e1071 - Misc Functions of the Department of Statistics, Probability Theory Group (Formerly: E1071), TU Wien

Functions for latent class analysis, short time Fourier transform, fuzzy clustering, support vector machines, shortest path computation, bagged clustering, naive Bayes classifier, generalized k-nearest neighbour ...

Last updated 3 months ago

cpp

14.47 score 27 stars 1.9k dependents 18k scripts 535k downloads

mgcv - Mixed GAM Computation Vehicle with Automatic Smoothness Estimation

Generalized additive (mixed) models, some of their extensions and other generalized ridge regression with multiple smoothing parameter estimation by (Restricted) Marginal Likelihood, Generalized Cross Validation and similar, or using iterated nested Laplace approximation for fully Bayesian inference. See Wood (2017) <doi:10.1201/9781315370279> for an overview. Includes a gam() function, a wide variety of smoothers, 'JAGS' support and distributions beyond the exponential family.

Last updated 1 years ago

openblasopenmp

12.86 score 32 stars 7.8k dependents 17k scripts 55k downloads

nlme - Linear and Nonlinear Mixed Effects Models

Fit and compare Gaussian linear and nonlinear mixed-effects models.

Last updated 4 months ago

fortran

12.58 score 6 stars 8.6k dependents 12k scripts 100k downloads

XML - Tools for Parsing and Generating XML Within R and S-Plus

Many approaches for both reading and creating XML (and HTML) documents (including DTDs), both local and accessible via HTTP or FTP. Also offers access to an 'XPath' "interpreter".

Last updated 6 months ago

12.16 score 3 stars 1.3k dependents 11k scripts 288k downloads

proxy - Distance and Similarity Measures

Provides an extensible framework for the efficient calculation of auto- and cross-proximities, along with implementations of the most popular ones.

Last updated 3 years ago

12.06 score 3 stars 2.0k dependents 1.4k scripts 473k downloads

boot - Bootstrap Functions (Originally by Angelo Canty for S)

Functions and datasets for bootstrapping from the book "Bootstrap Methods and Their Application" by A. C. Davison and D. V. Hinkley (1997, CUP), originally written by Angelo Canty for S.

Last updated 4 months ago

11.64 score 2 stars 2.2k dependents 14k scripts 82k downloads

nnet - Feed-Forward Neural Networks and Multinomial Log-Linear Models

Software for feed-forward neural networks with a single hidden layer, and for multinomial log-linear models.

Last updated 2 years ago

11.10 score 6 stars 2.3k dependents 7.1k scripts 43k downloads

vcd - Visualizing Categorical Data

Visualization techniques, data sets, summary and inference procedures aimed particularly at categorical data. Special emphasis is given to highly extensible grid graphics. The package was package was originally inspired by the book "Visualizing Categorical Data" by Michael Friendly and is now the main support package for a new book, "Discrete Data Analysis with R" by Michael Friendly and David Meyer (2015).

Last updated 3 months ago

11.01 score 5 stars 85 dependents 3.0k scripts 67k downloads

class - Functions for Classification

Various functions for classification, including k-nearest neighbour, Learning Vector Quantization and Self-Organizing Maps.

Last updated 2 years ago

10.30 score 1 stars 2.1k dependents 8.5k scripts 37k downloads

FNN - Fast Nearest Neighbor Search Algorithms and Applications

Cover-tree and kd-tree fast k-nearest neighbor search algorithms and related applications including KNN classification, regression and information measures are implemented.

Last updated 3 months ago

cpp

10.29 score 5 stars 582 dependents 2.2k scripts 103k downloads

MASS - Support Functions and Datasets for Venables and Ripley's MASS

Functions and datasets to support Venables and Ripley, "Modern Applied Statistics with S" (4th edition, 2002).

Last updated 6 months ago

10.27 score 19 stars 11k dependents 59k scripts 154k downloads

timeSeries - Financial Time Series Objects (Rmetrics)

'S4' classes and various tools for financial time series: Basic functions such as scaling and sorting, subsetting, mathematical operations and statistical functions.

Last updated 3 months ago

10.20 score 2 stars 145 dependents 1.2k scripts 38k downloads

fBasics - Rmetrics - Markets and Basic Statistics

Provides a collection of functions to explore and to investigate basic properties of financial returns and related quantities. The covered fields include techniques of explorative data analysis and the investigation of distributional properties, including parameter estimation and hypothesis testing. Even more there are several utility functions for data handling and management.

Last updated 4 months ago

9.56 score 2 stars 128 dependents 1.2k scripts 40k downloads

KernSmooth - Functions for Kernel Smoothing Supporting Wand & Jones (1995)

Functions for kernel smoothing (and density estimation) corresponding to the book: Wand, M.P. and Jones, M.C. (1995) "Kernel Smoothing".

Last updated 7 months ago

fortranopenblas

9.54 score 1 stars 2.5k dependents 1.1k scripts 43k downloads

sna - Tools for Social Network Analysis

A range of tools for social network analysis, including node and graph-level indices, structural distance and covariance methods, structural equivalence detection, network regression, random graph generation, and 2D/3D network visualization.

Last updated 4 months ago

9.50 score 8 stars 91 dependents 2.7k scripts 27k downloads

topicmodels - Topic Models

Provides an interface to the C code for Latent Dirichlet Allocation (LDA) models and Correlated Topics Models (CTM) by David M. Blei and co-authors and the C++ code for fitting LDA models using Gibbs sampling by Xuan-Hieu Phan and co-authors.

Last updated 4 months ago

gslcpp

9.42 score 8 stars 15 dependents 5.0k scripts 15k downloads

PMCMRplus - Calculate Pairwise Multiple Comparisons of Mean Rank Sums Extended

For one-way layout experiments the one-way ANOVA can be performed as an omnibus test. All-pairs multiple comparisons tests (Tukey-Kramer test, Scheffe test, LSD-test) and many-to-one tests (Dunnett test) for normally distributed residuals and equal within variance are available. Furthermore, all-pairs tests (Games-Howell test, Tamhane's T2 test, Dunnett T3 test, Ury-Wiggins-Hochberg test) and many-to-one (Tamhane-Dunnett Test) for normally distributed residuals and heterogeneous variances are provided. Van der Waerden's normal scores test for omnibus, all-pairs and many-to-one tests is provided for non-normally distributed residuals and homogeneous variances. The Kruskal-Wallis, BWS and Anderson-Darling omnibus test and all-pairs tests (Nemenyi test, Dunn test, Conover test, Dwass-Steele-Critchlow- Fligner test) as well as many-to-one (Nemenyi test, Dunn test, U-test) are given for the analysis of variance by ranks. Non-parametric trend tests (Jonckheere test, Cuzick test, Johnson-Mehrotra test, Spearman test) are included. In addition, a Friedman-test for one-way ANOVA with repeated measures on ranks (CRBD) and Skillings-Mack test for unbalanced CRBD is provided with consequent all-pairs tests (Nemenyi test, Siegel test, Miller test, Conover test, Exact test) and many-to-one tests (Nemenyi test, Demsar test, Exact test). A trend can be tested with Pages's test. Durbin's test for a two-way balanced incomplete block design (BIBD) is given in this package as well as Gore's test for CRBD with multiple observations per cell is given. Outlier tests, Mandel's k- and h statistic as well as functions for Type I error and Power analysis as well as generic summary, print and plot methods are provided.

Last updated 4 months ago

fortran

9.34 score 6 stars 12 dependents 426 scripts 24k downloads

futile.logger - A Logging Utility for R

Provides a simple yet powerful logging utility. Based loosely on log4j, futile.logger takes advantage of R idioms to make logging a convenient and easy to use replacement for cat and print statements.

Last updated 8 years ago

9.27 score 1.2k dependents 1.4k scripts 77k downloads

timeDate - Rmetrics - Chronological and Calendar Objects

The 'timeDate' class fulfils the conventions of the ISO 8601 standard as well as of the ANSI C and POSIX standards. Beyond these standards it provides the "Financial Center" concept which allows to handle data records collected in different time zones and mix them up to have always the proper time stamps with respect to your personal financial center, or alternatively to the GMT reference time. It can thus also handle time stamps from historical data records from the same time zone, even if the financial centers changed day light saving times at different calendar dates.

Last updated 3 months ago

9.27 score 1 stars 690 dependents 840 scripts 214k downloads

sn - The Skew-Normal and Related Distributions Such as the Skew-t and the SUN

Build and manipulate probability distributions of the skew-normal family and some related ones, notably the skew-t and the SUN families. For the skew-normal and the skew-t distributions, statistical methods are provided for data fitting and model diagnostics, in the univariate and the multivariate case.

Last updated 2 years ago

9.24 score 3 stars 84 dependents 680 scripts 16k downloads

interp - Interpolation Methods

Bivariate data interpolation on regular and irregular grids, either linear or using splines are the main part of this package. It is intended to provide FOSS replacement functions for the ACM licensed akima::interp and tripack::tri.mesh functions. Linear interpolation is implemented in interp::interp(..., method="linear"), this corresponds to the call akima::interp(..., linear=TRUE) which is the default setting and covers most of akima::interp use cases in depending packages. A re-implementation of Akimas irregular grid spline interpolation (akima::interp(..., linear=FALSE)) is now also available via interp::interp(..., method="akima"). Estimators for partial derivatives are now also available in interp::locpoly(), these are a prerequisite for the spline interpolation. The basic part is a GPLed triangulation algorithm (sweep hull algorithm by David Sinclair) providing the starting point for the irregular grid interpolator. As side effect this algorithm is also used to provide replacements for almost all functions of the tripack package which also suffers from the same ACM license restrictions. All functions are designed to be backward compatible with their akima / tripack counterparts.

Last updated 11 months ago

fortrancpp

9.02 score 1 stars 288 dependents 203 scripts 49k downloads

mnormt - The Multivariate Normal and t Distributions, and Their Truncated Versions

Functions are provided for computing the density and the distribution function of d-dimensional normal and "t" random variables, possibly truncated (on one side or two sides), and for generating random vectors sampled from these distributions, except sampling from the truncated "t". Moments of arbitrary order of a multivariate truncated normal are computed, and converted to cumulants up to order 4. Probabilities are computed via non-Monte Carlo methods; different routines are used in the case d=1, d=2, d=3, d>3, if d denotes the dimensionality.

Last updated 2 years ago

fortran

8.97 score 665 dependents 1.2k scripts 126k downloads

evd - Functions for Extreme Value Distributions

Extends simulation, distribution, quantile and density functions to univariate and multivariate parametric extreme value distributions, and provides fitting functions which calculate maximum likelihood estimates for univariate and bivariate maxima models, and for univariate and bivariate threshold models.

Last updated 3 months ago

8.87 score 2 stars 81 dependents 712 scripts 13k downloads

coxme - Mixed Effects Cox Models

Fit Cox proportional hazards models containing both fixed and random effects. The random effects can have a general form, of which familial interactions (a "kinship" matrix) is a particular special case. Note that the simplest case of a mixed effects Cox model, i.e. a single random per-group intercept, is also called a "frailty" model. The approach is based on Ripatti and Palmgren, Biometrics 2002.

Last updated 4 months ago

8.83 score 2 stars 16 dependents 590 scripts 9.9k downloads

MuMIn - Multi-Model Inference

Tools for model selection and model averaging with support for a wide range of statistical models. Automated model selection through subsets of the maximum model, with optional constraints for model inclusion. Averaging of model parameters and predictions based on model weights derived from information criteria (AICc and alike) or custom model weighting schemes.

Last updated 6 months ago

8.81 score 8 stars 24 dependents 5.4k scripts 21k downloads

fGarch - Rmetrics - Autoregressive Conditional Heteroskedastic Modelling

Analyze and model heteroskedastic behavior in financial time series.

Last updated 9 months ago

fortran

8.63 score 6 stars 50 dependents 1.1k scripts 14k downloads

drc - Analysis of Dose-Response Curves

Analysis of dose-response data is made available through a suite of flexible and versatile model fitting and after-fitting functions.

Last updated 8 years ago

8.41 score 8 stars 28 dependents 1.3k scripts 29k downloads

nleqslv - Solve Systems of Nonlinear Equations

Solve a system of nonlinear equations using a Broyden or a Newton method with a choice of global strategies such as line search and trust region. There are options for using a numerical or user supplied Jacobian, for specifying a banded numerical Jacobian and for allowing a singular or ill-conditioned Jacobian.

Last updated 1 years ago

fortranopenblas

8.40 score 3 stars 166 dependents 894 scripts 27k downloads

RCurl - General Network (HTTP/FTP/...) Client Interface for R

A wrapper for 'libcurl' <https://curl.se/libcurl/> Provides functions to allow one to compose general HTTP requests and provides convenient functions to fetch URIs, get & post forms, etc. and process the results returned by the Web server. This provides a great deal of control over the HTTP/FTP/... connection and the form of the request while providing a higher-level interface than is available just using R socket connections. Additionally, the underlying implementation is robust and extensive, supporting FTP/FTPS/TFTP (uploads and downloads), SSL/HTTPS, telnet, dict, ldap, and also supports cookies, redirects, authentication, etc.

Last updated 6 months ago

curl

8.36 score 2 stars 1.0k dependents 12k scripts 185k downloads

fdrtool - Estimation of (Local) False Discovery Rates and Higher Criticism

Estimates both tail area-based false discovery rates (Fdr) as well as local false discovery rates (fdr) for a variety of null models (p-values, z-scores, correlation coefficients, t-scores). The proportion of null values and the parameters of the null distribution are adaptively estimated from the data. In addition, the package contains functions for non-parametric density estimation (Grenander estimator), for monotone regression (isotonic regression and antitonic regression with weights), for computing the greatest convex minorant (GCM) and the least concave majorant (LCM), for the half-normal and correlation distributions, and for computing empirical higher criticism (HC) scores and the corresponding decision threshold.

Last updated 4 months ago

8.33 score 3 stars 116 dependents 804 scripts 25k downloads

flexmix - Flexible Mixture Modeling

A general framework for finite mixtures of regression models using the EM algorithm is implemented. The E-step and all data handling are provided, while the M-step can be supplied by the user to easily define new models. Existing drivers implement mixtures of standard linear models, generalized linear models and model-based clustering.

Last updated 2 years ago

8.23 score 5 stars 112 dependents 604 scripts 26k downloads

RJSONIO - Serialize R Objects to JSON, JavaScript Object Notation

This is a package that allows conversion to and from data in Javascript object notation (JSON) format. This allows R objects to be inserted into Javascript/ECMAScript/ActionScript code and allows R programmers to read and convert JSON content to R objects. This is an alternative to rjson package. Originally, that was too slow for converting large R objects to JSON and was not extensible. rjson's performance is now similar to this package, and perhaps slightly faster in some cases. This package uses methods and is readily extensible by defining methods for different classes, vectorized operations, and C code and callbacks to R functions for deserializing JSON objects to R. The two packages intentionally share the same basic interface. This package (RJSONIO) has many additional options to allow customizing the generation and processing of JSON content. This package uses libjson rather than implementing yet another JSON parser. The aim is to support other general projects by building on their work, providing feedback and benefit from their ongoing development.

Last updated 1 years ago

8.20 score 2 stars 76 dependents 1.6k scripts 22k downloads

epiR - Tools for the Analysis of Epidemiological Data

Tools for the analysis of epidemiological and surveillance data. Contains functions for directly and indirectly adjusting measures of disease frequency, quantifying measures of association on the basis of single or multiple strata of count data presented in a contingency table, computation of confidence intervals around incidence risk and incidence rate estimates and sample size calculations for cross-sectional, case-control and cohort studies. Surveillance tools include functions to calculate an appropriate sample size for 1- and 2-stage representative freedom surveys, functions to estimate surveillance system sensitivity and functions to support scenario tree modelling analyses.

Last updated 14 days ago

8.18 score 10 stars 10 dependents 680 scripts 14k downloads

Boruta - Wrapper Algorithm for All Relevant Feature Selection

An all relevant feature selection wrapper algorithm. It finds relevant features by comparing original attributes' importance with importance achievable at random, estimated using their permuted copies (shadows).

Last updated 2 years ago

8.17 score 7 stars 4 dependents 1.4k scripts 6.3k downloads

bayesm - Bayesian Inference for Marketing/Micro-Econometrics

Covers many important models used in marketing and micro-econometrics applications. The package includes: Bayes Regression (univariate or multivariate dep var), Bayes Seemingly Unrelated Regression (SUR), Binary and Ordinal Probit, Multinomial Logit (MNL) and Multinomial Probit (MNP), Multivariate Probit, Negative Binomial (Poisson) Regression, Multivariate Mixtures of Normals (including clustering), Dirichlet Process Prior Density Estimation with normal base, Hierarchical Linear Models with normal prior and covariates, Hierarchical Linear Models with a mixture of normals prior and covariates, Hierarchical Multinomial Logits with a mixture of normals prior and covariates, Hierarchical Multinomial Logits with a Dirichlet Process prior and covariates, Hierarchical Negative Binomial Regression Models, Bayesian analysis of choice-based conjoint data, Bayesian treatment of linear instrumental variables models, Analysis of Multivariate Ordinal survey data with scale usage heterogeneity (as in Rossi et al, JASA (01)), Bayesian Analysis of Aggregate Random Coefficient Logit Models as in BLP (see Jiang, Manchanda, Rossi 2009) For further reference, consult our book, Bayesian Statistics and Marketing by Rossi, Allenby and McCulloch (Wiley first edition 2005 and second forthcoming) and Bayesian Non- and Semi-Parametric Methods and Applications (Princeton U Press 2014).

Last updated 1 years ago

openblascpp

8.17 score 20 stars 42 dependents 323 scripts 9.1k downloads

foreign - Read Data Stored by 'Minitab', 'S', 'SAS', 'SPSS', 'Stata', 'Systat', 'Weka', 'dBase', ...

Reading and writing data stored by some versions of 'Epi Info', 'Minitab', 'S', 'SAS', 'SPSS', 'Stata', 'Systat', 'Weka', and for reading and writing some 'dBase' files.

Last updated 6 months ago

8.13 score 6 stars 886 dependents 15k scripts 85k downloads

ca - Simple, Multiple and Joint Correspondence Analysis

Computation and visualization of simple, multiple and joint correspondence analysis.

Last updated 5 years ago

8.03 score 2 stars 98 dependents 444 scripts 41k downloads

NbClust - Determining the Best Number of Clusters in a Data Set

It provides 30 indexes for determining the optimal number of clusters in a data set and offers the best clustering scheme from different results to the user.

Last updated 3 years ago

8.03 score 9 stars 18 dependents 1.4k scripts 15k downloads

beanplot - Visualization via Beanplots (Like Boxplot/Stripchart/Violin Plot)

Plots univariate comparison graphs, an alternative to boxplot/stripchart/violin plot.

Last updated 3 years ago

8.02 score 1 stars 44 dependents 390 scripts 4.1k downloads

snowfall - Easier Cluster Computing (Based on 'snow')

Usability wrapper around snow for easier development of parallel R programs. This package offers e.g. extended error checks, and additional functions. All functions work in sequential mode, too, if no cluster is present or wished. Package is also designed as connector to the cluster management tool sfCluster, but can also used without it.

Last updated 1 years ago

7.94 score 48 dependents 1.8k scripts 4.8k downloads

mc2d - Tools for Two-Dimensional Monte-Carlo Simulations

A complete framework to build and study Two-Dimensional Monte-Carlo simulations, aka Second-Order Monte-Carlo simulations. Also includes various distributions (pert, triangular, Bernoulli, empirical discrete and continuous).

Last updated 7 months ago

7.93 score 1 stars 16 dependents 364 scripts 4.8k downloads

gprofiler2 - Interface to the 'g:Profiler' Toolset

A toolset for functional enrichment analysis and visualization, gene/protein/SNP identifier conversion and mapping orthologous genes across species via 'g:Profiler' (<https://biit.cs.ut.ee/gprofiler/>). The main tools are: (1) 'g:GOSt' - functional enrichment analysis and visualization of gene lists; (2) 'g:Convert' - gene/protein/transcript identifier conversion across various namespaces; (3) 'g:Orth' - orthology search across species; (4) 'g:SNPense' - mapping SNP rs identifiers to chromosome positions, genes and variant effects. This package is an R interface corresponding to the 2019 update of 'g:Profiler' and provides access to 'g:Profiler' for versions 'e94_eg41_p11' and higher. See the package 'gProfileR' for accessing older versions from the 'g:Profiler' toolset.

Last updated 10 months ago

7.86 score 4 stars 14 dependents 1.4k scripts 3.0k downloads

network - Classes for Relational Data

Tools to create and modify network objects. The network class can represent a range of relational data types, and supports arbitrary vertex/edge/graph attributes.

Last updated 15 days ago

7.82 score 3 stars 143 dependents 3.1k scripts 26k downloads

glasso - Graphical Lasso: Estimation of Gaussian Graphical Models

Estimation of a sparse inverse covariance matrix using a lasso (L1) penalty. Facilities are provided for estimates along a path of values for the regularization parameter.

Last updated 5 years ago

fortran

7.81 score 2 stars 108 dependents 502 scripts 20k downloads

lpSolveAPI - R Interface to 'lp_solve' Version 5.5.2.0

The lpSolveAPI package provides an R interface to 'lp_solve', a Mixed Integer Linear Programming (MILP) solver with support for pure linear, (mixed) integer/binary, semi-continuous and special ordered sets (SOS) models.

Last updated 5 months ago

openblas

7.79 score 78 dependents 636 scripts 14k downloads

circular - Circular Statistics

Circular Statistics, from "Topics in circular Statistics" (2001) S. Rao Jammalamadaka and A. SenGupta, World Scientific.

Last updated 4 months ago

fortran

7.72 score 6 stars 39 dependents 1.1k scripts 6.7k downloads

bnlearn - Bayesian Network Structure Learning, Parameter Learning and Inference

Bayesian network structure learning, parameter learning and inference. This package implements constraint-based (PC, GS, IAMB, Inter-IAMB, Fast-IAMB, MMPC, Hiton-PC, HPC), pairwise (ARACNE and Chow-Liu), score-based (Hill-Climbing and Tabu Search) and hybrid (MMHC, RSMAX2, H2PC) structure learning algorithms for discrete, Gaussian and conditional Gaussian networks, along with many score functions and conditional independence tests. The Naive Bayes and the Tree-Augmented Naive Bayes (TAN) classifiers are also implemented. Some utility functions (model comparison and manipulation, random data generation, arc orientation testing, simple and advanced plots) are included, as well as support for parameter estimation (maximum likelihood and Bayesian) and inference, conditional probability queries, cross-validation, bootstrap and model averaging. Development snapshots with the latest bugfixes are available from <https://www.bnlearn.com/>.

Last updated 4 months ago

openblas

7.71 score 57 stars 32 dependents 1.6k scripts 23k downloads

jsonify - Convert Between 'R' Objects and Javascript Object Notation (JSON)

Conversions between 'R' objects and Javascript Object Notation (JSON) using the 'rapidjsonr' library <https://CRAN.R-project.org/package=rapidjsonr>.

Last updated 2 years ago

cpp

7.71 score 1 stars 127 dependents 78 scripts 34k downloads

cmprsk - Subdistribution Analysis of Competing Risks

Estimation, testing and regression modeling of subdistribution functions in competing risks, as described in Gray (1988), A class of K-sample tests for comparing the cumulative incidence of a competing risk, Ann. Stat. 16:1141-1154 <DOI:10.1214/aos/1176350951>, and Fine JP and Gray RJ (1999), A proportional hazards model for the subdistribution of a competing risk, JASA, 94:496-509, <DOI:10.1080/01621459.1999.10474144>.

Last updated 7 months ago

fortran

7.58 score 2 stars 60 dependents 604 scripts 18k downloads

BB - Solving and Optimizing Large-Scale Nonlinear Systems

Barzilai-Borwein spectral methods for solving nonlinear system of equations, and for optimizing nonlinear objective functions subject to simple constraints. A tutorial style introduction to this package is available in a vignette on the CRAN download page or, when the package is loaded in an R session, with vignette("BB").

Last updated 5 years ago

7.58 score 2 stars 60 dependents 133 scripts 4.0k downloads

MVN - Multivariate Normality Tests

Performs multivariate normality tests and graphical approaches and implements multivariate outlier detection and univariate normality of marginal distributions through plots and tests, and performs multivariate Box-Cox transformation (Korkmaz et al, (2014), <https://journal.r-project.org/archive/2014-2/korkmaz-goksuluk-zararsiz.pdf>).

Last updated 3 years ago

7.52 score 1 stars 4 dependents 600 scripts 9.3k downloads

mcmc - Markov Chain Monte Carlo

Simulates continuous distributions of random vectors using Markov chain Monte Carlo (MCMC). Users specify the distribution by an R function that evaluates the log unnormalized density. Algorithms are random walk Metropolis algorithm (function metrop), simulated tempering (function temper), and morphometric random walk Metropolis (Johnson and Geyer, 2012, <doi:10.1214/12-AOS1048>, function morph.metrop), which achieves geometric ergodicity by change of variable.

Last updated 1 years ago

7.45 score 153 dependents 302 scripts 15k downloads

RODBC - ODBC Database Access

An ODBC database interface.

Last updated 12 days ago

unixodbc

7.44 score 10 stars 38 dependents 3.0k scripts 24k downloads

registry - Infrastructure for R Package Registries

Provides a generic infrastructure for creating and using registries.

Last updated 6 years ago

7.41 score 169 dependents 131 scripts 38k downloads

irr - Various Coefficients of Interrater Reliability and Agreement

Coefficients of Interrater Reliability and Agreement for quantitative, ordinal and nominal data: ICC, Finn-Coefficient, Robinson's A, Kendall's W, Cohen's Kappa, ...

Last updated 6 years ago

7.40 score 3 stars 22 dependents 1.3k scripts 9.6k downloads

flexclust - Flexible Cluster Algorithms

The main function kcca implements a general framework for k-centroids cluster analysis supporting arbitrary distance measures and centroid computation. Further cluster methods include hard competitive learning, neural gas, and QT clustering. There are numerous visualization methods for cluster results (neighborhood graphs, convex cluster hulls, barcharts of centroids, ...), and bootstrap methods for the analysis of cluster stability.

Last updated 8 months ago

7.39 score 3 stars 51 dependents 768 scripts 7.0k downloads

spatial - Functions for Kriging and Point Pattern Analysis

Functions for kriging and point pattern analysis.

Last updated 1 years ago

7.34 score 133 dependents 276 scripts 20k downloads

wavethresh - Wavelets Statistics and Transforms

Performs 1, 2 and 3D real and complex-valued wavelet transforms, nondecimated transforms, wavelet packet transforms, nondecimated wavelet packet transforms, multiple wavelet transforms, complex-valued wavelet transforms, wavelet shrinkage for various kinds of data, locally stationary wavelet time series, nonstationary multiscale transfer function modeling, density estimation.

Last updated 4 months ago

7.27 score 40 dependents 362 scripts 54k downloads

sets - Sets, Generalized Sets, Customizable Sets and Intervals

Data structures and basic operations for ordinary sets, generalizations such as fuzzy sets, multisets, and fuzzy multisets, customizable sets, and intervals.

Last updated 1 years ago

7.23 score 1 stars 109 dependents 592 scripts 8.7k downloads

ppcor - Partial and Semi-Partial (Part) Correlation

Calculates partial and semi-partial (part) correlations along with p-value.

Last updated 9 years ago

7.18 score 27 dependents 1.1k scripts 16k downloads

exact2x2 - Exact Tests and Confidence Intervals for 2x2 Tables

Calculates conditional exact tests (Fisher's exact test, Blaker's exact test, or exact McNemar's test) and unconditional exact tests (including score-based tests on differences in proportions, ratios of proportions, and odds ratios, and Boshcloo's test) with appropriate matching confidence intervals, and provides power and sample size calculations. Gives melded confidence intervals for the binomial case (Fay, et al, 2015, <DOI:10.1111/biom.12231>). Gives boundary-optimized rejection region test (Gabriel, et al, 2018, <DOI:10.1002/sim.7579>), an unconditional exact test for the situation where the controls are all expected to fail. Gives confidence intervals compatible with exact McNemar's or sign tests (Fay and Lumbard, 2021, <DOI:10.1002/sim.8829>). For review of these kinds of exact tests see Fay and Hunsberger (2021, <DOI:10.1214/21-SS131>).

Last updated 11 months ago

7.18 score 3 stars 6 dependents 272 scripts 2.1k downloads

aod - Analysis of Overdispersed Data

Provides a set of functions to analyse overdispersed counts or proportions. Most of the methods are already available elsewhere but are scattered in different packages. The proposed functions should be considered as complements to more sophisticated methods such as generalized estimating equations (GEE) or generalized linear mixed effect models (GLMM).

Last updated 1 years ago

7.16 score 3 stars 14 dependents 1.0k scripts 11k downloads

trend - Non-Parametric Trend Tests and Change-Point Detection

The analysis of environmental data often requires the detection of trends and change-points. This package includes tests for trend detection (Cox-Stuart Trend Test, Mann-Kendall Trend Test, (correlated) Hirsch-Slack Test, partial Mann-Kendall Trend Test, multivariate (multisite) Mann-Kendall Trend Test, (Seasonal) Sen's slope, partial Pearson and Spearman correlation trend test), change-point detection (Lanzante's test procedures, Pettitt's test, Buishand Range Test, Buishand U Test, Standard Normal Homogeinity Test), detection of non-randomness (Wallis-Moore Phase Frequency Test, Bartels rank von Neumann's ratio test, Wald-Wolfowitz Test) and the two sample Robust Rank-Order Distributional Test.

Last updated 1 years ago

fortran

7.13 score 3 stars 9 dependents 592 scripts 4.0k downloads

futile.options - Futile Options Management

A scoped options management framework. Used in other packages.

Last updated 7 years ago

7.08 score 1.2k dependents 9 scripts 69k downloads

gaston - Genetic Data Handling (QC, GRM, LD, PCA) & Linear Mixed Models

Manipulation of genetic data (SNPs). Computation of GRM and dominance matrix, LD, heritability with efficient algorithms for linear mixed model (AIREML). Dandine et al <doi:10.1159/000488519>.

Last updated 1 years ago

zlibcpp

7.07 score 5 stars 11 dependents 140 scripts 4.3k downloads

agricolae - Statistical Procedures for Agricultural Research

Original idea was presented in the thesis "A statistical analysis tool for agricultural research" to obtain the degree of Master on science, National Engineering University (UNI), Lima-Peru. Some experimental data for the examples come from the CIP and others research. Agricolae offers extensive functionality on experimental design especially for agricultural and plant breeding experiments, which can also be useful for other purposes. It supports planning of lattice, Alpha, Cyclic, Complete Block, Latin Square, Graeco-Latin Squares, augmented block, factorial, split and strip plot designs. There are also various analysis facilities for experimental data, e.g. treatment comparison procedures and several non-parametric tests comparison, biodiversity indexes and consensus cluster.

Last updated 1 years ago

7.07 score 7 stars 14 dependents 2.4k scripts 40k downloads

GenSA - R Functions for Generalized Simulated Annealing

Performs search for global minimum of a very complex non-linear objective function with a very large number of optima.

Last updated 3 months ago

openblascpp

7.03 score 4 stars 27 dependents 250 scripts 9.5k downloads

enrichR - Provides an R Interface to 'Enrichr'

Provides an R interface to all 'Enrichr' databases. 'Enrichr' is a web-based tool for analysing gene sets and returns any enrichment of common annotated biological features. Quoting from their website 'Enrichment analysis is a computational method for inferring knowledge about an input gene set by comparing it to annotated gene sets representing prior biological knowledge.' See <https://maayanlab.cloud/Enrichr/> for further details.

Last updated 2 years ago

7.03 score 1 stars 8 dependents 888 scripts 209 downloads

scam - Shape Constrained Additive Models

Generalized additive models under shape constraints on the component functions of the linear predictor. Models can include multiple shape-constrained (univariate and bivariate) and unconstrained terms. Routines of the package 'mgcv' are used to set up the model matrix, print, and plot the results. Multiple smoothing parameter estimation by the Generalized Cross Validation or similar. See Pya and Wood (2015) <doi:10.1007/s11222-013-9448-7> for an overview. A broad selection of shape-constrained smoothers, linear functionals of smooths with shape constraints, and Gaussian models with AR1 residuals.

Last updated 6 months ago

7.03 score 5 stars 22 dependents 356 scripts 6.0k downloads

BGLR - Bayesian Generalized Linear Regression

Bayesian Generalized Linear Regression.

Last updated 3 months ago

openblas

7.02 score 2 stars 5 dependents 586 scripts 2.0k downloads

ggtern - An Extension to 'ggplot2', for the Creation of Ternary Diagrams

Extends the functionality of 'ggplot2', providing the capability to plot ternary diagrams for (subset of) the 'ggplot2' geometries. Additionally, 'ggtern' has implemented several NEW geometries which are unavailable to the standard 'ggplot2' release. For further examples and documentation, please proceed to the 'ggtern' website.

Last updated 9 months ago

6.99 score 4 stars 5 dependents 1.1k scripts 3.1k downloads

lambda.r - Modeling Data with Functional Programming

A language extension to efficiently write functional programs in R. Syntax extensions include multi-part function definitions, pattern matching, guard statements, built-in (optional) type safety.

Last updated 5 years ago

6.93 score 1 stars 1.2k dependents 31 scripts 78k downloads

polspline - Polynomial Spline Routines

Routines for the polynomial spline fitting routines hazard regression, hazard estimation with flexible tails, logspline, lspec, polyclass, and polymars, by C. Kooperberg and co-authors.

Last updated 8 months ago

fortranopenblas

6.86 score 126 dependents 181 scripts 21k downloads

epitools - Epidemiology Tools

Tools for training and practicing epidemiologists including methods for two-way and multi-way contingency tables.

Last updated 5 years ago

6.82 score 2 stars 12 dependents 774 scripts 12k downloads

vipor - Plot Categorical Data Using Quasirandom Noise and Density Estimates

Generate a violin point plot, a combination of a violin/histogram plot and a scatter plot by offsetting points within a category based on their density using quasirandom noise.

Last updated 1 years ago

6.82 score 88 dependents 36 scripts 25k downloads

airGR - Suite of GR Hydrological Models for Precipitation-Runoff Modelling

Hydrological modelling tools developed at INRAE-Antony (HYCAR Research Unit, France). The package includes several conceptual rainfall-runoff models (GR4H, GR5H, GR4J, GR5J, GR6J, GR2M, GR1A) that can be applied either on a lumped or semi-distributed way. A snow accumulation and melt model (CemaNeige) and the associated functions for the calibration and evaluation of models are also included. Use help(airGR) for package description and references.

Last updated 1 years ago

fortran

6.69 score 4 stars 4 dependents 184 scripts 1.9k downloads

dichromat - Color Schemes for Dichromats

Collapse red-green or green-blue distinctions to simulate the effects of different types of color-blindness.

Last updated 3 years ago

6.65 score 1 stars 115 dependents 482 scripts 27k downloads

lmom - L-Moments

Functions related to L-moments: computation of L-moments and trimmed L-moments of distributions and data samples; parameter estimation; L-moment ratio diagram; plot vs. quantiles of an extreme-value distribution.

Last updated 3 months ago

fortran

6.61 score 2 stars 138 dependents 95 scripts 52k downloads

compositions - Compositional Data Analysis

Provides functions for the consistent analysis of compositional data (e.g. portions of substances) and positive numbers (e.g. concentrations) in the way proposed by J. Aitchison and V. Pawlowsky-Glahn.

Last updated 11 months ago

openblas

6.60 score 1 stars 35 dependents 1.9k scripts 9.4k downloads

corpcor - Efficient Estimation of Covariance and (Partial) Correlation

Implements a James-Stein-type shrinkage estimator for the covariance matrix, with separate shrinkage for variances and correlations. The details of the method are explained in Schafer and Strimmer (2005) <DOI:10.2202/1544-6115.1175> and Opgen-Rhein and Strimmer (2007) <DOI:10.2202/1544-6115.1252>. The approach is both computationally as well as statistically very efficient, it is applicable to "small n, large p" data, and always returns a positive definite and well-conditioned covariance matrix. In addition to inferring the covariance matrix the package also provides shrinkage estimators for partial correlations and partial variances. The inverse of the covariance and correlation matrix can be efficiently computed, as well as any arbitrary power of the shrinkage correlation matrix. Furthermore, functions are available for fast singular value decomposition, for computing the pseudoinverse, and for checking the rank and positive definiteness of a matrix.

Last updated 3 years ago

6.57 score 289 dependents 956 scripts 43k downloads

tensorA - Advanced Tensor Arithmetic with Named Indices

Provides convenience functions for advanced linear algebra with tensors and computation with data sets of tensors on a higher level abstraction. It includes Einstein and Riemann summing conventions, dragging, co- and contravariate indices, parallel computations on sequences of tensors.

Last updated 1 years ago

6.55 score 381 dependents 60 scripts 52k downloads

SuppDists - Supplementary Distributions

Ten distributions supplementing those built into R. Inverse Gauss, Kruskal-Wallis, Kendall's Tau, Friedman's chi squared, Spearman's rho, maximum F ratio, the Pearson product moment correlation coefficient, Johnson distributions, normal scores and generalized hypergeometric distributions.

Last updated 4 months ago

cpp

6.54 score 76 dependents 196 scripts 26k downloads

TSA - Time Series Analysis

Contains R functions and datasets detailed in the book "Time Series Analysis with Applications in R (second edition)" by Jonathan Cryer and Kung-Sik Chan.

Last updated 2 years ago

6.52 score 2 stars 5 dependents 968 scripts 11k downloads

gamm4 - Generalized Additive Mixed Models using 'mgcv' and 'lme4'

Estimate generalized additive mixed models via a version of function gamm() from 'mgcv', using 'lme4' for estimation.

Last updated 5 years ago

6.49 score 1 stars 25 dependents 400 scripts 10k downloads

ica - Independent Component Analysis

Independent Component Analysis (ICA) using various algorithms: FastICA, Information-Maximization (Infomax), and Joint Approximate Diagonalization of Eigenmatrices (JADE).

Last updated 2 years ago

6.46 score 1 stars 78 dependents 78 scripts 20k downloads

aplpack - Another Plot Package: 'Bagplots', 'Iconplots', 'Summaryplots', Slider Functions and Others

Some functions for drawing some special plots: The function 'bagplot' plots a bagplot, 'faces' plots chernoff faces, 'iconplot' plots a representation of a frequency table or a data matrix, 'plothulls' plots hulls of a bivariate data set, 'plotsummary' plots a graphical summary of a data set, 'puticon' adds icons to a plot, 'skyline.hist' combines several histograms of a one dimensional data set in one plot, 'slider' functions supports some interactive graphics, 'spin3R' helps an inspection of a 3-dim point cloud, 'stem.leaf' plots a stem and leaf plot, 'stem.leaf.backback' plots back-to-back versions of stem and leaf plot.

Last updated 3 years ago

6.43 score 2 stars 3 dependents 348 scripts 14k downloads

sas7bdat - sas7bdat Reverse Engineering Documentation

Documentation and prototypes for the earliest (circa 2010) open-source effort to reverse engineer the sas7bdat file format. The package includes a prototype reader for sas7bdat files. However, newer packages may contain more robust readers for sas7bdat files.

Last updated 4 months ago

6.40 score 4 stars 4 dependents 516 scripts 3.4k downloads

akima - Interpolation of Irregularly and Regularly Spaced Data

Several cubic spline interpolation methods of H. Akima for irregular and regular gridded data are available through this package, both for the bivariate case (irregular data: ACM 761, regular data: ACM 760) and univariate case (ACM 433 and ACM 697). Linear interpolation of irregular gridded data is also covered by reusing D. J. Renkas triangulation code which is part of Akimas Fortran code. A bilinear interpolator for regular grids was also added for comparison with the bicubic interpolator on regular grids.

Last updated 3 years ago

fortran

6.39 score 5 stars 2 dependents 1.6k scripts 5.1k downloads

gss - General Smoothing Splines

A comprehensive package for structural multivariate function estimation using smoothing splines.

Last updated 2 months ago

fortranopenblas

6.39 score 3 stars 137 dependents 131 scripts 33k downloads

Rmpi - Interface (Wrapper) to MPI (Message-Passing Interface)

An interface (wrapper) to MPI. It also provides interactive R manager and worker environment.

Last updated 3 months ago

openmpi

6.37 score 5 stars 5 dependents 876 scripts 3.5k downloads

compare - Comparing Objects for Differences

Functions to compare a model object to a comparison object. If the objects are not identical, the functions can be instructed to explore various modifications of the objects (e.g., sorting rows, dropping names) to see if the modified versions are identical.

Last updated 9 years ago

6.35 score 5 dependents 472 scripts 1.6k downloads

lm.beta - Add Standardized Regression Coefficients to Linear-Model-Objects

Adds standardized regression coefficients to objects created by 'lm'. Also extends the S3 methods 'print', 'summary' and 'coef' with additional boolean argument 'standardized' and provides 'xtable'-support.

Last updated 2 years ago

6.34 score 6 dependents 572 scripts 11k downloads

survRM2 - Comparing Restricted Mean Survival Time

Performs two-sample comparisons using the restricted mean survival time (RMST) as a summary measure of the survival time distribution. Three kinds of between-group contrast metrics (i.e., the difference in RMST, the ratio of RMST and the ratio of the restricted mean time lost (RMTL)) are computed. It performs an ANCOVA-type covariate adjustment as well as unadjusted analyses for those measures.

Last updated 3 years ago

6.26 score 2 stars 5 dependents 93 scripts 1.3k downloads

dslabs - Data Science Labs

Datasets and functions that can be used for data analysis practice, homework and projects in data science courses and workshops. 26 datasets are available for case studies in data visualization, statistical inference, modeling, linear regression, data wrangling and machine learning.

Last updated 10 months ago

6.15 score 2 dependents 3.8k scripts 12k downloads

dotCall64 - Enhanced Foreign Function Interface Supporting Long Vectors

Provides .C64(), which is an enhanced version of .C() and .Fortran() from the foreign function interface. .C64() supports long vectors, arguments of type 64-bit integer, and provides a mechanism to avoid unnecessary copies of read-only and write-only arguments. This makes it a convenient and fast interface to C/C++ and Fortran code.

Last updated 3 months ago

fortranopenmp

6.14 score 422 dependents 15 scripts 73k downloads

fastICA - FastICA Algorithms to Perform ICA and Projection Pursuit

Implementation of FastICA algorithm to perform Independent Component Analysis (ICA) and Projection Pursuit.

Last updated 13 days ago

openblas

6.09 score 1 stars 88 dependents 412 scripts 24k downloads

ash - David Scott's ASH Routines

David Scott's ASH routines ported from S-PLUS to R.

Last updated 9 years ago

fortran

6.09 score 168 dependents 69 scripts 18k downloads

popbio - Construction and Analysis of Matrix Population Models

Construct and analyze projection matrix models from a demography study of marked individuals classified by age or stage. The package covers methods described in Matrix Population Models by Caswell (2001) and Quantitative Conservation Biology by Morris and Doak (2002).

Last updated 9 months ago

6.04 score 5 dependents 896 scripts 1.6k downloads

rehh - Searching for Footprints of Selection using 'Extended Haplotype Homozygosity' Based Tests

Population genetic data such as 'Single Nucleotide Polymorphisms' (SNPs) is often used to identify genomic regions that have been under recent natural or artificial selection and might provide clues about the molecular mechanisms of adaptation. One approach, the concept of an 'Extended Haplotype Homozygosity' (EHH), introduced by (Sabeti 2002) <doi:10.1038/nature01140>, has given rise to several statistics designed for whole genome scans. The package provides functions to compute three of these, namely: 'iHS' (Voight 2006) <doi:10.1371/journal.pbio.0040072> for detecting positive or 'Darwinian' selection within a single population as well as 'Rsb' (Tang 2007) <doi:10.1371/journal.pbio.0050171> and 'XP-EHH' (Sabeti 2007) <doi:10.1038/nature06250>, targeted at differential selection between two populations. Various plotting functions are included to facilitate visualization and interpretation of these statistics.

Last updated 3 years ago

openmp

6.03 score 8 stars 1 dependents 222 scripts 676 downloads

tensor - Tensor product of arrays

The tensor product of two arrays is notionally an outer product of the arrays collapsed in specific extents by summing along the appropriate diagonals.

Last updated 13 years ago

5.98 score 1 stars 158 dependents 73 scripts 28k downloads

kSamples - K-Sample Rank Tests and their Combinations

Compares k samples using the Anderson-Darling test, Kruskal-Wallis type tests with different rank score criteria, Steel's multiple comparison test, and the Jonckheere-Terpstra (JT) test. It computes asymptotic, simulated or (limited) exact P-values, all valid under randomization, with or without ties, or conditionally under random sampling from populations, given the observed tie pattern. Except for Steel's test and the JT test it also combines these tests across several blocks of samples. Also analyzed are 2 x t contingency tables and their blocked combinations using the Kruskal-Wallis criterion. Steel's test is inverted to provide simultaneous confidence bounds for shift parameters. A plotting function compares tail probabilities obtained under asymptotic approximation with those obtained via simulation or exact calculations.

Last updated 1 years ago

5.96 score 1 stars 47 dependents 99 scripts 16k downloads

bdsmatrix - Routines for Block Diagonal Symmetric Matrices

This is a special case of sparse matrices, used by coxme.

Last updated 10 months ago

5.92 score 1 stars 195 dependents 72 scripts 48k downloads

rapidjsonr - 'Rapidjson' C++ Header Files

Provides JSON parsing capability through the 'Rapidjson' 'C++' header-only library.

Last updated 5 years ago

5.91 score 137 dependents 3 scripts 39k downloads

VCA - Variance Component Analysis

ANOVA and REML estimation of linear mixed models is implemented, once following Searle et al. (1991, ANOVA for unbalanced data), once making use of the 'lme4' package. The primary objective of this package is to perform a variance component analysis (VCA) according to CLSI EP05-A3 guideline "Evaluation of Precision of Quantitative Measurement Procedures" (2014). There are plotting methods for visualization of an experimental design, plotting random effects and residuals. For ANOVA type estimation two methods for computing ANOVA mean squares are implemented (SWEEP and quadratic forms). The covariance matrix of variance components can be derived, which is used in estimating confidence intervals. Linear hypotheses of fixed effects and LS means can be computed. LS means can be computed at specific values of covariables and with custom weighting schemes for factor variables. See ?VCA for a more comprehensive description of the features.

Last updated 10 months ago

fortranopenblas

5.90 score 2 stars 4 dependents 167 scripts 928 downloads

GUniFrac - Generalized UniFrac Distances, Distance-Based Multivariate Methods and Feature-Based Univariate Methods for Microbiome Data Analysis

A suite of methods for powerful and robust microbiome data analysis including data normalization, data simulation, community-level association testing and differential abundance analysis. It implements generalized UniFrac distances, Geometric Mean of Pairwise Ratios (GMPR) normalization, semiparametric data simulator, distance-based statistical methods, and feature-based statistical methods. The distance-based statistical methods include three extensions of PERMANOVA: (1) PERMANOVA using the Freedman-Lane permutation scheme, (2) PERMANOVA omnibus test using multiple matrices, and (3) analytical approach to approximating PERMANOVA p-value. Feature-based statistical methods include linear model-based methods for differential abundance analysis of zero-inflated high-dimensional compositional data.

Last updated 1 years ago

cpp

5.90 score 7 dependents 261 scripts 1.5k downloads

grf - Generalized Random Forests

Forest-based statistical estimation and inference. GRF provides non-parametric methods for heterogeneous treatment effects estimation (optionally using right-censored outcomes, multiple treatment arms or outcomes, or instrumental variables), as well as least-squares regression, quantile regression, and survival regression, all with support for missing covariates.

Last updated 1 months ago

cpp

5.87 score 14 dependents 1.1k scripts 7.6k downloads

biclust - BiCluster Algorithms

The main function biclust() provides several algorithms to find biclusters in two-dimensional data: Cheng and Church (2000, ISBN:1-57735-115-0), spectral (2003) <doi:10.1101/gr.648603>, plaid model (2005) <doi:10.1016/j.csda.2004.02.003>, xmotifs (2003) <doi:10.1142/9789812776303_0008> and bimax (2006) <doi:10.1093/bioinformatics/btl060>. In addition, the package provides methods for data preprocessing (normalization and discretisation), visualisation, and validation of bicluster solutions.

Last updated 2 years ago

5.86 score 3 stars 16 dependents 170 scripts 2.9k downloads

matlab - 'MATLAB' Emulation Package

Emulate 'MATLAB' code using 'R'.

Last updated 6 months ago

5.83 score 19 dependents 516 scripts 2.3k downloads

fds - Functional Data Sets

Functional data sets.

Last updated 6 years ago

5.81 score 1 stars 145 dependents 110 scripts 13k downloads

rainbow - Bagplots, Boxplots and Rainbow Plots for Functional Data

Visualizing functional data and identifying functional outliers.

Last updated 11 months ago

5.73 score 146 dependents 84 scripts 15k downloads

FinTS - Companion to Tsay (2005) Analysis of Financial Time Series

R companion to Tsay (2005) Analysis of Financial Time Series, second edition (Wiley). Includes data sets, functions and script files required to work some of the examples. Version 0.3-x includes R objects for all data files used in the text and script files to recreate most of the analyses in chapters 1-3 and 9 plus parts of chapters 4 and 11.

Last updated 11 months ago

5.73 score 4 stars 6 dependents 984 scripts 7.5k downloads

pspline - Penalized Smoothing Splines

Smoothing splines with penalties on order m derivatives.

Last updated 13 days ago

fortran

5.72 score 1 stars 93 dependents 130 scripts 10k downloads

SELF - A Structural Equation Embedded Likelihood Framework for Causal Discovery

Provides the SELF criteria to learn causal structure. Please cite "Ruichu Cai, Jie Qiao, Zhenjie Zhang, Zhifeng Hao. SELF: Structural Equational Embedded Likelihood Framework for Causal Discovery. AAAI. 2018."

Last updated 7 years ago

5.72 score 15k scripts 189 downloads

rdrobust - Robust Data-Driven Statistical Inference in Regression-Discontinuity Designs

Regression-discontinuity (RD) designs are quasi-experimental research designs popular in social, behavioral and natural sciences. The RD design is usually employed to study the (local) causal effect of a treatment, intervention or policy. This package provides tools for data-driven graphical and analytical statistical inference in RD designs: rdrobust() to construct local-polynomial point estimators and robust confidence intervals for average treatment effects at the cutoff in Sharp, Fuzzy and Kink RD settings, rdbwselect() to perform bandwidth selection for the different procedures implemented, and rdplot() to conduct exploratory data analysis (RD plots).

Last updated 1 years ago

5.72 score 4 stars 4 dependents 670 scripts 4.0k downloads

pdfCluster - Cluster Analysis via Nonparametric Density Estimation

Cluster analysis via nonparametric density estimation is performed. Operationally, the kernel method is used throughout to estimate the density. Diagnostics methods for evaluating the quality of the clustering are available. The package includes also a routine to estimate the probability density function obtained by the kernel method, given a set of data with arbitrary dimensions.

Last updated 2 years ago

5.71 score 5 stars 11 dependents 191 scripts 2.7k downloads

googlePolylines - Encoding Coordinates into 'Google' Polylines

Encodes simple feature ('sf') objects and coordinates, and decodes polylines using the 'Google' polyline encoding algorithm (<https://developers.google.com/maps/documentation/utilities/polylinealgorithm>).

Last updated 2 months ago

cpp

5.70 score 9 dependents 79 scripts 4.7k downloads

evtree - Evolutionary Learning of Globally Optimal Trees

Commonly used classification and regression tree methods like the CART algorithm are recursive partitioning methods that build the model in a forward stepwise search. Although this approach is known to be an efficient heuristic, the results of recursive tree methods are only locally optimal, as splits are chosen to maximize homogeneity at the next step only. An alternative way to search over the parameter space of trees is to use global optimization methods like evolutionary algorithms. The 'evtree' package implements an evolutionary algorithm for learning globally optimal classification and regression trees in R. CPU and memory-intensive tasks are fully computed in C++ while the 'partykit' package is leveraged to represent the resulting trees in R, providing unified infrastructure for summaries, visualizations, and predictions.

Last updated 6 years ago

5.69 score 7 stars 2 dependents 126 scripts 1.6k downloads

restriktor - Restricted Statistical Estimation and Inference for Linear Models

Allow for easy-to-use testing or evaluating of linear equality and inequality restrictions about parameters and effects in (generalized) linear statistical models.

Last updated 5 days ago

5.65 score 4 dependents 94 scripts 881 downloads

entropy - Estimation of Entropy, Mutual Information and Related Quantities

Implements various estimators of entropy for discrete random variables, including the shrinkage estimator by Hausser and Strimmer (2009), the maximum likelihood and the Millow-Madow estimator, various Bayesian estimators, and the Chao-Shen estimator. It also offers an R interface to the NSB estimator. Furthermore, the package provides functions for estimating the Kullback-Leibler divergence, the chi-squared divergence, mutual information, and the chi-squared divergence of independence. It also computes the G statistic and the chi-squared statistic and corresponding p-values. Furthermore, there are functions for discretizing continuous random variables.

Last updated 3 years ago

5.63 score 4 stars 61 dependents 852 scripts 5.9k downloads

rcdd - Computational Geometry

R interface to (some of) cddlib (<https://github.com/cddlib/cddlib>). Converts back and forth between two representations of a convex polytope: as solution of a set of linear equalities and inequalities and as convex hull of set of points and rays. Also does linear programming and redundant generator elimination (for example, convex hull in n dimensions). All functions can use exact infinite-precision rational arithmetic.

Last updated 1 years ago

5.61 score 36 dependents 97 scripts 3.8k downloads

exactci - Exact P-Values and Matching Confidence Intervals for Simple Discrete Parametric Cases

Calculates exact tests and confidence intervals for one-sample binomial and one- or two-sample Poisson cases (see Fay (2010) <doi:10.32614/rj-2010-008>).

Last updated 1 years ago

5.57 score 10 dependents 36 scripts 2.1k downloads

sae - Small Area Estimation

Functions for small area estimation.

Last updated 5 years ago

5.57 score 6 stars 8 dependents 82 scripts 1.6k downloads

NADA - Nondetects and Data Analysis for Environmental Data

Contains methods described by Dennis Helsel in his book "Nondetects And Data Analysis: Statistics for Censored Environmental Data".

Last updated 5 years ago

5.56 score 2 stars 14 dependents 116 scripts 3.8k downloads

epiDisplay - Epidemiological Data Display Package

Package for data exploration and result presentation. Full 'epicalc' package with data management functions is available at '<https://medipe.psu.ac.th/epicalc/>'.

Last updated 3 years ago

5.51 score 1 stars 2 dependents 736 scripts 7.3k downloads

gee - Generalized Estimation Equation Solver

Generalized Estimation Equation solver.

Last updated 13 days ago

fortranopenblas

5.45 score 3 stars 17 dependents 610 scripts 9.2k downloads

rsatscan - Tools, Classes, and Methods for Interfacing with 'SaTScan' Stand-Alone Software

'SaTScan'(TM) <https://www.satscan.org> is software for finding regions in Time, Space, or Time-Space that have excess risk, based on scan statistics, and uses Monte Carlo hypothesis testing to generate P-values for these regions. The 'rsatscan' package provides functions for writing R data frames in 'SaTScan'-readable formats, for setting 'SaTScan' parameters, for running 'SaTScan' in the OS, and for reading the files that 'SaTScan' creates.

Last updated 6 months ago

5.45 score 8 stars 35 scripts 227 downloads

bigmemory.sri - A Shared Resource Interface for Bigmemory Project Packages

A shared resource interface for the bigmemory and synchronicity packages.

Last updated 12 months ago

5.43 score 67 dependents 16 scripts 8.4k downloads

mvnormtest - Normality Test for Multivariate Variables

Generalization of Shapiro-Wilk test for multivariate variables.

Last updated 9 months ago

5.36 score 5 dependents 274 scripts 6.2k downloads

pso - Particle Swarm Optimization

Provides an implementation of particle swarm optimisation consistent with the standard PSO 2007/2011 by Maurice Clerc. Additionally a number of ancillary routines are provided for easy testing and graphics.

Last updated 3 years ago

5.35 score 4 stars 23 dependents 89 scripts 4.6k downloads

frailtypack - Shared, Joint (Generalized) Frailty Models; Surrogate Endpoints

The following several classes of frailty models using a penalized likelihood estimation on the hazard function but also a parametric estimation can be fit using this R package: 1) A shared frailty model (with gamma or log-normal frailty distribution) and Cox proportional hazard model. Clustered and recurrent survival times can be studied. 2) Additive frailty models for proportional hazard models with two correlated random effects (intercept random effect with random slope). 3) Nested frailty models for hierarchically clustered data (with 2 levels of clustering) by including two iid gamma random effects. 4) Joint frailty models in the context of the joint modelling for recurrent events with terminal event for clustered data or not. A joint frailty model for two semi-competing risks and clustered data is also proposed. 5) Joint general frailty models in the context of the joint modelling for recurrent events with terminal event data with two independent frailty terms. 6) Joint Nested frailty models in the context of the joint modelling for recurrent events with terminal event, for hierarchically clustered data (with two levels of clustering) by including two iid gamma random effects. 7) Multivariate joint frailty models for two types of recurrent events and a terminal event. 8) Joint models for longitudinal data and a terminal event. 9) Trivariate joint models for longitudinal data, recurrent events and a terminal event. 10) Joint frailty models for the validation of surrogate endpoints in multiple randomized clinical trials with failure-time and/or longitudinal endpoints with the possibility to use a mediation analysis model. 11) Conditional and Marginal two-part joint models for longitudinal semicontinuous data and a terminal event. 12) Joint frailty-copula models for the validation of surrogate endpoints in multiple randomized clinical trials with failure-time endpoints. 13) Generalized shared and joint frailty models for recurrent and terminal events. Proportional hazards (PH), additive hazard (AH), proportional odds (PO) and probit models are available in a fully parametric framework. For PH and AH models, it is possible to consider type-varying coefficients and flexible semiparametric hazard function. Prediction values are available (for a terminal event or for a new recurrent event). Left-truncated (not for Joint model), right-censored data, interval-censored data (only for Cox proportional hazard and shared frailty model) and strata are allowed. In each model, the random effects have the gamma or normal distribution. Now, you can also consider time-varying covariates effects in Cox, shared and joint frailty models (1-5). The package includes concordance measures for Cox proportional hazards models and for shared frailty models. 14) Competing Joint Frailty Model: A single type of recurrent event and two terminal events. Moreover, the package can be used with its shiny application, in a local mode or by following the link below.

Last updated 10 days ago

fortranopenmp

5.35 score 7 stars 1 dependents 89 scripts 1.8k downloads

rbenchmark - Benchmarking routine for R

rbenchmark is inspired by the Perl module Benchmark, and is intended to facilitate benchmarking of arbitrary R code. The library consists of just one function, benchmark, which is a simple wrapper around system.time. Given a specification of the benchmarking process (counts of replications, evaluation environment) and an arbitrary number of expressions, benchmark evaluates each of the expressions in the specified environment, replicating the evaluation as many times as specified, and returning the results conveniently wrapped into a data frame.

Last updated 12 years ago

5.33 score 17 dependents 1.1k scripts 3.7k downloads

logspline - Routines for Logspline Density Estimation

Contains routines for logspline density estimation. The function oldlogspline() uses the same algorithm as the logspline package version 1.0.x; i.e. the Kooperberg and Stone (1992) algorithm (with an improved interface). The recommended routine logspline() uses an algorithm from Stone et al (1997) <DOI:10.1214/aos/1031594728>.

Last updated 8 months ago

fortranopenblas

5.31 score 12 dependents 265 scripts 7.1k downloads

Rfit - Rank-Based Estimation for Linear Models

Rank-based (R) estimation and inference for linear models. Estimation is for general scores and a library of commonly used score functions is included.

Last updated 7 months ago

5.29 score 8 dependents 104 scripts 1.6k downloads

multilevel - Multilevel Functions

Tools used by organizational researchers for the analysis of multilevel data. Includes four broad sets of tools. First, functions for estimating within-group agreement and reliability indices. Second, functions for manipulating multilevel and longitudinal (panel) data. Third, simulations for estimating power and generating multilevel data. Fourth, miscellaneous functions for estimating reliability and performing simple calculations and data transformations.

Last updated 3 years ago

5.28 score 4 dependents 238 scripts 6.7k downloads

CSTools - Assessing Skill of Climate Forecasts on Seasonal-to-Decadal Timescales

Exploits dynamical seasonal forecasts in order to provide information relevant to stakeholders at the seasonal timescale. The package contains process-based methods for forecast calibration, bias correction, statistical and stochastic downscaling, optimal forecast combination and multivariate verification, as well as basic and advanced tools to obtain tailored products. This package was developed in the context of the 'ERA4CS' project 'MEDSCOPE' and the 'H2020 S2S4E' project and includes contributions from 'ArticXchange' project founded by 'EU-PolarNet 2'. 'Pérez-Zanón et al. (2022) <doi:10.5194/gmd-15-6115-2022>'. 'Doblas-Reyes et al. (2005) <doi:10.1111/j.1600-0870.2005.00104.x>'. 'Mishra et al. (2018) <doi:10.1007/s00382-018-4404-z>'. 'Sanchez-Garcia et al. (2019) <doi:10.5194/asr-16-165-2019>'. 'Straus et al. (2007) <doi:10.1175/JCLI4070.1>'. 'Terzago et al. (2018) <doi:10.5194/nhess-18-2825-2018>'. 'Torralba et al. (2017) <doi:10.1175/JAMC-D-16-0204.1>'. 'D'Onofrio et al. (2014) <doi:10.1175/JHM-D-13-096.1>'. 'Verfaillie et al. (2017) <doi:10.5194/gmd-10-4257-2017>'. 'Van Schaeybroeck et al. (2019) <doi:10.1016/B978-0-12-812372-0.00010-8>'. 'Yiou et al. (2013) <doi:10.1007/s00382-012-1626-3>'.

Last updated 11 months ago

fortran

5.27 score 2 stars 1 dependents 62 scripts 938 downloads

PresenceAbsence - Presence-Absence Model Evaluation

Provides a set of functions useful when evaluating the results of presence-absence models. Package includes functions for calculating threshold dependent measures such as confusion matrices, pcc, sensitivity, specificity, and Kappa, and produces plots of each measure as the threshold is varied. It will calculate optimal threshold choice according to a choice of optimization criteria. It also includes functions to plot the threshold independent ROC curves along with the associated AUC (area under the curve).

Last updated 2 years ago

5.26 score 1 stars 9 dependents 208 scripts 3.3k downloads

airGRteaching - Teaching Hydrological Modelling with the GR Rainfall-Runoff Models ('Shiny' Interface Included)

Add-on package to the 'airGR' package that simplifies its use and is aimed at being used for teaching hydrology. The package provides 1) three functions that allow to complete very simply a hydrological modelling exercise 2) plotting functions to help students to explore observed data and to interpret the results of calibration and simulation of the GR ('Génie rural') models 3) a 'Shiny' graphical interface that allows for displaying the impact of model parameters on hydrographs and models internal variables.

Last updated 5 months ago

5.26 score 6 stars 44 scripts 1.7k downloads

orthopolynom - Collection of Functions for Orthogonal and Orthonormal Polynomials

A collection of functions to construct sets of orthogonal polynomials and their recurrence relations. Additional functions are provided to calculate the derivative, integral, value and roots of lists of polynomial objects.

Last updated 2 years ago

5.26 score 49 dependents 250 scripts 4.9k downloads

fossil - Palaeoecological and Palaeogeographical Analysis Tools

A set of analytical tools useful in analysing ecological and geographical data sets, both ancient and modern. The package includes functions for estimating species richness (Chao 1 and 2, ACE, ICE, Jacknife), shared species/beta diversity, species area curves and geographic distances and areas.

Last updated 5 years ago

5.23 score 1 stars 7 dependents 550 scripts 1.5k downloads

ICS - Tools for Exploring Multivariate Data via ICS/ICA

Implementation of Tyler, Critchley, Duembgen and Oja's (JRSS B, 2009, <doi:10.1111/j.1467-9868.2009.00706.x>) and Oja, Sirkia and Eriksson's (AJS, 2006, <https://www.ajs.or.at/index.php/ajs/article/view/vol35,%20no2%263%20-%207>) method of two different scatter matrices to obtain an invariant coordinate system or independent components, depending on the underlying assumptions.

Last updated 1 years ago

5.17 score 17 dependents 46 scripts 2.9k downloads

PairedData - Paired Data Analysis

Many datasets and a set of graphics (based on ggplot2), statistics, effect sizes and hypothesis tests are provided for analysing paired data with S4 class.

Last updated 7 years ago

5.14 score 2 stars 4 dependents 326 scripts 2.2k downloads

ClimProjDiags - Set of Tools to Compute Various Climate Indices

Set of tools to compute metrics and indices for climate analysis. The package provides functions to compute extreme indices, evaluate the agreement between models and combine theses models into an ensemble. Multi-model time series of climate indices can be computed either after averaging the 2-D fields from different models provided they share a common grid or by combining time series computed on the model native grid. Indices can be assigned weights and/or combined to construct new indices.

Last updated 11 months ago

5.14 score 4 dependents 58 scripts 462 downloads

Directional - A Collection of Functions for Directional Data Analysis

A collection of functions for directional data (including massive data, with millions of observations) analysis. Hypothesis testing, discriminant and regression analysis, MLE of distributions and more are included. The standard textbook for such data is the "Directional Statistics" by Mardia, K. V. and Jupp, P. E. (2000). Other references include: a) Paine J.P., Preston S.P., Tsagris M. and Wood A.T.A. (2018). "An elliptically symmetric angular Gaussian distribution". Statistics and Computing 28(3): 689-697. <doi:10.1007/s11222-017-9756-4>. b) Tsagris M. and Alenazi A. (2019). "Comparison of discriminant analysis methods on the sphere". Communications in Statistics: Case Studies, Data Analysis and Applications 5(4):467--491. <doi:10.1080/23737484.2019.1684854>. c) Paine J.P., Preston S.P., Tsagris M. and Wood A.T.A. (2020). "Spherical regression models with general covariates and anisotropic errors". Statistics and Computing 30(1): 153--165. <doi:10.1007/s11222-019-09872-2>. d) Tsagris M. and Alenazi A. (2024). "An investigation of hypothesis testing procedures for circular and spherical mean vectors". Communications in Statistics-Simulation and Computation, 53(3): 1387--1408. <doi:10.1080/03610918.2022.2045499>. e) Yu Z. and Huang X. (2024). A new parameterization for elliptically symmetric angular Gaussian distributions of arbitrary dimension. Electronic Journal of Statistics, 18(1): 301--334. <doi:10.1214/23-EJS2210>. f) Tsagris M. and Alzeley O. (2024). "Circular and spherical projected Cauchy distributions: A Novel Framework for Circular and Directional Data Modeling". Australian & New Zealand Journal of Statistics (Accepted for publication). <doi:10.48550/arXiv.2302.02468>. g) Tsagris M., Papastamoulis P. and Kato S. (2024). "Directional data analysis using the spherical Cauchy and the Poisson kernel-based distribution". <doi:10.48550/arXiv.2409.03292>.

Last updated 19 days ago

5.14 score 3 stars 3 dependents 127 scripts 1.4k downloads

JADE - Blind Source Separation Methods Based on Joint Diagonalization and Some BSS Performance Criteria

Cardoso's JADE algorithm as well as his functions for joint diagonalization are ported to R. Also several other blind source separation (BSS) methods, like AMUSE and SOBI, and some criteria for performance evaluation of BSS algorithms, are given. The package is described in Miettinen, Nordhausen and Taskinen (2017) <doi:10.18637/jss.v076.i02>.

Last updated 1 years ago

cpp

5.14 score 2 stars 18 dependents 67 scripts 1.3k downloads

survivalAnalysis - High-Level Interface for Survival Analysis and Associated Plots

A high-level interface to perform survival analysis, including Kaplan-Meier analysis and log-rank tests and Cox regression. Aims at providing a clear and elegant syntax, support for use in a pipeline, structured output and plotting. Builds upon the 'survminer' package for Kaplan-Meier plots and provides a customizable implementation for forest plots. Kaplan & Meier (1958) <doi:10.1080/01621459.1958.10501452> Cox (1972) <JSTOR:2985181> Peto & Peto (1972) <JSTOR:2344317>.

Last updated 3 years ago

5.12 score 3 stars 1 dependents 49 scripts 579 downloads

deming - Deming, Theil-Sen, Passing-Bablock and Total Least Squares Regression

Generalized Deming regression, Theil-Sen regression and Passing-Bablock regression functions.

Last updated 6 months ago

5.08 score 4 dependents 95 scripts 2.1k downloads

forestmodel - Forest Plots from Regression Models

Produces forest plots using 'ggplot2' from models produced by functions such as stats::lm(), stats::glm() and survival::coxph().

Last updated 4 years ago

5.07 score 1 stars 5 dependents 243 scripts 2.2k downloads

GSA - Gene Set Analysis

Gene Set Analysis.

Last updated 8 months ago

5.06 score 8 dependents 278 scripts 1.7k downloads

CohortCharacteristics - Summarise and Visualise Characteristics of Patients in the OMOP CDM

Summarise and visualise the characteristics of patients in data mapped to the Observational Medical Outcomes Partnership (OMOP) common data model (CDM).

Last updated 28 days ago

5.06 score 95 scripts 483 downloads

jetset - One-to-One Gene-Probeset Mapping for Affymetrix Human Microarrays

On Affymetrix gene expression microarrays, a single gene may be measured by multiple probe sets. This can present a mild conundrum when attempting to evaluate a gene "signature" that is defined by gene names rather than by specific probe sets. This package provides a one-to-one mapping from gene to "best" probe set for four Affymetrix human gene expression microarrays: hgu95av2, hgu133a, hgu133plus2, and u133x3p. This package also includes the pre-calculated probe set quality scores that were used to define the mapping.

Last updated 8 years ago

5.05 score 2 dependents 47 scripts 600 downloads

frbs - Fuzzy Rule-Based Systems for Classification and Regression Tasks

An implementation of various learning algorithms based on fuzzy rule-based systems (FRBSs) for dealing with classification and regression tasks. Moreover, it allows to construct an FRBS model defined by human experts. FRBSs are based on the concept of fuzzy sets, proposed by Zadeh in 1965, which aims at representing the reasoning of human experts in a set of IF-THEN rules, to handle real-life problems in, e.g., control, prediction and inference, data mining, bioinformatics data processing, and robotics. FRBSs are also known as fuzzy inference systems and fuzzy models. During the modeling of an FRBS, there are two important steps that need to be conducted: structure identification and parameter estimation. Nowadays, there exists a wide variety of algorithms to generate fuzzy IF-THEN rules automatically from numerical data, covering both steps. Approaches that have been used in the past are, e.g., heuristic procedures, neuro-fuzzy techniques, clustering methods, genetic algorithms, squares methods, etc. Furthermore, in this version we provide a universal framework named 'frbsPMML', which is adopted from the Predictive Model Markup Language (PMML), for representing FRBS models. PMML is an XML-based language to provide a standard for describing models produced by data mining and machine learning algorithms. Therefore, we are allowed to export and import an FRBS model to/from 'frbsPMML'. Finally, this package aims to implement the most widely used standard procedures, thus offering a standard package for FRBS modeling to the R community.

Last updated 5 years ago

5.02 score 10 stars 1 dependents 75 scripts 1.2k downloads

aTSA - Alternative Time Series Analysis

Contains some tools for testing, analyzing time series data and fitting popular time series models such as ARIMA, Moving Average and Holt Winters, etc. Most functions also provide nice and clear outputs like SAS does, such as identify, estimate and forecast, which are the same statements in PROC ARIMA in SAS.

Last updated 10 months ago

4.99 score 1 stars 5 dependents 378 scripts 8.6k downloads

HMM - Hidden Markov Models

Easy to use library to setup, apply and make inference with discrete time and discrete space Hidden Markov Models.

Last updated 3 years ago

4.98 score 3 stars 4 dependents 268 scripts 676 downloads

VAM - Variance-Adjusted Mahalanobis

Contains logic for cell-specific gene set scoring of single cell RNA sequencing data.

Last updated 1 years ago

4.98 score 4 dependents 16 scripts 480 downloads

ppclust - Probabilistic and Possibilistic Cluster Analysis

Partitioning clustering divides the objects in a data set into non-overlapping subsets or clusters by using the prototype-based probabilistic and possibilistic clustering algorithms. This package covers a set of the functions for Fuzzy C-Means (Bezdek, 1974) <doi:10.1080/01969727308546047>, Possibilistic C-Means (Krishnapuram & Keller, 1993) <doi:10.1109/91.227387>, Possibilistic Fuzzy C-Means (Pal et al, 2005) <doi:10.1109/TFUZZ.2004.840099>, Possibilistic Clustering Algorithm (Yang et al, 2006) <doi:10.1016/j.patcog.2005.07.005>, Possibilistic C-Means with Repulsion (Wachs et al, 2006) <doi:10.1007/3-540-31662-0_6> and the other variants of hard and soft clustering algorithms. The cluster prototypes and membership matrices required by these partitioning algorithms are initialized with different initialization techniques that are available in the package 'inaparc'. As the distance metrics, not only the Euclidean distance but also a set of the commonly used distance metrics are available to use with some of the algorithms in the package.

Last updated 1 years ago

4.93 score 1 stars 4 dependents 117 scripts 557 downloads

tree - Classification and Regression Trees

Classification and regression trees.

Last updated 13 days ago

4.91 score 1 stars 13 dependents 4.2k scripts 21k downloads

cba - Clustering for Business Analytics

Implements clustering techniques such as Proximus and Rock, utility functions for efficient computation of cross distances and data manipulation.

Last updated 4 months ago

4.85 score 3 dependents 171 scripts 2.6k downloads

mixAK - Multivariate Normal Mixture Models and Mixtures of Generalized Linear Mixed Models Including Model Based Clustering

Contains a mixture of statistical methods including the MCMC methods to analyze normal mixtures. Additionally, model based clustering methods are implemented to perform classification based on (multivariate) longitudinal (or otherwise correlated) data. The basis for such clustering is a mixture of multivariate generalized linear mixed models. The package is primarily related to the publications Komárek (2009, Comp. Stat. and Data Anal.) <doi:10.1016/j.csda.2009.05.006> and Komárek and Komárková (2014, J. of Stat. Soft.) <doi:10.18637/jss.v059.i12>. It also implements methods published in Komárek and Komárková (2013, Ann. of Appl. Stat.) <doi:10.1214/12-AOAS580>, Hughes, Komárek, Bonnett, Czanner, García-Fiñana (2017, Stat. in Med.) <doi:10.1002/sim.7397>, Jaspers, Komárek, Aerts (2018, Biom. J.) <doi:10.1002/bimj.201600253> and Hughes, Komárek, Czanner, García-Fiñana (2018, Stat. Meth. in Med. Res) <doi:10.1177/0962280216674496>.

Last updated 3 months ago

openblas

4.84 score 4 stars 3 dependents 108 scripts 899 downloads

fANCOVA - Nonparametric Analysis of Covariance

A collection of R functions to perform nonparametric analysis of covariance for regression curves or surfaces. Testing the equality or parallelism of nonparametric curves or surfaces is equivalent to analysis of variance (ANOVA) or analysis of covariance (ANCOVA) for one-sample functional data. Three different testing methods are available in the package, including one based on L-2 distance, one based on an ANOVA statistic, and one based on variance estimators.

Last updated 4 years ago

4.83 score 18 dependents 97 scripts 2.2k downloads

bst - Gradient Boosting

Functional gradient descent algorithm for a variety of convex and non-convex loss functions, for both classical and robust regression and classification problems. See Wang (2011) <doi:10.2202/1557-4679.1304>, Wang (2012) <doi:10.3414/ME11-02-0020>, Wang (2018) <doi:10.1080/10618600.2018.1424635>, Wang (2018) <doi:10.1214/18-EJS1404>.

Last updated 2 years ago

4.82 score 5 dependents 40 scripts 1.6k downloads

MetBrewer - Color Palettes Inspired by Works at the Metropolitan Museum of Art

Palettes Inspired by Works at the Metropolitan Museum of Art in New York. Currently contains over 50 color schemes and checks for colorblind-friendliness of palettes. Colorblind accessibility checked using the '{colorblindcheck} package by Jakub Nowosad'<https://jakubnowosad.com/colorblindcheck/>.

Last updated 3 years ago

4.81 score 5 dependents 2.1k scripts 2.1k downloads

IDPmisc - 'Utilities of Institute of Data Analyses and Process Design (www.zhaw.ch/idp)'

Different high-level graphics functions for displaying large datasets, displaying circular data in a very flexible way, finding local maxima, brewing color ramps, drawing nice arrows, zooming 2D-plots, creating figures with differently colored margin and plot region. In addition, the package contains auxiliary functions for data manipulation like omitting observations with irregular values or selecting data by logical vectors, which include NAs. Other functions are especially useful in spectroscopy and analyses of environmental data: robust baseline fitting, finding peaks in spectra, converting humidity measures.

Last updated 11 months ago

4.80 score 1 stars 23 dependents 171 scripts 2.7k downloads

propagate - Propagation of Uncertainty

Propagation of uncertainty using higher-order Taylor expansion and Monte Carlo simulation.

Last updated 7 years ago

cpp

4.80 score 2 stars 3 dependents 175 scripts 650 downloads

shiny.blueprint - Palantir's 'Blueprint' for 'Shiny' Apps

Easily use 'Blueprint', the popular 'React' library from Palantir, in your 'Shiny' app. 'Blueprint' provides a rich set of UI components for creating visually appealing applications and is optimized for building complex, data-dense web interfaces. This package provides most components from the underlying library, as well as special wrappers for some components to make it easy to use them in 'R' without writing 'JavaScript' code.

Last updated 7 months ago

4.78 score 120 scripts 298 downloads

tsModel - Time Series Modeling for Air Pollution and Health

Tools for specifying time series regression models.

Last updated 6 months ago

4.77 score 1 stars 6 dependents 176 scripts 3.1k downloads

ISOweek - Week of the year and weekday according to ISO 8601

This is an substitute for the %V and %u formats which are not implemented on Windows. In addition, the package offers functions to convert from standard calender format yyyy-mm-dd to and from ISO 8601 week format yyyy-Www-d.

Last updated 13 years ago

4.77 score 2 stars 9 dependents 210 scripts 5.2k downloads

perm - Exact or Asymptotic Permutation Tests

Perform Exact or Asymptotic permutation tests [see Fay and Shaw <doi:10.18637/jss.v036.i02>].

Last updated 1 years ago

4.76 score 9 dependents 117 scripts 1.8k downloads

monitoR - Acoustic Template Detection in R

Acoustic template detection and monitoring database interface. Create, modify, save, and use templates for detection of animal vocalizations. View, verify, and extract results. Upload a MySQL schema to a existing instance, manage survey metadata, write and read templates and detections locally or to the database.

Last updated 7 years ago

4.76 score 2 stars 5 dependents 95 scripts 630 downloads

irrCAC - Computing Chance-Corrected Agreement Coefficients (CAC)

Calculates various chance-corrected agreement coefficients (CAC) among 2 or more raters are provided. Among the CAC coefficients covered are Cohen's kappa, Conger's kappa, Fleiss' kappa, Brennan-Prediger coefficient, Gwet's AC1/AC2 coefficients, and Krippendorff's alpha. Multiple sets of weights are proposed for computing weighted analyses. All of these statistical procedures are described in details in Gwet, K.L. (2014,ISBN:978-0970806284): "Handbook of Inter-Rater Reliability," 4th edition, Advanced Analytics, LLC.

Last updated 5 years ago

4.73 score 3 dependents 48 scripts 521 downloads

shinycustomloader - Custom Loader for Shiny Outputs

A custom css/html or gif/image file for the loading screen in R 'shiny'. It also can use the marquee to have custom text loading screen.

Last updated 7 years ago

4.73 score 11 dependents 254 scripts 1.3k downloads

tmle - Targeted Maximum Likelihood Estimation

Targeted maximum likelihood estimation of point treatment effects (Targeted Maximum Likelihood Learning, The International Journal of Biostatistics, 2(1), 2006. This version automatically estimates the additive treatment effect among the treated (ATT) and among the controls (ATC). The tmle() function calculates the adjusted marginal difference in mean outcome associated with a binary point treatment, for continuous or binary outcomes. Relative risk and odds ratio estimates are also reported for binary outcomes. Missingness in the outcome is allowed, but not in treatment assignment or baseline covariate values. The population mean is calculated when there is missingness, and no variation in the treatment assignment. The tmleMSM() function estimates the parameters of a marginal structural model for a binary point treatment effect. Effect estimation stratified by a binary mediating variable is also available. An ID argument can be used to identify repeated measures. Default settings call 'SuperLearner' to estimate the Q and g portions of the likelihood, unless values or a user-supplied regression function are passed in as arguments.

Last updated 7 months ago

4.73 score 1 stars 3 dependents 296 scripts 679 downloads

clv - Cluster Validation Techniques

Package contains most of the popular internal and external cluster validation methods ready to use for the most of the outputs produced by functions coming from package "cluster". Package contains also functions and examples of usage for cluster stability approach that might be applied to algorithms implemented in "cluster" package as well as user defined clustering algorithms.

Last updated 1 years ago

4.71 score 1 stars 17 dependents 143 scripts 2.3k downloads

metRology - Support for Metrological Applications

Provides classes and calculation and plotting functions for metrology applications, including measurement uncertainty estimation and inter-laboratory metrology comparison studies.

Last updated 6 years ago

4.69 score 5 stars 7 dependents 201 scripts 1.2k downloads

multipanelfigure - Infrastructure to Assemble Multi-Panel Figures (from Grobs)

Tools to create a layout for figures made of multiple panels, and to fill the panels with base, 'lattice', 'ggplot2' and 'ComplexHeatmap' plots, grobs, as well as content from all image formats supported by 'ImageMagick' (accessed through 'magick').

Last updated 9 months ago

4.67 score 3 stars 155 scripts 636 downloads

BlandAltmanLeh - Plots (Slightly Extended) Bland-Altman Plots

Bland-Altman Plots using either base graphics or ggplot2, augmented with confidence intervals, with detailed return values and a sunflowerplot option for data with ties.

Last updated 9 years ago

4.66 score 2 dependents 77 scripts 936 downloads

tsoutliers - Detection of Outliers in Time Series

Detection of outliers in time series following the Chen and Liu (1993) <DOI:10.2307/2290724> procedure. Innovational outliers, additive outliers, level shifts, temporary changes and seasonal level shifts are considered.

Last updated 11 months ago

4.66 score 5 stars 5 dependents 160 scripts 2.0k downloads

psy - Various Procedures Used in Psychometrics

Kappa, ICC, reliability coefficient, parallel analysis, multi-traits multi-methods, spherical representation of a correlation matrix.

Last updated 3 years ago

4.65 score 4 dependents 266 scripts 1.4k downloads

soundgen - Sound Synthesis and Acoustic Analysis

Performs parametric synthesis of sounds with harmonic and noise components such as animal vocalizations or human voice. Also offers tools for audio manipulation and acoustic analysis, including pitch tracking, spectral analysis, audio segmentation, pitch and formant shifting, etc. Includes four interactive web apps for synthesizing and annotating audio, manually correcting pitch contours, and measuring formant frequencies. Reference: Anikin (2019) <doi:10.3758/s13428-018-1095-7>.

Last updated 2 months ago

4.65 score 1 stars 2 dependents 111 scripts 1.1k downloads

asnipe - Animal Social Network Inference and Permutations for Ecologists

Implements several tools that are used in animal social network analysis, as described in Whitehead (2007) Analyzing Animal Societies <University of Chicago Press> and Farine & Whitehead (2015) <doi: 10.1111/1365-2656.12418>. In particular, this package provides the tools to infer groups and generate networks from observation data, perform permutation tests on the data, calculate lagged association rates, and performed multiple regression analysis on social network data.

Last updated 1 years ago

4.62 score 2 stars 2 dependents 174 scripts 2.0k downloads

tis - Time Indexes and Time Indexed Series

Functions and S3 classes for time indexes and time indexed series, which are compatible with FAME frequencies.

Last updated 3 years ago

4.62 score 6 dependents 211 scripts 11k downloads

speedglm - Fitting Linear and Generalized Linear Models to Large Data Sets

Fitting linear models and generalized linear models to large data sets by updating algorithms, according to the method described in Enea (2009, ISBN: 9788861294257).

Last updated 2 years ago

4.59 score 9 stars 12 dependents 262 scripts 6.1k downloads

hmeasure - The H-Measure and Other Scalar Classification Performance Metrics

Classification performance metrics that are derived from the ROC curve of a classifier. The package includes the H-measure performance metric as described in <http://link.springer.com/article/10.1007/s10994-009-5119-5>, which computes the minimum total misclassification cost, integrating over any uncertainty about the relative misclassification costs, as per a user-defined prior. It also offers a one-stop-shop for other scalar metrics of performance, including sensitivity, specificity and many others, and also offers plotting tools for ROC curves and related statistics.

Last updated 6 years ago

4.59 score 1 dependents 129 scripts 606 downloads

mcr - Method Comparison Regression

Regression methods to quantify the relation between two measurement methods are provided by this package. In particular it addresses regression problems with errors in both variables and without repeated measurements. It implements the CLSI recommendations (see J. A. Budd et al. (2018, <https://clsi.org/standards/products/method-evaluation/documents/ep09/>) for analytical method comparison and bias estimation using patient samples. Furthermore, algorithms for Theil-Sen and equivariant Passing-Bablok estimators are implemented, see F. Dufey (2020, <doi:10.1515/ijb-2019-0157>) and J. Raymaekers and F. Dufey (2022, <arXiv:2202:08060>). A comprehensive overview over the implemented methods and references can be found in the manual pages "mcr-package" and "mcreg".

Last updated 3 months ago

fortran

4.58 score 1 stars 6 dependents 82 scripts 2.6k downloads

BMS - Bayesian Model Averaging Library

Bayesian Model Averaging for linear models with a wide choice of (customizable) priors. Built-in priors include coefficient priors (fixed, hyper-g and empirical priors), 5 kinds of model priors, moreover model sampling by enumeration or various MCMC approaches. Post-processing functions allow for inferring posterior inclusion and model probabilities, various moments, coefficient and predictive densities. Plotting functions available for posterior model size, MCMC convergence, predictive and coefficient densities, best models representation, BMA comparison. Also includes Bayesian normal-conjugate linear model with Zellner's g prior, and assorted methods.

Last updated 2 years ago

4.58 score 1 stars 382 scripts 709 downloads

Platypus - Single-Cell Immune Repertoire and Gene Expression Analysis

We present 'Platypus', an open-source software platform providing a user-friendly interface to investigate B-cell receptor and T-cell receptor repertoires from scSeq experiments. 'Platypus' provides a framework to automate and ease the analysis of single-cell immune repertoires while also incorporating transcriptional information involving unsupervised clustering, gene expression and gene ontology. This R version of 'Platypus' is part of the 'ePlatypus' ecosystem for computational analysis of immunogenomics data: Yermanos et al. (2021) <doi:10.1093/nargab/lqab023>, Cotet et al. (2023) <doi:10.1093/bioinformatics/btad553>.

Last updated 2 months ago

4.56 score 36 scripts 259 downloads

metaumbrella - Umbrella Review Package for R

A comprehensive range of facilities to perform umbrella reviews with stratification of the evidence in R. The package accomplishes this aim by building on three core functions that: (i) automatically perform all required calculations in an umbrella review (including but not limited to meta-analyses), (ii) stratify evidence according to various classification criteria, and (iii) generate a visual representation of the results. Note that if you are not familiar with R, the core features of this package are available from a web browser (<https://www.metaumbrella.org/>).

Last updated 10 months ago

4.56 score 9 stars 9 scripts 289 downloads

ftsa - Functional Time Series Analysis

Functions for visualizing, modeling, forecasting and hypothesis testing of functional time series.

Last updated 11 months ago

4.55 score 6 stars 9 dependents 94 scripts 2.3k downloads

locpol - Kernel Local Polynomial Regression

Computes local polynomial estimators for the regression and also density. It comprises several different utilities to handle kernel estimators.

Last updated 2 years ago

4.53 score 2 stars 22 dependents 123 scripts 2.1k downloads

GPfit - Gaussian Processes Modeling

A computationally stable approach of fitting a Gaussian Process (GP) model to a deterministic simulator.

Last updated 6 years ago

4.52 score 1 stars 42 dependents 102 scripts 26k downloads

Compositional - Compositional Data Analysis

Regression, classification, contour plots, hypothesis testing and fitting of distributions for compositional data are some of the functions included. We further include functions for percentages (or proportions). The standard textbook for such data is John Aitchison's (1986) "The statistical analysis of compositional data". Relevant papers include: a) Tsagris M.T., Preston S. and Wood A.T.A. (2011). "A data-based power transformation for compositional data". Fourth International International Workshop on Compositional Data Analysis. <doi:10.48550/arXiv.1106.1451> b) Tsagris M. (2014). "The k-NN algorithm for compositional data: a revised approach with and without zero values present". Journal of Data Science, 12(3): 519--534. <doi:10.6339/JDS.201407_12(3).0008>. c) Tsagris M. (2015). "A novel, divergence based, regression for compositional data". Proceedings of the 28th Panhellenic Statistics Conference, 15-18 April 2015, Athens, Greece, 430--444. <doi:10.48550/arXiv.1511.07600>. d) Tsagris M. (2015). "Regression analysis with compositional data containing zero values". Chilean Journal of Statistics, 6(2): 47--57. <https://soche.cl/chjs/volumes/06/02/Tsagris(2015).pdf>. e) Tsagris M., Preston S. and Wood A.T.A. (2016). "Improved supervised classification for compositional data using the alpha-transformation". Journal of Classification, 33(2): 243--261. <doi:10.1007/s00357-016-9207-5>. f) Tsagris M., Preston S. and Wood A.T.A. (2017). "Nonparametric hypothesis testing for equality of means on the simplex". Journal of Statistical Computation and Simulation, 87(2): 406--422. <doi:10.1080/00949655.2016.1216554>. g) Tsagris M. and Stewart C. (2018). "A Dirichlet regression model for compositional data with zeros". Lobachevskii Journal of Mathematics, 39(3): 398--412. <doi:10.1134/S1995080218030198>. h) Alenazi A. (2019). "Regression for compositional data with compositional data as predictor variables with or without zero values". Journal of Data Science, 17(1): 219--238. <doi:10.6339/JDS.201901_17(1).0010>. i) Tsagris M. and Stewart C. (2020). "A folded model for compositional data analysis". Australian and New Zealand Journal of Statistics, 62(2): 249--277. <doi:10.1111/anzs.12289>. j) Alenazi A.A. (2022). "f-divergence regression models for compositional data". Pakistan Journal of Statistics and Operation Research, 18(4): 867--882. <doi:10.18187/pjsor.v18i4.3969>. k) Tsagris M. and Stewart C. (2022). "A Review of Flexible Transformations for Modeling Compositional Data". In Advances and Innovations in Statistics and Data Science, pp. 225--234. <doi:10.1007/978-3-031-08329-7_10>. l) Alenazi A. (2023). "A review of compositional data analysis and recent advances". Communications in Statistics--Theory and Methods, 52(16): 5535--5567. <doi:10.1080/03610926.2021.2014890>. m) Tsagris M., Alenazi A. and Stewart C. (2023). "Flexible non-parametric regression models for compositional response data with zeros". Statistics and Computing, 33(106). <doi:10.1007/s11222-023-10277-5>. n) Tsagris. M. (2024). "Constrained least squares simplicial-simplicial regression". <doi:10.48550/arXiv.2403.19835>.

Last updated 20 days ago

4.51 score 2 stars 4 dependents 128 scripts 1.5k downloads

DImodels - Diversity-Interactions (DI) Models

The 'DImodels' package is suitable for analysing data from biodiversity and ecosystem function studies using the Diversity-Interactions (DI) modelling approach introduced by Kirwan et al. (2009) <doi:10.1890/08-1684.1>. Suitable data will contain proportions for each species and a community-level response variable, and may also include additional factors, such as blocks or treatments. The package can perform data manipulation tasks, such as computing pairwise interactions (the DI_data() function), can perform an automated model selection process (the autoDI() function) and has the flexibility to fit a wide range of user-defined DI models (the DI() function).

Last updated 10 months ago

4.49 score 2 dependents 52 scripts 320 downloads

overlapping - Estimation of Overlapping in Empirical Distributions

Functions for estimating the overlapping area of two or more kernel density estimations from empirical data.

Last updated 2 years ago

4.49 score 8 dependents 78 scripts 4.1k downloads

apc - Age-Period-Cohort Analysis

Functions for age-period-cohort analysis. Aggregate data can be organised in matrices indexed by age-cohort, age-period or cohort-period. The data can include dose and response or just doses. The statistical model is a generalized linear model (GLM) allowing for 3,2,1 or 0 of the age-period-cohort factors. Individual-level data should have a row for each individual and columns for each of age, period, and cohort. The statistical model for repeated cross-section is a generalized linear model. The statistical model for panel data is ordinary least squares. The canonical parametrisation of Kuang, Nielsen and Nielsen (2008) <DOI:10.1093/biomet/asn026> is used. Thus, the analysis does not rely on ad hoc identification.

Last updated 4 years ago

4.49 score 49 scripts 330 downloads

nsRFA - Non-Supervised Regional Frequency Analysis

A collection of statistical tools for objective (non-supervised) applications of the Regional Frequency Analysis methods in hydrology. The package refers to the index-value method and, more precisely, helps the hydrologist to: (1) regionalize the index-value; (2) form homogeneous regions with similar growth curves; (3) fit distribution functions to the empirical regional growth curves. Most of the methods are those described in the Flood Estimation Handbook (Centre for Ecology & Hydrology, 1999, ISBN:9781906698003). Homogeneity tests from Hosking and Wallis (1993) <doi:10.1029/92WR01980> and Viglione et al. (2007) <doi:10.1029/2006WR005095> are available.

Last updated 7 months ago

4.49 score 2 stars 51 scripts 757 downloads

PracTools - Designing and Weighting Survey Samples

Functions and datasets to support Valliant, Dever, and Kreuter (2018), <doi:10.1007/978-3-319-93632-1>, "Practical Tools for Designing and Weighting Survey Samples". Contains functions for sample size calculation for survey samples using stratified or clustered one-, two-, and three-stage sample designs, and single-stage audit sample designs. Functions are included that will group geographic units accounting for distances apart and measures of size. Other functions compute variance components for multistage designs and sample sizes in two-phase designs. A number of example data sets are included.

Last updated 6 months ago

4.48 score 1 stars 1 dependents 101 scripts 592 downloads

paleoTS - Analyze Paleontological Time-Series

Facilitates analysis of paleontological sequences of trait values. Functions are provided to fit, using maximum likelihood, simple evolutionary models (including unbiased random walks, directional evolution,stasis, Ornstein-Uhlenbeck, covariate-tracking) and complex models (punctuation, mode shifts).

Last updated 3 months ago

4.48 score 1 stars 2 dependents 247 scripts 584 downloads

heatmap3 - An Improved Heatmap Package

An improved heatmap package. Completely compatible with the original R function 'heatmap', and provides more powerful and convenient features.

Last updated 4 years ago

4.48 score 2 dependents 568 scripts 965 downloads

fmri - Analysis of fMRI Experiments

Contains R-functions to perform an fMRI analysis as described in Polzehl and Tabelow (2019) <DOI:10.1007/978-3-030-29184-6>, Tabelow et al. (2006) <DOI:10.1016/j.neuroimage.2006.06.029>, Polzehl et al. (2010) <DOI:10.1016/j.neuroimage.2010.04.241>, Tabelow and Polzehl (2011) <DOI:10.18637/jss.v044.i11>.

Last updated 5 months ago

fortranopenblas

4.47 score 2 stars 1 dependents 98 scripts 596 downloads

SAMBA - Selection and Misclassification Bias Adjustment for Logistic Regression Models

Health research using data from electronic health records (EHR) has gained popularity, but misclassification of EHR-derived disease status and lack of representativeness of the study sample can result in substantial bias in effect estimates and can impact power and type I error for association tests. Here, the assumed target of inference is the relationship between binary disease status and predictors modeled using a logistic regression model. 'SAMBA' implements several methods for obtaining bias-corrected point estimates along with valid standard errors as proposed in Beesley and Mukherjee (2020) <doi:10.1101/2019.12.26.19015859>, currently under review.

Last updated 5 years ago

4.43 score 1 dependents 18 scripts 129 downloads

PMCMR - Calculate Pairwise Multiple Comparisons of Mean Rank Sums

Note, that the 'PMCMR' package is superset by the novel 'PMCMRplus' package. The 'PMCMRplus' package contains all functions from 'PMCMR' and many more parametric and non-parametric multiple comparison procedures, one-factorial trend tests, as well as improved method functions, such as print, summary and plot. The 'PMCMR' package is no longer maintained, but kept for compatibility of reverse depending packages for some time.

Last updated 3 years ago

4.42 score 2 stars 1 dependents 198 scripts 2.2k downloads

OrgMassSpecR - Organic Mass Spectrometry

Organic/biological mass spectrometry data analysis.

Last updated 7 years ago

4.41 score 2 dependents 53 scripts 411 downloads

CUB - A Class of Mixture Models for Ordinal Data

For ordinal rating data, estimate and test models within the family of CUB models and their extensions (where CUB stands for Combination of a discrete Uniform and a shifted Binomial distributions); Simulation routines, plotting facilities and fitting measures are also provided.

Last updated 10 months ago

4.37 score 1 dependents 79 scripts 318 downloads

hce - Design and Analysis of Hierarchical Composite Endpoints

Simulate and analyze hierarchical composite endpoints. Win odds is the main analysis method, but other win statistics (win ratio, net benefit) are also implemented, provided there is no censoring. See Gasparyan SB et al (2023) "Hierarchical Composite Endpoints in COVID-19: The DARE-19 Trial." Case Studies in Innovative Clinical Trials, 95-148. Chapman; Hall/CRC. <doi:10.1201/9781003288640-7>.

Last updated 2 months ago

4.37 score 1 dependents 13 scripts 257 downloads

lisrelToR - Import Output from LISREL into R

This is an unofficial package aimed at automating the import of LISREL output in R. This package or its maintainer is not in any way affiliated with the creators of LISREL and SSI, Inc.

Last updated 11 months ago

4.36 score 13 dependents 2 scripts 12k downloads

mcclust - Process an MCMC Sample of Clusterings

Implements methods for processing a sample of (hard) clusterings, e.g. the MCMC output of a Bayesian clustering model. Among them are methods that find a single best clustering to represent the sample, which are based on the posterior similarity matrix or a relabelling algorithm.

Last updated 3 years ago

4.35 score 10 dependents 188 scripts 552 downloads

HMP - Hypothesis Testing and Power Calculations for Comparing Metagenomic Samples from HMP

Using Dirichlet-Multinomial distribution to provide several functions for formal hypothesis testing, power and sample size calculations for human microbiome experiments.

Last updated 5 years ago

4.35 score 1 stars 1 dependents 75 scripts 263 downloads

preseqR - Predicting Species Accumulation Curves

Originally as an R version of Preseq <doi:10.1038/nmeth.2375>, the package has extended its functionality to predict the r-species accumulation curve (r-SAC), which is the number of species represented at least r times as a function of the sampling effort. When r = 1, the curve is known as the species accumulation curve, or the library complexity curve in high-throughput genomic sequencing. The package includes both parametric and nonparametric methods, as described by Deng C, et al. (2018) <arXiv:1607.02804v3>.

Last updated 6 years ago

4.35 score 1 stars 3 dependents 123 scripts 534 downloads

Rlab - Functions and Datasets Required for ST370 Class

Provides functions and datasets required for the ST 370 course at North Carolina State University.

Last updated 3 years ago

4.34 score 8 dependents 614 scripts 1.5k downloads

Mercator - Clustering and Visualizing Distance Matrices

Defines the classes used to explore, cluster and visualize distance matrices, especially those arising from binary data. See Abrams and colleagues, 2021, <doi:10.1093/bioinformatics/btab037>.

Last updated 2 months ago

clustering

4.33 score 1 dependents 12 scripts 645 downloads

sdpt3r - Semi-Definite Quadratic Linear Programming Solver

Solves the general Semi-Definite Linear Programming formulation using an R implementation of SDPT3 (K.C. Toh, M.J. Todd, and R.H. Tutuncu (1999) <doi:10.1080/10556789908805762>). This includes problems such as the nearest correlation matrix problem (Higham (2002) <doi:10.1093/imanum/22.3.329>), D-optimal experimental design (Smith (1918) <doi:10.2307/2331929>), Distance Weighted Discrimination (Marron and Todd (2012) <doi:10.1198/016214507000001120>), as well as graph theory problems including the maximum cut problem. Technical details surrounding SDPT3 can be found in R.H Tutuncu, K.C. Toh, and M.J. Todd (2003) <doi:10.1007/s10107-002-0347-5>.

Last updated 6 years ago

4.33 score 1 stars 3 dependents 20 scripts 321 downloads

som - Self-Organizing Map

Self-Organizing Map (with application in gene clustering).

Last updated 3 months ago

cpp

4.32 score 14 dependents 69 scripts 5.6k downloads

interval - Weighted Logrank Tests and NPMLE for Interval Censored Data

Functions to fit nonparametric survival curves, plot them, and perform logrank or Wilcoxon type tests [see Fay and Shaw <doi:10.18637/jss.v036.i02>].

Last updated 1 years ago

4.32 score 4 dependents 43 scripts 1.3k downloads

optiSel - Optimum Contribution Selection and Population Genetics

A framework for the optimization of breeding programs via optimum contribution selection and mate allocation. An easy to use set of function for computation of optimum contributions of selection candidates, and of the population genetic parameters to be optimized. These parameters can be estimated using pedigree or genotype information, and include kinships, kinships at native haplotype segments, and breed composition of crossbred individuals. They are suitable for managing genetic diversity, removing introgressed genetic material, and accelerating genetic gain. Additionally, functions are provided for computing genetic contributions from ancestors, inbreeding coefficients, the native effective size, the native genome equivalent, pedigree completeness, and for preparing and plotting pedigrees. The methods are described in:\n Wellmann, R., and Pfeiffer, I. (2009) <doi:10.1017/S0016672309000202>.\n Wellmann, R., and Bennewitz, J. (2011) <doi:10.2527/jas.2010-3709>.\n Wellmann, R., Hartwig, S., Bennewitz, J. (2012) <doi:10.1186/1297-9686-44-34>.\n de Cara, M. A. R., Villanueva, B., Toro, M. A., Fernandez, J. (2013) <doi:10.1111/mec.12560>.\n Wellmann, R., Bennewitz, J., Meuwissen, T.H.E. (2014) <doi:10.1017/S0016672314000196>.\n Wellmann, R. (2019) <doi:10.1186/s12859-018-2450-5>.

Last updated 6 months ago

cpp

4.31 score 49 scripts 705 downloads

survC1 - C-Statistics for Risk Prediction Models with Censored Survival Data

Performs inference for C of risk prediction models with censored survival data, using the method proposed by Uno et al. (2011) <doi:10.1002/sim.4154>. Inference for the difference in C between two competing prediction models is also implemented.

Last updated 4 years ago

fortran

4.30 score 4 dependents 42 scripts 750 downloads

spcosa - Spatial Coverage Sampling and Random Sampling from Compact Geographical Strata

Spatial coverage sampling and random sampling from compact geographical strata created by k-means. See Walvoort et al. (2010) <doi:10.1016/j.cageo.2010.04.005> for details.

Last updated 2 years ago

openjdk

4.30 score 2 stars 1 dependents 67 scripts 488 downloads

ips - Interfaces to Phylogenetic Software in R

Functions that wrap popular phylogenetic software for sequence alignment, masking of sequence alignments, and estimation of phylogenies and ancestral character states.

Last updated 8 months ago

4.30 score 1 dependents 125 scripts 1.1k downloads

arcpullr - Pull Data from an 'ArcGIS REST' API

Functions to efficiently query 'ArcGIS REST' APIs <https://developers.arcgis.com/rest/>. Both spatial and SQL queries can be used to retrieve data. Simple Feature (sf) objects are utilized to perform spatial queries. This package was neither produced nor is maintained by Esri.

Last updated 10 months ago

4.30 score 1 dependents 44 scripts 498 downloads

SOMbrero - SOM Bound to Realize Euclidean and Relational Outputs

The stochastic (also called on-line) version of the Self-Organising Map (SOM) algorithm is provided. Different versions of the algorithm are implemented, for numeric and relational data and for contingency tables as described, respectively, in Kohonen (2001) <isbn:3-540-67921-9>, Olteanu & Villa-Vialaneix (2005) <doi:10.1016/j.neucom.2013.11.047> and Cottrell et al (2004) <doi:10.1016/j.neunet.2004.07.010>. The package also contains many plotting features (to help the user interpret the results), can handle (and impute) missing values and is delivered with a graphical user interface based on 'shiny'.

Last updated 11 months ago

4.30 score 1 stars 1 dependents 110 scripts 322 downloads

SNFtool - Similarity Network Fusion

Similarity Network Fusion takes multiple views of a network and fuses them together to construct an overall status matrix. The input to our algorithm can be feature vectors, pairwise distances, or pairwise similarities. The learned status matrix can then be used for retrieval, clustering, and classification.

Last updated 4 years ago

4.29 score 18 stars 4 dependents 478 scripts 445 downloads

mistr - Mixture and Composite Distributions

A flexible computational framework for mixture distributions with the focus on the composite models.

Last updated 2 years ago

4.28 score 4 dependents 80 scripts 230 downloads

PlayerRatings - Dynamic Updating Methods for Player Ratings Estimation

Implements schemes for estimating player or team skill based on dynamic updating. Implemented methods include Elo, Glicko, Glicko-2 and Stephenson. Contains pdf documentation of a reproducible analysis using approximately two million chess matches. Also contains an Elo based method for multi-player games where the result is a placing or a score. This includes zero-sum games such as poker and mahjong.

Last updated 5 years ago

4.28 score 9 stars 71 scripts 298 downloads

adlift - An Adaptive Lifting Scheme Algorithm

Adaptive wavelet lifting transforms for signal denoising using optimal local neighbourhood regression, from Nunes et al. (2006) <doi:10.1007/s11222-006-6560-y>.

Last updated 2 years ago

openblas

4.26 score 9 dependents 52 scripts 68k downloads

CTT - Classical Test Theory Functions

A collection of common test and item analyses from a classical test theory (CTT) framework. Analyses can be applied to both dichotomous and polytomous data. Functions provide reliability analyses (alpha), item statistics, disctractor analyses, disattenuated correlations, scoring routines, and empirical ICCs.

Last updated 6 years ago

4.25 score 5 dependents 73 scripts 1.6k downloads

rriskDistributions - Fitting Distributions to Given Data or Known Quantiles

Collection of functions for fitting distributions to given data or by known quantiles. Two main functions fit.perc() and fit.cont() provide users a GUI that allows to choose a most appropriate distribution without any knowledge of the R syntax. Note, this package is a part of the 'rrisk' project.

Last updated 8 years ago

4.25 score 1 dependents 170 scripts 1.4k downloads

PCDimension - Finding the Number of Significant Principal Components

Implements methods to automate the Auer-Gervini graphical Bayesian approach for determining the number of significant principal components. Automation uses clustering, change points, or simple statistical models to distinguish "long" from "short" steps in a graph showing the posterior number of components as a function of a prior parameter. See <doi:10.1101/237883>.

Last updated 2 years ago

clustering

4.23 score 4 dependents 22 scripts 1.6k downloads

GiRaF - Gibbs Random Fields Analysis

Allows calculation on, and sampling from Gibbs Random Fields, and more precisely general homogeneous Potts model. The primary tool is the exact computation of the intractable normalising constant for small rectangular lattices. Beside the latter function, it contains method that give exact sample from the likelihood for small enough rectangular lattices or approximate sample from the likelihood using MCMC samplers for large lattices.

Last updated 4 years ago

cpp

4.21 score 3 dependents 18 scripts 238 downloads

elasticnet - Elastic-Net for Sparse Estimation and Sparse PCA

Provides functions for fitting the entire solution path of the Elastic-Net and also provides functions for doing sparse PCA.

Last updated 5 years ago

4.21 score 1 stars 22 dependents 358 scripts 2.4k downloads

sparcl - Perform Sparse Hierarchical Clustering and Sparse K-Means Clustering

Implements the sparse clustering methods of Witten and Tibshirani (2010): "A framework for feature selection in clustering"; published in Journal of the American Statistical Association 105(490): 713-726.

Last updated 6 years ago

fortran

4.20 score 1 stars 4 dependents 132 scripts 626 downloads

textreg - n-Gram Text Regression, aka Concise Comparative Summarization

Function for sparse regression on raw text, regressing a labeling vector onto a feature space consisting of all possible phrases.

Last updated 6 years ago

cpp

4.18 score 1 stars 74 scripts 4.1k downloads

NlcOptim - Solve Nonlinear Optimization with Nonlinear Constraints

Optimization for nonlinear objective and constraint functions. Linear or nonlinear equality and inequality constraints are allowed. It accepts the input parameters as a constrained matrix.

Last updated 6 years ago

4.17 score 4 stars 11 dependents 31 scripts 3.6k downloads

languageR - Analyzing Linguistic Data: A Practical Introduction to Statistics

Data sets exemplifying statistical methods, and some facilitatory utility functions used in ``Analyzing Linguistic Data: A practical introduction to statistics using R'', Cambridge University Press, 2008.

Last updated 6 years ago

4.16 score 468 scripts 3.1k downloads

flux - Flux Rate Calculation from Dynamic Closed Chamber Measurements

Functions for the calculation of greenhouse gas flux rates from closed chamber concentration measurements. The package follows a modular concept: Fluxes can be calculated in just two simple steps or in several steps if more control in details is wanted. Additionally plot and preparation functions as well as functions for modelling gpp and reco are provided.

Last updated 2 years ago

4.16 score 2 stars 3 dependents 90 scripts 422 downloads

RSDA - R to Symbolic Data Analysis

Symbolic Data Analysis (SDA) was proposed by professor Edwin Diday in 1987, the main purpose of SDA is to substitute the set of rows (cases) in the data table for a concept (second order statistical unit). This package implements, to the symbolic case, certain techniques of automatic classification, as well as some linear models.

Last updated 1 years ago

4.15 score 1 stars 3 dependents 78 scripts 416 downloads

ConsRank - Compute the Median Ranking(s) According to the Kemeny's Axiomatic Approach

Compute the median ranking according to the Kemeny's axiomatic approach. Rankings can or cannot contain ties, rankings can be both complete or incomplete. The package contains both branch-and-bound algorithms and heuristic solutions recently proposed. The searching space of the solution can either be restricted to the universe of the permutations or unrestricted to all possible ties. The package also provide some useful utilities for deal with preference rankings, including both element-weight Kemeny distance and correlation coefficient. This release declare as deprecated some functions that are still in the package for compatibility. Next release will not contains these functions. Please type '?ConsRank-deprecated' Essential references: Emond, E.J., and Mason, D.W. (2002) <doi:10.1002/mcda.313>; D'Ambrosio, A., Amodio, S., and Iorio, C. (2015) <doi:10.1285/i20705948v8n2p198>; Amodio, S., D'Ambrosio, A., and Siciliano R. (2016) <doi:10.1016/j.ejor.2015.08.048>; D'Ambrosio, A., Mazzeo, G., Iorio, C., and Siciliano, R. (2017) <doi:10.1016/j.cor.2017.01.017>; Albano, A., and Plaia, A. (2021) <doi:10.1285/i20705948v14n1p117>.

Last updated 11 months ago

4.14 score 3 stars 8 dependents 23 scripts 4.2k downloads

glmertree - Generalized Linear Mixed Model Trees

Recursive partitioning based on (generalized) linear mixed models (GLMMs) combining lmer()/glmer() from 'lme4' and lmtree()/glmtree() from 'partykit'. The fitting algorithm is described in more detail in Fokkema, Smits, Zeileis, Hothorn & Kelderman (2018; <DOI:10.3758/s13428-017-0971-x>). For detecting and modeling subgroups in growth curves with GLMM trees see Fokkema & Zeileis (2024; <DOI:10.3758/s13428-024-02389-1>).

Last updated 2 months ago

4.11 score 1 dependents 41 scripts 1.8k downloads

LTASR - Functions to Replicate the Center for Disease Control and Prevention's 'LTAS' Software in R

A suite of functions for reading in a rate file in XML format, stratify a cohort, and calculate 'SMRs' from the stratified cohort and rate file.

Last updated 4 months ago

4.11 score 32 scripts 218 downloads

ecoCopula - Graphical Modelling and Ordination using Copulas

Creates 'graphs' of species associations (interactions) and ordination biplots from co-occurrence data by fitting discrete gaussian copula graphical models. Methods described in Popovic, GC., Hui, FKC., Warton, DI., (2018) <doi:10.1016/j.jmva.2017.12.002>.

Last updated 3 years ago

4.09 score 2 dependents 41 scripts 337 downloads

conf - Visualization and Analysis of Statistical Measures of Confidence

Enables: (1) plotting two-dimensional confidence regions, (2) coverage analysis of confidence region simulations, (3) calculating confidence intervals and the associated actual coverage for binomial proportions, (4) calculating the support values and the probability mass function of the Kaplan-Meier product-limit estimator, and (5) plotting the actual coverage function associated with a confidence interval for the survivor function from a randomly right-censored data set. Each is given in greater detail next. (1) Plots the two-dimensional confidence region for probability distribution parameters (supported distribution suffixes: cauchy, gamma, invgauss, logis, llogis, lnorm, norm, unif, weibull) corresponding to a user-given complete or right-censored dataset and level of significance. The crplot() algorithm plots more points in areas of greater curvature to ensure a smooth appearance throughout the confidence region boundary. An alternative heuristic plots a specified number of points at roughly uniform intervals along its boundary. Both heuristics build upon the radial profile log-likelihood ratio technique for plotting confidence regions given by Jaeger (2016) <doi:10.1080/00031305.2016.1182946>, and are detailed in a publication by Weld et al. (2019) <doi:10.1080/00031305.2018.1564696>. (2) Performs confidence region coverage simulations for a random sample drawn from a user- specified parametric population distribution, or for a user-specified dataset and point of interest with coversim(). (3) Calculates confidence interval bounds for a binomial proportion with binomTest(), calculates the actual coverage with binomTestCoverage(), and plots the actual coverage with binomTestCoveragePlot(). Calculates confidence interval bounds for the binomial proportion using an ensemble of constituent confidence intervals with binomTestEnsemble(). Calculates confidence interval bounds for the binomial proportion using a complete enumeration of all possible transitions from one actual coverage acceptance curve to another which minimizes the root mean square error for n <= 15 and follows the transitions for well-known confidence intervals for n > 15 using binomTestMSE(). (4) The km.support() function calculates the support values of the Kaplan-Meier product-limit estimator for a given sample size n using an induction algorithm described in Qin et al. (2023) <doi:10.1080/00031305.2022.2070279>. The km.outcomes() function generates a matrix containing all possible outcomes (all possible sequences of failure times and right-censoring times) of the value of the Kaplan-Meier product-limit estimator for a particular sample size n. The km.pmf() function generates the probability mass function for the support values of the Kaplan-Meier product-limit estimator for a particular sample size n, probability of observing a failure h at the time of interest expressed as the cumulative probability percentile associated with X = min(T, C), where T is the failure time and C is the censoring time under a random-censoring scheme. The km.surv() function generates multiple probability mass functions of the Kaplan-Meier product-limit estimator for the same arguments as those given for km.pmf(). (5) The km.coverage() function plots the actual coverage function associated with a confidence interval for the survivor function from a randomly right-censored data set for one or more of the following confidence intervals: Greenwood, log-minus-log, Peto, arcsine, and exponential Greenwood. The actual coverage function is plotted for a small number of items on test, stated coverage, failure rate, and censoring rate. The km.coverage() function can print an optional table containing all possible failure/censoring orderings, along with their contribution to the actual coverage function.

Last updated 8 months ago

4.08 score 85 scripts 894 downloads

ExpImage - Analysis of Images in Experiments

Tools created for image analysis in researches. There are functions associated with image editing, segmentation, and obtaining biometric measurements (Este pacote foi idealizado para para a analise de imagens em pesquisas. Ha funcoes associadas a edicao de imagens, segmentacao, e obtencao de medidas biometricas) <https://www.expstat.com/pacotes-do-r/expimage>.

Last updated 8 months ago

4.05 score 63 scripts 299 downloads

GeneNet - Modeling and Inferring Gene Networks

Analyzes gene expression (time series) data with focus on the inference of gene networks. In particular, GeneNet implements the methods of Schaefer and Strimmer (2005a,b,c) and Opgen-Rhein and Strimmer (2006, 2007) for learning large-scale gene association networks (including assignment of putative directions).

Last updated 3 years ago

4.03 score 4 dependents 89 scripts 529 downloads

mix - Estimation/Multiple Imputation for Mixed Categorical and Continuous Data

Estimation/multiple imputation programs for mixed categorical and continuous data.

Last updated 13 days ago

fortran

4.03 score 2 stars 5 dependents 30 scripts 2.5k downloads

pBrackets - Plot Brackets

Adds different kinds of brackets to a plot, including braces, chevrons, parentheses or square brackets.

Last updated 4 years ago

4.01 score 1 dependents 344 scripts 453 downloads

PRISMA - Protocol Inspection and State Machine Analysis

Loads and processes huge text corpora processed with the sally toolbox (<http://www.mlsec.org/sally/>). sally acts as a very fast preprocessor which splits the text files into tokens or n-grams. These output files can then be read with the PRISMA package which applies testing-based token selection and has some replicate-aware, highly tuned non-negative matrix factorization and principal component analysis implementation which allows the processing of very big data sets even on desktop machines.

Last updated 7 years ago

4.00 score 20 scripts 204 downloads

misty - Miscellaneous Functions 'T. Yanagida'

Miscellaneous functions for (1) data management (e.g., grand-mean and group-mean centering, coding variables and reverse coding items, scale and cluster scores, reading and writing Excel and SPSS files), (2) descriptive statistics (e.g., frequency table, cross tabulation, effect size measures), (3) missing data (e.g., descriptive statistics for missing data, missing data pattern, Little's test of Missing Completely at Random, and auxiliary variable analysis), (4) multilevel data (e.g., multilevel descriptive statistics, within-group and between-group correlation matrix, multilevel confirmatory factor analysis, level-specific fit indices, cross-level measurement equivalence evaluation, multilevel composite reliability, and multilevel R-squared measures), (5) item analysis (e.g., confirmatory factor analysis, coefficient alpha and omega, between-group and longitudinal measurement equivalence evaluation), (6) statistical analysis (e.g., confidence intervals, collinearity and residual diagnostics, dominance analysis, between- and within-subject analysis of variance, latent class analysis, t-test, z-test, sample size determination), and (7) functions to interact with 'Blimp' and 'Mplus'.

Last updated 2 months ago

3.98 score 1 stars 1 dependents 130 scripts 3.1k downloads

highs - 'HiGHS' Optimization Solver

R interface to 'HiGHS', an optimization solver for solving mixed integer optimization problems with quadratic or linear objective and linear constraints.

Last updated 2 years ago

fortrancpp

3.98 score 1 stars 8 dependents 44 scripts 1.8k downloads

preregr - Specify (Pre)Registrations and Export Them Human- And Machine-Readably

Preregistrations, or more generally, registrations, enable explicit timestamped and (often but not necessarily publicly) frozen documentation of plans and expectations as well as decisions and justifications. In research, preregistrations are commonly used to clearly document plans and facilitate justifications of deviations from those plans, as well as decreasing the effects of publication bias by enabling identification of research that was conducted but not published. Like reporting guidelines, (pre)registration forms often have specific structures that facilitate systematic reporting of important items. The 'preregr' package facilitates specifying (pre)registrations in R and exporting them to a human-readable format (using R Markdown partials or exporting to an 'HTML' file) as well as human-readable embedded data (using 'JSON'), as well as importing such exported (pre)registration specifications from such embedded 'JSON'.

Last updated 2 years ago

3.98 score 1 scripts 182 downloads

changepoint.np - Methods for Nonparametric Changepoint Detection

Implements the multiple changepoint algorithm PELT with a nonparametric cost function based on the empirical distribution of the data. This package extends the changepoint package (see Killick, R and Eckley, I (2014) <doi:10.18637/jss.v058.i03> ).

Last updated 2 years ago

3.97 score 2 stars 3 dependents 40 scripts 1.3k downloads

Thresher - Threshing and Reaping for Principal Components

Defines the classes used to identify outliers (threshing) and compute the number of significant principal components and number of clusters (reaping) in a joint application of PCA and hierarchical clustering. See Wang et al., 2018, <doi:10.1186/s12859-017-1998-9>.

Last updated 8 months ago

clustering

3.97 score 3 dependents 26 scripts 583 downloads

astrochron - A Computational Tool for Astrochronology

Routines for astrochronologic testing, astronomical time scale construction, and time series analysis <doi:10.1016/j.earscirev.2018.11.015>. Also included are a range of statistical analysis and modeling routines that are relevant to time scale development and paleoclimate analysis.

Last updated 3 months ago

fortran

3.96 score 6 stars 153 scripts 652 downloads

optimbase - R Port of the 'Scilab' Optimbase Module

Provides a set of commands to manage an abstract optimization method. The goal is to provide a building block for a large class of specialized optimization methods. This package manages: the number of variables, the minimum and maximum bounds, the number of non linear inequality constraints, the cost function, the logging system, various termination criteria, etc...

Last updated 3 years ago

3.95 score 6 dependents 31 scripts 451 downloads

qrnn - Quantile Regression Neural Network

Fit quantile regression neural network models with optional left censoring, partial monotonicity constraints, generalized additive model constraints, and the ability to fit multiple non-crossing quantile functions following Cannon (2011) <doi:10.1016/j.cageo.2010.07.005> and Cannon (2018) <doi:10.1007/s00477-018-1573-6>.

Last updated 10 months ago

3.95 score 8 stars 1 dependents 74 scripts 666 downloads

CVST - Fast Cross-Validation via Sequential Testing

The fast cross-validation via sequential testing (CVST) procedure is an improved cross-validation procedure which uses non-parametric testing coupled with sequential analysis to determine the best parameter set on linearly increasing subsets of the data. By eliminating under-performing candidates quickly and keeping promising candidates as long as possible, the method speeds up the computation while preserving the capability of a full cross-validation. Additionally to the CVST the package contains an implementation of the ordinary k-fold cross-validation with a flexible and powerful set of helper objects and methods to handle the overall model selection process. The implementations of the Cochran's Q test with permutations and the sequential testing framework of Wald are generic and can therefore also be used in other contexts.

Last updated 3 years ago

3.95 score 4 dependents 29 scripts 1.8k downloads

betapart - Partitioning Beta Diversity into Turnover and Nestedness Components

Functions to compute pair-wise dissimilarities (distance matrices) and multiple-site dissimilarities, separating the turnover and nestedness-resultant components of taxonomic (incidence and abundance based), functional and phylogenetic beta diversity.

Last updated 2 years ago

3.93 score 2 stars 6 dependents 506 scripts 2.4k downloads

MultiPhen - A Package to Test for Multi-Trait Association

Performs genetic association tests between SNPs (one-at-a-time) and multiple phenotypes (separately or in joint model).

Last updated 5 years ago

3.93 score 17 scripts 299 downloads

genpwr - Power Calculations Under Genetic Model Misspecification

Power and sample size calculations for genetic association studies allowing for misspecification of the model of genetic susceptibility. "Hum Hered. 2019;84(6):256-271.<doi:10.1159/000508558>. Epub 2020 Jul 28." Power and/or sample size can be calculated for logistic (case/control study design) and linear (continuous phenotype) regression models, using additive, dominant, recessive or degree of freedom coding of the genetic covariate while assuming a true dominant, recessive or additive genetic effect. In addition, power and sample size calculations can be performed for gene by environment interactions. These methods are extensions of Gauderman (2002) <doi:10.1093/aje/155.5.478> and Gauderman (2002) <doi:10.1002/sim.973> and are described in: Moore CM, Jacobson S, Fingerlin TE. Power and Sample Size Calculations for Genetic Association Studies in the Presence of Genetic Model Misspecification. American Society of Human Genetics. October 2018, San Diego.

Last updated 4 years ago

3.92 score 1 stars 42 scripts 242 downloads

agena.ai - R Wrapper for 'agena.ai' API

An R wrapper for 'agena.ai' <https://www.agena.ai> which provides users capabilities to work with 'agena.ai' using the R environment. Users can create Bayesian network models from scratch or import existing models in R and export to 'agena.ai' cloud or local API for calculations. Note: running calculations requires a valid 'agena.ai' API license (past the initial trial period of the local API).

Last updated 1 years ago

3.91 score 23 scripts 312 downloads

brnn - Bayesian Regularization for Feed-Forward Neural Networks

Bayesian regularization for feed-forward neural networks.

Last updated 1 years ago

openblasopenmp

3.89 score 5 dependents 106 scripts 1.6k downloads

pspearman - Spearman's Rank Correlation Test

Spearman's rank correlation test with precomputed exact null distribution for n <= 22.

Last updated 3 years ago

3.88 score 1 stars 3 dependents 35 scripts 3.4k downloads

eudract - Creates Safety Results Summary in XML to Upload to EudraCT, or ClinicalTrials.gov

The remit of the European Clinical Trials Data Base (EudraCT <https://eudract.ema.europa.eu/> ), or ClinicalTrials.gov <https://clinicaltrials.gov/>, is to provide open access to summaries of all registered clinical trial results; thus aiming to prevent non-reporting of negative results and provide open-access to results to inform future research. The amount of information required and the format of the results, however, imposes a large extra workload at the end of studies on clinical trial units. In particular, the adverse-event-reporting component requires entering: each unique combination of treatment group and safety event; for every such event above, a further 4 pieces of information (body system, number of occurrences, number of subjects, number exposed) for non-serious events, plus an extra three pieces of data for serious adverse events (numbers of causally related events, deaths, causally related deaths). This package prepares the required statistics needed by EudraCT and formats them into the precise requirements to directly upload an XML file into the web portal, with no further data entry by hand.

Last updated 26 days ago

3.86 score 24 scripts 299 downloads

Spillover - Spillover/Connectedness Index Based on VAR Modelling

A user-friendly tool for estimating both total and directional connectedness spillovers based on Diebold and Yilmaz (2009, 2012). It also provides the user with rolling estimation for total and net indices. User can find both orthogonalized and generalized versions for each kind of measures. See Diebold and Yilmaz (2009, 2012) find them at <doi:10.1111/j.1468-0297.2008.02208.x> and <doi:10.1016/j.ijforecast.2011.02.006>.

Last updated 10 months ago

3.86 score 8 stars 5 scripts 350 downloads

wavemulcor - Wavelet Routines for Global and Local Multiple Regression and Correlation

Wavelet routines that calculate single sets of wavelet multiple regressions and correlations, and cross-regressions and cross-correlations from a multivariate time series. Dynamic versions of the routines allow the wavelet local multiple (cross-)regressions and (cross-)correlations to evolve over time.

Last updated 3 years ago

3.86 score 2 dependents 24 scripts 308 downloads

TSdist - Distance Measures for Time Series Data

A set of commonly used distance measures and some additional functions which, although initially not designed for this purpose, can be used to measure the dissimilarity between time series. These measures can be used to perform clustering, classification or other data mining tasks which require the definition of a distance measure between time series. U. Mori, A. Mendiburu and J.A. Lozano (2016), <doi:10.32614/RJ-2016-058>.

Last updated 2 years ago

3.84 score 5 stars 5 dependents 93 scripts 702 downloads

ICSNP - Tools for Multivariate Nonparametrics

Tools for multivariate nonparametrics, as location tests based on marginal ranks, spatial median and spatial signs computation, Hotelling's T-test, estimates of shape are implemented.

Last updated 1 years ago

cpp

3.82 score 14 dependents 227 scripts 2.6k downloads

qmrparser - Parser Combinator in R

Basic functions for building parsers, with an application to PC-AXIS format files.

Last updated 3 years ago

3.82 score 1 stars 6 dependents 37 scripts 296 downloads

ibmdbR - IBM in-Database Analytics for R

Functionality required to efficiently use R with IBM(R) Db2(R) Warehouse offerings (formerly IBM dashDB(R)) and IBM Db2 for z/OS(R) in conjunction with IBM Db2 Analytics Accelerator for z/OS. Many basic and complex R operations are pushed down into the database, which removes the main memory boundary of R and allows to make full use of parallel processing in the underlying database. For executing R-functions in a multi-node environment in parallel the idaTApply() function requires the 'SparkR' package (<https://spark.apache.org/docs/latest/sparkr.html>). The optional 'ggplot2' package is needed for the plot.idaLm() function only.

Last updated 1 years ago

3.82 score 2 stars 66 scripts 249 downloads

mgwrsar - GWR and MGWR with Spatial Autocorrelation

Functions for computing (Mixed) Geographically Weighted Regression with spatial autocorrelation, Geniaux and Martinetti (2017) <doi:10.1016/j.regsciurbeco.2017.04.001>.

Last updated 1 years ago

cpp

3.81 score 7 stars 46 scripts 372 downloads

PoiClaClu - Classification and Clustering of Sequencing Data Based on a Poisson Model

Implements the methods described in the paper, Witten (2011) Classification and Clustering of Sequencing Data using a Poisson Model, Annals of Applied Statistics 5(4) 2493-2518.

Last updated 6 years ago

3.81 score 2 dependents 107 scripts 579 downloads

cusum - Cumulative Sum (CUSUM) Charts for Monitoring of Hospital Performance

Provides functions for constructing and evaluating CUSUM charts and RA-CUSUM charts with focus on false signal probability.

Last updated 5 years ago

cpp

3.81 score 16 scripts 275 downloads

MOCHA - Modeling for Single-Cell Open Chromatin Analysis

A statistical framework and analysis tool for open chromatin analysis designed specifically for single cell ATAC-seq (Assay for Transposase-Accessible Chromatin) data, after cell type/cluster identification. These novel modules remove unwanted technical variation, identify open chromatin, robustly models repeated measures in single cell data, implement advanced statistical frameworks to model zero-inflation for differential and co-accessibility analyses, and integrate with existing databases and modules for downstream analyses to reveal biological insights. MOCHA provides a statistical foundation for complex downstream analysis to help advance the potential of single cell ATAC-seq for applied studies. Methods for zero-inflated statistics are as described in: Ghazanfar, S., Lin, Y., Su, X. et al. (2020) <doi:10.1038/s41592-020-0885-x>. Pimentel, Ronald Silva, "Kendall's Tau and Spearman's Rho for Zero-Inflated Data" (2009) <https://scholarworks.wmich.edu/dissertations/721/>.

Last updated 11 months ago

3.79 score 31 scripts 196 downloads

Gmedian - Geometric Median, k-Medians Clustering and Robust Median PCA

Fast algorithms for robust estimation with large samples of multivariate observations. Estimation of the geometric median, robust k-Gmedian clustering, and robust PCA based on the Gmedian covariation matrix.

Last updated 3 years ago

cpp

3.79 score 3 stars 8 dependents 34 scripts 2.5k downloads

CytobankAPI - Cytobank API Wrapper for R

Tools to interface with Cytobank's API via R, organized by endpoints that represent various areas of Cytobank functionality. Learn more about Cytobank at <https://www.beckman.com/flow-cytometry/software>.

Last updated 2 years ago

3.79 score 61 scripts 791 downloads

convevol - Analysis of Convergent Evolution

Quantifies and assesses the significance of convergent evolution using multiple methods and measures as described in Stayton (2015) <DOI: 10.1111/evo.12729> and Grossnickle et al. 2023. Also displays results in various ways.

Last updated 4 months ago

3.78 score 30 scripts 375 downloads

randomUniformForest - Random Uniform Forests for Classification, Regression and Unsupervised Learning

Ensemble model, for classification, regression and unsupervised learning, based on a forest of unpruned and randomized binary decision trees. Each tree is grown by sampling, with replacement, a set of variables at each node. Each cut-point is generated randomly, according to the continuous Uniform distribution. For each tree, data are either bootstrapped or subsampled. The unsupervised mode introduces clustering, dimension reduction and variable importance, using a three-layer engine. Random Uniform Forests are mainly aimed to lower correlation between trees (or trees residuals), to provide a deep analysis of variable importance and to allow native distributed and incremental learning.

Last updated 3 years ago

cpp

3.77 score 3 stars 99 scripts 220 downloads

relsurv - Relative Survival

Contains functions for analysing relative survival data, including nonparametric estimators of net (marginal relative) survival, relative survival ratio, crude mortality, methods for fitting and checking additive and multiplicative regression models, transformation approach, methods for dealing with population mortality tables. Work has been described in Pohar Perme, Pavlic (2018) <doi:10.18637/jss.v087.i08>.

Last updated 2 years ago

3.77 score 3 stars 3 dependents 63 scripts 2.2k downloads

gtfs2emis - Estimating Public Transport Emissions from General Transit Feed Specification (GTFS) Data

A bottom up model to estimate the emission levels of public transport systems based on General Transit Feed Specification (GTFS) data. The package requires two main inputs: i) Public transport data in the GTFS standard format; and ii) Some basic information on fleet characteristics such as fleet age, technology, fuel and Euro stage. As it stands, the package estimates several pollutants at high spatial and temporal resolutions. Pollution levels can be calculated for specific transport routes, trips, time of the day or for the transport system as a whole. The output with emission estimates can be extracted in different formats, supporting analysis on how emission levels vary across space, time and by fleet characteristics. A full description of the methods used in the 'gtfs2emis' model is presented in Vieira, J. P. B.; Pereira, R. H. M.; Andrade, P. R. (2022) <doi:10.31219/osf.io/8m2cy>.

Last updated 22 days ago

3.76 score 29 scripts 14 downloads

mixdist - Finite Mixture Distribution Models

Fit finite mixture distribution models to grouped data and conditional data by maximum likelihood using a combination of a Newton-type algorithm and the EM algorithm.

Last updated 7 years ago

3.76 score 2 dependents 96 scripts 620 downloads

binhf - Haar-Fisz Functions for Binomial Data

Binomial Haar-Fisz transforms for Gaussianization as in Nunes and Nason (2009).

Last updated 6 years ago

3.76 score 3 dependents 279 scripts 63k downloads

evmix - Extreme Value Mixture Modelling, Threshold Estimation and Boundary Corrected Kernel Density Estimation

The usual distribution functions, maximum likelihood inference and model diagnostics for univariate stationary extreme value mixture models are provided. Kernel density estimation including various boundary corrected kernel density estimation methods and a wide choice of kernels, with cross-validation likelihood based bandwidth estimator. Reasonable consistency with the base functions in the 'evd' package is provided, so that users can safely interchange most code.

Last updated 5 years ago

3.76 score 1 stars 7 dependents 172 scripts 1.6k downloads

sgt - Skewed Generalized T Distribution Tree

Density, distribution function, quantile function and random generation for the skewed generalized t distribution. This package also provides a function that can fit data to the skewed generalized t distribution using maximum likelihood estimation.

Last updated 9 years ago

3.74 score 1 stars 111 scripts 465 downloads

forge - Casting Values into Shape

Helper functions with a consistent interface to coerce and verify the types and shapes of values for input checking.

Last updated 6 years ago

3.74 score 4 dependents 4 scripts 3.0k downloads

geigen - Calculate Generalized Eigenvalues, the Generalized Schur Decomposition and the Generalized Singular Value Decomposition of a Matrix Pair with Lapack

Functions to compute generalized eigenvalues and eigenvectors, the generalized Schur decomposition and the generalized Singular Value Decomposition of a matrix pair, using Lapack routines.

Last updated 6 years ago

fortranopenblas

3.74 score 1 stars 16 dependents 79 scripts 1.4k downloads

LogicReg - Logic Regression

Routines for fitting Logic Regression models. Logic Regression is described in Ruczinski, Kooperberg, and LeBlanc (2003) <DOI:10.1198/1061860032238>. Monte Carlo Logic Regression is described in and Kooperberg and Ruczinski (2005) <DOI:10.1002/gepi.20042>.

Last updated 1 years ago

fortran

3.74 score 3 dependents 73 scripts 1.7k downloads

fullfact - Full Factorial Breeding Analysis

We facilitate the analysis of full factorial mating designs with mixed-effects models. The package contains six vignettes containing detailed examples.

Last updated 11 months ago

3.73 score 45 scripts 234 downloads

ggenealogy - Visualization Tools for Genealogical Data

Methods for searching through genealogical data and displaying the results. Plotting algorithms assist with data exploration and publication-quality image generation. Includes interactive genealogy visualization tools. Provides parsing and calculation methods for variables in descendant branches of interest. Uses the Grammar of Graphics.

Last updated 10 months ago

3.72 score 2 stars 53 scripts 242 downloads

COUNT - Functions, Data and Code for Count Data

Functions, data and code for Hilbe, J.M. 2011. Negative Binomial Regression, 2nd Edition (Cambridge University Press) and Hilbe, J.M. 2014. Modeling Count Data (Cambridge University Press).

Last updated 8 years ago

3.72 score 1 dependents 154 scripts 1.1k downloads

haploR - Query 'HaploReg', 'RegulomeDB'

A set of utilities for querying 'HaploReg' <https://pubs.broadinstitute.org/mammals/haploreg/haploreg.php>, 'RegulomeDB' <https://www.regulomedb.org/regulome-search/> web-based tools. The package connects to 'HaploReg', 'RegulomeDB' searches and downloads results, without opening web pages, directly from R environment. Results are stored in a data frame that can be directly used in various kinds of downstream analyses.

Last updated 1 years ago

3.72 score 1 stars 35 scripts 880 downloads

chkptstanr - Checkpoint MCMC Sampling with 'Stan'

Fit Bayesian models in Stan <doi: 10.18637/jss.v076.i01> with checkpointing, that is, the ability to stop the MCMC sampler at will, and then pick right back up where the MCMC sampler left off. Custom 'Stan' models can be fitted, or the popular package 'brms' <doi: 10.18637/jss.v080.i01> can be used to generate the 'Stan' code. This package is fully compatible with the R packages 'brms', 'posterior', 'cmdstanr', and 'bayesplot'.

Last updated 3 years ago

3.72 score 2 stars 26 scripts 174 downloads

glmnetr - Nested Cross Validation for the Relaxed Lasso and Other Machine Learning Models

Cross validation informed Relaxed LASSO, Artificial Neural Network (ANN), gradient boosting machine ('xgboost'), Random Forest ('RandomForestSRC'), Oblique Random Forest ('aorsf'), Recursive Partitioning ('RPART') or step wise regression models are fit. Cross validation leave out samples (leading to nested cross validation) or bootstrap out-of-bag samples are used to evaluate and compare performances between these models with results presented in tabular or graphical means. Calibration plots can also be generated, again based upon (outer nested) cross validation or bootstrap leave out (out of bag) samples. For some datasets, for example when the design matrix is not of full rank, 'glmnet' may have very long run times when fitting the relaxed lasso model, from our experience when fitting Cox models on data with many predictors and many patients, making it difficult to get solutions from either glmnet() or cv.glmnet(). This may be remedied by using the 'path=TRUE' option when calling glmnet() and cv.glmnet(). Within the glmnetr package the approach of path=TRUE is taken by default. When fitting not a relaxed lasso model but an elastic-net model, then the R-packages 'nestedcv' <https://cran.r-project.org/package=nestedcv>, 'glmnetSE' <https://cran.r-project.org/package=glmnetSE> or others may provide greater functionality when performing a nested CV. Use of the 'glmnetr' has many similarities to the 'glmnet' package and it is recommended that the user of 'glmnetr' also become familiar with the 'glmnet' package <https://cran.r-project.org/package=glmnet>, with the "An Introduction to 'glmnet'" and "The Relaxed Lasso" being especially useful in this regard.

Last updated 2 months ago

3.70 score 2 scripts 787 downloads

RWsearch - Lazy Search in R Packages, Task Views, CRAN, the Web. All-in-One Download

Search by keywords in R packages, task views, CRAN, the web and display the results in the console or in txt, html or pdf files. Download the package documentation (html index, README, NEWS, pdf manual, vignettes, source code, binaries) with a single instruction. Visualize the package dependencies and CRAN checks. Compare the package versions, unload and install the packages and their dependencies in a safe order. Explore CRAN archives. Use the above functions for task view maintenance. Access web search engines from the console thanks to 80+ bookmarks. All functions accept standard and non-standard evaluation.

Last updated 2 months ago

3.70 score 9 scripts 221 downloads

cyjShiny - Cytoscape.js Shiny Widget (cyjShiny)

Wraps cytoscape.js as a shiny widget. cytoscape.js <https://js.cytoscape.org/> is a Javascript-based graph theory (network) library for visualization and analysis. This package supports the visualization of networks with custom visual styles and several available layouts. Demo Shiny applications are provided in the package code.

Last updated 2 years ago

3.70 score 100 scripts 227 downloads

SNPfiltR - Interactively Filter SNP Datasets

Is designed to interactively and reproducibly visualize and filter SNP (single-nucleotide polymorphism) datasets. This R-based implementation of SNP and genotype filters facilitates an interactive and iterative SNP filtering pipeline, which can be documented reproducibly via Rmarkdown. 'SNPfiltR' contains functions for visualizing various quality and missing data metrics for a SNP dataset, and then filtering the dataset based on user specified cutoffs. All functions take 'vcfR' objects as input, which can easily be generated by reading standard vcf (variant call format) files into R using the R package 'vcfR' (Knaus and Grünwald) (<doi:10.1111/1755-0998.12549>). Each 'SNPfiltR' function can return a newly filtered vcfR object, which can then be written to a local directory in standard vcf format using the 'vcfR' package, for downstream population genetic and phylogenetic analyses.

Last updated 2 years ago

3.70 score 100 scripts 343 downloads

support.CEs - Basic Functions for Supporting an Implementation of Choice Experiments

Provides basic functions that support an implementation of (discrete) choice experiments (CEs). CEs is a question-based survey method measuring people's preferences for goods/services and their characteristics. Refer to Louviere et al. (2000) <doi:10.1017/CBO9780511753831> for details on CEs, and Aizaki (2012) <doi:10.18637/jss.v050.c02> for the package.

Last updated 1 years ago

3.70 score 3 stars 4 dependents 46 scripts 956 downloads

tmcn - A Text Mining Toolkit for Chinese

A Text mining toolkit for Chinese, which includes facilities for Chinese string processing, Chinese NLP supporting, encoding detecting and converting. Moreover, it provides some functions to support 'tm' package in Chinese.

Last updated 5 years ago

3.68 score 1 stars 5 dependents 156 scripts 2.1k downloads

icmstate - Interval Censored Multi-State Models

Allows for the non-parametric estimation of transition intensities in interval-censored multi-state models using the approach of Gomon and Putter (2024) <doi:10.48550/arXiv.2409.07176> or Gu et al. (2023) <doi:10.1093/biomet/asad073>.

Last updated 2 months ago

cpp

3.65 score 15 scripts 466 downloads

glmpath - L1 Regularization Path for Generalized Linear Models and Cox Proportional Hazards Model

A path-following algorithm for L1 regularized generalized linear models and Cox proportional hazards model.

Last updated 7 years ago

3.65 score 2 dependents 75 scripts 394 downloads

vmr - Virtual Machines for R

Manage, provision and use Virtual Machines pre-configured for R. Develop, test and build package in a clean environment. 'Vagrant' tool and a provider (such as 'Virtualbox') have to be installed.

Last updated 2 years ago

3.65 score 3 scripts 192 downloads

optimsimplex - R Port of the 'Scilab' Optimsimplex Module

Provides a building block for optimization algorithms based on a simplex. The 'optimsimplex' package may be used in the following optimization methods: the simplex method of Spendley et al. (1962) <doi:10.1080/00401706.1962.10490033>, the method of Nelder and Mead (1965) <doi:10.1093/comjnl/7.4.308>, Box's algorithm for constrained optimization (1965) <doi:10.1093/comjnl/8.1.42>, the multi-dimensional search by Torczon (1989) <https://www.cs.wm.edu/~va/research/thesis.pdf>, etc...

Last updated 3 years ago

3.65 score 3 dependents 1 scripts 365 downloads

SSLR - Semi-Supervised Classification, Regression and Clustering Methods

Providing a collection of techniques for semi-supervised classification, regression and clustering. In semi-supervised problem, both labeled and unlabeled data are used to train a classifier. The package includes a collection of semi-supervised learning techniques: self-training, co-training, democratic, decision tree, random forest, 'S3VM' ... etc, with a fairly intuitive interface that is easy to use.

Last updated 3 years ago

cpp

3.64 score 1 stars 73 scripts 287 downloads

discretization - Data Preprocessing, Discretization for Classification

A collection of supervised discretization algorithms. It can also be grouped in terms of top-down or bottom-up, implementing the discretization algorithms.

Last updated 3 years ago

3.62 score 3 stars 5 dependents 64 scripts 1.5k downloads

tripack - Triangulation of Irregularly Spaced Data

A constrained two-dimensional Delaunay triangulation package providing both triangulation and generation of voronoi mosaics of irregular spaced data. Please note that most of the functions are now also covered in package interp, which is a re-implementation from scratch under a free license based on a different triangulation algorithm.

Last updated 2 months ago

3.62 score 1 dependents 176 scripts 3.9k downloads

FIT - Transcriptomic Dynamics Models in Field Conditions

Provides functionality for constructing statistical models of transcriptomic dynamics in field conditions. It further offers the function to predict expression of a gene given the attributes of samples and meteorological data. Nagano, A. J., Sato, Y., Mihara, M., Antonio, B. A., Motoyama, R., Itoh, H., Naganuma, Y., and Izawa, T. (2012). <doi:10.1016/j.cell.2012.10.048>. Iwayama, K., Aisaka, Y., Kutsuna, N., and Nagano, A. J. (2017). <doi:10.1093/bioinformatics/btx049>.

Last updated 6 years ago

cpp

3.61 score 41 scripts 233 downloads

expectreg - Expectile and Quantile Regression

Expectile and quantile regression of models with nonlinear effects e.g. spatial, random, ridge using least asymmetric weighed squares / absolutes as well as boosting; also supplies expectiles for common distributions.

Last updated 11 months ago

cpp

3.61 score 2 stars 2 dependents 34 scripts 479 downloads

metaplus - Robust Meta-Analysis and Meta-Regression

Performs meta-analysis and meta-regression using standard and robust methods with confidence intervals based on the profile likelihood. Robust methods are based on alternative distributions for the random effect, either the t-distribution (Lee and Thompson, 2008 <doi:10.1002/sim.2897> or Baker and Jackson, 2008 <doi:10.1007/s10729-007-9041-8>) or mixtures of normals (Beath, 2014 <doi:10.1002/jrsm.1114>).

Last updated 6 months ago

3.61 score 35 scripts 2.9k downloads

ChannelAttribution - Markov Model for Online Multi-Channel Attribution

Advertisers use a variety of online marketing channels to reach consumers and they want to know the degree each channel contributes to their marketing success. This is called online multi-channel attribution problem. This package contains a probabilistic algorithm for the attribution problem. The model uses a k-order Markov representation to identify structural correlations in the customer journey data. The package also contains three heuristic algorithms (first-touch, last-touch and linear-touch approach) for the same problem. The algorithms are implemented in C++.

Last updated 2 years ago

3.60 score 24 stars 1 dependents 49 scripts 1.1k downloads

RIA - Radiomics Image Analysis Toolbox for Medial Images

Radiomics image analysis toolbox for 2D and 3D radiological images. RIA supports DICOM, NIfTI, nrrd and npy (numpy array) file formats. RIA calculates first-order, gray level co-occurrence matrix, gray level run length matrix and geometry-based statistics. Almost all calculations are done using vectorized formulas to optimize run speeds. Calculation of several thousands of parameters only takes minutes on a single core of a conventional PC. Detailed methodology has been published: Kolossvary et al. Circ: Cardiovascular Imaging. 2017;10(12):e006843 <doi: 10.1161/CIRCIMAGING.117.006843>.

Last updated 12 months ago

3.60 score 7 stars 23 scripts 330 downloads

bpcp - Beta Product Confidence Procedure for Right Censored Data

Calculates nonparametric pointwise confidence intervals for the survival distribution for right censored data, and for medians [Fay and Brittain <DOI:10.1002/sim.6905>]. Has two-sample tests for dissimilarity (e.g., difference, ratio or odds ratio) in survival at a fixed time, and differences in medians [Fay, Proschan, and Brittain <DOI:10.1111/biom.12231>]. Basically, the package gives exact inference methods for one- and two-sample exact inferences for Kaplan-Meier curves (e.g., generalizing Fisher's exact test to allow for right censoring), which are especially important for latter parts of the survival curve, small sample sizes or heavily censored data. Includes mid-p options.

Last updated 3 years ago

3.60 score 3 dependents 32 scripts 1.4k downloads

matRiks - Generates Raven-Like Matrices According to Rules

Generates Raven like matrices according to different rules and the response list associated to the matrix. The package can generate matrices composed of 4 or 9 cells, along with a response list of 11 elements (the correct response + 10 incorrect responses). The matrices can be generated according to both logical rules (i.e., the relationships between the elements in the matrix are manipulated to create the matrix) and visual-spatial rules (i.e., the visual or spatial characteristics of the elements are manipulated to generate the matrix). The graphical elements of this package are based on the 'DescTools' package. This package has been developed within the PRIN2020 Project (Prot. 20209WKCLL) titled "Computerized, Adaptive and Personalized Assessment of Executive Functions and Fluid Intelligence" and founded by the Italian Ministry of Education and Research.

Last updated 10 months ago

3.60 score 40 scripts 155 downloads

EHR - Electronic Health Record (EHR) Data Processing and Analysis Tool

Process and analyze electronic health record (EHR) data. The 'EHR' package provides modules to perform diverse medication-related studies using data from EHR databases. Especially, the package includes modules to perform pharmacokinetic/pharmacodynamic (PK/PD) analyses using EHRs, as outlined in Choi, Beck, McNeer, Weeks, Williams, James, Niu, Abou-Khalil, Birdwell, Roden, Stein, Bejan, Denny, and Van Driest (2020) <doi:10.1002/cpt.1787>. Additional modules will be added in future. In addition, this package provides various functions useful to perform Phenome Wide Association Study (PheWAS) to explore associations between drug exposure and phenotypes obtained from EHR data, as outlined in Choi, Carroll, Beck, Mosley, Roden, Denny, and Van Driest (2018) <doi:10.1093/bioinformatics/bty306>.

Last updated 2 years ago

3.60 score 55 scripts 321 downloads

CB2 - CRISPR Pooled Screen Analysis using Beta-Binomial Test

Provides functions for hit gene identification and quantification of sgRNA (single-guided RNA) abundances for CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) pooled screen data analysis. Details are in Jeong et al. (2019) <doi:10.1101/gr.245571.118> and Baggerly et al. (2003) <doi:10.1093/bioinformatics/btg173>.

Last updated 4 years ago

cpp

3.60 score 40 scripts 303 downloads

SparseGrid - Sparse grid integration in R

SparseGrid is a package to create sparse grids for numerical integration, based on code from www.sparse-grids.de

Last updated 12 years ago

3.60 score 8 dependents 11 scripts 1.5k downloads

GenOrd - Simulation of Discrete Random Variables with Given Correlation Matrix and Marginal Distributions

A gaussian copula based procedure for generating samples from discrete random variables with prescribed correlation matrix and marginal distributions.

Last updated 9 years ago

3.59 score 2 stars 18 dependents 36 scripts 755 downloads

fclust - Fuzzy Clustering

Algorithms for fuzzy clustering, cluster validity indices and plots for cluster validity and visualizing fuzzy clustering results.

Last updated 2 years ago

openblascpp

3.58 score 1 stars 2 dependents 159 scripts 791 downloads

REAT - Regional Economic Analysis Toolbox

Collection of models and analysis methods used in regional and urban economics and (quantitative) economic geography, e.g. measures of inequality, regional disparities and convergence, regional specialization as well as accessibility and spatial interaction models.

Last updated 3 years ago

3.58 score 3 stars 127 scripts 942 downloads

aster - Aster Models

Aster models (Geyer, Wagenius, and Shaw, 2007, <doi:10.1093/biomet/asm030>; Shaw, Geyer, Wagenius, Hangelbroek, and Etterson, 2008, <doi:10.1086/588063>; Geyer, Ridley, Latta, Etterson, and Shaw, 2013, <doi:10.1214/13-AOAS653>) are exponential family regression models for life history analysis. They are like generalized linear models except that elements of the response vector can have different families (e. g., some Bernoulli, some Poisson, some zero-truncated Poisson, some normal) and can be dependent, the dependence indicated by a graphical structure. Discrete time survival analysis, life table analysis, zero-inflated Poisson regression, and generalized linear models that are exponential family (e. g., logistic regression and Poisson regression with log link) are special cases. Main use is for data in which there is survival over discrete time periods and there is additional data about what happens conditional on survival (e. g., number of offspring). Uses the exponential family canonical parameterization (aster transform of usual parameterization). There are also random effects versions of these models.

Last updated 1 years ago

3.56 score 1 dependents 198 scripts 654 downloads

Rdiagnosislist - Manipulate SNOMED CT Diagnosis Lists

Functions and methods for manipulating 'SNOMED CT' concepts. The package contains functions for loading the 'SNOMED CT' release into a convenient R environment, selecting 'SNOMED CT' concepts using regular expressions, and navigating the 'SNOMED CT' ontology. It provides the 'SNOMEDconcept' S3 class for a vector of 'SNOMED CT' concepts (stored as 64-bit integers) and the 'SNOMEDcodelist' S3 class for a table of concepts IDs with descriptions. For more information about 'SNOMED CT' visit <https://www.snomed.org/>.

Last updated 2 months ago

3.56 score 1 stars 18 scripts 659 downloads

Anthropometry - Statistical Methods for Anthropometric Data

Statistical methodologies especially developed to analyze anthropometric data. These methods are aimed at providing effective solutions to some commons problems related to Ergonomics and Anthropometry. They are based on clustering, the statistical concept of data depth, statistical shape analysis and archetypal analysis. Please see Vinue (2017) <doi:10.18637/jss.v077.i06>.

Last updated 2 years ago

3.56 score 1 stars 2 dependents 60 scripts 499 downloads

NBR - Network-Based R-Statistics using Mixed Effects Models

An implementation of network-based statistics in R using mixed effects models. Theoretical background for Network-Based Statistics can be found in Zalesky et al. (2010) <doi:10.1016/j.neuroimage.2010.06.041>. For Mixed Effects Models check the R package <https://CRAN.R-project.org/package=nlme>.

Last updated 2 years ago

3.56 score 36 scripts 157 downloads

StatMatch - Statistical Matching or Data Fusion

Integration of two data sources referred to the same target population which share a number of variables. Some functions can also be used to impute missing values in data sets through hot deck imputation methods. Methods to perform statistical matching when dealing with data from complex sample surveys are available too.

Last updated 7 months ago

3.55 score 10 dependents 197 scripts 1.2k downloads

MXM - Feature Selection (Including Multiple Solutions) and Bayesian Networks

Many feature selection methods for a wide range of response variables, including minimal, statistically-equivalent and equally-predictive feature subsets. Bayesian network algorithms and related functions are also included. The package name 'MXM' stands for "Mens eX Machina", meaning "Mind from the Machine" in Latin. References: a) Lagani, V. and Athineou, G. and Farcomeni, A. and Tsagris, M. and Tsamardinos, I. (2017). Feature Selection with the R Package MXM: Discovering Statistically Equivalent Feature Subsets. Journal of Statistical Software, 80(7). <doi:10.18637/jss.v080.i07>. b) Tsagris, M., Lagani, V. and Tsamardinos, I. (2018). Feature selection for high-dimensional temporal data. BMC Bioinformatics, 19:17. <doi:10.1186/s12859-018-2023-7>. c) Tsagris, M., Borboudakis, G., Lagani, V. and Tsamardinos, I. (2018). Constraint-based causal discovery with mixed data. International Journal of Data Science and Analytics, 6(1): 19-30. <doi:10.1007/s41060-018-0097-y>. d) Tsagris, M., Papadovasilakis, Z., Lakiotaki, K. and Tsamardinos, I. (2018). Efficient feature selection on gene expression data: Which algorithm to use? BioRxiv. <doi:10.1101/431734>. e) Tsagris, M. (2019). Bayesian Network Learning with the PC Algorithm: An Improved and Correct Variation. Applied Artificial Intelligence, 33(2):101-123. <doi:10.1080/08839514.2018.1526760>. f) Tsagris, M. and Tsamardinos, I. (2019). Feature selection with the R package MXM. F1000Research 7: 1505. <doi:10.12688/f1000research.16216.2>. g) Borboudakis, G. and Tsamardinos, I. (2019). Forward-Backward Selection with Early Dropping. Journal of Machine Learning Research 20: 1-39. h) The gamma-OMP algorithm for feature selection with application to gene expression data. IEEE/ACM Transactions on Computational Biology and Bioinformatics 19(2): 1214-1224. <doi:10.1109/TCBB.2020.3029952>.

Last updated 2 years ago

3.54 score 160 scripts 834 downloads

CornerstoneR - Collection of Scripts for Interface Between 'Cornerstone' and 'R'

Collection of generic 'R' scripts which enable you to use existing 'R' routines in 'Cornerstone'. . The desktop application 'Cornerstone' (<https://www.camline.com/en/products/cornerstone/cornerstone-core.html>) is a data analysis software provided by 'camLine' that empowers engineering teams to find solutions even faster. The engineers incorporate intensified hands-on statistics into their projects. They benefit from an intuitive and uniquely designed graphical Workmap concept: you design experiments (DoE) and explore data, analyze dependencies, and find answers you can act upon, immediately, interactively, and without any programming. . While 'Cornerstone's' interface to the statistical programming language 'R' has been available since version 6.0, the latest interface with 'R' is even much more efficient. 'Cornerstone' release 7.1.1 allows you to integrate user defined 'R' packages directly into the standard 'Cornerstone' GUI. Your engineering team stays in 'Cornerstone's' graphical working environment and can apply 'R' routines, immediately and without the need to deal with programming code. Additionally, your 'R' programming team develops corresponding 'R' packages detached from 'Cornerstone' in their favorite 'R' environment. . Learn how to use 'R' packages in 'Cornerstone' 7.1.1 on 'camLineTV' YouTube channel (<https://www.youtube.com/watch?v=HEQHwq_laXU>) (available in German).

Last updated 4 years ago

3.54 score 6 scripts 283 downloads

arulesSequences - Mining Frequent Sequences

Add-on for arules to handle and mine frequent sequences. Provides interfaces to the C++ implementation of cSPADE by Mohammed J. Zaki.

Last updated 4 months ago

3.54 score 11 stars 105 scripts 956 downloads

picasso - Pathwise Calibrated Sparse Shooting Algorithm

Computationally efficient tools for fitting generalized linear model with convex or non-convex penalty. Users can enjoy the superior statistical property of non-convex penalty such as SCAD and MCP which has significantly less estimation error and overfitting compared to convex penalty such as lasso and ridge. Computation is handled by multi-stage convex relaxation and the PathwIse CAlibrated Sparse Shooting algOrithm (PICASSO) which exploits warm start initialization, active set updating, and strong rule for coordinate preselection to boost computation, and attains a linear convergence to a unique sparse local optimum with optimal statistical properties. The computation is memory-optimized using the sparse matrix output.

Last updated 6 years ago

cpp

3.53 score 1 stars 3 dependents 38 scripts 320 downloads

smdi - Perform Structural Missing Data Investigations

An easy to use implementation of routine structural missing data diagnostics with functions to visualize the proportions of missing observations, investigate missing data patterns and conduct various empirical missing data diagnostic tests. Reference: Weberpals J, Raman SR, Shaw PA, Lee H, Hammill BG, Toh S, Connolly JG, Dandreo KJ, Tian F, Liu W, Li J, Hernández-Muñoz JJ, Glynn RJ, Desai RJ. smdi: an R package to perform structural missing data investigations on partially observed confounders in real-world evidence studies. JAMIA Open. 2024 Jan 31;7(1):ooae008. <doi:10.1093/jamiaopen/ooae008>.

Last updated 3 months ago

3.53 score 34 scripts 211 downloads

reportRmd - Tidy Presentation of Clinical Reporting

Streamlined statistical reporting in 'Rmarkdown' environments. Facilitates the automated reporting of descriptive statistics, multiple univariate models, multivariable models and tables combining these outputs. Plotting functions include customisable survival curves, forest plots from logistic and ordinal regression and bivariate comparison plots.

Last updated 1 years ago

3.52 score 1 dependents 22 scripts 169 downloads

shotGroups - Analyze Shot Group Data

Analyzes shooting data with respect to group shape, precision, and accuracy. This includes graphical methods, descriptive statistics, and inference tests using standard, but also non-parametric and robust statistical methods. Implements distributions for radial error in bivariate normal variables. Works with files exported by 'OnTarget PC/TDS', 'Silver Mountain' e-target, 'ShotMarker' e-target, or 'Taran', as well as with custom data files in text format. Supports inference from range statistics such as extreme spread. Includes a set of web-based graphical user interfaces.

Last updated 2 years ago

3.51 score 1 dependents 108 scripts 305 downloads

MonetDB.R - Connect MonetDB to R

Allows to pull data from MonetDB into R.

Last updated 4 years ago

3.49 score 2 stars 310 scripts 324 downloads

RCAL - Regularized Calibrated Estimation

Regularized calibrated estimation for causal inference and missing-data problems with high-dimensional data, based on Tan (2020a) <doi:10.1093/biomet/asz059>, Tan (2020b) <doi:10.1214/19-AOS1824> and Sun and Tan (2020) <arXiv:2009.09286>.

Last updated 4 years ago

3.49 score 1 dependents 17 scripts 174 downloads

multiway - Component Models for Multi-Way Data

Fits multi-way component models via alternating least squares algorithms with optional constraints. Fit models include N-way Canonical Polyadic Decomposition, Individual Differences Scaling, Multiway Covariates Regression, Parallel Factor Analysis (1 and 2), Simultaneous Component Analysis, and Tucker Factor Analysis.

Last updated 6 years ago

3.48 score 3 stars 5 dependents 54 scripts 1.3k downloads

datarobot - 'DataRobot' Predictive Modeling API

For working with the 'DataRobot' predictive modeling platform's API <https://www.datarobot.com/>.

Last updated 10 months ago

3.48 score 2 stars 334 scripts 545 downloads

neldermead - R Port of the 'Scilab' Neldermead Module

Provides several direct search optimization algorithms based on the simplex method. The provided algorithms are direct search algorithms, i.e. algorithms which do not use the derivative of the cost function. They are based on the update of a simplex. The following algorithms are available: the fixed shape simplex method of Spendley, Hext and Himsworth (unconstrained optimization with a fixed shape simplex, 1962) <doi:10.1080/00401706.1962.10490033>, the variable shape simplex method of Nelder and Mead (unconstrained optimization with a variable shape simplex made, 1965) <doi:10.1093/comjnl/7.4.308>, and Box's complex method (constrained optimization with a variable shape simplex, 1965) <doi: 10.1093/comjnl/8.1.42>.

Last updated 3 years ago

3.48 score 2 dependents 40 scripts 404 downloads

ODataQuery - Querying on 'OData'

Make querying on 'OData' easier. It exposes an 'ODataQuery' object that can be manipulated and provides features such as selection, filtering and ordering.

Last updated 3 years ago

3.48 score 1 dependents 8 scripts 242 downloads

crone - Structural Crystallography in 1d

Functions to carry out the most important crystallographic calculations for crystal structures made of 1d Gaussian-shaped atoms, especially useful for methods development. Main reference: E. Smith, G. Evans, J. Foadi (2017) <doi:10.1088/1361-6404/aa8188>.

Last updated 5 years ago

3.48 score 12 scripts 173 downloads

prevtoinc - Prevalence to Incidence Calculations for Point-Prevalence Studies in a Nosocomial Setting

Functions to simulate point prevalence studies (PPSs) of healthcare-associated infections (HAIs) and to convert prevalence to incidence in steady state setups. Companion package to the preprint Willrich et al., From prevalence to incidence - a new approach in the hospital setting; <doi:10.1101/554725> , where methods are explained in detail.

Last updated 6 years ago

3.48 score 1 dependents 20 scripts 256 downloads

Modeler - Classes and Methods for Training and Using Binary Prediction Models

Defines classes and methods to learn models and use them to predict binary outcomes. These are generic tools, but we also include specific examples for many common classifiers.

Last updated 6 years ago

microarrayclustering

3.48 score 1 dependents 8 scripts 203 downloads

pbs - Periodic B Splines

Periodic B Splines Basis

Last updated 12 years ago

3.47 score 21 dependents 30 scripts 1.6k downloads

gif - Graphical Independence Filtering

Provides a method of recovering the precision matrix for Gaussian graphical models efficiently. Our approach could be divided into three categories. First of all, we use Hard Graphical Thresholding for best subset selection problem of Gaussian graphical model, and the core concept of this method was proposed by Luo et al. (2014) <arXiv:1407.7819>. Secondly, a closed form solution for graphical lasso under acyclic graph structure is implemented in our package (Fattahi and Sojoudi (2019) <https://jmlr.org/papers/v20/17-501.html>). Furthermore, we implement block coordinate descent algorithm to efficiently solve the covariance selection problem (Dempster (1972) <doi:10.2307/2528966>). Our package is computationally efficient and can solve ultra-high-dimensional problems, e.g. p > 10,000, in a few minutes.

Last updated 12 months ago

cpp

3.47 score 59 scripts 183 downloads

ccRemover - Removes the Cell-Cycle Effect from Single-Cell RNA-Sequencing Data

Implements a method for identifying and removing the cell-cycle effect from scRNA-Seq data. The description of the method is in Barron M. and Li J. (2016) <doi:10.1038/srep33892>. Identifying and removing the cell-cycle effect from single-cell RNA-Sequencing data. Submitted. Different from previous methods, ccRemover implements a mechanism that formally tests whether a component is cell-cycle related or not, and thus while it often thoroughly removes the cell-cycle effect, it preserves other features/signals of interest in the data.

Last updated 7 years ago

3.46 score 2 stars 29 scripts 159 downloads

KneeArrower - Finds Cutoff Points on Knee Curves

Given a set of points around a knee curve, analyzes first and second derivatives to find knee points.

Last updated 4 years ago

3.45 score 1 dependents 19 scripts 161 downloads

osdatahub - Easier Interaction with the Ordnance Survey Data Hub

Ordnance Survey ('OS') is the national mapping agency for Great Britain and produces a large variety of mapping and geospatial products. Much of OS's data is available via the OS Data Hub <https://osdatahub.os.uk/>, a platform that hosts both free and premium data products. 'osdatahub' provides a user-friendly way to access, query, and download these data.

Last updated 1 years ago

3.45 score 14 scripts 569 downloads

Select - Determines Species Probabilities Based on Functional Traits

The objective of these functions is to derive a species assemblage that satisfies a functional trait profile. Restoring resilient ecosystems requires a flexible framework for selecting assemblages that are based on the functional traits of species. However, current trait-based models have been limited to algorithms that can only select species by optimising specific trait values, and could not elegantly accommodate the common desire among restoration ecologists to produce functionally diverse assemblages. We have solved this problem by applying a non-linear optimisation algorithm that optimises Rao Q, a closed-form functional trait diversity index that incorporates species abundances, subject to other linear constraints. This framework generalises previous models that only optimised the entropy of the community, and can optimise both functional diversity and entropy simultaneously. This package can also be used to generate experimental assemblages to test the effects of community-level traits on community dynamics and ecosystem function. The method is based on theory discussed in Laughlin (2014, Ecology Letters) <doi.org/10.1111/ele.12288>.

Last updated 7 years ago

3.45 score 28 scripts 507 downloads

XR - A Structure for Interfaces from R

Support for interfaces from R to other languages, built around a class for evaluators and a combination of functions, classes and methods for communication. Will be used through a specific language interface package. Described in the book "Extending R".

Last updated 7 years ago

3.45 score 3 dependents 31 scripts 222 downloads

FeaLect - Scores Features for Feature Selection

For each feature, a score is computed that can be useful for feature selection. Several random subsets are sampled from the input data and for each random subset, various linear models are fitted using lars method. A score is assigned to each feature based on the tendency of LASSO in including that feature in the models.Finally, the average score and the models are returned as the output. The features with relatively low scores are recommended to be ignored because they can lead to overfitting of the model to the training data. Moreover, for each random subset, the best set of features in terms of global error is returned. They are useful for applying Bolasso, the alternative feature selection method that recommends the intersection of features subsets.

Last updated 5 years ago

3.44 score 2 stars 23 scripts 209 downloads

FuzzySTs - Fuzzy Statistical Tools

The main goal of this package is to present various fuzzy statistical tools. It intends to provide an implementation of the theoretical and empirical approaches presented in the book entitled "The signed distance measure in fuzzy statistical analysis. Some theoretical, empirical and programming advances" <doi: 10.1007/978-3-030-76916-1>. For the theoretical approaches, see Berkachy R. and Donze L. (2019) <doi:10.1007/978-3-030-03368-2_1>. For the empirical approaches, see Berkachy R. and Donze L. (2016) <ISBN: 978-989-758-201-1>). Important (non-exhaustive) implementation highlights of this package are as follows: (1) a numerical procedure to estimate the fuzzy difference and the fuzzy square. (2) two numerical methods of fuzzification. (3) a function performing different possibilities of distances, including the signed distance and the generalized signed distance for instance with all its properties. (4) numerical estimations of fuzzy statistical measures such as the variance, the moment, etc. (5) two methods of estimation of the bootstrap distribution of the likelihood ratio in the fuzzy context. (6) an estimation of a fuzzy confidence interval by the likelihood ratio method. (7) testing fuzzy hypotheses and/or fuzzy data by fuzzy confidence intervals in the Kwakernaak - Kruse and Meyer sense. (8) a general method to estimate the fuzzy p-value with fuzzy hypotheses and/or fuzzy data. (9) a method of estimation of global and individual evaluations of linguistic questionnaires. (10) numerical estimations of multi-ways analysis of variance models in the fuzzy context. The unbalance in the considered designs are also foreseen.

Last updated 6 months ago

3.44 score 11 scripts 231 downloads

smidm - Statistical Modelling for Infectious Disease Management

Statistical models for specific coronavirus disease 2019 use cases at German local health authorities. All models of Statistical modelling for infectious disease management 'smidm' are part of the decision support toolkit in the 'EsteR' project. More information is published in Sonja Jäckle, Rieke Alpers, Lisa Kühne, Jakob Schumacher, Benjamin Geisler, Max Westphal "'EsteR' – A Digital Toolkit for COVID-19 Decision Support in Local Health Authorities" (2022) <doi:10.3233/SHTI220799> and Sonja Jäckle, Elias Röger, Volker Dicken, Benjamin Geisler, Jakob Schumacher, Max Westphal "A Statistical Model to Assess Risk for Supporting COVID-19 Quarantine Decisions" (2021) <doi:10.3390/ijerph18179166>.

Last updated 2 years ago

3.44 score 11 scripts 612 downloads

cdfquantreg - Quantile Regression for Random Variables on the Unit Interval

Employs a two-parameter family of distributions for modelling random variables on the (0, 1) interval by applying the cumulative distribution function (cdf) of one parent distribution to the quantile function of another.

Last updated 1 years ago

3.43 score 2 stars 34 scripts 372 downloads

gsynth - Generalized Synthetic Control Method

Provides causal inference with interactive fixed-effect models. It imputes counterfactuals for each treated unit using control group information based on a linear interactive fixed effects model that incorporates unit-specific intercepts interacted with time-varying coefficients. This method generalizes the synthetic control method to the case of multiple treated units and variable treatment periods, and improves efficiency and interpretability. This version supports unbalanced panels and implements the matrix completion method.

Last updated 3 years ago

openblascpp

3.43 score 2 stars 167 scripts 1.6k downloads

MultivariateAnalysis - Pacote Para Analise Multivariada

Package with multivariate analysis methodologies for experiment evaluation. The package estimates dissimilarity measures, builds dendrograms, obtains MANOVA, principal components, canonical variables, etc. (Pacote com metodologias de analise multivariada para avaliação de experimentos. O pacote estima medidas de dissimilaridade, construi de dendogramas, obtem a MANOVA, componentes principais, variaveis canonicas, etc.)

Last updated 9 months ago

3.42 score 29 scripts 532 downloads

ragtop - Pricing Equity Derivatives with Extensions of Black-Scholes

Algorithms to price American and European equity options, convertible bonds and a variety of other financial derivatives. It uses an extension of the usual Black-Scholes model in which jump to default may occur at a probability specified by a power-law link between stock price and hazard rate as found in the paper by Takahashi, Kobayashi, and Nakagawa (2001) <doi:10.3905/jfi.2001.319302>. We use ideas and techniques from Andersen and Buffum (2002) <doi:10.2139/ssrn.355308> and Linetsky (2006) <doi:10.1111/j.1467-9965.2006.00271.x>.

Last updated 5 years ago

3.41 score 52 scripts 287 downloads

statcomp - Statistical Complexity and Information Measures for Time Series Analysis

An implementation of local and global statistical complexity measures (aka Information Theory Quantifiers, ITQ) for time series analysis based on ordinal statistics (Bandt and Pompe (2002) <DOI:10.1103/PhysRevLett.88.174102>). Several distance measures that operate on ordinal pattern distributions, auxiliary functions for ordinal pattern analysis, and generating functions for stochastic and deterministic-chaotic processes for ITQ testing are provided.

Last updated 5 years ago

3.41 score 4 stars 1 dependents 72 scripts 151 downloads

mlVAR - Multi-Level Vector Autoregression

Estimates the multi-level vector autoregression model on time-series data. Three network structures are obtained: temporal networks, contemporaneous networks and between-subjects networks.

Last updated 11 months ago

3.41 score 2 dependents 72 scripts 894 downloads

sgeostat - An Object-Oriented Framework for Geostatistical Modeling in S+

An Object-oriented Framework for Geostatistical Modeling in S+ containing functions for variogram estimation, variogram fitting and kriging as well as some plot functions. Written entirely in S, therefore works only for small data sets in acceptable computing time.

Last updated 9 years ago

fortran

3.41 score 1 stars 23 dependents 57 scripts 3.7k downloads

ars - Adaptive Rejection Sampling

Adaptive Rejection Sampling, Original version.

Last updated 4 months ago

cpp

3.40 score 7 dependents 60 scripts 720 downloads

CEDA - CRISPR Screen and Gene Expression Differential Analysis

Provides analytical methods for analyzing CRISPR screen data at different levels of gene expression. Multi-component normal mixture models and EM algorithms are used for modeling.

Last updated 10 months ago

3.40 score 2 scripts 251 downloads

behaviorchange - Tools for Behavior Change Researchers and Professionals

Contains specialised analyses and visualisation tools for behavior change science. These facilitate conducting determinant studies (for example, using confidence interval-based estimation of relevance, CIBER, or CIBERlite plots, see Crutzen, Noijen & Peters (2017) <doi:10/ghtfz9>), systematically developing, reporting, and analysing interventions (for example, using Acyclic Behavior Change Diagrams), and reporting about intervention effectiveness (for example, using the Numbers Needed for Change, see Gruijters & Peters (2017) <doi:10/jzkt>), and computing the required sample size (using the Meaningful Change Definition, see Gruijters & Peters (2020) <doi:10/ghpnx8>). This package is especially useful for researchers in the field of behavior change or health psychology and to behavior change professionals such as intervention developers and prevention workers.

Last updated 2 years ago

3.40 score 9 scripts 447 downloads

erer - Empirical Research in Economics with R

Several functions, datasets, and sample codes related to empirical research in economics are included. They cover the marginal effects for binary or ordered choice models, static and dynamic Almost Ideal Demand System (AIDS) models, and a typical event analysis in finance.

Last updated 3 months ago

3.39 score 3 stars 1 dependents 213 scripts 1.3k downloads

pmsampsize - Sample Size for Development of a Prediction Model

Computes the minimum sample size required for the development of a new multivariable prediction model using the criteria proposed by Riley et al. (2018) <doi: 10.1002/sim.7992>. pmsampsize can be used to calculate the minimum sample size for the development of models with continuous, binary or survival (time-to-event) outcomes. Riley et al. (2018) <doi: 10.1002/sim.7992> lay out a series of criteria the sample size should meet. These aim to minimise the overfitting and to ensure precise estimation of key parameters in the prediction model.

Last updated 1 years ago

3.39 score 4 stars 1 dependents 29 scripts 948 downloads

ipw - Estimate Inverse Probability Weights

Functions to estimate the probability to receive the observed treatment, based on individual characteristics. The inverse of these probabilities can be used as weights when estimating causal effects from observational data via marginal structural models. Both point treatment situations and longitudinal studies can be analysed. The same functions can be used to correct for informative censoring.

Last updated 1 years ago

3.39 score 150 scripts 1.6k downloads

mixture - Mixture Models for Clustering and Classification

An implementation of 14 parsimonious mixture models for model-based clustering or model-based classification. Gaussian, Student's t, generalized hyperbolic, variance-gamma or skew-t mixtures are available. All approaches work with missing data. Celeux and Govaert (1995) <doi:10.1016/0031-3203(94)00125-6>, Browne and McNicholas (2014) <doi:10.1007/s11634-013-0139-1>, Browne and McNicholas (2015) <doi:10.1002/cjs.11246>.

Last updated 11 months ago

gslopenblascppopenmp

3.38 score 1 stars 10 dependents 20 scripts 920 downloads

randomizeR - Randomization for Clinical Trials

This tool enables the user to choose a randomization procedure based on sound scientific criteria. It comprises the generation of randomization sequences as well the assessment of randomization procedures based on carefully selected criteria. Furthermore, 'randomizeR' provides a function for the comparison of randomization procedures.

Last updated 1 years ago

3.38 score 2 stars 1 dependents 44 scripts 411 downloads

mhsmm - Inference for Hidden Markov and Semi-Markov Models

Parameter estimation and prediction for hidden Markov and semi-Markov models for data with multiple observation sequences. Suitable for equidistant time series data, with multivariate and/or missing data. Allows user defined emission distributions.

Last updated 1 years ago

3.38 score 2 stars 2 dependents 61 scripts 565 downloads

meboot - Maximum Entropy Bootstrap for Time Series

Maximum entropy density based dependent data bootstrap. An algorithm is provided to create a population of time series (ensemble) without assuming stationarity. The reference paper (Vinod, H.D., 2004 <DOI: 10.1016/j.jempfin.2003.06.002>) explains how the algorithm satisfies the ergodic theorem and the central limit theorem.

Last updated 1 years ago

3.38 score 2 stars 2 dependents 29 scripts 618 downloads

RSentiment - Analyse Sentiment of English Sentences

Analyses sentiment of a sentence in English and assigns score to it. It can classify sentences to the following categories of sentiments:- Positive, Negative, very Positive, very negative, Neutral. For a vector of sentences, it counts the number of sentences in each category of sentiment.In calculating the score, negation and various degrees of adjectives are taken into consideration. It deals only with English sentences.

Last updated 6 years ago

openjdk

3.37 score 47 scripts 425 downloads

rmcfs - The MCFS-ID Algorithm for Feature Selection and Interdependency Discovery

MCFS-ID (Monte Carlo Feature Selection and Interdependency Discovery) is a Monte Carlo method-based tool for feature selection. It also allows for the discovery of interdependencies between the relevant features. MCFS-ID is particularly suitable for the analysis of high-dimensional, 'small n large p' transactional and biological data. M. Draminski, J. Koronacki (2018) <doi:10.18637/jss.v085.i12>.

Last updated 4 months ago

openjdk

3.37 score 1 stars 1 dependents 26 scripts 542 downloads

kequate - The Kernel Method of Test Equating

Implements the kernel method of test equating as defined in von Davier, A. A., Holland, P. W. and Thayer, D. T. (2004) <doi:10.1007/b97446> and Andersson, B. and Wiberg, M. (2017) <doi:10.1007/s11336-016-9528-7> using the CB, EG, SG, NEAT CE/PSE and NEC designs, supporting Gaussian, logistic and uniform kernels and unsmoothed and pre-smoothed input data.

Last updated 3 years ago

3.37 score 2 stars 29 scripts 344 downloads

HiddenMarkov - Hidden Markov Models

Contains functions for the analysis of Discrete Time Hidden Markov Models, Markov Modulated GLMs and the Markov Modulated Poisson Process. It includes functions for simulation, parameter estimation, and the Viterbi algorithm. See the topic "HiddenMarkov" for an introduction to the package, and "Change Log" for a list of recent changes. The algorithms are based of those of Walter Zucchini.

Last updated 4 years ago

fortran

3.36 score 3 dependents 53 scripts 1.2k downloads

ATNr - Run Allometric Trophic Networks Models

Implements the differential equations associated to different versions of Allometric Trophic Models (ATN) to estimate the temporal dynamics of species biomasses in food webs. It offers several features to generate synthetic food webs and to parametrise models as well as a wrapper to the ODE solver deSolve.

Last updated 1 years ago

openblascppopenmp

3.36 score 23 scripts 271 downloads

BAMMtools - Analysis and Visualization of Macroevolutionary Dynamics on Phylogenetic Trees

Provides functions for analyzing and visualizing complex macroevolutionary dynamics on phylogenetic trees. It is a companion package to the command line program BAMM (Bayesian Analysis of Macroevolutionary Mixtures) and is entirely oriented towards the analysis, interpretation, and visualization of evolutionary rates. Functionality includes visualization of rate shifts on phylogenies, estimating evolutionary rates through time, comparing posterior distributions of evolutionary rates across clades, comparing diversification models using Bayes factors, and more.

Last updated 3 months ago

3.36 score 2 dependents 464 scripts 1.9k downloads

biganalytics - Utilities for 'big.matrix' Objects from Package 'bigmemory'

Extend the 'bigmemory' package with various analytics. Functions 'bigkmeans' and 'binit' may also be used with native R objects. For 'tapply'-like functions, the bigtabulate package may also be helpful. For linear algebra support, see 'bigalgebra'. For mutex (locking) support for advanced shared-memory usage, see 'synchronicity'.

Last updated 9 months ago

cpp

3.36 score 1 stars 4 dependents 190 scripts 709 downloads

MCS - Model Confidence Set Procedure

Perform the model confidence set procedure of Hansen et al (2011) <doi:10.3982/ECTA5771>.

Last updated 7 years ago

3.36 score 2 stars 1 dependents 38 scripts 392 downloads

dgof - Discrete Goodness-of-Fit Tests

A revision to the stats::ks.test() function and the associated ks.test.Rd help page. With one minor exception, it does not change the existing behavior of ks.test(), and it adds features necessary for doing one-sample tests with hypothesized discrete distributions. The package also contains cvm.test(), for doing one-sample Cramer-von Mises goodness-of-fit tests.

Last updated 3 months ago

3.36 score 1 stars 4 dependents 116 scripts 1.9k downloads

XRJulia - Structured Interface to Julia

A Julia interface structured according to the general form described in package 'XR' and in the book "Extending R".

Last updated 8 months ago

3.35 score 1 dependents 15 scripts 583 downloads

GB2 - Generalized Beta Distribution of the Second Kind: Properties, Likelihood, Estimation

Package GB2 explores the Generalized Beta distribution of the second kind. Density, cumulative distribution function, quantiles and moments of the distributions are given. Functions for the full log-likelihood, the profile log-likelihood and the scores are provided. Formulas for various indicators of inequality and poverty under the GB2 are implemented. The GB2 is fitted by the methods of maximum pseudo-likelihood estimation using the full and profile log-likelihood, and non-linear least squares estimation of the model parameters. Various plots for the visualization and analysis of the results are provided. Variance estimation of the parameters is provided for the method of maximum pseudo-likelihood estimation. A mixture distribution based on the compounding property of the GB2 is presented (denoted as "compound" in the documentation). This mixture distribution is based on the discretization of the distribution of the underlying random scale parameter. The discretization can be left or right tail. Density, cumulative distribution function, moments and quantiles for the mixture distribution are provided. The compound mixture distribution is fitted using the method of maximum pseudo-likelihood estimation. The fit can also incorporate the use of auxiliary information. In this new version of the package, the mixture case is complemented with new functions for variance estimation by linearization and comparative density plots.

Last updated 3 years ago

3.34 score 1 stars 3 dependents 81 scripts 319 downloads

runMCMCbtadjust - Runs Monte Carlo Markov Chain - With Either 'JAGS', 'nimble' or 'greta' - While Adjusting Burn-in and Thinning Parameters

The function runMCMC_btadjust() returns a mcmc.list object which is the output of a Markov Chain Monte Carlo obtained - from either 'JAGS', 'nimble' or 'greta' - after adjusting burn-in and thinning parameters to meet pre-specified criteria in terms of convergence & effective sample size. Used with 'nimble', runMCMC_btadjust() allows extra calculations (e.g. information criteria for model comparison and goodness-of-fit p-values for model diagnosis).

Last updated 4 months ago

3.33 score 18 scripts 245 downloads

ufs - A Collection of Utilities

This is a new version of the 'userfriendlyscience' package, which has grown a bit unwieldy. Therefore, distinct functionalities are being 'consciously uncoupled' into different packages. This package contains the general-purpose tools and utilities (see the 'behaviorchange' package, the 'rosetta' package, and the soon-to-be-released 'scd' package for other functionality), and is the most direct 'successor' of the original 'userfriendlyscience' package. For example, this package contains a number of basic functions to create higher level plots, such as diamond plots, to easily plot sampling distributions, to generate confidence intervals, to plan study sample sizes for confidence intervals, and to do some basic operations such as (dis)attenuate effect size estimates.

Last updated 10 months ago

3.33 score 3 dependents 24 scripts 908 downloads

SmartSVA - Fast and Robust Surrogate Variable Analysis

Introduces a fast and efficient Surrogate Variable Analysis algorithm that captures variation of unknown sources (batch effects) for high-dimensional data sets. The algorithm is built on the 'irwsva.build' function of the 'sva' package and proposes a revision on it that achieves an order of magnitude faster running time while trading no accuracy loss in return.

Last updated 8 years ago

3.33 score 2 dependents 36 scripts 291 downloads

hsphase - Phasing, Pedigree Reconstruction, Sire Imputation and Recombination Events Identification of Half-sib Families Using SNP Data

Identification of recombination events, haplotype reconstruction, sire imputation and pedigree reconstruction using half-sib family SNP data.

Last updated 10 months ago

cppopenmp

3.32 score 1 stars 1 dependents 27 scripts 280 downloads

MAVE - Methods for Dimension Reduction

Functions for dimension reduction, using MAVE (Minimum Average Variance Estimation), OPG (Outer Product of Gradient) and KSIR (sliced inverse regression of kernel version). Methods for selecting the best dimension are also included. Xia (2002) <doi:10.1111/1467-9868.03411>; Xia (2007) <doi:10.1214/009053607000000352>; Wang (2008) <doi:10.1198/016214508000000418>.

Last updated 4 years ago

3.32 score 1 stars 21 scripts 235 downloads

givitiR - The GiViTI Calibration Test and Belt

Functions to assess the calibration of logistic regression models with the GiViTI (Gruppo Italiano per la Valutazione degli interventi in Terapia Intensiva, Italian Group for the Evaluation of the Interventions in Intensive Care Units - see <http://www.giviti.marionegri.it/>) approach. The approach consists in a graphical tool, namely the GiViTI calibration belt, and in the associated statistical test. These tools can be used both to evaluate the internal calibration (i.e. the goodness of fit) and to assess the validity of an externally developed model.

Last updated 8 years ago

3.32 score 21 scripts 236 downloads

lordif - Logistic Ordinal Regression Differential Item Functioning using IRT

Analysis of Differential Item Functioning (DIF) for dichotomous and polytomous items using an iterative hybrid of ordinal logistic regression and item response theory (IRT).

Last updated 9 years ago

3.32 score 2 stars 1 dependents 35 scripts 675 downloads

ConfusionTableR - Confusion Matrix Toolset

Takes the outputs of a 'caret' confusion matrix and allows for the quick conversion of these list items to lists. The intended usage is to allow the tool to work with the outputs of machine learning classification models. This tool works with classification problems for binary and multi-classification problems and allows for the record level conversion of the confusion matrix outputs. This is useful, as it allows quick conversion of these objects for storage in database systems and to track ML model performance over time. Traditionally, this approach has been used for highlighting model representation and feature slippage.

Last updated 3 years ago

3.32 score 1 dependents 69 scripts 434 downloads

UPG - Efficient Bayesian Algorithms for Binary and Categorical Data Regression Models

Efficient Bayesian implementations of probit, logit, multinomial logit and binomial logit models. Functions for plotting and tabulating the estimation output are available as well. Estimation is based on Gibbs sampling where the Markov chain Monte Carlo algorithms are based on the latent variable representations and marginal data augmentation algorithms described in "Gregor Zens, Sylvia Frühwirth-Schnatter & Helga Wagner (2023). Ultimate Pólya Gamma Samplers – Efficient MCMC for possibly imbalanced binary and categorical data, Journal of the American Statistical Association <doi:10.1080/01621459.2023.2259030>".

Last updated 1 months ago

3.31 score 41 scripts 646 downloads

SPAtest - Score Test and Meta-Analysis Based on Saddlepoint Approximation

Performs score test using saddlepoint approximation to estimate the null distribution. Also prepares summary statistics for meta-analysis and performs meta-analysis to combine multiple association results. For the latest version, please check <https://github.com/leeshawn/SPAtest>.

Last updated 4 years ago

3.31 score 19 dependents 27 scripts 1.3k downloads

gasanalyzer - Import, Recompute and Analyze Data from Portable Gas Analyzers

The gasanalyzer R package offers methods for importing, preprocessing, and analyzing data related to photosynthetic characteristics (gas exchange, chlorophyll fluorescence and isotope ratios). It translates variable names into a standard format, and can recalculate derived, physiological quantities using imported or predefined equations. The package also allows users to assess the sensitivity of their results to different assumptions used in the calculations. See also Tholen (2024) <doi:10.1093/aobpla/plae035>.

Last updated 21 days ago

3.30 score 3 scripts 470 downloads

sparseSEM - Elastic Net Penalized Maximum Likelihood for Structural Equation Models with Network GPT Framework

Provides elastic net penalized maximum likelihood estimator for structural equation models (SEM). The package implements `lasso` and `elastic net` (l1/l2) penalized SEM and estimates the model parameters with an efficient block coordinate ascent algorithm that maximizes the penalized likelihood of the SEM. Hyperparameters are inferred from cross-validation (CV). A Stability Selection (STS) function is also available to provide accurate causal effect selection. The software achieves high accuracy performance through a `Network Generative Pre-trained Transformer` (Network GPT) Framework with two steps: 1) pre-trains the model to generate a complete (fully connected) graph; and 2) uses the complete graph as the initial state to fit the `elastic net` penalized SEM.

Last updated 2 months ago

openblas

3.30 score 20 scripts 557 downloads

ILSM - Analyze Interconnection Structure of Multilayer Interaction Networks

In view of the analysis of the structural characteristics of the multilayer network has been complete, however, there is still a lack of a unified operation that can quickly obtain the corresponding characteristics of the multilayer network. To solve this insufficiency, 'ILSM' was designed for supporting calculating such metrics of multilayer networks by functions of this R package.

Last updated 4 months ago

3.30 score 5 scripts 179 downloads

SIAtools - 'ShinyItemAnalysis' Modules Development Toolkit

A comprehensive suite of functions designed for constructing and managing 'ShinyItemAnalysis' modules, supplemented with detailed guides, ready-to-use templates, linters, and tests. This package allows developers to seamlessly create and integrate one or more modules into their existing packages or to start a new module project from scratch.

Last updated 6 months ago

3.30 score 144 downloads

ashapesampler - Generating Alpha Shapes

Understanding morphological variation is an important task in many applications. Recent studies in computational biology have focused on developing computational tools for the task of sub-image selection which aims at identifying structural features that best describe the variation between classes of shapes. A major part in assessing the utility of these approaches is to demonstrate their performance on both simulated and real datasets. However, when creating a model for shape statistics, real data can be difficult to access and the sample sizes for these data are often small due to them being expensive to collect. Meanwhile, the landscape of current shape simulation methods has been mostly limited to approaches that use black-box inference---making it difficult to systematically assess the power and calibration of sub-image models. In this R package, we introduce the alpha-shape sampler: a probabilistic framework for simulating realistic 2D and 3D shapes based on probability distributions which can be learned from real data or explicitly stated by the user. The 'ashapesampler' package supports two mechanisms for sampling shapes in two and three dimensions. The first, empirically sampling based on an existing data set, was highlighted in the original main text of the paper. The second, probabilistic sampling from a known distribution, is the computational implementation of the theory derived in that paper. Work based on Winn-Nunez et al. (2024) <doi:10.1101/2024.01.09.574919>.

Last updated 11 months ago

3.30 score 8 scripts 221 downloads

CSIndicators - Climate Services' Indicators Based on Sub-Seasonal to Decadal Predictions

Set of generalised tools for the flexible computation of climate related indicators defined by the user. Each method represents a specific mathematical approach which is combined with the possibility to select an arbitrary time period to define the indicator. This enables a wide range of possibilities to tailor the most suitable indicator for each particular climate service application (agriculture, food security, energy, water management, ...). This package is intended for sub-seasonal, seasonal and decadal climate predictions, but its methods are also applicable to other time-scales, provided the dimensional structure of the input is maintained. Additionally, the outputs of the functions in this package are compatible with 'CSTools'. This package is described in 'Pérez-Zanón et al. (2023) <doi:10.1016/j.cliser.2023.100393>' and it was developed in the context of 'H2020 MED-GOLD' (776467) and 'S2S4E' (776787) projects. See 'Lledó et al. (2019) <doi:10.1016/j.renene.2019.04.135>' and 'Chou et al., 2023 <doi:10.1016/j.cliser.2023.100345>' for details.

Last updated 11 months ago

3.30 score 6 scripts 246 downloads

mpwR - Standardized Comparison of Workflows in Mass Spectrometry-Based Bottom-Up Proteomics

Useful functions to analyze proteomic workflows including number of identifications, data completeness, missed cleavages, quantitative and retention time precision etc. Various software outputs are supported such as 'ProteomeDiscoverer', 'Spectronaut', 'DIA-NN' and 'MaxQuant'.

Last updated 1 years ago

3.30 score 8 scripts 255 downloads

zoomGroupStats - Analyze Text, Audio, and Video from 'Zoom' Meetings

Provides utilities for processing and analyzing the files that are exported from a recorded 'Zoom' Meeting. This includes analyzing data captured through video cameras and microphones, the text-based chat, and meta-data. You can analyze aspects of the conversation among meeting participants and their emotional expressions throughout the meeting.

Last updated 4 years ago

3.30 score 10 scripts 147 downloads

SDAR - Stratigraphic Data Analysis

A fast, consistent tool for plotting and facilitating the analysis of stratigraphic and sedimentological data. Taking advantage of the flexible plotting tools available in R, 'SDAR' uses stratigraphic and sedimentological data to produce detailed graphic logs for outcrop sections and borehole logs. These logs can include multiple features (e.g., bed thickness, lithology, samples, sedimentary structures, colors, fossil content, bioturbation index, gamma ray logs) (Johnson, 1992, <ISSN 0037-0738>).

Last updated 4 years ago

3.30 score 5 scripts 236 downloads

merlin - Mixed Effects Regression for Linear, Non-Linear and User-Defined Models

Fits linear, non-linear, and user-defined mixed effects regression models following the framework developed by Crowther (2017) <arXiv:1710.02223>. 'merlin' can fit multivariate outcome models of any type, each of which could be repeatedly measured (longitudinal), with any number of levels, and with any number of random effects at each level. Standard distributions/models available include the Bernoulli, Gaussian, Poisson, beta, negative-binomial, and time-to-event/survival models include the exponential, Gompertz, Royston-Parmar, Weibull and general hazard model. 'merlin' provides a flexible predictor syntax, allowing the user to define variables, random effects, spline and fractional polynomial functions, functions of other outcome models, and any interaction between each of them. Non-linear and time-dependent effects are seamlessly incorporated into the predictor. 'merlin' allows multivariate normal random effects, which are integrated out using Gaussian quadrature or Monte-Carlo integration. Note, 'merlin' is based on the 'Stata' package of the same name, described in Crowther (2018) <arXiv:1806.01615>.

Last updated 4 years ago

3.30 score 20 scripts 54 downloads

hglm - Hierarchical Generalized Linear Models

Implemented here are procedures for fitting hierarchical generalized linear models (HGLM). It can be used for linear mixed models and generalized linear mixed models with random effects for a variety of links and a variety of distributions for both the outcomes and the random effects. Fixed effects can also be fitted in the dispersion part of the mean model. As statistical models, HGLMs were initially developed by Lee and Nelder (1996) <https://www.jstor.org/stable/2346105?seq=1>. We provide an implementation (Ronnegard, Alam and Shen 2010) <https://journal.r-project.org/archive/2010-2/RJournal_2010-2_Roennegaard~et~al.pdf> following Lee, Nelder and Pawitan (2006) <ISBN: 9781420011340> with algorithms extended for spatial modeling (Alam, Ronnegard and Shen 2015) <https://journal.r-project.org/archive/2015/RJ-2015-017/RJ-2015-017.pdf>.

Last updated 6 years ago

3.30 score 2 stars 78 scripts 481 downloads

MLEcens - Computation of the MLE for Bivariate Interval Censored Data

We provide functions to compute the nonparametric maximum likelihood estimator (MLE) for the bivariate distribution of (X,Y), when realizations of (X,Y) cannot be observed directly. To be more precise, we consider the situation where we observe a set of rectangles in R^2 that are known to contain the unobservable realizations of (X,Y). We compute the MLE based on such a set of rectangles. The methods can also be used for univariate censored data (see data set 'cosmesis'), and for censored data with competing risks (see data set 'menopause'). We also provide functions to visualize the observed data and the MLE.

Last updated 3 months ago

openblas

3.30 score 17 dependents 20 scripts 1.9k downloads

scalreg - Scaled Sparse Linear Regression

Algorithms for fitting scaled sparse linear regression and estimating precision matrices.

Last updated 6 years ago

3.30 score 2 stars 11 dependents 28 scripts 1.1k downloads

ELISAtools - ELISA Data Analysis with Batch Correction

To run data analysis for enzyme-link immunosorbent assays (ELISAs). Either the five- or four-parameter logistic model will be fitted for data of single ELISA. Moreover, the batch effect correction/normalization will be carried out, when there are more than one batches of ELISAs. Feng (2018) <doi:10.1101/483800>.

Last updated 4 years ago

3.29 score 1 stars 39 scripts 190 downloads

caroline - A Collection of Database, Data Structure, Visualization, and Utility Functions for R

The caroline R library contains dozens of functions useful for: database migration (dbWriteTable2), database style joins & aggregation (nerge, groupBy, & bestBy), data structure conversion (nv, tab2df), legend table making (sstable & leghead), automatic legend positioning for scatter and box plots (), plot annotation (labsegs & mvlabs), data visualization (pies, sparge, confound.grid & raPlot), character string manipulation (m & pad), file I/O (write.delim), batch scripting, data exploration, and more. The package's greatest contributions lie in the database style merge, aggregation and interface functions as well as in it's extensive use and propagation of row, column and vector names in most functions.

Last updated 2 months ago

3.29 score 3 dependents 108 scripts 713 downloads

c3net - Inferring Large-Scale Gene Networks with C3NET

Allows inferring gene regulatory networks with direct physical interactions from microarray expression data using C3NET.

Last updated 3 years ago

3.28 score 2 stars 2 dependents 20 scripts 359 downloads

nparLD - Nonparametric Analysis of Longitudinal Data in Factorial Experiments

Performs nonparametric analysis of longitudinal data in factorial experiments. Longitudinal data are those which are collected from the same subjects over time, and they frequently arise in biological sciences. Nonparametric methods do not require distributional assumptions, and are applicable to a variety of data types (continuous, discrete, purely ordinal, and dichotomous). Such methods are also robust with respect to outliers and for small sample sizes.

Last updated 2 years ago

3.28 score 4 stars 48 scripts 553 downloads

jmuOutlier - Permutation Tests for Nonparametric Statistics

Performs a permutation test on the difference between two location parameters, a permutation correlation test, a permutation F-test, the Siegel-Tukey test, a ratio mean deviance test. Also performs some graphing techniques, such as for confidence intervals, vector addition, and Fourier analysis; and includes functions related to the Laplace (double exponential) and triangular distributions. Performs power calculations for the binomial test.

Last updated 5 years ago

3.28 score 1 dependents 106 scripts 549 downloads

difR - Collection of Methods to Detect Dichotomous Differential Item Functioning (DIF)

Provides a collection of standard methods to detect differential item functioning among dichotomously scored items. Methods for uniform and non-uniform DIF, based on test-score or IRT methods, for comparing two or more than two groups of respondents, are available (Magis, Beland, Tuerlinckx and De Boeck,A General Framework and an R Package for the Detection of Dichotomous Differential Item Functioning, Behavior Research Methods, 42, 2010, 847-862 <doi:10.3758/BRM.42.3.847>).

Last updated 5 years ago

3.28 score 5 dependents 122 scripts 1.4k downloads

sparseFLMM - Functional Linear Mixed Models for Irregularly or Sparsely Sampled Data

Estimation of functional linear mixed models for irregularly or sparsely sampled data based on functional principal component analysis.

Last updated 4 years ago

3.27 score 6 dependents 104 scripts 601 downloads

Rmosek - The R to MOSEK Optimization Interface

This is a meta-package designed to support the installation of Rmosek (>= 6.0) and bring the optimization facilities of MOSEK (>= 6.0) to the R-language. The interface supports large-scale optimization of many kinds: Mixed-integer and continuous linear, second-order cone, exponential cone and power cone optimization, as well as continuous semidefinite optimization. Rmosek and the R-language are open-source projects. MOSEK is a proprietary product, but unrestricted trial and academic licenses are available.

Last updated 5 years ago

3.27 score 2 stars 6 dependents 47 scripts 1.1k downloads

ModelMap - Modeling and Map Production using Random Forest and Related Stochastic Models

Creates sophisticated models of training data and validates the models with an independent test set, cross validation, or Out Of Bag (OOB) predictions on the training data. Create graphs and tables of the model validation results. Applies these models to GIS .img files of predictors to create detailed prediction surfaces. Handles large predictor files for map making, by reading in the .img files in chunks, and output to the .txt file the prediction for each data chunk, before reading the next chunk of data.

Last updated 2 years ago

3.26 score 1 stars 17 scripts 857 downloads

glarma - Generalized Linear Autoregressive Moving Average Models

Functions are provided for estimation, testing, diagnostic checking and forecasting of generalized linear autoregressive moving average (GLARMA) models for discrete valued time series with regression variables. These are a class of observation driven non-linear non-Gaussian state space models. The state vector consists of a linear regression component plus an observation driven component consisting of an autoregressive-moving average (ARMA) filter of past predictive residuals. Currently three distributions (Poisson, negative binomial and binomial) can be used for the response series. Three options (Pearson, score-type and unscaled) for the residuals in the observation driven component are available. Estimation is via maximum likelihood (conditional on initializing values for the ARMA process) optimized using Fisher scoring or Newton Raphson iterative methods. Likelihood ratio and Wald tests for the observation driven component allow testing for serial dependence in generalized linear model settings. Graphical diagnostics including model fits, autocorrelation functions and probability integral transform residuals are included in the package. Several standard data sets are included in the package.

Last updated 7 years ago

3.26 score 2 stars 1 dependents 65 scripts 298 downloads

vaccineff - Estimate Vaccine Effectiveness Based on Different Study Designs

Provides tools for estimating vaccine effectiveness and related metrics. The 'vaccineff_data' class manages key features for preparing, visualizing, and organizing cohort data, as well as estimating vaccine effectiveness. The results and model performance are assessed using the 'vaccineff' class.

Last updated 25 days ago

3.26 score 12 scripts

harmonicmeanp - Harmonic Mean p-Values and Model Averaging by Mean Maximum Likelihood

The harmonic mean p-value (HMP) test combines p-values and corrects for multiple testing while controlling the strong-sense family-wise error rate. It is more powerful than common alternatives including Bonferroni and Simes procedures when combining large proportions of all the p-values, at the cost of slightly lower power when combining small proportions of all the p-values. It is more stringent than controlling the false discovery rate, and possesses theoretical robustness to positive correlations between tests and unequal weights. It is a multi-level test in the sense that a superset of one or more significant tests is certain to be significant and conversely when the superset is non-significant, the constituent tests are certain to be non-significant. It is based on MAMML (model averaging by mean maximum likelihood), a frequentist analogue to Bayesian model averaging, and is theoretically grounded in generalized central limit theorem. For detailed examples type vignette("harmonicmeanp") after installation. Version 3.0 addresses errors in versions 1.0 and 2.0 that led function p.hmp to control the familywise error rate only in the weak sense, rather than the strong sense as intended.

Last updated 11 months ago

3.26 score 6 dependents 57 scripts 423 downloads

MRTSampleSizeBinary - Sample Size Calculator for MRT with Binary Outcomes

Provides a sample size calculator for micro-randomized trials (MRTs) with binary outcomes based on Cohn et al. (2023) <doi:10.1002/sim.9748>. Also provides a power calculator when the sample size is input by the user.

Last updated 1 years ago

3.26 score 36 scripts 243 downloads

symmoments - Symbolic Central and Noncentral Moments of the Multivariate Normal Distribution

Symbolic central and non-central moments of the multivariate normal distribution. Computes a standard representation, LateX code, and values at specified mean and covariance matrices.

Last updated 5 years ago

3.26 score 3 dependents 20 scripts 774 downloads

kendallRandomWalks - Simulate and Visualize Kendall Random Walks and Related Distributions

Kendall random walks are a continuous-space Markov chains generated by the Kendall generalized convolution. This package provides tools for simulating these random walks and studying distributions related to them. For more information about Kendall random walks see Jasiulis-Gołdyn (2014) <arXiv:1412.0220>.

Last updated 6 years ago

3.26 score 18 scripts 123 downloads

opdisDownsampling - Optimal Distribution Preserving Down-Sampling of Bio-Medical Data

An optimized method for distribution-preserving class-proportional down-sampling of bio-medical data.

Last updated 8 months ago

3.25 score 5 dependents 1 scripts 6.0k downloads

epandist - Statistical Functions for the Censored and Uncensored Epanechnikov Distribution

Analyzing censored variables usually requires the use of optimization algorithms. This package provides an alternative algebraic approach to the task of determining the expected value of a random censored variable with a known censoring point. Likewise this approach allows for the determination of the censoring point if the expected value is known. These results are derived under the assumption that the variable follows an Epanechnikov kernel distribution with known mean and range prior to censoring. Statistical functions related to the uncensored Epanechnikov distribution are also provided by this package.

Last updated 9 years ago

3.23 score 34 scripts 186 downloads

hnp - Half-Normal Plots with Simulation Envelopes

Generates (half-)normal plots with simulation envelopes using different diagnostics from a range of different fitted models. A few example datasets are included.

Last updated 7 years ago

3.23 score 1 stars 8 dependents 108 scripts 992 downloads

truncdist - Truncated Random Variables

A collection of tools to evaluate probability density functions, cumulative distribution functions, quantile functions and random numbers for truncated random variables. These functions are provided to also compute the expected value and variance. Nadarajah and Kotz (2006) developed most of the functions. QQ plots can be produced. All the probability functions in the stats, stats4 and evd packages are automatically available for truncation..

Last updated 8 years ago

3.22 score 20 dependents 307 scripts 2.8k downloads

DynNom - Visualising Statistical Models using Dynamic Nomograms

Demonstrate the results of a statistical model object as a dynamic nomogram in an RStudio panel or web browser. The package provides two generics functions: DynNom, which display statistical model objects as a dynamic nomogram; DNbuilder, which builds required scripts to publish a dynamic nomogram on a web server such as the <https://www.shinyapps.io/>. Current version of 'DynNom' supports stats::lm, stats::glm, survival::coxph, rms::ols, rms::Glm, rms::lrm, rms::cph, and mgcv::gam model objects.

Last updated 7 months ago

3.22 score 4 stars 33 scripts 1.3k downloads

MultinomialCI - Simultaneous Confidence Intervals for Multinomial Proportions According to the Method by Sison and Glaz

An implementation of a method for building simultaneous confidence intervals for the probabilities of a multinomial distribution given a set of observations, proposed by Sison and Glaz in their paper: Sison, C.P and J. Glaz. Simultaneous confidence intervals and sample size determination for multinomial proportions. Journal of the American Statistical Association, 90:366-369 (1995). The method is an R translation of the SAS code implemented by May and Johnson in their paper: May, W.L. and W.D. Johnson. Constructing two-sided simultaneous confidence intervals for multinomial proportions for small counts in a large number of cells. Journal of Statistical Software 5(6) (2000). Paper and code available at <DOI:10.18637/jss.v005.i06>.

Last updated 4 years ago

3.22 score 2 dependents 55 scripts 440 downloads

kappalab - Non-Additive Measure and Integral Manipulation Functions

S4 tool box for capacity (or non-additive measure, fuzzy measure) and integral manipulation in a finite setting. It contains routines for handling various types of set functions such as games or capacities. It can be used to compute several non-additive integrals: the Choquet integral, the Sugeno integral, and the symmetric and asymmetric Choquet integrals. An analysis of capacities in terms of decision behavior can be performed through the computation of various indices such as the Shapley value, the interaction index, the orness degree, etc. The well-known Möbius transform, as well as other equivalent representations of set functions can also be computed. Kappalab further contains seven capacity identification routines: three least squares based approaches, a method based on linear programming, a maximum entropy like method based on variance minimization, a minimum distance approach and an unsupervised approach based on parametric entropies. The functions contained in Kappalab can for instance be used in the framework of multicriteria decision making or cooperative game theory.

Last updated 1 years ago

3.20 score 5 dependents 85 scripts 1.2k downloads

sda - Shrinkage Discriminant Analysis and CAT Score Variable Selection

Provides an efficient framework for high-dimensional linear and diagonal discriminant analysis with variable selection. The classifier is trained using James-Stein-type shrinkage estimators and predictor variables are ranked using correlation-adjusted t-scores (CAT scores). Variable selection error is controlled using false non-discovery rates or higher criticism.

Last updated 3 years ago

3.20 score 3 dependents 49 scripts 1.7k downloads

pks - Probabilistic Knowledge Structures

Fitting and testing probabilistic knowledge structures, especially the basic local independence model (BLIM, Doignon & Flamagne, 1999) and the simple learning model (SLM), using the minimum discrepancy maximum likelihood (MDML) method (Heller & Wickelmaier, 2013 <doi:10.1016/j.endm.2013.05.145>).

Last updated 3 months ago

3.19 score 1 stars 2 dependents 26 scripts 304 downloads

stpp - Space-Time Point Pattern Simulation, Visualisation and Analysis

Many of the models encountered in applications of point process methods to the study of spatio-temporal phenomena are covered in 'stpp'. This package provides statistical tools for analyzing the global and local second-order properties of spatio-temporal point processes, including estimators of the space-time inhomogeneous K-function and pair correlation function. It also includes tools to get static and dynamic display of spatio-temporal point patterns. See Gabriel et al (2013) <doi:10.18637/jss.v053.i02>.

Last updated 6 months ago

fortran

3.19 score 2 stars 1 dependents 26 scripts 376 downloads

roots - Reconstructing Ordered Ontogenic Trajectories

A set of tools to reconstruct ordered ontogenic trajectories from single cell RNAseq data.

Last updated 7 years ago

3.19 score 31 scripts 175 downloads

ForestElementsR - Data Structures and Functions for Working with Forest Data

Provides generic data structures and algorithms for use with forest mensuration data in a consistent framework. The functions and objects included are a collection of broadly applicable tools. More specialized applications should be implemented in separate packages that build on this foundation. Documentation about 'ForestElementsR' is provided by three vignettes included in this package. For an introduction to the field of forest mensuration, refer to the textbooks by Kershaw et al. (2017) <doi:10.1002/9781118902028>, and van Laar and Akca (2007) <doi:10.1007/978-1-4020-5991-9>.

Last updated 1 days ago

3.18 score

catalytic - Tools for Applying Catalytic Priors in Statistical Modeling

To improve estimation accuracy and stability in statistical modeling, catalytic prior distributions are employed, integrating observed data with synthetic data generated from a simpler model's predictive distribution. This approach enhances model robustness, stability, and flexibility in complex data scenarios. The catalytic prior distributions are introduced by 'Huang et al.' (2020, <doi:10.1073/pnas.1920913117>), Li and Huang (2023, <doi:10.48550/arXiv.2312.01411>).

Last updated 6 days ago

3.18 score

neuroimaGene - Transcriptomic Atlas of Neuroimaging Derived Phenotypes

Contains functions to query and visualize the Neuroimaging features associated with genetically regulated gene expression (GReX). The primary utility, neuroimaGene(), relies on a list of user-defined genes and returns a table of neuroimaging features (NIDPs) associated with each gene. This resource is designed to assist in the interpretation of genome-wide and transcriptome-wide association studies that evaluate brain related traits. Bledsoe (2024) <doi:10.1016/j.ajhg.2024.06.002>. In addition there are several visualization functions that generate summary plots and 2-dimensional visualizations of regional brain measures. Mowinckel (2020).

Last updated 15 days ago

3.18 score 1 scripts 204 downloads

recforest - Random Survival Forest for Recurrent Events

Analyze recurrent events with right-censored data and the potential presence of a terminal event (that prevents further occurrences, like death). 'recofest' extends the random survival forest algorithm, adapting splitting rules and node estimators to handle complexities of recurrent events. The methodology is fully described in Murris, J., Bouaziz, O., Jakubczak, M., Katsahian, S., & Lavenu, A. (2024) (<https://hal.science/hal-04612431v1/document>).

Last updated 19 days ago

3.18 score 6 scripts

Rveg - Digitization of Phytosociological Relevés

Simple and fast tool for transforming phytosociological vegetation data into digital form for the following analysis. Danihelka, Chrtek, and Kaplan (2012, ISSN:00327786). Hennekens, and Schaminée (2001) <doi:10.2307/3237010>. Tichý (2002) <doi:10.1111/j.1654-1103.2002.tb02069.x>. Wickham, François, Henry, Müller (2022) <https://CRAN.R-project.org/package=dplyr>.

Last updated 1 months ago

3.18 score 3 scripts 261 downloads

care4cmodel - Carbon-Related Assessment of Silvicultural Concepts

A simulation model and accompanying functions that support assessing silvicultural concepts on the forest estate level with a focus on the CO2 uptake by wood growth and CO2 emissions by forest operations. For achieving this, a virtual forest estate area is split into the areas covered by typical phases of the silvicultural concept of interest. Given initial area shares of these phases, the dynamics of these areas is simulated. The typical carbon stocks and flows which are known for all phases are attributed post-hoc to the areas and upscaled to the estate level. CO2 emissions by forest operations are estimated based on the amounts and dimensions of the harvested timber. Probabilities of damage events are taken into account.

Last updated 1 months ago

3.18 score 3 scripts 260 downloads

mclustAddons - Addons for the 'mclust' Package

Extend the functionality of the 'mclust' package for Gaussian finite mixture modeling by including: density estimation for data with bounded support (Scrucca, 2019 <doi:10.1002/bimj.201800174>); modal clustering using MEM (Modal EM) algorithm for Gaussian mixtures (Scrucca, 2021 <doi:10.1002/sam.11527>); entropy estimation via Gaussian mixture modeling (Robin & Scrucca, 2023 <doi:10.1016/j.csda.2022.107582>); Gaussian mixtures modeling of financial log-returns (Scrucca, 2024 <doi:10.3390/e26110907>).

Last updated 1 months ago

cpp

3.18 score 7 scripts 430 downloads

BayesGP - Efficient Implementation of Gaussian Process in Bayesian Hierarchical Models

Implements Bayesian hierarchical models with flexible Gaussian process priors, focusing on Extended Latent Gaussian Models and incorporating various Gaussian process priors for Bayesian smoothing. Computations leverage finite element approximations and adaptive quadrature for efficient inference. Methods are detailed in Zhang, Stringer, Brown, and Stafford (2023) <doi:10.1177/09622802221134172>; Zhang, Stringer, Brown, and Stafford (2024) <doi:10.1080/10618600.2023.2289532>; Zhang, Brown, and Stafford (2023) <doi:10.48550/arXiv.2305.09914>; and Stringer, Brown, and Stafford (2021) <doi:10.1111/biom.13329>.

Last updated 1 months ago

cpp

3.18 score 71 scripts 489 downloads

pmxcode - Create Pharmacometric Models

Provides a user interface to create or modify pharmacometric models for various modeling and simulation software platforms.

Last updated 2 months ago

3.18 score 1 stars 347 downloads

vectorsurvR - Data Access and Analytical Tools for 'VectorSurv' Users

Allows registered 'VectorSurv' <https://vectorsurv.org/> users access to data through the 'VectorSurv API' <https://api.vectorsurv.org/>. Additionally provides functions for analysis and visualization.

Last updated 3 months ago

3.18 score 7 scripts 300 downloads

AFR - Toolkit for Regression Analysis of Kazakhstan Banking Sector Data

Tool is created for regression, prediction and forecast analysis of macroeconomic and credit data. The package includes functions from existing R packages adapted for banking sector of Kazakhstan. The purpose of the package is to optimize statistical functions for easier interpretation for bank analysts and non-statisticians.

Last updated 4 months ago

3.18 score 7 scripts 385 downloads

VisitorCounts - Modeling and Forecasting Visitor Counts Using Social Media

Performs modeling and forecasting of park visitor counts using social media data and (partial) on-site visitor counts. Specifically, the model is built based on an automatic decomposition of the trend and seasonal components of the social media-based park visitor counts, from which short-term forecasts of the visitor counts and percent changes in the visitor counts can be made. A reference for the underlying model that 'VisitorCounts' uses can be found at Russell Goebel, Austin Schmaltz, Beth Ann Brackett, Spencer A. Wood, Kimihiro Noguchi (2023) <doi:10.1002/for.2965> .

Last updated 4 months ago

3.18 score 8 scripts 206 downloads

wconf - Weighted Confusion Matrix

Allows users to create weighted confusion matrices and accuracy metrics that help with the model selection process for classification problems, where distance from the correct category is important. The package includes several weighting schemes which can be parameterized, as well as custom configuration options. Furthermore, users can decide whether they wish to positively or negatively affect the accuracy score as a result of applying weights to the confusion matrix. Functions are included to calculate accuracy metrics for imbalanced data. Finally, 'wconf' integrates well with the 'caret' package, but it can also work standalone when provided data in matrix form. References: Kuhn, M. (2008) "Building Perspective Models in R Using the caret Package" <doi:10.18637/jss.v028.i05> Monahov, A. (2021) "Model Evaluation with Weighted Threshold Optimization (and the mewto R package)" <doi:10.2139/ssrn.3805911> Monahov, A. (2024) "Improved Accuracy Metrics for Classification with Imbalanced Data and Where Distance from the Truth Matters, with the wconf R Package" <doi:10.2139/ssrn.4802336> Starovoitov, V., Golub, Y. (2020). New Function for Estimating Imbalanced Data Classification Results. Pattern Recognition and Image Analysis, 295–302 Van de Velden, M., Iodice D'Enza, A., Markos, A., Cavicchia, C. (2023) "A general framework for implementing distances for categorical variables" <doi:10.48550/arXiv.2301.02190>.

Last updated 4 months ago

3.18 score 186 downloads

spnaf - Spatial Network Autocorrelation for Flow Data

Identify statistically significant flow clusters using the local spatial network autocorrelation statistic G_ij* proposed by 'Berglund' and 'Karlström' (1999) <doi:10.1007/s101090050013>. The metric, an extended statistic of 'Getis/Ord' G ('Getis' and 'Ord' 1992) <doi:10.1111/j.1538-4632.1992.tb00261.x>, detects a group of flows having similar traits in terms of directionality. You provide OD data and the associated polygon to get results with several parameters, some of which are defined by spdep package.

Last updated 5 months ago

3.18 score 2 scripts 175 downloads

eggCounts - Hierarchical Modelling of Faecal Egg Counts

An implementation of Bayesian hierarchical models for faecal egg count data to assess anthelmintic efficacy. Bayesian inference is done via MCMC sampling using 'Stan' <https://mc-stan.org/>.

Last updated 1 years ago

cpp

3.18 score 15 scripts 405 downloads

jrSiCKLSNMF - Multimodal Single-Cell Omics Dimensionality Reduction

Methods to perform Joint graph Regularized Single-Cell Kullback-Leibler Sparse Non-negative Matrix Factorization ('jrSiCKLSNMF', pronounced "junior sickles NMF") on quality controlled single-cell multimodal omics count data. 'jrSiCKLSNMF' specifically deals with dual-assay scRNA-seq and scATAC-seq data. This package contains functions to extract meaningful latent factors that are shared across omics modalities. These factors enable accurate cell-type clustering and facilitate visualizations. Methods for pre-processing, clustering, and mini-batch updates and other adaptations for larger datasets are also included. For further details on the methods used in this package please see Ellis, Roy, and Datta (2023) <doi:10.3389/fgene.2023.1179439>.

Last updated 1 years ago

openblascppopenmp

3.18 score 6 scripts 228 downloads

SAPP - Statistical Analysis of Point Processes

Functions for statistical analysis of point processes.

Last updated 2 years ago

fortranglibc

3.18 score 15 scripts 230 downloads

bioSNR - Bioacoustic Basic Operations with Decibels and the Passive Sonar Equation

A beginners toolbox to help those in ecology who want to deepen their understanding or utilize Bioacoustics in their work. The package has a number of utilizations from calculating frequency from waveform, performing operations in dB, and determining acoustic range of recorders. The majority of this package is based on key concepts learned from the K. Lisa Yang Center for Conservation Bioacoustics at Cornell University and their associated course: Introduction to Bioacoustics course. More information can be found within the walk through vignettes at <https://github.com/MattyD797/bioSNR/tree/main/vignettes>.

Last updated 2 years ago

3.18 score 7 scripts 182 downloads

justifier - Human and Machine-Readable Justifications and Justified Decisions Based on 'YAML'

Leverages the 'yum' package to implement a 'YAML' ('YAML Ain't Markup Language', a human friendly standard for data serialization; see <https:yaml.org>) standard for documenting justifications, such as for decisions taken during the planning, execution and analysis of a study or during the development of a behavior change intervention as illustrated by Marques & Peters (2019) <doi:10.17605/osf.io/ndxha>. These justifications are both human- and machine-readable, facilitating efficient extraction and organisation.

Last updated 2 years ago

3.18 score 2 scripts 254 downloads

gsbm - Estimate Parameters in the Generalized SBM

Given an adjacency matrix drawn from a Generalized Stochastic Block Model with missing observations, this package robustly estimates the probabilities of connection between nodes and detects outliers nodes, as describes in Gaucher, Klopp and Robin (2019) <arXiv:1911.13122>.

Last updated 2 years ago

3.18 score 9 scripts 211 downloads

medExtractR - Extraction of Medication Information from Clinical Text

Function and support for medication and dosing information extraction from free-text clinical notes. Medication entities for the basic medExtractR implementation that can be extracted include drug name, strength, dose amount, dose, frequency, intake time, dose change, and time of last dose. The basic medExtractR is outlined in Weeks, Beck, McNeer, Williams, Bejan, Denny, Choi (2020) <doi: 10.1093/jamia/ocz207>. The extended medExtractR_tapering implementation is intended to extract dosing information for more tapering schedules, which are far more complex. The tapering extension allows for the extraction of additional entities including dispense amount, refills, dose schedule, time keyword, transition, and preposition.

Last updated 3 years ago

3.18 score 9 scripts 279 downloads

survIDINRI - IDI and NRI for Comparing Competing Risk Prediction Models with Censored Survival Data

Performs inference for a class of measures to compare competing risk prediction models with censored survival data. The class includes the integrated discrimination improvement index (IDI) and category-less net reclassification index (NRI).

Last updated 3 years ago

fortran

3.18 score 1 stars 1 dependents 27 scripts 594 downloads

iAdapt - Two-Stage Adaptive Dose-Finding Clinical Trial Design

Simulate and implement early phase two-stage adaptive dose-finding design for binary and quasi-continuous toxicity endpoints. See Chiuzan et al. (2018) for further reading <DOI:10.1080/19466315.2018.1462727>.

Last updated 3 years ago

3.18 score 7 scripts 148 downloads

oRus - Operational Research User Stories

A first implementation of automated parsing of user stories, when used to defined functional requirements for operational research mathematical models. It allows reading user stories, splitting them on the who-what-why template, and classifying them according to the parts of the mathematical model that they represent. Also provides semantic grouping of stories, for project management purposes.

Last updated 4 years ago

openjdk

3.18 score 475 downloads

samplingDataCRT - Sampling Data Within Different Study Designs for Cluster Randomized Trials

Package provides the possibility to sampling complete datasets from a normal distribution to simulate cluster randomized trails for different study designs.

Last updated 8 years ago

3.18 score 1 dependents 9 scripts 162 downloads

HSAR - Hierarchical Spatial Autoregressive Model

A Hierarchical Spatial Autoregressive Model (HSAR), based on a Bayesian Markov Chain Monte Carlo (MCMC) algorithm (Dong and Harris (2014) <doi:10.1111/gean.12049>). The creation of this package was supported by the Economic and Social Research Council (ESRC) through the Applied Quantitative Methods Network: Phase II, grant number ES/K006460/1.

Last updated 1 days ago

openblascppopenmp

3.16 score 1 stars 29 scripts 50 downloads

DiceOptim - Kriging-Based Optimization for Computer Experiments

Efficient Global Optimization (EGO) algorithm as described in "Roustant et al. (2012)" <doi:10.18637/jss.v051.i01> and adaptations for problems with noise ("Picheny and Ginsbourger, 2012") <doi:10.1016/j.csda.2013.03.018>, parallel infill, and problems with constraints.

Last updated 4 years ago

3.16 score 4 stars 1 dependents 107 scripts 1.1k downloads

causaldrf - Estimating Causal Dose Response Functions

Functions and data to estimate causal dose response functions given continuous, ordinal, or binary treatments. A description of the methods is given in Galagate (2016) <https://drum.lib.umd.edu/handle/1903/18170>.

Last updated 2 years ago

3.16 score 4 stars 36 scripts 261 downloads

yum - Utilities to Extract and Process 'YAML' Fragments

Provides a number of functions to facilitate extracting information in 'YAML' fragments from one or multiple files, optionally structuring the information in a 'data.tree'. 'YAML' (recursive acronym for "YAML ain't Markup Language") is a convention for specifying structured data in a format that is both machine- and human-readable. 'YAML' therefore lends itself well for embedding (meta)data in plain text files, such as Markdown files. This principle is implemented in 'yum' with minimal dependencies (i.e. only the 'yaml' packages, and the 'data.tree' package can be used to enable additional functionality).

Last updated 3 years ago

3.16 score 4 dependents 12 scripts 243 downloads

DFBA - Distribution-Free Bayesian Analysis

A set of functions to perform distribution-free Bayesian analyses. Included are Bayesian analogues to the frequentist Mann-Whitney U test, the Wilcoxon Signed-Ranks test, Kendall's Tau Rank Correlation Coefficient, Goodman and Kruskal's Gamma, McNemar's Test, the binomial test, the sign test, the median test, as well as distribution-free methods for testing contrasts among condition and for computing Bayes factors for hypotheses. The package also includes procedures to estimate the power of distribution-free Bayesian tests based on data simulations using various probability models for the data. The set of functions provide data analysts with a set of Bayesian procedures that avoids requiring parametric assumptions about measurement error and is robust to problem of extreme outlier scores.

Last updated 1 years ago

3.15 score 567 downloads

CALIBERrfimpute - Multiple Imputation Using MICE and Random Forest

Functions to impute using random forest under full conditional specifications (multivariate imputation by chained equations). The methods are described in Shah and others (2014) <doi:10.1093/aje/kwt312>.

Last updated 2 years ago

3.15 score 2 stars 35 scripts 380 downloads

di - Deficit Index (DI)

A set of utilities for calculating the Deficit (frailty) Index (DI) in gerontological studies. The deficit index was first proposed by Arnold Mitnitski and Kenneth Rockwood and represents a proxy measure of aging and also can be served as a sensitive predictor of survival. For more information, see (i)"Accumulation of Deficits as a Proxy Measure of Aging" by Arnold B. Mitnitski et al. (2001), The Scientific World Journal 1, <DOI:10.1100/tsw.2001.58>; (ii) "Frailty, fitness and late-life mortality in relation to chronological and biological age" by Arnold B Mitnitski et al. (2001), BMC Geriatrics2002 2(1), <DOI:10.1186/1471-2318-2-1>.

Last updated 7 years ago

3.15 score 14 scripts 200 downloads

Tlasso - Non-Convex Optimization and Statistical Inference for Sparse Tensor Graphical Models

An optimal alternating optimization algorithm for estimation of precision matrices of sparse tensor graphical models, and an efficient inference procedure for support recovery of the precision matrices.

Last updated 3 years ago

3.14 score 1 stars 2 dependents 23 scripts 180 downloads

hipread - Read Hierarchical Fixed Width Files

Read hierarchical fixed width files like those commonly used by many census data providers. Also allows for reading of data in chunks, and reading 'gzipped' files without storing the full file in memory.

Last updated 1 years ago

3.14 score 2 dependents 34 scripts 1.3k downloads

Sequential - Exact Sequential Analysis for Poisson and Binomial Data

Functions to calculate exact critical values, statistical power, expected time to signal, and required sample sizes for performing exact sequential analysis. All these calculations can be done for either Poisson or binomial data, for continuous or group sequential analyses, and for different types of rejection boundaries. In case of group sequential analyses, the group sizes do not have to be specified in advance and the alpha spending can be arbitrarily settled.

Last updated 2 months ago

3.14 score 2 stars 1 dependents 38 scripts 785 downloads

SemiPar - Semiparametic Regression

Functions for semiparametric regression analysis, to complement the book: Ruppert, D., Wand, M.P. and Carroll, R.J. (2003). Semiparametric Regression. Cambridge University Press.

Last updated 7 years ago

3.13 score 7 dependents 263 scripts 1.6k downloads

deident - Persistent Data Anonymization Pipeline

A framework for the replicable removal of personally identifiable data (PID) in data sets. The package implements a suite of methods to suit different data types based on the suggestions of Garfinkel (2015) <doi:10.6028/NIST.IR.8053> and the ICO "Guidelines on Anonymization" (2012) <https://ico.org.uk/media/1061/anonymisation-code.pdf>.

Last updated 1 months ago

3.13 score 15 scripts 110 downloads

rpsftm - Rank Preserving Structural Failure Time Models

Implements methods described by the paper Robins and Tsiatis (1991) <DOI:10.1080/03610929108830654>. These use g-estimation to estimate the causal effect of a treatment in a two-armed randomised control trial where non-compliance exists and is measured, under an assumption of an accelerated failure time model and no unmeasured confounders.

Last updated 10 months ago

3.13 score 27 scripts 314 downloads

tlrmvnmvt - Low-Rank Methods for MVN and MVT Probabilities

Implementation of the classic Genz algorithm and a novel tile-low-rank algorithm for computing relatively high-dimensional multivariate normal (MVN) and Student-t (MVT) probabilities. References used for this package: Foley, James, Andries van Dam, Steven Feiner, and John Hughes. "Computer Graphics: Principle and Practice". Addison-Wesley Publishing Company. Reading, Massachusetts (1987, ISBN:0-201-84840-6 1); Genz, A., "Numerical computation of multivariate normal probabilities," Journal of Computational and Graphical Statistics, 1, 141-149 (1992) <doi:10.1080/10618600.1992.10477010>; Cao, J., Genton, M. G., Keyes, D. E., & Turkiyyah, G. M. "Exploiting Low Rank Covariance Structures for Computing High-Dimensional Normal and Student- t Probabilities," Statistics and Computing, 31.1, 1-16 (2021) <doi:10.1007/s11222-020-09978-y>; Cao, J., Genton, M. G., Keyes, D. E., & Turkiyyah, G. M. "tlrmvnmvt: Computing High-Dimensional Multivariate Normal and Student-t Probabilities with Low-Rank Methods in R," Journal of Statistical Software, 101.4, 1-25 (2022) <doi:10.18637/jss.v101.i04>.

Last updated 3 years ago

fortranopenblascpp

3.13 score 1 stars 9 dependents 10 scripts 367 downloads

BAT - Biodiversity Assessment Tools

Includes algorithms to assess alpha and beta diversity in all their dimensions (taxonomic, phylogenetic and functional). It allows performing a number of analyses based on species identities/abundances, phylogenetic/functional distances, trees, convex-hulls or kernel density n-dimensional hypervolumes depicting species relationships. Cardoso et al. (2015) <doi:10.1111/2041-210X.12310>.

Last updated 10 months ago

3.12 score 3 dependents 65 scripts 1.5k downloads

randomLCA - Random Effects Latent Class Analysis

Fits standard and random effects latent class models. The single level random effects model is described in Qu et al <doi:10.2307/2533043> and the two level random effects model in Beath and Heller <doi:10.1177/1471082X0800900302>. Examples are given for their use in diagnostic testing.

Last updated 3 months ago

3.10 score 42 scripts 696 downloads

oaxaca - Blinder-Oaxaca Decomposition

An implementation of the Blinder-Oaxaca decomposition for linear regression models.

Last updated 3 years ago

3.09 score 3 stars 41 scripts 597 downloads

Evapotranspiration - Modelling Actual, Potential and Reference Crop Evapotranspiration

Uses data and constants to calculate potential evapotranspiration (PET) and actual evapotranspiration (AET) from 21 different formulations including Penman, Penman-Monteith FAO 56, Priestley-Taylor and Morton formulations.

Last updated 3 years ago

3.09 score 10 stars 61 scripts 899 downloads

binGroup - Evaluation and Experimental Design for Binomial Group Testing

Methods for estimation and hypothesis testing of proportions in group testing designs: methods for estimating a proportion in a single population (assuming sensitivity and specificity equal to 1 in designs with equal group sizes), as well as hypothesis tests and functions for experimental design for this situation. For estimating one proportion or the difference of proportions, a number of confidence interval methods are included, which can deal with various different pool sizes. Further, regression methods are implemented for simple pooling and matrix pooling designs. Methods for identification of positive items in group testing designs: Optimal testing configurations can be found for hierarchical and array-based algorithms. Operating characteristics can be calculated for testing configurations across a wide variety of situations.

Last updated 6 years ago

3.08 score 101 scripts 1.5k downloads

GGMselect - Gaussian Graphs Models Selection

Graph estimation in Gaussian Graphical Models, following the method developed by C. Giraud, S. Huet and N. Verzelen (2012) <doi:10.1515/1544-6115.1625>. The main functions return the adjacency matrix of an undirected graph estimated from a data matrix.

Last updated 1 months ago

fortranopenblas

3.08 score 1 stars 1 dependents 50 scripts 866 downloads

nonmem2R - Loading NONMEM Output Files with Functions for Visual Predictive Checks (VPC) and Goodness of Fit (GOF) Plots

Loading NONMEM (NONlinear Mixed-Effect Modeling, <https://www.iconplc.com/solutions/technologies/nonmem/>) and PSN (Perl-speaks-NONMEM, <https://uupharmacometrics.github.io/PsN/>) output files to extract parameter estimates, provide visual predictive check (VPC) and goodness of fit (GOF) plots, and simulate with parameter uncertainty.

Last updated 10 months ago

3.08 score 3 stars 20 scripts 449 downloads

MDSMap - High Density Genetic Linkage Mapping using Multidimensional Scaling

Estimate genetic linkage maps for markers on a single chromosome (or in a single linkage group) from pairwise recombination fractions or intermarker distances using weighted metric multidimensional scaling. The methods are suitable for autotetraploid as well as diploid populations. Options for assessing the fit to a known map are also provided. Methods are discussed in detail in Preedy and Hackett (2016) <doi:10.1007/s00122-016-2761-8>.

Last updated 6 years ago

3.08 score 1 dependents 15 scripts 245 downloads

tseriesTARMA - Analysis of Nonlinear Time Series Through Threshold Autoregressive Moving Average Models (TARMA) Models

Routines for nonlinear time series analysis based on Threshold Autoregressive Moving Average (TARMA) models. It provides functions and methods for: TARMA model fitting and forecasting, including robust estimators, see Goracci et al. JBES (2025) <doi:10.1080/07350015.2024.2412011>; tests for threshold effects, see Giannerini et al. JoE (2024) <doi:10.1016/j.jeconom.2023.01.004>, Goracci et al. Statistica Sinica (2023) <doi:10.5705/ss.202021.0120>, Angelini et al. (2024) <doi:10.48550/arXiv.2308.00444>; unit-root tests based on TARMA models, see Chan et al. Statistica Sinica (2024) <doi:10.5705/ss.202022.0125>.

Last updated 3 months ago

fortranopenblas

3.08 score 24k downloads

covsim - VITA, IG and PLSIM Simulation for Given Covariance and Marginals

Random sampling from distributions with user-specified population covariance matrix. Marginal information may be fully specified, for which the package implements the VITA (VIne-To-Anything) algorithm Grønneberg and Foldnes (2017) <doi:10.1007/s11336-017-9569-6>. See also Grønneberg, Foldnes and Marcoulides (2022) <doi:10.18637/jss.v102.i03>. Alternatively, marginal skewness and kurtosis may be specified, for which the package implements the IG (independent generator) and PLSIM (piecewise linear) algorithms, see Foldnes and Olsson (2016) <doi:10.1080/00273171.2015.1133274> and Foldnes and Grønneberg (2021) <doi:10.1080/10705511.2021.1949323>, respectively.

Last updated 7 months ago

3.06 score 23 scripts 274 downloads

rehh.data - Data Only: Searching for Footprints of Selection using Haplotype Homozygosity Based Tests

Contains example data for the 'rehh' package.

Last updated 8 years ago

3.06 score 2 dependents 19 scripts 389 downloads

sasLM - 'SAS' Linear Model

This is a core implementation of 'SAS' procedures for linear models - GLM, REG, ANOVA, TTEST, FREQ, and UNIVARIATE. Some R packages provide type II and type III SS. However, the results of nested and complex designs are often different from those of 'SAS.' Different results does not necessarily mean incorrectness. However, many wants the same results to SAS. This package aims to achieve that. Reference: Littell RC, Stroup WW, Freund RJ (2002, ISBN:0-471-22174-0).

Last updated 3 months ago

3.05 score 3 dependents 21 scripts 1.2k downloads

graphicalVAR - Graphical VAR for Experience Sampling Data

Estimates within and between time point interactions in experience sampling data, using the Graphical vector autoregression model in combination with regularization. See also Epskamp, Waldorp, Mottus & Borsboom (2018) <doi:10.1080/00273171.2018.1454823>.

Last updated 10 months ago

openblascpp

3.05 score 2 stars 4 dependents 46 scripts 1.0k downloads

qpcR - Modelling and Analysis of Real-Time PCR Data

Model fitting, optimal model selection and calculation of various features that are essential in the analysis of quantitative real-time polymerase chain reaction (qPCR).

Last updated 7 years ago

3.04 score 2 stars 1 dependents 1.1k scripts 1.8k downloads

BioVenn - Create Area-Proportional Venn Diagrams from Biological Lists

Creates an area-proportional Venn diagram of 2 or 3 circles. 'BioVenn' is the only R package that can automatically generate an accurate area-proportional Venn diagram by having only lists of (biological) identifiers as input. Also offers the option to map Entrez and/or Affymetrix IDs to Ensembl IDs. In SVG mode, text and numbers can be dragged and dropped. Based on the BioVenn web interface available at <https://www.biovenn.nl>. Hulsen (2021) <doi:10.3233/DS-210032>.

Last updated 4 years ago

3.04 score 1 stars 11 scripts 315 downloads

stratifyR - Optimal Stratification of Univariate Populations

The stratification of univariate populations under stratified sampling designs is implemented according to Khan et al. (2002) <doi:10.1177/0008068320020518> and Khan et al. (2015) <doi:10.1080/02664763.2015.1018674> in this library. It determines the Optimum Strata Boundaries (OSB) and Optimum Sample Sizes (OSS) for the study variable, y, using the best-fit frequency distribution of a survey variable (if data is available) or a hypothetical distribution (if data is not available). The method formulates the problem of determining the OSB as mathematical programming problem which is solved by using a dynamic programming technique. If a dataset of the population is available to the surveyor, the method estimates its best-fit distribution and determines the OSB and OSS under Neyman allocation directly. When the dataset is not available, stratification is made based on the assumption that the values of the study variable, y, are available as hypothetical realizations of proxy values of y from recent surveys. Thus, it requires certain distributional assumptions about the study variable. At present, it handles stratification for the populations where the study variable follows a continuous distribution, namely, Pareto, Triangular, Right-triangular, Weibull, Gamma, Exponential, Uniform, Normal, Log-normal and Cauchy distributions.

Last updated 3 years ago

3.04 score 22 scripts 186 downloads

JustifyAlpha - Justifying Alpha Levels for Hypothesis Tests

Functions to justify alpha levels for statistical hypothesis tests by avoiding Lindley's paradox, or by minimizing or balancing error rates. For more information about the package please read the following: Maier & Lakens (2021) <doi:10.31234/osf.io/ts4r6>).

Last updated 3 years ago

3.04 score 22 scripts 173 downloads

splm - Econometric Models for Spatial Panel Data

ML and GM estimation and diagnostic testing of econometric models for spatial panel data.

Last updated 1 years ago

3.04 score 10 stars 169 scripts 1.6k downloads

georob - Robust Geostatistical Analysis of Spatial Data

Provides functions for efficiently fitting linear models with spatially correlated errors by robust (Kuensch et al. (2011) <doi:10.3929/ethz-a-009900710>) and Gaussian (Harville (1977) <doi:10.1080/01621459.1977.10480998>) (Restricted) Maximum Likelihood and for computing robust and customary point and block external-drift Kriging predictions (Cressie (1993) <doi:10.1002/9781119115151>), along with utility functions for variogram modelling in ad hoc geostatistical analyses, model building, model evaluation by cross-validation, (conditional) simulation of Gaussian processes (Davies and Bryant (2013) <doi:10.18637/jss.v055.i09>), unbiased back-transformation of Kriging predictions of log-transformed data (Cressie (2006) <doi:10.1007/s11004-005-9022-8>).

Last updated 4 months ago

3.03 score 27 scripts 582 downloads

centiserve - Find Graph Centrality Indices

Calculates centrality indices additional to the 'igraph' package centrality functions.

Last updated 7 years ago

3.03 score 1 stars 1 dependents 89 scripts 311 downloads

hpfilter - The One- And Two-Sided Hodrick-Prescott Filter

Provides two functions that implement the one-sided and two-sided versions of the Hodrick-Prescott filter. The one-sided version is a Kalman filter-based implementation, whereas the two- sided version uses sparse matrices for improved efficiency. References: Hodrick, R. J., and Prescott, E. C. (1997) <doi:10.2307/2953682> Mcelroy, T. (2008) <doi:10.1111/j.1368-423X.2008.00230.x> Meyer-Gohde, A. (2010) <https://ideas.repec.org/c/dge/qmrbcd/181.html> For more references, see the vignette.

Last updated 2 years ago

3.02 score 1 stars 21 scripts 444 downloads

GenderInfer - This is a Collection of Functions to Analyse Gender Differences

Implementation of functions, which combines binomial calculation and data visualisation, to analyse the differences in publishing authorship by gender described in Day et al. (2020) <doi:10.1039/C9SC04090K>. It should only be used when self-reported gender is unavailable.

Last updated 3 years ago

3.02 score 21 scripts 178 downloads

ActivityIndex - Activity Index Calculation using Raw 'Accelerometry' Data

Reads raw 'accelerometry' from 'GT3X+' data and plain table data to calculate Activity Index from 'Bai et al.' (2016) <doi:10.1371/journal.pone.0160644>. The Activity Index refers to the square root of the second-level average variance of the three 'accelerometry' axes.

Last updated 4 years ago

3.02 score 21 scripts 300 downloads

forestinventory - Design-Based Global and Small-Area Estimations for Multiphase Forest Inventories

Extensive global and small-area estimation procedures for multiphase forest inventories under the design-based Monte-Carlo approach are provided. The implementation has been published in the Journal of Statistical Software (<doi:10.18637/jss.v097.i04>) and includes estimators for simple and cluster sampling published by Daniel Mandallaz in 2007 (<doi:10.1201/9781584889779>), 2013 (<doi:10.1139/cjfr-2012-0381>, <doi:10.1139/cjfr-2013-0181>, <doi:10.1139/cjfr-2013-0449>, <doi:10.3929/ethz-a-009990020>) and 2016 (<doi:10.3929/ethz-a-010579388>). It provides point estimates, their external- and design-based variances and confidence intervals, as well as a set of functions to analyze and visualize the produced estimates. The procedures have also been optimized for the use of remote sensing data as auxiliary information, as demonstrated in 2018 by Hill et al. (<doi:10.3390/rs10071052>).

Last updated 4 years ago

3.02 score 21 scripts 246 downloads

lctools - Local Correlation, Spatial Inequalities, Geographically Weighted Regression and Other Tools

Provides researchers and educators with easy-to-learn user friendly tools for calculating key spatial statistics and to apply simple as well as advanced methods of spatial analysis in real data. These include: Local Pearson and Geographically Weighted Pearson Correlation Coefficients, Spatial Inequality Measures (Gini, Spatial Gini, LQ, Focal LQ), Spatial Autocorrelation (Global and Local Moran's I), several Geographically Weighted Regression techniques and other Spatial Analysis tools (other geographically weighted statistics). This package also contains functions for measuring the significance of each statistic calculated, mainly based on Monte Carlo simulations.

Last updated 9 months ago

3.02 score 1 stars 52 scripts 352 downloads

sigclust - Statistical Significance of Clustering

SigClust is a statistical method for testing the significance of clustering results. SigClust can be applied to assess the statistical significance of splitting a data set into two clusters. For more than two clusters, SigClust can be used iteratively.

Last updated 2 years ago

3.01 score 2 dependents 43 scripts 407 downloads

synchronicity - Boost Mutex Functionality in R

Boost mutex functionality in R.

Last updated 12 months ago

cpp

3.01 score 2 dependents 23 scripts 1.5k downloads

VFP - Variance Function Program

Variance function estimation for models proposed by W. Sadler in his variance function program ('VFP', <http://www.aacb.asn.au/resources/useful-tools/variance-function-program-v14>). Here, the idea is to fit multiple variance functions to a data set and consequently assess which function reflects the relationship 'Var ~ Mean' best. For 'in-vitro diagnostic' ('IVD') assays modeling this relationship is of great importance when individual test-results are used for defining follow-up treatment of patients.

Last updated 2 years ago

3.01 score 17 scripts 185 downloads

gaussquad - Collection of Functions for Gaussian Quadrature

A collection of functions to perform Gaussian quadrature with different weight functions corresponding to the orthogonal polynomials in package orthopolynom. Examples verify the orthogonality and inner products of the polynomials.

Last updated 3 years ago

3.01 score 5 dependents 68 scripts 421 downloads

pgmm - Parsimonious Gaussian Mixture Models

Carries out model-based clustering or classification using parsimonious Gaussian mixture models. McNicholas and Murphy (2008) <doi:10.1007/s11222-008-9056-0>, McNicholas (2010) <doi:10.1016/j.jspi.2009.11.006>, McNicholas and Murphy (2010) <doi:10.1093/bioinformatics/btq498>, McNicholas et al. (2010) <doi:10.1016/j.csda.2009.02.011>.

Last updated 1 years ago

openblas

3.00 score 1 stars 2 dependents 167 scripts 838 downloads

itmsa - Information-Theoretic Measures for Spatial Association

Leveraging information-theoretic measures like mutual information and v-measure to quantify spatial associations between patterns (Nowosad and Stepinski (2018) <doi:10.1080/13658816.2018.1511794>; Bai, H. et al. (2023) <doi:10.1080/24694452.2023.2223700>).

Last updated 1 days ago

cpp

3.00 score

MultiTraits - Analyzing and Visualizing Multidimensional Plant Traits

Implements analytical methods for multidimensional plant traits, including Competitors-Stress tolerators-Ruderals strategy analysis using leaf traits, Leaf-Height-Seed strategy analysis, Niche Periodicity Table analysis, and Trait Network analysis. Provides functions for data analysis, visualization, and network metrics calculation. Methods are based on Grime (1974) <doi:10.1038/250026a0>, Pierce et al. (2017) <doi:10.1111/1365-2435.12882>, Westoby (1998) <doi:10.1023/A:1004327224729>, Yang et al. (2022) <doi:10.1016/j.foreco.2022.120540>, Winemiller et al. (2015) <doi:10.1111/ele.12462>, He et al. (2020) <doi:10.1016/j.tree.2020.06.003>.

Last updated 3 days ago

3.00 score 6 scripts 209 downloads

BioPred - An R Package for Biomarkers Analysis in Precision Medicine

Provides functions for training extreme gradient boosting model using propensity score A-learning and weight-learning methods. For further details, see Liu et al. (2024) <doi:10.1093/bioinformatics/btae592>.

Last updated 2 months ago

3.00 score 1 scripts 576 downloads

survcompare - Nested Cross-Validation to Compare Cox-PH, Cox-Lasso, Survival Random Forests

Performs repeated nested cross-validation for Cox Proportionate Hazards, Cox Lasso, Survival Random Forest, and their ensemble. Returns internally validated concordance index, time-dependent area under the curve, Brier score, calibration slope, and statistical testing of non-linear ensemble outperforming the baseline Cox model. In this, it helps researchers to quantify the gain of using a more complex survival model, or justify its redundancy. Equally, it shows the performance value of the non-linear and interaction terms, and may highlight the need of further feature transformation. Further details can be found in Shamsutdinova, Stamate, Roberts, & Stahl (2022) "Combining Cox Model and Tree-Based Algorithms to Boost Performance and Preserve Interpretability for Health Outcomes" <doi:10.1007/978-3-031-08337-2_15>, where the method is described as Ensemble 1.

Last updated 3 months ago

3.00 score 1 stars 10 scripts 219 downloads

tcl - Testing in Conditional Likelihood Context

An implementation of hypothesis testing in an extended Rasch modeling framework, including sample size planning procedures and power computations. Provides 4 statistical tests, i.e., gradient test (GR), likelihood ratio test (LR), Rao score or Lagrange multiplier test (RS), and Wald test, for testing a number of hypotheses referring to the Rasch model (RM), linear logistic test model (LLTM), rating scale model (RSM), and partial credit model (PCM). Three types of functions for power and sample size computations are provided. Firstly, functions to compute the sample size given a user-specified (predetermined) deviation from the hypothesis to be tested, the level alpha, and the power of the test. Secondly, functions to evaluate the power of the tests given a user-specified (predetermined) deviation from the hypothesis to be tested, the level alpha of the test, and the sample size. Thirdly, functions to evaluate the so-called post hoc power of the tests. This is the power of the tests given the observed deviation of the data from the hypothesis to be tested and a user-specified level alpha of the test. Power and sample size computations are based on a Monte Carlo simulation approach. It is computationally very efficient. The variance of the random error in computing power and sample size arising from the simulation approach is analytically derived by using the delta method. Draxler, C., & Alexandrowicz, R. W. (2015), <doi:10.1007/s11336-015-9472-y>.

Last updated 3 months ago

3.00 score 7 scripts 168 downloads

GeRnika - Simulation, Visualization and Comparison of Tumor Evolution Data

Simulating, visualizing and comparing tumor clonal data by using simple commands. This aims at providing a tool to help researchers to easily simulate tumor data and analyze the results of their approaches for studying the composition and the evolutionary history of tumors.

Last updated 4 months ago

3.00 score 157 downloads

Langevin - Langevin Analysis in One and Two Dimensions

Estimate drift and diffusion functions from time series and generate synthetic time series from given drift and diffusion coefficients.

Last updated 6 months ago

openblascppopenmp

3.00 score 6 scripts 269 downloads

PoPdesign - Posterior Predictive (PoP) Design for Phase I Clinical Trials

The primary goal of phase I clinical trials is to find the maximum tolerated dose (MTD). To reach this objective, we introduce a new design for phase I clinical trials, the posterior predictive (PoP) design. The PoP design is an innovative model-assisted design that is as simply as the conventional algorithmic designs as its decision rules can be pre-tabulated prior to the onset of trial, but is of more flexibility of selecting diverse target toxicity rates and cohort sizes. The PoP design has desirable properties, such as coherence and consistency. Moreover, the PoP design provides better empirical performance than the BOIN and Keyboard design with respect to high average probabilities of choosing the MTD and slightly lower risk of treating patients at subtherapeutic or overly toxic doses.

Last updated 6 months ago

3.00 score 4 scripts 240 downloads

rcausim - Generate Causally-Simulated Data

Generate causally-simulated data to serve as ground truth for evaluating methods in causal discovery and effect estimation. The package provides tools to assist in defining functions based on specified edges, and conversely, defining edges based on functions. It enables the generation of data according to these predefined functions and causal structures. This is particularly useful for researchers in fields such as artificial intelligence, statistics, biology, medicine, epidemiology, economics, and social sciences, who are developing a general or a domain-specific methods to discover causal structures and estimate causal effects. Data simulation adheres to principles of structural causal modeling. Detailed methodologies and examples are documented in our vignette, available at <https://htmlpreview.github.io/?https://github.com/herdiantrisufriyana/rcausim/blob/master/doc/causal_simulation_exemplar.html>.

Last updated 6 months ago

3.00 score 418 downloads

parallelPlot - `htmlwidget` for a Parallel Coordinates Plot

Create a parallel coordinates plot, using `htmlwidgets` package and `d3.js`.

Last updated 6 months ago

3.00 score 27 scripts 195 downloads

SpatialGEV - Fit Spatial Generalized Extreme Value Models

Fit latent variable models with the GEV distribution as the data likelihood and the GEV parameters following latent Gaussian processes. The models in this package are built using the template model builder 'TMB' in R, which has the fast ability to integrate out the latent variables using Laplace approximation. This package allows the users to choose in the fit function which GEV parameter(s) is considered as a spatially varying random effect following a Gaussian process, so the users can fit spatial GEV models with different complexities to their dataset without having to write the models in 'TMB' by themselves. This package also offers methods to sample from both fixed and random effects posteriors as well as the posterior predictive distributions at different spatial locations. Methods for fitting this class of models are described in Chen, Ramezan, and Lysy (2024) <doi:10.48550/arXiv.2110.07051>.

Last updated 7 months ago

3.00 score 20 scripts 163 downloads

ExactCIone - Admissible Exact Intervals for One-Dimensional Discrete Distributions

Construct the admissible exact intervals for the binomial proportion, the Poisson mean and the total number of subjects with a certain attribute or the total number of the subjects for the hypergeometric distribution. Both one-sided and two-sided intervals are of interest. This package can be used to calculate the intervals constructed methods developed by Wang (2014) <doi:10.5705/ss.2012.257> and Wang (2015) <doi:10.1111/biom.12360>.

Last updated 9 months ago

3.00 score 2 scripts 169 downloads

miselect - Variable Selection for Multiply Imputed Data

Penalized regression methods, such as lasso and elastic net, are used in many biomedical applications when simultaneous regression coefficient estimation and variable selection is desired. However, missing data complicates the implementation of these methods, particularly when missingness is handled using multiple imputation. Applying a variable selection algorithm on each imputed dataset will likely lead to different sets of selected predictors, making it difficult to ascertain a final active set without resorting to ad hoc combination rules. 'miselect' presents Stacked Adaptive Elastic Net (saenet) and Grouped Adaptive LASSO (galasso) for continuous and binary outcomes, developed by Du et al (2022) <doi:10.1080/10618600.2022.2035739>. They, by construction, force selection of the same variables across multiply imputed data. 'miselect' also provides cross validated variants of these methods.

Last updated 10 months ago

3.00 score 20 scripts 160 downloads

iperform - Time Series Performance

A tool to calculate the performance of a time series in a specific date or period. It is more intended for data analysis in the fields of finance, banking, telecommunications or operational marketing.

Last updated 11 months ago

3.00 score 108 downloads

gmGeostats - Geostatistics for Compositional Analysis

Support for geostatistical analysis of multivariate data, in particular data with restrictions, e.g. positive amounts, compositions, distributional data, microstructural data, etc. It includes descriptive analysis and modelling for such data, both from a two-point Gaussian perspective and multipoint perspective. The methods mainly follow Tolosana-Delgado, Mueller and van den Boogaart (2018) <doi:10.1007/s11004-018-9769-3>.

Last updated 2 years ago

openmp

3.00 score 1 stars 6 scripts 287 downloads

autoRasch - Semi-Automated Rasch Analysis

Performs Rasch analysis (semi-)automatically, which has been shown to be comparable with the standard Rasch analysis (Feri Wijayanto et al. (2021) <doi:10.1111/bmsp.12218>, Feri Wijayanto et al. (2022) <doi:10.3758/s13428-022-01947-9>, Feri Wijayanto et al. (2022) <doi:10.1177/01466216221125178>).

Last updated 2 years ago

openblascppopenmp

3.00 score 7 scripts 271 downloads

OTrecod - Data Fusion using Optimal Transportation Theory

In the context of data fusion, the package provides a set of functions dedicated to the solving of 'recoding problems' using optimal transportation theory (Gares, Guernec, Savy (2019) <doi:10.1515/ijb-2018-0106> and Gares, Omer (2020) <doi:10.1080/01621459.2020.1775615>). From two databases with no overlapping part except a subset of shared variables, the functions of the package assist users until obtaining a unique synthetic database, where the missing information is fully completed.

Last updated 2 years ago

3.00 score 20 scripts 174 downloads

litteR - Litter Analysis

Data sets on various litter types like beach litter, riverain litter, floating litter, and seafloor litter are rapidly growing. This package offers a simple user interface to analyse these litter data in a consistent and reproducible way. It also provides functions to facilitate several kinds of litter analysis, e.g., trend analysis, power analysis, and baseline analysis. Under the hood, these functions are also used by the user interface. See Schulz et al. (2019) <doi:10.1016/j.envpol.2019.02.030> for details. MS-Windows users are advised to run 'litteR' in 'RStudio'. See our vignette: Installation manual for 'RStudio' and 'litteR'.

Last updated 2 years ago

3.00 score 18 scripts 256 downloads

TriadSim - Simulating Triad Genomewide Genotypes

Simulate genotypes for case-parent triads, case-control, and quantitative trait samples with realistic linkage diequilibrium structure and allele frequency distribution. For studies of epistasis one can simulate models that involve specific SNPs at specific sets of loci, which we will refer to as "pathways". TriadSim generates genotype data by resampling triad genotypes from existing data. The details of the method is described in the manuscript under preparation "Simulating Autosomal Genotypes with Realistic Linkage Disequilibrium and a Spiked in Genetic Effect" Shi, M., Umbach, D.M., Wise A.S., Weinberg, C.R.

Last updated 3 years ago

snpstats

3.00 score 3 scripts 175 downloads

airGRdatassim - Ensemble-Based Data Assimilation with GR Hydrological Models

Add-on to the 'airGR' package which provides the tools to assimilate observed discharges in daily GR hydrological models. The package consists in two functions allowing to perform the assimilation of observed discharges via the Ensemble Kalman filter or the Particle filter as described in Piazzi et al. (2021) <doi:10.1029/2020WR028390>.

Last updated 4 years ago

3.00 score 2 stars 8 scripts 702 downloads

incidental - Implements Empirical Bayes Incidence Curves

Make empirical Bayes incidence curves from reported case data using a specified delay distribution.

Last updated 4 years ago

3.00 score 2 stars 10 scripts 118 downloads

GARCHIto - Class of GARCH-Ito Models

Provides functions to estimate model parameters and forecast future volatilities using the Unified GARCH-Ito [Kim and Wang (2016) <doi:10.1016/j.jeconom.2016.05.003>] and Realized GARCH-Ito [Song et. al. (2020) <doi:10.1016/j.jeconom.2020.07.007>] models. Optimization is done using augmented Lagrange multiplier method.

Last updated 4 years ago

3.00 score 2 stars 182 downloads

RNCEP - Obtain, Organize, and Visualize NCEP Weather Data

Contains functions to retrieve, organize, and visualize weather data from the NCEP/NCAR Reanalysis (<http://www.esrl.noaa.gov/psd/data/gridded/data.ncep.reanalysis.html>) and NCEP/DOE Reanalysis II (<http://www.esrl.noaa.gov/psd/data/gridded/data.ncep.reanalysis2.html>) datasets. Data are queried via the Internet and may be obtained for a specified spatial and temporal extent or interpolated to a point in space and time. We also provide functions to visualize these weather data on a map. There are also functions to simulate flight trajectories according to specified behavior using either NCEP wind data or data specified by the user.

Last updated 5 years ago

3.00 score 100 scripts 295 downloads

irrICC - Intraclass Correlations for Quantifying Inter-Rater Reliability

Calculates various intraclass correlation coefficients used to quantify inter-rater and intra-rater reliability. The assumption here is that the raters produced quantitative ratings. Most of the statistical procedures implemented in this package are described in details in Gwet, K.L. (2014, ISBN:978-0970806284): "Handbook of Inter-Rater Reliability," 4th edition, Advanced Analytics, LLC.

Last updated 5 years ago

3.00 score 79 scripts 119 downloads

SI - Stochastic Integrating

An implementation of four stochastic methods of integrating in R, including: 1. Stochastic Point Method (or Monte Carlo Method); 2. Mean Value Method; 3. Important Sampling Method; 4. Stratified Sampling Method. It can be used to estimate one-dimension or multi-dimension integration by Monte Carlo methods. And the estimated variance (precision) is given. Reference: Caflisch, R. E. (1998) <doi:10.1017/S0962492900002804>.

Last updated 6 years ago

3.00 score 311 scripts 123 downloads

SLIDE - Single Cell Linkage by Distance Estimation is SLIDE

This statistical method uses the nearest neighbor algorithm to estimate absolute distances between single cells based on a chosen constellation of surface proteins, with these distances being a measure of the similarity between the two cells being compared. Based on Sen, N., Mukherjee, G., and Arvin, A.M. (2015) <DOI:10.1016/j.ymeth.2015.07.008>.

Last updated 7 years ago

3.00 score 57 scripts 111 downloads

benthos - Marine Benthic Ecosystem Analysis

Preprocessing tools and biodiversity measures (species abundance, species richness, population heterogeneity and sensitivity) for analysing marine benthic data. See Van Loon et al. (2015) <doi:10.1016/j.seares.2015.05.002> for an application of these tools.

Last updated 2 years ago

3.00 score 1 dependents 33 scripts 325 downloads

cycleRtools - Tools for Cycling Data Analysis

A suite of functions for analysing cycling data.

Last updated 9 years ago

cpp

3.00 score 3 stars 33 scripts 556 downloads

lmomRFA - Regional Frequency Analysis using L-Moments

Functions for regional frequency analysis using the methods of J. R. M. Hosking and J. R. Wallis (1997), "Regional frequency analysis: an approach based on L-moments".

Last updated 3 months ago

fortran

2.98 score 1 stars 1 dependents 32 scripts 825 downloads

gvlma - Global Validation of Linear Models Assumptions

Methods from the paper: Pena, EA and Slate, EH, "Global Validation of Linear Model Assumptions," J. American Statistical Association, 101(473):341-354, 2006.

Last updated 6 years ago

2.97 score 1 stars 1 dependents 976 scripts 3.1k downloads

stratification - Univariate Stratification of Survey Populations

Univariate stratification of survey populations with a generalization of the Lavallee-Hidiroglou method of stratum construction. The generalized method takes into account a discrepancy between the stratification variable and the survey variable. The determination of the optimal boundaries also incorporate, if desired, an anticipated non-response, a take-all stratum for large units, a take-none stratum for small units, and a certainty stratum to ensure that some specific units are in the sample. The well known cumulative root frequency rule of Dalenius and Hodges and the geometric rule of Gunning and Horgan are also implemented.

Last updated 3 years ago

2.97 score 1 dependents 31 scripts 978 downloads

ctmcd - Estimating the Parameters of a Continuous-Time Markov Chain from Discrete-Time Data

Estimation of Markov generator matrices from discrete-time observations. The implemented approaches comprise diagonal and weighted adjustment of matrix logarithm based candidate solutions as in Israel (2001) <doi:10.1111/1467-9965.00114> as well as a quasi-optimization approach. Moreover, the expectation-maximization algorithm and the Gibbs sampling approach of Bladt and Sorensen (2005) <doi:10.1111/j.1467-9868.2005.00508.x> are included.

Last updated 11 months ago

openblascppopenmp

2.96 score 2 stars 23 scripts 449 downloads

smoother - Functions Relating to the Smoothing of Numerical Data

A collection of methods for smoothing numerical data, commencing with a port of the Matlab gaussian window smoothing function. In addition, several functions typically used in smoothing of financial data are included.

Last updated 9 months ago

2.96 score 4 dependents 68 scripts 1.1k downloads

IsingSampler - Sampling Methods and Distribution Functions for the Ising Model

Sample states from the Ising model and compute the probability of states. Sampling can be done for any number of nodes, but due to the intractibility of the Ising model the distribution can only be computed up to ~10 nodes.

Last updated 1 years ago

cpp

2.96 score 5 dependents 35 scripts 2.0k downloads

mvSLOUCH - Multivariate Stochastic Linear Ornstein-Uhlenbeck Models for Phylogenetic Comparative Hypotheses

Fits multivariate Ornstein-Uhlenbeck types of models to continues trait data from species related by a common evolutionary history. See K. Bartoszek, J, Pienaar, P. Mostad, S. Andersson, T. F. Hansen (2012) <doi:10.1016/j.jtbi.2012.08.005>. The suggested PCMBaseCpp package (which significantly speeds up the likelihood calculations) can be obtained from <https://github.com/venelin/PCMBaseCpp/>.

Last updated 1 years ago

2.95 score 1 dependents 60 scripts 683 downloads

MRTAnalysis - Primary and Secondary Analyses for Micro-Randomized Trials

Estimates marginal causal excursion effects and moderated causal excursion effects for micro-randomized trial (MRT). Applicable to MRT with binary treatment options and continuous or binary outcomes. The method for MRT with continuous outcomes is the weighted centered least squares (WCLS) by Boruvka et al. (2018) <doi:10.1080/01621459.2017.1305274>. The method for MRT with binary outcomes is the estimator for marginal excursion effect (EMEE) by Qian et al. (2021) <doi:10.1093/biomet/asaa070>.

Last updated 1 years ago

2.95 score 18 scripts 111 downloads

SolveSAPHE - Solver Suite for Alkalinity-PH Equations

Universal and robust algorithm for solving the total alkalinity-pH equation presented in G. Munhoven (2013) <doi:10.5194/gmd-6-1367-2013> and G. Munhoven (2021) <doi:10.5194/gmd-2020-447>. The total alkalinity-pH equation relates total alkalinity and pH for a given set of acid-base concentrations in a given water sample, among which carbonic acid. This package is particularly useful in marine chemistry involving dissolved inorganic carbon. Original package in Fortran can be found at <doi:10.5281/zenodo.4328965>.

Last updated 4 years ago

2.95 score 6 dependents 2 scripts 502 downloads

tableMatrix - Combines 'data.table' and 'matrix' Classes

Provides two classes extending 'data.table' class. Simple 'tableList' class wraps 'data.table' and any additional structures together. More complex 'tableMatrix' class combines 'data.table' and 'matrix'. See <http://github.com/InferenceTechnologies/tableMatrix> for more information and examples.

Last updated 7 years ago

2.95 score 18 scripts 159 downloads

keyringr - Decrypt Passwords from Gnome Keyring, Windows Data Protection API and macOS Keychain

Decrypts passwords stored in the Gnome Keyring, macOS Keychain and strings encrypted with the Windows Data Protection API.

Last updated 8 years ago

2.95 score 18 scripts 161 downloads

DISTRIB - Four Essential Functions for Statistical Distributions Analysis: A New Functional Approach

A different way for calculating pdf/pmf, cdf, quantile and random data such that the user is able to consider the name of related distribution as an argument and so easily can changed by a changing argument by user. It must be mentioned that the core and computation base of package 'DISTRIB' is package 'stats'. Although similar functions are introduced previously in package 'stats', but the package 'DISTRIB' has some special applications in some special computational programs.

Last updated 8 years ago

2.95 score 3 dependents 5 scripts 227 downloads

cluster.datasets - Cluster Analysis Data Sets

A collection of data sets for teaching cluster analysis.

Last updated 11 years ago

2.95 score 90 scripts 849 downloads

iCAMP - Infer Community Assembly Mechanisms by Phylogenetic-Bin-Based Null Model Analysis

To implement a general framework to quantitatively infer Community Assembly Mechanisms by Phylogenetic-bin-based null model analysis, abbreviated as 'iCAMP' (Ning et al 2020) <doi:10.1038/s41467-020-18560-z>. It can quantitatively assess the relative importance of different community assembly processes, such as selection, dispersal, and drift, for both communities and each phylogenetic group ('bin'). Each bin usually consists of different taxa from a family or an order. The package also provides functions to implement some other published methods, including neutral taxa percentage (Burns et al 2016) <doi:10.1038/ismej.2015.142> based on neutral theory model and quantifying assembly processes based on entire-community null models ('QPEN', Stegen et al 2013) <doi:10.1038/ismej.2013.93>. It also includes some handy functions, particularly for big datasets, such as phylogenetic and taxonomic null model analysis at both community and bin levels, between-taxa niche difference and phylogenetic distance calculation, phylogenetic signal test within phylogenetic groups, midpoint root of big trees, etc. Version 1.3.x mainly improved the function for 'QPEN' and added function 'icamp.cate()' to summarize 'iCAMP' results for different categories of taxa (e.g. core versus rare taxa).

Last updated 3 years ago

2.95 score 2 stars 1 dependents 49 scripts 841 downloads

rcbalance - Large, Sparse Optimal Matching with Refined Covariate Balance

Tools for large, sparse optimal matching of treated units and control units in observational studies. Provisions are made for refined covariate balance constraints, which include fine and near-fine balance as special cases. Matches are optimal in the sense that they are computed as solutions to network optimization problems rather than greedy algorithms. See Pimentel, et al.(2015) <doi:10.1080/01621459.2014.997879> and Pimentel (2016), Obs. Studies 2(1):4-23. The rrelaxiv package, which provides an alternative solver for the underlying network flow problems, carries an academic license and is not available on CRAN, but may be downloaded from Github at <https://github.com/josherrickson/rrelaxiv/>.

Last updated 3 years ago

2.94 score 1 stars 7 dependents 41 scripts 482 downloads

SpadeR - Species-Richness Prediction and Diversity Estimation with R

Estimation of various biodiversity indices and related (dis)similarity measures based on individual-based (abundance) data or sampling-unit-based (incidence) data taken from one or multiple communities/assemblages.

Last updated 8 years ago

2.93 score 86 scripts 343 downloads

bibliometrixData - Bibliometrix Example Datasets

It contains some example datasets used in 'bibliometrix'. The data are bibliographic datasets exported from the 'SCOPUS' (<https://scopus.com>) and 'Clarivate Analytics Web of Science' (<https://www.webofscience.com/>) databases. They can be used to test the different features of the package 'bibliometrix' (<https://bibliometrix.org>).

Last updated 3 years ago

2.93 score 3 dependents 9 scripts 9.5k downloads

capushe - CAlibrating Penalities Using Slope HEuristics

Calibration of penalized criteria for model selection. The calibration methods available are based on the slope heuristics.

Last updated 1 years ago

2.93 score 15 dependents 19 scripts 666 downloads

pubmed.mineR - Text Mining of PubMed Abstracts

Text mining of PubMed Abstracts (text and XML) from <https://pubmed.ncbi.nlm.nih.gov/>.

Last updated 4 months ago

2.93 score 5 stars 85 scripts 481 downloads

isingLenzMC - Monte Carlo for Classical Ising Model

Classical Ising Model is a land mark system in statistical physics.The model explains the physics of spin glasses and magnetic materials, and cooperative phenomenon in general, for example phase transitions and neural networks.This package provides utilities to simulate one dimensional Ising Model with Metropolis and Glauber Monte Carlo with single flip dynamics in periodic boundary conditions. Utility functions for exact solutions are provided.

Last updated 8 years ago

2.93 score 17 scripts 144 downloads

argosfilter - Argos Locations Filter

Filters animal satellite tracking data obtained from the Argos system(<https://www.argos-system.org/>), following the algorithm described in Freitas et al (2008) <doi:10.1111/j.1748-7692.2007.00180.x>. It is especially indicated for telemetry studies of marine animals, where Argos locations are predominantly of low-quality.

Last updated 2 years ago

2.92 score 84 scripts 462 downloads

OPI - Open Perimetry Interface

Implementation of the Open Perimetry Interface (OPI) for simulating and controlling visual field machines using R. The OPI is a standard for interfacing with visual field testing machines (perimeters) first started as an open source project with support of Haag-Streit in 2010. It specifies basic functions that allow many visual field tests to be constructed. As of February 2022 it is fully implemented on the Haag-Streit Octopus 900 and 'CrewT ImoVifa' ('Topcon Tempo') with partial implementations on the Centervue Compass, Kowa AP 7000 and Android phones. It also has a cousin: the R package 'visualFields', which has tools for analysing and manipulating visual field data.

Last updated 6 months ago

2.91 score 1 stars 18 scripts 432 downloads

separationplot - Separation Plots

Visual representations of model fit or predictive success in the form of "separation plots." See Greenhill, Brian, Michael D. Ward, and Audrey Sacks. "The separation plot: A new visual method for evaluating the fit of binary models." American Journal of Political Science 55.4 (2011): 991-1002.

Last updated 2 years ago

2.91 score 3 dependents 45 scripts 634 downloads

tipsae - Tools for Handling Indices and Proportions in Small Area Estimation

It allows for mapping proportions and indicators defined on the unit interval. It implements Beta-based small area methods comprising the classical Beta regression models, the Flexible Beta model and Zero and/or One Inflated extensions (Janicki 2020 <doi:10.1080/03610926.2019.1570266>). Such methods, developed within a Bayesian framework through Stan <https://mc-stan.org/>, come equipped with a set of diagnostics and complementary tools, visualizing and exporting functions. A Shiny application with a user-friendly interface can be launched to further simplify the process. For further details, refer to De Nicolò and Gardini (2024 <doi:10.18637/jss.v108.i01>).

Last updated 3 months ago

cpp

2.90 score 53 scripts 219 downloads

GPoM - Generalized Polynomial Modelling

Platform dedicated to the Global Modelling technique. Its aim is to obtain ordinary differential equations of polynomial form directly from time series. It can be applied to single or multiple time series under various conditions of noise, time series lengths, sampling, etc. This platform is developped at the Centre d'Etudes Spatiales de la Biosphere (CESBIO), UMR 5126 UPS/CNRS/CNES/IRD, 18 av. Edouard Belin, 31401 TOULOUSE, FRANCE. The developments were funded by the French program Les Enveloppes Fluides et l'Environnement (LEFE, MANU, projets GloMo, SpatioGloMo and MoMu). The French program Defi InFiNiTi (CNRS) and PNTS are also acknowledged (projects Crops'IChaos and Musc & SlowFast). The method is described in the article : Mangiarotti S. and Huc M. (2019) <doi:10.1063/1.5081448>.

Last updated 2 years ago

2.90 score 28 scripts 177 downloads

GCalcium - A Data Manipulation and Analysis Package for Calcium Indicator Data

Provides shortcuts in extracting useful data points and summarizing waveform data. It is optimized for speed to work efficiently with large data sets so you can get to the analysis phase more quickly. It also utilizes a user-friendly format for use by both beginners and seasoned R users.

Last updated 6 years ago

2.90 score 16 scripts 142 downloads

phyloclim - Integrating Phylogenetics and Climatic Niche Modeling

Implements some methods in phyloclimatic modeling: estimation of ancestral climatic niches, age-range-correlation, niche equivalency test and background-similarity test.

Last updated 7 years ago

2.90 score 2 stars 40 scripts 207 downloads

ssanv - Sample Size Adjusted for Nonadherence or Variability of Input Parameters

A set of functions to calculate sample size for two-sample difference in means tests. Does adjustments for either nonadherence or variability that comes from using data to estimate parameters.

Last updated 10 years ago

2.90 score 13 dependents 13 scripts 2.0k downloads

dHSIC - Independence Testing via Hilbert Schmidt Independence Criterion

Contains an implementation of the d-variable Hilbert Schmidt independence criterion and several hypothesis tests based on it, as described in Pfister et al. (2017) <doi:10.1111/rssb.12235>.

Last updated 6 years ago

2.89 score 3 dependents 87 scripts 515 downloads

LMERConvenienceFunctions - Model Selection and Post-Hoc Analysis for (G)LMER Models

The main function of the package is to perform backward selection of fixed effects, forward fitting of the random effects, and post-hoc analysis using parallel capabilities. Other functionality includes the computation of ANOVAs with upper- or lower-bound p-values and R-squared values for each model term, model criticism plots, data trimming on model residuals, and data visualization. The data to run examples is contained in package LCF_data.

Last updated 4 years ago

2.89 score 77 scripts 623 downloads

startR - Automatically Retrieve Multidimensional Distributed Data Sets

Tool to automatically fetch, transform and arrange subsets of multi- dimensional data sets (collections of files) stored in local and/or remote file systems or servers, using multicore capabilities where possible. The tool provides an interface to perceive a collection of data sets as a single large multidimensional data array, and enables the user to request for automatic retrieval, processing and arrangement of subsets of the large array. Wrapper functions to add support for custom file formats can be plugged in/out, making the tool suitable for any research field where large multidimensional data sets are involved.

Last updated 3 months ago

2.89 score 2 dependents 64 scripts 347 downloads

zetadiv - Functions to Compute Compositional Turnover Using Zeta Diversity

Functions to compute compositional turnover using zeta-diversity, the number of species shared by multiple assemblages. The package includes functions to compute zeta-diversity for a specific number of assemblages and to compute zeta-diversity for a range of numbers of assemblages. It also includes functions to explain how zeta-diversity varies with distance and with differences in environmental variables between assemblages, using generalised linear models, linear models with negative constraints, generalised additive models,shape constrained additive models, and I-splines.

Last updated 3 years ago

2.88 score 3 stars 63 scripts 258 downloads

conicfit - Algorithms for Fitting Circles, Ellipses and Conics Based on the Work by Prof. Nikolai Chernov

Geometric circle fitting with Levenberg-Marquardt (a, b, R), Levenberg-Marquardt reduced (a, b), Landau, Spath and Chernov-Lesort. Algebraic circle fitting with Taubin, Kasa, Pratt and Fitzgibbon-Pilu-Fisher. Geometric ellipse fitting with ellipse LMG (geometric parameters) and conic LMA (algebraic parameters). Algebraic ellipse fitting with Fitzgibbon-Pilu-Fisher and Taubin.

Last updated 9 years ago

2.88 score 2 dependents 126 scripts 684 downloads

interleave - Converts Tabular Data to Interleaved Vectors

Converts matrices and lists of matrices into a single vector by interleaving their values. That is, each element of the result vector is filled from the input matrices one row at a time. This is the same as transposing a matrix, then removing the dimension attribute, but is designed to operate on matrices in nested list structures.

Last updated 11 months ago

cpp

2.88 score 2 dependents 4 scripts 1.3k downloads

MNM - Multivariate Nonparametric Methods. An Approach Based on Spatial Signs and Ranks

Multivariate tests, estimates and methods based on the identity score, spatial sign score and spatial rank score are provided. The methods include one and c-sample problems, shape estimation and testing, linear regression and principal components. The methodology is described in Oja (2010) <doi:10.1007/978-1-4419-0468-3> and Nordhausen and Oja (2011) <doi:10.18637/jss.v043.i05>.

Last updated 1 years ago

2.88 score 1 dependents 25 scripts 282 downloads

PlaneGeometry - Plane Geometry

An extensive set of plane geometry routines. Provides R6 classes representing triangles, circles, circular arcs, ellipses, elliptical arcs, lines, hyperbolae, and their plot methods. Also provides R6 classes representing transformations: rotations, reflections, homotheties, scalings, general affine transformations, inversions, Möbius transformations.

Last updated 1 years ago

2.87 score 74 scripts 324 downloads

GPM - Gaussian Process Modeling of Multi-Response and Possibly Noisy Datasets

Provides a general and efficient tool for fitting a response surface to a dataset via Gaussian processes. The dataset can have multiple responses and be noisy (with stationary variance). The fitted GP model can predict the gradient as well. The package is based on the work of Bostanabad, R., Kearney, T., Tao, S. Y., Apley, D. W. & Chen, W. (2018) Leveraging the nugget parameter for efficient Gaussian process modeling. International Journal for Numerical Methods in Engineering, 114, 501-516.

Last updated 6 years ago

openblascppopenmp

2.86 score 73 scripts 196 downloads

sensitivitymv - Sensitivity Analysis in Observational Studies

The package performs a sensitivity analysis in an observational study using an M-statistic, for instance, the mean. The main function in the package is senmv(), but amplify() and truncatedP() are also useful. The method is developed in Rosenbaum Biometrics, 2007, 63, 456-464, <doi:10.1111/j.1541-0420.2006.00717.x>.

Last updated 7 years ago

2.86 score 4 dependents 60 scripts 210 downloads

HDMT - A Multiple Testing Procedure for High-Dimensional Mediation Hypotheses

A multiple-testing procedure for high-dimensional mediation hypotheses. Mediation analysis is of rising interest in epidemiology and clinical trials. Among existing methods for mediation analyses, the popular joint significance (JS) test yields an overly conservative type I error rate and therefore low power. In the R package 'HDMT' we implement a multiple-testing procedure that accurately controls the family-wise error rate (FWER) and the false discovery rate (FDR) when using JS for testing high-dimensional mediation hypotheses. The core of our procedure is based on estimating the proportions of three component null hypotheses and deriving the corresponding mixture distribution of null p-values. Results of the data examples include better-behaved quantile-quantile plots and improved detection of novel mediation relationships on the role of DNA methylation in genetic regulation of gene expression. With increasing interest in mediation by molecular intermediaries such as gene expression, the proposed method addresses an unmet methodological challenge. Methods used in the package refer to James Y. Dai, Janet L. Stanford & Michael LeBlanc (2020) <doi:10.1080/01621459.2020.1765785>.

Last updated 3 years ago

2.86 score 2 dependents 12 scripts 298 downloads

kappaSize - Sample Size Estimation Functions for Studies of Interobserver Agreement

Contains basic tools for sample size estimation in studies of interobserver/interrater agreement (reliability). Includes functions for both the power-based and confidence interval-based methods, with binary or multinomial outcomes and two through six raters.

Last updated 6 years ago

2.86 score 3 stars 2 dependents 14 scripts 306 downloads

ARIbrain - All-Resolution Inference

It performs All-Resolutions Inference (ARI) on functional Magnetic Resonance Image (fMRI) data. As a main feature, it estimates lower bounds for the proportion of active voxels in a set of clusters as, for example, given by a cluster-wise analysis. The method is described in Rosenblatt, Finos, Weeda, Solari, Goeman (2018) <doi:10.1016/j.neuroimage.2018.07.060>.

Last updated 6 years ago

2.86 score 1 stars 2 dependents 12 scripts 216 downloads

ThreeWay - Three-Way Component Analysis

Component analysis for three-way data arrays by means of Candecomp/Parafac, Tucker3, Tucker2 and Tucker1 models.

Last updated 9 years ago

2.86 score 8 dependents 60 scripts 545 downloads

batch - Batching Routines in Parallel and Passing Command-Line Arguments to R

Functions to allow you to easily pass command-line arguments into R, and functions to aid in submitting your R code in parallel on a cluster and joining the results afterward (e.g. multiple parameter values for simulations running in parallel, splitting up a permutation test in parallel, etc.). See `parseCommandArgs(...)' for the main example of how to use this package.

Last updated 7 years ago

2.85 score 179 scripts 299 downloads

msme - Functions and Datasets for "Methods of Statistical Model Estimation"

Functions and datasets from Hilbe, J.M., and Robinson, A.P. 2013. Methods of Statistical Model Estimation. Chapman & Hall / CRC.

Last updated 7 years ago

2.85 score 1 stars 2 dependents 117 scripts 664 downloads

mratios - Ratios of Coefficients in the General Linear Model

Performs (simultaneous) inferences for ratios of linear combinations of coefficients in the general linear model, linear mixed model, and for quantiles in a one-way layout. Multiple comparisons and simultaneous confidence interval estimations can be performed for ratios of treatment means in the normal one-way layout with homogeneous and heterogeneous treatment variances, according to Dilba et al. (2007) <https://cran.r-project.org/doc/Rnews/Rnews_2007-1.pdf> and Hasler and Hothorn (2008) <doi:10.1002/bimj.200710466>. Confidence interval estimations for ratios of linear combinations of linear model parameters like in (multiple) slope ratio and parallel line assays can be carried out. Moreover, it is possible to calculate the sample sizes required in comparisons with a control based on relative margins. For the simple two-sample problem, functions for a t-test for ratio-formatted hypotheses and the corresponding confidence interval are provided assuming homogeneous or heterogeneous group variances.

Last updated 5 years ago

2.85 score 4 dependents 54 scripts 1.1k downloads

espadon - Easy Study of Patient DICOM Data in Oncology

Exploitation, processing and 2D-3D visualization of DICOM-RT files (structures, dosimetry, imagery) for medical physics and clinical research, in a patient-oriented perspective.

Last updated 29 days ago

cpp

2.85 score 2 scripts 285 downloads

BAwiR - Analysis of Basketball Data

Collection of tools to work with European basketball data. Functions available are related to friendly web scraping, data management and visualization. Data were obtained from <https://www.euroleaguebasketball.net/euroleague/>, <https://www.euroleaguebasketball.net/eurocup/> and <https://www.acb.com/>, following the instructions of their respectives robots.txt files, when available. Box score data are available for the three leagues. Play-by-play data are also available for the Spanish league. Methods for analysis include a population pyramid, 2D plots, circular plots of players' percentiles, plots of players' monthly/yearly stats, team heatmaps, team shooting plots, team four factors plots, cross-tables with the results of regular season games, maps of nationalities, combinations of lineups, possessions-related variables, timeouts, performance by periods, personal fouls and offensive rebounds. Please see Vinue (2020) <doi:10.1089/big.2018.0124>.

Last updated 12 months ago

2.85 score 1 stars 35 scripts 461 downloads

mand - Multivariate Analysis for Neuroimaging Data

Several functions can be used to analyze neuroimaging data using multivariate methods based on the 'msma' package. The functions used in the book entitled "Multivariate Analysis for Neuroimaging Data" (2021, ISBN-13: 978-0367255329) are contained.

Last updated 1 years ago

2.85 score 10 scripts 245 downloads

pmmlTransformations - Transforms Input Data from a PMML Perspective

Allows for data to be transformed before using it to construct models. Builds structures to allow functions in the PMML package to output transformation details in addition to the model in the resulting PMML file. The Predictive Model Markup Language (PMML) is an XML-based language which provides a way for applications to define machine learning, statistical and data mining models and to share models between PMML compliant applications. More information about the PMML industry standard and the Data Mining Group can be found at <http://www.dmg.org>. The generated PMML can be imported into any PMML consuming application, such as Zementis Predictive Analytics products, which integrate with web services, relational database systems and deploy natively on Hadoop in conjunction with Hive, Spark or Storm, as well as allow predictive analytics to be executed for IBM z Systems mainframe applications and real-time, streaming analytics platforms.

Last updated 6 years ago

2.85 score 2 stars 35 scripts 234 downloads

ncappc - NCA Calculations and Population Model Diagnosis

A flexible tool that can perform (i) traditional non-compartmental analysis (NCA) and (ii) Simulation-based posterior predictive checks for population pharmacokinetic (PK) and/or pharmacodynamic (PKPD) models using NCA metrics.

Last updated 6 years ago

2.85 score 14 scripts 275 downloads

ordinalNet - Penalized Ordinal Regression

Fits ordinal regression models with elastic net penalty. Supported model families include cumulative probability, stopping ratio, continuation ratio, and adjacent category. These families are a subset of vector glm's which belong to a model class we call the elementwise link multinomial-ordinal (ELMO) class. Each family in this class links a vector of covariates to a vector of class probabilities. Each of these families has a parallel form, which is appropriate for ordinal response data, as well as a nonparallel form that is appropriate for an unordered categorical response, or as a more flexible model for ordinal data. The parallel model has a single set of coefficients, whereas the nonparallel model has a set of coefficients for each response category except the baseline category. It is also possible to fit a model with both parallel and nonparallel terms, which we call the semi-parallel model. The semi-parallel model has the flexibility of the nonparallel model, but the elastic net penalty shrinks it toward the parallel model. For details, refer to Wurm, Hanlon, and Rathouz (2021) <doi:10.18637/jss.v099.i06>.

Last updated 3 years ago

2.84 score 1 stars 4 dependents 29 scripts 501 downloads

rkt - Mann-Kendall Test, Seasonal and Regional Kendall Tests

Contains function rkt which computes the Mann-Kendall test (MK) and the Seasonal and the Regional Kendall Tests for trend (SKT and RKT) and Theil-Sen's slope estimator.

Last updated 11 months ago

2.84 score 1 stars 1 dependents 57 scripts 512 downloads

GoFKernel - Testing Goodness-of-Fit with the Kernel Density Estimator

Tests of goodness-of-fit based on a kernel smoothing of the data. References: Pavía (2015) <doi:10.18637/jss.v066.c01>.

Last updated 18 days ago

2.83 score 5 dependents 45 scripts 408 downloads

lunar - Calculate Lunar Phase & Distance, Seasons and Related Environmental Factors

Provides functions to calculate lunar and other related environmental covariates.

Last updated 3 years ago

2.82 score 1 dependents 74 scripts 329 downloads

RPointCloud - Visualizing Topological Loops and Voids

Visualizations to explain the results of a topological data analysis. The goal of topological data analysis is to identify persistent topological structures, such as loops (topological circles) and voids (topological spheres), in data sets. The output of an analysis using the 'TDA' package is a Rips diagram (named after the mathematician Eliyahu Rips). The goal of 'RPointCloud' is to fill in these holes in the data by providing tools to visualize the features that help explain the structures found in the Rips diagram. See McGee and colleagues (2024) <doi:10.1101/2024.05.16.593927>.

Last updated 4 months ago

2.82 score 11 scripts 158 downloads

IMTest - Information Matrix Test for Generalized Partial Credit Models

Implementation of the information matrix test for generalized partial credit models.

Last updated 8 years ago

2.82 score 6 scripts 1.3k downloads

trinROC - Statistical Tests for Assessing Trinormal ROC Data

Several statistical test functions as well as a function for exploratory data analysis to investigate classifiers allocating individuals to one of three disjoint and ordered classes. In a single classifier assessment the discriminatory power is compared to classification by chance. In a comparison of two classifiers the null hypothesis corresponds to equal discriminatory power of the two classifiers. See also "ROC Analysis for Classification and Prediction in Practice" by Nakas, Bantis and Gatsonis (2023), ISBN 9781482233704.

Last updated 3 months ago

2.81 score 13 scripts 190 downloads

unifed - The Unifed Distribution

Probability functions, family for glm() and Stan code for working with the unifed distribution (Quijano Xacur, 2019; <doi:10.1186/s40488-019-0102-6>).

Last updated 3 years ago

2.81 score 13 scripts 275 downloads

cdparcoord - Top Frequency-Based Parallel Coordinates

Parallel coordinate plotting with resolutions for large data sets and missing values.

Last updated 5 years ago

2.81 score 13 scripts 294 downloads

GAD - Analysis of Variance from General Principles

Analysis of complex ANOVA models with any combination of orthogonal/nested and fixed/random factors, as described by Underwood (1997). There are two restrictions: (i) data must be balanced; (ii) fixed nested factors are not allowed. Homogeneity of variances is checked using Cochran's C test and 'a posteriori' comparisons of means are done using Student-Newman-Keuls (SNK) procedure. For those terms with no denominator in the F-ratio calculation, pooled mean squares and quasi F-ratios are provided. Magnitute of effects are assessed by components of variation.

Last updated 8 months ago

2.81 score 53 scripts 1.2k downloads

PResiduals - Probability-Scale Residuals and Residual Correlations

Computes probability-scale residuals and residual correlations for continuous, ordinal, binary, count, and time-to-event data <doi:10.18637/jss.v094.i12>.

Last updated 4 years ago

2.81 score 2 stars 64 scripts 284 downloads

GeneCycle - Identification of Periodically Expressed Genes

The GeneCycle package implements the approaches of Wichert et al. (2004) <doi:10.1093/bioinformatics/btg364>, Ahdesmaki et al. (2005) <doi:10.1186/1471-2105-6-117> and Ahdesmaki et al. (2007) <DOI:10.1186/1471-2105-8-233> for detecting periodically expressed genes from gene expression time series data.

Last updated 4 years ago

2.81 score 1 stars 64 scripts 272 downloads

InterSIM - Simulation of Inter-Related Genomic Datasets

Generates three inter-related genomic datasets : methylation, gene expression and protein expression.

Last updated 6 years ago

2.80 score 2 dependents 35 scripts 229 downloads

pandocfilters - Pandoc Filters for R

The document converter 'pandoc' <https://pandoc.org/> is widely used in the R community. One feature of 'pandoc' is that it can produce and consume JSON-formatted abstract syntax trees (AST). This allows to transform a given source document into JSON-formatted AST, alter it by so called filters and pass the altered JSON-formatted AST back to 'pandoc'. This package provides functions which allow to write such filters in native R code. Although this package is inspired by the Python package 'pandocfilters' <https://github.com/jgm/pandocfilters/>, it provides additional convenience functions which make it simple to use the 'pandocfilters' package as a report generator. Since 'pandocfilters' inherits most of it's functionality from 'pandoc' it can create documents in many formats (for more information see <https://pandoc.org/>) but is also bound to the same limitations as 'pandoc'.

Last updated 2 years ago

2.80 score 63 scripts 261 downloads

XBRL - Extraction of Business Financial Information from 'XBRL' Documents

Functions to extract business financial information from an Extensible Business Reporting Language ('XBRL') instance file and the associated collection of files that defines its 'Discoverable' Taxonomy Set ('DTS').

Last updated 3 years ago

libxml2cpp

2.80 score 5 stars 1 dependents 42 scripts 552 downloads

ABCanalysis - Computed ABC Analysis

For a given data set, the package provides a novel method of computing precise limits to acquire subsets which are easily interpreted. Closely related to the Lorenz curve, the ABC curve visualizes the data by graphically representing the cumulative distribution function. Based on an ABC analysis the algorithm calculates, with the help of the ABC curve, the optimal limits by exploiting the mathematical properties pertaining to distribution of analyzed items. The data containing positive values is divided into three disjoint subsets A, B and C, with subset A comprising very profitable values, i.e. largest data values ("the important few"), subset B comprising values where the yield equals to the effort required to obtain it, and the subset C comprising of non-profitable values, i.e., the smallest data sets ("the trivial many"). Package is based on "Computed ABC Analysis for rational Selection of most informative Variables in multivariate Data", PLoS One. Ultsch. A., Lotsch J. (2015) <DOI:10.1371/journal.pone.0129767>.

Last updated 8 years ago

2.80 score 1 stars 3 dependents 9 scripts 987 downloads

yhat - Interpreting Regression Effects

The purpose of this package is to provide methods to interpret multiple linear regression and canonical correlation results including beta weights,structure coefficients, validity coefficients, product measures, relative weights, all-possible-subsets regression, dominance analysis, commonality analysis, and adjusted effect sizes.

Last updated 1 years ago

2.79 score 1 stars 62 scripts 565 downloads

NST - Normalized Stochasticity Ratio

To estimate ecological stochasticity in community assembly. Understanding the community assembly mechanisms controlling biodiversity patterns is a central issue in ecology. Although it is generally accepted that both deterministic and stochastic processes play important roles in community assembly, quantifying their relative importance is challenging. The new index, normalized stochasticity ratio (NST), is to estimate ecological stochasticity, i.e. relative importance of stochastic processes, in community assembly. With functions in this package, NST can be calculated based on different similarity metrics and/or different null model algorithms, as well as some previous indexes, e.g. previous Stochasticity Ratio (ST), Standard Effect Size (SES), modified Raup-Crick metrics (RC). Functions for permutational test and bootstrapping analysis are also included. Previous ST is published by Zhou et al (2014) <doi:10.1073/pnas.1324044111>. NST is modified from ST by considering two alternative situations and normalizing the index to range from 0 to 1 (Ning et al 2019) <doi:10.1073/pnas.1904623116>. A modified version, MST, is a special case of NST, used in some recent or upcoming publications, e.g. Liang et al (2020) <doi:10.1016/j.soilbio.2020.108023>. SES is calculated as described in Kraft et al (2011) <doi:10.1126/science.1208584>. RC is calculated as reported by Chase et al (2011) <doi:10.1890/ES10-00117.1> and Stegen et al (2013) <doi:10.1038/ismej.2013.93>. Version 3 added NST based on phylogenetic beta diversity, used by Ning et al (2020) <doi:10.1038/s41467-020-18560-z>.

Last updated 3 years ago

2.79 score 2 stars 31 scripts 584 downloads

queueing - Analysis of Queueing Networks and Models

It provides versatile tools for analysis of birth and death based Markovian Queueing Models and Single and Multiclass Product-Form Queueing Networks. It implements M/M/1, M/M/c, M/M/Infinite, M/M/1/K, M/M/c/K, M/M/c/c, M/M/1/K/K, M/M/c/K/K, M/M/c/K/m, M/M/Infinite/K/K, Multiple Channel Open Jackson Networks, Multiple Channel Closed Jackson Networks, Single Channel Multiple Class Open Networks, Single Channel Multiple Class Closed Networks and Single Channel Multiple Class Mixed Networks. Also it provides a B-Erlang, C-Erlang and Engset calculators. This work is dedicated to the memory of D. Sixto Rios Insua.

Last updated 5 years ago

2.79 score 376 scripts 1.6k downloads

tmvnsim - Truncated Multivariate Normal Simulation

Importance sampling from the truncated multivariate normal using the GHK (Geweke-Hajivassiliou-Keane) simulator. Unlike Gibbs sampling which can get stuck in one truncation sub-region depending on initial values, this package allows truncation based on disjoint regions that are created by truncation of absolute values. The GHK algorithm uses simple Cholesky transformation followed by recursive simulation of univariate truncated normals hence there are also no convergence issues. Importance sample is returned along with sampling weights, based on which, one can calculate integrals over truncated regions for multivariate normals.

Last updated 8 years ago

2.78 score 4 dependents 8 scripts 5.0k downloads

matchMulti - Optimal Multilevel Matching using a Network Algorithm

Performs multilevel matches for data with cluster- level treatments and individual-level outcomes using a network optimization algorithm. Functions for checking balance at the cluster and individual levels are also provided, as are methods for permutation-inference-based outcome analysis. Details in Pimentel et al. (2018) <doi:10.1214/17-AOAS1118>. The optmatch package, which is useful for running many of the provided functions, may be downloaded from Github at <https://github.com/markmfredrickson/optmatch> if not available on CRAN.

Last updated 6 months ago

2.78 score 1 stars 1 dependents 20 scripts 401 downloads

rumidas - Univariate GARCH-MIDAS, Double-Asymmetric GARCH-MIDAS and MEM-MIDAS

Adds the MIxing-Data Sampling (MIDAS, Ghysels et al. (2007) <doi:10.1080/07474930600972467>) components to a variety of GARCH and MEM (Engle (2002) <doi:10.1002/jae.683>, Engle and Gallo (2006) <doi:10.1016/j.jeconom.2005.01.018>, and Amendola et al. (2024) <doi:10.1016/j.seps.2023.101764>) models, with the aim of predicting the volatility with additional low-frequency (that is, MIDAS) terms. The estimation takes place through simple functions, which provide in-sample and (if present) and out-of-sample evaluations. 'rumidas' also offers a summary tool, which synthesizes the main information of the estimated model. There is also the possibility of generating one-step-ahead and multi-step-ahead forecasts.

Last updated 10 months ago

2.78 score 10 stars 2 dependents 4 scripts 201 downloads

mixKernel - Omics Data Integration Using Kernel Methods

Kernel-based methods are powerful methods for integrating heterogeneous types of data. mixKernel aims at providing methods to combine kernel for unsupervised exploratory analysis. Different solutions are provided to compute a meta-kernel, in a consensus way or in a way that best preserves the original topology of the data. mixKernel also integrates kernel PCA to visualize similarities between samples in a non linear space and from the multiple source point of view <doi:10.1093/bioinformatics/btx682>. A method to select (as well as funtions to display) important variables is also provided <doi:10.1093/nargab/lqac014>.

Last updated 11 months ago

2.78 score 9 scripts 232 downloads

RobPer - Robust Periodogram and Periodicity Detection Methods

Calculates periodograms based on (robustly) fitting periodic functions to light curves (irregularly observed time series, possibly with measurement accuracies, occurring in astroparticle physics). Three main functions are included: RobPer() calculates the periodogram. Outlying periodogram bars (indicating a period) can be detected with betaCvMfit(). Artificial light curves can be generated using the function tsgen(). For more details see the corresponding article: Thieler, Fried and Rathjens (2016), Journal of Statistical Software 69(9), 1-36, <doi:10.18637/jss.v069.i09>.

Last updated 3 years ago

2.78 score 2 stars 1 dependents 28 scripts 191 downloads

OptimalCutpoints - Computing Optimal Cutpoints in Diagnostic Tests

Computes optimal cutpoints for diagnostic tests or continuous markers. Various approaches for selecting optimal cutoffs have been implemented, including methods based on cost-benefit analysis and diagnostic test accuracy measures (Sensitivity/Specificity, Predictive Values and Diagnostic Likelihood Ratios). Numerical and graphical output for all methods is easily obtained.

Last updated 3 years ago

2.78 score 2 stars 1 dependents 136 scripts 793 downloads

Umpire - Simulating Realistic Gene Expression and Clinical Data

The Ultimate Microrray Prediction, Reality and Inference Engine (UMPIRE) is a package to facilitate the simulation of realistic microarray data sets with links to associated outcomes. See Zhang and Coombes (2012) <doi:10.1186/1471-2105-13-S13-S1>. Version 2.0 adds the ability to simulate realistic mixed-typed clinical data.

Last updated 4 years ago

2.78 score 58 scripts 213 downloads

iDINGO - Integrative Differential Network Analysis in Genomics

Fits covariate dependent partial correlation matrices for integrative models to identify differential networks between two groups. The methods are described in Class et. al., (2018) <doi:10.1093/bioinformatics/btx750> and Ha et. al., (2015) <doi:10.1093/bioinformatics/btv406>.

Last updated 4 years ago

2.78 score 3 stars 7 scripts 180 downloads

mnonr - A Generator of Multivariate Non-Normal Random Numbers

A data generator of multivariate non-normal data in R. It combines two different methods to generate non-normal data, one with user-specified multivariate skewness and kurtosis (more details can be found in the paper: Qu, Liu, & Zhang, 2019 <doi:10.3758/s13428-019-01291-5>), and the other with the given marginal skewness and kurtosis. The latter one is the widely-used Vale and Maurelli's method. It also contains a function to calculate univariate and multivariate (Mardia's Test) skew and kurtosis.

Last updated 5 years ago

2.78 score 2 dependents 2 scripts 261 downloads

sim1000G - Genotype Simulations for Rare or Common Variants Using Haplotypes from 1000 Genomes

Generates realistic simulated genetic data in families or unrelated individuals.

Last updated 6 years ago

2.78 score 1 stars 66 scripts 162 downloads

qtlhot - Inference for QTL Hotspots

Functions to infer co-mapping trait hotspots and causal models. Chaibub Neto E, Keller MP, Broman AF, Attie AD, Jansen RC, Broman KW, Yandell BS (2012) Quantile-based permutation thresholds for QTL hotspots. Genetics 191 : 1355-1365. <doi:10.1534/genetics.112.139451>. Chaibub Neto E, Broman AT, Keller MP, Attie AD, Zhang B, Zhu J, Yandell BS (2013) Modeling causality for pairs of phenotypes in system genetics. Genetics 193 : 1003-1013. <doi:10.1534/genetics.112.147124>.

Last updated 7 years ago

2.78 score 30 scripts 218 downloads

didimputation - Imputation Estimator from Borusyak, Jaravel, and Spiess (2021)

Estimates Two-way Fixed Effects difference-in-differences/event-study models using the imputation-based approach proposed by Borusyak, Jaravel, and Spiess (2021).

Last updated 2 years ago

openblascppopenmp

2.78 score 1 dependents 40 scripts 808 downloads

PCovR - Principal Covariates Regression

Analyzing regression data with many and/or highly collinear predictor variables, by simultaneously reducing the predictor variables to a limited number of components and regressing the criterion variables on these components (de Jong S. & Kiers H. A. L. (1992) <doi:10.1016/0169-7439(92)80100-I>). Several rotation and model selection options are provided.

Last updated 1 years ago

2.76 score 4 dependents 12 scripts 285 downloads

robslopes - Fast Algorithms for Robust Slopes

Fast algorithms for the Theil-Sen estimator, Siegel's repeated median slope estimator, and Passing-Bablok regression. The implementation is based on algorithms by Dillencourt et. al (1992) <doi:10.1142/S0218195992000020> and Matousek et. al (1998) <doi:10.1007/PL00009190>. The implementations are detailed in Raymaekers (2023) <doi:10.32614/RJ-2023-012> and Raymaekers J., Dufey F. (2022) <arXiv:2202.08060>. All algorithms run in quasilinear time.

Last updated 2 years ago

cpp

2.76 score 8 dependents 5 scripts 2.4k downloads

evclust - Evidential Clustering

Various clustering algorithms that produce a credal partition, i.e., a set of Dempster-Shafer mass functions representing the membership of objects to clusters. The mass functions quantify the cluster-membership uncertainty of the objects. The algorithms are: Evidential c-Means, Relational Evidential c-Means, Constrained Evidential c-Means, Evidential Clustering, Constrained Evidential Clustering, Evidential K-nearest-neighbor-based Clustering, Bootstrap Model-Based Evidential Clustering, Belief Peak Evidential Clustering, Neural-Network-based Evidential Clustering.

Last updated 1 years ago

2.76 score 1 dependents 19 scripts 310 downloads

MicrobiomeStat - Statistical Methods for Microbiome Compositional Data

A suite of methods for powerful and robust microbiome data analysis addressing zero-inflation, phylogenetic structure and compositional effects (Zhou et al. (2022)<doi:10.1186/s13059-022-02655-5>). The methods can be applied to the analysis of other (high-dimensional) compositional data arising from sequencing experiments.

Last updated 9 months ago

2.75 score 2 dependents 88 scripts 1.1k downloads

pwr2 - Power and Sample Size Analysis for One-way and Two-way ANOVA Models

User friendly functions for power and sample size analysis at one-way and two-way ANOVA settings take either effect size or delta and sigma as arguments. They are designed for both one-way and two-way ANOVA settings. In addition, a function for plotting power curves is available for power comparison, which can be easily visualized by statisticians and clinical researchers.

Last updated 8 years ago

2.75 score 1 dependents 47 scripts 842 downloads

siebanxicor - Query Data Series from Bank of Mexico

Allows to retrieve time series of all indicators available in the Bank of Mexico's Economic Information System (<http://www.banxico.org.mx/SieInternet/>).

Last updated 6 years ago

2.74 score 3 stars 37 scripts 298 downloads

KRIS - Keen and Reliable Interface Subroutines for Bioinformatic Analysis

Provides useful functions which are needed for bioinformatic analysis such as calculating linear principal components from numeric data and Single-nucleotide polymorphism (SNP) dataset, calculating fixation index (Fst) using Hudson method, creating scatter plots in 3 views, handling with PLINK binary file format, detecting rough structures and outliers using unsupervised clustering, and calculating matrix multiplication in the faster way for big data.

Last updated 4 years ago

2.73 score 2 dependents 18 scripts 175 downloads

EQL - Extended-Quasi-Likelihood-Function (EQL)

Computation of the EQL for a given family of variance functions, Saddlepoint-approximations and related auxiliary functions (e.g. Hermite polynomials).

Last updated 5 years ago

2.73 score 3 dependents 30 scripts 419 downloads

pgdraw - Generate Random Samples from the Polya-Gamma Distribution

Generates random samples from the Polya-Gamma distribution using an implementation of the algorithm described in J. Windle's PhD thesis (2013) <https://repositories.lib.utexas.edu/bitstream/handle/2152/21842/WINDLE-DISSERTATION-2013.pdf>. The underlying implementation is in C.

Last updated 6 years ago

cpp

2.73 score 5 dependents 36 scripts 484 downloads

AlphaPart - Partition/Decomposition of Breeding Values by Paths of Information

A software that implements a method for partitioning genetic trends to quantify the sources of genetic gain in breeding programmes. The partitioning method is described in Garcia-Cortes et al. (2008) <doi:10.1017/S175173110800205X>. The package includes the main function AlphaPart for partitioning breeding values and auxiliary functions for manipulating data and summarizing, visualizing, and saving results.

Last updated 2 years ago

cpp

2.72 score 26 scripts 497 downloads

NHPoisson - Modelling and Validation of Non Homogeneous Poisson Processes

Tools for modelling, ML estimation, validation analysis and simulation of non homogeneous Poisson processes in time.

Last updated 5 years ago

2.71 score 2 stars 2 dependents 43 scripts 254 downloads

SpatialML - Spatial Machine Learning

Implements a spatial extension of the random forest algorithm (Georganos et al. (2019) <doi:10.1080/10106049.2019.1595177>). Allows for a geographically weighted random forest regression including a function to find the optical bandwidth. (Georganos and Kalogirou (2022) <https://www.mdpi.com/2220-9964/11/9/471>).

Last updated 9 months ago

2.71 score 8 stars 32 scripts 294 downloads

joint.Cox - Joint Frailty-Copula Models for Tumour Progression and Death in Meta-Analysis

Fit survival data and perform dynamic prediction under joint frailty-copula models for tumour progression and death. Likelihood-based methods are employed for estimating model parameters, where the baseline hazard functions are modeled by the cubic M-spline or the Weibull model. The methods are applicable for meta-analytic data containing individual-patient information from several studies. Survival outcomes need information on both terminal event time (e.g., time-to-death) and non-terminal event time (e.g., time-to-tumour progression). Methodologies were published in Emura et al. (2017) <doi:10.1177/0962280215604510>, Emura et al. (2018) <doi:10.1177/0962280216688032>, Emura et al. (2020) <doi:10.1177/0962280219892295>, Shinohara et al. (2020) <doi:10.1080/03610918.2020.1855449>, Wu et al. (2020) <doi:10.1007/s00180-020-00977-1>, and Emura et al. (2021) <doi:10.1177/09622802211046390>. See also the book of Emura et al. (2019) <doi:10.1007/978-981-13-3516-7>. Survival data from ovarian cancer patients are also available.

Last updated 3 years ago

2.71 score 5 stars 2 dependents 17 scripts 573 downloads

DIDmultiplegtDYN - Estimation in Difference-in-Difference Designs with Multiple Groups and Periods

Estimation of event-study Difference-in-Difference (DID) estimators in designs with multiple groups and periods, and with a potentially non-binary treatment that may increase or decrease multiple times.

Last updated 3 months ago

openjdk

2.71 score 1 dependents 17 scripts 856 downloads

MARVEL - Revealing Splicing Dynamics at Single-Cell Resolution

Alternative splicing represents an additional and underappreciated layer of complexity underlying gene expression profiles. Nevertheless, there remains hitherto a paucity of software to investigate splicing dynamics at single-cell resolution. 'MARVEL' enables splicing analysis of single-cell RNA-sequencing data generated from plate- and droplet-based library preparation methods.

Last updated 2 years ago

2.71 score 51 scripts 209 downloads

edfReader - Reading EDF(+) and BDF(+) Files

Reads European Data Format files EDF and EDF+, see <http://www.edfplus.info>, BioSemi Data Format files BDF, see <http://www.biosemi.com/faq/file_format.htm>, and BDF+ files, see <http://www.teuniz.net/edfbrowser/bdfplus%20format%20description.html>. The files are read in two steps: first the header is read and then the signals (using the header object as a parameter).

Last updated 6 years ago

2.71 score 1 dependents 17 scripts 411 downloads

longitudinal - Analysis of Multiple Time Course Data

Contains general data structures and functions for longitudinal data with multiple variables, repeated measurements, and irregularly spaced time points. Also implements a shrinkage estimator of dynamical correlation and dynamical covariance.

Last updated 3 years ago

2.70 score 1 stars 7 dependents 24 scripts 690 downloads

XDNUTS - Discontinuous Hamiltonian Monte Carlo with Varying Trajectory Length

Hamiltonian Monte Carlo for both continuous and discontinuous posterior distributions with customisable trajectory length termination criterion. See Nishimura et al. (2020) <doi:10.1093/biomet/asz083> for the original Discontinuous Hamiltonian Monte Carlo, Hoffman et al. (2014) <doi:10.48550/arXiv.1111.4246> and Betancourt (2016) <doi:10.48550/arXiv.1601.00225> for the definition of possible Hamiltonian Monte Carlo termination criteria.

Last updated 2 days ago

openblascppopenmp

2.70 score 2 scripts 396 downloads

ggtaxplot - Create Plots to Visualize Taxonomy

Provides a comprehensive suite of functions for processing and visualizing taxonomic data. It includes functionality to clean and transform taxonomic data, categorize it into hierarchical ranks (such as Phylum, Class, Order, Family, and Genus), and calculate the relative abundance of each category. The package also generates a color palette for visual representation of the taxonomic data, allowing users to easily identify and differentiate between various taxonomic groups. Additionally, it features a river plot visualization to effectively display the distribution of individuals across different taxonomic ranks, facilitating insights into taxonomic visualization.

Last updated 4 days ago

2.70 score

qPRAentry - Quantitative Pest Risk Assessment at the Entry Step

Supports risk assessors in performing the entry step of the quantitative Pest Risk Assessment. It allows the estimation of the amount of a plant pest entering a risk assessment area (in terms of founder populations) through the calculation of the imported commodities that could be potential pathways of pest entry, and the development of a pathway model. Two 'Shiny' apps based on the functionalities of the package are included, that simplify the process of assessing the risk of entry of plant pests. The approach is based on the work of the European Food Safety Authority (EFSA PLH Panel et al., 2018) <doi:10.2903/j.efsa.2018.5350>.

Last updated 7 days ago

2.70 score

RCNA - Robust Copy Number Alteration Detection (RCNA)

Detects copy number alteration events in targeted exon sequencing data for tumor samples without matched normal controls. The advantage of this method is that it can be applied to smaller sequencing panels including evaluations of exon, transcript, gene, or even user specified genetic regions of interest. Functions in the package include steps for GC-content correction, calculation of quantile based normal karyotype ranges, and calculation of feature score. Cutoffs for "normal" quantile and score are user-adjustable.

Last updated 21 days ago

2.70 score 4 scripts

sleev - Semiparametric Likelihood Estimation with Errors in Variables

Efficient regression analysis under general two-phase sampling, where Phase I includes error-prone data and Phase II contains validated data on a subset.

Last updated 1 months ago

openblascppopenmp

2.70 score 5 scripts 220 downloads

PepMapViz - A Versatile Toolkit for Peptide Mapping, Visualization, and Comparative Exploration

A versatile R visualization package that empowers researchers with comprehensive visualization tools for seamlessly mapping peptides to protein sequences, identifying distinct domains and regions of interest, accentuating mutations, and highlighting post-translational modifications, all while enabling comparisons across diverse experimental conditions. Potential applications of 'PepMapViz' include the visualization of cross-software mass spectrometry results at the peptide level for specific protein and domain details in a linearized format and post-translational modification coverage across different experimental conditions; unraveling insights into disease mechanisms. It also enables visualization of major histocompatibility complex-presented peptides in different antibody regions predicting immunogenicity in antibody drug development.

Last updated 1 months ago

immunogenicitymassspectrometryproteomicspeptidomicssoftwarevisualization

2.70 score 4 scripts 495 downloads

heterocop - Semi-Parametric Estimation with Gaussian Copula

A method for generating random vectors which are linked by a Gaussian copula. It also enables to estimate the correlation matrix of the Gaussian copula in order to identify independencies within the data.

Last updated 2 months ago

2.70 score 496 downloads

atlasapprox - Cell Atlas Approximations

Provides an interface in R to cell atlas approximations. See the vignette under "Getting started" for instructions. You can also explore the reference documentation for specific functions. Additional interfaces and resources are available at <https://atlasapprox.readthedocs.io>.

Last updated 2 months ago

2.70 score 531 downloads

BoundaryStats - Boundary Overlap Statistics

Analysis workflow for finding geographic boundaries of ecological or landscape traits and comparing the placement of geographic boundaries of two traits. If data are trait values, trait data are transformed to boundary intensities based on approximate first derivatives across latitude and longitude. The package includes functions to create custom null models based on the input data. The boundary statistics are described in: Fortin, Drapeau, and Jacquez (1996) <doi:10.2307/3545584>.

Last updated 2 months ago

2.70 score 3 scripts 210 downloads

WQM - Wavelet-Based Quantile Mapping for Postprocessing Numerical Weather Predictions

The wavelet-based quantile mapping (WQM) technique is designed to correct biases in spatio-temporal precipitation forecasts across multiple time scales. The WQM method effectively enhances forecast accuracy by generating an ensemble of precipitation forecasts that account for uncertainties in the prediction process. For a comprehensive overview of the methodologies employed in this package, please refer to Jiang, Z., and Johnson, F. (2023) <doi:10.1029/2022EF003350>. The package relies on two packages for continuous wavelet transforms: 'WaveletComp', which can be installed automatically, and 'wmtsa', which is optional and available from the CRAN archive <https://cran.r-project.org/src/contrib/Archive/wmtsa/>. Users need to manually install 'wmtsa' from this archive if they prefer to use 'wmtsa' based decomposition.

Last updated 2 months ago

2.70 score 180 downloads

ChestVolume - Estimate the Chest Volume with Markers Data

Provides tools to process and analyze chest expansion using 3D marker data from motion capture systems. Includes functions for data processing, marker position adjustment, volume calculation using convex hulls, and visualization in 2D and 3D. Barber et al. (1996) <doi:10.1145/235815.235821>. TAMIYA Hiroyuki et al. (2021) <doi:10.1038/s41598-021-01033-8>.

Last updated 3 months ago

2.70 score 3 scripts 146 downloads

PytrendsLongitudinalR - Create Longitudinal Google Trends Data

'Google Trends' provides cross-sectional and time-series data on searches, but lacks readily available longitudinal data. Researchers, who want to create longitudinal 'Google Trends' on their own, face practical challenges, such as normalized counts that make it difficult to combine cross-sectional and time-series data and limitations in data formats and timelines that limit data granularity over extended time periods. This package addresses these issues and enables researchers to generate longitudinal 'Google Trends' data. This package is built on 'pytrends', a Python library that acts as the unofficial 'Google Trends API' to collect 'Google Trends' data. As long as the 'Google Trends API', 'pytrends' and all their dependencies are working, this package will work. During testing, we noticed that for the same input (keyword, topic, data_format, timeline), the output index can vary from time to time. Besides, if the keyword is not very popular, then the resulting dataset will contain a lot of zeros, which will greatly affect the final result. While this package has no control over the accuracy or quality of 'Google Trends' data, once the data is created, this package coverts it to longitudinal data. In addition, the user may encounter a 429 Too Many Requests error when using cross_section() and time_series() to collect 'Google Trends' data. This error indicates that the user has exceeded the rate limits set by the 'Google Trends API'. For more information about the 'Google Trends API' - 'pytrends', visit <https://pypi.org/project/pytrends/>.

Last updated 3 months ago

2.70 score 3 scripts 142 downloads

econet - Estimation of Parameter-Dependent Network Centrality Measures

Provides methods for estimating parameter-dependent network centrality measures with linear-in-means models. Both non linear least squares and maximum likelihood estimators are implemented. The methods allow for both link and node heterogeneity in network effects, endogenous network formation and the presence of unconnected nodes. The routines also compare the explanatory power of parameter-dependent network centrality measures with those of standard measures of network centrality. Benefits and features of the 'econet' package are illustrated using data from Battaglini and Patacchini (2018) and Battaglini, Patacchini, and Leone Sciabolazza (2020). For additional details, see the vignette <doi:10.18637/jss.v102.i08>.

Last updated 5 months ago

2.70 score 1 stars 4 scripts 278 downloads

FAfA - Factor Analysis for All

This Shiny application offers researchers a comprehensive tool for performing factor analysis. Users can upload datasets, validate assumptions, manage missing and outlier data, split data for different analyses, and run exploratory and confirmatory factor analyses ("EFA" and "CFA"). The software also offers reliability analysis, exploratory graph analysis, and item weighting. With a user-friendly interface, this tool simplifies the EFA and CFA processes. The main features are data submission and simple data inspection. Data manipulation (excluding variables, splitting data, checking for outliers), assumption checking (Tabachnik & Fidell (2012) <ISBN:978-0-205-84957-4> and Field (2009) <ISBN:978-1-84787-906-6>) for factor analysis, exploratory factor analysis (with various factor number determination methods (Lorenzo-Seva & Ferrando (2021) <doi:10.5964/meth.7185>)), confirmatory factor analysis (model definition and modification suggestions (Kline (2011) <ISBN:978-1-60623-877-6>)), reliability analysis (Cronbach's alpha, McDonald's omega, Armor's theta, structural reliability, stratified alpha), item weighting (Kilic & Dogan (2019) <doi:10.21031/epod.516057>).

Last updated 6 months ago

2.70 score 3 scripts 155 downloads

imanr - Identify the Racial Complex of Native Corns from Mexico

A model that provides researchers with a powerful tool for the classification and study of native corn by aiding in the identification of racial complexes which are fundamental to Mexico's agriculture and culture. This package has been developed based on data collected by "Proyecto Global de Maíces Nativos México", which has conducted exhaustive surveys across the country to document the qualitative and quantitative characteristics of different types of native maize. The trained model uses a robust and diverse dataset, enabling it to achieve an 80% accuracy in classifying maize racial complexes. The characteristics included in the analysis comprise geographic location, grain and cob colors, as well as various physical measurements, such as lengths and widths.

Last updated 6 months ago

2.70 score 125 downloads

scatterPlotMatrix - `htmlwidget` for a Scatter Plot Matrix

Create a scatter plot matrix, using `htmlwidgets` package and `d3.js`.

Last updated 6 months ago

2.70 score 42 scripts 412 downloads

colocPropTest - Proportional Testing for Colocalisation Analysis

Colocalisation analysis tests whether two traits share a causal genetic variant in a specified genomic region. Proportional testing for colocalisation has been previously proposed [Wallace (2013) <doi:10.1002/gepi.21765>], but is reimplemented here to overcome barriers to its adoption. Its use is complementary to the fine- mapping based colocalisation method in the 'coloc' package, and may be used in particular to identify false "H3" conclusions in 'coloc'.

Last updated 7 months ago

2.70 score 3 scripts 554 downloads

crosstalkr - Analysis of Graph-Structured Data with a Focus on Protein-Protein Interaction Networks

Provides a general toolkit for drug target identification. We include functionality to reduce large graphs to subgraphs and prioritize nodes. In addition to being optimized for use with generic graphs, we also provides support to analyze protein-protein interactions networks from online repositories. For more details on core method, refer to Weaver et al. (2021) <https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1008755>.

Last updated 7 months ago

cpp

2.70 score 7 scripts 620 downloads

sim.BA - Simulation-Based Bias Analysis for Observational Studies

Allows user to conduct a simulation based quantitative bias analysis using covariate structures generated with individual-level data to characterize the bias arising from unmeasured confounding. Users can specify their desired data generating mechanisms to simulate data and quantitatively summarize findings in an end-to-end application using this package.

Last updated 8 months ago

2.70 score 380 downloads

ADLP - Accident and Development Period Adjusted Linear Pools for Actuarial Stochastic Reserving

Loss reserving generally focuses on identifying a single model that can generate superior predictive performance. However, different loss reserving models specialise in capturing different aspects of loss data. This is recognised in practice in the sense that results from different models are often considered, and sometimes combined. For instance, actuaries may take a weighted average of the prediction outcomes from various loss reserving models, often based on subjective assessments. This package allows for the use of a systematic framework to objectively combine (i.e. ensemble) multiple stochastic loss reserving models such that the strengths offered by different models can be utilised effectively. Our framework is developed in Avanzi et al. (2023). Firstly, our criteria model combination considers the full distributional properties of the ensemble and not just the central estimate - which is of particular importance in the reserving context. Secondly, our framework is that it is tailored for the features inherent to reserving data. These include, for instance, accident, development, calendar, and claim maturity effects. Crucially, the relative importance and scarcity of data across accident periods renders the problem distinct from the traditional ensemble techniques in statistical learning. Our framework is illustrated with a complex synthetic dataset. In the results, the optimised ensemble outperforms both (i) traditional model selection strategies, and (ii) an equally weighted ensemble. In particular, the improvement occurs not only with central estimates but also relevant quantiles, such as the 75th percentile of reserves (typically of interest to both insurers and regulators). Reference: Avanzi B, Li Y, Wong B, Xian A (2023) "Ensemble distributional forecasting for insurance loss reserving" <doi:10.48550/arXiv.2206.08541>.

Last updated 8 months ago

2.70 score 251 downloads

CIfinder - Estimate the Confidence Intervals for Predictive Values

Computes confidence intervals for the positive predictive value (PPV) and negative predictive value (NPV) based on varied scenarios. In situations where the proportion of diseased subjects does not correspond to the disease prevalence (e.g. case-control studies), this package provides two types of solutions: 1) five methods for estimating confidence intervals for PPV and NPV via ratio of two binomial proportions including Gart & Nam (1988), Walter (1975), MOVER-J (Laud, 2017), Fieller (1954), and Bootstrap (Efron, 1979); 2) three direct methods that compute the confidence intervals including Pepe (2003), Zhou (2007), and Delta. In prospective studies where the proportion of diseased subjects is an unbiased estimate of the disease prevalence, this package provides several methods for calculating the confidence intervals for PPV and NPV including Clopper-Pearson, Wald, Wilson, Agresti-Coull, and Beta. See the Details and References sections in the corresponding functions.

Last updated 9 months ago

2.70 score 1 stars 4 scripts 210 downloads

bifurcatingr - Bifurcating Autoregressive Models

Estimation of bifurcating autoregressive models of any order, p, BAR(p) as well as several types of bias correction for the least squares estimators of the autoregressive parameters as described in Zhou and Basawa (2005) <doi:10.1016/j.spl.2005.04.024> and Elbayoumi and Mostafa (2020) <doi:10.1002/sta4.342>. Currently, the bias correction methods supported include bootstrap (single, double and fast-double) bias correction and linear-bias-function-based bias correction. Functions for generating and plotting bifurcating autoregressive data from any BAR(p) model are also included. This new version includes calculating several type of bias-corrected and -uncorrected confidence intervals for the least squares estimators of the autoregressive parameters as described in Elbayoumi and Mostafa (2023) <doi:10.6339/23-JDS1092>.

Last updated 9 months ago

2.70 score 3 scripts 257 downloads

BRVM - Retrieve Historical Data of Companies Listed on the 'BRVM' Stock Exchange

Provide real-time access to data from the Regional Securities Exchange SA(<https://www.brvm.org/en>), commonly known as the 'BRVM' stock exchange. The goal is to facilitate data access for users of the R programming language. The package includes a variety of data that can be accessed by calling functions.

Last updated 10 months ago

2.70 score 8 scripts 221 downloads

emery - Accuracy Statistic Estimation for Imperfect Gold Standards

Produce maximum likelihood estimates of common accuracy statistics for multiple measurement methods when a gold standard is not available. An R implementation of the expectation maximization algorithms described in Zhou et al. (2011) <doi:10.1002/9780470906514> with additional functions for creating simulated data and visualizing results. Supports binary, ordinal, and continuous measurement methods.

Last updated 10 months ago

2.70 score 1 scripts 141 downloads

HTRX - Haplotype Trend Regression with eXtra Flexibility (HTRX)

Detection of haplotype patterns that include single nucleotide polymorphisms (SNPs) and non-contiguous haplotypes that are associated with a phenotype. Methods for implementing HTRX are described in Yang Y, Lawson DJ (2023) <doi:10.1093/bioadv/vbad038> and Barrie W, Yang Y, Irving-Pease E.K, et al (2024) <doi:10.1038/s41586-023-06618-z>.

Last updated 11 months ago

2.70 score 5 scripts 209 downloads

rock - Reproducible Open Coding Kit

The Reproducible Open Coding Kit ('ROCK', and this package, 'rock') was developed to facilitate reproducible and open coding, specifically geared towards qualitative research methods. Although it is a general-purpose toolkit, three specific applications have been implemented, specifically an interface to the 'rENA' package that implements Epistemic Network Analysis ('ENA'), means to process notes from Cognitive Interviews ('CIs'), and means to work with decentralized construct taxonomies ('DCTs'). The 'ROCK' and this 'rock' package are described in the ROCK book <https://rockbook.org> and more information, such as tutorials, is available at <https://rock.science>.

Last updated 11 months ago

2.70 score 10 scripts 303 downloads

lddmm - Longitudinal Drift-Diffusion Mixed Models (LDDMM)

Implementation of the drift-diffusion mixed model for category learning as described in Paulon et al. (2021) <doi:10.1080/01621459.2020.1801448>.

Last updated 11 months ago

openblascppopenmp

2.70 score 4 scripts 145 downloads

hypergate - Machine Learning of Hyperrectangular Gating Strategies for High-Dimensional Cytometry

Given a high-dimensional dataset that typically represents a cytometry dataset, and a subset of the datapoints, this algorithm outputs an hyperrectangle so that datapoints within the hyperrectangle best correspond to the specified subset. In essence, this allows the conversion of clustering algorithms' outputs to gating strategies outputs.

Last updated 11 months ago

2.70 score 28 scripts 189 downloads

matrans - Model Averaging-Assisted Optimal Transfer Learning

Transfer learning, as a prevailing technique in computer sciences, aims to improve the performance of a target model by leveraging auxiliary information from heterogeneous source data. We provide novel tools for multi-source transfer learning under statistical models based on model averaging strategies, including linear regression models, partially linear models. Unlike existing transfer learning approaches, this method integrates the auxiliary information through data-driven weight assignments to avoid negative transfer. This is the first package for transfer learning based on the optimal model averaging frameworks, providing efficient implementations for practitioners in multi-source data modeling. The details are described in Hu and Zhang (2023) <https://jmlr.org/papers/v24/23-0030.html>.

Last updated 12 months ago

2.70 score 143 downloads

Glarmadillo - Solve the Graphical Lasso Problem with 'Armadillo'

Efficiently implements the Graphical Lasso algorithm, utilizing the 'Armadillo' 'C++' library for rapid computation. This algorithm introduces an L1 penalty to derive sparse inverse covariance matrices from observations of multivariate normal distributions. Features include the generation of random and structured sparse covariance matrices, beneficial for simulations, statistical method testing, and educational purposes in graphical modeling. A unique function for regularization parameter selection based on predefined sparsity levels is also offered, catering to users with specific sparsity requirements in their models. The methodology for sparse inverse covariance estimation implemented in this package is based on the work of Friedman, Hastie, and Tibshirani (2008) <doi:10.1093/biostatistics/kxm045>.

Last updated 1 years ago

openblascpp

2.70 score 133 downloads

WoodSimulatR - Generate Simulated Sawn Timber Strength Grading Data

Tools for generating simulated sawn timber strength grading data with a main focus on statistical simulation based on covariance matrices. Simulation data for Norway spruce sawn timber from Austria and reference values of means and standard deviations of grade determining properties from literature for a number of European countries are provided, as well.

Last updated 1 years ago

2.70 score 3 scripts 169 downloads

TestDimorph - Analysis of the Interpopulation Difference in Degree of Sexual Dimorphism Using Summary Statistics

Offers a solution for the unavailability of raw data in most anthropological studies by facilitating the calculations of several sexual dimorphism related analyses using the published summary statistics of metric data (mean, standard deviation and sex specific sample size) as illustrated by the works of Relethford, J. H., & Hodges, D. C. (1985) <doi:10.1002/ajpa.1330660105>, Greene, D. L. (1989) <doi:10.1002/ajpa.1330790113> and Konigsberg, L. W. (1991) <doi:10.1002/ajpa.1330840110>.

Last updated 1 years ago

2.70 score 1 stars 6 scripts 201 downloads

CLSIEP15 - Clinical and Laboratory Standards Institute (CLSI) EP15-A3 Calculations

Calculations of "EP15-A3 document. A manual for user verification of precision and estimation of bias" CLSI (2014, ISBN:1-56238-966-1).

Last updated 1 years ago

2.70 score 5 scripts 179 downloads

versioning - Settings and File I/O using a Configuration YAML File

R data pipelines commonly require reading and writing data to versioned directories. Each directory might correspond to one step of a multi-step process, where that version corresponds to particular settings for that step and a chain of previous steps that each have their own versions. This package creates a configuration object that makes it easy to read and write versioned data, based on YAML configuration files loaded and saved to each versioned folder.

Last updated 1 years ago

2.70 score 4 scripts 189 downloads

fqacalc - Calculate Floristic Quality Assessment Metrics

A collection of functions for calculating Floristic Quality Assessment (FQA) metrics using regional FQA databases that have been approved or approved with reservations as ecological planning models by the U.S. Army Corps of Engineers (USACE). For information on FQA see Spyreas (2019) <doi:10.1002/ecs2.2825>. These databases are stored in a sister R package, 'fqadata'. Both packages were developed for the USACE by the U.S. Army Engineer Research and Development Center’s Environmental Laboratory.

Last updated 1 years ago

2.70 score 8 scripts 160 downloads

PSIndependenceTest - Independence Tests for Two-Way, Three-Way and Four-Way Contingency Tables

Presentation two independence tests for two-way, three-way and four-way contingency tables. These tests are: the modular test and the logarithmic minimum test. For details on this method see: Sulewski (2017) <doi:10.18778/0208-6018.330.04>, Sulewski (2018) <doi:10.1080/02664763.2018.1424122>, Sulewski (2019) <doi:10.2478/bile-2019-0003>, Sulewski (2021) <doi:10.1080/00949655.2021.1908286>.

Last updated 1 years ago

2.70 score 5 scripts 138 downloads

PSDistr - Distributions Derived from Normal Distribution

Presentation of distributions such as: two-piece power normal (TPPN), plasticizing component (PC), DS normal (DSN), expnormal (EN), Sulewski plasticizing component (SPC), easily changeable kurtosis (ECK) distributions. Density, distribution function, quantile function and random generation are presented. For details on this method see: Sulewski (2019) <doi:10.1080/03610926.2019.1674871>, Sulewski (2021) <doi:10.1080/03610926.2020.1837881>, Sulewski (2021) <doi:10.1134/S1995080221120337>, Sulewski (2022) <"New members of the Johnson family of probability dis-tributions: properties and application">, Sulewski, Volodin (2022) <doi:10.1134/S1995080222110270>, Sulewski (2023) <doi:10.17713/ajs.v52i3.1434>.

Last updated 1 years ago

2.70 score 8 scripts 153 downloads

PSGoft - Modified Lilliefors Goodness-of-Fit Normality Test

Presentation of a new goodness-of-fit normality test based on the Lilliefors method. For details on this method see: Sulewski (2019) <doi:10.1080/03610918.2019.1664580>.

Last updated 1 years ago

2.70 score 5 scripts 146 downloads

ecopower - Power Estimates and Equivalence Testing for Multivariate Data

Estimates power by simulation for multivariate abundance data to be used for sample size estimates. Multivariate equivalence testing by simulation from a Gaussian copula model. The package also provides functions for parameterising multivariate effect sizes and simulating multivariate abundance data jointly. The discrete Gaussian copula approach is described in Popovic et al. (2018) <doi:10.1016/j.jmva.2017.12.002>.

Last updated 1 years ago

2.70 score 8 scripts 180 downloads

ref.ICAR - Objective Bayes Intrinsic Conditional Autoregressive Model for Areal Data

Implements an objective Bayes intrinsic conditional autoregressive prior. This model provides an objective Bayesian approach for modeling spatially correlated areal data using an intrinsic conditional autoregressive prior on a vector of spatial random effects.

Last updated 1 years ago

2.70 score 13 scripts 131 downloads

MLDS - Maximum Likelihood Difference Scaling

Difference scaling is a method for scaling perceived supra-threshold differences. The package contains functions that allow the user to design and run a difference scaling experiment, to fit the resulting data by maximum likelihood and test the internal validity of the estimated scale.

Last updated 1 years ago

2.70 score 36 scripts 494 downloads

drcarlate - Improving Estimation Efficiency in CAR with Imperfect Compliance

We provide a list of functions for replicating the results of the Monte Carlo simulations and empirical application of Jiang et al. (2022). In particular, we provide corresponding functions for generating the three types of random data described in this paper, as well as all the estimation strategies. Detailed information about the data generation process and estimation strategy can be found in Jiang et al. (2022) <doi:10.48550/arXiv.2201.13004>.

Last updated 2 years ago

2.70 score 3 scripts 180 downloads

flimo - Fixed Landscape Inference Method

Likelihood-free inference method for stochastic models. Uses a deterministic optimizer on simple simulations of the model that are performed with a prior drawn randomness by applying the inverse transform method. Is designed to work on its own and also by using the Julia package 'Jflimo' available on the git page of the project: <https://metabarcoding.org/flimo>.

Last updated 2 years ago

2.70 score 3 scripts 220 downloads

alpha.correction.bh - Benjamini-Hochberg Alpha Correction

Provides the alpha-adjustment correction from "Benjamini, Y., & Hochberg, Y. (1995) <doi:10.1111/j.2517-6161.1995.tb02031.x> Controlling the false discovery rate: a practical and powerful approach to multiple testing. Journal of the Royal statistical society: series B (Methodological), 57(1), 289-300". For researchers interested in using the exact mathematical formulas and procedures as used in the original paper.

Last updated 2 years ago

2.70 score 3 scripts 338 downloads

PCObw - Bandwidth Selector with Penalized Comparison to Overfitting Criterion

Bandwidth selector according to the Penalised Comparison to Overfitting (P.C.O.) criterion as described in Varet, S., Lacour, C., Massart, P., Rivoirard, V., (2019) <https://hal.archives-ouvertes.fr/hal-02002275>. It can be used with univariate and multivariate data.

Last updated 2 years ago

cpp

2.70 score 2 scripts 168 downloads

psyverse - Decentralized Unequivocality in Psychological Science

The constructs used to study the human psychology have many definitions and corresponding instructions for eliciting and coding qualitative data pertaining to constructs' content and for measuring the constructs. This plethora of definitions and instructions necessitates unequivocal reference to specific definitions and instructions in empirical and secondary research. This package implements a human- and machine-readable standard for specifying construct definitions and instructions for measurement and qualitative research based on 'YAML'. This standard facilitates systematic unequivocal reference to specific construct definitions and corresponding instructions in a decentralized manner (i.e. without requiring central curation; Peters (2020) <doi:10.31234/osf.io/xebhn>).

Last updated 2 years ago

2.70 score 127 downloads

rosetta - Parallel Use of Statistical Packages in Teaching

When teaching statistics, it can often be desirable to uncouple the content from specific software packages. To ease such efforts, the Rosetta Stats website (<https://rosettastats.com>) allows comparing analyses in different packages. This package is the companion to the Rosetta Stats website, aiming to provide functions that produce output that is similar to output from other statistical packages, thereby facilitating 'software-agnostic' teaching of statistics.

Last updated 2 years ago

2.70 score 10 scripts 430 downloads

AalenJohansen - Conditional Aalen-Johansen Estimation

Provides the conditional Nelson-Aalen and Aalen-Johansen estimators. The methods are based on Bladt & Furrer (2023), in preparation.

Last updated 2 years ago

2.70 score 9 scripts 547 downloads

PoolDilutionR - Calculate Gross Biogeochemical Flux Rates from Isotope Pool Dilution Data

Pool dilution is a isotope tracer technique wherein a biogeochemical pool is artifically enriched with its heavy isotopologue and the gross productive and consumptive fluxes of that pool are quantified by the change in pool size and isotopic composition over time. This package calculates gross production and consumption rates from closed-system isotopic pool dilution time series data. Pool size concentrations and heavy isotope (e.g., 15N) content are measured over time and the model optimizes production rate (P) and the first order rate constant (k) by minimizing error in the model-predicted total pool size, as well as the isotopic signature. The model optimizes rates by weighting information against the signal:noise ratio of concentration and heavy- isotope signatures using measurement precision as well as the magnitude of change over time. The calculations used here are based on von Fischer and Hedin (2002) <doi:10.1029/2001GB001448> with some modifications.

Last updated 2 years ago

2.70 score 8 scripts 151 downloads

dsample - Discretization-Based Direct Random Sample Generation

Discretization-based random sampling algorithm that is useful for a complex model in high dimension is implemented. The normalizing constant of a target distribution is not needed. Posterior summaries are compared with those by 'OpenBUGS'. The method is described: Wang and Lee (2014) <doi:10.1016/j.csda.2013.06.011> and exercised in Lee (2009) <http://hdl.handle.net/1993/21352>.

Last updated 2 years ago

2.70 score 7 scripts 208 downloads

imprecise101 - Introduction to Imprecise Probabilities

An imprecise inference presented in the study of Walley (1996) <doi:10.1111/j.2517-6161.1996.tb02065.x> is one of the statistical reasoning methods when prior information is unavailable. Functions and utils needed for illustrating this inferential paradigm are implemented for classroom teaching and further comprehensive research. Two imprecise models are demonstrated using multinomial data and 2x2 contingency table data. The concepts of prior ignorance and imprecision are discussed in lower and upper probabilities. Representation invariance principle, hypothesis testing, decision-making, and further generalization are also illustrated.

Last updated 2 years ago

2.70 score 2 scripts 160 downloads

harmonizer - Harmonizing CN8 and PC8 Product Codes

Several functions are provided to harmonize CN8 (Combined Nomenclature 8 digits) and PC8 (Production Communautaire 8 digits) product codes over time and the classification systems HS6 and BEC. Harmonization of CN8 codes are possible by default from 1995 to 2022 and of PC8 from 2001 to 2021, respectively.

Last updated 2 years ago

2.70 score 6 scripts 244 downloads

SimSST - Simulated Stop Signal Task Data

Stop signal task data of go and stop trials is generated per participant. The simulation process is based on the generally non-independent horse race model and fixed stop signal delay or tracking method. Each of go and stop process is assumed having exponentially modified Gaussian(ExG) or Shifted Wald (SW) distributions. The output data can be converted to 'BEESTS' software input data enabling researchers to test and evaluate various brain stopping processes manifested by ExG or SW distributional parameters of interest. Methods are described in: Soltanifar M (2020) <https://hdl.handle.net/1807/101208>, Matzke D, Love J, Wiecki TV, Brown SD, Logan GD and Wagenmakers E-J (2013) <doi:10.3389/fpsyg.2013.00918>, Logan GD, Van Zandt T, Verbruggen F, Wagenmakers EJ. (2014) <doi:10.1037/a0035230>.

Last updated 2 years ago

2.70 score 1 stars 6 scripts 134 downloads

Mestim - Computes the Variance-Covariance Matrix of Multidimensional Parameters Using M-Estimation

Provides a flexible framework for estimating the variance-covariance matrix of estimated parameters. Estimation relies on unbiased estimating functions to compute the empirical sandwich variance. (i.e., M-estimation in the vein of Tsiatis et al. (2019) <doi:10.1201/9780429192692>.

Last updated 2 years ago

2.70 score 6 scripts 180 downloads

PEIMAN2 - Post-Translational Modification Enrichment, Integration, and Matching Analysis

Functions and mined database from 'UniProt' focusing on post-translational modifications to do single enrichment analysis (SEA) and protein set enrichment analysis (PSEA). Payman Nickchi, Mehdi Mirzaie, Marc Baumann, Amir Ata Saei, Mohieddin Jafari (2022) <bioRxiv:10.1101/2022.11.09.515610>.

Last updated 2 years ago

2.70 score 6 scripts 162 downloads

deal - Learning Bayesian Networks with Mixed Variables

Bayesian networks with continuous and/or discrete variables can be learned and compared from data. The method is described in Boettcher and Dethlefsen (2003), <doi:10.18637/jss.v008.i20>.

Last updated 2 years ago

2.70 score 45 scripts 518 downloads

bangladesh - Provides Ready to Use Shapefiles for Geographical Map of Bangladesh

Usually, it is difficult to plot choropleth maps for Bangladesh in 'R'. The 'bangladesh' package provides ready-to-use shapefiles for different administrative regions of Bangladesh (e.g., Division, District, Upazila, and Union). This package helps users to draw thematic maps of administrative regions of Bangladesh easily as it comes with the 'sf' objects for the boundaries. It also provides functions allowing users to efficiently get specific area maps and center coordinates for regions. Users can also search for a specific area and calculate the centroids of those areas.

Last updated 2 years ago

2.70 score 1 stars 10 scripts 255 downloads

PesticideLoadIndicator - Computes Danish Pesticide Load Indicator

Computes the Danish Pesticide Load Indicator as described in Kudsk et al. (2018) <doi:10.1016/j.landusepol.2017.11.010> and Moehring et al. (2019) <doi:10.1016/j.scitotenv.2018.07.287> for pesticide use data. Additionally offers the possibility to directly link pesticide use data to pesticide properties given access to the Pesticide properties database (Lewis et al., 2016) <doi:10.1080/10807039.2015.1133242>.

Last updated 2 years ago

2.70 score 4 scripts 239 downloads

amanpg - Alternating Manifold Proximal Gradient Method for Sparse PCA

Alternating Manifold Proximal Gradient Method for Sparse PCA uses the Alternating Manifold Proximal Gradient (AManPG) method to find sparse principal components from a data or covariance matrix. Provides a novel algorithm for solving the sparse principal component analysis problem which provides advantages over existing methods in terms of efficiency and convergence guarantees. Chen, S., Ma, S., Xue, L., & Zou, H. (2020) <doi:10.1287/ijoo.2019.0032>. Zou, H., Hastie, T., & Tibshirani, R. (2006) <doi:10.1198/106186006X113430>. Zou, H., & Xue, L. (2018) <doi:10.1109/JPROC.2018.2846588>.

Last updated 2 years ago

2.70 score 3 scripts 300 downloads

neuronorm - Preprocessing of Structural MRI for Multiple Neurodegenerative Diseases

Preprocessing pipeline for normalizing and cleaning T1-weighted, T2-weighted and FLAIR MRI images coming from different sources, diseases, patients, scanners and sites.

Last updated 2 years ago

2.70 score 2 scripts 100 downloads

rwarrior - R Warrior - An AI Programming Game

A port of Ruby Warrior. Teaches R programming in a fun and interactive way.

Last updated 2 years ago

2.70 score 1 stars 4 scripts 157 downloads

stpm - Stochastic Process Model for Analysis of Longitudinal and Time-to-Event Outcomes

Utilities to estimate parameters of the models with survival functions induced by stochastic covariates. Miscellaneous functions for data preparation and simulation are also provided. For more information, see: (i)"Stochastic model for analysis of longitudinal data on aging and mortality" by Yashin A. et al. (2007), Mathematical Biosciences, 208(2), 538-551, <DOI:10.1016/j.mbs.2006.11.006>; (ii) "Health decline, aging and mortality: how are they related?" by Yashin A. et al. (2007), Biogerontology 8(3), 291(302), <DOI:10.1007/s10522-006-9073-3>.

Last updated 2 years ago

openblascppopenmp

2.70 score 95 scripts 285 downloads

evalR - Evaluation of Unverified Code

The purpose of this package is to generate trees and validate unverified code. Trees are made by parsing a statement into a verification tree data structure. This will make it easy to port the statement into another language. Safe statement evaluations are done by executing the verification trees.

Last updated 2 years ago

cpp

2.70 score 1 scripts 166 downloads

rTCRBCRr - Repertoire Analysis of the Detected Clonotype

The 'TRUST4' or 'MiXCR' is used to identify the clonotypes. The goal of 'rTCRBCRr' is to process the results from these clonotyping tools, and analyze the clonotype repertoire metrics based on chain names and IGH isotypes. The manuscript is still under preparation for publication for now. The references describing the methods in this package will be added later.

Last updated 2 years ago

2.70 score 148 downloads

WRI - Wasserstein Regression and Inference

Implementation of the methodologies described in 1) Alexander Petersen, Xi Liu and Afshin A. Divani (2021) <doi:10.1214/20-aos1971>, including global F tests, partial F tests, intrinsic Wasserstein-infinity bands and Wasserstein density bands, and 2) Chao Zhang, Piotr Kokoszka and Alexander Petersen (2022) <doi:10.1111/jtsa.12590>, including estimation, prediction, and inference of the Wasserstein autoregressive models.

Last updated 2 years ago

openblascpp

2.70 score 4 scripts 163 downloads

FGLMtrunc - Truncated Functional Generalized Linear Models

An implementation of the methodologies described in Xi Liu, Afshin A. Divani, and Alexander Petersen (2022) <doi:10.1016/j.csda.2022.107421>, including truncated functional linear and truncated functional logistic regression models.

Last updated 3 years ago

2.70 score 2 scripts 110 downloads

discnorm - Test for Discretized Normality in Ordinal Data

Tests whether multivariate ordinal data may stem from discretizing a multivariate normal distribution. The test is described by Foldnes and Grønneberg (2019) <doi:10.1080/10705511.2019.1673168>. In addition, an adjusted polychoric correlation estimator is provided that takes marginal knowledge into account, as described by Grønneberg and Foldnes (2022) <doi:10.1037/met0000495>.

Last updated 3 years ago

2.70 score 160 downloads

condGEE - Parameter Estimation in Conditional GEE for Recurrent Event Gap Times

Solves for the mean parameters, the variance parameter, and their asymptotic variance in a conditional GEE for recurrent event gap times, as described by Clement and Strawderman (2009) in the journal Biostatistics. Makes a parametric assumption for the length of the censored gap time.

Last updated 3 years ago

2.70 score 3 scripts 230 downloads

terminaldigits - Tests of Uniformity and Independence for Terminal Digits

Implements simulated tests for the hypothesis that terminal digits are uniformly distributed (chi-squared goodness-of-fit) and the hypothesis that terminal digits are independent from preceding digits (several tests of independence for r x c contingency tables). Also, for a number of distributions, implements Monte Carlo simulations for type I errors and power for the test of independence.

Last updated 3 years ago

cpp

2.70 score 4 scripts 160 downloads

PLORN - Prediction with Less Overfitting and Robust to Noise

A method for the quantitative prediction with much predictors. This package provides functions to construct the quantitative prediction model with less overfitting and robust to noise.

Last updated 3 years ago

2.70 score 4 scripts 335 downloads

rlcv - Robust Likelihood Cross Validation Bandwidth Selection

Robust likelihood cross validation bandwidth for uni- and multi-variate kernel densities. It is robust against fat-tailed distributions and/or outliers. Based on "Robust Likelihood Cross-Validation for Kernel Density Estimation," Wu (2019) <doi:10.1080/07350015.2018.1424633>.

Last updated 3 years ago

2.70 score 4 scripts 134 downloads

LogRegEquiv - Logistic Regression Equivalence

Tools for assessing equivalence of similar Logistic Regression models.

Last updated 3 years ago

2.70 score 3 scripts 148 downloads

QuESTr - Constructing Quantitative Environment Sensor using Transcriptomes

A method for prediction of environmental conditions based on transcriptome data linked with the environmental gradients. This package provides functions to overview gene-environment relationships, to construct the prediction model, and to predict environmental conditions where the transcriptomes were generated. This package can quest for candidate genes for the model construction even in non-model organisms' transcriptomes without any genetic information.

Last updated 3 years ago

2.70 score 4 scripts 341 downloads

RTTWebClient - Web Client to 'TickTrader'

R Web Client to 'TickTrader' platform. Provides you access to 'TickTrader' platform through Web API <https://ttlivewebapi.fxopen.net:8443/api/doc/index>.

Last updated 3 years ago

2.70 score 9 scripts 225 downloads

scaRabee - Optimization Toolkit for Pharmacokinetic-Pharmacodynamic Models

A port of the Scarabee toolkit originally written as a Matlab-based application. scaRabee provides a framework for simulation and optimization of pharmacokinetic-pharmacodynamic models at the individual and population level. It is built on top of the neldermead package, which provides the direct search algorithm proposed by Nelder and Mead for model optimization.

Last updated 3 years ago

2.70 score 3 scripts 208 downloads

gesso - Hierarchical GxE Interactions in a Regularized Regression Model

The method focuses on a single environmental exposure and induces a main-effect-before-interaction hierarchical structure for the joint selection of interaction terms in a regularized regression model. For details see Zemlianskaia et al. (2021) <arxiv:2103.13510>.

Last updated 3 years ago

cpp

2.70 score 7 scripts 207 downloads

rbooster - AdaBoost Framework for Any Classifier

This is a simple package which provides a function that boosts pre-ready or custom-made classifiers. Package uses Discrete AdaBoost (<doi:10.1006/jcss.1997.1504>) and Real AdaBoost (<doi:10.1214/aos/1016218223>) for two class, SAMME (<doi:10.4310/SII.2009.v2.n3.a8>) and SAMME.R (<doi:10.4310/SII.2009.v2.n3.a8>) for multiclass classification.

Last updated 3 years ago

2.70 score 6 scripts 150 downloads

MCID - Estimating the Minimal Clinically Important Difference

Apply the marginal classification method to achieve the purpose of providing the point and interval estimates for the minimal clinically important difference based on the classical anchor-based method. For more details of the methodology, please see Zehua Zhou, Leslie J. Bisson and Jiwei Zhao (2021) <arXiv:2108.11589>.

Last updated 3 years ago

2.70 score 1 stars 1 scripts 150 downloads

RADstackshelpR - Optimize the De Novo Stacks Pipeline via R

Offers a handful of useful wrapper functions which streamline the reading, analyzing, and visualizing of variant call format (vcf) files in R. This package was designed to facilitate an explicit pipeline for optimizing Stacks (Rochette et al., 2019) (<doi:10.1111/mec.15253>) parameters during de novo (without a reference genome) assembly and variant calling of restriction-enzyme associated DNA sequence (RADseq) data. The pipeline implemented here is based on the 2017 paper "Lost in Parameter Space" (Paris et al., 2017) (<doi:10.1111/2041-210X.12775>) which establishes clear recommendations for optimizing the parameters 'm', 'M', and 'n', during the process of assembling loci.

Last updated 3 years ago

2.70 score 30 scripts 177 downloads

ROCaggregator - Aggregate Multiple ROC Curves into One Global ROC

Aggregates multiple Receiver Operating Characteristic (ROC) curves obtained from different sources into one global ROC. Additionally, it’s also possible to calculate the aggregated precision-recall (PR) curve.

Last updated 3 years ago

2.70 score 5 scripts 161 downloads

colourvision - Colour Vision Models

Colour vision models, colour spaces and colour thresholds. Provides flexibility to build user-defined colour vision models for n number of photoreceptor types. Also includes Vorobyev & Osorio (1998) Receptor Noise Limited models <doi:10.1098/rspb.1998.0302>, Chittka (1992) colour hexagon <doi:10.1007/BF00199331>, and Endler & Mielke (2005) model <doi:10.1111/j.1095-8312.2005.00540.x>. Models have been extended to accept any number of photoreceptor types.

Last updated 3 years ago

2.70 score 25 scripts 205 downloads

uclust - Clustering and Classification Inference with U-Statistics

Clustering and classification inference for high dimension low sample size (HDLSS) data with U-statistics. The package contains implementations of nonparametric statistical tests for sample homogeneity, group separation, clustering, and classification of multivariate data. The methods have high statistical power and are tailored for data in which the dimension L is much larger than sample size n. See Gabriela B. Cybis, Marcio Valk and Sílvia RC Lopes (2018) <doi:10.1080/00949655.2017.1374387>, Marcio Valk and Gabriela B. Cybis (2020) <doi:10.1080/10618600.2020.1796398>, Debora Z. Bello, Marcio Valk and Gabriela B. Cybis (2021) <arXiv:2106.09115>.

Last updated 4 years ago

2.70 score 9 scripts 138 downloads

ez.combat - Easy ComBat Harmonization

A dataframe-friendly implementation of ComBat Harmonization which uses an empirical Bayesian framework to remove batch effects. Johnson WE & Li C (2007) <doi:10.1093/biostatistics/kxj037> "Adjusting batch effects in microarray expression data using empirical Bayes methods." Fortin J-P, Cullen N, Sheline YI, Taylor WD, Aselcioglu I, Cook PA, Adams P, Cooper C, Fava M, McGrath PJ, McInnes M, Phillips ML, Trivedi MH, Weissman MM, & Shinohara RT (2017) <doi:10.1016/j.neuroimage.2017.11.024> "Harmonization of cortical thickness measurements across scanners and sites." Fortin J-P, Parker D, Tun<e7> B, Watanabe T, Elliott MA, Ruparel K, Roalf DR, Satterthwaite TD, Gur RC, Gur RE, Schultz RT, Verma R, & Shinohara RT (2017) <doi:10.1016/j.neuroimage.2017.08.047> "Harmonization of multi-site diffusion tensor imaging data."

Last updated 4 years ago

2.70 score 190 downloads

mipplot - An Open-Source Tool for Visualization of Climate Mitigation Scenarios

Generic functions to produce area/bar/box/line plots of data following IAMC (Integrated Assessment Modeling Consortium) submission format.

Last updated 4 years ago

2.70 score 9 scripts 238 downloads

fipp - Induced Priors in Bayesian Mixture Models

Computes implicitly induced quantities from prior/hyperparameter specifications of three Mixtures of Finite Mixtures models: Dirichlet Process Mixtures (DPMs; Escobar and West (1995) <doi:10.1080/01621459.1995.10476550>), Static Mixtures of Finite Mixtures (Static MFMs; Miller and Harrison (2018) <doi:10.1080/01621459.2016.1255636>), and Dynamic Mixtures of Finite Mixtures (Dynamic MFMs; Frühwirth-Schnatter, Malsiner-Walli and Grün (2020) <arXiv:2005.09918>). For methodological details, please refer to Greve, Grün, Malsiner-Walli and Frühwirth-Schnatter (2020) <arXiv:2012.12337>) as well as the package vignette.

Last updated 4 years ago

2.70 score 1 scripts 127 downloads

cgmquantify - Analyzing Glucose and Glucose Variability

Continuous glucose monitoring (CGM) systems provide real-time, dynamic glucose information by tracking interstitial glucose values throughout the day. Glycemic variability, also known as glucose variability, is an established risk factor for hypoglycemia (Kovatchev) and has been shown to be a risk factor in diabetes complications. Over 20 metrics of glycemic variability have been identified. Here, we provide functions to calculate glucose summary metrics, glucose variability metrics (as defined in clinical publications), and visualizations to visualize trends in CGM data. Cho P, Bent B, Wittmann A, et al. (2020) <https://diabetes.diabetesjournals.org/content/69/Supplement_1/73-LB.abstract> American Diabetes Association (2020) <https://professional.diabetes.org/diapro/glucose_calc> Kovatchev B (2019) <doi:10.1177/1932296819826111> Kovdeatchev BP (2017) <doi:10.1038/nrendo.2017.3> Tamborlane W V., Beck RW, Bode BW, et al. (2008) <doi:10.1056/NEJMoa0805017> Umpierrez GE, P. Kovatchev B (2018) <doi:10.1016/j.amjms.2018.09.010>.

Last updated 4 years ago

2.70 score 3 scripts 211 downloads

borrowr - Estimate Causal Effects with Borrowing Between Data Sources

Estimate population average treatment effects from a primary data source with borrowing from supplemental sources. Causal estimation is done with either a Bayesian linear model or with Bayesian additive regression trees (BART) to adjust for confounding. Borrowing is done with multisource exchangeability models (MEMs). For information on BART, see Chipman, George, & McCulloch (2010) <doi:10.1214/09-AOAS285>. For information on MEMs, see Kaizer, Koopmeiners, & Hobbs (2018) <doi:10.1093/biostatistics/kxx031>.

Last updated 4 years ago

cpp

2.70 score 2 scripts 214 downloads

IMEC - Ising Model of Explanatory Coherence

Theories are one of the most important tools of science. Although psychologists discussed problems of theory in their discipline for a long time, weak theories are still widespread in most subfields. One possible reason for this is that psychologists lack the tools to systematically assess the quality of their theories. Previously a computational model for formal theory evaluation based on the concept of explanatory coherence was developed (Thagard, 1989, <doi:10.1017/S0140525X00057046>). However, there are possible improvements to this model and it is not available in software that psychologists typically use. Therefore, a new implementation of explanatory coherence based on the Ising model is available in this R-package.

Last updated 4 years ago

2.70 score 1 scripts 142 downloads

PubMedMining - Text-Mining of the 'PubMed' Repository

Easy function for text-mining the 'PubMed' repository based on defined sets of terms. The relationship between fix-terms (related to your research topic) and pub-terms (terms which pivot around your research focus) is calculated using the pointwise mutual information algorithm ('PMI'). Church, Kenneth Ward and Hanks, Patrick (1990) <https://www.aclweb.org/anthology/J90-1003/> A text file is generated with the 'PMI'-scores for each fix-term. Then for each collocation pairs (a fix-term + a pub-term), a text file is generated with related article titles and publishing years. Additional Author section will follow in the next version updates.

Last updated 4 years ago

2.70 score 2 scripts 141 downloads

SyScSelection - Systematic Scenario Selection for Stress Testing

Quasi-Monte-Carlo algorithm for systematic generation of shock scenarios from an arbitrary multivariate elliptical distribution. The algorithm selects a systematic mesh of arbitrary fineness that approximately evenly covers an isoprobability ellipsoid in d dimensions (Flood, Mark D. & Korenko, George G. (2013) <doi:10.1080/14697688.2014.926018>). This package is the 'R' analogy to the 'Matlab' code published by Flood & Korenko in above-mentioned paper.

Last updated 4 years ago

2.70 score 3 scripts 99 downloads

miRNAss - Genome-Wide Discovery of Pre-miRNAs with few Labeled Examples

Machine learning method specifically designed for pre-miRNA prediction. It takes advantage of unlabeled sequences to improve the prediction rates even when there are just a few positive examples, when the negative examples are unreliable or are not good representatives of its class. Furthermore, the method can automatically search for negative examples if the user is unable to provide them. MiRNAss can find a good boundary to divide the pre-miRNAs from other groups of sequences; it automatically optimizes the threshold that defines the classes boundaries, and thus, it is robust to high class imbalance. Each step of the method is scalable and can handle large volumes of data.

Last updated 4 years ago

cppopenmp

2.70 score 1 stars 3 scripts 168 downloads

discoverableresearch - Checks Title, Abstract and Keywords to Optimise Discoverability

A suite of tools are provided here to support authors in making their research more discoverable. check_keywords() - this function checks the keywords to assess whether they are already represented in the title and abstract. check_fields() - this function compares terminology used across the title, abstract and keywords to assess where terminological diversity (i.e. the use of synonyms) could increase the likelihood of the record being identified in a search. The function looks for terms in the title and abstract that also exist in other fields and highlights these as needing attention. suggest_keywords() - this function takes a full text document and produces a list of unigrams, bigrams and trigrams (1-, 2- or 2-word phrases) present in the full text after removing stop words (words with a low utility in natural language processing) that do not occur in the title or abstract that may be suitable candidates for keywords. suggest_title() - this function takes a full text document and produces a list of the most frequently used unigrams, bigrams and trigrams after removing stop words that do not occur in the abstract or keywords that may be suitable candidates for title words. check_title() - this function carries out a number of sub tasks: 1) it compares the length (number of words) of the title with the mean length of titles in major bibliographic databases to assess whether the title is likely to be too short; 2) it assesses the proportion of stop words in the title to highlight titles with low utility in search engines that strip out stop words; 3) it compares the title with a given sample of record titles from an .ris import and calculates a similarity score based on phrase overlap. This highlights the level of uniqueness of the title. This version of the package also contains functions currently in a non-CRAN package called 'litsearchr' <https://github.com/elizagrames/litsearchr>.

Last updated 4 years ago

2.70 score 154 downloads

hiphop - Parentage Assignment using Bi-Allelic Genetic Markers

Can be used for paternity and maternity assignment and outperforms conventional methods where closely related individuals occur in the pool of possible parents. The method compares the genotypes of offspring with any combination of potentials parents and scores the number of mismatches of these individuals at bi-allelic genetic markers (e.g. Single Nucleotide Polymorphisms). It elaborates on a prior exclusion method based on the Homozygous Opposite Test (HOT; Huisman 2017 <doi:10.1111/1755-0998.12665>) by introducing the additional exclusion criterion HIPHOP (Homozygous Identical Parents, Heterozygous Offspring are Precluded; Cockburn et al., in revision). Potential parents are excluded if they have more mismatches than can be expected due to genotyping error and mutation, and thereby one can identify the true genetic parents and detect situations where one (or both) of the true parents is not sampled. Package 'hiphop' can deal with (a) the case where there is contextual information about parentage of the mother (i.e. a female has been seen to be involved in reproductive tasks such as nest building), but paternity is unknown (e.g. due to promiscuity), (b) where both parents need to be assigned, because there is no contextual information on which female laid eggs and which male fertilized them (e.g. polygynandrous mating system where multiple females and males deposit young in a common nest, or organisms with external fertilisation that breed in aggregations). For details: Cockburn, A., Penalba, J.V.,Jaccoud, D.,Kilian, A., Brouwer, L., Double, M.C., Margraf, N., Osmond, H.L., van de Pol, M. and Kruuk, L.E.B. (in revision). HIPHOP: improved paternity assignment among close relatives using a simple exclusion method for bi-allelic markers. Molecular Ecology Resources, DOI to be added upon acceptance.

Last updated 4 years ago

2.70 score 1 stars 4 scripts 100 downloads

mosqcontrol - Mosquito Control Resource Optimization

This project aims to make an accessible model for mosquito control resource optimization. The model uses data provided by users to estimate the mosquito populations in the sampling area for the sampling time period, and the optimal time to apply a treatment or multiple treatments.

Last updated 4 years ago

2.70 score 4 scripts 154 downloads

SCOUTer - Simulate Controlled Outliers

Using principal component analysis as a base model, 'SCOUTer' offers a new approach to simulate outliers in a simple and precise way. The user can generate new observations defining them by a pair of well-known statistics: the Squared Prediction Error (SPE) and the Hotelling's T^2 (T^2) statistics. Just by introducing the target values of the SPE and T^2, 'SCOUTer' returns a new set of observations with the desired target properties. Authors: Alba González, Abel Folch-Fortuny, Francisco Arteaga and Alberto Ferrer (2020).

Last updated 4 years ago

2.70 score 2 scripts 140 downloads

higlasso - Hierarchical Integrative Group LASSO

Environmental health studies are increasingly measuring multiple pollutants to characterize the joint health effects attributable to exposure mixtures. However, the underlying dose-response relationship between toxicants and health outcomes of interest may be highly nonlinear, with possible nonlinear interaction effects. Hierarchical integrative group least absolute shrinkage and selection operator (HiGLASSO), developed by Boss et al (2020) <arXiv:2003.12844>, is a general framework to identify noteworthy nonlinear main and interaction effects in the presence of group structures among a set of exposures.

Last updated 5 years ago

openblascppopenmp

2.70 score 9 scripts 119 downloads

binomialRF - Binomial Random Forest Feature Selection

The 'binomialRF' is a new feature selection technique for decision trees that aims at providing an alternative approach to identify significant feature subsets using binomial distributional assumptions (Rachid Zaim, S., et al. (2019)) <doi:10.1101/681973>. Treating each splitting variable selection as a set of exchangeable correlated Bernoulli trials, 'binomialRF' then tests whether a feature is selected more often than by random chance.

Last updated 5 years ago

softwaregenepredictionstatisticalmethoddecisiontreedimensionreductionexperimentaldesign

2.70 score 1 scripts 262 downloads

TableHC - Higher Criticism Test of Two Frequency Counts Tables

Higher Criticism (HC) test between two frequency tables. Test is based on an adaptation of the Tukey-Donoho-Jin HC statistic to testing frequency tables described in Kipnis (2019) <arXiv:1911.01208>.

Last updated 5 years ago

2.70 score 1 scripts 118 downloads

LoopRig - Integration and Analysis of Chromatin Loop Data

Common coordinate-based workflows involving processed chromatin loop and genomic element data are considered and packaged into appropriate customizable functions. Includes methods for linking element sets via chromatin loops and creating consensus loop datasets.

Last updated 5 years ago

2.70 score 18 scripts 103 downloads

tvgeom - The Time-Varying (Right-Truncated) Geometric Distribution

Probability mass (d), distribution (p), quantile (q), and random number generating (r and rt) functions for the time-varying right-truncated geometric (tvgeom) distribution. Also provided are functions to calculate the first and second central moments of the distribution. The tvgeom distribution is similar to the geometric distribution, but the probability of success is allowed to vary at each time step, and there are a limited number of trials. This distribution is essentially a Markov chain, and it is useful for modeling Markov chain systems with a set number of time steps.

Last updated 5 years ago

2.70 score 1 stars 4 scripts 135 downloads

hdbm - High Dimensional Bayesian Mediation Analysis

Perform mediation analysis in the presence of high-dimensional mediators based on the potential outcome framework. High dimensional Bayesian mediation (HDBM), developed by Song et al (2018) <doi:10.1101/467399>, relies on two Bayesian sparse linear mixed models to simultaneously analyze a relatively large number of mediators for a continuous exposure and outcome assuming a small number of mediators are truly active. This sparsity assumption also allows the extension of univariate mediator analysis by casting the identification of active mediators as a variable selection problem and applying Bayesian methods with continuous shrinkage priors on the effects.

Last updated 5 years ago

openblascpp

2.70 score 6 scripts 111 downloads

ClussCluster - Simultaneous Detection of Clusters and Cluster-Specific Genes in High-Throughput Transcriptome Data

Implements a new method 'ClussCluster' descried in Ge Jiang and Jun Li, "Simultaneous Detection of Clusters and Cluster-Specific Genes in High-throughput Transcriptome Data" (Unpublished). Simultaneously perform clustering analysis and signature gene selection on high-dimensional transcriptome data sets. To do so, 'ClussCluster' incorporates a Lasso-type regularization penalty term to the objective function of K- means so that cell-type-specific signature genes can be identified while clustering the cells.

Last updated 5 years ago

2.70 score 4 scripts 149 downloads

IDmeasurer - Assessment of Individual Identity in Animal Signals

Provides tools for assessment and quantification of individual identity information in animal signals. This package accompanies a research article by Linhart et al. (2019) <doi:10.1101/546143>: "Measuring individual identity information in animal signals: Overview and performance of available identity metrics".

Last updated 6 years ago

2.70 score 4 scripts 133 downloads

dkanr - Client for the 'DKAN' API

Provides functions to facilitate access to the 'DKAN' API (<https://dkan.readthedocs.io/en/latest/apis/index.html>), including the 'DKAN' REST API (metadata), and the 'DKAN' datastore API (data). Includes functions to list, create, retrieve, update, and delete datasets and resources nodes. It also includes functions to search and retrieve data from the 'DKAN' datastore.

Last updated 6 years ago

2.70 score 25 scripts 163 downloads

fuser - Fused Lasso for High-Dimensional Regression over Groups

Enables high-dimensional penalized regression across heterogeneous subgroups. Fusion penalties are used to share information about the linear parameters across subgroups. The underlying model is described in detail in Dondelinger and Mukherjee (2017) <arXiv:1611.00953>.

Last updated 7 years ago

cpp

2.70 score 20 scripts 123 downloads

COCONUT - COmbat CO-Normalization Using conTrols (COCONUT)

Allows for pooled analysis of microarray data by batch-correcting control samples, and then applying the derived correction parameters to non-control samples to obtain bias-free, inter-dataset corrected data.

Last updated 7 years ago

2.70 score 1 stars 7 scripts 529 downloads

DES - Discrete Event Simulation

Discrete event simulation (DES) involves modeling of systems having discrete, i.e. abrupt, state changes. For instance, when a job arrives to a queue, the queue length abruptly increases by 1. This package is an R implementation of the event-oriented approach to DES; see the tutorial in Matloff (2008) <http://heather.cs.ucdavis.edu/~matloff/156/PLN/DESimIntro.pdf>.

Last updated 7 years ago

2.70 score 2 scripts 578 downloads

sfinx - Straightforward Filtering Index for AP-MS Data Analysis (SFINX)

The straightforward filtering index (SFINX) identifies true positive protein interactions in a fast, user-friendly, and highly accurate way. It is not only useful for the filtering of affinity purification - mass spectrometry (AP-MS) data, but also for similar types of data resulting from other co-complex interactomics technologies, such as TAP-MS, Virotrap and BioID. SFINX can also be used via the website interface at <http://sfinx.ugent.be>.

Last updated 7 years ago

2.70 score 6 scripts 128 downloads

SobolSequence - Sobol Sequences with Better Two-Dimensional Projections

R implementation of S. Joe and F. Y. Kuo(2008) <DOI:10.1137/070709359>. The implementation is based on the data file new-joe-kuo-6.21201 <http://web.maths.unsw.edu.au/~fkuo/sobol/>.

Last updated 7 years ago

cpp

2.70 score 13 scripts 108 downloads

slim - Singular Linear Models for Longitudinal Data

Fits singular linear models to longitudinal data. Singular linear models are useful when the number, or timing, of longitudinal observations may be informative about the observations themselves. They are described in Farewell (2010) <doi:10.1093/biomet/asp068>, and are extensions of the linear increments model <doi:10.1111/j.1467-9876.2007.00590.x> to general longitudinal data.

Last updated 8 years ago

2.70 score 4 scripts 185 downloads

BioM2 - Biologically Explainable Machine Learning Framework

Biologically Explainable Machine Learning Framework for Phenotype Prediction using omics data described in Chen and Schwarz (2017) <doi:10.48550/arXiv.1712.00336>.Identifying reproducible and interpretable biological patterns from high-dimensional omics data is a critical factor in understanding the risk mechanism of complex disease. As such, explainable machine learning can offer biological insight in addition to personalized risk scoring.In this process, a feature space of biological pathways will be generated, and the feature space can also be subsequently analyzed using WGCNA (Described in Horvath and Zhang (2005) <doi:10.2202/1544-6115.1128> and Langfelder and Horvath (2008) <doi:10.1186/1471-2105-9-559> ) methods.

Last updated 3 months ago

2.69 score 11 scripts 310 downloads

inaparc - Initialization Algorithms for Partitioning Cluster Analysis

Partitioning clustering algorithms divide data sets into k subsets or partitions so-called clusters. They require some initialization procedures for starting the algorithms. Initialization of cluster prototypes is one of such kind of procedures for most of the partitioning algorithms. Cluster prototypes are the centers of clusters, i.e. centroids or medoids, representing the clusters in a data set. In order to initialize cluster prototypes, the package 'inaparc' contains a set of the functions that are the implementations of several linear time-complexity and loglinear time-complexity methods in addition to some novel techniques. Initialization of fuzzy membership degrees matrices is another important task for starting the probabilistic and possibilistic partitioning algorithms. In order to initialize membership degrees matrices required by these algorithms, a number of functions based on some traditional and novel initialization techniques are also available in the package 'inaparc'.

Last updated 3 years ago

2.69 score 5 dependents 33 scripts 548 downloads

NISTnls - Nonlinear least squares examples from NIST

Datasets for testing nonlinear regression routines.

Last updated 12 years ago

2.69 score 99 scripts 232 downloads

QTLRel - Tools for Mapping of Quantitative Traits of Genetically Related Individuals and Calculating Identity Coefficients from Pedigrees

This software provides tools for quantitative trait mapping in populations such as advanced intercross lines where relatedness among individuals should not be ignored. It can estimate background genetic variance components, impute missing genotypes, simulate genotypes, perform a genome scan for putative quantitative trait loci (QTL), and plot mapping results. It also has functions to calculate identity coefficients from pedigrees, especially suitable for pedigrees that consist of a large number of generations, or estimate identity coefficients from genotypic data in certain circumstances.

Last updated 1 years ago

fortranopenblas

2.69 score 49 scripts 525 downloads

lsm - Estimation of the log Likelihood of the Saturated Model

When the values of the outcome variable Y are either 0 or 1, the function lsm() calculates the estimation of the log likelihood in the saturated model. This model is characterized by Llinas (2006, ISSN:2389-8976) in section 2.3 through the assumptions 1 and 2. The function LogLik() works (almost perfectly) when the number of independent variables K is high, but for small K it calculates wrong values in some cases. For this reason, when Y is dichotomous and the data are grouped in J populations, it is recommended to use the function lsm() because it works very well for all K.

Last updated 7 months ago

2.68 score 16 scripts 392 downloads

molaR - Dental Surface Complexity Measurement Tools

Surface topography calculations of Dirichlet's normal energy, relief index, surface slope, and orientation patch count for teeth using scans of enamel caps. Importantly, for the relief index and orientation patch count calculations to work, the scanned tooth files must be oriented with the occlusal plane parallel to the x and y axes, and perpendicular to the z axis. The files should also be simplified, and smoothed in some other software prior to uploading into R.

Last updated 2 years ago

2.68 score 1 stars 1 dependents 16 scripts 375 downloads

PhysicalActivity - Process Accelerometer Data for Physical Activity Measurement

It provides a function "wearingMarking" for classification of monitor wear and nonwear time intervals in accelerometer data collected to assess physical activity. The package also contains functions for making plot for accelerometer data and obtaining the summary of various information including daily monitor wear time and the mean monitor wear time during valid days. "deliveryPred" and "markDelivery" can classify days for ActiGraph delivery by mail; "deliveryPreprocess" can process accelerometry data for analysis by zeropadding incomplete days and removing low activity days; "markPAI" can categorize physical activity intensity level based on user-defined cut-points of accelerometer counts. It also supports importing ActiGraph AGD files with "readActigraph" and "queryActigraph" functions.

Last updated 4 years ago

2.68 score 1 stars 2 dependents 20 scripts 369 downloads

gamlss.inf - Fitting Mixed (Inflated and Adjusted) Distributions

This is an add-on package to 'gamlss'. The purpose of this package is to allow users to fit GAMLSS (Generalised Additive Models for Location Scale and Shape) models when the response variable is defined either in the intervals [0,1), (0,1] and [0,1] (inflated at zero and/or one distributions), or in the positive real line including zero (zero-adjusted distributions). The mass points at zero and/or one are treated as extra parameters with the possibility to include a linear predictor for both. The package also allows transformed or truncated distributions from the GAMLSS family to be used for the continuous part of the distribution. Standard methods and GAMLSS diagnostics can be used with the resulting fitted object.

Last updated 6 years ago

2.68 score 1 dependents 16 scripts 296 downloads

SimComp - Simultaneous Comparisons for Multiple Endpoints

Simultaneous tests and confidence intervals are provided for one-way experimental designs with one or many normally distributed, primary response variables (endpoints). Differences (Hasler and Hothorn, 2011 <doi:10.2202/1557-4679.1258>) or ratios (Hasler and Hothorn, 2012 <doi:10.1080/19466315.2011.633868>) of means can be considered. Various contrasts can be chosen, unbalanced sample sizes are allowed as well as heterogeneous variances (Hasler and Hothorn, 2008 <doi:10.1002/bimj.200710466>) or covariance matrices (Hasler, 2014 <doi:10.1515/ijb-2012-0015>).

Last updated 5 years ago

2.67 score 1 dependents 21 scripts 1.5k downloads

asht - Applied Statistical Hypothesis Tests

Gives some hypothesis test functions (sign test, median and other quantile tests, Wilcoxon signed rank test, coefficient of variation test, test of normal variance, test on weighted sums of Poisson [see Fay and Kim <doi:10.1002/bimj.201600111>], sample size for t-tests with different variances and non-equal n per arm, Behrens-Fisher test, nonparametric ABC intervals, Wilcoxon-Mann-Whitney test [with effect estimates and confidence intervals, see Fay and Malinovsky <doi:10.1002/sim.7890>], two-sample melding tests [see Fay, Proschan, and Brittain <doi:10.1111/biom.12231>], one-way ANOVA allowing var.equal=FALSE [see Brown and Forsythe, 1974, Biometrics]), prevalence confidence intervals that adjust for sensitivity and specificity [see Lang and Reiczigel, 2014 <doi:10.1016/j.prevetmed.2013.09.015>] or Bayer, Fay, and Graubard, 2023 <doi:10.48550/arXiv.2205.13494>). The focus is on hypothesis tests that have compatible confidence intervals, but some functions only have confidence intervals (e.g., prevSeSp).

Last updated 1 years ago

2.67 score 1 dependents 52 scripts 951 downloads

wbs - Wild Binary Segmentation for Multiple Change-Point Detection

Provides efficient implementation of the Wild Binary Segmentation and Binary Segmentation algorithms for estimation of the number and locations of multiple change-points in the piecewise constant function plus Gaussian noise model.

Last updated 2 months ago

2.67 score 3 stars 2 dependents 26 scripts 818 downloads

bios2mds - From Biological Sequences to Multidimensional Scaling

Utilities dedicated to the analysis of biological sequences by metric MultiDimensional Scaling with projection of supplementary data. It contains functions for reading multiple sequence alignment files, calculating distance matrices, performing metric multidimensional scaling and visualizing results.

Last updated 5 years ago

2.66 score 1 stars 57 scripts 446 downloads

JGL - Performs the Joint Graphical Lasso for Sparse Inverse Covariance Estimation on Multiple Classes

The Joint Graphical Lasso is a generalized method for estimating Gaussian graphical models/ sparse inverse covariance matrices/ biological networks on multiple classes of data. We solve JGL under two penalty functions: The Fused Graphical Lasso (FGL), which employs a fused penalty to encourage inverse covariance matrices to be similar across classes, and the Group Graphical Lasso (GGL), which encourages similar network structure between classes. FGL is recommended over GGL for most applications. Reference: Danaher P, Wang P, Witten DM. (2013) <doi:10.1111/rssb.12033>.

Last updated 1 years ago

2.65 score 1 stars 1 dependents 117 scripts 226 downloads

listr - Tools for Lists

Tools for common operations on lists. Provided are short-cuts to operations like selecting and merging data stored in lists. The functions in this package are designed to be used with pipes.

Last updated 2 years ago

2.65 score 45 scripts 213 downloads

Fragman - Fragment Analysis in R

Performs fragment analysis using genetic data coming from capillary electrophoresis machines. These are files with FSA extension which stands for FASTA-type file, and .txt files from Beckman CEQ 8000 system, both contain DNA fragment intensities read by machinery. In addition to visualization, it performs automatic scoring of SSRs (Sample Sequence Repeats; a type of genetic marker very common across the genome) and other type of PCR markers (standing for Polymerase Chain Reaction) in biparental populations such as F1, F2, BC (backcross), and diversity panels (collection of genetic diversity).

Last updated 7 years ago

2.65 score 5 stars 1 dependents 27 scripts 272 downloads

NaileR - Interpreting Latent Variables with AI

A small package designed for interpreting continuous and categorical latent variables. You provide a data set with a latent variable you want to understand and some other explanatory variables. It provides a description of the latent variable based on the explanatory variables. It also provides a name to the latent variable.

Last updated 1 months ago

2.65 score 1 dependents 49 scripts 561 downloads

TideHarmonics - Harmonic Analysis of Tides

Implements harmonic analysis of tidal and sea-level data. Over 400 harmonic tidal constituents can be estimated, all with daily nodal corrections. Time-varying mean sea-levels can also be used.

Last updated 8 years ago

2.65 score 1 dependents 15 scripts 196 downloads

localsolver - R API to LocalSolver

The package converts R data onto input and data for LocalSolver, executes optimization and exposes optimization results as R data. LocalSolver (http://www.localsolver.com/) is an optimization engine developed by Innovation24 (http://www.innovation24.fr/). It is designed to solve large-scale mixed-variable non-convex optimization problems. The localsolver package is developed and maintained by WLOG Solutions (http://www.wlogsolutions.com/en/) in collaboration with Decision Support and Analysis Division at Warsaw School of Economics (http://www.sgh.waw.pl/en/).

Last updated 11 years ago

2.65 score 3 stars 15 scripts 139 downloads

adimpro - Adaptive Smoothing of Digital Images

Implements tools for manipulation of digital images and the Propagation Separation approach by Polzehl and Spokoiny (2006) <DOI:10.1007/s00440-005-0464-1> for smoothing digital images, see Polzehl and Tabelow (2007) <DOI:10.18637/jss.v019.i01>.

Last updated 3 months ago

fortranopenblasopenmp

2.65 score 2 dependents 37 scripts 874 downloads

visualpred - Visualization 2D of Binary Classification Models

Visual contour and 2D point and contour plots for binary classification modeling under algorithms such as 'glm', 'rf', 'gbm', 'nnet' and 'svm', presented over two dimensions generated by 'famd' and 'mca' methods. Package 'FactoMineR' for multivariate reduction functions and package 'MBA' for interpolation functions are used. The package can be used to visualize the discriminant power of input variables and algorithmic modeling, explore outliers, compare algorithm behaviour, etc. It has been created initially for teaching purposes, but it has also many practical uses under the 'XAI' paradigm.

Last updated 2 months ago

2.64 score 11 scripts 540 downloads

ssfa - Spatial Stochastic Frontier Analysis

Spatial Stochastic Frontier Analysis (SSFA) is an original method for controlling the spatial heterogeneity in Stochastic Frontier Analysis (SFA) models, for cross-sectional data, by splitting the inefficiency term into three terms: the first one related to spatial peculiarities of the territory in which each single unit operates, the second one related to the specific production features and the third one representing the error term.

Last updated 1 years ago

2.64 score 2 stars 22 scripts 255 downloads

LTRCtrees - Survival Trees to Fit Left-Truncated and Right-Censored and Interval-Censored Survival Data

Recursive partition algorithms designed for fitting survival tree with left-truncated and right censored (LTRC) data, as well as interval-censored data. The LTRC trees can also be used to fit survival tree with time-varying covariates.

Last updated 4 years ago

2.64 score 22 scripts 229 downloads

BE - Bioequivalence Study Data Analysis

Analyze bioequivalence study data with industrial strength. Sample size could be determined for various crossover designs, such as 2x2 design, 2x4 design, 4x4 design, Balaam design, Two-sequence dual design, and William design. Reference: Chow SC, Liu JP. Design and Analysis of Bioavailability and Bioequivalence Studies. 3rd ed. (2009, ISBN:978-1-58488-668-6).

Last updated 2 years ago

2.63 score 1 stars 43 scripts 389 downloads

scbursts - Single Channel Bursts Analysis

Provides tools to import and export from several existing pieces of ion-channel analysis software such as 'TAC', 'QUB', 'SCAN', and 'Clampfit', implements procedures such as dwell-time correction and defining bursts with a critical time, and provides tools for analysis of bursts, such as tools for sorting and plotting.

Last updated 5 years ago

2.63 score 43 scripts 135 downloads

blockmodeling - Generalized and Classical Blockmodeling of Valued Networks

This is primarily meant as an implementation of generalized blockmodeling for valued networks. In addition, measures of similarity or dissimilarity based on structural equivalence and regular equivalence (REGE algorithms) can be computed and partitioned matrices can be plotted: Žiberna (2007)<doi:10.1016/j.socnet.2006.04.002>, Žiberna (2008)<doi:10.1080/00222500701790207>, Žiberna (2014)<doi:10.1016/j.socnet.2014.04.002>.

Last updated 1 years ago

fortran

2.63 score 12 dependents 78 scripts 1.2k downloads

NISTunits - Fundamental Physical Constants and Unit Conversions from NIST

Fundamental physical constants (Quantity, Value, Uncertainty, Unit) for SI (International System of Units) and non-SI units, plus unit conversions Based on the data from NIST (National Institute of Standards and Technology, USA)

Last updated 8 years ago

2.63 score 10 dependents 1.2k scripts 1.4k downloads

EL - Two-Sample Empirical Likelihood

Empirical likelihood (EL) inference for two-sample problems. The following statistics are included: the difference of two-sample means, smooth Huber estimators, quantile (qdiff) and cumulative distribution functions (ddiff), probability-probability (P-P) and quantile-quantile (Q-Q) plots as well as receiver operating characteristic (ROC) curves. EL calculations are based on J. Valeinis, E. Cers (2011) <http://home.lu.lv/~valeinis/lv/petnieciba/EL_TwoSample_2011.pdf>.

Last updated 2 months ago

2.62 score 42 scripts 719 downloads

bshazard - Nonparametric Smoothing of the Hazard Function

The function estimates the hazard function non parametrically from a survival object (possibly adjusted for covariates). The smoothed estimate is based on B-splines from the perspective of generalized linear mixed models. Left truncated and right censoring data are allowed. The package is based on the work in Rebora P (2014) <doi:10.32614/RJ-2014-028>.

Last updated 8 months ago

2.62 score 1 stars 2 dependents 73 scripts 582 downloads

EDISON - Network Reconstruction and Changepoint Detection

Package EDISON (Estimation of Directed Interactions from Sequences Of Non-homogeneous gene expression) runs an MCMC simulation to reconstruct networks from time series data, using a non-homogeneous, time-varying dynamic Bayesian network. Networks segments and changepoints are inferred concurrently, and information sharing priors provide a reduction of the inference uncertainty.

Last updated 9 years ago

2.62 score 2 stars 1 dependents 15 scripts 172 downloads

freqdom - Frequency Domain Based Analysis: Dynamic PCA

Implementation of dynamic principal component analysis (DPCA), simulation of VAR and VMA processes and frequency domain tools. These frequency domain methods for dimensionality reduction of multivariate time series were introduced by David Brillinger in his book Time Series (1974). We follow implementation guidelines as described in Hormann, Kidzinski and Hallin (2016), Dynamic Functional Principal Component <doi:10.1111/rssb.12076>.

Last updated 9 months ago

2.61 score 4 dependents 34 scripts 419 downloads

tsBSS - Blind Source Separation and Supervised Dimension Reduction for Time Series

Different estimators are provided to solve the blind source separation problem for multivariate time series with stochastic volatility and supervised dimension reduction problem for multivariate time series. Different functions based on AMUSE and SOBI are also provided for estimating the dimension of the white noise subspace. The package is fully described in Nordhausen, Matilainen, Miettinen, Virta and Taskinen (2021) <doi:10.18637/jss.v098.i15>.

Last updated 3 years ago

openblascpp

2.61 score 4 stars 2 dependents 17 scripts 344 downloads

AssocBin - Measuring Association with Recursive Binning

An iterative implementation of a recursive binary partitioning algorithm to measure pairwise dependence with a modular design that allows user specification of the splitting logic and stop criteria. Helper functions provide suggested versions of both and support visualization and the computation of summary statistics on final binnings. For a complete description of the functionality and algorithm, see Salahub and Oldford (2023) <doi:10.48550/arXiv.2311.08561>.

Last updated 14 days ago

2.60 score 10 scripts 152 downloads

sorcering - Soil Organic Carbon and CN Ratio Driven Nitrogen Modelling Framework

Can be used to model the fate of soil organic carbon and soil organic nitrogen and to calculate N mineralisation rates. Provides a framework that numerically solves differential equations of soil organic carbon models based on first-order kinetics and extends these models to include the nitrogen component. The name 'sorcering' is an acronym for 'Soil ORganic Carbon & CN Ratio drIven Nitrogen modellinG framework'.

Last updated 3 months ago

openblascpp

2.60 score 196 downloads

ggrcs - Draw Histograms and Restricted Cubic Splines (RCS)

You can use this function to easily draw a combined histogram and restricted cubic spline. The function draws the graph through 'ggplot2'. RCS fitting requires the use of the rcs() function of the 'rms' package. Can fit cox regression, logistic regression. This method was described by Per Kragh (2003) <doi:10.1002/sim.1497>.

Last updated 3 months ago

2.60 score 1 stars 7 scripts 811 downloads

geodetector - Stratified Heterogeneity Measure, Dominant Driving Force Detection, Interaction Relationship Investigation

Spatial stratified heterogeneity (SSH), referring to the within strata are more similar than the between strata, a model with global parameters would be confounded if input data is SSH. Note that the "spatial" here can be either geospatial or the space in mathematical meaning. Geographical detector is a novel tool to investigate SSH: (1) measure and find SSH of a variable Y; (2) test the power of determinant X of a dependent variable Y according to the consistency between their spatial distributions; and (3) investigate the interaction between two explanatory variables X1 and X2 to a dependent variable Y (Wang et al 2014 <doi:10.1080/13658810802443457>, Wang, Zhang, and Fu 2016 <doi:10.1016/j.ecolind.2016.02.052>).

Last updated 4 months ago

2.60 score 2 stars 10 scripts 335 downloads

GE - General Equilibrium Modeling

Some tools for developing general equilibrium models and some general equilibrium models. These models can be used for teaching economic theory and are built by the methods of new structural economics (see <https://www.nse.pku.edu.cn/> and LI Wu, 2019, ISBN: 9787521804225, General Equilibrium and Structural Dynamics: Perspectives of New Structural Economics. Beijing: Economic Science Press). The model form and mathematical methods can be traced back to J. von Neumann (1945, A Model of General Economic Equilibrium. The Review of Economic Studies, 13. pp. 1-9), J. G. Kemeny, O. Morgenstern and G. L. Thompson (1956, A Generalization of the von Neumann Model of an Expanding Economy, Econometrica, 24, pp. 115-135) et al. By the way, J. G. Kemeny is a co-inventor of the computer language BASIC.

Last updated 7 months ago

2.60 score 1 stars 511 downloads

dendRoAnalyst - A Tool for Processing and Analyzing Dendrometer Data

There are various functions for managing and cleaning data before the application of different approaches. This includes identifying and erasing sudden jumps in dendrometer data not related to environmental change, identifying the time gaps of recordings, and changing the temporal resolution of data to different frequencies. Furthermore, the package calculates daily statistics of dendrometer data, including the daily amplitude of tree growth. Various approaches can be applied to separate radial growth from daily cyclic shrinkage and expansion due to uptake and loss of stem water. In addition, it identifies periods of consecutive days with user-defined climatic conditions in daily meteorological data, then check what trees are doing during that period.

Last updated 9 months ago

2.60 score 2 stars 37 scripts 296 downloads

Monte.Carlo.se - Monte Carlo Standard Errors

Computes Monte Carlo standard errors for summaries of Monte Carlo output. Summaries and their standard errors are based on columns of Monte Carlo simulation output. Dennis D. Boos and Jason A. Osborne (2015) <doi:10.1111/insr.12087>.

Last updated 2 years ago

2.60 score 193 downloads

SFS - Similarity-First Search Seriation Algorithm

An implementation of the Similarity-First Search algorithm (SFS), a combinatorial algorithm which can be used to solve the seriation problem and to recognize some structured weighted graphs. The SFS algorithm represents a generalization to weighted graphs of the graph search algorithm Lexicographic Breadth-First Search (Lex-BFS), a variant of Breadth-First Search. The SFS algorithm reduces to Lex-BFS when applied to binary matrices (or, equivalently, unweighted graphs). Hence this library can be also considered for Lex-BFS applications such as recognition of graph classes like chordal or unit interval graphs. In fact, the SFS seriation algorithm implemented in this package is a multisweep algorithm, which consists in repeating a finite number of SFS iterations (at most n sweeps for a matrix of size n). If the data matrix has a Robinsonian structure, then the ranking returned by the multistep SFS algorithm is a Robinson ordering of the input matrix. Otherwise the algorithm can be used as a heuristic to return a ranking partially satisfying the Robinson property.

Last updated 6 years ago

cpp

2.60 score 6 scripts 131 downloads

locits - Test of Stationarity and Localized Autocovariance

Provides test of second-order stationarity for time series (for dyadic and arbitrary-n length data). Provides localized autocovariance, with confidence intervals, for locally stationary (nonstationary) time series. See Nason, G P (2013) "A test for second-order stationarity and approximate confidence intervals for localized autocovariance for locally stationary time series." Journal of the Royal Statistical Society, Series B, 75, 879-904. <doi:10.1111/rssb.12015>.

Last updated 1 years ago

2.60 score 1 stars 3 dependents 44 scripts 326 downloads

tmvmixnorm - Sampling from Truncated Multivariate Normal and t Distributions

Efficient sampling of truncated multivariate (scale) mixtures of normals under linear inequality constraints is nontrivial due to the analytically intractable normalizing constant. Meanwhile, traditional methods may subject to numerical issues, especially when the dimension is high and dependence is strong. Algorithms proposed by Li and Ghosh (2015) <doi: 10.1080/15598608.2014.996690> are adopted for overcoming difficulties in simulating truncated distributions. Efficient rejection sampling for simulating truncated univariate normal distribution is included in the package, which shows superiority in terms of acceptance rate and numerical stability compared to existing methods and R packages. An efficient function for sampling from truncated multivariate normal distribution subject to convex polytope restriction regions based on Gibbs sampler for conditional truncated univariate distribution is provided. By extending the sampling method, a function for sampling truncated multivariate Student's t distribution is also developed. Moreover, the proposed method and computation remain valid for high dimensional and strong dependence scenarios. Empirical results in Li and Ghosh (2015) <doi: 10.1080/15598608.2014.996690> illustrated the superior performance in terms of various criteria (e.g. mixing and integrated auto-correlation time).

Last updated 4 years ago

2.59 score 5 dependents 26 scripts 262 downloads

HDtweedie - The Lasso for Tweedie's Compound Poisson Model Using an IRLS-BMD Algorithm

The Tweedie lasso model implements an iteratively reweighed least square (IRLS) strategy that incorporates a blockwise majorization decent (BMD) method, for efficiently computing solution paths of the (grouped) lasso and the (grouped) elastic net methods.

Last updated 3 years ago

fortranopenblas

2.59 score 3 stars 1 dependents 43 scripts 276 downloads

stepPlr - L2 Penalized Logistic Regression with Stepwise Variable Selection

L2 penalized logistic regression for both continuous and discrete predictors, with forward stagewise/forward stepwise variable selection procedure.

Last updated 7 years ago

2.58 score 46 scripts 1.2k downloads

AMModels - Adaptive Management Model Manager

Helps enable adaptive management by codifying knowledge in the form of models generated from numerous analyses and data sets. Facilitates this process by storing all models and data sets in a single object that can be updated and saved, thus tracking changes in knowledge through time. A shiny application called AM Model Manager (modelMgr()) enables the use of these functions via a GUI.

Last updated 6 years ago

2.58 score 19 scripts 284 downloads

ensembleBMA - Probabilistic Forecasting using Ensembles and Bayesian Model Averaging

Bayesian Model Averaging to create probabilistic forecasts from ensemble forecasts and weather observations <https://stat.uw.edu/sites/default/files/files/reports/2007/tr516.pdf>.

Last updated 2 years ago

2.58 score 3 stars 1 dependents 42 scripts 711 downloads

ReAD - Powerful Replicability Analysis of Genome-Wide Association Studies

A robust and powerful approach is developed for replicability analysis of two Genome-wide association studies (GWASs) accounting for the linkage disequilibrium (LD) among genetic variants. The LD structure in two GWASs is captured by a four-state hidden Markov model (HMM). The unknowns involved in the HMM are estimated by an efficient expectation-maximization (EM) algorithm in combination with a non-parametric estimation of functions. By incorporating information from adjacent locations via the HMM, this approach identifies the entire clusters of genotype-phenotype associated signals, improving the power of replicability analysis while effectively controlling the false discovery rate.

Last updated 1 years ago

openblascppopenmp

2.57 score 372 scripts 357 downloads

intccr - Semiparametric Competing Risks Regression under Interval Censoring

Semiparametric regression models on the cumulative incidence function for interval-censored competing risks data as described in Bakoyannis, Yu, & Yiannoutsos (2017) /doi{10.1002/sim.7350} and the models with missing event types as described in Park, Bakoyannis, Zhang, & Yiannoutsos (2021) \doi{10.1093/biostatistics/kxaa052}. The proportional subdistribution hazards model (Fine-Gray model), the proportional odds model, and other models that belong to the class of semiparametric generalized odds rate transformation models.

Last updated 3 years ago

2.57 score 1 stars 37 scripts 364 downloads

CADFtest - A Package to Perform Covariate Augmented Dickey-Fuller Unit Root Tests

Hansen's (1995) Covariate-Augmented Dickey-Fuller (CADF) test. The only required argument is y, the Tx1 time series to be tested. If no stationary covariate X is passed to the procedure, then an ordinary ADF test is performed. The p-values of the test are computed using the procedure illustrated in Lupi (2009).

Last updated 8 years ago

2.57 score 37 scripts 686 downloads

ei - Ecological Inference

Software accompanying Gary King's book: A Solution to the Ecological Inference Problem. (1997). Princeton University Press. ISBN 978-0691012407.

Last updated 8 years ago

2.57 score 1 stars 37 scripts 239 downloads

BeSS - Best Subset Selection in Linear, Logistic and CoxPH Models

An implementation of best subset selection in generalized linear model and Cox proportional hazard model via the primal dual active set algorithm proposed by Wen, C., Zhang, A., Quan, S. and Wang, X. (2020) <doi:10.18637/jss.v094.i04>. The algorithm formulates coefficient parameters and residuals as primal and dual variables and utilizes efficient active set selection strategies based on the complementarity of the primal and dual variables.

Last updated 12 months ago

cpp

2.56 score 2 stars 26 scripts 484 downloads

marlod - Marginal Modeling for Exposure Data with Values Below the LOD

Functions of marginal mean and quantile regression models are used to analyze environmental exposure and biomonitoring data with repeated measurements and non-detects (i.e., values below the limit of detection (LOD)), as well as longitudinal exposure data that include non-detects and time-dependent covariates.

Last updated 25 days ago

2.56 score 12 scripts 176 downloads

MRCV - Methods for Analyzing Multiple Response Categorical Variables (MRCVs)

Provides functions for analyzing the association between one single response categorical variable (SRCV) and one multiple response categorical variable (MRCV), or between two or three MRCVs. A modified Pearson chi-square statistic can be used to test for marginal independence for the one or two MRCV case, or a more general loglinear modeling approach can be used to examine various other structures of association for the two or three MRCV case. Bootstrap- and asymptotic-based standardized residuals and model-predicted odds ratios are available, in addition to other descriptive information. Statisical methods implemented are described in Bilder et al. (2000) <doi:10.1080/03610910008813665>, Bilder and Loughin (2004) <doi:10.1111/j.0006-341X.2004.00147.x>, Bilder and Loughin (2007) <doi:10.1080/03610920600974419>, and Koziol and Bilder (2014) <https://journal.r-project.org/articles/RJ-2014-014/>.

Last updated 2 months ago

2.56 score 12 scripts 319 downloads

EntropyEstimation - Estimation of Entropy and Related Quantities

Contains methods for the estimation of Shannon's entropy, variants of Renyi's entropy, mutual information, Kullback-Leibler divergence, and generalized Simpson's indices. The estimators used have a bias that decays exponentially fast.

Last updated 3 months ago

2.56 score 4 dependents 22 scripts 614 downloads

elrm - Exact Logistic Regression via MCMC

Implements a Markov Chain Monte Carlo algorithm to approximate exact conditional inference for logistic regression models. Exact conditional inference is based on the distribution of the sufficient statistics for the parameters of interest given the sufficient statistics for the remaining nuisance parameters. Using model formula notation, users specify a logistic model and model terms of interest for exact inference. See Zamar et al. (2007) <doi:10.18637/jss.v021.i03> for more details.

Last updated 6 days ago

cpp

2.56 score 1 dependents 12 scripts 116 downloads

mable - Maximum Approximate Bernstein/Beta Likelihood Estimation

Fit data from a continuous population with a smooth density on finite interval by an approximate Bernstein polynomial model which is a mixture of certain beta distributions and find maximum approximate Bernstein likelihood estimator of the unknown coefficients. Consequently, maximum likelihood estimates of the unknown density, distribution functions, and more can be obtained. If the support of the density is not the unit interval then transformation can be applied. This is an implementation of the methods proposed by the author of this package published in the Journal of Nonparametric Statistics: Guan (2016) <doi:10.1080/10485252.2016.1163349> and Guan (2017) <doi:10.1080/10485252.2017.1374384>. For data with covariates, under some semiparametric regression models such as Cox proportional hazards model and the accelerated failure time model, the baseline survival function can be estimated smoothly based on general interval censored data.

Last updated 3 months ago

2.56 score 18 scripts 283 downloads

CMLS - Constrained Multivariate Least Squares

Solves multivariate least squares (MLS) problems subject to constraints on the coefficients, e.g., non-negativity, orthogonality, equality, inequality, monotonicity, unimodality, smoothness, etc. Includes flexible functions for solving MLS problems subject to user-specified equality and/or inequality constraints, as well as a wrapper function that implements 24 common constraint options. Also does k-fold or generalized cross-validation to tune constraint options for MLS problems. See ten Berge (1993, ISBN:9789066950832) for an overview of MLS problems, and see Goldfarb and Idnani (1983) <doi:10.1007/BF02591962> for a discussion of the underlying quadratic programming algorithm.

Last updated 2 years ago

2.56 score 6 dependents 6 scripts 779 downloads

varrank - Heuristics Tools Based on Mutual Information for Variable Ranking

A computational toolbox of heuristics approaches for performing variable ranking and feature selection based on mutual information well adapted for multivariate system epidemiology datasets. The core function is a general implementation of the minimum redundancy maximum relevance model. R. Battiti (1994) <doi:10.1109/72.298224>. Continuous variables are discretized using a large choice of rule. Variables ranking can be learned with a sequential forward/backward search algorithm. The two main problems that can be addressed by this package is the selection of the most representative variable within a group of variables of interest (i.e. dimension reduction) and variable ranking with respect to a set of features of interest.

Last updated 2 years ago

2.56 score 18 scripts 151 downloads

gamlss.foreach - Parallel Computations for Distributional Regression

Computational intensive calculations for Generalized Additive Models for Location Scale and Shape, <doi:10.1111/j.1467-9876.2005.00510.x>.

Last updated 2 years ago

2.56 score 1 dependents 12 scripts 253 downloads

etable - Easy Table

Creates simple to highly customized tables for a wide selection of descriptive statistics, with or without weighting the data.

Last updated 4 years ago

2.56 score 36 scripts 477 downloads

BayesGOF - Bayesian Modeling via Frequentist Goodness-of-Fit

A Bayesian data modeling scheme that performs four interconnected tasks: (i) characterizes the uncertainty of the elicited parametric prior; (ii) provides exploratory diagnostic for checking prior-data conflict; (iii) computes the final statistical prior density estimate; and (iv) executes macro- and micro-inference. Primary reference is Mukhopadhyay, S. and Fletcher, D. 2018 paper "Generalized Empirical Bayes via Frequentist Goodness of Fit" (<https://www.nature.com/articles/s41598-018-28130-5 >).

Last updated 6 years ago

2.56 score 1 dependents 12 scripts 270 downloads

deaR - Conventional and Fuzzy Data Envelopment Analysis

Set of functions for Data Envelopment Analysis. It runs both classic and fuzzy DEA models. See: Banker, R.; Charnes, A.; Cooper, W.W. (1984). <doi:10.1287/mnsc.30.9.1078>, Charnes, A.; Cooper, W.W.; Rhodes, E. (1978). <doi:10.1016/0377-2217(78)90138-8> and Charnes, A.; Cooper, W.W.; Rhodes, E. (1981). <doi:10.1287/mnsc.27.6.668>.

Last updated 2 years ago

2.55 score 146 scripts 1.2k downloads

BinaryEPPM - Mean and Scale-Factor Modeling of Under- And Over-Dispersed Binary Data

Under- and over-dispersed binary data are modeled using an extended Poisson process model (EPPM) appropriate for binary data. A feature of the model is that the under-dispersion relative to the binomial distribution only needs to be greater than zero, but the over-dispersion is restricted compared to other distributional models such as the beta and correlated binomials. Because of this, the examples focus on under-dispersed data and how, in combination with the beta or correlated distributions, flexible models can be fitted to data displaying both under- and over-dispersion. Using Generalized Linear Model (GLM) terminology, the functions utilize linear predictors for the probability of success and scale-factor with various link functions for p, and log link for scale-factor, to fit a variety of models relevant to areas such as bioassay. Details of the EPPM are in Faddy and Smith (2012) <doi:10.1002/bimj.201100214> and Smith and Faddy (2019) <doi:10.18637/jss.v090.i08>.

Last updated 7 months ago

2.54 score 35 scripts 253 downloads

tidysynth - A Tidy Implementation of the Synthetic Control Method

A synthetic control offers a way of evaluating the effect of an intervention in comparative case studies. The package makes a number of improvements when implementing the method in R. These improvements allow users to inspect, visualize, and tune the synthetic control more easily. A key benefit of a tidy implementation is that the entire preparation process for building the synthetic control can be accomplished in a single pipe.

Last updated 2 years ago

2.54 score 70 scripts 959 downloads

eSIR - Extended State-Space SIR Models

An implementation of extended state-space SIR models developed by Song Lab at UM school of Public Health. There are several functions available by 1) including a time-varying transmission modifier, 2) adding a time-dependent quarantine compartment, 3) adding a time-dependent antibody-immunization compartment. Wang L. (2020) <doi:10.6339/JDS.202007_18(3).0003>.

Last updated 3 years ago

jagscpp

2.54 score 1 stars 35 scripts 271 downloads

rtk - Rarefaction Tool Kit

Rarefy data, calculate diversity and plot the results.

Last updated 5 years ago

cpp

2.54 score 14 scripts 237 downloads

SRCS - Statistical Ranking Color Scheme for Multiple Pairwise Comparisons

Implementation of the SRCS method for a color-based visualization of the results of multiple pairwise tests on a large number of problem configurations, proposed in: I.G. del Amo, D.A. Pelta. SRCS: a technique for comparing multiple algorithms under several factors in dynamic optimization problems. In: E. Alba, A. Nakib, P. Siarry (Eds.), Metaheuristics for Dynamic Optimization. Series: Studies in Computational Intelligence 433, Springer, Berlin/Heidelberg, 2012.

Last updated 9 years ago

2.54 score 35 scripts 115 downloads

bda - Binned Data Analysis

Algorithms developed for binned data analysis, gene expression data analysis and measurement error models for ordinal data analysis.

Last updated 4 months ago

2.54 score 64 scripts 1.4k downloads

cg - Compare Groups, Analytically and Graphically

Comprehensive data analysis software, and the name "cg" stands for "compare groups." Its genesis and evolution are driven by common needs to compare administrations, conditions, etc. in medicine research and development. The current version provides comparisons of unpaired samples, i.e. a linear model with one factor of at least two levels. It also provides comparisons of two paired samples. Good data graphs, modern statistical methods, and useful displays of results are emphasized.

Last updated 9 years ago

2.54 score 86 scripts 259 downloads

MCPAN - Multiple Comparisons Using Normal Approximation

Multiple contrast tests and simultaneous confidence intervals based on normal approximation. With implementations for binomial proportions in a 2xk setting (risk difference and odds ratio), poly-3-adjusted tumour rates, biodiversity indices (multinomial data) and expected values under lognormal assumption. Approximative power calculation for multiple contrast tests of binomial and Gaussian data.

Last updated 7 years ago

2.53 score 1 stars 3 dependents 38 scripts 488 downloads

RCytoGPS - Using Cytogenetics Data in R

Defines classes and methods to process text-based cytogenetics using the CytoGPS web site, then import the results into R for further analysis and graphing.

Last updated 4 months ago

2.53 score 17 scripts 163 downloads

pointRes - Analyzing Pointer Years and Components of Resilience

Functions to calculate and plot event and pointer years as well as resilience indices. Designed for dendroecological applications, but also suitable to analyze patterns in other ecological time series.

Last updated 2 years ago

2.53 score 1 stars 17 scripts 368 downloads

bgw - Bunch-Gay-Welsch Statistical Estimation

Performs statistical estimation and inference-related computations by accessing and executing modified versions of 'Fortran' subroutines originally published in the Association for Computing Machinery (ACM) journal Transactions on Mathematical Software (TOMS) by Bunch, Gay and Welsch (1993) <doi:10.1145/151271.151279>. The acronym 'BGW' (from the authors' last names) will be used when making reference to technical content (e.g., algorithm, methodology) that originally appeared in ACM TOMS. A key feature of BGW is that it exploits the special structure of statistical estimation problems within a trust-region-based optimization approach to produce an estimation algorithm that is much more effective than the usual practice of using optimization methods and codes originally developed for general optimization. The 'bgw' package bundles 'R' wrapper (and related) functions with modified 'Fortran' source code so that it can be compiled and linked in the 'R' environment for fast execution. This version implements a function ('bgw_mle.R') that performs maximum likelihood estimation (MLE) for a user-provided model object that computes probabilities (a.k.a. probability densities). The original motivation for producing this package was to provide fast, efficient, and reliable MLE for discrete choice models that can be called from the 'Apollo' choice modelling 'R' package ( see <http://www.apollochoicemodelling.com>). Starting with the release of Apollo 3.0, BGW is the default estimation package. However, estimation can also be performed using BGW in a stand-alone fashion without using 'Apollo' (as shown in simple examples included in the package). Note also that BGW capabilities are not limited to MLE, and future extension to other estimators (e.g., nonlinear least squares, generalized method of moments, etc.) is possible. The 'Fortran' code included in 'bgw' was modified by one of the original BGW authors (Bunch) under his rights as confirmed by direct consultation with the ACM Intellectual Property and Rights Manager. See <https://authors.acm.org/author-resources/author-rights>. The main requirement is clear citation of the original publication (see above).

Last updated 9 months ago

fortran

2.53 score 1 dependents 3 scripts 1.1k downloads

MCI - Multiplicative Competitive Interaction (MCI) Model

Market area models are used to analyze and predict store choices and market areas concerning retail and service locations. This package implements two market area models (Huff Model, Multiplicative Competitive Interaction Model) into R, while the emphases lie on 1.) fitting these models based on empirical data via OLS regression and nonlinear techniques and 2.) data preparation and processing (esp. interaction matrices and data preparation for the MCI Model).

Last updated 7 years ago

2.53 score 42 scripts 180 downloads

PHENIX - Phenotypic Integration Index

Provides functions to estimate the size-controlled phenotypic integration index, a novel method by Torices & Méndez (2014) to solve problems due to individual size when estimating integration (namely, larger individuals have larger components, which will drive a correlation between components only due to resource availability that might obscure the observed measures of integration). In addition, the package also provides the classical estimation by Wagner (1984), bootstrapping and jackknife methods to calculate confidence intervals and a significance test for both integration indices.

Last updated 8 years ago

2.52 score 33 scripts 200 downloads

mexhaz - Mixed Effect Excess Hazard Models

Fit flexible (excess) hazard regression models with the possibility of including non-proportional effects of covariables and of adding a random effect at the cluster level (corresponding to a shared frailty). A detailed description of the package functionalities is provided in Charvat and Belot (2021) <doi: 10.18637/jss.v098.i14>.

Last updated 6 months ago

2.51 score 1 dependents 27 scripts 399 downloads

crrSC - Competing Risks Regression for Stratified and Clustered Data

Extension of 'cmprsk' to Stratified and Clustered data. A goodness of fit test for Fine-Gray model is also provided. Methods are detailed in the following articles: Zhou et al. (2011) <doi:10.1111/j.1541-0420.2010.01493.x>, Zhou et al. (2012) <doi:10.1093/biostatistics/kxr032>, Zhou et al. (2013) <doi: 10.1002/sim.5815>.

Last updated 3 years ago

2.51 score 1 dependents 18 scripts 272 downloads

sensitivitymult - Sensitivity Analysis for Observational Studies with Multiple Outcomes

Sensitivity analysis for multiple outcomes in observational studies. For instance, all linear combinations of several outcomes may be explored using Scheffe projections in the comparison() function; see Rosenbaum (2016, Annals of Applied Statistics) <doi:10.1214/16-AOAS942>. Alternatively, attention may focus on a few principal components in the principal() function. The package includes parallel methods for individual outcomes, including tests in the senm() function and confidence intervals in the senmCI() function.

Last updated 7 years ago

2.51 score 3 dependents 36 scripts 126 downloads

rcssci - Visualization of Restricted Cubic Splines

Restricted Cubic Splines were performed to explore the shape of association form of "U, inverted U, L" shape and test linearity or non-linearity base on "Cox,Logistic,linear,quasipoisson" regression, and auto output Restricted Cubic Splines figures. rcssci package could automatically draw RCS graphics with Y-axis "OR,HR,RR,beta". The Restricted Cubic Splines method were based on Suli Huang (2022) <doi:10.1016/j.ecoenv.2022.113183>,Amit Kaura (2019) <doi:10.1136/bmj.l6055>, and Harrell Jr (2015, ISBN:978-3-319-19424-0 (Print) 978-3-319-19425-7 (Online)).

Last updated 2 years ago

2.51 score 7 stars 46 scripts 490 downloads

robmixglm - Robust Generalized Linear Models (GLM) using Mixtures

Robust generalized linear models (GLM) using a mixture method, as described in Beath (2018) <doi:10.1080/02664763.2017.1414164>. This assumes that the data are a mixture of standard observations, being a generalised linear model, and outlier observations from an overdispersed generalized linear model. The overdispersed linear model is obtained by including a normally distributed random effect in the linear predictor of the generalized linear model.

Last updated 3 months ago

cpp

2.51 score 32 scripts 374 downloads

Delta - Measure of Agreement Between Two Raters

Measure of agreement delta was originally by Martín & Femia (2004) <DOI:10.1348/000711004849268>. Since then has been considered as agreement measure for different fields, since their behavior is usually better than the usual kappa index by Cohen (1960) <DOI:10.1177/001316446002000104>. The main issue with delta is that can not be computed by hand contrary to kappa. The current algorithm is based on the Version 5 of the delta windows program that can be found on <https://www.ugr.es/~bioest/software/delta/cmd.php?seccion=downloads>.

Last updated 5 years ago

2.51 score 1 stars 32 scripts 193 downloads

popReconstruct - Reconstruct Human Populations of the Recent Past

Implements the Bayesian hierarchical model described by Wheldon, Raftery, Clark and Gerland (see: <doi:10.1080/01621459.2012.737729>) for simultaneously estimating age-specific population counts, fertility rates, mortality rates and net international migration flows, at the national level.

Last updated 5 years ago

2.51 score 32 scripts 139 downloads

contoureR - Contouring of Non-Regular Three-Dimensional Data

Create contour lines for a non regular series of points, potentially from a non-regular canvas.

Last updated 9 years ago

2.51 score 2 stars 32 scripts 162 downloads

SSDforR - Functions to Analyze Single System Data

Functions to visually and statistically analyze single system data.

Last updated 8 days ago

2.51 score 80 scripts 774 downloads

whitening - Whitening and High-Dimensional Canonical Correlation Analysis

Implements the whitening methods (ZCA, PCA, Cholesky, ZCA-cor, and PCA-cor) discussed in Kessy, Lewin, and Strimmer (2018) "Optimal whitening and decorrelation", <doi:10.1080/00031305.2016.1277159>, as well as the whitening approach to canonical correlation analysis allowing negative canonical correlations described in Jendoubi and Strimmer (2019) "A whitening approach to probabilistic canonical correlation analysis for omics data integration", <doi:10.1186/s12859-018-2572-9>. The package also offers functions to simulate random orthogonal matrices, compute (correlation) loadings and explained variation. It also contains four example data sets (extended UCI wine data, TCGA LUSC data, nutrimouse data, extended pitprops data).

Last updated 3 years ago

2.50 score 2 dependents 53 scripts 412 downloads

eegkit - Toolkit for Electroencephalography Data

Analysis and visualization tools for electroencephalography (EEG) data. Includes functions for (i) plotting EEG data, (ii) filtering EEG data, (iii) smoothing EEG data; (iv) frequency domain (Fourier) analysis of EEG data, (v) Independent Component Analysis of EEG data, and (vi) simulating event-related potential EEG data.

Last updated 6 years ago

2.50 score 6 stars 53 scripts 308 downloads

marima - Multivariate ARIMA and ARIMA-X Analysis

Multivariate ARIMA and ARIMA-X estimation using Spliid's algorithm (marima()) and simulation (marima.sim()).

Last updated 8 years ago

2.50 score 1 dependents 106 scripts 262 downloads

gplm - Generalized Partial Linear Models (GPLM)

Provides functions for estimating a generalized partial linear model, a semiparametric variant of the generalized linear model (GLM) which replaces the linear predictor by the sum of a linear and a nonparametric function.

Last updated 8 years ago

2.49 score 31 scripts 344 downloads

GENLIB - Genealogical Data Analysis

Genealogical data analysis including descriptive statistics (e.g., kinship and inbreeding coefficients) and gene-dropping simulations. See: "GENLIB: an R package for the analysis of genealogical data" Gauvin et al. (2015) <doi:10.1186/s12859-015-0581-5>.

Last updated 10 months ago

cpp

2.49 score 1 dependents 51 scripts 317 downloads

schoRsch - Tools for Analyzing Factorial Experiments

Offers a helping hand to psychologists and other behavioral scientists who routinely deal with experimental data from factorial experiments. It includes several functions to format output from other R functions according to the style guidelines of the APA (American Psychological Association). This formatted output can be copied directly into manuscripts to facilitate data reporting. These features are backed up by a toolkit of several small helper functions, e.g., offering out-of-the-box outlier removal. The package lends its name to Georg "Schorsch" Schuessler, ingenious technician at the Department of Psychology III, University of Wuerzburg. For details on the implemented methods, see Roland Pfister and Markus Janczyk (2016) <doi: 10.20982/tqmp.12.2.p147>.

Last updated 1 months ago

2.48 score 2 stars 76 scripts 531 downloads

gains - Lift (Gains) Tables and Charts

Constructs gains tables and lift charts for prediction algorithms. Gains tables and lift charts are commonly used in direct marketing applications. The method is described in Drozdenko and Drake (2002), "Optimal Database Marketing", Chapter 11.

Last updated 7 years ago

2.48 score 130 scripts 2.3k downloads

salad - Simple Automatic Differentiation

Handles both vector and matrices, using a flexible S4 class for automatic differentiation. The method used is forward automatic differentiation. Many functions and methods have been defined, so that in most cases, functions written without automatic differentiation in mind can be used without change.

Last updated 6 days ago

2.48 score 9 scripts 459 downloads

excessmort - Excess Mortality

Implementation of method for estimating excess mortality and other health related outcomes from weekly or daily count data described in Acosta and Irizarry (2021) "A Flexible Statistical Framework for Estimating Excess Mortality".

Last updated 1 months ago

2.48 score 15 scripts 406 downloads

FishResp - Analytical Tool for Aquatic Respirometry

Calculates metabolic rate of fish and other aquatic organisms measured using an intermittent-flow respirometry approach. The tool is used to run a set of graphical QC tests of raw respirometry data, correct it for background respiration and chamber effect, filter and extract target values of absolute and mass-specific metabolic rate. Experimental design should include background respiration tests and measuring of one or more metabolic rate traits. The R package is ideally integrated with the pump controller 'PumpResp' and the DO meter 'SensResp' (open-source hardware by FishResp). Raw respirometry data can be also imported from 'AquaResp' (free software), 'AutoResp' ('LoligoSystems'), 'OxyView' ('PreSens'), 'Pyro Oxygen Logger' ('PyroScience') and 'Q-box Aqua' ('QubitSystems'). More information about the R package 'FishResp'is available in the publication by Morozov et al. (2019) <doi:10.1093/conphys/coz003>.

Last updated 1 months ago

2.48 score 2 stars 33 scripts 721 downloads

EIEntropy - Ecological Inference Applying Entropy

Implements two estimations related to the foundations of info metrics applied to ecological inference. These methodologies assess the lack of disaggregated data and provide an approach to obtaining disaggregated territorial-level data. For more details, see the following references: Fernández-Vázquez, E., Díaz-Dapena, A., Rubiera-Morollón, F. et al. (2020) "Spatial Disaggregation of Social Indicators: An Info-Metrics Approach." <doi:10.1007/s11205-020-02455-z>. Díaz-Dapena, A., Fernández-Vázquez, E., Rubiera-Morollón, F., & Vinuela, A. (2021) "Mapping poverty at the local level in Europe: A consistent spatial disaggregation of the AROPE indicator for France, Spain, Portugal and the United Kingdom." <doi:10.1111/rsp3.12379>.

Last updated 2 months ago

2.48 score 549 downloads

wintime - Win Time Methods for Time-to-Event Data in Clinical Trials

Performs an analysis of time-to-event clinical trial data using various "win time" methods, including 'ewt', 'ewtr', 'rmt', 'max', 'wtr', 'rwtr', and 'pwt'. These methods are used to calculate and compare treatment effects on ordered composite endpoints. The package handles event times, event indicators, and treatment arm indicators and supports calculations on observed and resampled data. Detailed explanations of each method and usage examples are provided in "Use of win time for ordered composite endpoints in clinical trials," by Troendle et al. (2024)<https://pubmed.ncbi.nlm.nih.gov/38417455/>. For more information, see the package documentation or the vignette titled "Introduction to wintime."

Last updated 2 months ago

2.48 score 5 scripts 505 downloads

rPDBapi - A Comprehensive Interface for Accessing the Protein Data Bank

Streamlines the interaction with the 'RCSB' Protein Data Bank ('PDB') <https://www.rcsb.org/>. This interface offers an intuitive and powerful tool for searching and retrieving a diverse range of data types from the 'PDB'. It includes advanced functionalities like BLAST and sequence motif queries. Built upon the existing XML-based API of the 'PDB', it simplifies the creation of custom requests, thereby enhancing usability and flexibility for researchers.

Last updated 2 months ago

2.48 score 2 scripts 298 downloads

robustmatrix - Robust Matrix-Variate Parameter Estimation

Robust covariance estimation for matrix-valued data and data with Kronecker-covariance structure using the Matrix Minimum Covariance Determinant (MMCD) estimators and outlier explanation using and Shapley values.

Last updated 2 months ago

openblascppopenmp

2.48 score 2 scripts 169 downloads

CommonDataModel - OMOP CDM DDL and Documentation Generator

Generates the scripts required to create an Observational Medical Outcomes Partnership (OMOP) Common Data Model (CDM) database and associated documentation for supported database platforms. Leverages the 'SqlRender' package to convert the Data Definition Language (DDL) script written in parameterized Structured Query Language (SQL) to the other supported dialects.

Last updated 3 months ago

openjdk

2.48 score 1 dependents 6 scripts 549 downloads

Numero - Statistical Framework to Define Subgroups in Complex Datasets

High-dimensional datasets that do not exhibit a clear intrinsic clustered structure pose a challenge to conventional clustering algorithms. For this reason, we developed an unsupervised framework that helps scientists to better subgroup their datasets based on visual cues, please see Gao S, Mutter S, Casey A, Makinen V-P (2019) Numero: a statistical framework to define multivariable subgroups in complex population-based datasets, Int J Epidemiology, 48:369-37, <doi:10.1093/ije/dyy113>. The framework includes the necessary functions to construct a self-organizing map of the data, to evaluate the statistical significance of the observed data patterns, and to visualize the results.

Last updated 3 months ago

cpp

2.48 score 3 scripts 354 downloads

CGNM - Cluster Gauss-Newton Method

Find multiple solutions of a nonlinear least squares problem. Cluster Gauss-Newton method does not assume uniqueness of the solution of the nonlinear least squares problem and compute multiple minimizers. Please cite the following paper when this software is used in your research: Aoki et al. (2020) <doi:10.1007/s11081-020-09571-2>. Cluster Gauss–Newton method. Optimization and Engineering, 1-31. Please cite the following paper when profile likelihood plot is drawn with this software and used in your research: Aoki and Sugiyama (2024) <doi:10.1002/psp4.13055>. Cluster Gauss-Newton method for a quick approximation of profile likelihood: With application to physiologically-based pharmacokinetic models. CPT Pharmacometrics Syst Pharmacol.13(1):54-67.

Last updated 6 months ago

2.48 score 6 scripts 593 downloads

SNSeg - Self-Normalization(SN) Based Change-Point Estimation for Time Series

Implementations self-normalization (SN) based algorithms for change-points estimation in time series data. This comprises nested local-window algorithms for detecting changes in both univariate and multivariate time series developed in Zhao, Jiang and Shao (2022) <doi:10.1111/rssb.12552>.

Last updated 7 months ago

2.48 score 1 stars 2 scripts 439 downloads

rocbc - Statistical Inference for Box-Cox Based Receiver Operating Characteristic Curves

Generation of Box-Cox based ROC curves and several aspects of inferences and hypothesis testing. Can be used when inferences for one biomarker (Bantis LE, Nakas CT, Reiser B. (2018)<doi:10.1002/bimj.201700107>) are of interest or when comparisons of two correlated biomarkers (Bantis LE, Nakas CT, Reiser B. (2021)<doi:10.1002/bimj.202000128>) are of interest. Provides inferences and comparisons around the AUC, the Youden index, the sensitivity at a given specificity level (and vice versa), the optimal operating point of the ROC curve (in the Youden sense), and the Youden based cutoff.

Last updated 8 months ago

2.48 score 2 scripts 582 downloads

opGMMassessment - Optimized Automated Gaussian Mixture Assessment

Necessary functions for optimized automated evaluation of the number and parameters of Gaussian mixtures in one-dimensional data. Various methods are available for parameter estimation and for determining the number of modes in the mixture. A detailed description of the methods ca ben found in Lotsch, J., Malkusch, S. and A. Ultsch. (2022) <doi:10.1016/j.imu.2022.101113>.

Last updated 8 months ago

2.48 score 1 dependents 205 downloads

ipanema - Read Data from 'LimeSurvey'

Read data from 'LimeSurvey' (<https://www.limesurvey.org/>) in a comfortable way. Heavily inspired by 'limer' (<https://github.com/cloudyr/limer/>), which lacked a few comfort features for me.

Last updated 10 months ago

2.48 score 233 downloads

msma - Multiblock Sparse Multivariable Analysis

Several functions can be used to analyze multiblock multivariable data. If the input is a single matrix, then principal components analysis (PCA) is implemented. If the input is a list of matrices, then multiblock PCA is implemented. If the input is two matrices, for exploratory and objective variables, then partial least squares (PLS) analysis is implemented. If the input is two lists of matrices, for exploratory and objective variables, then multiblock PLS analysis is implemented. Additionally, if an extra outcome variable is specified, then a supervised version of the methods above is implemented. For each method, sparse modeling is also incorporated. Functions for selecting the number of components and regularized parameters are also provided.

Last updated 10 months ago

2.48 score 1 dependents 11 scripts 194 downloads

CountsEPPM - Mean and Variance Modeling of Count Data

Modeling under- and over-dispersed count data using extended Poisson process models as in the article Faddy and Smith (2011) <doi:10.18637/jss.v069.i06> .

Last updated 12 months ago

2.48 score 30 scripts 236 downloads

critpath - Setting the Critical Path in Project Management

Solving the problem of project management using CPM (Critical Path Method), PERT (Program Evaluation and Review Technique) and LESS (Least Cost Estimating and Scheduling) methods. The package sets the critical path, schedule and Gantt chart. In addition, it allows to draw a graph even with marked critical activities. For more information about project management see: Taha H. A. "Operations Research. An Introduction" (2017, ISBN:978-1-292-16554-7), Rama Murthy P. "Operations Research" (2007, ISBN:978-81-224-2944-2), Yuval Cohen & Arik Sadeh (2006) "A New Approach for Constructing and Generating AOA Networks", Journal of Engineering, Computing and Architecture 1. 1-13, Konarzewska I., Jewczak M., Kucharski A. (2020, ISBN:978-83-8220-112-3), Miszczyńska D., Miszczyński M. "Wybrane metody badań operacyjnych" (2000, ISBN:83-907712-0-9).

Last updated 12 months ago

2.48 score 6 scripts 380 downloads

SPECK - Receptor Abundance Estimation using Reduced Rank Reconstruction and Clustered Thresholding

Surface Protein abundance Estimation using CKmeans-based clustered thresholding ('SPECK') is an unsupervised learning-based method that performs receptor abundance estimation for single cell RNA-sequencing data based on reduced rank reconstruction (RRR) and a clustered thresholding mechanism. Seurat's normalization method is described in: Hao et al., (2021) <doi:10.1016/j.cell.2021.04.048>, Stuart et al., (2019) <doi:10.1016/j.cell.2019.05.031>, Butler et al., (2018) <doi:10.1038/nbt.4096> and Satija et al., (2015) <doi:10.1038/nbt.3192>. Method for the RRR is further detailed in: Erichson et al., (2019) <doi:10.18637/jss.v089.i11> and Halko et al., (2009) <arXiv:0909.4061>. Clustering method is outlined in: Song et al., (2020) <doi:10.1093/bioinformatics/btaa613> and Wang et al., (2011) <doi:10.32614/RJ-2011-015>.

Last updated 1 years ago

2.48 score 1 dependents 3 scripts 172 downloads

HeteroGGM - Gaussian Graphical Model-Based Heterogeneity Analysis

The goal of this package is to user-friendly realizing Gaussian graphical model-based heterogeneity analysis. Recently, several Gaussian graphical model-based heterogeneity analysis techniques have been developed. A common methodological limitation is that the number of subgroups is assumed to be known a priori, which is not realistic. In a very recent study (Ren et al., 2022), a novel approach based on the penalized fusion technique is developed to fully data-dependently determine the number and structure of subgroups in Gaussian graphical model-based heterogeneity analysis. It opens the door for utilizing the Gaussian graphical model technique in more practical settings. Beyond Ren et al. (2022), more estimations and functions are added, so that the package is self-contained and more comprehensive and can provide ``more direct'' insights to practitioners (with the visualization function). Reference: Ren, M., Zhang S., Zhang Q. and Ma S. (2022). Gaussian Graphical Model-based Heterogeneity Analysis via Penalized Fusion. Biometrics, 78 (2), 524-535.

Last updated 1 years ago

2.48 score 1 dependents 226 downloads

schoolmath - Functions and Datasets for Math Used in School

Contains functions and datasets for math taught in school. A main focus is set to prime-calculation.

Last updated 1 years ago

2.48 score 2 dependents 103 scripts 741 downloads

SpatialBSS - Blind Source Separation for Multivariate Spatial Data

Blind source separation for multivariate spatial data based on simultaneous/joint diagonalization of (robust) local covariance matrices. This package is an implementation of the methods described in Bachoc, Genton, Nordhausen, Ruiz-Gazen and Virta (2020) <doi:10.1093/biomet/asz079>.

Last updated 1 years ago

openblascppopenmp

2.48 score 1 dependents 230 downloads

hydropeak - Detect and Characterize Sub-Daily Flow Fluctuations

An important environmental impact on running water ecosystems is caused by hydropeaking - the discontinuous release of turbine water because of peaks of energy demand. An event-based algorithm is implemented to detect flow fluctuations referring to increase events (IC) and decrease events (DC). For each event, a set of parameters related to the fluctuation intensity is calculated. The framework is introduced in Greimel et al. (2016) "A method to detect and characterize sub-daily flow fluctuations" <doi:10.1002/hyp.10773> and can be used to identify different fluctuation types according to the potential source: e.g., sub-daily flow fluctuations caused by hydropeaking, rainfall, or snow and glacier melt. This is a companion to the package 'hydroroute', which is used to detect and follow hydropower plant-specific hydropeaking waves at the sub-catchment scale and to describe how hydropeaking flow parameters change along the longitudinal flow path as proposed and validated in Greimel et al. (2022).

Last updated 2 years ago

2.48 score 1 dependents 217 downloads

BSL - Bayesian Synthetic Likelihood

Bayesian synthetic likelihood (BSL, Price et al. (2018) <doi:10.1080/10618600.2017.1302882>) is an alternative to standard, non-parametric approximate Bayesian computation (ABC). BSL assumes a multivariate normal distribution for the summary statistic likelihood and it is suitable when the distribution of the model summary statistics is sufficiently regular. This package provides a Metropolis Hastings Markov chain Monte Carlo implementation of four methods (BSL, uBSL, semiBSL and BSLmisspec) and two shrinkage estimators (graphical lasso and Warton's estimator). uBSL (Price et al. (2018) <doi:10.1080/10618600.2017.1302882>) uses an unbiased estimator to the normal density. A semi-parametric version of BSL (semiBSL, An et al. (2018) <arXiv:1809.05800>) is more robust to non-normal summary statistics. BSLmisspec (Frazier et al. 2019 <arXiv:1904.04551>) estimates the Gaussian synthetic likelihood whilst acknowledging that there may be incompatibility between the model and the observed summary statistic. Shrinkage estimation can help to decrease the number of model simulations when the dimension of the summary statistic is high (e.g., BSLasso, An et al. (2019) <doi:10.1080/10618600.2018.1537928>). Extensions to this package are planned. For a journal article describing how to use this package, see An et al. (2022) <doi:10.18637/jss.v101.i11>.

Last updated 2 years ago

2.48 score 3 stars 9 scripts 294 downloads

multiridge - Fast Cross-Validation for Multi-Penalty Ridge Regression

Multi-penalty linear, logistic and cox ridge regression, including estimation of the penalty parameters by efficient (repeated) cross-validation and marginal likelihood maximization. Multiple high-dimensional data types that require penalization are allowed, as well as unpenalized variables. Paired and preferential data types can be specified. See Van de Wiel et al. (2021), <arXiv:2005.09301>.

Last updated 3 years ago

2.48 score 2 dependents 2 scripts 151 downloads

cqrReg - Quantile, Composite Quantile Regression and Regularized Versions

Estimate quantile regression(QR) and composite quantile regression (cqr) and with adaptive lasso penalty using interior point (IP), majorize and minimize(MM), coordinate descent (CD), and alternating direction method of multipliers algorithms(ADMM).

Last updated 3 years ago

openblascpp

2.48 score 5 stars 1 dependents 20 scripts 266 downloads

compareC - Compare Two Correlated C Indices with Right-Censored Survival Outcome

Proposed by Harrell, the C index or concordance C, is considered an overall measure of discrimination in survival analysis between a survival outcome that is possibly right censored and a predictive-score variable, which can represent a measured biomarker or a composite-score output from an algorithm that combines multiple biomarkers. This package aims to statistically compare two C indices with right-censored survival outcome, which commonly arise from a paired design and thus resulting two correlated C indices.

Last updated 3 years ago

2.48 score 30 scripts 521 downloads

tidytidbits - A Collection of Tools and Helpers Extending the Tidyverse

A selection of various tools to extend a data analysis workflow based on the 'tidyverse' packages. This includes high-level data frame editing methods (in the style of 'mutate'/'mutate_at'), some methods in the style of 'purrr' and 'forcats', 'lookup' methods for dict-like lists, a generic method for lumping a data frame by a given count, various low-level methods for special treatment of 'NA' values, 'python'-style tuple-assignment and 'truthy'/'falsy' checks, saving to PDF and PNG from a pipe and various small utilities.

Last updated 3 years ago

2.48 score 2 dependents 46 scripts 555 downloads

yacca - Yet Another Canonical Correlation Analysis Package

An alternative canonical correlation/redundancy analysis function, with associated print, plot, and summary methods. A method for generating helio plots is also included.

Last updated 3 years ago

2.48 score 1 stars 1 dependents 27 scripts 606 downloads

geneExpressionFromGEO - Easily Downloads a Gene Expression Dataset from a GEO Code and Retrieves the Gene Symbols of Its Probesets

A function that reads in the GEO code of a gene expression dataset, retrieves its data from GEO, (optionally) retrieves the gene symbols of the dataset, and returns a simple dataframe table containing all the data. Platforms available: GPL11532, GPL23126, GPL6244, GPL8300, GPL80, GPL96, GPL570, GPL571, GPL20115, GPL1293, GPL6102, GPL6104, GPL6883, GPL6884, GPL13497, GPL14550, GPL17077, GPL6480. GEO: Gene Expression Omnibus. ID: identifier code. The GEO datasets are downloaded from the URL <https://ftp.ncbi.nlm.nih.gov/geo/series/>. More information can be found in the following manuscript: Davide Chicco, "geneExpressionFromGEO: an R package to facilitate data reading from Gene Expression Omnibus (GEO)". Microarray Data Analysis, Methods in Molecular Biology, volume 2401, chapter 12, pages 187-194, Springer Protocols, 2021, <doi:10.1007/978-1-0716-1839-4_12>.

Last updated 3 years ago

2.48 score 1 dependents 7 scripts 300 downloads

eatDB - Spreadsheet Interface for Relational Databases

Use 'SQLite3' as a database system via a complete SQL free R interface, treating the data as if it was a single spreadsheet.

Last updated 3 years ago

2.48 score 2 dependents 5 scripts 410 downloads

edcpR - Ecological Data Collection and Processing Package

This is the course package for the exercise portion of the "Ecological Data Collection and Processing" course.

Last updated 3 years ago

2.48 score 4 scripts 187 downloads

heatmapFlex - Tools to Generate Flexible Heatmaps

A set of tools supporting more flexible heatmaps. The graphics is grid-like using the old graphics system. The main function is heatmap.n2(), which is a wrapper around the various functions constructing individual parts of the heatmap, like sidebars, picket plots, legends etc. The function supports zooming and splitting, i.e., having (unlimited) small heatmaps underneath each other in one plot deriving from the same data set, e.g., clustered and ordered by a supervised clustering method.

Last updated 3 years ago

2.48 score 1 dependents 2 scripts 148 downloads

tRnslate - Translate R Code in Source Files

Evaluate inline or chunks of R code in template files and replace with their output modifying the resulting template.

Last updated 3 years ago

2.48 score 1 dependents 4 scripts 126 downloads

ensembleTax - Ensemble Taxonomic Assignments of Amplicon Sequencing Data

Creates ensemble taxonomic assignments of amplicon sequencing data in R using outputs of multiple taxonomic assignment algorithms and/or reference databases. Includes flexible algorithms for mapping taxonomic nomenclatures onto one another and for computing ensemble taxonomic assignments.

Last updated 4 years ago

2.48 score 7 scripts 175 downloads

rNeighborGWAS - Testing Neighbor Effects in Marker-Based Regressions

To incorporate neighbor genotypic identity into genome-wide association studies, the package provides a set of functions for variation partitioning and association mapping. The theoretical background of the method is described in Sato et al. (2021) <doi:10.1038/s41437-020-00401-w>.

Last updated 4 years ago

2.48 score 15 scripts 193 downloads

vcvComp - Comparison of Variance - Covariance Patterns

Comparison of variance - covariance patterns using relative principal component analysis (relative eigenanalysis), as described in Le Maitre and Mitteroecker (2019) <doi:10.1111/2041-210X.13253>. Also provides functions to compute group covariance matrices, distance matrices, and perform proportionality tests. A worked sample on the body shape of cichlid fishes is included, based on the dataset from Kerschbaumer et al. (2013) <doi:10.5061/dryad.fc02f>.

Last updated 4 years ago

2.48 score 10 scripts 182 downloads

CGE - Computing General Equilibrium

Developing general equilibrium models, computing general equilibrium and simulating economic dynamics with structural dynamic models in LI (2019, ISBN: 9787521804225) "General Equilibrium and Structural Dynamics: Perspectives of New Structural Economics. Beijing: Economic Science Press". When developing complex general equilibrium models, GE package should be used in addition to this package.

Last updated 5 years ago

2.48 score 1 dependents 3 scripts 228 downloads

BimodalIndex - The Bimodality Index

Defines the functions used to compute the bimodal index as defined by Wang et al. (2009) <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2730180/>, <doi:10.4137/CIN.S2846>.

Last updated 6 years ago

microarray

2.48 score 1 dependents 5 scripts 201 downloads

hglm.data - Data for the 'hglm' Package

This data-only package was created for distributing data used in the examples of the 'hglm' package.

Last updated 6 years ago

2.48 score 1 dependents 316 downloads

RationalExp - Rationalizing Rational Expectations. Tests and Deviations

We implement a test of the rational expectations hypothesis based on the marginal distributions of realizations and subjective beliefs from D'Haultfoeuille, Gaillac, and Maurel (2018) <doi:10.3386/w25274>. This test can be used in cases where realizations and subjective beliefs are observed in two different datasets that cannot be matched, or when they are observed in the same dataset. The package also computes the estimator of the minimal deviations from rational expectations than can be rationalized by the data.

Last updated 6 years ago

2.48 score 1 dependents 4 scripts 147 downloads

FinancialMath - Financial Mathematics for Actuaries

Contains financial math functions and introductory derivative functions included in the Society of Actuaries and Casualty Actuarial Society 'Financial Mathematics' exam, and some topics in the 'Models for Financial Economics' exam.

Last updated 8 years ago

2.47 score 4 stars 73 scripts 990 downloads

aniDom - Inferring Dominance Hierarchies and Estimating Uncertainty

Provides: (1) Tools to infer dominance hierarchies based on calculating Elo scores, but with custom functions to improve estimates in animals with relatively stable dominance ranks. (2) Tools to plot the shape of the dominance hierarchy and estimate the uncertainty of a given data set.

Last updated 4 years ago

2.46 score 1 stars 1 dependents 24 scripts 356 downloads

icd.data - International Classifcation of Diseases (ICD) Data

Data from the United States Center for Medicare and Medicaid Services (CMS) is included in this package. There are ICD-9 and ICD-10 diagnostic and procedure codes, and lists of the chapter and sub-chapter headings and the ranges of ICD codes they encompass. There are also two sample datasets. These data are used by the 'icd' package for finding comorbidities.

Last updated 7 years ago

2.45 score 56 scripts 214 downloads

dagR - Directed Acyclic Graphs: Analysis and Data Simulation

Draw, manipulate, and evaluate directed acyclic graphs and simulate corresponding data, as described in International Journal of Epidemiology 50(6):1772-1777.

Last updated 2 years ago

2.44 score 5 stars 55 scripts 258 downloads

normalp - Routines for Exponential Power Distribution

A collection of utilities referred to Exponential Power distribution, also known as General Error Distribution (see Mineo, A.M. and Ruggieri, M. (2005), A software Tool for the Exponential Power Distribution: The normalp package. In Journal of Statistical Software, Vol. 12, Issue 4).

Last updated 1 years ago

2.43 score 5 dependents 18 scripts 476 downloads

assortnet - Calculate the Assortativity Coefficient of Weighted and Binary Networks

Functions to calculate the assortment of vertices in social networks. This can be measured on both weighted and binary networks, with discrete or continuous vertex values.

Last updated 2 years ago

2.43 score 54 scripts 406 downloads

Rcapture - Loglinear Models for Capture-Recapture Experiments

Estimation of abundance and other demographic parameters for closed populations, open populations and the robust design in capture-recapture experiments using loglinear models.

Last updated 3 years ago

2.43 score 1 stars 1 dependents 102 scripts 859 downloads

st - Shrinkage t Statistic and Correlation-Adjusted t-Score

Implements the "shrinkage t" statistic introduced in Opgen-Rhein and Strimmer (2007) <DOI:10.2202/1544-6115.1252> and a shrinkage estimate of the "correlation-adjusted t-score" (CAT score) described in Zuber and Strimmer (2009) <DOI:10.1093/bioinformatics/btp460>. It also offers a convenient interface to a number of other regularized t-statistics commonly employed in high-dimensional case-control studies.

Last updated 3 years ago

2.43 score 1 dependents 69 scripts 920 downloads

PROSPER - Simulation of Weed Population Dynamics

An environment to simulate the development of annual plant populations with regard to population dynamics and genetics, especially herbicide resistance. It combines genetics on the individual level (Renton et al. 2011) with a stochastic development on the population level (Daedlow, 2015). Renton, M, Diggle, A, Manalil, S and Powles, S (2011) <doi:10.1016/j.jtbi.2011.05.010> Daedlow, Daniel (2015, doctoral dissertation: University of Rostock, Faculty of Agriculture and Environmental Sciences.)

Last updated 4 years ago

2.43 score 27 scripts 187 downloads

senstrat - Sensitivity Analysis for Stratified Observational Studies

Sensitivity analysis in unmatched observational studies, with or without strata. The main functions are sen2sample() and senstrat(). See Rosenbaum, P. R. and Krieger, A. M. (1990), JASA, 85, 493-498, <doi:10.1080/01621459.1990.10476226> and Gastwirth, Krieger and Rosenbaum (2000), JRSS-B, 62, 545–555 <doi:10.1111/1467-9868.00249> .

Last updated 7 years ago

2.43 score 3 dependents 30 scripts 224 downloads

ART - Aligned Rank Transform for Nonparametric Factorial Analysis

An implementation of the Aligned Rank Transform technique for factorial analysis (see references below for details) including models with missing terms (unsaturated factorial models). The function first computes a separate aligned ranked response variable for each effect of the user-specified model, and then runs a classic ANOVA on each of the aligned ranked responses. For further details, see Higgins, J. J. and Tashtoush, S. (1994). An aligned rank transform test for interaction. Nonlinear World 1 (2), pp. 201-211. Wobbrock, J.O., Findlater, L., Gergle, D. and Higgins,J.J. (2011). The Aligned Rank Transform for nonparametric factorial analyses using only ANOVA procedures. Proceedings of the ACM Conference on Human Factors in Computing Systems (CHI '11). New York: ACM Press, pp. 143-146. <doi:10.1145/1978942.1978963>.

Last updated 9 years ago

2.43 score 27 scripts 251 downloads

REEMtree - Regression Trees with Random Effects for Longitudinal (Panel) Data

A data mining approach for longitudinal and clustered data, which combines the structure of mixed effects model with tree-based estimation methods. See Sela, R.J. and Simonoff, J.S. (2012) RE-EM trees: a data mining approach for longitudinal and clustered data <doi:10.1007/s10994-011-5258-3>.

Last updated 1 years ago

2.43 score 2 stars 67 scripts 226 downloads

OasisR - Outright Tool for the Analysis of Spatial Inequalities and Segregation

A comprehensive set of indexes and tests for social segregation analysis, as described in Tivadar (2019) - 'OasisR': An R Package to Bring Some Order to the World of Segregation Measurement <doi:10.18637/jss.v089.i07>. The package is the most complete existing tool and it clarifies many ambiguities and errors regarding the definition of segregation indices. Additionally, 'OasisR' introduces several resampling methods that enable testing their statistical significance (randomization tests, bootstrapping, and jackknife methods).

Last updated 2 months ago

2.43 score 1 stars 1 dependents 89 scripts 468 downloads

FMStable - Finite Moment Stable Distributions

Some basic procedures for dealing with log maximally skew stable distributions, which are also called finite moment log stable distributions.

Last updated 3 years ago

2.42 score 8 dependents 9 scripts 1.1k downloads

nopaco - Non-Parametric Concordance Coefficient

A non-parametric test for multi-observer concordance and differences between concordances in (un)balanced data.

Last updated 2 months ago

cpp

2.41 score 13 scripts 206 downloads

WayFindR - Computing Graph Structures on WikiPathways

Converts pathways from 'WikiPathways' GPML format into 'igraph' objects. Includes tools to find all cycles in the resulting graphs and determine which ones involve negative feedback (inhibition).

Last updated 9 months ago

2.41 score 13 scripts 519 downloads

purgeR - Inbreeding-Purging Estimation in Pedigreed Populations

Inbreeding-purging analysis of pedigreed populations, including the computation of the inbreeding coefficient, partial, ancestral and purged inbreeding coefficients, and measures of the opportunity of purging related to the individual reduction of inbreeding load. In addition, functions to calculate the effective population size and other parameters relevant to population genetics are included. See López-Cortegano E. (2021) <doi:10.1093/bioinformatics/btab599>.

Last updated 1 years ago

cpp

2.41 score 13 scripts 244 downloads

SpTe2M - Nonparametric Modeling and Monitoring of Spatio-Temporal Data

Spatio-temporal data have become increasingly popular in many research fields. Such data often have complex structures that are difficult to describe and estimate. This package provides reliable tools for modeling complicated spatio-temporal data. It also includes tools of online process monitoring to detect possible change-points in a spatio-temporal process over time. More specifically, the package implements the spatio-temporal mean estimation procedure described in Yang and Qiu (2018) <doi:10.1002/sim.7622>, the spatio-temporal covariance estimation procedure discussed in Yang and Qiu (2019) <doi:10.1002/sim.8315>, the three-step method for the joint estimation of spatio-temporal mean and covariance functions suggested by Yang and Qiu (2022) <doi:10.1007/s10463-021-00787-2>, the spatio-temporal disease surveillance method discussed in Qiu and Yang (2021) <doi:10.1002/sim.9150> that can accommodate the covariate effect, the spatial-LASSO-based process monitoring method proposed by Qiu and Yang (2023) <doi:10.1080/00224065.2022.2081104>, and the online spatio-temporal disease surveillance method described in Yang and Qiu (2020) <doi:10.1080/24725854.2019.1696496>.

Last updated 1 years ago

fortran

2.41 score 26 scripts 148 downloads

pdR - Threshold Model and Unit Root Tests in Cross-Section and Time Series Data

Threshold model, panel version of Hylleberg et al. (1990) <DOI:10.1016/0304-4076(90)90080-D> seasonal unit root tests, and panel unit root test of Chang (2002) <DOI:10.1016/S0304-4076(02)00095-7>.

Last updated 4 months ago

2.41 score 4 stars 32 scripts 523 downloads

ttutils - Utility Functions

Contains some auxiliary functions.

Last updated 3 years ago

2.41 score 5 dependents 17 scripts 589 downloads

rpms - Recursive Partitioning for Modeling Survey Data

Functions to allow users to build and analyze design consistent tree and random forest models using survey data from a complex sample design. The tree model algorithm can fit a linear model to survey data in each node obtained by recursively partitioning the data. The splitting variables and selected splits are obtained using a randomized permutation test procedure which adjusted for complex sample design features used to obtain the data. Likewise the model fitting algorithm produces design-consistent coefficients to any specified least squares linear model between the dependent and independent variables used in the end nodes. The main functions return the resulting binary tree or random forest as an object of "rpms" or "rpms_forest" type. The package also provides methods modeling a "boosted" tree or forest model and a tree model for zero-inflated data as well as a number of functions and methods available for use with these object types.

Last updated 4 years ago

openblascpp

2.40 score 3 dependents 28 scripts 434 downloads

scitb - Provides Some Useful Functions for Making Statistical Tables

You can use the functions provided by the package to make various statistical tables, such as baseline data tables. Creates 'Table 1', i.e., a description of the baseline patient characteristics, which is essential in every medical research. Supports both continuous and categorical variables, as well as p-values and standardized mean differences. This method was described by Mary L McHugh (2013) <doi:10.11613/bm.2013.018>.

Last updated 3 months ago

2.40 score 1 stars 9 scripts 387 downloads

npbr - Nonparametric Boundary Regression

A variety of functions for the best known and most innovative approaches to nonparametric boundary estimation. The selected methods are concerned with empirical, smoothed, unrestricted as well as constrained fits under both separate and multiple shape constraints. They cover robust approaches to outliers as well as data envelopment techniques based on piecewise polynomials, splines, local linear fitting, extreme values and kernel smoothing. The package also seamlessly allows for Monte Carlo comparisons among these different estimation methods. Its use is illustrated via a number of empirical applications and simulated examples.

Last updated 2 years ago

2.40 score 1 stars 25 scripts 251 downloads

BHSBVAR - Structural Bayesian Vector Autoregression Models

Provides a function for estimating the parameters of Structural Bayesian Vector Autoregression models with the method developed by Baumeister and Hamilton (2015) <doi:10.3982/ECTA12356>, Baumeister and Hamilton (2017) <doi:10.3386/w24167>, and Baumeister and Hamilton (2018) <doi:10.1016/j.jmoneco.2018.06.005>. Functions for plotting impulse responses, historical decompositions, and posterior distributions of model parameters are also provided.

Last updated 2 years ago

openblascppopenmp

2.40 score 25 scripts 391 downloads

MASSTIMATE - Body Mass Estimation Equations for Vertebrates

Estimation equations are from a variety of sources and associated error estimation.

Last updated 4 years ago

2.40 score 7 scripts 230 downloads

ega - Error Grid Analysis

Functions for assigning Clarke or Parkes (Consensus) error grid zones to blood glucose values, and for plotting both types of error grids in both mg/mL and mmol/L units.

Last updated 8 years ago

2.40 score 25 scripts 511 downloads

equivalence - Provides Tests and Graphics for Assessing Tests of Equivalence

Provides statistical tests and graphics for assessing tests of equivalence. Such tests have similarity as the alternative hypothesis instead of the null. Sample data sets are included.

Last updated 9 years ago

2.39 score 4 stars 49 scripts 1.3k downloads

OPTS - Optimization via Subsampling (OPTS)

Subsampling based variable selection for low dimensional generalized linear models. The methods repeatedly subsample the data minimizing an information criterion (AIC/BIC) over a sequence of nested models for each subsample. Marinela Capanu, Mihai Giurcanu, Colin B Begg, Mithat Gonen, Subsampling based variable selection for generalized linear models.

Last updated 3 years ago

2.39 score 244 scripts 114 downloads

lm.br - Linear Model with Breakpoint

Exact significance tests for a changepoint in linear or multiple linear regression. Confidence regions with exact coverage probabilities for the changepoint. Based on Knowles, Siegmund and Zhang (1991) <doi:10.1093/biomet/78.1.15>.

Last updated 3 months ago

openblascpp

2.38 score 12 scripts 335 downloads

qtlnet - Causal Inference of QTL Networks

Functions to Simultaneously Infer Causal Graphs and Genetic Architecture. Includes acyclic and cyclic graphs for data from an experimental cross with a modest number (<10) of phenotypes driven by a few genetic loci (QTL). Chaibub Neto E, Keller MP, Attie AD, Yandell BS (2010) Causal Graphical Models in Systems Genetics: a unified framework for joint inference of causal network and genetic architecture for correlated phenotypes. Annals of Applied Statistics 4: 320-339. <doi:10.1214/09-AOAS288>.

Last updated 5 years ago

2.38 score 12 scripts 204 downloads

YatchewTest - Yatchew (1997), De Chaisemartin & D'Haultfoeuille (2024) Linearity Test

Test of linearity originally proposed by Yatchew (1997) <doi:10.1016/S0165-1765(97)00218-8> and improved by de Chaisemartin & D'Haultfoeuille (2024) <doi:10.2139/ssrn.4284811> to be robust under heteroskedasticity.

Last updated 5 months ago

cpp

2.38 score 2 dependents 370 downloads

zoib - Bayesian Inference for Beta Regression and Zero-or-One Inflated Beta Regression

Fits beta regression and zero-or-one inflated beta regression and obtains Bayesian Inference of the model via the Markov Chain Monte Carlo approach implemented in JAGS.

Last updated 2 years ago

jagscpp

2.38 score 3 stars 40 scripts 370 downloads

rateratio.test - Exact Rate Ratio Test

Performs exact rate ratio tests.

Last updated 3 years ago

2.38 score 24 scripts 288 downloads

AF - Model-Based Estimation of Confounder-Adjusted Attributable Fractions

Estimates the attributable fraction in different sampling designs adjusted for measured confounders using logistic regression (cross-sectional and case-control designs), conditional logistic regression (matched case-control design), Cox proportional hazard regression (cohort design with time-to- event outcome), gamma-frailty model with a Weibull baseline hazard and instrumental variables analysis. An exploration of the AF with a genetic exposure can be found in the package 'AFheritability' Dahlqwist E et al. (2019) <doi:10.1007/s00439-019-02006-8>.

Last updated 6 years ago

2.38 score 24 scripts 467 downloads

FuzzyNumbers.Ext.2 - Apply Two Fuzzy Numbers on a Monotone Function

One can easily draw the membership function of f(x,y) by package 'FuzzyNumbers.Ext.2' in which f(.,.) is supposed monotone and x and y are two fuzzy numbers. This work is possible using function f2apply() which is an extension of function fapply() from Package 'FuzzyNumbers' for two-variable monotone functions. Moreover, this package has the ability of computing the core, support and alpha-cuts of the fuzzy-valued final result.

Last updated 7 years ago

2.38 score 8 dependents 10 scripts 425 downloads

iRafNet - Integrative Random Forest for Gene Regulatory Network Inference

Provides a flexible integrative algorithm that allows information from prior data, such as protein protein interactions and gene knock-down, to be jointly considered for gene regulatory network inference.

Last updated 8 years ago

2.38 score 3 stars 6 scripts 58 downloads

vita - Variable Importance Testing Approaches

Implements the novel testing approach by Janitza et al.(2015) <http://nbn-resolving.de/urn/resolver.pl?urn=nbn:de:bvb:19-epub-25587-4> for the permutation variable importance measure in a random forest and the PIMP-algorithm by Altmann et al.(2010) <doi:10.1093/bioinformatics/btq134>. Janitza et al.(2015) <http://nbn-resolving.de/urn/resolver.pl?urn=nbn:de:bvb:19-epub-25587-4> do not use the "standard" permutation variable importance but the cross-validated permutation variable importance for the novel test approach. The cross-validated permutation variable importance is not based on the out-of-bag observations but uses a similar strategy which is inspired by the cross-validation procedure. The novel test approach can be applied for classification trees as well as for regression trees. However, the use of the novel testing approach has not been tested for regression trees so far, so this routine is meant for the expert user only and its current state is rather experimental.

Last updated 9 years ago

cpp

2.37 score 2 dependents 39 scripts 122 downloads

noweb - The 'noweb' System for R

The noweb system for source code, implemented in R.

Last updated 11 months ago

2.36 score 23 scripts 262 downloads

MBHdesign - Spatial Designs for Ecological and Environmental Surveys

Provides spatially survey balanced designs using the quasi-random number method described Robinson et al. (2013) <doi:10.1111/biom.12059> and adjusted in Robinson et al. (2017) <doi:10.1016/j.spl.2017.05.004>. Designs using MBHdesign can: 1) accommodate, without substantial detrimental effects on spatial balance, legacy sites (Foster et al., 2017 <doi:10.1111/2041-210X.12782>); 2) be based on points or transects (foster et al. 2020 <doi:10.1111/2041-210X.13321> and produce clustered samples (Foster et al. (in press). Additional information about the package use itself is given in Foster (2021) <doi:10.1111/2041-210X.13535>.

Last updated 1 years ago

2.36 score 23 scripts 361 downloads

GNAR - Methods for Fitting Network Time Series Models

Simulation of, and fitting models for, Generalised Network Autoregressive (GNAR) time series models which take account of network structure, potentially with exogenous variables. Such models are described in Knight et al. (2020) <doi:10.18637/jss.v096.i05> and Nason and Wei (2021) <doi:10.1111/rssa.12875>. Diagnostic tools for GNAR(X) models can be found in Nason et al. (2023) <doi:10.48550/arXiv.2312.00530>.

Last updated 3 months ago

2.36 score 2 stars 57 scripts 352 downloads

pgnorm - The p-Generalized Normal Distribution

Evaluation of the pdf and the cdf of the univariate, noncentral, p-generalized normal distribution. Sampling from the univariate, noncentral, p-generalized normal distribution using either the p-generalized polar method, the p-generalized rejecting polar method, the Monty Python method, the Ziggurat method or the method of Nardon and Pianca. The package also includes routines for the simulation of the bivariate, p-generalized uniform distribution and the simulation of the corresponding angular distribution.

Last updated 9 years ago

2.36 score 4 dependents 19 scripts 324 downloads

InvariantCausalPrediction - Invariant Causal Prediction

Confidence intervals for causal effects, using data collected in different experimental or environmental conditions. Hidden variables can be included in the model with a more experimental version.

Last updated 5 years ago

2.35 score 3 stars 1 dependents 25 scripts 340 downloads

survPresmooth - Presmoothed Estimation in Survival Analysis

Presmoothed estimators of survival, density, cumulative and non-cumulative hazard functions with right-censored survival data. For details, see Lopez-de-Ullibarri and Jacome (2013) <doi:10.18637/jss.v054.i11>.

Last updated 3 years ago

2.35 score 6 dependents 4 scripts 1.2k downloads

clusterSEs - Calculate Cluster-Robust p-Values and Confidence Intervals

Calculate p-values and confidence intervals using cluster-adjusted t-statistics (based on Ibragimov and Muller (2010) <DOI:10.1198/jbes.2009.08046>, pairs cluster bootstrapped t-statistics, and wild cluster bootstrapped t-statistics (the latter two techniques based on Cameron, Gelbach, and Miller (2008) <DOI:10.1162/rest.90.3.414>. Procedures are included for use with GLM, ivreg, plm (pooling or fixed effects), and mlogit models.

Last updated 4 years ago

2.35 score 2 stars 1 dependents 37 scripts 579 downloads

nprobust - Nonparametric Robust Estimation and Inference Methods using Local Polynomial Regression and Kernel Density Estimation

Tools for data-driven statistical analysis using local polynomial regression and kernel density estimation methods as described in Calonico, Cattaneo and Farrell (2018, <doi:10.1080/01621459.2017.1285776>): lprobust() for local polynomial point estimation and robust bias-corrected inference, lpbwselect() for local polynomial bandwidth selection, kdrobust() for kernel density point estimation and robust bias-corrected inference, kdbwselect() for kernel density bandwidth selection, and nprobust.plot() for plotting results. The main methodological and numerical features of this package are described in Calonico, Cattaneo and Farrell (2019, <doi:10.18637/jss.v091.i08>).

Last updated 4 years ago

openblascppopenmp

2.35 score 1 stars 2 dependents 37 scripts 397 downloads

MAMS - Designing Multi-Arm Multi-Stage Studies

Designing multi-arm multi-stage studies with (asymptotically) normal endpoints and known variance.

Last updated 3 months ago

2.34 score 11 scripts 442 downloads

IDF - Estimation and Plotting of IDF Curves

Intensity-duration-frequency (IDF) curves are a widely used analysis-tool in hydrology to assess extreme values of precipitation [e.g. Mailhot et al., 2007, <doi:10.1016/j.jhydrol.2007.09.019>]. The package 'IDF' provides functions to estimate IDF parameters for given precipitation time series on the basis of a duration-dependent generalized extreme value distribution [Koutsoyiannis et al., 1998, <doi:10.1016/S0022-1694(98)00097-3>].

Last updated 2 years ago

2.34 score 11 scripts 195 downloads

siland - Spatial Influence of Landscape

Method to estimate the spatial influence scales of landscape variables on a response variable. The method is based on Chandler and Hepinstall-Cymerman (2016) Estimating the spatial scales of landscape effects on abundance, Landscape ecology, 31: 1383-1394, <doi:10.1007/s10980-016-0380-z>.

Last updated 2 years ago

2.34 score 22 scripts 204 downloads

cubing - Rubik's Cube Solving

Functions for visualizing, animating, solving and analyzing the Rubik's cube. Includes data structures for solvable and unsolvable cubes, random moves and random state scrambles and cubes, 3D displays and animations using 'OpenGL', patterned cube generation, and lightweight solvers. See Rokicki, T. (2008) <arXiv:0803.3435> for the Kociemba solver.

Last updated 7 years ago

2.34 score 1 stars 22 scripts 211 downloads

CEoptim - Cross-Entropy R Package for Optimization

Optimization solver based on the Cross-Entropy method.

Last updated 1 years ago

2.33 score 2 stars 1 dependents 12 scripts 242 downloads

rasterImage - An Improved Wrapper of image()

This is a wrapper function for image(), which makes reasonable raster plots with nice axis and other useful features.

Last updated 5 years ago

2.33 score 4 dependents 18 scripts 406 downloads

deltaPlotR - Identification of Dichotomous Differential Item Functioning (DIF) using Angoff's Delta Plot Method

The deltaPlotR package implements Angoff's Delta Plot method to detect dichotomous DIF. Several detection thresholds are included, either from multivariate normality assumption or by prior determination. Item purification is supported (Magis and Facon (2014) <doi:10.18637/jss.v059.c01>).

Last updated 7 years ago

2.33 score 6 dependents 12 scripts 958 downloads

notebookutils - Dummy R APIs Used in 'Azure Synapse Analytics' for Local Developments

This is a pure dummy interfaces package which mirrors 'MsSparkUtils' APIs <https://learn.microsoft.com/en-us/azure/synapse-analytics/spark/microsoft-spark-utilities?pivots=programming-language-r> of 'Azure Synapse Analytics' <https://learn.microsoft.com/en-us/azure/synapse-analytics/> for R users, customer of Azure Synapse can download this package from CRAN for local development.

Last updated 9 months ago

2.32 score 21 scripts 191 downloads

GSM - Gamma Shape Mixture

Implementation of a Bayesian approach for estimating a mixture of gamma distributions in which the mixing occurs over the shape parameter. This family provides a flexible and novel approach for modeling heavy-tailed distributions, it is computationally efficient, and it only requires to specify a prior distribution for a single parameter.

Last updated 9 years ago

2.32 score 21 scripts 215 downloads

INFOSET - Computing a New Informative Distribution Set of Asset Returns

Estimation of the most-left informative set of gross returns (i.e., the informative set). The procedure to compute the informative set adjusts the method proposed by Mariani et al. (2022a) <doi:10.1007/s11205-020-02440-6> and Mariani et al. (2022b) <doi:10.1007/s10287-022-00422-2> to gross returns of financial assets. This is accomplished through an adaptive algorithm that identifies sub-groups of gross returns in each iteration by approximating their distribution with a sequence of two-component log-normal mixtures. These sub-groups emerge when a significant change in the distribution occurs below the median of the financial returns, with their boundary termed as the “change point" of the mixture. The process concludes when no further change points are detected. The outcome encompasses parameters of the leftmost mixture distributions and change points of the analyzed financial time series. The functionalities of the INFOSET package include: (i) modelling asset distribution detecting the parameters which describe left tail behaviour (infoset function), (ii) clustering, (iii) labeling of the financial series for predictive and classification purposes through a Left Risk measure based on the first change point (LR_cp function) (iv) portfolio construction (ptf_construction function). The package also provide a specific function to construct rolling windows of different length size and overlapping time.

Last updated 1 months ago

2.30 score 3 scripts 236 downloads

CDsampling - 'CDsampling': Constraint Sampling in Paid Research Studies

In the context of paid research studies and clinical trials, budget considerations and patient sampling from available populations are subject to inherent constraints. We introduce the 'CDsampling' package, which integrates optimal design theories within the framework of constrained sampling. This package offers the possibility to find both D-optimal approximate and exact allocations for samplings with or without constraints. Additionally, it provides functions to find constrained uniform sampling as a robust sampling strategy with limited model information. Our package offers functions for the computation of the Fisher information matrix under generalized linear models (including regular linear regression model) and multinomial logistic models.To demonstrate the applications, we also provide a simulated dataset and a real dataset embedded in the package. Yifei Huang, Liping Tong, and Jie Yang (2025)<doi:10.5705/ss.202022.0414>.

Last updated 1 months ago

2.30 score 2 scripts 191 downloads

lpcde - Boundary Adaptive Local Polynomial Conditional Density Estimator

Tools for estimation and inference of conditional densities, derivatives and functions. This is the companion software for Cattaneo, Chandak, Jansson and Ma (2024) <doi:10.3150/23-BEJ1711>.

Last updated 1 months ago

cpp

2.30 score 2 scripts 395 downloads

dawai - Discriminant Analysis with Additional Information

In applications it is usual that some additional information is available. This package dawai (an acronym for Discriminant Analysis With Additional Information) performs linear and quadratic discriminant analysis with additional information expressed as inequality restrictions among the populations means. It also computes several estimations of the true error rate.

Last updated 2 months ago

2.30 score 10 scripts 286 downloads

RALSA - R Analyzer for Large-Scale Assessments

Prepare and analyze data from large-scale assessments and surveys with complex sampling and assessment design (see 'Rutkowski', 2010 <doi:10.3102/0013189X10363170>). Such studies are, for example, international assessments like 'TIMSS', 'PIRLS' and 'PISA'. A graphical interface is available for the non-technical user.The package includes functions to covert the original data from 'SPSS' into 'R' data sets keeping the user-defined missing values, merge data from different respondents and/or countries, generate variable dictionaries, modify data, produce descriptive statistics (percentages, means, percentiles, benchmarks) and multivariate statistics (correlations, linear regression, binary logistic regression). The number of supported studies and analysis types will increase in future. For a general presentation of the package, see 'Mirazchiyski', 2021a (<doi:10.1186/s40536-021-00114-4>). For detailed technical aspects of the package, see 'Mirazchiyski', 2021b (<doi:10.3390/psych3020018>).

Last updated 3 months ago

2.30 score 370 downloads

PRANA - Pseudo-Value Regression Approach for Network Analysis (PRANA)

A novel pseudo-value regression approach for the differential co-expression network analysis in expression data, which can incorporate additional clinical variables in the model. This is a direct regression modeling for the differential network analysis, and it is therefore computationally amenable for the most users. The full methodological details can be found in Ahn S et al (2023) <doi:10.1186/s12859-022-05123-w>.

Last updated 3 months ago

2.30 score 4 scripts 160 downloads

wishmom - Compute Moments Related to Beta-Wishart and Inverse Beta-Wishart Distributions

Provides functions for computing moments and coefficients related to the Beta-Wishart and Inverse Beta-Wishart distributions. It includes functions for calculating the expectation of matrix-valued functions of the Beta-Wishart distribution, coefficient matrices C_k and H_k, expectation of matrix-valued functions of the inverse Beta-Wishart distribution, and coefficient matrices \tilde{C}_k and \tilde{H}_k. For more details, refer Hillier and Kan (2024) <https://www-2.rotman.utoronto.ca/~kan/papers/wishmom.pdf>, "On the Expectations of Equivariant Matrix-valued Functions of Wishart and Inverse Wishart Matrices".

Last updated 4 months ago

2.30 score 158 downloads

mlrv - Long-Run Variance Estimation in Time Series Regression

Plug-in and difference-based long-run covariance matrix estimation for time series regression. Two applications of hypothesis testing are also provided. The first one is for testing for structural stability in coefficient functions. The second one is aimed at detecting long memory in time series regression. Lujia Bai and Weichi Wu (2024)<doi:10.3150/23-BEJ1680> Zhou Zhou and Wei Biao Wu(2010)<doi:10.1111/j.1467-9868.2010.00743.x> Jianqing Fan and Wenyang Zhang<doi:10.1214/aos/1017939139> Lujia Bai and Weichi Wu(2024)<doi:10.1093/biomet/asae013> Dimitris N. Politis, Joseph P. Romano, Michael Wolf(1999)<doi:10.1007/978-1-4612-1554-7> Weichi Wu and Zhou Zhou(2018)<doi:10.1214/17-AOS1582>.

Last updated 5 months ago

openblascppopenmp

2.30 score 4 scripts 175 downloads

callback - Computes Statistics from Discrimination Experimental Data

In discrimination experiments candidates are sent on the same test (e.g. job, house rental) and one examines whether they receive the same outcome. The number of non negative answers are first examined in details looking for outcome differences. Then various answering rates and their exacts confidence intervals are computed. Last, exact and asymptotic discrimination tests are performed. Graphical methods are also available.

Last updated 5 months ago

2.30 score 118 scripts 184 downloads

LatentBMA - Bayesian Model Averaging for Univariate Link Latent Gaussian Models

Bayesian model averaging (BMA) algorithms for univariate link latent Gaussian models (ULLGMs). For detailed information, refer to Steel M.F.J. & Zens G. (2024) "Model Uncertainty in Latent Gaussian Models with Univariate Link Function" <doi:10.48550/arXiv.2406.17318>. The package supports various g-priors and a beta-binomial prior on the model space. It also includes auxiliary functions for visualizing and tabulating BMA results. Currently, it offers an out-of-the-box solution for model averaging of Poisson log-normal (PLN) and binomial logistic-normal (BiL) models. The codebase is designed to be easily extendable to other likelihoods, priors, and link functions.

Last updated 6 months ago

2.30 score 1 scripts 190 downloads

evreg - Evidential Regression

An implementation of the 'Evidential Neural Network for Regression' model recently introduced in Denoeux (2023) <doi:10.1109/TFUZZ.2023.3268200>. In this model, prediction uncertainty is quantified by Gaussian random fuzzy numbers as introduced in Denoeux (2023) <doi:10.1016/j.fss.2022.06.004>. The package contains functions for training the network, tuning hyperparameters by cross-validation or the hold-out method, and making predictions. It also contains utilities for making calculations with Gaussian random fuzzy numbers (such as, e.g., computing the degrees of belief and plausibility of an interval, or combining Gaussian random fuzzy numbers).

Last updated 8 months ago

2.30 score 2 scripts 289 downloads

BiSEp - Toolkit to Identify Candidate Synthetic Lethality

Enables the user to infer potential synthetic lethal relationships by analysing relationships between bimodally distributed gene pairs in big gene expression datasets. Enables the user to visualise these candidate synthetic lethal relationships.

Last updated 8 months ago

2.30 score 280 downloads

prWarp - Warping Landmark Configurations

Compute bending energies, principal warps, partial warp scores, and the non-affine component of shape variation for 2D landmark configurations, as well as Mardia-Dryden distributions and self-similar distributions of landmarks, as described in Mitteroecker et al. (2020) <doi:10.1093/sysbio/syaa007>. Working examples to decompose shape variation into small-scale and large-scale components, and to decompose the total shape variation into outline and residual shape components are provided. Two landmark datasets are provided, that quantify skull morphology in humans and papionin primates, respectively from Mitteroecker et al. (2020) <doi:10.5061/dryad.j6q573n8s> and Grunstra et al. (2020) <doi:10.5061/dryad.zkh189373>.

Last updated 9 months ago

2.30 score 98 downloads

ssd4mosaic - Web Application for the SSD Module of the MOSAIC Platform

Web application using 'shiny' for the SSD (Species Sensitivity Distribution) module of the MOSAIC (MOdeling and StAtistical tools for ecotoxICology) platform. It estimates the Hazardous Concentration for x% of the species (HCx) from toxicity values that can be censored and provides various plotting options for a better understanding of the results. See our companion paper Kon Kam King et al. (2014) <doi:10.48550/arXiv.1311.5772>.

Last updated 9 months ago

2.30 score 99 downloads

GenTwoArmsTrialSize - Generalized Two Arms Clinical Trial Sample Size Calculation

Two arms clinical trials required sample size is calculated in the comprehensive parametric context. The calculation is based on the type of endpoints(continuous/binary/time-to-event/ordinal), design (parallel/crossover), hypothesis tests (equality/noninferiority/superiority/equivalence), trial arms noncompliance rates and expected loss of follow-up. Methods are described in: Chow SC, Shao J, Wang H, Lokhnygina Y (2017) <doi:10.1201/9781315183084>, Wittes, J (2002) <doi:10.1093/epirev/24.1.39>, Sato, T (2000) <doi:10.1002/1097-0258(20001015)19:19%3C2689::aid-sim555%3E3.0.co;2-0>, Lachin J M, Foulkes, M A (1986) <doi:10.2307/2531201>, Whitehead J(1993) <doi:10.1002/sim.4780122404>, Julious SA (2023) <doi:10.1201/9780429503658>.

Last updated 9 months ago

2.30 score 2 scripts 178 downloads

RESET - Reconstruction Set Test

Contains logic for sample-level variable set scoring using randomized reduced rank reconstruction error. Frost, H. Robert (2023) "Reconstruction Set Test (RESET): a computationally efficient method for single sample gene set testing based on randomized reduced rank reconstruction error" <doi:10.1101/2023.04.03.535366>.

Last updated 10 months ago

2.30 score 6 scripts 245 downloads

gcxgclab - GCxGC Preprocessing and Analysis

Provides complete detailed preprocessing of two-dimensional gas chromatogram (GCxGC) samples. Baseline correction, smoothing, peak detection, and peak alignment. Also provided are some analysis functions, such as finding extracted ion chromatograms, finding mass spectral data, targeted analysis, and nontargeted analysis with either the 'National Institute of Standards and Technology Mass Spectral Library' or with the mass data. There are also several visualization methods provided for each step of the preprocessing and analysis.

Last updated 11 months ago

2.30 score 1 scripts 111 downloads

wwntests - Hypothesis Tests for Functional Time Series

Provides a collection of white noise hypothesis tests for functional time series and related visualizations. These include tests based on the norms of autocovariance operators that are built under both strong and weak white noise assumptions. Additionally, tests based on the spectral density operator and on principal component dimensional reduction are included, which are built under strong white noise assumptions. Also, this package provides goodness-of-fit tests for functional autoregressive of order 1 models. These methods are described in Kokoszka et al. (2017) <doi:10.1016/j.jmva.2017.08.004>, Characiejus and Rice (2019) <doi:10.1016/j.ecosta.2019.01.003>, Gabrys and Kokoszka (2007) <doi:10.1198/016214507000001111>, and Kim et al. (2023) <doi: 10.1214/23-SS143> respectively.

Last updated 1 years ago

2.30 score 2 stars 3 scripts 160 downloads

scaper - Single Cell Transcriptomics-Level Cytokine Activity Prediction and Estimation

Generates cell-level cytokine activity estimates using relevant information from gene sets constructed with the 'CytoSig' and the 'Reactome' databases and scored using the modified 'Variance-adjusted Mahalanobis (VAM)' framework for single-cell RNA-sequencing (scRNA-seq) data. 'CytoSig' database is described in: Jiang at al., (2021) <doi:10.1038/s41592-021-01274-5>. 'Reactome' database is described in: Gillespie et al., (2021) <doi:10.1093/nar/gkab1028>. The 'VAM' method is outlined in: Frost (2020) <doi:10.1093/nar/gkaa582>.

Last updated 1 years ago

2.30 score 4 scripts 139 downloads

mvngGrAd - Moving Grid Adjustment in Plant Breeding Field Trials

Package for moving grid adjustment in plant breeding field trials.

Last updated 1 years ago

2.30 score 10 scripts 263 downloads

hbim - Hill/Bliss Independence Model for Combination Vaccines

Calculate expected relative risk and proportion protected assuming normally distributed log10 transformed antibody dose for a several component vaccine. Uses Hill models for each component which are combined under Bliss independence. See Saul and Fay, 2007 <DOI:10.1371/journal.pone.0000850>.

Last updated 1 years ago

2.30 score 9 scripts 274 downloads

bujar - Buckley-James Regression for Survival Data with High-Dimensional Covariates

Buckley-James regression for right-censoring survival data with high-dimensional covariates. Implementations for survival data include boosting with componentwise linear least squares, componentwise smoothing splines, regression trees and MARS. Other high-dimensional tools include penalized regression for survival data. See Wang and Wang (2010) <doi:10.2202/1544-6115.1550>.

Last updated 2 years ago

2.30 score 5 scripts 375 downloads

DCEtool - Efficient and Accessible Discrete Choice Experiments

Design, conduct and analyze 'DCEs' from a virtual interface in shiny. Reference: Perez-Troncoso, D. (2022) <https://github.com/danielpereztr/DCEtool>.

Last updated 2 years ago

2.30 score 2 stars 3 scripts 376 downloads

sparseDFM - Estimate Dynamic Factor Models with Sparse Loadings

Implementation of various estimation methods for dynamic factor models (DFMs) including principal components analysis (PCA) Stock and Watson (2002) <doi:10.1198/016214502388618960>, 2Stage Giannone et al. (2008) <doi:10.1016/j.jmoneco.2008.05.010>, expectation-maximisation (EM) Banbura and Modugno (2014) <doi:10.1002/jae.2306>, and the novel EM-sparse approach for sparse DFMs Mosley et al. (2023) <arXiv:2303.11892>. Options to use classic multivariate Kalman filter and smoother (KFS) equations from Shumway and Stoffer (1982) <doi:10.1111/j.1467-9892.1982.tb00349.x> or fast univariate KFS equations from Koopman and Durbin (2000) <doi:10.1111/1467-9892.00186>, and options for independent and identically distributed (IID) white noise or auto-regressive (AR(1)) idiosyncratic errors. Algorithms coded in 'C++' and linked to R via 'RcppArmadillo'.

Last updated 2 years ago

openblascppopenmp

2.30 score 1 stars 7 scripts 250 downloads

aweSOM - Interactive Self-Organizing Maps

Self-organizing maps (also known as SOM, see Kohonen (2001) <doi:10.1007/978-3-642-56927-2>) are a method for dimensionality reduction and clustering of continuous data. This package introduces interactive (html) graphics for easier analysis of SOM results. It also features an interactive interface, for push-button training and visualization of SOM on numeric, categorical or mixed data, as well as tools to evaluate the quality of SOM.

Last updated 2 years ago

2.30 score 2 stars 45 scripts 413 downloads

circularEV - Extreme Value Analysis for Circular Data

General functions for performing extreme value analysis on a circular domain as part of the statistical methodology in the paper by Konzen, E., Neves, C., and Jonathan, P. (2021). Modeling nonstationary extremes of storm severity: Comparing parametric and semiparametric inference. Environmetrics, 32(4), e2667.

Last updated 3 years ago

2.30 score 8 scripts 196 downloads

BayesRGMM - Bayesian Robust Generalized Mixed Models for Longitudinal Data

To perform model estimation using MCMC algorithms with Bayesian methods for incomplete longitudinal studies on binary and ordinal outcomes that are measured repeatedly on subjects over time with drop-outs. Details about the method can be found in the vignette or <https://sites.google.com/view/kuojunglee/r-packages/bayesrgmm>.

Last updated 3 years ago

openblascppopenmp

2.30 score 20 scripts 227 downloads

integIRTy - Integrating Multiple Modalities of High Throughput Assays Using Item Response Theory

Provides a systematic framework for integrating multiple modalities of assays profiled on the same set of samples. The goal is to identify genes that are altered in cancer either marginally or consistently across different assays. The heterogeneity among different platforms and different samples are automatically adjusted so that the overall alteration magnitude can be accurately inferred. See Tong and Coombes (2012) <doi:10.1093/bioinformatics/bts561>.

Last updated 3 years ago

2.30 score 20 scripts 154 downloads

audiometry - Standard Conform Pure Tone Audiometry (PTA) Plots

Facilitates plotting audiometric data (mostly) by preparing the coordinate system according to standards, given e. g. in American Speech-Language-Hearing Association (2005), <doi:10.1044/policy.GL2005-00014>.

Last updated 4 years ago

2.30 score 4 scripts 233 downloads

rADA - Statistical Analysis and Cut-Point Determination of Immunoassays

Systematically transform immunoassay data, evaluate if the data is normally distributed, and pick the right method for cut point determination based on that evaluation. This package can also produce plots that are needed for reports, so data analysis and visualization can be done easily.

Last updated 4 years ago

2.30 score 1 stars 3 scripts 129 downloads

scSorter - Implementation of 'scSorter' Algorithm

Implements the algorithm described in Guo, H., and Li, J., "scSorter: assigning cells to known cell types according to known marker genes". Cluster cells to known cell types based on marker genes specified for each cell type.

Last updated 4 years ago

2.30 score 46 scripts 145 downloads

vimpclust - Variable Importance in Clustering

An implementation of methods related to sparse clustering and variable importance in clustering. The package currently allows to perform sparse k-means clustering with a group penalty, so that it automatically selects groups of numerical features. It also allows to perform sparse clustering and variable selection on mixed data (categorical and numerical features), by preprocessing each categorical feature as a group of numerical features. Several methods for visualizing and exploring the results are also provided. M. Chavent, J. Lacaille, A. Mourer and M. Olteanu (2020)<https://www.esann.org/sites/default/files/proceedings/2020/ES2020-103.pdf>.

Last updated 4 years ago

2.30 score 4 scripts 153 downloads

varitas - Variant Calling in Targeted Analysis Sequencing Data

Multi-caller variant analysis pipeline for targeted analysis sequencing (TAS) data. Features a modular, automated workflow that can start with raw reads and produces a user-friendly PDF summary and a spreadsheet containing consensus variant information.

Last updated 4 years ago

2.30 score 7 scripts 135 downloads

BENMMI - Benthic Multi-Metric Index

Analysis tool for evaluating benthic multimetric indices (BENMMIs). It generates reproducible reports on the analysis of benthic data, e.g., validation and correction of species names, sample pooling, automatic conversion of genus to species names, outlier detection, benthic indicator calculation, optimization of single and multimetric indicators against a pressure gradient, and spatial aggregation of benthic indicators. One of its use cases was the development of a common benthic indicator for <https://www.ospar.org> (publication accepted by Ecological Indicators). See Van Loon et al. (2018) <doi:10.1016/j.ecolind.2017.09.029> for details.

Last updated 4 years ago

2.30 score 4 scripts 70 downloads

base.rms - Convert Regression Between Base Function and 'rms' Package

We perform linear, logistic, and cox regression using the base functions lm(), glm(), and coxph() in the R software and the 'survival' package. Likewise, we can use ols(), lrm() and cph() from the 'rms' package for the same functionality. Each of these two sets of commands has a different focus. In many cases, we need to use both sets of commands in the same situation, e.g. we need to filter the full subset model using AIC, and we need to build a visualization graph for the final model. 'base.rms' package can help you to switch between the two sets of commands easily.

Last updated 4 years ago

2.30 score 2 scripts 724 downloads

VALERIE - Visualising Splicing at Single-Cell Resolution

Alternative splicing produces a variety of different protein products from a given gene. 'VALERIE' enables visualisation of alternative splicing events from high-throughput single-cell RNA-sequencing experiments. 'VALERIE' computes percent spliced-in (PSI) values for user-specified genomic coordinates corresponding to alternative splicing events. PSI is the proportion of sequencing reads supporting the included exon/intron as defined by Shiozawa (2018) <doi:10.1038/s41467-018-06063-x>. PSI are inferred from sequencing reads data based on specialised infrastructures for representing and computing annotated genomic ranges by Lawrence (2013) <doi:10.1371/journal.pcbi.1003118>. Computed PSI for each single cell are subsequently presented in the form of a heatmap implemented using the 'pheatmap' package by Kolde (2010) <https://CRAN.R-project.org/package=pheatmap>. Board overview of the mean PSI difference and associated p-values across different user-defined groups of single cells are presented in the form of a line graph using the 'ggplot2' package by Wickham (2007) <https://CRAN.R-project.org/package=ggplot2>.

Last updated 4 years ago

2.30 score 2 scripts 151 downloads

ds - Descriptive Statistics

Performs various analyzes of descriptive statistics, including correlations, graphics and tables.

Last updated 5 years ago

2.30 score 40 scripts 206 downloads

SeqFeatR - A Tool to Associate FASTA Sequences and Features

Provides user friendly methods for the identification of sequence patterns that are statistically significantly associated with a property of the sequence. For instance, SeqFeatR allows to identify viral immune escape mutations for hosts of given HLA types. The underlying statistical method is Fisher's exact test, with appropriate corrections for multiple testing, or Bayes. Patterns may be point mutations or n-tuple of mutations. SeqFeatR offers several ways to visualize the results of the statistical analyses, see Budeus (2016) <doi:10.1371/journal.pone.0146409>.

Last updated 6 years ago

jagscpp

2.30 score 261 downloads

BICORN - Integrative Inference of De Novo Cis-Regulatory Modules

Prior transcription factor binding knowledge and target gene expression data are integrated in a Bayesian framework for functional cis-regulatory module inference. Using Gibbs sampling, we iteratively estimate transcription factor associations for each gene, regulation strength for each binding event and the hidden activity for each transcription factor.

Last updated 7 years ago

2.30 score 4 scripts 167 downloads

alleHap - Allele Imputation and Haplotype Reconstruction from Pedigree Databases

Tools to simulate alphanumeric alleles, impute genetic missing data and reconstruct non-recombinant haplotypes from pedigree databases in a deterministic way. Allelic simulations can be implemented taking into account many factors (such as number of families, markers, alleles per marker, probability and proportion of missing genotypes, recombination rate, etc). Genotype imputation can be used with simulated datasets or real databases (previously loaded in .ped format). Haplotype reconstruction can be carried out even with missing data, since the program firstly imputes each family genotype (without a reference panel), to later reconstruct the corresponding haplotypes for each family member. All this considering that each individual (due to meiosis) should unequivocally have two alleles per marker (one inherited from each parent) and thus imputation and reconstruction results can be deterministically calculated.

Last updated 7 years ago

2.30 score 9 scripts 305 downloads

EFS - Tool for Ensemble Feature Selection

Provides a function to check the importance of a feature based on a dependent classification variable. An ensemble of feature selection methods is used to determine the normalized importance value of all features. Combining these methods in one function (building the cumulative importance values) provides a stable feature selection tool. This selection can also be viewed in a barplot using the barplot_fs() function and proved using the evaluation function efs_eval().

Last updated 7 years ago

2.30 score 2 stars 7 scripts 163 downloads

kpcalg - Kernel PC Algorithm for Causal Structure Detection

Kernel PC (kPC) algorithm for causal structure learning and causal inference using graphical models. kPC is a version of PC algorithm that uses kernel based independence criteria in order to be able to deal with non-linear relationships and non-Gaussian noise.

Last updated 8 years ago

2.30 score 2 stars 36 scripts 251 downloads

vietnamcode - Convert Vietnam Provincial Codes

Converts Vietnam's provinces' names and ID across different formats. Handles diacritics and different spellings.

Last updated 8 years ago

2.30 score 40 scripts 121 downloads

decode - Differential Co-Expression and Differential Expression Analysis

Integrated differential expression (DE) and differential co-expression (DC) analysis on gene expression data based on DECODE (DifferEntial CO-expression and Differential Expression) algorithm.

Last updated 9 years ago

2.30 score 2 stars 5 scripts 160 downloads

compound.Cox - Univariate Feature Selection and Compound Covariate for Predicting Survival, Including Copula-Based Analyses for Dependent Censoring

Univariate feature selection and compound covariate methods under the Cox model with high-dimensional features (e.g., gene expressions). Available are survival data for non-small-cell lung cancer patients with gene expressions (Chen et al 2007 New Engl J Med) <DOI:10.1056/NEJMoa060096>, statistical methods in Emura et al (2012 PLoS ONE) <DOI:10.1371/journal.pone.0047627>, Emura & Chen (2016 Stat Methods Med Res) <DOI:10.1177/0962280214533378>, and Emura et al (2019)<DOI:10.1016/j.cmpb.2018.10.020>. Algorithms for generating correlated gene expressions are also available. Estimation of survival functions via copula-graphic (CG) estimators is also implemented, which is useful for sensitivity analyses under dependent censoring (Yeh et al 2023 Biomedicines) <DOI:10.3390/biomedicines11030797> and factorial survival analyses (Emura et al 2024 Stat Methods Med Res) <DOI:10.1177/09622802231215805>.

Last updated 3 months ago

2.30 score 3 dependents 22 scripts 679 downloads

ratesci - Confidence Intervals for Comparisons of Binomial or Poisson Rates

Computes confidence intervals for the rate (or risk) difference ('RD') or rate ratio (or relative risk, 'RR') for binomial proportions or Poisson rates, or for odds ratio ('OR', binomial only). Also confidence intervals for a single binomial or Poisson rate, and intervals for matched pairs. Includes skewness-corrected asymptotic score ('SCAS') methods, which have been developed in Laud (2017) <doi:10.1002/pst.1813> from Miettinen & Nurminen (1985) <doi:10.1002/sim.4780040211> and Gart & Nam (1988) <doi:10.2307/2531848>. The same score produces hypothesis tests analogous to the test for binomial RD and RR by Farrington & Manning (1990) <doi:10.1002/sim.4780091208>. The package also includes MOVER methods (Method Of Variance Estimates Recovery) for all contrasts, derived from the Newcombe method but using equal-tailed Jeffreys intervals, and generalised for Bayesian applications incorporating prior information. So-called 'exact' methods for strictly conservative coverage are approximated using continuity corrections. Also includes methods for stratified calculations (e.g. meta-analysis), either assuming fixed effects (matching the CMH test) or incorporating stratum heterogeneity.

Last updated 3 years ago

2.30 score 3 dependents 22 scripts 236 downloads

BOIN - Bayesian Optimal INterval (BOIN) Design for Single-Agent and Drug- Combination Phase I Clinical Trials

The Bayesian optimal interval (BOIN) design is a novel phase I clinical trial design for finding the maximum tolerated dose (MTD). It can be used to design both single-agent and drug-combination trials. The BOIN design is motivated by the top priority and concern of clinicians when testing a new drug, which is to effectively treat patients and minimize the chance of exposing them to subtherapeutic or overly toxic doses. The prominent advantage of the BOIN design is that it achieves simplicity and superior performance at the same time. The BOIN design is algorithm-based and can be implemented in a simple way similar to the traditional 3+3 design. The BOIN design yields an average performance that is comparable to that of the continual reassessment method (CRM, one of the best model-based designs) in terms of selecting the MTD, but has a substantially lower risk of assigning patients to subtherapeutic or overly toxic doses. For tutorial, please check Yan et al. (2020) <doi:10.18637/jss.v094.i13>.

Last updated 4 years ago

2.30 score 1 stars 2 dependents 33 scripts 549 downloads

DTWBI - Imputation of Time Series Based on Dynamic Time Warping

Functions to impute large gaps within time series based on Dynamic Time Warping methods. It contains all required functions to create large missing consecutive values within time series and to fill them, according to the paper Phan et al. (2017), <DOI:10.1016/j.patrec.2017.08.019>. Performance criteria are added to compare similarity between two signals (query and reference).

Last updated 6 years ago

2.30 score 1 dependents 66 scripts 197 downloads

poliscidata - Datasets and Functions Featured in Pollock and Edwards, an R Companion to Essentials of Political Analysis, Second Edition

Bundles the datasets and functions used in the textbook by Philip Pollock and Barry Edwards, an R Companion to Essentials of Political Analysis, Second Edition.

Last updated 4 years ago

2.29 score 195 scripts 777 downloads

rtsdata - R Time Series Intelligent Data Storage

A tool that allows to download and save historical time series data for future use offline. The intelligent updating functionality will only download the new available information; thus, saving you time and Internet bandwidth. It will only re-download the full data-set if any inconsistencies are detected. This package supports following data provides: 'Yahoo' (finance.yahoo.com), 'FRED' (fred.stlouisfed.org), 'Quandl' (data.nasdaq.com), 'AlphaVantage' (www.alphavantage.co), 'Tiingo' (www.tiingo.com).

Last updated 1 years ago

2.29 score 1 stars 39 scripts 217 downloads

pmr - Probability Models for Ranking Data

Descriptive statistics (mean rank, pairwise frequencies, and marginal matrix), Analytic Hierarchy Process models (with Saaty's and Koczkodaj's inconsistencies), probability models (Luce models, distance-based models, and rank-ordered logit models) and visualization with multidimensional preference analysis for ranking data are provided. Current, only complete rankings are supported by this package.

Last updated 3 years ago

2.28 score 1 dependents 64 scripts 736 downloads

weightr - Estimating Weight-Function Models for Publication Bias

Estimates the Vevea and Hedges (1995) weight-function model. By specifying arguments, users can also estimate the modified model described in Vevea and Woods (2005), which may be more practical with small datasets. Users can also specify moderators to estimate a linear model. The package functionality allows users to easily extract the results of these analyses as R objects for other uses. In addition, the package includes a function to launch both models as a Shiny application. Although the Shiny application is also available online, this function allows users to launch it locally if they choose.

Last updated 5 years ago

2.28 score 32 scripts 759 downloads

fluxweb - Estimate Energy Fluxes in Food Webs

Compute energy fluxes in trophic networks, from resources to their consumers, and can be applied to systems ranging from simple two-species interactions to highly complex food webs. It implements the approach described in Gauzens et al. (2017) <doi:10.1101/229450> to calculate energy fluxes, which are also used to calculate equilibrium stability.

Last updated 6 years ago

2.28 score 1 stars 19 scripts 173 downloads

gamair - Data for 'GAMs: An Introduction with R'

Data sets and scripts used in the book 'Generalized Additive Models: An Introduction with R', Wood (2006,2017) CRC.

Last updated 5 years ago

2.28 score 162 scripts 1.2k downloads

ContaminatedMixt - Clustering and Classification with the Contaminated Normal

Fits mixtures of multivariate contaminated normal distributions (with eigen-decomposed scale matrices) via the expectation conditional- maximization algorithm under a clustering or classification paradigm Methods are described in Antonio Punzo, Angelo Mazza, and Paul D McNicholas (2018) <doi:10.18637/jss.v085.i10>.

Last updated 2 years ago

openblas

2.28 score 1 dependents 63 scripts 592 downloads

chinese.misc - Miscellaneous Tools for Chinese Text Mining and More

Efforts are made to make Chinese text mining easier, faster, and robust to errors. Document term matrix can be generated by only one line of code; detecting encoding, segmenting and removing stop words are done automatically. Some convenient tools are also supplied.

Last updated 4 years ago

2.27 score 2 dependents 31 scripts 429 downloads

samplingVarEst - Sampling Variance Estimation

Functions to calculate some point estimators and estimate their variance under unequal probability sampling without replacement. Single and two-stage sampling designs are considered. Some approximations for the second-order inclusion probabilities (joint inclusion probabilities) are available (sample and population based). A variety of Jackknife variance estimators are implemented. Almost every function is written in C (compiled) code for faster results. The functions incorporate some performance improvements for faster results with large datasets.

Last updated 2 years ago

2.27 score 1 stars 1 dependents 62 scripts 325 downloads

acc - Exploring Accelerometer Data

Processes accelerometer data from uni-axial and tri-axial devices, and generates data summaries. Also includes functions to plot, analyze, and simulate accelerometer data.

Last updated 8 years ago

openblascpp

2.27 score 1 stars 31 scripts 377 downloads

apt - Asymmetric Price Transmission

The transmission between two time-series prices is assessed. It contains several functions for linear and nonlinear threshold co-integration, and furthermore, symmetric and asymmetric error correction models.

Last updated 3 months ago

2.26 score 23 scripts 545 downloads

CBCgrps - Compare Baseline Characteristics Between Groups

Compare baseline characteristics between two or more groups. The variables being compared can be factor and numeric variables. The function will automatically judge the type and distribution of the variables, and make statistical description and bivariate analysis.

Last updated 4 years ago

2.26 score 17 scripts 1.3k downloads

HDclust - Clustering High Dimensional Data with Hidden Markov Model on Variable Blocks

Clustering of high dimensional data with Hidden Markov Model on Variable Blocks (HMM-VB) fitted via Baum-Welch algorithm. Clustering is performed by the Modal Baum-Welch algorithm (MBW), which finds modes of the density function. Lin Lin and Jia Li (2017) <https://jmlr.org/papers/v18/16-342.html>.

Last updated 3 months ago

2.26 score 18 scripts 200 downloads

pch - Piecewise Constant Hazard Models for Censored and Truncated Data

Piecewise constant hazard models for survival data. The package allows for right-censored, left-truncated, and interval-censored data.

Last updated 11 months ago

2.26 score 6 dependents 9 scripts 352 downloads

iWeigReg - Improved Methods for Causal Inference and Missing Data Problems

Improved methods based on inverse probability weighting and outcome regression for causal inference and missing data problems.

Last updated 3 years ago

2.26 score 18 scripts 142 downloads

shinySIR - Interactive Plotting for Mathematical Models of Infectious Disease Spread

Provides interactive plotting for mathematical models of infectious disease spread. Users can choose from a variety of common built-in ordinary differential equation (ODE) models (such as the SIR, SIRS, and SIS models), or create their own. This latter flexibility allows 'shinySIR' to be applied to simple ODEs from any discipline. The package is a useful teaching tool as students can visualize how changing different parameters can impact model dynamics, with minimal knowledge of coding in R. The built-in models are inspired by those featured in Keeling and Rohani (2008) <doi:10.2307/j.ctvcm4gk0> and Bjornstad (2018) <doi:10.1007/978-3-319-97487-3>.

Last updated 4 years ago

2.26 score 18 scripts 172 downloads

kpeaks - Determination of K Using Peak Counts of Features for Clustering

The number of clusters (k) is needed to start all the partitioning clustering algorithms. An optimal value of this input argument is widely determined by using some internal validity indices. Since most of the existing internal indices suggest a k value which is computed from the clustering results after several runs of a clustering algorithm they are computationally expensive. On the contrary, the package 'kpeaks' enables to estimate k before running any clustering algorithm. It is based on a simple novel technique using the descriptive statistics of peak counts of the features in a data set.

Last updated 5 years ago

2.26 score 6 dependents 6 scripts 461 downloads

BLR - Bayesian Linear Regression

Bayesian Linear Regression.

Last updated 5 years ago

2.26 score 18 scripts 312 downloads

gamlss.countKinf - Generating and Fitting K-Inflated 'discrete gamlss.family' Distributions

This is an add on package to 'GAMLSS'. The main purpose of this package is generating and fitting inflated distributions at any desired point (0, 1, 2, ...). The function gen.Kinf() generates K-inflated version of an existing discrete 'GAMLSS' family distribution.

Last updated 6 years ago

2.26 score 18 scripts 121 downloads

CANSIM2R - Directly Extracts Complete CANSIM Data Tables

Extract CANSIM (Statistics Canada) tables and transform them into readily usable data in panel (wide) format. It can also extract more than one table at a time and produce the resulting merge by time period and geographical region.

Last updated 6 years ago

2.26 score 6 stars 30 scripts 304 downloads

SILGGM - Statistical Inference of Large-Scale Gaussian Graphical Model in Gene Networks

Provides a general framework to perform statistical inference of each gene pair and global inference of whole-scale gene pairs in gene networks using the well known Gaussian graphical model (GGM) in a time-efficient manner. We focus on the high-dimensional settings where p (the number of genes) is allowed to be far larger than n (the number of subjects). Four main approaches are supported in this package: (1) the bivariate nodewise scaled Lasso (Ren et al (2015) <doi:10.1214/14-AOS1286>) (2) the de-sparsified nodewise scaled Lasso (Jankova and van de Geer (2017) <doi:10.1007/s11749-016-0503-5>) (3) the de-sparsified graphical Lasso (Jankova and van de Geer (2015) <doi:10.1214/15-EJS1031>) (4) the GGM estimation with false discovery rate control (FDR) using scaled Lasso or Lasso (Liu (2013) <doi:10.1214/13-AOS1169>). Windows users should install 'Rtools' before the installation of this package.

Last updated 7 years ago

cpp

2.26 score 3 stars 1 dependents 8 scripts 155 downloads

conclust - Pairwise Constraints Clustering

There are 4 main functions in this package: ckmeans(), lcvqe(), mpckm() and ccls(). They take an unlabeled dataset and two lists of must-link and cannot-link constraints as input and produce a clustering as output.

Last updated 8 years ago

2.26 score 2 stars 3 dependents 6 scripts 264 downloads

DiscreteWeibull - Discrete Weibull Distributions (Type 1 and 3)

Probability mass function, distribution function, quantile function, random generation and parameter estimation for the type I and III discrete Weibull distributions.

Last updated 9 years ago

2.26 score 6 dependents 17 scripts 310 downloads

dice - Calculate probabilities of various dice-rolling events

This package provides utilities to calculate the probabilities of various dice-rolling events, such as the probability of rolling a four-sided die six times and getting a 4, a 3, and either a 1 or 2 among the six rolls (in any order); the probability of rolling two six-sided dice three times and getting a 10 on the first roll, followed by a 4 on the second roll, followed by anything but a 7 on the third roll; or the probabilities of each possible sum of rolling five six-sided dice, dropping the lowest two rolls, and summing the remaining dice.

Last updated 10 years ago

2.25 score 46 scripts 3.9k downloads

gendist - Generated Probability Distribution Models

Computes the probability density function (pdf), cumulative distribution function (cdf), quantile function (qf) and generates random values (rg) for the following general models : mixture models, composite models, folded models, skewed symmetric models and arc tan models.

Last updated 6 years ago

2.25 score 22 scripts 136 downloads

ggplotlyExtra - Extra Convenience Functions for 'Plotly'

Convenience functions for smooth conversion from 'ggplot' to 'plotly' where the conversion using ggplotly() usually gives an unexpected labels. The package ease the process of making a 'plotly' figures generated from 'ggplot2' object more aesthetic in terms of labels and customizability.

Last updated 5 years ago

2.24 score 35 scripts 565 downloads

Weighted.Desc.Stat - Weighted Descriptive Statistics

Weighted descriptive statistics is the discipline of quantitatively describing the main features of real-valued fuzzy data which usually given from a fuzzy population. One can summarize this special kind of fuzzy data numerically or graphically using this package. To interpret some of the properties of one or several sets of real-valued fuzzy data, numerically summarize is possible by some weighted statistics which are designed in this package such as mean, variance, covariance and correlation coefficent. Also, graphically interpretation can be given by weighted histogram and weighted scatter plot using this package to describe properties of real-valued fuzzy data set.

Last updated 9 years ago

2.24 score 2 dependents 29 scripts 539 downloads

NonCompart - Noncompartmental Analysis for Pharmacokinetic Data

Conduct a noncompartmental analysis with industrial strength. Some features are 1) Use of CDISC SDTM terms 2) Automatic or manual slope selection 3) Supporting both 'linear-up linear-down' and 'linear-up log-down' method 4) Interval(partial) AUCs with 'linear' or 'log' interpolation method * Reference: Gabrielsson J, Weiner D. Pharmacokinetic and Pharmacodynamic Data Analysis - Concepts and Applications. 5th ed. 2016. (ISBN:9198299107).

Last updated 1 years ago

2.23 score 1 stars 1 dependents 57 scripts 693 downloads

Newdistns - Computes Pdf, Cdf, Quantile and Random Numbers, Measures of Inference for 19 General Families of Distributions

Computes the probability density function, cumulative distribution function, quantile function, random numbers and measures of inference for the following general families of distributions (each family defined in terms of an arbitrary cdf G): Marshall Olkin G distributions, exponentiated G distributions, beta G distributions, gamma G distributions, Kumaraswamy G distributions, generalized beta G distributions, beta extended G distributions, gamma G distributions, gamma uniform G distributions, beta exponential G distributions, Weibull G distributions, log gamma G I distributions, log gamma G II distributions, exponentiated generalized G distributions, exponentiated Kumaraswamy G distributions, geometric exponential Poisson G distributions, truncated-exponential skew-symmetric G distributions, modified beta G distributions, and exponentiated exponential Poisson G distributions.

Last updated 9 years ago

2.23 score 1 dependents 19 scripts 198 downloads

evclass - Evidential Distance-Based Classification

Different evidential classifiers, which provide outputs in the form of Dempster-Shafer mass functions. The methods are: the evidential K-nearest neighbor rule, the evidential neural network, radial basis function neural networks, logistic regression, feed-forward neural networks.

Last updated 1 years ago

2.23 score 1 stars 17 scripts 296 downloads

EBglmnet - Empirical Bayesian Lasso and Elastic Net Methods for Generalized Linear Models

Provides empirical Bayesian lasso and elastic net algorithms for variable selection and effect estimation. Key features include sparse variable selection and effect estimation via generalized linear regression models, high dimensionality with p>>n, and significance test for nonzero effects. This package outperforms other popular methods such as lasso and elastic net methods in terms of power of detection, false discovery rate, and power of detecting grouping effects. Please reference its use as A Huang and D Liu (2016) <doi: 10.1093/bioinformatics/btw143>.

Last updated 2 years ago

openblas

2.23 score 17 scripts 82 downloads

DOS - Design of Observational Studies

Contains data sets, examples and software from the book Design of Observational Studies by Paul R. Rosenbaum, New York: Springer, <doi:10.1007/978-1-4419-1213-8>, ISBN 978-1-4419-1212-1.

Last updated 6 years ago

2.23 score 17 scripts 146 downloads

rhosp - Side Effect Risks in Hospital : Simulation and Estimation

Evaluating risk (that a patient arises a side effect) during hospitalization is the main purpose of this package. Several methods (Parametric, non parametric and De Vielder estimation) to estimate the risk constant (R) are implemented in this package. There are also functions to simulate the different models of this issue in order to quantify the previous estimators. It is necessary to read at least the first six pages of the report to understand the topic.

Last updated 6 years ago

2.23 score 17 scripts 196 downloads

ManifoldOptim - An R Interface to the 'ROPTLIB' Library for Riemannian Manifold Optimization

An R interface to version 0.3 of the 'ROPTLIB' optimization library (see <https://www.math.fsu.edu/~whuang2/> for more information). Optimize real- valued functions over manifolds such as Stiefel, Grassmann, and Symmetric Positive Definite matrices. For details see Martin et. al. (2020) <doi:10.18637/jss.v093.i01>. Note that the optional ldr package used in some of this package's examples can be obtained from either JSS <https://www.jstatsoft.org/index.php/jss/article/view/v061i03/2886> or from the CRAN archives <https://cran.r-project.org/src/contrib/Archive/ldr/ldr_1.3.3.tar.gz>.

Last updated 3 years ago

openblascpp

2.23 score 2 dependents 28 scripts 331 downloads

survexp.fr - Relative Survival, AER and SMR Based on French Death Rates

It computes Relative survival, AER and SMR based on French death rates.

Last updated 3 years ago

2.22 score 1 stars 1 dependents 11 scripts 158 downloads

tdROC - Nonparametric Estimation of Time-Dependent ROC, Brier Score, and Survival Difference from Right Censored Time-to-Event Data with or without Competing Risks

The tdROC package facilitates the estimation of time-dependent ROC (Receiver Operating Characteristic) curves and the Area Under the time-dependent ROC Curve (AUC) in the context of survival data, accommodating scenarios with right censored data and the option to account for competing risks. In addition to the ROC/AUC estimation, the package also estimates time-dependent Brier score and survival difference. Confidence intervals of various estimated quantities can be obtained from bootstrap. The package also offers plotting functions for visualizing time-dependent ROC curves.

Last updated 1 years ago

cpp

2.21 score 23 scripts 223 downloads

polyapost - Simulating from the Polya Posterior

Simulate via Markov chain Monte Carlo (hit-and-run algorithm) a Dirichlet distribution conditioned to satisfy a finite set of linear equality and inequality constraints (hence to lie in a convex polytope that is a subset of the unit simplex).

Last updated 3 months ago

openblas

2.20 score 16 scripts 314 downloads

bartMan - Create Visualisations for BART Models

Investigating and visualising Bayesian Additive Regression Tree (BART) (Chipman, H. A., George, E. I., & McCulloch, R. E. 2010) <doi:10.1214/09-AOAS285> model fits. We construct conventional plots to analyze a model’s performance and stability as well as create new tree-based plots to analyze variable importance, interaction, and tree structure. We employ Value Suppressing Uncertainty Palettes (VSUP) to construct heatmaps that display variable importance and interactions jointly using colour scale to represent posterior uncertainty. Our visualisations are designed to work with the most popular BART R packages available, namely 'BART' Rodney Sparapani and Charles Spanbauer and Robert McCulloch 2021 <doi:10.18637/jss.v097.i01>, 'dbarts' (Vincent Dorie 2023) <https://CRAN.R-project.org/package=dbarts>, and 'bartMachine' (Adam Kapelner and Justin Bleich 2016) <doi:10.18637/jss.v070.i04>.

Last updated 5 months ago

openjdk

2.20 score 16 scripts 222 downloads

HMR - Flux Estimation with Static Chamber Data

Statistical analysis of static chamber concentration data for trace gas flux estimation.

Last updated 6 months ago

2.20 score 7 scripts 419 downloads

gie - API Wrapper for the Natural Gas Transparency Platforms of Gas Infrastructure Europe

Providing access to the API for Gas Infrastructure Europe's natural gas transparency platforms <https://agsi.gie.eu/> and <https://alsi.gie.eu/>. Lets the user easily download metadata on companies and gas storage units covered by the API as well as the respective data on regional, country, company or facility level.

Last updated 7 months ago

2.20 score 16 scripts 489 downloads

dynRB - Dynamic Range Boxes

Improves the concept of multivariate range boxes, which is highly susceptible for outliers and does not consider the distribution of the data. The package uses dynamic range boxes to overcome these problems.

Last updated 2 years ago

2.20 score 16 scripts 357 downloads

SIBERG - Systematic Identification of Bimodally Expressed Genes Using RNAseq Data

Provides models to identify bimodally expressed genes from RNAseq data based on the Bimodality Index. SIBERG models the RNAseq data in the finite mixture modeling framework and incorporates mechanisms for dealing with RNAseq normalization. Three types of mixture models are implemented, namely, the mixture of log normal, negative binomial, or generalized Poisson distribution. See Tong et al. (2013) <doi:10.1093/bioinformatics/bts713>.

Last updated 3 years ago

2.20 score 16 scripts 168 downloads

GFD - Tests for General Factorial Designs

Implemented are the Wald-type statistic, a permuted version thereof as well as the ANOVA-type statistic for general factorial designs, even with non-normal error terms and/or heteroscedastic variances, for crossed designs with an arbitrary number of factors and nested designs with up to three factors. Friedrich et al. (2017) <doi:10.18637/jss.v079.c01>.

Last updated 3 years ago

2.20 score 16 scripts 387 downloads

GenAlgo - Classes and Methods to Use Genetic Algorithms for Feature Selection

Defines classes and methods that can be used to implement genetic algorithms for feature selection. The idea is that we want to select a fixed number of features to combine into a linear classifier that can predict a binary outcome, and can use a genetic algorithm heuristically to select an optimal set of features.

Last updated 4 years ago

microarrayclustering

2.20 score 16 scripts 186 downloads

cPCG - Efficient and Customized Preconditioned Conjugate Gradient Method for Solving System of Linear Equations

Solves system of linear equations using (preconditioned) conjugate gradient algorithm, with improved efficiency using Armadillo templated 'C++' linear algebra library, and flexibility for user-specified preconditioning method. Please check <https://github.com/styvon/cPCG> for latest updates.

Last updated 6 years ago

openblascpp

2.20 score 16 scripts 161 downloads

DAKS - Data Analysis and Knowledge Spaces

Functions and an example dataset for the psychometric theory of knowledge spaces. This package implements data analysis methods and procedures for simulating data and quasi orders and transforming different formulations in knowledge space theory. See package?DAKS for an overview.

Last updated 9 years ago

2.20 score 16 scripts 234 downloads

cmaes - Covariance Matrix Adapting Evolutionary Strategy

Single objective optimization using a CMA-ES.

Last updated 3 years ago

2.19 score 1 stars 4 dependents 13 scripts 1.0k downloads

flip - Multivariate Permutation Tests

It implements many univariate and multivariate permutation (and rotation) tests. Allowed tests: the t one and two samples, ANOVA, linear models, Chi Squared test, rank tests (i.e. Wilcoxon, Mann-Whitney, Kruskal-Wallis), Sign test and Mc Nemar. Test on Linear Models are performed also in presence of covariates (i.e. nuisance parameters). The permutation and the rotation methods to get the null distribution of the test statistics are available. It also implements methods for multiplicity control such as Westfall & Young minP procedure and Closed Testing (Marcus, 1976) and k-FWER. Moreover, it allows to test for fixed effects in mixed effects models.

Last updated 6 years ago

2.19 score 2 dependents 13 scripts 356 downloads

bigsplines - Smoothing Splines for Large Samples

Fits smoothing spline regression models using scalable algorithms designed for large samples. Seven marginal spline types are supported: linear, cubic, different cubic, cubic periodic, cubic thin-plate, ordinal, and nominal. Random effects and parametric effects are also supported. Response can be Gaussian or non-Gaussian: Binomial, Poisson, Gamma, Inverse Gaussian, or Negative Binomial.

Last updated 7 years ago

fortran

2.19 score 2 dependents 26 scripts 505 downloads

easyanova - Analysis of Variance and Other Important Complementary Analyses

Perform analysis of variance and other important complementary analyses. The functions are easy to use. Performs analysis in various designs, with balanced and unbalanced data.

Last updated 3 months ago

2.19 score 1 stars 65 scripts 1.2k downloads

ACDm - Tools for Autoregressive Conditional Duration Models

Package for Autoregressive Conditional Duration (ACD, Engle and Russell, 1998) models. Creates trade, price or volume durations from transactions (tic) data, performs diurnal adjustments, fits various ACD models and tests them.

Last updated 10 months ago

2.18 score 3 stars 1 dependents 17 scripts 433 downloads

steadyICA - ICA and Tests of Independence via Multivariate Distance Covariance

Functions related to multivariate measures of independence and ICA: -estimate independent components by minimizing distance covariance; -conduct a test of mutual independence based on distance covariance; -estimate independent components via infomax (a popular method but generally performs poorer than mdcovica, ProDenICA, and/or fastICA, but is useful for comparisons); -order indepedent components by skewness; -match independent components from multiple estimates; -other functions useful in ICA.

Last updated 1 months ago

cpp

2.18 score 1 dependents 49 scripts 1.0k downloads

fastml - Fast Machine Learning Model Training and Evaluation

Streamlines the training, evaluation, and comparison of multiple machine learning models with minimal code by providing comprehensive data preprocessing and support for a wide range of algorithms with hyperparameter tuning. It offers performance metrics and visualization tools to facilitate efficient and effective machine learning workflows.

Last updated 8 days ago

2.18 score 1 scripts 621 downloads

stoppingrule - Create and Evaluate Stopping Rules for Safety Monitoring

Provides functions for creating, displaying, and evaluating stopping rules for safety monitoring in clinical studies. Implements stopping rule methods described in Goldman (1987) <doi:10.1016/0197-2456(87)90153-X>; Geller et al. (2003, ISBN:9781135524388); Ivanova, Qaqish, and Schell (2005) <doi:10.1111/j.1541-0420.2005.00311.x>; Chen and Chaloner (2006) <doi:10.1002/sim.2429>; and Kulldorff et al. (2011) <doi:10.1080/07474946.2011.539924>.

Last updated 18 days ago

2.18 score 210 downloads

BANAM - Bayesian Analysis of the Network Autocorrelation Model

The network autocorrelation model (NAM) can be used for studying the degree of social influence regarding an outcome variable based on one or more known networks. The degree of social influence is quantified via the network autocorrelation parameters. In case of a single network, the Bayesian methods of Dittrich, Leenders, and Mulder (2017) <DOI:10.1016/j.socnet.2016.09.002> and Dittrich, Leenders, and Mulder (2019) <DOI:10.1177/0049124117729712> are implemented using a normal, flat, or independence Jeffreys prior for the network autocorrelation. In the case of multiple networks, the Bayesian methods of Dittrich, Leenders, and Mulder (2020) <DOI:10.1177/0081175020913899> are implemented using a multivariate normal prior for the network autocorrelation parameters. Flat priors are implemented for estimating the coefficients. For Bayesian testing of equality and order-constrained hypotheses, the default Bayes factor of Gu, Mulder, and Hoijtink, (2018) <DOI:10.1111/bmsp.12110> is used with the posterior mean and posterior covariance matrix of the NAM parameters based on flat priors as input.

Last updated 21 days ago

2.18 score 1 scripts 214 downloads

EBEN - Empirical Bayesian Elastic Net

Provides the Empirical Bayesian Elastic Net for handling multicollinearity in generalized linear regression models. As a special case of the 'EBglmnet' package (also available on CRAN), this package encourages a grouping effects to select relevant variables and estimate the corresponding non-zero effects.

Last updated 2 months ago

openblas

2.18 score 30 scripts 601 downloads

MoNAn - Mobility Network Analysis

Implements the method to analyse weighted mobility networks or distribution networks as outlined in: Block, P., Stadtfeld, C., & Robins, G. (2022) <doi:10.1016/j.socnet.2021.08.003>. The purpose of the model is to analyse the structure of mobility, incorporating exogenous predictors pertaining to individuals and locations known from classical mobility analyses, as well as modelling emergent mobility patterns akin to structural patterns known from the statistical analysis of social networks.

Last updated 3 months ago

2.18 score 3 scripts 119 downloads

quantilogram - Cross-Quantilogram

Estimation and inference methods for the cross-quantilogram. The cross-quantilogram is a measure of nonlinear dependence between two variables, based on either unconditional or conditional quantile functions. It can be considered an extension of the correlogram, which is a correlation function over multiple lag periods that mainly focuses on linear dependency. One can use the cross-quantilogram to detect the presence of directional predictability from one time series to another. This package provides a statistical inference method based on the stationary bootstrap. For detailed theoretical and empirical explanations, see Linton and Whang (2007) for univariate time series analysis and Han, Linton, Oka and Whang (2016) for multivariate time series analysis. The full references for these key publications are as follows: (1) Linton, O., and Whang, Y. J. (2007). The quantilogram: with an application to evaluating directional predictability. Journal of Econometrics, 141(1), 250-282 <doi:10.1016/j.jeconom.2007.01.004>; (2) Han, H., Linton, O., Oka, T., and Whang, Y. J. (2016). The cross-quantilogram: measuring quantile dependence and testing directional predictability between time series. Journal of Econometrics, 193(1), 251-270 <doi:10.1016/j.jeconom.2016.03.001>.

Last updated 4 months ago

2.18 score 3 stars 8 scripts 242 downloads

refineR - Reference Interval Estimation using Real-World Data

Indirect method for the estimation of reference intervals using Real-World Data ('RWD'). It takes routine measurements of diagnostic tests, containing pathological and non-pathological samples as input and uses sophisticated statistical methods to derive a model describing the distribution of the non-pathological samples. This distribution can then be used to derive reference intervals. Furthermore, the package offers functions for printing and plotting the results of the algorithm. See ?refineR for a more comprehensive description of the features. Version 1.0 of the algorithm is described in detail in 'Ammer et al. (2021)' <doi:10.1038/s41598-021-95301-2>. Additional guidance on the usage of the algorithm is given in 'Ammer et al. (2023)' <doi:10.1093/jalm/jfac101>.

Last updated 4 months ago

2.18 score 1 stars 15 scripts 257 downloads

jgsbook - Package of the German Book "Statistik mit R und RStudio" by Joerg grosse Schlarmann

All datasets and functions used in the german book "Statistik mit R und RStudio" by grosse Schlarmann (2010-2024) <https://www.produnis.de/R/>.

Last updated 6 months ago

2.18 score 604 downloads

cryptotrackr - An Interface to Crypto Data Sources

Allows you to connect to data sources across the crypto ecosystem. This data can enable a range of activity such as portfolio tracking, programmatic trading, or industry analysis. The package is described in French (2024) <https://github.com/TrevorFrench/cryptotrackr/wiki>.

Last updated 7 months ago

2.18 score 1 stars 1 scripts 202 downloads

rifreg - Estimate Recentered Influence Function Regression

Provides functions to compute recentered influence functions (RIF) of a distributional variable at the mean, quantiles, variance, gini or any custom functional of interest. The package allows to regress the RIF on any number of covariates. Generic print, plot and summary functions are also provided. Reference: Firpo, Sergio, Nicole M. Fortin, and Thomas Lemieux. (2009) <doi:10.3982/ECTA6822>. "Unconditional Quantile Regressions.".

Last updated 8 months ago

2.18 score 1 dependents 3 scripts 169 downloads

GRIDCOPULA - Bivariate Copula Functions Based on Regular Grid

Estimates grid type bivariate copula functions, calculates some association measures and provides several copula graphics.

Last updated 9 months ago

2.18 score 1 dependents 2 scripts 214 downloads

npreg - Nonparametric Regression via Smoothing Splines

Multiple and generalized nonparametric regression using smoothing spline ANOVA models and generalized additive models, as described in Helwig (2020) <doi:10.4135/9781526421036885885>. Includes support for Gaussian and non-Gaussian responses, smoothers for multiple types of predictors (including random intercepts), interactions between smoothers of mixed types, eight different methods for smoothing parameter selection, and flexible tools for diagnostics, inference, and prediction.

Last updated 9 months ago

2.18 score 150 scripts 595 downloads

GABB - Facilitation of Data Preparation and Plotting Procedures for RDA and PCA Analyses

Help to the occasional R user for synthesis and enhanced graphical visualization of redundancy analysis (RDA) and principal component analysis (PCA) methods and objects. Inputs are : data frame, RDA (package 'vegan') and PCA (package 'FactoMineR') objects. Outputs are : synthesized results of RDA, displayed in console and saved in tables ; displayed and saved objects of PCA graphic visualization of individuals and variables projections with multiple graphic parameters.

Last updated 10 months ago

2.18 score 2 scripts 269 downloads

regda - Regularised Discriminant Analysis

Regularised discriminant analysis functions. The classical regularised discriminant analysis proposed by Friedman in 1989, including cross-validation, of which the linear and quadratic discriminant analyses are special cases. Further, the regularised maximum likelihood linear discriminant analysis, including cross-validation. References: Friedman J.H. (1989): "Regularized Discriminant Analysis". Journal of the American Statistical Association 84(405): 165--175. <doi:10.2307/2289860>. Friedman J., Hastie T. and Tibshirani R. (2009). "The elements of statistical learning", 2nd edition. Springer, Berlin. <doi:10.1007/978-0-387-84858-7>. Tsagris M., Preston S. and Wood A.T.A. (2016). "Improved classification for compositional data using the alpha-transformation". Journal of Classification, 33(2): 243--261. <doi:10.1007/s00357-016-9207-5>.

Last updated 1 years ago

2.18 score 5 dependents 278 downloads

fqadata - Contains Regional Floristic Quality Assessment Databases

Contains regional Floristic Quality Assessment databases that have been approved or approved with reservations by the U.S. Army Corps of Engineers (USACE). Paired with the 'fqacalc' R package, these data sets allow for Floristic Quality Assessment metrics to be calculated. For information on FQA see Spyreas (2019) <doi:10.1002/ecs2.2825>. Both packages were developed for the USACE by the U.S. Army Engineer Research and Development Center's Environmental Laboratory.

Last updated 1 years ago

2.18 score 1 dependents 2 scripts 186 downloads

aghq - Adaptive Gauss Hermite Quadrature for Bayesian Inference

Adaptive Gauss Hermite Quadrature for Bayesian inference. The AGHQ method for normalizing posterior distributions and making Bayesian inferences based on them. Functions are provided for doing quadrature and marginal Laplace approximations, and summary methods are provided for making inferences based on the results. See Stringer (2021). "Implementing Adaptive Quadrature for Bayesian Inference: the aghq Package" <arXiv:2101.04468>.

Last updated 2 years ago

2.18 score 1 dependents 62 scripts 382 downloads

PEtests - Power-Enhanced (PE) Tests for High-Dimensional Data

Two-sample power-enhanced mean tests, covariance tests, and simultaneous tests on mean vectors and covariance matrices for high-dimensional data. Methods of these PE tests are presented in Yu, Li, and Xue (2022) <doi:10.1080/01621459.2022.2126781>; Yu, Li, Xue, and Li (2022) <doi:10.1080/01621459.2022.2061354>.

Last updated 2 years ago

2.18 score 3 stars 1 scripts 132 downloads

HyRiM - Multicriteria Risk Management using Zero-Sum Games with Vector-Valued Payoffs that are Probability Distributions

Construction and analysis of multivalued zero-sum matrix games over the abstract space of probability distributions, which describe the losses in each scenario of defense vs. attack action. The distributions can be compiled directly from expert opinions or other empirical data (insofar available). The package implements the methods put forth in the EU project HyRiM (Hybrid Risk Management for Utility Networks), FP7 EU Project Number 608090. The method has been published in Rass, S., König, S., Schauer, S., 2016. Decisions with Uncertain Consequences-A Total Ordering on Loss-Distributions. PLoS ONE 11, e0168583. <doi:10.1371/journal.pone.0168583>, and applied for advanced persistent thread modeling in Rass, S., König, S., Schauer, S., 2017. Defending Against Advanced Persistent Threats Using Game-Theory. PLoS ONE 12, e0168675. <doi:10.1371/journal.pone.0168675>. A volume covering the wider range of aspects of risk management, partially based on the theory implemented in the package is the book edited by S. Rass and S. Schauer, 2018. Game Theory for Security and Risk Management: From Theory to Practice. Springer, <doi:10.1007/978-3-319-75268-6>, ISBN 978-3-319-75267-9.

Last updated 2 years ago

2.18 score 15 scripts 224 downloads

twopartm - Two-Part Model with Marginal Effects

Fit two-part regression models for zero-inflated data. The models and their components are represented using S4 classes and methods. Average Marginal effects and predictive margins with standard errors and confidence intervals can be calculated from two-part model objects. Belotti, F., Deb, P., Manning, W. G., & Norton, E. C. (2015) <doi:10.1177/1536867X1501500102>.

Last updated 2 years ago

2.18 score 3 stars 8 scripts 407 downloads

mvdalab - Multivariate Data Analysis Laboratory

An open-source implementation of latent variable methods and multivariate modeling tools. The focus is on exploratory analyses using dimensionality reduction methods including low dimensional embedding, classical multivariate statistical tools, and tools for enhanced interpretation of machine learning methods (i.e. intelligible models to provide important information for end-users). Target domains include extension to dedicated applications e.g. for manufacturing process modeling, spectroscopic analyses, and data mining.

Last updated 2 years ago

2.18 score 1 dependents 74 scripts 296 downloads

KGode - Kernel Based Gradient Matching for Parameter Inference in Ordinary Differential Equations

The kernel ridge regression and the gradient matching algorithm proposed in Niu et al. (2016) <https://proceedings.mlr.press/v48/niu16.html> and the warping algorithm proposed in Niu et al. (2017) <DOI:10.1007/s00180-017-0753-z> are implemented for parameter inference in differential equations. Four schemes are provided for improving parameter estimation in odes by using the odes regularisation and warping.

Last updated 2 years ago

2.18 score 1 dependents 8 scripts 213 downloads

mlergm - Multilevel Exponential-Family Random Graph Models

Estimates exponential-family random graph models for multilevel network data, assuming the multilevel structure is observed. The scope, at present, covers multilevel models where the set of nodes is nested within known blocks. The estimation method uses Monte-Carlo maximum likelihood estimation (MCMLE) methods to estimate a variety of canonical or curved exponential family models for binary random graphs. MCMLE methods for curved exponential-family random graph models can be found in Hunter and Handcock (2006) <DOI: 10.1198/106186006X133069>. The package supports parallel computing, and provides methods for assessing goodness-of-fit of models and visualization of networks.

Last updated 3 years ago

2.18 score 1 stars 15 scripts 265 downloads

ibelief - Belief Function Implementation

Some basic functions to implement belief functions including: transformation between belief functions using the method introduced by Philippe Smets <arXiv:1304.1122>, evidence combination, evidence discounting, decision-making, and constructing masses. Currently, thirteen combination rules and six decision rules are supported. It can also be used to generate different types of random masses when working on belief combination and conflict management.

Last updated 4 years ago

2.18 score 1 stars 1 dependents 8 scripts 234 downloads

StempCens - Spatio-Temporal Estimation and Prediction for Censored/Missing Responses

It estimates the parameters of a censored or missing data in spatio-temporal models using the SAEM algorithm (Delyon et al., 1999). This algorithm is a stochastic approximation of the widely used EM algorithm and an important tool for models in which the E-step does not have an analytic form. Besides the expressions obtained to estimate the parameters to the proposed model, we include the calculations for the observed information matrix using the method developed by Louis (1982). To examine the performance of the fitted model, case-deletion measure are provided.

Last updated 4 years ago

2.18 score 1 dependents 8 scripts 217 downloads

estimraw - Estimation of Four-Fold Table Cell Frequencies (Raw Data) from Effect Size Measures

Estimation of four-fold table cell frequencies (raw data) from risk ratios (relative risks), risk differences and odds ratios. While raw data can be useful for doing meta-analysis, such data is often not provided by primary studies (with summary statistics being solely presented). Therefore, based on summary statistics (namely, risk ratios, risk differences and odds ratios), this package estimates the value of each cell in a 2x2 table according to the equations described in Di Pietrantonj C (2006) <doi:10.1002/sim.2287>.

Last updated 4 years ago

2.18 score 1 dependents 198 downloads

dcov - A Fast Implementation of Distance Covariance

Efficient methods for computing distance covariance and relevant statistics. See Székely et al.(2007) <doi:10.1214/009053607000000505>; Székely and Rizzo (2013) <doi:10.1016/j.jmva.2013.02.012>; Székely and Rizzo (2014) <doi:10.1214/14-AOS1255>; Huo and Székely (2016) <doi:10.1080/00401706.2015.1054435>.

Last updated 5 years ago

openblascpp

2.18 score 5 dependents 2 scripts 265 downloads

cctools - Tools for the Continuous Convolution Trick in Nonparametric Estimation

Implements the uniform scaled beta distribution and the continuous convolution kernel density estimator.

Last updated 6 years ago

cpp

2.18 score 1 dependents 5 scripts 202 downloads

aiRthermo - Atmospheric Thermodynamics and Visualization

Deals with many computations related to the thermodynamics of atmospheric processes. It includes many functions designed to consider the density of air with varying degrees of water vapour in it, saturation pressures and mixing ratios, conversion of moisture indices, computation of atmospheric states of parcels subject to dry or pseudoadiabatic vertical evolutions and atmospheric instability indices that are routinely used for operational weather forecasts or meteorological diagnostics.

Last updated 6 years ago

2.18 score 1 dependents 50 scripts 321 downloads

freqparcoord - Novel Methods for Parallel Coordinates

New approaches to parallel coordinates plots for multivariate data visualization, including applications to clustering, outlier hunting and regression diagnostics. Includes general functions for multivariate nonparametric density and regression estimation, using parallel computation.

Last updated 9 years ago

2.18 score 2 dependents 25 scripts 486 downloads

threewords - Represent Precise Coordinates in Three Words

A connector to the 'What3Words' (http://what3words.com/) service, which represents each 3m by 3m square on earth with a unique trio of English-language words.

Last updated 9 years ago

2.18 score 1 stars 1 dependents 4 scripts 117 downloads

MVar.pt - Analise multivariada (brazilian portuguese)

Analise multivariada, tendo funcoes que executam analise de correspondencia simples (CA) e multipla (MCA), analise de componentes principais (PCA), analise de correlacao canonica (CCA), analise fatorial (FA), escalonamento multidimensional (MDS), analise discriminante linear (LDA) e quadratica (QDA), analise de cluster hierarquico e nao hierarquico, regressao linear simples e multipla, analise de multiplos fatores (MFA) para dados quantitativos, qualitativos, de frequencia (MFACT) e dados mistos, biplot, scatter plot, projection pursuit (PP), grant tour e outras funcoes uteis para a analise multivariada.

Last updated 1 months ago

2.17 score 37 scripts 724 downloads

pairwiseCI - Confidence Intervals for Two Sample Comparisons

Calculation of the parametric, nonparametric confidence intervals for the difference or ratio of location parameters, nonparametric confidence interval for the Behrens-Fisher problem and for the difference, ratio and odds-ratio of binomial proportions for comparison of independent samples. Common wrapper functions to split data sets and apply confidence intervals or tests to these subsets. A by-statement allows calculation of CI separately for the levels of further factors. CI are not adjusted for multiplicity.

Last updated 6 years ago

2.17 score 74 scripts 491 downloads

insuranceData - A Collection of Insurance Datasets Useful in Risk Classification in Non-life Insurance.

Insurance datasets, which are often used in claims severity and claims frequency modelling. It helps testing new regression models in those problems, such as GLM, GLMM, HGLM, non-linear mixed models etc. Most of the data sets are applied in the project "Mixed models in ratemaking" supported by grant NN 111461540 from Polish National Science Center.

Last updated 10 years ago

2.17 score 2 stars 74 scripts 914 downloads

Umatrix - Visualization of Structures in High-Dimensional Data

By gaining the property of emergence through self-organization, the enhancement of SOMs(self organizing maps) is called Emergent SOM (ESOM). The result of the projection by ESOM is a grid of neurons which can be visualised as a three dimensional landscape in form of the Umatrix. Further details can be found in the referenced publications (see url). This package offers tools for calculating and visualising the ESOM as well as Umatrix, Pmatrix and UStarMatrix. All the functionality is also available through graphical user interfaces implemented in 'shiny'. Based on the recognized data structures, the method can be used to generate new data.

Last updated 4 months ago

cpp

2.16 score 1 stars 12 scripts 247 downloads

fTrading - Rmetrics - Trading and Rebalancing Financial Instruments

A collection of functions for trading and rebalancing financial instruments. It implements various technical indicators to analyse time series such as moving averages or stochastic oscillators.

Last updated 7 years ago

2.16 score 3 stars 48 scripts 989 downloads

TExPosition - Two-Table ExPosition

An extension of ExPosition for two table analyses, specifically, discriminant analyses.

Last updated 6 years ago

2.15 score 71 scripts 194 downloads

anomaly - Detecting Anomalies in Data

Implements Collective And Point Anomaly (CAPA) Fisch, Eckley, and Fearnhead (2022) <doi:10.1002/sam.11586>, Multi-Variate Collective And Point Anomaly (MVCAPA) Fisch, Eckley, and Fearnhead (2021) <doi:10.1080/10618600.2021.1987257>, Proportion Adaptive Segment Selection (PASS) Jeng, Cai, and Li (2012) <doi:10.1093/biomet/ass059>, and Bayesian Abnormal Region Detector (BARD) Bardwell and Fearnhead (2015) <doi:10.1214/16-BA998>. These methods are for the detection of anomalies in time series data. Further information regarding the use of this package along with detailed examples can be found in Fisch, Grose, Eckley, Fearnhead, and Bardwell (2024) <doi:10.18637/jss.v110.i01>.

Last updated 4 months ago

2.15 score 1 stars 47 scripts 516 downloads

redcas - An Interface to the Computer Algebra System 'REDUCE'

'REDUCE' is a portable general-purpose computer algebra system supporting scalar, vector, matrix and tensor algebra, symbolic differential and integral calculus, arbitrary precision numerical calculations and output in 'LaTeX' format. 'REDUCE' is based on 'Lisp' and is available on the two dialects 'Portable Standard Lisp' ('PSL') and 'Codemist Standard Lisp' ('CSL'). The 'redcas' package provides an interface for executing arbitrary 'REDUCE' code interactively from 'R', returning output as character vectors. 'R' code and 'REDUCE' code can be interspersed. It also provides a specialized function for calling the 'REDUCE' feature for solving systems of equations, returning the output as an 'R' object designed for the purpose. A further specialized function uses 'REDUCE' features to generate 'LaTeX' output and post-processes this for direct use in 'LaTeX' documents, e.g. using 'Sweave'.

Last updated 2 months ago

2.15 score 28 scripts 107 downloads

ggBubbles - Mini Bubble Plots for Comparison of Discrete Data with 'ggplot2'

When comparing discrete data mini bubble plots allow displaying more information than traditional bubble plots via colour, shape or labels. Exact overlapping coordinates will be transformed so they surround the original point circularly without overlapping. This is implemented as a position_surround() function for 'ggplot2'.

Last updated 5 years ago

2.15 score 14 scripts 139 downloads

episcan - Scan Pairwise Epistasis

Searching genomic interactions with linear/logistic regression in a high-dimensional dataset is a time-consuming task. This package provides some efficient ways to scan epistasis in genome-wide interaction studies (GWIS). Both case-control status (binary outcome) and quantitative phenotype (continuous outcome) are supported (the main references: 1. Kam-Thong, T., D. Czamara, K. Tsuda, K. Borgwardt, C. M. Lewis, A. Erhardt-Lehmann, B. Hemmer, et al. (2011). <doi:10.1038/ejhg.2010.196>. 2. Kam-Thong, T., B. Pütz, N. Karbalai, B. Müller-Myhsok, and K. Borgwardt. (2011). <doi:10.1093/bioinformatics/btr218>.)

Last updated 6 years ago

2.15 score 14 scripts 143 downloads

woeBinning - Supervised Weight of Evidence Binning of Numeric Variables and Factors

Implements an automated binning of numeric variables and factors with respect to a dichotomous target variable. Two approaches are provided: An implementation of fine and coarse classing that merges granular classes and levels step by step. And a tree-like approach that iteratively segments the initial bins via binary splits. Both procedures merge, respectively split, bins based on similar weight of evidence (WOE) values and stop via an information value (IV) based criteria. The package can be used with single variables or an entire data frame. It provides flexible tools for exploring different binning solutions and for deploying them to (new) data.

Last updated 6 years ago

2.15 score 5 stars 28 scripts 719 downloads

cowbell - Performs Segmented Linear Regression on Two Independent Variables

Implements a specific form of segmented linear regression with two independent variables. The visualization of that function looks like a quarter segment of a cowbell giving the package its name. The package has been specifically constructed for the case where minimum and maximum value of the dependent and two independent variables are known a prior, which is usually the case when those values are derived from Likert scales.

Last updated 8 years ago

2.15 score 14 scripts 160 downloads

fastSOM - Fast Calculation of Spillover Measures

Functions for computing spillover measures, especially spillover tables and spillover indices, as well as their average, minimal, and maximal values.

Last updated 5 years ago

2.14 score 2 stars 1 dependents 23 scripts 267 downloads

InPosition - Inference Tests for ExPosition

Non-parametric resampling-based inference tests for ExPosition.

Last updated 6 years ago

2.14 score 69 scripts 131 downloads

SpatialVx - Spatial Forecast Verification

Spatial forecast verification refers to verifying weather forecasts when the verification set (forecast and observations) is on a spatial field, usually a high-resolution gridded spatial field. Most of the functions here require the forecast and observed fields to be gridded and on the same grid. For a thorough review of most of the methods in this package, please see Gilleland et al. (2009) <doi: 10.1175/2009WAF2222269.1> and for a tutorial on some of the main functions available here, see Gilleland (2022) <doi: 10.5065/4px3-5a05>.

Last updated 28 days ago

2.13 score 1 stars 68 scripts 482 downloads

FlexParamCurve - Tools to Fit Flexible Parametric Curves

Model selection tools and 'selfStart' functions to fit parametric curves in 'nls', 'nlsList' and 'nlme' frameworks.

Last updated 1 years ago

2.13 score 17 scripts 306 downloads

RCPA3 - Data and Functions for R Companion to Political Analysis 3rd Ed

Bundles the datasets and functions featured in Philip H. Pollock and Barry C. Edwards<https://edge.sagepub.com/pollock>, "An R Companion to Political Analysis, 3rd Edition," Thousand Oaks, CA: Sage Publications.

Last updated 19 days ago

2.13 score 67 scripts 771 downloads

rankdist - Distance Based Ranking Models

Implements distance based probability models for ranking data. The supported distance metrics include Kendall distance, Spearman distance, Footrule distance, Hamming distance, Weighted-tau distance and Weighted Kendall distance. Phi-component model and mixture models are also supported.

Last updated 5 years ago

cpp

2.12 score 1 dependents 44 scripts 252 downloads

pbr - Find a Cold One Near You

In short, this package is a locator for cool, refreshing beverages. It will find and return the nearest location where you can get a cold one.

Last updated 1 years ago

2.11 score 13 scripts 94 downloads

RNentropy - Entropy Based Method for the Detection of Significant Variation in Gene Expression Data

An implementation of a method based on information theory devised for the identification of genes showing a significant variation of expression across multiple conditions. Given expression estimates from any number of RNA-Seq samples and conditions it identifies genes or transcripts with a significant variation of expression across all the conditions studied, together with the samples in which they are over- or under-expressed. Zambelli et al. (2018) <doi:10.1093/nar/gky055>.

Last updated 3 years ago

2.11 score 13 scripts 221 downloads

simpleRCache - Simple R Cache

Simple result caching in R based on R.cache. The global environment is not considered when caching results simplifying moving files between multiple instances of R. Relies on more base functions than R.cache (e.g. cached results are saved using saveRDS() and readRDS()).

Last updated 3 years ago

2.11 score 13 scripts 179 downloads

ccoptimalmatch - Implementation of Case-Control Optimal Matching

Cases are matched to controls in an efficient, optimal and computationally flexible way. It uses the idea of sub-sampling in the level of the case, by creating pseudo-observations of controls. The user can select between replacement and without replacement, the number of controls, and several covariates to match upon. See Mamouris (2021) <doi:10.1186/s12874-021-01256-3> for an overview.

Last updated 4 years ago

2.11 score 13 scripts 266 downloads

bdlp - Transparent and Reproducible Artificial Data Generation

The main function generateDataset() processes a user-supplied .R file that contains metadata parameters in order to generate actual data. The metadata parameters have to be structured in the form of metadata objects, the format of which is outlined in the package vignette. This approach allows to generate artificial data in a transparent and reproducible manner.

Last updated 4 years ago

2.11 score 13 scripts 237 downloads

shinyaframe - 'WebVR' Data Visualizations with 'RStudio Shiny' and 'Mozilla A-Frame'

Make R data available in Web-based virtual reality experiences for immersive, cross-platform data visualizations. Includes the 'gg-aframe' JavaScript package for a Grammar of Graphics declarative HTML syntax to create 3-dimensional data visualizations with 'Mozilla A-Frame' <https://aframe.io>.

Last updated 7 years ago

2.11 score 1 stars 13 scripts 115 downloads

HMPTrees - Statistical Object Oriented Data Analysis of RDP-Based Taxonomic Trees from Human Microbiome Data

Tools to model, compare, and visualize populations of taxonomic tree objects.

Last updated 7 years ago

2.11 score 1 stars 13 scripts 198 downloads

rxSeq - Combined Total and Allele Specific Reads Sequencing Study

Analysis of combined total and allele specific reads from the reciprocal cross study with RNA-seq data.

Last updated 8 years ago

2.11 score 13 scripts 116 downloads

DCchoice - Analyzing Dichotomous Choice Contingent Valuation Data

Functions for analyzing dichotomous choice contingent valuation (CV) data. It provides functions for estimating parametric and nonparametric models for single-, one-and-one-half-, and double-bounded CV data. For details, see Aizaki et al. (2022) <doi:10.1007/s42081-022-00171-1>.

Last updated 1 years ago

2.11 score 1 stars 1 dependents 30 scripts 1.4k downloads

Rfmtool - Fuzzy Measure Tools

Various tools for handling fuzzy measures, calculating Shapley value and interaction index, Choquet and Sugeno integrals, as well as fitting fuzzy measures to empirical data are provided. Construction of fuzzy measures from empirical data is done by solving a linear programming problem by using 'lpsolve' package, whose source in C adapted to the R environment is included. The description of the basic theory of fuzzy measures is in the manual in the Doc folder in this package. Please refer to the following: [1] <https://personal-sites.deakin.edu.au/~gleb/fmtools.html> [2] G. Beliakov, H. Bustince, T. Calvo, 'A Practical Guide to Averaging', Springer, (2016, ISBN: 978-3-319-24753-3). [3] G. Beliakov, S. James, J-Z. Wu, 'Discrete Fuzzy Measures', Springer, (2020, ISBN: 978-3-030-15305-2).

Last updated 7 months ago

2.10 score 63 scripts 606 downloads

discSurv - Discrete Time Survival Analysis

Provides data transformations, estimation utilities, predictive evaluation measures and simulation functions for discrete time survival analysis.

Last updated 3 years ago

2.10 score 2 stars 63 scripts 453 downloads

serial - The Serial Interface Package

Enables reading and writing binary and ASCII data to RS232/RS422/RS485 or any other virtual serial interface of the computer.

Last updated 5 years ago

2.10 score 1 dependents 42 scripts 291 downloads

MVar - Multivariate Analysis

Multivariate analysis, having functions that perform simple correspondence analysis (CA) and multiple correspondence analysis (MCA), principal components analysis (PCA), canonical correlation analysis (CCA), factorial analysis (FA), multidimensional scaling (MDS), linear (LDA) and quadratic discriminant analysis (QDA), hierarchical and non-hierarchical cluster analysis, simple and multiple linear regression, multiple factor analysis (MFA) for quantitative, qualitative, frequency (MFACT) and mixed data, biplot, scatter plot, projection pursuit (PP), grant tour method and other useful functions for the multivariate analysis.

Last updated 1 months ago

2.09 score 31 scripts 564 downloads

bayesmix - Bayesian Mixture Models with JAGS

Fits finite mixture models of univariate Gaussian distributions using JAGS within a Bayesian framework.

Last updated 2 years ago

2.09 score 1 dependents 41 scripts 538 downloads

NewmanOmics - Extending the Newman Studentized Range Statistic to Transcriptomics

Extends the classical Newman studentized range statistic in various ways that can be applied to genome-scale transcriptomic or other expression data.

Last updated 8 months ago

2.08 score 12 scripts 549 downloads

bivpois - Bivariate Poisson Distribution

Maximum likelihood estimation, random values generation, density computation and other functions for the bivariate Poisson distribution. References include: Kawamura K. (1984). "Direct calculation of maximum likelihood estimator for the bivariate Poisson distribution". Kodai Mathematical Journal, 7(2): 211--221. <doi:10.2996/kmj/1138036908>. Kocherlakota S. and Kocherlakota K. (1992). "Bivariate discrete distributions". CRC Press. <doi:10.1201/9781315138480>. Karlis D. and Ntzoufras I. (2003). "Analysis of sports data by using bivariate Poisson models". Journal of the Royal Statistical Society: Series D (The Statistician), 52(3): 381--393. <doi:10.1111/1467-9884.00366>.

Last updated 1 years ago

2.08 score 4 stars 1 dependents 26 scripts 269 downloads

ConfZIC - Confidence Envelopes for Model Selection Criteria Based on Minimum ZIC

Narrow down the number of models to look at in model selection using the confidence envelopes based on the minimum ZIC (Generalized Information Criteria) values for regression and time series data. Functions involve the computation of multivariate normal-probabilities with covariance matrices based on minimum ZIC inverting the CDF of the minimum ZIC. It involves both the computation of singular and non-singular probabilities as described in Genz (1992) <[https:doi.org/10.2307/1390838]https:doi.org/10.2307/1390838>.

Last updated 2 years ago

2.08 score 12 scripts 159 downloads

BSSprep - Whitening Data as Preparation for Blind Source Separation

Whitening is the first step of almost all blind source separation (BSS) methods. A fast implementation of whitening for BSS is implemented to serve as a lightweight dependency for packages providing BSS methods.

Last updated 4 years ago

2.08 score 4 dependents 226 downloads

welchADF - Welch-James Statistic for Robust Hypothesis Testing under Heterocedasticity and Non-Normality

Implementation of Johansen's general formulation of Welch-James's statistic with Approximate Degrees of Freedom, which makes it suitable for testing any linear hypothesis concerning cell means in univariate and multivariate mixed model designs when the data pose non-normality and non-homogeneous variance. Some improvements, namely trimmed means and Winsorized variances, and bootstrapping for calculating an empirical critical value, have been added to the classical formulation. The code departs from a previous SAS implementation by L.M. Lix and H.J. Keselman, available at <http://supp.apa.org/psycarticles/supplemental/met_13_2_110/SAS_Program.pdf> and published in Keselman, H.J., Wilcox, R.R., and Lix, L.M. (2003) <DOI:10.1111/1469-8986.00060>.

Last updated 5 years ago

2.08 score 12 scripts 153 downloads

CrossValidate - Classes and Methods for Cross Validation of "Class Prediction" Algorithms

Defines classes and methods to cross-validate various binary classification algorithms used for "class prediction" problems.

Last updated 6 years ago

microarrayclustering

2.08 score 12 scripts 197 downloads

nlt - A Nondecimated Lifting Transform for Signal Denoising

Uses a modified lifting algorithm on which it builds the nondecimated lifting transform. It has applications in wavelet shrinkage.

Last updated 6 years ago

2.08 score 4 dependents 4 scripts 195 downloads

DDM - Death Registration Coverage Estimation

A set of three two-census methods to the estimate the degree of death registration coverage for a population. Implemented methods include the Generalized Growth Balance method (GGB), the Synthetic Extinct Generation method (SEG), and a hybrid of the two, GGB-SEG. Each method offers automatic estimation, but users may also specify exact parameters or use a graphical interface to guess parameters in the traditional way if desired.

Last updated 8 years ago

2.08 score 12 scripts 145 downloads

FLLat - Fused Lasso Latent Feature Model

Fits the Fused Lasso Latent Feature model, which is used for modeling multi-sample aCGH data to identify regions of copy number variation (CNV). Produces a set of features that describe the patterns of CNV and a set of weights that describe the composition of each sample. Also provides functions for choosing the optimal tuning parameters and the appropriate number of features, and for estimating the false discovery rate.

Last updated 8 years ago

cpp

2.08 score 12 scripts 257 downloads

GESE - Gene-Based Segregation Test

Implements the gene-based segregation test(GESE) and the weighted GESE test for identifying genes with causal variants of large effects for family-based sequencing data. The methods are described in Qiao, D. Lange, C., Laird, N.M., Won, S., Hersh, C.P., et al. (2017). <DOI:10.1002/gepi.22037>. Gene-based segregation method for identifying rare variants for family-based sequencing studies. Genet Epidemiol 41(4):309-319. More details can be found at <http://scholar.harvard.edu/dqiao/gese>.

Last updated 8 years ago

2.08 score 12 scripts 513 downloads

ABC.RAP - Array Based CpG Region Analysis Pipeline

It aims to identify candidate genes that are “differentially methylated” between cases and controls. It applies Student’s t-test and delta beta analysis to identify candidate genes containing multiple “CpG sites”.

Last updated 8 years ago

2.08 score 12 scripts 388 downloads

multichull - A Generic Convex-Hull-Based Model Selection Method

Given a set of models for which a measure of model (mis)fit and model complexity is provided, CHull(), developed by Ceulemans and Kiers (2006) <doi:10.1348/000711005X64817>, determines the models that are located on the boundary of the convex hull and selects an optimal model by means of the scree test values.

Last updated 1 months ago

2.08 score 2 dependents 5 scripts 412 downloads

datanugget - Create, and Refine Data Nuggets

Creating, and refining data nuggets. Data nuggets reduce a large dataset into a small collection of nuggets of data, each containing a center (location), weight (importance), and scale (variability) parameter. Data nugget centers are created by choosing observations in the dataset which are as equally spaced apart as possible. Data nugget weights are created by counting the number observations closest to a given data nugget center. We then say the data nugget 'contains' these observations and the data nugget center is recalculated as the mean of these observations. Data nugget scales are created by calculating the trace of the covariance matrix of the observations contained within a data nugget divided by the dimension of the dataset. Data nuggets are refined by 'splitting' data nuggets which have scales or shapes (defined as the ratio of the two largest eigenvalues of the covariance matrix of the observations contained within the data nugget) Reference paper: [1] Beavers, T. E., Cheng, G., Duan, Y., Cabrera, J., Lubomirski, M., Amaratunga, D., & Teigler, J. E. (2024). Data Nuggets: A Method for Reducing Big Data While Preserving Data Structure. Journal of Computational and Graphical Statistics, 1-21. [2] Cherasia, K. E., Cabrera, J., Fernholz, L. T., & Fernholz, R. (2022). Data Nuggets in Supervised Learning. \emph{In Robust and Multivariate Statistical Methods: Festschrift in Honor of David E. Tyler} (pp. 429-449). Cham: Springer International Publishing.

Last updated 3 months ago

2.08 score 1 stars 2 dependents 1 scripts 232 downloads

smoothSurv - Survival Regression with Smoothed Error Distribution

Contains, as a main contribution, a function to fit a regression model with possibly right, left or interval censored observations and with the error distribution expressed as a mixture of G-splines. Core part of the computation is done in compiled 'C++' written using the 'Scythe' Statistical Library Version 0.3.

Last updated 1 years ago

cpp

2.08 score 2 dependents 20 scripts 567 downloads

rtsplot - Time Series Plot

A fast and elegant time series visualization package. In addition to the standard R plot types, this package supports candle sticks, open-high-low-close, and volume plots. Useful for visualizing any time series data, e.g., stock prices and technical indicators.

Last updated 1 years ago

2.08 score 1 stars 24 scripts 210 downloads

ecespa - Functions for Spatial Point Pattern Analysis

Some wrappers, functions and data sets for for spatial point pattern analysis (mainly based on 'spatstat'), used in the book "Introduccion al Analisis Espacial de Datos en Ecologia y Ciencias Ambientales: Metodos y Aplicaciones" and in the papers by De la Cruz et al. (2008) <doi:10.1111/j.0906-7590.2008.05299.x> and Olano et al. (2009) <doi:10.1051/forest:2008074>.

Last updated 2 years ago

fortran

2.08 score 1 dependents 40 scripts 527 downloads

NPBayesImputeCat - Non-Parametric Bayesian Multiple Imputation for Categorical Data

These routines create multiple imputations of missing at random categorical data, and create multiply imputed synthesis of categorical data, with or without structural zeros. Imputations and syntheses are based on Dirichlet process mixtures of multinomial distributions, which is a non-parametric Bayesian modeling approach that allows for flexible joint modeling, described in Manrique-Vallier and Reiter (2014) <doi:10.1080/10618600.2013.844700>.

Last updated 2 years ago

cpp

2.08 score 1 dependents 40 scripts 290 downloads

sparktf - Interface for 'TensorFlow' 'TFRecord' Files with 'Apache Spark'

A 'sparklyr' extension that enables reading and writing 'TensorFlow' TFRecord files via 'Apache Spark'.

Last updated 6 years ago

2.08 score 24 scripts 112 downloads

CircNNTSR - Statistical Analysis of Circular Data using Nonnegative Trigonometric Sums (NNTS) Models

Includes functions for the analysis of circular data using distributions based on Nonnegative Trigonometric Sums (NNTS). The package includes functions for calculation of densities and distributions, for the estimation of parameters, for plotting and more.

Last updated 1 years ago

2.07 score 1 dependents 39 scripts 330 downloads

vannstats - Simplified Statistics for PA 606

Simplifies functions assess normality for bivariate and multivariate statistical techniques. Includes functions designed to replicate plots and tables that would result from similar calls in 'SPSS', including hst(), box(), qq(), tab(), cormat(), and residplot(). Also includes simplified formulae, such as mode(), scatter(), p.corr(), ow.anova(), and rm.anova().

Last updated 2 years ago

2.06 score 23 scripts 402 downloads

nptest - Nonparametric Bootstrap and Permutation Tests

Robust nonparametric bootstrap and permutation tests for location, correlation, and regression problems, as described in Helwig (2019a) <doi:10.1002/wics.1457> and Helwig (2019b) <doi:10.1016/j.neuroimage.2019.116030>. Univariate and multivariate tests are supported. For each problem, exact tests and Monte Carlo approximations are available. Five different nonparametric bootstrap confidence intervals are implemented. Parallel computing is implemented via the 'parallel' package.

Last updated 2 years ago

2.06 score 2 dependents 19 scripts 442 downloads

mccr - The Matthews Correlation Coefficient

The Matthews correlation coefficient (MCC) score is calculated (Matthews BW (1975) <DOI:10.1016/0005-2795(75)90109-9>).

Last updated 8 years ago

2.06 score 1 dependents 38 scripts 180 downloads

EngrExpt - Data sets from "Introductory Statistics for Engineering Experimentation"

Datasets from Nelson, Coffin and Copeland "Introductory Statistics for Engineering Experimentation" (Elsevier, 2003) with sample code.

Last updated 15 years ago

2.05 score 113 scripts 142 downloads

MSinference - Multiscale Inference for Nonparametric Time Trend(s)

Performs a multiscale analysis of a nonparametric regression or nonparametric regressions with time series errors. In case of one regression, with the help of this package it is possible to detect the regions where the trend function is increasing or decreasing. In case of multiple regressions, the test identifies regions where the trend functions are different from each other. See Khismatullina and Vogt (2020) <doi:10.1111/rssb.12347>, Khismatullina and Vogt (2022) <doi:10.48550/arXiv.2209.10841> and Khismatullina and Vogt (2023) <doi:10.1016/j.jeconom.2021.04.010> for more details on theory and applications.

Last updated 4 months ago

2.04 score 11 scripts 197 downloads

binseqtest - Exact Binary Sequential Designs and Analysis

For a series of binary responses, create stopping boundary with exact results after stopping, allowing updating for missing assessments.

Last updated 1 years ago

2.04 score 11 scripts 252 downloads

msBP - Multiscale Bernstein Polynomials for Densities

Performs Bayesian nonparametric multiscale density estimation and multiscale testing of group differences with multiscale Bernstein polynomials (msBP) mixtures as in Canale and Dunson (2016).

Last updated 1 years ago

cpp

2.04 score 11 scripts 195 downloads

smoothy - Automatic Estimation of the Most Likely Drug Combination using Smooth Algorithm

A flexible moving average algorithm for modeling drug exposure in pharmacoepidemiology studies as presented in the article: Ouchi, D., Giner-Soriano, M., Gómez-Lumbreras, A., Vedia Urgell, C.,Torres, F., & Morros, R. (2022). "Automatic Estimation of the Most Likely Drug Combination in Electronic Health Records Using the Smooth Algorithm : Development and Validation Study." JMIR medical informatics, 10(11), e37976. <doi:10.2196/37976>.

Last updated 1 years ago

2.04 score 11 scripts 92 downloads

AUtests - Approximate Unconditional and Permutation Tests

Performs approximate unconditional and permutation testing for 2x2 contingency tables. Motivated by testing for disease association with rare genetic variants in case-control studies. When variants are extremely rare, these tests give better control of Type I error than standard tests.

Last updated 4 years ago

2.04 score 11 scripts 190 downloads

epibasix - Elementary Epidemiological Functions for Epidemiology and Biostatistics

Contains elementary tools for analysis of common epidemiological problems, ranging from sample size estimation, through 2x2 contingency table analysis and basic measures of agreement (kappa, sensitivity/specificity). Appropriate print and summary statements are also written to facilitate interpretation wherever possible. Source code is commented throughout to facilitate modification. The target audience includes advanced undergraduate and graduate students in epidemiology or biostatistics courses, and clinical researchers.

Last updated 6 years ago

2.04 score 22 scripts 518 downloads

eDMA - Dynamic Model Averaging with Grid Search

Perform dynamic model averaging with grid search as in Dangl and Halling (2012) <doi:10.1016/j.jfineco.2012.04.003> using parallel computing.

Last updated 6 years ago

openblascppopenmp

2.04 score 22 scripts 184 downloads

expandFunctions - Feature Matrix Builder

Generates feature matrix outputs from R object inputs using a variety of expansion functions. The generated feature matrices have applications as inputs for a variety of machine learning algorithms. The expansion functions are based on coercing the input to a matrix, treating the columns as features and converting individual columns or combinations into blocks of columns. Currently these include expansion of columns by efficient sparse embedding by vectors of lags, quadratic expansion into squares and unique products, powers by vectors of degree, vectors of orthogonal polynomials functions, and block random affine projection transformations (RAPTs). The transformations are magrittr- and cbind-friendly, and can be used in a building block fashion. For instance, taking the cos() of the output of the RAPT transformation generates a stationary kernel expansion via Bochner's theorem, and this expansion can then be cbind-ed with other features. Additionally, there are utilities for replacing features, removing rows with NAs, creating matrix samples of a given distribution, a simple wrapper for LASSO with CV, a Freeman-Tukey transform, generalizations of the outer function, matrix size-preserving discrete difference by row, plotting, etc.

Last updated 8 years ago

2.04 score 22 scripts 159 downloads

md - Selecting Bandwidth for Kernel Density Estimator with Minimum Distance Method

Selects bandwidth for the kernel density estimator with minimum distance method as proposed by Devroye and Lugosi (1996). The minimum distance method directly selects the optimal kernel density estimator from countably infinite kernel density estimators and indirectly selects the optimal bandwidth. This package selects the optimal bandwidth from finite kernel density estimators.

Last updated 9 years ago

2.03 score 12 scripts 108 downloads

mixsmsn - Fitting Finite Mixture of Scale Mixture of Skew-Normal Distributions

Functions to fit finite mixture of scale mixture of skew-normal (FM-SMSN) distributions, details in Prates, Lachos and Cabral (2013) <doi: 10.18637/jss.v054.i12>, Cabral, Lachos and Prates (2012) <doi:10.1016/j.csda.2011.06.026> and Basso, Lachos, Cabral and Ghosh (2010) <doi:10.1016/j.csda.2009.09.031>.

Last updated 3 years ago

2.03 score 1 stars 1 dependents 36 scripts 646 downloads

vocaldia - Create and Manipulate Vocalisation Diagrams

Create adjacency matrices of vocalisation graphs from dataframes containing sequences of speech and silence intervals, transforming these matrices into Markov diagrams, and generating datasets for classification of these diagrams by 'flattening' them and adding global properties (functionals) etc. Vocalisation diagrams date back to early work in psychiatry (Jaffe and Feldstein, 1970) and social psychology (Dabbs and Ruback, 1987) but have only recently been employed as a data representation method for machine learning tasks including meeting segmentation (Luz, 2012) <doi:10.1145/2328967.2328970> and classification (Luz, 2013) <doi:10.1145/2522848.2533788>.

Last updated 2 years ago

2.02 score 21 scripts 167 downloads

easynls - Easy Nonlinear Model

Fit and plot some nonlinear models.

Last updated 7 years ago

2.02 score 1 stars 13 scripts 414 downloads

gp - Maximum Likelihood Estimation of the Generalized Poisson Distribution

Functions to estimate the parameters of the generalized Poisson distribution with or without covariates using maximum likelihood. The references include Nikoloulopoulos A.K. & Karlis D. (2008). "On modeling count data: a comparison of some well-known discrete distributions". Journal of Statistical Computation and Simulation, 78(3): 437--457, <doi:10.1080/10629360601010760> and Consul P.C. & Famoye F. (1992). "Generalized Poisson regression model". Communications in Statistics - Theory and Methods, 21(1): 89--109, <doi:10.1080/03610929208830766>.

Last updated 1 years ago

2.01 score 2 dependents 17 scripts 248 downloads

FRACTION - Numeric Number into Fraction

Turn numeric,data.frame,matrix into fraction form.

Last updated 1 years ago

2.01 score 1 dependents 17 scripts 325 downloads

MixGHD - Model Based Clustering, Classification and Discriminant Analysis Using the Mixture of Generalized Hyperbolic Distributions

Carries out model-based clustering, classification and discriminant analysis using five different models. The models are all based on the generalized hyperbolic distribution. The first model 'MGHD' (Browne and McNicholas (2015) <doi:10.1002/cjs.11246>) is the classical mixture of generalized hyperbolic distributions. The 'MGHFA' (Tortora et al. (2016) <doi:10.1007/s11634-015-0204-z>) is the mixture of generalized hyperbolic factor analyzers for high dimensional data sets. The 'MSGHD' is the mixture of multiple scaled generalized hyperbolic distributions, the 'cMSGHD' is a 'MSGHD' with convex contour plots and the 'MCGHD', mixture of coalesced generalized hyperbolic distributions is a new more flexible model (Tortora et al. (2019)<doi:10.1007/s00357-019-09319-3>. The paper related to the software can be found at <doi:10.18637/jss.v098.i03>.

Last updated 3 years ago

2.01 score 1 stars 1 dependents 34 scripts 500 downloads

NPCD - Nonparametric Methods for Cognitive Diagnosis

An array of nonparametric and parametric estimation methods for cognitive diagnostic models, including nonparametric classification of examinee attribute profiles, joint maximum likelihood estimation (JMLE) of examinee attribute profiles and item parameters, and nonparametric refinement of the Q-matrix, as well as conditional maximum likelihood estimation (CMLE) of examinee attribute profiles given item parameters and CMLE of item parameters given examinee attribute profiles. Currently the nonparametric methods in the package support both conjunctive and disjunctive models, and the parametric methods in the package support the DINA model, the DINO model, the NIDA model, the G-NIDA model, and the R-RUM model.

Last updated 5 years ago

2.01 score 1 stars 2 dependents 17 scripts 253 downloads

PSS.Health - Power and Sample Size for Health Researchers via Shiny

Power and Sample Size for Health Researchers is a Shiny application that brings together a series of functions related to sample size and power calculations for common analysis in the healthcare field. There are functionalities to calculate the power, sample size to estimate or test hypotheses for means and proportions (including test for correlated groups, equivalence, non-inferiority and superiority), association, correlations coefficients, regression coefficients (linear, logistic, gamma, and Cox), linear mixed model, Cronbach's alpha, interobserver agreement, intraclass correlation coefficients, limit of agreement on Bland-Altman plots, area under the curve, sensitivity and specificity incorporating the prevalence of disease. You can also use the online version at <https://hcpa-unidade-bioestatistica.shinyapps.io/PSS_Health/>.

Last updated 4 days ago

2.00 score 1 scripts 217 downloads

rGV - Analysis of Continuous Glucose Monitor Data

Reads in continuous glucose monitor data of many different formats, calculates a host of glycemic variability metrics, and plots glucose over time.

Last updated 5 days ago

2.00 score 2 stars 2 scripts 154 downloads

scR - Estimate Vapnik-Chervonenkis Dimension and Sample Complexity

We provide a suite of tools for estimating the sample complexity of a chosen model through theoretical bounds and simulation. The package incorporates methods for estimating the Vapnik-Chervonenkis dimension (VCD) of a chosen algorithm, which can be used to estimate its sample complexity. Alternatively, we provide simulation methods to estimate sample complexity directly. For more details, see Carter, P & Choi, D (2024). "Learning from Noise: Applying Sample Complexity for Political Science Research" <doi:10.31219/osf.io/evrcj>.

Last updated 6 days ago

2.00 score 4 scripts 183 downloads

jointest - Multivariate Testing Through Joint Resampling-Based Tests

Runs resampling-based tests jointly, e.g., sign-flip score tests from Hemerik et al., (2020) <doi:10.1111/rssb.12369>, to allow for multivariate testing, i.e., weak and strong control of the Familywise Error Rate or True Discovery Proportion.

Last updated 8 days ago

2.00 score 9 scripts

Simile - Interact with Simile Models

Allows a Simile model saved as a compiled binary to be loaded, parameterized, executed and interrogated. This version works with Simile v6 on.

Last updated 13 days ago

2.00 score 18 scripts 124 downloads

SSHAARP - Searching Shared HLA Amino Acid Residue Prevalence

Processes amino acid alignments produced by the 'IPD-IMGT/HLA (Immuno Polymorphism-ImMunoGeneTics/Human Leukocyte Antigen) Database' to identify user-defined amino acid residue motifs shared across HLA alleles, HLA alleles, or HLA haplotypes, and calculates frequencies based on HLA allele frequency data. 'SSHAARP' (Searching Shared HLA Amino Acid Residue Prevalence) uses 'Generic Mapping Tools (GMT)' software and the 'GMT' R package to generate global frequency heat maps that illustrate the distribution of each user-defined map around the globe. 'SSHAARP' analyzes the allele frequency data described by Solberg et al. (2008) <doi:10.1016/j.humimm.2008.05.001>, a global set of 497 population samples from 185 published datasets, representing 66,800 individuals total. Users may also specify their own datasets, but file conventions must follow the prebundled Solberg dataset, or the mock haplotype dataset.

Last updated 13 days ago

2.00 score 170 downloads

bplsr - Bayesian partial least squares regression

Fits the Bayesian partial least squares regression model introduced in Urbas et al. (2024) <doi:10.1214/24-AOAS1947>. Suitable for univariate and multivariate regression with high-dimensional data.

Last updated 22 days ago

2.00 score 2 scripts 281 downloads

visachartR - Wrapper for 'Visa Chart Components'

Provides a set of wrapper functions for 'Visa Chart Components'. 'Visa Chart Components' <https://github.com/visa/visa-chart-components> is an accessibility focused, framework agnostic set of data experience design systems components for the web.

Last updated 1 months ago

2.00 score 7 scripts 362 downloads

graphicalEvidence - Graphical Evidence

Computes marginal likelihood in Gaussian graphical models through a novel telescoping block decomposition of the precision matrix which allows estimation of model evidence. The top level function used to estimate marginal likelihood is called evidence(), which expects the prior name, data, and relevant prior specific parameters. This package also provides an MCMC prior sampler using the same underlying approach, implemented in prior_sampling(), which expects a prior name and prior specific parameters. Both functions also expect the number of burn-in iterations and the number of sampling iterations for the underlying MCMC sampler.

Last updated 2 months ago

openblascppopenmp

2.00 score 575 downloads

siren - Hybrid FA-CFA for Controlling Acquiescence in Restricted Factorial Solutions

Performs hybrid multi-stage factor analytic procedure for controlling acquiescence in restricted solutions (Ferrando & Lorenzo-Seva, 2000 <https://www.uv.es/revispsi/articulos3.00/ferran7.pdf>).

Last updated 2 months ago

2.00 score 2 scripts 555 downloads

NPFD - N-Power Fourier Deconvolution

Provides tools for non-parametric Fourier deconvolution using the N-Power Fourier Deconvolution (NPFD) method. This package includes methods for density estimation (densprf()) and sample generation (createSample()), enabling users to perform statistical analyses on mixed or replicated data sets.

Last updated 2 months ago

2.00 score 470 downloads

CADF - Customer Analytics Data Formatting

Converts customer transaction data (ID, purchase date) into a R6 class called customer. The class stores various customer analytics calculations at the customer level. The package also contains functionality to convert data in the R6 class to data.frames that can serve as inputs for various customer analytics models.

Last updated 2 months ago

2.00 score 535 downloads

DisaggregateTS - High-Dimensional Temporal Disaggregation

Provides tools for temporal disaggregation, including: (1) High-dimensional and low-dimensional series generation for simulation studies; (2) A toolkit for temporal disaggregation and benchmarking using low-dimensional indicator series as proposed by Dagum and Cholette (2006, ISBN:978-0-387-35439-2); (3) Novel techniques by Mosley, Gibberd, and Eckley (2022, <doi:10.1111/rssa.12952>) for disaggregating low-frequency series in the presence of high-dimensional indicator matrices.

Last updated 2 months ago

2.00 score 3 scripts 611 downloads

UnplanSimon - Methods for Managing Enrollment Deviation in Simon's Two-Stage Design

Methods for managing under- and over-enrollment in Simon's Two-Stage Design are offered by providing adaptive threshold adjustments and sample size recalibration. It also includes post-inference analysis tools to support clinical trial design and evaluation. The package is designed to enhance flexibility and accuracy in trial design, ensuring better outcomes in oncology and other clinical studies. Yunhe Liu, Haitao Pan (2024). Submitted.

Last updated 2 months ago

2.00 score 489 downloads

MLCOPULA - Classification Models with Copula Functions

Provides several classifiers based on probabilistic models. These classifiers allow to model the dependence structure of continuous features through bivariate copula functions and graphical models, see Salinas-Gutiérrez et al. (2014) <doi:10.1007/s00180-013-0457-y>.

Last updated 2 months ago

2.00 score 478 downloads

ShapleyOutlier - Multivariate Outlier Explanations using Shapley Values and Mahalanobis Distances

Based on Shapley values to explain multivariate outlyingness and to detect and impute cellwise outliers. Includes implementations of methods described in Mayrhofer and Filzmoser (2023) <doi:10.1016/j.ecosta.2023.04.003>.

Last updated 2 months ago

2.00 score 3 scripts 196 downloads

codecountR - Counting Codes in a Text and Preparing Data for Analysis

Data analysis often requires coding, especially when data are collected through interviews, observations, or questionnaires. As a result, code counting and data preparation are essential steps in the analysis process. Analysts may need to count the codes in a text (tokenization and counting of pre-established codes) and prepare the data (e.g., min-max normalization, Z-score, robust scaling, Box-Cox transformation, and non-parametric bootstrap). For the Box-Cox transformation (Box & Cox, 1964, <https://www.jstor.org/stable/2984418>), the optimal Lambda is determined using the log-likelihood method. Non-parametric bootstrap involves randomly sampling data with replacement. Two random number generators are also integrated: a Lehmer congruential generator for uniform distribution and a Box-Muller generator for normal distribution. Package for educational purposes.

Last updated 2 months ago

2.00 score 2 scripts 193 downloads

mpt - Multinomial Processing Tree Models

Fitting and testing multinomial processing tree (MPT) models, a class of nonlinear models for categorical data. The parameters are the link probabilities of a tree-like graph and represent the latent cognitive processing steps executed to arrive at observable response categories (Batchelder & Riefer, 1999 <doi:10.3758/bf03210812>; Erdfelder et al., 2009 <doi:10.1027/0044-3409.217.3.108>; Riefer & Batchelder, 1988 <doi:10.1037/0033-295x.95.3.318>).

Last updated 2 months ago

2.00 score 23 scripts 328 downloads

DDHFm - Variance Stabilization by Data-Driven Haar-Fisz (for Microarrays)

Contains the normalizing and variance stabilizing Data-Driven Haar-Fisz algorithm. Also contains related algorithms for simulating from certain microarray gene intensity models and evaluation of certain transformations. Contains cDNA and shipping credit flow data.

Last updated 3 months ago

2.00 score 6 scripts 310 downloads

pMEM - Predictive Moran's Eigenvector Maps

Calculation of Predictive Moran's eigenvector maps (pMEM), as defined by Guénard and Legendre (In Press) "Spatially-explicit predictions using spatial eigenvector maps" <doi:10.5281/zenodo.13356457>. Methods in Ecology and Evolution. This method enables scientists to predict the values of spatially-structured environmental variables. Multiple types of pMEM are defined, each one implemented on the basis of spatial weighting function taking a range parameter, and sometimes also a shape parameter. The code's modular nature enables programers to implement new pMEM by defining new spatial weighting functions.

Last updated 3 months ago

cpp

2.00 score 7 scripts 125 downloads

MethodOpt - Advanced Method Optimization for Spectra-Generating Sampling and Analysis Instrumentation

A graphical user interface to apply an advanced method optimization algorithm to various sampling and analysis instruments. This includes generating experimental designs, uploading and viewing data, and performing various analyses to determine the optimal method. Details of the techniques used in this package are published in Gamble, Granger, & Mannion (2024) <doi:10.1021/acs.analchem.3c05763>.

Last updated 3 months ago

2.00 score 136 downloads

microbiomeMQC - Calculate 4 Key Reporting Measures

Perform calculations for the WHO International Reference Reagents for the microbiome. Using strain, species or genera abundance tables generated through analysis of 16S ribosomal RNA sequencing or shotgun sequencing which included a reference reagent. This package will calculate measures of sensitivity, False positive relative abundance, diversity, and similarity based on mean average abundances with respect to the reference reagent.

Last updated 3 months ago

2.00 score 170 downloads

biostats101 - Practical Functions for Biostatistics Beginners

A set of user-friendly functions designed to fill gaps in existing introductory biostatistics R tools, making it easier for newcomers to perform basic biostatistical analyses without needing advanced programming skills. The methods implemented in this package are based on the works: Connor (1987) <doi:10.2307/2531961> Fleiss, Levin, & Paik (2013, ISBN:978-1-118-62561-3) Levin & Chen (1999) <doi:10.1080/00031305.1999.10474431> McNemar (1947) <doi:10.1007/BF02295996>.

Last updated 3 months ago

2.00 score 2 scripts 200 downloads

psvmSDR - Unified Principal Sufficient Dimension Reduction Package

A unified and user-friendly framework for applying the principal sufficient dimension reduction methods for both linear and nonlinear cases. The package has an extendable power by varying loss functions for the support vector machine, even for an user-defined arbitrary function, unless those are convex and differentiable everywhere over the support (Li et al. (2011) <doi:10.1214/11-AOS932>). Also, it provides a real-time sufficient dimension reduction update procedure using the principal least squares support vector machine (Artemiou et al. (2021) <doi:10.1016/j.patcog.2020.107768>).

Last updated 4 months ago

2.00 score 1 stars 1 scripts 130 downloads

lab2clean - Automation and Standardization of Cleaning Clinical Lab Data

Navigating the shift of clinical laboratory data from primary everyday clinical use to secondary research purposes presents a significant challenge. Given the substantial time and expertise required for lab data pre-processing and cleaning and the lack of all-in-one tools tailored for this need, we developed our algorithm 'lab2clean' as an open-source R-package. 'lab2clean' package is set to automate and standardize the intricate process of cleaning clinical laboratory results. With a keen focus on improving the data quality of laboratory result values, our goal is to equip researchers with a straightforward, plug-and-play tool, making it smoother for them to unlock the true potential of clinical laboratory data in clinical research and clinical machine learning (ML) model development. Version 1.0 of the algorithm is described in detail in 'Zayed et al. (2024)' <doi:10.1186/s12911-024-02652-7>.

Last updated 4 months ago

2.00 score 3 scripts 208 downloads

PoweREST - A Bootstrap-Based Power Estimation Tool for Spatial Transcriptomics

Power estimation and sample size calculation for 10X Visium Spatial Transcriptomics data to detect differential expressed genes between two conditions based on bootstrap resampling. See Shui et al. (2024) <doi:10.1101/2024.08.30.610564> for method details.

Last updated 4 months ago

2.00 score 5 scripts 144 downloads

mstDIF - A Collection of DIF Tests for Multistage Tests

A collection of statistical tests for the detection of differential item functioning (DIF) in multistage tests. Methods entail logistic regression, an adaptation of the simultaneous item bias test (SIBTEST), and various score-based tests. The presented tests provide itemwise test for DIF along categorical, ordinal or metric covariates. Methods for uniform and non-uniform DIF effects are available depending on which method is used.

Last updated 4 months ago

2.00 score 8 scripts 214 downloads

tRigon - Toolbox for Integrative Pathomics Analysis

Processing and analysis of pathomics, omics and other medical datasets. 'tRigon' serves as a toolbox for descriptive and statistical analysis, correlations, plotting and many other methods for exploratory analysis of high-dimensional datasets.

Last updated 4 months ago

2.00 score 2 scripts 187 downloads

ssMRCD - Spatially Smoothed MRCD Estimator

Estimation of the Spatially Smoothed Minimum Regularized Determinant (ssMRCD) estimator and its usage in an ssMRCD-based outlier detection method as described in Puchhammer and Filzmoser (2023) <doi:10.1080/10618600.2023.2277875> and for sparse robust PCA for multi-source data described in Puchhammer, Wilms and Filzmoser (2024) <doi:10.48550/arXiv.2407.16299>. Included are also complementary visualization and parameter tuning tools.

Last updated 4 months ago

2.00 score 3 scripts 155 downloads

SRTsim - Simulator for Spatially Resolved Transcriptomics

An independent, reproducible, and flexible Spatially Resolved Transcriptomics (SRT) simulation framework that can be used to facilitate the development of SRT analytical methods for a wide variety of SRT-specific analyses. It utilizes spatial localization information to simulate SRT expression count data in a reproducible and scalable fashion. Two major simulation schemes are implemented in 'SRTsim': reference-based and reference-free.

Last updated 4 months ago

2.00 score 9 scripts 188 downloads

metaGE - Meta-Analysis for Detecting Genotype x Environment Associations

Provides functions to perform all steps of genome-wide association meta-analysis for studying Genotype x Environment interactions, from collecting the data to the manhattan plot. The procedure accounts for the potential correlation between studies. In addition to the Fixed and Random models, one can investigate the relationship between QTL effects and some qualitative or quantitative covariate via the test of contrast and the meta-regression, respectively. The methodology is available from: (De Walsche, A., et al. (2023) \doi{10.1101/2023.03.01.530237}).

Last updated 5 months ago

2.00 score 1 scripts 291 downloads

StuteTest - Stute (1997) Linearity Test

Non-parametric test, originally proposed by Stute (1997) <https://www.jstor.org/stable/2242560>, that the expectation of a dependent variable Y given an independent variable D is linear in D.

Last updated 5 months ago

2.00 score 142 downloads

bdsvd - Block Structure Detection Using Singular Vectors

Performs block diagonal covariance matrix detection using singular vectors (BD-SVD), which can be extended to hierarchical variable clustering (HC-SVD). The methods are described in Bauer (202Xa) <doi:10.48550/arXiv.2211.16155> and Bauer (202Xb) <doi:10.48550/arXiv.2308.06820>.

Last updated 6 months ago

2.00 score 207 downloads

lincom - Linear Biomarker Combination: Empirical Performance Optimization

Perform two linear combination methods for biomarkers: (1) Empirical performance optimization for specificity (or sensitivity) at a controlled sensitivity (or specificity) level of Huang and Sanda (2022) <doi:10.1214/22-aos2210>, and (2) weighted maximum score estimator with empirical minimization of averaged false positive rate and false negative rate. Both adopt the algorithms of Huang and Sanda (2022) <doi:10.1214/22-aos2210>. 'MOSEK' solver is used and needs to be installed; an academic license for 'MOSEK' is free.

Last updated 6 months ago

fortran

2.00 score 2 scripts 229 downloads

dartR.sexlinked - Analysing SNP Data to Identify Sex-Linked Markers

Identifies, filters and exports sex linked markers using 'SNP' (single nucleotide polymorphism) data. To install the other packages, we recommend to install the 'dartRverse' package, that supports the installation of all packages in the 'dartRverse'. If you want understand the applied rational to identify sexlinked markers and/or want to cite 'dartR.sexlinked', you find the information by typing citation('dartR.sexlinked') in the console.

Last updated 6 months ago

2.00 score 4 scripts 501 downloads

milorGWAS - Mixed Logistic Regression for Genome-Wide Analysis Studies (GWAS)

Fast approximate methods for mixed logistic regression in genome-wide analysis studies (GWAS). Two computationnally efficient methods are proposed for obtaining effect size estimates (beta) in Mixed Logistic Regression in GWAS: the Approximate Maximum Likelihood Estimate (AMLE), and the Offset method. The wald test obtained with AMLE is identical to the score test. Data can be genotype matrices in plink format, or dosage (VCF files). The methods are described in details in Milet et al (2020) <doi:10.1101/2020.01.17.910109>.

Last updated 6 months ago

zlibcpp

2.00 score 8 scripts 510 downloads

FlowerMate - Reciprocity Indices for Style-Polymorphic Plants

Computes unidimensional and multidimensional Reciprocity and Inaccuracy indices. These indices are applicable to common heterostylous populations and to any other type of stylar dimorphic and trimorphic populations, such as in enantiostylous and three-dimensional heterostylous plants. Simón-Porcar, V., A. J. Muñoz-Pajares, J. Arroyo, and S. D. Johnson. (in press) "FlowerMate: multidimensional reciprocity and inaccuracy indices for style-polymorphic plant populations."

Last updated 6 months ago

2.00 score 123 downloads

PerMat - Performance Metrics in Predictive Modeling

Performance metric provides different performance measures like mean squared error, root mean square error, mean absolute deviation, mean absolute percentage error etc. of a fitted model. These can provide a way for forecasters to quantitatively compare the performance of competing models. For method details see (i) Pankaj Das (2020) <http://krishi.icar.gov.in/jspui/handle/123456789/44138>.

Last updated 6 months ago

2.00 score 2 scripts 460 downloads

TRMF - Temporally Regularized Matrix Factorization

Functions to estimate temporally regularized matrix factorizations (TRMF) for forecasting and imputing values in short but high-dimensional time series. Uses regularized alternating least squares to compute the factorization, allows for several types of constraints on matrix factors and natively handles weighted and missing data.

Last updated 6 months ago

2.00 score 518 downloads

SoilSaltIndex - Soil Salinity Indices Generation using Satellite Data

The developed function generates soil salinity indices using satellite data, utilizing multiple spectral bands such as Blue, Green, Red, Near-Infrared (NIR), and Shortwave Infrared (SWIR1, SWIR2). It computes 24 different salinity indices crucial for monitoring and analyzing salt-affected soils efficiently. For more details see, Rani, et al. (2022). <DOI: 10.1007/s12517-022-09682-3>. One of the key features of the developed function is its flexibility. Users can provide any combination of the required spectral bands, and the function will automatically calculate only the relevant indices based on the available data. This dynamic capability ensures that users can maximize the utility of their data without the need for all spectral bands, making the package versatile and user-friendly. Outputs are provided as GeoTIFF file format, facilitating easy integration with GIS workflows.

Last updated 7 months ago

2.00 score 1 stars 1 scripts 467 downloads

svgtools - Manipulate SVG (Template) Files of Charts

The purpose of this package is to manipulate SVG files that are templates of charts the user wants to produce. In vector graphics one copes with x-/y-coordinates of elements (e.g. lines, rectangles, text). Their scale is often dependent on the program that is used to produce the graphics. In applied statistics one usually has numeric values on a fixed scale (e.g. percentage values between 0 and 100) to show in a chart. Basically, 'svgtools' transforms the statistical values into coordinates and widths/heights of the vector graphics. This is done by stackedBar() for bar charts, by linesSymbols() for charts with lines and/or symbols (dot markers) and scatterSymbols() for scatterplots.

Last updated 7 months ago

2.00 score 597 downloads

MFSIS - Model-Free Sure Independent Screening Procedures

An implementation of popular screening methods that are commonly employed in ultra-high and high dimensional data. Through this publicly available package, we provide a unified framework to carry out model-free screening procedures including SIS (Fan and Lv (2008) <doi:10.1111/j.1467-9868.2008.00674.x>), SIRS(Zhu et al. (2011)<doi:10.1198/jasa.2011.tm10563>), DC-SIS (Li et al. (2012) <doi:10.1080/01621459.2012.695654>), MDC-SIS(Shao and Zhang (2014) <doi:10.1080/01621459.2014.887012>), Bcor-SIS (Pan et al. (2019) <doi:10.1080/01621459.2018.1462709>), PC-Screen (Liu et al. (2020) <doi:10.1080/01621459.2020.1783274>), WLS (Zhong et al.(2021) <doi:10.1080/01621459.2021.1918554>), Kfilter (Mai and Zou (2015) <doi:10.1214/14-AOS1303>), MVSIS (Cui et al. (2015) <doi:10.1080/01621459.2014.920256>), PSIS (Pan et al. (2016) <doi:10.1080/01621459.2014.998760>), CAS (Xie et al. (2020) <doi:10.1080/01621459.2019.1573734>), CI-SIS (Cheng and Wang. (2023) <doi:10.1016/j.cmpb.2022.107269>) and CSIS (Cheng et al. (2023) <doi:10.1007/s00180-023-01399-5>).

Last updated 7 months ago

2.00 score 2 stars 3 scripts 611 downloads

pathling - A Library for using 'Pathling'

R API for 'Pathling', a tool for querying and transforming electronic health record data that is represented using the 'Fast Healthcare Interoperability Resources' (FHIR) standard - see <https://pathling.csiro.au/docs>.

Last updated 7 months ago

2.00 score 10 scripts 556 downloads

ClusTCR2 - Identifying Similar T Cell Receptor Hyper-Variable Sequences with 'ClusTCR2'

Enhancing T cell receptor (TCR) sequence analysis, 'ClusTCR2', based on 'ClusTCR' python program, leverages Hamming distance to compare the complement-determining region three (CDR3) sequences for sequence similarity, variable gene (V gene) and length. The second step employs the Markov Cluster Algorithm to identify clusters within an undirected graph, providing a summary of amino acid motifs and matrix for generating network plots. Tailored for single-cell RNA-seq data with integrated TCR-seq information, 'ClusTCR2' is integrated into the Single Cell TCR and Expression Grouped Ontologies (STEGO) R application or 'STEGO.R'. See the two publications for more details. Sebastiaan Valkiers, Max Van Houcke, Kris Laukens, Pieter Meysman (2021) <doi:10.1093/bioinformatics/btab446>, Kerry A. Mullan, My Ha, Sebastiaan Valkiers, Nicky de Vrij, Benson Ogunjimi, Kris Laukens, Pieter Meysman (2023) <doi:10.1101/2023.09.27.559702>.

Last updated 7 months ago

genetargetsinglecell

2.00 score 1 scripts 175 downloads

hmmm - Hierarchical Multinomial Marginal Models

Functions for specifying and fitting marginal models for contingency tables proposed by Bergsma and Rudas (2002) <doi:10.1214/aos/1015362188> here called hierarchical multinomial marginal models (hmmm) and their extensions presented by Bartolucci, Colombi and Forcina (2007) <https://www.jstor.org/stable/24307737>; multinomial Poisson homogeneous (mph) models and homogeneous linear predictor (hlp) models for contingency tables proposed by Lang (2004) <doi:10.1214/aos/1079120140> and Lang (2005) <doi:10.1198/016214504000001042>. Inequality constraints on the parameters are allowed and can be tested.

Last updated 7 months ago

2.00 score 54 scripts 538 downloads

GWASinspector - Comprehensive and Easy to Use Quality Control of GWAS Results

When evaluating the results of a genome-wide association study (GWAS), it is important to perform a quality control to ensure that the results are valid, complete, correctly formatted, and, in case of meta-analysis, consistent with other studies that have applied the same analysis. This package was developed to facilitate and streamline this process and provide the user with a comprehensive report.

Last updated 8 months ago

2.00 score 4 scripts 523 downloads

nmaplateplot - The Plate Plot for Network Meta-Analysis Results

A graphical display of results from network meta-analysis (NMA). It is suitable for outcomes like odds ratio (OR), risk ratio (RR), risk difference (RD) and standardized mean difference (SMD). It also has an option to visually display and compare the surface under the cumulative ranking (SUCRA) of different treatments.

Last updated 9 months ago

2.00 score 2 scripts 153 downloads

wflo - Data Set and Helper Functions for Wind Farm Layout Optimization Problems

Provides a convenient data set, a set of helper functions, and a benchmark function for economically (profit) driven wind farm layout optimization. This enables researchers in the field of the NP-hard (non-deterministic polynomial-time hard) problem of wind farm layout optimization to focus on their optimization methodology contribution and also provides a realistic benchmark setting for comparability among contributions. See Croonenbroeck, Carsten & Hennecke, David (2020) <doi:10.1016/j.energy.2020.119244>.

Last updated 9 months ago

2.00 score 2 scripts 202 downloads

LogicForest - Logic Forest

Two classification ensemble methods based on logic regression models. LogForest() uses a bagging approach to construct an ensemble of logic regression models. LBoost() uses a combination of boosting and cross-validation to construct an ensemble of logic regression models. Both methods are used for classification of binary responses based on binary predictors and for identification of important variables and variable interactions predictive of a binary outcome. Wolf, B.J., Slate, E.H., Hill, E.G. (2010) <doi:10.1093/bioinformatics/btq354>.

Last updated 10 months ago

2.00 score 3 scripts 234 downloads

OptimModel - Perform Nonlinear Regression Using 'optim' as the Optimization Engine

A wrapper for 'optim' for nonlinear regression problems; see Nocedal J and Write S (2006, ISBN: 978-0387-30303-1). Performs ordinary least squares (OLS), iterative re-weighted least squares (IRWLS), and maximum likelihood (MLE). Also includes the robust outlier detection (ROUT) algorithm; see Motulsky, H and Brown, R (2006)<doi:10.1186/1471-2105-7-123>.

Last updated 10 months ago

2.00 score 1 stars 142 downloads

BElikelihood - Likelihood Method for Evaluating Bioequivalence

A likelihood method is implemented to present evidence for evaluating bioequivalence (BE). The functions use bioequivalence data [area under the blood concentration-time curve (AUC) and peak concentration (Cmax)] from various crossover designs commonly used in BE studies including a fully replicated, a partially replicated design, and a conventional 2x2 crossover design. They will calculate the profile likelihoods for the mean difference, total standard deviation ratio, and within subject standard deviation ratio for a test and a reference drug. A plot of a standardized profile likelihood can be generated along with the maximum likelihood estimate and likelihood intervals, which present evidence for bioequivalence. See Liping Du and Leena Choi (2015) <doi:10.1002/pst.1661>.

Last updated 10 months ago

2.00 score 191 downloads

psBayesborrow - Bayesian Information Borrowing with Propensity Score Matching

Hybrid control design is a way to borrow information from external controls to augment concurrent controls in a randomized controlled trial and is expected to overcome the feasibility issue when adequate randomized controlled trials cannot be conducted. A major challenge in the hybrid control design is its inability to eliminate a prior-data conflict caused by systematic imbalances in measured or unmeasured confounding factors between patients in the concurrent treatment/control group and external controls. To prevent the prior-data conflict, a combined use of propensity score matching and Bayesian commensurate prior has been proposed in the context of hybrid control design. The propensity score matching is first performed to guarantee the balance in baseline characteristics, and then the Bayesian commensurate prior is constructed while discounting the information based on the similarity in outcomes between the concurrent and external controls. 'psBayesborrow' is a package to implement the propensity score matching and the Bayesian analysis with commensurate prior, as well as to conduct a simulation study to assess operating characteristics of the hybrid control design, where users can choose design parameters in flexible and straightforward ways depending on their own application.

Last updated 10 months ago

cpp

2.00 score 2 scripts 157 downloads

iwaqr - Irrigation Water Quality Assessment and Visualizations

Calculates irrigation water quality ratios and has functions that could be used to plot several popular diagrams for irrigation water quality classification.

Last updated 10 months ago

2.00 score 167 downloads

absorber - Variable Selection in Nonparametric Models using B-Splines

A variable selection method using B-Splines in multivariate nOnparametric Regression models Based on partial dErivatives Regularization (ABSORBER) implements a novel variable selection method in a nonlinear multivariate model using B-splines. For further details we refer the reader to the paper Savino, M. E. and Lévy-Leduc, C. (2024), <https://hal.science/hal-04434820>.

Last updated 10 months ago

2.00 score 327 downloads

VIMPS - Calculate Variable Importance with Knock Off Variables

The variable importance is calculated using knock off variables. Then output can be provided in numerical and graphical form. Meredith L Wallace (2023) <doi:10.1186/s12874-023-01965-x>.

Last updated 10 months ago

2.00 score 121 downloads

RNAseqNet - Log-Linear Poisson Graphical Model with Hot-Deck Multiple Imputation

Infer log-linear Poisson Graphical Model with an auxiliary data set. Hot-deck multiple imputation method is used to improve the reliability of the inference with an auxiliary dataset. Standard log-linear Poisson graphical model can also be used for the inference and the Stability Approach for Regularization Selection (StARS) is implemented to drive the selection of the regularization parameter. The method is fully described in <doi:10.1093/bioinformatics/btx819>.

Last updated 10 months ago

2.00 score 10 scripts 188 downloads

SillyPutty - Silly Putty Clustering

Implements a simple, novel clustering algorithm based on optimizing the silhouette width. See <doi:10.1101/2023.11.07.566055> for details.

Last updated 11 months ago

clustering

2.00 score 3 scripts 148 downloads

easyDifferentialGeneCoexpression - Easily Performs Differential Coexpression Analysis

A function that reads in the GEO code of a list of probesets or gene symbols, a gene expression dataset GEO accession code, the name of the dataset feature discriminating the two conditions for the differential coexpression, and the values of the two different conditions for the differential coexpression, and returns the significant pairs of genes/probesets with highest differential coexpression (p-value < 0.005). If the input gene list is made of gene symbols, this package associates the probesets to these gene symbols, if found. Platforms available: GPL80, GPL8300, GPL80, GPL96, GPL570, GPL571, GPL20115, GPL1293, GPL6102, GPL6104, GPL6883, GPL6884, GPL13497, GPL14550, GPL17077, GPL6480. GEO: Gene Expression Omnibus. ID: identifier code. The GEO datasets are downloaded from the URL <https://ftp.ncbi.nlm.nih.gov/geo/series/>.

Last updated 11 months ago

2.00 score 2 scripts 234 downloads

curephEM - NPMLE for Logistic-Cox Cure-Rate Model

Expectation-Maximization (EM) algorithm for point estimation and variance estimation to the nonparametric maximum likelihood estimator (NPMLE) for logistic-Cox cure-rate model with left truncation and right- censoring. See Hou, Chambers and Xu (2017) <doi:10.1007/s10985-017-9415-2>.

Last updated 11 months ago

2.00 score 5 scripts 206 downloads

ammiBayes - Bayesian Ammi Model for Continuous Data

Flexible multi-environment trials analysis via MCMC method for Additive Main Effects and Multiplicative Model (AMMI) for continuous data. Biplot with the averages and regions of confidence can be generated. The chains run in parallel on Linux systems and run serially on Windows.

Last updated 11 months ago

2.00 score 8 scripts 333 downloads

g.data - Delayed-Data Packages

Create and maintain delayed-data packages (ddp's). Data stored in a ddp are available on demand, but do not take up memory until requested. You attach a ddp with g.data.attach(), then read from it and assign to it in a manner similar to S-PLUS, except that you must run g.data.save() to actually commit to disk.

Last updated 11 months ago

2.00 score 10 scripts 560 downloads

choplump - Permutation Test for Some Positive and Many Zero Responses

Calculates permutation tests that can be powerful for comparing two groups with some positive but many zero responses (see Follmann, Fay, and Proschan <DOI:10.1111/j.1541-0420.2008.01131.x>).

Last updated 11 months ago

2.00 score 6 scripts 272 downloads

bSi - Modeling and Computing Biogenic Silica ('bSi') from Inland and Pelagic Sediments

A collection of integrated tools designed to seamlessly interact with each other for the analysis of biogenic silica 'bSi' in inland and marine sediments. These tools share common data representations and follow a consistent 'API' design. The primary goal of the 'bSi' package is to simplify the installation process, facilitate data loading, and enable the analysis of multiple samples for biogenic silica fluxes. This package is designed to enhance the efficiency and coherence of the entire 'bSi' analytic workflow, from data loading to model construction and visualization tailored towards reconstructing productivity in aquatic ecosystems.

Last updated 11 months ago

2.00 score 4 scripts 191 downloads

mwlaxeref - Cross-References Lake Identifiers Between Different Data Sets

Handy helper package for cross-referencing lake identifiers among different data sets in the Midwestern United States. There are multiple different state, regional, and federal agencies that have different identifiers on lakes. This package helps you to go between them.

Last updated 11 months ago

2.00 score 12 scripts 92 downloads

CLimd - Generating Rainfall Rasters from IMD NetCDF Data

The developed function is a comprehensive tool for the analysis of India Meteorological Department (IMD) NetCDF rainfall data. Specifically designed to process high-resolution daily gridded rainfall datasets. It provides four key functions to process IMD NetCDF rainfall data and create rasters for various temporal scales, including annual, seasonal, monthly, and weekly rainfall. For method details see, Malik, A. (2019).<DOI:10.1007/s12517-019-4454-5>. It supports different aggregation methods, such as sum, min, max, mean, and standard deviation. These functions are designed for spatio-temporal analysis of rainfall patterns, trend analysis,geostatistical modeling of rainfall variability, identifying rainfall anomalies and extreme events and can be an input for hydrological and agricultural models.

Last updated 12 months ago

2.00 score 1 scripts 182 downloads

SenSpe - Estimating Specificity at Controlled Sensitivity, or Vice Versa

Perform biomarker evaluation and comparison in terms of specificity at a controlled sensitivity level, or sensitivity at a controlled specificity level. Point estimation and exact bootstrap of Huang, Parakati, Patil, and Sanda (2023) <doi:10.5705/ss.202021.0020> for the one- and two-biomarker problems are implemented.

Last updated 12 months ago

2.00 score 175 downloads

frontiles - Partial Frontier Efficiency Analysis

It calculates the alpha-quantile proposed by Daouia and Simar (2007) <doi:10.1016/j.jeconom.2006.07.002> and order-m efficiency score in multi-dimension proposed by Daouia and Gijbels (2011) <doi:10.1016/j.jeconom.2010.12.002> and computes several summaries and representation of the associated frontiers in 2d and 3d.

Last updated 1 years ago

2.00 score 1 stars 13 scripts 263 downloads

SpatGRID - Spatial Grid Generation from Longitude and Latitude List

The developed function is designed for the generation of spatial grids based on user-specified longitude and latitude coordinates. The function first validates the input longitude and latitude values, ensuring they fall within the appropriate geographic ranges. It then creates a polygon from the coordinates and determines the appropriate Universal Transverse Mercator zone based on the provided hemisphere and longitude values. Subsequently, transforming the input Shapefile to the Universal Transverse Mercator projection when necessary. Finally, a spatial grid is generated with the specified interval and saved as a Shapefile. For method details see, Brus,D.J.(2022).<DOI:10.1201/9781003258940>. The function takes into account crucial parameters such as the hemisphere (north or south), desired grid interval, and the output Shapefile path. The developed function is an efficient tool, simplifying the process of empty spatial grid generation for applications such as, geo-statistical analysis, digital soil mapping product generation, etc. Whether for environmental studies, urban planning, or any other geo-spatial analysis, this package caters to the diverse needs of users working with spatial data, enhancing the accessibility and ease of spatial data processing and visualization.

Last updated 1 years ago

2.00 score 1 scripts 137 downloads

WRestimates - Sample Size, Power and CI for the Win Ratio

Calculates non-parametric estimates of the sample size, power and confidence intervals for the win-ratio. For more detail on the theory behind the methodologies implemented see Yu, R. X. and Ganju, J. (2022) <doi:10.1002/sim.9297>.

Last updated 1 years ago

2.00 score 121 downloads

halk - Methods to Create Hierarchical Age Length Keys for Age Assignment

Provides methods for implementing hierarchical age length keys to estimate fish ages from lengths using data borrowing. Users can create hierarchical age length keys and use them to assign ages given length.

Last updated 1 years ago

2.00 score 3 scripts 214 downloads

SQRL - Enhances Interaction with 'ODBC' Databases

Provides simple and powerful interfaces that facilitate interaction with 'ODBC' data sources. Each data source gets its own unique and dedicated interface, wrapped around 'RODBC'. Communication settings are remembered between queries, and are managed silently in the background. The interfaces support multi-statement 'SQL' scripts, which can be parameterised via metaprogramming structures and embedded 'R' expressions.

Last updated 1 years ago

2.00 score 9 scripts 466 downloads

BayesPPD - Bayesian Power Prior Design

Bayesian power/type I error calculation and model fitting using the power prior and the normalized power prior for generalized linear models. Detailed examples of applying the package are available at <doi:10.32614/RJ-2023-016>. The Bayesian clinical trial design methodology is described in Chen et al. (2011) <doi:10.1111/j.1541-0420.2011.01561.x>, and Psioda and Ibrahim (2019) <doi:10.1093/biostatistics/kxy009>. The normalized power prior is described in Duan et al. (2006) <doi:10.1002/env.752> and Ibrahim et al. (2015) <doi:10.1002/sim.6728>.

Last updated 1 years ago

2.00 score 7 scripts 406 downloads

sqlcaser - 'SQL' Case Statement Generator

Includes built-in methods for generating long 'SQL' CASE statements, and other 'SQL' statements that may otherwise be arduous to construct by hand. The generated statement can easily be concatenated to string literals to form queries to 'SQL'-like databases, such as when using the 'RODBC' package. The current methods include casewhen() for building CASE statements, inlist() for building IN statements, and updatetable() for building UPDATE statements.

Last updated 1 years ago

2.00 score 116 downloads

GPArotateDF - Derivative Free Gradient Projection Factor Rotation

Derivative Free Gradient Projection Algorithms for Factor Rotation. For more details see ?GPArotateDF. Theory for these functions can be found in the following publications: Jennrich (2004) <doi:10.1007/BF02295647>. Bernaards and Jennrich (2005) <doi:10.1177/0013164404272507>.

Last updated 1 years ago

2.00 score 4 scripts 242 downloads

revert - Reversion Mutation Identifier for Sequencing Data

A tool for detecting reversions for a given pathogenic mutation from next-generation DNA sequencing data. It analyses reads aligned to the locus of the pathogenic mutation and reports reversion events where secondary mutations have restored or undone the deleterious effect of the original pathogenic mutation, e.g., secondary indels complement to a frameshift pathogenic mutation converting the orignal frameshift mutation into inframe mutaions, deletions or SNVs that replaced the original pathogenic mutation restoring the open reading frame, SNVs changing the stop codon caused by the original nonsense SNV into an amino acid, etc.

Last updated 1 years ago

2.00 score 120 downloads

STREAK - Receptor Abundance Estimation using Feature Selection and Gene Set Scoring

Performs receptor abundance estimation for single cell RNA-sequencing data using a supervised feature selection mechanism and a thresholded gene set scoring procedure. Seurat's normalization method is described in: Hao et al., (2021) <doi:10.1016/j.cell.2021.04.048>, Stuart et al., (2019) <doi:10.1016/j.cell.2019.05.031>, Butler et al., (2018) <doi:10.1038/nbt.4096> and Satija et al., (2015) <doi:10.1038/nbt.3192>. Method for reduced rank reconstruction and rank-k selection is detailed in: Javaid et al., (2022) <doi:10.1101/2022.10.08.511197>. Gene set scoring procedure is described in: Frost et al., (2020) <doi:10.1093/nar/gkaa582>. Clustering method is outlined in: Song et al., (2020) <doi:10.1093/bioinformatics/btaa613> and Wang et al., (2011) <doi:10.32614/RJ-2011-015>.

Last updated 1 years ago

2.00 score 2 scripts 151 downloads

landmulti - Landmark Prediction with Multiple Short-Term Events

Contains functions for a flexible varying-coefficient landmark model by incorporating multiple short-term events into the prediction of long-term survival probability. For more information about landmark prediction please see Li, W., Ning, J., Zhang, J., Li, Z., Savitz, S.I., Tahanan, A., Rahbar.M.H., (2023+). "Enhancing Long-term Survival Prediction with Multiple Short-term Events: Landmarking with A Flexible Varying Coefficient Model".

Last updated 1 years ago

2.00 score 143 downloads

localScore - Package for Sequence Analysis by Local Score

Functionalities for calculating the local score and calculating statistical relevance (p-value) to find a local Score in a sequence of given distribution (S. Mercier and J.-J. Daudin (2001) <https://hal.science/hal-00714174/>) ; S. Karlin and S. Altschul (1990) <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC53667/> ; S. Mercier, D. Cellier and F. Charlot (2003) <https://hal.science/hal-00937529v1/> ; A. Lagnoux, S. Mercier and P. Valois (2017) <doi:10.1093/bioinformatics/btw699> ).

Last updated 1 years ago

cpp

2.00 score 4 scripts 187 downloads

sara4r - An R-GUI for Spatial Analysis of Surface Runoff using the NRCS-CN Method

A Graphical user interface to calculate the rainfall-runoff relation using the Natural Resources Conservation Service - Curve Number method (NRCS-CN method) but include modifications by Hawkins et al., (2002) about the Initial Abstraction. This GUI follows the programming logic of a previously published software (Hernandez-Guzman et al., 2011)<doi:10.1016/j.envsoft.2011.07.006>. It is a raster-based GIS tool that outputs runoff estimates from Land use/land cover and hydrologic soil group maps. This package has already been published in Journal of Hydroinformatics (Hernandez-Guzman et al., 2021)<doi:10.2166/hydro.2020.087> but it is under constant development at the Institute about Natural Resources Research (INIRENA) from the Universidad Michoacana de San Nicolas de Hidalgo and represents a collaborative effort between the Hydro-Geomatic Lab (INIRENA) with the Environmental Management Lab (CIAD, A.C.).

Last updated 1 years ago

2.00 score 2 scripts 145 downloads

TPAC - Tissue-Adjusted Pathway Analysis of Cancer (TPAC)

Contains logic for single sample gene set testing of cancer transcriptomic data with adjustment for normal tissue-specificity. Frost, H. Robert (2023) "Tissue-adjusted pathway analysis of cancer (TPAC)" <doi:10.1101/2022.03.17.484779>.

Last updated 1 years ago

2.00 score 182 downloads

wdnr.gis - Pull Spatial Layers from 'WDNR ArcGIS REST API'

Functions for finding and pulling data from the 'Wisconsin Department of Natural Resources ArcGIS REST APIs' <https://dnrmaps.wi.gov/arcgis/rest/services> and <https://dnrmaps.wi.gov/arcgis2/rest/services>.

Last updated 1 years ago

2.00 score 1 stars 3 scripts 188 downloads

RFPM - Floating Percentile Model

Floating Percentile Model with additional functions for optimizing inputs and evaluating outputs and assumptions.

Last updated 1 years ago

2.00 score 2 scripts 556 downloads

SOHPIE - Statistical Approach via Pseudo-Value Information and Estimation

'SOHPIE' (pronounced as SOFIE) is a novel pseudo-value regression approach for differential co-abundance network analysis of microbiome data, which can include additional clinical covariate in the model. The full methodological details can be found in Ahn S and Datta S (2023) <arXiv:2303.13702v1>.

Last updated 1 years ago

2.00 score 3 scripts 562 downloads

TransGraph - Transfer Graph Learning

Transfer learning, aiming to use auxiliary domains to help improve learning of the target domain of interest when multiple heterogeneous datasets are available, has always been a hot topic in statistical machine learning. The recent transfer learning methods with statistical guarantees mainly focus on the overall parameter transfer for supervised models in the ideal case with the informative auxiliary domains with overall similarity. In contrast, transfer learning for unsupervised graph learning is in its infancy and largely follows the idea of overall parameter transfer as for supervised learning. In this package, the transfer learning for several complex graphical models is implemented, including Tensor Gaussian graphical models, non-Gaussian directed acyclic graph (DAG), and Gaussian graphical mixture models. Notably, this package promotes local transfer at node-level and subgroup-level in DAG structural learning and Gaussian graphical mixture models, respectively, which are more flexible and robust than the existing overall parameter transfer. As by-products, transfer learning for undirected graphical model (precision matrix) via D-trace loss, transfer learning for mean vector estimation, and single non-Gaussian learning via topological layer method are also included in this package. Moreover, the aggregation of auxiliary information is an important issue in transfer learning, and this package provides multiple user-friendly aggregation methods, including sample weighting, similarity weighting, and most informative selection. Reference: Ren, M., Zhen Y., and Wang J. (2022) <arXiv:2211.09391> "Transfer learning for tensor graphical models". Ren, M., He X., and Wang J. (2023) <arXiv:2310.10239> "Structural transfer learning of non-Gaussian DAG". Zhao, R., He X., and Wang J. (2022) <https://jmlr.org/papers/v23/21-1173.html> "Learning linear non-Gaussian directed acyclic graph with diverging number of nodes".

Last updated 1 years ago

2.00 score 11 scripts 122 downloads

BetaPASS - Calculate Power and Sample Size with Beta Regression

Power calculations are a critical component of any research study to determine the minimum sample size necessary to detect differences between multiple groups. Researchers often work with data taking the form of proportions that can be modeled with a beta distribution. Here we present an R package, 'BetaPASS', that perform power and sample size calculations for data following a beta distribution with comparative nonparametric output. This package allows flexibility with multiple options for link functions to fit the data and graphing functionality for visual comparisons.

Last updated 1 years ago

2.00 score 2 scripts 189 downloads

PASSED - Calculate Power and Sample Size for Two Sample Mean Tests

Power calculations are a critical component of any research study to determine the minimum sample size necessary to detect differences between multiple groups. Here we present an 'R' package, 'PASSED', that performs power and sample size calculations for the test of two-sample means or ratios with data following beta, gamma (Chang et al. (2011), <doi:10.1007/s00180-010-0209-1>), normal, Poisson (Gu et al. (2008), <doi:10.1002/bimj.200710403>), binomial, geometric, and negative binomial (Zhu and Lakkis (2014), <doi:10.1002/sim.5947>) distributions.

Last updated 1 years ago

2.00 score 8 scripts 313 downloads

VectorCodeR - Easily Analyze Your Gait Patterns Using Vector Coding Technique

Facilitate the analysis of inter-limb and intra-limb coordination in human movement. It provides functions for calculating the phase angle between two segments, enabling researchers and practitioners to quantify the coordination patterns within and between limbs during various motor tasks. Needham, R., Naemi, R., & Chockalingam, N. (2014) <doi:10.1016/j.jbiomech.2013.12.032>. Needham, R., Naemi, R., & Chockalingam, N. (2015) <doi:10.1016/j.jbiomech.2015.07.023>. Tepavac, D., & Field-Fote, E. C. (2001) <doi:10.1123/jab.17.3.259>. Park, J.H., Lee, H., Cho, Js. et al. (2021) <doi:10.1038/s41598-020-80237-w>.

Last updated 1 years ago

2.00 score 3 scripts 161 downloads

EMDSVRhybrid - Empirical Mode Decomposition Based Support Vector Regression Model

Description: Application of empirical mode decomposition based support vector regression model for nonlinear and non stationary univariate time series forecasting. For method details see (i) Choudhury (2019) <http://krishi.icar.gov.in/jspui/handle/123456789/44873>; (ii) Das (2020) <http://krishi.icar.gov.in/jspui/handle/123456789/43174>; (iii) Das (2023) <http://krishi.icar.gov.in/jspui/handle/123456789/77772>.

Last updated 1 years ago

2.00 score 3 scripts 197 downloads

LabourMarketAreas - Identification, Tuning, Visualisation and Analysis of Labour Market Areas

Produces Labour Market Areas from commuting flows available at elementary territorial units. It provides tools for automatic tuning based on spatial contiguity. It also allows for statistical analyses and visualisation of the new functional geography.

Last updated 1 years ago

2.00 score 6 scripts 357 downloads

OneArm2stage - Phase II Single-Arm Two-Stage Designs with Time-to-Event Outcomes

Two-stage design for single-arm phase II trials with time-to-event endpoints (e.g., clinical trials on immunotherapies among cancer patients) can be calculated using this package. Two notable advantages of the package: 1) It provides flexible choices from three design methods (optimal, minmax, and admissible), and 2) the power of the design is more accurately calculated using the exact variance in the one-sample log-rank test. The package can be used for 1) planning the sample sizes and other design parameters, and 2) conducting the interim and final analyses for the Go/No-go decisions. More details about the design method can be found in: Wu, J, Chen L, Wei J, Weiss H, Chauhan A. (2020). <doi:10.1002/pst.1983>.

Last updated 1 years ago

2.00 score 2 scripts 205 downloads

UniExactFunTest - Uniform Exact Functional Tests for Contingency Tables

Testing whether two discrete variables have a functional relationship under null distributions where the two variables are statistically independent with fixed marginal counts. The fast enumeration algorithm was based on (Nguyen et al. 2020) <doi:10.24963/ijcai.2020/372>.

Last updated 1 years ago

cpp

2.00 score 4 scripts 138 downloads

reappraised - Statistical Tools for Assessing Publication Integrity of Groups of Trials

Takes user-provided baseline data from groups of randomised controlled data and assesses whether the observed distribution of baseline p-values, numbers of participants in each group, or categorical variables are consistent with the expected distribution, as an aid to the assessment of integrity concerns in published randomised controlled trials. References (citations in PubMed format in details of each function): Bolland MJ, Avenell A, Gamble GD, Grey A. (2016) <doi:10.1212/WNL.0000000000003387>. Bolland MJ, Gamble GD, Avenell A, Grey A, Lumley T. (2019) <doi:10.1016/j.jclinepi.2019.05.006>. Bolland MJ, Gamble GD, Avenell A, Grey A. (2019) <doi:10.1016/j.jclinepi.2019.03.001>. Bolland MJ, Gamble GD, Grey A, Avenell A. (2020) <doi:10.1111/anae.15165>. Bolland MJ, Gamble GD, Avenell A, Cooper DJ, Grey A. (2021) <doi:10.1016/j.jclinepi.2020.11.012>. Bolland MJ, Gamble GD, Avenell A, Grey A. (2021) <doi:10.1016/j.jclinepi.2021.05.002>. Bolland MJ, Gamble GD, Avenell A, Cooper DJ, Grey A. (2023) <doi:10.1016/j.jclinepi.2022.12.018>. Carlisle JB, Loadsman JA. (2017) <doi:10.1111/anae.13650>. Carlisle JB. (2017) <doi:10.1111/anae.13938>.

Last updated 1 years ago

2.00 score 2 scripts 272 downloads

markophylo - Markov Chain Models for Phylogenetic Trees

Allows for fitting of maximum likelihood models using Markov chains on phylogenetic trees for analysis of discrete character data. Examples of such discrete character data include restriction sites, gene family presence/absence, intron presence/absence, and gene family size data. Hypothesis-driven user- specified substitution rate matrices can be estimated. Allows for biologically realistic models combining constrained substitution rate matrices, site rate variation, site partitioning, branch-specific rates, allowing for non-stationary prior root probabilities, correcting for sampling bias, etc. See Dang and Golding (2016) <doi:10.1093/bioinformatics/btv541> for more details.

Last updated 1 years ago

openblascpp

2.00 score 13 scripts 204 downloads

NiLeDAM - Monazite Dating for the NiLeDAM Team

Th-U-Pb electron microprobe age dating of monazite, as originally described in <doi:10.1016/0009-2541(96)00024-1>.

Last updated 1 years ago

2.00 score 4 scripts 164 downloads

EMDANNhybrid - Empirical Mode Decomposition Based Artificial Neural Network Model

Application of empirical mode decomposition based artificial neural network model for nonlinear and non stationary univariate time series forecasting. For method details see (i) Choudhury (2019) <https://www.indianjournals.com/ijor.aspx?target=ijor:ijee3&volume=55&issue=1&article=013>; (ii) Das (2020) <https://www.indianjournals.com/ijor.aspx?target=ijor:ijee3&volume=56&issue=2&article=002>.

Last updated 1 years ago

2.00 score 3 scripts 191 downloads

mergingTools - Tools to Merge Hardware Event Monitors (HEMs) Coming from Separate Subexperiments into One Single Dataframe

Implementation of two tools to merge Hardware Event Monitors (HEMs) from different subexperiments. Hardware Reading and Merging (HRM), which uses order statistics to merge; and MUlti-Correlation HEM (MUCH) which merges using a multivariate normal distribution. The reference paper for HRM is: S. Vilardell, I. Serra, R. Santalla, E. Mezzetti, J. Abella and F. J. Cazorla, "HRM: Merging Hardware Event Monitors for Improved Timing Analysis of Complex MPSoCs," in IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems, vol. 39, no. 11, pp. 3662-3673, Nov. 2020, <doi:10.1109/TCAD.2020.3013051>. For MUCH: S. Vilardell, I. Serra, E. Mezzetti, J. Abella, and F. J. Cazorla. 2021. "MUCH: exploiting pairwise hardware event monitor correlations for improved timing analysis of complex MPSoCs". In Proceedings of the 36th Annual ACM Symposium on Applied Computing (SAC '21). Association for Computing Machinery. <doi:10.1145/3412841.3441931>. This work has been supported by the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (grant agreement No. 772773).

Last updated 1 years ago

2.00 score 5 scripts 92 downloads

QuadRoot - Quadratic Root for any Quadratic Equation

It will assist the user to find simple quadratic roots from any quadratic equation.

Last updated 1 years ago

2.00 score 7 scripts 172 downloads

meta.shrinkage - Meta-Analyses for Simultaneously Estimating Individual Means

Implement meta-analyses for simultaneously estimating individual means with shrinkage, isotonic regression and pretests. Include our original implementation of the isotonic regression via the pool-adjacent-violators algorithm (PAVA) algorithm. For the pretest estimator, the confidence interval for individual means are provided. Methodologies were published in Taketomi et al. (2021) <doi:10.3390/axioms10040267>, Taketomi et al. (2022) <doi:10.3390/a15010026>, Taketomi et al. (2023-) (under review).

Last updated 1 years ago

2.00 score 280 downloads

TSTutorial - Fitting and Predict Time Series Interactive Laboratory

Interactive laboratory of Time Series based in Box-Jenkins methodology.

Last updated 1 years ago

2.00 score 7 scripts 297 downloads

ECTSVR - Cointegration Based Support Vector Regression Model

The cointegration based support vector regression model enables researchers to use data obtained from the cointegrating vector as input in the support vector regression model.

Last updated 1 years ago

2.00 score 3 scripts 164 downloads

GWRLASSO - A Hybrid Model for Spatial Prediction Through Local Regression

It implements a hybrid spatial model for improved spatial prediction by combining the variable selection capability of LASSO (Least Absolute Shrinkage and Selection Operator) with the Geographically Weighted Regression (GWR) model that captures the spatially varying relationship efficiently. For method details see, Wheeler, D.C.(2009).<DOI:10.1068/a40256>. The developed hybrid model efficiently selects the relevant variables by using LASSO as the first step; these selected variables are then incorporated into the GWR framework, allowing the estimation of spatially varying regression coefficients at unknown locations and finally predicting the values of the response variable at unknown test locations while taking into account the spatial heterogeneity of the data. Integrating the LASSO and GWR models enhances prediction accuracy by considering spatial heterogeneity and capturing the local relationships between the predictors and the response variable. The developed hybrid spatial model can be useful for spatial modeling, especially in scenarios involving complex spatial patterns and large datasets with multiple predictor variables.

Last updated 1 years ago

2.00 score 3 scripts 163 downloads

VMDML - Variational Mode Decomposition Based Machine Learning Models

Application of Variational Mode Decomposition based different Machine Learning models for univariate time series forecasting. For method details see (i) K. Dragomiretskiy and D. Zosso (2014) <doi:10.1109/TSP.2013.2288675>; (ii) Pankaj Das (2020) <http://krishi.icar.gov.in/jspui/handle/123456789/44138>.

Last updated 1 years ago

2.00 score 3 scripts 160 downloads

HealthCal - Health Calculator

Health Calculator helps to find different parameters like basal metabolic rate, body mass index etc. related to fitness and health of a person.

Last updated 1 years ago

2.00 score 2 scripts 159 downloads

optistock - Determine Optimum Stocking Times Used in Fishery Enhancements

A collection of functions that aid in calculating the optimum time to stock hatchery reared fish into a body of water given the growth, mortality and cost of raising a particular number of individuals to a certain length.

Last updated 1 years ago

2.00 score 10 scripts 144 downloads

oceCens - Ordered Composite Endpoints with Censoring

Estimates win ratio or Mann-Whitney parameter for two group comparisons using ordered composite endpoints with right censoring as described in Follmann, Fay, Hamasaki, and Evans (2020)<doi:10.1002/sim.7890>.

Last updated 1 years ago

2.00 score 3 scripts 121 downloads

endogeneity - Recursive Two-Stage Models to Address Endogeneity

Various recursive two-stage models to address the endogeneity issue of treatment variables in observational study or mediators in experiments. The details of the models are discussed in Peng (2023) <doi:10.1287/isre.2022.1113>.

Last updated 1 years ago

cpp

2.00 score 2 scripts 264 downloads

PanelCount - Random Effects and/or Sample Selection Models for Panel Count Data

A high performance package implementing random effects and/or sample selection models for panel count data. The details of the models are discussed in Peng and Van den Bulte (2023) <doi:10.2139/ssrn.2702053>.

Last updated 1 years ago

cpp

2.00 score 8 scripts 141 downloads

NameNeedle - Using Needleman-Wunsch to Match Sample Names

The Needleman-Wunsch global alignment algorithm can be used to find approximate matches between sample names in different data sets. See Wang et al. (2010) <doi:10.4137/CIN.S5613>.

Last updated 1 years ago

2.00 score 1 stars 16 scripts 191 downloads

invgamstochvol - Obtains the Log Likelihood for an Inverse Gamma Stochastic Volatility Model

Computes the log likelihood for an inverse gamma stochastic volatility model using a closed form expression of the likelihood. The details of the computation of this closed form expression are given in Gonzalez and Majoni (2023) <http://rcea.org/RePEc/pdf/wp23-11.pdf> . The closed form expression is obtained for a stationary inverse gamma stochastic volatility model by marginalising out the volatility. This allows the user to obtain the maximum likelihood estimator for this non linear non Gaussian state space model. In addition, the user can obtain the estimates of the smoothed volatility using the exact smoothing distributions.

Last updated 1 years ago

cppopenmp

2.00 score 2 scripts 134 downloads

M3JF - Multi-Modal Matrix Joint Factorization for Integrative Multi-Omics Data Analysis

Multi modality data matrices are factorized conjointly into the multiplication of a shared sub-matrix and multiple modality specific sub-matrices, group sparse constraint is applied to the shared sub-matrix to capture the homogeneous and heterogeneous information, respectively. Then the samples are classified by clustering the shared sub-matrix with kmeanspp(), a new version of kmeans() developed here to obtain concordant results. The package also provides the cluster number estimation by rotation cost. Moreover, cluster specific features could be retrieved using hypergeometric tests.

Last updated 1 years ago

2.00 score 2 scripts 161 downloads

visit - Vaccine Phase I Design with Simultaneous Evaluation of Immunogenicity and Toxicity

Phase I clinical trials are the first step in drug development to test a new drug or drug combination on humans. Typical designs of Phase I trials use toxicity as the primary endpoint and aim to find the maximum tolerable dosage. However, these designs are poorly applicable for the development of cancer therapeutic vaccines because the expected safety concerns for these vaccines are not as much as cytotoxic agents. The primary objectives of a cancer therapeutic vaccine phase I trial thus often include determining whether the vaccine shows biologic activity and the minimum dose necessary to achieve a full immune or even clinical response. This package implements a Bayesian Phase I cancer vaccine trial design that allows simultaneous evaluation of safety and immunogenicity outcomes. See Wang et al. (2019) <DOI:10.1002/sim.8021> for further details.

Last updated 1 years ago

cpp

2.00 score 132 downloads

beanz - Bayesian Analysis of Heterogeneous Treatment Effect

It is vital to assess the heterogeneity of treatment effects (HTE) when making health care decisions for an individual patient or a group of patients. Nevertheless, it remains challenging to evaluate HTE based on information collected from clinical studies that are often designed and conducted to evaluate the efficacy of a treatment for the overall population. The Bayesian framework offers a principled and flexible approach to estimate and compare treatment effects across subgroups of patients defined by their characteristics. This package allows users to explore a wide range of Bayesian HTE analysis models, and produce posterior inferences about HTE. See Wang et al. (2018) <DOI:10.18637/jss.v085.i07> for further details.

Last updated 1 years ago

cpp

2.00 score 1 stars 7 scripts 358 downloads

MissCP - Change Point Detection with Missing Values

A four step change point detection method that can detect break points with the presence of missing values proposed by Liu and Safikhani (2023) <https://drive.google.com/file/d/1a8sV3RJ8VofLWikTDTQ7W4XJ76cEj4Fg/view?usp=drive_link>.

Last updated 1 years ago

openblascpp

2.00 score 2 scripts 128 downloads

SEARS - Seamless Dose Escalation/Expansion with Adaptive Randomization Scheme

A seamless design that combines phase I dose escalation based on toxicity with phase II dose expansion and dose comparison based on efficacy.

Last updated 1 years ago

2.00 score 2 scripts 125 downloads

coxerr - Cox Regression with Dependent Error in Covariates

Perform the functional modeling methods of Huang and Wang (2018) <doi:10.1111/biom.12741> to accommodate dependent error in covariates of the proportional hazards model. The adopted measurement error model has minimal assumptions on the dependence structure, and an instrumental variable is supposed to be available.

Last updated 1 years ago

fortran

2.00 score 2 scripts 155 downloads

orsk - Converting Odds Ratio to Relative Risk in Cohort Studies with Partial Data Information

Convert odds ratio to relative risk in cohort studies with partial data information (Wang (2013) <doi:10.18637/jss.v055.i05>).

Last updated 2 years ago

fortran

2.00 score 2 scripts 257 downloads

fastAFT - Fast Regression for the Accelerated Failure Time (AFT) Model

Fast censored linear regression for the accelerated failure time (AFT) model of Huang (2013) <doi:10.1111/sjos.12031>.

Last updated 2 years ago

fortran

2.00 score 2 scripts 181 downloads

cequre - Censored Quantile Regression & Monotonicity-Respecting Restoring

Perform censored quantile regression of Huang (2010) <doi:10.1214/09-AOS771>, and restore monotonicity respecting via adaptive interpolation for dynamic regression of Huang (2017) <doi:10.1080/01621459.2016.1149070>. The monotonicity-respecting restoration applies to general dynamic regression models including (uncensored or censored) quantile regression model, additive hazards model, and dynamic survival models of Peng and Huang (2007) <doi:10.1093/biomet/asm058>, among others.

Last updated 2 years ago

fortran

2.00 score 3 scripts 218 downloads

ExtremeBounds - Extreme Bounds Analysis (EBA)

An implementation of Extreme Bounds Analysis (EBA), a global sensitivity analysis that examines the robustness of determinants in regression models. The package supports both Leamer's and Sala-i-Martin's versions of EBA, and allows users to customize all aspects of the analysis.

Last updated 2 years ago

2.00 score 1 stars 7 scripts 398 downloads

gnrprod - Estimates Gross Output Functions

Estimation of gross output production functions and productivity in the presence of numerous fixed (nonflexible) and a single flexible input using the nonparametric identification strategy specified in Gandhi, Navarro, and Rivers (2020) <doi:10.1086/707736>. Monte Carlo evidence from the paper demonstrates high performance in estimating production function elasticities.

Last updated 2 years ago

2.00 score 2 stars 4 scripts 242 downloads

AlteredPQR - Detection of Altered Protein Quantitative Relationships

Inference of protein complex states from quantitative proteomics data. The package takes information on known stable protein interactions (i.e. protein components of the same complex) and assesses how protein quantitative ratios change between different conditions. It reports protein pairs for which relative protein quantities to each other have been significantly altered in the tested condition.

Last updated 2 years ago

2.00 score 2 scripts 298 downloads

glober - Estimating Functions with Multivariate B-Splines

Generalized LassO applied to knot selection in multivariate B-splinE Regression (GLOBER) implements a novel approach for estimating functions in a multivariate nonparametric regression model based on an adaptive knot selection for B-splines using the Generalized Lasso. For further details we refer the reader to the paper Savino, M. E. and Lévy-Leduc, C. (2023), <arXiv:2306.00686>.

Last updated 2 years ago

2.00 score 3 scripts 128 downloads

intrinsicKappa - Sample Size Planning Based on Intrinsic Kappa Value

Kappa statistics is one of the most used methods to evaluate the effectiveness of inpsections based on attribute assessments in industry. However, its estimation by available methods does not provide its "real" or "intrinstic" value. This package provides functions for the computation of the intrinsic kappa value as it is described in: Rafael Sanchez-Marquez, Frank Gerhorst and David Schindler (2023) "Effectiveness of quality inspections of attributive characteristics – A novel and practical method for estimating the “intrinsic” value of kappa based on alpha and beta statistics." <doi:10.1016/j.cie.2023.109006>.

Last updated 2 years ago

2.00 score 2 scripts 102 downloads

metevalue - E-Value in the Omics Data Association Studies

In the omics data association studies, it is common to conduct the p-value corrections to control the false significance. Beyond the P-value corrections, E-value is recently studied to facilitate multiple testing correction based on V. Vovk and R. Wang (2021) <doi:10.1214/20-AOS2020>. This package provides E-value calculation for DNA methylation data and RNA-seq data. Currently, five data formats are supported: DNA methylation levels using DMR detection tools (BiSeq, DMRfinder, MethylKit, Metilene and other DNA methylation tools) and RNA-seq data. The relevant references are listed below: Katja Hebestreit and Hans-Ulrich Klein (2022) <doi:10.18129/B9.bioc.BiSeq>; Altuna Akalin et.al (2012) <doi:10.18129/B9.bioc.methylKit>.

Last updated 2 years ago

2.00 score 2 scripts 170 downloads

SecDim - The Second Dimension of Spatial Association

Most of the current methods explore spatial association using observations at sample locations, which are defined as the first dimension of spatial association (FDA). The proposed concept of the second dimension of spatial association (SDA), as described in Yongze Song (2022) <doi:10.1016/j.jag.2022.102834>, aims to extract in-depth information about the geographical environment from locations outside sample locations for exploring spatial association.

Last updated 2 years ago

2.00 score 2 scripts 38 downloads

hdiVAR - Statistical Inference for Noisy Vector Autoregression

The model is high-dimensional vector autoregression with measurement error, also known as linear gaussian state-space model. Provable sparse expectation-maximization algorithm is provided for the estimation of transition matrix and noise variances. Global and simultaneous testings are implemented for transition matrix with false discovery rate control. For more information, see the accompanying paper: Lyu, X., Kang, J., & Li, L. (2023). "Statistical inference for high-dimensional vector autoregression with measurement error", Statistica Sinica.

Last updated 2 years ago

2.00 score 3 scripts 171 downloads

anabel - Analysis of Binding Events + l

A free software for a fast and easy analysis of 1:1 molecular interaction studies. This package is suitable for a high-throughput data analysis. Both the online app and the package are completely open source. You provide a table of sensogram, tell 'anabel' which method to use, and it takes care of all fitting details. The first two releases of 'anabel' were created and implemented as in (<doi:10.1177/1177932218821383>, <doi:10.1093/database/baz101>).

Last updated 2 years ago

2.00 score 4 scripts 267 downloads

npcurePK - Mixture Cure Model Estimation with Cure Status Partially Known

Performs nonparametric estimation in mixture cure models when the cure status is partially known. For details, see Safari et al (2021) <doi:10.1002/bimj.202100156>, Safari et al (2022) <doi:10.1177/09622802221115880> and Safari et al (2023) <doi:10.1007/s10985-023-09591-x>.

Last updated 2 years ago

2.00 score 9 scripts 104 downloads

stockR - Identifying Stocks in Genetic Data

Provides a mixture model for clustering individuals (or sampling groups) into stocks based on their genetic profile. Here, sampling groups are individuals that are sure to come from the same stock (e.g. breeding adults or larvae). The mixture (log-)likelihood is maximised using the EM-algorithm after finding good starting values via a K-means clustering of the genetic data. Details can be found in: Foster, S. D.; Feutry, P.; Grewe, P. M.; Berry, O.; Hui, F. K. C. & Davies (2020) <doi:10.1111/1755-0998.12920>.

Last updated 2 years ago

fortran

2.00 score 5 scripts 145 downloads

SpPOP - Generation of Spatial Population under Different Levels of Relationships among Variables

The developed package can be used to generate a spatial population for different levels of relationships among the dependent and auxiliary variables along with spatially varying model parameters. A spatial layout is designed as a [0,k-1]x[0,k-1] square region on which observations are collected at (k x k) lattice points with a unit distance between any two neighbouring points along the horizontal and vertical axes. For method details see Chao, Liu., Chuanhua, Wei. and Yunan, Su. (2018).<doi:10.1080/10485252.2018.1499907>. The generated spatial population can be utilized in Geographically Weighted Regression model based analysis for studying the spatially varying relationships among the variables. Furthermore, various statistical analysis can be performed on this spatially generated data.

Last updated 2 years ago

2.00 score 2 scripts 580 downloads

overlapptest - Test Overlapping of Polygons Against Random Rotation

Tests the observed overlapping polygon area in a collection of polygons against a null model of random rotation, as explained in De la Cruz et al. (2017) <doi:10.13140/RG.2.2.12825.72801>.

Last updated 2 years ago

2.00 score 10 scripts 572 downloads

InflectSSP - Melt Curve Fitting and Melt Shift Analysis

Analyzes raw abundance data from a cellular thermal shift experiment and calculates melt temperatures and melt shifts for each protein in the experiment. McCracken (2022) <doi:10.1101/2022.12.30.522131>.

Last updated 2 years ago

openjdk

2.00 score 3 scripts 782 downloads

nfer - Event Stream Abstraction using Interval Logic

This is the R API for the 'nfer' formalism (<http://nfer.io/>). 'nfer' was developed to specify event stream abstractions for spacecraft telemetry such as the Mars Science Laboratory. Users write rules using a syntax that borrows heavily from Allen's Temporal Logic that, when applied to an event stream, construct a hierarchy of temporal intervals with data. The R API supports loading rules from a file or mining them from historical data. Traces of events or pools of intervals are provided as data frames.

Last updated 2 years ago

2.00 score 3 scripts 216 downloads

NScluster - Simulation and Estimation of the Neyman-Scott Type Spatial Cluster Models

Simulation and estimation for Neyman-Scott spatial cluster point process models and their extensions, based on the methodology in Tanaka, Ogata, and Stoyan (2008) <doi:10.1002/bimj.200610339>. To estimate parameters by the simplex method, parallel computation using 'OpenMP' application programming interface is available. For more details see Tanaka, Saga and Nakano <doi:10.18637/jss.v098.i06>.

Last updated 2 years ago

fortranopenmp

2.00 score 1 stars 4 scripts 267 downloads

countdata - The Beta-Binomial Test for Count Data

The beta-binomial test is used for significance analysis of independent samples by Pham et al. (2010) <doi:10.1093/bioinformatics/btp677>. The inverted beta-binomial test is used for paired sample testing, e.g. pre-treatment and post-treatment data, by Pham and Jimenez (2012) <doi:10.1093/bioinformatics/bts394>.

Last updated 2 years ago

2.00 score 9 scripts 223 downloads

BRACE - Bias Reduction Through Analysis of Competing Events (BRACE)

Adjusting the bias due to residual confounding (often called treatment selection bias) in estimating the treatment effect in a proportional hazard model, as described in Williamson et al. (2022) <doi:10.1158/1078-0432.ccr-21-2468>.

Last updated 2 years ago

2.00 score 3 scripts 212 downloads

PPLasso - Prognostic Predictive Lasso for Biomarker Selection

We provide new tools for the identification of prognostic and predictive biomarkers. For further details we refer the reader to the paper: Zhu et al. Identification of prognostic and predictive biomarkers in high-dimensional data with PPLasso. BMC Bioinformatics. 2023 Jan 23;24(1):25.

Last updated 2 years ago

2.00 score 5 scripts 150 downloads

qPCRhelper - qPCR Ct Values to Expression Values

Computes normalized cycle threshold (Ct) values (delta Ct) from raw quantitative polymerase chain reaction (qPCR) Ct values and conducts test of significance using t.test(). Plots expression values based from log2(2^(-1*delta delta Ct)) across groups per gene of interest. Methods for calculation of delta delta Ct and relative expression (2^(-1*delta delta Ct)) values are described in: Livak & Schmittgen, (2001) <doi:10.1006/meth.2001.1262>.

Last updated 2 years ago

2.00 score 4 scripts 197 downloads

forplo - Flexible Forest Plots

Simplifies the creation and customization of forest plots (alternatively called dot-and-whisker plots). Input classes accepted by 'forplo' are data.frame, matrix, lm, glm, and coxph. 'forplo' was written in base R and does not depend on other packages.

Last updated 2 years ago

2.00 score 3 scripts 264 downloads

OCA - Optimal Capital Allocations

Computes optimal capital allocations based on some standard principles such as Haircut, Overbeck type II and the Covariance Allocation Principle. It also provides some shortcuts for obtaining the Value at Risk and the Expectation Shortfall, using both the normal and the t-student distribution, see Urbina and Guillén (2014)<doi:10.1016/j.eswa.2014.05.017> and Urbina (2013)<http://hdl.handle.net/2099.1/19443>.

Last updated 2 years ago

2.00 score 8 scripts 185 downloads

hydroroute - Trace Longitudinal Hydropeaking Waves

Implements an empirical approach referred to as PeakTrace which uses multiple hydrographs to detect and follow hydropower plant-specific hydropeaking waves at the sub-catchment scale and to describe how hydropeaking flow parameters change along the longitudinal flow path. The method is based on the identification of associated events and uses (linear) regression models to describe translation and retention processes between neighboring hydrographs. Several regression model results are combined to arrive at a power plant-specific model. The approach is proposed and validated in Greimel et al. (2022) <doi:10.1002/rra.3978>. The identification of associated events is based on the event detection implemented in 'hydropeak'.

Last updated 2 years ago

2.00 score 130 downloads

siie - Superior Identification Index and Its Extensions

Calculate superior identification index and its extensions. Measure the performance of journals based on how well they could identify the top papers by any index (e.g. citation indices) according to Huang & Yang. (2022) <doi:10.1007/s11192-022-04372-z>. These methods could be extended to evaluate other entities such as institutes, countries, etc.

Last updated 2 years ago

2.00 score 3 scripts 258 downloads

Allspice - RNA-Seq Profile Classifier

We developed a lightweight machine learning tool for RNA profiling of acute lymphoblastic leukemia (ALL), however, it can be used for any problem where multiple classes need to be identified from multi-dimensional data. The methodology is described in Makinen V-P, Rehn J, Breen J, Yeung D, White DL (2022) Multi-cohort transcriptomic subtyping of B-cell acute lymphoblastic leukemia, International Journal of Molecular Sciences 23:4574, <doi:10.3390/ijms23094574>. The classifier contains optimized mean profiles of the classes (centroids) as observed in the training data, and new samples are matched to these centroids using the shortest Euclidean distance. Centroids derived from a dataset of 1,598 ALL patients are included, but users can train the models with their own data as well. The output includes both numerical and visual presentations of the classification results. Samples with mixed features from multiple classes or atypical values are also identified.

Last updated 2 years ago

2.00 score 374 downloads

cencrne - Consistent Estimation of the Number of Communities via Regularized Network Embedding

The network analysis plays an important role in numerous application domains including biomedicine. Estimation of the number of communities is a fundamental and critical issue in network analysis. Most existing studies assume that the number of communities is known a priori, or lack of rigorous theoretical guarantee on the estimation consistency. This method proposes a regularized network embedding model to simultaneously estimate the community structure and the number of communities in a unified formulation. The proposed model equips network embedding with a novel composite regularization term, which pushes the embedding vector towards its center and collapses similar community centers with each other. A rigorous theoretical analysis is conducted, establishing asymptotic consistency in terms of community detection and estimation of the number of communities. Reference: Ren, M., Zhang S. and Wang J. (2022). "Consistent Estimation of the Number of Communities via Regularized Network Embedding". Biometrics, <doi:10.1111/biom.13815>.

Last updated 2 years ago

2.00 score 7 scripts 165 downloads

MB - The Use of Marginal Distributions in Conditional Forecasting

A new way to predict time series using the marginal distribution table in the absence of the significance of traditional models.

Last updated 2 years ago

2.00 score 6 scripts 131 downloads

PlatformDesign - Optimal Two-Period Multiarm Platform Design with New Experimental Arms Added During the Trial

Design parameters of the optimal two-period multiarm platform design (controlling for either family-wise error rate or pair-wise error rate) can be calculated using this package, allowing pre-planned deferred arms to be added during the trial. More details about the design method can be found in the paper: Pan, H., Yuan, X. and Ye, J. (2022) "An optimal two-period multiarm platform design with new experimental arms added during the trial". Manuscript submitted for publication. For additional references: Dunnett, C. W. (1955) <doi:10.2307/2281208>.

Last updated 2 years ago

2.00 score 3 scripts 170 downloads

ddc - Distance Density Clustering Algorithm

A distance density clustering (DDC) algorithm in R. DDC uses dynamic time warping (DTW) to compute a similarity matrix, based on which cluster centers and cluster assignments are found. DDC inherits dynamic time warping (DTW) arguments and constraints. The cluster centers are centroid points that are calculated using the DTW Barycenter Averaging (DBA) algorithm. The clustering process is divisive. At each iteration, cluster centers are updated and data is reassigned to cluster centers. Early stopping is possible. The output includes cluster centers and clustering assignment, as described in the paper (Ma et al (2017) <doi:10.1109/ICDMW.2017.11>).

Last updated 2 years ago

2.00 score 9 scripts 135 downloads

hdcate - Estimation of Conditional Average Treatment Effects with High-Dimensional Data

A two-step double-robust method to estimate the conditional average treatment effects (CATE) with potentially high-dimensional covariate(s). In the first stage, the nuisance functions necessary for identifying CATE are estimated by machine learning methods, allowing the number of covariates to be comparable to or larger than the sample size. The second stage consists of a low-dimensional local linear regression, reducing CATE to a function of the covariate(s) of interest. The CATE estimator implemented in this package not only allows for high-dimensional data, but also has the “double robustness” property: either the model for the propensity score or the models for the conditional means of the potential outcomes are allowed to be misspecified (but not both). This package is based on the paper by Fan et al., "Estimation of Conditional Average Treatment Effects With High-Dimensional Data" (2022), Journal of Business & Economic Statistics <doi:10.1080/07350015.2020.1811102>.

Last updated 2 years ago

2.00 score 4 scripts 193 downloads

goalp - Weighted and Lexicographic Goal Programming Interface

Solves goal programming problems of the weighted and lexicographic type, as well as combinations of the two, as described by Ignizio (1983) <doi:10.1016/0305-0548(83)90003-5>. Allows for a simple human-readable input describing the problem as a series of equations. Relies on the 'lpSolve' package to solve the underlying linear optimisation problem.

Last updated 2 years ago

2.00 score 3 scripts 431 downloads

RIbench - Benchmark Suite for Indirect Methods for RI Estimation

The provided benchmark suite enables the automated evaluation and comparison of any existing and novel indirect method for reference interval ('RI') estimation in a systematic way. Indirect methods take routine measurements of diagnostic tests, containing pathological and non-pathological samples as input and use sophisticated statistical methods to derive a model describing the distribution of the non-pathological samples, which can then be used to derive reference intervals. The benchmark suite contains 5,760 simulated test sets with varying difficulty. To include any indirect method, a custom wrapper function needs to be provided. The package offers functions for generating the test sets, executing the indirect method and evaluating the results. See ?RIbench or vignette("RIbench_package") for a more comprehensive description of the features. A detailed description and application is described in Ammer T., Schuetzenmeister A., Prokosch H.-U., Zierk J., Rank C.M., Rauh M. "RIbench: A Proposed Benchmark for the Standardized Evaluation of Indirect Methods for Reference Interval Estimation". Clinical Chemistry (2022) <doi:10.1093/clinchem/hvac142>.

Last updated 2 years ago

2.00 score 1 stars 2 scripts 230 downloads

SIMICO - Set-Based Inference for Multiple Interval-Censored Outcomes

Contains tests for association between a set of genetic variants and multiple correlated outcomes that are interval censored. Interval-censored data arises when the exact time of the onset of an outcome of interest is unknown but known to fall between two time points.

Last updated 2 years ago

2.00 score 2 scripts 189 downloads

HhP - Hierarchical Heterogeneity Analysis via Penalization

In medical research, supervised heterogeneity analysis has important implications. Assume that there are two types of features. Using both types of features, our goal is to conduct the first supervised heterogeneity analysis that satisfies a hierarchical structure. That is, the first type of features defines a rough structure, and the second type defines a nested and more refined structure. A penalization approach is developed, which has been motivated by but differs significantly from penalized fusion and sparse group penalization. Reference: Ren, M., Zhang, Q., Zhang, S., Zhong, T., Huang, J. & Ma, S. (2022). "Hierarchical cancer heterogeneity analysis based on histopathological imaging features". Biometrics, <doi:10.1111/biom.13426>.

Last updated 2 years ago

2.00 score 7 scripts 142 downloads

TransTGGM - Transfer Learning for Tensor Graphical Models

Tensor Gaussian graphical models (GGMs) have important applications in numerous areas, which can interpret conditional independence structures within tensor data. Yet, the available tensor data in one single study is often limited due to high acquisition costs. Although relevant studies can provide additional data, it remains an open question how to pool such heterogeneous data. This package implements a transfer learning framework for tensor GGMs, which takes full advantage of informative auxiliary domains even when non-informative auxiliary domains are present, benefiting from the carefully designed data-adaptive weights. Reference: Ren, M., Zhen Y., and Wang J. (2022). "Transfer learning for tensor graphical models" <arXiv:2211.09391>.

Last updated 2 years ago

2.00 score 5 scripts 172 downloads

BSSoverSpace - Blind Source Separation for Multivariate Spatial Data using Eigen Analysis

Provides functions for blind source separation over multivariate spatial data, and useful statistics for evaluating performance of estimation on mixing matrix. 'BSSoverSpace' is based on an eigen analysis of a positive definite matrix defined in terms of multiple normalized spatial local covariance matrices, and thus can handle moderately high-dimensional random fields. This package is an implementation of the method described in Zhang, Hao and Yao (2022)<arXiv:2201.02023>.

Last updated 2 years ago

2.00 score 2 scripts 197 downloads

BAR - Bayesian Adaptive Randomization

Bayesian adaptive randomization is also called outcome adaptive randomization, which is increasingly used in clinical trials.

Last updated 2 years ago

2.00 score 41 scripts 221 downloads

CSCNet - Fitting and Tuning Regularized Cause-Specific Cox Models with Elastic-Net Penalty

Flexible tools to fit, tune and obtain absolute risk predictions from regularized cause-specific cox models with elastic-net penalty.

Last updated 2 years ago

2.00 score 3 scripts 178 downloads

Ease - Simulating Explicit Population Genetics Models

Implementation in a simple and efficient way of fully customisable population genetics simulations, considering multiple loci that have epistatic interactions. Specifically suited to the modelling of multilocus nucleocytoplasmic systems (with both diploid and haploid loci), it is nevertheless possible to simulate purely diploid (or purely haploid) genetic models. Examples of models that can be simulated with Ease are numerous, for example models of genetic incompatibilities as presented by Marie-Orleach et al. (2022) <doi:10.1101/2022.07.25.501356>. Many others are conceivable, although few are actually explored, Ease having been developed in particular to provide a solution so that these kinds of models can be simulated simply.

Last updated 2 years ago

cpp

2.00 score 4 scripts 212 downloads

SoftBart - Implements the SoftBart Algorithm

Implements the SoftBart model of described by Linero and Yang (2018) <doi:10.1111/rssb.12293>, with the optional use of a sparsity-inducing prior to allow for variable selection. For usability, the package maintains the same style as the 'BayesTree' package.

Last updated 2 years ago

openblascpp

2.00 score 35 scripts 641 downloads

socialh - Rank and Social Hierarchy for Gregarious Animals

Tools developed to facilitate the establishment of the rank and social hierarchy for gregarious animals by the Si method developed by Kondo & Hurnik (1990)<doi:10.1016/0168-1591(90)90125-W>. It is also possible to determine the number of agonistic interactions between two individuals, sociometric and dyadics matrix from dataset obtained through electronic bins. In addition, it is possible plotting the results using a bar plot, box plot, and sociogram.

Last updated 2 years ago

2.00 score 3 scripts 252 downloads

brassica - 1970s BASIC Interpreter

Executes BASIC programs from the 1970s, for historical and educational purposes. This enables famous examples of early machine learning, artificial intelligence, natural language processing, cellular automata, and so on, to be run in their original form.

Last updated 2 years ago

2.00 score 275 downloads

ISEtools - Ion Selective Electrodes Analysis Methods

Characterisation and calibration of single or multiple Ion Selective Electrodes (ISEs); activity estimation of experimental samples. Implements methods described in: Dillingham, P.W., Radu, T., Diamond, D., Radu, A. and McGraw, C.M. (2012) <doi:10.1002/elan.201100510>, Dillingham, P.W., Alsaedi, B.S.O. and McGraw, C.M. (2017) <doi:10.1109/ICSENS.2017.8233898>, Dillingham, P.W., Alsaedi, B.S.O., Radu, A., and McGraw, C.M. (2019) <doi:10.3390/s19204544>, and Dillingham, P.W., Alsaedi, B.S.O., Granados-Focil, S., Radu, A., and McGraw, C.M. (2020) <doi:10.1021/acssensors.9b02133>.

Last updated 2 years ago

2.00 score 10 scripts 153 downloads

noisemodel - Noise Models for Classification Datasets

Implementation of models for the controlled introduction of errors in classification datasets. This package contains the noise models described in Saez (2022) <doi:10.3390/math10203736> that allow corrupting class labels, attributes and both simultaneously.

Last updated 2 years ago

2.00 score 5 scripts 197 downloads

Rgff - R Utilities for GFF Files

R utilities for gff files, either general feature format (GFF3) or gene transfer format (GTF) formatted files. This package includes functions for producing summary stats, check for consistency and sorting errors, conversion from GTF to GFF3 format, file sorting, visualization and plotting of feature hierarchy, and exporting user defined feature subsets to SAF format. This tool was developed by the BioinfoGP core facility at CNB-CSIC.

Last updated 2 years ago

2.00 score 3 scripts 215 downloads

varycoef - Modeling Spatially Varying Coefficients

Implements a maximum likelihood estimation (MLE) method for estimation and prediction of Gaussian process-based spatially varying coefficient (SVC) models (Dambon et al. (2021a) <doi:10.1016/j.spasta.2020.100470>). Covariance tapering (Furrer et al. (2006) <doi:10.1198/106186006X132178>) can be applied such that the method scales to large data. Further, it implements a joint variable selection of the fixed and random effects (Dambon et al. (2021b) <doi:10.1080/13658816.2022.2097684>). The package and its capabilities are described in (Dambon et al. (2021c) <arXiv:2106.02364>).

Last updated 2 years ago

2.00 score 16 scripts 221 downloads

MultiGlarmaVarSel - Variable Selection in Sparse Multivariate GLARMA Models

Performs variable selection in high-dimensional sparse GLARMA models. For further details we refer the reader to the paper Gomtsyan et al. (2022), <arXiv:2208.14721>.

Last updated 2 years ago

2.00 score 2 scripts 193 downloads

RAT - Research Assessment Tools

Includes algorithms to assess research productivity and patterns, such as the h-index and i-index. Cardoso et al. (2022) Cardoso, P., Fukushima, C.S. & Mammola, S. (2022) Quantifying the internationalization and representativeness in research. Trends in Ecology and Evolution, 37: 725-728.

Last updated 2 years ago

2.00 score 3 scripts 152 downloads

mlrpro - Stepwise Regression with Assumptions Checking

The stepwise regression with assumptions checking and the possible Box-Cox transformation.

Last updated 2 years ago

2.00 score 3 scripts 187 downloads

lnmCluster - Perform Logistic Normal Multinomial Clustering for Microbiome Compositional Data

An implementation of logistic normal multinomial (LNM) clustering. It is an extension of LNM mixture model proposed by Fang and Subedi (2020) <arXiv:2011.06682>, and is designed for clustering compositional data. The package includes 3 extended models: LNM Factor Analyzer (LNM-FA), LNM Bicluster Mixture Model (LNM-BMM) and Penalized LNM Factor Analyzer (LNM-FA). There are several advantages of LNM models: 1. LNM provides more flexible covariance structure; 2. Factor analyzer can reduce the number of parameters to estimate; 3. Bicluster can simultaneously cluster subjects and taxa, and provides significant biological insights; 4. Penalty term allows sparse estimation in the covariance matrix. Details for model assumptions and interpretation can be found in papers: Tu and Subedi (2021) <arXiv:2101.01871> and Tu and Subedi (2022) <doi:10.1002/sam.11555>.

Last updated 2 years ago

cpp

2.00 score 2 scripts 123 downloads

CloneSeeker - Seeking and Finding Clones in Copy Number and Sequencing Data

Defines the classes and functions used to simulate and to analyze data sets describing copy number variants and, optionally, sequencing mutations in order to detect clonal subsets. See Zucker et al. (2019) <doi:10.1093/bioinformatics/btz057>.

Last updated 2 years ago

2.00 score 8 scripts 177 downloads

EESPCA - Eigenvectors from Eigenvalues Sparse Principal Component Analysis (EESPCA)

Contains logic for computing sparse principal components via the EESPCA method, which is based on an approximation of the eigenvector/eigenvalue identity. Includes logic to support execution of the TPower and rifle sparse PCA methods, as well as logic to estimate the sparsity parameters used by EESPCA, TPower and rifle via cross-validation to minimize the out-of-sample reconstruction error. H. Robert Frost (2021) <doi:10.1080/10618600.2021.1987254>.

Last updated 3 years ago

2.00 score 1 stars 2 scripts 183 downloads

pwlmm - PWIGLS for Two-Level Multivariate and Multilevel Linear Models

Estimates two-level multilevel linear model and two-level multivariate linear multilevel model with weights following Probability Weighted Iterative Generalised Least Squares approach. For details see Veiga et al.(2014) <doi:10.1111/rssc.12020>.

Last updated 3 years ago

cpp

2.00 score 4 scripts 126 downloads

geno2proteo - Finding the DNA and Protein Sequences of Any Genomic or Proteomic Loci

Using the DNA sequence and gene annotation files provided in 'ENSEMBL' <https://www.ensembl.org/index.html>, the functions implemented in the package try to find the DNA sequences and protein sequences of any given genomic loci, and to find the genomic coordinates and protein sequences of any given protein locations, which are the frequent tasks in the analysis of genomic and proteomic data.

Last updated 3 years ago

geneticsproteomicssequencingannotationgenomeannotationgenomeassembly

2.00 score 9 scripts 172 downloads

onlineBcp - Online Bayesian Methods for Change Point Analysis

It implements the online Bayesian methods for change point analysis. It can also perform missing data imputation with methods from 'VIM'. The reference is Yigiter A, Chen J, An L, Danacioglu N (2015) <doi:10.1080/02664763.2014.1001330>. The link to the package is <https://CRAN.R-project.org/package=onlineBcp>.

Last updated 3 years ago

2.00 score 1 stars 7 scripts 214 downloads

EUfootball - Football Match Data of European Leagues

Contains match results from seven European men's football leagues, namely Premier League (England), Ligue 1 (France), Bundesliga (Germany), Serie A (Italy), Primera Division (Spain), Eredivisie (The Netherlands), Super Lig (Turkey). Includes Seasons 2010/2011 until 2019/2020 and a set of interesting covariates. Can be used all purposes.

Last updated 3 years ago

2.00 score 3 scripts 181 downloads

htestClust - Reweighted Marginal Hypothesis Tests for Clustered Data

A collection of reweighted marginal hypothesis tests for clustered data, based on reweighting methods of Williamson, J., Datta, S., and Satten, G. (2003) <doi:10.1111/1541-0420.00005>. The tests in this collection are clustered analogs to well-known hypothesis tests in the classical setting, and are appropriate for data with cluster- and/or group-size informativeness. The syntax and output of functions are modeled after common, recognizable functions native to R. Methods used in the package refer to Gregg, M., Datta, S., and Lorenz, D. (2020) <doi:10.1177/0962280220928572>, Nevalainen, J., Oja, H., and Datta, S. (2017) <doi:10.1002/sim.7288> Dutta, S. and Datta, S. (2015) <doi:10.1111/biom.12447>, Lorenz, D., Datta, S., and Harkema, S. (2011) <doi:10.1002/sim.4368>, Datta, S. and Satten, G. (2008) <doi:10.1111/j.1541-0420.2007.00923.x>, Datta, S. and Satten, G. (2005) <doi:10.1198/016214504000001583>.

Last updated 3 years ago

2.00 score 6 scripts 203 downloads

primate - Tools and Methods for Primatological Data Science

Data from All the World's Primates relational SQL database and other tabular datasets are made available via drivers and connection functions. Additionally we provide several functions and examples to facilitate the merging and aggregation of these tabular inputs.

Last updated 3 years ago

2.00 score 2 scripts 118 downloads

diffeRenTES - Computation of TES-Based Cell Differentiation Trees

Computes the ATM (Attractor Transition Matrix) structure and the tree-like structure describing the cell differentiation process (based on the Threshold Ergodic Set concept introduced by Serra and Villani), starting from the Boolean networks with synchronous updating scheme of the 'BoolNet' R package. TESs (Threshold Ergodic Sets) are the mathematical abstractions that represent the different cell types arising during ontogenesis. TESs and the powerful model of biological differentiation based on Boolean networks to which it belongs have been firstly described in "A Dynamical Model of Genetic Networks for Cell Differentiation" Villani M, Barbieri A, Serra R (2011) A Dynamical Model of Genetic Networks for Cell Differentiation. PLOS ONE 6(3): e17703.

Last updated 3 years ago

2.00 score 2 scripts 98 downloads

sealasso - Standard Error Adjusted Adaptive Lasso

Standard error adjusted adaptive lasso (SEA-lasso) is a version of the adaptive lasso, which incorporates OLS standard error to the L1 penalty weight. This method is intended for variable selection under linear regression settings (n > p). This new weight assignment strategy is especially useful when the collinearity of the design matrix is a concern.

Last updated 3 years ago

2.00 score 4 scripts 214 downloads

Markovchart - Markov Chain-Based Cost-Optimal Control Charts

Functions for cost-optimal control charts with a focus on health care applications. Compared to assumptions in traditional control chart theory, here, we allow random shift sizes, random repair and random sampling times. The package focuses on X-bar charts with a sample size of 1 (representing the monitoring of a single patient at a time). The methods are described in Zempleni et al. (2004) <doi:10.1002/asmb.521>, Dobi and Zempleni (2019) <doi:10.1002/qre.2518> and Dobi and Zempleni (2019) <http://ac.inf.elte.hu/Vol_049_2019/129_49.pdf>.

Last updated 3 years ago

2.00 score 206 downloads

complexity - Calculate the Proportion of Permutations in Line with an Informative Hypothesis

Allows for the easy computation of complexity: the proportion of the parameter space in line with the hypothesis by chance. The package comes with a Shiny application in which the calculations can be conducted as well.

Last updated 3 years ago

2.00 score 5 scripts 214 downloads

ahMLE - Methods for the Additive Hazard Model

Methods for fitting additive hazards model. Perform the maximum likelihood method as well as the traditional Aalen's method for estimating the additive hazards model. For details see Chengyuan Lu(2021) <arXiv:2004.06156>.

Last updated 3 years ago

openblascpp

2.00 score 2 scripts 380 downloads

LogisticRCI - Linear and Logistic Regression-Based Reliable Change Index

Here we provide an implementation of the linear and logistic regression-based Reliable Change Index (RCI), to be used with lm and binomial glm model objects, respectively, following Moral et al. <https://psyarxiv.com/gq7az/>. The RCI function returns a score assumed to be approximately normally distributed, which is helpful to detect patients that may present cognitive decline.

Last updated 3 years ago

2.00 score 2 scripts 171 downloads

bbreg - Bessel and Beta Regressions via Expectation-Maximization Algorithm for Continuous Bounded Data

Functions to fit, via Expectation-Maximization (EM) algorithm, the Bessel and Beta regressions to a data set with a bounded continuous response variable. The Bessel regression is a new and robust approach proposed in the literature. The EM version for the well known Beta regression is another major contribution of this package. See details in the references Barreto-Souza, Mayrink and Simas (2022) <doi:10.1111/anzs.12354> and Barreto-Souza, Mayrink and Simas (2020) <arXiv:2003.05157>.

Last updated 3 years ago

2.00 score 4 scripts 475 downloads

probout - Unsupervised Multivariate Outlier Probabilities for Large Datasets

Estimates unsupervised outlier probabilities for multivariate numeric data with many observations from a nonparametric outlier statistic.

Last updated 3 years ago

fortran

2.00 score 7 scripts 162 downloads

PHclust - Poisson Hurdle Clustering for Sparse Microbiome Data

Clustering analysis for sparse microbiome data, based on a Poisson hurdle model.

Last updated 3 years ago

2.00 score 5 scripts 91 downloads

LARisk - Estimation of Lifetime Attributable Risk of Cancer from Radiation Exposure

Compute lifetime attributable risk of radiation-induced cancer reveals that it can be helpful with enhancement of the flexibility in research with fast calculation and various options. Important reference papers include Berrington de Gonzalez et al. (2012) <doi:10.1088/0952-4746/32/3/205>, National Research Council (2006, ISBN:978-0-309-09156-5).

Last updated 3 years ago

2.00 score 2 scripts 141 downloads

kko - Kernel Knockoffs Selection for Nonparametric Additive Models

A variable selection procedure, dubbed KKO, for nonparametric additive model with finite-sample false discovery rate control guarantee. The method integrates three key components: knockoffs, subsampling for stability, and random feature mapping for nonparametric function approximation. For more information, see the accompanying paper: Dai, X., Lyu, X., & Li, L. (2021). “Kernel Knockoffs Selection for Nonparametric Additive Models”. arXiv preprint <arXiv:2105.11659>.

Last updated 3 years ago

2.00 score 1 stars 2 scripts 154 downloads

PhitestR - Analyzing the Heterogeneity of Single-Cell Populations

A bioinformatics method developed for analyzing the heterogeneity of single-cell populations. Phitest provides an objective and automatic method to evaluate the performance of clustering and quality of cell clusters.

Last updated 3 years ago

2.00 score 95 downloads

dataprep - Efficient and Flexible Data Preprocessing Tools

Efficiently and flexibly preprocess data using a set of data filtering, deletion, and interpolation tools. These data preprocessing methods are developed based on the principles of completeness, accuracy, threshold method, and linear interpolation and through the setting of constraint conditions, time completion & recovery, and fast & efficient calculation and grouping. Key preprocessing steps include deletions of variables and observations, outlier removal, and missing values (NA) interpolation, which are dependent on the incomplete and dispersed degrees of raw data. They clean data more accurately, keep more samples, and add no outliers after interpolation, compared with ordinary methods. Auto-identification of consecutive NA via run-length based grouping is used in observation deletion, outlier removal, and NA interpolation; thus, new outliers are not generated in interpolation. Conditional extremum is proposed to realize point-by-point weighed outlier removal that saves non-outliers from being removed. Plus, time series interpolation with values to refer to within short periods further ensures reliable interpolation. These methods are based on and improved from the reference: Liang, C.-S., Wu, H., Li, H.-Y., Zhang, Q., Li, Z. & He, K.-B. (2020) <doi:10.1016/j.scitotenv.2020.140923>.

Last updated 3 years ago

2.00 score 2 scripts 282 downloads

gfboost - Gradient-Free Gradient Boosting

Implementation of routines of the author's PhD thesis on gradient-free Gradient Boosting (Werner, Tino (2020) "Gradient-Free Gradient Boosting", URL '<https://oops.uni-oldenburg.de/id/eprint/4290>').

Last updated 3 years ago

2.00 score 3 scripts 132 downloads

NAP - Non-Local Alternative Priors in Psychology

Conducts Bayesian Hypothesis tests of a point null hypothesis against a two-sided alternative using Non-local Alternative Prior (NAP) for one- and two-sample z- and t-tests (Pramanik and Johnson, 2022). Under the alternative, the NAP is assumed on the standardized effects size in one-sample tests and on their differences in two-sample tests. The package considers two types of NAP densities: (1) the normal moment prior, and (2) the composite alternative. In fixed design tests, the functions calculate the Bayes factors and the expected weight of evidence for varied effect size and sample size. The package also provides a sequential testing framework using the Sequential Bayes Factor (SBF) design. The functions calculate the operating characteristics (OC) and the average sample number (ASN), and also conducts sequential tests for a sequentially observed data.

Last updated 3 years ago

2.00 score 133 downloads

BOJ - Interface to Bank of Japan Statistics

Provides an interface to Bank of Japan <https://www.boj.or.jp> statistics.

Last updated 3 years ago

2.00 score 203 downloads

GEVACO - Joint Test of Gene and GxE Interactions via Varying Coefficients

A novel statistical model to detect the joint genetic and dynamic gene-environment (GxE) interaction with continuous traits in genetic association studies. It uses varying-coefficient models to account for different GxE trajectories, regardless whether the relationship is linear or not. The package includes one function, GxEtest(), to test a single genetic variant (e.g., a single nucleotide polymorphism or SNP), and another function, GxEscreen(), to test for a set of genetic variants. The method involves a likelihood ratio test described in Crainiceanu, C. M., and Ruppert, D. (2004) <doi:10.1111/j.1467-9868.2004.00438.x>.

Last updated 3 years ago

2.00 score 2 scripts 198 downloads

OSTE - Optimal Survival Trees Ensemble

Function for growing survival trees ensemble ('Naz Gul', 'Nosheen Faiz', 'Dan Brawn', 'Rafal Kulakowski', 'Zardad Khan', and 'Berthold Lausen' (2020) <arXiv:2005.09043>) is given. The trees are grown by the method of random survival forest ('Marvin Wright', 'Andreas Ziegler' (2017) <doi:10.18637/jss.v077.i01>). The survival trees grown are assessed for both individual and collective performances. The ensemble can give promising results on fewer survival trees selected in the final ensemble.

Last updated 3 years ago

2.00 score 1 stars 151 downloads

meerva - Analysis of Data with Measurement Error Using a Validation Subsample

Sometimes data for analysis are obtained using more convenient or less expensive means yielding "surrogate" variables for what could be obtained more accurately, albeit with less convenience; or less conveniently or at more expense yielding "reference" variables, thought of as being measured without error. Analysis of the surrogate variables measured with error generally yields biased estimates when the objective is to make inference about the reference variables. Often it is thought that ignoring the measurement error in surrogate variables only biases effects toward the null hypothesis, but this need not be the case. Measurement errors may bias parameter estimates either toward or away from the null hypothesis. If one has a data set with surrogate variable data from the full sample, and also reference variable data from a randomly selected subsample, then one can assess the bias introduced by measurement error in parameter estimation, and use this information to derive improved estimates based upon all available data. Formulaically these estimates based upon the reference variables from the validation subsample combined with the surrogate variables from the whole sample can be interpreted as starting with the estimate from reference variables in the validation subsample, and "augmenting" this with additional information from the surrogate variables. This suggests the term "augmented" estimate. The meerva package calculates these augmented estimates in the regression setting when there is a randomly selected subsample with both surrogate and reference variables. Measurement errors may be differential or non-differential, in any or all predictors (simultaneously) as well as outcome. The augmented estimates derive, in part, from the multivariate correlation between regression model parameter estimates from the reference variables and the surrogate variables, both from the validation subset. Because the validation subsample is chosen at random any biases imposed by measurement error, whether non-differential or differential, are reflected in this correlation and these correlations can be used to derive estimates for the reference variables using data from the whole sample. The main functions in the package are meerva.fit which calculates estimates for a dataset, and meerva.sim.block which simulates multiple datasets as described by the user, and analyzes these datasets, storing the regression coefficient estimates for inspection. The augmented estimates, as well as how measurement error may arise in practice, is described in more detail by Kremers WK (2021) <arXiv:2106.14063> and is an extension of the works by Chen Y-H, Chen H. (2000) <doi:10.1111/1467-9868.00243>, Chen Y-H. (2002) <doi:10.1111/1467-9868.00324>, Wang X, Wang Q (2015) <doi:10.1016/j.jmva.2015.05.017> and Tong J, Huang J, Chubak J, et al. (2020) <doi:10.1093/jamia/ocz180>.

Last updated 3 years ago

2.00 score 665 downloads

DCEmgmt - DCE Data Reshaping and Processing

Prepare the results of a DCE to be analysed through choice models.'DCEmgmt' reshapes DCE data from wide to long format considering the special characteristics of a DCE. 'DCEmgmt' includes the function 'DCEestm' which estimates choice models once the database has been reshaped with 'DCEmgmt'.

Last updated 3 years ago

2.00 score 2 scripts 142 downloads

SDAResources - Datasets and Functions for 'Sampling: Design and Analysis, 3rd Edition'

Includes all the datasets of 'Sampling: Design and Analysis' (3rd edition by Sharon Lohr) in R format and additional functions for analyzing and graphing probability samples.

Last updated 3 years ago

2.00 score 26 scripts 428 downloads

GlarmaVarSel - Variable Selection in Sparse GLARMA Models

Performs variable selection in high-dimensional sparse GLARMA models. For further details we refer the reader to the paper Gomtsyan et al. (2020), <arXiv:2007.08623v1>.

Last updated 3 years ago

2.00 score 2 scripts 151 downloads

PAMhm - Generate Heatmaps Based on Partitioning Around Medoids (PAM)

Data are partitioned (clustered) into k clusters "around medoids", which is a more robust version of K-means implemented in the function pam() in the 'cluster' package. The PAM algorithm is described in Kaufman and Rousseeuw (1990) <doi:10.1002/9780470316801>. Please refer to the pam() function documentation for more references. Clustered data is plotted as a split heatmap allowing visualisation of representative "group-clusters" (medoids) in the data as separated fractions of the graph while those "sub-clusters" are visualised as a traditional heatmap based on hierarchical clustering.

Last updated 3 years ago

2.00 score 2 scripts 113 downloads

cmprskcoxmsm - Use IPW to Estimate Treatment Effect under Competing Risks

Uses inverse probability weighting methods to estimate treatment effect under marginal structure model for the cause-specific hazard of competing risk events. Estimates also the cumulative incidence function (i.e. risk) of the potential outcomes, and provides inference on risk difference and risk ratio. Reference: Kalbfleisch & Prentice (2002)<doi:10.1002/9781118032985>; Hernan et al (2001)<doi:10.1198/016214501753168154>.

Last updated 3 years ago

2.00 score 1 stars 3 scripts 214 downloads

isni - Index of Local Sensitivity to Nonignorability

The current version provides functions to compute, print and summarize the Index of Sensitivity to Nonignorability (ISNI) in the generalized linear model for independent data, and in the marginal multivariate Gaussian model and the mixed-effects models for continuous and binary longitudinal/clustered data. It allows for arbitrary patterns of missingness in the regression outcomes caused by dropout and/or intermittent missingness. One can compute the sensitivity index without estimating any nonignorable models or positing specific magnitude of nonignorability. Thus ISNI provides a simple quantitative assessment of how robust the standard estimates assuming missing at random is with respect to the assumption of ignorability. For a tutorial, download at <https://huixie.people.uic.edu/Research/ISNI_R_tutorial.pdf>. For more details, see Troxel Ma and Heitjan (2004) and Xie and Heitjan (2004) <doi:10.1191/1740774504cn005oa> and Ma Troxel and Heitjan (2005) <doi:10.1002/sim.2107> and Xie (2008) <doi:10.1002/sim.3117> and Xie (2012) <doi:10.1016/j.csda.2010.11.021> and Xie and Qian (2012) <doi:10.1002/jae.1157>.

Last updated 3 years ago

2.00 score 7 scripts 323 downloads

RHybridFinder - Identification of Hybrid Peptides in Immunopeptidomic Analyses

Tool for the analysis Mass Spectrometry (MS) data in the context of immunopeptidomic analysis for the identification of hybrid peptides and the predictions of binding affinity of all peptides using 'netMHCpan' <doi:10.1093/nar/gkaa379> while providing a summary of the netMHCpan output. 'RHybridFinder' (RHF) is destined for researchers who are looking to analyze their MS data for the purpose of identification of potential spliced peptides. This package, developed mainly in base R, is based on the workflow published by Faridi et al. in 2018 <doi:10.1126/sciimmunol.aar3947>.

Last updated 3 years ago

2.00 score 5 scripts 196 downloads

ADP - Adoption Probability, Triers and Users Rate of a New Product

Calculate users prevalence of a product based on the prevalence of triers in the population. The measurement of triers is relatively easy. It is just a question of whether a person tried a product even once in his life or not. On the other hand, The measurement of people who also adopt it as part of their life is more complicated since adopting an innovative product is a subjective view of the individual. Mickey Kislev and Shira Kislev developed a formula to calculate the prevalence of a product's users to overcome this difficulty. The current package assists in calculating the users prevalence of a product based on the prevalence of triers in the population. See for: Kislev, M. M., and S. Kislev (2020) <doi:10.5539/ijms.v12n4p63>.

Last updated 3 years ago

2.00 score 281 downloads

DMtest - Differential Methylation Tests (DMtest)

Several tests for differential methylation in methylation array data, including one-sided differential mean and variance test. Methods used in the package refer to Dai, J, Wang, X, Chen, H and others (2021) "Incorporating increased variability in discovering cancer methylation markers", Biostatistics, submitted.

Last updated 3 years ago

2.00 score 3 scripts 145 downloads

tmplate - Code Generation Based on Templates

Define general templates with tags that can be replaced by content depending on arguments and objects to modify the final output of the document.

Last updated 3 years ago

2.00 score 5 scripts 158 downloads

comsimitv - Flexible Framework for Simulating Community Assembly

Flexible framework for trait-based simulation of community assembly, where components could be replaced by user-defined function and that allows variation of traits within species.

Last updated 3 years ago

2.00 score 3 scripts 191 downloads

FeatureTerminatoR - Feature Selection Engine to Remove Features with Minimal Predictive Power

The aim is to take in data.frame inputs and utilises methods, such as recursive feature engineering, to enable the features to be removed. What this does differently from the other packages, is that it gives you the choice to remove the variables manually, or it automated this process. Feature selection is a concept in machine learning, and statistical pipelines, whereby unimportant, or less predictive variables are eliminated from the analysis, see Boughaci (2018) <doi:10.1007/s40595-018-0107-y>.

Last updated 3 years ago

2.00 score 7 scripts 194 downloads

NHSDataDictionaRy - NHS Data Dictionary Toolset for NHS Lookups

Providing a common set of simplified web scraping tools for working with the NHS Data Dictionary <https://datadictionary.nhs.uk/data_elements_overview.html>. The intended usage is to access the data elements section of the NHS Data Dictionary to access key lookups. The benefits of having it in this package are that the lookups are the live lookups on the website and will not need to be maintained. This package was commissioned by the NHS-R community <https://nhsrcommunity.com/> to provide this consistency of lookups. The OpenSafely lookups have now been added <https://www.opencodelists.org/docs/>.

Last updated 3 years ago

2.00 score 5 scripts 193 downloads

intcensROC - AUC Estimation of Interval Censored Survival Data

The kernel of this 'Rcpp' based package is an efficient implementation of the generalized gradient projection method for spline function based constrained maximum likelihood estimator for interval censored survival data (Wu, Yuan; Zhang, Ying. Partially monotone tensor spline estimation of the joint distribution function with bivariate current status data. Ann. Statist. 40, 2012, 1609-1636 <doi:10.1214/12-AOS1016>). The key function computes the density function of the joint distribution of event time and the marker and returns the receiver operating characteristic (ROC) curve for the interval censored survival data as well as area under the curve (AUC).

Last updated 4 years ago

cpp

2.00 score 8 scripts 180 downloads

hybridogram - Function that Creates a Heat Map from Hybridization Data

Using hybrid data, this package created a vividly colored hybrid heat map. The input is two files which are auto-selected. The first file has three columns, the first two for pairs of species, with the third column for the hybrid experiment code (an integer). The second file is a list of code and their descriptions in two columns. The output is a figure showing the hybrid heat map with a color legend.

Last updated 4 years ago

2.00 score 2 scripts 108 downloads

IIVpredictor - Modeling Within Individual Variability as Predictor

Time parceling method and Bayesian variability modeling methods for modeling within individual variability indicators as predictors.For more details, see <https://github.com/xliu12/IIVpredicitor>.

Last updated 4 years ago

jagscpp

2.00 score 2 scripts 186 downloads

vtype - Estimates the Variable Type in Error Afflicted Data

Estimates the type of variables in non-quality controlled data. The prediction is based on a random forest model, trained on over 5000 medical variables with accuracy of 99%. The accuracy can hardy depend on type and coding style of data.

Last updated 4 years ago

2.00 score 2 scripts 114 downloads

SunsVoc - Constructing Suns-Voc from Outdoor Time-Series I-V Curves

Suns-Voc (or Isc-Voc) curves can provide the current-voltage (I-V) characteristics of the diode of photovoltaic cells without the effect of series resistance. Here, Suns-Voc curves can be constructed with outdoor time-series I-V curves [1,2,3] of full-size photovoltaic (PV) modules instead of having to be measured in the lab. Time series of four different power loss modes can be calculated based on obtained Isc-Voc curves. This material is based upon work supported by the U.S. Department of Energy's Office of Energy Efficiency and Renewable Energy (EERE) under Solar Energy Technologies Office (SETO) Agreement Number DE-EE0008172. Jennifer L. Braid is supported by the U.S. Department of Energy (DOE) Office of Energy Efficiency and Renewable Energy administered by the Oak Ridge Institute for Science and Education (ORISE) for the DOE. ORISE is managed by Oak Ridge Associated Universities (ORAU) under DOE contract number DE-SC0014664. [1] Wang, M. et al, 2018. <doi:10.1109/PVSC.2018.8547772>. [2] Walters et al, 2018 <doi:10.1109/PVSC.2018.8548187>. [3] Guo, S. et al, 2016. <doi:10.1117/12.2236939>.

Last updated 4 years ago

2.00 score 3 scripts 185 downloads

RRTCS - Randomized Response Techniques for Complex Surveys

Point and interval estimation of linear parameters with data obtained from complex surveys (including stratified and clustered samples) when randomization techniques are used. The randomized response technique was developed to obtain estimates that are more valid when studying sensitive topics. Estimators and variances for 14 randomized response methods for qualitative variables and 7 randomized response methods for quantitative variables are also implemented. In addition, some data sets from surveys with these randomization methods are included in the package.

Last updated 4 years ago

2.00 score 43 scripts 167 downloads

rNeighborQTL - Interval Mapping for Quantitative Trait Loci Underlying Neighbor Effects

To enable quantitative trait loci mapping of neighbor effects, this package extends a single-marker regression to interval mapping. The theoretical background of the method is described in Sato et al. (2021) <doi:10.1093/g3journal/jkab017>.

Last updated 4 years ago

2.00 score 3 scripts 670 downloads

svplots - Sample Variance Plots (Sv-Plots)

Two versions of sample variance plots, Sv-plot1 and Sv-plot2, will be provided illustrating the squared deviations from sample variance. Besides indicating the contribution of squared deviations for the sample variability, these plots are capable of detecting characteristics of the distribution such as symmetry, skewness and outliers. A remarkable graphical method based on Sv-plot2 can determine the decision on testing hypotheses over one or two population means. In sum, Sv-plots will be appealing visualization tools. Complete description of this methodology can be found in the article, Wijesuriya (2020) <doi:10.1080/03610918.2020.1851716>.

Last updated 4 years ago

2.00 score 4 scripts 134 downloads

AdvancedBasketballStats - Advanced Basketball Statistics

Provides different functionalities and calculations used in the world of basketball to analyze the statistics of the players, the statistics of the teams, the statistics of the quintets and the statistics of the plays. For more details of the calculations included in the package can be found in the book Basketball on Paper written by Dean Oliver.

Last updated 4 years ago

2.00 score 3 scripts 259 downloads

spotidy - Providing Convenience Functions to Connect R with the Spotify API

Providing convenience functions to connect R with the 'Spotify' application programming interface ('API'). At first it aims to help setting up the OAuth2.0 Authentication flow. The default output of the get_*() functions is tidy, but optionally the functions could return the raw response from the 'API' as well. The search_*() and get_*() functions can be combined. See the vignette for more information and examples and the official Spotify for Developers website <https://developer.spotify.com/documentation/web-api/> for information about the Web 'API'.

Last updated 4 years ago

2.00 score 5 scripts 126 downloads

BOSSreg - Best Orthogonalized Subset Selection (BOSS)

Best Orthogonalized Subset Selection (BOSS) is a least-squares (LS) based subset selection method, that performs best subset selection upon an orthogonalized basis of ordered predictors, with the computational effort of a single ordinary LS fit. This package provides a highly optimized implementation of BOSS and estimates a heuristic degrees of freedom for BOSS, which can be plugged into an information criterion (IC) such as AICc in order to select the subset from candidates. It provides various choices of IC, including AIC, BIC, AICc, Cp and GCV. It also implements the forward stepwise selection (FS) with no additional computational cost, where the subset of FS is selected via cross-validation (CV). CV is also an option for BOSS. For details see: Tian, Hurvich and Simonoff (2021), "On the Use of Information Criteria for Subset Selection in Least Squares Regression", <arXiv:1911.10191>.

Last updated 4 years ago

2.00 score 4 scripts 173 downloads

lwqs - Lagged Weighted Quantile Sum Regression

Wrapper functions for the implementation of lagged weighted quantile sum regression, as per 'Gennings et al' (2020) <doi:10.1016/j.envres.2020.109529>.

Last updated 4 years ago

2.00 score 2 scripts 222 downloads

IPCAPS - Iterative Pruning to Capture Population Structure

An unsupervised clustering algorithm based on iterative pruning is for capturing population structure. This version supports ordinal data which can be applied directly to SNP data to identify fine-level population structure and it is built on the iterative pruning Principal Component Analysis ('ipPCA') algorithm as explained in Intarapanich et al. (2009) <doi:10.1186/1471-2105-10-382>. The 'IPCAPS' involves an iterative process using multiple splits based on multivariate Gaussian mixture modeling of principal components and 'Expectation-Maximization' clustering as explained in Lebret et al. (2015) <doi:10.18637/jss.v067.i06>. In each iteration, rough clusters and outliers are also identified using the function rubikclust() from the R package 'KRIS'.

Last updated 4 years ago

2.00 score 10 scripts 490 downloads

PEACH - Pareto Enrichment Analysis for Combining Heterogeneous Datasets

A meta gene set analysis tool developed based on principles of Pareto dominance (William B T Mock (2011) <doi:10.1007/978-1-4020-9160-5_341>). It is designed to combine gene set analysis p-values from multiple transcriptome datasets (e.g., microarray and RNA-Seq). The novel Pareto method for p-value combination allows PEACH to properly model heterogeneity and correlation in Omics datasets.

Last updated 4 years ago

2.00 score 142 downloads

Snake - Game of Snake

Implements snake in R as a programming example, see <https://en.wikipedia.org/wiki/Snake_(video_game_genre)>.

Last updated 4 years ago

2.00 score 1 scripts 142 downloads

PBIR - Estimating the Probability of Being in Response and Related Outcomes

Make statistical inference on the probability of being in response, the duration of response, and the cumulative response rate up to a given time point. The method can be applied to analyze phase II randomized clinical trials with the endpoints being time to treatment response and time to progression or death.

Last updated 4 years ago

2.00 score 2 scripts 129 downloads

fairsubset - Choose Representative Subsets

Allows user to obtain subsets of columns of data or vectors within a list. These subsets will match the original data in terms of average and variation, but have a consistent length of data per column. It is intended for use on automated data generation which may not always output the same N per replicate or sample.

Last updated 4 years ago

2.00 score 2 scripts 165 downloads

genset - Generates Data Sets for Class Demonstrations

For educational purposes to demonstrate the importance of multiple regression. The genset function generates a data set from an initial data set to have the same summary statistics (mean, median, and standard deviation) but opposing regression results.

Last updated 4 years ago

2.00 score 98 downloads

credsubs - Credible Subsets

Functions for constructing simultaneous credible bands and identifying subsets via the "credible subsets" (also called "credible subgroups") method. Package documentation includes the vignette included in this package, and the paper by Schnell, Fiecas, and Carlin (2020, <doi:10.18637/jss.v094.i07>).

Last updated 4 years ago

2.00 score 8 scripts 204 downloads

scLink - Inferring Functional Gene Co-Expression Networks from Single Cell Data

Uses statistical network modeling to understand the co-expression relationships among genes and to construct sparse gene co-expression networks from single-cell gene expression data.

Last updated 4 years ago

2.00 score 10 scripts 122 downloads

MixOptim - Mixture Optimization Algorithm

Simple tools to perform mixture optimization based on the 'desirability' package by Max Kuhn. It also provides a plot routine using 'ggplot2' and 'patchwork'.

Last updated 4 years ago

2.00 score 10 scripts 114 downloads

BSS - Brownian Semistationary Processes

Efficient simulation of Brownian semistationary (BSS) processes using the hybrid simulation scheme, as described in Bennedsen, Lunde, Pakkannen (2017) <arXiv:1507.03004v4>, as well as functions to fit BSS processes to data, and functions to estimate the stochastic volatility process of a BSS process.

Last updated 5 years ago

2.00 score 2 scripts 146 downloads

unitedR - Assessment and Evaluation of Formations in United

United is a software tool which can be downloaded at the following website <http://www.schroepl.net/pbm/software/united/>. In general, it is a virtual manager game for football teams. This package contains helpful functions for determining an optimal formation for a virtual match in United. E.g. knowing that the opponent has a strong defensive it is advisable to beat him in the midfield. Furthermore, this package contains functions for computing the optimal usage of hardness in a game.

Last updated 5 years ago

2.00 score 6 scripts 141 downloads

addScales - Adds Labeled Center Line and Scale Lines/Regions to Trellis Plots

Modifies trellis objects by adding horizontal and/or vertical reference lines or shaded regions that provide visual scaling information. This is mostly useful in multi-panel plots that use the relation = 'free' option in their 'scales' argument list.

Last updated 5 years ago

2.00 score 2 scripts 210 downloads

RSqlParser - Parse 'SQL' Statements

Parser for 'SQL' statements. Currently, it supports parsing of only 'SELECT' statements.

Last updated 5 years ago

2.00 score 4 scripts 107 downloads

CASMAP - Detection of Statistically Significant Combinations of SNPs in Association Mapping

A significant pattern mining-based toolbox for region-based genome-wide association studies and higher-order epistasis analyses, implementing the methods described in Llinares-López et al. (2017) <doi:10.1093/bioinformatics/btx071>.

Last updated 5 years ago

cpp

2.00 score 9 scripts 181 downloads

starm - Spatio-Temporal Autologistic Regression Model

Estimates the coefficients of the two-time centered autologistic regression model based on Gegout-Petit A., Guerin-Dubrana L., Li S. "A new centered spatio-temporal autologistic regression model. Application to local spread of plant diseases." 2019. <arXiv:1811.06782>, using a grid of binary variables to estimate the spread of a disease on the grid over the years.

Last updated 5 years ago

2.00 score 114 downloads

survCurve - Plots Survival Curves Element by Element

Plots survival models from the 'survival' package. Additionally, it plots curves of multistate models from the 'mstate' package. Typically, a plot is drawn by the sequence survplot(), confIntArea(), survCurve() and nrAtRisk(). The separation of the plot in this 4 functions allows for great flexibility to make a custom plot for publication.

Last updated 5 years ago

2.00 score 3 scripts 141 downloads

DevTreatRules - Develop Treatment Rules with Observational Data

Develop and evaluate treatment rules based on: (1) the standard indirect approach of split-regression, which fits regressions separately in both treatment groups and assigns an individual to the treatment option under which predicted outcome is more desirable; (2) the direct approach of outcome-weighted-learning proposed by Yingqi Zhao, Donglin Zeng, A. John Rush, and Michael Kosorok (2012) <doi:10.1080/01621459.2012.695674>; (3) the direct approach, which we refer to as direct-interactions, proposed by Shuai Chen, Lu Tian, Tianxi Cai, and Menggang Yu (2017) <doi:10.1111/biom.12676>. Please see the vignette for a walk-through of how to start with an observational dataset whose design is understood scientifically and end up with a treatment rule that is trustworthy statistically, along with an estimation of rule benefit in an independent sample.

Last updated 5 years ago

2.00 score 2 scripts 157 downloads

tukeytrend - Tukeys Trend Test via Multiple Marginal Models

Provides wrapper functions to the multiple marginal model function mmm() of package 'multcomp' to implement the trend test of Tukey, Ciminera and Heyse (1985) <DOI:10.2307/2530666> for general parametric models.

Last updated 5 years ago

2.00 score 5 scripts 122 downloads

clusterability - Performs Tests for Cluster Tendency of a Data Set

Test for cluster tendency (clusterability) of a data set. The methods implemented - reducing the data set to a single dimension using principal component analysis or computing pairwise distances, and performing a multimodality test like the Dip Test or Silverman's Critical Bandwidth Test - are described in Adolfsson, Ackerman, and Brownstein (2019) <doi:10.1016/j.patcog.2018.10.026>. Such methods can inform whether clustering algorithms are appropriate for a data set.

Last updated 5 years ago

2.00 score 20 scripts 192 downloads

SeqDetect - Sequence and Latent Process Detector

Sequence detector in this package contains a specific automaton model that can be used to learn and detect data and process sequences. Automaton model in this package is capable of learning and tracing sequences. Automaton model can be found in Krleža, Vrdoljak, Brčić (2019) <doi:10.1109/ACCESS.2019.2955245>. This research has been partly supported under Competitiveness and Cohesion Operational Programme from the European Regional and Development Fund, as part of the Integrated Anti-Fraud System project no. KK.01.2.1.01.0041. This research has also been partly supported by the European Regional Development Fund under the grant KK.01.1.1.01.0009.

Last updated 5 years ago

2.00 score 2 scripts 143 downloads

optionstrat - Utilizes the Black-Scholes Option Pricing Model to Perform Strategic Option Analysis and Plot Option Strategies

Utilizes the Black-Scholes-Merton option pricing model to calculate key option analytics and perform graphical analysis of various option strategies. Provides functions to calculate the option premium and option greeks of European-style options.

Last updated 5 years ago

2.00 score 33 scripts 159 downloads

capitalR - Capital Budgeting Analysis, Annuity Loan Calculations and Amortization Schedules

Provides Capital Budgeting Analysis functionality and the essential Annuity loan functions. Also computes Loan Amortization Schedules including schedules with irregular payments.

Last updated 5 years ago

2.00 score 10 scripts 332 downloads

placer - PLastic ACcumulation Estimate using R (PLACER)

Assessment of the prevalence of plastic debris in bird nests based on bootstrap replicates. The package allows for calculating bootstrapped 95% confidence intervals for the estimated prevalence of debris. Combined with a Bayesian approach, the resampling simulations can be also used to define appropriate sample sizes to detect prevalence of plastics. The method has wide application, and can also be applied to estimate confidence intervals and define sample sizes for the prevalence of plastics ingested by any other organisms. The method is described in Tavares et al. (Submitted).

Last updated 5 years ago

2.00 score 99 downloads

BESTree - Branch-Exclusive Splits Trees

Decision tree algorithm with a major feature added. Allows for users to define an ordering on the partitioning process. Resulting in Branch-Exclusive Splits Trees (BEST). Cedric Beaulac and Jeffrey S. Rosentahl (2019) <arXiv:1804.10168>.

Last updated 5 years ago

2.00 score 2 scripts 161 downloads

mlmm.gwas - Pipeline for GWAS Using MLMM

Pipeline for Genome-Wide Association Study using Multi-Locus Mixed Model from Segura V, Vilhjálmsson BJ et al. (2012) <doi:10.1038/ng.2314>. The pipeline include detection of associated SNPs with MLMM, model selection by lowest eBIC and p-value threshold, estimation of the effects of the SNPs in the selected model and graphical functions.

Last updated 5 years ago

2.00 score 1 stars 5 scripts 167 downloads

BALLI - Expression RNA-Seq Data Analysis Based on Linear Mixed Model

Analysis of gene expression RNA-seq data using Bartlett-Adjusted Likelihood-based LInear model (BALLI). Based on likelihood ratio test, it provides comparisons for effect of one or more variables. See Kyungtaek Park (2018) <doi:10.1101/344929> for more information.

Last updated 6 years ago

2.00 score 199 downloads

PoA - Finds the Price of Anarchy for Routing Games

Computes the optimal flow, Nash flow and the Price of Anarchy for any routing game defined within the game theoretical framework. The input is a routing game in the form of it’s cost and flow functions. Then transforms this into an optimisation problem, allowing both Nash and Optimal flows to be solved by nonlinear optimisation. See <https://en.wikipedia.org/wiki/Congestion_game> and Knight and Harper (2013) <doi:10.1016/j.ejor.2013.04.003> for more information.

Last updated 6 years ago

2.00 score 1 scripts 127 downloads

MFT - The Multiple Filter Test for Change Point Detection

Provides statistical tests and algorithms for the detection of change points in time series and point processes - particularly for changes in the mean in time series and for changes in the rate and in the variance in point processes. References - Michael Messer, Marietta Kirchner, Julia Schiemann, Jochen Roeper, Ralph Neininger and Gaby Schneider (2014), A multiple filter test for the detection of rate changes in renewal processes with varying variance <doi:10.1214/14-AOAS782>. Stefan Albert, Michael Messer, Julia Schiemann, Jochen Roeper, Gaby Schneider (2017), Multi-scale detection of variance changes in renewal processes in the presence of rate change points <doi:10.1111/jtsa.12254>. Michael Messer, Kaue M. Costa, Jochen Roeper and Gaby Schneider (2017), Multi-scale detection of rate changes in spike trains with weak dependencies <doi:10.1007/s10827-016-0635-3>. Michael Messer, Stefan Albert and Gaby Schneider (2018), The multiple filter test for change point detection in time series <doi:10.1007/s00184-018-0672-1>. Michael Messer, Hendrik Backhaus, Albrecht Stroh and Gaby Schneider (2019+) Peak detection in time series.

Last updated 6 years ago

2.00 score 9 scripts 118 downloads

FuzzyStatProb - Fuzzy Stationary Probabilities from a Sequence of Observations of an Unknown Markov Chain

An implementation of a method for computing fuzzy numbers representing stationary probabilities of an unknown Markov chain, from which a sequence of observations along time has been obtained. The algorithm is based on the proposal presented by James Buckley in his book on Fuzzy probabilities (Springer, 2005), chapter 6. Package 'FuzzyNumbers' is used to represent the output probabilities.

Last updated 6 years ago

2.00 score 1 scripts 192 downloads

COST - Copula-Based Semiparametric Models for Spatio-Temporal Data

Parameter estimation, one-step ahead forecast and new location prediction methods for spatio-temporal data.

Last updated 6 years ago

2.00 score 10 scripts 127 downloads

BPM - Bayesian Purity Model to Estimate Tumor Purity

Bayesian purity model to estimate tumor purity using methylation array data (DNA methylation Infinium 450K array data) without reference samples.

Last updated 6 years ago

2.00 score 1 stars 5 scripts 137 downloads

mMPA - Implementation of Marker-Assisted Mini-Pooling with Algorithm

To determine the number of quantitative assays needed for a sample of data using pooled testing methods, which include mini-pooling (MP), MP with algorithm (MPA), and marker-assisted MPA (mMPA). To estimate the number of assays needed, the package also provides a tool to conduct Monte Carlo (MC) to simulate different orders in which the sample would be collected to form pools. Using MC avoids the dependence of the estimated number of assays on any specific ordering of the samples to form pools.

Last updated 6 years ago

2.00 score 6 scripts 107 downloads

MCSim - Determine the Optimal Number of Clusters

Identifies the optimal number of clusters by calculating the similarity between two clustering methods at the same number of clusters using the corrected indices of Rand and Jaccard as described in Albatineh and Niewiadomska-Bugaj (2011). The number of clusters at which the index attain its maximum more frequently is a candidate for being the optimal number of clusters.

Last updated 6 years ago

2.00 score 5 scripts 126 downloads

Rfolding - The Folding Test of Unimodality

The basic algorithm to perform the folding test of unimodality. Given a dataset X (d dimensional, n samples), the test checks whether the distribution of the data are rather unimodal or rather multimodal. This package stems from the following research publication: Siffer Alban, Pierre-Alain Fouque, Alexandre Termier, and Christine Largouët. "Are your data gathered?" In Proceedings of the 24th ACM SIGKDD International Conference on Knowledge Discovery Data Mining, pp. 2210-2218. ACM, 2018. <doi:10.1145/3219819.3219994>.

Last updated 6 years ago

2.00 score 6 scripts 101 downloads

CRM - Continual Reassessment Method (CRM) for Phase I Clinical Trials

Functions for phase I clinical trials using the continual reassessment method.

Last updated 6 years ago

2.00 score 8 scripts 150 downloads

SparseMDC - Implementation of SparseMDC Algorithm

Implements the algorithm described in Barron, M., and Li, J. (Not yet published). This algorithm clusters samples from multiple ordered populations, links the clusters across the conditions and identifies marker genes for these changes. The package was designed for scRNA-Seq data but is also applicable to many other data types, just replace cells with samples and genes with variables. The package also contains functions for estimating the parameters for SparseMDC as outlined in the paper. We recommend that users further select their marker genes using the magnitude of the cluster centers.

Last updated 6 years ago

2.00 score 7 scripts 118 downloads

dhh - A Heavy-Headed Distribution

The density, cumulative distribution, quantiles, and i.i.d random variables of a heavy-headed distribution. For more information, please see the vignette.

Last updated 6 years ago

2.00 score 6 scripts 140 downloads

RanglaPunjab - Displays Palette of 5 Colors

Displays palette of 5 colors based on photos depicting the unique and vibrant culture of Punjab in Northern India. Since Punjab translates to ``Land of 5 Rivers'' there are 5 colors per palette. If users need more than 5 colors, they can merge 2 to 3 palettes to create their own color-combination, or they can cherry-pick their own custom colors. Users can view up to 3 palettes together. Users can also list all the palette choices. And last but not least, users can see the photo that inspired a particular palette.

Last updated 6 years ago

2.00 score 7 scripts 143 downloads

sft - Functions for Systems Factorial Technology Analysis of Data

A series of tools for analyzing Systems Factorial Technology data. This includes functions for plotting and statistically testing capacity coefficient functions and survivor interaction contrast functions. Houpt, Blaha, McIntire, Havig, and Townsend (2013) <doi:10.3758/s13428-013-0377-3> provide a basic introduction to Systems Factorial Technology along with examples using the sft R package.

Last updated 6 years ago

2.00 score 1 stars 46 scripts 206 downloads

ACA - Abrupt Change-Point or Aberration Detection in Point Series

Offers an interactive function for the detection of breakpoints in series.

Last updated 6 years ago

2.00 score 5 scripts 319 downloads

oglmx - Estimation of Ordered Generalized Linear Models

Ordered models such as ordered probit and ordered logit presume that the error variance is constant across observations. In the case that this assumption does not hold estimates of marginal effects are typically biased (Weiss (1997)). This package allows for generalization of ordered probit and ordered logit models by allowing the user to specify a model for the variance. Furthermore, the package includes functions to calculate the marginal effects. Wrapper functions to estimate the standard limited dependent variable models are also included.

Last updated 7 years ago

2.00 score 11 scripts 256 downloads

AR - Another Look at the Acceptance-Rejection Method

In mathematics, 'rejection sampling' is a basic technique used to generate observations from a distribution. It is also commonly called 'the Acceptance-Rejection method' or 'Accept-Reject algorithm' and is a type of Monte Carlo method. 'Acceptance-Rejection method' is based on the observation that to sample a random variable one can perform a uniformly random sampling of the 2D cartesian graph, and keep the samples in the region under the graph of its density function. Package 'AR' is able to generate/simulate random data from a probability density function by Acceptance-Rejection method. Moreover, this package is a useful teaching resource for graphical presentation of Acceptance-Rejection method. From the practical point of view, the user needs to calculate a constant in Acceptance-Rejection method, which package 'AR' is able to compute this constant by optimization tools. Several numerical examples are provided to illustrate the graphical presentation for the Acceptance-Rejection Method.

Last updated 7 years ago

2.00 score 2 scripts 309 downloads

multisensi - Multivariate Sensitivity Analysis

Functions to perform sensitivity analysis on a model with multivariate output.

Last updated 7 years ago

2.00 score 1 stars 24 scripts 188 downloads

confSAM - Estimates and Bounds for the False Discovery Proportion, by Permutation

For multiple testing. Computes estimates and confidence bounds for the False Discovery Proportion (FDP), the fraction of false positives among all rejected hypotheses. The methods in the package use permutations of the data. Doing so, they take into account the dependence structure in the data.

Last updated 7 years ago

2.00 score 4 scripts 126 downloads

valection - Sampler for Verification Studies

A binding for the 'valection' program which offers various ways to sample the outputs of competing algorithms or parameterizations, and fairly assess their performance against each other. The 'valection' C library is required to use this package and can be downloaded from: <http://labs.oicr.on.ca/boutros-lab/software/valection>. Cooper CI, et al; Valection: Design Optimization for Validation and Verification Studies; Biorxiv 2018; <doi:10.1101/254839>.

Last updated 7 years ago

2.00 score 7 scripts 98 downloads

SDT - Self-Determination Theory Measures

Functions for self-determination motivation theory (SDT) to compute measures of motivation internalization, motivation simplex structure, and of the original and adjusted self-determination or relative autonomy index. SDT was introduced by Deci and Ryan (1985) <doi:10.1007/978-1-4899-2271-7>. See package?SDT for an overview.

Last updated 7 years ago

2.00 score 1 stars 8 scripts 103 downloads

rlme - Rank-Based Estimation and Prediction in Random Effects Nested Models

Estimates robust rank-based fixed effects and predicts robust random effects in two- and three- level random effects nested models. The methodology is described in Bilgic & Susmann (2013) <https://journal.r-project.org/archive/2013/RJ-2013-027/>.

Last updated 7 years ago

cpp

2.00 score 20 scripts 928 downloads

SparseDC - Implementation of SparseDC Algorithm

Implements the algorithm described in Barron, M., Zhang, S. and Li, J. 2017, "A sparse differential clustering algorithm for tracing cell type changes via single-cell RNA-sequencing data", Nucleic Acids Research, gkx1113, <doi:10.1093/nar/gkx1113>. This algorithm clusters samples from two different populations, links the clusters across the conditions and identifies marker genes for these changes. The package was designed for scRNA-Seq data but is also applicable to many other data types, just replace cells with samples and genes with variables. The package also contains functions for estimating the parameters for SparseDC as outlined in the paper. We recommend that users further select their marker genes using the magnitude of the cluster centers.

Last updated 7 years ago

2.00 score 8 scripts 202 downloads

TSCS - Time Series Cointegrated System

A set of functions to implement Time Series Cointegrated System (TSCS) spatial interpolation and relevant data visualization.

Last updated 7 years ago

2.00 score 13 scripts 114 downloads

confidence - Confidence Estimation of Environmental State Classifications

Functions for estimating and reporting multi-year averages and corresponding confidence intervals and distributions. A potential use case is reporting the chemical and ecological status of surface waters according to the European Water Framework Directive.

Last updated 7 years ago

2.00 score 5 scripts 186 downloads

tpAUC - Estimation and Inference of Two-Way pAUC, pAUC and pODC

Tools for estimating and inferring two-way partial area under receiver operating characteristic curves (two-way pAUC), partial area under receiver operating characteristic curves (pAUC), and partial area under ordinal dominance curves (pODC). Methods includes Mann-Whitney statistic and Jackknife, etc.

Last updated 8 years ago

2.00 score 9 scripts 123 downloads

afmToolkit - Functions for Atomic Force Microscope Force-Distance Curves Analysis

Set of functions for analyzing Atomic Force Microscope (AFM) force-distance curves. It allows to obtain the contact and unbinding points, perform the baseline correction, estimate the Young's modulus, fit up to two exponential decay function to a stress-relaxation / creep experiment, obtain adhesion energies. These operations can be done either over a single F-d curve or over a set of F-d curves in batch mode.

Last updated 8 years ago

2.00 score 20 scripts 607 downloads

remindR - Insert and Extract "Reminders" from Function Comments

Insert/extract text "reminders" into/from function source code comments or as the "comment" attribute of any object. The former can be handy in development as reminders of e.g. argument requirements, expected objects in the calling environment, required options settings, etc. The latter can be used to provide information of the object and as simple manual "tooltips" for users, among other things.

Last updated 8 years ago

2.00 score 4 scripts 420 downloads

rope - Model Selection with FDR Control of Selected Variables

Selects one model with variable selection FDR controlled at a specified level. A q-value for each potential variable is also returned. The input, variable selection counts over many bootstraps for several levels of penalization, is modeled as coming from a beta-binomial mixture distribution.

Last updated 8 years ago

2.00 score 3 scripts 393 downloads

SOFIA - Making Sophisticated and Aesthetical Figures in R

Software that leverages the capabilities of Circos by manipulating data, preparing configuration files, and running the Perl-native Circos directly from the R environment with minimal user intervention. Circos is a novel software that addresses the challenges in visualizing genetic data by creating circular ideograms composed of tracks of heatmaps, scatter plots, line plots, histograms, links between common markers, glyphs, text, and etc. Please see <http://www.circos.ca>.

Last updated 8 years ago

2.00 score 32 scripts 94 downloads

tsdecomp - Decomposition of Time Series Data

ARIMA-model-based decomposition of quarterly and monthly time series data. The methodology is developed and described, among others, in Burman (1980) <DOI:10.2307/2982132> and Hillmer and Tiao (1982) <DOI:10.2307/2287770>.

Last updated 8 years ago

2.00 score 10 scripts 168 downloads

INSPIRE - Inferring Shared Modules from Multiple Gene Expression Datasets with Partially Overlapping Gene Sets

A method to infer modules of co-expressed genes and the dependencies among the modules from multiple expression datasets that may contain different sets of genes. Please refer to: Extracting a low-dimensional description of multiple gene expression datasets reveals a potential driver for tumor-associated stroma in ovarian cancer, Safiye Celik, Benjamin A. Logsdon, Stephanie Battle, Charles W. Drescher, Mara Rendi, R. David Hawkins and Su-In Lee (2016) <DOI:10.1186/s13073-016-0319-7>.

Last updated 8 years ago

2.00 score 7 scripts 122 downloads

stripless - Structured Trellis Displays Without Strips for Lattice Graphics

For making Trellis-type conditioning plots without strip labels. This is useful for displaying the structure of results from factorial designs and other studies when many conditioning variables would clutter the display with layers of redundant strip labels. Settings of the variables are encoded by layout and spacing in the trellis array and decoded by a separate legend. The functionality is implemented by a single S3 generic strucplot() function that is a wrapper for the Lattice package's xyplot() function. This allows access to all Lattice graphics capabilities in the usual way.

Last updated 8 years ago

2.00 score 1 stars 6 scripts 120 downloads

ClusteredMutations - Location and Visualization of Clustered Somatic Mutations

Identification and visualization of groups of closely spaced mutations in the DNA sequence of cancer genome. The extremely mutated zones are searched in the symmetric dissimilarity matrix using the anti-Robinson matrix properties. Different data sets are obtained to describe and plot the clustered mutations information.

Last updated 9 years ago

2.00 score 8 scripts 149 downloads

exploreR - Tools for Quickly Exploring Data

Simplifies some complicated and labor intensive processes involved in exploring and explaining data. Allows you to quickly and efficiently visualize the interaction between variables and simplifies the process of discovering covariation in your data. Also includes some convenience features designed to remove as much redundant typing as possible.

Last updated 9 years ago

2.00 score 15 scripts 169 downloads

CovSel - Model-Free Covariate Selection

Model-free selection of covariates under unconfoundedness for situations where the parameter of interest is an average causal effect. This package is based on model-free backward elimination algorithms proposed in de Luna, Waernbaum and Richardson (2011). Marginal co-ordinate hypothesis testing is used in situations where all covariates are continuous while kernel-based smoothing appropriate for mixed data is used otherwise.

Last updated 9 years ago

2.00 score 1 stars 20 scripts 186 downloads

AlgebraicHaploPackage - Haplotype Two Snips Out of a Paired Group of Patients

Two unordered pairs of data of two different snips positions is haplotyped by resolving a small number ob closed equations.

Last updated 9 years ago

2.00 score 9 scripts 264 downloads

STAND - Statistical Analysis of Non-Detects

Provides functions for the analysis of occupational and environmental data with non-detects. Maximum likelihood (ML) methods for censored log-normal data and non-parametric methods based on the product limit estimate (PLE) for left censored data are used to calculate all of the statistics recommended by the American Industrial Hygiene Association (AIHA) for the complete data case. Functions for the analysis of complete samples using exact methods are also provided for the lognormal model. Revised from 2007-11-05 'survfit~1'.

Last updated 9 years ago

2.00 score 69 scripts 103 downloads

gamlss.demo - Demos for GAMLSS

Demos for smoothing and gamlss.family distributions.

Last updated 9 years ago

2.00 score 1 stars 4 scripts 242 downloads

MGL - Module Graphical Lasso

An aggressive dimensionality reduction and network estimation technique for a high-dimensional Gaussian graphical model (GGM). Please refer to: Efficient Dimensionality Reduction for High-Dimensional Network Estimation, Safiye Celik, Benjamin A. Logsdon, Su-In Lee, Proceedings of The 31st International Conference on Machine Learning, 2014, p. 1953--1961.

Last updated 10 years ago

2.00 score 4 scripts 115 downloads

fgui - Function GUI

Rapidly create a GUI interface for a function you created by automatically creating widgets for arguments of the function. Automatically parses help routines for context-sensitive help to these arguments. The interface essentially a wrapper to some Tcl/Tk routines to both simplify and facilitate GUI creation. More advanced Tcl/Tk routines/GUI objects can be incorporated into the interface for greater customization for the more experienced.

Last updated 7 years ago

2.00 score 3 dependents 11 scripts 288 downloads

BSagri - Safety Assessment in Agricultural Field Trials

Collection of functions, data sets and code examples for evaluations of field trials with the objective of equivalence assessment.

Last updated 7 years ago

2.00 score 1 stars 33 scripts 189 downloads

NHLData - Scores for Every Season Since the Founding of the NHL in 1917

Each dataset contains scores for every game during a specific season of the NHL.

Last updated 8 years ago

2.00 score 99 scripts 520 downloads

bayesSurv - Bayesian Survival Regression with Flexible Error and Random Effects Distributions

Contains Bayesian implementations of the Mixed-Effects Accelerated Failure Time (MEAFT) models for censored data. Those can be not only right-censored but also interval-censored, doubly-interval-censored or misclassified interval-censored. The methods implemented in the package have been published in Komárek and Lesaffre (2006, Stat. Modelling) <doi:10.1191/1471082X06st107oa>, Komárek, Lesaffre and Legrand (2007, Stat. in Medicine) <doi:10.1002/sim.3083>, Komárek and Lesaffre (2007, Stat. Sinica) <https://www3.stat.sinica.edu.tw/statistica/oldpdf/A17n27.pdf>, Komárek and Lesaffre (2008, JASA) <doi:10.1198/016214507000000563>, García-Zattera, Jara and Komárek (2016, Biometrics) <doi:10.1111/biom.12424>.

Last updated 3 months ago

openblascpp

1.99 score 49 scripts 595 downloads

MPDiR - Data Sets and Scripts for Modeling Psychophysical Data in R

Data sets and scripts for Modeling Psychophysical Data in R (Springer).

Last updated 1 years ago

1.99 score 97 scripts 519 downloads

svydiags - Regression Model Diagnostics for Survey Data

Diagnostics for fixed effects linear and general linear regression models fitted with survey data. Extensions of standard diagnostics to complex survey data are included: standardized residuals, leverages, Cook's D, dfbetas, dffits, condition indexes, and variance inflation factors as found in Li and Valliant (Surv. Meth., 2009, 35(1), pp. 15-24; Jnl. of Off. Stat., 2011, 27(1), pp. 99-119; Jnl. of Off. Stat., 2015, 31(1), pp. 61-75); Liao and Valliant (Surv. Meth., 2012, 38(1), pp. 53-62; Surv. Meth., 2012, 38(2), pp. 189-202). Variance inflation factors and condition indexes are also computed for some general linear models as described in Liao (U. Maryland thesis, 2010).

Last updated 2 months ago

1.98 score 1 stars 16 scripts 481 downloads

SCCS - The Self-Controlled Case Series Method

Various self-controlled case series models used to investigate associations between time-varying exposures such as vaccines or other drugs or non drug exposures and an adverse event can be fitted. Detailed information on the self-controlled case series method and its extensions with more examples can be found in Farrington, P., Whitaker, H., and Ghebremichael Weldeselassie, Y. (2018, ISBN: 978-1-4987-8159-6. Self-controlled Case Series studies: A modelling Guide with R. Boca Raton: Chapman & Hall/CRC Press) and <https://sccs-studies.info/index.html>.

Last updated 9 months ago

1.98 score 24 scripts 264 downloads

ClickClust - Model-Based Clustering of Categorical Sequences

Clustering categorical sequences by means of finite mixtures with Markov model components is the main utility of ClickClust. The package also allows detecting blocks of equivalent states by forward and backward state selection procedures.

Last updated 1 years ago

1.98 score 2 stars 1 dependents 16 scripts 417 downloads

mltest - Classification Evaluation Metrics

A fast, robust and easy-to-use calculation of multi-class classification evaluation metrics based on confusion matrix.

Last updated 6 years ago

1.98 score 32 scripts 182 downloads

clustMD - Model Based Clustering for Mixed Data

Model-based clustering of mixed data (i.e. data which consist of continuous, binary, ordinal or nominal variables) using a parsimonious mixture of latent Gaussian variable models.

Last updated 8 years ago

1.98 score 1 stars 19 scripts 272 downloads

GeomComb - (Geometric) Forecast Combination Methods

Provides eigenvector-based (geometric) forecast combination methods; also includes simple approaches (simple average, median, trimmed and winsorized mean, inverse rank method) and regression-based combination. Tools for data pre-processing are available in order to deal with common problems in forecast combination (missingness, collinearity).

Last updated 8 years ago

1.98 score 19 scripts 166 downloads

Renvlp - Computing Envelope Estimators

Provides a general routine, envMU, which allows estimation of the M envelope of span(U) given root n consistent estimators of M and U. The routine envMU does not presume a model. This package implements response envelopes, partial response envelopes, envelopes in the predictor space, heteroscedastic envelopes, simultaneous envelopes, scaled response envelopes, scaled envelopes in the predictor space, groupwise envelopes, weighted envelopes, envelopes in logistic regression, envelopes in Poisson regression envelopes in function-on-function linear regression, envelope-based Partial Partial Least Squares, envelopes with non-constant error covariance, envelopes with t-distributed errors, reduced rank envelopes and reduced rank envelopes with non-constant error covariance. For each of these model-based routines the package provides inference tools including bootstrap, cross validation, estimation and prediction, hypothesis testing on coefficients are included except for weighted envelopes. Tools for selection of dimension include AIC, BIC and likelihood ratio testing. Background is available at Cook, R. D., Forzani, L. and Su, Z. (2016) <doi:10.1016/j.jmva.2016.05.006>. Optimization is based on a clockwise coordinate descent algorithm.

Last updated 1 years ago

1.97 score 93 scripts 235 downloads

spgs - Statistical Patterns in Genomic Sequences

A collection of statistical hypothesis tests and other techniques for identifying certain spatial relationships/phenomena in DNA sequences. In particular, it provides tests and graphical methods for determining whether or not DNA sequences comply with Chargaff's second parity rule or exhibit purine-pyrimidine parity. In addition, there are functions for efficiently simulating discrete state space Markov chains and testing arbitrary symbolic sequences of symbols for the presence of first-order Markovianness. Also, it has functions for counting words/k-mers (and cylinder patterns) in arbitrary symbolic sequences. Functions which take a DNA sequence as input can handle sequences stored as SeqFastadna objects from the 'seqinr' package.

Last updated 1 years ago

1.97 score 93 scripts 409 downloads

designmatch - Matched Samples that are Balanced and Representative by Design

Includes functions for the construction of matched samples that are balanced and representative by design. Among others, these functions can be used for matching in observational studies with treated and control units, with cases and controls, in related settings with instrumental variables, and in discontinuity designs. Also, they can be used for the design of randomized experiments, for example, for matching before randomization. By default, 'designmatch' uses the 'highs' optimization solver, but its performance is greatly enhanced by the 'Gurobi' optimization solver and its associated R interface. For their installation, please follow the instructions at <https://www.gurobi.com/documentation/quickstart.html> and <https://www.gurobi.com/documentation/7.0/refman/r_api_overview.html>. We have also included directions in the gurobi_installation file in the inst folder.

Last updated 1 years ago

1.97 score 1 stars 75 scripts 1.2k downloads

ganGenerativeData - Generate Generative Data for a Data Source

Generative Adversarial Networks are applied to generate generative data for a data source. A generative model consisting of a generator and a discriminator network is trained. During iterative training the distribution of generated data is converging to that of the data source. Direct applications of generative data are the created functions for data evaluation, missing data completion and data classification. A software service for accelerated training of generative models on graphics processing units is available. Reference: Goodfellow et al. (2014) <doi:10.48550/arXiv.1406.2661>.

Last updated 12 days ago

cpp

1.95 score 1 stars 5 scripts 353 downloads

s2dv - A Set of Common Tools for Seasonal to Decadal Verification

The advanced version of package 's2dverification'. It is intended for 'seasonal to decadal' (s2d) climate forecast verification, but it can also be used in other kinds of forecasts or general climate analysis. This package is specially designed for the comparison between the experimental and observational datasets. The functionality of the included functions covers from data retrieval, data post-processing, skill scores against observation, to visualization. Compared to 's2dverification', 's2dv' is more compatible with the package 'startR', able to use multiple cores for computation and handle multi-dimensional arrays with a higher flexibility. The CDO version used in development is 1.9.8.

Last updated 2 months ago

1.95 score 3 dependents 38 scripts 358 downloads

policytree - Policy Learning via Doubly Robust Empirical Welfare Maximization over Trees

Learn optimal policies via doubly robust empirical welfare maximization over trees. Given doubly robust reward estimates, this package finds a rule-based treatment prescription policy, where the policy takes the form of a shallow decision tree that is globally (or close to) optimal.

Last updated 6 months ago

cpp

1.95 score 3 dependents 57 scripts 521 downloads

support.BWS3 - Tools for Case 3 Best-Worst Scaling

Provides basic functions that support an implementation of multi-profile case (Case 3) best-worst scaling (BWS). Case 3 BWS is a question-based survey method to elicit people's preferences for attribute levels. Case 3 BWS constructs various combinations of attribute levels (profiles) and then asks respondents to select the best and worst profiles in each choice set. A main function creates a dataset for the analysis from the choice sets and the responses to the questions. For details on Case 3 BWS, refer to Louviere et al. (2015) <doi:10.1017/CBO9781107337855>.

Last updated 11 months ago

1.95 score 1 dependents 348 downloads

mvhtests - Multivariate Hypothesis Tests

Hypothesis tests for multivariate data. Tests for one and two mean vectors, multivariate analysis of variance, tests for one, two or more covariance matrices. References include: Mardia K.V., Kent J.T. and Bibby J.M. (1979). Multivariate Analysis. ISBN: 978-0124712522. London: Academic Press.

Last updated 1 years ago

1.95 score 3 dependents 373 downloads

LDRTools - Tools for Linear Dimension Reduction

Linear dimension reduction subspaces can be uniquely defined using orthogonal projection matrices. This package provides tools to compute distances between such subspaces and to compute the average subspace. For details see Liski, E.Nordhausen K., Oja H., Ruiz-Gazen A. (2016) Combining Linear Dimension Reduction Subspaces <doi:10.1007/978-81-322-3643-6_7>.

Last updated 1 years ago

1.95 score 3 dependents 6 scripts 844 downloads

crossval - Generic Functions for Cross Validation

Contains generic functions for performing cross validation and for computing diagnostic errors.

Last updated 2 years ago

1.95 score 1 dependents 45 scripts 912 downloads

parSim - Parallel Simulation Studies

Perform flexible simulation studies using one or multiple computer cores. The package is set up to be usable on high-performance clusters in addition to being run locally, see examples on <https://github.com/SachaEpskamp/parSim>.

Last updated 2 years ago

1.95 score 18 scripts 258 downloads

ssym - Fitting Semi-Parametric log-Symmetric Regression Models

Set of tools to fit a semi-parametric regression model suitable for analysis of data sets in which the response variable is continuous, strictly positive, asymmetric and possibly, censored. Under this setup, both the median and the skewness of the response variable distribution are explicitly modeled by using semi-parametric functions, whose non-parametric components may be approximated by natural cubic splines or P-splines. Supported distributions for the model error include log-normal, log-Student-t, log-power-exponential, log-hyperbolic, log-contaminated-normal, log-slash, Birnbaum-Saunders and Birnbaum-Saunders-t distributions.

Last updated 2 years ago

1.95 score 1 dependents 30 scripts 290 downloads

support.BWS - Tools for Case 1 Best-Worst Scaling

Provides basic functions that support an implementation of object case (Case 1) best-worst scaling: a function for converting a two-level orthogonal main-effect design/balanced incomplete block design into questions; two functions for creating a data set suitable for analysis; a function for calculating count-based scores; a function for calculating shares of preference; and a function for generating artificial responses to questions. See Louviere et al. (2015) <doi:10.1017/CBO9781107337855> for details on best-worst scaling, and Aizaki and Fogarty (2023) <doi:10.1016/j.jocm.2022.100394> for the package.

Last updated 2 years ago

1.95 score 1 stars 1 dependents 8 scripts 707 downloads

ICsurv - Semiparametric Regression Analysis of Interval-Censored Data

Currently using the proportional hazards (PH) model. More methods under other semiparametric regression models will be included in later versions.

Last updated 3 years ago

1.95 score 3 dependents 4 scripts 204 downloads

support.BWS2 - Tools for Case 2 Best-Worst Scaling

Provides three basic functions that support an implementation of Case 2 (profile case) best-worst scaling. The first is to convert an orthogonal main-effect design into questions, the second is to create a dataset suitable for analysis, and the third is to calculate count-based scores. For details, see Aizaki and Fogarty (2019) <doi:10.1016/j.jocm.2019.100171>.

Last updated 3 years ago

1.95 score 1 dependents 6 scripts 926 downloads

smcure - Fit Semiparametric Mixture Cure Models

An R-package for Estimating Semiparametric PH and AFT Mixture Cure Models.

Last updated 3 years ago

1.95 score 1 stars 1 dependents 25 scripts 287 downloads

HDoutliers - Leland Wilkinson's Algorithm for Detecting Multidimensional Outliers

An implementation of an algorithm for outlier detection that can handle a) data with a mixed categorical and continuous variables, b) many columns of data, c) many rows of data, d) outliers that mask other outliers, and e) both unidimensional and multidimensional datasets. Unlike ad hoc methods found in many machine learning papers, HDoutliers is based on a distributional model that uses probabilities to determine outliers.

Last updated 3 years ago

1.95 score 3 stars 1 dependents 17 scripts 312 downloads

EFA.MRFA - Dimensionality Assessment Using Minimum Rank Factor Analysis

Performs parallel analysis (Timmerman & Lorenzo-Seva, 2011 <doi:10.1037/a0023353>) and hull method (Lorenzo-Seva, Timmerman, & Kiers, 2011 <doi:10.1080/00273171.2011.564527>) for assessing the dimensionality of a set of variables using minimum rank factor analysis (see ten Berge & Kiers, 1991 <doi:10.1007/BF02294464> for more information). The package also includes the option to compute minimum rank factor analysis by itself, as well as the greater lower bound calculation.

Last updated 4 years ago

1.95 score 3 dependents 319 downloads

eba - Elimination-by-Aspects Models

Fitting and testing multi-attribute probabilistic choice models, especially the Bradley-Terry-Luce (BTL) model (Bradley & Terry, 1952 <doi:10.1093/biomet/39.3-4.324>; Luce, 1959), elimination-by-aspects (EBA) models (Tversky, 1972 <doi:10.1037/h0032955>), and preference tree (Pretree) models (Tversky & Sattath, 1979 <doi:10.1037/0033-295X.86.6.542>).

Last updated 4 years ago

1.95 score 1 dependents 30 scripts 420 downloads

interactionTest - Calculates Critical Test Statistics to Control False Discovery Rates in Marginal Effects Plots

Implements the procedures suggested in Esarey and Sumner (2017) <http://justinesarey.com/interaction-overconfidence.pdf> for controlling the false discovery rate when constructing marginal effects plots for models with interaction terms.

Last updated 6 years ago

1.95 score 3 dependents 2 scripts 999 downloads

bayesdistreg - Bayesian Distribution Regression

Implements Bayesian Distribution Regression methods. This package contains functions for three estimators (non-asymptotic, semi-asymptotic and asymptotic) and related routines for Bayesian Distribution Regression in Huang and Tsyawo (2018) <doi:10.2139/ssrn.3048658> which is also the recommended reference to cite for this package. The functions can be grouped into three (3) categories. The first computes the logit likelihood function and posterior densities under uniform and normal priors. The second contains Independence and Random Walk Metropolis-Hastings Markov Chain Monte Carlo (MCMC) algorithms as functions and the third category of functions are useful for semi-asymptotic and asymptotic Bayesian distribution regression inference.

Last updated 6 years ago

1.95 score 18 scripts 241 downloads

CBT - Confidence Bound Target Algorithm

The Confidence Bound Target (CBT) algorithm is designed for infinite arms bandit problem. It is shown that CBT algorithm achieves the regret lower bound for general reward distributions. Reference: Hock Peng Chan and Shouri Hu (2018) <arXiv:1805.11793>.

Last updated 7 years ago

1.95 score 1 scripts 137 downloads

PGEE - Penalized Generalized Estimating Equations in High-Dimension

Fits penalized generalized estimating equations to longitudinal data with high-dimensional covariates.

Last updated 8 years ago

1.95 score 1 dependents 25 scripts 305 downloads

RSKC - Robust Sparse K-Means

This RSKC package contains a function RSKC which runs the robust sparse K-means clustering algorithm.

Last updated 8 years ago

1.95 score 1 dependents 30 scripts 273 downloads

rpnf - Point and Figure Package

A set of functions to analyze and print the development of a commodity using the Point and Figure (P&F) approach. A P&F processor can be used to calculate daily statistics for the time series. These statistics can be used for deeper investigations as well as to create plots. Plots can be generated as well known X/O Plots in plain text format, and additionally in a more graphical format.

Last updated 8 years ago

1.95 score 3 stars 30 scripts 110 downloads

score - A Package to Score Behavioral Questionnaires

Provides routines for scoring behavioral questionnaires. Includes scoring procedures for the 'International Physical Activity Questionnaire (IPAQ)' <http://www.ipaq.ki.se>. Compares physical functional performance to the age- and gender-specific normal ranges.

Last updated 10 years ago

1.95 score 1 stars 2 scripts 149 downloads

bvls - The Stark-Parker algorithm for bounded-variable least squares

An R interface to the Stark-Parker implementation of an algorithm for bounded-variable least squares

Last updated 11 years ago

fortran

1.95 score 3 dependents 7 scripts 953 downloads

RJSplot - Interactive Graphs with R

Creates interactive graphs with 'R'. It joins the data analysis power of R and the visualization libraries of JavaScript in one package.

Last updated 3 years ago

1.94 score 4 stars 22 scripts 185 downloads

revgeo - Reverse Geocoding with the Photon Geocoder for OpenStreetMap, Google Maps, and Bing

Function revgeo() allows you to use the Photon geocoder for OpenStreetMap <http://photon.komoot.de>, Google Maps <http://maps.google.com>, and Bing <https://www.bingmapsportal.com> to reverse geocode coordinate pairs with minimal hassle.

Last updated 7 years ago

1.94 score 88 scripts 218 downloads

vecsets - Like Set Tools in 'Base' Package but Keeps Duplicate Elements

The 'base' tools union() intersect(), etc., follow the algebraic definition that each element of a set must be unique. Since it's often helpful to compare all elements of two vectors, this toolset treats every element as unique for counting purposes. For ease of use, all functions in vecsets have an argument 'multiple' which, when set to FALSE, reverts them to the base::sets (alias for all the items) tools functionality.

Last updated 1 years ago

1.94 score 1 dependents 29 scripts 249 downloads

DOS2 - Design of Observational Studies, Companion to the Second Edition

Contains data sets, examples and software from the Second Edition of "Design of Observational Studies"; see Rosenbaum, P.R. (2010) <doi:10.1007/978-1-4419-1213-8>.

Last updated 5 years ago

1.94 score 1 stars 1 dependents 29 scripts 164 downloads

metaBLUE - BLUE for Combining Location and Scale Information in a Meta-Analysis

The sample mean and standard deviation are two commonly used statistics in meta-analyses, but some trials use other summary statistics such as the median and quartiles to report the results. Therefore, researchers need to transform those information back to the sample mean and standard deviation. This package implemented sample mean estimators by Luo et al. (2016) <arXiv:1505.05687>, sample standard deviation estimators by Wan et al. (2014) <arXiv:1407.8038>, and the best linear unbiased estimators (BLUEs) of location and scale parameters by Yang et al. (2018, submitted) based on sample quantiles derived summaries in a meta-analysis.

Last updated 7 years ago

1.93 score 2 dependents 5 scripts 1.4k downloads

airGRdatasets - Hydro-Meteorological Catchments Datasets for the 'airGR' Packages

Sample of hydro-meteorological datasets extracted from the 'CAMELS-FR' French database <https://hal.inrae.fr/hal-03687235>. It provides metadata and catchment-scale aggregated hydro-meteorological time series on a pool of French catchments for use by the 'airGR' packages.

Last updated 1 years ago

1.93 score 17 scripts 331 downloads

constrainedKriging - Constrained, Covariance-Matching Constrained and Universal Point or Block Kriging

Provides functions for efficient computation of non-linear spatial predictions with local change of support (Hofer, C. and Papritz, A. (2011) "constrainedKriging: An R-package for customary, constrained and covariance-matching constrained point or block kriging" <doi:10.1016/j.cageo.2011.02.009>). This package supplies functions for two-dimensional spatial interpolation by constrained (Cressie, N. (1993) "Aggregation in geostatistical problems" <doi:10.1007/978-94-011-1739-5_3>), covariance-matching constrained (Aldworth, J. and Cressie, N. (2003) "Prediction of nonlinear spatial functionals" <doi:10.1016/S0378-3758(02)00321-X>) and universal (external drift) Kriging for points or blocks of any shape from data with a non-stationary mean function and an isotropic weakly stationary covariance function. The linear spatial interpolation methods, constrained and covariance-matching constrained Kriging, provide approximately unbiased prediction for non-linear target values under change of support. This package extends the range of tools for spatial predictions available in R and provides an alternative to conditional simulation for non-linear spatial prediction problems with local change of support.

Last updated 4 months ago

1.92 score 1 dependents 14 scripts 400 downloads

PtProcess - Time Dependent Point Process Modelling

Fits and analyses time dependent marked point process models with an emphasis on earthquake modelling. For a more detailed introduction to the package, see the topic "PtProcess". A list of recent changes can be found in the topic "Change Log".

Last updated 4 years ago

1.92 score 3 stars 28 scripts 579 downloads

acid - Analysing Conditional Income Distributions

Functions for the analysis of income distributions for subgroups of the population as defined by a set of variables like age, gender, region, etc. This entails a Kolmogorov-Smirnov test for a mixture distribution as well as functions for moments, inequality measures, entropy measures and polarisation measures of income distributions. This package thus aides the analysis of income inequality by offering tools for the exploratory analysis of income distributions at the disaggregated level.

Last updated 9 years ago

1.92 score 84 scripts 395 downloads

sensitivity2x2xk - Sensitivity Analysis for 2x2xk Tables in Observational Studies

Performs exact or approximate adaptive or nonadaptive Cochran-Mantel-Haenszel-Birch tests and sensitivity analyses for one or two 2x2xk tables in observational studies.

Last updated 9 years ago

1.92 score 2 dependents 14 scripts 159 downloads

ICSOutlier - Outlier Detection Using Invariant Coordinate Selection

Multivariate outlier detection is performed using invariant coordinates where the package offers different methods to choose the appropriate components. ICS is a general multivariate technique with many applications in multivariate analysis. ICSOutlier offers a selection of functions for automated detection of outliers in the data based on a fitted ICS object or by specifying the dataset and the scatters of interest. The current implementation targets data sets with only a small percentage of outliers.

Last updated 1 years ago

1.91 score 1 dependents 18 scripts 1.5k downloads

robfilter - Robust Time Series Filters

Implementations for several robust procedures that allow for (online) extraction of the signal of univariate or multivariate time series by applying robust regression techniques to a moving time window are provided. Included are univariate filtering procedures based on repeated-median regression as well as hybrid and trimmed filters derived from it; see Schettlinger et al. (2006) <doi:10.1515/BMT.2006.010>. The adaptive online repeated median by Schettlinger et al. (2010) <doi:10.1002/acs.1105> and the slope comparing adaptive repeated median by Borowski and Fried (2013) <doi:10.1007/s11222-013-9391-7> choose the width of the moving time window adaptively. Multivariate versions are also provided; see Borowski et al. (2009) <doi:10.1080/03610910802514972> for a multivariate online adaptive repeated median and Borowski (2012) <doi:10.17877/DE290R-14393> for a multivariate slope comparing adaptive repeated median. Furthermore, a repeated-median based filter with automatic outlier replacement and shift detection is provided; see Fried (2004) <doi:10.1080/10485250410001656444>.

Last updated 5 months ago

cpp

1.90 score 2 stars 44 scripts 649 downloads

DIDmultiplegt - Estimators DID with Multiple Groups and Periods

Estimators of Difference-in-Differences based on de Chaisemartin and D'Haultfoeuille.

Last updated 5 months ago

openjdk

1.90 score 2 stars 41 scripts 531 downloads

HWEintrinsic - Objective Bayesian Testing for the Hardy-Weinberg Equilibrium Problem

General (multi-allelic) Hardy-Weinberg equilibrium problem from an objective Bayesian testing standpoint. This aim is achieved through the identification of a class of priors specifically designed for this testing problem. A class of intrinsic priors under the full model is considered. This class is indexed by a tuning quantity, the training sample size, as discussed in Consonni, Moreno and Venturini (2010). These priors are objective, satisfy Savage's continuity condition and have proved to behave extremely well for many statistical testing problems.

Last updated 1 years ago

1.90 score 16 scripts 302 downloads

wearables - Tools to Read and Convert Wearables Data

Package to read Empatica E4 data, perform several transformations, perform signal processing and analyses, including batch analyses.

Last updated 3 years ago

1.90 score 1 stars 16 scripts 158 downloads

CFO - CFO-Type Designs in Phase I/II Clinical Trials

In phase I clinical trials, the primary objective is to ascertain the maximum tolerated dose (MTD) corresponding to a specified target toxicity rate. The subsequent phase II trials are designed to examine the potential efficacy of the drug based on the MTD obtained from the phase I trials, with the aim of identifying the optimal biological dose (OBD). The 'CFO' package facilitates the implementation of dose-finding trials by utilizing calibration-free odds type (CFO-type) designs. Specifically, it encompasses the calibration-free odds (CFO) (Jin and Yin (2022) <doi:10.1177/09622802221079353>), randomized CFO (rCFO), precision CFO (pCFO), two-dimensional CFO (2dCFO) (Wang et al. (2023) <doi:10.3389/fonc.2023.1294258>), time-to-event CFO (TITE-CFO) (Jin and Yin (2023) <doi:10.1002/pst.2304>), fractional CFO (fCFO), accumulative CFO (aCFO), TITE-aCFO, and f-aCFO (Fang and Yin (2024) <doi: 10.1002/sim.10127>). It supports phase I/II trials for the CFO design and only phase I trials for the other CFO-type designs. The ‘CFO' package accommodates diverse CFO-type designs, allowing users to tailor the approach based on factors such as dose information inclusion, handling of late-onset toxicity, and the nature of the target drug (single-drug or drug-combination). The functionalities embedded in 'CFO' package include the determination of the dose level for the next cohort, the selection of the MTD for a real trial, and the execution of single or multiple simulations to obtain operating characteristics. Moreover, these functions are equipped with early stopping and dose elimination rules to address safety considerations. Users have the flexibility to choose different distributions, thresholds, and cohort sizes among others for their specific needs. The output of the 'CFO' package can be summary statistics as well as various plots for better visualization. An interactive web application for CFO is available at the provided URL.

Last updated 1 months ago

1.90 score 568 downloads

crossmatch - The Cross-Match Test

Performs the cross-match test that is an exact, distribution free test of equality of 2 high dimensional multivariate distributions. The input is a distance matrix and the labels of the two groups to be compared, the output is the number of cross-matches and a p-value. See Rosenbaum (2005) <doi:10.1111/j.1467-9868.2005.00513.x>.

Last updated 6 months ago

1.90 score 1 stars 6 scripts 249 downloads

aspace - Functions for Estimating Centrographic Statistics

A collection of functions for computing centrographic statistics (e.g., standard distance, standard deviation ellipse, standard deviation box) for observations taken at point locations. Separate plotting functions have been developed for each measure. Users interested in writing results to ESRI shapefiles can do so by using results from 'aspace' functions as inputs to the convert.to.shapefile() and write.shapefile() functions in the 'shapefiles' library. We intend to provide 'terra' integration for geographic data in a future release. The 'aspace' package was originally conceived to aid in the analysis of spatial patterns of travel behaviour (see Buliung and Remmel 2008 <doi:10.1007/s10109-008-0063-7>).

Last updated 8 months ago

1.90 score 1 stars 79 scripts 830 downloads

BNPdensity - Ferguson-Klass Type Algorithm for Posterior Normalized Random Measures

Bayesian nonparametric density estimation modeling mixtures by a Ferguson-Klass type algorithm for posterior normalized random measures.

Last updated 2 years ago

1.90 score 79 scripts 347 downloads

denseFLMM - Functional Linear Mixed Models for Densely Sampled Data

Estimation of functional linear mixed models for densely sampled data based on functional principal component analysis.

Last updated 7 years ago

1.89 score 2 dependents 13 scripts 217 downloads

ecotoxicology - Methods for Ecotoxicology

Implementation of the EPA's Ecological Exposure Research Division (EERD) tools (discontinued in 1999) for Probit and Trimmed Spearman-Karber Analysis. Probit and Spearman-Karber methods from Finney's book "Probit analysis a statistical treatment of the sigmoid response curve" with options for most accurate results or identical results to the book. Probit and all the tables from Finney's book (code-generated, not copied) with the generating functions included. Control correction: Abbott, Schneider-Orelli, Henderson-Tilton, Sun-Shepard. Toxicity scales: Horsfall-Barratt, Archer, Gauhl-Stover, Fullerton-Olsen, etc.

Last updated 9 years ago

1.89 score 3 stars 26 scripts 137 downloads

tea - Threshold Estimation Approaches

Different approaches for selecting the threshold in generalized Pareto distributions. Most of them are based on minimizing the AMSE-criterion or at least by reducing the bias of the assumed GPD-model. Others are heuristically motivated by searching for stable sample paths, i.e. a nearly constant region of the tail index estimator with respect to k, which is the number of data in the tail. The third class is motivated by graphical inspection. In addition, a sequential testing procedure for GPD-GoF-tests is also implemented here.

Last updated 5 years ago

1.89 score 77 scripts 197 downloads

scplot - Plot Function for Single-Case Data Frames

Add-on for the 'scan' package that creates plots from single-case data frames ('scdf'). It includes functions for styling single-case plots, adding phase-based lines to indicate various statistical parameters, and predefined themes for presentations and publications. More information and in depth examples can be found in the online book "Analyzing Single-Case Data with R and 'scan" Jürgen Wilbert (2023) <https://jazznbass.github.io/scan-Book/>.

Last updated 6 months ago

1.88 score 15 scripts 298 downloads

orders - Sampling from k-th Order Statistics of New Families of Distributions

Set of tools to generate samples of k-th order statistics and others quantities of interest from new families of distributions. The main references for this package are: C. Kleiber and S. Kotz (2003) Statistical size distributions in economics and actuarial sciences; Gentle, J. (2009), Computational Statistics, Springer-Verlag; Naradajah, S. and Rocha, R. (2016), <DOI:10.18637/jss.v069.i10> and Stasinopoulos, M. and Rigby, R. (2015), <DOI:10.1111/j.1467-9876.2005.00510.x>. The families of distributions are: Benini distributions, Burr distributions, Dagum distributions, Feller-Pareto distributions, Generalized Pareto distributions, Inverse Pareto distributions, The Inverse Paralogistic distributions, Marshall-Olkin G distributions, exponentiated G distributions, beta G distributions, gamma G distributions, Kumaraswamy G distributions, generalized beta G distributions, beta extended G distributions, gamma G distributions, gamma uniform G distributions, beta exponential G distributions, Weibull G distributions, log gamma G I distributions, log gamma G II distributions, exponentiated generalized G distributions, exponentiated Kumaraswamy G distributions, geometric exponential Poisson G distributions, truncated-exponential skew-symmetric G distributions, modified beta G distributions, exponentiated exponential Poisson G distributions, Poisson-inverse gaussian distributions, Skew normal type 1 distributions, Skew student t distributions, Singh-Maddala distributions, Sinh-Arcsinh distributions, Sichel distributions, Zero inflated Poisson distributions.

Last updated 1 years ago

1.86 score 73 scripts 308 downloads

Libra - Linearized Bregman Algorithms for Generalized Linear Models

Efficient procedures for fitting the regularization path for linear, binomial, multinomial, Ising and Potts models with lasso, group lasso or column lasso(only for multinomial) penalty. The package uses Linearized Bregman Algorithm to solve the regularization path through iterations. Bregman Inverse Scale Space Differential Inclusion solver is also provided for linear model with lasso penalty.

Last updated 3 years ago

gsl

1.86 score 73 scripts 277 downloads

SMPracticals - Practicals for Use with Davison (2003) Statistical Models

Contains the datasets and a few functions for use with the practicals outlined in Appendix A of the book Statistical Models (Davison, 2003, Cambridge University Press), which can be found at <doi:10.1017/CBO9780511815850>.

Last updated 11 months ago

1.86 score 1 dependents 24 scripts 744 downloads

fairml - Fair Models in Machine Learning

Fair machine learning regression models which take sensitive attributes into account in model estimation. Currently implementing Komiyama et al. (2018) <http://proceedings.mlr.press/v80/komiyama18a/komiyama18a.pdf>, Zafar et al. (2019) <https://www.jmlr.org/papers/volume20/18-262/18-262.pdf> and my own approach from Scutari, Panero and Proissl (2022) <https://link.springer.com/content/pdf/10.1007/s11222-022-10143-w.pdf> that uses ridge regression to enforce fairness.

Last updated 2 years ago

1.86 score 1 stars 1 dependents 24 scripts 548 downloads

CRTSize - Sample Size Estimation Functions for Cluster Randomized Trials

Sample size estimation in cluster (group) randomized trials. Contains traditional power-based methods, empirical smoothing (Rotondi and Donner, 2009), and updated meta-analysis techniques (Rotondi and Donner, 2012).

Last updated 2 years ago

1.86 score 12 scripts 365 downloads

mvLSW - Multivariate, Locally Stationary Wavelet Process Estimation

Tools for analysing multivariate time series with wavelets. This includes: simulation of a multivariate locally stationary wavelet (mvLSW) process from a multivariate evolutionary wavelet spectrum (mvEWS); estimation of the mvEWS, local coherence and local partial coherence. See Park, Eckley and Ombao (2014) <doi:10.1109/TSP.2014.2343937> for details.

Last updated 3 years ago

1.86 score 2 dependents 12 scripts 288 downloads

MCPMod - Design and Analysis of Dose-Finding Studies

Implements a methodology for the design and analysis of dose-response studies that combines aspects of multiple comparison procedures and modeling approaches (Bretz, Pinheiro and Branson, 2005, Biometrics 61, 738-748, <doi: 10.1111/j.1541-0420.2005.00344.x>). The package provides tools for the analysis of dose finding trials as well as a variety of tools necessary to plan a trial to be conducted with the MCP-Mod methodology. Please note: The 'MCPMod' package will not be further developed, all future development of the MCP-Mod methodology will be done in the 'DoseFinding' R-package.

Last updated 5 years ago

1.86 score 18 scripts 355 downloads

bdpv - Inference and Design for Predictive Values in Diagnostic Tests

Computation of asymptotic confidence intervals for negative and positive predictive values in binary diagnostic tests in case-control studies. Experimental design for hypothesis tests on predictive values.

Last updated 6 years ago

1.86 score 36 scripts 232 downloads

MultiLCIRT - Multidimensional Latent Class Item Response Theory Models

Framework for the Item Response Theory analysis of dichotomous and ordinal polytomous outcomes under the assumption of multidimensionality and discreteness of the latent traits. The fitting algorithms allow for missing responses and for different item parameterizations and are based on the Expectation-Maximization paradigm. Individual covariates affecting the class weights may be included in the new version (since 2.1).

Last updated 8 years ago

fortran

1.86 score 1 stars 2 dependents 12 scripts 454 downloads

oaColors - OpenAnalytics Colors Package

Provides carefully chosen color palettes as used a.o. at OpenAnalytics <http://www.openanalytics.eu>.

Last updated 9 years ago

1.86 score 1 dependents 24 scripts 102 downloads

sate - Scientific Analysis of Trial Errors (SATE)

Bundles functions used to analyze the harmfulness of trial errors in criminal trials. Functions in the Scientific Analysis of Trial Errors ('SATE') package help users estimate the probability that a jury will find a defendant guilty given jurors' preferences for a guilty verdict and the uncertainty of that estimate. Users can also compare actual and hypothetical trial conditions to conduct harmful error analysis. The relationship between individual jurors' verdict preferences and the probability that a jury returns a guilty verdict has been studied by Davis (1973) <doi:10.1037/h0033951>; MacCoun & Kerr (1988) <doi:10.1037/0022-3514.54.1.21>, and Devine et el. (2001) <doi:10.1037/1076-8971.7.3.622>, among others.

Last updated 19 days ago

1.86 score 24 scripts 127 downloads

care - High-Dimensional Regression and CAR Score Variable Selection

Implements the regression approach of Zuber and Strimmer (2011) "High-dimensional regression and variable selection using CAR scores" SAGMB 10: 34, <DOI:10.2202/1544-6115.1730>. CAR scores measure the correlation between the response and the Mahalanobis-decorrelated predictors. The squared CAR score is a natural measure of variable importance and provides a canonical ordering of variables. This package provides functions for estimating CAR scores, for variable selection using CAR scores, and for estimating corresponding regression coefficients. Both shrinkage as well as empirical estimators are available.

Last updated 3 years ago

1.85 score 1 stars 19 scripts 1.2k downloads

LBI - Likelihood Based Inference

Maximum likelihood estimation and likelihood ratio test are essential for modern statistics. This package supports in calculating likelihood based inference. Reference: Pawitan Y. (2001, ISBN:0-19-850765-8).

Last updated 1 months ago

1.85 score 1 scripts 539 downloads

quarks - Simple Methods for Calculating and Backtesting Value at Risk and Expected Shortfall

Enables the user to calculate Value at Risk (VaR) and Expected Shortfall (ES) by means of various types of historical simulation. Currently plain-, age-, volatility-weighted- and filtered historical simulation are implemented in this package. Volatility weighting can be carried out via an exponentially weighted moving average model (EWMA) or other GARCH-type models. The performance can be assessed via Traffic Light Test, Coverage Tests and Loss Functions. The methods of the package are described in Gurrola-Perez, P. and Murphy, D. (2015) <https://EconPapers.repec.org/RePEc:boe:boeewp:0525> as well as McNeil, J., Frey, R., and Embrechts, P. (2015) <https://ideas.repec.org/b/pup/pbooks/10496.html>.

Last updated 7 months ago

1.85 score 1 stars 14 scripts 357 downloads

dccmidas - DCC Models with GARCH and GARCH-MIDAS Specifications in the Univariate Step, RiskMetrics, Moving Covariance and Scalar and Diagonal BEKK Models

Estimates a variety of Dynamic Conditional Correlation (DCC) models. More in detail, the 'dccmidas' package allows the estimation of the corrected DCC (cDCC) of Aielli (2013) <doi:10.1080/07350015.2013.771027>, the DCC-MIDAS of Colacito et al. (2011) <doi:10.1016/j.jeconom.2011.02.013>, the Asymmetric DCC of Cappiello et al. <doi:10.1093/jjfinec/nbl005>, and the Dynamic Equicorrelation (DECO) of Engle and Kelly (2012) <doi:10.1080/07350015.2011.652048>. 'dccmidas' offers the possibility of including standard GARCH <doi:10.1016/0304-4076(86)90063-1>, GARCH-MIDAS <doi:10.1162/REST_a_00300> and Double Asymmetric GARCH-MIDAS <doi:10.1016/j.econmod.2018.07.025> models in the univariate estimation. Moreover, also the scalar and diagonal BEKK <doi:10.1017/S0266466600009063> models can be estimated. Finally, the package calculates also the var-cov matrix under two non-parametric models: the Moving Covariance and the RiskMetrics specifications.

Last updated 10 months ago

1.85 score 7 stars 1 scripts 204 downloads

mederrRank - Bayesian Methods for Identifying the Most Harmful Medication Errors

Two distinct but related statistical approaches to the problem of identifying the combinations of medication error characteristics that are more likely to result in harm are implemented in this package: 1) a Bayesian hierarchical model with optimal Bayesian ranking on the log odds of harm, and 2) an empirical Bayes model that estimates the ratio of the observed count of harm to the count that would be expected if error characteristics and harm were independent. In addition, for the Bayesian hierarchical model, the package provides functions to assess the sensitivity of results to different specifications of the random effects distributions.

Last updated 1 years ago

1.85 score 14 scripts 174 downloads

CoDiNA - Co-Expression Differential Network Analysis

Categorize links and nodes from multiple networks in 3 categories: Common links (alpha) specific links (gamma), and different links (beta). Also categorizes the links into sub-categories and groups. The package includes a visualization tool for the networks. More information about the methodology can be found at: Gysi et. al., 2018 <arXiv:1802.00828>.

Last updated 4 years ago

1.85 score 23 scripts 261 downloads

waterYearType - Sacramento and San Joaquin Valley Water Year Types

Provides Water Year Hydrologic Classification Indices based on measured unimpaired runoff (in million acre-feet). Data is provided by California Department of Water Resources and subject to revision.

Last updated 6 years ago

1.85 score 14 scripts 113 downloads

ttScreening - Genome-Wide DNA Methylation Sites Screening by Use of Training and Testing Samples

A screening process utilizing training and testing samples to filter out uninformative DNA methylation sites. Surrogate variables (SVs) of DNA methylation are included in the filtering process to explain unknown factor effects.

Last updated 6 years ago

1.85 score 156 downloads

portes - Portmanteau Tests for Time Series Models

Contains common univariate and multivariate portmanteau test statistics for time series models. These tests are based on using asymptotic distributions such as chi-square distribution and based on using the Monte Carlo significance tests. Also, it can be used to simulate from univariate and multivariate seasonal time series models.

Last updated 2 years ago

1.84 score 69 scripts 652 downloads

lmf - Functions for Estimation and Inference of Selection in Age-Structured Populations

Provides methods for estimation and statistical inference on directional and fluctuating selection in age-structured populations.

Last updated 3 years ago

1.84 score 1 dependents 23 scripts 258 downloads

truncSP - Semi-parametric estimators of truncated regression models

Semi-parametric estimation of truncated linear regression models

Last updated 11 years ago

1.84 score 1 dependents 23 scripts 185 downloads

panelView - Visualizing Panel Data

Visualizes panel data. It has three main functionalities: (1) it plots the treatment status and missing values in a panel dataset; (2) it visualizes the temporal dynamics of a main variable of interest; (3) it depicts the bivariate relationships between a treatment variable and an outcome variable either by unit or in aggregate. For details, see <doi:10.18637/jss.v107.i07>.

Last updated 6 months ago

1.82 score 1 dependents 175 scripts 2.2k downloads

GenBinomApps - Clopper-Pearson Confidence Interval and Generalized Binomial Distribution

Density, distribution function, quantile function and random generation for the Generalized Binomial Distribution. Functions to compute the Clopper-Pearson Confidence Interval and the required sample size. Enhanced model for burn-in studies, where failures are tackled by countermeasures.

Last updated 10 months ago

1.82 score 2 dependents 11 scripts 520 downloads

rcbsubset - Optimal Subset Matching with Refined Covariate Balance

Tools for optimal subset matching of treated units and control units in observational studies, with support for refined covariate balance constraints, (including fine and near-fine balance as special cases). A close relative is the 'rcbalance' package. See Pimentel, et al.(2015) <doi:10.1080/01621459.2014.997879> and Pimentel and Kelz (2020) <doi:10.1080/01621459.2020.1720693>. The rrelaxiv package, which provides an alternative solver for the underlying network flow problems, carries an academic license and is not available on CRAN, but may be downloaded from Github at <https://github.com/josherrickson/rrelaxiv/>.

Last updated 3 years ago

1.82 score 2 dependents 11 scripts 276 downloads

VALIDICLUST - VALID Inference for Clusters Separation Testing

Given a partition resulting from any clustering algorithm, the implemented tests allow valid post-clustering inference by testing if a given variable significantly separates two of the estimated clusters. Methods are detailed in: Hivert B, Agniel D, Thiebaut R & Hejblum BP (2022). "Post-clustering difference testing: valid inference and practical considerations", <arXiv:2210.13172>.

Last updated 2 years ago

1.81 score 13 scripts 193 downloads

RobKF - Innovative and/or Additive Outlier Robust Kalman Filtering

Implements a series of robust Kalman filtering approaches. It implements the additive outlier robust filters of Ruckdeschel et al. (2014) <arXiv:1204.3358> and Agamennoni et al. (2018) <doi:10.1109/ICRA.2011.5979605>, the innovative outlier robust filter of Ruckdeschel et al. (2014) <arXiv:1204.3358>, as well as the innovative and additive outlier robust filter of Fisch et al. (2020) <arXiv:2007.03238>.

Last updated 3 years ago

cpp

1.81 score 13 scripts 221 downloads

fastmit - Fast Mutual Information Based Independence Test

A mutual information estimator based on k-nearest neighbor method proposed by A. Kraskov, et al. (2004) <doi:10.1103/PhysRevE.69.066138> to measure general dependence and the time complexity for our estimator is only squared to the sample size, which is faster than other statistics. Besides, an implementation of mutual information based independence test is provided for analyzing multivariate data in Euclidean space (T B. Berrett, et al. (2019) <doi:10.1093/biomet/asz024>); furthermore, we extend it to tackle datasets in metric spaces.

Last updated 5 years ago

cpp

1.81 score 13 scripts 156 downloads

regexPipes - Wrappers Around 'base::grep()' for Use with Pipes

Provides wrappers around base::grep() where the first argument is standardized to take the data object. This makes it less of a pain to use regular expressions with 'magrittr' or other pipe operators.

Last updated 8 years ago

1.81 score 1 stars 13 scripts 128 downloads

GVARX - Perform Global Vector Autoregression Estimation and Inference

Light procedures for learning Global Vector Autoregression model (GVAR) of Pesaran, Schuermann and Weiner (2004) <DOI:10.1198/073500104000000019> and Dees, di Mauro, Pesaran and Smith (2007) <DOI:10.1002/jae.932>.

Last updated 2 years ago

1.81 score 4 stars 16 scripts 169 downloads

biosignalEMG - Tools for Electromyogram Signals (EMG) Analysis

Data processing tools to compute the rectified, integrated and the averaged EMG. Routines for automatic detection of activation phases. A routine to compute and plot the ensemble average of the EMG. An EMG signal simulator for general purposes.

Last updated 7 years ago

1.81 score 2 stars 32 scripts 580 downloads

VGAMextra - Additions and Extensions of the 'VGAM' Package

Extending the functionalities of the 'VGAM' package with additional functions and datasets. At present, 'VGAMextra' comprises new family functions (ffs) to estimate several time series models by maximum likelihood using Fisher scoring, unlike popular packages in CRAN relying on optim(), including ARMA-GARCH-like models, the Order-(p, d, q) ARIMAX model (non- seasonal), the Order-(p) VAR model, error correction models for cointegrated time series, and ARMA-structures with Student-t errors. For independent data, new ffs to estimate the inverse- Weibull, the inverse-gamma, the generalized beta of the second kind and the general multivariate normal distributions are available. In addition, 'VGAMextra' incorporates new VGLM-links for the mean-function, and the quantile-function (as an alternative to ordinary quantile modelling) of several 1-parameter distributions, that are compatible with the class of VGLM/VGAM family functions. Currently, only fixed-effects models are implemented. All functions are subject to change; see the NEWS for further details on the latest changes.

Last updated 1 years ago

1.80 score 63 scripts 855 downloads

SetMethods - Functions for Set-Theoretic Multi-Method Research and Advanced QCA

Functions for performing set-theoretic multi-method research, QCA for clustered data, theory evaluation, Enhanced Standard Analysis, indirect calibration, radar visualisations. Additionally it includes data to replicate the examples in the books by Oana, I.E, C. Q. Schneider, and E. Thomann. Qualitative Comparative Analysis (QCA) using R: A Beginner's Guide. Cambridge University Press and C. Q. Schneider and C. Wagemann "Set Theoretic Methods for the Social Sciences", Cambridge University Press.

Last updated 2 years ago

1.80 score 1 stars 63 scripts 963 downloads

R1magic - Compressive Sampling: Sparse Signal Recovery Utilities

Utilities for sparse signal recovery suitable for compressed sensing. L1, L2 and TV penalties, DFT basis matrix, simple sparse signal generator, mutual cumulative coherence between two matrices and examples, Lp complex norm, scaling back regression coefficients.

Last updated 1 years ago

1.78 score 12 scripts 286 downloads

intRvals - Analysis of Time-Ordered Event Data with Missed Observations

Calculates event rates and compares means and variances of groups of interval data corrected for missed arrival observations.

Last updated 3 years ago

1.78 score 12 scripts 133 downloads

reinsureR - Reinsurance Treaties Application

Application of reinsurance treaties to claims portfolios. The package creates a class Claims whose objective is to store claims and premiums, on which different treaties can be applied. A statistical analysis can then be applied to measure the impact of reinsurance, producing a table or graphical output. This package can be used for estimating the impact of reinsurance on several portfolios or for pricing treaties through statistical analysis. Documentation for the implemented methods can be found in "Reinsurance: Actuarial and Statistical Aspects" by Hansjöerg Albrecher, Jan Beirlant, Jozef L. Teugels (2017, ISBN: 978-0-470-77268-3) and "REINSURANCE: A Basic Guide to Facultative and Treaty Reinsurance" by Munich Re (2010) <https://www.munichre.com/site/mram/get/documents_E96160999/mram/assetpool.mr_america/PDFs/3_Publications/reinsurance_basic_guide.pdf>.

Last updated 7 years ago

1.78 score 12 scripts 202 downloads

SKNN - A Super K-Nearest Neighbor (SKNN) Classification Algorithm

It's a Super K-Nearest Neighbor classification method with using kernel density to describe weight of the distance between a training observation and the testing sample.

Last updated 3 months ago

1.78 score 238 downloads

DIDHAD - Difference-in-Differences in Heterogeneous Adoption Designs with Quasi Stayers

Estimation of Difference-in-Differences (DiD) estimators from de Chaisemartin and D'Haultfoeuille (2024) <doi:10.2139/ssrn.4284811> in Heterogeneous Adoption Designs with no stayers but with quasi stayers.

Last updated 5 months ago

1.78 score 1 dependents 346 downloads

bigBits - Perform Boolean Operations on Large Numbers

A set of Boolean operators which accept integers of any size, in any base from 2 to 36, including 2's complement format, and perform actions like "AND," "OR", "NOT", "SHIFTR/L" etc. The output can be in any base specified. A direct base to base converter is included.

Last updated 6 months ago

1.78 score 1 dependents 268 downloads

Pursuit - Projection Pursuit

Projection pursuit (PP) with 17 methods and grand tour with 3 methods. Being that projection pursuit searches for low-dimensional linear projections in high-dimensional data structures, while grand tour is a technique used to explore multivariate statistical data through animation.

Last updated 6 months ago

1.78 score 1 dependents 556 downloads

qrcm - Quantile Regression Coefficients Modeling

Parametric modeling of quantile regression coefficient functions.

Last updated 10 months ago

1.78 score 2 dependents 8 scripts 194 downloads

pbatR - Pedigree/Family-Based Genetic Association Tests Analysis and Power

This R package provides power calculations via internal simulation methods. The package also provides a frontend to the now abandoned PBAT program (developed by Christoph Lange), and reads in the corresponding output and displays results and figures when appropriate. The license of this R package itself is GPL. However, to have the program interact with the PBAT program for some functionality of the R package, users must additionally obtain the PBAT program from Christoph Lange, and accept his license. Both the data analysis and power calculations have command line and graphical interfaces using tcltk.

Last updated 11 months ago

cpp

1.78 score 2 stars 1 dependents 7 scripts 426 downloads

SpatEntropy - Spatial Entropy Measures

The heterogeneity of spatial data presenting a finite number of categories can be measured via computation of spatial entropy. Functions are available for the computation of the main entropy and spatial entropy measures in the literature. They include the traditional version of Shannon's entropy (Shannon, 1948 <doi:10.1002/j.1538-7305.1948.tb01338.x>), Batty's spatial entropy (Batty, 1974 <doi:10.1111/j.1538-4632.1974.tb01014.x>), O'Neill's entropy (O'Neill et al., 1998 <doi:10.1007/BF00162741>), Li and Reynolds' contagion index (Li and Reynolds, 1993 <doi:10.1007/BF00125347>), Karlstrom and Ceccato's entropy (Karlstrom and Ceccato, 2002 <https://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-61351>), Leibovici's entropy (Leibovici, 2009 <doi:10.1007/978-3-642-03832-7_24>), Parresol and Edwards' entropy (Parresol and Edwards, 2014 <doi:10.3390/e16041842>) and Altieri's entropy (Altieri et al., 2018, <doi:10.1007/s10651-017-0383-1>). Full references for all measures can be found under the topic 'SpatEntropy'. The package is able to work with lattice and point data. The updated version works with the updated 'spatstat' package (>= 3.0-2).

Last updated 1 years ago

1.78 score 2 stars 1 dependents 24 scripts 253 downloads

TSSS - Time Series Analysis with State Space Model

Functions for statistical analysis, modeling and simulation of time series with state space model, based on the methodology in Kitagawa (2020, ISBN: 978-0-367-18733-0).

Last updated 1 years ago

fortran

1.78 score 2 stars 2 scripts 365 downloads

liftLRD - Wavelet Lifting Estimators of the Hurst Exponent for Regularly and Irregularly Sampled Time Series

Implementations of Hurst exponent estimators based on the relationship between wavelet lifting scales and wavelet energy of Knight et al (2017) <doi:10.1007/s11222-016-9698-2>.

Last updated 1 years ago

1.78 score 2 stars 1 dependents 5 scripts 178 downloads

psyphy - Functions for Analyzing Psychophysical Data in R

An assortment of functions that could be useful in analyzing data from psychophysical experiments. It includes functions for calculating d' from several different experimental designs, links for m-alternative forced-choice (mafc) data to be used with the binomial family in glm (and possibly other contexts) and self-Start functions for estimating gamma values for CRT screen calibrations.

Last updated 1 years ago

1.78 score 53 scripts 414 downloads

ChernoffDist - Chernoff's Distribution

Computes Chernoff's distribution based on the method in Piet Groeneboom & Jon A Wellner (2001) Computing Chernoff's Distribution, Journal of Computational and Graphical Statistics, 10:2, 388-400, <doi:10.1198/10618600152627997>. Chernoff's distribution is defined as the distribution of the maximizer of the two-sided Brownian motion minus quadratic drift. That is, Z = argmax (B(t)-t^2).

Last updated 2 years ago

1.78 score 2 dependents 2 scripts 263 downloads

RSC - Robust and Sparse Correlation Matrix

Performs robust and sparse correlation matrix estimation. Robustness is achieved based on a simple robust pairwise correlation estimator, while sparsity is obtained based on thresholding. The optimal thresholding is tuned via cross-validation. See Serra, Coretto, Fratello and Tagliaferri (2018) <doi:10.1093/bioinformatics/btx642>.

Last updated 2 years ago

1.78 score 5 scripts 210 downloads

phase - Analyse Biological Time-Series Data

Compiles functions to trim, bin, visualise, and analyse activity/sleep time-series data collected from the Drosophila Activity Monitor (DAM) system (Trikinetics, USA). The following methods were used to compute periodograms - Chi-square periodogram: Sokolove and Bushell (1978) <doi:10.1016/0022-5193(78)90022-X>, Lomb-Scargle periodogram: Lomb (1976) <doi:10.1007/BF00648343>, Scargle (1982) <doi:10.1086/160554> and Ruf (1999) <doi:10.1076/brhm.30.2.178.1422>, and Autocorrelation: Eijzenbach et al. (1986) <doi:10.1111/j.1440-1681.1986.tb00943.x>. Identification of activity peaks is done after using a Savitzky-Golay filter (Savitzky and Golay (1964) <doi:10.1021/ac60214a047>) to smooth raw activity data. Three methods to estimate anticipation of activity are used based on the following papers - Slope method: Fernandez et al. (2020) <doi:10.1016/j.cub.2020.04.025>, Harrisingh method: Harrisingh et al. (2007) <doi:10.1523/JNEUROSCI.3680-07.2007>, and Stoleru method: Stoleru et al. (2004) <doi:10.1038/nature02926>. Rose plots and circular analysis are based on methods from - Batschelet (1981) <ISBN:0120810506> and Zar (2010) <ISBN:0321656865>.

Last updated 2 years ago

1.78 score 227 downloads

morph - 3D Segmentation of Voxels into Morphologic Classes

Automatically segments a 3D array of voxels into mutually exclusive morphological elements. This package extends existing work for segmenting 2D binary raster data. A paper documenting this approach has been accepted for publication in the journal Landscape Ecology. Detailed references will be updated here once those are known.

Last updated 2 years ago

1.78 score 1 scripts 150 downloads

geoTS - Methods for Handling and Analyzing Time Series of Satellite Images

Provides functions and methods for: splitting large raster objects into smaller chunks, transferring images from a binary format into raster layers, transferring raster layers into an 'RData' file, calculating the maximum gap (amount of consecutive missing values) of a numeric vector, and fitting harmonic regression models to periodic time series. The homoscedastic harmonic regression model is based on G. Roerink, M. Menenti and W. Verhoef (2000) <doi:10.1080/014311600209814>.

Last updated 2 years ago

1.78 score 2 dependents 9 scripts 199 downloads

NPCirc - Nonparametric Circular Methods

Nonparametric smoothing methods for density and regression estimation involving circular data, including the estimation of the mean regression function and other conditional characteristics.

Last updated 2 years ago

openblascppopenmp

1.78 score 2 dependents 56 scripts 306 downloads

HUM - Compute HUM Value and Visualize ROC Curves

Tools for computing HUM (Hypervolume Under the Manifold) value to estimate features ability to discriminate the class labels, visualizing the ROC curve for two or three class labels (Natalia Novoselova, Cristina Della Beffa, Junxi Wang, Jialiang Li, Frank Pessler, Frank Klawonn (2014) <doi:10.1093/bioinformatics/btu086>).

Last updated 3 years ago

cpp

1.78 score 1 stars 12 scripts 117 downloads

mAr - Multivariate AutoRegressive Analysis

R functions for the estimation and eigen-decomposition of multivariate autoregressive models.

Last updated 3 years ago

1.78 score 1 stars 2 dependents 84 scripts 402 downloads

univOutl - Detection of Univariate Outliers

Well known outlier detection techniques in the univariate case. Methods to deal with skewed distribution are included too. The Hidiroglou-Berthelot (1986) method to search for outliers in ratios of historical data is implemented as well. When available, survey weights can be used in outliers detection.

Last updated 3 years ago

1.78 score 1 dependents 20 scripts 251 downloads

pheno - Auxiliary Functions for Phenological Data Analysis

Provides some easy-to-use functions for time series analyses of (plant-) phenological data sets. These functions mainly deal with the estimation of combined phenological time series and are usually wrappers for functions that are already implemented in other R packages adapted to the special structure of phenological data and the needs of phenologists. Some date conversion functions to handle Julian dates are also provided.

Last updated 3 years ago

1.78 score 1 stars 1 dependents 20 scripts 216 downloads

PermAlgo - Permutational Algorithm to Simulate Survival Data

This version of the permutational algorithm generates a dataset in which event and censoring times are conditional on an user-specified list of covariates, some or all of which are time-dependent.

Last updated 3 years ago

1.78 score 2 dependents 36 scripts 540 downloads

twinning - Data Twinning

An efficient algorithm for data twinning. This work is supported by U.S. National Science Foundation grants DMREF-1921873 and CMMI-1921646.

Last updated 3 years ago

cppopenmp

1.78 score 2 dependents 6 scripts 159 downloads

ggrisk - Risk Score Plot for Cox Regression

The risk plot may be one of the most commonly used figures in tumor genetic data analysis. We can conclude the following two points: Comparing the prediction results of the model with the real survival situation to see whether the survival rate of the high-risk group is lower than that of the low-level group, and whether the survival time of the high-risk group is shorter than that of the low-risk group. The other is to compare the heat map and scatter plot to see the correlation between the predictors and the outcome.

Last updated 3 years ago

1.78 score 1 stars 25 scripts 281 downloads

ShinyQuickStarter - 'RStudio' Addin for Building Shiny Apps per Drag & Drop

This 'RStudio' addin makes the creation of 'Shiny' and 'ShinyDashboard' apps more efficient. Besides the necessary folder structure, entire apps can be created using a drag and drop interface and customized with respect to a specific use case. The addin allows the export of the required user interface and server code at any time. By allowing the creation of modules, the addin can be used throughout the entire app development process.

Last updated 3 years ago

1.78 score 6 stars 301 downloads

EWS - Early Warning System

The purpose of Early Warning Systems (EWS) is to detect accurately the occurrence of a crisis, which is represented by a binary variable which takes the value of one when the event occurs, and the value of zero otherwise. EWS are a toolbox for policymakers to prevent or attenuate the impact of economic downturns. Modern EWS are based on the econometric framework of Kauppi and Saikkonen (2008) <doi:10.1162/rest.90.4.777>. Specifically, this framework includes four dichotomous models, relying on a logit approach to model the relationship between yield spreads and future recessions, controlling for recession risk factors. These models can be estimated in a univariate or a balanced panel framework as in Candelon, Dumitrescu and Hurlin (2014) <doi:10.1016/j.ijforecast.2014.03.015>. This package provides both methods for estimating these models and a dataset covering 13 OECD countries over a period of 45 years. In addition, this package also provides methods for the analysis of the propagation mechanisms of an exogenous shock, as well as robust confidence intervals for these response functions using a block-bootstrap method as in Lajaunie (2021). This package constitutes a useful toolbox (data and functions) for scholars as well as policymakers.

Last updated 4 years ago

1.78 score 4 scripts 187 downloads

DistributionOptimization - Distribution Optimization

Fits Gaussian Mixtures by applying evolution. As fitness function a mixture of the chi square test for distributions and a novel measure for approximating the common area under curves between multiple Gaussians is used. The package presents an alternative to the commonly used Likelihood Maximization as is used in Expectation Maximization. The algorithm and applications of this package are published under: Lerch, F., Ultsch, A., Lotsch, J. (2020) <doi:10.1038/s41598-020-57432-w>. The evolution is based on the 'GA' package: Scrucca, L. (2013) <doi:10.18637/jss.v053.i04> while the Gaussian Mixture Logic stems from 'AdaptGauss': Ultsch, A, et al. (2015) <doi:10.3390/ijms161025897>.

Last updated 5 years ago

1.78 score 2 dependents 5 scripts 185 downloads

LPGraph - Nonparametric Smoothing of Laplacian Graph Spectra

A nonparametric method to approximate Laplacian graph spectra of a network with ordered vertices. This provides a computationally efficient algorithm for obtaining an accurate and smooth estimate of the graph Laplacian basis. The approximation results can then be used for tasks like change point detection, k-sample testing, and so on. The primary reference is Mukhopadhyay, S. and Wang, K. (2018, Technical Report).

Last updated 5 years ago

1.78 score 2 dependents 138 downloads

PersianStemmer - Persian Stemmer for Text Analysis

Allows users to stem Persian texts for text analysis.

Last updated 5 years ago

1.78 score 2 dependents 7 scripts 107 downloads

IBDsim - Simulation of Chromosomal Regions Shared by Family Members

Simulation of segments shared identical-by-descent (IBD) by pedigree members. Using sex specific recombination rates along the human genome (Kong et. al (2010) <doi:10.1038/nature09525>), phased chromosomes are simulated for all pedigree members, either by unconditional gene dropping or conditional on a specified IBD pattern. Additional functions provide summaries and further analysis of the simulated genomes.

Last updated 6 years ago

1.78 score 11 scripts 203 downloads

SPSL - Site Percolation on Square Lattices (SPSL)

Provides basic functionality for labeling iso- & anisotropic percolation clusters on 2D & 3D square lattices with various lattice sizes, occupation probabilities, von Neumann & Moore (1,d)-neighborhoods, and random variables weighting the percolation lattice sites.

Last updated 6 years ago

1.78 score 1 dependents 20 scripts 158 downloads

CNLTreg - Complex-Valued Wavelet Lifting for Signal Denoising

Implementations of recent complex-valued wavelet shrinkage procedures for smoothing irregularly sampled signals, see Hamilton et al (2018) <doi:10.1080/00401706.2017.1281846>.

Last updated 6 years ago

1.78 score 2 dependents 6 scripts 182 downloads

multiROC - Calculating and Visualizing ROC and PR Curves Across Multi-Class Classifications

Tools to solve real-world problems with multiple classes classifications by computing the areas under ROC and PR curve via micro-averaging and macro-averaging. The vignettes of this package can be found via <https://github.com/WandeRum/multiROC>. The methodology is described in V. Van Asch (2013) <https://www.clips.uantwerpen.be/~vincent/pdf/microaverage.pdf> and Pedregosa et al. (2011) <http://scikit-learn.org/stable/auto_examples/model_selection/plot_roc.html>.

Last updated 7 years ago

1.78 score 61 scripts 237 downloads

groupICA - Independent Component Analysis for Grouped Data

Contains an implementation of an independent component analysis (ICA) for grouped data. The main function groupICA() performs a blind source separation, by maximizing an independence across sources and allows to adjust for varying confounding for user-specified groups. Additionally, the package contains the function uwedge() which can be used to approximately jointly diagonalize a list of matrices. For more details see the project website <https://sweichwald.de/groupICA/>.

Last updated 7 years ago

1.78 score 2 dependents 2 scripts 153 downloads

OGI - Objective General Index

Consider a data matrix of n individuals with p variates. The objective general index (OGI) is a general index that combines the p variates into a univariate index in order to rank the n individuals. The OGI is always positively correlated with each of the variates. More details can be found in Sei (2016) <doi:10.1016/j.jmva.2016.02.005>.

Last updated 7 years ago

1.78 score 4 scripts 124 downloads

MOQA - Basic Quality Data Assurance for Epidemiological Research

With the provision of several tools and templates the MOSAIC project (DFG-Grant Number HO 1937/2-1) supports the implementation of a central data management in epidemiological research projects. The 'MOQA' package enables epidemiologists with none or low experience in R to generate basic data quality reports for a wide range of application scenarios. See <https://mosaic-greifswald.de/> for more information. Please read and cite the corresponding open access publication (using the former package-name) in METHODS OF INFORMATION IN MEDICINE by M. Bialke, H. Rau, T. Schwaneberg, R. Walk, T. Bahls and W. Hoffmann (2017) <doi:10.3414/ME16-01-0123>. <https://methods.schattauer.de/en/contents/most-recent-articles/issue/2483/issue/special/manuscript/27573/show.html>.

Last updated 8 years ago

1.78 score 8 scripts 134 downloads

hapsim - Haplotype Data Simulation

Package for haplotype-based genotype simulations. Haplotypes are generated such that their allele frequencies and linkage disequilibrium coefficients match those estimated from an input data set.

Last updated 8 years ago

1.78 score 1 stars 1 dependents 7 scripts 185 downloads

CVD - Color Vision Deficiencies

Methods for color vision deficiencies (CVD), to help understanding and mitigating issues with CVDs and to generate tests for diagnosis and interpretation.

Last updated 8 years ago

1.78 score 67 scripts 145 downloads

LARF - Local Average Response Functions for Instrumental Variable Estimation of Treatment Effects

Provides instrumental variable estimation of treatment effects when both the endogenous treatment and its instrument are binary. Applicable to both binary and continuous outcomes.

Last updated 8 years ago

1.78 score 2 stars 1 dependents 3 scripts 543 downloads

NAEPprimer - The NAEP Primer

Contains a sample of the 2005 Grade 8 Mathematics data from the National Assessment of Educational Progress (NAEP). This data set is called the NAEP Primer.

Last updated 9 years ago

1.78 score 2 dependents 316 downloads

falcon - Finding Allele-Specific Copy Number in Next-Generation Sequencing Data

This is a method for Allele-specific DNA Copy Number Profiling using Next-Generation Sequencing. Given the allele-specific coverage at the variant loci, this program segments the genome into regions of homogeneous allele-specific copy number. It requires, as input, the read counts for each variant allele in a pair of case and control samples. For detection of somatic mutations, the case and control samples can be the tumor and normal sample from the same individual.

Last updated 9 years ago

1.78 score 15 scripts 135 downloads

geesmv - Modified Variance Estimators for Generalized Estimating Equations

Generalized estimating equations with the original sandwich variance estimator proposed by Liang and Zeger (1986), and eight types of more recent modified variance estimators for improving the finite small-sample performance.

Last updated 9 years ago

1.78 score 43 scripts 181 downloads

spatialCovariance - Computation of Spatial Covariance Matrices for Data on Rectangles

Functions that compute the spatial covariance matrix for the matern and power classes of spatial models, for data that arise on rectangular units. This code can also be used for the change of support problem and for spatial data that arise on irregularly shaped regions like counties or zipcodes by laying a fine grid of rectangles and aggregating the integrals in a form of Riemann integration.

Last updated 9 years ago

1.78 score 2 dependents 8 scripts 344 downloads

rFerns - Random Ferns Classifier

Provides the random ferns classifier by Ozuysal, Calonder, Lepetit and Fua (2009) <doi:10.1109/TPAMI.2009.23>, modified for generic and multi-label classification and featuring OOB error approximation and importance measure as introduced in Kursa (2014) <doi:10.18637/jss.v061.i10>.

Last updated 3 years ago

openmp

1.77 score 27 scripts 1.1k downloads

ggversa - Graficas Versatiles Con 'ggplot2'

A collection of datasets for the upcoming book "Graficas versatiles con ggplot: Analisis visuales de datos", by Raymond L. Tremblay and Julian Hernandez-Serano.

Last updated 7 years ago

1.76 score 58 scripts 124 downloads

rpartScore - Classification Trees for Ordinal Responses

Recursive partitioning methods to build classification trees for ordinal responses within the CART framework. Trees are grown using the Generalized Gini impurity function, where the misclassification costs are given by the absolute or squared differences in scores assigned to the categories of the response. Pruning is based on the total misclassification rate or on the total misclassification cost.

Last updated 3 years ago

1.76 score 1 dependents 19 scripts 335 downloads

HiDimDA - High Dimensional Discriminant Analysis

Performs linear discriminant analysis in high dimensional problems based on reliable covariance estimators for problems with (many) more variables than observations. Includes routines for classifier training, prediction, cross-validation and variable selection.

Last updated 3 months ago

fortranopenblascpp

1.75 score 28 scripts 313 downloads

birdring - Methods to Analyse Ring Re-Encounter Data

R functions to read EURING data and analyse re-encounter data of birds marked by metal rings. For a tutorial, go to <doi:10.1080/03078698.2014.933053>.

Last updated 1 years ago

1.75 score 28 scripts 238 downloads

IntNMF - Integrative Clustering of Multiple Genomic Dataset

Carries out integrative clustering analysis using multiple types of genomic dataset using integrative Non-negative Matrix factorization.

Last updated 6 years ago

1.75 score 2 stars 28 scripts 226 downloads

twl - Two-Way Latent Structure Clustering Model

Implementation of a Bayesian two-way latent structure model for integrative genomic clustering. The model clusters samples in relation to distinct data sources, with each subject-dataset receiving a latent cluster label, though cluster labels have across-dataset meaning because of the model formulation. A common scaling across data sources is unneeded, and inference is obtained by a Gibbs Sampler. The model can fit multivariate Gaussian distributed clusters or a heavier-tailed modification of a Gaussian density. Uniquely among integrative clustering models, the formulation makes no nestedness assumptions of samples across data sources -- the user can still fit the model if a study subject only has information from one data source. The package provides a variety of post-processing functions for model examination including ones for quantifying observed alignment of clusterings across genomic data sources. Run time is optimized so that analyses of datasets on the order of thousands of features on fewer than 5 datasets and hundreds of subjects can converge in 1 or 2 days on a single CPU. See "Swanson DM, Lien T, Bergholtz H, Sorlie T, Frigessi A, Investigating Coordinated Architectures Across Clusters in Integrative Studies: a Bayesian Two-Way Latent Structure Model, 2018, <doi:10.1101/387076>, Cold Spring Harbor Laboratory" at <https://www.biorxiv.org/content/early/2018/08/07/387076.full.pdf> for model details.

Last updated 6 years ago

1.75 score 56 scripts 151 downloads

gbRd - Utilities for Processing Rd Objects and Files

Provides utilities for processing Rd objects and files. Extract argument descriptions and other parts of the help pages of functions.

Last updated 7 months ago

1.74 score 13 scripts 1.1k downloads

funFEM - Clustering in the Discriminative Functional Subspace

The funFEM algorithm (Bouveyron et al., 2014) allows to cluster functional data by modeling the curves within a common and discriminative functional subspace.

Last updated 3 years ago

1.73 score 1 dependents 18 scripts 417 downloads

aster2 - Aster Models

Aster models are exponential family regression models for life history analysis. They are like generalized linear models except that elements of the response vector can have different families (e. g., some Bernoulli, some Poisson, some zero-truncated Poisson, some normal) and can be dependent, the dependence indicated by a graphical structure. Discrete time survival analysis, zero-inflated Poisson regression, and generalized linear models that are exponential family (e. g., logistic regression and Poisson regression with log link) are special cases. Main use is for data in which there is survival over discrete time periods and there is additional data about what happens conditional on survival (e. g., number of offspring). Uses the exponential family canonical parameterization (aster transform of usual parameterization). Unlike the aster package, this package does dependence groups (nodes of the graph need not be conditionally independent given their predecessor node), including multinomial and two-parameter normal as families. Thus this package also generalizes mark-capture-recapture analysis.

Last updated 3 months ago

1.72 score 52 scripts 259 downloads

RcmdrPlugin.FactoMineR - Graphical User Interface for FactoMineR

Rcmdr Plugin for the 'FactoMineR' package.

Last updated 1 years ago

1.72 score 1 stars 2 scripts 1.0k downloads

tightClust - Tight Clustering

The functions needed to perform tight clustering Algorithm.

Last updated 7 years ago

1.71 score 1 dependents 17 scripts 134 downloads

mstR - Procedures to Generate Patterns under Multistage Testing

Generation of response patterns under dichotomous and polytomous computerized multistage testing (MST) framework. It holds various item response theory (IRT) and score-based methods to select the next module and estimate ability levels (Magis, Yan and von Davier (2017, ISBN:978-3-319-69218-0)).

Last updated 7 years ago

1.71 score 3 stars 17 scripts 158 downloads

powdist - Power and Reversal Power Distributions

Density, distribution function, quantile function and random generation for the family of power and reversal power distributions.

Last updated 7 years ago

1.71 score 1 dependents 17 scripts 150 downloads

iso8601 - Working with ISO8601 Dates and Times

Functions to parse strings with ISO8601 dates, times, and date-times into R-objects. Additionally, there are functions to determine the type of ISO8601 string and to standardise ISO8601 strings.

Last updated 4 days ago

cpp

1.70 score 71 downloads

multvardiv - Multivariate Probability Distributions, Statistical Divergence

Multivariate generalized Gaussian distribution, Multivariate Cauchy distribution, Multivariate t distribution. Distance between two distributions (see N. Bouhlel and A. Dziri (2019): <doi:10.1109/LSP.2019.2915000>, N. Bouhlel and D. Rousseau (2022): <doi:10.3390/e24060838>, N. Bouhlel and D. Rousseau (2023): <doi:10.1109/LSP.2023.3324594>). Manipulation of these multivariate probability distributions.

Last updated 4 days ago

1.70 score

ADSIHT - Adaptive Double Sparse Iterative Hard Thresholding

Solving the high-dimensional double sparse linear regression via iterative hard thresholding algorithm. For more details, please see Zhang et al. (2024, <DOI:10.48550/arXiv.2305.04182>).

Last updated 13 days ago

cpp

1.70 score 2 scripts

opengraph - Process Metadata from the Open Graph Protocol

Social media sites often embed cards when links are shared, based on metadata in the 'Open Graph Protocol' (<https://ogp.me/>). This supports extracting that metadata from a website. It further allows for the creation of tags to add to a website to support the 'Open Graph Protocol' and provides a list of the standard tags and their required properties.

Last updated 14 days ago

1.70 score 5 scripts

gg1d - Exploratory Data Analysis using Tiled One-Dimensional Graphics

Streamlines exploratory data analysis by providing a turnkey approach to visualising n-dimensional data which graphically reveals correlative or associative relationships between 2 or more features. Represents all dataset features as distinct, vertically aligned bar or tile plots, with plot types auto-selected based on whether variables are categorical or numeric.

Last updated 15 days ago

1.70 score 6 scripts

tinylens - Minimal Implementation of Functional Lenses

Provides utilities to create and use lenses to simplify data manipulation. Lenses are composable getter/setter pairs that provide a functional approach to manipulating deeply nested data structures, e.g., elements within list columns in data frames. The implementation is based on the earlier 'lenses' R package <https://github.com/cfhammill/lenses>, which was inspired by the Haskell 'lens' package by Kmett (2012) <https://github.com/ekmett/lens>, one of the most widely referenced implementations of lenses. For additional background and history on the theory of lenses, see the 'lens' package wiki: <https://github.com/ekmett/lens/wiki/History-of-Lenses>.

Last updated 15 days ago

1.70 score 3 scripts

sooty - Data Source Catalogues Online for Southern Ocean Ecosystem Research

Obtains lists of files of remote sensing collections for Southern Ocean surface properties. Commonly used data sources of sea surface temperature, sea ice concentration, and altimetry products such as sea surface height and sea surface currents are cached in object storage on the Pawsey Supercomputing Research Centre facility. Functions to retrieve these object storage catalogues are provided. The catalogues include complete collections of datasets Reynolds et al. (2008) "NOAA Optimum Interpolation Sea Surface Temperature (OISST) Analysis, Version 2.1" <doi:10.7289/V5SQ8XB5>, Spreen et al. (2008) "Artist Advanced Microwave Scanning Radiometer for Earth Observing System (AMSR-E) sea ice concentration" <doi:10.1029/2005JC003384>. In future releases helpers will be added to identify particular data collections and target specific dates for earth observation data for reading, as well as helpers to retrieve data set citation and provenance details.

Last updated 18 days ago

1.70 score 4 scripts

iclogcondist - Log-Concave Distribution Estimation with Interval-Censored Data

We consider the non-parametric maximum likelihood estimation of the underlying distribution function, assuming log-concavity, based on mixed-case interval-censored data. The algorithm implemented is base on Chi Wing Chu, Hok Kan Ling and Chaoyu Yuan (2024, <doi:10.48550/arXiv.2411.19878>).

Last updated 19 days ago

cpp

1.70 score 2 scripts

ErlangC - Solve Erlang-C Model

Provides a set of functions to solve Erlang-C model. The Erlang C formula was invented by the Danish Mathematician A.K. Erlang and is used to calculate the number of advisors and the service level.

Last updated 19 days ago

1.70 score 3 scripts

gfoRmulaICE - Parametric Iterative Conditional Expectation G-Formula

Implements iterative conditional expectation (ICE) estimators of the plug-in g-formula (Wen, Young, Robins, and Hernán (2020) <doi: 10.1111/biom.13321>). Both singly robust and doubly robust ICE estimators based on parametric models are available. The package can be used to estimate survival curves under sustained treatment strategies (interventions) using longitudinal data with time-varying treatments, time-varying confounders, censoring, and competing events. The interventions can be static or dynamic, and deterministic or stochastic (including threshold interventions). Both prespecified and user-defined interventions are available.

Last updated 22 days ago

1.70 score 2 scripts

wdiEF - Calculation of the Water Deficit Index (WDI) and the Evaporative Fraction (EF) on Rasters

Calculates the Water Deficit Index (WDI) and the Evaporative Fraction (EF) using geospatial data, such as fractional vegetation cover (FVC) and surface-air temperature difference (TS-TA). Terms like "raster", "CRS" are part of standard geospatial terminology.

Last updated 22 days ago

1.70 score 4 scripts

PolisheR - Interfacing 'NaileR' with 'Shiny'

A very small package for more convenient use of 'NaileR'. You provide a data set containing a latent variable you want to understand. It generates a description and an interpretation of this latent variable using a Large Language Model. For perceptual data, it describes the stimuli used in the experiment.

Last updated 25 days ago

1.70 score 2 scripts

bayeslist - Bayesian Analysis of List Experiments with Prior Information

Estimates Bayesian models of list experiments with informative priors. It includes functionalities to estimate different types of list experiment models with varying prior information. See Lu and Traunmüller (2021) <doi:10.2139/ssrn.3871089> for examples and details of estimation.

Last updated 26 days ago

cpp

1.70 score

AnomalyScore - Anomaly Scoring for Multivariate Time Series

Compute an anomaly score for multivariate time series based on the k-nearest neighbors algorithm. Different computations of distances between time series are provided.

Last updated 1 months ago

1.70 score 1 scripts 562 downloads

RCognito - A Simplified Interface for 'Amazon Cognito'

Simplifies integration with 'Amazon Cognito' (<https://aws.amazon.com/cognito/>) for R developers, enabling easy management of user authentication, registration, and password flows.

Last updated 1 months ago

1.70 score 500 downloads

CIMPLE - Analysis of Longitudinal Electronic Health Record (EHR) Data with Possibly Informative Observational Time

Analyzes longitudinal Electronic Health Record (EHR) data with possibly informative observational time. These methods are grouped into two classes depending on the inferential task. One group focuses on estimating the effect of an exposure on a longitudinal biomarker while the other group assesses the impact of a longitudinal biomarker on time-to-diagnosis outcomes. The accompanying paper is Du et al (2024) <doi:10.48550/arXiv.2410.13113>.

Last updated 1 months ago

1.70 score 2 scripts 470 downloads

mcmapper - Mapping First Moment and C-Statistic to the Parameters of Distributions for Risk

Provides a series of numerical methods for extracting parameters of distributions for risks based on knowing the expected value and c-statistics (e.g., from a published report on the performance of a risk prediction model). This package implements the methodology described in Sadatsafavi et al (2024) <doi:10.48550/arXiv.2409.09178>. The core of the package is mcmap(), which takes a pair of (mean, c-statistic) and the distribution type requested. This function provides a generic interface to more customized functions (mcmap_beta(), mcmap_logitnorm(), mcmap_probitnorm()) for specific distributions.

Last updated 2 months ago

1.70 score 3 scripts 435 downloads

Copula.surv - Analysis of Bivariate Survival Data Based on Copulas

Simulating bivariate survival data from copula models. Estimation of the association parameter in copula models. Two different ways to estimate the association parameter in copula models are implemented. A goodness-of-fit test for a given copula model is implemented. See Emura, Lin and Wang (2010) <doi:10.1016/j.csda.2010.03.013> for details.

Last updated 2 months ago

1.70 score 3 scripts 753 downloads

roseRF - ROSE Random Forests for Robust Semiparametric Efficient Estimation

ROSE (RObust Semiparametric Efficient) random forests for robust semiparametric efficient estimation in partially parametric models (containing generalised partially linear models). Details can be found in the paper by Young and Shah (2024) <doi:10.48550/arXiv.2410.03471>.

Last updated 2 months ago

1.70 score 2 scripts 98 downloads

logconcens - Maximum Likelihood Estimation of a Log-Concave Density Based on Censored Data

Based on right or interval censored data, compute the maximum likelihood estimator of a (sub)probability density under the assumption that it is log-concave. For further information see Duembgen, Rufibach and Schuhmacher (2014) <doi:10.1214/14-EJS930>.

Last updated 3 months ago

openblas

1.70 score 7 scripts 278 downloads

shrinkem - Approximate Bayesian Regularization for Parsimonious Estimates

Approximate Bayesian regularization using Gaussian approximations. The input is a vector of estimates and a Gaussian error covariance matrix of the key parameters. Bayesian shrinkage is then applied to obtain parsimonious solutions. The method is described on Karimova, van Erp, Leenders, and Mulder (2024) <DOI:10.31234/osf.io/2g8qm>. Gibbs samplers are used for model fitting. The shrinkage priors that are supported are Gaussian (ridge) priors, Laplace (lasso) priors (Park and Casella, 2008 <DOI:10.1198/016214508000000337>), and horseshoe priors (Carvalho, et al., 2010; <DOI:10.1093/biomet/asq017>). These priors include an option for grouped regularization of different subsets of parameters (Meier et al., 2008; <DOI:10.1111/j.1467-9868.2007.00627.x>). F priors are used for the penalty parameters lambda^2 (Mulder and Pericchi, 2018 <DOI:10.1214/17-BA1092>). This correspond to half-Cauchy priors on lambda (Carvalho, Polson, Scott, 2010 <DOI:10.1093/biomet/asq017>).

Last updated 3 months ago

1.70 score 3 scripts 119 downloads

IGC.CSM - Simulate Impact of Different Urban Policies Through a General Equilibrium Model

Develops a General Equilibrium (GE) Model, which estimates key variables such as wages, the number of residents and workers, the prices of the floor space, and its distribution between commercial and residential use, as in Ahlfeldt et al., (2015) <doi:10.3982/ECTA10876>. By doing so, the model allows understanding the economic influence of different urban policies.

Last updated 3 months ago

1.70 score 261 downloads

permutest - Run Permutation Tests and Construct Associated Confidence Intervals

Implements permutation tests for any test statistic and randomization scheme and constructs associated confidence intervals as described in Glazer and Stark (2024) <doi:10.48550/arXiv.2405.05238>.

Last updated 3 months ago

1.70 score 2 scripts 129 downloads

staticryptR - Encrypt HTML Files Using 'staticrypt'

Provides a convenient interface to the 'staticrypt' by Robin Moisson <https://github.com/robinmoisson/staticrypt>---'Node.js' package for adding a password protection layer to static HTML pages. This package can be integrated into the post-render process of 'quarto' documents to secure them with a password.

Last updated 3 months ago

1.70 score 340 downloads

WAnova - Welch's Anova from Summary Statistics

Provides the functions to perform a Welch's one-way Anova with fixed effects based on summary statistics (sample size, means, standard deviation) and the Games-Howell post hoc test for multiple comparisons and provides the effect size estimator adjusted omega squared. In addition sample size estimation can be computed based on Levy's method, and a Monte Carlo simulation is included to bootstrap residual normality and homoscedasticity Welch, B. L. (1951) <doi:10.1093/biomet/38.3-4.330> Kirk, R. E. (1996) <doi:10.1177/0013164496056005002> Carroll, R. M., & Nordholm, L. A. (1975) <doi:10.1177/001316447503500304> Albers, C., & Lakens, D. (2018) <doi:10.1016/j.jesp.2017.09.004> Games, P. A., & Howell, J. F. (1976) <doi:10.2307/1164979> Levy, K. J. (1978a) <doi:10.1080/00949657808810246> Show-Li, J., & Gwowen, S. (2014) <doi:10.1111/bmsp.12006>.

Last updated 3 months ago

1.70 score 3 scripts 112 downloads

DEXiR - 'DEXi' Library

A software package for using 'DEXi' models. 'DEXi' models are hierarchical qualitative multi-criteria decision models developed according to the method DEX (Decision EXpert, <https://dex.ijs.si/documentation/DEX_Method/DEX_Method.html>), using the program 'DEXi' (<https://kt.ijs.si/MarkoBohanec/dexi.html>) or 'DEXiWin' (<https://dex.ijs.si/dexisuite/dexiwin.html>). A typical workflow with 'DEXiR' consists of: (1) reading a '.dxi' file, previously made using the 'DEXi' software (function read_dexi()), (2) making a data frame containing input values of one or more decision alternatives, (3) evaluating those alternatives (function evaluate()), (4) analyzing alternatives (selective_explanation(), plus_minus(), compare_alternatives()), (5) drawing charts. 'DEXiR' is restricted to using models produced externally by the 'DEXi' software and does not provide functionality for creating and/or editing 'DEXi' models directly in 'R'.

Last updated 3 months ago

1.70 score 139 downloads

maxstablePCA - Apply a PCA Like Procedure Suited for Multivariate Extreme Value Distributions

Dimension reduction for multivariate data of extreme events with a PCA like procedure as described in Reinbott, Janßen, (2024), <doi:10.48550/arXiv.2408.10650>. Tools for necessary transformations of the data are provided.

Last updated 4 months ago

1.70 score 1 scripts 149 downloads

Kira - Machine Learning

Machine learning, containing several algorithms for supervised and unsupervised classification, in addition to a function that plots the Receiver Operating Characteristic (ROC) and Precision-Recall (PRC) curve graphs, and also a function that returns several metrics used for model evaluation, the latter can be used in ranking results from other packs.

Last updated 4 months ago

1.70 score 1 scripts 191 downloads

QuICSeedR - Analyze Data for Fluorophore-Assisted Seed Amplification Assays

A toolkit for analysis and visualization of data from fluorophore-assisted seed amplification assays, such as Real-Time Quaking-Induced Conversion (RT-QuIC) and Fluorophore-Assisted Protein Misfolding Cyclic Amplification (PMCA). 'QuICSeedR' addresses limitations in existing software by automating data processing, supporting large-scale analysis, and enabling comparative studies of analysis methods. It incorporates methods described in Henderson et al. (2015) <doi:10.1099/vir.0.069906-0>, Li et al. (2020) <doi:10.1038/s41598-021-96127-8>, Rowden et al. (2023) <doi:10.3390/pathogens12020309>, Haley et al. (2013) <doi:10.1371/journal.pone.0081488>, and Mair and Wilcox (2020) <doi:10.3758/s13428-019-01246-w>. Please refer to the original publications for details.

Last updated 4 months ago

1.70 score 2 scripts 110 downloads

mvs - Methods for High-Dimensional Multi-View Learning

Methods for high-dimensional multi-view learning based on the multi-view stacking (MVS) framework. For technical details on the MVS and stacked penalized logistic regression (StaPLR) methods see Van Loon, Fokkema, Szabo, & De Rooij (2020) <doi:10.1016/j.inffus.2020.03.007> and Van Loon et al. (2022) <doi:10.3389/fnins.2022.830630>.

Last updated 4 months ago

1.70 score 1 scripts 156 downloads

PoSIAdjRSquared - Post-Selection Inference for Adjusted R Squared

Conduct post-selection inference for regression coefficients in linear models after they have been selected by adjusted R squared. The p-values and confidence intervals are valid after model selection with the same data. This allows the user to use all data for both model selection and inference without losing control over the type I error rate. The provided tests are more powerful than data splitting, which bases inference on less data since it discards all information used for selection.

Last updated 4 months ago

1.70 score 1 scripts 139 downloads

boinet - Conduct Simulation Study of Bayesian Optimal Interval Design with BOIN-ET Family

Bayesian optimal interval based on both efficacy and toxicity outcomes (BOIN-ET) design is a model-assisted oncology phase I/II trial design, aiming to establish an optimal biological dose accounting for efficacy and toxicity in the framework of dose-finding. Some extensions of BOIN-ET design are also available to allow for time-to-event efficacy and toxicity outcomes based on cumulative and pending data (time-to-event BOIN-ET: TITE-BOIN-ET), ordinal graded efficacy and toxicity outcomes (generalized BOIN-ET: gBOIN-ET), and their combination (TITE-gBOIN-ET). 'boinet' is a package to implement the BOIN-ET design family and supports the conduct of simulation studies to assess operating characteristics of BOIN-ET, TITE-BOIN-ET, gBOIN-ET, and TITE-gBOIN-ET, where users can choose design parameters in flexible and straightforward ways depending on their own application.

Last updated 4 months ago

1.70 score 1 scripts 203 downloads

triplesmatch - Match Triples Consisting of Two Controls and a Treated Unit or Vice Versa

Attain excellent covariate balance by matching two treated units and one control unit or vice versa within strata. Using such triples, as opposed to also allowing pairs of treated and control units, allows easier interpretation of the two possible weights of observations and better insensitivity to unmeasured bias in the test statistic. Using triples instead of matching in a fixed 1:2 or 2:1 ratio allows for the match to be feasible in more situations. The 'rrelaxiv' package, which provides an alternative solver for the underlying network flow problems, carries an academic license and is not available on CRAN, but may be downloaded from 'GitHub' at <https://github.com/josherrickson/rrelaxiv/>. The 'Gurobi' commercial optimization software is required to use the two functions [infsentrip()] and [triplesIP()]. These functions are not essential to the main purpose of this package. A free academic license can be obtained at <https://www.gurobi.com/features/academic-named-user-license/>. The 'gurobi' R package can then be installed following the instructions at <https://www.gurobi.com/documentation/9.1/refman/ins_the_r_package.html>.

Last updated 5 months ago

1.70 score 1 scripts 158 downloads

fwlplot - Scatter Plot After Residualizing Using 'fixest' Package

Creates a scatter plot after residualizing using a set of covariates. The residuals are calculated using the 'fixest' package which allows very fast estimation that scales. Details of the (Yule-)Frisch-Waugh-Lovell theorem is given in Basu (2023) <doi:10.48550/arXiv.2307.00369>.

Last updated 6 months ago

1.70 score 9 scripts 532 downloads

avidaR - A Computational Biologist’s Toolkit To Get Data From 'avidaDB'

Easy-to-use tools for performing complex queries on 'avidaDB', a semantic database that stores genomic and transcriptomic data of self-replicating computer programs (known as digital organisms) that mutate and evolve within a user-defined computational environment.

Last updated 6 months ago

1.70 score 2 scripts 283 downloads

probs - Elementary Probability on Finite Sample Spaces

Performs elementary probability calculations on finite sample spaces, which may be represented by data frames or lists. This package is meant to rescue some widely used functions from the archived 'prob' package (see <https://cran.r-project.org/src/contrib/Archive/prob/>). Functionality includes setting up sample spaces, counting tools, defining probability spaces, performing set algebra, calculating probability and conditional probability, tools for simulation and checking the law of large numbers, adding random variables, and finding marginal distributions. Characteristic functions for all base R distributions are included.

Last updated 6 months ago

1.70 score 3 scripts 856 downloads

crossurr - Cross-Fitting for Doubly Robust Evaluation of High-Dimensional Surrogate Markers

Doubly robust methods for evaluating surrogate markers as outlined in: Agniel D, Hejblum BP, Thiebaut R & Parast L (2022). "Doubly robust evaluation of high-dimensional surrogate markers", Biostatistics <doi:10.1093/biostatistics/kxac020>. You can use these methods to determine how much of the overall treatment effect is explained by a (possibly high-dimensional) set of surrogate markers.

Last updated 6 months ago

1.70 score 198 downloads

SeaVal - Validation of Seasonal Weather Forecasts

Provides tools for processing and evaluating seasonal weather forecasts, with an emphasis on tercile forecasts. We follow the World Meteorological Organization's "Guidance on Verification of Operational Seasonal Climate Forecasts", S.J.Mason (2018, ISBN: 978-92-63-11220-0, URL: <https://library.wmo.int/idurl/4/56227>). The development was supported by the European Union’s Horizon 2020 research and innovation programme under grant agreement no. 869730 (CONFER). A comprehensive online tutorial is available at <https://seasonalforecastingengine.github.io/SeaValDoc/>.

Last updated 6 months ago

1.70 score 14 scripts 547 downloads

ppgm - PaleoPhyloGeographic Modeling of Climate Niches and Species Distributions

Reconstruction of paleoclimate niches using phylogenetic comparative methods and projection reconstructed niches onto paleoclimate maps. The user can specify various models of trait evolution or estimate the best fit model, include fossils, use one or multiple phylogenies for inference, and make animations of shifting suitable habitat through time. This model was first used in Lawing and Polly (2011), and further implemented in Lawing et al (2016) and Rivera et al (2020). Lawing and Polly (2011) <doi:10.1371/journal.pone.0028554> "Pleistocene climate, phylogeny and climate envelope models: An integrative approach to better understand species' response to climate change" Lawing et al (2016) <doi:10.1086/687202> "Including fossils in phylogenetic climate reconstructions: A deep time perspective on the climatic niche evolution and diversification of spiny lizards (Sceloporus)" Rivera et al (2020) <doi:10.1111/jbi.13915> "Reconstructing historical shifts in suitable habitat of Sceloporus lineages using phylogenetic niche modelling.".

Last updated 7 months ago

1.70 score 5 scripts 439 downloads

KnockoffHybrid - Hybrid Analysis of Population and Trio Data with Knockoff Statistics for FDR Control

Identification of putative causal variants in genome-wide association studies using hybrid analysis of both the trio and population designs. The package implements the method in the paper: Yang, Y., Wang, Q., Wang, C., Buxbaum, J., & Ionita-Laza, I. (2024). KnockoffHybrid: A knockoff framework for hybrid analysis of trio and population designs in genome-wide association studies. The American Journal of Human Genetics, in press.

Last updated 7 months ago

1.70 score 483 downloads

HDCD - High-Dimensional Changepoint Detection

Efficient implementations of the following multiple changepoint detection algorithms: Efficient Sparsity Adaptive Change-point estimator by Moen, Glad and Tveten (2023) <doi:10.48550/arXiv.2306.04702> , Informative Sparse Projection for Estimating Changepoints by Wang and Samworth (2017) <doi:10.1111/rssb.12243>, and the method of Pilliat et al (2023) <doi:10.1214/23-EJS2126>.

Last updated 7 months ago

1.70 score 3 scripts 488 downloads

ggscidca - Plotting Decision Curve Analysis with Coloured Bars

Decision curve analysis is a method for evaluating and comparing prediction models that incorporates clinical consequences, requires only the data set on which the models are tested, and can be applied to models that have either continuous or dichotomous results. The 'ggscidca' package adds coloured bars of discriminant relevance to the traditional decision curve. Improved practicality and aesthetics. This method was described by Balachandran VP (2015) <doi:10.1016/S1470-2045(14)71116-7>.

Last updated 7 months ago

1.70 score 248 downloads

clarkeTest - Distribution-Free Tests of Non-Nested Models

Implementation of Clarke's distribution-free test of non-nested models. Currently supported model functions are: lm(), glm() ('binomial', 'poisson', 'negative binomial' links), polr() ('MASS'), clm() ('ordinal'), and multinom() ('nnet'). For more information on the test, see Clarke (2007) <doi:10.1093/pan/mpm004>.

Last updated 7 months ago

1.70 score 8 scripts 540 downloads

hdmed - Methods for Mediation Analysis with High-Dimensional Mediators

A suite of functions for performing mediation analysis with high-dimensional mediators. In addition to centralizing code from several existing packages for high-dimensional mediation analysis, we provide organized, well-documented functions for a handle of methods which, though programmed their original authors, have not previously been formalized into R packages or been made presentable for public use. The methods we include cover a broad array of approaches and objectives, and are described in detail by both our companion manuscript---"Methods for Mediation Analysis with High-Dimensional DNA Methylation Data: Possible Choices and Comparison"---and the original publications that proposed them. The specific methods offered by our package include the Bayesian sparse linear mixed model (BSLMM) by Song et al. (2019); high-dimensional mediation analysis (HDMA) by Gao et al. (2019); high-dimensional multivariate mediation (HDMM) by Chén et al. (2018); high-dimensional linear mediation analysis (HILMA) by Zhou et al. (2020); high-dimensional mediation analysis (HIMA) by Zhang et al. (2016); latent variable mediation analysis (LVMA) by Derkach et al. (2019); mediation by fixed-effect model (MedFix) by Zhang (2021); pathway LASSO by Zhao & Luo (2022); principal component mediation analysis (PCMA) by Huang & Pan (2016); and sparse principal component mediation analysis (SPCMA) by Zhao et al. (2020). Citations for the corresponding papers can be found in their respective functions.

Last updated 7 months ago

1.70 score 7 scripts 515 downloads

shinymgr - A Framework for Building, Managing, and Stitching 'shiny' Modules into Reproducible Workflows

A unifying framework for managing and deploying 'shiny' applications that consist of modules, where an "app" is a tab-based workflow that guides a user step-by-step through an analysis. The 'shinymgr' app builder "stitches" 'shiny' modules together so that outputs from one module serve as inputs to the next, creating an analysis pipeline that is easy to implement and maintain. Users of 'shinymgr' apps can save analyses as an RDS file that fully reproduces the analytic steps and can be ingested into an R Markdown report for rapid reporting. In short, developers use the 'shinymgr' framework to write modules and seamlessly combine them into 'shiny' apps, and users of these apps can execute reproducible analyses that can be incorporated into reports for rapid dissemination.

Last updated 8 months ago

1.70 score 1 scripts 498 downloads

ddecompose - Detailed Distributional Decomposition

Implements the Oaxaca-Blinder decomposition method and generalizations of it that decompose differences in distributional statistics beyond the mean. The function ob_decompose() decomposes differences in the mean outcome between two groups into one part explained by different covariates (composition effect) and into another part due to differences in the way covariates are linked to the outcome variable (structure effect). The function further divides the two effects into the contribution of each covariate and allows for weighted doubly robust decompositions. For distributional statistics beyond the mean, the function performs the recentered influence function (RIF) decomposition proposed by Firpo, Fortin, and Lemieux (2018). The function dfl_decompose() divides differences in distributional statistics into an composition effect and a structure effect using inverse probability weighting as introduced by DiNardo, Fortin, and Lemieux (1996). The function also allows to sequentially decompose the composition effect into the contribution of single covariates. References: Firpo, Sergio, Nicole M. Fortin, and Thomas Lemieux. (2018) <doi:10.3390/econometrics6020028>. "Decomposing Wage Distributions Using Recentered Influence Function Regressions." Fortin, Nicole M., Thomas Lemieux, and Sergio Firpo. (2011) <doi:10.3386/w16045>. "Decomposition Methods in Economics." DiNardo, John, Nicole M. Fortin, and Thomas Lemieux. (1996) <doi:10.2307/2171954>. "Labor Market Institutions and the Distribution of Wages, 1973-1992: A Semiparametric Approach." Oaxaca, Ronald. (1973) <doi:10.2307/2525981>. "Male-Female Wage Differentials in Urban Labor Markets." Blinder, Alan S. (1973) <doi:10.2307/144855>. "Wage Discrimination: Reduced Form and Structural Estimates."

Last updated 8 months ago

1.70 score 1 stars 3 scripts 156 downloads

mlr3summary - Model and Learner Summaries for 'mlr3'

Concise and interpretable summaries for machine learning models and learners of the 'mlr3' ecosystem. The package takes inspiration from the summary function for (generalized) linear models but extends it to non-parametric machine learning models, based on generalization performance, model complexity, feature importances and effects, and fairness metrics.

Last updated 8 months ago

1.70 score 4 scripts 199 downloads

LDAandLDAS - Linkage Disequilibrium of Ancestry (LDA) and LDA Score (LDAS)

Computation of linkage disequilibrium of ancestry (LDA) and linkage disequilibrium of ancestry score (LDAS). LDA calculates the pairwise linkage disequilibrium of ancestry between single nucleotide polymorphisms (SNPs). LDAS calculates the LDA score of SNPs. The methods are described in Barrie W, Yang Y, Irving-Pease E.K, et al (2024) <doi:10.1038/s41586-023-06618-z>.

Last updated 11 months ago

cpp

1.70 score 2 scripts 184 downloads

WhatsR - Parsing, Anonymizing and Visualizing Exported 'WhatsApp' Chat Logs

Imports 'WhatsApp' chat logs and parses them into a usable dataframe object. The parser works on chats exported from Android or iOS phones and on Linux, macOS and Windows. The parser has multiple options for extracting smileys and emojis from the messages, extracting URLs and domains from the messages, extracting names and types of sent media files from the messages, extracting timestamps from messages, extracting and anonymizing author names from messages. Can be used to create anonymized versions of data.

Last updated 11 months ago

openjdk

1.70 score 3 scripts 247 downloads

GAGAs - Global Adaptive Generative Adjustment Algorithm for Generalized Linear Models

Fits linear regression, logistic and multinomial regression models, Poisson regression, Cox model via Global Adaptive Generative Adjustment Algorithm. For more detailed information, see Bin Wang, Xiaofei Wang and Jianhua Guo (2022) <arXiv:1911.00658>. This paper provides the theoretical properties of Gaga linear model when the load matrix is orthogonal. Further study is going on for the nonorthogonal cases and generalized linear models. These works are in part supported by the National Natural Foundation of China (No.12171076).

Last updated 11 months ago

1.70 score 190 downloads

EVchargcost - Computes and Plot the Optimal Charging Strategy for Electric Vehicles

The purpose of this library is to compute the optimal charging cost function for a electric vehicle (EV). It is well known that the charging function of a EV is a concave function that can be approximated by a piece-wise linear function, so bigger the state of charge, slower the charging process is. Moreover, the other important function is the one that gives the electricity price. This function is usually step-wise, since depending on the time of the day, the price of the electricity is different. Then, the problem of charging an EV to a certain state of charge is not trivial. This library implements an algorithm to compute the optimal charging cost function, that is, it plots for a given state of charge r (between 0 and 1) the minimum cost we need to pay in order to charge the EV to that state of charge r. The details of the algorithm are described in González-Rodríguez et at (2023) <https://inria.hal.science/hal-04362876v1>.

Last updated 12 months ago

1.70 score 151 downloads

vectorbitops - Vector Bitwise Operations

A tool for fast, efficient bitwise operations along the elements within a vector. Provides such functionality for AND, OR and XOR, as well as infix operators for all of the binary bitwise operations.

Last updated 12 months ago

1.70 score 135 downloads

DeBoinR - Box-Plots and Outlier Detection for Probability Density Functions

Orders a data-set consisting of an ensemble of probability density functions on the same x-grid. Visualizes a box-plot of these functions based on the notion of distance determined by the user. Reports outliers based on the distance chosen and the scaling factor for an interquartile range rule. For further details, see: Alexander C. Murph et al. (2023). "Visualization and Outlier Detection for Probability Density Function Ensembles." <https://sirmurphalot.github.io/publications>.

Last updated 1 years ago

1.70 score 1 scripts 139 downloads

rlc - Create Interactive Linked Charts with Minimal Code

An easy-to-use tool to employ interactivity in every-day exploratory analysis. It contains a collection of most commonly used types of charts (such as scatter plots, line plots, heatmaps, bar charts), which can be linked to each other or to other interactive elements with just few lines of code.

Last updated 1 years ago

1.70 score 29 scripts 181 downloads

BayesFluxR - Implementation of Bayesian Neural Networks

Implementation of 'BayesFlux.jl' for R; It extends the famous 'Flux.jl' machine learning library to Bayesian Neural Networks. The goal is not to have the fastest production ready library, but rather to allow more people to be able to use and research on Bayesian Neural Networks.

Last updated 1 years ago

1.70 score 4 scripts 247 downloads

KnockoffTrio - Trio Data Analysis with Knockoff Statistics for FDR Control

Identification of putative causal variants in genome-wide association studies with the trio design. The package implements the methods in the paper: Yang, Y., Wang, C., Liu, L., Buxbaum, J., He, Z., & Ionita-Laza, I. (2022). KnockoffTrio: A knockoff framework for the identification of putative causal variants in genome-wide association studies with trio design. The American Journal of Human Genetics, 109(10), 1761-1776.

Last updated 1 years ago

1.70 score 365 downloads

datetoiso - Modify Dates to ISO Standard ("International Organization for Standardization")

Transfer any date type to ISO standard. Package recognizes dates in given data frame and transform to ISO format. Only one date format can be applied within one data frame column.

Last updated 1 years ago

1.70 score 1 scripts 177 downloads

Rrepest - An Analyzer of International Large Scale Assessments in Education

A fast way to analyze International Large-Scale Assessments (ILSAs) or any other dataset that includes replicated weights (Balanced Repeated Replication (BRR) weights, Jackknife replicate weights,...) and/or plausible values. 'Rrepest' contains functionalities that enable you to calculate basic statistics (means, correlations, etc.), frequencies, linear regression, or any other model already implemented in R that takes a data frame and weights as parameters. It also includes options to prepare the results for publication, following the table formatting standards of the Organization for Economic Cooperation and Development (OECD).

Last updated 1 years ago

1.70 score 1 stars 2 scripts 126 downloads

exceldata - Streamline Data Import, Cleaning and Recoding from 'Excel'

A small group of functions to read in a data dictionary and the corresponding data table from 'Excel' and to automate the cleaning, re-coding and creation of simple calculated variables. This package was designed to be a companion to the macro-enabled 'Excel' template available on the GitHub site, but works with any similarly-formatted 'Excel' data.

Last updated 1 years ago

1.70 score 1 scripts 434 downloads

nlopt - Call Optimization Solvers with .nl Files

The purpose of this library is to to call different optimization solvers (such as Gonzalez Rodriguez et al. (2022) <doi:10.1007/s10898-022-01229-w>, Tawarmalani and Sahinidis (2005) <doi:10.1007/s10107-005-0581-8>, and Byrd et al. (2006) <doi:10.1007/0-387-30065-1_4>) to solve problems given by a standard nl file.

Last updated 1 years ago

1.70 score 2 scripts 219 downloads

MTAFT - Data-Driven Estimation for Multi-Threshold Accelerate Failure Time Model

Developed a data-driven estimation framework for the multi-threshold accelerate failure time (MTAFT) model. The MTAFT model features different linear forms in different subdomains, and one of the major challenges is determining the number of threshold effects. The package introduces a data-driven approach that utilizes a Schwarz' information criterion, which demonstrates consistency under mild conditions. Additionally, a cross-validation (CV) criterion with an order-preserved sample-splitting scheme is proposed to achieve consistent estimation, without the need for additional parameters. The package establishes the asymptotic properties of the parameter estimates and includes an efficient score-type test to examine the existence of threshold effects. The methodologies are supported by numerical experiments and theoretical results, showcasing their reliable performance in finite-sample cases.

Last updated 1 years ago

1.70 score 1 scripts 144 downloads

MigrationDetectR - Segment-Based Migration Detection Algorithm

Detection of migration events and segments of continuous residence based on irregular time series of location data as published in Chi et al. (2020) <doi:10.1371/journal.pone.0239408>.

Last updated 1 years ago

1.70 score 1 scripts 151 downloads

BeQut - Bayesian Estimation for Quantile Regression Mixed Models

Using a Bayesian estimation procedure, this package fits linear quantile regression models such as linear quantile models, linear quantile mixed models, quantile regression joint models for time-to-event and longitudinal data. The estimation procedure is based on the asymmetric Laplace distribution and the 'JAGS' software is used to get posterior samples (Yang, Luo, DeSantis (2019) <doi:10.1177/0962280218784757>).

Last updated 1 years ago

jagscpp

1.70 score 1 stars 235 downloads

dualScale - Dual Scaling Analysis of Data

Dual Scaling, developed by Professor Shizuhiko Nishisato (1994, ISBN: 0-9691785-3-6), is a fundamental technique in multivariate analysis used for data scaling and correspondence analysis. Its utility lies in its ability to represent multidimensional data in a lower-dimensional space, making it easier to visualize and understand underlying patterns in complex data. This technique has been implemented to handle various types of data, including Contingency and Frequency data (CF), Multiple-Choice data (MC), Sorting data (SO), Paired-Comparison data (PC), and Rank-Order data (RO), providing users with a powerful tool to explore relationships between variables and observations in various fields, from sociology to ecology, enabling deeper and more efficient analysis of multivariate datasets.

Last updated 1 years ago

1.70 score 1 scripts 180 downloads

dotsViolin - Dot Plots Mimicking Violin Plots

Modifies dot plots to have different sizes of dots mimicking violin plots and identifies modes or peaks for them based on frequency and kernel density estimates (Rosenblatt, 1956) <doi:10.1214/aoms/1177728190> (Parzen, 1962) <doi:10.1214/aoms/1177704472>.

Last updated 1 years ago

1.70 score 1 scripts 129 downloads

ufRisk - Risk Measure Calculation in Financial TS

Enables the user to calculate Value at Risk (VaR) and Expected Shortfall (ES) by means of various parametric and semiparametric GARCH-type models. For the latter the estimation of the nonparametric scale function is carried out by means of a data-driven smoothing approach. Model quality, in terms of forecasting VaR and ES, can be assessed by means of various backtesting methods such as the traffic light test for VaR and a newly developed traffic light test for ES. The approaches implemented in this package are described in e.g. Feng Y., Beran J., Letmathe S. and Ghosh S. (2020) <https://ideas.repec.org/p/pdn/ciepap/137.html> as well as Letmathe S., Feng Y. and Uhde A. (2021) <https://ideas.repec.org/p/pdn/ciepap/141.html>.

Last updated 1 years ago

1.70 score 1 scripts 201 downloads

dCUR - Dimension Reduction with Dynamic CUR

Dynamic CUR (dCUR) boosts the CUR decomposition (Mahoney MW., Drineas P. (2009) <doi:10.1073/pnas.0803205106>) varying the k, the number of columns and rows used, and its final purposes to help find the stage, which minimizes the relative error to reduce matrix dimension. The goal of CUR Decomposition is to give a better interpretation of the matrix decomposition employing proper variable selection in the data matrix, in a way that yields a simplified structure. Its origins come from analysis in genetics. The goal of this package is to show an alternative to variable selection (columns) or individuals (rows). The idea proposed consists of adjusting the probability distributions to the leverage scores and selecting the best columns and rows that minimize the reconstruction error of the matrix approximation ||A-CUR||. It also includes a method that recalibrates the relative importance of the leverage scores according to an external variable of the user's interest.

Last updated 1 years ago

1.70 score 6 scripts 161 downloads

popstudy - Applied Techniques to Demographic and Time Series Analysis

The use of overparameterization is proposed with combinatorial analysis to test a broader spectrum of possible ARIMA models. In the selection of ARIMA models, the most traditional methods such as correlograms or others, do not usually cover many alternatives to define the number of coefficients to be estimated in the model, which represents an estimation method that is not the best. The popstudy package contains several tools for statistical analysis in demography and time series based in Shryock research (Shryock et. al. (1980) <https://books.google.co.cr/books?id=8Oo6AQAAMAAJ>).

Last updated 1 years ago

1.70 score 1 scripts 574 downloads

GeoAdjust - Accounting for Random Displacements of True GPS Coordinates of Data

The purpose is to account for the random displacements (jittering) of true survey household cluster center coordinates in geostatistical analyses of Demographic and Health Surveys program (DHS) data. Adjustment for jittering can be implemented either in the spatial random effect, or in the raster/distance based covariates, or in both. Detailed information about the methods behind the package functionality can be found in two preprints. Umut Altay, John Paige, Andrea Riebler, Geir-Arne Fuglstad (2022) <arXiv:2202.11035v2>. Umut Altay, John Paige, Andrea Riebler, Geir-Arne Fuglstad (2022) <arXiv:2211.07442v1>.

Last updated 1 years ago

cpp

1.70 score 1 scripts 218 downloads

blsBandit - Data Viewer for Bureau of Labor Statistics Data

Allows users to easily visualize data from the BLS (United States of America Bureau of Labor Statistics) <https://www.bls.gov>. Currently unemployment data series U1-U6 are available. Not affiliated with the Bureau of Labor Statistics or United States Government.

Last updated 1 years ago

1.70 score 161 downloads

pisaRT - Small Example Response and Response Time Data from PISA 2018

Scored responses and responses times from the Canadian subsample of the PISA 2018 assessment, accessible as the "Cognitive items total time/visits data file" by OECD (2020) <https://www.oecd.org/pisa/data/2018database/>.

Last updated 1 years ago

1.70 score 2 scripts 134 downloads

foodquotient - Food Quotient and Nutrient Analysis for HSFFQ

Aids in analysing data from a food frequency questionnaire known as the Harvard Service Food Frequency Questionnaire (HSFFQ). Functions from this package use answers from the HSFFQ to generate estimates of daily consumed micronutrients, calories, macronutrients on an individual level. The package also calculates food quotients on individual and group levels. Foodquotient calculation is an often tedious step in the calculation of total human energy expenditure (TEE) using the doubly labeled water method, which is the gold standard for measuring TEE.

Last updated 1 years ago

1.70 score 194 downloads

saeME - Small Area Estimation with Measurement Error

A set of functions and datasets implementation of small area estimation when auxiliary variable is measured with error. These functions provide a empirical best linear unbiased prediction (EBLUP) estimator and mean squared error (MSE) estimator of the EBLUP. These models were developed by Ybarra and Lohr (2008) <doi:10.1093/biomet/asn048>.

Last updated 1 years ago

1.70 score 183 downloads

responsePatterns - Screening for Careless Responding Patterns

Some survey participants tend to respond carelessly which complicates data analysis. This package provides functions that make it easier to explore responses and identify those that may be problematic. See Gottfried et al. (2022) <doi:10.7275/vyxb-gt24> for more information.

Last updated 1 years ago

1.70 score 6 scripts 170 downloads

ROI.plugin.highs - 'HiGHS' Plugin for the 'R' Optimization Infrastructure

Enhances the 'R' Optimization Infrastructure ('ROI') package with the quadratic solver 'HiGHS'. More information about 'HiGHS' can be found at <https://highs.dev>.

Last updated 1 years ago

1.70 score 173 downloads

doudpackage - Create Elegant Table 1 in HTML for Bio-Statistics

Creates the "table one" of bio-medical papers. Fill it with your data and the name of the variable which you'll make the group(s) out of and it will make univariate, bivariate analysis and parse it into HTML. It also allows you to visualize all your data with graphic representation.

Last updated 1 years ago

1.70 score 1 scripts 151 downloads

TrumpetPlots - Visualization of Genetic Association Studies

Visualizes the relationship between allele frequency and effect size in genetic association studies. The input is a data frame containing association results. The output is a plot with the effect size of risk variants in the Y axis, and the allele frequency spectrum in the X axis. Corte et al (2023) <doi:10.1101/2023.04.21.23288923>.

Last updated 2 years ago

1.70 score 1 stars 1 scripts 186 downloads

REDI - Robust Exponential Decreasing Index

Implementation of the Robust Exponential Decreasing Index (REDI), proposed in the article by Issa Moussa, Arthur Leroy et al. (2019) <https://bmjopensem.bmj.com/content/bmjosem/5/1/e000573.full.pdf>. The REDI represents a measure of cumulated workload, robust to missing data, providing control of the decreasing influence of workload over time. Various functions are provided to format data, compute REDI, and visualise results in a simple and convenient way.

Last updated 2 years ago

1.70 score 1 scripts 148 downloads

agghoo - Aggregated Hold-Out Cross Validation

The 'agghoo' procedure is an alternative to usual cross-validation. Instead of choosing the best model trained on V subsamples, it determines a winner model for each subsample, and then aggregates the V outputs. For the details, see "Aggregated hold-out" by Guillaume Maillard, Sylvain Arlot, Matthieu Lerasle (2021) <arXiv:1909.04890> published in Journal of Machine Learning Research 22(20):1--55.

Last updated 2 years ago

1.70 score 1 scripts 248 downloads

wrappr - A Collection of Helper and Wrapper Functions

Helper functions to easily add functionality to functions. The package can assign functions to have an lazy evaluation allowing you to save and update the arguments before and after each function call. You can set a temporary working directory within functions and wrap console messages around other functions.

Last updated 2 years ago

1.70 score 2 scripts 122 downloads

validateIt - Validating Topic Coherence and Topic Labels

By creating crowd-sourcing tasks that can be easily posted and results retrieved using Amazon's Mechanical Turk (MTurk) API, researchers can use this solution to validate the quality of topics obtained from unsupervised or semi-supervised learning methods, and the relevance of topic labels assigned. This helps ensure that the topic modeling results are accurate and useful for research purposes. See Ying and others (2022) <doi:10.1101/2023.05.02.538599>. For more information, please visit <https://github.com/Triads-Developer/Topic_Model_Validation>.

Last updated 2 years ago

1.70 score 2 scripts 114 downloads

animl - A Collection of ML Tools for Conservation Research

Functions required to classify subjects within camera trap field data. The package can handle both images and videos. The authors recommend a two-step approach using Microsoft's 'MegaDector' model and then a second model trained on the classes of interest.

Last updated 2 years ago

1.70 score 9 scripts 287 downloads

penAFT - Fit the Regularized Gehan Estimator with Elastic Net and Sparse Group Lasso Penalties

The semiparametric accelerated failure time (AFT) model is an attractive alternative to the Cox proportional hazards model. This package provides a suite of functions for fitting one popular estimator of the semiparametric AFT model, the regularized Gehan estimator. Specifically, we provide functions for cross-validation, prediction, coefficient extraction, and visualizing both trace plots and cross-validation curves. For further details, please see Suder, P. M. and Molstad, A. J., (2022+) Scalable algorithms for semiparametric accelerated failure time models in high dimensions, to appear in Statistics in Medicine <doi:10.1002/sim.9264>.

Last updated 2 years ago

openblascpp

1.70 score 9 scripts 176 downloads

TensorComplete - Tensor Noise Reduction and Completion Methods

Efficient algorithms for tensor noise reduction and completion. This package includes a suite of parametric and nonparametric tools for estimating tensor signals from noisy, possibly incomplete observations. The methods allow a broad range of data types, including continuous, binary, and ordinal-valued tensor entries. The algorithms employ the alternating optimization. The detailed algorithm description can be found in the following three references.

Last updated 2 years ago

1.70 score 184 downloads

MaximinInfer - Inference for Maximin Effects in High-Dimensional Settings

Implementation of the sampling and aggregation method for the covariate shift maximin effect, which was proposed in <arXiv:2011.07568>. It constructs the confidence interval for any linear combination of the high-dimensional maximin effect.

Last updated 2 years ago

1.70 score 1 scripts 207 downloads

DDL - Doubly Debiased Lasso (DDL)

Statistical inference for the regression coefficients in high-dimensional linear models with hidden confounders. The Doubly Debiased Lasso method was proposed in <arXiv:2004.03758>.

Last updated 2 years ago

1.70 score 1 scripts 218 downloads

cbq - Conditional Binary Quantile Models

Estimates conditional binary quantile models developed by Lu (2020) <doi:10.1017/pan.2019.29>. The estimation procedure is implemented based on Markov chain Monte Carlo methods.

Last updated 2 years ago

cpp

1.70 score 1 scripts 244 downloads

rfieldclimate - Client for the 'FieldClimate' API

Provides functionality to interact with the 'FieldClimate' API <https://api.fieldclimate.com/v2/docs/>.

Last updated 2 years ago

1.70 score 1 scripts 126 downloads

diffval - Vegetation Patterns

Find, visualize and explore patterns of differential taxa in vegetation data (namely in a phytosociological table), using the Differential Value (DiffVal). Patterns are searched through mathematical optimization algorithms. Ultimately, Total Differential Value (TDV) optimization aims at obtaining classifications of vegetation data based on differential taxa, as in the traditional geobotanical approach. The Gurobi optimizer, as well as the R package 'gurobi', can be installed from <https://www.gurobi.com/products/gurobi-optimizer/>. The useful vignette Gurobi Installation Guide, from package 'prioritizr', can be found here: <https://prioritizr.net/articles/gurobi_installation_guide.html>.

Last updated 2 years ago

1.70 score 218 downloads

oesr - Methods for the Office of Evaluation Sciences

Methods for statistical analysis and reporting preferred by the US Office of Evaluation Sciences (OES). This package prepares data from standard model output objects (such as from \code{lm()} and \code{estimatr::lm_robust()}) and creates visualizations of treatment effects from the prepared quantities, according to the standards of the US Office of Evaluation Sciences.

Last updated 2 years ago

1.70 score 6 scripts 150 downloads

FuzzyStatTraEOO - Package 'FuzzyStatTra' in Encapsulated Object Oriented Programming

The aim of the package is to contain the package 'FuzzyStatTra' in Encapsulated Object Oriented Programming using R6. 'FuzzyStatTra' contains Statistical Methods for Trapezoidal Fuzzy Numbers, whose aim is to provide some basic functions for doing statistical analysis with trapezoidal fuzzy numbers. For more details, you can visit the website of the SMIRE+CoDiRE (Statistical Methods with Imprecise Random Elements and Comparison of Distributions of Random Elements) Research Group (<https://bellman.ciencias.uniovi.es/smire+codire/>). The most related paper can be found in References. Now, those functions are organized in specific classes and methods. This object-based approach is an important step in making statistical computing more accessible to users.

Last updated 2 years ago

1.70 score 1 scripts 180 downloads

exactLTRE - An Exact Method for Life Table Response Experiment (LTRE) Analysis

Life Table Response Experiments (LTREs) are a method of comparative demographic analysis. The purpose is to quantify how the difference or variance in vital rates (stage-specific survival, growth, and fertility) among populations contributes to difference or variance in the population growth rate, "lambda." We provide functions for one-way fixed design and random design LTRE, using either the classical methods that have been in use for several decades, or an fANOVA-based exact method that directly calculates the impact on lambda of changes in matrix elements, for matrix elements and their interactions. The equations and descriptions for the classical methods of LTRE analysis can be found in "Matrix Population Models: Construction, Analysis, and Interpretation (2nd edition)" Caswell (2001, ISBN: 0878930965), and the fANOVA-based exact methods will be published in a forthcoming paper. We also provide some demographic functions, including generation time from Bienvenu and Legendre (2015) <doi:10.1086/681104>. For implementation of exactLTRE where all possible interactions are calculated, we use an operator matrix presented in Poelwijk, Krishna, and Ranganathan (2016) <doi:10.1371/journal.pcbi.1004771>.

Last updated 2 years ago

1.70 score 9 scripts 181 downloads

simplifyNet - Network Sparsification

Network sparsification with a variety of novel and known network sparsification techniques. All network sparsification techniques reduce the number of edges, not the number of nodes. Network sparsification is sometimes referred to as network dimensionality reduction. This package is based on the work of Spielman, D., Srivastava, N. (2009)<arXiv:0803.0929>. Koutis I., Levin, A., Peng, R. (2013)<arXiv:1209.5821>. Toivonen, H., Mahler, S., Zhou, F. (2010)<doi:10.1007>. Foti, N., Hughes, J., Rockmore, D. (2011)<doi:10.1371>.

Last updated 2 years ago

1.70 score 1 stars 156 downloads

rheroicons - A Zero Dependency 'SVG' Icon Library for 'Shiny'

An implementation of the 'Heroicons' icon library for 'shiny' applications and other 'R' web-based projects. You can search, render, and customize icons without 'CSS' or 'JavaScript' dependencies.

Last updated 2 years ago

1.70 score 1 scripts 154 downloads

gstsm - Generalized Spatial-Time Sequence Miner

Implementations of the algorithms present article Generalized Spatial-Time Sequence Miner, original title (Castro, Antonio; Borges, Heraldo ; Pacitti, Esther ; Porto, Fabio ; Coutinho, Rafaelli ; Ogasawara, Eduardo . Generalização de Mineração de Sequências Restritas no Espaço e no Tempo. In: XXXVI SBBD - Simpósio Brasileiro de Banco de Dados, 2021 <doi:10.5753/sbbd.2021.17891>).

Last updated 2 years ago

1.70 score 3 scripts 155 downloads

simuclustfactor - Simultaneous Clustering and Factorial Decomposition of Three-Way Datasets

Implements two iterative techniques called T3Clus and 3Fkmeans, aimed at simultaneously clustering objects and a factorial dimensionality reduction of variables and occasions on three-mode datasets developed by Vichi et al. (2007) <doi:10.1007/s00357-007-0006-x>. Also, we provide a convex combination of these two simultaneous procedures called CT3Clus and based on a hyperparameter alpha (alpha in [0,1], with 3FKMeans for alpha=0 and T3Clus for alpha= 1) also developed by Vichi et al. (2007) <doi:10.1007/s00357-007-0006-x>. Furthermore, we implemented the traditional tandem procedures of T3Clus (TWCFTA) and 3FKMeans (TWFCTA) for sequential clustering-factorial decomposition (TWCFTA), and vice-versa (TWFCTA) proposed by P. Arabie and L. Hubert (1996) <doi:10.1007/978-3-642-79999-0_1>.

Last updated 2 years ago

1.70 score 12 scripts 135 downloads

LOCUS - Low-Rank Decomposition of Brain Connectivity Matrices with Uniform Sparsity

To decompose symmetric matrices such as brain connectivity matrices so that one can extract sparse latent component matrices and also estimate mixing coefficients, a blind source separation (BSS) method named LOCUS was proposed in Wang and Guo (2023) <arXiv:2008.08915>. For brain connectivity matrices, the outputs correspond to sparse latent connectivity traits and individual-level trait loadings.

Last updated 2 years ago

1.70 score 1 scripts 130 downloads

YieldCurve - Modelling and Estimation of the Yield Curve

Modelling the yield curve with some parametric models. The models implemented are: Nelson, C.R., and A.F. Siegel (1987) <doi: 10.1086/296409>, Diebold, F.X. and Li, C. (2006) <doi: 10.1016/j.jeconom.2005.03.005> and Svensson, L.E. (1994) <doi: 10.3386/w4871>. The package also includes the data of the term structure of interest rate of Federal Reserve Bank and European Central Bank.

Last updated 2 years ago

1.70 score 5 stars 54 scripts 532 downloads

survout - Excel Conversion of R Surival Analysis Output

Simple and quick method of exporting the most often used survival analysis results to an Excel sheet.

Last updated 2 years ago

1.70 score 1 scripts 164 downloads

mpower - Power Analysis via Monte Carlo Simulation for Correlated Data

A flexible framework for power analysis using Monte Carlo simulation for settings in which considerations of the correlations between predictors are important. Users can set up a data generative model that preserves dependence structures among predictors given existing data (continuous, binary, or ordinal). Users can also generate power curves to assess the trade-offs between sample size, effect size, and power of a design. This package includes several statistical models common in environmental mixtures studies. For more details and tutorials, see Nguyen et al. (2022) <arXiv:2209.08036>.

Last updated 2 years ago

1.70 score 1 stars 8 scripts 187 downloads

sansa - Synthetic Data Generation for Imbalanced Learning in 'R'

Machine learning is widely used in information-systems design. Yet, training algorithms on imbalanced datasets may severely affect performance on unseen data. For example, in some cases in healthcare, financial, or internet-security contexts, certain sub-classes are difficult to learn because they are underrepresented in training data. This 'R' package offers a flexible and efficient solution based on a new synthetic average neighborhood sampling algorithm ('SANSA'), which, in contrast to other solutions, introduces a novel “placement” parameter that can be tuned to adapt to each datasets unique manifestation of the imbalance. More information about the algorithm's parameters can be found at Nasir et al. (2022) <https://murtaza.cc/SANSA/>.

Last updated 2 years ago

1.70 score 4 scripts 216 downloads

bws - Bayesian Weighted Sums

An interface to the Bayesian Weighted Sums model implemented in 'RStan'. It estimates the summed effect of multiple, often moderately to highly correlated, continuous predictors. Its applications can be found in analysis of exposure mixtures. The model was proposed by Hamra, Maclehose, Croen, Kauffman, and Newschaffer (2021) <doi:10.3390/ijerph18041373>. This implementation includes an extension to model binary outcome.

Last updated 2 years ago

cpp

1.70 score 5 scripts 257 downloads

rdaisi - R Client for the Daisi Microservice Platform

Connect, execute, and parse results from the Daisi Microservice Platform <https://www.daisi.io/>. The rdaisi client includes a set of functionality that allows remote execution of microservices directly from R. Daisis allow R users to access a wide variety of Python functionality and interact with them natively.

Last updated 2 years ago

1.70 score 2 scripts 146 downloads

ivaBSS - Tools for Independent Vector Analysis

Independent vector analysis (IVA) is a blind source separation (BSS) model where several datasets are jointly unmixed. This package provides several methods for the unmixing together with some performance measures. For details, see Anderson et al. (2011) <doi:10.1109/TSP.2011.2181836> and Lee et al. (2007) <doi:10.1016/j.sigpro.2007.01.010>.

Last updated 3 years ago

1.70 score 97 downloads

kmodR - K-Means with Simultaneous Outlier Detection

An implementation of the 'k-means--' algorithm proposed by Chawla and Gionis, 2013 in their paper, "k-means-- : A unified approach to clustering and outlier detection. SIAM International Conference on Data Mining (SDM13)", <doi:10.1137/1.9781611972832.21> and using 'ordering' described by Howe, 2013 in the thesis, Clustering and anomaly detection in tropical cyclones". Useful for creating (potentially) tighter clusters than standard k-means and simultaneously finding outliers inexpensively in multidimensional space.

Last updated 3 years ago

1.70 score 6 scripts 200 downloads

wikibooks - Functions and Datasets of the German WikiBook "GNU R"

The german Wikibook "GNU R" introduces R to new users. This package is a collection of functions and datas used in the german WikiBook "GNU R".

Last updated 3 years ago

1.70 score 5 scripts 183 downloads

time.slots - Display Data in a Weekly Calendar View

Generate weekly timetables as a ggplot2 layer. Add informative timeslots with elements such as title, key-value pairs, or colour to reveal trends.

Last updated 3 years ago

1.70 score 1 scripts 165 downloads

googleTagManageR - Access the 'Google Tag Manager' API using R

Interact with the 'Google Tag Manager' API <https://developers.google.com/tag-platform/tag-manager/api/v2>, enabling scripted deployments and updates across multiple tags, triggers, variables and containers.

Last updated 3 years ago

1.70 score 4 scripts 188 downloads

Linkage - Clustering Communication Networks Using the Stochastic Topic Block Model Through Linkage.fr

It allows to cluster communication networks using the Stochastic Topic Block Model <doi:10.1007/s11222-016-9713-7> by posting jobs through the API of the linkage.fr server, which implements the clustering method. The package also allows to visualize the clustering results returned by the server.

Last updated 3 years ago

1.70 score 50 scripts 147 downloads

irrNA - Coefficients of Interrater Reliability – Generalized for Randomly Incomplete Datasets

Provides coefficients of interrater reliability that are generalized to cope with randomly incomplete (i.e. unbalanced) datasets without any imputation of missing values or any (row-wise or column-wise) omissions of actually available data. Applied to complete (balanced) datasets, these generalizations yield the same results as the common procedures, namely the Intraclass Correlation according to McGraw & Wong (1996) \doi{10.1037/1082-989X.1.1.30} and the Coefficient of Concordance according to Kendall & Babington Smith (1939) \doi{10.1214/aoms/1177732186}.

Last updated 3 years ago

1.70 score 6 scripts 316 downloads

weakARMA - Tools for the Analysis of Weak ARMA Models

Numerous time series admit autoregressive moving average (ARMA) representations, in which the errors are uncorrelated but not necessarily independent. These models are called weak ARMA by opposition to the standard ARMA models, also called strong ARMA models, in which the error terms are supposed to be independent and identically distributed (iid). This package allows the study of nonlinear time series models through weak ARMA representations. It determines identification, estimation and validation for ARMA models and for AR and MA models in particular. Functions can also be used in the strong case. This package also works on white noises by omitting arguments 'p', 'q', 'ar' and 'ma'. See Francq, C. and Zakoïan, J. (1998) <doi:10.1016/S0378-3758(97)00139-0> and Boubacar Maïnassara, Y. and Saussereau, B. (2018) <doi:10.1080/01621459.2017.1380030> for more details.

Last updated 3 years ago

1.70 score 2 scripts 181 downloads

consolechoice - An Easy and Quick Way to Loop a Character Vector as a Menu in the Console

A fast way to loop a character vector or file names as a menu in the console for the user to choose an option.

Last updated 3 years ago

1.70 score 2 scripts 169 downloads

sistmr - A Collection of Utility Function from the Inserm/Inria SISTM Team

Functions common to members of the SISTM team.

Last updated 3 years ago

1.70 score 116 downloads

bayesGAM - Fit Multivariate Response Generalized Additive Models using Hamiltonian Monte Carlo

The 'bayesGAM' package is designed to provide a user friendly option to fit univariate and multivariate response Generalized Additive Models (GAM) using Hamiltonian Monte Carlo (HMC) with few technical burdens. The functions in this package use 'rstan' (Stan Development Team 2020) to call 'Stan' routines that run the HMC simulations. The 'Stan' code for these models is already pre-compiled for the user. The programming formulation for models in 'bayesGAM' is designed to be familiar to analysts who fit statistical models in 'R'. Carpenter, B., Gelman, A., Hoffman, M. D., Lee, D., Goodrich, B., Betancourt, M., ... & Riddell, A. (2017). Stan: A probabilistic programming language. Journal of statistical software, 76(1). Stan Development Team. 2018. RStan: the R interface to Stan. R package version 2.17.3. <https://mc-stan.org/> Neal, Radford (2011) "Handbook of Markov Chain Monte Carlo" ISBN: 978-1420079418. Betancourt, Michael, and Mark Girolami. "Hamiltonian Monte Carlo for hierarchical models." Current trends in Bayesian methodology with applications 79.30 (2015): 2-4. Thomas, S., Tu, W. (2020) "Learning Hamiltonian Monte Carlo in R" <arXiv:2006.16194>, Gelman, A., Carlin, J. B., Stern, H. S., Dunson, D. B., Vehtari, A., & Rubin, D. B. (2013) "Bayesian Data Analysis" ISBN: 978-1439840955, Agresti, Alan (2015) "Foundations of Linear and Generalized Linear Models ISBN: 978-1118730034, Pinheiro, J., Bates, D. (2006) "Mixed-effects Models in S and S-Plus" ISBN: 978-1441903174. Ruppert, D., Wand, M. P., & Carroll, R. J. (2003). Semiparametric regression (No. 12). Cambridge university press. ISBN: 978-0521785167.

Last updated 3 years ago

cpp

1.70 score 2 scripts 295 downloads

cabootcrs - Bootstrap Confidence Regions for Simple and Multiple Correspondence Analysis

Performs simple correspondence analysis on a two-way contingency table, or multiple correspondence analysis (homogeneity analysis) on data with p categorical variables, and produces bootstrap-based elliptical confidence regions around the projected coordinates for the category points. Includes routines to plot the results in a variety of styles. Also reports the standard numerical output for correspondence analysis.

Last updated 3 years ago

1.70 score 14 scripts 303 downloads

ETC - Equivalence to Control

Treatments of a one-way layout, being equivalent to a control, can be selected with this package. Bonferroni adjusted "two one-sided t-tests" (TOST) and related simultaneous confidence intervals are given for both differences or ratios of means of normally distributed data. For the case of equal variances and balanced sample sizes for the treatment groups, the single-step procedure of Bofinger and Bofinger (1995) <doi:10.1111/j.2517-6161.1995.tb02058.x> can be chosen. For non-normal data, the Wilcoxon test is applied.

Last updated 3 years ago

1.70 score 9 scripts 213 downloads

FuzzyM - Fuzzy Cognitive Maps Operations

Contains functions for operations with fuzzy cognitive maps using t-norm and s-norm operators. T-norms and S-norms are described by Dov M. Gabbay and George Metcalfe (2007) <doi:10.1007/s00153-007-0047-1>. System indicators are described by Cox, Earl D. (1995) <isbn:1886801010>. Executable examples are provided in the "inst/examples" folder.

Last updated 3 years ago

1.70 score 1 scripts 150 downloads

bootComb - Combine Parameter Estimates via Parametric Bootstrap

Propagate uncertainty from several estimates when combining these estimates via a function. This is done by using the parametric bootstrap to simulate values from the distribution of each estimate to build up an empirical distribution of the combined parameter. Finally either the percentile method is used or the highest density interval is chosen to derive a confidence interval for the combined parameter with the desired coverage. Gaussian copulas are used for when parameters are assumed to be dependent / correlated. References: Davison and Hinkley (1997,ISBN:0-521-57471-4) for the parametric bootstrap and percentile method, Gelman et al. (2014,ISBN:978-1-4398-4095-5) for the highest density interval, Stockdale et al. (2020)<doi:10.1016/j.jhep.2020.04.008> for an example of combining conditional prevalences.

Last updated 3 years ago

1.70 score 6 scripts 232 downloads

citationchaser - Perform Forward and Backwards Chasing in Evidence Syntheses

In searching for research articles, we often want to obtain lists of references from across studies, and also obtain lists of articles that cite a particular study. In systematic reviews, this supplementary search technique is known as 'citation chasing': forward citation chasing looks for all records citing one or more articles of known relevance; backward citation chasing looks for all records referenced in one or more articles. Traditionally, this process would be done manually, and the resulting records would need to be checked one-by-one against included studies in a review to identify potentially relevant records that should be included in a review. This package contains functions to automate this process by making use of the Lens.org API. An input article list can be used to return a list of all referenced records, and/or all citing records in the Lens.org database (consisting of PubMed, PubMed Central, CrossRef, Microsoft Academic Graph and CORE; <https://www.lens.org>).

Last updated 3 years ago

1.70 score 3 scripts 326 downloads

leprechaun - Create Simple 'Shiny' Applications as Packages

Code generator for robust dependency-free 'Shiny' applications in the form of packages. It includes numerous convenience functions to create modules, include utility functions to create common 'Bootstrap' elements, setup a project from the ground-up, and much more.

Last updated 3 years ago

1.70 score 8 scripts 173 downloads

podcleaner - Legacy Scottish Post Office Directories Cleaner

Attempts to clean optical character recognition (OCR) errors in legacy Scottish Post Office Directories. Further attempts to match records from trades and general directories.

Last updated 3 years ago

1.70 score 4 scripts 134 downloads

MLCM - Maximum Likelihood Conjoint Measurement

Conjoint measurement is a psychophysical procedure in which stimulus pairs are presented that vary along 2 or more dimensions and the observer is required to compare the stimuli along one of them. This package contains functions to estimate the contribution of the n scales to the judgment by a maximum likelihood method under several hypotheses of how the perceptual dimensions interact. Reference: Knoblauch & Maloney (2012) "Modeling Psychophysical Data in R". <doi:10.1007/978-1-4614-4475-6>.

Last updated 3 years ago

1.70 score 1 stars 1 scripts 341 downloads

icardaFIGSr - Subsetting using Focused Identification of the Germplasm Strategy (FIGS)

Running Focused Identification of the Germplasm Strategy (FIGS) to make best subsets from Genebank Collection.

Last updated 3 years ago

1.70 score 4 scripts 155 downloads

ZIPBayes - Bayesian Methods in the Analysis of Zero-Inflated Poisson Model

Implementation of zero-inflated Poisson models under Bayesian framework using data augmentation as discussed in Chapter 5 of Zhang (2020) <https://hdl.handle.net/10012/16378>. This package is constructed in accommodating four different scenarios: the general scenario, the scenario with measurement error in responses, the external validation scenario, and the internal validation scenario.

Last updated 3 years ago

1.70 score 160 downloads

SmoothTensor - A Collection of Smooth Tensor Estimation Methods

A list of methods for estimating a smooth tensor with an unknown permutation. It also contains several multi-variate functions for generating permuted signal tensors and corresponding observed tensors. For a detailed introduction for the model and estimation techniques, see the paper by Chanwoo Lee and Miaoyan Wang (2021) "Smooth tensor estimation with unknown permutations" <arXiv:2111.04681>.

Last updated 3 years ago

1.70 score 136 downloads

pecora - Permutation Conditional Random Tests

It provides functions to perform permutation conditional random one-sample and two-samples t-tests in a multivariate framework.

Last updated 3 years ago

openblascpp

1.70 score 9 scripts 141 downloads

OEFPIL - Optimal Estimation of Function Parameters by Iterated Linearization

Package for estimating the parameters of a nonlinear function using iterated linearization via Taylor series. Method is based on Kubáček (2000) ISBN: 80-244-0093-6. The algorithm is a generalization of the procedure given in Köning, R., Wimmer, G. and Witkovský, V. (2014) <doi:10.1088/0957-0233/25/11/115001>.

Last updated 3 years ago

1.70 score 1 scripts 156 downloads

crrcbcv - Bias-Corrected Variance for Competing Risks Regression with Clustered Data

A user friendly function 'crrcbcv' to compute bias-corrected variances for competing risks regression models using proportional subdistribution hazards with small-sample clustered data. Four types of bias correction are included: the MD-type bias correction by Mancl and DeRouen (2001) <doi:10.1111/j.0006-341X.2001.00126.x>, the KC-type bias correction by Kauermann and Carroll (2001) <doi:10.1198/016214501753382309>, the FG-type bias correction by Fay and Graubard (2001) <doi:10.1111/j.0006-341X.2001.01198.x>, and the MBN-type bias correction by Morel, Bokossa, and Neerchal (2003) <doi:10.1002/bimj.200390021>.

Last updated 3 years ago

1.70 score 7 scripts 147 downloads

KingCountyHouses - Data on House Sales in King County WA

Data on houses in and around Seattle WA are included. Basic characteristics are given along with sale prices.

Last updated 3 years ago

1.70 score 9 scripts 160 downloads

ToxCrit - Calculates Safety Stopping Boundaries for a Single-Arm Trial using Bayes

Computation of stopping boundaries for a single-arm trial using a Bayesian criterion; i.e., for each m<=n (n= total patient number of the trial) the smallest number of observed toxicities is calculated leading to the termination of the trial/accrual according to the specified criteria. The probabilities of stopping the trial/accrual at and up until (resp.) the m-th patient (m<=n) is also calculated. This design is more conservative than the frequentist approach (using Clopper Pearson CIs) which might be preferred as it concerns safety.See also Aamot et.al.(2010) "Continuous monitoring of toxicity in clinical trials - simulating the risk of stopping prematurely" <doi:10.5414/cpp48476>.

Last updated 3 years ago

1.70 score 191 downloads

miRetrieve - miRNA Text Mining in Abstracts

Providing tools for microRNA (miRNA) text mining. miRetrieve summarizes miRNA literature by extracting, counting, and analyzing miRNA names, thus aiming at gaining biological insights into a large amount of text within a short period of time. To do so, miRetrieve uses regular expressions to extract miRNAs and tokenization to identify meaningful miRNA associations. In addition, miRetrieve uses the latest miRTarBase version 8.0 (Hsi-Yuan Huang et al. (2020) "miRTarBase 2020: updates to the experimentally validated microRNA–target interaction database" <doi:10.1093/nar/gkz896>) to display field-specific miRNA-mRNA interactions. The most important functions are available as a Shiny web application under <https://miretrieve.shinyapps.io/miRetrieve/>.

Last updated 3 years ago

1.70 score 31 scripts 150 downloads

droll - Analyze Roll Distributions

A toolkit for parsing dice notation, analyzing rolls, calculating success probabilities, and plotting outcome distributions.

Last updated 3 years ago

1.70 score 9 scripts 163 downloads

refitME - Measurement Error Modelling using MCEM

Fits measurement error models using Monte Carlo Expectation Maximization (MCEM). For specific details on the methodology, see: Greg C. G. Wei & Martin A. Tanner (1990) A Monte Carlo Implementation of the EM Algorithm and the Poor Man's Data Augmentation Algorithms, Journal of the American Statistical Association, 85:411, 699-704 <doi:10.1080/01621459.1990.10474930> For more examples on measurement error modelling using MCEM, see the 'RMarkdown' vignette: "'refitME' R-package tutorial".

Last updated 3 years ago

1.70 score 9 scripts 133 downloads

MGBT - Multiple Grubbs-Beck Low-Outlier Test

Compute the multiple Grubbs-Beck low-outlier test on positively distributed data and utilities for noninterpretive U.S. Geological Survey annual peak-streamflow data processing discussed in Cohn et al. (2013) <doi:10.1002/wrcr.20392> and England et al. (2017) <doi:10.3133/tm4B5>.

Last updated 3 years ago

1.70 score 1 stars 3 scripts 161 downloads

genSEIR - Predict Epidemic Curves with Generalized SEIR Modeling

Performs generalized Susceptible-Exposed-Infected-Recovered (SEIR) modeling to predict epidemic curves. The method is described in Peng et al. (2020) <doi:10.1101/2020.02.16.20023465>.

Last updated 3 years ago

1.70 score 147 downloads

kdpee - Fast Multidimensional Entropy Estimation by k-d Partitioning

Estimate entropy of multidimensional data set.

Last updated 3 years ago

1.70 score 43 downloads

TensorClustering - Model-Based Tensor Clustering

Performs model-based tensor clustering methods including Tensor Gaussian Mixture Model (TGMM), Tensor Envelope Mixture Model (TEMM) by Deng and Zhang (2021) <DOI: 10.1111/biom.13486>, Doubly-Enhanced EM (DEEM) algorithm by Mai, Zhang, Pan and Deng (2021) <DOI: 10.1080/01621459.2021.1904959>.

Last updated 3 years ago

fortran

1.70 score 1 scripts 145 downloads

dbglm - Generalised Linear Models by Subsampling and One-Step Polishing

Fast fitting of generalised linear models on moderately large datasets, by taking an initial sample, fitting in memory, then evaluating the score function for the full data in the database. Thomas Lumley <doi:10.1080/10618600.2019.1610312>.

Last updated 4 years ago

1.70 score 5 scripts 203 downloads

nifti.io - Read and Write NIfTI Files

Tools for reading and writing NIfTI-1.1 (NII) files, including optimized voxelwise read/write operations and a simplified method to write dataframes to NII. Specification of the NIfTI-1.1 format can be found here <https://nifti.nimh.nih.gov/nifti-1>. Scientific publication first using these tools Koscik TR, Man V, Jahn A, Lee CH, Cunningham WA (2020) <doi:10.1016/j.neuroimage.2020.116764> "Decomposing the neural pathways in a simple, value-based choice." Neuroimage, 214, 116764.

Last updated 4 years ago

1.70 score 5 scripts 163 downloads

ebreg - Implementation of the Empirical Bayes Method

Implements a Bayesian-like approach to the high-dimensional sparse linear regression problem based on an empirical or data-dependent prior distribution, which can be used for estimation/inference on the model parameters, variable selection, and prediction of a future response. The method was first presented in Martin, Ryan and Mess, Raymond and Walker, Stephen G (2017) <doi:10.3150/15-BEJ797>. More details focused on the prediction problem are given in Martin, Ryan and Tang, Yiqi (2019) <arXiv:1903.00961>.

Last updated 4 years ago

1.70 score 8 scripts 153 downloads

TraceAssist - Nonparametric Trace Regression via Sign Series Representation

Efficient method for fitting nonparametric matrix trace regression model. The detailed description can be found in C. Lee, L. Li, H. Zhang, and M. Wang (2021). Nonparametric Trace Regression via Sign Series Representation. <arXiv:2105.01783>. The method employs the aggregation of structured sign series for trace regression (ASSIST) algorithm.

Last updated 4 years ago

1.70 score 108 downloads

sdpdth - M-Estimator for Threshold Spatial Dynamic Panel Data Model

M-estimator for threshold and non-threshold spatial dynamic panel data model. Yang, Z (2018) <doi:10.1016/j.jeconom.2017.08.019>. Wu, J., Matsuda, Y (2021) <doi:10.1007/s43071-021-00008-1>.

Last updated 4 years ago

openblascppopenjdk

1.70 score 1 stars 91 downloads

multicastR - A Companion to the Multi-CAST Collection

Provides a basic interface for accessing annotation data from the Multi-CAST collection, a database of spoken natural language texts edited by Geoffrey Haig and Stefan Schnell. The collection draws from a diverse set of languages and has been annotated across multiple levels. Annotation data is downloaded on request from the servers of the University of Bamberg. See the Multi-CAST website <https://multicast.aspra.uni-bamberg.de/> for more information and a list of related publications.

Last updated 4 years ago

1.70 score 6 scripts 167 downloads

FILEST - Fine-Level Structure Simulator

A population genetic simulator, which is able to generate synthetic datasets for single-nucleotide polymorphisms (SNP) for multiple populations. The genetic distances among populations can be set according to the Fixation Index (Fst) as explained in Balding and Nichols (1995) <doi:10.1007/BF01441146>. This tool is able to simulate outlying individuals and missing SNPs can be specified. For Genome-wide association study (GWAS), disease status can be set in desired level according risk ratio.

Last updated 4 years ago

1.70 score 6 scripts 141 downloads

mongopipe - Query MongoDB Documents with R

Translate R code into MongoDB aggregation pipelines.

Last updated 4 years ago

1.70 score 2 scripts 160 downloads

rzentra - Client for the 'ZENTRA Cloud' API

Provides functionality to read settings, statuses and readings of weather stations from the 'ZENTRA Cloud' API <https://zentracloud.com/api/v1/guide#APIGuidelines>.

Last updated 4 years ago

1.70 score 1 scripts 155 downloads

fastlogitME - Basic Marginal Effects for Logit Models

Calculates marginal effects based on logistic model objects such as 'glm' or 'speedglm' at the average (default) or at given values using finite differences. It also returns confidence intervals for said marginal effects and the p-values, which can easily be used as input in stargazer. The function only returns the essentials and is therefore much faster but not as detailed as other functions available to calculate marginal effects. As a result, it is highly suitable for large datasets for which other packages may require too much time or calculating power.

Last updated 4 years ago

1.70 score 153 downloads

smfishHmrf - Hidden Markov Random Field for Spatial Transcriptomic Data

Discovery of spatial patterns with Hidden Markov Random Field. This package is designed for spatial transcriptomic data and single molecule fluorescent in situ hybridization (FISH) data such as sequential fluorescence in situ hybridization (seqFISH) and multiplexed error-robust fluorescence in situ hybridization (MERFISH). The methods implemented in this package are described in Zhu et al. (2018) <doi:10.1038/nbt.4260>.

Last updated 4 years ago

1.70 score 16 scripts 109 downloads

ocd - High-Dimensional Multiscale Online Changepoint Detection

Implements the algorithm in Chen, Wang and Samworth (2020) <arxiv:2003.03668> for online detection of sudden mean changes in a sequence of high-dimensional observations. It also implements methods by Mei (2010) <doi:10.1093/biomet/asq010>, Xie and Siegmund (2013) <doi:10.1214/13-AOS1094> and Chan (2017) <doi:10.1214/17-AOS1546>.

Last updated 4 years ago

1.70 score 6 scripts 173 downloads

sazedR - Parameter-Free Domain-Agnostic Season Length Detection in Time Series

Spectral and Average Autocorrelation Zero Distance Density ('sazed') is a method for estimating the season length of a seasonal time series. 'sazed' is aimed at practitioners, as it employs only domain-agnostic preprocessing and does not depend on parameter tuning or empirical constants. The computation of 'sazed' relies on the efficient autocorrelation computation methods suggested by Thibauld Nion (2012, URL: <https://etudes.tibonihoo.net/literate_musing/autocorrelations.html>) and by Bob Carpenter (2012, URL: <https://lingpipe-blog.com/2012/06/08/autocorrelation-fft-kiss-eigen/>).

Last updated 4 years ago

1.70 score 10 scripts 236 downloads

SphereOptimize - Optimization on a Unit Sphere

A simple tool for numerical optimization on the unit sphere. This is achieved by combining the spherical coordinating system with L-BFGS-B optimization. This algorithm is implemented in Kolkiewicz, A., Rice, G., & Xie, Y. (2020) <doi:10.1016/j.jspi.2020.07.001>.

Last updated 4 years ago

1.70 score 89 downloads

IOHexperimenter - Benchmarking Part of the 'IOHprofiler'

The benchmarking module for the Iterative Optimization Heuristics Profiler ('IOHprofiler'). This module provides benchmarking in the 'IOHprofiler' format, which can be visualized using the 'IOHanalyzer' module.

Last updated 4 years ago

cpp

1.70 score 3 scripts 136 downloads

ROI.models.globalOptTests - 'ROI' Optimization Problems Based on 'globalOptTests'

A collection of non-linear optimization problems with box bounds transformed into 'ROI' optimization problems. This package provides a wrapper around the 'globalOptTests' which provides a collection of global optimization problems. More information can be found in the 'README' file.

Last updated 4 years ago

1.70 score 3 scripts 168 downloads

lmviz - A Package to Visualize Linear Models Features and Play with Them

Contains a suite of shiny applications meant to explore linear model inference feature through simulation and games.

Last updated 4 years ago

1.70 score 7 scripts 170 downloads

radlibs - Build Your Own Madlibs!

Make your phrase or sentence into something funny! Pass a string with the keywords in, and get out a bit of humor.

Last updated 4 years ago

1.70 score 1 scripts 243 downloads

pdfminer - Read Portable Document Format (PDF) Files

Provides an interface to 'PDFMiner' <https://github.com/pdfminer/pdfminer.six> a 'Python' package for extracting information from 'PDF'-files. 'PDFMiner' has the goal to get all information available in a 'PDF'-file, position of the characters, font type, font size and informations about lines. Which makes it the perfect starting point for extracting tables from 'PDF'-files. More information can be found in the package 'README'-file.

Last updated 5 years ago

1.70 score 4 scripts 171 downloads

openblender - Request <https://openblender.io> API Services

Interface to make HTTP requests to 'OpenBlender' API services. Go to <https://openblender.io> for more information.

Last updated 5 years ago

1.70 score 4 scripts 235 downloads

dvqcc - Dynamic VAR - Based Control Charts for Batch Process Monitoring

A set of control charts for batch processes based on the VAR model. The package contains the implementation of T2.var and W.var control charts based on VAR model coefficients using the couple vectors theory. In each time-instant the VAR coefficients are estimated from a historical in-control dataset and a decision rule is made for online classifying of a new batch data. Those charts allow efficient online monitoring since the very first time-instant. The offline version is available too. In order to evaluate the chart's performance, this package contains functions to generate batch data for offline and online monitoring.See in Danilo Marcondes Filho and Marcio Valk (2020) <doi:10.1016/j.ejor.2019.12.038>.

Last updated 5 years ago

1.70 score 138 downloads

epxToR - Import 'Epidata' XML Files '.epx'

Import data from 'Epidata' XML files '.epx' and convert it to R data structures.

Last updated 5 years ago

1.70 score 3 scripts 194 downloads

MGMS2 - 'MGMS2' for Polymicrobial Samples

A glycolipid mass spectrometry technology has the potential to accurately identify individual bacterial species from polymicrobial samples. To develop bacterial identification algorithms (e.g. machine learning) using this glycolipid technology, it is necessary to generate a large number of various in-silico polymicrobial mass spectra that are similar to real mass spectra. 'MGMS2' (Membrane Glycolipid Mass Spectrum Simulator) generates such in-silico mass spectra, considering errors in m/z (mass-to-charge ratio) and variances of intensity values, occasions of missing signature ions, and noise peaks. It estimates summary statistics of monomicrobial mass spectra for each strain or species and simulates polymicrobial glycolipid mass spectra using the summary statistics of monomicrobial mass spectra. References: Ryu, S.Y., Wendt, G.A., Chandler, C.E., Ernst, R.K. and Goodlett, D.R. (2019) <doi:10.1021/acs.analchem.9b03340> "Model-based Spectral Library Approach for Bacterial Identification via Membrane Glycolipids." Gibb, S. and Strimmer, K. (2012) <doi:10.1093/bioinformatics/bts447> "MALDIquant: a versatile R package for the analysis of mass spectrometry data."

Last updated 5 years ago

1.70 score 2 scripts 140 downloads

OTE - Optimal Trees Ensembles for Regression, Classification and Class Membership Probability Estimation

Functions for creating ensembles of optimal trees for regression, classification (Khan, Z., Gul, A., Perperoglou, A., Miftahuddin, M., Mahmoud, O., Adler, W., & Lausen, B. (2019). (2019) <doi:10.1007/s11634-019-00364-9>) and class membership probability estimation (Khan, Z, Gul, A, Mahmoud, O, Miftahuddin, M, Perperoglou, A, Adler, W & Lausen, B (2016) <doi:10.1007/978-3-319-25226-1_34>) are given. A few trees are selected from an initial set of trees grown by random forest for the ensemble on the basis of their individual and collective performance. Three different methods of tree selection for the case of classification are given. The prediction functions return estimates of the test responses and their class membership probabilities. Unexplained variations, error rates, confusion matrix, Brier scores, etc. are also returned for the test data.

Last updated 5 years ago

1.70 score 8 scripts 104 downloads

infinitefactor - Bayesian Infinite Factor Models

Sampler and post-processing functions for semi-parametric Bayesian infinite factor models, motivated by the Multiplicative Gamma Shrinkage Prior of Bhattacharya and Dunson (2011) <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3419391/>. Contains component C++ functions for building samplers for linear and 2-way interaction factor models using the multiplicative gamma and Dirichlet-Laplace shrinkage priors. The package also contains post processing functions to return matrices that display rotational ambiguity to identifiability through successive application of orthogonalization procedures and resolution of column label and sign switching. This package was developed with the support of the National Institute of Environmental Health Sciences grant 1R01ES028804-01.

Last updated 5 years ago

openblascppopenmp

1.70 score 7 scripts 128 downloads

varjmcm - Estimations for the Covariance of Estimated Parameters in Joint Mean-Covariance Models

The goal of the package is to equip the 'jmcm' package (current version 0.2.1) with estimations of the covariance of estimated parameters. Two methods are provided. The first method is to use the inverse of estimated Fisher's information matrix, see M. Pourahmadi (2000) <doi:10.1093/biomet/87.2.425>, M. Maadooliat, M. Pourahmadi and J. Z. Huang (2013) <doi:10.1007/s11222-011-9284-6>, and W. Zhang, C. Leng, C. Tang (2015) <doi:10.1111/rssb.12065>. The second method is bootstrap based, see Liu, R.Y. (1988) <doi:10.1214/aos/1176351062> for reference.

Last updated 5 years ago

1.70 score 5 scripts 99 downloads

lipidomeR - Integrative Visualizations of the Lipidome

Create lipidome-wide heatmaps of statistics with the 'lipidomeR'. The 'lipidomeR' provides a streamlined pipeline for the systematic interpretation of the lipidome through publication-ready visualizations of regression models fitted on lipidomics data. With 'lipidomeR', associations between covariates and the lipidome can be interpreted systematically and intuitively through heatmaps, where lipids are categorized by the lipid class and are presented on two-dimensional maps organized by the lipid size and level of saturation. This way, the 'lipidomeR' helps you gain an immediate understanding of the multivariate patterns in the lipidome already at first glance. You can create lipidome-wide heatmaps of statistical associations, changes, differences, variation, or other lipid-specific values. The heatmaps are provided with publication-ready quality and the results behind the visualizations are based on rigorous statistical models.

Last updated 5 years ago

1.70 score 1 scripts 175 downloads

hindex - Simulating the Development of h-Index Values

H-index and h-alpha are a bibliometric indicators. This package provides functions to simulate how these indicators may develop over time for a given set of researchers and to visualize the simulation data. The implementation is based on the 'STATA' ado h-index and is described in more detail in Bornmann et al. (2019) <arXiv:1905.11052>.

Last updated 5 years ago

1.70 score 2 scripts 121 downloads

poisFErobust - Poisson Fixed Effects Robust

Computation of robust standard errors of Poisson fixed effects models, following Wooldridge (1999).

Last updated 5 years ago

1.70 score 7 scripts 194 downloads

l0ara - Sparse Generalized Linear Model with L0 Approximation for Feature Selection

An efficient procedure for feature selection for generalized linear models with L0 penalty, including linear, logistic, Poisson, gamma, inverse Gaussian regression. Adaptive ridge algorithms are used to fit the models.

Last updated 5 years ago

openblascpp

1.70 score 5 scripts 137 downloads

oncrawlR - Machine Learning for S.E.O

Measures different aspects of page content, structure and performance for SEO (Search Engine Optimization). Aspects covered include HTML tags used in SEO, duplicate and near-duplicate content, structured data, on-site linking structure and popularity transfer, and many other amazing things. This package can be used to generate a real, full SEO audit report, which serves to detect errors or inefficiencies on a page that can be corrected in order to optimise its performance on search engines.

Last updated 5 years ago

1.70 score 1 scripts 140 downloads

RonFHIR - Read and Search Interface to the 'HL7 FHIR' REST API

R on FHIR is an easy to use wrapper around the 'HL7 FHIR' REST API (STU 3 and R4). It provides tools to easily read and search resources on a FHIR server and brings the results into the R environment. R on FHIR is based on the FhirClient of the official 'HL7 FHIR .NET API', also made by Firely.

Last updated 5 years ago

1.70 score 11 scripts 138 downloads

sparkhail - A 'Sparklyr' Extension for 'Hail'

'Hail' is an open-source, general-purpose, 'python' based data analysis tool with additional data types and methods for working with genomic data, see <https://hail.is/>. 'Hail' is built to scale and has first-class support for multi-dimensional structured data, like the genomic data in a genome-wide association study (GWAS). 'Hail' is exposed as a 'python' library, using primitives for distributed queries and linear algebra implemented in 'scala', 'spark', and increasingly 'C++'. The 'sparkhail' is an R extension using 'sparklyr' package. The idea is to help R users to use 'hail' functionalities with the well-know 'tidyverse' syntax, see <https://www.tidyverse.org/>.

Last updated 5 years ago

1.70 score 9 scripts 101 downloads

NLPclient - Stanford 'CoreNLP' Annotation Client

Stanford 'CoreNLP' annotation client. Stanford 'CoreNLP' <https://stanfordnlp.github.io/CoreNLP/index.html> integrates all NLP tools from the Stanford Natural Language Processing Group, including a part-of-speech (POS) tagger, a named entity recognizer (NER), a parser, and a coreference resolution system, and provides model files for the analysis of English. More information can be found in the README.

Last updated 5 years ago

1.70 score 111 downloads

BCA1SG - Block Coordinate Ascent with One-Step Generalized Rosen Algorithm

Implementing the Block Coordinate Ascent with One-Step Generalized Rosen (BCA1SG) algorithm on the semiparametric models for panel count data, interval-censored survival data, and degradation data. A comprehensive description of the BCA1SG algorithm can be found in Wang et al. (2020) <https://github.com/yudongstat/BCA1SG/blob/master/BCA1SG.pdf>. For details of the semiparametric models for panel count data, interval-censored survival data, and degradation data, please see Wellner and Zhang (2007) <doi:10.1214/009053607000000181>, Huang and Wellner (1997) <ISBN:978-0-387-94992-5>, and Wang and Xu (2010) <doi:10.1198/TECH.2009.08197>, respectively.

Last updated 5 years ago

1.70 score 163 downloads

nbconvertR - Vignette Engine Wrapping Jupyter Notebooks

Calls the 'Jupyter' script 'nbconvert' to create vignettes from notebooks. Those notebooks ('.ipynb' files) are files containing rich text, code, and its output. Code cells can be edited and evaluated interactively. See <https://jupyter.org/> for more information.

Last updated 5 years ago

1.70 score 7 scripts 129 downloads

AnimalHabitatNetwork - Networks Characterising the Physical Configurations of Animal Habitats

Functions for generating and visualising networks for characterising the physical attributes and spatial organisations of habitat components (i.e. habitat physical configurations). The network generating algorithm first determines the X and Y coordinates of N nodes within a rectangle with a side length of L and an area of A. Then it computes the pair-wise Euclidean distance Dij between node i and j, and then a complete network with 1/Dij as link weights is constructed. Then, the algorithm removes links from the complete network with the probability as shown in the function ahn_prob(). Such link removals can make the network disconnected whereas a connected network is wanted. In such cases, the algorithm rewires one network component to its spatially nearest neighbouring component and repeat doing this until the network is connected again. Finally, it outputs an undirected network (weighted or unweighted, connected or disconnected). This package came with a manuscript on modelling the physical configurations of animal habitats using networks (in preparation).

Last updated 5 years ago

1.70 score 1 scripts 237 downloads

NMVANOVA - Novice Model Variation ANOVA

Due to 'Rstudio's' status as open source software, we believe it will be utilized frequently for future data analysis by users whom lack formal training or experience with 'R'. The 'NMVANOVA' (Novice Model Variation ANOVA) a streamlined variation of experimental design functions that allows novice 'Rstudio' users to perform different model variations one-way analysis of variance without downloading multiple libraries or packages. Users can easily manipulate the data block, and needed inputs so that users only have to plugin the four designed variables/values.

Last updated 5 years ago

1.70 score 94 downloads

mSTEM - Multiple Testing of Local Extrema for Detection of Change Points

A new approach to detect change points based on smoothing and multiple testing, which is for long data sequence modeled as piecewise constant functions plus stationary Gaussian noise, see Dan Cheng and Armin Schwartzman (2015) <arXiv:1504.06384>.

Last updated 5 years ago

1.70 score 1 scripts 102 downloads

hans - Haversines are not Slow

The haversine is a function used to calculate the distance between a pair of latitude and longitude points while accounting for the assumption that the points are on a spherical globe. This package provides a fast, dataframe compatible, haversine function. For the first publication on the haversine calculation see Joseph de Mendoza y Ríos (1795) <https://books.google.cat/books?id=030t0OqlX2AC> (In Spanish).

Last updated 5 years ago

cpp

1.70 score 1 scripts 131 downloads

geosed - Smallest Enclosing Disc for Latitude and Longitude Points

Find the smallest circle that contains all longitude and latitude input points. From the generated center and radius, variable side polygons can be created, navigation based on bearing and distance can be applied, and more. Based on a modified version of Welzl's algorithm for smallest circle. Distance calculations are based on the haversine formula. Calculations for distance, midpoint, bearing and more are derived from <https://www.movable-type.co.uk>.

Last updated 5 years ago

1.70 score 105 downloads

variantspark - A 'Sparklyr' Extension for 'VariantSpark'

This is a 'sparklyr' extension integrating 'VariantSpark' and R. 'VariantSpark' is a framework based on 'scala' and 'spark' to analyze genome datasets, see <https://bioinformatics.csiro.au/>. It was tested on datasets with 3000 samples each one containing 80 million features in either unsupervised clustering approaches and supervised applications, like classification and regression. The genome datasets are usually writing in VCF, a specific text file format used in bioinformatics for storing gene sequence variations. So, 'VariantSpark' is a great tool for genome research, because it is able to read VCF files, run analyses and return the output in a 'spark' data frame.

Last updated 6 years ago

1.70 score 16 scripts 101 downloads

cluscov - Clustered Covariate Regression

Clustered covariate regression enables estimation and inference in both linear and non-linear models with linear predictor functions even when the design matrix is column rank deficient. Routines in this package implement algorithms in Soale and Tsyawo (2019) <doi:10.13140/RG.2.2.32355.81441>.

Last updated 6 years ago

1.70 score 161 downloads

rapidxmlr - 'Rapidxml' C++ Header Files

Provides XML parsing capability through the 'Rapidxml' 'C++' header-only library.

Last updated 6 years ago

1.70 score 108 downloads

packHV - A few Useful Functions for Statisticians

Various useful functions for statisticians: describe data, plot Kaplan-Meier curves with numbers of subjects at risk, compare data sets, display spaghetti-plot, build multi-contingency tables...

Last updated 6 years ago

1.70 score 36 scripts 408 downloads

fugue - Sensitivity Analysis Optimized for Matched Sets of Varied Sizes

As in music, a fugue statistic repeats a theme in small variations. Here, the psi-function that defines an m-statistic is slightly altered to maintain the same design sensitivity in matched sets of different sizes. The main functions in the package are sen() and senCI(). For sensitivity analyses for m-statistics, see Rosenbaum (2007) Biometrics 63 456-464 <doi:10.1111/j.1541-0420.2006.00717.x>.

Last updated 6 years ago

1.70 score 4 scripts 126 downloads

raws.profile - Managing Profiles on Amazon Web Service

This is an R wrapper from the AWS Command Line Interface that provides methods to manage the user configuration on Amazon Web Service. You can create as many profiles as you want, manage them, and delete them. The profiles created with this tool work with all AWS products such as S3, Glacier, and EC2. It also provides a function to automatically install AWS CLI, but you can download it and install it manually if you prefer.

Last updated 6 years ago

1.70 score 4 scripts 114 downloads

kernhaz - Kernel Estimation of Hazard Function in Survival Analysis

Producing kernel estimates of the unconditional and conditional hazard function for right-censored data including methods of bandwidth selection.

Last updated 6 years ago

1.70 score 1 stars 4 scripts 133 downloads

AutoStepwiseGLM - Builds Stepwise GLMs via Train and Test Approach

Randomly splits data into testing and training sets. Then, uses stepwise selection to fit numerous multiple regression models on the training data, and tests them on the test data. Returned for each model are plots comparing model Akaike Information Criterion (AIC), Pearson correlation coefficient (r) between the predicted and actual values, Mean Absolute Error (MAE), and R-Squared among the models. Each model is ranked relative to the other models by the model evaluation metrics (i.e., AIC, r, MAE, and R-Squared) and the model with the best mean ranking among the model evaluation metrics is returned. Model evaluation metric weights for AIC, r, MAE, and R-Squared are taken in as arguments as aic_wt, r_wt, mae_wt, and r_squ_wt, respectively. They are equally weighted as default but may be adjusted relative to each other if the user prefers one or more metrics to the others, Field, A. (2013, ISBN:978-1-4462-4918-5).

Last updated 6 years ago

1.70 score 2 scripts 168 downloads

mixedsde - Estimation Methods for Stochastic Differential Mixed Effects Models

Inference on stochastic differential models Ornstein-Uhlenbeck or Cox-Ingersoll-Ross, with one or two random effects in the drift function.

Last updated 6 years ago

1.70 score 7 scripts 157 downloads

IMmailgun - Send Emails using 'Mailgun'

Send emails using the 'mailgun' api. To use this package you will need an account from <https://www.mailgun.com> .

Last updated 6 years ago

1.70 score 5 scripts 104 downloads

ECLRMC - Ensemble Correlation-Based Low-Rank Matrix Completion

Ensemble correlation-based low-rank matrix completion method (ECLRMC) is an extension to the LRMC based methods. Traditionally, the LRMC based methods give identical importance to the whole data which results in emphasizing on the commonality of the data and overlooking the subtle but crucial differences. This method aims to overcome the equality assumption problem that exists in the current LRMS based methods. Ensemble correlation-based low-rank matrix completion (ECLRMC) takes consideration of the specific characteristic of each sample and performs LRMC on the set of samples with a strong correlation. It uses an ensemble learning method to improve the imputation performance. Since each sample is analyzed independently this method can be parallelized by distributing imputation across many computation units or GPU platforms. This package provides three different methods (LRMC, CLRMC and ECLRMC) for data imputation. There is also an NRMS function for evaluating the result. Chen, Xiaobo, et al (2017) <doi:10.1016/j.knosys.2017.06.010>.

Last updated 6 years ago

1.70 score 1 stars 4 scripts 139 downloads

dyncomp - Complexity of Short and Coarse-Grained Time Series

While there are many well-established measures for identifying critical fluctuations and phase transitions, these measures only work with many points of measurement and thus are unreliable when studying short and coarse-grained time series. This package provides a measure for complexity in a time series that does not rely on long time series (Kaiser (2017), <doi:10.17605/OSF.IO/GWTKX>).

Last updated 6 years ago

1.70 score 3 scripts 150 downloads

rmi - Mutual Information Estimators

Provides mutual information estimators based on k-nearest neighbor estimators by A. Kraskov, et al. (2004) <doi:10.1103/PhysRevE.69.066138>, S. Gao, et al. (2015) <http://proceedings.mlr.press/v38/gao15.pdf> and local density estimators by W. Gao, et al. (2017) <doi:10.1109/ISIT.2017.8006749>.

Last updated 6 years ago

openblascpp

1.70 score 7 scripts 99 downloads

adwordsR - Access the 'Google Adwords' API

Allows access to selected services that are part of the 'Google Adwords' API <https://developers.google.com/adwords/api/docs/guides/start>. 'Google Adwords' is an online advertising service by 'Google', that delivers Ads to users. This package offers a authentication process using 'OAUTH2'. Currently, there are two methods of data of accessing the API, depending on the type of request. One method uses 'SOAP' requests which require building an 'XML' structure and then sent to the API. These are used for the 'ManagedCustomerService' and the 'TargetingIdeaService'. The second method is by building 'AWQL' queries for the reporting side of the 'Google Adwords' API.

Last updated 7 years ago

1.70 score 7 scripts 229 downloads

gimmeTools - Supplemental Tools for the 'gimme' R Package

Supplemental tools for the 'gimme' R package. It contains an interactive graphical user interface, allowing for the flexible specification of a variety of both basic and advanced options. It will expand to include a variety of tools for navigating output.

Last updated 7 years ago

1.70 score 2 scripts 135 downloads

stringformattr - Dynamic String Formatting

Pass named and unnamed character vectors into specified positions in strings. This represents an attempt to replicate some of python's string formatting.

Last updated 7 years ago

1.70 score 2 scripts 133 downloads

XKCDdata - Get XKCD Comic Data

Download data from individual XKCD comics, written by Randall Munroe <https://xkcd.com/>.

Last updated 7 years ago

1.70 score 10 scripts 112 downloads

BrownDog - Brown Dog R Interface

An R interface for the Brown Dog which allows researchers to leverage Brown Dog Services that provides modules to identify the conversion options for a file, to convert file to appropriate format, or to extract data from a file. See <http://browndog.ncsa.illinois.edu/> for more information.

Last updated 7 years ago

1.70 score 8 scripts 180 downloads

Sunclarco - Survival Analysis using Copulas

Survival analysis for unbalanced clusters using Archimedean copulas (Prenen et al. (2016) <DOI:10.1111/rssb.12174>).

Last updated 7 years ago

1.70 score 1 scripts 91 downloads

d3plus - Seamless 'D3Plus' Integration

Provides functions that offer seamless 'D3Plus' integration. The examples provided here are taken from the official 'D3Plus' website <http://d3plus.org>.

Last updated 7 years ago

1.70 score 16 scripts 446 downloads

TNC - Temporal Network Centrality (TNC) Measures

Node centrality measures for temporal networks. Available measures are temporal degree centrality, temporal closeness centrality and temporal betweenness centrality defined by Kim and Anderson (2012) <doi:10.1103/PhysRevE.85.026107>. Applying the REN algorithm by Hanke and Foraita (2017) <doi:10.1186/s12859-017-1677-x> when calculating the centrality measures keeps the computational running time linear in the number of graph snapshots. Further, all methods can run in parallel up to the number of nodes in the network.

Last updated 7 years ago

1.70 score 7 scripts 112 downloads

pcdpca - Dynamic Principal Components for Periodically Correlated Functional Time Series

Method extends multivariate and functional dynamic principal components to periodically correlated multivariate time series. This package allows you to compute true dynamic principal components in the presence of periodicity. We follow implementation guidelines as described in Kidzinski, Kokoszka and Jouzdani (2017), in Principal component analysis of periodically correlated functional time series <arXiv:1612.00040>.

Last updated 7 years ago

1.70 score 8 scripts 154 downloads

MicroMacroMultilevel - Micro-Macro Multilevel Modeling

Most multilevel methodologies can only model macro-micro multilevel situations in an unbiased way, wherein group-level predictors (e.g., city temperature) are used to predict an individual-level outcome variable (e.g., citizen personality). In contrast, this R package enables researchers to model micro-macro situations, wherein individual-level (micro) predictors (and other group-level predictors) are used to predict a group-level (macro) outcome variable in an unbiased way.

Last updated 7 years ago

1.70 score 4 scripts 497 downloads

SanFranBeachWater - Downloads and Tidies the San Francisco Public Utilities Commission Beach Water Quality Monitoring Program Data

Downloads and tidies the San Francisco Public Utilities Commission Beach Water Quality Monitoring Program data. Data sets can be downloaded per beach, or the raw data can be downloaded. See <https://sfwater.org/cfapps/lims/beachmain1.cfm>.

Last updated 8 years ago

1.70 score 4 scripts 154 downloads

CVR - Canonical Variate Regression

Perform canonical variate regression (CVR) for two sets of covariates and a univariate response, with regularization and weight parameters tuned by cross validation.

Last updated 8 years ago

openblascpp

1.70 score 10 scripts 502 downloads

QCAtools - Helper Functions for QCA in R

Helper functions for Qualitative Comparative Analysis: evaluate and plot Boolean formulae on fuzzy set score data, apply Boolean operations, compute consistency and coverage measures.

Last updated 8 years ago

1.70 score 6 scripts 137 downloads

apdesign - An Implementation of the Additive Polynomial Design Matrix

An implementation of the additive polynomial (AP) design matrix. It constructs and appends an AP design matrix to a data frame for use with longitudinal data subject to seasonality.

Last updated 8 years ago

1.70 score 2 scripts 517 downloads

ordcrm - Likelihood-Based Continual Reassessment Method (CRM) Dose Finding Designs

Provides the setup and calculations needed to run a likelihood-based continual reassessment method (CRM) dose finding trial and performs simulations to assess design performance under various scenarios. 3 dose finding designs are included in this package: ordinal proportional odds model (POM) CRM, ordinal continuation ratio (CR) model CRM, and the binary 2-parameter logistic model CRM. These functions allow customization of design characteristics to vary sample size, cohort sizes, target dose-limiting toxicity (DLT) rates, discrete or continuous dose levels, combining ordinal grades 0 and 1 into one category, and incorporate safety and/or stopping rules. For POM and CR model designs, ordinal toxicity grades are specified by common terminology criteria for adverse events (CTCAE) version 4.0. Function 'pseudodata' creates the necessary starting models for these 3 designs, and function 'nextdose' estimates the next dose to test in a cohort of patients for a target DLT rate. We also provide the function 'crmsimulations' to assess the performance of these 3 dose finding designs under various scenarios.

Last updated 8 years ago

1.70 score 3 scripts 97 downloads

CUMP - Analyze Multivariate Phenotypes by Combining Univariate Results

Combining Univariate Association Test Results of Multiple Phenotypes for Detecting Pleiotropy.

Last updated 8 years ago

1.70 score 1 scripts 124 downloads

RRate - Estimating Replication Rate for Genome-Wide Association Studies

Replication Rate (RR) is the probability of replicating a statistically significant association in genome-wide association studies. This R-package provide the estimation method for replication rate which makes use of the summary statistics from the primary study. We can use the estimated RR to determine the sample size of the replication study, and to check the consistency between the results of the primary study and those of the replication study.

Last updated 8 years ago

1.70 score 5 scripts 110 downloads

stmCorrViz - A Tool for Structural Topic Model Visualizations

Generates an interactive visualization of topic correlations/ hierarchy in a Structural Topic Model (STM) of Roberts, Stewart, and Tingley. The package performs a hierarchical clustering of topics which are then exported to a JSON object and visualized using D3.

Last updated 8 years ago

1.70 score 5 stars 22 scripts 155 downloads

depth.plot - Multivariate Analogy of Quantiles

Could be used to obtain spatial depths, spatial ranks and outliers of multivariate random variables. Could also be used to visualize DD-plots (a multivariate generalization of QQ-plots).

Last updated 9 years ago

1.70 score 5 scripts 169 downloads

favnums - A Dataset of Favourite Numbers

A dataset of favourite numbers, selected from an online poll of over 30,000 people by Alex Bellos (http://pages.bloomsbury.com/favouritenumber).

Last updated 9 years ago

1.70 score 1 scripts 106 downloads

missDeaths - Simulating and Analyzing Time to Event Data in the Presence of Population Mortality

Implements two methods: a nonparametric risk adjustment and a data imputation method that use general population mortality tables to allow a correct analysis of time to disease recurrence. Also includes a powerful set of object oriented survival data simulation functions.

Last updated 3 months ago

cpp

1.69 score 49 scripts 201 downloads

beyondWhittle - Bayesian Spectral Inference for Time Series

Implementations of Bayesian parametric, nonparametric and semiparametric procedures for univariate and multivariate time series. The package is based on the methods presented in C. Kirch et al (2018) <doi:10.1214/18-BA1126>, A. Meier (2018) <https://opendata.uni-halle.de//handle/1981185920/13470> and Y. Tang et al (2023) <doi:10.48550/arXiv.2303.11561>. It was supported by DFG grants KI 1443/3-1 and KI 1443/3-2.

Last updated 29 days ago

openblascpp

1.68 score 2 stars 12 scripts 431 downloads

wavScalogram - Wavelet Scalogram Tools for Time Series Analysis

Provides scalogram based wavelet tools for time series analysis: wavelet power spectrum, scalogram, windowed scalogram, windowed scalogram difference (see Bolos et al. (2017) <doi:10.1016/j.amc.2017.05.046>), scale index and windowed scale index (Benitez et al. (2010) <doi:10.1016/j.camwa.2010.05.010>).

Last updated 10 months ago

1.68 score 1 dependents 16 scripts 327 downloads

netClust - Model-Based Clustering of Network Data

Clustering unilayer and multilayer network data by means of finite mixtures is the main utility of 'netClust'.

Last updated 4 years ago

openblascppopenmp

1.68 score 48 scripts 101 downloads

wPerm - Permutation Tests

Supplies permutation-test alternatives to traditional hypothesis-test procedures such as two-sample tests for means, medians, and standard deviations; correlation tests; tests for homogeneity and independence; and more. Suitable for general audiences, including individual and group users, introductory statistics courses, and more advanced statistics courses that desire an introduction to permutation tests.

Last updated 9 years ago

1.68 score 24 scripts 129 downloads

thermocouple - Temperature Measurement with Thermocouples, RTD and IC Sensors

Temperature measurement data, equations and methods for thermocouples, wire RTD, thermistors, IC thermometers, bimetallic strips and the ITS-90.

Last updated 9 years ago

1.68 score 48 scripts 114 downloads

SpatialAcc - Spatial Accessibility Measures

Provides a set of spatial accessibility measures from a set of locations (demand) to another set of locations (supply). It aims, among others, to support research on spatial accessibility to health care facilities. Includes the locations and some characteristics of major public hospitals in Greece.

Last updated 9 months ago

1.67 score 47 scripts 206 downloads

VBLPCM - Variational Bayes Latent Position Cluster Model for Networks

Fit and simulate latent position and cluster models for network data, using a fast Variational Bayes approximation developed in Salter-Townshend and Murphy (2013) <doi:10.1016/j.csda.2012.08.004>.

Last updated 2 years ago

1.66 score 2 stars 23 scripts 292 downloads

fastGraph - Fast Drawing and Shading of Graphs of Statistical Distributions

Provides functionality to produce graphs of probability density functions and cumulative distribution functions with few keystrokes, allows shading under the curve of the probability density function to illustrate concepts such as p-values and critical values, and fits a simple linear regression line on a scatter plot with the equation as the main title.

Last updated 5 years ago

1.65 score 45 scripts 662 downloads

spuRs - Functions and Datasets for "Introduction to Scientific Programming and Simulation Using R"

Provides functions and datasets from Jones, O.D., R. Maillardet, and A.P. Robinson. 2014. An Introduction to Scientific Programming and Simulation, Using R. 2nd Ed. Chapman And Hall/CRC.

Last updated 7 years ago

1.65 score 1 stars 45 scripts 328 downloads

spectralGP - Approximate Gaussian Processes Using the Fourier Basis

Routines for creating, manipulating, and performing Bayesian inference about Gaussian processes in one and two dimensions using the Fourier basis approximation: simulation and plotting of processes, calculation of coefficient variances, calculation of process density, coefficient proposals (for use in MCMC). It uses R environments to store GP objects as references/pointers.

Last updated 9 years ago

1.65 score 1 stars 45 scripts 195 downloads

optiSolve - Linear, Quadratic, and Rational Optimization

Solver for linear, quadratic, and rational programs with linear, quadratic, and rational constraints. A unified interface to different R packages is provided. Optimization problems are transformed into equivalent formulations and solved by the respective package. For example, quadratic programming problems with linear, quadratic and rational constraints can be solved by augmented Lagrangian minimization using package 'alabama', or by sequential quadratic programming using solver 'slsqp'. Alternatively, they can be reformulated as optimization problems with second order cone constraints and solved with package 'cccp'.

Last updated 3 years ago

1.65 score 1 dependents 15 scripts 431 downloads

ctrlGene - Assess the Stability of Candidate Housekeeping Genes

A simple way to assess the stability of candidate housekeeping genes is implemented in this package.

Last updated 5 years ago

1.65 score 1 dependents 15 scripts 230 downloads

adamethods - Archetypoid Algorithms and Anomaly Detection

Collection of several algorithms to obtain archetypoids with small and large databases, and with both classical multivariate data and functional data (univariate and multivariate). Some of these algorithms also allow to detect anomalies (outliers). Please see Vinue and Epifanio (2020) <doi:10.1007/s11634-020-00412-9>.

Last updated 4 years ago

1.63 score 43 scripts 283 downloads

BivRegBLS - Tolerance Interval and EIV Regression - Method Comparison Studies

Assess the agreement in method comparison studies by tolerance intervals and errors-in-variables (EIV) regressions. The Ordinary Least Square regressions (OLSv and OLSh), the Deming Regression (DR), and the (Correlated)-Bivariate Least Square regressions (BLS and CBLS) can be used with unreplicated or replicated data. The BLS() and CBLS() are the two main functions to estimate a regression line, while XY.plot() and MD.plot() are the two main graphical functions to display, respectively an (X,Y) plot or (M,D) plot with the BLS or CBLS results. Four hyperbolic statistical intervals are provided: the Confidence Interval (CI), the Confidence Bands (CB), the Prediction Interval and the Generalized prediction Interval. Assuming no proportional bias, the (M,D) plot (Band-Altman plot) may be simplified by calculating univariate tolerance intervals (beta-expectation (type I) or beta-gamma content (type II)). Major updates from last version 1.0.0 are: title shortened, include the new functions BLS.fit() and CBLS.fit() as shortcut of the, respectively, functions BLS() and CBLS(). References: B.G. Francq, B. Govaerts (2016) <doi:10.1002/sim.6872>, B.G. Francq, B. Govaerts (2014) <doi:10.1016/j.chemolab.2014.03.006>, B.G. Francq, B. Govaerts (2014) <http://publications-sfds.fr/index.php/J-SFdS/article/view/262>, B.G. Francq (2013), PhD Thesis, UCLouvain, Errors-in-variables regressions to assess equivalence in method comparison studies, <https://dial.uclouvain.be/pr/boreal/object/boreal%3A135862/datastream/PDF_01/view>.

Last updated 5 years ago

1.63 score 43 scripts 191 downloads

cumstats - Cumulative Descriptive Statistics

Cumulative descriptive statistics for (arithmetic, geometric, harmonic) mean, median, mode, variance, skewness and kurtosis.

Last updated 8 years ago

1.63 score 43 scripts 313 downloads

SparseTSCGM - Sparse Time Series Chain Graphical Models

Computes sparse vector autoregressive coefficients and precision matrices for time series chain graphical models. Fentaw Abegaz and Ernst Wit (2013) <doi:10.1093/biostatistics/kxt005>.

Last updated 4 years ago

1.62 score 2 stars 21 scripts 197 downloads

unbalhaar - Function Estimation via Unbalanced Haar Wavelets

Top-down and bottom-up algorithms for nonparametric function estimation in Gaussian noise using Unbalanced Haar wavelets.

Last updated 3 years ago

1.62 score 1 dependents 14 scripts 250 downloads

globalOptTests - Objective functions for benchmarking the performance of global optimization algorithms

This package makes available 50 objective functions for benchmarking the performance of global optimization algorithms

Last updated 10 years ago

1.62 score 1 stars 1 dependents 14 scripts 174 downloads

soilassessment - Assessment Models for Agriculture Soil Conditions and Crop Suitability

Soil assessment builds information for improved decision in soil management. It analyzes soil conditions with regard to agriculture crop suitability requirements [such as those given by FAO <https://www.fao.org/land-water/databases-and-software/crop-information/en/>] soil fertility classes, soil erosion, and soil salinity classification [<doi:10.1002/ldr.4211>]. Suitability requirements are for crops grouped into cereal crops, nuts, legumes, fruits, vegetables, industrial crops, and root crops.

Last updated 1 years ago

1.61 score 1 stars 41 scripts 306 downloads

timsac - Time Series Analysis and Control Package

Functions for statistical analysis, prediction and control of time series based mainly on Akaike and Nakagawa (1988) <ISBN 978-90-277-2786-2>.

Last updated 1 years ago

fortran

1.60 score 1 stars 1 dependents 87 scripts 1.3k downloads

cols - Constrained Ordinary Least Squares

Constrained ordinary least squares is performed. One constraint is that all beta coefficients (including the constant) cannot be negative. They can be either 0 or strictly positive. Another constraint is that the sum of the beta coefficients equals a constant. References: Hansen, B. E. (2022). Econometrics, Princeton University Press. <ISBN:9780691235899>.

Last updated 4 days ago

1.60 score 8 scripts 591 downloads

MLE - Maximum Likelihood Estimation of Various Univariate and Multivariate Distributions

Several functions for maximum likelihood estimation of various univariate and multivariate distributions. The list includes more than 100 functions for univariate continuous and discrete distributions, distributions that lie on the real line, the positive line, interval restricted, circular distributions. Further, multivariate continuous and discrete distributions, distributions for compositional and directional data, etc. Some references include Johnson N. L., Kotz S. and Balakrishnan N. (1994). "Continuous Univariate Distributions, Volume 1" <ISBN:978-0-471-58495-7>, Johnson, Norman L. Kemp, Adrianne W. Kotz, Samuel (2005). "Univariate Discrete Distributions". <ISBN:978-0-471-71580-1> and Mardia, K. V. and Jupp, P. E. (2000). "Directional Statistics". <ISBN:978-0-471-95333-3>.

Last updated 8 days ago

1.60 score 2 scripts 524 downloads

phoenics - Pathways Longitudinal and Differential Analysis in Metabolomics

Perform a differential analysis at pathway level based on metabolite quantifications and information on pathway metabolite composition. The method is based on a Principal Component Analysis step and on a linear mixed model. Automatic query of metabolic pathways is also implemented.

Last updated 12 days ago

1.60 score 148 downloads

smof - Scoring Methodology for Ordered Factors

Starting from a given object representing a fitted model (within a certain set of model classes) whose (non-)linear predictor includes some ordered factor(s) among the explanatory variables, a new model is constructed and fitted where each named factor is replaced by a single numeric score, suitably chosen so that the new variable produces a fit comparable with the standard methodology based on a set of polynomial contrasts. Two variants of the present approach have been developed, one in each of the next references: Azzalini (2023) <doi:10.1002/sta4.624>, (2024) <doi:10.48550/arXiv.2406.15933>.

Last updated 14 days ago

1.60 score 499 downloads

Xplortext - Statistical Analysis of Textual Data

Provides a set of functions devoted to multivariate exploratory statistics on textual data. Classical methods such as correspondence analysis and agglomerative hierarchical clustering are available. Chronologically constrained agglomerative hierarchical clustering enriched with labelled-by-words trees is offered. Given a division of the corpus into parts, their characteristic words and documents are identified. Further, accessing to 'FactoMineR' functions is very easy. Two of them are relevant in textual domain. MFA() addresses multiple lexical table allowing applications such as dealing with multilingual corpora as well as simultaneously analyzing both open-ended and closed questions in surveys. See <http://xplortext.unileon.es> for examples.

Last updated 1 months ago

1.60 score 2 stars 20 scripts 496 downloads

CopulaREMADA - Copula Mixed Models for Multivariate Meta-Analysis of Diagnostic Test Accuracy Studies

The bivariate copula mixed model for meta-analysis of diagnostic test accuracy studies in Nikoloulopoulos (2015) <doi:10.1002/sim.6595> and Nikoloulopoulos (2018) <doi:10.1007/s10182-017-0299-y>. The vine copula mixed model for meta-analysis of diagnostic test accuracy studies accounting for disease prevalence in Nikoloulopoulos (2017) <doi:10.1177/0962280215596769> and also accounting for non-evaluable subjects in Nikoloulopoulos (2020) <doi:10.1515/ijb-2019-0107>. The hybrid vine copula mixed model for meta-analysis of diagnostic test accuracy case-control and cohort studies in Nikoloulopoulos (2018) <doi:10.1177/0962280216682376>. The D-vine copula mixed model for meta-analysis and comparison of two diagnostic tests in Nikoloulopoulos (2019) <doi:10.1177/0962280218796685>. The multinomial quadrivariate D-vine copula mixed model for meta-analysis of diagnostic tests with non-evaluable subjects in Nikoloulopoulos (2020) <doi:10.1177/0962280220913898>. The one-factor copula mixed model for joint meta-analysis of multiple diagnostic tests in Nikoloulopoulos (2022) <doi:10.1111/rssa.12838>. The multinomial six-variate 1-truncated D-vine copula mixed model for meta-analysis of two diagnostic tests accounting for within and between studies dependence in Nikoloulopoulos (2024) <doi:10.1177/09622802241269645>. The 1-truncated D-vine copula mixed models for meta-analysis of diagnostic accuracy studies without a gold standard (Nikoloulopoulos, 2024).

Last updated 2 months ago

1.60 score 2 stars 10 scripts 295 downloads

grpnet - Group Elastic Net Regularized GLMs and GAMs

Efficient algorithms for fitting generalized linear and additive models with group elastic net penalties as described in Helwig (2024) <doi:10.1080/10618600.2024.2362232>. Implements group LASSO, group MCP, and group SCAD with an optional group ridge penalty. Computes the regularization path for linear regression (gaussian), logistic regression (binomial), multinomial logistic regression (multinomial), log-linear count regression (poisson and negative.binomial), and log-linear continuous regression (gamma and inverse gaussian). Supports default and formula methods for model specification, k-fold cross-validation for tuning the regularization parameters, and nonparametric regression via tensor product reproducing kernel (smoothing spline) basis function expansion.

Last updated 2 months ago

fortran

1.60 score 1 scripts 339 downloads

extrafrail - Estimation and Additional Tools for Alternative Shared Frailty Models

Provide estimation and data generation tools for some new multivariate frailty models. This version includes the gamma, inverse Gaussian, weighted Lindley, Birnbaum-Saunders, truncated normal, mixture of inverse Gaussian and mixture of Birnbaum-Saunders as the distribution for the frailty terms. For the basal model, it is considered a parametric approach based on the exponential, Weibull and the piecewise exponential distributions as well as a semiparametric approach. For details, see Gallardo and Bourguignon (2022) <doi:10.48550/arXiv.2206.12973> and Gallardo et al. (2024) <doi:10.1007/s11222-024-10458-w>.

Last updated 3 months ago

1.60 score 281 downloads

BayesFBHborrow - Bayesian Dynamic Borrowing with Flexible Baseline Hazard Function

Allows Bayesian borrowing from a historical dataset for time-to- event data. A flexible baseline hazard function is achieved via a piecewise exponential likelihood with time varying split points and smoothing prior on the historic baseline hazards. The method is described in Scott and Lewin (2024) <doi:10.48550/arXiv.2401.06082>, and the software paper is in Axillus et al. (2024) <doi:10.48550/arXiv.2408.04327>.

Last updated 3 months ago

1.60 score 1 scripts 203 downloads

JFE - Tools for Analyzing Time Series Data of Just Finance and Econometrics

Offers procedures to support financial-economic time series modelling and enhanced procedures for computing the investment performance indices of Bacon (2004) <DOI:10.1002/9781119206309>.

Last updated 7 months ago

1.60 score 2 stars 631 downloads

moderate.mediation - Causal Moderated Mediation Analysis

Causal moderated mediation analysis using the methods proposed by Qin and Wang (2023) <doi:10.3758/s13428-023-02095-4>. Causal moderated mediation analysis is crucial for investigating how, for whom, and where a treatment is effective by assessing the heterogeneity of mediation mechanism across individuals and contexts. This package enables researchers to estimate and test the conditional and moderated mediation effects, assess their sensitivity to unmeasured pre-treatment confounding, and visualize the results. The package is built based on the quasi-Bayesian Monte Carlo method, because it has relatively better performance at small sample sizes, and its running speed is the fastest. The package is applicable to a treatment of any scale, a binary or continuous mediator, a binary or continuous outcome, and one or more moderators of any scale.

Last updated 7 months ago

1.60 score 295 downloads

gausscov - The Gaussian Covariate Method for Variable Selection

The standard linear regression theory whether frequentist or Bayesian is based on an 'assumed (revealed?) truth' (John Tukey) attitude to models. This is reflected in the language of statistical inference which involves a concept of truth, for example confidence intervals, hypothesis testing and consistency. The motivation behind this package was to remove the word true from the theory and practice of linear regression and to replace it by approximation. The approximations considered are the least squares approximations. An approximation is called valid if it contains no irrelevant covariates. This is operationalized using the concept of a Gaussian P-value which is the probability that pure Gaussian noise is better in term of least squares than the covariate. The precise definition given in the paper, it is intuitive and requires only four simple equations. Its overwhelming advantage compared with a standard F P-value is that is is exact and valid whatever the data. In contrast F P-values are only valid for specially designed simulations. Given this a valid approximation is one where all the Gaussian P-values are less than a threshold p0 specified by the statistician, in this package with the default value 0.01. This approximations approach is not only much simpler it is overwhelmingly better than the standard model based approach. The will be demonstrated using six real data sets, four from high dimensional regression and two from vector autoregression. The simplicity and superiority of Gaussian P-values derive from their universal exactness and validity. This is in complete contrast to standard F P-values which are valid only for carefully designed simulations. The function f1st is the most important function. It is a greedy forward selection procedure which results in either just one or no approximations which may however not be valid. If the size is less than than a threshold with default value 21 then an all subset procedure is called which returns the best valid subset. A good default start is f1st(y,x,kmn=15) The best function for returning multiple approximations is f3st which repeatedly calls f1st. For more information see the web site below and the accompanying papers: L. Davies and L. Duembgen, "Covariate Selection Based on a Model-free Approach to Linear Regression with Exact Probabilities", 2202, <doi:10.48550/arXiv.2202.01553>. L. Davies, "An Approximation Based Theory of Linear Regression", 2402, <doi:10.48550/arXiv.2402.09858>.

Last updated 7 months ago

1.60 score 1 stars 53 scripts 657 downloads

RcmdrPlugin.DCE - R Commander Plug-in for Discrete Choice Experiments

Adds menu items for discrete choice experiments (DCEs) to the R Commander. DCE is a question-based survey method that designs various combinations (profiles) of attribute levels using the experimental designs, asks respondents to select the most preferred profile in each choice set, and then measures preferences for the attribute levels by analyzing the responses. For details on DCEs, refer to Louviere et al. (2000) <doi:10.1017/CBO9780511753831>.

Last updated 7 months ago

1.60 score 2 stars 2 scripts 433 downloads

RcmdrPlugin.BWS3 - R Commander Plug-in for Case 3 Best-Worst Scaling

Adds menu items for case 3 (multi-profile) best-worst scaling (BWS3) to the R Commander. BWS3 is a question-based survey method that designs various combinations of attribute levels (profiles), asks respondents to select the best and worst profiles in each choice set, and then measures preferences for the attribute levels by analyzing the responses. For details on BWS3, refer to Louviere et al. (2015) <doi:10.1017/CBO9781107337855>.

Last updated 7 months ago

1.60 score 2 scripts 762 downloads

topologyGSA - Gene Set Analysis Exploiting Pathway Topology

Using Gaussian graphical models we propose a novel approach to perform pathway analysis using gene expression. Given the structure of a graph (a pathway) we introduce two statistical tests to compare the mean and the concentration matrices between two groups. Specifically, these tests can be performed on the graph and on its connected components (cliques). The package is based on the method described in Massa M.S., Chiogna M., Romualdi C. (2010) <doi:10.1186/1752-0509-4-121>.

Last updated 1 years ago

1.60 score 9 scripts 301 downloads

epade - Easy Plots

A collection of nice plotting functions directly from a data.frame with limited customisation possibilities.

Last updated 2 years ago

1.60 score 32 scripts 366 downloads

Keyboard - Bayesian Designs for Early Phase Clinical Trials

We developed a package 'Keyboard' for designing single-agent, drug-combination, or phase I/II dose-finding clinical trials. The 'Keyboard' designs are novel early phase trial designs that can be implemented simply and transparently, similar to the 3+3 design, but yield excellent performance, comparable to those of more-complicated, model-based designs (Yan F, Mandrekar SJ, Yuan Y (2017) <doi:10.1158/1078-0432.CCR-17-0220>, Li DH, Whitmore JB, Guo W, Ji Y. (2017) <doi:10.1158/1078-0432.CCR-16-1125>, Liu S, Johnson VE (2016) <doi:10.1093/biostatistics/kxv040>, Zhou Y, Lee JJ, Yuan Y (2019) <doi:10.1002/sim.8475>, Pan H, Lin R, Yuan Y (2020) <doi:10.1016/j.cct.2020.105972>). The 'Keyboard' package provides tools for designing, conducting, and analyzing single-agent, drug-combination, and phase I/II dose-finding clinical trials. For more details about how to use this packge, please refer to Li C, Sun H, Cheng C, Tang L, and Pan H. (2022) "A software tool for both the maximum tolerated dose and the optimal biological dose finding trials in early phase designs". Manuscript submitted for publication.

Last updated 2 years ago

1.60 score 1 stars 3 scripts 213 downloads

POCRE - Penalized Orthogonal-Components Regression

Penalized orthogonal-components regression (POCRE) is a supervised dimension reduction method for high-dimensional data. It sequentially constructs orthogonal components (with selected features) which are maximally correlated to the response residuals. POCRE can also construct common components for multiple responses and thus build up latent-variable models.

Last updated 3 years ago

1.60 score 10 scripts 180 downloads

Kurt - Performs Kurtosis-Based Statistical Analyses

Computes measures of multivariate kurtosis, matrices of fourth-order moments and cumulants, kurtosis-based projection pursuit. Franceschini, C. and Loperfido, N. (2018, ISBN:978-3-319-73905-2). "An Algorithm for Finding Projections with Extreme Kurtosis". Loperfido, N. (2017,ISSN:0024-3795). "A New Kurtosis Matrix, with Statistical Applications".

Last updated 3 years ago

1.60 score 147 downloads

STB - Simultaneous Tolerance Bounds

Provides an implementation of simultaneous tolerance bounds (STB), useful for checking whether a numeric vector fits to a hypothetical null-distribution or not. Furthermore, there are functions for computing STB (bands, intervals) for random variates of linear mixed models fitted with package 'VCA'. All kinds of, possibly transformed (studentized, standardized, Pearson-type transformed) random variates (residuals, random effects), can be assessed employing STB-methodology.

Last updated 3 years ago

openmp

1.60 score 22 scripts 211 downloads

PQLseq - Efficient Mixed Model Analysis of Count Data in Large-Scale Genomic Sequencing Studies

An efficient tool designed for differential analysis of large-scale RNA sequencing (RNAseq) data and Bisulfite sequencing (BSseq) data in the presence of individual relatedness and population structure. 'PQLseq' first fits a Generalized Linear Mixed Model (GLMM) with adjusted covariates, predictor of interest and random effects to account for population structure and individual relatedness, and then performs Wald tests for each gene in RNAseq or site in BSseq.

Last updated 4 years ago

openblascppopenmp

1.60 score 5 scripts 177 downloads

USP - U-Statistic Permutation Tests of Independence for all Data Types

Implements various independence tests for discrete, continuous, and infinite-dimensional data. The tests are based on a U-statistic permutation test, the USP of Berrett, Kontoyiannis and Samworth (2020) <arXiv:2001.05513>, and shown to be minimax rate optimal in a wide range of settings. As the permutation principle is used, all tests have exact, non-asymptotic Type I error control at the nominal level.

Last updated 4 years ago

1.60 score 1 scripts 136 downloads

wmwpow - Precise and Accurate Power of the Wilcoxon-Mann-Whitney Rank-Sum Test for a Continuous Variable

Power calculator for the two-sample Wilcoxon-Mann-Whitney rank-sum test for a continuous outcome (Mollan, Trumble, Reifeis et. al., Mar. 2020) <doi:10.1080/10543406.2020.1730866> <arXiv:1901.04597>, (Mann and Whitney 1947) <doi:10.1214/aoms/1177730491>, (Shieh, Jan, and Randles 2006) <doi:10.1080/10485250500473099>.

Last updated 4 years ago

1.60 score 9 scripts 203 downloads

OptimalDesign - A Toolbox for Computing Efficient Designs of Experiments

Algorithms for D-, A-, I-, and c-optimal designs. Some of the functions in this package require the 'gurobi' software and its accompanying R package. For their installation, please follow the instructions at <https://www.gurobi.com> and the file gurobi_inst.txt, respectively.

Last updated 5 years ago

1.60 score 20 scripts 175 downloads

BNPTSclust - A Bayesian Nonparametric Algorithm for Time Series Clustering

Performs the algorithm for time series clustering described in Nieto-Barajas and Contreras-Cristan (2014).

Last updated 5 years ago

1.60 score 4 stars 9 scripts 230 downloads

xsp - The Chi-Square Periodogram

The circadian period of a time series data is predicted and the statistical significance of the periodicity are calculated using the chi-square periodogram.

Last updated 8 years ago

1.60 score 2 scripts 158 downloads

lrmest - Different Types of Estimators to Deal with Multicollinearity

When multicollinearity exists among predictor variables of the linear model, least square estimators does not provide a better solution for estimating parameters. To deal with multicollinearity several estimators are proposed in the literature. Some of these estimators are Ordinary Least Square Estimator (OLSE), Ordinary Generalized Ordinary Least Square Estimator (OGOLSE), Ordinary Ridge Regression Estimator (ORRE), Ordinary Generalized Ridge Regression Estimator (OGRRE), Restricted Least Square Estimator (RLSE), Ordinary Generalized Restricted Least Square Estimator (OGRLSE), Ordinary Mixed Regression Estimator (OMRE), Ordinary Generalized Mixed Regression Estimator (OGMRE), Liu Estimator (LE), Ordinary Generalized Liu Estimator (OGLE), Restricted Liu Estimator (RLE), Ordinary Generalized Restricted Liu Estimator (OGRLE), Stochastic Restricted Liu Estimator (SRLE), Ordinary Generalized Stochastic Restricted Liu Estimator (OGSRLE), Type (1),(2),(3) Liu Estimator (Type-1,2,3 LTE), Ordinary Generalized Type (1),(2),(3) Liu Estimator (Type-1,2,3 OGLTE), Type (1),(2),(3) Adjusted Liu Estimator (Type-1,2,3 ALTE), Ordinary Generalized Type (1),(2),(3) Adjusted Liu Estimator (Type-1,2,3 OGALTE), Almost Unbiased Ridge Estimator (AURE), Ordinary Generalized Almost Unbiased Ridge Estimator (OGAURE), Almost Unbiased Liu Estimator (AULE), Ordinary Generalized Almost Unbiased Liu Estimator (OGAULE), Stochastic Restricted Ridge Estimator (SRRE), Ordinary Generalized Stochastic Restricted Ridge Estimator (OGSRRE), Restricted Ridge Regression Estimator (RRRE) and Ordinary Generalized Restricted Ridge Regression Estimator (OGRRRE). To select the best estimator in a practical situation the Mean Square Error (MSE) is used. Using this package scalar MSE value of all the above estimators and Prediction Sum of Square (PRESS) values of some of the estimators can be obtained, and the variation of the MSE and PRESS values for the relevant estimators can be shown graphically.

Last updated 9 years ago

1.60 score 40 scripts 177 downloads

ZRA - Dynamic Plots for Time Series Forecasting

Combines a forecast of a time series, using the function forecast(), with the dynamic plots from dygraphs.

Last updated 9 years ago

1.60 score 4 scripts 186 downloads

BenfordTests - Statistical Tests for Evaluating Conformity to Benford's Law

Several specialized statistical tests and support functions for determining if numerical data could conform to Benford's law.

Last updated 9 years ago

1.60 score 40 scripts 468 downloads

RSpincalc - Conversion Between Attitude Representations of DCM, Euler Angles, Quaternions, and Euler Vectors

Conversion between attitude representations: DCM, Euler angles, Quaternions, and Euler vectors. Plus conversion between 2 Euler angle set types (xyx, yzy, zxz, xzx, yxy, zyz, xyz, yzx, zxy, xzy, yxz, zyx). Fully vectorized code, with warnings/errors for Euler angles (singularity, out of range, invalid angle order), DCM (orthogonality, not proper, exceeded tolerance to unity determinant) and Euler vectors(not unity). Also quaternion and other useful functions. Based on SpinCalc by John Fuller and SpinConv by Paolo de Leva.

Last updated 9 years ago

1.60 score 40 scripts 120 downloads

Records - Record Values and Record Times

Functions for generating k-record values and k-record times

Last updated 14 years ago

1.60 score 4 scripts 112 downloads

CreditRisk - Evaluation of Credit Risk with Structural and Reduced Form Models

Evaluation of default probability of sovereign and corporate entities based on structural or intensity based models and calibration on market Credit Default Swap quotes. References: Damiano Brigo, Massimo Morini, Andrea Pallavicini (2013) <doi:10.1002/9781118818589>. Print ISBN: 9780470748466, Online ISBN: 9781118818589. © 2013 John Wiley & Sons Ltd.

Last updated 8 months ago

1.59 score 3 stars 13 scripts 190 downloads

lira - LInear Regression in Astronomy

Performs Bayesian linear regression and forecasting in astronomy. The method accounts for heteroscedastic errors in both the independent and the dependent variables, intrinsic scatters (in both variables) and scatter correlation, time evolution of slopes, normalization, scatters, Malmquist and Eddington bias, upper limits and break of linearity. The posterior distribution of the regression parameters is sampled with a Gibbs method exploiting the JAGS library.

Last updated 7 years ago

jagscpp

1.59 score 39 scripts 208 downloads

BurStFin - Burns Statistics Financial

A suite of functions for finance, including the estimation of variance matrices via a statistical factor model or Ledoit-Wolf shrinkage.

Last updated 3 years ago

1.58 score 2 stars 19 scripts 264 downloads

sensitivitymw - Sensitivity Analysis for Observational Studies Using Weighted M-Statistics

Sensitivity analysis for tests, confidence intervals and estimates in matched observational studies with one or more controls using weighted or unweighted Huber-Maritz M-tests (including the permutational t-test). The method is from Rosenbaum (2014) Weighted M-statistics with superior design sensitivity in matched observational studies with multiple controls JASA, 109(507), 1145-1158 <doi:10.1080/01621459.2013.879261>.

Last updated 3 years ago

1.58 score 1 stars 38 scripts 323 downloads

nsROC - Non-Standard ROC Curve Analysis

Tools for estimating Receiver Operating Characteristic (ROC) curves, building confidence bands, comparing several curves both for dependent and independent data, estimating the cumulative-dynamic ROC curve in presence of censored data, and performing meta-analysis studies, among others.

Last updated 6 years ago

1.58 score 1 stars 19 scripts 256 downloads

sudoku - Sudoku Puzzle Generator and Solver

Generates, plays, and solves Sudoku puzzles. The GUI playSudoku() needs package "tkrplot" if you are not on Windows.

Last updated 3 years ago

1.57 score 37 scripts 296 downloads

sidier - Substitution and Indel Distances to Infer Evolutionary Relationships

Evolutionary reconstruction based on substitutions and insertion-deletion (indels) analyses in a distance-based framework.

Last updated 4 years ago

1.57 score 37 scripts 198 downloads

ppcc - Probability Plot Correlation Coefficient Test

Calculates the Probability Plot Correlation Coefficient (PPCC) between a continuous variable X and a specified distribution. The corresponding composite hypothesis test that was first introduced by Filliben (1975) <doi: 10.1080/00401706.1975.10489279> can be performed to test whether the sample X is element of either the Normal, log-Normal, Exponential, Uniform, Cauchy, Logistic, Generalized Logistic, Gumbel (GEVI), Weibull, Generalized Extreme Value, Pearson III (Gamma 2), Mielke's Kappa, Rayleigh or Generalized Logistic Distribution. The PPCC test is performed with a fast Monte-Carlo simulation.

Last updated 5 years ago

1.57 score 37 scripts 181 downloads

CompR - Paired Comparison Data Analysis

Different tools for describing and analysing paired comparison data are presented. Main methods are estimation of products scores according Bradley Terry Luce model. A segmentation of the individual could be conducted on the basis of a mixture distribution approach. The number of classes can be tested by the use of Monte Carlo simulations. This package deals also with multi-criteria paired comparison data.

Last updated 9 years ago

1.57 score 37 scripts 449 downloads

bqtl - Bayesian QTL Mapping Toolkit

QTL mapping toolkit for inbred crosses and recombinant inbred lines. Includes maximum likelihood and Bayesian tools.

Last updated 3 months ago

fortranopenblas

1.56 score 18 scripts 842 downloads

groupTesting - Simulating and Modeling Group (Pooled) Testing Data

Provides an expectation-maximization (EM) algorithm using the approach introduced in Warasi (2023) <doi:10.1080/03610918.2021.2009867>. The EM algorithm can be used to estimate the prevalence (overall proportion) of a disease and to estimate a binary regression model from among the class of generalized linear models based on group testing data. The estimation framework we consider offers a flexible and general approach; i.e., its application is not limited to any specific group testing protocol. Consequently, the EM algorithm can model data arising from simple pooling as well as advanced pooling such as hierarchical testing, array testing, and quality control pooling. Also, provided are functions that can be used to conduct the Wald tests described in Buse (1982) <doi:10.1080/00031305.1982.10482817> and to simulate the group testing data described in Kim et al. (2007) <doi:10.1111/j.1541-0420.2007.00817.x>. We offer a function to compute relative efficiency measures, which can be used to optimize the maximum likelihood estimator of disease prevalence.

Last updated 4 months ago

1.56 score 18 scripts 255 downloads

PTAk - Principal Tensor Analysis on k Modes

A multiway method to decompose a tensor (array) of any order, as a generalisation of SVD also supporting non-identity metrics and penalisations. 2-way SVD with these extensions is also available. The package includes also some other multiway methods: PCAn (Tucker-n) and PARAFAC/CANDECOMP with these extensions.

Last updated 2 years ago

1.56 score 1 stars 18 scripts 578 downloads

PDSCE - Positive Definite Sparse Covariance Estimators

Compute and tune some positive definite and sparse covariance estimators.

Last updated 3 years ago

1.56 score 1 stars 1 dependents 12 scripts 241 downloads

ssize.fdr - Sample Size Calculations for Microarray Experiments

Functions that calculate appropriate sample sizes for one-sample t-tests, two-sample t-tests, and F-tests for microarray experiments based on desired power while controlling for false discovery rates. For all tests, the standard deviations (variances) among genes can be assumed fixed or random. This is also true for effect sizes among genes in one-sample and two sample experiments. Functions also output a chart of power versus sample size, a table of power at different sample sizes, and a table of critical test values at different sample sizes.

Last updated 3 years ago

1.56 score 1 stars 1 dependents 12 scripts 284 downloads

SLBDD - Statistical Learning for Big Dependent Data

Programs for analyzing large-scale time series data. They include functions for automatic specification and estimation of univariate time series, for clustering time series, for multivariate outlier detections, for quantile plotting of many time series, for dynamic factor models and for creating input data for deep learning programs. Examples of using the package can be found in the Wiley book 'Statistical Learning with Big Dependent Data' by Daniel Peña and Ruey S. Tsay (2021). ISBN 9781119417385.

Last updated 3 years ago

1.56 score 1 dependents 12 scripts 271 downloads

demu - Optimal Design Emulators via Point Processes

Implements the Determinantal point process (DPP) based optimal design emulator described in Pratola, Lin and Craigmile (2018) <arXiv:1804.02089> for Gaussian process regression models. See <http://www.matthewpratola.com/software> for more information and examples.

Last updated 5 years ago

openblascppopenmp

1.56 score 36 scripts 155 downloads

Phase123 - Simulating and Conducting Phase 123 Trials

Contains three simulation functions for implementing the entire Phase 123 trial and the separate Eff-Tox and Phase 3 portions of the trial, which may be beneficial for use on clusters. The functions AssignEffTox() and RandomizeEffTox() assign doses to patient cohorts during phase 12 and Reoptimize() determines the optimal dose to continue with during Phase 3. The functions ReturnMeansAgent() and ReturnMeanControl() gives the true mean survival for the agent doses and control and ReturnOCS() gives the operating characteristics of the design.

Last updated 6 years ago

1.56 score 1 stars 1 dependents 12 scripts 183 downloads

comato - Analysis of Concept Maps and Concept Landscapes

Provides methods for the import/export and automated analysis of concept maps and concept landscapes (sets of concept maps).

Last updated 7 years ago

1.56 score 36 scripts 161 downloads

subspace - Interface to OpenSubspace

An interface to 'OpenSubspace', an open source framework for evaluation and exploration of subspace clustering algorithms in WEKA (see <http://dme.rwth-aachen.de/de/opensubspace> for more information). Also performs visualization.

Last updated 9 years ago

openjdk

1.56 score 1 dependents 12 scripts 223 downloads

conjoint - An Implementation of Conjoint Analysis Method

This is a simple R package that allows to measure the stated preferences using traditional conjoint analysis method.

Last updated 6 years ago

1.56 score 1 stars 87 scripts 1.8k downloads

astroFns - Astronomy: Time and Position Functions, Misc. Utilities

Miscellaneous astronomy functions, utilities, and data.

Last updated 3 years ago

1.54 score 35 scripts 314 downloads

SpaCCI - Spatially Aware Cell-Cell Interaction Analysis

Provides tools for analyzing spatial cell-cell interactions based on ligand-receptor pairs, including functions for local, regional, and global analysis using spatial transcriptomics data. Integrates with databases like 'CellChat' <http://www.cellchat.org/>, 'CellPhoneDB' <https://www.cellphonedb.org/>, 'Cellinker' <https://www.rna-society.org/cellinker/>, 'ICELLNET' <https://github.com/soumelis-lab/ICELLNET>, and 'ConnectomeDB' <https://humanconnectome.org/software/connectomedb/> to identify ligand-receptor pairs, visualize interactions through heatmaps, chord diagrams, and infer interactions on different spatial scales.

Last updated 2 months ago

openblascpp

1.53 score 17 scripts 463 downloads

DCL - Claims Reserving under the Double Chain Ladder Model

Statistical modelling and forecasting in claims reserving in non-life insurance under the Double Chain Ladder framework by Martinez-Miranda, Nielsen and Verrall (2012).

Last updated 3 years ago

1.53 score 1 stars 34 scripts 190 downloads

npordtests - Nonparametric Tests for Equality of Location Against Ordered Alternatives

Performs nonparametric tests for equality of location against ordered alternatives.

Last updated 5 years ago

1.53 score 34 scripts 141 downloads

OBsMD - Objective Bayesian Model Discrimination in Follow-Up Designs

Implements the objective Bayesian methodology proposed in Consonni and Deldossi in order to choose the optimal experiment that better discriminate between competing models, see Deldossi and Nai Ruscone (2020) <doi:10.18637/jss.v094.i02>.

Last updated 4 months ago

fortran

1.52 score 33 scripts 303 downloads

reddPrec - Reconstruction of Daily Data - Precipitation

Applies quality control to daily precipitation observations; reconstructs the original series by estimating precipitation in missing values; and creates gridded datasets of daily precipitation.

Last updated 8 months ago

1.52 score 11 scripts 213 downloads

pkr - Pharmacokinetics in R

Conduct a noncompartmental analysis as closely as possible to the most widely used commercial software. Some features are 1) CDISC SDTM terms 2) Automatic slope selection with the same criterion of WinNonlin(R) 3) Supporting both 'linear-up linear-down' and 'linear-up log-down' method 4) Interval(partial) AUCs with 'linear' or 'log' interpolation method * Reference: Gabrielsson J, Weiner D. Pharmacokinetic and Pharmacodynamic Data Analysis - Concepts and Applications. 5th ed. 2016. (ISBN:9198299107).

Last updated 3 years ago

1.52 score 33 scripts 233 downloads

CDFt - Downscaling and Bias Correction via Non-Parametric CDF-Transform

Statistical downscaling and bias correction (model output statistics) method based on cumulative distribution functions (CDF) transformation. See Michelangeli, Vrac, Loukos (2009) Probabilistic downscaling approaches: Application to wind cumulative distribution functions. Geophysical Research Letters, 36, L11708, <doi:10.1029/2009GL038401>. ; and Vrac, Drobinski, Merlo, Herrmann, Lavaysse, Li, Somot (2012) Dynamical and statistical downscaling of the French Mediterranean climate: uncertainty assessment. Nat. Hazards Earth Syst. Sci., 12, 2769-2784, www.nat-hazards-earth-syst-sci.net/12/2769/2012/, <doi:10.5194/nhess-12-2769-2012>.

Last updated 4 years ago

1.52 score 1 dependents 11 scripts 275 downloads

LCAextend - Latent Class Analysis (LCA) with Familial Dependence in Extended Pedigrees

Latent Class Analysis of phenotypic measurements in pedigrees and model selection based on one of two methods: likelihood-based cross-validation and Bayesian Information Criterion. Computation of individual and triplet child-parents weights in a pedigree is performed using an upward-downward algorithm. The model takes into account the familial dependence defined by the pedigree structure by considering that a class of a child depends on his parents classes via triplet-transition probabilities of the classes. The package handles the case where measurements are available on all subjects and the case where measurements are available only on symptomatic (i.e. affected) subjects. Distributions for discrete (or ordinal) and continuous data are currently implemented. The package can deal with missing data.

Last updated 6 years ago

1.52 score 33 scripts 124 downloads

QCApro - Advanced Functionality for Performing and Evaluating Qualitative Comparative Analysis

Provides advanced functionality for performing configurational comparative research with Qualitative Comparative Analysis (QCA), including crisp-set, multi-value, and fuzzy-set QCA. It also offers advanced tools for sensitivity diagnostics and methodological evaluations of QCA.

Last updated 7 years ago

1.52 score 1 stars 33 scripts 394 downloads

complexplus - Functions of Complex or Real Variable

Extension of several functions to the complex domain, including the matrix exponential and logarithm, and the determinant.

Last updated 8 years ago

1.52 score 1 dependents 11 scripts 229 downloads

ljr - Logistic Joinpoint Regression

Fits and tests logistic joinpoint models.

Last updated 9 years ago

openblas

1.52 score 1 stars 11 scripts 205 downloads

maq - Multi-Armed Qini

Policy evaluation using generalized Qini curves: Evaluate data-driven treatment targeting rules for one or more treatment arms over different budget constraints in experimental or observational settings under unconfoundedness.

Last updated 1 months ago

cpp

1.51 score 16 scripts 366 downloads

selectiongain - A Tool for Calculation and Optimization of the Expected Gain from Multi-Stage Selection

Multi-stage selection is practiced in numerous fields of life and social sciences and particularly in breeding. A special characteristic of multi-stage selection is that candidates are evaluated in successive stages with increasing intensity and effort, and only a fraction of the superior candidates is selected and promoted to the next stage. For the optimum design of such selection programs, the selection gain plays a crucial role. It can be calculated by integration of a truncated multivariate normal (MVN) distribution. While mathematical formulas for calculating the selection gain and the variance among selected candidates were developed long time ago, solutions for numerical calculation were not available. This package can also be used for optimizing multi-stage selection programs for a given total budget and different costs of evaluating the candidates in each stage.

Last updated 2 years ago

1.51 score 2 stars 16 scripts 336 downloads

NetCluster - Clustering for networks

Facilitates network clustering and evaluation of cluster configurations.

Last updated 15 years ago

1.51 score 2 stars 16 scripts 135 downloads

bigtabulate - Table, Apply, and Split Functionality for Matrix and 'big.matrix' Objects

Extend the bigmemory package with 'table', 'tapply', and 'split' support for 'big.matrix' objects. The functions may also be used with native R matrices for improving speed and memory-efficiency.

Last updated 3 years ago

cpp

1.49 score 31 scripts 429 downloads

ebmc - Ensemble-Based Methods for Class Imbalance Problem

Four ensemble-based methods (SMOTEBoost, RUSBoost, UnderBagging, and SMOTEBagging) for class imbalance problem are implemented for binary classification. Such methods adopt ensemble methods and data re-sampling techniques to improve model performance in presence of class imbalance problem. One special feature offers the possibility to choose multiple supervised learning algorithms to build weak learners within ensemble models. References: Nitesh V. Chawla, Aleksandar Lazarevic, Lawrence O. Hall, and Kevin W. Bowyer (2003) <doi:10.1007/978-3-540-39804-2_12>, Chris Seiffert, Taghi M. Khoshgoftaar, Jason Van Hulse, and Amri Napolitano (2010) <doi:10.1109/TSMCA.2009.2029559>, R. Barandela, J. S. Sanchez, R. M. Valdovinos (2003) <doi:10.1007/s10044-003-0192-z>, Shuo Wang and Xin Yao (2009) <doi:10.1109/CIDM.2009.4938667>, Yoav Freund and Robert E. Schapire (1997) <doi:10.1006/jcss.1997.1504>.

Last updated 3 years ago

1.49 score 31 scripts 140 downloads

mpr - Multi-Parameter Regression (MPR)

Fitting Multi-Parameter Regression (MPR) models to right-censored survival data. These are flexible parametric regression models which extend standard models, for example, proportional hazards. See Burke & MacKenzie (2016) <doi:10.1111/biom.12625> and Burke et al (2020) <doi:10.1111/rssc.12398>.

Last updated 3 years ago

1.49 score 31 scripts 136 downloads

rem - Relational Event Models (REM)

Calculate endogenous network effects in event sequences and fit relational event models (REM): Using network event sequences (where each tie between a sender and a target in a network is time-stamped), REMs can measure how networks form and evolve over time. Endogenous patterns such as popularity effects, inertia, similarities, cycles or triads can be calculated and analyzed over time.

Last updated 6 years ago

cpp

1.49 score 31 scripts 207 downloads

noncompliance - Causal Inference in the Presence of Treatment Noncompliance Under the Binary Instrumental Variable Model

A finite-population significance test of the 'sharp' causal null hypothesis that treatment exposure X has no effect on final outcome Y, within the principal stratum of Compliers. A generalized likelihood ratio test statistic is used, and the resulting p-value is exact. Currently, it is assumed that there are only Compliers and Never Takers in the population.

Last updated 9 years ago

1.49 score 31 scripts 180 downloads

FamEvent - Family Age-at-Onset Data Simulation and Penetrance Estimation

Simulates age-at-onset traits associated with a segregating major gene in family data obtained from population-based, clinic-based, or multi-stage designs. Appropriate ascertainment correction is utilized to estimate age-dependent penetrance functions either parametrically from the fitted model or nonparametrically from the data. The Expectation and Maximization algorithm can infer missing genotypes and carrier probabilities estimated from family's genotype and phenotype information or from a fitted model. Plot functions include pedigrees of simulated families and predicted penetrance curves based on specified parameter values. For more information see Choi, Y.-H., Briollais, L., He, W. and Kopciuk, K. (2021) FamEvent: An R Package for Generating and Modeling Time-to-Event Data in Family Designs, Journal of Statistical Software 97 (7), 1-30.

Last updated 6 months ago

1.48 score 15 scripts 292 downloads

sgr - Sample Generation by Replacement

Sample Generation by Replacement simulations (SGR; Lombardi & Pastore, 2014; Pastore & Lombardi, 2014). The package can be used to perform fake data analysis according to the sample generation by replacement approach. It includes functions for making simple inferences about discrete/ordinal fake data. The package allows to study the implications of fake data for empirical results.

Last updated 3 years ago

1.48 score 15 scripts 227 downloads

BCRA - Breast Cancer Risk Assessment

Functions provide risk projections of invasive breast cancer based on Gail model according to National Cancer Institute's Breast Cancer Risk Assessment Tool algorithm for specified race/ethnic groups and age intervals. Gail MH, Brinton LA, et al (1989) <doi:10.1093/jnci/81.24.1879>. Marthew PB, Gail MH, et al (2016) <doi:10.1093/jnci/djw215>.

Last updated 4 years ago

1.48 score 1 stars 15 scripts 293 downloads

CoImp - Parametric and Non-Parametric Copula-Based Imputation Methods

Copula-based imputation methods: parametric and non-parametric algorithms for missing multivariate data through conditional copulas.

Last updated 4 days ago

1.48 score 1 stars 8 scripts 266 downloads

HQM - Superefficient Estimation of Future Conditional Hazards Based on Marker Information

Provides a nonparametric smoothed kernel density estimator for the future conditional hazard when time-dependent covariates are present. It also provides pointwise and uniform confidence bands and a bandwidth selection.

Last updated 12 days ago

1.48 score 309 downloads

FPDclustering - PD-Clustering and Related Methods

Probabilistic distance clustering (PD-clustering) is an iterative, distribution-free, probabilistic clustering method. PD-clustering assigns units to a cluster according to their probability of membership under the constraint that the product of the probability and the distance of each point to any cluster center is a constant. PD-clustering is a flexible method that can be used with elliptical clusters, outliers, or noisy data. PDQ is an extension of the algorithm for clusters of different sizes. GPDC and TPDC use a dissimilarity measure based on densities. Factor PD-clustering (FPDC) is a factor clustering method that involves a linear transformation of variables and a cluster optimizing the PD-clustering criterion. It works on high-dimensional data sets.

Last updated 12 days ago

1.48 score 13 scripts 295 downloads

CICI - Causal Inference with Continuous (Multiple Time Point) Interventions

Estimation of counterfactual outcomes for multiple values of continuous interventions at different time points, and plotting of causal dose-response curves. Details are given in Schomaker, McIlleron, Denti, Diaz (2024) <doi:10.48550/arXiv.2305.06645>.

Last updated 14 days ago

1.48 score 1 stars 529 downloads

sts - Estimation of the Structural Topic and Sentiment-Discourse Model for Text Analysis

The Structural Topic and Sentiment-Discourse (STS) model allows researchers to estimate topic models with document-level metadata that determines both topic prevalence and sentiment-discourse. The sentiment-discourse is modeled as a document-level latent variable for each topic that modulates the word frequency within a topic. These latent topic sentiment-discourse variables are controlled by the document-level metadata. The STS model can be useful for regression analysis with text data in addition to topic modeling’s traditional use of descriptive analysis. The method was developed in Chen and Mankad (2024) <doi:10.1287/mnsc.2022.00261>.

Last updated 29 days ago

openblascpp

1.48 score 402 downloads

ordinalpattern - Tests Based on Ordinal Patterns

Ordinal patterns describe the dynamics of a time series by looking at the ranks of subsequent observations. By comparing ordinal patterns of two times series, Schnurr (2014) <doi:10.1007/s00362-013-0536-8> defines a robust and non-parametric dependence measure: the ordinal pattern coefficient. Functions to calculate this and a method to detect a change in the pattern coefficient proposed in Schnurr and Dehling (2017) <doi:10.1080/01621459.2016.1164706> are provided. Furthermore, the package contains a function for calculating the ordinal pattern frequencies. Generalized ordinal patterns as proposed by Schnurr and Fischer (2022) <doi:10.1016/j.csda.2022.107472> are also considered.

Last updated 1 months ago

1.48 score 382 downloads

MCARtest - Optimal Nonparametric Testing of Missing Completely at Random

Provides functions for carrying out nonparametric hypothesis tests of the MCAR hypothesis based on the theory of Frechet classes and compatibility. Also gives functions for computing halfspace representations of the marginal polytope and related geometric objects.

Last updated 2 months ago

1.48 score 1 scripts 205 downloads

sc2sc - Spatial Transfer of Statistics among Spanish Census Sections

Transfers/imputes statistics among Spanish spatial polygons (census sections or postal code areas) from different moments in time (2001-2023) without need of spatial files, just linking statistics to the ID codes of the spatial units. The data available in the census sections of a partition/division (cartography) into force in a moment of time is transferred to the census sections of another partition/division employing the geometric approach (also known as areal weighting or polygon overlay). References: Goerlich (2022) <doi:10.12842/WPIVIE_0322>. Pavía and Cantarino (2017a, b) <doi:10.1111/gean.12112>, <doi:10.1016/j.apgeog.2017.06.021>. Pérez and Pavía (2024a, b) <doi:10.4995/CARMA2024.2024.17796>, <doi:10.38191/iirr-jorr.24.057>. Acknowledgements: The authors wish to thank Consellería de Educación, Universidades y Empleo, Generalitat Valenciana (grant AICO/2021/257), Ministerio de Economía e Innovación (grant PID2021-128228NB-I00) and Fundación Mapfre for supporting this research.

Last updated 2 months ago

1.48 score 675 downloads

multilevLCA - Estimates and Plots Single-Level and Multilevel Latent Class Models

Efficiently estimates single- and multilevel latent class models with covariates, allowing for output visualization in all specifications. For more technical details, see Lyrvall et al (2023) <doi:10.48550/arXiv.2305.07276>.

Last updated 2 months ago

openblascpp

1.48 score 1 scripts 315 downloads

BayesianFactorZoo - Bayesian Solutions for the Factor Zoo: We Just Ran Two Quadrillion Models

Contains the functions to use the econometric methods in the paper Bryzgalova, Huang, and Julliard (2023) <doi:10.1111/jofi.13197>. In this package, we provide a novel Bayesian framework for analyzing linear asset pricing models: simple, robust, and applicable to high-dimensional problems. For a stand-alone model, we provide functions including BayesianFM() and BayesianSDF() to deliver reliable price of risk estimates for both tradable and nontradable factors. For competing factors and possibly nonnested models, we provide functions including continuous_ss_sdf(), continuous_ss_sdf_v2(), and dirac_ss_sdf_pvalue() to analyze high-dimensional models. If you use this package, please cite the paper. We are thankful to Yunan Ding and Jingtong Zhang for their research assistance. Any errors or omissions are the responsibility of the authors.

Last updated 3 months ago

1.48 score 3 stars 309 downloads

bayesreg - Bayesian Regression Models with Global-Local Shrinkage Priors

Fits linear or generalized linear regression models using Bayesian global-local shrinkage prior hierarchies as described in Polson and Scott (2010) <doi:10.1093/acprof:oso/9780199694587.003.0017>. Provides an efficient implementation of ridge, lasso, horseshoe and horseshoe+ regression with logistic, Gaussian, Laplace, Student-t, Poisson or geometric distributed targets using the algorithms summarized in Makalic and Schmidt (2016) <doi:10.48550/arXiv.1611.06649>.

Last updated 3 months ago

1.48 score 1 stars 1 dependents 8 scripts 575 downloads

diffcor - Fisher's z-Tests Concerning Differences Between Correlations

Computations of Fisher's z-tests concerning different kinds of correlation differences. The 'diffpwr' family entails approaches to estimating statistical power via Monte Carlo simulations. Important to note, the Pearson correlation coefficient is sensitive to linear association, but also to a host of statistical issues such as univariate and bivariate outliers, range restrictions, and heteroscedasticity (e.g., Duncan & Layard, 1973 <doi:10.1093/BIOMET/60.3.551>; Wilcox, 2013 <doi:10.1016/C2010-0-67044-1>). Thus, every power analysis requires that specific statistical prerequisites are fulfilled and can be invalid if the prerequisites do not hold. To this end, the 'bootcor' family provides bootstrapping confidence intervals for the incorporated correlation difference tests.

Last updated 3 months ago

1.48 score 1 scripts 332 downloads

geppe - Generalised Exponential Poisson and Poisson Exponential Distributions

Maximum likelihood estimation, random values generation, density computation and other functions for the exponential-Poisson generalised exponential-Poisson and Poisson-exponential distributions. References include: Rodrigues G. C., Louzada F. and Ramos P. L. (2018). "Poisson-exponential distribution: different methods of estimation". Journal of Applied Statistics, 45(1): 128--144. <doi:10.1080/02664763.2016.1268571>. Louzada F., Ramos, P. L. and Ferreira, H. P. (2020). "Exponential-Poisson distribution: estimation and applications to rainfall and aircraft data with zero occurrence". Communications in Statistics--Simulation and Computation, 49(4): 1024--1043. <doi:10.1080/03610918.2018.1491988>. Barreto-Souza W. and Cribari-Neto F. (2009). "A generalization of the exponential-Poisson distribution". Statistics and Probability Letters, 79(24): 2493--2500. <doi:10.1016/j.spl.2009.09.003>.

Last updated 6 months ago

1.48 score 1 dependents 518 downloads

SINRELEF.LD - Reliability and Relative Efficiency in Locally-Dependent Measures

Implements an approach aimed at assessing the accuracy and effectiveness of raw scores obtained in scales that contain locally dependent items. The program uses as input the calibration (structural) item estimates obtained from fitting extended unidimensional factor-analytic solutions in which the existing local dependencies are included. Measures of reliability (Omega) and information are proposed at three levels: (a) total score, (b) bivariate-doublet, and (c) item-by-item deletion, and are compared to those that would be obtained if all the items had been locally independent. All the implemented procedures can be obtained from: (a) linear factor-analytic solutions in which the item scores are treated as approximately continuous, and (b) non-linear solutions in which the item scores are treated as ordered-categorical. A detailed guide can be obtained at the following url.

Last updated 7 months ago

1.48 score 202 downloads

BayesMortalityPlus - Bayesian Mortality Modelling

Fit Bayesian graduation mortality using the Heligman-Pollard model, as seen in Heligman, L., & Pollard, J. H. (1980) <doi:10.1017/S0020268100040257> and Dellaportas, Petros, et al. (2001) <doi:10.1111/1467-985X.00202>, and dynamic linear model (Campagnoli, P., Petris, G., and Petrone, S. (2009) <doi:10.1007/b135794_2>). While Heligman-Pollard has parameters with a straightforward interpretation yielding some rich analysis, the dynamic linear model provides a very flexible adjustment of the mortality curves by controlling the discount factor value. Closing methods for both Heligman-Pollard and dynamic linear model were also implemented according to Dodd, Erengul, et al. (2018) <https://www.jstor.org/stable/48547511>. The Bayesian Lee-Carter model is also implemented to fit historical mortality tables time series to predict the mortality in the following years and to do improvement analysis, as seen in Lee, R. D., & Carter, L. R. (1992) <doi:10.1080/01621459.1992.10475265> and Pedroza, C. (2006) <doi:10.1093/biostatistics/kxj024>.

Last updated 7 months ago

1.48 score 1 scripts 647 downloads

cpop - Detection of Multiple Changes in Slope in Univariate Time-Series

Detects multiple changes in slope using the CPOP dynamic programming approach of Fearnhead, Maidstone, and Letchford (2019) <doi:10.1080/10618600.2018.1512868>. This method finds the best continuous piecewise linear fit to data under a criterion that measures fit to data using the residual sum of squares, but penalizes complexity based on an L0 penalty on changes in slope. Further information regarding the use of this package with detailed examples can be found in Fearnhead and Grose (2024) <doi:10.18637/jss.v109.i07>.

Last updated 7 months ago

cpp

1.48 score 30 scripts 648 downloads

MN - Matrix Normal Distribution

Density computation, random matrix generation and maximum likelihood estimation of the matrix normal distribution. References: Pocuca N., Gallaugher M. P., Clark K. M. & McNicholas P. D. (2019). Assessing and Visualizing Matrix Variate Normality. <doi:10.48550/arXiv.1910.02859> and the relevant wikipedia page.

Last updated 7 months ago

1.48 score 1 dependents 2 scripts 197 downloads

fsemipar - Estimation, Variable Selection and Prediction for Functional Semiparametric Models

Routines for the estimation or simultaneous estimation and variable selection in several functional semiparametric models with scalar responses are provided. These models include the functional single-index model, the semi-functional partial linear model, and the semi-functional partial linear single-index model. Additionally, the package offers algorithms for handling scalar covariates with linear effects that originate from the discretization of a curve. This functionality is applicable in the context of the linear model, the multi-functional partial linear model, and the multi-functional partial linear single-index model.

Last updated 7 months ago

1.48 score 2 scripts 175 downloads

RcmdrPlugin.DCCV - R Commander Plug-in for Dichotomous Choice Contingent Valuation

Adds menu items to the R Commander for parametric analysis of dichotomous choice contingent valuation (DCCV) data. CV is a question-based survey method to elicit individuals' preferences for goods and services. This package depends on functions regarding parametric DCCV analysis in the package DCchoice. See Carson and Hanemann (2005) <doi:10.1016/S1574-0099(05)02017-6> for DCCV.

Last updated 7 months ago

1.48 score 1 stars 2 scripts 867 downloads

RcmdrPlugin.BWS2 - R Commander Plug-in for Case 2 Best-Worst Scaling

Adds menu items for case 2 (profile case) best-worst scaling (BWS2) to the R Commander. BWS2 is a question-based survey method that constructs profiles (combinations of attribute levels) using an orthogonal array, asks respondents to select the best and worst levels in each profile, and measures preferences for attribute levels by analyzing the responses. For details, see Aizaki and Fogarty (2019) <doi:10.1016/j.jocm.2019.100171>.

Last updated 7 months ago

1.48 score 1 stars 2 scripts 778 downloads

RcmdrPlugin.BWS1 - R Commander Plug-in for Case 1 Best-Worst Scaling

Adds menu items to the R Commander for implementing case 1 (object case) best-worst scaling (BWS1) from designing choice sets to measuring preferences for items. BWS1 is a question-based survey method that constructs various combinations of items (choice sets) using the experimental designs, asks respondents to select the best and worst items in each choice set, and then measures preferences for the items by analyzing the responses. For details on BWS1, refer to Louviere et al. (2015) <doi:10.1017/CBO9781107337855>.

Last updated 7 months ago

1.48 score 1 stars 2 scripts 546 downloads

BayesPPDSurv - Bayesian Power Prior Design for Survival Data

Bayesian power/type I error calculation and model fitting using the power prior and the normalized power prior for proportional hazards models with piecewise constant hazard. The methodology and examples of applying the package are detailed in <doi:10.48550/arXiv.2404.05118>. The Bayesian clinical trial design methodology is described in Chen et al. (2011) <doi:10.1111/j.1541-0420.2011.01561.x>, and Psioda and Ibrahim (2019) <doi:10.1093/biostatistics/kxy009>. The proportional hazards model with piecewise constant hazard is detailed in Ibrahim et al. (2001) <doi:10.1007/978-1-4757-3447-8>.

Last updated 9 months ago

openblascppopenmp

1.48 score 230 downloads

biogeom - Biological Geometries

Is used to simulate and fit biological geometries. 'biogeom' incorporates several novel universal parametric equations that can generate the profiles of bird eggs, flowers, linear and lanceolate leaves, seeds, starfish, and tree-rings (Gielis (2003) <doi:10.3732/ajb.90.3.333>; Shi et al. (2020) <doi:10.3390/sym12040645>), three growth-rate curves representing the ontogenetic growth trajectories of animals and plants against time, and the axially symmetrical and integral forms of all these functions (Shi et al. (2017) <doi:10.1016/j.ecolmodel.2017.01.012>; Shi et al. (2021) <doi:10.3390/sym13081524>). The optimization method proposed by Nelder and Mead (1965) <doi:10.1093/comjnl/7.4.308> was used to estimate model parameters. 'biogeom' includes several real data sets of the boundary coordinates of natural shapes, including avian eggs, fruit, lanceolate and ovate leaves, tree rings, seeds, and sea stars,and can be potentially applied to other natural shapes. 'biogeom' can quantify the conspecific or interspecific similarity of natural outlines, and provides information with important ecological and evolutionary implications for the growth and form of living organisms. Please see Shi et al. (2022) <doi:10.1111/nyas.14862> for details.

Last updated 9 months ago

1.48 score 1 stars 1 scripts 318 downloads

bibliorefer - Generator of Main Scientific References

Generates a list, with a size defined by the user, containing the main scientific references and the frequency distribution of authors and journals in the list obtained. The database is a dataframe with academic production metadata made available by bibliographic collections such as Scopus, Web of Science, etc. The temporal evolution of scientific production on a given topic is presented and ordered lists of articles are constructed by number of citations and of authors and journals by level of productivity. Massimo Aria, Corrado Cuccurullo. (2017) <doi:10.1016/j.joi.2017.08.007>. Caibo Zhou, Wenyan Song. (2021) <doi:10.1016/j.jclepro.2021.126943>.

Last updated 10 months ago

1.48 score 1 stars 1 dependents 355 downloads

FatTailsR - Kiener Distributions and Fat Tails in Finance

Kiener distributions K1, K2, K3, K4 and K7 to characterize distributions with left and right, symmetric or asymmetric fat tails in market finance, neuroscience and other disciplines. Two algorithms to estimate with a high accuracy distribution parameters, quantiles, value-at-risk and expected shortfall. Include power hyperbolas and power hyperbolic functions.

Last updated 10 months ago

1.48 score 30 scripts 376 downloads

HTMLUtils - Facilitates Automated HTML Report Creation

Facilitates automated HTML report creation, in particular framed HTML pages and dynamically sortable tables.

Last updated 11 months ago

1.48 score 1 dependents 9 scripts 381 downloads

HDMFA - High-Dimensional Matrix Factor Analysis

High-dimensional matrix factor models have drawn much attention in view of the fact that observations are usually well structured to be an array such as in macroeconomics and finance. In addition, data often exhibit heavy-tails and thus it is also important to develop robust procedures. We aim to address this issue by replacing the least square loss with Huber loss function. We propose two algorithms to do robust factor analysis by considering the Huber loss. One is based on minimizing the Huber loss of the idiosyncratic error's Frobenius norm, which leads to a weighted iterative projection approach to compute and learn the parameters and thereby named as Robust-Matrix-Factor-Analysis (RMFA), see the details in He et al. (2023)<doi:10.1080/07350015.2023.2191676>. The other one is based on minimizing the element-wise Huber loss, which can be solved by an iterative Huber regression algorithm (IHR), see the details in He et al. (2023) <arXiv:2306.03317>. In this package, we also provide the algorithm for alpha-PCA by Chen & Fan (2021) <doi:10.1080/01621459.2021.1970569>, the Projected estimation (PE) method by Yu et al. (2022)<doi:10.1016/j.jeconom.2021.04.001>. In addition, the methods for determining the pair of factor numbers are also given.

Last updated 11 months ago

1.48 score 1 dependents 133 downloads

IPEC - Root Mean Square Curvature Calculation

Calculates the RMS intrinsic and parameter-effects curvatures of a nonlinear regression model. The curvatures are global measures of assessing whether a model/data set combination is close-to-linear or not. See Bates and Watts (1980) <doi:10.1002/9780470316757> and Ratkowsky and Reddy (2017) <doi:10.1093/aesa/saw098> for details.

Last updated 12 months ago

1.48 score 12 scripts 209 downloads

dixon - Nearest Neighbour Contingency Table Analysis

Function to test spatial segregation and association based in contingency table analysis of nearest neighbour counts following Dixon (2002) <doi:10.1080/11956860.2002.11682700>. Some 'Fortran' code has been included to the original dixon2002() function of the 'ecespa' package to improve speed.

Last updated 12 months ago

fortran

1.48 score 1 dependents 7 scripts 401 downloads

RBE3 - Estimation and Additional Tools for Quantile Generalized Beta Regression Model

Provide estimation and data generation tools for the quantile generalized beta regression model. For details, see Bourguignon, Gallardo and Saulo <arXiv:2110.04428> The package also provides tools to perform covariates selection.

Last updated 1 years ago

1.48 score 1 dependents 145 downloads

treebalance - Computation of Tree (Im)Balance Indices

The aim of the 'R' package 'treebalance' is to provide functions for the computation of a large variety of (im)balance indices for rooted trees. The package accompanies the book ''Tree balance indices: a comprehensive survey'' by M. Fischer, L. Herbst, S. Kersting, L. Kuehn and K. Wicke (2023) <ISBN: 978-3-031-39799-8>, <doi:10.1007/978-3-031-39800-1>, which gives a precise definition for the terms 'balance index' and 'imbalance index' (Chapter 4) and provides an overview of the terminology in this manual (Chapter 2). For further information on (im)balance indices, see also Fischer et al. (2021) <https://treebalance.wordpress.com>. Considering both established and new (im)balance indices, 'treebalance' provides (among others) functions for calculating the following 18 established indices and index families: the average leaf depth, the B1 and B2 index, the Colijn-Plazzotta rank, the normal, corrected, quadratic and equal weights Colless index, the family of Colless-like indices, the family of I-based indices, the Rogers J index, the Furnas rank, the rooted quartet index, the s-shape statistic, the Sackin index, the symmetry nodes index, the total cophenetic index and the variance of leaf depths. Additionally, we include 9 tree shape statistics that satisfy the definition of an (im)balance index but have not been thoroughly analyzed in terms of tree balance in the literature yet. These are: the total internal path length, the total path length, the average vertex depth, the maximum width, the modified maximum difference in widths, the maximum depth, the maximum width over maximum depth, the stairs1 and the stairs2 index. As input, most functions of 'treebalance' require a rooted (phylogenetic) tree in 'phylo' format (as introduced in 'ape' 1.9 in November 2006). 'phylo' is used to store (phylogenetic) trees with no vertices of out-degree one. For further information on the format we kindly refer the reader to E. Paradis (2012) <http://ape-package.ird.fr/misc/FormatTreeR_24Oct2012.pdf>.

Last updated 1 years ago

1.48 score 1 dependents 7 scripts 204 downloads

LINselect - Selection of Linear Estimators

Estimate the mean of a Gaussian vector, by choosing among a large collection of estimators, following the method developed by Y. Baraud, C. Giraud and S. Huet (2014) <doi:10.1214/13-AIHP539>. In particular it solves the problem of variable selection by choosing the best predictor among predictors emanating from different methods as lasso, elastic-net, adaptive lasso, pls, randomForest. Moreover, it can be applied for choosing the tuning parameter in a Gauss-lasso procedure.

Last updated 1 years ago

1.48 score 1 dependents 2 scripts 275 downloads

TPACData - Human Protein Atlas Data for Tissue-Adjusted Pathway Analysis of Cancer (TPAC)

Contains summary data on gene expression in normal human tissues from the Human Protein Atlas for use with the Tissue-Adjusted Pathway Analysis of cancer (TPAC) method. Frost, H. Robert (2023) "Tissue-adjusted pathway analysis of cancer (TPAC)" <doi:10.1101/2022.03.17.484779>.

Last updated 1 years ago

1.48 score 1 dependents 228 downloads

sgPLS - Sparse Group Partial Least Square Methods

Regularized version of partial least square approaches providing sparse, group, and sparse group versions of partial least square regression models (Liquet, B., Lafaye de Micheaux, P., Hejblum B., Thiebaut, R. (2016) <doi:10.1093/bioinformatics/btv535>). Version of PLS Discriminant analysis is also provided.

Last updated 1 years ago

1.48 score 1 stars 7 scripts 209 downloads

pycno - Pycnophylactic Interpolation

Given a SpatialPolygonsDataFrame and a set of populations for each polygon, compute a population density estimate based on Tobler's pycnophylactic interpolation algorithm. The result is a SpatialGridDataFrame. Methods are described in Tobler Waldo R. (1979) <doi:10.1080/01621459.1979.10481647>.

Last updated 1 years ago

1.48 score 3 stars 20 scripts 131 downloads

riskSimul - Risk Quantification for Stock Portfolios under the T-Copula Model

Implements efficient simulation procedures to estimate tail loss probabilities and conditional excess for a stock portfolio. The log-returns are assumed to follow a t-copula model with generalized hyperbolic or t marginals.

Last updated 1 years ago

1.48 score 3 stars 2 scripts 175 downloads

elitism - Equipment for Logarithmic and Linear Time Stepwise Multiple Hypothesis Testing

Recently many new p-value based multiple test procedures have been proposed, and these new methods are more powerful than the widely used Hochberg procedure. These procedures strongly control the familywise error rate (FWER). This is a comprehensive collection of p-value based FWER-control stepwise multiple test procedures, including six procedure families and thirty multiple test procedures. In this collection, the conservative Hochberg procedure, linear time Hommel procedures, asymptotic Rom procedure, Gou-Tamhane-Xi-Rom procedures, and Quick procedures are all developed in recent five years since 2014. The package name "elitism" is an acronym of "e"quipment for "l"ogarithmic and l"i"near "ti"me "s"tepwise "m"ultiple hypothesis testing. See Gou, J. (2022), "Quick multiple test procedures and p-value adjustments", Statistics in Biopharmaceutical Research 14(4), 636-650.

Last updated 1 years ago

1.48 score 1 dependents 7 scripts 161 downloads

go2bigq - Convert Large Numbers to Bigq Format

This function converts mfpr, numeric, or character strings representing numbers to bigq format without loss of precision.

Last updated 1 years ago

1.48 score 1 dependents 207 downloads

fitConic - Fit Data to Any Conic Section

Fit data to an ellipse, hyperbola, or parabola. Bootstrapping is available when needed. The conic curve can be rotated through an arbitrary angle and the fit will still succeed. Helper functions are provided to convert generator coefficients from one style to another, generate test data sets, rotate conic section parameters, and so on. References include Nikolai Chernov (2014) "Fitting ellipses, circles, and lines by least squares" <https://people.cas.uab.edu/~mosya/cl/>; A. W. Fitzgibbon, M. Pilu, R. B. Fisher (1999) "Direct Least Squares Fitting of Ellipses" IEEE Trans. PAMI, Vol. 21, pages 476-48; N. Chernov, Q. Huang, and H. Ma (2014) "Fitting quadratic curves to data points", British Journal of Mathematics & Computer Science, 4, 33-60; N. Chernov and H. Ma (2011) "Least squares fitting of quadratic curves and surfaces", Computer Vision, Editor S. R. Yoshida, Nova Science Publishers, pp. 285-302.

Last updated 1 years ago

1.48 score 1 dependents 4 scripts 259 downloads

PCGSE - Principal Component Gene Set Enrichment

Contains logic for computing the statistical association of variable groups, i.e., gene sets, with respect to the principal components of genomic data.

Last updated 1 years ago

1.48 score 1 scripts 140 downloads

BGFD - Bell-G and Complementary Bell-G Family of Distributions

Evaluates the probability density function, cumulative distribution function, quantile function, random numbers, survival function, hazard rate function, and maximum likelihood estimates for the following distributions: Bell exponential, Bell extended exponential, Bell Weibull, Bell extended Weibull, Bell-Fisk, Bell-Lomax, Bell Burr-XII, Bell Burr-X, complementary Bell exponential, complementary Bell extended exponential, complementary Bell Weibull, complementary Bell extended Weibull, complementary Bell-Fisk, complementary Bell-Lomax, complementary Bell Burr-XII and complementary Bell Burr-X distribution. Related work includes: a) Fayomi A., Tahir M. H., Algarni A., Imran M. and Jamal F. (2022). "A new useful exponential model with applications to quality control and actuarial data". Computational Intelligence and Neuroscience, 2022. <doi:10.1155/2022/2489998>. b) Alanzi, A. R., Imran M., Tahir M. H., Chesneau C., Jamal F. Shakoor S. and Sami, W. (2023). "Simulation analysis, properties and applications on a new Burr XII model based on the Bell-X functionalities". AIMS Mathematics, 8(3): 6970-7004. <doi:10.3934/math.2023352>. c) Algarni A. (2022). "Group Acceptance Sampling Plan Based on New Compounded Three-Parameter Weibull Model". Axioms, 11(9): 438. <doi:10.3390/axioms11090438>.

Last updated 2 years ago

1.48 score 1 dependents 342 downloads

relevent - Relational Event Models

Tools to fit and simulate realizations from relational event models.

Last updated 2 years ago

1.48 score 1 stars 1 dependents 33 scripts 411 downloads

bcfrailph - Semiparametric Bivariate Correlated Frailty Models Fit

Fit and simulate a semiparametric bivariate correlated frailty models with proportional hazard structure. Frailty distributions, such as gamma and lognormal models are supported. Bivariate gamma fit is obtained using the approach given in Iachine (1995) and lognormal fit is based on the approach by Ripatti and Palmgren (2000) <doi:10.1111/j.0006-341X.2000.01016.x>.

Last updated 2 years ago

1.48 score 1 dependents 705 downloads

shrinkDSM - Efficient Bayesian Inference for Dynamic Survival Models with Shrinkage

Efficient Markov chain Monte Carlo (MCMC) algorithms for fully Bayesian estimation of dynamic survival models with shrinkage priors. Details on the algorithms used are provided in Wagner (2011) <doi:10.1007/s11222-009-9164-5>, Bitto and Frühwirth-Schnatter (2019) <doi:10.1016/j.jeconom.2018.11.006> and Cadonna et al. (2020) <doi:10.3390/econometrics8020020>.

Last updated 2 years ago

openblascpp

1.48 score 3 stars 2 scripts 158 downloads

manifold - Operations for Riemannian Manifolds

Implements operations for Riemannian manifolds, e.g., geodesic distance, Riemannian metric, exponential and logarithm maps, etc. Also incorporates random object generator on the manifolds. See Dai, Lin, and Müller (2021) <doi:10.1111/biom.13385>.

Last updated 2 years ago

openblascpp

1.48 score 1 stars 1 dependents 4 scripts 166 downloads

dixonTest - Dixon's Ratio Test for Outlier Detection

For outlier detection in small and normally distributed samples the ratio test of Dixon (Q-test) can be used. Density, distribution function, quantile function and random generation for Dixon's ratio statistics are provided as wrapper functions. The core applies McBane's Fortran functions <doi:10.18637/jss.v016.i03> that use Gaussian quadrature for a numerical solution.

Last updated 2 years ago

fortran

1.48 score 1 dependents 3 scripts 299 downloads

nilde - Nonnegative Integer Solutions of Linear Diophantine Equations with Applications

Routines for enumerating all existing nonnegative integer solutions of a linear Diophantine equation. The package provides routines for solving 0-1, bounded and unbounded knapsack problems; 0-1, bounded and unbounded subset sum problems; additive partitioning of natural numbers; and one-dimensional bin-packing problem.

Last updated 2 years ago

1.48 score 1 dependents 8 scripts 207 downloads

crops - Changepoints for a Range of Penalties (CROPS)

Implements the Changepoints for a Range of Penalties (CROPS) algorithm of Haynes et al. (2017) <doi:10.1080/10618600.2015.1116445> for finding all of the optimal segmentations for multiple penalty values over a continuous range.

Last updated 2 years ago

1.48 score 1 dependents 2 scripts 231 downloads

RockFab - Rock Fabric and Strain Analysis Tools

Provides functions to complete three-dimensional rock fabric and strain analyses following the Rf Phi, Fry, and normalized Fry methods. Also allows for plotting of results and interactive 3D visualization functionality.

Last updated 3 years ago

1.48 score 1 dependents 184 downloads

ProbYX - Inference for the Stress-Strength Model R = P(Y<X)

Confidence intervals and point estimation for R under various parametric model assumptions; likelihood inference based on classical first-order approximations and higher-order asymptotic procedures.

Last updated 3 years ago

1.48 score 1 dependents 8 scripts 230 downloads

pmledecon - Deconvolution Density Estimation using Penalized MLE

Given a sample with additive measurement error, the package estimates the deconvolution density - that is, the density of the underlying distribution of the sample without measurement error. The method maximises the log-likelihood of the estimated density, plus a quadratic smoothness penalty. The distribution of the measurement error can be either a known family, or can be estimated from a "pure error" sample. For known error distributions, the package supports Normal, Laplace or Beta distributed error. For unknown error distribution, a pure error sample independent from the data is used.

Last updated 3 years ago

1.48 score 1 dependents 152 downloads

UWHAM - Unbinned Weighted Histogram Analysis Method (UWHAM)

A method for estimating log-normalizing constants (or free energies) and expectations from multiple distributions (such as multiple generalized ensembles).

Last updated 3 years ago

1.48 score 4 scripts 173 downloads

eegkitdata - Electroencephalography Toolkit Datasets

Contains the example EEG data used in the package eegkit. Also contains code for easily creating larger EEG datasets from the EEG Database on the UCI Machine Learning Repository.

Last updated 3 years ago

1.48 score 1 dependents 9 scripts 317 downloads

clordr - Composite Likelihood Inference and Diagnostics for Replicated Spatial Ordinal Data

Composite likelihood parameter estimate and asymptotic covariance matrix are calculated for the spatial ordinal data with replications, where spatial ordinal response with covariate and both spatial exponential covariance within subject and independent and identically distributed measurement error. Parameter estimation can be performed by either solving the gradient function or maximizing composite log-likelihood. Parametric bootstrapping is used to estimate the Godambe information matrix and hence the asymptotic standard error and covariance matrix with parallel processing option. Moreover, the proposed surrogate residual, which extends the results of Liu and Zhang (2017) <doi: 10.1080/01621459.2017.1292915>, can act as a useful tool for model diagnostics.

Last updated 3 years ago

1.48 score 1 dependents 6 scripts 225 downloads

matpow - Matrix Powers

A general framework for computing powers of matrices. A key feature is the capability for users to write callback functions, called after each iteration, thus enabling customization for specific applications. Diverse types of matrix classes/matrix multiplication are accommodated. If the multiplication type computes in parallel, then the package computation is also parallel.

Last updated 3 years ago

1.48 score 1 dependents 8 scripts 210 downloads

Copula.Markov - Copula-Based Estimation and Statistical Process Control for Serially Correlated Time Series

Estimation and statistical process control are performed under copula-based time-series models. Available are statistical methods in Long and Emura (2014 JCSA), Emura et al. (2017 Commun Stat-Simul) <DOI:10.1080/03610918.2015.1073303>, Huang and Emura (2021 Commun Stat-Simul) <DOI:10.1080/03610918.2019.1602647>, Lin et al. (2021 Comm Stat-Simul) <DOI:10.1080/03610918.2019.1652318>, Sun et al. (2020 JSS Series in Statistics)<DOI:10.1007/978-981-15-4998-4>, and Huang and Emura (2021, in revision).

Last updated 3 years ago

1.48 score 3 stars 9 scripts 333 downloads

skewMLRM - Estimation for Scale-Shape Mixtures of Skew-Normal Distributions

Provide data generation and estimation tools for the multivariate scale mixtures of normal presented in Lange and Sinsheimer (1993) <doi:10.2307/1390698>, the multivariate scale mixtures of skew-normal presented in Zeller, Lachos and Vilca (2011) <doi:10.1080/02664760903406504>, the multivariate skew scale mixtures of normal presented in Louredo, Zeller and Ferreira (2021) <doi:10.1007/s13571-021-00257-y> and the multivariate scale mixtures of skew-normal-Cauchy presented in Kahrari et al. (2020) <doi:10.1080/03610918.2020.1804582>.

Last updated 3 years ago

1.48 score 1 dependents 184 downloads

sClust - R Toolbox for Unsupervised Spectral Clustering

Toolbox containing a variety of spectral clustering tools functions. Among the tools available are the hierarchical spectral clustering algorithm, the Shi and Malik clustering algorithm, the Perona and Freeman algorithm, the non-normalized clustering, the Von Luxburg algorithm, the Partition Around Medoids clustering algorithm, a multi-level clustering algorithm, recursive clustering and the fast method for all clustering algorithm. As well as other tools needed to run these algorithms or useful for unsupervised spectral clustering. This toolbox aims to gather the main tools for unsupervised spectral classification. See <http://mawenzi.univ-littoral.fr/> for more information and documentation.

Last updated 3 years ago

1.48 score 1 dependents 3 scripts 206 downloads

readmoRe - Utilities for Importing and Manipulating Biomedical Data Files

Tools to read various file types into one list of data structures, usually, but not limited to, data frames. Excel files are read sheet-wise, i.e., all or a selection of sheets can be read. Field delimiters and decimal separators are determined automatically.

Last updated 3 years ago

1.48 score 1 dependents 165 downloads

CatReg - Solution Paths for Linear and Logistic Regression Models with Categorical Predictors, with SCOPE Penalty

Computes solutions for linear and logistic regression models with potentially high-dimensional categorical predictors. This is done by applying a nonconvex penalty (SCOPE) and computing solutions in an efficient path-wise fashion. The scaling of the solution paths is selected automatically. Includes functionality for selecting tuning parameter lambda by k-fold cross-validation and early termination based on information criteria. Solutions are computed by cyclical block-coordinate descent, iterating an innovative dynamic programming algorithm to compute exact solutions for each block.

Last updated 4 years ago

cpp

1.48 score 243 downloads

otrimle - Robust Model-Based Clustering

Performs robust cluster analysis allowing for outliers and noise that cannot be fitted by any cluster. The data are modelled by a mixture of Gaussian distributions and a noise component, which is an improper uniform distribution covering the whole Euclidean space. Parameters are estimated by (pseudo) maximum likelihood. This is fitted by a EM-type algorithm. See Coretto and Hennig (2016) <doi:10.1080/01621459.2015.1100996>, and Coretto and Hennig (2017) <https://jmlr.org/papers/v18/16-382.html>.

Last updated 4 years ago

1.48 score 1 stars 1 dependents 9 scripts 314 downloads

FuzzyR - Fuzzy Logic Toolkit for R

Design and simulate fuzzy logic systems using Type-1 and Interval Type-2 Fuzzy Logic. This toolkit includes with graphical user interface (GUI) and an adaptive neuro- fuzzy inference system (ANFIS). This toolkit is a continuation from the previous package ('FuzzyToolkitUoN'). Produced by the Intelligent Modelling & Analysis Group (IMA) and Lab for UnCertainty In Data and decision making (LUCID), University of Nottingham. A big thank you to the many people who have contributed to the development/evaluation of the toolbox. Please cite the toolbox and the corresponding paper <doi:10.1109/FUZZ48607.2020.9177780> when using it. More related papers can be found in the NEWS.

Last updated 4 years ago

1.48 score 3 stars 41 scripts 271 downloads

catseyes - Create Catseye Plots Illustrating the Normal Distribution of the Means

Provides the tools to produce catseye plots, principally by catseyesplot() function which calls R's standard plot() function internally, or alternatively by the catseyes() function to overlay the catseye plot onto an existing R plot window. Catseye plots illustrate the normal distribution of the mean (picture a normal bell curve reflected over its base and rotated 90 degrees), with a shaded confidence interval; they are an intuitive way of illustrating and comparing normally distributed estimates, and are arguably a superior alternative to standard confidence intervals, since they show the full distribution rather than fixed quantile bounds. The catseyesplot and catseyes functions require pre-calculated means and standard errors (or standard deviations), provided as numeric vectors; this allows the flexibility of obtaining this information from a variety of sources, such as direct calculation or prediction from a model. Catseye plots, as illustrations of the normal distribution of the means, are described in Cumming (2013 & 2014). Cumming, G. (2013). The new statistics: Why and how. Psychological Science, 27, 7-29. <doi:10.1177/0956797613504966> pmid:24220629.

Last updated 5 years ago

1.48 score 2 scripts 146 downloads

ShiftConvolvePoibin - Exactly Computing the Tail of the Poisson-Binomial Distribution

An exact method for computing the Poisson-Binomial Distribution (PBD). The package provides a function for generating a random sample from the PBD, as well as two distinct approaches for computing the density, distribution, and quantile functions of the PBD. The first method uses direct-convolution, or a dynamic-programming approach which is numerically stable but can be slow for a large input due to its quadratic complexity. The second method is much faster on large inputs thanks to its use of Fast Fourier Transform (FFT) based convolutions. Notably in this case the package uses an exponential shift to practically guarantee the relative accuracy of the computation of an arbitrarily small tail of the PBD -- something that FFT-based methods often struggle with. This ShiftConvolvePoiBin method is described in Peres, Lee and Keich (2020) <arXiv:2004.07429> where it is also shown to be competitive with the fastest implementations for exactly computing the entire Poisson-Binomial distribution.

Last updated 5 years ago

1.48 score 1 dependents 2 scripts 184 downloads

nonpar - A Collection of Nonparametric Hypothesis Tests

Contains the following 5 nonparametric hypothesis tests: The Sign Test, The 2 Sample Median Test, Miller's Jackknife Procedure, Cochran's Q Test, & The Stuart-Maxwell Test.

Last updated 5 years ago

1.48 score 24 scripts 311 downloads

riceidconverter - Convert Biological ID from RAP or MSU to SYMBOL for Oryza Sativa

Convert one biological ID to another of rice (Oryza sativa). Rice(Oryza sativa) has more than one form gene ID for the genome. The two main gene ID for rice genome are the RAP (The Rice Annotation Project, <https://rapdb.dna.affrc.go.jp/>, and the MSU(The Rice Genome Annotation Project, <http://rice.plantbiology.msu.edu/>. All RAP rice gene IDs are of the form Os##g####### as explained on the website <https://rapdb.dna.affrc.go.jp/>. All MSU rice gene IDs are of the form LOC_Os##g##### as explained on the website <http://rice.plantbiology.msu.edu/analyses_nomenclature.shtml>. All SYMBOL rice gene IDs are the unique name on the NCBI(National Center for Biotechnology Information, <https://www.ncbi.nlm.nih.gov/>. The TRANSCRIPTID, is the transcript id of rice, are of the form Os##t#######. The researchers usually need to converter between various IDs. Such as converter RAP to SYMBOLS for function searching on NCBI. There are a lot of websites with the function for converting RAP to MSU or MSU to RA, such as 'ID Converter' <https://rapdb.dna.affrc.go.jp/tools/converter>. But it is difficult to convert super multiple IDs on these websites. The package can convert all IDs between the three IDs (RAP, MSU and SYMBOL) regardless of the number.

Last updated 5 years ago

1.48 score 1 dependents 1 scripts 192 downloads

SCRT - Single-Case Randomization Tests

Design single-case phase, alternation and multiple-baseline experiments, and conduct randomization tests on data gathered by means of such designs, as discussed in Bulte and Onghena (2013) <doi:10.22237/jmasm/1383280020>.

Last updated 5 years ago

1.48 score 1 stars 21 scripts 258 downloads

ClusVis - Gaussian-Based Visualization of Gaussian and Non-Gaussian Model-Based Clustering

Gaussian-Based Visualization of Gaussian and Non-Gaussian Model-Based Clustering done on any type of data. Visualization is based on the probabilities of classification.

Last updated 6 years ago

openblascpp

1.48 score 10 scripts 185 downloads

MultiwayRegression - Perform Tensor-on-Tensor Regression

Functions to predict one multi-way array (i.e., a tensor) from another multi-way array, using a low-rank CANDECOMP/PARAFAC (CP) factorization and a ridge (L_2) penalty [Lock, EF (2018) <doi:10.1080/10618600.2017.1401544>]. Also includes functions to sample from the Bayesian posterior of a tensor-on-tensor model.

Last updated 6 years ago

1.48 score 1 dependents 7 scripts 107 downloads

clogitL1 - Fitting Exact Conditional Logistic Regression with Lasso and Elastic Net Penalties

Tools for the fitting and cross validation of exact conditional logistic regression models with lasso and elastic net penalties. Uses cyclic coordinate descent and warm starts to compute the entire path efficiently.

Last updated 6 years ago

cpp

1.48 score 1 stars 1 dependents 8 scripts 298 downloads

Fgmutils - Forest Growth Model Utilities

Growth models and forest production require existing data manipulation and the creation of new data, structured from basic forest inventory data. The purpose of this package is provide functions to support these activities.

Last updated 6 years ago

1.48 score 1 dependents 29 scripts 385 downloads

kofnGA - A Genetic Algorithm for Fixed-Size Subset Selection

Provides a function that uses a genetic algorithm to search for a subset of size k from the integers 1:n, such that a user-supplied objective function is minimized at that subset. The selection step is done by tournament selection based on ranks, and elitism may be used to retain a portion of the best solutions from one generation to the next. Population objective function values may optionally be evaluated in parallel.

Last updated 6 years ago

1.48 score 1 dependents 10 scripts 218 downloads

EcoVirtual - Simulation of Ecological Models

Computer simulations of classical ecological models as a learning resource.

Last updated 6 years ago

1.48 score 1 dependents 22 scripts 303 downloads

rifle - Sparse Generalized Eigenvalue Problem

Implements the algorithms for solving sparse generalized eigenvalue problem by Tan, et. al. (2018). Sparse Generalized Eigenvalue Problem: Optimal Statistical Rates via Truncated Rayleigh Flow. To appear in Journal of the Royal Statistical Society: Series B. <arXiv:1604.08697>.

Last updated 6 years ago

1.48 score 1 dependents 9 scripts 125 downloads

xmlrpc2 - Implementation of the Remote Procedure Call Protocol ('XML-RPC')

The 'XML-RPC' is a remote procedure call protocol based on 'XML'. The 'xmlrpc2' package is inspired by the 'XMLRPC' package but uses the 'curl' and 'xml2' packages instead 'RCurl' and 'XML'.

Last updated 6 years ago

1.48 score 1 dependents 5 scripts 240 downloads

hermite - Generalized Hermite Distribution

Probability functions and other utilities for the generalized Hermite distribution.

Last updated 7 years ago

1.48 score 1 dependents 5 scripts 251 downloads

IDetect - Isolate-Detect Methodology for Multiple Change-Point Detection

Provides efficient implementation of the Isolate-Detect methodology for the consistent estimation of the number and location of multiple change-points in one-dimensional data sequences from the "deterministic + noise" model. For details on the Isolate-Detect methodology, please see Anastasiou and Fryzlewicz (2018) <https://docs.wixstatic.com/ugd/24cdcc_6a0866c574654163b8255e272bc0001b.pdf>. Currently implemented scenarios are: piecewise-constant signal with Gaussian noise, piecewise-constant signal with heavy-tailed noise, continuous piecewise-linear signal with Gaussian noise, continuous piecewise-linear signal with heavy-tailed noise.

Last updated 7 years ago

1.48 score 1 dependents 24 scripts 119 downloads

tgram - Compute and Plot Tracheidograms

Functions to compute and plot tracheidograms, as in De Soto et al. (2011) <doi:10.1139/x11-045>.

Last updated 7 years ago

1.48 score 1 dependents 4 scripts 133 downloads

thregI - Threshold Regression for Interval-Censored Data with a Cure Rate Option

Fit a threshold regression model for Interval Censored Data based on the first-hitting-time of a boundary by the sample path of a Wiener diffusion process. The threshold regression methodology is well suited to applications involving survival and time-to-event data.

Last updated 7 years ago

1.48 score 1 dependents 8 scripts 150 downloads

cenGAM - Censored Regression with Smooth Terms

Implementation of Tobit type I and type II families for censored regression using the 'mgcv' package, based on methods detailed in Woods (2016) <doi:10.1080/01621459.2016.1180986>.

Last updated 7 years ago

1.48 score 1 dependents 14 scripts 246 downloads

DoEstRare - Rare Variant Association Test Based on Position Density Estimation

Rare variant association test integrating variant position information. It aims to identify the presence of clusters of disease-risk variants in specific gene regions. For more details, please read the publication from Persyn et al. (2017) <doi:10.1371/journal.pone.0179364>.

Last updated 7 years ago

1.48 score 1 scripts 124 downloads

CDVineCopulaConditional - Sampling from Conditional C- and D-Vine Copulas

Provides tools for sampling from a conditional copula density decomposed via Pair-Copula Constructions as C- or D- vine. Here, the vines which can be used for such a sampling are those which sample as first the conditioning variables (when following the sampling algorithms shown in Aas et al. (2009) <DOI:10.1016/j.insmatheco.2007.02.001>). The used sampling algorithm is presented and discussed in Bevacqua et al. (2017) <DOI:10.5194/hess-2016-652>, and it is a modified version of that from Aas et al. (2009) <DOI:10.1016/j.insmatheco.2007.02.001>. A function is available to select the best vine (based on information criteria) among those which allow for such a conditional sampling. The package includes a function to compare scatterplot matrices and pair-dependencies of two multivariate datasets.

Last updated 7 years ago

1.48 score 3 stars 7 scripts 249 downloads

TPEA - A Novel Topology-Based Pathway Enrichment Analysis Approach

We described a novel Topology-based pathway enrichment analysis, which integrated the global position of the nodes and the topological property of the pathways in Kyoto Encyclopedia of Genes and Genomes Database. We also provide some functions to obtain the latest information about pathways to finish pathway enrichment analysis using this method.

Last updated 8 years ago

1.48 score 1 stars 1 dependents 3 scripts 173 downloads

MaxSkew - Orthogonal Data Projections with Maximal Skewness

It finds Orthogonal Data Projections with Maximal Skewness. The first data projection in the output is the most skewed among all linear data projections. The second data projection in the output is the most skewed among all data projections orthogonal to the first one, and so on.

Last updated 8 years ago

1.48 score 1 dependents 7 scripts 132 downloads

sensitivityfull - Sensitivity Analysis for Full Matching in Observational Studies

Sensitivity to unmeasured biases in an observational study that is a full match. Function senfm() performs tests and function senfmCI() creates confidence intervals. The method uses Huber's M-statistics, including least squares, and is described in Rosenbaum (2007, Biometrics) <DOI:10.1111/j.1541-0420.2006.00717.x>.

Last updated 8 years ago

1.48 score 1 dependents 23 scripts 500 downloads

TTCA - Transcript Time Course Analysis

The analysis of microarray time series promises a deeper insight into the dynamics of the cellular response following stimulation. A common observation in this type of data is that some genes respond with quick, transient dynamics, while other genes change their expression slowly over time. The existing methods for detecting significant expression dynamics often fail when the expression dynamics show a large heterogeneity. Moreover, these methods often cannot cope with irregular and sparse measurements. The method proposed here is specifically designed for the analysis of perturbation responses. It combines different scores to capture fast and transient dynamics as well as slow expression changes, and performs well in the presence of low replicate numbers and irregular sampling times. The results are given in the form of tables including links to figures showing the expression dynamics of the respective transcript. These allow to quickly recognise the relevance of detection, to identify possible false positives and to discriminate early and late changes in gene expression. An extension of the method allows the analysis of the expression dynamics of functional groups of genes, providing a quick overview of the cellular response. The performance of this package was tested on microarray data derived from lung cancer cells stimulated with epidermal growth factor (EGF). Paper: Albrecht, Marco, et al. (2017)<DOI:10.1186/s12859-016-1440-8>.

Last updated 8 years ago

1.48 score 5 scripts 125 downloads

RDStreeboot - RDS Tree Bootstrap Method

A tree bootstrap method for estimating uncertainty in respondent-driven samples (RDS). Quantiles are estimated by multilevel resampling in such a way that preserves the dependencies of and accounts for the high variability of the RDS process.

Last updated 8 years ago

1.48 score 1 dependents 6 scripts 103 downloads

momentchi2 - Moment-Matching Methods for Weighted Sums of Chi-Squared Random Variables

A collection of moment-matching methods for computing the cumulative distribution function of a positively-weighted sum of chi-squared random variables. Methods include the Satterthwaite-Welch method, Hall-Buckley-Eagleson method, Wood's F method, and the Lindsay-Pilla-Basak method.

Last updated 8 years ago

1.48 score 1 stars 1 dependents 8 scripts 208 downloads

GameTheoryAllocation - Tools for Calculating Allocations in Game Theory

Many situations can be modeled as game theoretic situations. Some procedures are included in this package to calculate the most important allocations rules in Game Theory: Shapley value, Owen value or nucleolus, among other. First, we must define as an argument the value of the unions of the envolved agents with the characteristic function.

Last updated 8 years ago

1.48 score 1 stars 1 dependents 9 scripts 165 downloads

DWreg - Parametric Regression for Discrete Response

Regression for a discrete response, where the conditional distribution is modelled via a discrete Weibull distribution.

Last updated 8 years ago

1.48 score 1 dependents 5 scripts 157 downloads

uniReg - Unimodal Penalized Spline Regression using B-Splines

Univariate spline regression. It is possible to add the shape constraint of unimodality and predefined or self-defined penalties on the B-spline coefficients.

Last updated 9 years ago

1.48 score 1 dependents 8 scripts 182 downloads

GiNA - High Throughput Phenotyping

Performs image segmentation in fruit or seeds pictures in order to measure physical features in a high-throughput manner for genome-wide association (GWAS) and genomic selection programs.

Last updated 9 years ago

1.48 score 8 scripts 133 downloads

robreg3S - Three-Step Regression and Inference for Cellwise and Casewise Contamination

Three-step regression and inference for cellwise and casewise contamination.

Last updated 9 years ago

1.48 score 1 dependents 3 scripts 101 downloads

ForecastCombinations - Forecast Combinations

Aim: Supports the most frequently used methods to combine forecasts. Among others: Simple average, Ordinary Least Squares, Least Absolute Deviation, Constrained Least Squares, Variance-based, Best Individual model, Complete subset regressions and Information-theoretic (information criteria based).

Last updated 9 years ago

1.48 score 1 dependents 3 scripts 173 downloads

BCBCSF - Bias-Corrected Bayesian Classification with Selected Features

Fully Bayesian Classification with a subset of high-dimensional features, such as expression levels of genes. The data are modeled with a hierarchical Bayesian models using heavy-tailed t distributions as priors. When a large number of features are available, one may like to select only a subset of features to use, typically those features strongly correlated with the response in training cases. Such a feature selection procedure is however invalid since the relationship between the response and the features has be exaggerated by feature selection. This package provides a way to avoid this bias and yield better-calibrated predictions for future cases when one uses F-statistic to select features.

Last updated 9 years ago

1.48 score 1 dependents 1 scripts 243 downloads

ICC.Sample.Size - Calculation of Sample Size and Power for ICC

Provides functions to calculate the requisite sample size for studies where ICC is the primary outcome. Can also be used for calculation of power. In both cases it allows the user to test the impact of changing input variables by calculating the outcome for several different values of input variables. Based off the work of Zou. Zou, G. Y. (2012). Sample size formulas for estimating intraclass correlation coefficients with precision and assurance. Statistics in medicine, 31(29), 3972-3981.

Last updated 9 years ago

1.48 score 1 dependents 8 scripts 209 downloads

LCFdata - Data sets for package ``LMERConvenienceFunctions''

This package contains (1) event-related brain potential data recorded from 10 participants at electrodes Fz, Cz, Pz, and Oz (0--300 ms) in the context of Antoine Tremblay's PhD thesis (Tremblay, 2009); (2) ERP amplitudes at electrode Fz restricted to the 100 to 175 millisecond time window; and (3) plotting data generated from a linear mixed-effects model.

Last updated 11 years ago

1.48 score 1 dependents 7 scripts 338 downloads

qrmix - Quantile Regression Mixture Models

Implements the robust algorithm for fitting finite mixture models based on quantile regression proposed by Emir et al., 2017 (unpublished).

Last updated 8 years ago

1.46 score 1 stars 29 scripts 124 downloads

spagmix - Artificial Spatial and Spatio-Temporal Densities on Bounded Windows

Simple utilities to design and generate density functions on bounded regions in space and space-time, and simulate independent, identically distributed data therefrom. See Davies & Lawson (2019) <doi:10.1080/00949655.2019.1575066> for example.

Last updated 6 months ago

1.45 score 14 scripts 514 downloads

ppmSuite - A Collection of Models that Employ Product Partition Distributions as a Prior on Partitions

Provides a suite of functions that fit models that use PPM type priors for partitions. Models include hierarchical Gaussian and probit ordinal models with a (covariate dependent) PPM. If a covariate dependent product partition model is selected, then all the options detailed in Page, G.L.; Quintana, F.A. (2018) <doi:10.1007/s11222-017-9777-z> are available. If covariate values are missing, then the approach detailed in Page, G.L.; Quintana, F.A.; Mueller, P (2020) <doi:10.1080/10618600.2021.1999824> is employed. Also included in the package is a function that fits a Gaussian likelihood spatial product partition model that is detailed in Page, G.L.; Quintana, F.A. (2016) <doi:10.1214/15-BA971>, and multivariate PPM change point models that are detailed in Quinlan, J.J.; Page, G.L.; Castro, L.M. (2023) <doi:10.1214/22-BA1344>. In addition, a function that fits a univariate or bivariate functional data model that employs a PPM or a PPMx to cluster curves based on B-spline coefficients is provided.

Last updated 1 years ago

fortran

1.45 score 2 stars 14 scripts 277 downloads

rankFD - Rank-Based Tests for General Factorial Designs

The rankFD() function calculates the Wald-type statistic (WTS) and the ANOVA-type statistic (ATS) for nonparametric factorial designs, e.g., for count, ordinal or score data in a crossed design with an arbitrary number of factors. Brunner, E., Bathke, A. and Konietschke, F. (2018) <doi:10.1007/978-3-030-02914-2>.

Last updated 3 years ago

1.45 score 14 scripts 246 downloads

rLDCP - Text Generation from Data

Linguistic Descriptions of Complex Phenomena (LDCP) is an architecture and methodology that allows us to model complex phenomena, interpreting input data, and generating automatic text reports customized to the user needs (see <doi:10.1016/j.ins.2016.11.002> and <doi:10.1007/s00500-016-2430-5>). The proposed package contains a set of methods that facilitates the development of LDCP systems. It main goal is increasing the visibility and practical use of this research line.

Last updated 7 years ago

1.43 score 27 scripts 114 downloads

SampleSizeMeans - Sample Size Calculations for Normal Means

Sample size requirements calculation using three different Bayesian criteria in the context of designing an experiment to estimate a normal mean or the difference between two normal means. Functions for calculation of required sample sizes for the Average Length Criterion, the Average Coverage Criterion and the Worst Outcome Criterion in the context of normal means are provided. Functions for both the fully Bayesian and the mixed Bayesian/likelihood approaches are provided. For reference see Joseph L. and Bélisle P. (1997) <https://www.jstor.org/stable/2988525>.

Last updated 1 years ago

1.41 score 26 scripts 242 downloads

CalibratR - Mapping ML Scores to Calibrated Predictions

Transforms your uncalibrated Machine Learning scores to well-calibrated prediction estimates that can be interpreted as probability estimates. The implemented BBQ (Bayes Binning in Quantiles) model is taken from Naeini (2015, ISBN:0-262-51129-0). Please cite this paper: Schwarz J and Heider D, Bioinformatics 2019, 35(14):2458-2465.

Last updated 5 years ago

1.41 score 2 stars 13 scripts 295 downloads

tropAlgebra - Tropical Algebraic Functions

It includes functions like tropical addition, tropical multiplication for vectors and matrices. In tropical algebra, the tropical sum of two numbers is their minimum and the tropical product of two numbers is their ordinary sum. For more information see also I. Simon (1988) Recognizable sets with multiplicities in the tropical semi ring: Volume 324 Lecture Notes I Computer Science, pages 107-120 <doi: 10.1007/BFb0017135>.

Last updated 7 years ago

1.41 score 2 stars 13 scripts 98 downloads

assocInd - Implements New and Existing Association Indices for Constructing Animal Social Networks

Implements several new association indices that can control for various types of errors. Also includes existing association indices and functions for simulating the effects of different rates of error on estimates of association strength between individuals using each method.

Last updated 7 years ago

1.41 score 26 scripts 186 downloads

SteinIV - Semi-Parametric Stein-Like Estimator with Instrumental Variables

Routines for computing different types of linear estimators, based on instrumental variables (IVs), including the semi-parametric Stein-like (SPS) estimator, originally introduced by Judge and Mittelhammer (2004) <DOI:10.1198/016214504000000430>.

Last updated 9 years ago

1.41 score 2 stars 13 scripts 161 downloads

hwwntest - Tests of White Noise using Wavelets

Provides methods to test whether time series is consistent with white noise. Two new tests based on Haar wavelets and general wavelets described by Nason and Savchev (2014) <doi:10.1002/sta4.69> are provided and, for comparison purposes this package also implements the B test of Bartlett (1967) <doi:10.2307/2333850>. Functionality is provided to compute an approximation to the theoretical power of the general wavelet test in the case of general ARMA alternatives.

Last updated 1 years ago

1.40 score 1 stars 25 scripts 206 downloads

Rmalschains - Continuous Optimization using Memetic Algorithms with Local Search Chains (MA-LS-Chains)

An implementation of an algorithm family for continuous optimization called memetic algorithms with local search chains (MA-LS-Chains), as proposed in Molina et al. (2010) <doi:10.1162/evco.2010.18.1.18102> and Molina et al. (2011) <doi:10.1007/s00500-010-0647-2>. Rmalschains is further discussed in Bergmeir et al. (2016) <doi:10.18637/jss.v075.i04>. Memetic algorithms are hybridizations of genetic algorithms with local search methods. They are especially suited for continuous optimization.

Last updated 2 years ago

1.40 score 25 scripts 443 downloads

FunctanSNP - Functional Analysis (with Interactions) for Dense SNP Data

An implementation of revised functional regression models for multiple genetic variation data, such as single nucleotide polymorphism (SNP) data, which provides revised functional linear regression models, partially functional interaction regression analysis with penalty-based techniques and corresponding drawing functions, etc.(Ruzong Fan, Yifan Wang, James L. Mills, Alexander F. Wilson, Joan E. Bailey-Wilson, and Momiao Xiong (2013) <doi:10.1002/gepi.21757>).

Last updated 2 years ago

1.40 score 25 scripts 154 downloads

IndTestPP - Tests of Independence and Analysis of Dependence Between Point Processes in Time

It provides a general framework to analyse dependence between point processes in time. It includes parametric and non-parametric tests to study independence, and functions for generating and analysing different types of dependence.

Last updated 4 years ago

1.40 score 25 scripts 171 downloads

miLineage - Association Tests for Microbial Lineages on a Taxonomic Tree

A variety of association tests for microbiome data analysis including Quasi-Conditional Association Tests (QCAT) described in Tang Z.-Z. et al.(2017) <doi:10.1093/bioinformatics/btw804> and Zero-Inflated Generalized Dirichlet Multinomial (ZIGDM) tests described in Tang Z.-Z. & Chen G. (2017, submitted).

Last updated 7 years ago

1.40 score 25 scripts 200 downloads

SigOptR - R API Wrapper for SigOpt

Interfaces with the 'SigOpt' API. More info at <https://sigopt.com>.

Last updated 8 years ago

1.40 score 25 scripts 405 downloads

lgarch - Simulation and Estimation of Log-GARCH Models

Simulation and estimation of univariate and multivariate log-GARCH models. The main functions of the package are: lgarchSim(), mlgarchSim(), lgarch() and mlgarch(). The first two functions simulate from a univariate and a multivariate log-GARCH model, respectively, whereas the latter two estimate a univariate and multivariate log-GARCH model, respectively.

Last updated 9 years ago

1.40 score 1 stars 25 scripts 260 downloads

sbw - Stable Balancing Weights for Causal Inference and Missing Data

Implements the Stable Balancing Weights by Zubizarreta (2015) <DOI:10.1080/01621459.2015.1023805>. These are the weights of minimum variance that approximately balance the empirical distribution of the observed covariates. For an overview, see Chattopadhyay, Hase and Zubizarreta (2020) <DOI:10.1002/sim.8659>. To solve the optimization problem in 'sbw', the default solver is 'quadprog', which is readily available through CRAN. The solver 'osqp' is also posted on CRAN. To enhance the performance of 'sbw', users are encouraged to install other solvers such as 'gurobi' and 'Rmosek', which require special installation. For the installation of gurobi and pogs, please follow the instructions at <https://www.gurobi.com/documentation/current/refman/r_ins_the_r_package.html> and <http://foges.github.io/pogs/stp/r>.

Last updated 5 months ago

1.38 score 1 stars 11 scripts 1.1k downloads

phenmod - Auxiliary Functions for Phenological Data Processing, Modelling and Result Handling

Provides functions for phenological data preprocessing, modelling and result handling. For more information, please refer to Lange et al. (2016) <doi:10.1007/s00484-016-1161-8>.

Last updated 3 years ago

1.38 score 24 scripts 164 downloads

bio.infer - Predict Environmental Conditions from Biological Observations

Imports benthic count data, reformats this data, and computes environmental inferences from this data.

Last updated 4 years ago

1.38 score 24 scripts 386 downloads

wskm - Weighted k-Means Clustering

Entropy weighted k-means (ewkm) by Liping Jing, Michael K. Ng and Joshua Zhexue Huang (2007) <doi:10.1109/TKDE.2007.1048> is a weighted subspace clustering algorithm that is well suited to very high dimensional data. Weights are calculated as the importance of a variable with regard to cluster membership. The two-level variable weighting clustering algorithm tw-k-means (twkm) by Xiaojun Chen, Xiaofei Xu, Joshua Zhexue Huang and Yunming Ye (2013) <doi:10.1109/TKDE.2011.262> introduces two types of weights, the weights on individual variables and the weights on variable groups, and they are calculated during the clustering process. The feature group weighted k-means (fgkm) by Xiaojun Chen, Yunminng Ye, Xiaofei Xu and Joshua Zhexue Huang (2012) <doi:10.1016/j.patcog.2011.06.004> extends this concept by grouping features and weighting the group in addition to weighting individual features.

Last updated 5 years ago

1.38 score 1 stars 24 scripts 269 downloads

FreeSortR - Free Sorting Data Analysis

Provides tools for describing and analysing free sorting data. Main methods are computation of consensus partition and factorial analysis of the dissimilarity matrix between stimuli (using multidimensional scaling approach).

Last updated 7 years ago

1.38 score 24 scripts 233 downloads

capn - Capital Asset Pricing for Nature

Implements approximation methods for natural capital asset prices suggested by Fenichel and Abbott (2014) <doi:10.1086/676034> in Journal of the Associations of Environmental and Resource Economists (JAERE), Fenichel et al. (2016) <doi:10.1073/pnas.1513779113> in Proceedings of the National Academy of Sciences (PNAS), and Yun et al. (2017) in PNAS (accepted), and their extensions: creating Chebyshev polynomial nodes and grids, calculating basis of Chebyshev polynomials, approximation and their simulations for: V-approximation (single and multiple stocks, PNAS), P-approximation (single stock, PNAS), and Pdot-approximation (single stock, JAERE). Development of this package was generously supported by the Knobloch Family Foundation.

Last updated 8 years ago

1.38 score 24 scripts 162 downloads

woe - Computes Weight of Evidence and Information Values

Shows the relationship between an independent and dependent variable through Weight of Evidence and Information Value.

Last updated 9 years ago

1.38 score 1 stars 24 scripts 278 downloads

BlakerCI - Blaker's Binomial and Poisson Confidence Limits

Fast and accurate calculation of Blaker's binomial and Poisson confidence limits (and some related stuff).

Last updated 6 years ago

1.37 score 8 scripts 1.2k downloads

ClustBlock - Clustering of Datasets

Hierarchical and partitioning algorithms to cluster blocks of variables. The partitioning algorithm includes an option called noise cluster to set aside atypical blocks of variables. The CLUSTATIS method (for quantitative blocks) (Llobell, Cariou, Vigneau, Labenne & Qannari (2020) <doi:10.1016/j.foodqual.2018.05.013>, Llobell, Vigneau & Qannari (2019) <doi:10.1016/j.foodqual.2019.02.017>) and the CLUSCATA method (for Check-All-That-Apply data) (Llobell, Cariou, Vigneau, Labenne & Qannari (2019) <doi:10.1016/j.foodqual.2018.09.006>, Llobell, Giacalone, Labenne & Qannari (2019) <doi:10.1016/j.foodqual.2019.05.017>) are the core of this package. The CATATIS methods allows to compute some indices and tests to control the quality of CATA data. Multivariate analysis and clustering of subjects for quantitative multiblock data, CATA, RATA, Free Sorting and JAR experiments are available. Clustering of rows in multi-block context (notably with ClusMB strategy) is also included.

Last updated 7 months ago

1.36 score 23 scripts 331 downloads

votesys - Voting Systems, Instant-Runoff Voting, Borda Method, Various Condorcet Methods

Various methods to count ballots in voting systems are provided. Functions to check validity of ballots are also provided to ensure flexibility.

Last updated 7 years ago

1.36 score 1 stars 23 scripts 228 downloads

newTestSurvRec - Statistical Tests to Compare Curves with Recurrent Events

Implements the routines to compare the survival curves with recurrent events, including the estimations of survival curves. The first model is a model for recurrent event, when the data are correlated or not correlated. It was proposed by Wang and Chang (1999) <doi:10.2307/2669690>. In the independent case, the survival function can be estimated by the generalization of the limit product model of Pena (2001) <doi:10.1198/016214501753381922>.

Last updated 7 years ago

1.36 score 23 scripts 111 downloads

RGenData - Generates Multivariate Nonnormal Data and Determines How Many Factors to Retain

The GenDataSample() and GenDataPopulation() functions create, respectively, a sample or population of multivariate nonnormal data using methods described in Ruscio and Kaczetow (2008). Both of these functions call a FactorAnalysis() function to reproduce a correlation matrix. The EFACompData() function allows users to determine how many factors to retain in an exploratory factor analysis of an empirical data set using a method described in Ruscio and Roche (2012). The latter function uses populations of comparison data created by calling the GenDataPopulation() function. <DOI: 10.1080/00273170802285693>. <DOI: 10.1037/a0025697>.

Last updated 6 years ago

1.34 score 1 stars 11 scripts 106 downloads

Pstat - Assessing Pst Statistics

Calculating Pst values to assess differentiation among populations from a set of quantitative traits is the primary purpose of such a package. The bootstrap method provides confidence intervals and distribution histograms of Pst. Variations of Pst in function of the parameter c/h^2 are studied as well. Finally, the package proposes different transformations especially to eliminate any variation resulting from allometric growth (calculation of residuals from linear regressions, Reist standardizations or Aitchison transformation).

Last updated 7 years ago

1.34 score 11 scripts 477 downloads

geoBayes - Analysis of Geostatistical Data using Bayes and Empirical Bayes Methods

Functions to fit geostatistical data. The data can be continuous, binary or count data and the models implemented are flexible. Conjugate priors are assumed on some parameters while inference on the other parameters can be done through a full Bayesian analysis of by empirical Bayes methods.

Last updated 3 months ago

fortranopenblas

1.34 score 22 scripts 409 downloads

EvCombR - Evidence Combination in R

Combine pieces of evidence in the form of uncertainty representations.

Last updated 3 years ago

1.34 score 22 scripts 296 downloads

RProbSup - Calculates Probability of Superiority

The A() function calculates the A statistic, a nonparametric measure of effect size for two independent groups that’s also known as the probability of superiority (Ruscio, 2008), along with its standard error and a confidence interval constructed using bootstrap methods (Ruscio & Mullen, 2012). Optional arguments can be specified to calculate variants of the A statistic developed for other research designs (e.g., related samples, more than two independent groups or related samples; Ruscio & Gera, 2013). <DOI: 10.1037/1082-989X.13.1.19>. <DOI: 10.1080/00273171.2012.658329>. <DOI: 10.1080/00273171.2012.738184>.

Last updated 4 years ago

1.34 score 22 scripts 155 downloads

GFGM.copula - Generalized Farlie-Gumbel-Morgenstern Copula

Compute bivariate dependence measures and perform bivariate competing risks analysis under the generalized Farlie-Gumbel-Morgenstern (FGM) copula. See Shih and Emura (2018) <doi:10.1007/s00180-018-0804-0> and Shih and Emura (2019) <doi:10.1007/s00362-016-0865-5> for details.

Last updated 5 years ago

1.34 score 22 scripts 185 downloads

hhi - Calculate and Visualize the Herfindahl-Hirschman Index

Based on the aggregated shares retained by individual firms or actors within a market or space, the Herfindahl-Hirschman Index (HHI) measures the level of concentration in a space. This package allows for intuitive and straightforward computation of HHI scores, requiring placement of objects of interest directly into the function. The package also includes a plot function for quick visual display of an HHI time series using any measure of time (year, quarter, month, etc.). For usage, please cite the Journal of Open Source Software paper associated with the package: Waggoner, Philip D. (2018) <doi:10.21105/joss.00828>.

Last updated 6 years ago

1.34 score 1 stars 22 scripts 183 downloads

phiDelta - Tool for Phi Delta Analysis of Features

Analysis of features by phi delta diagrams. In particular, functions for reading data and calculating phi and delta as well as the functionality to plot it. Moreover it is possible to do further analysis on the data by generating rankings. For more information on phi delta diagrams, see also Giuliano Armano (2015) <doi:10.1016/j.ins.2015.07.028>.

Last updated 7 years ago

1.34 score 22 scripts 86 downloads

radar - Fundamental Formulas for Radar

Fundamental formulas for Radar, for attenuation, range, velocity, effectiveness, power, scatter, doppler, geometry, radar equations, etc. Based on Nick Guy's Python package PyRadarMet

Last updated 10 years ago

1.34 score 1 stars 22 scripts 148 downloads

optimStrat - Choosing the Sample Strategy

Intended to assist in the choice of the sampling strategy to implement in a survey.

Last updated 1 years ago

1.32 score 21 scripts 168 downloads

linearModel - Linear Model Functions

Functions to access and test results from a linear model.

Last updated 3 years ago

1.32 score 21 scripts 234 downloads

RcppHMM - Rcpp Hidden Markov Model

Collection of functions to evaluate sequences, decode hidden states and estimate parameters from a single or multiple sequences of a discrete time Hidden Markov Model. The observed values can be modeled by a multinomial distribution for categorical/labeled emissions, a mixture of Gaussians for continuous data and also a mixture of Poissons for discrete values. It includes functions for random initialization, simulation, backward or forward sequence evaluation, Viterbi or forward-backward decoding and parameter estimation using an Expectation-Maximization approach.

Last updated 7 years ago

1.32 score 1 stars 21 scripts 222 downloads

CCTpack - Consensus Analysis, Model-Based Clustering, and Cultural Consensus Theory Applications

Consensus analysis, model-based clustering, and cultural consensus theory applications to response data (e.g. questionnaires). The models are applied using hierarchical Bayesian inference. The current package version supports binary, ordinal, and continuous data formats.

Last updated 7 years ago

1.32 score 1 stars 21 scripts 282 downloads

epilogi - The 'epilogi' Variable Selection Algorithm for Continuous Data

The 'epilogi' variable selection algorithm is implemented for the case of continuous response and predictor variables. The relevant paper is: Lakiotaki K., Papadovasilakis Z., Lagani V., Fafalios S., Charonyktakis P., Tsagris M. and Tsamardinos I. (2023). "Automated machine learning for Genome Wide Association Studies". Bioinformatics, 39(9): btad545. <doi:10.1093/bioinformatics/btad545>.

Last updated 23 hours ago

1.30 score 145 downloads

flipscores - Robust Score Testing in GLMs, by Sign-Flip Contributions

Provides robust tests for testing in GLMs, by sign-flipping score contributions. The tests are robust against overdispersion, heteroscedasticity and, in some cases, ignored nuisance variables. See Hemerik, Goeman and Finos (2020) <doi:10.1111/rssb.12369>.

Last updated 13 days ago

1.30 score 14 scripts 263 downloads

rjaf - Regularized Joint Assignment Forest with Treatment Arm Clustering

Personalized assignment to one of many treatment arms via regularized and clustered joint assignment forests as described in Ladhania, Spiess, Ungar, and Wu (2023) <doi:10.48550/arXiv.2311.00577>. The algorithm pools information across treatment arms: it considers a regularized forest-based assignment algorithm based on greedy recursive partitioning that shrinks effect estimates across arms; and it incorporates a clustering scheme that combines treatment arms with consistently similar outcomes.

Last updated 16 days ago

cpp

1.30 score 4 scripts 420 downloads

CCd - The Cauchy-Cacoullos (Discrete Cauchy) Distribution

Maximum likelihood estimation of the Cauchy-Cacoullos (discrete Cauchy) distribution. Probability mass, distribution and quantile function are also included. The reference paper is: Papadatos N. (2022). "The Characteristic Function of the Discrete Cauchy Distribution in Memory of T. Cacoullos". Journal of Statistical Theory Practice, 16(3): 47. <doi:10.1007/s42519-022-00268-6>.

Last updated 17 days ago

1.30 score 3 scripts 193 downloads

VisCov - Visualizing of Distributions of Covariance Matrices

Visualizing of distributions of covariance matrices. The package implements the methodology described in Tokuda, T., Goodrich, B., Van Mechelen, I., Gelman, A., & Tuerlinckx, F. (2012) <https://stat.columbia.edu/~gelman/research/unpublished/Visualization.pdf>.

Last updated 20 days ago

1.30 score 483 downloads

WMAP - Weighted Meta-Analysis with Pseudo-Populations

Implementation of integrative weighting approaches for multiple observational studies and causal inferences. The package features three weighting approaches, each representing a special case of the unified weighting framework, introduced by Guha and Li (2024) <doi:10.1093/biomtc/ujae070>, which includes an extension of inverse probability weights for data integration settings.

Last updated 24 days ago

1.30 score 350 downloads

AOboot - Bootstrapping in Different One-Way and Two-Way ANOVA

To address the violation of the assumption of normally distributed variables, researchers frequently employ bootstrapping. Building upon established packages for R (Sigmann et al. (2024) <doi:10.32614/CRAN.package.afex>, Lenth (2024) <doi:10.32614/CRAN.package.emmeans>), we provide bootstrapping functions to approximate a normal distribution of the parameter estimates for between-subject, within-subject, and mixed one-way and two-way ANOVA.

Last updated 1 months ago

1.30 score 270 downloads

synMicrodata - Synthetic Microdata Generator

This tool fits a non-parametric Bayesian model called a "hierarchically coupled mixture model with local dependence (HCMM-LD)" to the original microdata in order to generate synthetic microdata for privacy protection. The non-parametric feature of the adopted model is useful for capturing the joint distribution of the original input data in a highly flexible manner, leading to the generation of synthetic data whose distributional features are similar to that of the input data. The package allows the original input data to have missing values and impute them with the posterior predictive distribution, so no missing values exist in the synthetic data output. The method builds on the work of Murray and Reiter (2016) <doi:10.1080/01621459.2016.1174132>.

Last updated 1 months ago

openblascpp

1.30 score 207 downloads

TWW - Growth Models

A model for the growth of self-limiting populations using three, four, or five parameter functions, which have wide applications in a variety of fields. The dependent variable in a dynamical modeling could be the population size at time x, where x is the independent variable. In the analysis of quantitative polymerase chain reaction (qPCR), the dependent variable would be the fluorescence intensity and the independent variable the cycle number. This package then would calculate the TWW cycle threshold.

Last updated 1 months ago

1.30 score 1 scripts 463 downloads

HMMRel - Hidden Markov Models for Reliability and Maintenance

Reliability Analysis and Maintenance Optimization using Hidden Markov Models (HMM). The use of HMMs to model the state of a system which is not directly observable and instead certain indicators (signals) of the true situation are provided via a control system. A hidden model can provide key information about the system dependability, such as the reliability of the system and related measures. An estimation procedure is implemented based on the Baum-Welch algorithm. Classical structures such as K-out-of-N systems and Shock models are illustrated. Finally, the maintenance of the system is considered in the HMM context and two functions for new preventive maintenance strategies are considered. Maintenance efficiency is measured in terms of expected cost. Methods are described in Gamiz, Limnios, and Segovia-Garcia (2023) <doi:10.1016/j.ejor.2022.05.006>.

Last updated 1 months ago

1.30 score 47 downloads

RadEro - Cs-137 Conversion Model

A straightforward model to estimate soil migration rates across various soil contexts. Based on the compartmental, vertically-resolved, physically-based mass balance model of Soto and Navas (2004) <doi:10.1016/j.jaridenv.2004.02.003> and Soto and Navas (2008) <doi:10.1016/j.radmeas.2008.02.024>. 'RadEro' provides a user-friendly interface in R, utilizing input data such as 137Cs inventories and parameters directly derived from soil samples (e.g., fine fraction density, effective volume) to accurately capture the 137Cs distribution within the soil profile. The model simulates annual 137Cs fallout, radioactive decay, and vertical diffusion, with the diffusion coefficient calculated from 137Cs reference inventory profiles. Additionally, it allows users to input custom parameters as calibration coefficients. The RadEro user manual and protocol, including detailed instructions on how to format input data and configuration files, can be found at the following link: <https://github.com/eead-csic-eesa/RadEro>.

Last updated 1 months ago

cpp

1.30 score 467 downloads

gerefer - Preparer of Main Scientific References for Automatic Insertion in Academic Papers

Generates a file, containing the main scientific references, prepared to be automatically inserted into an academic paper. The articles present in the list are chosen from the main references generated, by function principal_lister(), of the package 'bibliorefer'. The generated file contains the list of metadata of the principal references in 'BibTex' format. Massimo Aria, Corrado Cuccurullo. (2017) <doi:10.1016/j.joi.2017.08.007>. Caibo Zhou, Wenyan Song. (2021) <doi:10.1016/j.jclepro.2021.126943>. Hamid Derviş. (2019) <doi:10.5530/jscires.8.3.32>.

Last updated 1 months ago

1.30 score 182 downloads

tpn - Truncated Positive Normal Model and Extensions

Provide data generation and estimation tools for the truncated positive normal (tpn) model discussed in Gomez, Olmos, Varela and Bolfarine (2018) <doi:10.1007/s11766-018-3354-x>, the slash tpn distribution discussed in Gomez, Gallardo and Santoro (2021) <doi:10.3390/sym13112164>, the bimodal tpn distribution discussed in Gomez et al. (2022) <doi:10.3390/sym14040665> and the flexible tpn model.

Last updated 1 months ago

1.30 score 342 downloads

cchs - Cox Model for Case-Cohort Data with Stratified Subcohort-Selection

Contains a function, also called 'cchs', that calculates Estimator III of Borgan et al (2000), <DOI:10.1023/A:1009661900674>. This estimator is for fitting a Cox proportional hazards model to data from a case-cohort study where the subcohort was selected by stratified simple random sampling.

Last updated 1 months ago

1.30 score 1 stars 1 scripts 632 downloads

regressoR - Regression Data Analysis System

Perform a supervised data analysis on a database through a 'shiny' graphical interface. It includes methods such as linear regression, penalized regression, k-nearest neighbors, decision trees, ada boosting, extreme gradient boosting, random forest, neural networks, deep learning and support vector machines.

Last updated 1 months ago

1.30 score 2 stars 522 downloads

CTxCC - Multivariate Normal Mean Monitoring Through Critical-to-X Control Chart

A comprehensive set of functions designed for multivariate mean monitoring using the Critical-to-X Control Chart. These functions enable the determination of optimal control limits based on a specified in-control Average Run Length (ARL), the calculation of out-of-control ARL for a given control limit, and post-signal analysis to identify the specific variable responsible for a detected shift in the mean. This suite of tools provides robust support for precise and effective process monitoring and analysis.

Last updated 2 months ago

1.30 score 524 downloads

waveband - Computes Credible Intervals for Bayesian Wavelet Shrinkage

Computes Bayesian wavelet shrinkage credible intervals for nonparametric regression. The method uses cumulants to derive Bayesian credible intervals for wavelet regression estimates. The first four cumulants of the posterior distribution of the estimates are expressed in terms of the observed data and integer powers of the mother wavelet functions. These powers are closely approximated by linear combinations of wavelet scaling functions at an appropriate finer scale. Hence, a suitable modification of the discrete wavelet transform allows the posterior cumulants to be found efficiently for any data set. Johnson transformations then yield the credible intervals themselves. Barber, S., Nason, G.P. and Silverman, B.W. (2002) <doi:10.1111/1467-9868.00332>.

Last updated 2 months ago

fortran

1.30 score 8 scripts 604 downloads

NetworkReg - Generalized Linear Regression Models on Network-Linked Data with Statistical Inference

Linear regression model and generalized linear models with nonparametric network effects on network-linked observations. The model is originally proposed by Le and Li (2022) <doi:10.48550/arXiv.2007.00803> and is assumed on observations that are connected by a network or similar relational data structure. A more recent work by Wang, Le and Li (2024) <doi:10.48550/arXiv.2410.01163> further extends the framework to generalized linear models. All these models are implemented in the current package. The model does not assume that the relational data or network structure to be precisely observed; thus, the method is provably robust to a certain level of perturbation of the network structure. The package contains the estimation and inference function for the model.

Last updated 2 months ago

1.30 score 1 scripts 477 downloads

iForecast - Machine Learning Time Series Forecasting

Compute static, onestep and multistep time series forecasts for machine learning models.

Last updated 2 months ago

1.30 score 1 scripts 741 downloads

elhmc - Sampling from a Empirical Likelihood Bayesian Posterior of Parameters Using Hamiltonian Monte Carlo

A tool to draw samples from a Empirical Likelihood Bayesian posterior of parameters using Hamiltonian Monte Carlo.

Last updated 2 months ago

1.30 score 2 scripts 178 downloads

CIpostSelect - Confidence Interval Post-Selection of Variable

Calculates confidence intervals after variable selection using repeated data splits. The package offers methods to address the challenges of post-selection inference, ensuring more accurate confidence intervals in models involving variable selection. The two main functions are 'lmps', which records the different models selected across multiple data splits as well as the corresponding coefficient estimates, and 'cips', which takes the lmps object as input to select variables and perform inferences using two types of voting.

Last updated 2 months ago

1.30 score 168 downloads

npcp - Some Nonparametric CUSUM Tests for Change-Point Detection in Possibly Multivariate Observations

Provides nonparametric CUSUM tests for detecting changes in possibly serially dependent univariate or low-dimensional multivariate observations. Retrospective tests sensitive to changes in the expectation, the variance, the covariance, the autocovariance, the distribution function, Spearman's rho, Kendall's tau, Gini's mean difference, and the copula are provided, as well as a test for detecting changes in the distribution of independent block maxima (with environmental studies in mind). The package also contains a test sensitive to changes in the autocopula and a combined test of stationarity sensitive to changes in the distribution function and the autocopula. The latest additions are an open-end sequential test based on the retrospective CUSUM statistic that can be used for monitoring changes in the mean of possibly serially dependent univariate observations, as well as closed-end and open-end sequential tests based on empirical distribution functions that can be used for monitoring changes in the contemporary distribution of possibly serially dependent univariate or low-dimensional multivariate observations.

Last updated 2 months ago

1.30 score 2 stars 9 scripts 230 downloads

MHDA - Massive Hierarchically Data Analysis

Three main functions about analyzing massive data (missing observations are allowed) considered from multiple layers of categories.

Last updated 2 months ago

1.30 score 343 downloads

eummd - Efficient Univariate Maximum Mean Discrepancy

Computes maximum mean discrepancy two-sample test for univariate data using the Laplacian kernel, as described in Bodenham and Kawahara (2023) <doi:10.1007/s11222-023-10271-x>. The p-value is computed using permutations. Also includes implementation for computing the robust median difference statistic 'Q_n' from Croux and Rousseeuw (1992) <doi:10.1007/978-3-662-26811-7_58> based on Johnson and Mizoguchi (1978) <doi:10.1137/0207013>.

Last updated 2 months ago

cpp

1.30 score 5 scripts 172 downloads

QWDAP - Quantum Walk-Based Data Analysis and Prediction

The modeling and prediction of graph-associated time series(GATS) based on continuous time quantum walk. This software is mainly used for feature extraction, modeling, prediction and result evaluation of GATS, including continuous time quantum walk simulation, feature selection, regression analysis, time series prediction, and series fit calculation. A paper is attached to the package for reference.

Last updated 3 months ago

cpp

1.30 score 249 downloads

MKMeans - A Modern K-Means (MKMeans) Clustering Algorithm

It's a Modern K-Means clustering algorithm allowing data of any number of dimensions, any initial center, and any number of clusters to expect.

Last updated 3 months ago

1.30 score 319 downloads

cctest - Canonical Correlations and Tests of Independence

A simple interface for multivariate correlation analysis that unifies various classical statistical procedures including t-tests, tests in univariate and multivariate linear models, parametric and nonparametric tests for correlation, Kruskal-Wallis tests, common approximate versions of Wilcoxon rank-sum and signed rank tests, chi-squared tests of independence, score tests of particular hypotheses in generalized linear models, canonical correlation analysis and linear discriminant analysis.

Last updated 3 months ago

1.30 score 258 downloads

DNAmotif - DNA Sequence Motifs

Motifs within biological sequences show a significant role. This package utilizes a user-defined threshold value (window size and similarity) to create consensus segments or motifs through local alignment of dynamic programming with gap and it calculates the frequency of each identified motif, offering a detailed view of their prevalence within the dataset. It allows for thorough exploration and understanding of sequence patterns and their biological importance.

Last updated 3 months ago

cpp

1.30 score 155 downloads

changepointTests - Change Point Tests for Joint Distributions and Copulas

Change point tests for joint distributions and copulas using pseudo-observations with multipliers or bootstrap. The processes used here have been defined in Bucher, Kojadinovic, Rohmer & Segers <doi:10.1016/j.jmva.2014.07.012> and Nasri & Remillard <doi:10.1016/j.jmva.2019.03.002>.

Last updated 3 months ago

1.30 score 190 downloads

EQUALSTATS - Algorithm Driven Statistical Analysis for Researchers without Coding Skills

Support functions for R-based 'EQUAL-STATS' software which automatically classifies the data and performs appropriate statistical tests. 'EQUAL-STATS' software is a shiny application with an user-friendly interface to perform complex statistical analysis. Gurusamy,K (2024)<doi:10.5281/zenodo.13354162>.

Last updated 3 months ago

1.30 score 252 downloads

SurveyDefense - Survey Defense Tool

This tool is designed to analyze up to 5 Fraud Detection Questions integrated into a survey, focusing on potential fraudulent participants to clean the survey dataset from potential fraud. Fraud Detection Questions and further information available at <https://surveydefense.org>.

Last updated 3 months ago

1.30 score 123 downloads

hytest - Hypothesis Testing Based on Neyman-Pearson Lemma and Likelihood Ratio Test

Error type I and Optimal critical values to test statistical hypothesis based on Neyman-Pearson Lemma and Likelihood ratio test based on random samples from several distributions. The families of distributions are Bernoulli, Exponential, Geometric, Inverse Normal, Normal, Gamma, Gumbel, Lognormal, Poisson, and Weibull. This package is an ideal resource to help with the teaching of Statistics. The main references for this package are Casella G. and Berger R. (2003,ISBN:0-534-24312-6 , "Statistical Inference. Second Edition", Duxbury Press) and Hogg, R., McKean, J., and Craig, A. (2019,ISBN:013468699, "Introduction to Mathematical Statistic. Eighth edition", Pearson).

Last updated 4 months ago

1.30 score 143 downloads

tetRys - Game of 'tetRys'

A game inspired by 'Tetris'. Opens a plot window device and starts a game of 'tetRys' in it. Steer the tetrominos with the arrow keys, press Pause to pause and Esc to end the game.

Last updated 4 months ago

1.30 score 150 downloads

decp - Complete Change Point Analysis

Provides a comprehensive approach for identifying and estimating change points in multivariate time series through various statistical methods. Implements the multiple change point detection methodology from Ryan & Killick (2023) <doi:10.1080/00401706.2023.2183261> and a novel estimation methodology from Fotopoulos et al. (2023) <doi:10.1007/s00362-023-01495-0> generalized to fit the detection methodologies. Performs both detection and estimation of change points, providing visualization and summary information of the estimation process for each detected change point.

Last updated 4 months ago

1.30 score 1 scripts 160 downloads

squant - Subgroup Identification Based on Quantitative Objectives

A subgroup identification method for precision medicine based on quantitative objectives. This method can handle continuous, binary and survival endpoint for both prognostic and predictive case. For the predictive case, the method aims at identifying a subgroup for which treatment is better than control by at least a pre-specified or auto-selected constant. For the prognostic case, the method aims at identifying a subgroup that is at least better than a pre-specified/auto-selected constant. The derived signature is a linear combination of predictors, and the selected subgroup are subjects with the signature > 0. The false discover rate when no true subgroup exists is controlled at a user-specified level.

Last updated 4 months ago

1.30 score 144 downloads

heteromixgm - Copula Graphical Models for Heterogeneous Mixed Data

A multi-core R package that allows for the statistical modeling of multi-group multivariate mixed data using Gaussian graphical models. Combining the Gaussian copula framework with the fused graphical lasso penalty, the 'heteromixgm' package can handle a wide variety of datasets found in various sciences. The package also includes an option to perform model selection using the AIC, BIC and EBIC information criteria, a function that plots partial correlation graphs based on the selected precision matrices, as well as simulate mixed heterogeneous data for exploratory or simulation purposes and one multi-group multivariate mixed agricultural dataset pertaining to maize yields. The package implements the methodological developments found in Hermes et al. (2024) <doi:10.1080/10618600.2023.2289545>.

Last updated 4 months ago

1.30 score 182 downloads

HMC - High Dimensional Mean Comparison with Projection and Cross-Fitting

Provides interpretable High-dimensional Mean Comparison methods (HMC). For example, users can use them to assess the difference in gene expression between two treatment groups. It is not a gene-by-gene comparison. Instead, we focus on the interplay between features and are interested in those that are predictive of the group label. The methods are valid frequentist tests and give sparse estimates indicating which features contribute to the test results.

Last updated 4 months ago

1.30 score 5 scripts 145 downloads

octopucs - Statistical Support for Hierarchical Clusters

Generates n hierarchical clustering hypotheses on subsets of classifiers (usually species in community ecology studies). The n clustering hypotheses are combined to generate a generalized cluster, and computes three metrics of support. 1) The average proportion of elements conforming the group in each of the n clusters (integrity). And 2) the contamination, i.e., the average proportion of elements from other groups that enter a focal group. 3) The probability of existence of the group gives the integrity and contamination in a Bayesian approach.

Last updated 4 months ago

1.30 score 159 downloads

GUEST - Graphical Models in Ultrahigh-Dimensional and Error-Prone Data via Boosting Algorithm

We consider the ultrahigh-dimensional and error-prone data. Our goal aims to estimate the precision matrix and identify the graphical structure of the random variables with measurement error corrected. We further adopt the estimated precision matrix to the linear discriminant function to do classification for multi-label classes.

Last updated 5 months ago

1.30 score 166 downloads

ganDataModel - Build a Metric Subspaces Data Model for a Data Source

Neural networks are applied to create a density value function which approximates density values for a data source. The trained neural network is analyzed for different levels. For each level metric subspaces with density values above a level are determined. The obtained set of metric subspaces and the trained neural network are assembled into a data model. A prerequisite is the definition of a data source, the generation of generative data and the calculation of density values. These tasks are executed using package 'ganGenerativeData' <https://cran.r-project.org/package=ganGenerativeData>.

Last updated 5 months ago

cpp

1.30 score 2 scripts 238 downloads

syllogi - Collection of Data Sets for Teaching Purposes

Collection (syllogi in greek) of real and fictitious data sets for teaching purposes. The datasets were manually entered by the author from the respective references as listed in the individual dataset documentation. The fictions datasets are the creation of the author, that he has found useful for teaching statistics.

Last updated 6 months ago

1.30 score 285 downloads

qlifetable - Managing and Building of Quarterly Life Tables

Manages, builds and computes statistics and datasets for the construction of quarterly (sub-annual) life tables by exploiting micro-data from either a general or an insured population. References: Pavía and Lledó (2022) <doi:10.1111/rssa.12769>. Pavía and Lledó (2023) <doi:10.1017/asb.2023.16>. Acknowledgements: The authors wish to thank Consellería de Educación, Universidades y Empleo, Generalitat Valenciana (grant AICO/2021/257), Ministerio de Ciencia e Innovación (grant PID2021-128228NB-I00) and Fundación Mapfre (grant 'Modelización espacial e intra-anual de la mortalidad en España. Una herramienta automática para el cálculo de productos de vida') for supporting this research.

Last updated 6 months ago

1.30 score 173 downloads

predhy.GUI - Genomic Prediction of Hybrid Performance with Graphical User Interface

Performs genomic prediction of hybrid performance using eight GS methods including GBLUP, BayesB, RKHS, PLS, LASSO, Elastic net, XGBoost and LightGBM. GBLUP: genomic best liner unbiased prediction, RKHS: reproducing kernel Hilbert space, PLS: partial least squares regression, LASSO: least absolute shrinkage and selection operator, XGBoost: extreme gradient boosting, LightGBM: light gradient boosting machine. It also provides fast cross-validation and mating design scheme for training population (Xu S et al (2016) <doi:10.1111/tpj.13242>; Xu S (2017) <doi:10.1534/g3.116.038059>).

Last updated 6 months ago

1.30 score 215 downloads

RsSimulx - Extension of 'lixoftConnectors' for 'Simulx'

Provides useful tools which supplement the use of 'Simulx' software and 'R' connectors ('Monolix Suite'). 'Simulx' is an easy, efficient and flexible application for clinical trial simulations. You need 'Simulx' software to be installed in order to use 'RsSimulx' package. Among others tasks, 'RsSimulx' provides the same functions as package 'mlxR' does with a compatibility with 'Simulx' software.

Last updated 7 months ago

1.30 score 2 stars 1 scripts 218 downloads

mvcauchy - Multivariate Cauchy Distribution

The Cauchy distribution is a special case of the t distribution when the degrees of freedom are equal to 1. The functions are related to the multivariate Cauchy distribution and include simulation, computation of the density, maximum likelihood estimation, contour plot of the bivariate Cauchy distribution, and discriminant analysis. References include: Nadarajah S. and Kotz S. (2008). "Estimation methods for the multivariate t distribution". Acta Applicandae Mathematicae, 102(1): 99--118. <doi:10.1007/s10440-008-9212-8>, and Kanti V. Mardia, John T. Kent and John M. Bibby (1979). "Multivariate analysis", ISBN:978-0124712522. Academic Press, London.

Last updated 7 months ago

1.30 score 489 downloads

wnl - Minimization Tool for Pharmacokinetic-Pharmacodynamic Data Analysis

This is a set of minimization tools (maximum likelihood estimation and least square fitting) to solve examples in the Johan Gabrielsson and Dan Weiner's book "Pharmacokinetic and Pharmacodynamic Data Analysis - Concepts and Applications" 5th ed. (ISBN:9198299107). Examples include linear and nonlinear compartmental model, turn-over model, single or multiple dosing bolus/infusion/oral models, allometry, toxicokinetics, reversible metabolism, in-vitro/in-vivo extrapolation, enterohepatic circulation, metabolite modeling, Emax model, inhibitory model, tolerance model, oscillating response model, enantiomer interaction model, effect compartment model, drug-drug interaction model, receptor occupancy model, and rebound phenomena model.

Last updated 7 months ago

1.30 score 1 stars 6 scripts 716 downloads

powerindexR - Measuring the Power in Voting Systems

This R package allows the determination of some distributions of the voters' power when passing laws in weighted voting situations.

Last updated 7 months ago

1.30 score 321 downloads

SurvEval - Methods for the Evaluation of Survival Models

Provides predictive accuracy tools to evaluate time-to-event survival models. This includes calculating the concordance probability estimate that incorporates the follow-up time for a particular study developed by Devlin, Gonen, Heller (2020)<doi:10.1007/s10985-020-09503-3>. It also evaluates the concordance probability estimate for nested Cox proportional hazards models using a projection-based approach by Heller and Devlin (under review).

Last updated 7 months ago

cpp

1.30 score 124 downloads

QuantileGH - Quantile Least Mahalanobis Distance Estimator for Tukey g-&-h Mixture

Functions for simulation, estimation, and model selection of finite mixtures of Tukey g-and-h distributions.

Last updated 8 months ago

1.30 score 333 downloads

Oncofilterfast - Aids in the Analysis of Genes Influencing Cancer Survival

Aids in the analysis of genes influencing cancer survival by including a principal function, calculator(), which calculates the P-value for each provided gene under the optimal cutoff in cancer survival studies. Grounded in methodologies from significant works, this package references Therneau's 'survival' package (Therneau, 2024; <https://CRAN.R-project.org/package=survival>) and the survival analysis extensions by Therneau and Grambsch (2000, ISBN 0-387-98784-3). It also integrates the 'survminer' package by Kassambara et al. (2021; <https://CRAN.R-project.org/package=survminer>), enhancing survival curve visualizations with 'ggplot2'.

Last updated 9 months ago

1.30 score 2 stars 1 scripts 111 downloads

eiCircles - Ecological Inference of RxC Tables by Overdispersed-Multinomial Models

Estimates RxC (R by C) vote transfer matrices (ecological contingency tables) from aggregate data using the model described in Forcina et al. (2012), as extension of the model proposed in Brown and Payne (1986). Allows incorporation of covariates. References: Brown, P. and Payne, C. (1986). ''Aggregate data, ecological regression and voting transitions''. Journal of the American Statistical Association, 81, 453–460. <DOI:10.1080/01621459.1986.10478290>. Forcina, A., Gnaldi, M. and Bracalente, B. (2012). ''A revised Brown and Payne model of voting behaviour applied to the 2009 elections in Italy''. Statistical Methods & Applications, 21, 109–119. <DOI:10.1007/s10260-011-0184-x>.

Last updated 9 months ago

1.30 score 158 downloads

cliot - Clinical Indices and Outcomes Tools

Collection of indices and tools relating to cardiovascular, nephrology, and hepatic research that aid epidemiological chort or retrospective chart review with big data. All indices and tools take commonly used lab values and patient demographics and measurements to compute various risk and predictive values for survival. References to original literature and validation contained in each function documentation.

Last updated 9 months ago

1.30 score 258 downloads

lphom - Ecological Inference by Linear Programming under Homogeneity

Provides a bunch of algorithms based on linear programming for estimating, under the homogeneity hypothesis, RxC ecological contingency tables (or vote transition matrices) using mainly aggregate data (from voting units). References: Pavía and Romero (2022) <doi:10.1177/00491241221092725>. Pavía (2023) <doi:10.1007/s43545-023-00658-y>. Pavía and Romero (2024) <doi:10.1093/jrsssa/qnae013>. Pavía (2024) A local convergent ecological inference algorithm for RxC tables. Pavía and Penadés (2024). A bottom-up approach for ecological inference. Romero, Pavía, Martín and Romero (2020) <doi:10.1080/02664763.2020.1804842>. Acknowledgements: The authors wish to thank Consellería de Educación, Universidades y Empleo, Generalitat Valenciana (grant AICO/2021/257) and Ministerio de Economía e Innovación (grant PID2021-128228NB-I00) for supporting this research.

Last updated 10 months ago

1.30 score 1 scripts 261 downloads

SKFCPD - Fast Online Changepoint Detection for Temporally Correlated Data

Sequential Kalman filter for scalable online changepoint detection by temporally correlated data. It enables fast single and multiple change points with missing values. See the reference: Hanmo Li, Yuedong Wang, Mengyang Gu (2023), <arXiv:2310.18611>.

Last updated 10 months ago

cpp

1.30 score 5 scripts 134 downloads

first - Factor Importance Ranking and Selection using Total Indices

A model-independent factor importance ranking and selection procedure that is based on total Sobol' indices. Please see Huang and Joseph (2024) <arXiv:2401.00800>. This research is supported by U.S. National Science Foundation grants DMS-2310637 and DMREF-1921873.

Last updated 10 months ago

1.30 score 11 scripts 184 downloads

IALS - Iterative Alternating Least Square Estimation for Large-Dimensional Matrix Factor Model

The matrix factor model has drawn growing attention for its advantage in achieving two-directional dimension reduction simultaneously for matrix-structured observations. In contrast to the Principal Component Analysis (PCA)-based methods, we propose a simple Iterative Alternating Least Squares (IALS) algorithm for matrix factor model, see the details in He et al. (2023) <arXiv:2301.00360>.

Last updated 10 months ago

1.30 score 138 downloads

multipleNCC - Weighted Cox-Regression for Nested Case-Control Data

Fit Cox proportional hazard models with a weighted partial likelihood. It handles one or multiple endpoints, additional matching and makes it possible to reuse controls for other endpoints Stoer NC and Samuelsen SO (2016) <doi:10.32614/rj-2016-030>.

Last updated 11 months ago

1.30 score 10 scripts 214 downloads

fbati - Gene by Environment Interaction and Conditional Gene Tests for Nuclear Families

Does family-based gene by environment interaction tests, joint gene, gene-environment interaction test, and a test of a set of genes conditional on another set of genes.

Last updated 11 months ago

cpp

1.30 score 5 scripts 348 downloads

dbstats - Distance-Based Statistics

Prediction methods where explanatory information is coded as a matrix of distances between individuals. Distances can either be directly input as a distances matrix, a squared distances matrix, an inner-products matrix or computed from observed predictors.

Last updated 11 months ago

1.30 score 1 stars 20 scripts 254 downloads

Branching - Simulation and Estimation for Branching Processes

Simulation and parameter estimation of multitype Bienayme - Galton - Watson processes.

Last updated 12 months ago

cpp

1.30 score 5 scripts 332 downloads

psbcGroup - Penalized Parametric and Semiparametric Bayesian Survival Models with Shrinkage and Grouping Priors

Algorithms to implement various Bayesian penalized survival regression models including: semiparametric proportional hazards models with lasso priors (Lee et al., Int J Biostat, 2011 <doi:10.2202/1557-4679.1301>) and three other shrinkage and group priors (Lee et al., Stat Anal Data Min, 2015 <doi:10.1002/sam.11266>); parametric accelerated failure time models with group/ordinary lasso prior (Lee et al. Comput Stat Data Anal, 2017 <doi:10.1016/j.csda.2017.02.014>).

Last updated 12 months ago

gsl

1.30 score 2 stars 4 scripts 198 downloads

longclust - Model-Based Clustering and Classification for Longitudinal Data

Clustering or classification of longitudinal data based on a mixture of multivariate t or Gaussian distributions with a Cholesky-decomposed covariance structure. Details in McNicholas and Murphy (2010) <doi:10.1002/cjs.10047> and McNicholas and Subedi (2012) <doi:10.1016/j.jspi.2011.11.026>.

Last updated 1 years ago

openblas

1.30 score 5 scripts 166 downloads

onlinePCA - Online Principal Component Analysis

Online PCA for multivariate and functional data using perturbation methods, low-rank incremental methods, and stochastic optimization methods.

Last updated 1 years ago

openblascpp

1.30 score 2 stars 28 scripts 156 downloads

EcoIndR - Ecological Indicators

Calculates several indices, such as of diversity, fluctuation, etc., and they are used to estimate ecological indicators.

Last updated 1 years ago

1.30 score 1 stars 1 scripts 271 downloads

EnvNicheR - Niche Estimation

A plot overlying the niche of multiple species is obtained: 1) to determine the niche conditions which favor a higher species richness, 2) to create a box plot with the range of environmental variables of the species, 3) to obtain a list of species in an area of the niche selected by the user and, 4) to estimate niche overlap among the species.

Last updated 1 years ago

1.30 score 3 scripts 198 downloads

OptionPricing - Option Pricing with Efficient Simulation Algorithms

Efficient Monte Carlo Algorithms for the price and the sensitivities of Asian and European Options under Geometric Brownian Motion.

Last updated 1 years ago

1.30 score 2 stars 5 scripts 356 downloads

sae2 - Small Area Estimation: Time-Series Models

Time series area-level models for small area estimation. The package supplements the functionality of the sae package. Specifically, it includes EBLUP fitting of the original Rao-Yu model, which in the original form did not have a spatial component. The package also offers a modified ('dynamic') version of the Rao-Yu model, replacing the assumption of stationarity. Both univariate and multivariate applications are supported. Of particular note is the allowance for covariance of the area-level sample estimates over time, as encountered in rotating panel designs such as the U.S. National Crime Victimization Survey or present in a time-series of 5-year estimates from the American Community Survey. Key references to the methods include J.N.K. Rao and I. Molina (2015, ISBN:9781118735787), J.N.K. Rao and M. Yu (1994) <doi:10.2307/3315407>, and R.E. Fay and R.A. Herriot (1979) <doi:10.1080/01621459.1979.10482505>.

Last updated 1 years ago

1.30 score 2 stars 6 scripts 151 downloads

GMMBoost - Likelihood-Based Boosting for Generalized Mixed Models

Likelihood-based boosting approaches for generalized mixed models are provided.

Last updated 1 years ago

1.30 score 9 scripts 323 downloads

lillies - Estimation of Life Years Lost

Estimation of life expectancy and Life Years Lost (LYL, or lillies for short) for a given population, for example those with a given disease or condition. In addition, the package can be used to compare estimates from different populations, or to estimate confidence intervals. Technical details of the method are available in Plana-Ripoll et al. (2020) <doi:10.1371/journal.pone.0228073> and Andersen (2017) <doi:10.1002/sim.7357>.

Last updated 1 years ago

1.30 score 2 stars 2 scripts 360 downloads

MBSP - Multivariate Bayesian Model with Shrinkage Priors

Gibbs sampler for fitting multivariate Bayesian linear regression with shrinkage priors (MBSP), using the three parameter beta normal family. The method is described in Bai and Ghosh (2018) <doi:10.1016/j.jmva.2018.04.010>.

Last updated 2 years ago

1.30 score 6 scripts 240 downloads

cml - Conditional Manifold Learning

Finds a low-dimensional embedding of high-dimensional data, conditioning on available manifold information. The current version supports conditional MDS (based on either conditional SMACOF in Bui (2021) <arXiv:2111.13646> or closed-form solution in Bui (2022) <doi:10.1016/j.patrec.2022.11.007>) and conditional ISOMAP in Bui (2021) <arXiv:2111.13646>.

Last updated 2 years ago

1.30 score 2 scripts 243 downloads

CPE - Concordance Probability Estimates in Survival Analysis

Concordance probability estimate (CPE) is a commonly used performance measure in survival analysis that evaluates the predictive accuracy of a survival model. It measures how well a model can distinguish between pairs of individuals with different survival times. Specifically, it calculate the proportion of all pairs of individuals whose predicted survival times are correctly ordered.

Last updated 2 years ago

1.30 score 2 stars 10 scripts 267 downloads

ChaosGame - Chaos Game

The main objective of the package is to enter a word of at least two letters based on which an Iterated Function System with Probabilities is constructed, and a two-dimensional fractal containing the chosen word infinitely often is generated via the Chaos Game. Additionally, the package allows to project the two-dimensional fractal on several three-dimensional surfaces and to transform the fractal into another fractal with uniform marginals.

Last updated 2 years ago

1.30 score 2 stars 3 scripts 309 downloads

ARIMAANN - Time Series Forecasting using ARIMA-ANN Hybrid Model

Testing, Implementation, and Forecasting of the ARIMA-ANN hybrid model. The ARIMA-ANN hybrid model combines the distinct strengths of the Auto-Regressive Integrated Moving Average (ARIMA) model and the Artificial Neural Network (ANN) model for time series forecasting.For method details see Zhang, GP (2003) <doi:10.1016/S0925-2312(01)00702-0>.

Last updated 2 years ago

1.30 score 2 stars 295 downloads

ExactCIdiff - Inductive Confidence Intervals for the Difference Between Two Proportions

This is a package for exact Confidence Intervals for the difference between two independent or dependent proportions.

Last updated 2 years ago

1.30 score 5 scripts 229 downloads

sumFREGAT - Fast Region-Based Association Tests on Summary Statistics

An adaptation of classical region/gene-based association analysis techniques to the use of summary statistics (P values and effect sizes) and correlations between genetic variants as input. It is a tool to perform the most popular and efficient gene-based tests using the results of genome-wide association (meta-)analyses without having the original genotypes and phenotypes at hand. See for details: Svishcheva et al (2019) Gene-based association tests using GWAS summary statistics. Bioinformatics. Belonogova et al (2022) SumSTAAR: A flexible framework for gene-based association studies using GWAS summary statistics. PLOS Comp Biol.

Last updated 3 years ago

cpp

1.30 score 2 stars 6 scripts 272 downloads

sta - Seasonal Trend Analysis for Time Series Imagery in R

Efficiently estimate shape parameters of periodic time series imagery with which a statistical seasonal trend analysis (STA) is subsequently performed. STA output can be exported in conventional raster formats. Methods to visualize STA output are also implemented as well as the calculation of additional basic statistics. STA is based on (R. Eastman, F. Sangermano, B. Ghimire, H. Zhu, H. Chen, N. Neeti, Y. Cai, E. Machado and S. Crema, 2009) <doi:10.1080/01431160902755338>.

Last updated 3 years ago

1.30 score 9 scripts 114 downloads

NSAE - Nonstationary Small Area Estimation

Executes nonstationary Fay-Herriot model and nonstationary generalized linear mixed model for small area estimation.The empirical best linear unbiased predictor (EBLUP) under stationary and nonstationary Fay-Herriot models and empirical best predictor (EBP) under nonstationary generalized linear mixed model along with the mean squared error estimation are included. EBLUP for prediction of non-sample area is also included under both stationary and nonstationary Fay-Herriot models. This extension to the Fay-Herriot model that accounts for the presence of spatial nonstationarity was developed by Hukum Chandra, Nicola Salvati and Ray Chambers (2015) <doi:10.1093/jssam/smu026> and nonstationary generalized linear mixed model was developed by Hukum Chandra, Nicola Salvati and Ray Chambers (2017) <doi:10.1016/j.spasta.2017.01.004>. This package is dedicated to the memory of Dr. Hukum Chandra who passed away while the package creation was in progress.

Last updated 3 years ago

1.30 score 2 stars 186 downloads

tsrobprep - Robust Preprocessing of Time Series Data

Methods for handling the missing values outliers are introduced in this package. The recognized missing values and outliers are replaced using a model-based approach. The model may consist of both autoregressive components and external regressors. The methods work robust and efficient, and they are fully tunable. The primary motivation for writing the package was preprocessing of the energy systems data, e.g. power plant production time series, but the package could be used with any time series data. For details, see Narajewski et al. (2021) <doi:10.1016/j.softx.2021.100809>.

Last updated 3 years ago

1.30 score 2 stars 236 downloads

RGE - Response from Genotype to Environment

Compute yield-stability index based on Bayesian methodology, which is useful for analyze multi-environment trials in plant breeding programs. References: Cotes Torres JM, Gonzalez Jaimes EP, and Cotes Torres A (2016) <https://revistas.unimilitar.edu.co/index.php/rfcb/article/view/2037> Seleccion de Genotipos con Alta Respuesta y Estabilidad Fenotipica en Pruebas Regionales: Recuperando el Concepto Biologico.

Last updated 3 years ago

1.30 score 6 scripts 156 downloads

GreyModel - Fitting and Forecasting of Grey Model

Testing, Implementation and Forecasting of Grey Model (GM(1, 1)). For method details see Hsu, L. and Wang, C. (2007). <doi:10.1016/j.techfore.2006.02.005>.

Last updated 3 years ago

1.30 score 2 stars 4 scripts 189 downloads

EQUIVNONINF - Testing for Equivalence and Noninferiority

Making available in R the complete set of programs accompanying S. Wellek's (2010) monograph ''Testing Statistical Hypotheses of Equivalence and Noninferiority. Second Edition'' (Chapman&Hall/CRC).

Last updated 3 years ago

1.30 score 41 scripts 190 downloads

FertBoot - Fertilizer Response Curve Analysis by Bootstrapping Residuals

Quantify variability (such as confidence interval) of fertilizer response curves and optimum fertilizer rates using bootstrapping residuals with several popular non-linear and linear models.

Last updated 4 years ago

1.30 score 2 stars 1 scripts 143 downloads

NonlinearTSA - Nonlinear Time Series Analysis

Function and data sets in the book entitled "Nonlinear Time Series Analysis with R Applications" B.Guris (2020). The book will be published in Turkish and the original name of this book will be "R Uygulamali Dogrusal Olmayan Zaman Serileri Analizi". It is possible to perform nonlinearity tests, nonlinear unit root tests, nonlinear cointegration tests and estimate nonlinear error correction models by using the functions written in this package. The Momentum Threshold Autoregressive (MTAR), the Smooth Threshold Autoregressive (STAR) and the Self Exciting Threshold Autoregressive (SETAR) type unit root tests can be performed using the functions written. In addition, cointegration tests using the Momentum Threshold Autoregressive (MTAR), the Smooth Threshold Autoregressive (STAR) and the Self Exciting Threshold Autoregressive (SETAR) models can be applied. It is possible to estimate nonlinear error correction models. The Granger causality test performed using nonlinear models can also be applied.

Last updated 4 years ago

1.30 score 2 stars 213 downloads

nlsmsn - Fitting Nonlinear Models with Scale Mixture of Skew-Normal Distributions

Fit univariate non-linear scale mixture of skew-normal(NL-SMSN) regression, details in Garay, Lachos and Abanto-Valle (2011) <doi:10.1016/j.jkss.2010.08.003> and Lachos, Bandyopadhyay and Garay (2011) <doi:10.1016/j.spl.2011.03.019>.

Last updated 4 years ago

1.30 score 2 stars 3 scripts 218 downloads

spass - Study Planning and Adaptation of Sample Size

Sample size estimation and blinded sample size reestimation in Adaptive Study Design.

Last updated 4 years ago

cpp

1.30 score 122 downloads

miCoPTCM - Promotion Time Cure Model with Mis-Measured Covariates

Fits Semiparametric Promotion Time Cure Models, taking into account (using a corrected score approach or the SIMEX algorithm) or not the measurement error in the covariates, using a backfitting approach to maximize the likelihood.

Last updated 4 years ago

1.30 score 5 scripts 263 downloads

FAwR - Functions and Datasets for "Forest Analytics with R"

Provides functions and datasets from the book "Forest Analytics with R".

Last updated 4 years ago

1.30 score 2 stars 15 scripts 282 downloads

FHDI - Fractional Hot Deck and Fully Efficient Fractional Imputation

Impute general multivariate missing data with the fractional hot deck imputation based on Jaekwang Kim (2011) <doi:10.1093/biomet/asq073>.

Last updated 4 years ago

1.30 score 2 stars 4 scripts 240 downloads

PhysActBedRest - Marks Periods of 'Bedrest' in Actigraph Accelerometer Data

Contains a function to categorize accelerometer readings collected in free-living (e.g., for 24 hours/day for 7 days), preprocessed and compressed as counts (unit-less value) in a specified time period termed epoch (e.g., 1 minute) as either bedrest (sleep) or active. The input is a matrix with a timestamp column and a column with number of counts per epoch. The output is the same dataframe with an additional column termed bedrest. In the bedrest column each line (epoch) contains a function-generated classification 'br' or 'a' denoting bedrest/sleep and activity, respectively. The package is designed to be used after wear/nonwear marking function in the 'PhysicalActivity' package. Version 1.1 adds preschool thresholds and corrects for possible errors in algorithm implementation.

Last updated 4 years ago

1.30 score 1 stars 2 scripts 165 downloads

sanon - Stratified Analysis with Nonparametric Covariable Adjustment

There are several functions to implement the method for analysis in a randomized clinical trial with strata with following key features. A stratified Mann-Whitney estimator addresses the comparison between two randomized groups for a strictly ordinal response variable. The multivariate vector of such stratified Mann-Whitney estimators for multivariate response variables can be considered for one or more response variables such as in repeated measurements and these can have missing completely at random (MCAR) data. Non-parametric covariance adjustment is also considered with the minimal assumption of randomization. The p-value for hypothesis test and confidence interval are provided.

Last updated 5 years ago

1.30 score 1 stars 6 scripts 221 downloads

ecipex - Efficient Calculation of Fine Structure Isotope Patterns via Fourier Transforms of Simplex-Based Elemental Models

Provides a function that quickly computes the fine structure isotope patterns of a set of chemical formulas to a given degree of accuracy (up to the limit set by errors in floating point arithmetic). A data-set comprising the masses and isotopic abundances of individual elements is also provided and calculation of isotopic gross structures is also supported.

Last updated 5 years ago

1.30 score 1 stars 1 scripts 154 downloads

Bivariate.Pareto - Bivariate Pareto Models

Perform competing risks analysis under bivariate Pareto models. See Shih et al. (2019) <doi:10.1080/03610926.2018.1425450> for details.

Last updated 5 years ago

1.30 score 20 scripts 209 downloads

gStream - Graph-Based Sequential Change-Point Detection for Streaming Data

Uses an approach based on k-nearest neighbor information to sequentially detect change-points. Offers analytic approximations for false discovery control given user-specified average run length. Can be applied to any type of data (high-dimensional, non-Euclidean, etc.) as long as a reasonable similarity measure is available. See references (1) Chen, H. (2019) Sequential change-point detection based on nearest neighbors. The Annals of Statistics, 47(3):1381-1407. (2) Chu, L. and Chen, H. (2018) Sequential change-point detection for high-dimensional and non-Euclidean data <arXiv:1810.05973>.

Last updated 6 years ago

1.30 score 2 stars 70 scripts 116 downloads

texteffect - Discovering Latent Treatments in Text Corpora and Estimating Their Causal Effects

Implements the approach described in Fong and Grimmer (2016) <https://aclweb.org/anthology/P/P16/P16-1151.pdf> for automatically discovering latent treatments from a corpus and estimating the average marginal component effect (AMCE) of each treatment. The data is divided into a training and test set. The supervised Indian Buffet Process (sibp) is used to discover latent treatments in the training set. The fitted model is then applied to the test set to infer the values of the latent treatments in the test set. Finally, Y is regressed on the latent treatments in the test set to estimate the causal effect of each treatment.

Last updated 6 years ago

1.30 score 2 stars 7 scripts 113 downloads

BNSL - Bayesian Network Structure Learning

From a given data frame, this package learns its Bayesian network structure based on a selected score.

Last updated 6 years ago

cpp

1.30 score 8 scripts 216 downloads

glmc - Fitting Generalized Linear Models Subject to Constraints

Fits generalized linear models where the parameters are subject to linear constraints. The model is specified by giving a symbolic description of the linear predictor, a description of the error distribution, and a matrix of constraints on the parameters.

Last updated 6 years ago

1.30 score 1 stars 20 scripts 195 downloads

ELYP - Empirical Likelihood Analysis for the Cox Model and Yang-Prentice (2005) Model

Empirical likelihood ratio tests for the Yang and Prentice (short/long term hazards ratio) models. Empirical likelihood tests within a Cox model, for parameters defined via both baseline hazard function and regression parameters.

Last updated 6 years ago

1.30 score 23 scripts 166 downloads

PlasmaMutationDetector - Tumor Mutation Detection in Plasma

Aims at detecting single nucleotide variation (SNV) and insertion/deletion (INDEL) in circulating tumor DNA (ctDNA), used as a surrogate marker for tumor, at each base position of an Next Generation Sequencing (NGS) analysis. Mutations are assessed by comparing the minor-allele frequency at each position to the measured PER in control samples.

Last updated 7 years ago

1.30 score 160 downloads

PBNPA - Permutation Based Non-Parametric Analysis of CRISPR Screen Data

Permutation based non-parametric analysis of CRISPR screen data. Details about this algorithm are published in the following paper published on BMC genomics, Jia et al. (2017) <doi:10.1186/s12864-017-3938-5>: A permutation-based non-parametric analysis of CRISPR screen data. Please cite this paper if you use this algorithm for your paper.

Last updated 7 years ago

1.30 score 4 scripts 115 downloads

SBSDiff - Satorra-Bentler Scaled Chi-Squared Difference Test

Calculates a Satorra-Bentler scaled chi-squared difference test between nested models that were estimated using maximum likelihood (ML) with robust standard errors, which cannot be calculated the traditional way. For details see Satorra & Bentler (2001) <doi:10.1007/bf02296192> and Satorra & Bentler (2010) <doi:10.1007/s11336-009-9135-y>. This package may be particularly helpful when used in conjunction with 'Mplus' software, specifically when implementing the complex survey option. In such cases, the model estimator in 'Mplus' defaults to ML with robust standard errors.

Last updated 7 years ago

1.30 score 3 scripts 143 downloads

gb - Generalize Lambda Distribution and Generalized Bootstrapping

A collection of algorithms and functions for fitting data to a generalized lambda distribution via moment matching methods, and generalized bootstrapping.

Last updated 7 years ago

1.30 score 7 scripts 201 downloads

mogavs - Multiobjective Genetic Algorithm for Variable Selection in Regression

Functions for exploring the best subsets in regression with a genetic algorithm. The package is much faster than methods relying on complete enumeration, and is suitable for data sets with large number of variables. For more information, see Sinha, Malo & Kuosmanen (2015) <doi:10.1080/10618600.2014.899236>.

Last updated 7 years ago

1.30 score 20 scripts 114 downloads

CoClust - Copula Based Cluster Analysis

A copula based clustering algorithm that finds clusters according to the complex multivariate dependence structure of the data generating process. The updated version of the algorithm is described in Di Lascio, F.M.L. and Giannerini, S. (2016). "Clustering dependent observations with copula functions". Statistical Papers, p.1-17. <doi:10.1007/s00362-016-0822-3>.

Last updated 7 years ago

1.30 score 2 stars 10 scripts 228 downloads

SegCorr - Detecting Correlated Genomic Regions

Performs correlation matrix segmentation and applies a test procedure to detect highly correlated regions in gene expression.

Last updated 7 years ago

1.30 score 1 stars 7 scripts 107 downloads

ConSpline - Partial Linear Least-Squares Regression using Constrained Splines

Given response y, continuous predictor x, and covariate matrix, the relationship between E(y) and x is estimated with a shape constrained regression spline. Function outputs fits and various types of inference.

Last updated 7 years ago

1.30 score 2 stars 5 scripts 154 downloads

LGEWIS - Tests for Genetic Association/Gene-Environment Interaction in Longitudinal Studies

Functions for genome-wide association studies (GWAS)/gene-environment-wide interaction studies (GEWIS) with longitudinal outcomes and exposures. He et al. (2017) "Set-Based Tests for Gene-Environment Interaction in Longitudinal Studies" and He et al. (2017) "Rare-variant association tests in longitudinal studies, with an application to the Multi-Ethnic Study of Atherosclerosis (MESA)".

Last updated 7 years ago

1.30 score 9 scripts 127 downloads

plaqr - Partially Linear Additive Quantile Regression

Estimation, prediction, thresholding, transformation, and plotting for partially linear additive quantile regression. Intuitive functions for fitting and plotting partially linear additive quantile regression models. Uses and works with functions from the 'quantreg' package.

Last updated 7 years ago

1.30 score 2 stars 8 scripts 149 downloads

highmean - Two-Sample Tests for High-Dimensional Mean Vectors

Provides various tests for comparing high-dimensional mean vectors in two sample populations.

Last updated 8 years ago

1.30 score 2 stars 13 scripts 127 downloads

GMDH - Short Term Forecasting via GMDH-Type Neural Network Algorithms

Group method of data handling (GMDH) - type neural network algorithm is the heuristic self-organization method for modelling the complex systems. In this package, GMDH-type neural network algorithms are applied to make short term forecasting for a univariate time series.

Last updated 8 years ago

1.30 score 2 stars 8 scripts 213 downloads

AntAngioCOOL - Anti-Angiogenic Peptide Prediction

Machine learning based package to predict anti-angiogenic peptides using heterogeneous sequence descriptors. 'AntAngioCOOL' exploits five descriptor types of a peptide of interest to do prediction including: pseudo amino acid composition, k-mer composition, k-mer composition (reduced alphabet), physico-chemical profile and atomic profile. According to the obtained results, 'AntAngioCOOL' reached to a satisfactory performance in anti-angiogenic peptide prediction on a benchmark non-redundant independent test dataset.

Last updated 8 years ago

openjdk

1.30 score 1 scripts 179 downloads

MCMC4Extremes - Posterior Distribution of Extreme Value Models in R

Provides some function to perform posterior estimation for some distribution, with emphasis to extreme value distributions. It contains some extreme datasets, and functions that perform the runs of posterior points of the GPD and GEV distribution. The package calculate some important extreme measures like return level for each t periods of time, and some plots as the predictive distribution, and return level plots.

Last updated 8 years ago

1.30 score 20 scripts 175 downloads

rasclass - Supervised Raster Image Classification

Software to perform supervised and pixel based raster image classification. It has been designed to facilitate land-cover analysis. Five classification algorithms can be used: Maximum Likelihood Classification, Multinomial Logistic Regression, Neural Networks, Random Forests and Support Vector Machines. The output includes the classified raster and standard classification accuracy assessment such as the accuracy matrix, the overall accuracy and the kappa coefficient. An option for in-sample verification is available.

Last updated 9 years ago

1.30 score 2 stars 8 scripts 140 downloads

seqtest - Sequential Triangular Test

Sequential triangular test for the arithmetic mean in one- and two- samples, proportions in one- and two-samples, and the Pearson's correlation coefficient.

Last updated 9 years ago

1.30 score 20 scripts 123 downloads

GroupTest - Multiple Testing Procedure for Grouped Hypotheses

Contains functions for a two-stage multiple testing procedure for grouped hypothesis, aiming at controlling both the total posterior false discovery rate and within-group false discovery rate.

Last updated 9 years ago

1.30 score 6 scripts 130 downloads

pco - Panel Cointegration Tests

Computation of the Pedroni (1999) panel cointegration test statistics. Reported are the empirical and the standardized values.

Last updated 9 years ago

1.30 score 10 scripts 340 downloads

modMax - Community Structure Detection via Modularity Maximization

The algorithms implemented here are used to detect the community structure of a network. These algorithms follow different approaches, but are all based on the concept of modularity maximization.

Last updated 9 years ago

1.30 score 2 stars 10 scripts 116 downloads

OptHedging - Estimation of value and hedging strategy of call and put options.

Estimation of value and hedging strategy of call and put options, based on optimal hedging and Monte Carlo method, from Chapter 3 of 'Statistical Methods for Financial Engineering', by Bruno Remillard, CRC Press, (2013).

Last updated 11 years ago

1.30 score 2 stars 3 scripts 143 downloads

Inventorymodel - Inventory Models

Determination of the optimal policy in inventory problems from a game-theoretic perspective.

Last updated 1 years ago

1.28 score 1 stars 19 scripts 262 downloads

SALTSampler - Efficient Sampling on the Simplex

The SALTSampler package facilitates Monte Carlo Markov Chain (MCMC) sampling of random variables on a simplex. A Self-Adjusting Logit Transform (SALT) proposal is used so that sampling is still efficient even in difficult cases, such as those in high dimensions or with parameters that differ by orders of magnitude. Special care is also taken to maintain accuracy even when some coordinates approach 0 or 1 numerically. Diagnostic and graphic functions are included in the package, enabling easy assessment of the convergence and mixing of the chain within the constrained space.

Last updated 7 years ago

1.28 score 19 scripts 106 downloads

bingat - Binary Graph Analysis Tools

Tools to analyze binary graph objects.

Last updated 7 years ago

1.28 score 19 scripts 216 downloads

gmDatabase - Accessing a Geometallurgical Database with R

A template for a geometallurgical database and a fast and easy interface for accessing it is provided in this package.

Last updated 9 years ago

1.28 score 19 scripts 119 downloads

diffIRT - Diffusion IRT Models for Response and Response Time Data

Package to fit diffusion-based IRT models to response and response time data. Models are fit using marginal maximum likelihood. Parameter restrictions (fixed value and equality constraints) are possible. In addition, factor scores (person drift rate and person boundary separation) can be estimated. Model fit assessment tools are also available. The traditional diffusion model can be estimated as well.

Last updated 9 years ago

1.28 score 19 scripts 162 downloads

PROreg - Patient Reported Outcomes Regression Analysis

It offers a wide variety of techniques, such as graphics, recoding, or regression models, for a comprehensive analysis of patient-reported outcomes (PRO). Especially novel is the broad range of regression models based on the beta-binomial distribution useful for analyzing binomial data with over-dispersion in cross-sectional, longitudinal, or multidimensional response studies (see Najera-Zuloaga J., Lee D.-J. and Arostegui I. (2019) <doi:10.1002/bimj.201700251>).

Last updated 10 months ago

1.27 score 41 scripts 1.9k downloads

perms - Fast Permutation Computation

Implements the algorithm of Christensen (2024) <doi:10.1214/22-BA1353> for estimating marginal likelihoods via permutation counting.

Last updated 4 months ago

1.26 score 18 scripts 172 downloads

D3GB - Interactive Genome Browser

Creates interactive genome browser. It joins the data analysis power of 'R' and the visualization libraries of 'JavaScript' in one package. Barrios, D. & Prieto, C. (2017) <doi:10.1089/cmb.2016.0213>.

Last updated 7 months ago

1.26 score 18 scripts 516 downloads

highriskzone - Determining and Evaluating High-Risk Zones

Functions for determining and evaluating high-risk zones and simulating and thinning point process data, as described in 'Determining high risk zones using point process methodology - Realization by building an R package' Seibold (2012) <http://highriskzone.r-forge.r-project.org/Bachelorarbeit.pdf> and 'Determining high-risk zones for unexploded World War II bombs by using point process methodology', Mahling et al. (2013) <doi:10.1111/j.1467-9876.2012.01055.x>.

Last updated 1 years ago

1.26 score 18 scripts 283 downloads

discoveR - Exploratory Data Analysis System

Performs an exploratory data analysis through a 'shiny' interface. It includes basic methods such as the mean, median, mode, normality test, among others. It also includes clustering techniques such as Principal Components Analysis, Hierarchical Clustering and the K-Means Method.

Last updated 2 years ago

1.26 score 1 stars 18 scripts 418 downloads

csci - Current Status Confidence Intervals

Calculates pointwise confidence intervals for the cumulative distribution function of the event time for current status data, data where each individual is assessed at one time to see if they had the event or not by the assessment time.

Last updated 4 years ago

1.26 score 18 scripts 162 downloads

RobustLinearReg - Robust Linear Regressions

Provides an easy way to compute the Theil Sehn Regression method and also the Siegel Regression Method which are both robust methods base on the median of slopes between all pairs of data. In contrast with the least squared linear regression, these methods are not sensitive to outliers. Theil, H. (1992) <doi:10.1007/978-94-011-2546-8_20>, Sen, P. K. (1968) <doi:10.1080/01621459.1968.10480934>.

Last updated 5 years ago

1.26 score 18 scripts 238 downloads

naivereg - Nonparametric Additive Instrumental Variable Estimator and Related IV Methods

In empirical studies, instrumental variable (IV) regression is the signature method to solve the endogeneity problem. If we enforce the exogeneity condition of the IV, it is likely that we end up with a large set of IVs without knowing which ones are good. Also, one could face the model uncertainty for structural equation, as large micro dataset is commonly available nowadays. This package uses adaptive group lasso and B-spline methods to select the nonparametric components of the IV function, with the linear function being a special case (naivereg). The package also incorporates two stage least squares estimator (2SLS), generalized method of moment (GMM), generalized empirical likelihood (GEL) methods post instrument selection, logistic-regression instrumental variables estimator (LIVE, for dummy endogenous variable problem), double-selection plus instrumental variable estimator (DS-IV) and double selection plus logistic regression instrumental variable estimator (DS-LIVE), where the double selection methods are useful for high-dimensional structural equation models. The naivereg is nonparametric version of 'ivregress' in 'Stata' with IV selection and high dimensional features. The package is based on the paper by Q. Fan and W. Zhong, "Nonparametric Additive Instrumental Variable Estimator: A Group Shrinkage Estimation Perspective" (2018), Journal of Business & Economic Statistics <doi:10.1080/07350015.2016.1180991> as well as a series of working papers led by the same authors.

Last updated 5 years ago

1.26 score 1 stars 18 scripts 121 downloads

stilt - Separable Gaussian Process Interpolation (Emulation)

Functions for simplified emulation of time series computer model output in model parameter space using Gaussian processes. Stilt can be used more generally for Kriging of spatio-temporal fields. There are functions to predict at new parameter settings, to test the emulator using cross-validation (which includes information on 95% confidence interval empirical coverage), and to produce contour plots over 2D slices in model parameter space.

Last updated 6 years ago

1.26 score 18 scripts 139 downloads

activegp - Gaussian Process Based Design and Analysis for the Active Subspace Method

The active subspace method is a sensitivity analysis technique that finds important linear combinations of input variables for a simulator. This package provides functions allowing estimation of the active subspace without gradient information using Gaussian processes as well as sequential experimental design tools to minimize the amount of data required to do so. Implements Wycoff et al. (JCGS, 2021) <doi:10.48550/arXiv.1907.11572>.

Last updated 7 months ago

cpp

1.23 score 17 scripts 379 downloads

psgp - Projected Spatial Gaussian Process Methods

Implements projected sparse Gaussian process Kriging (Ingram 'et. al.', 2008, <doi:10.1007/s00477-007-0163-9>) as an additional method for the 'intamap' package. More details on implementation (Barillec 'et. al.', 2010, <doi:10.1016/j.cageo.2010.05.008>).

Last updated 1 years ago

openblascpp

1.23 score 17 scripts 320 downloads

PLRModels - Statistical Inference in Partial Linear Regression Models

Contains statistical inference tools applied to Partial Linear Regression (PLR) models. Specifically, point estimation, confidence intervals estimation, bandwidth selection, goodness-of-fit tests and analysis of covariance are considered. Kernel-based methods, combined with ordinary least squares estimation, are used and time series errors are allowed. In addition, these techniques are also implemented for both parametric (linear) and nonparametric regression models.

Last updated 1 years ago

1.23 score 17 scripts 281 downloads

cosso - Fit Regularized Nonparametric Regression Models Using COSSO Penalty

The COSSO regularization method automatically estimates and selects important function components by a soft-thresholding penalty in the context of smoothing spline ANOVA models. Implemented models include mean regression, quantile regression, logistic regression and the Cox regression models.

Last updated 2 years ago

1.23 score 1 stars 17 scripts 223 downloads

ImportanceIndice - Analyzing Data Through of Percentage of Importance Indice and Its Derivations

The Percentage of Importance Indice (Percentage_I.I.) bases in magnitudes, frequencies, and distributions of occurrence of an event (DEMOLIN-LEITE, 2021) <http://cjascience.com/index.php/CJAS/article/view/1009/1350>. This index can detect the key loss sources (L.S) and solution sources (S.S.), classifying them according to their importance in terms of loss or income gain, on the productive system. The Percentage_I.I. = [(ks1 x c1 x ds1)/SUM (ks1 x c1 x ds1) + (ks2 x c2 x ds2) + (ksn x cn x dsn)] x 100. key source (ks) is obtained using simple regression analysis and magnitude (abundance). Constancy (c) is SUM of occurrence of L.S. or S.S. on the samples (absence = 0 or presence = 1), and distribution source (ds) is obtained using chi-square test. This index has derivations: i.e., i) Loss estimates and solutions effectiveness and ii) Attention and non-attention levels (DEMOLIN-LEITE,2024) <DOI: 10.1590/1519-6984.253215>.

Last updated 2 years ago

1.23 score 17 scripts 178 downloads

currentSurvival - Estimation of CCI and CLFS Functions

The currentSurvival package contains functions for the estimation of the current cumulative incidence (CCI) and the current leukaemia-free survival (CLFS). The CCI is the probability that a patient is alive and in any disease remission (e.g. complete cytogenetic remission in chronic myeloid leukaemia) after initiating his or her therapy (e.g. tyrosine kinase therapy for chronic myeloid leukaemia). The CLFS is the probability that a patient is alive and in any disease remission after achieving the first disease remission.

Last updated 3 years ago

1.23 score 17 scripts 401 downloads

influence.SEM - Case Influence in Structural Equation Models

A set of tools for evaluating several measures of case influence for structural equation models.

Last updated 3 years ago

1.23 score 1 stars 17 scripts 296 downloads

WWGbook - Functions and Datasets for WWGbook

Book is "Linear Mixed Models: A Practical Guide Using Statistical Software" published in 2006 by Chapman Hall / CRC Press.

Last updated 3 years ago

1.23 score 1 stars 17 scripts 797 downloads

randcorr - Generate a Random p x p Correlation Matrix

Implements the algorithm by Pourahmadi and Wang (2015) <doi:10.1016/j.spl.2015.06.015> for generating a random p x p correlation matrix. Briefly, the idea is to represent the correlation matrix using Cholesky factorization and p(p-1)/2 hyperspherical coordinates (i.e., angles), sample the angles from a particular distribution and then convert to the standard correlation matrix form. The angles are sampled from a distribution with pdf proportional to sin^k(theta) (0 < theta < pi, k >= 1) using the efficient sampling algorithm described in Enes Makalic and Daniel F. Schmidt (2018) <arXiv:1809.05212>.

Last updated 6 years ago

1.23 score 1 stars 17 scripts 121 downloads

DOvalidation - Kernel Hazard Estimation with Best One-Sided and Double One-Sided Cross-Validation

Local linear hazard estimator and its multiplicatively bias correction, including three bandwidth selection methods: best one-sided cross-validation, double one-sided cross-validation, and standard cross-validation.

Last updated 7 years ago

1.23 score 1 stars 17 scripts 123 downloads

modelwordcloud - Model Word Clouds

Makes a word cloud of text, sized by the frequency of the word, and colored either by user-specified colors or colored by the strength of the coefficient of that text derived from a regression model.

Last updated 7 years ago

1.23 score 17 scripts 164 downloads

factorplot - Presenting Pairwise Comparisons

The tools herein calculate, print, summarize and plot pairwise differences that result from generalized linear models, general linear hypothesis tests and multinomial logistic regression models. For more information, see Armstrong (2013) <doi:10.32614/RJ-2013-021>.

Last updated 7 months ago

1.20 score 16 scripts 253 downloads

GsymPoint - Estimation of the Generalized Symmetry Point, an Optimal Cutpoint in Continuous Diagnostic Tests

Estimation of the cutpoint defined by the Generalized Symmetry point in a binary classification setting based on a continuous diagnostic test or marker. Two methods have been implemented to construct confidence intervals for this optimal cutpoint, one based on the Generalized Pivotal Quantity and the other based on Empirical Likelihood. Numerical and graphical outputs for these two methods are easily obtained.

Last updated 1 years ago

1.20 score 16 scripts 209 downloads

sglg - Fitting Semi-Parametric Generalized log-Gamma Regression Models

Set of tools to fit a linear multiple or semi-parametric regression models with the possibility of non-informative random right-censoring. Under this setup, the localization parameter of the response variable distribution is modeled by using linear multiple regression or semi-parametric functions, whose non-parametric components may be approximated by natural cubic spline or P-splines. The supported distribution for the model error is a generalized log-gamma distribution which includes the generalized extreme value and standard normal distributions as important special cases. Inference is based on penalized likelihood and bootstrap methods. Also, some numerical and graphical devices for diagnostic of the fitted models are offered.

Last updated 2 years ago

1.20 score 16 scripts 320 downloads

pocrm - Dose Finding in Drug Combination Phase I Trials Using PO-CRM

Provides functions to implement and simulate the partial order continual reassessment method (PO-CRM) of Wages, Conaway and O'Quigley (2011) <doi:10.1177/1740774511408748> for use in Phase I trials of combinations of agents. Provides a function for generating a set of initial guesses (skeleton) for the toxicity probabilities at each combination that correspond to the set of possible orderings of the toxicity probabilities specified by the user.

Last updated 3 years ago

1.20 score 16 scripts 191 downloads

LNIRT - LogNormal Response Time Item Response Theory Models

Allows the simultaneous analysis of responses and response times in an Item Response Theory (IRT) modelling framework. Supports variable person speed functions (intercept, trend, quadratic), and covariates for item and person (random) parameters. Data missing-by-design can be specified. Parameter estimation is done with a MCMC algorithm. LNIRT replaces the package CIRT, which was written by Rinke Klein Entink. For reference, see the paper by Fox, Klein Entink and Van der Linden (2007), "Modeling of Responses and Response Times with the Package cirt", Journal of Statistical Software, <doi:10.18637/jss.v020.i07>.

Last updated 4 years ago

1.20 score 1 stars 16 scripts 295 downloads

dadjoke - Displays a Dad Joke

Displays a terrible joke, the kind only dads crack.

Last updated 4 years ago

1.20 score 16 scripts 161 downloads

serieslcb - Lower Confidence Bounds for Binomial Series System

Calculate and compare lower confidence bounds for binomial series system reliability. The R 'shiny' application, launched by the function launch_app(), weaves together a workflow of customized simulations and delta coverage calculations to output recommended lower confidence bound methods.

Last updated 5 years ago

1.20 score 16 scripts 156 downloads

RSSampling - Ranked Set Sampling

Ranked set sampling (RSS) is introduced as an advanced method for data collection which is substantial for the statistical and methodological analysis in scientific studies by McIntyre (1952) (reprinted in 2005) <doi:10.1198/000313005X54180>. This package introduces the first package that implements the RSS and its modified versions for sampling. With 'RSSampling', the researchers can sample with basic RSS and the modified versions, namely, Median RSS, Extreme RSS, Percentile RSS, Balanced groups RSS, Double RSS, L-RSS, Truncation-based RSS, Robust extreme RSS. The 'RSSampling' also allows imperfect ranking using an auxiliary variable (concomitant) which is widely used in the real life applications. Applicants can also use this package for parametric and nonparametric inference such as mean, median and variance estimation, regression analysis and some distribution-free tests where the the samples are obtained via basic RSS.

Last updated 7 years ago

1.20 score 16 scripts 136 downloads

seqICP - Sequential Invariant Causal Prediction

Contains an implementation of invariant causal prediction for sequential data. The main function in the package is 'seqICP', which performs linear sequential invariant causal prediction and has guaranteed type I error control. For non-linear dependencies the package also contains a non-linear method 'seqICPnl', which allows to input any regression procedure and performs tests based on a permutation approach that is only approximately correct. In order to test whether an individual set S is invariant the package contains the subroutines 'seqICP.s' and 'seqICPnl.s' corresponding to the respective main methods.

Last updated 7 years ago

1.20 score 1 stars 16 scripts 407 downloads

optR - Optimization Toolbox for Solving Linear Systems

Solves linear systems of form Ax=b via Gauss elimination, LU decomposition, Gauss-Seidel, Conjugate Gradient Method (CGM) and Cholesky methods.

Last updated 8 years ago

1.20 score 1 stars 16 scripts 162 downloads

acss - Algorithmic Complexity for Short Strings

Main functionality is to provide the algorithmic complexity for short strings, an approximation of the Kolmogorov Complexity of a short string using the coding theorem method (see ?acss). The database containing the complexity is provided in the data only package acss.data, this package provides functions accessing the data such as prob_random returning the posterior probability that a given string was produced by a random process. In addition, two traditional (but problematic) measures of complexity are also provided: entropy and change complexity.

Last updated 10 years ago

1.20 score 16 scripts 350 downloads

forward - Robust Analysis using Forward Search

Robust analysis using forward search in linear and generalized linear regression models, as described in Atkinson, A.C. and Riani, M. (2000), Robust Diagnostic Regression Analysis, First Edition. New York: Springer.

Last updated 3 months ago

1.18 score 15 scripts 310 downloads

gsrsb - Group Sequential Refined Secondary Boundary

A gate-keeping procedure to test a primary and a secondary endpoint in a group sequential design with multiple interim looks. Computations related to group sequential primary and secondary boundaries. Refined secondary boundaries are calculated for a gate-keeping test on a primary and a secondary endpoint in a group sequential design with multiple interim looks. The choices include both the standard boundaries and the boundaries using error spending functions. See Tamhane et al. (2018), "A gatekeeping procedure to test a primary and a secondary endpoint in a group sequential design with multiple interim looks", Biometrics, 74(1), 40-48.

Last updated 1 years ago

1.18 score 15 scripts 140 downloads

hudr - Providing Data from the US Department of Housing and Urban Development

Provides functions to access data from the US Department of Housing and Urban Development <https://www.huduser.gov/portal/dataset/fmr-api.html>.

Last updated 2 years ago

1.18 score 15 scripts 249 downloads

weightedScores - Weighted Scores Method for Regression Models with Dependent Data

The weighted scores method and composite likelihood information criteria as an intermediate step for variable/correlation selection for longitudinal ordinal and count data in Nikoloulopoulos, Joe and Chaganty (2011) <doi:10.1093/biostatistics/kxr005>, Nikoloulopoulos (2016) <doi:10.1002/sim.6871> and Nikoloulopoulos (2017) <arXiv:1510.07376>.

Last updated 5 years ago

1.18 score 15 scripts 161 downloads

NPHazardRate - Nonparametric Hazard Rate Estimation

Provides functions and examples for histogram, kernel (classical, variable bandwidth and transformations based), discrete and semiparametric hazard rate estimators.

Last updated 6 years ago

1.18 score 15 scripts 129 downloads

bigdatadist - Distances for Machine Learning and Statistics in the Context of Big Data

Functions to compute distances between probability measures or any other data object than can be posed in this way, entropy measures for samples of curves, distances and depth measures for functional data, and the Generalized Mahalanobis Kernel distance for high dimensional data. For further details about the metrics please refer to Martos et al (2014) <doi:10.3233/IDA-140706>; Martos et al (2018) <doi:10.3390/e20010033>; Hernandez et al (2018, submitted); Martos et al (2018, submitted).

Last updated 6 years ago

1.18 score 15 scripts 213 downloads

OPDOE - Optimal Design of Experiments

Several function related to Experimental Design are implemented here, see "Optimal Experimental Design with R" by Rasch D. et. al (ISBN 9781439816974).

Last updated 7 years ago

1.18 score 15 scripts 183 downloads

StrainRanking - Ranking of Pathogen Strains

Regression-based ranking of pathogen strains with respect to their contributions to natural epidemics, using demographic and genetic data sampled in the curse of the epidemics. This package also includes the GMCPIC test.

Last updated 7 years ago

1.18 score 15 scripts 136 downloads

afc - Generalized Discrimination Score

This is an implementation of the Generalized Discrimination Score (also known as Two Alternatives Forced Choice Score, 2AFC) for various representations of forecasts and verifying observations. The Generalized Discrimination Score is a generic forecast verification framework which can be applied to any of the following verification contexts: dichotomous, polychotomous (ordinal and nominal), continuous, probabilistic, and ensemble. A comprehensive description of the Generalized Discrimination Score, including all equations used in this package, is provided by Mason and Weigel (2009) <doi:10.1175/MWR-D-10-05069.1>.

Last updated 8 years ago

1.18 score 15 scripts 246 downloads

ShinyTester - Functions to Minimize Bonehead Moves While Working with 'shiny'

It's my experience that working with 'shiny' is intuitive once you're into it, but can be quite daunting at first. Several common mistakes are fairly predictable, and therefore we can control for these. The functions in this package help match up the assets listed in the UI and the SERVER files, and Visualize the ad hoc structure of the 'shiny' App.

Last updated 8 years ago

1.18 score 15 scripts 125 downloads

wqs - Weighted Quantile Sum Regression

Fits weighted quantile sum regression models, calculates weighted quantile sum index and estimated component weights.

Last updated 9 years ago

1.18 score 15 scripts 152 downloads

MAINT.Data - Model and Analyse Interval Data

Implements methodologies for modelling interval data by Normal and Skew-Normal distributions, considering appropriate parameterizations of the variance-covariance matrix that takes into account the intrinsic nature of interval data, and lead to four different possible configuration structures. The Skew-Normal parameters can be estimated by maximum likelihood, while Normal parameters may be estimated by maximum likelihood or robust trimmed maximum likelihood methods.

Last updated 2 years ago

1.15 score 14 scripts 503 downloads

evdbayes - Bayesian Analysis in Extreme Value Theory

Provides functions for the Bayesian analysis of extreme value models, using Markov chain Monte Carlo methods. Allows the construction of both uninformative and informed prior distributions for common statistical models applied to extreme event data, including the generalized extreme value distribution.

Last updated 2 years ago

1.15 score 14 scripts 322 downloads

randomizationInference - Flexible Randomization-Based Inference

Allows the user to conduct randomization-based inference for a wide variety of experimental scenarios. The package leverages a potential outcomes framework to output randomization-based p-values and null intervals for test statistics geared toward any estimands of interest, according to the specified null and alternative hypotheses. Users can define custom randomization schemes so that the randomization distributions are accurate for their experimental settings. The package also creates visualizations of randomization distributions and can test multiple test statistics simultaneously.

Last updated 3 years ago

1.15 score 14 scripts 182 downloads

SPlit - Split a Dataset for Training and Testing

Procedure to optimally split a dataset for training and testing. 'SPlit' is based on the method of support points, which is independent of modeling methods. Please see Joseph and Vakayil (2021) <doi:10.1080/00401706.2021.1921037> for details. This work is supported by U.S. National Science Foundation grant DMREF-1921873.

Last updated 3 years ago

cppopenmp

1.15 score 1 stars 14 scripts 245 downloads

genomicper - Circular Genomic Permutation using Genome Wide Association p-Values

Circular genomic permutation approach uses genome wide association studies (GWAS) results to establish the significance of pathway/gene-set associations whilst accounting for genomic structure(Cabrera et al (2012) <doi:10.1534/g3.112.002618>). All single nucleotide polymorphisms (SNPs) in the GWAS are placed in a 'circular genome' according to their location. Then the complete set of SNP association p-values are permuted by rotation with respect to the SNPs' genomic locations. Two testing frameworks are available: permutations at the gene level, and permutations at the SNP level. The permutation at the gene level uses Fisher's combination test to calculate a single gene p-value, followed by the hypergeometric test. The SNP count methodology maps each SNP to pathways/gene-sets and calculates the proportion of SNPs for the real and the permutated datasets above a pre-defined threshold. Genomicper requires a matrix of GWAS association p-values and SNPs annotation to genes. Pathways can be obtained from within the package or can be provided by the user.

Last updated 4 years ago

1.15 score 1 stars 14 scripts 540 downloads

subcopem2D - Bivariate Empirical Subcopula

Calculate empirical subcopula and dependence measures from a given bivariate sample, and Bernstein copula approximations.

Last updated 6 years ago

1.15 score 14 scripts 145 downloads

bivgeom - Roy's Bivariate Geometric Distribution

Implements Roy's bivariate geometric model (Roy (1993) <doi:10.1006/jmva.1993.1065>): joint probability mass function, distribution function, survival function, random generation, parameter estimation, and more.

Last updated 6 years ago

1.15 score 14 scripts 185 downloads

rocsvm.path - The Entire Solution Paths for ROC-SVM

We develop the entire solution paths for ROC-SVM presented by Rakotomamonjy. The ROC-SVM solution path algorithm greatly facilitates the tuning procedure for regularization parameter, lambda in ROC-SVM by avoiding grid search algorithm which may be computationally too intensive. For more information on the ROC-SVM, see the report in the ROC Analysis in AI workshop(ROCAI-2004) : Hernàndez-Orallo, José, et al. (2004) <doi:10.1145/1046456.1046489>.

Last updated 6 years ago

1.15 score 14 scripts 122 downloads

bcgam - Bayesian Constrained Generalised Linear Models

Fits generalised partial linear regression models using a Bayesian approach, where shape and smoothness constraints are imposed on nonparametrically modelled predictors through shape-restricted splines, and no constraints are imposed on optional parametrically modelled covariates. See Meyer et al. (2011) <doi/10.1080/10485252.2011.597852> for more details. IMPORTANT: before installing 'bcgam', you need to install 'Rtools' (Windows) or 'Xcode' (Mac OS X). These are required for the correct installation of 'nimble' (<https://r-nimble.org/download>).

Last updated 7 years ago

1.15 score 14 scripts 270 downloads

flood - Statistical Methods for the (Regional) Analysis of Flood Frequency

Includes several statistical methods for the estimation of parameters and high quantiles of river flow distributions. The focus is on regional estimation based on homogeneity assumptions and computed from multivariate observations (multiple measurement stations). For details see Kinsvater et al. (2017) <arXiv:1701.06455>.

Last updated 8 years ago

1.15 score 14 scripts 134 downloads

triangulation - Determine Position of Observer

Measuring angles between points in a landscape is much easier than measuring distances. When the location of three points is known the position of the observer can be determined based solely on the angles between these points as seen by the observer. This task (known as triangulation) however requires onerous calculations - these calculations are automated by this package.

Last updated 8 years ago

1.15 score 14 scripts 107 downloads

VDAP - Peptide Array Analysis Tools

Analyze Peptide Array Data and characterize peptide sequence space. Allows for high level visualization of global signal, Quality control based on replicate correlation and/or relative Kd, calculation of peptide Length/Charge/Kd parameters, Hits selection based on RFU Signal, and amino acid composition/basic motif recognition with RFU signal weighting. Basic signal trends can be used to generate peptides that follow the observed compositional trends.

Last updated 9 years ago

1.15 score 14 scripts 117 downloads

LGRF - Set-Based Tests for Genetic Association in Longitudinal Studies

Functions for the longitudinal genetic random field method (He et al., 2015, <doi:10.1111/biom.12310>) to test the association between a longitudinally measured quantitative outcome and a set of genetic variants in a gene/region.

Last updated 9 years ago

1.15 score 14 scripts 127 downloads

LSMonteCarlo - American options pricing with Least Squares Monte Carlo method

The package compiles functions for calculating prices of American put options with Least Squares Monte Carlo method. The option types are plain vanilla American put, Asian American put, and Quanto American put. The pricing algorithms include variance reduction techniques such as Antithetic Variates and Control Variates. Additional functions are given to derive "price surfaces" at different volatilities and strikes, create 3-D plots, quickly generate Geometric Brownian motion, and calculate prices of European options with Black & Scholes analytical solution.

Last updated 11 years ago

1.15 score 14 scripts 166 downloads

pRepDesigns - Partially Replicated (p-Rep) Designs

Early generation breeding trials are to be conducted in multiple environments where it may not be possible to replicate all the lines in each environment due to scarcity of resources. For such situations, partially replicated (p-Rep) designs have wide application potential as only a proportion of the test lines are replicated at each environment. A collection of several utility functions related to p-Rep designs have been developed. Here, the package contains six functions for a complete stepwise analytical study of these designs. Five functions pRep1(), pRep2(), pRep3(), pRep4() and pRep5(), are used to generate five new series of p-Rep designs and also compute average variance factors and canonical efficiency factors of generated designs. A fourth function NCEV() is used to generate incidence matrix (N), information matrix (C), canonical efficiency factor (E) and average variance factor (V). This function is general in nature and can be used for studying the characterization properties of any block design. A construction procedure for p-Rep designs was given by Williams et al.(2011) <doi:10.1002/bimj.201000102> which was tedious and time consuming. Here, in this package, five different methods have been given to generate p-Rep designs easily.

Last updated 9 months ago

1.11 score 13 scripts 166 downloads

mvst - Bayesian Inference for the Multivariate Skew-t Model

Estimates the multivariate skew-t and nested models, as described in the articles Liseo, B., Parisi, A. (2013). Bayesian inference for the multivariate skew-normal model: a population Monte Carlo approach. Comput. Statist. Data Anal. <doi:10.1016/j.csda.2013.02.007> and in Parisi, A., Liseo, B. (2017). Objective Bayesian analysis for the multivariate skew-t model. Statistical Methods & Applications <doi: 10.1007/s10260-017-0404-0>.

Last updated 1 years ago

gsl

1.11 score 13 scripts 161 downloads

dCovTS - Distance Covariance and Correlation for Time Series Analysis

Computing and plotting the distance covariance and correlation function of a univariate or a multivariate time series. Both versions of biased and unbiased estimators of distance covariance and correlation are provided. Test statistics for testing pairwise independence are also implemented. Some data sets are also included. References include: a) Edelmann Dominic, Fokianos Konstantinos and Pitsillou Maria (2019). 'An Updated Literature Review of Distance Correlation and Its Applications to Time Series'. International Statistical Review, 87(2): 237--262. <doi:10.1111/insr.12294>. b) Fokianos Konstantinos and Pitsillou Maria (2018). 'Testing independence for multivariate time series via the auto-distance correlation matrix'. Biometrika, 105(2): 337--352. <doi:10.1093/biomet/asx082>. c) Fokianos Konstantinos and Pitsillou Maria (2017). 'Consistent testing for pairwise dependence in time series'. Technometrics, 59(2): 262--270. <doi:10.1080/00401706.2016.1156024>. d) Pitsillou Maria and Fokianos Konstantinos (2016). 'dCovTS: Distance Covariance/Correlation for Time Series'. R Journal, 8(2):324-340. <doi:10.32614/RJ-2016-049>.

Last updated 1 years ago

1.11 score 1 stars 13 scripts 315 downloads

crimCV - Group-Based Modelling of Longitudinal Data

A finite mixture of Zero-Inflated Poisson (ZIP) models for analyzing criminal trajectories.

Last updated 1 years ago

fortranopenblas

1.11 score 13 scripts 420 downloads

CASCORE - Covariate Assisted Spectral Clustering on Ratios of Eigenvectors

Functions for implementing the novel algorithm CASCORE, which is designed to detect latent community structure in graphs with node covariates. This algorithm can handle models such as the covariate-assisted degree corrected stochastic block model (CADCSBM). CASCORE specifically addresses the disagreement between the community structure inferred from the adjacency information and the community structure inferred from the covariate information. For more detailed information, please refer to the reference paper: Yaofang Hu and Wanjie Wang (2022) <arXiv:2306.15616>. In addition to CASCORE, this package includes several classical community detection algorithms that are compared to CASCORE in our paper. These algorithms are: Spectral Clustering On Ratios-of Eigenvectors (SCORE), normalized PCA, ordinary PCA, network-based clustering, covariates-based clustering and covariate-assisted spectral clustering (CASC). By providing these additional algorithms, the package enables users to compare their performance with CASCORE in community detection tasks.

Last updated 1 years ago

1.11 score 13 scripts 179 downloads

bentcableAR - Bent-Cable Regression for Independent Data or Autoregressive Time Series

Included are two main interfaces, bentcable.ar() and bentcable.dev.plot(), for fitting and diagnosing bent-cable regressions for autoregressive time-series data (Chiu and Lockhart 2010, <doi:10.1002/cjs.10070>) or independent data (time series or otherwise - Chiu, Lockhart and Routledge 2006, <doi:10.1198/016214505000001177>). Some components in the package can also be used as stand-alone functions. The bent cable (linear-quadratic-linear) generalizes the broken stick (linear-linear), which is also handled by this package. Version 0.2 corrected a glitch in the computation of confidence intervals for the CTP. References that were updated from Versions 0.2.1 and 0.2.2 appear in Version 0.2.3 and up. Version 0.3.0 improved robustness of the error-message producing mechanism. Version 0.3.1 improves the NAMESPACE file of the package. It is the author's intention to distribute any future updates via GitHub.

Last updated 2 years ago

1.11 score 1 stars 13 scripts 393 downloads

mycobacrvR - Integrative Immunoinformatics for Mycobacterial Diseases in R Platform

The mycobacrvR package contains utilities to provide detailed information for B cell and T cell epitopes for predicted adhesins from various servers such as ABCpred, Bcepred, Bimas, Propred, NetMHC and IEDB. Please refer the URL below to download data files (data_mycobacrvR.zip) used in functions of this package.

Last updated 3 years ago

1.11 score 1 stars 13 scripts 190 downloads

cosmoFns - Functions for Cosmological Distances, Times, Luminosities, Etc

Package encapsulates standard expressions for distances, times, luminosities, and other quantities useful in observational cosmology, including molecular line observations. Currently coded for a flat universe only.

Last updated 3 years ago

1.11 score 13 scripts 235 downloads

freqdom.fda - Functional Time Series: Dynamic Functional Principal Components

Implementations of functional dynamic principle components analysis. Related graphic tools and frequency domain methods. These methods directly use multivariate dynamic principal components implementation, following the guidelines from Hormann, Kidzinski and Hallin (2016), Dynamic Functional Principal Component <doi:10.1111/rssb.12076>.

Last updated 3 years ago

1.11 score 13 scripts 204 downloads

SignifReg - Consistent Significance Controlled Variable Selection in Generalized Linear Regression

Provides significance controlled variable selection algorithms with different directions (forward, backward, stepwise) based on diverse criteria (AIC, BIC, adjusted r-square, PRESS, or p-value). The algorithm selects a final model with only significant variables defined as those with significant p-values after multiple testing correction such as Bonferroni, False Discovery Rate, etc. See Zambom and Kim (2018) <doi:10.1002/sta4.210>.

Last updated 3 years ago

1.11 score 13 scripts 424 downloads

SCMA - Single-Case Meta-Analysis

Perform meta-analysis of single-case experiments, including calculating various effect size measures (SMD, PND, PEM and NAP) and probability combining (additive and multiplicative method), as discussed in Bulte and Onghena (2013) <doi:10.22237/jmasm/1383280020>.

Last updated 5 years ago

1.11 score 13 scripts 242 downloads

NNMIS - Nearest Neighbor Based Multiple Imputation for Survival Data with Missing Covariates

Imputation for both missing covariates and censored observations (optional) for survival data with missing covariates by the nearest neighbor based multiple imputation algorithm as described in Hsu et al. (2006) <doi:10.1002/sim.2452>, and Hsu and Yu (2018) <doi: 10.1177/0962280218772592>. Note that the current version can only impute for a situation with one missing covariate.

Last updated 6 years ago

1.11 score 1 stars 13 scripts 139 downloads

Calculator.LR.FNs - Calculator for LR Fuzzy Numbers

Arithmetic operations scalar multiplication, addition, subtraction, multiplication and division of LR fuzzy numbers (which are on the basis of extension principle) have a complicate form for using in fuzzy Statistics, fuzzy Mathematics, machine learning, fuzzy data analysis and etc. Calculator for LR Fuzzy Numbers package relieve and aid applied users to achieve a simple and closed form for some complicated operator based on LR fuzzy numbers and also the user can easily draw the membership function of the obtained result by this package.

Last updated 7 years ago

1.11 score 13 scripts 204 downloads

fence - Using Fence Methods for Model Selection

This method is a new class of model selection strategies, for mixed model selection, which includes linear and generalized linear mixed models. The idea involves a procedure to isolate a subgroup of what are known as correct models (of which the optimal model is a member). This is accomplished by constructing a statistical fence, or barrier, to carefully eliminate incorrect models. Once the fence is constructed, the optimal model is selected from among those within the fence according to a criterion which can be made flexible. References: 1. Jiang J., Rao J.S., Gu Z., Nguyen T. (2008), Fence Methods for Mixed Model Selection. The Annals of Statistics, 36(4): 1669-1692. <DOI:10.1214/07-AOS517> <https://projecteuclid.org/euclid.aos/1216237296>. 2. Jiang J., Nguyen T., Rao J.S. (2009), A Simplified Adaptive Fence Procedure. Statistics and Probability Letters, 79, 625-629. <DOI:10.1016/j.spl.2008.10.014> <https://www.researchgate.net/publication/23991417_A_simplified_adaptive_fence_procedure> 3. Jiang J., Nguyen T., Rao J.S. (2010), Fence Method for Nonparametric Small Area Estimation. Survey Methodology, 36(1), 3-11. <http://publications.gc.ca/collections/collection_2010/statcan/12-001-X/12-001-x2010001-eng.pdf>. 4. Jiming Jiang, Thuan Nguyen and J. Sunil Rao (2011), Invisible fence methods and the identification of differentially expressed gene sets. Statistics and Its Interface, Volume 4, 403-415. <http://www.intlpress.com/site/pub/files/_fulltext/journals/sii/2011/0004/0003/SII-2011-0004-0003-a014.pdf>. 5. Thuan Nguyen & Jiming Jiang (2012), Restricted fence method for covariate selection in longitudinal data analysis. Biostatistics, 13(2), 303-314. <DOI:10.1093/biostatistics/kxr046> <https://academic.oup.com/biostatistics/article/13/2/303/263903/Restricted-fence-method-for-covariate-selection-in>. 6. Thuan Nguyen, Jie Peng, Jiming Jiang (2014), Fence Methods for Backcross Experiments. Statistical Computation and Simulation, 84(3), 644-662. <DOI:10.1080/00949655.2012.721885> <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3891925/>. 7. Jiang, J. (2014), The fence methods, in Advances in Statistics, Hindawi Publishing Corp., Cairo. <DOI:10.1155/2014/830821>. 8. Jiming Jiang and Thuan Nguyen (2015), The Fence Methods, World Scientific, Singapore. <https://www.abebooks.com/9789814596060/Fence-Methods-Jiming-Jiang-981459606X/plp>.

Last updated 7 years ago

1.11 score 13 scripts 143 downloads

NCSampling - Nearest Centroid (NC) Sampling

Provides functionality for performing Nearest Centroid (NC) Sampling. The NC sampling procedure was developed for forestry applications and selects plots for ground measurement so as to maximize the efficiency of imputation estimates. It uses multiple auxiliary variables and multivariate clustering to search for an optimal sample. Further details are given in Melville G. & Stone C. (2016) <doi:10.1080/00049158.2016.1218265>.

Last updated 7 years ago

1.11 score 13 scripts 122 downloads

pvclass - P-Values for Classification

Computes nonparametric p-values for the potential class memberships of new observations as well as cross-validated p-values for the training data. The p-values are based on permutation tests applied to an estimated Bayesian likelihood ratio, using a plug-in statistic for the Gaussian model, 'k nearest neighbors', 'weighted nearest neighbors' or 'penalized logistic regression'. Additionally, it provides graphical displays and quantitative analyses of the p-values.

Last updated 8 years ago

1.11 score 13 scripts 153 downloads

SCBmeanfd - Simultaneous Confidence Bands for the Mean of Functional Data

Statistical methods for estimating and inferring the mean of functional data. The methods include simultaneous confidence bands, local polynomial fitting, bandwidth selection by plug-in and cross-validation, goodness-of-fit tests for parametric models, equality tests for two-sample problems, and plotting functions.

Last updated 8 years ago

1.11 score 1 stars 13 scripts 196 downloads

extremogram - Estimation of Extreme Value Dependence for Time Series Data

Estimation of the sample univariate, cross and return time extremograms. The package can also adds empirical confidence bands to each of the extremogram plots via a permutation procedure under the assumption that the data are independent. Finally, the stationary bootstrap allows us to construct credible confidence bands for the extremograms.

Last updated 8 years ago

1.11 score 13 scripts 162 downloads

MonoInc - Monotonic Increasing

Various imputation methods are utilized in this package, where one can flag and impute non-monotonic data that is outside of a prespecified range.

Last updated 9 years ago

1.11 score 13 scripts 104 downloads

Skillings.Mack - The Skillings-Mack Test Statistic for Block Designs with Missing Observations

A generalization of the statistic used in Friedman's ANOVA method and in Durbin's rank test. This nonparametric statistical test is useful for the data obtained from block designs with missing observations occurring randomly. A resulting p-value is based on the chi-squared distribution and Monte Carlo method.

Last updated 9 years ago

1.11 score 13 scripts 164 downloads

mded - Measuring the Difference Between Two Empirical Distributions

Provides a function for measuring the difference between two independent or non-independent empirical distributions and returning a significance level of the difference.

Last updated 10 years ago

1.11 score 13 scripts 212 downloads

accrual - Bayesian Accrual Prediction

Participant recruitment for medical research is challenging. Slow accrual leads to delays in research. Accrual monitoring during the process of recruitment is critical. Researchers need reliable tools to manage the accrual rate. We developed a Bayesian method that integrates the researcher's experience with previous trials and data from the current study, providing reliable predictions on accrual rate for clinical studies. For more details and background on these methodologies, see the publications of Byron, Stephen and Susan (2008) <doi:10.1002/sim.3128>, and Yu et al. (2015) <doi:10.1002/sim.6359>. In this R package, Bayesian accrual prediction functions are presented, which can be easily used by statisticians and clinical researchers.

Last updated 1 years ago

1.08 score 1 stars 12 scripts 380 downloads

argus - Random Variate Generator for the Argus Distribution

Random variate generation, density, CDF and quantile function for the Argus distribution. Especially, it includes for random variate generation a flexible inversion method that is also fast in the varying parameter case. A Ratio-of-Uniforms method is provided as second alternative.

Last updated 1 years ago

1.08 score 12 scripts 201 downloads

SoftClustering - Soft Clustering Algorithms

It contains soft clustering algorithms, in particular approaches derived from rough set theory: Lingras & West original rough k-means, Peters' refined rough k-means, and PI rough k-means. It also contains classic k-means and a corresponding illustrative demo.

Last updated 1 years ago

1.08 score 12 scripts 189 downloads

Neighboot - Neighborhood Bootstrap Method for RDS

A bootstrap method for Respondent-Driven Sampling (RDS) that relies on the underlying structure of the RDS network to estimate uncertainty.

Last updated 3 years ago

1.08 score 12 scripts 126 downloads

sac - Semiparametric Analysis of Change-Point

Semiparametric empirical likelihood ratio based tests of change-point with one-change or epidemic alternatives with data-based model diagnostic are contained.

Last updated 4 years ago

1.08 score 12 scripts 143 downloads

jmdem - Fitting Joint Mean and Dispersion Effects Models

Joint mean and dispersion effects models fit the mean and dispersion parameters of a response variable by two separate linear models, the mean and dispersion submodels, simultaneously. It also allows the users to choose either the deviance or the Pearson residuals as the response variable of the dispersion submodel. Furthermore, the package provides the possibility to nest the submodels in one another, if one of the parameters has significant explanatory power on the other. Wu & Li (2016) <doi:10.1016/j.csda.2016.04.015>.

Last updated 5 years ago

1.08 score 12 scripts 141 downloads

easyreg - Easy Regression

Performs analysis of regression in simple designs with quantitative treatments, including mixed models and non linear models.

Last updated 5 years ago

1.08 score 12 scripts 152 downloads

MiDA - Microarray Data Analysis

Set of functions designed to simplify transcriptome analysis and identification of marker molecules using microarrays data. The package includes a set of functions that allows performing full pipeline of analysis including data normalization, summarisation, binary classification, FDR (False Discovery Rate) multiple comparison and the definition of potential biological markers.

Last updated 6 years ago

1.08 score 12 scripts 124 downloads

sparseBC - Sparse Biclustering of Transposable Data

Implements the sparse biclustering proposal of Tan and Witten (2014), Sparse biclustering of transposable data. Journal of Computational and Graphical Statistics 23(4):985-1008.

Last updated 6 years ago

1.08 score 12 scripts 128 downloads

longROC - Time-Dependent Prognostic Accuracy with Multiply Evaluated Bio Markers or Scores

Time-dependent Receiver Operating Characteristic curves, Area Under the Curve, and Net Reclassification Indexes for repeated measures. It is based on methods in Barbati and Farcomeni (2017) <doi:10.1007/s10260-017-0410-2>.

Last updated 7 years ago

1.08 score 12 scripts 97 downloads

StakeholderAnalysis - Measuring Stakeholder Influence

Proposes an original instrument for measuring stakeholder influence on the development of an infrastructure project that is carried through by a municipality, drawing on stakeholder classifications (Mitchell, Agle, & Wood, 1997) and input-output modelling (Hester & Adams, 2013). Mitchell R., Agle B.R., & Wood D.J. <doi:10.2307/259247> Hester, P.T., & Adams, K.M. (2013) <doi:10.1016/j.procs.2013.09.282>.

Last updated 7 years ago

1.08 score 12 scripts 146 downloads

IntegratedJM - Joint Modeling of the Gene-Expression and Bioassay Data, Taking Care of the Effect Due to a Fingerprint Feature

Offers modeling the association between gene-expression and bioassay data, taking care of the effect due to a fingerprint feature and helps with several plots to better understand the analysis.

Last updated 7 years ago

1.08 score 12 scripts 210 downloads

BurStMisc - Burns Statistics Miscellaneous

Script search, corner, genetic optimization, permutation tests, write expect test.

Last updated 8 years ago

1.08 score 12 scripts 221 downloads

SeqAlloc - Sequential Allocation for Prospective Experiments

Potential randomization schemes are prospectively evaluated when units are assigned to treatment arms upon entry into the experiment. The schemes are evaluated for balance on covariates and on predictability (i.e., how well could a site worker guess the treatment of the next unit enrolled).

Last updated 8 years ago

1.08 score 12 scripts 115 downloads

AdvBinomApps - Upper Clopper-Pearson Confidence Limits for Burn-in Studies under Additional Available Information

Functions to compute upper Clopper-Pearson confidence limits of early life failure probabilities and required sample sizes of burn-in studies under further available information, e.g. from other products or technologies.

Last updated 9 years ago

1.08 score 12 scripts 198 downloads

TwoStepCLogit - Conditional Logistic Regression: A Two-Step Estimation Method

Conditional logistic regression with longitudinal follow up and individual-level random coefficients: A stable and efficient two-step estimation method.

Last updated 9 years ago

1.08 score 12 scripts 205 downloads

jvnVaR - Value at Risk

Many method to compute, predict and back-test VaR. For more detail, see the report: Value at Risk <researchgate.net>.

Last updated 9 years ago

1.08 score 12 scripts 147 downloads

LifeTables - Two-Parameter HMD Model Life Table System

Functions supplied in this package will implement discriminant analysis to select an appropriate life table family, select an appropriate alpha level based on a desired life expectancy at birth, produce a model mortality pattern based on family and level as well as plot the results.

Last updated 9 years ago

1.08 score 12 scripts 203 downloads

double.truncation - Analysis of Doubly-Truncated Data

Likelihood-based inference methods with doubly-truncated data are developed under various models. Nonparametric models are based on Efron and Petrosian (1999) <doi:10.1080/01621459.1999.10474187> and Emura, Konno, and Michimae (2015) <doi:10.1007/s10985-014-9297-5>. Parametric models from the special exponential family (SEF) are based on Hu and Emura (2015) <doi:10.1007/s00180-015-0564-z> and Emura, Hu and Konno (2017) <doi:10.1007/s00362-015-0730-y>. The parametric location-scale models are based on Dorre et al. (2021) <doi:10.1007/s00180-020-01027-6>.

Last updated 19 days ago

1.04 score 11 scripts 258 downloads

rPAex - Automatic Detection of Experimental Unit in Precision Agriculture

A part of precision agriculture is linked to the spectral image obtained from the cameras. With the image information of the agricultural experiment, the included functions facilitate the collection of spectral data associated with the experimental units. Some designs generated in R are linked to the images, which allows the use of the information of each pixel of the image in the experimental unit and the treatment. Tables and images are generated for the analysis of the precision agriculture experiment during the entire vegetative period of the crop.

Last updated 1 years ago

1.04 score 11 scripts 189 downloads

GameTheory - Cooperative Game Theory

Implementation of a common set of punctual solutions for Cooperative Game Theory.

Last updated 1 years ago

1.04 score 11 scripts 326 downloads

indelmiss - Insertion Deletion Analysis While Accounting for Possible Missing Data

Genome-wide gene insertion and deletion rates can be modelled in a maximum likelihood framework with the additional flexibility of modelling potential missing data using the models included within. These models simultaneously estimate insertion and deletion (indel) rates of gene families and proportions of "missing" data for (multiple) taxa of interest. The likelihood framework is utilized for parameter estimation. A phylogenetic tree of the taxa and gene presence/absence patterns (with data ordered by the tips of the tree) are required. See Dang et al. (2016) <doi:10.1534/genetics.116.191973> for more details.

Last updated 1 years ago

cpp

1.04 score 11 scripts 157 downloads

SQL - Executes 'SQL' Statements

Runs 'SQL' statements on in-memory data frames within a temporary in-memory 'duckdb' data base.

Last updated 2 years ago

1.04 score 11 scripts 301 downloads

sregsurvey - Semiparametric Model-Assisted Estimation in Finite Populations

It is a framework to fit semiparametric regression estimators for the total parameter of a finite population when the interest variable is asymmetric distributed. The main references for this package are Sarndal C.E., Swensson B., and Wretman J. (2003,ISBN: 978-0-387-40620-6, "Model Assisted Survey Sampling." Springer-Verlag) Cardozo C.A, Paula G.A. and Vanegas L.H. (2022) "Generalized log-gamma additive partial linear mdoels with P-spline smoothing", Statistical Papers. Cardozo C.A and Alonso-Malaver C.E. (2022). "Semi-parametric model assisted estimation in finite populations." In preparation.

Last updated 2 years ago

1.04 score 11 scripts 666 downloads

idar - Individual Diversity-Area Relationships

Computes and tests individual (species, phylogenetic and functional) diversity-area relationships, i.e., how species-, phylogenetic- and functional-diversity varies with spatial scale around the individuals of some species in a community. See applications of these methods in Wiegand et al. (2007) <doi:10.1073/pnas.0705621104> or Chacon-Labella et al. (2016) <doi:10.1007/s00442-016-3547-z>.

Last updated 2 years ago

fortran

1.04 score 11 scripts 249 downloads

pogit - Bayesian Variable Selection for a Poisson-Logistic Model

Bayesian variable selection for regression models of under-reported count data as well as for (overdispersed) Poisson, negative binomal and binomial logit regression models using spike and slab priors.

Last updated 3 years ago

1.04 score 11 scripts 162 downloads

Tushare - Interface to 'Tushare Pro' API

Helps the R users to get data from 'Tushare Pro'<https://tushare.pro>. 'Tushare Pro' is a platform as well as a community with a lot of staffs working in financial area. We support financial data such as stock price, financial report statements and digital coins data.

Last updated 3 years ago

1.04 score 11 scripts 377 downloads

wsbackfit - Weighted Smooth Backfitting for Structured Models

Non- and semiparametric regression for generalized additive, partial linear, and varying coefficient models as well as their combinations via smoothed backfitting. Based on Roca-Pardinas J and Sperlich S (2010) <doi:10.1007/s11222-009-9130-2>; Mammen E, Linton O and Nielsen J (1999) <doi:10.1214/aos/1017939138>; Lee YK, Mammen E, Park BU (2012) <doi:10.1214/12-AOS1026>.

Last updated 4 years ago

1.04 score 11 scripts 159 downloads

SeleMix - Selective Editing via Mixture Models

Detection of outliers and influential errors using a latent variable model.

Last updated 4 years ago

1.04 score 11 scripts 201 downloads

lbreg - Log-Binomial Regression with Constrained Optimization

Maximum likelihood estimation of log-binomial regression with special functionality when the MLE is on the boundary of the parameter space.

Last updated 5 years ago

1.04 score 11 scripts 167 downloads

detpack - Density Estimation and Random Number Generation with Distribution Element Trees

Density estimation for possibly large data sets and conditional/unconditional random number generation or bootstrapping with distribution element trees. The function 'det.construct' translates a dataset into a distribution element tree. To evaluate the probability density based on a previously computed tree at arbitrary query points, the function 'det.query' is available. The functions 'det1' and 'det2' provide density estimation and plotting for one- and two-dimensional datasets. Conditional/unconditional smooth bootstrapping from an available distribution element tree can be performed by 'det.rnd'. For more details on distribution element trees, see: Meyer, D.W. (2016) <arXiv:1610.00345> or Meyer, D.W., Statistics and Computing (2017) <doi:10.1007/s11222-017-9751-9> and Meyer, D.W. (2017) <arXiv:1711.04632> or Meyer, D.W., Journal of Computational and Graphical Statistics (2018) <doi:10.1080/10618600.2018.1482768>.

Last updated 5 years ago

1.04 score 11 scripts 170 downloads

EntropyMCMC - MCMC Simulation and Convergence Evaluation using Entropy and Kullback-Leibler Divergence Estimation

Tools for Markov Chain Monte Carlo (MCMC) simulation and performance analysis. Simulate MCMC algorithms including adaptive MCMC, evaluate their convergence rate, and compare candidate MCMC algorithms for a same target density, based on entropy and Kullback-Leibler divergence criteria. MCMC algorithms can be simulated using provided functions, or imported from external codes. This package is based upon work starting with Chauveau, D. and Vandekerkhove, P. (2013) <doi:10.1051/ps/2012004> and next articles.

Last updated 6 years ago

1.04 score 1 stars 11 scripts 206 downloads

populationPDXdesign - Designing Population PDX Studies

Run simulations to assess the impact of various designs features and the underlying biological behaviour on the outcome of a Patient Derived Xenograft (PDX) population study. This project can either be deployed to a server as a 'shiny' app or installed locally as a package and run the app using the command 'populationPDXdesignApp()'.

Last updated 6 years ago

1.04 score 11 scripts 134 downloads

sievetest - Laboratory Sieve Test Reporting Functions

Functions for making particle-size analysis. Sieve tests are widely used to obtain particle-size distribution of powders or granular materials.

Last updated 7 years ago

1.04 score 11 scripts 123 downloads

carSurv - Correlation-Adjusted Regression Survival (CARS) Scores

Contains functions to estimate the Correlation-Adjusted Regression Survival (CARS) Scores. The method is described in Welchowski, T. and Zuber, V. and Schmid, M., (2018), Correlation-Adjusted Regression Survival Scores for High-Dimensional Variable Selection, <arXiv:1802.08178>.

Last updated 7 years ago

1.04 score 11 scripts 418 downloads

Sim.PLFN - Simulation of Piecewise Linear Fuzzy Numbers

The definition of fuzzy random variable and the methods of simulation from fuzzy random variables are two challenging statistical problems in three recent decades. This package is organized based on a special definition of fuzzy random variable and simulate fuzzy random variable by Piecewise Linear Fuzzy Numbers (PLFNs); see Coroianua et al. (2013) <doi:10.1016/j.fss.2013.02.005> for details about PLFNs. Some important statistical functions are considered for obtaining the membership function of main statistics, such as mean, variance, summation, standard deviation and coefficient of variance. Some of applied advantages of 'Sim.PLFN' package are: (1) Easily generating / simulation a random sample of PLFN, (2) drawing the membership functions of the simulated PLFNs or the membership function of the statistical result, and (3) Considering the simulated PLFNs for arithmetic operation or importing into some statistical computation. Finally, it must be mentioned that 'Sim.PLFN' package works on the basis of 'FuzzyNumbers' package.

Last updated 7 years ago

1.04 score 11 scripts 89 downloads

epr - Easy Polynomial Regression

Performs analysis of polynomial regression in simple designs with quantitative treatments.

Last updated 7 years ago

1.04 score 11 scripts 131 downloads

OptimalTiming - Optimal Timing Identification

Identify the optimal timing for new treatment initiation during multiple state disease transition, including multistate model fitting, simulation of mean residual lifetime for a given transition state, and estimation of confidence interval. The method is referred to de Wreede, L., Fiocco, M., & Putter, H. (2011) <doi:10.18637/jss.v038.i07>.

Last updated 7 years ago

1.04 score 11 scripts 119 downloads

DWLasso - Degree Weighted Lasso

Infers networks with hubs using degree weighted Lasso method.

Last updated 7 years ago

1.04 score 1 stars 11 scripts 160 downloads

T2EQ - Functions for Applying the T^2-Test for Equivalence

Contains functions for applying the T^2-test for equivalence. The T^2-test for equivalence is a multivariate two-sample equivalence test. Distance measure of the test is the Mahalanobis distance. For multivariate normally distributed data the T^2-test for equivalence is exact and UMPI. The function T2EQ() implements the T^2-test for equivalence according to Wellek (2010) <DOI:10.1201/ebk1439808184>. The function T2EQ.dissolution.profiles.hoffelder() implements a variant of the T^2-test for equivalence according to Hoffelder (2016) <http://www.ecv.de/suse_item.php?suseId=Z|pi|8430> for the equivalence comparison of highly variable dissolution profiles.

Last updated 8 years ago

1.04 score 11 scripts 105 downloads

DiscreteLaplace - Discrete Laplace Distributions

Probability mass function, distribution function, quantile function, random generation and estimation for the skew discrete Laplace distributions.

Last updated 9 years ago

1.04 score 11 scripts 170 downloads

pAnalysis - Benchmarking and Rescaling R2 using Noise Percentile Analysis

Provides the tools needed to benchmark the R2 value corresponding to a certain acceptable noise level while also providing a rescaling function based on that noise level yielding a new value of R2 we refer to as R2k which is independent of both the number of degrees of freedom and the noise distribution function.

Last updated 9 years ago

1.04 score 11 scripts 103 downloads

JPEN - Covariance and Inverse Covariance Matrix Estimation Using Joint Penalty

A Joint PENalty Estimation of Covariance and Inverse Covariance Matrices.

Last updated 9 years ago

1.04 score 11 scripts 139 downloads

hdthreshold - Inference on Many Jumps in Nonparametric Panel Regression Models

Provides uniform testing procedures for existence and heterogeneity of threshold effects in high-dimensional nonparametric panel regression models. The package accompanies the paper Chen, Keilbar, Su and Wang (2023) "Inference on many jumps in nonparametric panel regression models". arXiv preprint <doi:10.48550/arXiv.2312.01162>.

Last updated 1 days ago

1.00 score

sTSD - Simulate Time Series Diagnostics

These are tools that allow users to do time series diagnostics, primarily tests of unit root, by way of simulation. While there is nothing necessarily wrong with the received wisdom of critical values generated decades ago, simulation provides its own perks. Not only is simulation broadly informative as to what these various test statistics do and what are their plausible values, simulation provides more flexibility for assessing unit root by way of different thresholds or different hypothesized distributions.

Last updated 4 days ago

1.00 score

Cronbach - Cronbach's Alpha

Cronbach's alpha and various formulas for confidence intervals. The relevant paper is Tsagris M., Frangos C.C. and Frangos C.C. (2013). "Confidence intervals for Cronbach's reliability coefficient". Recent Techniques in Educational Science, 14-16 May, Athens, Greece.

Last updated 7 days ago

1.00 score 1 scripts 225 downloads

displease - Numeric and Color Sequences with Non-Linear Interpolation

When visualising changes between two values over time, a strict linear interpolation can look jarring and unnatural. By applying a non-linear easing to the transition, the motion between values can appear smoother and more natural. This package includes functions for applying such non-linear easings to colors and numeric values, and is useful where smooth animated movement and transitions are desired.

Last updated 8 days ago

1.00 score 4 scripts

sisireg - Sign-Simplicity-Regression-Solver

Implementation of the SSR-Algorithm. The Sign-Simplicity-Regression model is a nonparametric statistical model which is based on residual signs and simplicity assumptions on the regression function. Goal is to calculate the most parsimonious regression function satisfying the statistical adequacy requirements. Theory and functions are specified in Metzner (2020, ISBN: 979-8-68239-420-3, "Trendbasierte Prognostik") and Metzner (2021, ISBN: 979-8-59347-027-0, "Adäquates Maschinelles Lernen").

Last updated 11 days ago

1.00 score 182 downloads

spphpr - Spring Phenological Prediction

Predicts the occurrence times (in day of year) of spring phenological events. Three methods, including the accumulated degree days (ADD) method, the accumulated days transferred to a standardized temperature (ADTS) method, and the accumulated developmental progress (ADP) method, were used. See Shi et al. (2017a) <doi:10.1016/j.agrformet.2017.04.001> and Shi et al. (2017b) <doi:10.1093/aesa/sax063> for details.

Last updated 11 days ago

1.00 score

MAICtools - Performing Matched-Adjusted Indirect Comparisons (MAIC)

A generalised workflow for Matching-Adjusted Indirect Comparison (MAIC) analysis, which supports both anchored and non-anchored MAIC methods. In MAIC, unbiased trial outcome comparison is achieved by weighting the subject-level outcomes of the intervention trial so that the weighted aggregate measures of prognostic or effect-modifying variables match those of the comparator trial. Measurements supported include time-to-event (e.g., overall survival) and binary (e.g., objective tumor response). The method is described in Signorovitch et al. (2010) <doi:10.2165/11538370-000000000-00000> and Signorovitch et al. (2012) <doi:10.1016/j.jval.2012.05.004>.

Last updated 13 days ago

1.00 score

fastPLS - A Fast Implementation of Partial Least Square

An implementation in 'Rcpp' / 'RcppArmadillo' of Partial Least Square algorithms. This package includes other functions to perform the double cross-validation and a fast correlation.

Last updated 13 days ago

openblascpp

1.00 score 3 scripts

fsn - Rosenthal's Fail Safe Number and Related Functions

Estimation of Rosenthal's fail safe number including confidence intervals. The relevant papers are the following. Konstantinos C. Fragkos, Michail Tsagris and Christos C. Frangos (2014). "Publication Bias in Meta-Analysis: Confidence Intervals for Rosenthal's Fail-Safe Number". International Scholarly Research Notices, Volume 2014. <doi:10.1155/2014/825383>. Konstantinos C. Fragkos, Michail Tsagris and Christos C. Frangos (2017). "Exploring the distribution for the estimator of Rosenthal's fail-safe number of unpublished studies in meta-analysis". Communications in Statistics-Theory and Methods, 46(11):5672--5684. <doi:10.1080/03610926.2015.1109664>.

Last updated 14 days ago

1.00 score 1 scripts 209 downloads

dcorVS - Variable Selection Algorithms Using the Distance Correlation

The 'FBED' and 'mmpc' variable selection algorithms have been implemented using the distance correlation. The references include: Tsamardinos I., Aliferis C. F. and Statnikov A. (2003). "Time and sample efficient discovery of Markovblankets and direct causal relations". In Proceedings of the ninth ACM SIGKDD international Conference. <doi:10.1145/956750.956838>. Borboudakis G. and Tsamardinos I. (2019). "Forward-backward selection with early dropping". Journal of Machine Learning Research, 20(8): 1--39. <doi:10.48550/arXiv.1705.10770>. Huo X. and Szekely G.J. (2016). "Fast computing for distance covariance". Technometrics, 58(4): 435--447. <doi:10.1080/00401706.2015.1054435>.

Last updated 14 days ago

1.00 score 137 downloads

ShapePattern - Tools for Analyzing Shapes and Patterns

This is an evolving and growing collection of tools for the quantification, assessment, and comparison of shape and pattern. This collection provides tools for: (1) the spatial decomposition of planar shapes using 'ShrinkShape' to incrementally shrink shapes to extinction while computing area, perimeter, and number of parts at each iteration of shrinking; the spectra of results are returned in graphic and tabular formats (Remmel 2015) <doi:10.1111/cag.12222>, (2) simulating landscape patterns, (3) provision of tools for estimating composition and configuration parameters from a categorical (binary) landscape map (grid) and then simulates a selected number of statistically similar landscapes. Class-focused pattern metrics are computed for each simulated map to produce empirical distributions against which statistical comparisons can be made. The code permits the analysis of single maps or pairs of maps (Remmel and Fortin 2013) <doi:10.1007/s10980-013-9905-x>, (4) counting the number of each first-order pattern element and converting that information into both frequency and empirical probability vectors (Remmel 2020) <doi:10.3390/e22040420>, and (5) computing the porosity of raster patches <doi:10.3390/su10103413>. NOTE: This is a consolidation of existing packages ('PatternClass', 'ShapePattern') to begin warehousing all shape and pattern code in a common package. Additional utility tools for handling data are provided and this package will be added to as more tools are created, cleaned-up, and documented. Note that all future developments will appear in this package and that 'PatternClass' will eventually be archived.

Last updated 14 days ago

1.00 score 5 scripts 209 downloads

SurrogateParadoxTest - Empirical Testing of Surrogate Paradox Assumptions

Provides functions to nonparametrically assess assumptions necessary to prevent the surrogate paradox through hypothesis tests of stochastic dominance, monotonicity of regression functions, and non-negative residual treatment effects. More details are available in Hsiao et al 2024 (under review).

Last updated 16 days ago

1.00 score

pchc - Bayesian Network Learning with the PCHC and Related Algorithms

Bayesian network learning using the PCHC, FEDHC, MMHC and variants of these algorithms. PCHC stands for PC Hill-Climbing, a new hybrid algorithm that uses PC to construct the skeleton of the BN and then applies the Hill-Climbing greedy search. More algorithms and variants have been added, such as MMHC, FEDHC, and the Tabu search variants, PCTABU, MMTABU and FEDTABU. The relevant papers are: a) Tsagris M. (2021). "A new scalable Bayesian network learning algorithm with applications to economics". Computational Economics, 57(1): 341-367. <doi:10.1007/s10614-020-10065-7>. b) Tsagris M. (2022). "The FEDHC Bayesian Network Learning Algorithm". Mathematics 2022, 10(15): 2604. <doi:10.3390/math10152604>.

Last updated 18 days ago

1.00 score 4 scripts 347 downloads

qcluster - Clustering via Quadratic Scoring

Performs tuning of clustering models, methods and algorithms including the problem of determining an appropriate number of clusters. Validation of cluster analysis results is performed via quadratic scoring using resampling methods, as in Coraggio, L. and Coretto, P. (2023) <doi:10.1016/j.jmva.2023.105181>.

Last updated 18 days ago

openblas

1.00 score

rectpacker - Rectangle Packing

Rectangle packing is a packing problem where rectangles are placed into a larger rectangular region (without overlapping) in order to maximise the use space. Rectangles are packed using the skyline heuristic as discussed in Lijun et al (2011) 'A Skyline-Based Heuristic for the 2D Rectangular Strip Packing Problem' <doi:10.1007/978-3-642-21827-9_29>. A function is also included for determining a good small-sized box for containing a given set of rectangles.

Last updated 19 days ago

1.00 score 3 scripts

robqda - Robust Quadratic Discriminant Analysis

The minimum covariance determinant estimator is used to perform robust quadratic discriminant analysis, including cross-validation. References: Friedman J., Hastie T. and Tibshirani R. (2009). "The elements of statistical learning", 2nd edition. Springer, Berlin. <doi:10.1007/978-0-387-84858-7>.

Last updated 19 days ago

1.00 score

plattice - Lattice Plot for Panel Data

It creates a lattice plot to visualize panel or longitudinal data. The observed values are plotted as dots and the fitted values as lines, both against time. The plot is customizable and easy to edit, even if you do not know how to construct a lattice plot from scratch.

Last updated 20 days ago

1.00 score 138 downloads

npclust - Nonparametric Tests for Incomplete Clustered Data

Nonparametric tests for clustered data in pre-post intervention design documented in Cui and Harrar (2021) <doi:10.1002/bimj.201900310> and Harrar and Cui (2022) <doi:10.1016/j.jspi.2022.05.009>. Other than the main test results mentioned in the reference paper, this package also provides a function to calculate the sample size allocations for the input long format data set, and also a function for adjusted/unadjusted confidence intervals calculations. There are also functions to visualize the distribution of data across different intervention groups over time, and also the adjusted/unadjusted confidence intervals.

Last updated 21 days ago

1.00 score 1 scripts 624 downloads

fertilmodel - Fertility Models

Four fertility models are fitted using non-linear least squares. These are the Hadwiger, the Gamma, the Model1 and Model2, following the terminology of the following paper: Peristera P. and Kostaki A. (2007). "Modeling fertility in modern populations". Demographic Research, 16(6): 141--194. <doi:10.4054/DemRes.2007.16.6>. Model based averaging is also supported.

Last updated 25 days ago

1.00 score 1 scripts 227 downloads

braQCA - Bootstrapped Robustness Assessment for Qualitative Comparative Analysis

Test the robustness of a user's Qualitative Comparative Analysis solutions to randomness, using the bootstrapped assessment: baQCA(). This package also includes a function that provides recommendations for improving solutions to reach typical significance levels: brQCA(). Data included come from McVeigh et al. (2014) <doi:10.1177/0003122414534065>.

Last updated 27 days ago

1.00 score 3 scripts 288 downloads

binomCI - Confidence Intervals for a Binomial Proportion

Twelve confidence intervals for one binomial proportion or a vector of binomial proportions are computed. The confidence intervals are: Jeffreys, Wald, Wald corrected, Wald, Blyth and Still, Agresti and Coull, Wilson, Score, Score corrected, Wald logit, Wald logit corrected, Arcsine and Exact binomial. References include, among others: Vollset, S. E. (1993). "Confidence intervals for a binomial proportion". Statistics in Medicine, 12(9): 809-824. <doi:10.1002/sim.4780120902>.

Last updated 29 days ago

1.00 score 1 stars 244 downloads

transDA - Transformation Discriminant Analysis

Performs transformation discrimination analysis and non-transformation discrimination analysis. It also includes functions for Linear Discriminant Analysis, Quadratic Discriminant Analysis, and Mixture Discriminant Analysis. In the context of mixture discriminant analysis, it offers options for both common covariance matrix (common sigma) and individual covariance matrices (uncommon sigma) for the mixture components.

Last updated 1 months ago

1.00 score 60 downloads

cohetsurr - Assessing Complex Heterogeneity in Surrogacy

Provides functions to assess and test for complex heterogeneity in the utility of a surrogate marker with respect to multiple baseline covariates, using both a parametric model and a semiparametric two-step model. More details will be available in the future in: Knowlton, R., Tian, L., Parast, L. (2024) ``A General Framework to Assess Complex Heterogeneity in the Strength of a Surrogate Marker."

Last updated 1 months ago

1.00 score 61 downloads

consrq - Constrained Quantile Regression

Constrained quantile regression is performed. One constraint is that all beta coefficients (including the constant) cannot be negative, they can be either 0 or strictly positive. Another constraint is that the beta coefficients lie within an interval. References: Koenker R. (2005) Quantile Regression, Cambridge University Press. <doi:10.1017/CBO9780511754098>.

Last updated 1 months ago

1.00 score 71 downloads

watson - Fitting and Simulating Mixtures of Watson Distributions

Tools for fitting and simulating mixtures of Watson distributions. The random sampling scheme of the package offers two sampling algorithms that are based of the results of Sablica, Hornik and Leydold (2022) <https://research.wu.ac.at/en/publications/random-sampling-from-the-watson-distribution>. What is more, the package offers a smart tool to combine these two methods, and based on the selected parameters, it approximates the relative sampling speed for both methods and picks the faster one. In addition, the package offers a fitting function for the mixtures of Watson distribution, that uses the expectation-maximization (EM) algorithm. Special features are the possibility to use multiple variants of the E-step and M-step, sparse matrices for the data representation and state of the art methods for numerical evaluation of needed special functions using the results of Sablica and Hornik (2022) <https://www.ams.org/journals/mcom/2022-91-334/S0025-5718-2021-03690-X/>.

Last updated 1 months ago

openblascppopenmp

1.00 score 4 scripts 354 downloads

Bios2cor - From Biological Sequences and Simulations to Correlation Analysis

Utilities for computation and analysis of correlation/covariation in multiple sequence alignments and in side chain motions during molecular dynamics simulations. Features include the computation of correlation/covariation scores using a variety of scoring functions between either sequence positions in alignments or side chain dihedral angles in molecular dynamics simulations and utilities to analyze the correlation/covariation matrix through a variety of tools including network representation and principal components analysis. In addition, several utility functions are based on the R graphical environment to provide friendly tools for help in data interpretation. Examples of sequence covariation analysis are provided in: (1) Pele J, Moreau M, Abdi H, Rodien P, Castel H, Chabbert M (2014) <doi:10.1002/prot.24570> and (2) Taddese B, Deniaud M, Garnier A, Tiss A, Guissouma H, Abdi H, Henrion D, Chabbert M (2018) <doi:10.1371/journal.pcbi.1006209>. An example of side chain correlated motion analysis is provided in: Taddese B, Garnier A, Abdi H, Henrion D, Chabbert M (2020) <doi:10.1038/s41598-020-72766-1>. This work was supported by the French National Research Agency (Grant number: ANR-11-BSV2-026) and by GENCI (Grant number: 100567).

Last updated 1 months ago

1.00 score 1 stars 40 scripts 635 downloads

SegEnvIneq - Environmental Inequality Indices Based on Segregation Measures

A set of segregation-based indices and randomization methods to make robust environmental inequality assessments, as described in Schaeffer and Tivadar (2019) "Measuring Environmental Inequalities: Insights from the Residential Segregation Literature" <doi:10.1016/j.ecolecon.2019.05.009>.

Last updated 1 months ago

1.00 score 300 downloads

FGRepo - Functional Genomics Repository for POST-GWAS Analysis

A collection of datasets essential for functional genomic analysis. Gene names, gene positions, cytoband information, sourced from Ensembl and phenotypes association graph prepared from GWAScatalog are included. Data is available in both GRCh37 and 38 builds. These datasets facilitate a wide range of genomic studies, including the identification of genetic variants, exploration of genomic features, and post-GWAS functional analysis.

Last updated 2 months ago

1.00 score 457 downloads

rbc - Regression by Composition

Flexible statistical modelling using a modular framework for regression, in which groups of transformations are composed together and act on probability distributions.

Last updated 2 months ago

1.00 score 487 downloads

ABRSQOL - Quality-of-Life Solver for "Measuring Quality of Life under Spatial Frictions"

This toolkit implements a numerical solution algorithm to invert a quality of life measure from observed data. Unlike the traditional Rosen-Roback measure, this measure accounts for mobility frictions—generated by idiosyncratic tastes and local ties — and trade frictions — generated by trade costs and non-tradable services, thereby reducing non-classical measurement error. The QoL measure is based on Ahlfeldt, Bald, Roth, Seidel (2024) <https://econpapers.repec.org/RePEc:boc:bocode:s459382> "Measuring Quality of Life under Spatial Frictions". When using this programme or the toolkit in your work, please cite the paper.

Last updated 2 months ago

1.00 score 3 scripts 692 downloads

minFactorial - All Possible Minimally Changed Factorial Run Orders

In many agricultural, engineering, industrial, post-harvest and processing experiments, the number of factor level changes and hence the total number of changes is of serious concern as such experiments may consists of hard-to-change factors where it is physically very difficult to change levels of some factors or sometime such experiments may require normalization time to obtain adequate operating condition. For this reason, run orders that offer the minimum number of factor level changes and at the same time minimize the possible influence of systematic trend effects on the experimentation have been sought. Factorial designs with minimum changes in factors level may be preferred for such situations as these minimally changed run orders will minimize the cost of the experiments. For method details see, Bhowmik, A.,Varghese, E., Jaggi, S. and Varghese, C. (2017)<doi:10.1080/03610926.2016.1152490>.This package used to construct all possible minimally changed factorial run orders for different experimental set ups along with different statistical criteria to measure the performance of these designs. It consist of the function minFactDesign().

Last updated 2 months ago

1.00 score 432 downloads

sicure - Single-Index Mixture Cure Models

Single-index mixture cure models allow estimating the probability of cure and the latency depending on a vector (or functional) covariate, avoiding the curse of dimensionality. The vector of parameters that defines the model can be estimated by maximum likelihood. A nonparametric estimator for the conditional density of the susceptible population is provided. For more details, see Piñeiro-Lamas (2024) (<https://ruc.udc.es/dspace/handle/2183/37035>).

Last updated 2 months ago

1.00 score 448 downloads

optbin - Optimal Binning of Data

Defines thresholds for breaking data into a number of discrete levels, minimizing the (mean) squared error within all bins.

Last updated 2 months ago

1.00 score 2 scripts 567 downloads

classicaltest - Classical Test Theory (CTT) Analysis

Functions for classical test theory analysis, following methods presented by Wu et al. (2006) <doi:10.1007/978-981-10-3302-5>.

Last updated 2 months ago

1.00 score 500 downloads

SUMO - Generating Multi-Omics Datasets

Designed to generate multi-omics datasets that closely reflect biological complexity, the package allows for testing, validation, and benchmarking of multi-omics integrative methods. The simulated data includes one or multiple predefined signals (latent/unobserved factors), giving users complete control over the data-generated characteristics. Tini, Giulia, et al (2019) <doi:10.1093/bib/bbx167>.

Last updated 2 months ago

1.00 score 7 scripts 446 downloads

likelihoodR - Likelihood Analyses for Common Statistical Tests

A collection of functions that calculate the log likelihood (support) for a range of statistical tests. Where possible the likelihood function and likelihood interval for the observed data are displayed. The evidential approach used here is based on the book "Likelihood" by A.W.F. Edwards (1992, ISBN-13 : 978-0801844430), "Statistical Evidence" by R. Royall (1997, ISBN-13 : 978-0412044113), S.N. Goodman & R. Royall (2011) <doi:10.2105/AJPH.78.12.1568>, "Understanding Psychology as a Science" by Z. Dienes (2008, ISBN-13 : 978-0230542310), S. Glover & P. Dixon <doi:10.3758/BF03196706> and others. This package accompanies "Evidence-Based Statistics" by P. Cahusac (2020, ISBN-13 : 978-1119549802) <doi:10.1002/9781119549833>.

Last updated 2 months ago

1.00 score 1 stars 1 scripts 264 downloads

Equalden.HD - Testing the Equality of a High Dimensional Set of Densities

The equality of a large number k of densities is tested by measuring the L2 distance between the corresponding kernel density estimators and the one based on the pooled sample. The test even works for sample sizes as small as 2.

Last updated 2 months ago

1.00 score 8 scripts 382 downloads

deFit - Fitting Differential Equations to Time Series Data

Use numerical optimization to fit ordinary differential equations (ODEs) to time series data to examine the dynamic relationships between variables or the characteristics of a dynamical system. It can now be used to estimate the parameters of ODEs up to second order, and can also apply to multilevel systems. See <https://github.com/yueqinhu/defit> for details.

Last updated 2 months ago

1.00 score 2 scripts 196 downloads

circlus - Clustering and Simulation of Spherical Cauchy and PKBD Models

Provides tools for estimation and clustering of spherical data, seamlessly integrated with the 'flexmix' package. Includes the necessary M-step implementations for both Poisson Kernel-Based Distribution (PKBD) and spherical Cauchy distribution. Additionally, the package provides random number generators for PKBD and spherical Cauchy distribution. Methods are based on Golzy M., Markatou M. (2020) <doi:10.1080/10618600.2020.1740713>, Kato S., McCullagh P. (2020) <doi:10.3150/20-bej1222> and Sablica L., Hornik K., Leydold J. (2023) <doi:10.1214/23-ejs2149>.

Last updated 2 months ago

openblascppopenmp

1.00 score 1 scripts 159 downloads

MixLFA - Mixture of Longitudinal Factor Analysis Methods

Provides a function for the estimation of mixture of longitudinal factor analysis models using the iterative expectation-maximization algorithm (Ounajim, Slaoui, Louis, Billot, Frasca, Rigoard (2023) <doi:10.1002/sim.9804>) and several tools for visualizing and interpreting the models' parameters.

Last updated 2 months ago

cpp

1.00 score 206 downloads

SSRA - Sakai Sequential Relation Analysis

'Takea Semantic Structure Analysis' (TSSA) and 'Sakai Sequential Relation Analysis' (SSRA) for polytomous items. Package includes functions for generating a sequential relation table and a treegram to visualize the sequential relations between pairs of items.

Last updated 2 months ago

1.00 score 9 scripts 116 downloads

BTTL - Bradley-Terry Transfer Learning

Implements the methodological developments found in Hermes, van Heerwaarden, and Behrouzi (2024) <doi:10.48550/arXiv.2408.10558>, and allows for the statistical modeling of multi-attribute pairwise comparison data.

Last updated 3 months ago

1.00 score 265 downloads

HMMcopula - Markov Regime Switching Copula Models Estimation and Goodness-of-Fit

Estimation procedures and goodness-of-fit test for several Markov regime switching models and mixtures of bivariate copula models. The goodness-of-fit test is based on a Cramer-von Mises statistic and uses Rosenblatt's transform and parametric bootstrap to estimate the p-value. The proposed methodologies are described in Nasri, Remillard and Thioub (2020) <doi:10.1002/cjs.11534>.

Last updated 3 months ago

1.00 score 1 stars 4 scripts 193 downloads

CompositionalRF - Multivariate Random Forest with Compositional Responses

Non linear regression with compositional responses and Euclidean predictors is performed. The compositional data are first transformed using the additive log-ratio transformation, and then the multivariate random forest of Rahman R., Otridge J. and Pal R. (2017), <doi:10.1093/bioinformatics/btw765>, is applied.

Last updated 3 months ago

1.00 score 155 downloads

optRF - Optimising Random Forest Stability Through Selection of the Optimal Number of Trees

Calculating the stability of random forest with certain numbers of trees. The non-linear relationship between stability and numbers of trees is described using a logistic regression model and used to estimate the optimal number of trees.

Last updated 3 months ago

1.00 score 85 downloads

AnimalSequences - Analyse Animal Sequential Behaviour and Communication

All animal behaviour occurs sequentially. The package has a number of functions to format sequence data from different sources, to analyse sequential behaviour and communication in animals. It also has functions to plot the data and to calculate the entropy of sequences.

Last updated 3 months ago

1.00 score 231 downloads

affluenceIndex - Affluence (Richness) Indices

Enables to compute the statistical indices of affluence (richness) with bootstrap errors, and inequality and polarization indices. Moreover, gives the possibility of calculation of affluence line. Some simple errors are fixed and it works with new version of Spatial Statistics packaged.

Last updated 3 months ago

1.00 score 9 scripts 336 downloads

twingp - A Fast Global-Local Gaussian Process Approximation

A global-local approximation framework for large-scale Gaussian process modeling. Please see Vakayil and Joseph (2024) <doi:10.1080/00401706.2023.2296451> for details. This work is supported by U.S. NSF grants CMMI-1921646 and DMREF-1921873.

Last updated 3 months ago

1.00 score 456 downloads

R4HCR - R for Health Care Research

A collection of datasets that accompany the forthcoming book "R for Health Care Research".

Last updated 3 months ago

1.00 score 304 downloads

mvcor - Correlation Coefficients for Multivariate Data

Correlation coefficients for multivariate data, namely the squared correlation coefficient and the RV coefficient (multivariate generalization of the squared Pearson correlation coefficient). References include Mardia K.V., Kent J.T. and Bibby J.M. (1979). "Multivariate Analysis". ISBN: 978-0124712522. London: Academic Press.

Last updated 3 months ago

1.00 score 130 downloads

gammi - Generalized Additive Mixed Model Interface

An interface for fitting generalized additive models (GAMs) and generalized additive mixed models (GAMMs) using the 'lme4' package as the computational engine, as described in Helwig (2024) <doi:10.3390/stats7010003>. Supports default and formula methods for model specification, additive and tensor product splines for capturing nonlinear effects, and automatic determination of spline type based on the class of each predictor. Includes an S3 plot method for visualizing the (nonlinear) model terms, an S3 predict method for forming predictions from a fit model, and an S3 summary method for conducting significance testing using the Bayesian interpretation of a smoothing spline.

Last updated 3 months ago

1.00 score 129 downloads

equiBSPD - Equivalent Estimation Balanced Split Plot Designs

In agricultural, post-harvest and processing, engineering and industrial experiments factors are often differentiated with ease with which they can change from experimental run to experimental run. This is due to the fact that one or more factors may be expensive or time consuming to change i.e. hard-to-change factors. These factors restrict the use of complete randomization as it may make the experiment expensive and time consuming. Split plot designs can be used for such situations. In general model estimation of split plot designs require the use of generalized least squares (GLS). However for some split-plot designs ordinary least squares (OLS) estimates are equivalent to generalized least squares (GLS) estimates. These types of designs are known in literature as equivalent-estimation split-plot design. For method details see, Macharia, H. and Goos, P.(2010) <doi:10.1080/00224065.2010.11917833>.Balanced split plot designs are designs which have an equal number of subplots within every whole plot. This package used to construct equivalent estimation balanced split plot designs for different experimental set ups along with different statistical criteria to measure the performance of these designs. It consist of the function equivalent_BSPD().

Last updated 3 months ago

1.00 score 218 downloads

RMX - Rasch Models -- eXtensions

Extend Rasch and Item Response Theory (IRT) analyses by providing tools for post-processing the output from five major IRT packages (i.e., 'eRm', 'psychotools', 'ltm', 'mirt', and 'TAM'). The current version provides the plotPIccc() function, which extracts from the return object of the originating package all information required to draw an extended Person-Item-Map (PIccc), showing any combination of * category characteristic curves (CCCs), * threshold characteristic curves (TCCs), * item characteristic curves (ICCs), * category information functions (CIFs), * item information functions (IIFs), * test information function (TIF), and the * standard error curve (S.E.). for uni- and multidimensional models (as far as supported by each package). It allows for selecting dimensions, items, and categories to plot and offers numerous options to adapt the output. The return object contains all calculated values for further processing.

Last updated 3 months ago

1.00 score 7 scripts 432 downloads

GenomicSig - Computation of Genomic Signatures

Genomic signatures represent unique features within a species' DNA, enabling the differentiation of species and offering broad applications across various fields. This package provides essential tools for calculating these specific signatures, streamlining the process for researchers and offering a comprehensive and time-saving solution for genomic analysis.The amino acid contents are identified based on the work published by Sandberg et al. (2003) <doi:10.1016/s0378-1119(03)00581-x> and Xiao et al. (2015) <doi:10.1093/bioinformatics/btv042>. The Average Mutual Information Profiles (AMIP) values are calculated based on the work of Bauer et al. (2008) <doi:10.1186/1471-2105-9-48>. The Chaos Game Representation (CGR) plot visualization was done based on the work of Deschavanne et al. (1999) <doi:10.1093/oxfordjournals.molbev.a026048> and Jeffrey et al. (1990) <doi:10.1093/nar/18.8.2163>. The GC content is calculated based on the work published by Nakabachi et al. (2006) <doi:10.1126/science.1134196> and Barbu et al. (1956) <https://pubmed.ncbi.nlm.nih.gov/13363015>. The Oligonucleotide Frequency Derived Error Gradient (OFDEG) values are computed based on the work published by Saeed et al. (2009) <doi:10.1186/1471-2164-10-S3-S10>. The Relative Synonymous Codon Usage (RSCU) values are calculated based on the work published by Elek (2018) <https://urn.nsk.hr/urn:nbn:hr:217:686131>.

Last updated 3 months ago

1.00 score 6 scripts 128 downloads

AquaAnalytix - Water Quality Analysis

A varied array of mathematical derivations from various titrimetric and colorimetric methods for analyzing water quality parameters were condensed and integrated for the better physicochemical analysis. It is indispensable for managing any aquatic ecosystem, including aquaculture facilities. By substituting titrant and spectrophotometric absorbance readings, accurate determination of the concentrations of critical parameters such as Dissolved Oxygen, Free Carbon Dioxide, Total Alkalinity, Water Hardness, Hydrogen Sulfide, Total Ammonia Nitrogen, Nitrite, Nitrate, Chlorinity, Salinity, Inorganic Phosphate, and Transparency can be facilitated APHA(2017,ISBN:9780875532875).

Last updated 3 months ago

1.00 score 277 downloads

uni.shrinkage - Shrinkage Estimation for Univariate Normal Mean

Implement a shrinkage estimation for the univariate normal mean based on a preliminary test (pretest) estimator. This package also provides the confidence interval based on pivoting the cumulative density function. The methodologies are published in Taketomi et al.(2024) <doi:10.1007/s42081-023-00221-2> and Taketomi et al.(2024-)(under review).

Last updated 3 months ago

1.00 score 204 downloads

EQUALrepeat - Algorithm Driven Time Series Analysis for Researchers without Coding Skills

Support functions for R-based 'EQUAL-STATS' software which automatically classifies the data and performs appropriate statistical tests. 'EQUAL-STATS' software is a shiny application with an user-friendly interface to perform complex statistical analysis. Gurusamy,K (2024)<doi:10.5281/zenodo.13354162>.

Last updated 4 months ago

1.00 score 379 downloads

iTOS - Methods and Examples from Introduction to the Theory of Observational Studies

Supplements for a book, "iTOS" = "Introduction to the Theory of Observational Studies." Data sets are 'aHDL' from Rosenbaum (2023a) <doi:10.1111/biom.13558> and 'bingeM' from Rosenbaum (2023b) <doi:10.1111/biom.13921>. The function makematch() uses two-criteria matching from Zhang et al. (2023) <doi:10.1080/01621459.2021.1981337> to create the matched data 'bingeM' from 'binge'. The makematch() function also implements optimal matching (Rosenbaum (1989) <doi:10.2307/2290079>) and matching with fine or near-fine balance (Rosenbaum et al. (2007) <doi:10.1198/016214506000001059> and Yang et al (2012) <doi:10.1111/j.1541-0420.2011.01691.x>). The book makes use of two other R packages, 'weightedRank' and 'tightenBlock'.

Last updated 4 months ago

1.00 score 1 scripts 143 downloads

PNAR - Poisson Network Autoregressive Models

Quasi likelihood-based methods for estimating linear and log-linear Poisson Network Autoregression models with p lags and covariates. Tools for testing the linearity versus several non-linear alternatives. Tools for simulation of multivariate count distributions, from linear and non-linear PNAR models, by using a specific copula construction. References include: Armillotta, M. and K. Fokianos (2023). "Nonlinear network autoregression". Annals of Statistics, 51(6): 2526--2552. <doi:10.1214/23-AOS2345>. Armillotta, M. and K. Fokianos (2024). "Count network autoregression". Journal of Time Series Analysis, 45(4): 584--612. <doi:10.1111/jtsa.12728>. Armillotta, M., Tsagris, M. and Fokianos, K. (2024). "Inference for Network Count Time Series with the R Package PNAR". The R Journal, 15/4: 255--269. <doi:10.32614/RJ-2023-094>.

Last updated 4 months ago

1.00 score 5 scripts 197 downloads

pandemics - Monitoring a Developing Pandemic with Available Data

Full dynamic system to describe and forecast the spread and the severity of a developing pandemic, based on available data. These data are number of infections, hospitalizations, deaths and recoveries notified each day. The system consists of three transitions, infection-infection, infection-hospital and hospital-death/recovery. The intensities of these transitions are dynamic and estimated using non-parametric local linear estimators. The package can be used to provide forecasts and survival indicators such as the median time spent in hospital and the probability that a patient who has been in hospital for a number of days can leave it alive. Methods are described in Gámiz, Mammen, Martínez-Miranda, and Nielsen (2024) <doi:10.48550/arXiv.2308.09918> and <doi:10.48550/arXiv.2308.09919>.

Last updated 4 months ago

1.00 score 221 downloads

hrtlFMC - Half Replicate of Two Level Factorial Run Order with Minimum Level Changes

It is used to construct run sequences with minimum changes for half replicate of two level factorial run order. Experimenter can save time and resources by minimizing the number of changes in levels of individual factor and therefore the total number of changes. It consists of the function minimal_hrtlf(). This technique can be employed to any half replicate of two level factorial run order where the number of factors are greater than two. In Design of Experiments (DOE) theory, two level of a factor can be represented as integers e.g. - 1 for low and 1 for high. User is expected to enter total number of factors to be considered in the experiment. minimal_hrtlf() provides the required run sequences for the input number of factors. The output also gives the number of changes of each factor along with total number of changes in the run sequence. Due to restricted randomization the minimally changed run sequences of half replicate of two level factorial run order will be affected by trend effect. The output also provides the Trend Factor value of the run order. Trend factor value will lies between 0 to 1. Higher the values, lesser the influence of trend effects on the run order.

Last updated 4 months ago

1.00 score 231 downloads

fdesigns - Optimal Experimental Designs for Functional/Dynamic Models

Optimal experimental designs for functional linear and functional generalised linear models, for scalar responses and profile/dynamic factors. The designs are optimised using the coordinate exchange algorithm. The methods are discussed by Michaelides (2023) <https://eprints.soton.ac.uk/474982/1/Thesis_DamianosMichaelides_Final_pdfa_1_.pdf>.

Last updated 4 months ago

openblascppopenmp

1.00 score 138 downloads

AirExposure - Exposure Model to Air Pollutants Based on Mobility and Daily Activities

Model that assesses daily exposure to air pollution, which considers daily population mobility on a geographical scale and the spatial and temporal variability of pollutant concentrations, in addition to traditional parameters such as exposure time and pollutant concentration.

Last updated 4 months ago

1.00 score 223 downloads

WOAkMedoids - Whale Optimization Algorithm for K-Medoids Clustering

Implements the Whale Optimization Algorithm(WOA) for k-medoids clustering, providing tools for effective and efficient cluster analysis in various data sets. The methodology is based on "The Whale Optimization Algorithm" by Mirjalili and Lewis (2016) <doi:10.1016/j.advengsoft.2016.01.008>.

Last updated 4 months ago

cpp

1.00 score 123 downloads

MatrixHMM - Parsimonious Families of Hidden Markov Models for Matrix-Variate Longitudinal Data

Implements three families of parsimonious hidden Markov models (HMMs) for matrix-variate longitudinal data using the Expectation-Conditional Maximization (ECM) algorithm. The package supports matrix-variate normal, t, and contaminated normal distributions as emission distributions. For each hidden state, parsimony is achieved through the eigen-decomposition of the covariance matrices associated with the emission distribution. This approach results in a comprehensive set of 98 parsimonious HMMs for each type of emission distribution. Atypical matrix detection is also supported, utilizing the fitted (heavy-tailed) models.

Last updated 4 months ago

1.00 score 222 downloads

FishProxCompAnalyzer - Proximate Composition Analysis of Fish and Feed Ingredients

The proximate composition analysis is the quantification of main components that constitutes nutritional profile of any food and food products including fish, shellfish, fish feed and their ingredients. Understanding this composition is essential for evaluating their nutritional value and for making informed dietary choices. The primary components typically analyzed include; moisture/ water in foods, crude protein, crude fat/ lipid, total ash, fiber and carbohydrates AOAC(2005,ISBN:0-935584-77-3). In case of fish, shellfish and its products, the proximate composition consists of four primary constituents - water, protein, fat, and ash (mostly minerals). Fish exhibit significant variation in their chemical makeup based on age, sex, environment, and season, both within the same species and between individual fish. There is minimal fluctuation in the content of ash and protein. The lipid concentration varies remarkably and is inversely correlated with the water content. In case of fish, carbohydrates are present in minor quantity so that are quantified by subtracting total of other components from 100 to get percentage of carbohydrates.

Last updated 4 months ago

1.00 score 247 downloads

scdensity - Shape-Constrained Kernel Density Estimation

Implements methods for obtaining kernel density estimates subject to a variety of shape constraints (unimodality, bimodality, symmetry, tail monotonicity, bounds, and constraints on the number of inflection points). Enforcing constraints can eliminate unwanted waves or kinks in the estimate, which improves its subjective appearance and can also improve statistical performance. The main function scdensity() is very similar to the density() function in 'stats', allowing shape-restricted estimates to be obtained with little effort. The methods implemented in this package are described in Wolters and Braun (2017) <doi:10.1080/03610918.2017.1288247>, Wolters (2012) <doi:10.18637/jss.v047.i06>, and Hall and Huang (2002) <https://www3.stat.sinica.edu.tw/statistica/j12n4/j12n41/j12n41.htm>. See the scdensity() help for for full citations.

Last updated 4 months ago

1.00 score 10 scripts 143 downloads

GephiForR - 'Gephi' Network Visualization

Implements key features of 'Gephi' for network visualization, including 'ForceAtlas2' (with LinLog mode), network scaling, and network rotations. It also includes easy network visualization tools such as edge and node color assignment for recreating 'Gephi'-style graphs in R. The package references layout algorithms developed by Jacomy, M., Venturini T., Heymann S., and Bastian M. (2014) <doi:10.1371/journal.pone.0098679> and Noack, A. (2009) <doi:10.48550/arXiv.0807.4052>.

Last updated 4 months ago

1.00 score 162 downloads

bexy - Visualize and Parse the Output of 'BeXY'

Provides functions for summarizing and plotting the output of the command-line tool 'BeXY' (<https://bitbucket.org/wegmannlab/bexy>), a tool that performs Bayesian inference of sex chromosome karyotypes and sex-linked scaffolds from low-depth sequencing data.

Last updated 4 months ago

1.00 score 179 downloads

highd2means - High-Dimensional Tests for Two Population Mean Vectors

Tests for two high-dimensional population mean vectors. The user has the option to compute the asymptotic, the permutation or the bootstrap based p-value of the test. Some references are: Chen S.X. and Qin Y.L. (2010). <doi:10.1214/09-AOS716>, Cai T.T., Liu W., and Xia Y. (2014) <doi:10.1111/rssb.12034> and Yu X., Li D., Xue L. and Li, R. (2023) <doi:10.1080/01621459.2022.2061354>.

Last updated 4 months ago

1.00 score 139 downloads

PermCor - Robust Permutation Tests of Correlation Coefficients

Provides tools for statistical testing of correlation coefficients through robust permutation method and large sample approximation method. Tailored to different types of correlation coefficients including Pearson correlation coefficient, weighted Pearson correlation coefficient, Spearman correlation coefficient, and Lin's concordance correlation coefficient.The robust permutation test controls type I error under general scenarios when sample size is small and two variables are dependent but uncorrelated. The large sample approximation test generally controls type I error when the sample size is large (>200).

Last updated 4 months ago

1.00 score 217 downloads

CCSRfind - Convert ICD-10 Codes to CCSR Codes

Provides a tool for matching ICD-10 codes to corresponding Clinical Classification Software Refined (CCSR) codes. The main function, CCSRfind(), identifies each CCSR code that applies to an individual given their diagnosis codes. It also provides a summary of CCSR codes that are matched to a dataset. The package contains 3 datasets: 'DXCCSR' (mapping of ICD-10 codes to CCSR codes), 'Legend' (conversion of DXCCSR to CCSRfind-usable format for CCSR codes with less than or equal to 1000 ICD-10 diagnosis codes), and 'LegendExtend' (conversion of DXCCSR to CCSRfind-usable format for CCSR codes with more than 1000 ICD-10 dx codes). The disc() function applies grepl() ('base') to multiple columns and is used in CCSRfind().

Last updated 4 months ago

1.00 score 184 downloads

SISIR - Select Intervals Suited for Functional Regression

Interval fusion and selection procedures for regression with functional inputs. Methods include a semiparametric approach based on Sliced Inverse Regression (SIR), as described in <doi:10.1007/s11222-018-9806-6> (standard ridge and sparse SIR are also included in the package) and a random forest based approach, as described in <doi:10.1002/sam.11705>.

Last updated 4 months ago

1.00 score 8 scripts 188 downloads

ORIONZ.G - EAP Scoring in Exploratory FA Solutions with Correlated Residuals

Obtaining Bayes Expected A Posteriori (EAP) individual score estimates based on linear and non-linear extended Exploratoy Factor Analysis solutions that include a correlated-residual structure.

Last updated 5 months ago

1.00 score 202 downloads

SFPL - Sparse Fused Plackett-Luce

Implements the methodological developments found in Hermes, van Heerwaarden, and Behrouzi (2024) <doi:10.48550/arXiv.2308.04325>, and allows for the statistical modeling of multi-group rank data in combination with object variables. The package also allows for the simulation of synthetic multi-group rank data.

Last updated 5 months ago

1.00 score 132 downloads

ElectDecomp - Decomposition of Seats-to-Votes Distortion in Multimember Elections

Decomposes the seat-to-vote distortion for every party (individual party bias or individual party deviation from proportional representation) into segments that can be attributed to separate causes for the party infra or over-representation: the electoral system effect (separating the mean and the variance effect within it) and the population effect (separating malapportionment and unequal participation effect within it). It works on (single tired) districted electoral systems with any number of seats per district. In addition, the package aggregates the individual party distortion into an index of deviation from proportionality (the Losemore-Hanby index) whose value is also decomposed into segments attributed to the major causes of deviation from proportionality (plus the interactions among them).

Last updated 5 months ago

1.00 score 248 downloads

AdIsMF - Adsorption Isotherm Model Fitting

The Langmuir and Freundlich adsorption isotherms are pivotal in characterizing adsorption processes, essential across various scientific disciplines. Proper interpretation of adsorption isotherms involves robust fitting of data to the models, accurate estimation of parameters, and efficiency evaluation of the models, both in linear and non-linear forms. For researchers and practitioners in the fields of chemistry, environmental science, soil science, and engineering, a comprehensive package that satisfies all these requirements would be ideal for accurate and efficient analysis of adsorption data, precise model selection and validation for rigorous scientific inquiry and real-world applications. Details can be found in Langmuir (1918) <doi:10.1021/ja02242a004> and Giles (1973) <doi:10.1111/j.1478-4408.1973.tb03158.x>.

Last updated 5 months ago

1.00 score 263 downloads

pm3 - Propensity Score Matching for Unordered 3-Group Data

You can use this program for 3 sets of categorical data for propensity score matching. Assume that the data has 3 different categorical variables. You can use it to perform propensity matching of baseline indicator groupings. The matching will make the differences in the baseline data smaller. This method was described by Alvaro Fuentes (2022) <doi:10.1080/00273171.2021.1925521>.

Last updated 5 months ago

1.00 score 257 downloads

HDRFA - High-Dimensional Robust Factor Analysis

Factor models have been widely applied in areas such as economics and finance, and the well-known heavy-tailedness of macroeconomic/financial data should be taken into account when conducting factor analysis. We propose two algorithms to do robust factor analysis by considering the Huber loss. One is based on minimizing the Huber loss of the idiosyncratic error's L2 norm, which turns out to do Principal Component Analysis (PCA) on the weighted sample covariance matrix and thereby named as Huber PCA. The other one is based on minimizing the element-wise Huber loss, which can be solved by an iterative Huber regression algorithm. In this package we also provide the code for traditional PCA, the Robust Two Step (RTS) method by He et al. (2022) and the Quantile Factor Analysis (QFA) method by Chen et al. (2021) and He et al. (2023).

Last updated 5 months ago

1.00 score 1 scripts 246 downloads

trdist - Univariate Proability Distributions with Truncation

Truncation of univariate probability distributions. The probability distribution can come from other packages so long as the function names follow the standard d, p, q, r naming format. Also other univariate probability distributions are included.

Last updated 5 months ago

1.00 score 269 downloads

kpcaIG - Variables Interpretability with Kernel PCA

The kernelized version of principal component analysis (KPCA) has proven to be a valid nonlinear alternative for tackling the nonlinearity of biological sample spaces. However, it poses new challenges in terms of the interpretability of the original variables. 'kpcaIG' aims to provide a tool to select the most relevant variables based on the kernel PCA representation of the data as in Briscik et al. (2023) <doi:10.1186/s12859-023-05404-y>. It also includes functions for 2D and 3D visualization of the original variables (as arrows) into the kernel principal components axes, highlighting the contribution of the most important ones.

Last updated 5 months ago

1.00 score 1 stars 133 downloads

geotoolsR - Tools to Improve the Use of Geostatistic

The basic idea of this package is provides some tools to help the researcher to work with geostatistics. Initially, we present a collection of functions that allow the researchers to deal with spatial data using bootstrap procedure. There are five methods available and two ways to display them: bootstrap confidence interval - provides a two-sided bootstrap confidence interval; bootstrap plot - a graphic with the original variogram and each of the B bootstrap variograms.

Last updated 5 months ago

1.00 score 5 scripts 150 downloads

flexmsm - A General Framework for Flexible Multi-State Survival Modelling

A general estimation framework for multi-state Markov processes with flexible specification of the transition intensities. The log-transition intensities can be specified through Generalised Additive Models which allow for virtually any type of covariate effect. Elementary specifications such as time-homogeneous processes and simple parametric forms are also supported. There are no limitations on the type of process one can assume, with both forward and backward transitions allowed and virtually any number of states.

Last updated 5 months ago

1.00 score 7 scripts 168 downloads

EWOC.Comb - Escalation with Overdose Control using 2 Drug Combinations

Implements Escalation With Overdose Control trial designs using two drug combinations described by this paper <doi:10.1002/sim.6961>(Tighiouart et al., 2016). It calculates the recommended dose for next cohorts and perform simulations to obtain operating characteristics.

Last updated 5 months ago

jagscpp

1.00 score 161 downloads

hedgedrf - An Implementation of the Hedged Random Forest Algorithm

This algorithm is described in detail in the paper "Hedging Forecast Combinations With an Application to the Random Forest" by Beck et al. (2023) <doi:10.48550/arXiv.2308.15384>. The package provides a function hedgedrf() that can be used to train a Hedged Random Forest model on a dataset, and a function predict.hedgedrf() that can be used to make predictions with the model.

Last updated 5 months ago

1.00 score 132 downloads

ltable - Easy to Make (Lazy) Tables

Constructs tables of counts and proportions out of data sets with possibility to insert tables to Excel, Word, HTML, and PDF documents. Transforms tables to data suitable for modelling. Features Gibbs sampling based log-linear (NB2) and power analyses (original by Oleksandr Ocheredko <doi:10.35566/isdsa2019c5>) for tabulated data.

Last updated 6 months ago

1.00 score 3 scripts 143 downloads

weightedRank - Sensitivity Analysis Using Weighted Rank Statistics

Performs a sensitivity analysis using weighted rank tests in observational studies with I blocks of size J; see Rosenbaum (2024) <doi:10.1080/01621459.2023.2221402>. The package can perform adaptive inference in block designs; see Rosenbaum (2012) <doi:10.1093/biomet/ass032>. The main functions are wgtRank(), wgtRankCI() and wgtRanktt().

Last updated 6 months ago

1.00 score 153 downloads

SILFS - Subgroup Identification with Latent Factor Structure

In various domains, many datasets exhibit both high variable dependency and group structures, which necessitates their simultaneous estimation. This package provides functions for two subgroup identification methods based on penalized functions, both of which utilize factor model structures to adapt to data with cross-sectional dependency. The first method is the Subgroup Identification with Latent Factor Structure Method (SILFSM) we proposed. By employing Center-Augmented Regularization and factor structures, the SILFSM effectively eliminates data dependencies while identifying subgroups within datasets. For this model, we offer optimization functions based on two different methods: Coordinate Descent and our newly developed Difference of Convex-Alternating Direction Method of Multipliers (DC-ADMM) algorithms; the latter can be applied to cases where the distance function in Center-Augmented Regularization takes L1 and L2 forms. The other method is the Factor-Adjusted Pairwise Fusion Penalty (FA-PFP) model, which incorporates factor augmentation into the Pairwise Fusion Penalty (PFP) developed by Ma, S. and Huang, J. (2017) <doi:10.1080/01621459.2016.1148039>. Additionally, we provide a function for the Standard CAR (S-CAR) method, which does not consider the dependency and is for comparative analysis with other approaches. Furthermore, functions based on the Bayesian Information Criterion (BIC) of the SILFSM and the FA-PFP method are also included in 'SILFS' for selecting tuning parameters. For more details of Subgroup Identification with Latent Factor Structure Method, please refer to He et al. (2024) <doi:10.48550/arXiv.2407.00882>.

Last updated 6 months ago

1.00 score 145 downloads

latcontrol - Evaluation of the Role of Control Variables in Structural Equation Models

Various opportunities to evaluate the effects of including one or more control variable(s) in structural equation models onto model-implied variances, covariances, and parameter estimates. The derivation of the methodology employed in this package can be obtained from Blötner (2023) <doi:10.31234/osf.io/dy79z>.

Last updated 6 months ago

1.00 score 116 downloads

convertBCD - Convert Decimal to Binary-Coded Decimal (BCD) Form and Vice Versa

Convert BCD (raw bytes) to decimal numbers and vice versa. BCD format is used to preserve decimals exactly, as opposed to the binary rounding errors inherent in "numeric" or "floating-point" formats.

Last updated 6 months ago

1.00 score 160 downloads

LogisticCopula - A Copula Based Extension of Logistic Regression

An implementation of a method of extending a logistic regression model beyond linear effects of the co-variates. The extension in is constructed by first equating the logistic regression model to a naive Bayes model where all the margins are specified to follow natural exponential distributions conditional on Y, that is, a model for Y given X that is specified through the distribution of X given Y, where the columns of X are assumed to be mutually independent conditional on Y. Subsequently, the model is expanded by adding vine - copulas to relax the assumption of mutual independence, where pair-copulas are added in a stage-wise, forward selection manner. Some heuristics are employed during the process of selecting edges, as well as the families of pair-copula models. After each component is added, the parameters are updated by a (smaller) number of gradient steps to maximise the likelihood. When the algorithm has stopped adding edges, based the criterion that a new edge should improve the likelihood more than k times the number new parameters, the parameters are updated with a larger number of gradient steps, or until convergence.

Last updated 6 months ago

1.00 score 146 downloads

frequentistSSDBinary - Screened Selection Design with Binary Endpoints

A study based on the screened selection design (SSD) is an exploratory phase II randomized trial with two or more arms but without concurrent control. The primary aim of the SSD trial is to pick a desirable treatment arm (e.g., in terms of the response rate) to recommend to the subsequent randomized phase IIb (with the concurrent control) or phase III. The proposed designs can “partially” control or provide the empirical type I error/false positive rate by an optimal algorithm (implemented by the optimal_2arm_binary() or optimal_3arm_binary() function) for each arm. All the design needed components (sample size, operating characteristics) are supported.

Last updated 6 months ago

1.00 score 141 downloads

phylopairs - Comparative Analyses of Lineage-Pair Traits

Facilitates the testing of causal relationships among lineage-pair traits in a phylogenetically informed context. Lineage-pair traits are characters that are defined for pairs of lineages instead of individual taxa. Examples include the strength of reproductive isolation, range overlap, competition coefficient, diet niche similarity, and relative hybrid fitness. Users supply a lineage-pair dataset and a phylogeny. 'phylopairs' calculates a covariance matrix for the pairwise-defined data and provides built-in models to test for relationships among variables while taking this covariance into account. Bayesian sampling is run through built-in 'Stan' programs via the 'rstan' package. The various models and methods that this package makes available are described in Anderson et al. (In Review), Coyne and Orr (1989) <doi:10.1111/j.1558-5646.1989.tb04233.x>, Fitzpatrick (2002) <doi:10.1111/j.0014-3820.2002.tb00860.x>, and Castillo (2007) <doi:10.1002/ece3.3093>.

Last updated 6 months ago

cpp

1.00 score 143 downloads

ExactCox - Exact Test and Exact Confidence Interval for the Cox Model

Performs the exact test on whether there is a difference between two survival curves. Exact confidence interval for the hazard ratio can also be generated for the Cox model.

Last updated 6 months ago

1.00 score 460 downloads

RMaCzek - Czekanowski's Diagrams

Allows for production of Czekanowski's Diagrams with clusters. See K. Bartoszek, A. Vasterlund (2020) <doi:10.2478/bile-2020-0008> and K. Bartoszek, Y. Luo (2023) <doi:10.14708/ma.v51i2.7259>.

Last updated 6 months ago

1.00 score 6 scripts 246 downloads

MFAg - Multiple Factor Analysis (MFA)

Performs Multiple Factor Analysis method for quantitative, categorical, frequency and mixed data, in addition to generating a lot of graphics, also has other useful functions.

Last updated 6 months ago

1.00 score 8 scripts 707 downloads

Blendstat - Joint Analysis of Experiments with Mixtures and Random Effects

Performs a joint analysis of experiments with mixtures and random effects, taking on a process variable represented by a covariable.

Last updated 6 months ago

1.00 score 4 scripts 550 downloads

ultrapolaRplot - Plotting Ultrasound Tongue Traces

Plots traced ultrasound tongue imaging data according to a polar coordinate system. There is currently support for plotting means and standard deviations of each category's trace; Smoothing Splines Analysis of Variance (SSANOVA) could be implemented as well. The origin of the polar coordinates may be defined manually or automatically determined based on different algorithms. Currently 'ultrapolaRplot' supports ultrasound tongue imaging trace data from 'UltraTrace' (<https://github.com/SwatPhonLab/UltraTrace>). 'UltraTrace' is capable of importing data from Articulate Instruments AAA. 'read_textgrid.R' is required for opening TextGrids to determine category and alignment information of ultrasound traces.

Last updated 6 months ago

1.00 score 3 scripts 474 downloads

splmm - Simultaneous Penalized Linear Mixed Effects Models

Contains functions that fit linear mixed-effects models for high-dimensional data (p>>n) with penalty for both the fixed effects and random effects for variable selection. The details of the algorithm can be found in Luoying Yang PhD thesis (Yang and Wu 2020). The algorithm implementation is based on the R package 'lmmlasso'. Reference: Yang L, Wu TT (2020). Model-Based Clustering of Longitudinal Data in High-Dimensionality. Unpublished thesis.

Last updated 6 months ago

openblascppopenmp

1.00 score 3 scripts 197 downloads

oceanic - Location Identify Tool

Determine the sea area where the fishing boat operates. The latitude and longitude of geographic coordinates are used to match oceanic areas and economic sea areas. You can plot the distribution map with dotplot() function. Please refer to Flanders Marine Institute (2020) <doi:10.14284/403>.

Last updated 7 months ago

1.00 score 556 downloads

VAR.spec - Allows Specifying a Bivariate VAR (Vector Autoregression) with Desired Spectral Characteristics

The spectral characteristics of a bivariate series (Marginal Spectra, Coherency- and Phase-Spectrum) determine whether there is a strong presence of short-, medium-, or long-term fluctuations (components of certain frequencies in the spectral representation of the series) in each one of them. These are induced by strong peaks of the marginal spectra of each series at the corresponding frequencies. The spectral characteristics also determine how strongly these short-, medium-, or long-term fluctuations of the two series are correlated between the two series. Information on this is provided by the Coherency spectrum at the corresponding frequencies. Finally, certain fluctuations of the two series may be lagged to each other. Information on this is provided by the Phase spectrum at the corresponding frequencies. The idea in this package is to define a VAR (Vector autoregression) model with desired spectral characteristics by specifying a number of polynomials, required to define the VAR. See Ioannidis(2007) <doi:10.1016/j.jspi.2005.12.013>. These are specified via their roots, instead of via their coefficients. This is an idea borrowed from the Time Series Library of R. Dahlhaus, where it is used for defining ARMA models for univariate time series. This way, one may e.g. specify a VAR inducing a strong presence of long-term fluctuations in series 1 and in series 2, which are weakly correlated, but lagged by a number of time units to each other, while short-term fluctuations in series 1 and in series 2, are strongly present only in one of the two series, while they are strongly correlated to each other between the two series. Simulation from such models allows studying the behavior of data-analysis tools, such as estimation of the spectra, under different circumstances, as e.g. peaks in the spectra, generating bias, induced by leakage.

Last updated 7 months ago

1.00 score 455 downloads

rsides - SIDES-Based Subgroup Search Algorithms

R implementation of SIDES-based subgroup search algorithms (Lipkovich et al. (2017) <doi:10.1002/sim.7064>).

Last updated 7 months ago

cpp

1.00 score 142 downloads

PredictorSelect - Out-of-Sample Predictability in Predictive Regressions with Many Predictor Candidates

Consider a linear predictive regression setting with a potentially large set of candidate predictors. This work is concerned with detecting the presence of out of sample predictability based on out of sample mean squared error comparisons given in Gonzalo and Pitarakis (2023) <doi:10.1016/j.ijforecast.2023.10.005>.

Last updated 7 months ago

1.00 score 473 downloads

iccde - Computation of the Double-Entry Intraclass Correlation

The functions compute the double-entry intraclass correlation, which is an index of profile similarity (Furr, 2010; McCrae, 2008). The double-entry intraclass correlation is a more precise index of the agreement of two empirically observed profiles than the often-used intraclass correlation (McCrae, 2008). Profiles comprising correlations are automatically transformed according to the Fisher z-transformation before the double-entry intraclass correlation is calculated. If the profiles comprise scores such as sum scores from various personality scales, it is recommended to standardize each individual score prior to computation of the double-entry intraclass correlation (McCrae, 2008). See Furr (2010) <doi:10.1080/00223890903379134> or McCrae (2008) <doi:10.1080/00223890701845104> for details.

Last updated 7 months ago

1.00 score 581 downloads

SeedVigorIndex - Seed Vigor Index

Seed vigor is defined as the sum total of those properties of the seed which determine the level of activity and performance of the seed or seed lot during germination and seedling emergence. Testing for vigor becomes more important for carryover seeds, especially if seeds were stored under unknown conditions or under unfavorable storage conditions. Seed vigor testing is also used as indicator of the storage potential of a seed lot and in ranking various seed lots with different qualities. The vigour index is calculated using the equation given by (Ling et al. 2014) <doi:10.1038/srep05859>.

Last updated 7 months ago

1.00 score 471 downloads

SeedImbibition - Seed Imbibition Percentage

Imbibition causes seeds to expand, which results in the seed coat or testa being broken. Seed germination begins with imbibition. Imbibition aids in the transport of water into the developing ovules. Imbibition is required during the first stages of root water absorption.

Last updated 7 months ago

1.00 score 470 downloads

SpaceTimeBSS - Blind Source Separation for Multivariate Spatio-Temporal Data

Simultaneous/joint diagonalization of local autocovariance matrices to estimate spatio-temporally uncorrelated random fields.

Last updated 7 months ago

openblascppopenmp

1.00 score 559 downloads

EconAndProdEfficiency - Economic and Production Efficiency

Production efficiency and economic efficiency are crucial concepts in agriculture/horticulture for sustainable and profitable practices. It helps to determine the optimal use of resources to maximize outputs and profitability. Production efficiency focuses on the optimal use of resources to produce goods, while economic efficiency ensures these goods are produced and allocated in a way that maximizes economic welfare. Production efficiency and economic efficiency are calculated with the help of the formula given by (Kumar et al., 2017) <doi:10.21921/jas.v4i04.10202>.

Last updated 7 months ago

1.00 score 536 downloads

outliers.ts.oga - Efficient Outlier Detection in Heterogeneous Time Series Databases

Programs for detecting and cleaning outliers in single time series and in time series from homogeneous and heterogeneous databases using an Orthogonal Greedy Algorithm (OGA) for saturated linear regression models. The programs implement the procedures presented in the paper entitled "Efficient outlier detection in heterogeneous time series databases" by Pedro Galeano, Daniel Peña and Ruey S. Tsay (2024), working paper, Universidad Carlos III de Madrid.

Last updated 7 months ago

1.00 score 448 downloads

SoilFDA - Fractal Dimension Analysis of Soil Particle Size Distribution

Function for the computation of fractal dimension based on mass of soil particle size distribution by Tyler & Wheatcraft (1992) <doi:10.2136/sssaj1992.03615995005600020005x>. It also provides functions for calculation of mean weight and geometric mean diameter of particle size distribution by Perfect et al. (1992) <doi:10.2136/sssaj1992.03615995005600050012x>.

Last updated 7 months ago

1.00 score 207 downloads

TDSTNN - Time Delay Spatio Temporal Neural Network

STARMA (Space-Time Autoregressive Moving Average) models are commonly utilized in modeling and forecasting spatiotemporal time series data. However, the intricate nonlinear dynamics observed in many space-time rainfall patterns often exceed the capabilities of conventional STARMA models. This R package enables the fitting of Time Delay Spatio-Temporal Neural Networks, which are adept at handling such complex nonlinear dynamics efficiently. For detailed methodology, please refer to Saha et al. (2020) <doi:10.1007/s00704-020-03374-2>.

Last updated 7 months ago

1.00 score 68 downloads

vsmi - Variable Selection for Multiple Imputed Data

Penalized weighted least-squares estimate for variable selection on correlated multiply imputed data and penalized estimating equations for generalized linear models with multiple imputation. Reference: Li, Y., Yang, H., Yu, H., Huang, H., Shen, Y*. (2023) "Penalized estimating equations for generalized linear models with multiple imputation", <doi:10.1214/22-AOAS1721>. Li, Y., Yang, H., Yu, H., Huang, H., Shen, Y*. (2023) "Penalized weighted least-squares estimate for variable selection on correlated multiply imputed data", <doi:10.1093/jrsssc/qlad028>.

Last updated 7 months ago

1.00 score 132 downloads

SoilFunctionality - Soil Functionality Measurement

Generally, soil functionality is characterized by its capability to sustain microbial activity, nutritional element supply, structural stability and aid for crop production. Since soil functions can be linked to 80% of ecosystem services, conservation of degraded land should strive to restore not only the capacity of soil to sustain flora but also ecosystem provisions. The primary ecosystem services of soil are carbon sequestration, food or biomass production, provision of microbial habitat, nutrient recycling. However, the actual magnitude of soil functions provided by agricultural land uses has never been quantified. Nutrient supply capacity (NSC) is a measure of nutrient dynamics in restored land uses. Carbon accumulation proficiency (CAP) is a measure of ecosystem carbon sequestration. Biological activity index (BAI) is the average of responses of all enzyme activities in treated land over control/reference land. The CAP parameter investigates how land uses may affect carbon flows, retention, and sequestration. The CAP provides a signal for C cycles, flows, and the systems' relative operational supremacy.

Last updated 7 months ago

1.00 score 232 downloads

seqmon - Group Sequential Design Class for Clinical Trials

S4 class object for creating and managing group sequential designs. It calculates the efficacy and futility boundaries at each look. It allows modifying the design and tracking the design update history.

Last updated 7 months ago

1.00 score 24 scripts 157 downloads

good - Good Regression

Fit Good regression models to count data (Tur et al., 2021) <doi:10.48550/arXiv.2105.01557>. The package provides functions for model estimation and model prediction. Density, distribution function, quantile function and random generation for the Good distribution are also provided.

Last updated 7 months ago

1.00 score 1 scripts 53 downloads

HydroMe - Estimating Water Retention and Infiltration Model Parameters using Experimental Data

Contains functions for estimating the parameters of infiltration and water retention models using the curve-fitting methods as discussed in Omuto and Gumbe (2009) ("Estimating water infiltration and retention characteristics using a computer program in R"<doi:10.1016/j.cageo.2008.08.011>). The models considered are those that are commonly used in soil science. Version 2 of the package has new models for water retention characteristic curves.

Last updated 7 months ago

1.00 score 1 stars 27 scripts 216 downloads

optiscale - Optimal Scaling

Optimal scaling of a data vector, relative to a set of targets, is obtained through a least-squares transformation subject to appropriate measurement constraints. The targets are usually predicted values from a statistical model. If the data are nominal level, then the transformation must be identity-preserving. If the data are ordinal level, then the transformation must be monotonic. If the data are discrete, then tied data values must remain tied in the optimal transformation. If the data are continuous, then tied data values can be untied in the optimal transformation.

Last updated 7 months ago

1.00 score 1 stars 15 scripts 590 downloads

SplitSplitPlot - Analysis of Split-Split-Plot Experiments (Analise De Experimentos Em Parcela Subsubdividida)

Performs analysis of split-split plot experiments in both completely randomized and randomized complete block designs. With the results, you can obtain ANOVA, mean tests, and regression analysis (Este pacote faz a analise de experimentos em parcela subsubdivididas no delineamento inteiramente casualizado e delineamento em blocos casualizados. Com resultados e possível obter a ANOVA, testes de medias e análise de regressao) <https://www.expstat.com/pacotes-do-r>.

Last updated 7 months ago

1.00 score 211 downloads

biologicalActivityIndices - Biological Activity Indices

Ecological alteration of degraded lands can improve their sustainability by addition of large amount of biomass to soil resulting in improved soil health. Soil biological parameters (such as carbon, nitrogen and phosphorus cycling enzyme activity) are reactive to minute variations in soils [Ghosh et al. (2021) <doi:10.1016/j.ecoleng.2021.106176> ]. Hence, biological activity index combining Urease, Alkaline Phosphatase, Dehydrogenase (DHA) & Beta-Glucosidase activity will assist in detecting early changes in restored land use systems [Patidar et al. (2023) <doi:10.3389/fsufs.2023.1230156>]. This package helps to calculate Biological Activity Index (BAI) based on vectors of Land Use System/treatment and control/reference Land Use System containing four values of Urease, Alkaline Phosphatase, DHA & Beta-Glucosidase. (DHA), urease (URE), fluorescein diacetate hydrolysis (FDA) and alkaline phosphatase (ALP) activities are measured in soil samples using triphenyl tetrazolium chloride, urea, fluorescein diacetate and p-nitro phenyl-phosphate as substrates, respectively.

Last updated 7 months ago

1.00 score 265 downloads

LTCDM - Latent Transition Cognitive Diagnosis Model with Covariates

Implementation of the three-step approach of latent transition cognitive diagnosis model (CDM) with covariates. This approach can be used to assess changes in attribute mastery status and to evaluate the covariate effects on both the initial states and transition probabilities over time using latent logistic regression. Because stepwise approaches often yield biased estimates, correction for classification error probabilities (CEPs) is considered in this approach. The three-step approach for latent transition CDM with covariates involves the following steps: (1) fitting a CDM to the response data without covariates at each time point separately, (2) assigning examinees to latent states at each time point and computing the associated CEPs, and (3) estimating the latent transition CDM with the known CEPs and computing the regression coefficients. The method was proposed in Liang et al. (2023) <doi:10.3102/10769986231163320> and demonstrated using mental health data in Liang et al. (in press; annotated R code and data utilized in this example are available in Mendeley data) <doi:10.17632/kpjp3gnwbt.1>.

Last updated 7 months ago

1.00 score 143 downloads

IADT - Interaction Difference Test for Prediction Models

Provides functions to conduct a model-agnostic asymptotic hypothesis test for the identification of interaction effects in black-box machine learning models. The null hypothesis assumes that a given set of covariates does not contribute to interaction effects in the prediction model. The test statistic is based on the difference of variances of partial dependence functions (Friedman (2008) <doi:10.1214/07-AOAS148> and Welchowski (2022) <doi:10.1007/s13253-021-00479-7>) with respect to the original black-box predictions and the predictions under the null hypothesis. The hypothesis test can be applied to any black-box prediction model, and the null hypothesis of the test can be flexibly specified according to the research question of interest. Furthermore, the test is computationally fast to apply as the null distribution does not require resampling or refitting black-box prediction models.

Last updated 7 months ago

1.00 score 1 stars 161 downloads

RAFS - Robust Aggregative Feature Selection

A cross-validated minimal-optimal feature selection algorithm. It utilises popularity counting, hierarchical clustering with feature dissimilarity measures, and prefiltering with all-relevant feature selection method to obtain the minimal-optimal set of features.

Last updated 8 months ago

1.00 score 2 scripts 68 downloads

CleanBSequences - Curing of Biological Sequences

Curates biological sequences massively, quickly, without errors and without internet connection. Biological sequences curing is performed by aligning the forward and / or revers primers or ends of cloning vectors with the sequences to be cleaned. After the alignment, new subsequences are generated without biological fragment not desired by the user. Pozzi et al (2020) <doi:10.1007/s00438-020-01671-z>.

Last updated 8 months ago

1.00 score 317 downloads

BlythStillCasellaCI - Blyth-Still-Casella Exact Binomial Confidence Intervals

Computes Blyth-Still-Casella exact binomial confidence intervals based on a refining procedure proposed by George Casella (1986) <doi:10.2307/3314658>.

Last updated 8 months ago

1.00 score 284 downloads

BMconcor - CONCOR for Structural- And Regular-Equivalence Blockmodeling

The four functions svdcp() ('cp' for column partitioned), svdbip() or svdbip2() ('bip' for bipartitioned), and svdbips() ('s' for a simultaneous optimization of a set of 'r' solutions), correspond to a singular value decomposition (SVD) by blocks notion, by supposing each block depending on relative subspaces, rather than on two whole spaces as usual SVD does. The other functions, based on this notion, are relative to two column partitioned data matrices x and y defining two sets of subsets x_i and y_j of variables and amount to estimate a link between x_i and y_j for the pair (x_i, y_j) relatively to the links associated to all the other pairs. These methods were first presented in: Lafosse R. & Hanafi M.,(1997) <https://eudml.org/doc/106424> and Hanafi M. & Lafosse, R. (2001) <https://eudml.org/doc/106494>.

Last updated 8 months ago

1.00 score 282 downloads

PPbigdata - Projection Pursuit for Big Data Based on Data Nuggets

Perform 1-dim/2-dim projection pursuit, grand tour and guided tour for big data based on data nuggets. Reference papers: [1] Beavers et al., (2024) <doi:10.1080/10618600.2024.2341896>. [2] Duan, Y., Cabrera, J., & Emir, B. (2023). "A New Projection Pursuit Index for Big Data." <doi:10.48550/arXiv.2312.06465>.

Last updated 8 months ago

1.00 score 159 downloads

KMLtoSHAPE - Preserving Attribute Values: Converting KML to Shapefile

The developed function is designed to facilitate the seamless conversion of KML (Keyhole Markup Language) files to Shapefiles while preserving attribute values. It provides a straightforward interface for users to effortlessly import KML data, extract relevant attributes, and export them into the widely compatible Shapefile format. The package ensures accurate representation of spatial data while maintaining the integrity of associated attribute information. For details see, Flores, G. (2021). <DOI:10.1007/978-3-030-63665-4_15>. Whether for spatial analysis, visualization, or data interoperability, it simplifies the conversion process and empowers users to seamlessly work with geospatial datasets.

Last updated 8 months ago

1.00 score 1 scripts 179 downloads

nFunNN - Nonlinear Functional Principal Component Analysis using Neural Networks

Implementation for 'nFunNN' method, which is a novel nonlinear functional principal component analysis method using neural networks. The crucial function of this package is nFunNNmodel().

Last updated 8 months ago

1.00 score 497 downloads

drclust - Simultaneous Clustering and (or) Dimensionality Reduction

Methods for simultaneous clustering and dimensionality reduction such as: Double k-means, Reduced k-means, Factorial k-means, Clustering with Disjoint PCA but also methods for exclusively dimensionality reduction: Disjoint PCA, Disjoint FA. The statistical methods implemented refer to the following articles: de Soete G., Carroll J. (1994) "K-means clustering in a low-dimensional Euclidean space" <doi:10.1007/978-3-642-51175-2_24> ; Vichi M. (2001) "Double k-means Clustering for Simultaneous Classification of Objects and Variables" <doi:10.1007/978-3-642-59471-7_6> ; Vichi M., Kiers H.A.L. (2001) "Factorial k-means analysis for two-way data" <doi:10.1016/S0167-9473(00)00064-5> ; Vichi M., Saporta G. (2009) "Clustering and disjoint principal component analysis" <doi:10.1016/j.csda.2008.05.028> ; Vichi M. (2017) "Disjoint factor analysis with cross-loadings" <doi:10.1007/s11634-016-0263-9>.

Last updated 8 months ago

1.00 score 124 downloads

PanelTM - Two- And Three-Way Dynamic Panel Threshold Regression Model for Change Point Detection

Estimation of two- and three-way dynamic panel threshold regression models (Di Lascio and Perazzini (2024) <https://repec.unibz.it/bemps104.pdf>; Di Lascio and Perazzini (2022, ISBN:978-88-9193-231-0); Seo and Shin (2016) <doi:10.1016/j.jeconom.2016.03.005>) through the generalized method of moments based on the first difference transformation and the use of instrumental variables. The models can be used to find a change point detection in the time series. In addition, random number generation is also implemented.

Last updated 8 months ago

1.00 score 80 downloads

MSclust - Multiple-Scaled Clustering

Model based clustering using the multivariate multiple Scaled t (MST) and multivariate multiple scaled contaminated normal (MSCN) distributions. The MST is an extension of the multivariate Student-t distribution to include flexible tail behaviors, Forbes, F. & Wraith, D. (2014) <doi:10.1007/s11222-013-9414-4>. The MSCN represents a heavy-tailed generalization of the multivariate normal (MN) distribution to model elliptical contoured scatters in the presence of mild outliers (also referred to as "bad" points) and automatically detect bad points, Punzo, A. & Tortora, C. (2021) <doi:10.1177/1471082X19890935>.

Last updated 8 months ago

1.00 score 570 downloads

EDOtrans - Euclidean Distance-Optimized Data Transformation

A data transformation method which takes into account the special property of scale non-invariance with a breakpoint at 1 of the Euclidean distance.

Last updated 8 months ago

1.00 score 195 downloads

ntranova - Two Way Neutrosophic ANOVA

Dealing with neutrosophic data of the form N=D+I(where N is a Neutrosophic number ,D is the determinant part of the number and I is the indeterminacy part) using the neutrosophic two way anova test keeps the type I error low. This algorithm calculates the fisher statistics when we have a neutrosophic data, also tests two hypothesizes, first is to test differences between treatments, and second is to test differences between sectors. For more information see Miari, Mahmoud; Anan, Mohamad Taher; Zeina, Mohamed Bisher(2022) <https://www.americaspg.com/articleinfo/21/show/1058>.

Last updated 9 months ago

1.00 score 220 downloads

flippant - Dithionite Scramblase Assay Analysis

The lipid scrambling activity of protein extracts and purified scramblases is often determined using a fluorescence-based assay involving many manual steps. flippant offers an integrated solution for the analysis and publication-grade graphical presentation of dithionite scramblase assays, as well as a platform for review, dissemination and extension of the strategies it employs. The package's name derives from a play on the fact that lipid scrambling is also sometimes referred to as 'flipping'. The package is originally published as Cotton, R.J., Ploier, B., Goren, M.A., Menon, A.K., and Graumann, J. (2017). "flippant–An R package for the automated analysis of fluorescence-based scramblase assays." BMC Bioinformatics 18, 146. <DOI:10.1186/s12859-017-1542-y>.

Last updated 9 months ago

1.00 score 3 scripts 279 downloads

mtanan - Single Valued Neutrosophic Kruskal-Wallis and Mann Whitney Tests

Dealing with neutrosophic data in single valued form using score, accuracy and certainty functions to calculate ranks of Single Valued Neutrosophic Set (SVNS), also to calculate the Mann-Whitney test, and making a post-hoc test after rejecting the null hypothesis using the Neutrosophic Statistics Kruskal-Wallis test. For more information see Miari, Mahmoud; Anan, Mohamad Taher; Zeina, Mohamed Bisher(2022) <https://digitalrepository.unm.edu/nss_journal/vol51/iss1/60/>.

Last updated 9 months ago

1.00 score 207 downloads

MatchGATE - Estimate Group Average Treatment Effects with Matching

Two novel matching-based methods for estimating group average treatment effects (GATEs). The match_y1y0() and match_y1y0_bc() functions are used for imputing the potential outcomes based on matching and bias-corrected matching techniques, respectively. The EstGATE() function is employed to estimate the GATE after imputing the potential outcomes.

Last updated 9 months ago

1.00 score 227 downloads

HeckmanEM - Fit Normal, Student-t or Contaminated Normal Heckman Selection Models

It performs maximum likelihood estimation for the Heckman selection model (Normal, Student-t or Contaminated normal) using an EM-algorithm <doi:10.1016/j.jmva.2021.104737>. It also performs influence diagnostic through global and local influence for four possible perturbation schema.

Last updated 9 months ago

1.00 score 232 downloads

FunWithNumbers - Fun with Fractions and Number Sequences

A collection of toys to do things like generate Collatz and other interesting sequences, calculate a fraction which is a close approximation to some value (e.g., 22/7 or 355/113 for pi), and so on.

Last updated 9 months ago

1.00 score 227 downloads

fableCount - INGARCH and GLARMA Models for Count Time Series in Fable Framework

Provides a tidy R interface for count time series analysis. It includes implementation of the INGARCH (Integer Generalized Autoregressive Conditional Heteroskedasticity) model from the 'tscount' package and the GLARMA (Generalized Linear Autoregressive Moving Averages) model from the 'glarma' package. Additionally, it offers automated parameter selection algorithms based on the minimization of a penalized likelihood.

Last updated 9 months ago

1.00 score 1 stars 217 downloads

CDVI - Cuddy-Della Valle Index for Capturing the Instability in Time Series Data

Cuddy-Della valle index gives the degree of instability present in the data by accommodating the effect of a trend. The adjusted R squared value of the best fitted model is chosen. The index is obtained by multiplying the coefficient of variation with square root of one minus the adjusted R-squared value. This package has been developed using concept of Shankar et al. (2022)<doi:10.3389/fsufs.2023.1208898>.

Last updated 9 months ago

1.00 score 1 scripts 217 downloads

CoreMicrobiomeR - Identification of Core Microbiome

The Core Microbiome refers to the group of microorganisms that are consistently present in a particular environment, habitat, or host species. These microorganisms play a crucial role in the functioning and stability of that ecosystem. Identifying these microorganisms can contribute to the emerging field of personalized medicine. The 'CoreMicrobiomeR' is designed to facilitate the identification, statistical testing, and visualization of this group of microorganisms.This package offers three key functions to analyze and visualize microbial community data. This package has been developed based on the research papers published by Pereira et al.(2018) <doi:10.1186/s12864-018-4637-6> and Beule L, Karlovsky P. (2020) <doi:10.7717/peerj.9593>.

Last updated 9 months ago

1.00 score 175 downloads

CGR - Compound Growth Rate for Capturing the Growth Rate Over the Period

The compound growth rate indicates the percentage change of a specific variable over a defined period. It is calculated using non-linear models, particularly the exponential model. To estimate the compound growth rates, the growth model is first converted to semilog form and then analyzed using Ordinary Least Squares (OLS) regression. This package has been developed using concept of Shankar et al. (2022)<doi:10.3389/fsufs.2023.1208898>.

Last updated 9 months ago

1.00 score 1 scripts 218 downloads

PolyTree - Estimate Causal Polytree from Data

Given a data matrix with rows representing data vectors and columns representing variables, produces a directed polytree for the underlying causal structure. Based on the algorithm developed in Chatterjee and Vidyasagar (2022) <arxiv:2209.07028>. The method is fully nonparametric, making no use of linearity assumptions, and especially useful when the number of variables is large.

Last updated 9 months ago

1.00 score 131 downloads

Dtableone - Tabular Comparison of Paired Diagnostic Tests

Offers statistical methods to compare diagnostic performance between two binary diagnostic tests on the same subject in clinical studies. Includes functions for generating formatted tables to display diagnostic outcomes, facilitating a clear and comprehensive comparison directly through the R console. Inspired by and extending the functionalities of the 'DTComPair', 'tableone', and 'gtsummary' packages.

Last updated 9 months ago

1.00 score 116 downloads

welo - Weighted and Standard Elo Rates

Estimates the standard and weighted Elo (WElo, Angelini et al., 2022 <doi:10.1016/j.ejor.2021.04.011>) rates. The current version provides Elo and WElo rates for tennis, according to different systems of weights (games or sets) and scale factors (constant, proportional to the number of matches, with more weight on Grand Slam matches or matches played on a specific surface). Moreover, the package gives the possibility of estimating the (bootstrap) standard errors for the rates. Finally, the package includes betting functions that automatically select the matches on which place a bet.

Last updated 9 months ago

1.00 score 6 scripts 184 downloads

CompositionalML - Machine Learning with Compositional Data

Machine learning algorithms for predictor variables that are compositional data and the response variable is either continuous or categorical. Specifically, the Boruta variable selection algorithm, random forest, support vector machines and projection pursuit regression are included. Relevant papers include: Tsagris M.T., Preston S. and Wood A.T.A. (2011). "A data-based power transformation for compositional data". Fourth International International Workshop on Compositional Data Analysis. <doi:10.48550/arXiv.1106.1451> and Alenazi, A. (2023). "A review of compositional data analysis and recent advances". Communications in Statistics--Theory and Methods, 52(16): 5535--5567. <doi:10.1080/03610926.2021.2014890>.

Last updated 9 months ago

1.00 score 154 downloads

Inquilab - Dissipation Kinetics Analysis, Half Life Period, Rate Constant, Plots

For environmental chemists, ecologists, researchers and agricultural scientists to understand the dissipation kinetics, calculate the half-life periods and rate constants of compounds, pesticides, contaminants in different matrices.

Last updated 10 months ago

1.00 score 231 downloads

iGasso - Statistical Tests and Utilities for Genetic Association

A collection of statistical tests for genetic association studies and summary data based Mendelian randomization.

Last updated 10 months ago

1.00 score 6 scripts 248 downloads

rid - Multiple Change-Point Detection in Multivariate Time Series

Provides efficient functions for detecting multiple change points in multidimensional time series. The models can be piecewise constant or polynomial. Adaptive threshold selection methods are available, see Fan and Wu (2024) <arXiv:2403.00600>.

Last updated 10 months ago

cpp

1.00 score 1 scripts 140 downloads

FastCUB - Fast Estimation of CUB Models via Louis' Identity

For ordinal rating data, consider the accelerated EM algorithm to estimate and test models within the family of CUB models (where CUB stands for Combination of a discrete Uniform and a shifted Binomial distributions). The procedure is built upon Louis' identity for the observed information matrix. Best-subset variable selection is then implemented since it becomes more feasible from the computational point of view.

Last updated 10 months ago

1.00 score 1 stars 180 downloads

CBnetworkMA - Contrast-Based Bayesian Network Meta Analysis

A function that facilitates fitting three types of models for contrast-based Bayesian Network Meta Analysis. The first model is that which is described in Lu and Ades (2006) <doi:10.1198/016214505000001302>. The other two models are based on a Bayesian nonparametric methods that permit ties when comparing treatment or for a treatment effect to be exactly equal to zero. In addition to the model fits, the package provides a summary of the interplay between treatment effects based on the procedure described in Barrientos, Page, and Lin (2023) <doi:10.48550/arXiv.2207.06561>.

Last updated 10 months ago

1.00 score 147 downloads

rmpw - Causal Mediation Analysis Using Weighting Approach

We implement causal mediation analysis using the methods proposed by Hong (2010) and Hong, Deutsch & Hill (2015) <doi:10.3102/1076998615583902>. It allows the estimation and hypothesis testing of causal mediation effects through ratio of mediator probability weights (RMPW). This strategy conveniently relaxes the assumption of no treatment-by-mediator interaction while greatly simplifying the outcome model specification without invoking strong distributional assumptions. We also implement a sensitivity analysis by extending the RMPW method to assess potential bias in the presence of omitted pretreatment or posttreatment covariates. The sensitivity analysis strategy was proposed by Hong, Qin, and Yang (2018) <doi:10.3102/1076998617749561>.

Last updated 10 months ago

1.00 score 3 scripts 156 downloads

mediationsens - Simulation-Based Sensitivity Analysis for Causal Mediation Studies

Simulation-based sensitivity analysis for causal mediation studies. It numerically and graphically evaluates the sensitivity of causal mediation analysis results to the presence of unmeasured pretreatment confounding. The proposed method has primary advantages over existing methods. First, using an unmeasured pretreatment confounder conditional associations with the treatment, mediator, and outcome as sensitivity parameters, the method enables users to intuitively assess sensitivity in reference to prior knowledge about the strength of a potential unmeasured pretreatment confounder. Second, the method accurately reflects the influence of unmeasured pretreatment confounding on the efficiency of estimation of the causal effects. Third, the method can be implemented in different causal mediation analysis approaches, including regression-based, simulation-based, and propensity score-based methods. It is applicable to both randomized experiments and observational studies.

Last updated 10 months ago

1.00 score 171 downloads

effClust - Calculate Effective Number of Clusters for a Linear Model

Calculates the (approximate) effective number of clusters for a regression model, as described in Carter, Schnepel, and Steigerwald (2017) <doi:10.1162/REST_a_00639>. The effective number of clusters is a statistic to assess the reliability of asymptotic inference when sampling or treatment assignment is clustered. Methods are implemented for stats::lm(), plm::plm(), and fixest::feols(). There is also a formula method.

Last updated 10 months ago

1.00 score 217 downloads

pda - Privacy-Preserving Distributed Algorithms

A collection of privacy-preserving distributed algorithms for conducting multi-site data analyses. The regression analyses can be linear regression for continuous outcome, logistic regression for binary outcome, Cox proportional hazard regression for time-to event outcome, Poisson regression for count outcome, or multi-categorical regression for nominal or ordinal outcome. The PDA algorithm runs on a lead site and only requires summary statistics from collaborating sites, with one or few iterations. The package can be used together with the online system (<https://pda-ota.pdamethods.org/>) for safe and convenient collaboration. For more information, please visit our software websites: <https://github.com/Penncil/pda>, and <https://pdamethods.org/>.

Last updated 10 months ago

1.00 score 9 scripts 213 downloads

CAGR - Compound Annual Growth Rate

A time series usually does not have a uniform growth rate. Compound Annual Growth Rate measures the average annual growth over a given period. More details can be found in Bardhan et al. (2022) <DOI:10.18805/ag.D-5418>.

Last updated 10 months ago

1.00 score 278 downloads

MSoutcomes - CORe Multiple Sclerosis Outcomes Toolkit

Enable operationalized evaluation of disease outcomes in multiple sclerosis. ‘MSoutcomes’ requires longitudinally recorded clinical data structured in long format. The package is based on the research developed at Clinical Outcomes Research unit (CORe), University of Melbourne and Neuroimmunology Centre, Royal Melbourne Hospital. Kalincik et al. (2015) <doi:10.1093/brain/awv258>. Lorscheider et al. (2016) <doi:10.1093/brain/aww173>. Sharmin et al. (2022) <doi:10.1111/ene.15406>. Dzau et al. (2023) <doi:10.1136/jnnp-2023-331748>.

Last updated 10 months ago

1.00 score 1 stars 564 downloads

Lifertable - Life and Fertility Tables Specially for Insects

Life and Fertility Tables are appropriate to study the dynamics of arthropods populations. This package provides utilities for constructing Life Tables and Fertility Tables, related demographic parameters, and some simple graphs of interest. It also offers functions to transform the obtained data into a known format for better manipulation. This document is based on the article by Maia, Luiz, and Campanhola "Statistical Inference on Associated Fertility Life Table Parameters Using Jackknife Technique Computational Aspects" (April 2000, Journal of Economic Entomology, Volume 93, Issue 2) <doi:10.1603/0022-0493-93.2.511>.

Last updated 10 months ago

1.00 score 542 downloads

ARMALSTM - Fitting of Hybrid ARMA-LSTM Models

The real-life time series data are hardly pure linear or nonlinear. Merging a linear time series model like the autoregressive moving average (ARMA) model with a nonlinear neural network model such as the Long Short-Term Memory (LSTM) model can be used as a hybrid model for more accurate modeling purposes. Both the autoregressive integrated moving average (ARIMA) and autoregressive fractionally integrated moving average (ARFIMA) models can be implemented. Details can be found in Box et al. (2015, ISBN: 978-1-118-67502-1) and Hochreiter and Schmidhuber (1997) <doi:10.1162/neco.1997.9.8.1735>.

Last updated 10 months ago

1.00 score 222 downloads

RclusTool - Graphical Toolbox for Clustering and Classification of Data Frames

Graphical toolbox for clustering and classification of data frames. It proposes a graphical interface to process clustering and classification methods on features data-frames, and to view initial data as well as resulted cluster or classes. According to the level of available labels, different approaches are proposed: unsupervised clustering, semi-supervised clustering and supervised classification. To assess the processed clusters or classes, the toolbox can import and show some supplementary data formats: either profile/time series, or images. These added information can help the expert to label clusters (clustering), or to constrain data frame rows (semi-supervised clustering), using Constrained spectral embedding algorithm by Wacquet et al. (2013) <doi:10.1016/j.patrec.2013.02.003> and the methodology provided by Wacquet et al. (2013) <doi:10.1007/978-3-642-35638-4_21>.

Last updated 10 months ago

1.00 score 205 downloads

metainc - Assessment of Inconsistency in Meta-Analysis using Decision Thresholds

Assessment of inconsistency in meta-analysis by calculating the Decision Inconsistency index (DI) and the Across-Studies Inconsistency (ASI) index. These indices quantify inconsistency taking into account outcome-level decision thresholds.

Last updated 10 months ago

1.00 score 154 downloads

EncompassTest - Direct Multi-Step Forecast Based Comparison of Nested Models via an Encompassing Test

The encompassing test is developed based on multi-step-ahead predictions of two nested models as in Pitarakis, J. (2023) <doi:10.48550/arXiv.2312.16099>. The statistics are standardised to a normal distribution, and the null hypothesis is that the larger model contains no additional useful information. P-values will be provided in the output.

Last updated 10 months ago

1.00 score 133 downloads

treediff - Testing Differences Between Families of Trees

Perform test to detect differences in structure between families of trees. The method is based on cophenetic distances and aggregated Student's tests.

Last updated 10 months ago

1.00 score 216 downloads

axisandallies - Axis and Allies Spring

Simulates battles in the board game Axis and Allies Spring 1942, and calculates your probability of winning a battle. This speeds the game up significantly.

Last updated 10 months ago

1.00 score 269 downloads

sbde - Semiparametric Bayesian Density Estimation

Offers Bayesian semiparametric density estimation and tail-index estimation for heavy tailed data, by using a parametric, tail-respecting transformation of the data to the unit interval and then modeling the transformed data with a purely nonparametric logistic Gaussian process density prior. Based on Tokdar et al. (2022) <doi:10.1080/01621459.2022.2104727>.

Last updated 10 months ago

1.00 score 1 scripts 124 downloads

CASMI - 'CASMI'-Based Functions

Contains Coverage Adjusted Standardized Mutual Information ('CASMI')-based functions. 'CASMI' is a fundamental concept of a series of methods. For more information about 'CASMI' and 'CASMI'-related methods, please refer to the corresponding publications (e.g., a feature selection method, Shi, J., Zhang, J., & Ge, Y. (2019) <doi:10.3390/e21121179>, and a dataset quality measurement method, Shi, J., Zhang, J., & Ge, Y. (2019) <doi:10.1109/ICHI.2019.8904553>) or contact the package author for the latest updates.

Last updated 10 months ago

1.00 score 297 downloads

WCE - Weighted Cumulative Exposure Models

A flexible method for modeling cumulative effects of time-varying exposures, weighted according to their relative proximity in time, and represented by time-dependent covariates. The current implementation estimates the weight function in the Cox proportional hazards model. The function that assigns weights to doses taken in the past is estimated using cubic regression splines.

Last updated 10 months ago

1.00 score 1 stars 18 scripts 117 downloads

ctqr - Censored and Truncated Quantile Regression

Estimation of quantile regression models for survival data.

Last updated 11 months ago

1.00 score 1 stars 3 scripts 244 downloads

Mqrcm - M-Quantile Regression Coefficients Modeling

Parametric modeling of M-quantile regression coefficient functions.

Last updated 11 months ago

1.00 score 8 scripts 149 downloads

SPEDInstabR - Estimation of the Relative Importance of Factors Affecting Species Distribution Based on Stability Concept

From output files obtained from the software 'ModestR', the relative contribution of factors to explain species distribution is depicted using several plots. A global geographic raster file for each environmental variable may be also obtained with the mean relative contribution, considering all species present in each raster cell, of the factor to explain species distribution. Finally, for each variable it is also possible to compare the frequencies of any variable obtained in the cells where the species is present with the frequencies of the same variable in the cells of the extent.

Last updated 11 months ago

1.00 score 3 scripts 258 downloads

echelon - The Echelon Analysis and the Detection of Spatial Clusters using Echelon Scan Method

Functions for the echelon analysis proposed by Myers et al. (1997) <doi:10.1023/A:1018518327329>, and the detection of spatial clusters using echelon scan method proposed by Kurihara (2003) <doi:10.20551/jscswabun.15.2_171>.

Last updated 11 months ago

1.00 score 190 downloads

SwissAir - Air Quality Data of Switzerland for One Year in 30 Min Resolution

Ozone, NOx (= Sum of nitrogen monoxide and nitrogen dioxide), nitrogen monoxide, ambient temperature, dew point, wind speed and wind direction at 3 sites around lake of Lucerne in Central Switzerland in 30 min time resolution for year 2004.

Last updated 11 months ago

1.00 score 1 stars 5 scripts 239 downloads

pgKDEsphere - Parametrically Guided Kernel Density Estimator for Spherical Data

Nonparametric density estimation for (hyper)spherical data by means of a parametrically guided kernel estimator (adaptation of the method of Hjort and Glad (1995) <doi:10.1214/aos/1176324627> to the spherical setting). The package also allows the data-driven selection of the smoothing parameter and the representation of the estimated density for circular and spherical data. Estimators of the density without guide can also be obtained.

Last updated 11 months ago

openblascppopenmp

1.00 score 126 downloads

SeqAlignR - Sequence Alignment and Visualization Tool

Computes the optimal alignment of two character sequences. Visualizes the result of the alignment in a matrix plot. Needleman, Saul B.; Wunsch, Christian D. (1970) "A general method applicable to the search for similarities in the amino acid sequence of two proteins" <doi:10.1016/0022-2836(70)90057-4>.

Last updated 11 months ago

1.00 score 4 scripts 138 downloads

fdWasserstein - Application of Optimal Transport to Functional Data Analysis

These functions were developed to support statistical analysis on functional covariance operators. The package contains functions to: - compute 2-Wasserstein distances between Gaussian Processes as in Masarotto, Panaretos & Zemel (2019) <doi:10.1007/s13171-018-0130-1>; - compute the Wasserstein barycenter (Frechet mean) as in Masarotto, Panaretos & Zemel (2019) <doi:10.1007/s13171-018-0130-1>; - perform analysis of variance testing procedures for functional covariances and tangent space principal component analysis of covariance operators as in Masarotto, Panaretos & Zemel (2022) <arXiv:2212.04797>. - perform a soft-clustering based on the Wasserstein distance where functional data are classified based on their covariance structure as in Masarotto & Masarotto (2023) <doi:10.1111/sjos.12692>.

Last updated 11 months ago

1.00 score 1 scripts 132 downloads

SAGM - Spatial Autoregressive Graphical Model

Implements the methodological developments found in Hermes, van Heerwaarden, and Behrouzi (2023) <doi:10.48550/arXiv.2308.04325>, and allows for the statistical modeling of asymmetric between-location effects, as well as within-location effects using spatial autoregressive graphical models. The package allows for the generation of spatial weight matrices to capture asymmetric effects for strip-type intercropping designs, although it can handle any type of spatial data commonly found in other sciences.

Last updated 11 months ago

1.00 score 137 downloads

fastliu - Fast Functions for Liu Regression with Regularization Parameter and Statistics

Efficient computation of the Liu regression coefficient paths, Liu-related statistics and information criteria for a grid of the regularization parameter. The computations are based on the 'C++' library 'Armadillo' through the 'R' package 'Rcpp'.

Last updated 11 months ago

openblascppopenmp

1.00 score 139 downloads

jage - Estimation of Developmental Age

Bayesian methods for estimating developmental age from ordinal dental data. For an explanation of the model used, see Konigsberg (2015) <doi:10.3109/03014460.2015.1045430>. For details on the conditional correlation correction, see Sgheiza (2022) <doi:10.1016/j.forsciint.2021.111135>. Dental scoring is based on Moorrees, Fanning, and Hunt (1963) <doi:10.1177/00220345630420062701>.

Last updated 11 months ago

1.00 score 201 downloads

SubgrpID - Patient Subgroup Identification for Clinical Drug Development

Implementation of Sequential BATTing (bootstrapping and aggregating of thresholds from trees) for developing threshold-based multivariate (prognostic/predictive) biomarker signatures. Variable selection is automatically built-in. Final signatures are returned with interaction plots for predictive signatures. Cross-validation performance evaluation and testing dataset results are also output. Detail algorithms are described in Huang et al (2017) <doi:10.1002/sim.7236>.

Last updated 11 months ago

1.00 score 3 scripts 158 downloads

stodom - Estimating Consistent Tests for Stochastic Dominance

Stochastic dominance tests help ranking different distributions. The package implements the consistent test for stochastic dominance by Barrett and Donald (2003) <doi:10.1111/1468-0262.00390>. Specifically, it implements Barrett and Donald's Kolmogorov-Smirnov type tests for first- and second-order stochastic dominance based on bootstrapping 2 and 1.

Last updated 11 months ago

1.00 score 140 downloads

ProbSamplingI - Probabilistic Sampling Design and Strategies

It allows the user to determine sample sizes, select probabilistic samples, make estimates of different parameters for the total finite population and in studio domains, using the main design drawings.

Last updated 11 months ago

1.00 score 256 downloads

EnviroPRA2 - Environmental Probabilistic Risk Assessment Tools

It contains functions for dose calculation for different routes, fitting data to probability distributions, random number generation (Monte Carlo simulation) and calculation of systemic and carcinogenic risks. For more information see the publication: Barrio-Parra et al. (2019) "Human-health probabilistic risk assessment: the role of exposure factors in an urban garden scenario" <doi:10.1016/j.landurbplan.2019.02.005>.

Last updated 11 months ago

1.00 score 152 downloads

zfa - Zoom-Focus Algorithm

Performs Zoom-Focus Algorithm (ZFA) to optimize testing regions for rare variant association tests in exome sequencing data.

Last updated 11 months ago

1.00 score 1 scripts 130 downloads

nivm - Noninferiority Tests with Variable Margins

Noninferiority tests for difference in failure rates at a prespecified control rate or prespecified time. For details, see Fay and Follmann, 2016 <DOI:10.1177/1740774516654861>.

Last updated 11 months ago

1.00 score 6 scripts 125 downloads

mccca - Visualizing Class Specific Heterogeneous Tendencies in Categorical Data

Performing multiple-class cluster correspondence analysis(MCCCA). The main functions are create.MCCCAdata() to create a list to be applied to MCCCA, MCCCA() to apply MCCCA, and plot.mccca() for visualizing MCCCA result. Methods used in the package refers to Mariko Takagishi and Michel van de Velden (2022)<doi:10.1080/10618600.2022.2035737>.

Last updated 11 months ago

1.00 score 184 downloads

gldrm - Generalized Linear Density Ratio Models

Fits a generalized linear density ratio model (GLDRM). A GLDRM is a semiparametric generalized linear model. In contrast to a GLM, which assumes a particular exponential family distribution, the GLDRM uses a semiparametric likelihood to estimate the reference distribution. The reference distribution may be any discrete, continuous, or mixed exponential family distribution. The model parameters, which include both the regression coefficients and the cdf of the unspecified reference distribution, are estimated by maximizing a semiparametric likelihood. Regression coefficients are estimated with no loss of efficiency, i.e. the asymptotic variance is the same as if the true exponential family distribution were known. Huang (2014) <doi:10.1080/01621459.2013.824892>. Huang and Rathouz (2012) <doi:10.1093/biomet/asr075>. Rathouz and Gao (2008) <doi:10.1093/biostatistics/kxn030>.

Last updated 11 months ago

1.00 score 7 scripts 201 downloads

cauchypca - Robust Principal Component Analysis Using the Cauchy Distribution

A new robust principal component analysis algorithm is implemented that relies upon the Cauchy Distribution. The algorithm is suitable for high dimensional data even if the sample size is less than the number of variables. The methodology is described in this paper: Fayomi A., Pantazis Y., Tsagris M. and Wood A.T.A. (2024). "Cauchy robust principal component analysis with applications to high-dimensional data sets". Statistics and Computing, 34: 26. <doi:10.1007/s11222-023-10328-x>.

Last updated 11 months ago

1.00 score 221 downloads

karaoke - Remove Vocals from a Song

Attempts to remove vocals from a stereo '.wav' recording of a song.

Last updated 11 months ago

1.00 score 1 scripts 165 downloads

gbm2sas - Convert GBM Object Trees to SAS Code

Writes SAS code to get predicted values from every tree of a gbm.object.

Last updated 11 months ago

1.00 score 1 scripts 223 downloads

bpAcc - Blood Pressure Device Accuracy Evaluation: Statistical Considerations

A comprehensive statistical analysis of the accuracy of blood pressure devices based on the method of AAMI/ANSI SP10 standards developed by the AAMI Sphygmomanometer Committee for indirect measurement of blood pressure, incorporated into IS0 81060-2. The 'bpAcc' package gives the exact probability 'of accepting a device D' derived from the join distribution of the sample standard deviation and a non-linear transformation of the sample mean for a specified sample size introduced by Chandel et al. (2023) and by the Association for the Advancement of Medical Instrumentation (2003, ISBN:1-57020-183-8).

Last updated 11 months ago

1.00 score 332 downloads

sephora - Statistical Estimation of Phenological Parameters

Provides functions and methods for estimating phenological dates (green up, start of a season, maturity, senescence, end of a season and dormancy) from (nearly) periodic Earth Observation time series. These dates are critical points of some derivatives of an idealized curve which, in turn, is obtained through a functional principal component analysis-based regression model. Some of the methods implemented here are based on T. Krivobokova, P. Serra and F. Rosales (2022) <https://www.sciencedirect.com/science/article/pii/S0167947322000998>. Methods for handling and plotting Earth observation time series are also provided.

Last updated 11 months ago

1.00 score 1 scripts 117 downloads

fiberLD - Fiber Length Determination

Routines for estimating tree fiber (tracheid) length distributions in the standing tree based on increment core samples. Two types of data can be used with the package, increment core data measured by means of an optical fiber analyzer (OFA), e.g. such as the Kajaani Fiber Lab, or measured by microscopy. Increment core data analyzed by OFAs consist of the cell lengths of both cut and uncut fibres (tracheids) and fines (such as ray parenchyma cells) without being able to identify which cells are cut or if they are fines or fibres. The microscopy measured data consist of the observed lengths of the uncut fibres in the increment core. A censored version of a mixture of the fine and fiber length distributions is proposed to fit the OFA data, under distributional assumptions (Svensson et al., 2006) <doi:10.1111/j.1467-9469.2006.00501.x>. The package offers two choices for the assumptions of the underlying density functions of the true fiber (fine) lenghts of those fibers (fines) that at least partially appear in the increment core, being the generalized gamma and the log normal densities.

Last updated 11 months ago

cpp

1.00 score 11 scripts 149 downloads

ConcordanceTest - An Alternative to the Kruskal-Wallis Based on the Kendall Tau Distance

The Concordance Test is a non-parametric method for testing whether two o more samples originate from the same distribution. It extends the Kendall Tau correlation coefficient when there are only two groups. For details, see Alcaraz J., Anton-Sanchez L., Monge J.F. (2022) The Concordance Test, an Alternative to Kruskal-Wallis Based on the Kendall-tau Distance: An R Package. The R Journal 14, 26–53 <doi:10.32614/RJ-2022-039>.

Last updated 11 months ago

1.00 score 298 downloads

SIRmcmc - Compartmental Susceptible-Infectious-Recovered (SIR) Model of Community and Household Infection

We build an Susceptible-Infectious-Recovered (SIR) model where the rate of infection is the sum of the household rate and the community rate. We estimate the posterior distribution of the parameters using the Metropolis algorithm. Further details may be found in: F Scott Dahlgren, Ivo M Foppa, Melissa S Stockwell, Celibell Y Vargas, Philip LaRussa, Carrie Reed (2021) "Household transmission of influenza A and B within a prospective cohort during the 2013-2014 and 2014-2015 seasons" <doi:10.1002/sim.9181>.

Last updated 12 months ago

cpp

1.00 score 151 downloads

semicontMANOVA - Multivariate ANalysis of VAriance with Ridge Regularization for Semicontinuous High-Dimensional Data

Implements Multivariate ANalysis Of VAriance (MANOVA) parameters' inference and test with regularization for semicontinuous high-dimensional data. The method can be applied also in presence of low-dimensional data. The p-value can be obtained through asymptotic distribution or using a permutation procedure. The package gives also the possibility to simulate this type of data. Method is described in Elena Sabbioni, Claudio Agostinelli and Alessio Farcomeni (2024) <arXiv:2401.04036>.

Last updated 12 months ago

1.00 score 133 downloads

hbal - Hierarchically Regularized Entropy Balancing

Implements hierarchically regularized entropy balancing proposed by Xu and Yang (2022) <doi:10.1017/pan.2022.12>. The method adjusts the covariate distributions of the control group to match those of the treatment group. 'hbal' automatically expands the covariate space to include higher order terms and uses cross-validation to select variable penalties for the balancing conditions.

Last updated 12 months ago

cpp

1.00 score 8 scripts 248 downloads

cocotest - Dependence Condition Test Using Ranked Correlation Coefficients

A common misconception is that the Hochberg procedure comes up with adequate overall type I error control when test statistics are positively correlated. However, unless the test statistics follow some standard distributions, the Hochberg procedure requires a more stringent positive dependence assumption, beyond mere positive correlation, to ensure valid overall type I error control. To fill this gap, we formulate statistical tests grounded in rank correlation coefficients to validate fulfillment of the positive dependence through stochastic ordering (PDS) condition. See Gou, J., Wu, K. and Chen, O. Y. (2024). Rank correlation coefficient based tests on positive dependence through stochastic ordering with application in cancer studies, Technical Report.

Last updated 12 months ago

1.00 score 126 downloads

LiftTest - A Bootstrap Proportion Test for Brand Lift Testing

A bootstrap proportion test for Brand Lift Testing to quantify the effectiveness of online advertising. Methods of the bootstrap proportion test are presented in Liu, Yu, Mao, Wu, Dyer (2023) <doi:10.1145/3583780.3615021>.

Last updated 12 months ago

1.00 score 148 downloads

PUPMCR - Image-Based Identification of Color Based on Rayner (1970) Terminology and Known Fungal Pigments

Image-based color matching using the "Mycological Colour Chart" by Rayner (1970, ISBN:9780851980263) and its associated fungal pigments. This package will assist mycologists in identifying color during morphological analysis.

Last updated 12 months ago

1.00 score 1 scripts 176 downloads

ADER - Data Analysis in Ecology

Data sets used in Cayuela and De la Cruz (2022, ISBN:978-84-8476-833-3).

Last updated 12 months ago

1.00 score 426 downloads

dirttee - Distributional Regression for Time to Event Data

Semiparametric distributional regression methods (expectile, quantile and mode regression) for time-to-event variables with right-censoring; uses inverse probability of censoring weights or accelerated failure time models with auxiliary likelihoods. Expectile regression using inverse probability of censoring weights has been introduced in Seipp et al. (2021) ``Weighted Expectile Regression for Right-Censored Data'' <doi:10.1002/sim.9137>, mode regression for time-to-event variables has been introduced in Seipp et al. (2022) ``Flexible Semiparametric Mode Regression for Time-to-Event Data'' <doi:10.1177/09622802221122406>.

Last updated 1 years ago

1.00 score 194 downloads

icensBKL - Accompanion to the Book on Interval Censoring by Bogaerts, Komarek, and Lesaffre

Contains datasets and several smaller functions suitable for analysis of interval-censored data. The package complements the book Bogaerts, Komárek and Lesaffre (2017, ISBN: 978-1-4200-7747-6) "Survival Analysis with Interval-Censored Data: A Practical Approach" <https://www.routledge.com/Survival-Analysis-with-Interval-Censored-Data-A-Practical-Approach-with/Bogaerts-Komarek-Lesaffre/p/book/9781420077476>. Full R code related to the examples presented in the book can be found at <https://ibiostat.be/online-resources/icbook/supplemental>. Packages mentioned in the "Suggests" section are used in those examples.

Last updated 1 years ago

1.00 score 1 stars 3 scripts 251 downloads

THREC - Tree Height Response Calibration for Swedish Forests

A tool that allows users to estimate tree height in the long-term forest experiments in Sweden. It utilizes the multilevel nonlinear mixed-effect height models developed for the forest experiments and consists of four functions for the main species, other conifer species, and other broadleaves. Each function within the system returns a data frame that includes the input data and the estimated heights for any missing values. Ogana et al. (2023) <doi:10.1016/j.foreco.2023.120843>\n Arias-Rodil et al. (2015) <doi:10.1371/JOURNAL.PONE.0143521>.

Last updated 1 years ago

1.00 score 1 scripts 529 downloads

GenMarkov - Multivariate Markov Chains

Provides routines to estimate the Mixture Transition Distribution Model based on Raftery (1985) <http://www.jstor.org/stable/2345788> and Nicolau (2014) <doi:10.1111/sjos.12087> specifications, for multivariate data. Additionally, provides a function for the estimation of a new model for multivariate non-homogeneous Markov chains. This new specification, Generalized Multivariate Markov Chains (GMMC) was proposed by Carolina Vasconcelos and Bruno Damasio and considers (continuous or discrete) covariates exogenous to the Markov chain.

Last updated 1 years ago

1.00 score 179 downloads

tightenBlock - Tightens an Observational Block Design by Balanced Subset Matching

Tightens an observational block design into a smaller design with either smaller or fewer blocks while controlling for covariates. The method uses fine balance, optimal subset matching (Rosenbaum, 2012 <doi:10.1198/jcgs.2011.09219>) and two-criteria matching (Zhang et al 2023 <doi:10.1080/01621459.2021.1981337>). The main function is tighten(). The suggested 'rrelaxiv' package for solving minimum cost flow problems: (i) derives from Bertsekas and Tseng (1988) <doi:10.1007/BF02288322>, (ii) is not available on CRAN due to its academic license, (iii) may be downloaded from GitHub at <https://github.com/josherrickson/rrelaxiv/>, (iv) is not essential to use the package.

Last updated 1 years ago

1.00 score 109 downloads

nice - Get or Set UNIX Niceness

Get or set UNIX priority (niceness) of running R process.

Last updated 1 years ago

1.00 score 4 scripts 105 downloads

InterfaceqPCR - GUI to Analyse qPCR Results after PMA Treatment or not

Graphical User Interface allowing to determine the concentration in the sample in CFU per mL or in number of copies per mL provided to qPCR results after with or without PMA treatment. This package is simply to use because no knowledge in R commands is necessary. A graphic represents the standard curve, and a table containing the result for each sample is created.

Last updated 1 years ago

openjdk

1.00 score 3 scripts 189 downloads

Gammareg - Classic Gamma Regression: Joint Modeling of Mean and Shape Parameters

Performs Gamma regression, where both mean and shape parameters follows lineal regression structures.

Last updated 1 years ago

1.00 score 2 scripts 284 downloads

rmp - Rounded Mixture Package

Performs univariate probability mass function estimation via Bayesian nonparametric mixtures of rounded kernels as in Canale and Dunson (2011) <doi:10.1198/jasa.2011.tm10552>.

Last updated 1 years ago

1.00 score 257 downloads

elections - USA Presidential Elections Data

This includes a dataset on the outcomes of the USA presidential elections since 1920, and various predictors, as used in <https://www.vanderwalresearch.com/blog/15-elections>.

Last updated 1 years ago

1.00 score 8 scripts 330 downloads

sMSROC - Assessment of Diagnostic and Prognostic Markers

Provides estimations of the Receiver Operating Characteristic (ROC) curve and the Area Under the Curve (AUC) based on the two-stages mixed-subjects ROC curve estimator (Diaz-Coto et al. (2020) <doi:10.1515/ijb-2019-0097> and Diaz-Coto et al. (2020) <doi:10.1080/00949655.2020.1736071>).

Last updated 1 years ago

1.00 score 5 scripts 158 downloads

g.ridge - Generalized Ridge Regression for Linear Models

Ridge regression due to Hoerl and Kennard (1970)<DOI:10.1080/00401706.1970.10488634> and generalized ridge regression due to Yang and Emura (2017)<DOI:10.1080/03610918.2016.1193195> with optimized tuning parameters. These ridge regression estimators (the HK estimator and the YE estimator) are computed by minimizing the cross-validated mean squared errors. Both the ridge and generalized ridge estimators are applicable for high-dimensional regressors (p>n), where p is the number of regressors, and n is the sample size.

Last updated 1 years ago

1.00 score 255 downloads

covadap - Implement Covariate-Adaptive Randomization

Implementing seven Covariate-Adaptive Randomization to assign patients to two treatments. Three of these procedures can also accommodate quantitative and mixed covariates. Given a set of covariates, the user can generate a single sequence of allocations or replicate the design multiple times by simulating the patients' covariate profiles. At the end, an extensive assessment of the performance of the randomization procedures is provided, calculating several imbalance measures. See Baldi Antognini A, Frieri R, Zagoraiou M and Novelli M (2022) <doi:10.1007/s00362-022-01381-1> for details.

Last updated 1 years ago

1.00 score 231 downloads

NAC - Network-Adjusted Covariates for Community Detection

Incorporating node-level covariates for community detection has gained increasing attention these years. This package provides the function for implementing the novel community detection algorithm known as Network-Adjusted Covariates for Community Detection (NAC), which is designed to detect latent community structure in graphs with node-level information, i.e., covariates. This algorithm can handle models such as the degree-corrected stochastic block model (DCSBM) with covariates. NAC specifically addresses the discrepancy between the community structure inferred from the adjacency information and the community structure inferred from the covariates information. For more detailed information, please refer to the reference paper: Yaofang Hu and Wanjie Wang (2023) <arXiv:2306.15616>. In addition to NAC, this package includes several other existing community detection algorithms that are compared to NAC in the reference paper. These algorithms are Spectral Clustering On Ratios-of Eigenvectors (SCORE), network-based regularized spectral clustering (Net-based), covariate-based spectral clustering (Cov-based), covariate-assisted spectral clustering (CAclustering) and semidefinite programming (SDP).

Last updated 1 years ago

1.00 score 102 downloads

poistweedie - Poisson-Tweedie Exponential Family Models

Simulation of models Poisson-Tweedie.

Last updated 1 years ago

1.00 score 6 scripts 288 downloads

CopulaGAMM - Copula-Based Mixed Regression Models

Estimation of 2-level factor copula-based regression models for clustered data where the response variable can be either discrete or continuous.

Last updated 1 years ago

1.00 score 237 downloads

countts - Thomson Sampling for Zero-Inflated Count Outcomes

A specialized tool is designed for assessing contextual bandit algorithms, particularly those aimed at handling overdispersed and zero-inflated count data. It offers a simulated testing environment that includes various models like Poisson, Overdispersed Poisson, Zero-inflated Poisson, and Zero-inflated Overdispersed Poisson. The package is capable of executing five specific algorithms: Linear Thompson sampling with log transformation on the outcome, Thompson sampling Poisson, Thompson sampling Negative Binomial, Thompson sampling Zero-inflated Poisson, and Thompson sampling Zero-inflated Negative Binomial. Additionally, it can generate regret plots to evaluate the performance of contextual bandit algorithms. This package is based on the algorithms by Liu et al. (2023) <arXiv:2311.14359>.

Last updated 1 years ago

1.00 score 151 downloads

convertid - Convert Gene IDs Between Each Other and Fetch Annotations from Biomart

Gene Symbols or Ensembl Gene IDs are converted using the Bimap interface in 'AnnotationDbi' in convertId2() but that function is only provided as fallback mechanism for the most common use cases in data analysis. The main function in the package is convert.bm() which queries BioMart using the full capacity of the API provided through the 'biomaRt' package. Presets and defaults are provided for convenience but all "marts", "filters" and "attributes" can be set by the user. Function convert.alias() converts Gene Symbols to Aliases and vice versa and function likely_symbol() attempts to determine the most likely current Gene Symbol.

Last updated 1 years ago

1.00 score 260 downloads

slfm - Fitting a Bayesian Sparse Latent Factor Model in Gene Expression Analysis

Set of tools to find coherent patterns in gene expression (microarray) data using a Bayesian Sparse Latent Factor Model (SLFM) <DOI:10.1007/978-3-319-12454-4_15>. Considerable effort has been put to build a fast and memory efficient package, which makes this proposal an interesting and computationally convenient alternative to study patterns of gene expressions exhibited in matrices. The package contains the implementation of two versions of the model based on different mixture priors for the loadings: one relies on a degenerate component at zero and the other uses a small variance normal distribution for the spike part of the mixture.

Last updated 1 years ago

openblascpp

1.00 score 1 scripts 146 downloads

modernVA - An Implementation of Two Modern Education-Based Value-Added Models

Provides functions that fit two modern education-based value-added models. One of these models is the quantile value-added model. This model permits estimating a school's value-added based on specific quantiles of the post-test distribution. Estimating value-added based on quantiles of the post-test distribution provides a more complete picture of an education institution's contribution to learning for students of all abilities. See Page, G.L.; San Martín, E.; Orellana, J.; Gonzalez, J. (2017) <doi:10.1111/rssa.12195> for more details. The second model is a temporally dependent value-added model. This model takes into account the temporal dependence that may exist in school performance between two cohorts in one of two ways. The first is by modeling school random effects with a non-stationary AR(1) process. The second is by modeling school effects based on previous cohort's post-test performance. In addition to more efficiently estimating value-added, this model permits making statements about the persistence of a schools effectiveness. The standard value-added model is also an option.

Last updated 1 years ago

1.00 score 297 downloads

engression - Engression Modelling

Fits engression models for nonlinear distributional regression. Predictors and targets can be univariate or multivariate. Functionality includes estimation of conditional mean, estimation of conditional quantiles, or sampling from the fitted distribution. Training is done full-batch on CPU (the python version offers GPU-accelerated stochastic gradient descent). Based on "Engression: Extrapolation for nonlinear regression?" by Xinwei Shen and Nicolai Meinshausen (2023). Also supports classification (experimental). <arxiv:2307.00835>.

Last updated 1 years ago

1.00 score 162 downloads

PoolBal - Balancing Central and Marginal Rejection of Pooled p-Values

When using pooled p-values to adjust for multiple testing, there is an inherent balance that must be struck between rejection based on weak evidence spread among many tests and strong evidence in a few, explored in Salahub and Olford (2023) <arXiv:2310.16600>. This package provides functionality to compute marginal and central rejection levels and the centrality quotient for p-value pooling functions and provides implementations of the chi-squared quantile pooled p-value (described in Salahub and Oldford (2023)) and a proposal from Heard and Rubin-Delanchy (2018) <doi:10.1093/biomet/asx076> to control the quotient's value.

Last updated 1 years ago

1.00 score 2 scripts 179 downloads

rSPARCS - Sites, Population, and Records Cleaning Skills

Data cleaning including 1) generating datasets for time-series and case-crossover analyses based on raw hospital records, 2) linking individuals to an areal map, 3) picking out cases living within a buffer of certain size surrounding a site, etc. For more information, please refer to Zhang W,etc. (2018) <doi:10.1016/j.envpol.2018.08.030>.

Last updated 1 years ago

1.00 score 4 scripts 306 downloads

marradistrees - Plots a Tree-Like Representation of a Numerical Variable (Marradi's Tree)

Provides a single function plotting Marradi's trees: a graphical representation of a numerical variable for comparing the variable mean and standard deviation across subgroups. See A. Marradi "L'analisi monovariata" (1993, ISBN: 9788820496876).

Last updated 1 years ago

1.00 score 206 downloads

ncar - Noncompartmental Analysis for Pharmacokinetic Report

Conduct a noncompartmental analysis with industrial strength. Some features are 1) CDISC SDTM terms 2) Automatic or manual slope selection 3) Supporting both 'linear-up linear-down' and 'linear-up log-down' method 4) Interval(partial) AUCs with 'linear' or 'log' interpolation method 5) Produce pdf, rtf, text report files. * Reference: Gabrielsson J, Weiner D. Pharmacokinetic and Pharmacodynamic Data Analysis - Concepts and Applications. 5th ed. 2016. (ISBN:9198299107).

Last updated 1 years ago

1.00 score 1 stars 25 scripts 427 downloads

WCluster - Clustering and PCA with Weights, and Data Nuggets Clustering

K-means clustering, hierarchical clustering, and PCA with observational weights and/or variable weights. It also includes the corresponding functions for data nuggets which serve as representative samples of large datasets. Cherasia et al., (2022) <doi:10.1007/978-3-031-22687-8_20>. Amaratunga et al., (2009) <doi:10.1002/9780470317129>.

Last updated 1 years ago

1.00 score 1 scripts 169 downloads

pmvalsampsize - Sample Size for External Validation of a Prediction Model

Computes the minimum sample size required for the external validation of an existing multivariable prediction model using the criteria proposed by Archer (2020) <doi:10.1002/sim.8766> and Riley (2021) <doi:10.1002/sim.9025>.

Last updated 1 years ago

1.00 score 1 scripts 173 downloads

SIMEXBoost - Boosting Method for High-Dimensional Error-Prone Data

Implementation of the boosting procedure with the simulation and extrapolation approach to address variable selection and estimation for high-dimensional data subject to measurement error in predictors. It can be used to address generalized linear models (GLM) in Chen (2023) <doi: 10.1007/s11222-023-10209-3> and the accelerated failure time (AFT) model in Chen and Qiu (2023) <doi: 10.1111/biom.13898>. Some relevant references include Chen and Yi (2021) <doi:10.1111/biom.13331> and Hastie, Tibshirani, and Friedman (2008, ISBN:978-0387848570).

Last updated 1 years ago

1.00 score 9 scripts 126 downloads

RcmdrPlugin.TeachStat - R Commander Plugin for Teaching Statistical Methods

R Commander plugin for teaching statistical methods. It adds a new menu for making easier the teaching of the main concepts about the main statistical methods.

Last updated 1 years ago

1.00 score 11 scripts 560 downloads

MSigSeg - Multiple SIGnal SEGmentation

Traditional methods typically detect breakpoints from individual signals, which means that when applied separately to multiple signals, the breakpoints are not aligned. However, this package implements a common breakpoint detection approach for multiple piecewise constant signals, resulting in increased detection sensitivity and specificity. By employing various techniques, optimal performance is ensured, and computation is accelerated. We hope that this package will be beneficial for researchers in signal processing, bioinformatics, economy, and other related fields. The segmentation(), lambda_estimator() functions are the main functions of this package.

Last updated 1 years ago

1.00 score 148 downloads

EMAR - Empirical Model Assessment

A tool that allows users to generate various indices for evaluating statistical models. The fitstat() function computes indices based on the fitting data. The valstat() function computes indices based on the validation data set. Both fitstat() and valstat() will return 16 indices SSR: residual sum of squares, TRE: total relative error, Bias: mean bias, MRB: mean relative bias, MAB: mean absolute bias, MAPE: mean absolute percentage error, MSE: mean squared error, RMSE: root mean square error, Percent.RMSE: percentage root mean squared error, R2: coefficient of determination, R2adj: adjusted coefficient of determination, APC: Amemiya's prediction criterion, logL: Log-likelihood, AIC: Akaike information criterion, AICc: corrected Akaike information criterion, BIC: Bayesian information criterion, HQC: Hannan-Quin information criterion. The lower the better for the SSR, TRE, Bias, MRB, MAB, MAPE, MSE, RMSE, Percent.RMSE, APC, AIC, AICc, BIC and HQC indices. The higher the better for R2 and R2adj indices. Petre Stoica, P., Selén, Y. (2004) <doi:10.1109/MSP.2004.1311138>\n Zhou et al. (2023) <doi:10.3389/fpls.2023.1186250>\n Ogana, F.N., Ercanli, I. (2021) <doi:10.1007/s11676-021-01373-1>\n Musabbikhah et al. (2019) <doi:10.1088/1742-6596/1175/1/012270>.

Last updated 1 years ago

1.00 score 4 scripts 568 downloads

bild - A Package for BInary Longitudinal Data

Performs logistic regression for binary longitudinal data, allowing for serial dependence among observations from a given individual and a random intercept term. Estimation is via maximization of the exact likelihood of a suitably defined model. Missing values and unbalanced data are allowed, with some restrictions. M. Helena Goncalves et al.(2007) <DOI: 10.18637/jss.v046.i09>.

Last updated 1 years ago

fortran

1.00 score 1 stars 8 scripts 480 downloads

bioclim - Bioclimatic Analysis and Classification

Using numeric or raster data, this package contains functions to calculate: complete water balance, bioclimatic balance, bioclimatic intensities, reports for individual locations, multi-layered rasters for spatial analysis.

Last updated 1 years ago

1.00 score 323 downloads

SurvSparse - Survival Analysis with Sparse Longitudinal Covariates

Survival analysis with sparse longitudinal covariates under right censoring scheme. Different hazards models are involved. Please cite the manuscripts corresponding to this package: Sun, Z. et al. (2022) <doi:10.1007/s10985-022-09548-6>, Sun, Z. and Cao, H. (2023) <arXiv:2310.15877> and Sun, D. et al. (2023) <arXiv:2308.15549>.

Last updated 1 years ago

1.00 score 121 downloads

simdd - Simulation of Fisher Bingham and Related Directional Distributions

Simulation methods for the Fisher Bingham distribution on the unit sphere, the matrix Bingham distribution on a Grassmann manifold, the matrix Fisher distribution on SO(3), and the bivariate von Mises sine model on the torus. The methods use an acceptance/rejection simulation algorithm for the Bingham distribution and are described fully by Kent, Ganeiber and Mardia (2018) <doi:10.1080/10618600.2017.1390468>. These methods supersede earlier MCMC simulation methods and are more general than earlier simulation methods. The methods can be slower in specific situations where there are existing non-MCMC simulation methods (see Section 8 of Kent, Ganeiber and Mardia (2018) <doi:10.1080/10618600.2017.1390468> for further details).

Last updated 1 years ago

1.00 score 1 scripts 183 downloads

TailClassifier - Tail Classifier

The function TailClassifier() suggests one of the following types of tail for your discrete data: 1) Power decaying tail; 2) Sub-exponential decaying tail; and 3) Near-exponential decaying tail. The function also provides an estimate of the parameter for the classified-distribution as a reference.

Last updated 1 years ago

1.00 score 127 downloads

DMQ - Dynamic Multiple Quantile (DMQ) Model

Perform estimation, prediction, and simulations using the Dynamic Multiple Quantile model of Catania and Luati (2023) <doi:10.1016/j.jeconom.2022.11.002>. Can be used to estimate a set of conditional time-varying quantiles of a time series that do not cross.

Last updated 1 years ago

openblascpp

1.00 score 7 scripts 130 downloads

corrfuns - Correlation Coefficient Related Functions

Many correlation coefficient related functions are offered, such as correlations, partial correlations and hypothesis testing using asymptotic tests and computer intensive methods (bootstrap and permutation). References include Mardia K.V., Kent J.T. and Bibby J.M. (1979). "Multivariate Analysis". ISBN: 978-0124712522. London: Academic Press.

Last updated 1 years ago

1.00 score 156 downloads

kcpRS - Kernel Change Point Detection on the Running Statistics

The running statistics of interest is first extracted using a time window which is slid across the time series, and in each window, the running statistics value is computed. KCP (Kernel Change Point) detection proposed by Arlot et al. (2012) <arXiv:1202.3878> is then implemented to flag the change points on the running statistics (Cabrieto et al., 2018, <doi:10.1016/j.ins.2018.03.010>). Change points are located by minimizing a variance criterion based on the pairwise similarities between running statistics which are computed via the Gaussian kernel. KCP can locate change points for a given k number of change points. To determine the optimal k, the KCP permutation test is first carried out by comparing the variance of the running statistics extracted from the original data to that of permuted data. If this test is significant, then there is sufficient evidence for at least one change point in the data. Model selection is then used to determine the optimal k>0.

Last updated 1 years ago

cpp

1.00 score 7 scripts 185 downloads

GFE - Gross Flows Estimation under Complex Surveys

The philosophy in the package is described in Stasny (1988) <doi:10.2307/1391558> and Gutierrez, A., Trujillo, L. & Silva, N. (2014), <ISSN:1492-0921> to estimate the gross flows under complex surveys using a Markov chain approach with non response.

Last updated 1 years ago

1.00 score 4 scripts 314 downloads

choosepc - Choose the Number of Principal Components via Recistruction Error

One way to choose the number of principal components is via the reconstruction error. This package is designed mainly for this purpose. Graphical representation is also supported, plus some other principal component analysis related functions. References include: Jolliffe I.T. (2002). Principal Component Analysis. <doi:10.1007/b98835> and Mardia K.V., Kent J.T. and Bibby J.M. (1979). Multivariate Analysis. ISBN: 978-0124712522. London: Academic Press.

Last updated 1 years ago

1.00 score 146 downloads

cgwtools - Miscellaneous Tools

Functions for performing quick observations or evaluations of data, including a variety of ways to list objects by size, class, etc. The functions 'seqle' and 'reverse.seqle' mimic the base 'rle' but can search for linear sequences. The function 'splatnd' allows the user to generate zero-argument commands without the need for 'makeActiveBinding' . Functions provided to convert from any base to any other base, and to find the n-th greatest max or n-th least min. In addition, functions which mimic Unix shell commands, including 'head', 'tail' ,'pushd' ,and 'popd'. Various other goodies included as well.

Last updated 1 years ago

1.00 score 79 scripts 315 downloads

SuessR - Suess and Laws Corrections for Marine Stable Carbon Isotope Data

Generates region-specific Suess and Laws corrections for stable carbon isotope data from marine organisms collected between 1850 and 2022. Version 0.1.5 of 'SuessR' contains four built-in regions: the Bering Sea ('Bering Sea'), the Aleutian archipelago ('Aleutian Islands'), the Gulf of Alaska ('Gulf of Alaska'), and the subpolar North Atlantic ('Subpolar North Atlantic'). Users can supply their own environmental data for regions currently not built into the package to generate corrections for those regions.

Last updated 1 years ago

1.00 score 2 scripts 285 downloads

pretest - A Novel Approach to Predictive Accuracy Testing in Nested Environments

This repository contains the codes for using the predictive accuracy comparison tests developed in Pitarakis, J. (2023) <doi:10.1017/S0266466623000154>.

Last updated 1 years ago

1.00 score 186 downloads

crwbmetareg - Cluster Robust Wild Bootstrap Meta Regression

In meta regression sometimes the studies have multiple effects that are correlated. For this reason cluster robust standard errors must be computed. However, since the clusters are unbalanced the wild bootstrap is suggested. See Oczkowski E. and Doucouliagos H. (2015). "Wine prices and quality ratings: a meta-regression analysis". American Journal of Agricultural Economics, 97(1): 103--121. <doi:10.1093/ajae/aau057> and Cameron A. C., Gelbach J. B. and Miller D. L. (2008). "Bootstrap-based improvements for inference with clustered errors". The Review of Economics and Statistics, 90(3): 414--427. <doi:10.1162/rest.90.3.414>.

Last updated 1 years ago

1.00 score 206 downloads

vscc - Variable Selection for Clustering and Classification

Performs variable selection/feature reduction under a clustering or classification framework. In particular, it can be used in an automated fashion using mixture model-based methods ('teigen' and 'mclust' are currently supported). Can account for mixtures of non-Gaussian distributions via Manly transform (via 'ManlyMix'). See Andrews and McNicholas (2014) <doi:10.1007/s00357-013-9139-2> and Neal and McNicholas (2023) <doi:10.48550/arXiv.2305.16464>.

Last updated 1 years ago

1.00 score 14 scripts 610 downloads

mixSPE - Mixtures of Power Exponential and Skew Power Exponential Distributions for Use in Model-Based Clustering and Classification

Mixtures of skewed and elliptical distributions are implemented using mixtures of multivariate skew power exponential and power exponential distributions, respectively. A generalized expectation-maximization framework is used for parameter estimation. See citation() for how to cite.

Last updated 1 years ago

1.00 score 1 scripts 170 downloads

RegCombin - Partially Linear Regression under Data Combination

We implement linear regression when the outcome of interest and some of the covariates are observed in two different datasets that cannot be linked, based on D'Haultfoeuille, Gaillac, Maurel (2022) <doi:10.3386/w29953>. The package allows for common regressors observed in both datasets, and for various shape constraints on the effect of covariates on the outcome of interest. It also provides the tools to perform a test of point identification. See the associated vignette <https://github.com/cgaillac/RegCombin/blob/master/RegCombin_vignette.pdf> for theory and code examples.

Last updated 1 years ago

1.00 score 1 stars 151 downloads

longitudinalANAL - Longitudinal Data Analysis

Regression analysis of mixed sparse synchronous and asynchronous longitudinal covariates. Please cite the manuscripts corresponding to this package: Sun, Z. et al. (2023) <arXiv:2305.17715> and Liu, C. et al. (2023) <arXiv:2305.17662>.

Last updated 1 years ago

1.00 score 178 downloads

BosonSampling - Classical Boson Sampling

Classical Boson Sampling using the algorithm of Clifford and Clifford (2017) <arXiv:1706.01260>. Also provides functions for generating random unitary matrices, evaluation of matrix permanents (both real and complex) and evaluation of complex permanent minors.

Last updated 1 years ago

cpp

1.00 score 3 scripts 233 downloads

KnowBR - Discriminating Well Surveyed Spatial Units from Exhaustive Biodiversity Databases

It uses species accumulation curves and diverse estimators to assess, at the same time, the levels of survey coverage in multiple geographic cells of a size defined by the user or polygons. It also enables the geographical depiction of observed species richness, survey effort and completeness values including a background with administrative areas.

Last updated 1 years ago

1.00 score 8 scripts 255 downloads

GGRidge - Graphical Group Ridge

The Graphical Group Ridge 'GGRidge' package package classifies ridge regression predictors in disjoint groups of conditionally correlated variables and derives different penalties (shrinkage parameters) for these groups of predictors. It combines the ridge regression method with the graphical model for high-dimensional data (i.e. the number of predictors exceeds the number of cases) or ill-conditioned data (e.g. in the presence of multicollinearity among predictors). The package reduces the mean square errors and the extent of over-shrinking of predictors as compared to the ridge method.Aldahmani, S. and Zoubeidi, T. (2020) <DOI:10.1080/00949655.2020.1803320>.

Last updated 1 years ago

1.00 score 1 scripts 656 downloads

viking - State-Space Models Inference by Kalman or Viking

Inference methods for state-space models, relying on the Kalman Filter or on Viking (Variational Bayesian VarIance tracKING). See J. de Vilmarest (2022) <https://theses.hal.science/tel-03716104/>.

Last updated 1 years ago

1.00 score 167 downloads

FlexReg - Regression Models for Bounded Continuous and Discrete Responses

Functions to fit regression models for bounded continuous and discrete responses. In case of bounded continuous responses (e.g., proportions and rates), available models are the flexible beta (Migliorati, S., Di Brisco, A. M., Ongaro, A. (2018) <doi:10.1214/17-BA1079>), the variance-inflated beta (Di Brisco, A. M., Migliorati, S., Ongaro, A. (2020) <doi:10.1177/1471082X18821213>), the beta (Ferrari, S.L.P., Cribari-Neto, F. (2004) <doi:10.1080/0266476042000214501>), and their augmented versions to handle the presence of zero/one values (Di Brisco, A. M., Migliorati, S. (2020) <doi:10.1002/sim.8406>) are implemented. In case of bounded discrete responses (e.g., bounded counts, such as the number of successes in n trials), available models are the flexible beta-binomial (Ascari, R., Migliorati, S. (2021) <doi:10.1002/sim.9005>), the beta-binomial, and the binomial are implemented. Inference is dealt with a Bayesian approach based on the Hamiltonian Monte Carlo (HMC) algorithm (Gelman, A., Carlin, J. B., Stern, H. S., Rubin, D. B. (2014) <doi:10.1201/b16018>). Besides, functions to compute residuals, posterior predictives, goodness of fit measures, convergence diagnostics, and graphical representations are provided.

Last updated 1 years ago

cpp

1.00 score 3 scripts 280 downloads

ExpAnalysis3d - Pacote Para Analise De Experimentos Com Graficos De Superficie Resposta

Pacote para a analise de experimentos havendo duas variaveis explicativas quantitativas e uma variavel dependente quantitativa. Os experimentos podem ser sem repeticoes ou com delineamento estatistico. Sao ajustados 12 modelos de regressao multipla e plotados graficos de superficie resposta (Hair JF, 2016) <ISBN:13:978-0138132637>.(Package for the analysis of experiments having two explanatory quantitative variables and one quantitative dependent variable. The experiments can be without repetitions or with a statistical design. Twelve multiple regression models are fitted and response surface graphs are plotted (Hair JF, 2016) <ISBN:13:978-0138132637>).

Last updated 1 years ago

1.00 score 216 downloads

REPPlabShiny - 'REPPlab' via a Shiny Application

Performs exploratory projection pursuit via 'REPPlab' (Daniel Fischer, Alain Berro, Klaus Nordhausen & Anne Ruiz-Gazen (2019) <doi:10.1080/03610918.2019.1626880>) using a Shiny app.

Last updated 1 years ago

openjdk

1.00 score 138 downloads

ISRaD - Tools and Data for the International Soil Radiocarbon Database

This is the central location for data and tools for the development, maintenance, analysis, and deployment of the International Soil Radiocarbon Database (ISRaD). ISRaD was developed as a collaboration between the U.S. Geological Survey Powell Center and the Max Planck Institute for Biogeochemistry. This R package provides tools for accessing and manipulating ISRaD data, compiling local data using the ISRaD data structure, and simple query and reporting functions for ISRaD. For more detailed information visit the ISRaD website at: <https://soilradiocarbon.org/>.

Last updated 1 years ago

1.00 score 12 scripts 223 downloads

prolsirm - Procrustes Matching for Latent Space Item Response Model

Procrustes matching of the posterior samples of person and item latent positions from latent space item response models. The methods implemented in this package are based on work by Borg, I., Groenen, P. (1997, ISBN:978-0-387-94845-4), Jeon, M., Jin, I. H., Schweinberger, M., Baugh, S. (2021) <doi:10.1007/s11336-021-09762-5>, and Andrew, D. M., Kevin M. Q., Jong Hee Park. (2011) <doi:10.18637/jss.v042.i09>.

Last updated 1 years ago

1.00 score 4 scripts 121 downloads

GPSeqClus - Sequential Clustering Algorithm for Location Data

Applies sequential clustering algorithm to animal location data based on user-defined parameters. Plots interactive cluster maps and provides a summary dataframe with attributes for each cluster commonly used as covariates in subsequent modeling efforts. Additional functions provide individual keyhole markup language plots for quick assessment, and export of global positioning system exchange format files for navigation purposes. Methods can be found at <doi:10.1111/2041-210X.13572>.

Last updated 1 years ago

1.00 score 2 scripts 227 downloads

SQMtools - Analyze Results Generated by the 'SqueezeMeta' Pipeline

'SqueezeMeta' is a versatile pipeline for the automated analysis of metagenomics/metatranscriptomics data (<https://github.com/jtamames/SqueezeMeta>). This package provides functions loading 'SqueezeMeta' results into R, filtering them based on different criteria, and visualizing the results using basic plots. The 'SqueezeMeta' project (and any subsets of it generated by the different filtering functions) is parsed into a single object, whose different components (e.g. tables with the taxonomic or functional composition across samples, contig/gene abundance profiles) can be easily analyzed using other R packages such as 'vegan' or 'DESeq2'. The methods in this package are further described in Puente-Sánchez et al., (2020) <doi:10.1186/s12859-020-03703-2>.

Last updated 1 years ago

1.00 score 1 stars 23 scripts 287 downloads

NVCSSL - Nonparametric Varying Coefficient Spike-and-Slab Lasso

Fits Bayesian regularized varying coefficient models with the Nonparametric Varying Coefficient Spike-and-Slab Lasso (NVC-SSL) introduced by Bai et al. (2023) <arXiv:1907.06477>. Functions to fit frequentist penalized varying coefficients are also provided, with the option of employing the group lasso penalty of Yuan and Lin (2006) <doi:10.1111/j.1467-9868.2005.00532.x>, the group minimax concave penalty (MCP) of Breheny and Huang <doi:10.1007/s11222-013-9424-2>, or the group smoothly clipped absolute deviation (SCAD) penalty of Breheny and Huang (2015) <doi:10.1007/s11222-013-9424-2>.

Last updated 1 years ago

1.00 score 121 downloads

LS2Wstat - A Multiscale Test of Spatial Stationarity for LS2W Processes

Wavelet-based methods for testing stationarity and quadtree segmenting of images, see Taylor et al (2014) <doi:10.1080/00401706.2013.823890>.

Last updated 1 years ago

1.00 score 1 stars 16 scripts 231 downloads

ivDiag - Estimation and Diagnostic Tools for Instrumental Variables Designs

Estimation and diagnostic tools for instrumental variables designs, which implements the guidelines proposed in Lal et al. (2023) <arXiv:2303.11399>, including bootstrapped confidence intervals, effective F-statistic, Anderson-Rubin test, valid-t ratio test, and local-to-zero tests.

Last updated 1 years ago

1.00 score 12 scripts 202 downloads

AutoTransQF - A Novel Automatic Shifted Log Transformation

A novel parametrization of log transformation and a shift parameter to automate the transformation process are proposed in R package 'AutoTransQF' based on Feng et al. (2016). Please read Feng et al. (2016) <doi:10.1002/sta4.104> for more details of the method.

Last updated 1 years ago

1.00 score 174 downloads

prome - Patient-Reported Outcome Data Analysis with Stan

Algorithms and subroutines for patient-reported outcome data analysis.

Last updated 1 years ago

cpp

1.00 score 180 downloads

CircNNTSRmult - Multivariate Circular Data using MNNTS Models

A collection of utilities for the statistical analysis of multivariate circular data using distributions based on Multivariate Nonnegative Trigonometric Sums (MNNTS). The package includes functions for calculation of densities and distributions, for the estimation of parameters, and more.

Last updated 1 years ago

1.00 score 186 downloads

BlockMissingData - Integrating Multi-Source Block-Wise Missing Data in Model Selection

Model selection method with multiple block-wise imputation for block-wise missing data; see Xue, F., and Qu, A. (2021) <doi:10.1080/01621459.2020.1751176>.

Last updated 1 years ago

1.00 score 174 downloads

acopula - Modelling Dependence with Multivariate Archimax (or any User-Defined Continuous) Copulas

Archimax copulas are mixture of Archimedean and EV copulas. The package provides definitions of several parametric families of generator and dependence function, computes CDF and PDF, estimates parameters, tests for goodness of fit, generates random sample and checks copula properties for custom constructs. In 2-dimensional case explicit formulas for density are used, contrary to higher dimensions when all derivatives are linearly approximated. Several non-archimax families (normal, FGM, Plackett) are provided as well.

Last updated 1 years ago

1.00 score 9 scripts 390 downloads

modelSSE - Modelling Infectious Disease Superspreading from Contact Tracing Data

Comprehensive analytical tools are provided to characterize infectious disease superspreading from contact tracing surveillance data. The underlying theoretical frameworks of this toolkit include branching process with transmission heterogeneity (Lloyd-Smith et al. (2005) <doi:10.1038/nature04153>), case cluster size distribution (Nishiura et al. (2012) <doi:10.1016/j.jtbi.2011.10.039>, Blumberg et al. (2014) <doi:10.1371/journal.ppat.1004452>, and Kucharski and Althaus (2015) <doi:10.2807/1560-7917.ES2015.20.25.21167>), and decomposition of reproduction number (Zhao et al. (2022) <doi:10.1371/journal.pcbi.1010281>).

Last updated 1 years ago

1.00 score 178 downloads

costat - Time Series Costationarity Determination

Contains functions that can determine whether a time series is second-order stationary or not (and hence evidence for locally stationarity). Given two non-stationary series (i.e. locally stationary series) this package can then discover time-varying linear combinations that are second-order stationary. Cardinali, A. and Nason, G.P. (2013) <doi:10.18637/jss.v055.i01>.

Last updated 1 years ago

1.00 score 33 scripts 279 downloads

IASD - Model Selection for Index of Asymmetry Distribution

Calculate AIC's and AICc's of unimodal model (one normal distribution) and bimodal model(a mixture of two normal distributions) which fit the distribution of indices of asymmetry (IAS), and plot their density, to help determine IAS distribution is unimodal or bimodal.

Last updated 1 years ago

1.00 score 2 scripts 216 downloads

GAGBLUP - Genetic Algorithm Assisted Genomic Best Liner Unbiased Prediction

Performs genetic algorithm (Scrucca, L (2013) <doi:10.18637/jss.v053.i04>) assisted genomic best liner unbiased prediction for genomic selection. It also provides a binning method in natural population for genomic selection under the principle of linkage disequilibrium for dimensional reduction.

Last updated 1 years ago

1.00 score 125 downloads

haarfisz - Software to Perform Haar Fisz Transforms

A Haar-Fisz algorithm for Poisson intensity estimation. Will denoise Poisson distributed sequences where underlying intensity is not constant. Uses the multiscale variance-stabilization method called the Haar-Fisz transform. Contains functions to carry out the forward and inverse Haar-Fisz transform and denoising on near-Gaussian sequences. Can also carry out cycle-spinning. Main reference: Fryzlewicz, P. and Nason, G.P. (2004) "A Haar-Fisz algorithm for Poisson intensity estimation." Journal of Computational and Graphical Statistics, 13, 621-638. <doi:10.1198/106186004X2697>.

Last updated 1 years ago

1.00 score 8 scripts 147 downloads

TELP - Social Representation Theory Application: The Free Evocation of Words Technique

Using The Free Evocation of Words Technique method with some functions, this package will make a social representation and other analysis. The Free Evocation of Words Technique consists of collecting a number of words evoked by a subject facing exposure to an inducer term. The purpose of this technique is to understand the relationships created between words evoked by the individual and the inducer term. This technique is included in the theory of social representations, therefore, on the information transmitted by an individual, seeks to create a profile that define a social group.

Last updated 1 years ago

1.00 score 2 scripts 98 downloads

SpectralClMixed - Spectral Clustering for Mixed Type Data

Performs cluster analysis of mixed-type data using Spectral Clustering, see F. Mbuga and, C. Tortora (2022) <doi:10.3390/stats5010001>.

Last updated 1 years ago

1.00 score 6 scripts 159 downloads

ktsolve - Configurable Function for Solving Families of Nonlinear Equations

This is designed for use with an arbitrary set of equations with an arbitrary set of unknowns. The user selects "fixed" values for enough unknowns to leave as many variables as there are equations, which in most cases means the system is properly defined and a unique solution exists. The function, the fixed values and initial values for the remaining unknowns are fed to a nonlinear backsolver. The original version of "TK!Solver" , now a product of Universal Technical Systems (<https://www.uts.com>) was the inspiration for this function.

Last updated 1 years ago

1.00 score 1 stars 1 scripts 199 downloads

Rfractran - A 'FRACTRAN' Interpreter and Some Helper Functions

'FRACTRAN' is an obscure yet tantalizing programming language invented by John Conway of 'Game of Life' fame. The code consists of a sequence of fractions. The rules are simple. First, select an integer to initialize the process. Second, multiply the integer by the first fraction. If an integer results, start again with the new integer. If not, try the next fraction. Finally, if no such multiplication yields an integer, terminate the program. For more information, see <https://en.wikipedia.org/wiki/FRACTRAN> .

Last updated 1 years ago

1.00 score 133 downloads

pkmon - Least-Squares Estimator under k-Monotony Constraint for Discrete Functions

We implement two least-squares estimators under k-monotony constraint using a method based on the Support Reduction Algorithm from Groeneboom et al (2008) <DOI:10.1111/j.1467-9469.2007.00588.x>. The first one is a projection estimator on the set of k-monotone discrete functions. The second one is a projection on the set of k-monotone discrete probabilities. This package provides functions to generate samples from the spline basis from Lefevre and Loisel (2013) <DOI:10.1239/jap/1378401239>, and from mixtures of splines.

Last updated 1 years ago

1.00 score 7 scripts 209 downloads

crov - Constrained Regression Model for an Ordinal Response and Ordinal Predictors

Fits a constrained regression model for an ordinal response with ordinal predictors and possibly others, Espinosa and Hennig (2019) <DOI:10.1007/s11222-018-9842-2>. The parameter estimates associated with an ordinal predictor are constrained to be monotonic. If a monotonicity direction (isotonic or antitonic) is not specified for an ordinal predictor by the user, then one of the available methods will either establish it or drop the monotonicity assumption. Two monotonicity tests are also available to test the null hypothesis of monotonicity over a set of parameters associated with an ordinal predictor.

Last updated 1 years ago

1.00 score 2 scripts 173 downloads

lamle - Maximum Likelihood Estimation of Latent Variable Models

Approximate marginal maximum likelihood estimation of multidimensional latent variable models via adaptive quadrature or Laplace approximations to the integrals in the likelihood function, as presented for confirmatory factor analysis models in Jin, S., Noh, M., and Lee, Y. (2018) <doi:10.1080/10705511.2017.1403287>, for item response theory models in Andersson, B., and Xin, T. (2021) <doi:10.3102/1076998620945199>, and for generalized linear latent variable models in Andersson, B., Jin, S., and Zhang, M. (2023) <doi:10.1016/j.csda.2023.107710>. Models implemented include the generalized partial credit model, the graded response model, and generalized linear latent variable models for Poisson, negative-binomial and normal distributions. Supports a combination of binary, ordinal, count and continuous observed variables and multiple group models.

Last updated 1 years ago

openblascppopenmp

1.00 score 123 downloads

CoMiRe - Convex Mixture Regression

Posterior inference under the convex mixture regression (CoMiRe) models introduced by Canale, Durante, and Dunson (2018) <doi:10.1111/biom.12917>.

Last updated 1 years ago

cpp

1.00 score 200 downloads

SampleSizeProportions - Calculating Sample Size Requirements when Estimating the Difference Between Two Binomial Proportions

Sample size requirements calculation using three different Bayesian criteria in the context of designing an experiment to estimate the difference between two binomial proportions. Functions for calculation of required sample sizes for the Average Length Criterion, the Average Coverage Criterion and the Worst Outcome Criterion in the context of binomial observations are provided. In all cases, estimation of the difference between two binomial proportions is considered. Functions for both the fully Bayesian and the mixed Bayesian/likelihood approaches are provided. For reference see Joseph L., du Berger R. and Bélisle P. (1997) <doi:10.1002/(sici)1097-0258(19970415)16:7%3C769::aid-sim495%3E3.0.co;2-v>.

Last updated 1 years ago

1.00 score 10 scripts 251 downloads

kerTests - Generalized Kernel Two-Sample Tests

New kernel-based test and fast tests for testing whether two samples are from the same distribution. They work well particularly for high-dimensional data. Song, H. and Chen, H. (2023) <arXiv:2011.06127>.

Last updated 1 years ago

1.00 score 269 downloads

kerSeg - New Kernel-Based Change-Point Detection

New kernel-based test and fast tests for detecting change-points or changed-intervals where the distributions abruptly change. They work well particularly for high-dimensional data. Song, H. and Chen, H. (2022) <arXiv:2206.01853>.

Last updated 1 years ago

cpp

1.00 score 144 downloads

kerDAA - New Kernel-Based Test for Differential Association Analysis

A new practical method to evaluate whether relationships between two sets of high-dimensional variables are different or not across two conditions. Song, H. and Wu, M.C. (2023) <arXiv:2307.15268>.

Last updated 1 years ago

1.00 score 136 downloads

gTestsMulti - New Graph-Based Multi-Sample Tests

New multi-sample tests for testing whether multiple samples are from the same distribution. They work well particularly for high-dimensional data. Song, H. and Chen, H. (2022) <arXiv:2205.13787>.

Last updated 1 years ago

1.00 score 176 downloads

RESTK - An Implementation of the RESTK Algorithm

Implementation of the RESTK algorithm based on Markov's Inequality from Vilardell, Sergi, Serra, Isabel, Mezzetti, Enrico, Abella, Jaume, Cazorla, Francisco J. and Del Castillo, J. (2022). "Using Markov's Inequality with Power-Of-k Function for Probabilistic WCET Estimation". In 34th Euromicro Conference on Real-Time Systems (ECRTS 2022). Leibniz International Proceedings in Informatics (LIPIcs) 231 20:1-20:24. <doi:10.4230/LIPIcs.ECRTS.2022.20>. This work has been supported by the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (grant agreement No. 772773).

Last updated 1 years ago

1.00 score 118 downloads

assist - A Suite of R Functions Implementing Spline Smoothing Techniques

Fit various smoothing spline models. Includes an ssr() function for smoothing spline regression, an nnr() function for nonparametric nonlinear regression, an snr() function for semiparametric nonlinear regression, an slm() function for semiparametric linear mixed-effects models, and an snm() function for semiparametric nonlinear mixed-effects models. See Wang (2011) <doi:10.1201/b10954> for an overview.

Last updated 1 years ago

fortranopenblas

1.00 score 56 scripts 461 downloads

RobustAFT - Truncated Maximum Likelihood Fit and Robust Accelerated Failure Time Regression for Gaussian and Log-Weibull Case

R functions for the computation of the truncated maximum likelihood and the robust accelerated failure time regression for gaussian and log-Weibull case.

Last updated 1 years ago

fortran

1.00 score 20 scripts 215 downloads

qape - Quantile of Absolute Prediction Errors

Estimates QAPE using bootstrap procedures. The residual, parametric and double bootstrap is used. The test of normality using Cholesky decomposition is added. Y pop is defined.

Last updated 1 years ago

1.00 score 2 scripts 158 downloads

MKLE - Maximum Kernel Likelihood Estimation

Package for fast computation of the maximum kernel likelihood estimator (mkle).

Last updated 1 years ago

1.00 score 6 scripts 211 downloads

saeHB.ME - Small Area Estimation with Measurement Error using Hierarchical Bayesian Method

Implementation of small area estimation using Hierarchical Bayesian (HB) Method when auxiliary variable measured with error. The 'rjags' package is employed to obtain parameter estimates. For the references, see Rao and Molina (2015) <doi:10.1002/9781118735855>, Ybarra and Lohr (2008) <doi:10.1093/biomet/asn048>, and Ntzoufras (2009, ISBN-10: 1118210352).

Last updated 1 years ago

jagscpp

1.00 score 1 stars 127 downloads

contFracR - Continued Fraction Generators and Evaluators

Converts numbers to continued fractions and back again. A solver for Pell's Equation is provided. The method for calculating roots in continued fraction form is provided without published attribution in such places as Professor Emeritus Jonathan Lubin, <http://www.math.brown.edu/jlubin/> and his post to StackOverflow, <https://math.stackexchange.com/questions/2215918> , or Professor Ron Knott, e.g., <https://r-knott.surrey.ac.uk/Fibonacci/cfINTRO.html> .

Last updated 1 years ago

1.00 score 257 downloads

sEparaTe - Maximum Likelihood Estimation and Likelihood Ratio Test Functions for Separable Variance-Covariance Structures

Maximum likelihood estimation of the parameters of matrix and 3rd-order tensor normal distributions with unstructured factor variance covariance matrices, two procedures, and for unbiased modified likelihood ratio testing of simple and double separability for variance-covariance structures, two procedures. References: Dutilleul P. (1999) <doi:10.1080/00949659908811970>, Manceur AM, Dutilleul P. (2013) <doi:10.1016/j.cam.2012.09.017>, and Manceur AM, Dutilleul P. (2013) <doi:10.1016/j.spl.2012.10.020>.

Last updated 1 years ago

1.00 score 5 scripts 283 downloads

mrct - Outlier Detection of Functional Data Based on the Minimum Regularized Covariance Trace Estimator

Detect outlying observations in functional data sets based on the minimum regularized covariance trace (MRCT) estimator. Includes implementation of Oguamalam et al. (2023) <arXiv:2307.13509>.

Last updated 1 years ago

1.00 score 111 downloads

graposas - Graphical Approach Optimal Sample Size

Graphical approach provides a useful framework for multiplicity adjustment in clinical trials with multiple endpoints. This package includes statistical methods to optimize sample size over initial weight and transition probability in a graphical approach under a common setting, which is to use marginal power for each endpoint in a trial design. See Zhang, F. and Gou, J. (2023). Sample size optimization for clinical trials using graphical approaches for multiplicity adjustment, Technical Report.

Last updated 1 years ago

1.00 score 1 stars 99 downloads

TP.idm - Estimation of Transition Probabilities for the Illness-Death Model

Estimation of transition probabilities for the illness-death model. Both the Aalen-Johansen estimator for a Markov model and a novel non-Markovian estimator by de Una-Alvarez and Meira-Machado (2015) <doi:10.1111/biom.12288>, see also Balboa and de Una-Alvarez (2018) <doi:10.18637/jss.v083.i10>, are included.

Last updated 1 years ago

1.00 score 7 scripts 240 downloads

StReg - Student's t Regression Models

It contains functions to estimate multivariate Student's t dynamic and static regression models for given degrees of freedom and lag length. Users can also specify the trends and dummies of any kind in matrix form. Poudyal, N., and Spanos, A. (2022) <doi:10.3390/econometrics10020017>. Spanos, A. (1994) <http://www.jstor.org/stable/3532870>.

Last updated 1 years ago

1.00 score 133 downloads

STAREG - An Empirical Bayes Approach for Replicability Analysis Across Two Studies

A robust and powerful empirical Bayesian approach is developed for replicability analysis of two large-scale experimental studies. The method controls the false discovery rate by using the joint local false discovery rate based on the replicability null as the test statistic. An EM algorithm combined with a shape constraint nonparametric method is used to estimate unknown parameters and functions. [Li, Y. et al., (2023), <https://www.biorxiv.org/content/10.1101/2023.05.30.542607v1>].

Last updated 1 years ago

openblascppopenmp

1.00 score 4 scripts 149 downloads

RHclust - Vector in Partition

Non-parametric clustering of joint pattern multi-genetic/epigenetic factors. This package contains functions designed to cluster subjects based on gene features including single nucleotide polymorphisms (SNPs), DNA methylation (CPG), gene expression (GE), and covariate data. The novel concept follows the general K-means (Hartigan and Wong (1979) <doi:10.2307/2346830> framework but uses weighted Euclidean distances across the gene features to cluster subjects. This approach is unique in that it attempts to capture all pairwise interactions in an effort to cluster based on their complex biological interactions.

Last updated 1 years ago

1.00 score 163 downloads

NetworkComparr - Statistical Comparison of Networks

A permutation-based hypothesis test for statistical comparison of two networks based on the invariance measures of the R package 'NetworkComparisonTest' by van Borkulo et al. (2022), <doi:10.1037/met0000476>: network structure invariance, global strength invariance, edge invariance, and various centrality measures. Edgelists from dependent or independent samples are used as input. These edgelists are generated from concept maps and summed into two comparable group networks. The networks can be directed or undirected.

Last updated 1 years ago

1.00 score 143 downloads

rego - Automatic Time Series Forecasting and Missing Value Imputation

Machine learning algorithm for predicting and imputing time series. It can automatically set all the parameters needed, thus in the minimal configuration it only requires the target variable and the dependent variables if present. It can address large problems with hundreds or thousands of dependent variables and problems in which the number of dependent variables is greater than the number of observations. Moreover it can be used not only for time series but also for any other real valued target variable. The algorithm implemented includes a Bayesian stochastic search methodology for model selection and a robust estimation based on bootstrapping. 'rego' is fast because all the code is C++.

Last updated 1 years ago

cpp

1.00 score 9 scripts 211 downloads

MSclassifR - Automated Classification of Mass Spectra

Functions to classify mass spectra in known categories, and to determine discriminant mass-over-charge values. It includes easy-to-use functions for pre-processing mass spectra, functions to determine discriminant mass-over-charge values (m/z) from a library of mass spectra corresponding to different categories, and functions to predict the category (species, phenotypes, etc.) associated to a mass spectrum from a list of selected mass-over-charge values. Three vignettes illustrating how to use the functions of this package from real data sets are also available online to help users: <https://agodmer.github.io/MSclassifR_examples/Vignettes/Vignettemsclassifr_Ecrobiav3.html>, <https://agodmer.github.io/MSclassifR_examples/Vignettes/Vignettemsclassifr_Klebsiellav3.html> and <https://agodmer.github.io/MSclassifR_examples/Vignettes/Vignettemsclassifr_DAv3.html>.

Last updated 1 years ago

1.00 score 1 stars 210 downloads

atRisk - At-Risk

The at-Risk (aR) approach is based on a two-step parametric estimation procedure that allows to forecast the full conditional distribution of an economic variable at a given horizon, as a function of a set of factors. These density forecasts are then be used to produce coherent forecasts for any downside risk measure, e.g., value-at-risk, expected shortfall, downside entropy. Initially introduced by Adrian et al. (2019) <doi:10.1257/aer.20161923> to reveal the vulnerability of economic growth to financial conditions, the aR approach is currently extensively used by international financial institutions to provide Value-at-Risk (VaR) type forecasts for GDP growth (Growth-at-Risk) or inflation (Inflation-at-Risk). This package provides methods for estimating these models. Datasets for the US and the Eurozone are available to allow testing of the Adrian et al. (2019) model. This package constitutes a useful toolbox (data and functions) for private practitioners, scholars as well as policymakers.

Last updated 1 years ago

1.00 score 204 downloads

iRepro - Reproducibility for Interval-Censored Data

Calculates intraclass correlation coefficient (ICC) for assessing reproducibility of interval-censored data with two repeated measurements (Kovacic and Varnai (2014) <doi:10.1097/EDE.0000000000000139>). ICC is estimated by maximum likelihood from model with one fixed and one random effect (both intercepts). Help in model checking (normality of subjects' means and residuals) is provided.

Last updated 1 years ago

1.00 score 7 scripts 238 downloads

MultiClassROC - ROC Curves for Multi-Class Analysis

Function multiroc() can be used for computing and visualizing Receiver Operating Characteristics (ROC) and Area Under the Curve (AUC) for multi-class classification problems. It supports both One-vs-One approach by M.Bishop, C. (2006, ISBN:978-0-387-31073-2) and One-vs-All approach by Murphy P., K. (2012, ISBN:9780262018029).

Last updated 1 years ago

1.00 score 152 downloads

EXPARMA - Fitting of Exponential Autoregressive Moving Average (EXPARMA) Model

The amplitude-dependent autoregressive time series model (EXPAR) proposed by Haggan and Ozaki (1981) <doi:10.2307/2335819> was improved by incorporating the moving average (MA) framework for capturing the variability efficiently. Parameters of the EXPARMA model can be estimated using this package. The user is provided with the best fitted EXPARMA model for the data set under consideration.

Last updated 1 years ago

1.00 score 216 downloads

random.polychor.pa - A Parallel Analysis with Polychoric Correlation Matrices

The Function performs a parallel analysis using simulated polychoric correlation matrices. The nth-percentile of the eigenvalues distribution obtained from both the randomly generated and the real data polychoric correlation matrices is returned. A plot comparing the two types of eigenvalues (real and simulated) will help determine the number of real eigenvalues that outperform random data. The function is based on the idea that if real data are non-normal and the polychoric correlation matrix is needed to perform a Factor Analysis, then the Parallel Analysis method used to choose a non-random number of factors should also be based on randomly generated polychoric correlation matrices and not on Pearson correlation matrices. Random data sets are simulated assuming or a uniform or a multinomial distribution or via the bootstrap method of resampling (i.e., random permutations of cases). Also Multigroup Parallel analysis is made available for random (uniform and multinomial distribution and with or without difficulty factor) and bootstrap methods. An option to choose between default or full output is also available as well as a parameter to print Fit Statistics (Chi-squared, TLI, RMSEA, RMR and BIC) for the factor solutions indicated by the Parallel Analysis. Also weighted correlation matrices may be considered for PA.

Last updated 1 years ago

1.00 score 4 scripts 286 downloads

coat - Conditional Method Agreement Trees (COAT)

Agreement of continuously scaled measurements made by two techniques, devices or methods is usually evaluated by the well-established Bland-Altman analysis or plot. Conditional method agreement trees (COAT), proposed by Karapetyan, Zeileis, Henriksen, and Hapfelmeier (2023) <doi:10.48550/arXiv.2306.04456>, embed the Bland-Altman analysis in the framework of recursive partitioning to explore heterogeneous method agreement in dependence of covariates. COAT can also be used to perform a Bland-Altman test for differences in method agreement.

Last updated 1 years ago

1.00 score 141 downloads

MMAD - MM Algorithm Based on the Assembly-Decomposition Technology

The Minorize-Maximization(MM) algorithm based on Assembly-Decomposition(AD) technology can be used for model estimation of parametric models, semi-parametric models and non-parametric models. We selected parametric models including left truncated normal distribution, type I multivariate zero-inflated generalized poisson distribution and multivariate compound zero-inflated generalized poisson distribution; semiparametric models include Cox model and gamma frailty model; nonparametric model is estimated for type II interval-censored data. These general methods are proposed based on the following papers, Tian, Huang and Xu (2019) <doi:10.5705/SS.202016.0488>, Huang, Xu and Tian (2019) <doi:10.5705/ss.202016.0516>, Zhang and Huang (2022) <doi:10.1117/12.2642737>.

Last updated 1 years ago

1.00 score 3 scripts 142 downloads

EzGP - Easy-to-Interpret Gaussian Process Models for Computer Experiments

Fit model for datasets with easy-to-interpret Gaussian process modeling, predict responses for new inputs. The input variables of the datasets can be quantitative, qualitative/categorical or mixed. The output variable of the datasets is a scalar (quantitative). The optimization of the likelihood function can be chosen by the users (see the documentation of EzGP_fit()). The modeling method is published in "EzGP: Easy-to-Interpret Gaussian Process Models for Computer Experiments with Both Quantitative and Qualitative Factors" by Qian Xiao, Abhyuday Mandal, C. Devon Lin, and Xinwei Deng (2022) <doi:10.1137/19M1288462>.

Last updated 1 years ago

1.00 score 93 downloads

vstdct - Nonparametric Estimation of Toeplitz Covariance Matrices

A nonparametric method to estimate Toeplitz covariance matrices from a sample of n independently and identically distributed p-dimensional vectors with mean zero. The data is preprocessed with the discrete cosine matrix and a variance stabilization transformation to obtain an approximate Gaussian regression setting for the log-spectral density function. Estimates of the spectral density function and the inverse of the covariance matrix are provided as well. Functions for simulating data and a protein data example are included. For details see (Klockmann, Krivobokova; 2023), <arXiv:2303.10018>.

Last updated 1 years ago

1.00 score 1 scripts 128 downloads

triggerstrategy - Trigger Strategy in Clinical Trials

The trigger strategy is a general framework for a multistage statistical design with multiple hypotheses, allowing an adaptive selection of interim analyses. The selection of interim stages can be associated with some prespecified endpoints which serve as the trigger. This selection allows us to refine the critical boundaries in hypotheses testing procedures, and potentially increase the statistical power. This package includes several trial designs using the trigger strategy. See Gou, J. (2023), "Trigger strategy in repeated tests on multiple hypotheses", Statistics in Biopharmaceutical Research, 15(1), 133-140, and Gou, J. (2022), "Sample size optimization and initial allocation of the significance levels in group sequential trials with multiple endpoints", Biometrical Journal, 64(2), 301-311.

Last updated 1 years ago

1.00 score 116 downloads

IndGenErrors - Tests of Independence Between Innovations of Generalized Error Models

Computation of test statistics of independence between (continuous) innovations of time series. They Can be used with stochastic volatility models and Hidden Markov Models (HMM). This improves the results in Duchesne, Ghoudi & Remillard (2012) <doi:10.1002/cjs.11141>.

Last updated 1 years ago

1.00 score 130 downloads

rbmn - Handling Linear Gaussian Bayesian Networks

Creation, manipulation, simulation of linear Gaussian Bayesian networks from text files and more...

Last updated 1 years ago

1.00 score 75 scripts 180 downloads

dbacf - Autocovariance Estimation via Difference-Based Methods

Provides methods for (auto)covariance/correlation function estimation in change point regression with stationary errors circumventing the pre-estimation of the underlying signal of the observations. Generic, first-order, (m+1)-gapped, difference-based autocovariance function estimator is based on M. Levine and I. Tecuapetla-Gómez (2023) <doi:10.48550/arXiv.1905.04578>. Bias-reducing, second-order, (m+1)-gapped, difference-based estimator is based on I. Tecuapetla-Gómez and A. Munk (2017) <doi:10.1111/sjos.12256>. Robust autocovariance estimator for change point regression with autoregressive errors is based on S. Chakar et al. (2017) <doi:10.3150/15-BEJ782>. It also includes a general projection-based method for covariance matrix estimation.

Last updated 1 years ago

1.00 score 2 scripts 148 downloads

SSGL - Spike-and-Slab Group Lasso for Group-Regularized Generalized Linear Models

Fits group-regularized generalized linear models (GLMs) using the spike-and-slab group lasso (SSGL) prior introduced by Bai et al. (2022) <doi:10.1080/01621459.2020.1765784> and extended to GLMs by Bai (2023) <arXiv:2007.07021>. This package supports fitting the SSGL model for the following GLMs with group sparsity: Gaussian linear regression, binary logistic regression, Poisson regression, negative binomial regression, and gamma regression. Stand-alone functions for group-regularized negative binomial regression and group-regularized gamma regression are also available, with the option of employing the group lasso penalty of Yuan and Lin (2006) <doi:10.1111/j.1467-9868.2005.00532.x>, the group minimax concave penalty (MCP) of Breheny and Huang <doi:10.1007/s11222-013-9424-2>, or the group smoothly clipped absolute deviation (SCAD) penalty of Breheny and Huang (2015) <doi:10.1007/s11222-013-9424-2>.

Last updated 1 years ago

1.00 score 1 scripts 153 downloads

dSTEM - Multiple Testing of Local Extrema for Detection of Change Points

Simultaneously detect the number and locations of change points in piecewise linear models under stationary Gaussian noise allowing autocorrelated random noise. The core idea is to transform the problem of detecting change points into the detection of local extrema (local maxima and local minima)through kernel smoothing and differentiation of the data sequence, see Cheng et al. (2020) <doi:10.1214/20-EJS1751>. A low-computational and fast algorithm call 'dSTEM' is introduced to detect change points based on the 'STEM' algorithm in D. Cheng and A. Schwartzman (2017) <doi:10.1214/16-AOS1458>.

Last updated 2 years ago

1.00 score 3 scripts 152 downloads

dfphase1 - Phase I Control Charts (with Emphasis on Distribution-Free Methods)

Statistical methods for retrospectively detecting changes in location and/or dispersion of univariate and multivariate variables. Data values are assumed to be independent, can be individual (one observation at each instant of time) or subgrouped (more than one observation at each instant of time). Control limits are computed, often using a permutation approach, so that a prescribed false alarm probability is guaranteed without making any parametric assumptions on the stable (in-control) distribution. See G. Capizzi and G. Masarotto (2018) <doi:10.1007/978-3-319-75295-2_1> for an introduction to the package.

Last updated 2 years ago

openblascpp

1.00 score 13 scripts 247 downloads

tdsc - Time Domain Signal Coding

Functions for performing time domain signal coding as used in Chesmore (2001) <doi:10.1016/S0003-682X(01)00009-3>, and related tasks. This package creates the standard S-matrix and A-matrix (with variable lag), has tools to convert coding matrices into distributed matrices, provides published codebooks and allows for extraction of code sequences.

Last updated 2 years ago

1.00 score 8 scripts 184 downloads

epmrob - Robust Estimation of Probit Models with Endogeneity

Package provides a set of tools for robust estimation and inference for probit model with endogenous covariates. The current version contains a robust two-step estimator. For technical details, see Naghi, Varadi and Zhelonkin (2022), <doi:10.1016/j.ecosta.2022.05.001>.

Last updated 2 years ago

1.00 score 140 downloads

fixedpointproperty - Determine and Test the Fixed-Point Property in Binary Mixture Data

Determine and test the fixed-point property in binary mixture data. This package was originally developed in the context of detecting mixture of cognitive processing strategies, based on observed response time distributions. The method is explain in more detail by Van Maanen, De Jong, Van Rijn (2014) <doi:10.1371/journal.pone.0106113> and Van Maanen, Couto, Lebreton, (2016) <doi:10.1371/journal.pone.0167377>.

Last updated 2 years ago

1.00 score 134 downloads

OBRE - Optimal B-Robust Estimator Tools

An implementation for computing Optimal B-Robust Estimators of two-parameter distribution. The procedure is composed of some equations that are evaluated alternatively until the solution is reached. Some tools for analyzing the estimates are included. The most relevant is covariance matrix computation using a closed formula.

Last updated 2 years ago

1.00 score 5 scripts 135 downloads

cvmaPLFAM - Cross-Validation Model Averaging for Partial Linear Functional Additive Models

Produce an averaging estimate/prediction by combining all candidate models for partial linear functional additive models, using multi-fold cross-validation criterion. More details can be referred to Shishi Liu and Jingxiao Zhang. (2021) <arXiv:2105.00966>.

Last updated 2 years ago

1.00 score 159 downloads

catdap - Categorical Data Analysis Program Package

Categorical data analysis by AIC. The methodology is described in Sakamoto (1992) <ISBN 978-0-7923-1429-5>.

Last updated 2 years ago

fortran

1.00 score 3 scripts 292 downloads

RTaxometrics - Taxometric Analysis

We provide functions to perform taxometric analyses. This package contains 46 functions, but only 5 should be called directly by users. CheckData() should be run prior to any taxometric analysis to ensure that the data are appropriate for taxometric analysis. RunTaxometrics() performs taxometric analyses for a sample of data. RunCCFIProfile() performs a series of taxometric analyses to generate a CCFI profile. CreateData() generates a sample of categorical or dimensional data. ClassifyCases() assigns cases to groups using the base-rate classification method.

Last updated 2 years ago

1.00 score 3 scripts 303 downloads

adapt4pv - Adaptive Approaches for Signal Detection in Pharmacovigilance

A collection of several pharmacovigilance signal detection methods based on adaptive lasso. Additional lasso-based and propensity score-based signal detection approaches are also supplied. See Courtois et al <doi:10.1186/s12874-021-01450-3>.

Last updated 2 years ago

1.00 score 1 stars 344 downloads

EntropicStatistics - Functions Based on Entropic Statistics

Contains methods for data analysis in entropic perspective. These entropic perspective methods are nonparametric, and perform better on non-ordinal data. Currently, the package has a function HeatMap() for visualizing distributional characteristics among multiple populations (groups).

Last updated 2 years ago

1.00 score 1 scripts 189 downloads

JUMP - Replicability Analysis of High-Throughput Experiments

Implementing a computationally scalable false discovery rate control procedure for replicability analysis based on maximum of p-values. Please cite the manuscript corresponding to this package [Lyu, P. et al., (2023), <https://www.biorxiv.org/content/10.1101/2023.02.13.528417v2>].

Last updated 2 years ago

cpp

1.00 score 122 downloads

lmtestrob - Outlier Robust Specification Testing

Robust test(s) for model diagnostics in regression. The current version contains a robust test for functional specification (linearity). The test is based on the robust bounded-influence test by Heritier and Ronchetti (1994) <doi:10.1080/01621459.1994.10476822>.

Last updated 2 years ago

1.00 score 165 downloads

MCPModBC - Improved Inference in Multiple Comparison Procedure – Modelling

Implementation of Multiple Comparison Procedures with Modeling (MCP-Mod) procedure with bias-corrected estimators and second-order covariance matrices as described in Diniz, Gallardo and Magalhaes (2023) <doi:10.1002/pst.2303>.

Last updated 2 years ago

1.00 score 9 scripts 188 downloads

StepGWR - A Hybrid Spatial Model for Prediction and Capturing Spatial Variation in the Data

It is a hybrid spatial model that combines the variable selection capabilities of stepwise regression methods with the predictive power of the Geographically Weighted Regression(GWR) model.The developed hybrid model follows a two-step approach where the stepwise variable selection method is applied first to identify the subset of predictors that have the most significant impact on the response variable, and then a GWR model is fitted using those selected variables for spatial prediction at test or unknown locations. For method details,see Leung, Y., Mei, C. L. and Zhang, W. X. (2000).<DOI:10.1068/a3162>.This hybrid spatial model aims to improve the accuracy and interpretability of GWR predictions by selecting a subset of relevant variables through a stepwise selection process.This approach is particularly useful for modeling spatially varying relationships and improving the accuracy of spatial predictions.

Last updated 2 years ago

1.00 score 1 scripts 141 downloads

estadistica - Fundamentos De Estadistica Descriptiva e Inferencial

Este paquete pretende apoyar el proceso enseñanza-aprendizaje de estadística descriptiva e inferencial. Las funciones contenidas en el paquete 'estadistica' cubren los conceptos básicos estudiados en un curso introductorio. Muchos conceptos son ilustrados con gráficos dinámicos o web apps para facilitar su comprensión. This package aims to help the teaching-learning process of descriptive and inferential statistics. The functions contained in the package 'estadistica' cover the basic concepts studied in a statistics introductory course. Many concepts are illustrated with dynamic graphs or web apps to make the understanding easier. See: Esteban et al. (2005, ISBN: 9788497323741), Newbold et al.(2019, ISBN:9781292315034 ), Murgui et al. (2002, ISBN:9788484424673) .

Last updated 2 years ago

1.00 score 2 scripts 687 downloads

OPC - The Online Principal Component Estimation Method

The online principal component method can process the online data set. The philosophy of the package is described in Guo G. (2018) <doi:10.1080/10485252.2018.1531130>.

Last updated 2 years ago

1.00 score 1 scripts 137 downloads

Tex4exams - Generating 'Sweave' Code for 'R/exams' Questions in Mathematics

When using the R package 'exams' to write mathematics questions in 'Sweave' files, the output of a lot of R functions need to be adjusted for display in mathematical formulas. Specifically, the functions were accumulated when writing questions for the topics of the mathematics courses College Algebra, Precalculus, Calculus, Differential Equations, Introduction to Probability, and Linear Algebra. The output of the developed functions can be used in 'Sweave' files.

Last updated 2 years ago

1.00 score 147 downloads

nmw - Understanding Nonlinear Mixed Effects Modeling for Population Pharmacokinetics

This shows how NONMEM(R) software works. NONMEM's classical estimation methods like 'First Order(FO) approximation', 'First Order Conditional Estimation(FOCE)', and 'Laplacian approximation' are explained.

Last updated 2 years ago

1.00 score 1 stars 8 scripts 274 downloads

PrInDT - Prediction and Interpretation in Decision Trees for Classification and Regression

Optimization of conditional inference trees from the package 'party' for classification and regression. For optimization, the model space is searched for the best tree on the full sample by means of repeated subsampling. Restrictions are allowed so that only trees are accepted which do not include pre-specified uninterpretable split results (cf. Weihs & Buschfeld, 2021a). The function PrInDT() represents the basic resampling loop for 2-class classification (cf. Weihs & Buschfeld, 2021a). The function RePrInDT() (repeated PrInDT()) allows for repeated applications of PrInDT() for different percentages of the observations of the large and the small classes (cf. Weihs & Buschfeld, 2021c). The function NesPrInDT() (nested PrInDT()) allows for an extra layer of subsampling for a specific factor variable (cf. Weihs & Buschfeld, 2021b). The functions PrInDTMulev() and PrInDTMulab() deal with multilevel and multilabel classification. In addition to these PrInDT() variants for classification, the function PrInDTreg() has been developed for regression problems. Finally, the function PostPrInDT() allows for a posterior analysis of the distribution of a specified variable in the terminal nodes of a given tree. References are: -- Weihs, C., Buschfeld, S. (2021a) "Combining Prediction and Interpretation in Decision Trees (PrInDT) - a Linguistic Example" <arXiv:2103.02336>; -- Weihs, C., Buschfeld, S. (2021b) "NesPrInDT: Nested undersampling in PrInDT" <arXiv:2103.14931>; -- Weihs, C., Buschfeld, S. (2021c) "Repeated undersampling in PrInDT (RePrInDT): Variation in undersampling and prediction, and ranking of predictors in ensembles" <arXiv:2108.05129>.

Last updated 2 years ago

1.00 score 170 downloads

MARSGWR - A Hybrid Spatial Model for Capturing Spatially Varying Relationships Between Variables in the Data

It is a hybrid spatial model that combines the strength of two widely used regression models, MARS (Multivariate Adaptive Regression Splines) and GWR (Geographically Weighted Regression) to provide an effective approach for predicting a response variable at unknown locations. The MARS model is used in the first step of the development of a hybrid model to identify the most important predictor variables that assist in predicting the response variable. For method details see, Friedman, J.H. (1991). <DOI:10.1214/aos/1176347963>.The GWR model is then used to predict the response variable at testing locations based on these selected variables that account for spatial variations in the relationships between the variables. This hybrid model can improve the accuracy of the predictions compared to using an individual model alone.This developed hybrid spatial model can be useful particularly in cases where the relationship between the response variable and predictor variables is complex and non-linear, and varies across locations.

Last updated 2 years ago

1.00 score 157 downloads

dstabledist - The Discrete Stable Distribution Functions

Probability generating function, formulae for the probabilities (discrete density) and random generation for discrete stable random variables.

Last updated 2 years ago

1.00 score 177 downloads

gor - Algorithms for the Subject Graphs and Network Optimization

Informal implementation of some algorithms from Graph Theory and Combinatorial Optimization which arise in the subject "Graphs and Network Optimization" from first course of the EUPLA (Escuela Universitaria Politecnica de La Almunia) degree of Data Engineering in Industrial Processes. References used are: Cook et al (1998, ISBN:0-471-55894-X), Korte, Vygen (2018) <doi:10.1007/978-3-662-56039-6>, Hromkovic (2004) <doi:10.1007/978-3-662-05269-3>, Hartmann, Weigt (2005, ISBN:978-3-527-40473-5).

Last updated 2 years ago

1.00 score 1 scripts 161 downloads

matrisk - Macroeconomic-at-Risk

The Macroeconomics-at-Risk (MaR) approach is based on a two-step semi-parametric estimation procedure that allows to forecast the full conditional distribution of an economic variable at a given horizon, as a function of a set of factors. These density forecasts are then be used to produce coherent forecasts for any downside risk measure, e.g., value-at-risk, expected shortfall, downside entropy. Initially introduced by Adrian et al. (2019) <doi:10.1257/aer.20161923> to reveal the vulnerability of economic growth to financial conditions, the MaR approach is currently extensively used by international financial institutions to provide Value-at-Risk (VaR) type forecasts for GDP growth (Growth-at-Risk) or inflation (Inflation-at-Risk). This package provides methods for estimating these models. Datasets for the US and the Eurozone are available to allow testing of the Adrian et al (2019) model. This package constitutes a useful toolbox (data and functions) for private practitioners, scholars as well as policymakers.

Last updated 2 years ago

1.00 score 141 downloads

MiRNAQCD - Micro-RNA Quality Control and Diagnosis

A complete and dedicated analytical toolbox for quality control and diagnosis based on subject-related measurements of micro-RNA (miRNA) expressions. The package consists of a set of functions that allow to train, optimize and use a Bayesian classifier that relies on multiplets of measured miRNA expressions. The package also implements the quality control tools required to preprocess input datasets. In addition, the package provides a function to carry out a statistical analysis of miRNA expressions, which can give insights to improve the classifier's performance. The method implemented in the package was first introduced in L. Ricci, V. Del Vescovo, C. Cantaloni, M. Grasso, M. Barbareschi and M. A. Denti, "Statistical analysis of a Bayesian classifier based on the expression of miRNAs", BMC Bioinformatics 16:287, 2015 <doi:10.1186/s12859-015-0715-9>. The package is thoroughly described in M. Castelluzzo, A. Perinelli, S. Detassis, M. A. Denti and L. Ricci, "MiRNA-QC-and-Diagnosis: An R package for diagnosis based on MiRNA expression", SoftwareX 12:100569, 2020 <doi:10.1016/j.softx.2020.100569>. Please cite both these works if you use the package for your analysis. DISCLAIMER: The software in this package is for general research purposes only and is thus provided WITHOUT ANY WARRANTY. It is NOT intended to form the basis of clinical decisions. Please refer to the GNU General Public License 3.0 (GPLv3) for further information.

Last updated 2 years ago

1.00 score 7 scripts 205 downloads

monoreg - Bayesian Monotonic Regression Using a Marked Point Process Construction

An extended version of the nonparametric Bayesian monotonic regression procedure described in Saarela & Arjas (2011) <DOI:10.1111/j.1467-9469.2010.00716.x>, allowing for multiple additive monotonic components in the linear predictor, and time-to-event outcomes through case-base sampling. The extension and its applications, including estimation of absolute risks, are described in Saarela & Arjas (2015) <DOI:10.1111/sjos.12125>. The package also implements the nonparametric ordinal regression model described in Saarela, Rohrbeck & Arjas <DOI:10.1214/22-BA1310>.

Last updated 2 years ago

gsl

1.00 score 8 scripts 270 downloads

hset - Sets of Numbers Implemented with Hash Tables

Implementation of S4 class of sets and multisets of numbers. The implementation is based on the hash table from the package 'hash'. Quick operations are allowed when the set is a dynamic object. The implementation is discussed in detail in Ceoldo and Wit (2023) <arXiv:2304.09809>.

Last updated 2 years ago

1.00 score 160 downloads

VARSELECTEXPOSURE - Variable Selection Methods Including an Exposure Variable

Utilizes multiple variable selection methods to estimate Average Treatment Effect.

Last updated 2 years ago

1.00 score 192 downloads

lmerPerm - Perform Permutation Test on General Linear and Mixed Linear Regression

We provide a solution for performing permutation tests on linear and mixed linear regression models. It allows users to obtain accurate p-values without making distributional assumptions about the data. By generating a null distribution of the test statistics through repeated permutations of the response variable, permutation tests provide a powerful alternative to traditional parameter tests (Holt et al. (2023) <doi:10.1007/s10683-023-09799-6>). In this early version, we focus on the permutation tests over observed t values of beta coefficients, i.e.original t values generated by parameter tests. After generating a null distribution of the test statistic through repeated permutations of the response variable, each observed t values would be compared to the null distribution to generate a p-value. To improve the efficiency,a stop criterion (Anscombe (1953) <doi:10.1111/j.2517-6161.1953.tb00121.x>) is adopted to force permutation to stop if the estimated standard deviation of the value falls below a fraction of the estimated p-value. By doing so, we avoid the need for massive calculations in exact permutation methods while still generating stable and accurate p-values.

Last updated 2 years ago

1.00 score 177 downloads

ROI.models.netlib - 'ROI' Optimization Problems Based on 'NETLIB-LP'

A collection of 'ROI' optimization problems based on the 'NETLIB-LP' collection. 'Netlib' is a software repository, which amongst many other software for scientific computing contains a collection of linear programming problems. The purpose of this package is to make this problems easily accessible from 'R' as 'ROI' optimization problems.

Last updated 2 years ago

1.00 score 8 scripts 258 downloads

nlstac - An R Package for Fitting Separable Nonlinear Models

Set of functions implementing the algorithm described in Fernandez Torvisco et al. (2018) for fitting separable nonlinear regression curves. See Fernandez Torvisco, Rodriguez-Arias Fernandez and Cabello Sanchez (2018) <doi:10.2298/FIL1812233T>.

Last updated 2 years ago

1.00 score 2 scripts 177 downloads

hybridts - Hybrid Time Series Forecasting Using Error Remodeling Approach

Method and tool for generating hybrid time series forecasts using an error remodeling approach. These forecasting approaches utilize a recursive technique for modeling the linearity of the series using a linear method (e.g., ARIMA, Theta, etc.) and then models (forecasts) the residuals of the linear forecaster using non-linear neural networks (e.g., ANN, ARNN, etc.). The hybrid architectures comprise three steps: firstly, the linear patterns of the series are forecasted which are followed by an error re-modeling step, and finally, the forecasts from both the steps are combined to produce the final output. This method additionally provides the confidence intervals as needed. Ten different models can be implemented using this package. This package generates different types of hybrid error correction models for time series forecasting based on the algorithms by Zhang. (2003), Chakraborty et al. (2019), Chakraborty et al. (2020), Bhattacharyya et al. (2021), Chakraborty et al. (2022), and Bhattacharyya et al. (2022) <doi:10.1016/S0925-2312(01)00702-0> <doi:10.1016/j.physa.2019.121266> <doi:10.1016/j.chaos.2020.109850> <doi:10.1109/IJCNN52387.2021.9533747> <doi:10.1007/978-3-030-72834-2_29> <doi:10.1007/s11071-021-07099-3>.

Last updated 2 years ago

1.00 score 608 downloads

RTFA - Robust Factor Analysis for Tensor Time Series

Tensor Factor Models (TFM) are appealing dimension reduction tools for high-order tensor time series, and have wide applications in economics, finance and medical imaging. We propose an one-step projection estimator by minimizing the least-square loss function, and further propose a robust estimator with an iterative weighted projection technique by utilizing the Huber loss function. The methods are discussed in Barigozzi et al. (2022) <arXiv:2206.09800>, and Barigozzi et al. (2023) <arXiv:2303.18163>.

Last updated 2 years ago

1.00 score 293 downloads

qrjoint - Joint Estimation in Linear Quantile Regression

Joint estimation of quantile specific intercept and slope parameters in a linear regression setting.

Last updated 2 years ago

1.00 score 12 scripts 157 downloads

align - A Modified DTW Algorithm for Stratigraphic Time Series Alignment

A dynamic time warping (DTW) algorithm for stratigraphic alignment, translated into R from the original published 'MATLAB' code by Hay et al. (2019) <doi:10.1130/G46019.1>. The DTW algorithm incorporates two geologically relevant parameters (g and edge) for augmenting the typical DTW cost matrix, allowing for a range of sedimentologic and chronologic conditions to be explored, as well as the generation of an alignment library (as opposed to a single alignment solution). The g parameter relates to the relative sediment accumulation rate between the two time series records, while the edge parameter relates to the amount of total shared time between the records. Note that this algorithm is used for all DTW alignments in the Align Shiny application, detailed in Hagen et al. (in review).

Last updated 2 years ago

1.00 score 3 scripts 320 downloads

ecolRxC - Ecological Inference of RxC Tables by Latent Structure Approaches

Estimates RxC (R by C) vote transfer matrices (ecological contingency tables) from aggregate data building on Thomsen (1987) and Park (2008) approaches. References: Park, W.-H. (2008). ''Ecological Inference and Aggregate Analysis of Election''. PhD Dissertation. University of Michigan. <https://deepblue.lib.umich.edu/bitstream/handle/2027.42/58525/wpark_1.pdf> Thomsen, S.R. (1987, ISBN:87-7335-037-2). ''Danish Elections 1920 79: a Logit Approach to Ecological Analysis and Inference''. Politica, Aarhus, Denmark.

Last updated 2 years ago

1.00 score 142 downloads

HDCurves - Hierarchical Derivative Curve Estimation

A procedure that fits derivative curves based on a sequence of quotient differences. In a hierarchical setting the package produces estimates of subject-specific and group-specific derivative curves. In a non-hierarchical setting the package produces a single derivative curve.

Last updated 2 years ago

1.00 score 3 scripts 207 downloads

cenROC - Estimating Time-Dependent ROC Curve and AUC for Censored Data

Contains functions to estimate a smoothed and a non-smoothed (empirical) time-dependent receiver operating characteristic curve and the corresponding area under the receiver operating characteristic curve and the optimal cutoff point for the right and interval censored survival data. See Beyene and El Ghouch (2020)<doi:10.1002/sim.8671> and Beyene and El Ghouch (2022) <doi:10.1002/bimj.202000382>.

Last updated 2 years ago

cpp

1.00 score 29 scripts 192 downloads

HydroCode - Hydrological Codes

Pfafstetter Hydrological Codes as cited in Verdin and Verdin (1999) <doi: 10.1016/S0022-1694(99)00011-6> are decoded for upstream or downstream queries.

Last updated 2 years ago

1.00 score 227 downloads

matrixcut - Determines Clustering Threshold Based on Similarity Values

The user must supply a matrix filled with similarity values. The software will search for significant differences between similarity values at different hierarchical levels. The algorithm will return a Loess-smoothed plot of the similarity values along with the inflection point, if there are any. There is the option to search for an inflection point within a specified range. The package also has a function that will return the matrix components at a specified cutoff. References: Mullner. <ArXiv:1109.2378>; Cserhati, Carter. (2020, Journal of Creation 34(3):41-50), <https://dl0.creation.com/articles/p137/c13759/j34-3_64-73.pdf>.

Last updated 2 years ago

1.00 score 162 downloads

mcen - Multivariate Cluster Elastic Net

Fits the Multivariate Cluster Elastic Net (MCEN) presented in Price & Sherwood (2018) <arXiv:1707.03530>. The MCEN model simultaneously estimates regression coefficients and a clustering of the responses for a multivariate response model. Currently accommodates the Gaussian and binomial likelihood.

Last updated 2 years ago

1.00 score 1 stars 8 scripts 262 downloads

windAC - Area Correction Methods

Post-construction fatality monitoring studies at wind facilities are based on data from searches for bird and bat carcasses in plots beneath turbines. Bird and bat carcasses can fall outside of the search plot. Bird and bat carcasses from wind turbines often fall outside of the searched area. To compensate, area correction (AC) estimations are calculated to estimate the percentage of fatalities that fall within the searched area versus those that fall outside of it. This package provides two likelihood based methods and one physics based method (Hull and Muir (2010) <doi:10.1080/14486563.2010.9725253>, Huso and Dalthorp (2014) <doi:10.1002/jwmg.663>) to estimate the carcass fall distribution. There are also functions for calculating the proportion of area searched within one unit annuli, log logistic distribution functions, and truncated distribution functions.

Last updated 2 years ago

1.00 score 189 downloads

epicasting - Ewnet: An Ensemble Wavelet Neural Network for Forecasting and Epicasting

Method and tool for generating time series forecasts using an ensemble wavelet-based auto-regressive neural network architecture. This method provides additional support of exogenous variables and also generates confidence interval. This package provides EWNet model for time series forecasting based on the algorithm by Panja, et al. (2022) and Panja, et al. (2023) <arXiv:2206.10696> <doi:10.1016/j.chaos.2023.113124>.

Last updated 2 years ago

1.00 score 185 downloads

rciplot - Plot Jacobson-Truax Reliable Change Indices

The concept of reliable and clinically significant change (Jacobson & Truax, 1991) helps you answer the following questions for a sample with two measurements at different points in time (pre & post): Which proportion of my sample has a (considering the reliability of the instrument) probably not-just-by-chance difference in pre- vs. post-scores? Which proportion of my sample does not only change in a statistically significant way (see question one), but also in a clinically significant way (e.g. change from a test score regarded "dysfunctional" to a score regarded "functional")? This package allows you to very easily create a scatterplot of your sample in which the x-axis maps to the pre-scores, the y-axis maps to the post-scores and several graphical elements (lines, colors) allow you to gain a quick overview about reliable changes in these scores. An example of this kind of plot is Figure 2 of Jacobson & Truax (1991). Referenced article: Jacobson, N. S., & Truax, P. (1991) <doi:10.1037/0022-006X.59.1.12>.

Last updated 2 years ago

1.00 score 1 scripts 186 downloads

rplotengine - R as a Plotting Engine

Generate basic charts either by custom applications, or from a small script launched from the system console, or within the R console. Two ASCII text files are necessary: (1) The graph parameters file, which name is passed to the function 'rplotengine()'. The user can specify the titles, choose the type of the graph, graph output formats (e.g. png, eps), proportion of the X-axis and Y-axis, position of the legend, whether to show or not a grid at the background, etc. (2) The data to be plotted, which name is specified as a parameter ('data_filename') in the previous file. This data file has a tabulated format, with a single character (e.g. tab) between each column. Optionally, the file could include data columns for showing confidence intervals.

Last updated 2 years ago

1.00 score 3 scripts 205 downloads

metaSDTreg - Regression Models for Meta Signal Detection Theory

Regression methods for the meta-SDT model. The package implements methods for cognitive experiments of metacognition as described in Kristensen, S. B., Sandberg, K., & Bibby, B. M. (2020). Regression methods for metacognitive sensitivity. Journal of Mathematical Psychology, 94. <doi:10.1016/j.jmp.2019.102297>.

Last updated 2 years ago

1.00 score 164 downloads

symmetry - Testing for Symmetry of Data and Model Residuals

Implementations of a large number of tests for symmetry and their bootstrap variants, which can be used for testing the symmetry of random samples around a known or unknown mean. Functions are also there for testing the symmetry of model residuals around zero. Currently, the supported models are linear models and generalized autoregressive conditional heteroskedasticity (GARCH) models (fitted with the 'fGarch' package). All tests are implemented using the 'Rcpp' package which ensures great performance of the code.

Last updated 2 years ago

openblascpp

1.00 score 6 scripts 713 downloads

IGoRRR - A Shiny Interface for Simple Data Management

Launches a shiny application generating code to view tables in several ways, import/export tables, modify tables, make some basic graphics. 'IGoR' is a graphic user interface designed to help beginners using simple functions around table management and exploration. Inspired by 'Rcmdr', 'IGoR' is a code generator that, with simple inputs under a Shiny application, provides R code mainly built around the 'tidyverse' or some packages in the direct line of the Mosaic project: the 'rio' and 'ggformula' packages. The generated code doesn't depend on IGoR and can be manually modified by the user or copied elsewhere.

Last updated 2 years ago

1.00 score 228 downloads

evilDice - Test Dice Sets for Intransitive Properties

Checks to see whether a supplied set of dice (their face values) are transitive, returning pair-win and group-roll win probabilities. Expected returns (mean magnitude of win/loss) are presented as well.

Last updated 2 years ago

1.00 score 216 downloads

MacroZooBenthosWaterA - Fresh Water Quality Analysis Based on Macrozoobenthos

Includes functions for calculating basic indices of macrozoobenthos for water quality and is designed to provide researchers and environmental professionals with a comprehensive tool for evaluating the ecological health of aquatic ecosystems.The package is based on the following references: Paisley, M. F., Trigg, D. J. and Walley, W. J. (2014)<doi:10.1002/rra.2686>. Arslan, N., Salur, A., Kalyoncu, H. et al.(2016) <doi:10.1515/biolog-2016-0005>. Hilsenhoff W.L. (1987). Hilsenhoff. W.L. (1988) Barbour, M.T., Gerritsen, J., Snyder, B.D., and Stribling, J.B. (1999).

Last updated 2 years ago

1.00 score 205 downloads

FactorCopula - Factor, Bi-Factor, Second-Order and Factor Tree Copula Models

Estimation, model selection and goodness-of-fit of (1) factor copula models for mixed continuous and discrete data in Kadhem and Nikoloulopoulos (2021) <doi:10.1111/bmsp.12231>; (2) bi-factor and second-order copula models for item response data in Kadhem and Nikoloulopoulos (2023) <doi:10.1007/s11336-022-09894-2>; (3) factor tree copula models for item response data in Kadhem and Nikoloulopoulos (2022) <arXiv:2201.00339>.

Last updated 2 years ago

fortran

1.00 score 3 scripts 196 downloads

StatDataML - Read and Write StatDataML Files

Support for reading and writing files in StatDataML---an XML-based data exchange format.

Last updated 2 years ago

1.00 score 6 scripts 422 downloads

DNetFinder - Estimating Differential Networks under Semiparametric Gaussian Graphical Models

Provides a modified hierarchical test (Liu (2017) <doi:10.1214/17-AOS1539>) for detecting the structural difference between two Semiparametric Gaussian graphical models. The multiple testing procedure asymptotically controls the false discovery rate (FDR) at a user-specified level. To construct the test statistic, a truncated estimator is used to approximate the transformation functions and two R functions including lassoGGM() and lassoNPN() are provided to compute the lasso estimates of the regression coefficients.

Last updated 2 years ago

1.00 score 1 stars 8 scripts 174 downloads

TwoSampleTest.HD - A Two-Sample Test for the Equality of Distributions for High-Dimensional Data

For high-dimensional data whose main feature is a large number, p, of variables but a small sample size, the null hypothesis that the marginal distributions of p variables are the same for two groups is tested. We propose a test statistic motivated by the simple idea of comparing, for each of the p variables, the empirical characteristic functions computed from the two samples. If one rejects this global null hypothesis of no differences in distributions between the two groups, a set of permutation p-values is reported to identify which variables are not equally distributed in both groups.

Last updated 2 years ago

1.00 score 5 scripts 147 downloads

HYDROCAL - Hydraulic Roughness Calculator

Estimates frictional constants for hydraulic analysis of rivers. This HYDRaulic ROughness CALculator (HYDROCAL) was previously developed as a spreadsheet tool and accompanying documentation by McKay and Fischenich (2011, <https://erdc-library.erdc.dren.mil/jspui/bitstream/11681/2034/1/CHETN-VII-11.pdf>).

Last updated 2 years ago

1.00 score 180 downloads

clickb - Web Data Analysis by Bayesian Mixture of Markov Models

Designed for web usage data analysis, it implements tools to process web sequences and identify web browsing profiles through sequential classification. Sequences' clusters are identified by using a model-based approach, specifically mixture of discrete time first-order Markov models for categorical web sequences. A Bayesian approach is used to estimate model parameters and identify sequences classification as proposed by Fruehwirth-Schnatter and Pamminger (2010) <doi:10.1214/10-BA606>.

Last updated 2 years ago

1.00 score 204 downloads

cpmBigData - Fitting Semiparametric Cumulative Probability Models for Big Data

A big data version for fitting cumulative probability models using the orm() function from the 'rms' package. See Liu et al. (2017) <DOI:10.1002/sim.7433> for details.

Last updated 2 years ago

1.00 score 183 downloads

clustering.sc.dp - Optimal Distance-Based Clustering for Multidimensional Data with Sequential Constraint

A dynamic programming algorithm for optimal clustering multidimensional data with sequential constraint. The algorithm minimizes the sum of squares of within-cluster distances. The sequential constraint allows only subsequent items of the input data to form a cluster. The sequential constraint is typically required in clustering data streams or items with time stamps such as video frames, GPS signals of a vehicle, movement data of a person, e-pen data, etc. The algorithm represents an extension of 'Ckmeans.1d.dp' to multiple dimensional spaces. Similarly to the one-dimensional case, the algorithm guarantees optimality and repeatability of clustering. Method clustering.sc.dp() can find the optimal clustering if the number of clusters is known. Otherwise, methods findwithinss.sc.dp() and backtracking.sc.dp() can be used. See Szkaliczki, T. (2016) "clustering.sc.dp: Optimal Clustering with Sequential Constraint by Using Dynamic Programming" <doi: 10.32614/RJ-2016-022> for more information.

Last updated 2 years ago

cpp

1.00 score 4 scripts 205 downloads

CMHNPA - Cochran-Mantel-Haenszel and Nonparametric ANOVA

Cochran-Mantel-Haenszel methods (Cochran (1954) <doi:10.2307/3001616>; Mantel and Haenszel (1959) <doi:10.1093/jnci/22.4.719>; Landis et al. (1978) <doi:10.2307/1402373>) are a suite of tests applicable to categorical data. A competitor to those tests is the procedure of Nonparametric ANOVA which was initially introduced in Rayner and Best (2013) <doi:10.1111/anzs.12041>. The methodology was then extended in Rayner et al. (2015) <doi:10.1111/anzs.12113>. This package employs functions related to both methodologies and serves as an accompaniment to the book: An Introduction to Cochran–Mantel–Haenszel and Non-Parametric ANOVA. The package also contains the data sets used in that text.

Last updated 2 years ago

1.00 score 193 downloads

IIProductionUnknown - Analyzing Data Through of Percentage of Importance Indice (Production Unknown) and Its Derivations

The Importance Index (I.I.) can determine the loss and solution sources for a system in certain knowledge areas (e.g., agronomy), when production (e.g., fruits) is known (Demolin-Leite, 2021). Events (e.g., agricultural pest) can have different magnitudes (numerical measurements), frequencies, and distributions (aggregate, random, or regular) of event occurrence, and I.I. bases in this triplet (Demolin-Leite, 2021) <https://cjascience.com/index.php/CJAS/article/view/1009/1319>. Usually, the higher the magnitude and frequency of aggregated distribution, the greater the problem or the solution (e.g., natural enemies versus pests) for the system (Demolin-Leite, 2021). However, the final production of the system is not always known or is difficult to determine (e.g., degraded area recovery). A derivation of the I.I. is the percentage of Importance Index-Production Unknown (% I.I.-PU) that can detect the loss or solution sources, when production is unknown for the system (Demolin-Leite, 2024) <DOI:10.1590/1519-6984.253218>.

Last updated 2 years ago

1.00 score 148 downloads

penalizedcdf - Estimate a Penalized Linear Model using the CDF Penalty Function

Utilize the CDF penalty function to estimate a penalized linear model. It enables you to display some graphical representations and determine whether the Karush-Kuhn-Tucker conditions are met. For more details about the theory, please refer to Cuntrera, D., Augugliaro, L., & Muggeo, V. M. (2022) <arXiv:2212.08582>.

Last updated 2 years ago

1.00 score 123 downloads

L2DensityGoFtest - Density Goodness-of-Fit Test

Provides functions for the implementation of a density goodness-of-fit test, based on piecewise approximation of the L2 distance.

Last updated 2 years ago

1.00 score 231 downloads

p3state.msm - Analyzing Survival Data from an Illness-Death Model

Contains functions for data preparation, prediction of transition probabilities, estimating semi-parametric regression models and for implementing nonparametric estimators for other quantities. See Meira-Machado and Roca-Pardiñas (2011) <doi:10.18637/jss.v038.i03>.

Last updated 2 years ago

1.00 score 1 stars 5 scripts 218 downloads

SNPannotator - Investigating the Functional Characteristics of Selected SNPs and Their Vicinity Genomic Region

To investigate the functional characteristics of selected SNPs and their vicinity genomic region. Linked SNPs in moderate to high linkage disequilibrium (e.g. r2>0.50) with the corresponding index SNPs will be selected for further analysis.

Last updated 2 years ago

1.00 score 259 downloads

KFPLS - Kernel Functional Partial Least Squares

Implementation for kernel functional partial least squares (KFPLS) method. KFPLS method is developed for functional nonlinear models, and the method does not require strict constraints for the nonlinear structures. The crucial function of this package is KFPLS().

Last updated 2 years ago

1.00 score 143 downloads

IBFS - Initial Basic Feasible Solution for Transportation Problem

The initial basic feasible solution (IBFS) is a significant step to achieve the minimal total cost (optimal solution) of the transportation problem. However, the existing methods of IBFS do not always provide a good feasible solution which can reduce the number of iterations to find the optimal solution. This initial basic feasible solution can be obtained by using any of the following methods. a) North West Corner Method. b) Least Cost Method. c) Row Minimum Method. d) Column Minimum Method. e) Vogel's Approximation Method. etc. For more technical details about the algorithms please refer below URLs. <https://theintactone.com/2018/05/24/ds-u2-topic-8-transportation-problems-initial-basic-feasible-solution/>. <https://www.brainkart.com/article/Methods-of-finding-initial-Basic-Feasible-Solutions_39037/>. <https://myhomeworkhelp.com/row-minima-method/>. <https://myhomeworkhelp.com/column-minima-method/>.

Last updated 2 years ago

1.00 score 202 downloads

replicatedpp2w - Two-Way ANOVA-Like Method to Analyze Replicated Point Patterns

Test for effects of both individual factors and their interaction on replicated spatial patterns in a two factorial design, as explained in Ramon et al. (2016) <doi:10.1111/ecog.01848>.

Last updated 2 years ago

1.00 score 2 scripts 141 downloads

selectspm - Select Point Pattern Models Based on Minimum Contrast, AIC and Goodness of Fit

Fit and selects point pattern models based on minimum contrast, AIC and and goodness of fit.

Last updated 2 years ago

1.00 score 3 scripts 184 downloads

ockc - Order Constrained Solutions in k-Means Clustering

Extends 'flexclust' with an R implementation of order constrained solutions in k-means clustering (Steinley and Hubert, 2008, <doi:10.1007/s11336-008-9058-z>).

Last updated 2 years ago

1.00 score 2 scripts 125 downloads

istacr - Obtaining Open Data from Instituto Canario De Estadistica (ISTAC) API

You can access to open data published in Instituto Canario De Estadistica (ISTAC) APIs at <https://datos.canarias.es/api/estadisticas/>.

Last updated 2 years ago

1.00 score 1 scripts 199 downloads

ExNRuleEnsemble - A k Nearest Neibour Ensemble Based on Extended Neighbourhood Rule

The extended neighbourhood rule for the k nearest neighbour ensemble where the neighbours are determined in k steps. Starting from the first nearest observation of the test point, the algorithm identifies a single observation that is closest to the observation at the previous step. At each base learner in the ensemble, this search is extended to k steps on a random bootstrap sample with a random subset of features selected from the feature space. The final predicted class of the test point is determined by using a majority vote in the predicted classes given by all base models. Amjad Ali, Muhammad Hamraz, Naz Gul, Dost Muhammad Khan, Saeed Aldahmani, Zardad Khan (2022) <doi:10.48550/arXiv.2205.15111>.

Last updated 2 years ago

1.00 score 203 downloads

binomialtrend - Calculates the Statistical Significance of a Trend in a Set of Measurements

Detection of a statistically significant trend in the data provided by the user. This is based on the a signed test based on the binomial distribution. The package returns a trend test value, T, and also a p-value. A T value close to 1 indicates a rising trend, whereas a T value close to -1 indicates a decreasing trend. A T value close to 0 indicates no trend. There is also a command to visualize the trend. A test data set called gtsa_data is also available, which has global mean temperatures for January, April, July, and October for the years 1851 to 2022. Reference: Walpole, Myers, Myers, Ye. (2007, ISBN: 0-13-187711-9).

Last updated 2 years ago

1.00 score 1 scripts 224 downloads

FMAdist - Frequentist Model Averaging Distribution

Creation of an input model (fitted distribution) via the frequentist model averaging (FMA) approach and generate random-variates from the distribution specified by "myfit" which is the fitted input model via the FMA approach. See W. X. Jiang and B. L. Nelson (2018), "Better Input Modeling via Model Averaging," Proceedings of the 2018 Winter Simulation Conference, IEEE Press, 1575-1586.

Last updated 2 years ago

1.00 score 2 scripts 192 downloads

HybridDesign - Hybrid Design for Phase I Dose-Finding Studies

The Hybrid design is a combination of model-assisted design (e.g., the modified Toxicity Probability Interval design) with dose-toxicity model-based design for phase I dose-finding studies. The hybrid design controls the overdosing toxicity well and leads to a recommended dose closer to the true maximum tolerated dose (MTD) due to its ability to calibrate for an intermediate dose. More details can be found in Liao et al. 2022 <doi:10.1002/ijc.34203>.

Last updated 2 years ago

1.00 score 159 downloads

diverge - Evolutionary Trait Divergence Between Sister Species and Other Paired Lineages

Compares the fit of alternative models of continuous trait differentiation between sister species and other paired lineages. Differences in trait means between two lineages arise as they diverge from a common ancestor, and alternative processes of evolutionary divergence are expected to leave unique signatures in the distribution of trait differentiation in datasets comprised of many lineage pairs. Models include approximations of divergent selection, drift, and stabilizing selection. A variety of model extensions facilitate the testing of process-to-pattern hypotheses. Users supply trait data and divergence times for each lineage pair. The fit of alternative models is compared in a likelihood framework.

Last updated 2 years ago

1.00 score 10 scripts 218 downloads

BlockmodelingGUI - GUI for the Generalised Blockmodeling of Valued Networks

This app provides some useful tools for Offering an accessible GUI for generalised blockmodeling of single-relation, one-mode networks. The user can execute blockmodeling without having to write a line code by using the app's visual helps. Moreover, there are several ways to visualisations networks and their partitions. Finally, the results can be exported as if they were produced by writing code. The development of this package is financially supported by the Slovenian Research Agency (www.arrs.gov.si) within the research project J5-2557 (Comparison and evaluation of different approaches to blockmodeling dynamic networks by simulations with application to Slovenian co-authorship networks).

Last updated 2 years ago

1.00 score 243 downloads

bcfrailphdv - Bivariate Correlated Frailty Models with Varied Variances

Fit and simulate bivariate correlated frailty models with proportional hazard structure. Frailty distributions, such as gamma and lognormal models are supported for semiparametric procedures. Frailty variances of the two subjects can be varied or equal. Details on the models are available in book of Wienke (2011,ISBN:978-1-4200-7388-1). Bivariate gamma fit is obtained using the approach given in Iachine (1995) with modifications. Lognormal fit is based on the approach by Ripatti and Palmgren (2000) <doi:10.1111/j.0006-341X.2000.01016.x>. Frailty distributions, such as gamma, inverse gaussian and power variance frailty models are supported for parametric approach.

Last updated 2 years ago

1.00 score 717 downloads

SLFPCA - Sparse Logistic Functional Principal Component Analysis

Implementation for sparse logistic functional principal component analysis (SLFPCA). SLFPCA is specifically developed for functional binary data, and the estimated eigenfunction can be strictly zero on some sub-intervals, which is helpful for interpretation. The crucial function of this package is SLFPCA().

Last updated 2 years ago

1.00 score 1 stars 3 scripts 167 downloads

RobustANOVA - Robust One-Way ANOVA Tests under Heteroscedasticity and Nonnormality

Robust tests (RW, RPB and RGF) are provided for testing the equality of several long-tailed symmetric (LTS) means when the variances are unknown and arbitrary. RW, RPB and RGF tests are robust versions of Welch's F test proposed by Welch (1951) <doi:10.2307/2332579>, parametric bootstrap test proposed by Krishnamoorthy et. al (2007) <doi:10.1016/j.csda.2006.09.039>; and generalized F test proposed by Weerahandi (1995) <doi:10.2307/2532947>;, respectively. These tests are based on the modified maximum likelihood (MML) estimators proposed by Tiku(1967, 1968) <doi:10.2307/2333859>, <doi:10.1080/01621459.1968.11009228>.

Last updated 2 years ago

1.00 score 5 scripts 199 downloads

BayesBEKK - Bayesian Estimation of Bivariate Volatility Model

The Multivariate Generalized Autoregressive Conditional Heteroskedasticity (MGARCH) models are used for modelling the volatile multivariate data sets. In this package a variant of MGARCH called BEKK (Baba, Engle, Kraft, Kroner) proposed by Engle and Kroner (1995) <http://www.jstor.org/stable/3532933> has been used to estimate the bivariate time series data using Bayesian technique.

Last updated 2 years ago

1.00 score 232 downloads

TSSVM - Time Series Forecasting using SVM Model

Implementation and forecasting univariate time series data using the Support Vector Machine model. Support Vector Machine is one of the prominent machine learning approach for non-linear time series forecasting. For method details see Kim, K. (2003) <doi:10.1016/S0925-2312(03)00372-2>.

Last updated 2 years ago

1.00 score 174 downloads

ssaBSS - Stationary Subspace Analysis

Stationary subspace analysis (SSA) is a blind source separation (BSS) variant where stationary components are separated from non-stationary components. Several SSA methods for multivariate time series are provided here (Flumian et al. (2021); Hara et al. (2010) <doi:10.1007/978-3-642-17537-4_52>) along with functions to simulate time series with time-varying variance and autocovariance (Patilea and Raissi(2014) <doi:10.1080/01621459.2014.884504>).

Last updated 2 years ago

1.00 score 132 downloads

ciu - Contextual Importance and Utility

Implementation of the Contextual Importance and Utility (CIU) concepts for Explainable AI (XAI). A recent description of CIU can be found in e.g. Främling (2020) <arXiv:2009.13996>.

Last updated 2 years ago

1.00 score 7 scripts 258 downloads

nlgm - Non Linear Growth Models

Six growth models are fitted using non-linear least squares. These are the Richards, the 3, 4 and 5 parameter logistic, the Gompetz and the Weibull growth models. Reference: Reddy T., Shkedy Z., van Rensburg C. J., Mwambi H., Debba P., Zuma K. and Manda, S. (2021). "Short-term real-time prediction of total number of reported COVID-19 cases and deaths in South Africa: a data driven approach". BMC medical research methodology, 21(1), 1-11. <doi:10.1186/s12874-020-01165-x>.

Last updated 2 years ago

1.00 score 166 downloads

quadraticSD - Visualizing the SD using a Quadratic Curve

Given a dataset, the user is invited to utilize the Empirical Cumulative Distribution Function (ECDF) to guess interactively the mean and the mean deviation. Thereafter, using the quadratic curve the user can guess the Root Mean Squared Deviation (RMSD) and visualize the standard deviation (SD). For details, see Sarkar and Rashid (2019)<doi:10.3126/njs.v3i0.25574>, Have You Seen the Standard Deviaton?, Nepalese Journal of Statistics, Vol. 3, 1-10.

Last updated 2 years ago

1.00 score 195 downloads

ttbary - Barycenter Methods for Spatial Point Patterns

Computes a point pattern in R^2 or on a graph that is representative of a collection of many data patterns. The result is an approximate barycenter (also known as Fréchet mean or prototype) based on a transport-transform metric. Possible choices include Optimal SubPattern Assignment (OSPA) and Spike Time metrics. Details can be found in Müller, Schuhmacher and Mateu (2020) <doi:10.1007/s11222-020-09932-y>.

Last updated 2 years ago

cpp

1.00 score 204 downloads

HDiR - Directional Highest Density Regions

We provide an R tool for computation and nonparametric plug-in estimation of Highest Density Regions (HDRs) and general level sets in the directional setting. Concretely, circular and spherical HDRs can be reconstructed from a data sample following Saavedra-Nieves and Crujeiras (2021) <doi:10.1007/s11634-021-00457-4>. This library also contains two real datasets in the circular and spherical settings. The first one concerns a problem from animal orientation studies and the second one is related to earthquakes occurrences.

Last updated 2 years ago

1.00 score 1 scripts 268 downloads

loedata - Data Sets from "Lectures on Econometrics" by Chirok Han

Data sets for Chirok Han (2022, ISBN:979-11-303-1497-6, "Lectures on Econometrics"). Students, teachers, and self-learners will find the data sets essential for replicating the results in the book.

Last updated 2 years ago

1.00 score 1 scripts 482 downloads

LatticeDesign - Lattice-Based Space-Filling Designs

Lattice-based space-filling designs with fill or separation distance properties including interleaved lattice-based minimax distance designs proposed in Xu He (2017) <doi:10.1093/biomet/asx036>, interleaved lattice-based maximin distance designs proposed in Xu He (2018) <doi:10.1093/biomet/asy069>, (sliced) rotated sphere packing designs proposed in Xu He (2017) <doi:10.1080/01621459.2016.1222289> and Xu He (2019) <doi:10.1080/00401706.2018.1458655>, and densest packing-based maximum projections designs proposed in Xu He (2020) <doi:10.1093/biomet/asaa057> and Xu He (2018) <arXiv:1709.02062v2>.

Last updated 2 years ago

1.00 score 6 scripts 309 downloads

netcmc - Spatio-Network Generalised Linear Mixed Models for Areal Unit and Network Data

Implements a class of univariate and multivariate spatio-network generalised linear mixed models for areal unit and network data, with inference in a Bayesian setting using Markov chain Monte Carlo (MCMC) simulation. The response variable can be binomial, Gaussian, or Poisson. Spatial autocorrelation is modelled by a set of random effects that are assigned a conditional autoregressive (CAR) prior distribution following the Leroux model (Leroux et al. (2000) <doi:10.1007/978-1-4612-1284-3_4>). Network structures are modelled by a set of random effects that reflect a multiple membership structure (Browne et al. (2001) <doi:10.1177/1471082X0100100202>).

Last updated 2 years ago

openblascpp

1.00 score 1 scripts 175 downloads

FADPclust - Functional Data Clustering Using Adaptive Density Peak Detection

An implementation of a clustering algorithm for functional data based on adaptive density peak detection technique, in which the density is estimated by functional k-nearest neighbor density estimation based on a proposed semi-metric between functions. The proposed functional data clustering algorithm is computationally fast since it does not need iterative process. (Alex Rodriguez and Alessandro Laio (2014) <doi:10.1126/science.1242072>; Xiao-Feng Wang and Yifan Xu (2016) <doi:10.1177/0962280215609948>).

Last updated 2 years ago

1.00 score 1 stars 8 scripts 257 downloads

cmbClust - Conditional Mixture Modeling and Model-Based Clustering

Conditional mixture model fitted via EM (Expectation Maximization) algorithm for model-based clustering, including parsimonious procedure, optimal conditional order exploration, and visualization.

Last updated 2 years ago

1.00 score 206 downloads

ZINAR1 - Simulates ZINAR(1) Model and Estimates Its Parameters Under Frequentist Approach

Generates Realizations of First-Order Integer Valued Autoregressive Processes with Zero-Inflated Innovations (ZINAR(1)) and Estimates its Parameters as described in Garay et al. (2021) <doi:10.1007/978-3-030-82110-4_2>.

Last updated 2 years ago

1.00 score 128 downloads

ResPBIBD - "Resolvable Partially Balanced Incomplete Block Designs (PBIBDs)"

A collection of several utility functions related to resolvable and affine resolvable Partially Balanced Incomplete Block Designs (PBIBDs), have been developed. In the class of resolvable designs, affine resolvable designs are said to be optimal, Bailey (1995) <doi:10.2307/2337638>. Here, the package contains three functions to generate and study the characterization properties of these designs. Developed functions are named as PBIBD1(), PBIBD2() and PBIBD3(), in which first two functions are used to generate two new series of affine resolvable PBIBDs and last one is used to generate a new series of resolvable PBIBDs, respectively. In addition, these functions can also be used to generate design parameters (v, b, r and k), canonical efficiency factors, variance factor between associates and average variance factors of the generated designs. Here v is the number of treatments, b (= b1 + b2, in case of non-proper design) is the number of blocks, r is the number of replications and k (= k1 + k2; k1 is the size of b1 and k2 is the size of b2) is the block size.

Last updated 2 years ago

1.00 score 7 scripts 152 downloads

OnboardClient - Bindings for Onboard Data's Building Data API

Provides a wrapper for the Onboard Data building data API <https://api.onboarddata.io/swagger>. Along with streamlining access to the API, this package simplifies access to sensor time series data, metadata (sensors, equipment, and buildings), and details about the Onboard data model/ontology.

Last updated 2 years ago

1.00 score 6 scripts 202 downloads

FRCC - Fast Regularized Canonical Correlation Analysis

Contains the core functions associated with Fast Regularized Canonical Correlation Analysis. Please see the following for details: Raul Cruz-Cano, Mei-Ling Ting Lee, Fast regularized canonical correlation analysis, Computational Statistics & Data Analysis, Volume 70, 2014, Pages 88-100, ISSN 0167-9473 <doi:10.1016/j.csda.2013.09.020>.

Last updated 2 years ago

1.00 score 11 scripts 155 downloads

FBCRM - Phase I Optimal Dose Assignment using the FBCRM and MFBCRM Methods

Performs dose assignment and trial simulation for the FBCRM (Fully Bayesian Continual Reassessment Method) and MFBCRM (Mixture Fully Bayesian Continual Reassessment Method) phase I clinical trial designs. These trial designs extend the Continual Reassessment Method (CRM) and Bayesian Model Averaging Continual Reassessment Method (BMA-CRM) by allowing the prior toxicity skeleton itself to be random, with posterior distributions obtained from Markov Chain Monte Carlo. On average, the FBCRM and MFBCRM methods outperformed the CRM and BMA-CRM methods in terms of selecting an optimal dose level across thousands of randomly generated simulation scenarios. Details on the methods and results of this simulation study are available on request, and the manuscript is currently under review.

Last updated 2 years ago

cpp

1.00 score 161 downloads

BayesReversePLLH - Fits the Bayesian Piecewise Linear Log-Hazard Model

Contains posterior samplers for the Bayesian piecewise linear log-hazard and piecewise exponential hazard models, including Cox models. Posterior mean restricted survival times are also computed for non-Cox an Cox models with only treatment indicators. The ApproxMean() function can be used to estimate restricted posterior mean survival times given a vector of patient covariates in the Cox model. Functions included to return the posterior mean hazard and survival functions for the piecewise exponential and piecewise linear log-hazard models. Chapple, AG, Peak, T, Hemal, A (2020). Under Revision.

Last updated 2 years ago

openblascppopenmp

1.00 score 264 downloads

sAIC - Akaike Information Criterion for Sparse Estimation

Computes the Akaike information criterion for the generalized linear models (logistic regression, Poisson regression, and Gaussian graphical models) estimated by the lasso.

Last updated 2 years ago

1.00 score 2 scripts 105 downloads

gridOT - Approximate Optimal Transport Between Two-Dimensional Grids

Can be used for optimal transport between two-dimensional grids with respect to separable cost functions of l^p form. It utilizes the Frank-Wolfe algorithm to approximate so-called pivot measures: one-dimensional transport plans that fully describe the full transport, see G. Auricchio (2021) <arXiv:2105.07278>. For these, it offers methods for visualization and to extract the corresponding transport plans and costs. Additionally, related functions for one-dimensional optimal transport are available.

Last updated 2 years ago

openblascppopenmp

1.00 score 1 scripts 146 downloads

gllm - Generalised log-Linear Model

Routines for log-linear models of incomplete contingency tables, including some latent class models, via EM and Fisher scoring approaches. Allows bootstrapping. See Espeland and Hui (1987) <doi:10.2307/2531553> for general approach.

Last updated 2 years ago

1.00 score 8 scripts 344 downloads

spcr - Sparse Principal Component Regression

The sparse principal component regression is computed. The regularization parameters are optimized by cross-validation.

Last updated 2 years ago

1.00 score 1 stars 4 scripts 287 downloads

UnifiedDoseFinding - Dose-Finding Methods for Non-Binary Outcomes

In many phase I trials, the design goal is to find the dose associated with a certain target toxicity rate. In some trials, the goal can be to find the dose with a certain weighted sum of rates of various toxicity grades. For others, the goal is to find the dose with a certain mean value of a continuous response. This package provides the setup and calculations needed to run a dose-finding trial with non-binary endpoints and performs simulations to assess design’s operating characteristics under various scenarios. Three dose finding designs are included in this package: unified phase I design (Ivanova et al. (2009) <doi:10.1111/j.1541-0420.2008.01045.x>), Quasi-CRM/Robust-Quasi-CRM (Yuan et al. (2007) <doi:10.1111/j.1541-0420.2006.00666.x>, Pan et al. (2014) <doi:10.1371/journal.pone.0098147>) and generalized BOIN design (Mu et al. (2018) <doi:10.1111/rssc.12263>). The toxicity endpoints can be handled with these functions including equivalent toxicity score (ETS), total toxicity burden (TTB), general continuous toxicity endpoints, with incorporating ordinal grade toxicity information into dose-finding procedure. These functions allow customization of design characteristics to vary sample size, cohort sizes, target dose-limiting toxicity (DLT) rates, discrete or continuous toxicity score, and incorporate safety and/or stopping rules.

Last updated 2 years ago

1.00 score 256 downloads

MplusTrees - Decision Trees with Structural Equation Models Fit in 'Mplus'

Uses recursive partitioning to create homogeneous subgroups based on structural equation models fit in 'Mplus', a stand-alone program developed by Muthen and Muthen.

Last updated 2 years ago

1.00 score 170 downloads

TOU - Transformed Ornstein-Uhlenbeck Model for Adsorption Kinetics

Estimates the parameters of a Transformed Ornstein-Uhlenbeck (TOU) stochastic model for adsorption data and also the parameters of the related pseudo-n-order (PNO) model, such as the maximum adsorption capacity (qe), the adsorption rate constant (kn) and the order of the model (n).

Last updated 2 years ago

1.00 score 123 downloads

weightedCL - Efficient and Feasible Inference for High-Dimensional Normal Copula Regression Models

Estimates high-dimensional multivariate normal copula regression models with the weighted composite likelihood estimating equations in Nikoloulopoulos (2022) <arXiv:2203.04619>. It provides autoregressive moving average correlation structures and binary, ordinal, Poisson, and negative binomial regressions.

Last updated 2 years ago

fortran

1.00 score 128 downloads

TemporalGSSA - Outputs Temporal Profile of Molecules from Stochastic Simulation Algorithm Generated Datasets

The data that is generated from independent and consecutive 'GillespieSSA' runs for a generic biochemical network is formatted as rows and constitutes an observation. The first column of each row is the computed timestep for each run. Subsequent columns are used for the number of molecules of each participating molecular species or "metabolite" of a generic biochemical network. In this way 'TemporalGSSA', is a wrapper for the R-package 'GillespieSSA'. The number of observations must be at least 30. This will generate data that is statistically significant. 'TemporalGSSA', transforms this raw data into a simulation time-dependent and metabolite-specific trial. Each such trial is defined as a set of linear models (n >= 30) between a timestep and number of molecules for a metabolite. Each linear model is characterized by coefficients such as the slope, arbitrary constant, etc. The user must enter an integer from 1-4. These specify the statistical modality utilized to compute a representative timestep (mean, median, random, all). These arguments are mandatory and will be checked. Whilst, the numeric indicator "0" indicates suitability, "1" prompts the user to revise and re-enter their data. An optional logical argument controls the output to the console with the default being "TRUE" (curtailed) whilst "FALSE" (verbose). The coefficients of each linear model are averaged (mean slope, mean constant) and are incorporated into a metabolite-specific linear regression model as the dependent variable. The independent variable is the representative timestep chosen previously. The generated data is the imputed molecule number for an in silico experiment with (n >=30) observations. These steps can be replicated with multiple set of observations. The generated "technical replicates" can be statistically evaluated (mean, standard deviation) and will constitute simulation time-dependent molecules for each metabolite. For SSA-generated datasets with varying simulation times 'TemporalGSSA' will generate a simulation time-dependent trajectory for each metabolite of the biochemical network under study. The relevant publication with the mathematical derivation of the algorithm is (2022, Journal of Bioinformatics and Computational Biology) <doi:10.1142/S0219720022500184>. The algorithm has been deployed in the following publications (2021, Heliyon) <doi:10.1016/j.heliyon.2021.e07466> and (2016, Journal of Theoretical Biology) <doi:10.1016/j.jtbi.2016.07.002>.

Last updated 2 years ago

1.00 score 1 scripts 117 downloads

Design.parameters - Parameters of the Experimental Designs

Here, a function has been developed to generate parameters of the input designs, as well as incidence matrices. This is a general function that can be used to investigate the characterization properties of any block design.

Last updated 2 years ago

1.00 score 3 scripts 184 downloads

adaptsmoFMRI - Adaptive Smoothing of FMRI Data

Adaptive smoothing functions for estimating the blood oxygenation level dependent (BOLD) effect by using functional Magnetic Resonance Imaging (fMRI) data, based on adaptive Gauss Markov random fields, for real as well as simulated data. The implemented models make use of efficient Markov Chain Monte Carlo methods. Implemented methods are based on the research developed by A. Brezger, L. Fahrmeir, A. Hennerfeind (2007) <https://www.jstor.org/stable/4626770>.

Last updated 2 years ago

1.00 score 6 scripts 287 downloads

washeR - Time Series Outlier Detection

Time series outlier detection with non parametric test. This is a new outlier detection methodology (washer): efficient for time saving elaboration and implementation procedures, adaptable for general assumptions and for needing very short time series, reliable and effective as involving robust non parametric test. You can find two approaches: single time series (a vector) and grouped time series (a data frame). For other informations: Andrea Venturini (2011) Statistica - Universita di Bologna, Vol.71, pp.329-344. For an informal explanation look at R-bloggers on web.

Last updated 2 years ago

1.00 score 1 scripts 148 downloads

SurvTrunc - Analysis of Doubly Truncated Data

Package performs Cox regression and survival distribution function estimation when the survival times are subject to double truncation. In case that the survival and truncation times are quasi-independent, the estimation procedure for each method involves inverse probability weighting, where the weights correspond to the inverse of the selection probabilities and are estimated using the survival times and truncation times only. A test for checking this independence assumption is also included in this package. The functions available in this package for Cox regression, survival distribution function estimation, and testing independence under double truncation are based on the following methods, respectively: Rennert and Xie (2018) <doi:10.1111/biom.12809>, Shen (2010) <doi:10.1007/s10463-008-0192-2>, Martin and Betensky (2005) <doi:10.1198/016214504000001538>. When the survival times are dependent on at least one of the truncation times, an EM algorithm is employed to obtain point estimates for the regression coefficients. The standard errors are calculated using the bootstrap method. See Rennert and Xie (2022) <doi:10.1111/biom.13451>. Both the independent and dependent cases assume no censoring is present in the data. Please contact Lior Rennert <[email protected]> for questions regarding function coxDT and Yidan Shi <[email protected]> for questions regarding function coxDTdep.

Last updated 2 years ago

1.00 score 10 scripts 133 downloads

Tratamentos.ad - Pacote Para Analise De Experimentos Com Testemunhas Adicionais

Pacote para a analise de experimentos com um ou dois fatores com testemunhas adicionais conduzidos no delineamento inteiramente casualizado ou em blocos casualizados. "Package for the analysis of one or two-way experiments with additional controls conducted in a completely randomized design or in a randomized block design".

Last updated 2 years ago

1.00 score 9 scripts 330 downloads

CpmERCCutoff - Calculation of Log2 Counts per Million Cutoff from ERCC Controls

Implementation of the empirical method to derive log2 counts per million (CPM) cutoff to filter out lowly expressed genes using ERCC spike-ins as described in Goll and Bosinger et.al (2022)<doi:10.1101/2022.06.23.497396>. This package utilizes the synthetic mRNA control pairs developed by the External RNA Controls Consortium (ERCC) (ERCC 1 / ERCC 2) that are spiked into sample pairs at known ratios at various absolute abundances. The relationship between the observed and expected fold changes is then used to empirically determine an optimal log2 CPM cutoff for filtering out lowly expressed genes.

Last updated 2 years ago

1.00 score 5 scripts 631 downloads

OneArmTTE - One-Arm Clinical Trial Designs for Time-to-Event Endpoint

Get operating characteristics of one-arm clinical trial designs for time-to-event endpoint through simulation and perform analysis with time-to-event data.

Last updated 2 years ago

1.00 score 186 downloads

fmt - Variance Estimation of FMT Method (Fully Moderated T-Statistic)

The FMT method computes posterior residual variances to be used in the denominator of a moderated t-statistic from a linear model analysis of gene expression data. It is an extension of the moderated t-statistic originally proposed by Smyth (2004) <doi:10.2202/1544-6115.1027>. LOESS local regression and empirical Bayesian method are used to estimate gene specific prior degrees of freedom and prior variance based on average gene intensity levels. The posterior residual variance in the denominator is a weighted average of prior and residual variance and the weights are prior degrees of freedom and residual variance degrees of freedom. The degrees of freedom of the moderated t-statistic is simply the sum of prior and residual variance degrees of freedom.

Last updated 2 years ago

1.00 score 73 scripts 214 downloads

GiniDistance - A New Gini Correlation Between Quantitative and Qualitative Variables

An implementation of a new Gini covariance and correlation to measure dependence between a categorical and numerical variables. Dang, X., Nguyen, D., Chen, Y. and Zhang, J., (2018) <arXiv:1809.09793>.

Last updated 2 years ago

cpp

1.00 score 1 scripts 181 downloads

MultiplierDEA - Multiplier Data Envelopment Analysis and Cross Efficiency

Functions are provided for calculating efficiency using multiplier DEA (Data Envelopment Analysis): Measuring the efficiency of decision making units (Charnes et al., 1978 <doi:10.1016/0377-2217(78)90138-8>) and cross efficiency using single and two-phase approach. In addition, it includes some datasets for calculating efficiency and cross efficiency.

Last updated 2 years ago

1.00 score 1 stars 26 scripts 157 downloads

soilhypfit - Modelling of Soil Water Retention and Hydraulic Conductivity Data

Provides functions for efficiently estimating properties of the Van Genuchten-Mualem model for soil hydraulic parameters from possibly sparse soil water retention and hydraulic conductivity data by multi-response parameter estimation methods (Stewart, W.E., Caracotsios, M. Soerensen, J.P. (1992) "Parameter estimation from multi-response data" <doi:10.1002/aic.690380502>). Parameter estimation is simplified by exploiting the fact that residual and saturated water contents and saturated conductivity are conditionally linear parameters (Bates, D. M. and Watts, D. G. (1988) "Nonlinear Regression Analysis and Its Applications" <doi:10.1002/9780470316757>). Estimated parameters are optionally constrained by the evaporation characteristic length (Lehmann, P., Bickel, S., Wei, Z. and Or, D. (2020) "Physical Constraints for Improved Soil Hydraulic Parameter Estimation by Pedotransfer Functions" <doi:10.1029/2019WR025963>) to ensure that the estimated parameters are physically valid. Common S3 methods and further utility functions allow to process, explore and visualise estimation results.

Last updated 2 years ago

1.00 score 174 downloads

AutoWeatherIndices - Calculating Weather Indices

Weather indices are formed from weather variables in this package. The users can input any number of weather variables recorded over any number of weeks. This package has no restriction on the number of weeks and weather variables to be taken as input.The details of the method can be seen (i)'Joint effects of weather variables on rice yields' by R. Agrawal, R. C. Jain and M. P. Jha in Mausam, vol. 34, pp. 189-194, 1983,<doi:10.54302/mausam.v34i2.2392>,(ii)'Improved weather indices based Bayesian regression model for forecasting crop yield' by M. Yeasin, K. N. Singh, A. Lama and B. Gurung in Mausam, vol. 72, pp.879-886, 2021,<doi:10.54302/mausam.v72i4.670>.

Last updated 2 years ago

1.00 score 191 downloads

ROCSI - Receiver Operating Characteristic Based Signature Identification

Optimal linear combination predictive signatures for maximizing the area between two Receiver Operating Characteristic (ROC) curves (treatment vs. control).

Last updated 2 years ago

1.00 score 180 downloads

arakno - ARAchnid KNowledge Online

Allows the user to connect with the World Spider Catalogue (WSC; <https://wsc.nmbe.ch/>) and the World Spider Trait (WST; <https://spidertraits.sci.muni.cz/>) databases. Also performs several basic functions such as checking names validity, retrieving coordinate data from the Global Biodiversity Information Facility (GBIF; <https://www.gbif.org/>), and mapping.

Last updated 2 years ago

1.00 score 289 downloads

copulaboost - Fitting Additive Copula Regression Models for Binary Outcome Regression

Additive copula regression for regression problems with binary outcome via gradient boosting [Brant, Hobæk Haff (2022); <arXiv:2208.04669>]. The fitting process includes a specialised model selection algorithm for each component, where each component is found (by greedy optimisation) among all the D-vines with only Gaussian pair-copulas of a fixed dimension, as specified by the user. When the variables and structure have been selected, the algorithm then re-fits the component where the pair-copula distributions can be different from Gaussian, if specified.

Last updated 2 years ago

1.00 score 179 downloads

mFDP - Flexible Control of the mFDP

Computes bounds for the median of the false discovery proportion (mFDP). These 50 percent confidence bounds for the FDP are simultaneously valid. The method takes a vector of p-values as input. Also provides mFDP-adjusted p-values. Can be used for flexible mFDP control.

Last updated 2 years ago

1.00 score 200 downloads

qmd - Quantification of Multivariate Dependence

A multivariate copula-based dependence measure. For more information, see Griessenberger, Junker, Trutschnig (2022), On a multivariate copula-based dependence measure and its estimation, Electronic Journal of Statistics, 16, 2206-2251.

Last updated 2 years ago

cpp

1.00 score 218 downloads

JSparO - Joint Sparse Optimization via Proximal Gradient Method for Cell Fate Conversion

Implementation of joint sparse optimization (JSparO) to infer the gene regulatory network for cell fate conversion. The proximal gradient method is implemented to solve different low-order regularization models for JSparO.

Last updated 2 years ago

1.00 score 1 stars 156 downloads

dyads - Dyadic Network Analysis

Contains functions for the MCMC simulation of dyadic network models j2 (Zijlstra, 2017, <doi:10.1080/0022250X.2017.1387858>) and p2 (Van Duijn, Snijders & Zijlstra, 2004, <doi: 10.1046/j.0039-0402.2003.00258.x>), the multilevel p2 model (Zijlstra, Van Duijn & Snijders (2009) <doi: 10.1348/000711007X255336>), and the bidirectional (multilevel) counterpart of the the multilevel p2 model as described in Zijlstra, Van Duijn & Snijders (2009) <doi: 10.1348/000711007X255336>, the (multilevel) b2 model.

Last updated 2 years ago

1.00 score 3 scripts 241 downloads

mvLSWimpute - Imputation Methods for Multivariate Locally Stationary Time Series

Implementation of imputation techniques based on locally stationary wavelet time series forecasting methods from Wilson, R. E. et al. (2021) <doi:10.1007/s11222-021-09998-2>.

Last updated 2 years ago

1.00 score 1 scripts 192 downloads

SPB - Simple Progress Bars for Procedural Coding

Provides a simple progress bar to use for basic and advanced users that suits all those who prefer procedural programming. It is especially useful for integration into markdown files thanks to the progress bar's customisable appearance.

Last updated 2 years ago

1.00 score 253 downloads

clusterHD - Tools for Clustering High-Dimensional Data

Tools for clustering high-dimensional data. In particular, it contains the methods described in <doi:10.1093/bioinformatics/btaa243>, <arXiv:2010.00950>.

Last updated 2 years ago

cpp

1.00 score 2 scripts 231 downloads

Omisc - Univariate Bootstrapping and Other Things

Primarily devoted to implementing the Univariate Bootstrap (as well as the Traditional Bootstrap). In addition there are multiple functions for DeFries-Fulker behavioral genetics models. The univariate bootstrapping functions, DeFries-Fulker functions, regression and traditional bootstrapping functions form the original core. Additional features may come online later, however this software is a work in progress. For more information about univariate bootstrapping see: Lee and Rodgers (1998) and Beasley et al (2007) <doi:10.1037/1082-989X.12.4.414>.

Last updated 2 years ago

1.00 score 37 scripts 202 downloads

stlELM - Hybrid Forecasting Model Based on STL Decomposition and ELM

Univariate time series forecasting with STL decomposition based Extreme Learning Machine hybrid model. For method details see Xiong T, Li C, Bao Y (2018). <doi:10.1016/j.neucom.2017.11.053>.

Last updated 2 years ago

1.00 score 139 downloads

EEMDelm - Ensemble Empirical Mode Decomposition and Its Variant Based ELM Model

Forecasting univariate time series with different decomposition based Extreme Learning Machine models. For method details see Yu L, Wang S, Lai KK (2008). <doi:10.1016/j.eneco.2008.05.003>, Parida M, Behera MK, Nayak N (2018). <doi:10.1109/ICSESP.2018.8376723>.

Last updated 2 years ago

1.00 score 224 downloads

fdaMocca - Model-Based Clustering for Functional Data with Covariates

Routines for model-based functional cluster analysis for functional data with optional covariates. The idea is to cluster functional subjects (often called functional objects) into homogenous groups by using spline smoothers (for functional data) together with scalar covariates. The spline coefficients and the covariates are modelled as a multivariate Gaussian mixture model, where the number of mixtures corresponds to the number of clusters. The parameters of the model are estimated by maximizing the observed mixture likelihood via an EM algorithm (Arnqvist and Sjöstedt de Luna, 2019) <arXiv:1904.10265>. The clustering method is used to analyze annual lake sediment from lake Kassjön (Northern Sweden) which cover more than 6400 years and can be seen as historical records of weather and climate.

Last updated 2 years ago

1.00 score 3 scripts 149 downloads

PUPAK - Parameter Estimation, and Plot Visualization of Adsorption Kinetic Models

Contains model fitting functions for linear and non-linear adsorption kinetic and diffusion models. Adsorption kinetics is used for characterizing the rate of solute adsorption and the time necessary for the adsorption process. Adsorption kinetics offers vital information on adsorption rate, adsorbent performance in response time, and mass transfer processes. In addition, diffusion models are included in the package as solute diffusion affects the adsorption kinetic experiments. This package consists of 20 adsorption and diffusion models, including Pseudo First Order (PFO), Pseudo Second Order (PSO), Elovich, and Weber-Morris model (commonly called the intraparticle model) stated by Plazinski et al. (2009) <doi:10.1016/j.cis.2009.07.009>. This package also contains a summary function where the statistical errors of each model are ranked for a more straightforward determination of the best fit model.

Last updated 2 years ago

1.00 score 112 downloads

CREDS - Calibrated Ratio Estimator under Double Sampling Design

Population ratio estimator (calibrated) under two-phase random sampling design has gained enormous popularity in the recent time. This package provides functions for estimation population ratio (calibrated) under two phase sampling design, including the approximate variance of the ratio estimator. The improved ratio estimator can be applicable for both the case, when auxiliary data is available at unit level or aggregate level (eg., mean or total) for first phase sampled. Calibration weight of each unit of the second phase sample was calculated. Single and combined inclusion probabilities were also estimated for both phases under two phase random [simple random sampling without replacement (SRSWOR)] sampling. The improved ratio estimator's percentage coefficient of variation was also determined as a measure of accuracy. This package has been developed based on the theoretical development of Islam et al. (2021) and Ozgul (2020) <doi:10.1080/00949655.2020.1844702>.

Last updated 2 years ago

1.00 score 8 scripts 140 downloads

dbcsp - Distance-Based Common Spatial Patterns

A way to apply Distance-Based Common Spatial Patterns (DB-CSP) techniques in different fields, both classical Common Spatial Patterns (CSP) as well as DB-CSP. The method is composed of two phases: applying the DB-CSP algorithm and performing a classification. The main idea behind the CSP is to use a linear transform to project data into low-dimensional subspace with a projection matrix, in such a way that each row consists of weights for signals. This transformation maximizes the variance of two-class signal matrices.The dbcsp object is created to compute the projection vectors. For exploratory and descriptive purpose, plot and boxplot functions can be used. Functions train, predict and selectQ are implemented for the classification step.

Last updated 2 years ago

1.00 score 1 scripts 178 downloads

mod2rm - Moderation Analysis for Two-Instance Repeated Measures Designs

Multiple moderation analysis for two-instance repeated measures designs, with up to three simultaneous moderators (dichotomous and/or continuous) with additive or multiplicative relationship. Includes analyses of simple slopes and conditional effects at (automatically determined or manually set) values of the moderator(s), as well as an implementation of the Johnson-Neyman procedure for determining regions of significance in single moderator models. Based on Montoya, A. K. (2018) "Moderation analysis in two-instance repeated measures designs: Probing methods and multiple moderator models" <doi:10.3758/s13428-018-1088-6> .

Last updated 2 years ago

1.00 score 123 downloads

ARpLMEC - Censored Mixed-Effects Models with Different Correlation Structures

Left, right or interval censored mixed-effects linear model with autoregressive errors of order p or DEC correlation structure using the type-EM algorithm. The error distribution can be Normal or t-Student. It provides the parameter estimates, the standard errors and prediction of future observations (available only for the normal case). Olivari et all (2021) <doi:10.1080/10543406.2020.1852246>.

Last updated 2 years ago

1.00 score 3 scripts 359 downloads

mined - Minimum Energy Designs

This is a method (MinED) for mining probability distributions using deterministic sampling which is proposed by Joseph, Wang, Gu, Lv, and Tuo (2019) <DOI:10.1080/00401706.2018.1552203>. The MinED samples can be used for approximating the target distribution. They can be generated from a density function that is known only up to a proportionality constant and thus, it might find applications in Bayesian computation. Moreover, the MinED samples are generated with much fewer evaluations of the density function compared to random sampling-based methods such as MCMC and therefore, this method will be especially useful when the unnormalized posterior is expensive or time consuming to evaluate. This research is supported by a U.S. National Science Foundation grant DMS-1712642.

Last updated 2 years ago

cpp

1.00 score 6 scripts 150 downloads

hpcwld - High Performance Cluster Models Based on Kiefer-Wolfowitz Recursion

Probabilistic models describing the behavior of workload and queue on a High Performance Cluster and computing GRID under FIFO service discipline basing on modified Kiefer-Wolfowitz recursion. Also sample data for inter-arrival times, service times, number of cores per task and waiting times of HPC of Karelian Research Centre are included, measurements took place from 06/03/2009 to 02/30/2011. Functions provided to import/export workload traces in Standard Workload Format (swf). Stability condition of the model may be verified either exactly, or approximately. Stability analysis: see Rumyantsev and Morozov (2017) <doi:10.1007/s10479-015-1917-2>, workload recursion: see Rumyantsev (2014) <doi:10.1109/PDCAT.2014.36>.

Last updated 2 years ago

1.00 score 1 stars 10 scripts 247 downloads

saws - Small-Sample Adjustments for Wald Tests Using Sandwich Estimators

Tests coefficients with sandwich estimator of variance and with small samples. Regression types supported are gee, linear regression, and conditional logistic regression.

Last updated 3 years ago

1.00 score 12 scripts 208 downloads

ORIClust - Order-Restricted Information Criterion-Based Clustering Algorithm

A user-friendly R-based software package for gene clustering. Clusters are given by genes matched to prespecified profiles across various ordered treatment groups. It is particularly useful for analyzing data obtained from short time-course or dose-response microarray experiments.

Last updated 3 years ago

1.00 score 2 scripts 247 downloads

HDOMDesign - High-Dimensional Orthogonal Maximin Distance Designs

Contains functions to construct high-dimensional orthogonal maximin distance designs in two, four, eight, and sixteen levels from rotating the Kronecker product of sub-Hadamard matrices.

Last updated 3 years ago

1.00 score 96 downloads

packMBPLSDA - Multi-Block Partial Least Squares Discriminant Analysis

Several functions are provided to implement a MBPLSDA : components search, optimal model components number search, optimal model validity test by permutation tests, observed values evaluation of optimal model parameters and predicted categories, bootstrap values evaluation of optimal model parameters and predicted cross-validated categories. The use of this package is described in Brandolini-Bunlon et al (2019. Multi-block PLS discriminant analysis for the joint analysis of metabolomic and epidemiological data. Metabolomics, 15(10):134).

Last updated 3 years ago

1.00 score 3 scripts 144 downloads

leapp - Latent Effect Adjustment After Primary Projection

These functions take a gene expression value matrix, a primary covariate vector, an additional known covariates matrix. A two stage analysis is applied to counter the effects of latent variables on the rankings of hypotheses. The estimation and adjustment of latent effects are proposed by Sun, Zhang and Owen (2011). "leapp" is developed in the context of microarray experiments, but may be used as a general tool for high throughput data sets where dependence may be involved.

Last updated 3 years ago

1.00 score 9 scripts 180 downloads

ExcessMass - Excess Mass Calculation and Plots

Implementation of a function which calculates the empirical excess mass for given \eqn{\lambda} and given maximal number of modes (excessm()). Offering powerful plot features to visualize empirical excess mass (exmplot()). This includes the possibility of drawing several plots (with different maximal number of modes / cut off values) in a single graph.

Last updated 3 years ago

1.00 score 7 scripts 118 downloads

UNPaC - Non-Parametric Cluster Significance Testing with Reference to a Unimodal Null Distribution

Assess the significance of identified clusters and estimates the true number of clusters by comparing the explained variation due to the clustering from the original data to that produced by clustering a unimodal reference distribution which preserves the covariance structure in the data. The reference distribution is generated using kernel density estimation and a Gaussian copula framework. A dimension reduction strategy and sparse covariance estimation optimize this method for the high-dimensional, low-sample size setting. This method is described in Helgeson, Vock, and Bair (2021) <doi:10.1111/biom.13376>.

Last updated 3 years ago

1.00 score 142 downloads

SCBiclust - Identifies Mean, Variance, and Hierarchically Clustered Biclusters

Identifies a bicluster, a submatrix of the data such that the features and observations within the submatrix differ from those not contained in submatrix, using a two-step method. In the first step, observations in the bicluster are identified to maximize the sum of weighted between cluster feature differences. The method is described in Helgeson et al. (2020) <doi:10.1111/biom.13136>. 'SCBiclust' can be used to identify biclusters which differ based on feature means, feature variances, or more general differences.

Last updated 3 years ago

1.00 score 153 downloads

seedCCA - Seeded Canonical Correlation Analysis

Functions for dimension reduction through the seeded canonical correlation analysis are provided. A classical canonical correlation analysis (CCA) is one of useful statistical methods in multivariate data analysis, but it is limited in use due to the matrix inversion for large p small n data. To overcome this, a seeded CCA has been proposed in Im, Gang and Yoo (2015) \doi{10.1002/cem.2691}. The seeded CCA is a two-step procedure. The sets of variables are initially reduced by successively projecting cov(X,Y) or cov(Y,X) onto cov(X) and cov(Y), respectively, without loss of information on canonical correlation analysis, following Cook, Li and Chiaromonte (2007) \doi{10.1093/biomet/asm038} and Lee and Yoo (2014) \doi{10.1111/anzs.12057}. Then, the canonical correlation is finalized with the initially-reduced two sets of variables.

Last updated 3 years ago

1.00 score 9 scripts 171 downloads

gCat - Graph-Based Two-Sample Tests for Categorical Data

These are two-sample tests for categorical data utilizing similarity information among the categories. They are useful when there is underlying structure on the categories.

Last updated 3 years ago

cpp

1.00 score 1 stars 3 scripts 196 downloads

cpa - Confirmatory Path Analysis Through 'd-sep' Tests

Functions to test and compare causal models using Confirmatory Path Analysis.

Last updated 3 years ago

1.00 score 2 scripts 211 downloads

SMNCensReg - Fitting Univariate Censored Regression Model Under the Family of Scale Mixture of Normal Distributions

Fit univariate right, left or interval censored regression model under the scale mixture of normal distributions.

Last updated 3 years ago

1.00 score 4 scripts 219 downloads

DBNMFrank - Rank Selection for Non-Negative Matrix Factorization

Given the non-negative data and its distribution, the package estimates the rank parameter for Non-negative Matrix Factorization. The method is based on hypothesis testing, using a deconvolved bootstrap distribution to assess the significance level accurately despite the large amount of optimization error. The distribution of the non-negative data can be either Normal distributed or Poisson distributed.

Last updated 3 years ago

1.00 score 144 downloads

modesto - Modeling and Analysis of Stochastic Systems

Compute important quantities when we consider stochastic systems that are observed continuously. Such as, Cost model, Limiting distribution, Transition matrix, Transition distribution and Occupancy matrix. The methods are described, for example, Ross S. (2014), Introduction to Probability Models. Eleven Edition. Academic Press.

Last updated 3 years ago

cpp

1.00 score 17 scripts 145 downloads

PUPMSI - Moisture Sorption Isotherm Modeling Program

Contains sixteen moisture sorption isotherm models, which evaluate the fitness of adsorption and desorption curves for further understanding of the relationship between moisture content and water activity. Fitness evaluation is conducted through parameter estimation and error analysis. Moreover, graphical representation, hysteresis area estimation, and isotherm classification through the equation of Blahovec & Yanniotis (2009) <doi:10.1016/j.jfoodeng.2008.08.007> which is based on the classification system introduced by Brunauer et. al. (1940) <doi:10.1021/ja01864a025> are also included for the visualization of models and hysteresis.

Last updated 3 years ago

1.00 score 119 downloads

cccm - Crossed Classification Credibility Model

Calculates the credit debt for the next period based on the available data using the cross-classification credibility model.

Last updated 3 years ago

1.00 score 137 downloads

BondValuation - Fixed Coupon Bond Valuation Allowing for Odd Coupon Periods and Various Day Count Conventions

Analysis of large datasets of fixed coupon bonds, allowing for irregular first and last coupon periods and various day count conventions. With this package you can compute the yield to maturity, the modified and MacAulay durations and the convexity of fixed-rate bonds. It provides the function AnnivDates, which can be used to evaluate the quality of the data and return time-invariant properties and temporal structure of a bond.

Last updated 3 years ago

cpp

1.00 score 8 scripts 192 downloads

HBSTM - Hierarchical Bayesian Space-Time Models for Gaussian Space-Time Data

Fits Hierarchical Bayesian space-Time models for Gaussian data. Furthermore, its functions have been implemented for analysing the fitting qualities of those models.

Last updated 3 years ago

1.00 score 1 stars 6 scripts 153 downloads

cmenet - Bi-Level Selection of Conditional Main Effects

Provides functions for implementing cmenet - a bi-level variable selection method for conditional main effects (see Mak and Wu (2018) <doi:10.1080/01621459.2018.1448828>). CMEs are reparametrized interaction effects which capture the conditional impact of a factor at a fixed level of another factor. Compared to traditional two-factor interactions, CMEs can quantify more interpretable interaction effects in many problems. The current implementation performs variable selection on only binary CMEs; we are working on an extension for the continuous setting.

Last updated 3 years ago

cpp

1.00 score 9 scripts 173 downloads

OPTtesting - Optimal Testing

Optimal testing under general dependence. The R package implements procedures proposed in Wang, Han, and Tong (2022). The package includes parameter estimation procedures, the computation for the posterior probabilities, and the testing procedure.

Last updated 3 years ago

1.00 score 116 downloads

GAIPE - Graphical Extension with Accuracy in Parameter Estimation (GAIPE)

Implements graphical extension with accuracy in parameter estimation (AIPE) on RMSEA for sample size planning in structural equation modeling based on Lin, T.-Z. & Weng, L.-J. (2014) <doi: 10.1080/10705511.2014.915380>. And, it can also implement AIPE on RMSEA and power analysis on RMSEA.

Last updated 3 years ago

1.00 score 4 scripts 155 downloads

spc4sts - Statistical Process Control for Stochastic Textured Surfaces

Provides statistical process control tools for stochastic textured surfaces. The current version supports the following tools: (1) generic modeling of stochastic textured surfaces. (2) local defect monitoring and diagnostics in stochastic textured surfaces, which was proposed by Bui and Apley (2018a) <doi:10.1080/00401706.2017.1302362>. (3) global change monitoring in the nature of stochastic textured surfaces, which was proposed by Bui and Apley (2018b) <doi:10.1080/00224065.2018.1507559>. (4) computation of dissimilarity matrix of stochastic textured surface images, which was proposed by Bui and Apley (2019b) <doi:10.1016/j.csda.2019.01.019>.

Last updated 3 years ago

1.00 score 16 scripts 242 downloads

wowa - Weighted Ordered Weighted Average

Introduce weights into Ordered Weighted Averages and extend bivariate means based on n-ary tree construction. Please refer to the following: G. Beliakov, H. Bustince, and T. Calvo (2016, ISBN: 978-3-319-24753-3), G. Beliakov(2018) <doi:10.1002/int.21913>, G. Beliakov, J.J. Dujmovic (2016) <doi:10.1016/j.ins.2015.10.040>, J.J. Dujmovic and G. Beliakov (2017) <doi:10.1002/int.21828>.

Last updated 3 years ago

cpp

1.00 score 148 downloads

BootWPTOS - Test Stationarity using Bootstrap Wavelet Packet Tests

Provides significance tests for second-order stationarity for time series using bootstrap wavelet packet tests. Provides functionality to visualize the time series with the results of the hypothesis tests superimposed. The methodology is described in Cardinali, A and Nason, G P (2016) "Practical powerful wavelet packet tests for second-order stationarity." Applied and Computational Harmonic Analysis, 44, 558-585 <doi:10.1016/j.acha.2016.06.006>.

Last updated 3 years ago

1.00 score 7 scripts 175 downloads

GEInter - Robust Gene-Environment Interaction Analysis

Description: For the risk, progression, and response to treatment of many complex diseases, it has been increasingly recognized that gene-environment interactions play important roles beyond the main genetic and environmental effects. In practical interaction analyses, outliers in response variables and covariates are not uncommon. In addition, missingness in environmental factors is routinely encountered in epidemiological studies. The developed package consists of five robust approaches to address the outliers problems, among which two approaches can also accommodate missingness in environmental factors. Both continuous and right censored responses are considered. The proposed approaches are based on penalization and sparse boosting techniques for identifying important interactions, which are realized using efficient algorithms. Beyond the gene-environment analysis, the developed package can also be adopted to conduct analysis on interactions between other types of low-dimensional and high-dimensional data. (Mengyun Wu et al (2017), <doi:10.1080/00949655.2018.1523411>; Mengyun Wu et al (2017), <doi:10.1002/gepi.22055>; Yaqing Xu et al (2018), <doi:10.1080/00949655.2018.1523411>; Yaqing Xu et al (2019), <doi:10.1016/j.ygeno.2018.07.006>; Mengyun Wu et al (2021), <doi:10.1093/bioinformatics/btab318>).

Last updated 3 years ago

1.00 score 1 scripts 208 downloads

DEM - The Distributed EM Algorithms in Multivariate Gaussian Mixture Models

The distributed expectation maximization algorithms are used to solve parameters of multivariate Gaussian mixture models. The philosophy of the package is described in Guo, G. (2022) <doi:10.1080/02664763.2022.2053949>.

Last updated 3 years ago

1.00 score 3 scripts 173 downloads

PhageCocktail - Design of the Best Phage Cocktail

There are 4 possible methods: "ExhaustiveSearch"; "ExhaustivePhi"; "ClusteringSearch"; and "ClusteringPhi". "ExhaustiveSearch"--> gives you the best phage cocktail from a phage-bacteria infection network. It checks different phage cocktail sizes from 1 to 7 and only stops before if it lyses all bacteria. Other option is when users have decided not to obtain a phage cocktail size higher than a limit value. "ExhaustivePhi"--> firstly, it finds Phi out. Phi is a formula indicating the necessary phage cocktail size. Phi needs nestedness temperature and fill, which are internally calculated. This function will only look for the best combination (phage cocktail) with a Phi size. "ClusteringSearch"--> firstly, an agglomerative hierarchical clustering using Ward's algorithm is calculated for phages. They will be clustered according to bacteria lysed by them. PhageCocktail() chooses how many clusters are needed in order to select 1 phage per cluster. Using the phages selected during the clustering, it checks different phage cocktail sizes from 1 to 7 and only stops before if it lyses all bacteria. Other option is when users have decided not to obtain a phage cocktail size higher than a limit value. "ClusteringPhi"--> firstly, an agglomerative hierarchical clustering using Ward's algorithm is calculated for phages. They will be clustered according to bacteria lysed by them. PhageCocktail() chooses how many clusters are needed in order to select 1 phage per cluster. Once the function has one phage per cluster, it calculates Phi. If the number of clusters is less than Phi number, it will be changed to obtain, as minimum, this quantity of candidates (phages). Then, it calculates the best combination of Phi phages using those selected during the clustering with Ward algorithm. If you use PhageCocktail, please cite it as: "PhageCocktail: An R Package to Design Phage Cocktails from Experimental Phage-Bacteria Infection Networks". María Victoria Díaz-Galián, Miguel A. Vega-Rodríguez, Felipe Molina. Computer Methods and Programs in Biomedicine, 221, 106865, Elsevier Ireland, Clare, Ireland, 2022, pp. 1-9, ISSN: 0169-2607. <doi:10.1016/j.cmpb.2022.106865>.

Last updated 3 years ago

1.00 score 1 stars 214 downloads

modQR - Multiple-Output Directional Quantile Regression

Contains basic tools for performing multiple-output quantile regression and computing regression quantile contours by means of directional regression quantiles. In the location case, one can thus obtain halfspace depth contours in two to six dimensions. Hallin, M., Paindaveine, D. and Šiman, M. (2010) Multivariate quantiles and multiple-output regression quantiles: from L1 optimization to halfspace depth. Annals of Statistics 38, 635-669 For more references about the method, see Help pages.

Last updated 3 years ago

1.00 score 5 scripts 609 downloads

RankResponse - Ranking Responses in a Single Response Question or a Multiple Response Question

Methods for ranking responses of a single response question or a multiple response question are described in the two papers: 1. Wang, H. (2008). Ranking Responses in Multiple-Choice Questions. Journal of Applied Statistics, 35, 465-474. <DOI:10.1080/02664760801924533> 2. Wang, H. and Huang, W. H. (2014). Bayesian Ranking Responses in Multiple Response Questions. Journal of the Royal Statistical Society: Series A (Statistics in Society), 177, 191-208. <DOI:10.1111/rssa.12009>.

Last updated 3 years ago

1.00 score 7 scripts 223 downloads

SECP - Statistical Estimation of Cluster Parameters

Estimating parameters of site clusters on 2D & 3D square lattice with various lattice sizes, relative fractions of open sites (occupation probability), iso- & anisotropy, von Neumann & Moore (1,d)-neighborhoods, described by Moskalev P.V. et al. (2011) <arXiv:1105.2334v1>.

Last updated 3 years ago

1.00 score 8 scripts 140 downloads

GeneF - Package for Generalized F-Statistics

Implementation of several generalized F-statistics. The current version includes a generalized F-statistic based on the flexible isotonic/monotonic regression or order restricted hypothesis testing. Based on: Y. Lai (2011) <doi:10.1371/journal.pone.0019754>.

Last updated 3 years ago

1.00 score 2 scripts 228 downloads

ZINARp - Simulate INAR/ZINAR(p) Models and Estimate Its Parameters

Simulation, exploratory data analysis and Bayesian analysis of the p-order Integer-valued Autoregressive (INAR(p)) and Zero-inflated p-order Integer-valued Autoregressive (ZINAR(p)) processes, as described in Garay et al. (2020) <doi:10.1080/00949655.2020.1754819>.

Last updated 3 years ago

1.00 score 154 downloads

Voss - Generic Voss Algorithm (Random Sequential Additions)

Generating realizations of a fractal Brownian function on uniform 1D & 2D grid with classic and generic versions of the Voss algorithm (random sequential additions).

Last updated 3 years ago

1.00 score 6 scripts 135 downloads

pcmabc - Approximate Bayesian Computations for Phylogenetic Comparative Methods

Fits by ABC, the parameters of a stochastic process modelling the phylogeny and evolution of a suite of traits following the tree. The user may define an arbitrary Markov process for the trait and phylogeny. Importantly, trait-dependent speciation models are handled and fitted to data. See K. Bartoszek, P. Lio' (2019) <doi:10.5506/APhysPolBSupp.12.25>. The suggested geiger package can be obtained from CRAN's archive <https://cran.r-project.org/src/contrib/Archive/geiger/>, suggested to take latest version. Otherwise its required code is present in the pcmabc package. The suggested distory package can be obtained from CRAN's archive <https://cran.r-project.org/src/contrib/Archive/distory/>, suggested to take latest version.

Last updated 3 years ago

1.00 score 8 scripts 221 downloads

RIFS - Random Iterated Function System

Pointwise generation and display of attractors (prefractals) of the random iterated function system (RIFS) for various combinations of probabilistic and geometric parameters of some fixed point sets (protofractals), described by Bukhovets A.G. (2012) <doi:10.1134/S0005117912020154>.

Last updated 3 years ago

1.00 score 4 scripts 203 downloads

NPHMC - Sample Size Calculation for the Proportional Hazards Mixture Cure Model

An R-package for calculating sample size of a survival trial with or without cure fractions.

Last updated 3 years ago

1.00 score 4 scripts 222 downloads

InspectChangepoint - High-Dimensional Changepoint Estimation via Sparse Projection

Provides a data-driven projection-based method for estimating changepoints in high-dimensional time series. Multiple changepoints are estimated using a (wild) binary segmentation scheme.

Last updated 3 years ago

1.00 score 1 stars 33 scripts 234 downloads

LTPDvar - LTPD and AOQL Plans for Acceptance Sampling Inspection by Variables

Calculation of rectifying LTPD and AOQL plans for sampling inspection by variables which minimize mean inspection cost per lot of process average quality.

Last updated 3 years ago

1.00 score 10 scripts 188 downloads

semicmprskcoxmsm - Use Inverse Probability Weighting to Estimate Treatment Effect for Semi Competing Risks Data

Use inverse probability weighting methods to estimate treatment effect under marginal structure model (MSM) for the transition hazard of semi competing risk data, i.e. illness death model. We implement two specific such models, the usual Markov illness death structural model and the general Markov illness death structural model. We also provide the predicted three risks functions from the marginal structure models. Zhang, Y. and Xu, R. (2022) <arXiv:2204.10426>.

Last updated 3 years ago

1.00 score 127 downloads

LinCal - Static Univariate Frequentist and Bayesian Linear Calibration

Estimate and confidence/credible intervals for an unknown regressor x0 given an observed y0.

Last updated 3 years ago

1.00 score 8 scripts 167 downloads

SPOUSE - Scatter Plots Over-Viewed Using Summary Ellipses

Summary ellipses superimposed on a scatter plot contain all bi-variate summary statistics for regression analysis. Furthermore, the outer ellipse flags potential outliers. Multiple groups can be compared in terms of centers and spreads as illustrated in the examples.

Last updated 3 years ago

1.00 score 149 downloads

ei.Datasets - Real Datasets for Assessing Ecological Inference Algorithms

Provides more than 550 data sets of actual election results. Each of the data sets includes aggregate party and candidate outcomes at the voting unit (polling stations) level and two-way cross-tabulated results at the district level. These data sets can be used to assess ecological inference algorithms devised for estimating RxC (global) ecological contingency tables using exclusively aggregate results from voting units. Reference: Pavía (2022) <doi:10.1177/08944393211040808>.

Last updated 3 years ago

1.00 score 184 downloads

cellVolumeDist - Functions to Fit Cell Volume Distributions and Thereby Estimate Cell Growth Rates and Division Times

Implements a methodology for using cell volume distributions to estimate cell growth rates and division times that is described in the paper entitled, "Cell Volume Distributions Reveal Cell Growth Rates and Division Times", by Michael Halter, John T. Elliott, Joseph B. Hubbard, Alessandro Tona and Anne L. Plant, which is in press in the Journal of Theoretical Biology. In order to reproduce the analysis used to obtain Table 1 in the paper, execute the command "example(fitVolDist)".

Last updated 3 years ago

1.00 score 3 scripts 212 downloads

msae - Multivariate Fay Herriot Models for Small Area Estimation

Implements multivariate Fay-Herriot models for small area estimation. It uses empirical best linear unbiased prediction (EBLUP) estimator. Multivariate models consider the correlation of several target variables and borrow strength from auxiliary variables to improve the effectiveness of a domain sample size. Models which accommodated by this package are univariate model with several target variables (model 0), multivariate model (model 1), autoregressive multivariate model (model 2), and heteroscedastic autoregressive multivariate model (model 3). Functions provide EBLUP estimators and mean squared error (MSE) estimator for each model. These models were developed by Roberto Benavent and Domingo Morales (2015) <doi:10.1016/j.csda.2015.07.013>.

Last updated 3 years ago

1.00 score 213 downloads

Rivivc - In Vitro in Vivo Correlation Linear Level "A"

It is devoted to the IVIVC linear level A with numerical deconvolution method. The latter is working for inequal and incompatible timepoints between impulse and response curves. A numerical convolution method is also available. Application domains include pharamaceutical industry QA/QC and R&D together with academic research.

Last updated 3 years ago

1.00 score 3 scripts 138 downloads

HCT - Calculates Significance Criteria and Power for a Single Arm Trial

Given a database of previous treatment/placebo estimates, their standard errors and sample sizes, the program calculates a significance criteria and power estimate that takes into account the among trial variation.

Last updated 3 years ago

1.00 score 6 scripts 172 downloads

refreg - Conditional Multivariate Reference Regions

An R package for estimating conditional multivariate reference regions. The reference region is non parametrically estimated using a kernel density estimator. Covariates effects on the multivariate response means vector and variance-covariance matrix, thus on the region shape, are estimated by flexible additive predictors. Continuous covariates non linear effects might be estimated using penalized splines smoothers. Confidence intervals for the covariates estimated effects might be derived from bootstrap resampling. Kernel density bandwidth can be estimated with different methods, including a method that optimize the region coverage. Numerical, and graphical, summaries can be obtained by the user in order to evaluate reference region performance with real data. Full mathematical details can be found in <doi:10.1002/sim.9163> and <doi:10.1007/s00477-020-01901-1>.

Last updated 3 years ago

1.00 score 4 scripts 185 downloads

gte - Generalized Turnbull's Estimator

Generalized Turnbull's estimator proposed by Dehghan and Duchesne (2011).

Last updated 3 years ago

1.00 score 5 scripts 177 downloads

frequentistSSD - Screened Selection Design with Survival Endpoints

A study based on the screened selection design (SSD) is an exploratory phase II randomized trial with two or more arms but without concurrent control. The primary aim of the SSD trial is to pick a desirable treatment arm (e.g., in terms of the median survival time) to recommend to the subsequent randomized phase IIb (with the concurrent control) or phase III. Though The survival endpoint is often encountered in phase II trials, the existing SSD methods cannot deal with the survival endpoint. Furthermore, the existing SSD won’t control the type I error rate. The proposed designs can “partially” control or provide the empirical type I error/false positive rate by an optimal algorithm (implemented by the optimal() function) for each arm. All the design needed components (sample size, operating characteristics) are supported.

Last updated 3 years ago

1.00 score 193 downloads

caribou - Estimation of Caribou Abundance Based on Radio Telemetry Data

Estimation of population size of migratory caribou herds based on large scale aggregations monitored by radio telemetry. It implements the methodology found in the article by Rivest et al. (1998) about caribou abundance estimation. It also includes a function based on the Lincoln-Petersen Index as applied to radio telemetry data by White and Garrott (1990).

Last updated 3 years ago

1.00 score 8 scripts 272 downloads

funLBM - Model-Based Co-Clustering of Functional Data

The funLBM algorithm allows to simultaneously cluster the rows and the columns of a data matrix where each entry of the matrix is a function or a time series.

Last updated 3 years ago

1.00 score 7 scripts 197 downloads

dstat2x2xk - Demonstrated Insensitivity to Bias in 2x2xK Contingency Tables

For an observational study with binary treatment, binary outcome and K strata, implements a d-statistic that uses those strata most insensitive to unmeasured bias in treatment assignment.<doi:10.1093/biomet/asaa032> The package has one function, dstat2x2xk.

Last updated 3 years ago

1.00 score 210 downloads

DOEM - The Distributed Online Expectation Maximization Algorithms to Solve Parameters of Poisson Mixture Models

The distributed online expectation maximization algorithms are used to solve parameters of Poisson mixture models. The philosophy of the package is described in Guo, G. (2022) <doi:10.1080/02664763.2022.2053949>.

Last updated 3 years ago

1.00 score 1 scripts 142 downloads

LocKer - Locally Sparse Estimator of Generalized Varying Coefficient Model for Asynchronous Longitudinal Data

Locally sparse estimator of generalized varying coefficient model for asynchronous longitudinal data by kernel-weighted estimating equation.

Last updated 3 years ago

1.00 score 171 downloads

BRACoD.R - BRACoD: Bayesian Regression Analysis of Compositional Data

The goal of this method is to identify associations between bacteria and an environmental variable in 16S or other compositional data. The environmental variable is any variable which is measure for each microbiome sample, for example, a butyrate measurement paired with every sample in the data. Microbiome data is compositional, meaning that the total abundance of each sample sums to 1, and this introduces severe statistical distortions. This method takes a Bayesian approach to correcting for these statistical distortions, in which the total abundance is treated as an unknown variable. This package runs the python implementation using reticulate.

Last updated 3 years ago

1.00 score 1 scripts 167 downloads

dagwood - DAGs with Omitted Objects Displayed (DAGWOOD)

DAGs With Omitted Objects Displayed (DAGWOOD) is a framework to help reveal key hidden assumptions in a causal DAG. This package provides an implementation of the DAGWOOD algorithm. Further description can be found in Haber et al (2022) <DOI:10.1016/j.annepidem.2022.01.001>.

Last updated 3 years ago

1.00 score 180 downloads

tailTransform - Symmetric Transformation of Tails for Plotting Differences

When plotting treated-minus-control differences, after-minus-before changes, or difference-in-differences, the ttrans() function symmetrically transforms the positive and negative tails to aid plotting. The package includes an observational study with three control groups and an unaffected outcome; see Rosenbaum (2020) <doi:10.1111/biom.13558>.

Last updated 3 years ago

1.00 score 210 downloads

disprose - Discriminating Probes Selection

Set of tools for molecular probes selection and design of a microarray, e.g. the assessment of physical and chemical properties, blast performance, selection according to sensitivity and selectivity. Methods used in package are described in: Lorenz R., Stephan H.B., Höner zu Siederdissen C. et al. (2011) <doi:10.1186/1748-7188-6-26>; Camacho C., Coulouris G., Avagyan V. et al. (2009) <doi:10.1186/1471-2105-10-421>.

Last updated 3 years ago

1.00 score 250 downloads

mcount - Marginalized Count Regression Models

Implementation of marginalized models for zero-inflated count data. This package provides a tool to implement an estimation algorithm for the marginalized count models, which directly makes inference on the effect of each covariate on the marginal mean of the outcome. The method involves the marginalized zero-inflated Poisson model described in Long et al. (2014) <doi:10.1002/sim.6293>.

Last updated 3 years ago

1.00 score 126 downloads

msaeHB - Multivariate Small Area Estimation using Hierarchical Bayesian Method

Implements area level of multivariate small area estimation using Hierarchical Bayesian method under Normal and T distribution. The 'rjags' package is employed to obtain parameter estimates. For the reference, see Rao and Molina (2015) <doi:10.1002/9781118735855>.

Last updated 3 years ago

jagscpp

1.00 score 153 downloads

nparMD - Nonparametric Analysis of Multivariate Data in Factorial Designs

Analysis of multivariate data with two-way completely randomized factorial design. The analysis is based on fully nonparametric, rank-based methods and uses test statistics based on the Dempster's ANOVA, Wilk's Lambda, Lawley-Hotelling and Bartlett-Nanda-Pillai criteria. The multivariate response is allowed to be ordinal, quantitative, binary or a mixture of the different variable types. The package offers two functions performing the analysis, one for small and the other for large sample sizes. The underlying methodology is largely described in Bathke and Harrar (2016) <doi:10.1007/978-3-319-39065-9_7> and in Munzel and Brunner (2000) <doi:10.1016/S0378-3758(99)00212-8>.

Last updated 3 years ago

1.00 score 6 scripts 197 downloads

LSWPlib - Simulation and Spectral Estimation of Locally Stationary Wavelet Packet Processes

Library of functions for the statistical analysis and simulation of Locally Stationary Wavelet Packet (LSWP) processes. The methods implemented by this library are described in Cardinali and Nason (2017) <doi:10.1111/jtsa.12230>.

Last updated 3 years ago

1.00 score 238 downloads

OSDR - Finds an Optimal System of Distinct Representatives

Provides routines for finding an Optimal System of Distinct Representatives (OSDR), as defined by D.Gale (1968) <doi:10.1016/S0021-9800(68)80039-0>.

Last updated 3 years ago

1.00 score 5 scripts 233 downloads

uwedragon - Data Research, Access, Governance Network : Statistical Disclosure Control

A tool for checking how much information is disclosed when reporting summary statistics.

Last updated 3 years ago

1.00 score 124 downloads

cif - Cointegrated ICU Forecasting

Set of forecasting tools to predict ICU beds using a Vector Error Correction model with a single cointegrating vector. Method described in Berta, P. Lovaglio, P.G. Paruolo, P. Verzillo, S., 2020. "Real Time Forecasting of Covid-19 Intensive Care Units demand" Health, Econometrics and Data Group (HEDG) Working Papers 20/16, HEDG, Department of Economics, University of York, <https://www.york.ac.uk/media/economics/documents/hedg/workingpapers/2020/2016.pdf>.

Last updated 3 years ago

1.00 score 3 scripts 175 downloads

MultEq - Multiple Equivalence Tests and Simultaneous Confidence Intervals

Equivalence tests and related confidence intervals for the comparison of two treatments, simultaneously for one or many normally distributed, primary response variables (endpoints). The step-up procedure of Quan et al. (2001) is both applied for differences and extended to ratios of means. A related single-step procedure is also available.

Last updated 3 years ago

1.00 score 6 scripts 191 downloads

adana - Adaptive Nature-Inspired Algorithms for Hybrid Genetic Optimization

The Genetic Algorithm (GA) is a type of optimization method of Evolutionary Algorithms. It uses the biologically inspired operators such as mutation, crossover, selection and replacement.Because of their global search and robustness abilities, GAs have been widely utilized in machine learning, expert systems, data science, engineering, life sciences and many other areas of research and business. However, the regular GAs need the techniques to improve their efficiency in computing time and performance in finding global optimum using some adaptation and hybridization strategies. The adaptive GAs (AGA) increase the convergence speed and success of regular GAs by setting the parameters crossover and mutation probabilities dynamically. The hybrid GAs combine the exploration strength of a stochastic GAs with the exact convergence ability of any type of deterministic local search algorithms such as simulated-annealing, in addition to other nature-inspired algorithms such as ant colony optimization, particle swarm optimization etc. The package 'adana' includes a rich working environment with its many functions that make possible to build and work regular GA, adaptive GA, hybrid GA and hybrid adaptive GA for any kind of optimization problems. Cebeci, Z. (2021, ISBN: 9786254397448).

Last updated 3 years ago

1.00 score 6 scripts 286 downloads

SOPIE - Non-Parametric Estimation of the Off-Pulse Interval of a Pulsar

Provides functions to non-parametrically estimate the off-pulse interval of a source function originating from a pulsar. The technique is based on a sequential application of P-values obtained from goodness-of-fit tests for the uniform distribution, such as the Kolmogorov-Smirnov, Cramer-von Mises, Anderson-Darling and Rayleigh goodness-of-fit tests.

Last updated 3 years ago

1.00 score 10 scripts 187 downloads

evident - Evidence Factors in Observational Studies

Contains a collection of examples of evidence factors in observational studies from the book Replication and Evidence Factors in Observational Studies by Paul R. Rosenbaum (2021) <doi:10.1201/9781003039648>.

Last updated 3 years ago

1.00 score 1 scripts 150 downloads

BSPADATA - Bayesian Proposal to Fit Spatial Econometric Models

The purpose of this package is to fit the three Spatial Econometric Models proposed in Anselin (1988, ISBN:9024737354) in the homoscedastic and the heteroscedatic case. The fit is made through MCMC algorithms and observational working variables approach.

Last updated 3 years ago

1.00 score 8 scripts 187 downloads

DArand - Differential Analysis with Random Reference Genes

Differential Analysis of short RNA transcripts that can be modeled by either Poisson or Negative binomial distribution. The statistical methodology implemented in this package is based on the random selection of references genes (Desaulle et al. (2021) <arXiv:2103.09872>).

Last updated 3 years ago

1.00 score 168 downloads

KFPCA - Kendall Functional Principal Component Analysis

Implementation for Kendall functional principal component analysis. Kendall functional principal component analysis is a robust functional principal component analysis technique for non-Gaussian functional/longitudinal data. The crucial function of this package is KFPCA() and KFPCA_reg(). Moreover, least square estimates of functional principal component scores are also provided. Refer to Rou Zhong, Shishi Liu, Haocheng Li, Jingxiao Zhang. (2021) <arXiv:2102.01286>. Rou Zhong, Shishi Liu, Haocheng Li, Jingxiao Zhang. (2021) <doi:10.1016/j.jmva.2021.104864>.

Last updated 3 years ago

1.00 score 160 downloads

acca - A Canonical Correlation Analysis with Inferential Guaranties

It performs Canonical Correlation Analysis and provides inferential guaranties on the correlation components. The p-values are computed following the resampling method developed in Winkler, A. M., Renaud, O., Smith, S. M., & Nichols, T. E. (2020). Permutation inference for canonical correlation analysis. NeuroImage, <doi:10.1016/j.neuroimage.2020.117065>. Furthermore, it provides plotting tools to visualize the results.

Last updated 3 years ago

1.00 score 345 downloads

l1spectral - An L1-Version of the Spectral Clustering

Provides an l1-version of the spectral clustering algorithm devoted to robustly clustering highly perturbed graphs using l1-penalty. This algorithm is described with more details in the preprint C. Champion, M. Champion, M. Blazère, R. Burcelin and J.M. Loubes, "l1-spectral clustering algorithm: a spectral clustering method using l1-regularization" (2022).

Last updated 3 years ago

openblascpp

1.00 score 226 downloads

mbrdr - Model-Based Response Dimension Reduction

Functions for model-based response dimension reduction. Usual dimension reduction methods in multivariate regression focus on the reduction of predictors, not responses. The response dimension reduction is theoretically founded in Yoo and Cook (2008) <doi:10.1016/j.csda.2008.07.029>. Later, three model-based response dimension reduction approaches are proposed in Yoo (2016) <doi:10.1080/02331888.2017.1410152> and Yoo (2019) <doi:10.1016/j.jkss.2019.02.001>. The method by Yoo and Cook (2008) is based on non-parametric ordinary least squares, but the model-based approaches are done through maximum likelihood estimation. For two model-based response dimension reduction methods called principal fitted response reduction and unstructured principal fitted response reduction, chi-squared tests are provided for determining the dimension of the response subspace.

Last updated 3 years ago

1.00 score 264 downloads

icertool - Calculate and Plot ICER

The app will calculate the ICER (incremental cost-effectiveness ratio) Rawlins (2012) <doi:10.1016/B978-0-7020-4084-9.00044-6> from the mean costs and quality-adjusted life years (QALY) Torrance and Feeny (2009) <doi:10.1017/S0266462300008461> for a set of treatment options, and draw the efficiency frontier in the costs-effectiveness plane. The app automatically identifies and excludes dominated and extended-dominated options from the ICER calculation.

Last updated 3 years ago

1.00 score 135 downloads

polimetrics - R Tools for Political Measures

This is a collection of data and functions for common metrics in political science research. Data measuring ideology, and functions calculating geographical diffusion and ideological diffusion - geog.diffuse() and ideo.dist(), respectively. Functions derived from methods developed in: Soule and King (2006) <doi:10.1086/499908>, Berry et al. (1998) <doi:10.2307/2991759>, Cruz-Aceves and Mallinson (2019) <doi:10.1177/0160323X20902818>, and Grossback et al. (2004) <doi:10.1177/1532673X04263801>.

Last updated 3 years ago

1.00 score 161 downloads

supercompress - Supervised Compression of Big Data

A supervised compression method that incorporates the response for reducing big data to a carefully selected subset. Please see Joseph and Mak (2021) <doi:10.1002/sam.11508>. This research is supported by a U.S. National Science Foundation (NSF) grant CMMI-1921646.

Last updated 3 years ago

1.00 score 1 stars 164 downloads

GEInfo - Gene-Environment Interaction Analysis Incorporating Prior Information

Realize three approaches for Gene-Environment interaction analysis. All of them adopt Sparse Group Minimax Concave Penalty to identify important G variables and G-E interactions, and simultaneously respect the hierarchy between main G and G-E interaction effects. All the three approaches are available for Linear, Logistic, and Poisson regression. Also realize to mine and construct prior information for G variables and G-E interactions.

Last updated 3 years ago

1.00 score 126 downloads

logitFD - Functional Principal Components Logistic Regression

Functions for fitting a functional principal components logit regression model in four different situations: ordinary and filtered functional principal components of functional predictors, included in the model according to their variability explanation power, and according to their prediction ability by stepwise methods. The proposed methods were developed in Escabias et al (2004) <doi:10.1080/10485250310001624738> and Escabias et al (2005) <doi:10.1016/j.csda.2005.03.011>.

Last updated 3 years ago

1.00 score 2 scripts 112 downloads

plfMA - A GUI to View, Design and Export Various Graphs of Data

Provides a graphical user interface for viewing and designing various types of graphs of the data. The graphs can be saved in different formats of an image.

Last updated 3 years ago

1.00 score 176 downloads

phd - Permutation Testing in High-Dimensional Linear Models

Provides permutation methods for testing in high-dimensional linear models. The tests are often robust against heteroscedasticity and non-normality and usually perform well under anti-sparsity. See Hemerik, Thoresen and Finos (2021) <doi:10.1080/00949655.2020.1836183>.

Last updated 3 years ago

1.00 score 3 scripts 161 downloads

vdar - Discriminant Analysis Incorporating Individual Uncertainties

The qda() function from package 'MASS' is extended to calculate a weighted linear (LDA) and quadratic discriminant analysis (QDA) by changing the group variances and group means based on cell-wise uncertainties. The uncertainties can be derived e.g. through relative errors for each individual measurement (cell), not only row-wise or column-wise uncertainties. The method can be applied compositional data (e.g. portions of substances, concentrations) and non-compositional data.

Last updated 3 years ago

1.00 score 145 downloads

MRCE - Multivariate Regression with Covariance Estimation

Compute and select tuning parameters for the MRCE estimator proposed by Rothman, Levina, and Zhu (2010) <doi:10.1198/jcgs.2010.09188>. This estimator fits the multiple output linear regression model with a sparse estimator of the error precision matrix and a sparse estimator of the regression coefficient matrix.

Last updated 3 years ago

1.00 score 1 stars 6 scripts 244 downloads

cogmapr - Cognitive Mapping Tools Based on Coding of Textual Sources

Functions for building cognitive maps based on qualitative data. Inputs are textual sources (articles, transcription of qualitative interviews of agents,...). These sources have been coded using relations and are linked to (i) a table describing the variables (or concepts) used for the coding and (ii) a table describing the sources (typology of agents, ...). Main outputs are Individual Cognitive Maps (ICM), Social Cognitive Maps (all sources or group of sources) and a list of quotes linked to relations. This package is linked to the work done during the PhD of Frederic M. Vanwindekens (CRA-W / UCL) hold the 13 of May 2014 at University of Louvain in collaboration with the Walloon Agricultural Research Centre (project MIMOSA, MOERMAN fund).

Last updated 3 years ago

graphrgraphviz

1.00 score 1 stars 1 scripts 197 downloads

abundant - High-Dimensional Principal Fitted Components and Abundant Regression

Fit and predict with the high-dimensional principal fitted components model. This model is described by Cook, Forzani, and Rothman (2012) <doi:10.1214/11-AOS962>.

Last updated 3 years ago

1.00 score 3 scripts 419 downloads

fat2Lpoly - Two-Locus Family-Based Association Test with Polytomous Outcome

Performs family-based association tests with a polytomous outcome under 2-locus and 1-locus models defined by some design matrix.

Last updated 3 years ago

1.00 score 6 scripts 197 downloads

CommonMean.Copula - Common Mean Vector under Copula Models

Estimate bivariate common mean vector under copula models with known correlation. In the current version, available copulas are the Clayton, Gumbel, Frank, Farlie-Gumbel-Morgenstern (FGM), and normal copulas. See Shih et al. (2019) <doi:10.1080/02331888.2019.1581782> and Shih et al. (2021) <under review> for details under the FGM and general copulas, respectively.

Last updated 3 years ago

1.00 score 3 scripts 234 downloads

rerandPower - Power and Sample Size Calculations for Completely Randomized and Rerandomized Experiments

Computes the power resulting from completely randomized and rerandomized experiments with two groups. Furthermore, computes the sample size necessary to obtain a desired level of power for completely randomized and rerandomized experiments.

Last updated 3 years ago

1.00 score 128 downloads

iSFun - Integrative Dimension Reduction Analysis for Multi-Source Data

The implement of integrative analysis methods based on a two-part penalization, which realizes dimension reduction analysis and mining the heterogeneity and association of multiple studies with compatible designs. The software package provides the integrative analysis methods including integrative sparse principal component analysis (Fang et al., 2018), integrative sparse partial least squares (Liang et al., 2021) and integrative sparse canonical correlation analysis, as well as corresponding individual analysis and meta-analysis versions. References: (1) Fang, K., Fan, X., Zhang, Q., and Ma, S. (2018). Integrative sparse principal component analysis. Journal of Multivariate Analysis, <doi:10.1016/j.jmva.2018.02.002>. (2) Liang, W., Ma, S., Zhang, Q., and Zhu, T. (2021). Integrative sparse partial least squares. Statistics in Medicine, <doi:10.1002/sim.8900>.

Last updated 3 years ago

1.00 score 37 scripts 138 downloads

nsp - Inference for Multiple Change-Points in Linear Models

Implementation of Narrowest Significance Pursuit, a general and flexible methodology for automatically detecting localised regions in data sequences which each must contain a change-point (understood as an abrupt change in the parameters of an underlying linear model), at a prescribed global significance level. Narrowest Significance Pursuit works with a wide range of distributional assumptions on the errors, and yields exact desired finite-sample coverage probabilities, regardless of the form or number of the covariates. For details, see P. Fryzlewicz (2021) <https://stats.lse.ac.uk/fryzlewicz/nsp/nsp.pdf>.

Last updated 3 years ago

1.00 score 2 scripts 147 downloads

rcDEA - Robust and Conditional Data Envelopment Analysis (DEA)

With this package we provide an easy method to compute robust and conditional Data Envelopment Analysis (DEA), Free Disposal Hull (FDH) and Benefit of the Doubt (BOD) scores. The robust approach is based on the work of Cazals, Florens and Simar (2002) <doi:10.1016/S0304-4076(01)00080-X>. The conditional approach is based on Daraio and Simar (2007) <doi:10.1007/s11123-007-0049-3>. Besides we provide graphs to help with the choice of m. We relay on the 'Benchmarking' package to compute the efficiency scores and on the 'np' package to compute non parametric estimation of similarity among units.

Last updated 3 years ago

1.00 score 173 downloads

matman - Material Management

A set of functions, classes and methods for performing ABC and ABC/XYZ analyses, identifying overperforming, underperforming and constantly performing items, and plotting, analyzing as well as predicting the temporal development of items.

Last updated 3 years ago

1.00 score 281 downloads

FWRGB - Fresh Weight Determination from Visual Image of the Plant

Fresh biomass determination is the key to evaluating crop genotypes' response to diverse input and stress conditions and forms the basis for calculating net primary production. However, as conventional phenotyping approaches for measuring fresh biomass is time-consuming, laborious and destructive, image-based phenotyping methods are being widely used now. In the image-based approach, the fresh weight of the above-ground part of the plant depends on the projected area. For determining the projected area, the visual image of the plant is converted into the grayscale image by simply averaging the Red(R), Green (G) and Blue (B) pixel values. Grayscale image is then converted into a binary image using Otsu’s thresholding method Otsu, N. (1979) <doi:10.1109/TSMC.1979.4310076> to separate plant area from the background (image segmentation). The segmentation process was accomplished by selecting the pixels with values over the threshold value belonging to the plant region and other pixels to the background region. The resulting binary image consists of white and black pixels representing the plant and background regions. Finally, the number of pixels inside the plant region was counted and converted to square centimetres (cm2) using the reference object (any object whose actual area is known previously) to get the projected area. After that, the projected area is used as input to the machine learning model (Linear Model, Artificial Neural Network, and Support Vector Regression) to determine the plant's fresh weight.

Last updated 3 years ago

1.00 score 166 downloads

agrifeature - Agriculture Image Feature

Functions to calculate Gray Level Co-occurrence Matrix(GLCM), RGB-based Vegetative Index(RGB VI) and Normalized Difference Vegetation Index(NDVI) family image features. GLCM calculations are based on Haralick (1973) <doi:10.1109/TSMC.1973.4309314>.

Last updated 3 years ago

1.00 score 313 downloads

ClusPred - Simultaneous Semi-Parametric Estimation of Clustering and Regression

Parameter estimation of regression models with fixed group effects, when the group variable is missing while group-related variables are available. Parametric and semi-parametric approaches described in Marbac et al. (2020) <arXiv:2012.14159> are implemented.

Last updated 3 years ago

openblascpp

1.00 score 190 downloads

MNARclust - Clustering Data with Non-Ignorable Missingness using Semi-Parametric Mixture Models

Clustering of data under a non-ignorable missingness mechanism. Clustering is achieved by a semi-parametric mixture model and missingness is managed by using the pattern-mixture approach. More details of the approach are available in Du Roy de Chaumaray et al. (2020) <arXiv:2009.07662>.

Last updated 3 years ago

openblascpp

1.00 score 151 downloads

FourWayHMM - Parsimonious Hidden Markov Models for Four-Way Data

Implements parsimonious hidden Markov models for four-way data via expectation- conditional maximization algorithm, as described in Tomarchio et al. (2020) <arXiv:2107.04330>. The matrix-variate normal distribution is used as emission distribution. For each hidden state, parsimony is reached via the eigen-decomposition of the covariance matrices of the emission distribution. This produces a family of 98 parsimonious hidden Markov models.

Last updated 3 years ago

1.00 score 235 downloads

GhostKnockoff - The Knockoff Inference Using Summary Statistics

Functions for multiple knockoff inference using summary statistics, e.g. Z-scores. The knockoff inference is a general procedure for controlling the false discovery rate (FDR) when performing variable selection. This package provides a procedure which performs knockoff inference without ever constructing individual knockoffs (GhostKnockoff). It additionally supports multiple knockoff inference for improved stability and reproducibility. Moreover, it supports meta-analysis of multiple overlapping studies.

Last updated 3 years ago

1.00 score 1 stars 15 scripts 142 downloads

binda - Multi-Class Discriminant Analysis using Binary Predictors

Implements functions for multi-class discriminant analysis using binary predictors, for corresponding variable selection, and for dichotomizing continuous data.

Last updated 3 years ago

1.00 score 9 scripts 910 downloads

KnockoffScreen - Whole-Genome Sequencing Data Analysis via Knockoff Statistics

Functions for identification of putative causal loci in whole-genome sequencing data. The functions allow genome-wide association scan. It also includes an efficient knockoff generator for genetic data.

Last updated 3 years ago

1.00 score 1 stars 5 scripts 211 downloads

FairMclus - Clustering for Data with Sensitive Attribute

Clustering for categorical and mixed-type of data, to preventing classification biases due to race, gender or others sensitive attributes. This algorithm is an extension of the methodology proposed by "Santos & Heras (2020) <doi:10.28945/4643>".

Last updated 3 years ago

1.00 score 3 scripts 226 downloads

MultipleBreakpoints - Estimating Multiple Breakpoints for a Sequence of Realizations of Bernoulli Variables

The iterative procedure estimates structural changes in the success probability of Bernoulli variables. It estimates the number and location of the breakpoints as well as the success probability of the different sequences between the breakpoints. In addition, it provides a graphical illustration of the result.

Last updated 3 years ago

1.00 score 143 downloads

RobustBF - Robust Solution to the Behrens-Fisher Problem

Robust tests (RW and RF) are provided for testing the equality of two long-tailed symmetric (LTS) means when the variances are unknown and arbitrary. RW test is a robust version of Welch's two sample t test and the RF is a robust fiducial based test. The RW and RF tests are proposed using the adaptive modified maximum likelihood (AMML) estimators derived by Tiku and Surucu (2009) <doi:10.1016/j.spl.2008.12.001> and Donmez (2010) <https://open.metu.edu.tr/bitstream/handle/11511/19440/index.pdf>.

Last updated 3 years ago

1.00 score 2 scripts 159 downloads

MultipleRegression - Multiple Regression Analysis

Tools to analysis of experiments having two or more quantitative explanatory variables and one quantitative dependent variable. Experiments can be without repetitions or with a statistical design (Hair JF, 2016) <ISBN: 13: 978-0138132637>. Pacote para uma analise de experimentos havendo duas ou mais variaveis explicativas quantitativas e uma variavel dependente quantitativa. Os experimentos podem ser sem repeticoes ou com delineamento estatistico (Hair JF, 2016) <ISBN: 13: 978-0138132637>.

Last updated 3 years ago

1.00 score 161 downloads

autoharp - Semi-Automatic Grading of R and Rmd Scripts

A customisable set of tools for assessing and grading R or R-markdown scripts from students. It allows for checking correctness of code output, runtime statistics and static code analysis. The latter feature is made possible by representing R expressions using a tree structure.

Last updated 3 years ago

1.00 score 1 stars 8 scripts 317 downloads

ICglm - Information Criteria for Generalized Linear Regression

Calculate various information criteria in literature for "lm" and "glm" objects.

Last updated 3 years ago

1.00 score 5 scripts 240 downloads

jcp - Joint Change Point Detection

Procedures for joint detection of changes in both expectation and variance in univariate sequences. Performs a statistical test of the null hypothesis of the absence of change points. In case of rejection performs an algorithm for change point detection. Reference - Bivariate change point detection - joint detection of changes in expectation and variance, Scandinavian Journal of Statistics, DOI 10.1111/sjos.12547.

Last updated 3 years ago

1.00 score 3 scripts 174 downloads

simpleFDR - Simple False Discovery Rate Calculation

Using the adjustment method from Benjamini & Hochberg (1995) <doi:10.1111/j.2517-6161.1995.tb02031.x>, this package determines which variables are significant under repeated testing with a given dataframe of p values and an user defined "q" threshold. It then returns the original dataframe along with a significance column where an asterisk denotes a significant p value after FDR calculation, and NA denotes all other p values. This package uses the Benjamini & Hochberg method specifically as described in Lee, S., & Lee, D. K. (2018) <doi:10.4097/kja.d.18.00242>.

Last updated 3 years ago

1.00 score 146 downloads

SenTinMixt - Parsimonious Mixtures of MSEN and MTIN Distributions

Implements parsimonious mixtures of MSEN and MTIN distributions via expectation- maximization based algorithms for model-based clustering. For each mixture component, parsimony is reached via the eigen-decomposition of the scale matrices and by imposing a constraint on the tailedness parameter. This produces a family of 28 parsimonious mixture models for each distribution.

Last updated 3 years ago

1.00 score 216 downloads

spidR - Spider Knowledge Online

Allows the user to connect with the World Spider Catalogue (WSC; <https://wsc.nmbe.ch/>) and the World Spider Trait (WST; <https://spidertraits.sci.muni.cz/>) databases. Also performs several basic functions such as checking names validity, retrieving coordinate data from the Global Biodiversity Information Facility (GBIF; <https://www.gbif.org/>), and mapping.

Last updated 3 years ago

1.00 score 144 downloads

transmdl - Semiparametric Transformation Models

To make the semiparametric transformation models easier to apply in real studies, we introduce this R package, in which the MLE in transformation models via an EM algorithm proposed by Zeng D, Lin DY(2007) <doi:10.1111/j.1369-7412.2007.00606.x> and adaptive lasso method in transformation models proposed by Liu XX, Zeng D(2013) <doi:10.1093/biomet/ast029> are implemented. C++ functions are used to compute complex loops. The coefficient vector and cumulative baseline hazard function can be estimated, along with the corresponding standard errors and P values.

Last updated 3 years ago

1.00 score 153 downloads

CLONETv2 - Clonality Estimates in Tumor

Analyze data from next-generation sequencing experiments on genomic samples. 'CLONETv2' offers a set of functions to compute allele specific copy number and clonality from segmented data and SNPs position pileup. The package has also calculated the clonality of single nucleotide variants given read counts at mutated positions. The package has been developed at the laboratory of Computational and Functional Oncology, Department of CIBIO, University of Trento (Italy), under the supervision of prof Francesca Demichelis. References: Prandi et al. (2014) <doi:10.1186/s13059-014-0439-6>; Carreira et al. (2014) <doi:10.1126/scitranslmed.3009448>; Romanel et al. (2015) <doi:10.1126/scitranslmed.aac9511>.

Last updated 3 years ago

1.00 score 3 scripts 207 downloads

CorrectedFDR - Correcting False Discovery Rates

There are many estimators of false discovery rate. In this package we compute the Nonlocal False Discovery Rate (NFDR) and the estimators of local false discovery rate: Corrected False discovery Rate (CFDR), Re-ranked False Discovery rate (RFDR) and the blended estimator. Bickel, D.R., Rahal, A. (2019) <https://tinyurl.com/kkdc9rk8>.

Last updated 3 years ago

bayesian statisticsmathematicalbiology

1.00 score 2 scripts 192 downloads

ReDirection - Predict Dominant Direction of Reactions of a Biochemical Network

Biologically relevant, yet mathematically sound constraints are used to compute the propensity and thence infer the dominant direction of reactions of a generic biochemical network. The reactions must be unique and their number must exceed that of the reactants,i.e., reactions >= reactants + 2. 'ReDirection', computes the null space of a user-defined stoichiometry matrix. The spanning non-zero and unique reaction vectors (RVs) are combinatorially summed to generate one or more subspaces recursively. Every reaction is represented as a sequence of identical components across all RVs of a particular subspace. The terms are evaluated with (biologically relevant bounds, linear maps, tests of convergence, descriptive statistics, vector norms) and the terms are classified into forward-, reverse- and equivalent-subsets. Since, these are mutually exclusive the probability of occurrence is binary (all, 1; none, 0). The combined propensity of a reaction is the p1-norm of the sub-propensities, i.e., sum of the products of the probability and maximum numeric value of a subset (least upper bound, greatest lower bound). This, if strictly positive is the probable rate constant, is used to infer dominant direction and annotate a reaction as "Forward (f)", "Reverse (b)" or "Equivalent (e)". The inherent computational complexity (NP-hard) per iteration suggests that a suitable value for the number of reactions is around 20. Three functions comprise ReDirection. These are check_matrix() and reaction_vector() which are internal, and calculate_reaction_vector() which is external.

Last updated 3 years ago

1.00 score 1 scripts 174 downloads

BDEsize - Efficient Determination of Sample Size in Balanced Design of Experiments

For a balanced design of experiments, this package calculates the sample size required to detect a certain standardized effect size, under a significance level. This package also provides three graphs; detectable standardized effect size vs power, sample size vs detectable standardized effect size, and sample size vs power, which show the mutual relationship between the sample size, power and the detectable standardized effect size. The detailed procedure is described in R. V. Lenth (2006-9) <https://homepage.divms.uiowa.edu/~rlenth/Power/>, Y. B. Lim (1998), M. A. Kastenbaum, D. G. Hoel and K. O. Bowman (1970) <doi:10.2307/2334851>, and Douglas C. Montgomery (2013, ISBN: 0849323312).

Last updated 3 years ago

1.00 score 247 downloads

ConsRankClass - Classification and Clustering of Preference Rankings

Tree-based classification and soft-clustering method for preference rankings, with tools for external validation of fuzzy clustering. It contains the recursive partitioning algorithm for preference rankings, non-parametric tree-based method for a matrix of preference rankings as a response variable. It contains also the distribution-free soft clustering method for preference rankings, namely the K-median cluster component analysis (CCA). The package depends on the 'ConsRank' R package. Options for validate the tree-based method are both test-set procedure and V-fold cross validation. The package contains the routines to compute the adjusted concordance index (a fuzzy version of the adjusted rand index) and the normalized degree of concordance (the corresponding fuzzy version of the rand index). Essential references: D'Ambrosio, A., Amodio, S., Iorio, C., Pandolfo, G., and Siciliano, R. (2021) <doi:10.1007/s00357-020-09367-0> D'Ambrosio, A., and Heiser, W.J. (2019) <doi:10.1007/s41237-018-0069-5>; D'Ambrosio, A., and Heiser W.J. (2016) <doi:10.1007/s11336-016-9505-1>; Hullermeier, E., Rifqi, M., Henzgen, S., and Senge, R. (2012) <doi:10.1109/TFUZZ.2011.2179303>.

Last updated 3 years ago

1.00 score 208 downloads

tsfngm - Time Series Forecasting using Nonlinear Growth Models

Nonlinear growth models are extremely useful in gaining insight into the underlying mechanism. These models are generally 'mechanistic,' with parameters that have biological meaning. This package allows you to fit and forecast time series data using nonlinear growth models.

Last updated 3 years ago

1.00 score 175 downloads

EEMDSVR - Ensemble Empirical Mode Decomposition and Its Variant Based Support Vector Regression Model

Application of Ensemble Empirical Mode Decomposition and its variant based Support Vector regression model for univariate time series forecasting. For method details see Das (2020).<http://krishi.icar.gov.in/jspui/handle/123456789/44138>.

Last updated 3 years ago

1.00 score 165 downloads

SubTite - Subgroup Specific Optimal Dose Assignment

Chooses subgroup specific optimal doses in a phase I dose finding clinical trial allowing for subgroup combination and simulates clinical trials under the subgroup specific time to event continual reassessment method. Chapple, A.G., Thall, P.F. (2018) <doi:10.1002/pst.1891>.

Last updated 3 years ago

1.00 score 4 scripts 251 downloads

BAGofT - A Binary Regression Adaptive Goodness-of-Fit Test (BAGofT)

The BAGofT assesses the goodness-of-fit of binary classifiers. Details can be found in Zhang, Ding and Yang (2021) <arXiv:1911.03063v2>.

Last updated 3 years ago

1.00 score 237 downloads

papci - Prevalence Adjusted PPV Confidence Interval

Positive predictive value (PPV) defined as the conditional probability of clinical trial assay (CTA) being positive given Companion diagnostic device (CDx) being positive is a key performance parameter for evaluating the clinical validity utility of a companion diagnostic test in clinical bridging studies. When bridging study patients are enrolled based on CTA assay results, Binomial-based confidence intervals (CI) may are not appropriate for PPV CI estimation. Bootstrap CIs which are not restricted by the Binomial assumption may be used for PPV CI estimation only when PPV is not 100%. Bootstrap CI is not valid when PPV is 100% and becomes a single value of [1, 1]. We proposed a risk ratio-based method for constructing CI for PPV. By simulation we illustrated that the coverage probability of the proposed CI is close to the nominal value even when PPV is high and negative percent agreement (NPA) is close to 100%. There is a lack of R package for PPV CI calculation. we developed a publicly available R package along with this shiny app to implement the proposed approach and some other existing methods.

Last updated 3 years ago

1.00 score 1 stars 189 downloads

hrt - Heteroskedasticity Robust Testing

Functions for testing affine hypotheses on the regression coefficient vector in regression models with heteroskedastic errors: (i) a function for computing various test statistics (in particular using HC0-HC4 covariance estimators based on unrestricted or restricted residuals); (ii) a function for numerically approximating the size of a test based on such test statistics and a user-supplied critical value; and, most importantly, (iii) a function for determining size-controlling critical values for such test statistics and a user-supplied significance level (also incorporating a check of conditions under which such a size-controlling critical value exists). The three functions are based on results in Poetscher and Preinerstorfer (2021) "Valid Heteroskedasticity Robust Testing" <arXiv:2104.12597>.

Last updated 3 years ago

cppopenmp

1.00 score 171 downloads

combinationpvalues - Combination of Independent P-Values

Provides access to six fundamental statistics that can be used for the purpose of combination p-values. All methods used can referenced here: Heard & Rubin-Delanchy (2017) <arXiv:1707.06897>.

Last updated 3 years ago

1.00 score 2 scripts 204 downloads

MINTplates - Encode "License-Plates" from Sequences and Decode Them Back

It can be used to create/encode molecular "license-plates" from sequences and to also decode the "license-plates" back to sequences. While initially created for transfer RNA-derived small fragments (tRFs), this tool can be used for any genomic sequences including but not limited to: tRFs, microRNAs, etc. The detailed information can reference to Pliatsika V, Loher P, Telonis AG, Rigoutsos I (2016) <doi:10.1093/bioinformatics/btw194>. It can also be used to annotate tRFs. The detailed information can reference to Loher P, Telonis AG, Rigoutsos I (2017) <doi:10.1038/srep41184>.

Last updated 3 years ago

1.00 score 166 downloads

cold - Count Longitudinal Data

Performs regression analysis for longitudinal count data, allowing for serial dependence among observations from a given individual and two dimensional random effects on the linear predictor. Estimation is via maximization of the exact likelihood of a suitably defined model. Missing values and unbalanced data are allowed. Details can be found in the accompanying scientific papers: Goncalves & Cabral (2021, Journal of Statistical Software, <doi:10.18637/jss.v099.i03>) and Goncalves et al. (2007, Computational Statistics & Data Analysis, <doi:10.1016/j.csda.2007.03.002>).

Last updated 3 years ago

fortran

1.00 score 3 scripts 288 downloads

cta - Contingency Table Analysis Based on ML Fitting of MPH Models

Contingency table analysis is performed based on maximum likelihood (ML) fitting of multinomial-Poisson homogeneous (MPH) and homogeneous linear predictor (HLP) models. See Lang (2004) <doi:10.1214/aos/1079120140> and Lang (2005) <doi:10.1198/016214504000001042> for MPH and HLP models. Objects computed include model goodness-of-fit statistics; likelihood- based (cell- and link-specific) residuals; and cell probability and expected count estimates along with standard errors. This package can also compute test-inversion--e.g. Wald, profile likelihood, score, power-divergence--confidence intervals for contingency table estimands, when table probabilities are potentially subject to equality constraints. For test-inversion intervals, see Lang (2008) <doi:10.1002/sim.3391> and Zhu (2020) <doi:10.17077/etd.005331>.

Last updated 3 years ago

1.00 score 180 downloads

conmet - Construct Measurement Evaluation Tool

With this package you can run 'ConMET' locally in R. 'ConMET' is an R-shiny application that facilitates performing and evaluating confirmatory factor analyses (CFAs) and is useful for running and reporting typical measurement models in applied psychology and management journals. 'ConMET' automatically creates, compares and summarizes CFA models. Most common fit indices (E.g., CFI and SRMR) are put in an overview table. ConMET also allows to test for common method variance. The application is particularly useful for teaching and instruction of measurement issues in survey research. The application uses the 'lavaan' package (Rosseel, 2012) to run CFAs.

Last updated 3 years ago

1.00 score 4 scripts 193 downloads

onc.api - Oceans 2.0 API Client Library

Allows users to discover and retrieve Ocean Networks Canada's oceanographic data in raw, text, image, audio, video or any other format available. Provides a class that wraps web service calls and business logic so that users can download data with a single line of code.

Last updated 3 years ago

1.00 score 1 scripts 167 downloads

ssmrob - Robust Estimation and Inference in Sample Selection Models

Package provides a set of tools for robust estimation and inference for models with sample selectivity and endogenous treatment model. For details, see Zhelonkin and Ronchetti (2021) <doi:10.18637/jss.v099.i04>.

Last updated 3 years ago

1.00 score 9 scripts 364 downloads

glvmfit - Methods to Assess Generalized Latent Variable Model Fit

Provides residual global fit indices for generalized latent variable models.

Last updated 3 years ago

1.00 score 179 downloads

primePCA - Projected Refinement for Imputation of Missing Entries in PCA

Implements the primePCA algorithm, developed and analysed in Zhu, Z., Wang, T. and Samworth, R. J. (2019) High-dimensional principal component analysis with heterogeneous missingness. <arXiv:1906.12125>.

Last updated 3 years ago

1.00 score 7 scripts 207 downloads

PICBayes - Bayesian Models for Partly Interval-Censored Data

Contains functions to fit proportional hazards (PH) model to partly interval-censored (PIC) data (Pan et al. (2020) <doi:10.1177/0962280220921552>), PH model with spatial frailty to spatially dependent PIC data (Pan and Cai (2021) <doi:10.1080/03610918.2020.1839497>), and mixed effects PH model to clustered PIC data. Each random intercept/random effect can follow both a normal prior and a Dirichlet process mixture prior. It also includes the corresponding functions for general interval-censored data.

Last updated 3 years ago

1.00 score 118 downloads

informedSen - Sensitivity Analysis Informed by a Test for Bias

After testing for biased treatment assignment in an observational study using an unaffected outcome, the sensitivity analysis is constrained to be compatible with that test. The package uses the optimization software gurobi obtainable from <https://www.gurobi.com/>, together with its associated R package, also called gurobi; see: <https://www.gurobi.com/documentation/7.0/refman/installing_the_r_package.html>. The method is a substantial computational and practical enhancement of a concept introduced in Rosenbaum (1992) Detecting bias with confidence in observational studies Biometrika, 79(2), 367-374 <doi:10.1093/biomet/79.2.367>.

Last updated 3 years ago

1.00 score 166 downloads

HMMextra0s - Hidden Markov Models with Extra Zeros

Contains functions for hidden Markov models with observations having extra zeros as defined in the following two publications, Wang, T., Zhuang, J., Obara, K. and Tsuruoka, H. (2016) <doi:10.1111/rssc.12194>; Wang, T., Zhuang, J., Buckby, J., Obara, K. and Tsuruoka, H. (2018) <doi:10.1029/2017JB015360>. The observed response variable is either univariate or bivariate Gaussian conditioning on presence of events, and extra zeros mean that the response variable takes on the value zero if nothing is happening. Hence the response is modelled as a mixture distribution of a Bernoulli variable and a continuous variable. That is, if the Bernoulli variable takes on the value 1, then the response variable is Gaussian, and if the Bernoulli variable takes on the value 0, then the response is zero too. This package includes functions for simulation, parameter estimation, goodness-of-fit, the Viterbi algorithm, and plotting the classified 2-D data. Some of the functions in the package are based on those of the R package 'HiddenMarkov' by David Harte. This updated version has included an example dataset and R code examples to show how to transform the data into the objects needed in the main functions. We have also made changes to increase the speed of some of the functions.

Last updated 3 years ago

1.00 score 9 scripts 121 downloads

GIplot - Gaussian Interval Plot (GIplot)

The Gaussian Interval Plot (GIplot) is a pictorial representation of the mean and the standard deviation of a quantitative variable. It also flags potential outliers (together with their frequencies) that are c standard deviations away from the mean.

Last updated 3 years ago

1.00 score 133 downloads

gsrs - A Group-Specific Recommendation System

A group-specific recommendation system to use dependency information from users and items which share similar characteristics under the singular value decomposition framework. Refer to paper A Group-Specific Recommender System <doi:10.1080/01621459.2016.1219261> for the details.

Last updated 3 years ago

1.00 score 92 downloads

predfairness - Discrimination Mitigation for Machine Learning Models

Based on different statistical definitions of discrimination, several methods have been proposed to detect and mitigate social inequality in machine learning models. This package aims to provide an alternative to fairness treatment in predictive models. The ROC method implemented in this package is described by Kamiran, Karim and Zhang (2012) <https://ieeexplore.ieee.org/document/6413831/>.

Last updated 3 years ago

1.00 score 120 downloads

gds - Descriptive Statistics of Grouped Data

Contains a function called gds() which accepts three input parameters like lower limits, upper limits and the frequencies of the corresponding classes. The gds() function calculate and return the values of mean ('gmean'), median ('gmedian'), mode ('gmode'), variance ('gvar'), standard deviation ('gstdev'), coefficient of variance ('gcv'), quartiles ('gq1', 'gq2', 'gq3'), inter-quartile range ('gIQR'), skewness ('g1'), and kurtosis ('g2') which facilitate effective data analysis. For skewness and kurtosis calculations we use moments.

Last updated 3 years ago

1.00 score 5 scripts 332 downloads

benford - Benford's Analysis on Large Data Sets

Perform the Benford's Analysis to a data set in order to evaluate if it contains human fabricated data. For more details on the method see Moreau, 2021, Model Assist. Statist. Appl., 16 (2021) 73–79. <doi:10.3233/MAS-210517>.

Last updated 3 years ago

1.00 score 337 downloads

bikm1 - Co-Clustering Adjusted Rand Index and Bikm1 Procedure for Contingency and Binary Data-Sets

Co-clustering of the rows and columns of a contingency or binary matrix, or double binary matrices and model selection for the number of row and column clusters. Three models are considered: the Poisson latent block model for contingency matrix, the binary latent block model for binary matrix and a new model we develop: the multiple latent block model for double binary matrices. A new procedure named bikm1 is implemented to investigate more efficiently the grid of numbers of clusters. Then, the studied model selection criteria are the integrated completed likelihood (ICL) and the Bayesian integrated likelihood (BIC). Finally, the co-clustering adjusted Rand index (CARI) to measure agreement between co-clustering partitions is implemented. Robert Valerie, Vasseur Yann, Brault Vincent (2021) <doi:10.1007/s00357-020-09379-w>.

Last updated 3 years ago

1.00 score 1 stars 1 scripts 239 downloads

geovol - Geopolitical Volatility (GEOVOL) Modelling

Simulation, estimation and inference for the geopolitical volatility (GEOVOL) model of Engle and Campos-Martins (2020) <doi:10.2139/ssrn.3685213>, where GEOVOL is modelled as a latent multiplicative volatility factor with heterogeneous factor loadings. Estimation is carried out as a maximization-maximization procedure, where GEOVOL and the GEOVOL loadings are estimated iteratively until convergence.

Last updated 3 years ago

1.00 score 1 scripts 117 downloads

npwbs - Nonparametric Multiple Change Point Detection Using WBS

Implements the procedure from G. J. Ross (2021) - "Nonparametric Detection of Multiple Location-Scale Change Points via Wild Binary Segmentation" <arxiv:2107.01742>. This uses a version of Wild Binary Segmentation to detect multiple location-scale (i.e. mean and/or variance) change points in a sequence of univariate observations, with a strict control on the probability of incorrectly detecting a change point in a sequence which does not contain any.

Last updated 3 years ago

1.00 score 181 downloads

newFocus - True Discovery Guarantee by Combining Partial Closed Testings

Closed testing has been proved powerful for true discovery guarantee. The computation of closed testing is, however, quite burdensome. A general way to reduce computational complexity is to combine partial closed testings for some prespecified feature sets of interest. Partial closed testings are performed at Bonferroni-corrected alpha level to guarantee the lower bounds for the number of true discoveries in prespecified sets are simultaneously valid. For any post hoc chosen sets of interest, coherence property is used to get the lower bound. In this package, we implement closed testing with globaltest to calculate the lower bound for number of true discoveries, see Ningning Xu et.al (2021) <arXiv:2001.01541> for detailed description.

Last updated 3 years ago

1.00 score 158 downloads

EuclideanSD - An Euclidean View of Center and Spread

Illustrates the concepts developed in Sarkar and Rashid (2019, ISSN:0025-5742) <http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=&cad=rja&uact=8&ved=2ahUKEwiH4deL3q3xAhWX73MBHR_wDaYQFnoECAUQAw&url=https%3A%2F%2Fwww.indianmathsociety.org.in%2Fmathstudent-part-2-2019.pdf&usg=AOvVaw3SY--3T6UAWUnH5-Nj6bSc>. This package helps a user guess four things (mean, MD, scaled MSD, and RMSD) before they get the SD. 1) The package displays the Empirical Cumulative Distribution Function (ECDF) of the given data. The user must choose the value of the mean by equating the areas of two colored (blue and green) regions. The package gives feedback to improve the choice until it is correct. Alternatively, the reader may continue with a different guess for the center (not necessarily the mean). 2) The user chooses the values of the Mean Deviation (MD) based on the ECDF of the deviations by equating the areas of two newly colored (blue and green) regions, with feedback from the package until the user guesses correctly. 3) The user chooses the Scaled Mean Squared Deviation (MSD) based on the ECDF of the scaled square deviations by equating the areas of two newly colored (blue and green) regions, with feedback from the package until the user guesses correctly. 4) The user chooses the Root Mean Squared Deviation (RMSD) by ensuring that its intersection with the ECDF of the deviations is at the same height as the intersection between the scaled MSD and the ECDF of the scaled squared deviations. Additionally, the intersection of two blue lines (the green dot) should fall on the vertical line at the maximum deviation. 5) Finally, if the mean is chosen correctly, only then the user can view the population SD (the same as the RMSD) and the sample SD (sqrt(n/(n-1))*RMSD) by clicking the respective buttons. If the mean is chosen incorrectly, the user is asked to correct it.

Last updated 3 years ago

1.00 score 194 downloads

ProbitSpatial - Probit with Spatial Dependence, SAR, SEM and SARAR Models

Fast estimation of binomial spatial probit regression models with spatial autocorrelation for big datasets.

Last updated 3 years ago

cpp

1.00 score 10 scripts 224 downloads

msig - An R Package for Exploring Molecular Signatures Database

The Molecular Signatures Database ('MSigDB') is one of the most widely used and comprehensive databases of gene sets for performing gene set enrichment analysis <doi:10.1016/j.cels.2015.12.004>. The 'msig' package provides you with powerful, easy-to-use and flexible query functions for the 'MsigDB' database. There are 2 query modes in the 'msig' package: online query and local query. Both queries contain 2 steps: gene set name and gene. The online search is divided into 2 modes: registered search and non-registered browse. For registered search, email that you registered should be provided. Local queries can be made from local database, which can be updated by msig_update() function.

Last updated 3 years ago

1.00 score 105 downloads

SAMTx - Sensitivity Assessment to Unmeasured Confounding with Multiple Treatments

A sensitivity analysis approach for unmeasured confounding in observational data with multiple treatments and a binary outcome. This approach derives the general bias formula and provides adjusted causal effect estimates in response to various assumptions about the degree of unmeasured confounding. Nested multiple imputation is embedded within the Bayesian framework to integrate uncertainty about the sensitivity parameters and sampling variability. Bayesian Additive Regression Model (BART) is used for outcome modeling. The causal estimands are the conditional average treatment effects (CATE) based on the risk difference. For more details, see paper: Hu L et al. (2020) A flexible sensitivity analysis approach for unmeasured confounding with multiple treatments and a binary outcome with application to SEER-Medicare lung cancer data <arXiv:2012.06093>.

Last updated 3 years ago

1.00 score 133 downloads

PreProcessing - Various Preprocessing Transformations of Numeric Data Matrices

Preprocess numeric data matrices into desired transformed representations. Standardization, Unitization, Cubitization and adaptive intervals are offered.

Last updated 4 years ago

1.00 score 145 downloads

BioInsight - Filter and Plot RNA Biotypes

Analyze and plot the abundance of different RNA biotypes present in a count matrix, this evaluation can be useful if you want to test different strategies of normalization or analyze a particular biotype in a differential gene expression analysis.

Last updated 4 years ago

1.00 score 1 scripts 232 downloads

vampyr - Factor Analysis Controlling the Effects of Response Bias

Vampirize the response biases from a dataset! Performs factor analysis controlling the effects of social desirability and acquiescence using the method described in Ferrando, Lorenzo-Seva & Chico (2009) <doi:10.1080/10705510902751374>.

Last updated 4 years ago

1.00 score 163 downloads

InDisc - Obtaining and Estimating Unidimensional and Multidimensional IRT Dual Models

Performs a unified approach for obtaining and estimating unidimensional and multidimensional Item Response Theory (IRT) Dual Models (DMs), proposed by Ferrando (2019 <doi:10.1177/0146621618817779>).

Last updated 4 years ago

1.00 score 183 downloads

unival - Assessing Essential Unidimensionality Using External Validity Information

Assess essential unidimensionality using external validity information using the procedure proposed by Ferrando & Lorenzo-Seva (2019) <doi:10.1177/0013164418824755>. Provides two indices for assessing differential and incremental validity, both based on a second-order modelling schema for the general factor.

Last updated 4 years ago

1.00 score 4 scripts 142 downloads

ormBigData - Fitting Semiparametric Cumulative Probability Models for Big Data

A big data version for fitting cumulative probability models using the orm() function. See Liu et al. (2017) <DOI:10.1002/sim.7433> for details.

Last updated 4 years ago

1.00 score 125 downloads

LavaCvxr - Lava Estimation for the Sum of Sparse and Dense Signals(3 Methods)

The lava estimation is used to recover signals that is the sum of a sparse signal and a dense signal. The post-lava method corrects the shrinkage bias of lava. For more information on the lava estimation, see Chernozhukov, Hansen, and Liao (2017) <doi:10.1214/16-AOS1434>.

Last updated 4 years ago

1.00 score 153 downloads

audit - Bounds for Accounting Populations

Find an upper bound for the total amount of overstatement of assets in a set of accounts, or estimate the amount of sales tax owed on a collection of transactions (Meeden and Sargent, 2007, <doi:10.1080/03610920701386802>).

Last updated 4 years ago

1.00 score 4 scripts 232 downloads

simml - Single-Index Models with Multiple-Links

A major challenge in estimating treatment decision rules from a randomized clinical trial dataset with covariates measured at baseline lies in detecting relatively small treatment effect modification-related variability (i.e., the treatment-by-covariates interaction effects on treatment outcomes) against a relatively large non-treatment-related variability (i.e., the main effects of covariates on treatment outcomes). The class of Single-Index Models with Multiple-Links is a novel single-index model specifically designed to estimate a single-index (a linear combination) of the covariates associated with the treatment effect modification-related variability, while allowing a nonlinear association with the treatment outcomes via flexible link functions. The models provide a flexible regression approach to developing treatment decision rules based on patients' data measured at baseline. We refer to Park, Petkova, Tarpey, and Ogden (2020) <doi:10.1016/j.jspi.2019.05.008> and Park, Petkova, Tarpey, and Ogden (2020) <doi:10.1111/biom.13320> (that allows an unspecified X main effect) for detail of the method. The main function of this package is simml().

Last updated 4 years ago

1.00 score 4 scripts 146 downloads

DICOMread - Reading and Saving DICOM Image Files

This function provides an interface between 'Matlab' and 'R' in facilitating fast processing for reading and saving DICOM images.

Last updated 4 years ago

1.00 score 192 downloads

SportsTour - Display Tournament Fixtures using Knock Out and Round Robin Techniques

Use of Knock Out and Round Robin Techniques in preparing tournament fixtures as discussed in the Book Health and Physical Education by 'Dr. V K Sharma'(2018,ISBN:978-93-5272-134-4).

Last updated 4 years ago

1.00 score 94 downloads

BayesDesign - Bayesian Single-Arm Design with Survival Endpoints

The proposed event-driven approach for Bayesian two-stage single-arm phase II trial design is a novel clinical trial design and can be regarded as an extension of the Simon’s two-stage design with the time-to-event endpoint. This design is motivated by cancer clinical trials with immunotherapy and molecularly targeted therapy, in which time-to-event endpoint is often a desired endpoint.

Last updated 4 years ago

1.00 score 196 downloads

isoboost - Isotonic Boosting Classification Rules

In classification problems a monotone relation between some predictors and the classes may be assumed. In this package 'isoboost' we propose new boosting algorithms, based on LogitBoost, that incorporate this isotonicity information, yielding more accurate and easily interpretable rules.

Last updated 4 years ago

1.00 score 155 downloads

DBfit - A Double Bootstrap Method for Analyzing Linear Models with Autoregressive Errors

Computes the double bootstrap as discussed in McKnight, McKean, and Huitema (2000) <doi:10.1037/1082-989X.5.1.87>. The double bootstrap method provides a better fit for a linear model with autoregressive errors than ARIMA when the sample size is small.

Last updated 4 years ago

1.00 score 7 scripts 138 downloads

BBSSL - Bayesian Bootstrap Spike-and-Slab LASSO

Posterior sampling for Spike-and-Slab LASSO prior in linear models from Nie and Rockova <arXiv:2011.14279>.

Last updated 4 years ago

1.00 score 2 scripts 148 downloads

neuromplex - Neural Multiplexing Analysis

Statistical methods for whole-trial and time-domain analysis of single cell neural response to multiple stimuli presented simultaneously. The package is based on the paper by C Glynn, ST Tokdar, A Zaman, VC Caruso, JT Mohl, SM Willett, and JM Groh (2021) "Analyzing second order stochasticity of neural spiking under stimuli-bundle exposure", is in press for publication by the Annals of Applied Statistics. A preprint may be found at <arXiv:1911.04387>.

Last updated 4 years ago

1.00 score 125 downloads

VDSM - Visualization of Distribution of Selected Model

Although model selection is ubiquitous in scientific discovery, the stability and uncertainty of the selected model is often hard to evaluate. How to characterize the random behavior of the model selection procedure is the key to understand and quantify the model selection uncertainty. This R package offers several graphical tools to visualize the distribution of the selected model. For example, Gplot(), Hplot(), VDSM_scatterplot() and VDSM_heatmap(). To the best of our knowledge, this is the first attempt to visualize such a distribution. About what distribution of selected model is and how it work please see Qin,Y.and Wang,L. (2021) "Visualization of Model Selection Uncertainty" <https://homepages.uc.edu/~qinyn/VDSM/VDSM.html>.

Last updated 4 years ago

1.00 score 2 scripts 113 downloads

jlctree - Joint Latent Class Trees for Joint Modeling of Time-to-Event and Longitudinal Data

Implements the tree-based approach to joint modeling of time-to-event and longitudinal data. This approach looks for a tree-based partitioning such that within each estimated latent class defined by a terminal node, the time-to-event and longitudinal responses display a lack of association. See Zhang and Simonoff (2018) <arXiv:1812.01774>.

Last updated 4 years ago

1.00 score 6 scripts 123 downloads

RegKink - Regression Kink with a Time-Varying Threshold

An algorithm is proposed to estimate regression kink model proposed by the paper, Lixiong Yang and Jen-Je Su (2018) <doi:10.1016/j.jimonfin.2018.06.002>.

Last updated 4 years ago

1.00 score 86 downloads

ellipticalsymmetry - Elliptical Symmetry Tests

Given the omnipresence of the assumption of elliptical symmetry, it is essential to be able to test whether that assumption actually holds true or not for the data at hand. This package provides several statistical tests for elliptical symmetry that are described in Babic et al. (2021) <arXiv:2011.12560v2>.

Last updated 4 years ago

1.00 score 172 downloads

textile - Textile Images

Contains real images of the same textile material with/without local defects, which were used in Bui and Apley (2018) <doi:10.1080/00401706.2017.1302362>.

Last updated 4 years ago

1.00 score 1 scripts 163 downloads

FITSio - FITS (Flexible Image Transport System) Utilities

Utilities to read and write files in the FITS (Flexible Image Transport System) format, a standard format in astronomy (see e.g. <https://en.wikipedia.org/wiki/FITS> for more information). Present low-level routines allow: reading, parsing, and modifying FITS headers; reading FITS images (multi-dimensional arrays); reading FITS binary and ASCII tables; and writing FITS images (multi-dimensional arrays). Higher-level functions allow: reading files composed of one or more headers and a single (perhaps multidimensional) image or single table; reading tables into data frames; generating vectors for image array axes; scaling and writing images as 16-bit integers. Known incompletenesses are reading random group extensions, as well as complex and array descriptor data types in binary tables.

Last updated 4 years ago

1.00 score 1 stars 50 scripts 366 downloads

bbdetection - Identification of Bull and Bear States of the Market

Implements two algorithms of detecting Bull and Bear markets in stock prices: the algorithm of Pagan and Sossounov (2002, <doi:10.1002/jae.664>) and the algorithm of Lunde and Timmermann (2004, <doi:10.1198/073500104000000136>). The package also contains functions for printing out the dating of the Bull and Bear states of the market, the descriptive statistics of the states, and functions for plotting the results. For the sake of convenience, the package includes the monthly and daily data on the prices (not adjusted for dividends) of the S&P 500 stock market index.

Last updated 4 years ago

cpp

1.00 score 5 scripts 226 downloads

Taba - Taba Robust Correlations

Calculates the robust Taba linear, Taba rank (monotonic), TabWil, and TabWil rank correlations. Test statistics as well as one sided or two sided p-values are provided for all correlations. Multiple correlations and p-values can be calculated simultaneously across multiple variables. In addition, users will have the option to use the partial, semipartial, and generalized partial correlations; where the partial and semipartial correlations use linear, logistic, or Poisson regression to modify the specified variable.

Last updated 4 years ago

1.00 score 2 scripts 146 downloads

SPORTSCausal - Spillover Time Series Causal Inference

A time series causal inference model for Randomized Controlled Trial (RCT) under spillover effect. 'SPORTSCausal' (Spillover Time Series Causal Inference) separates treatment effect and spillover effect from given responses of experiment group and control group by predicting the response without treatment. It reports both effects by fitting the Bayesian Structural Time Series (BSTS) model based on 'CausalImpact', as described in Brodersen et al. (2015) <doi:10.1214/14-AOAS788>.

Last updated 4 years ago

1.00 score 140 downloads

RSizeBiased - Hypothesis Testing Based on R-Size Biased Samples

Provides functions and examples for testing hypothesis about the population mean and variance on samples drawn by r-size biased sampling schemes.

Last updated 4 years ago

1.00 score 150 downloads

uni.survival.tree - A Survival Tree Based on Stabilized Score Tests for High-dimensional Covariates

A classification (decision) tree is constructed from survival data with high-dimensional covariates. The method is a robust version of the logrank tree, where the variance is stabilized. The main function "uni.tree" returns a classification tree for a given survival dataset. The inner nodes (splitting criterion) are selected by minimizing the P-value of the two-sample the score tests. The decision of declaring terminal nodes (stopping criterion) is the P-value threshold given by an argument (specified by user). This tree construction algorithm is proposed by Emura et al. (2021, in review).

Last updated 4 years ago

1.00 score 117 downloads

randChecks - Covariate Balance Checks: Randomization Tests and Graphical Diagnostics

Provides randomization tests and graphical diagnostics for assessing randomized assignment and covariate balance for a binary treatment variable. See Branson (2021) <arXiv:1804.08760> for details.

Last updated 4 years ago

1.00 score 8 scripts 156 downloads

MDOLS - Inference of Quadratic Functional for Moderate-Dimensional OLS

Statistical inference for quadratic functional of the moderate-dimensional linear model in Guo and Cheng (2021) <DOI:10.1080/01621459.2021.1893177>.

Last updated 4 years ago

1.00 score 88 downloads

IndexNumber - Index Numbers in Social Sciences

We provide an R tool for teaching in Social Sciences. It allows the computation of index numbers. It is a measure of the evolution of a fixed magnitude for only a product of for several products. It is very useful in Social Sciences. Among others, we obtain simple index numbers (in chain or in serie), index numbers for not only a product or weighted index numbers as the Laspeyres index (Laspeyres, 1864), the Paasche index (Paasche, 1874) or the Fisher index (Lapedes, 1978).

Last updated 4 years ago

1.00 score 234 downloads

shapeNA - M-Estimation of Shape for Data with Missing Values

M-estimators of location and shape following the power family (Frahm, Nordhausen, Oja (2020) <doi:10.1016/j.jmva.2019.104569>) are provided in the case of complete data and also when observations have missing values together with functions aiding their visualization.

Last updated 4 years ago

1.00 score 93 downloads

MABOUST - Multi-Armed Bayesian Ordinal Utility-Based Sequential Trial

Conducts and simulates the MABOUST design, including making interim decisions to stop a treatment for inferiority or stop the trial early for superiority or equivalency.

Last updated 4 years ago

openblascppopenmp

1.00 score 110 downloads

oreo - Large Amplitude Oscillatory Shear (LAOS)

The Sequence of Physical Processes (SPP) framework is a way of interpreting the transient data derived from oscillatory rheological tests. It is designed to allow both the linear and non-linear deformation regimes to be understood within a single unified framework. This code provides a convenient way to determine the SPP framework metrics for a given sample of oscillatory data. It will produce a text file containing the SPP metrics, which the user can then plot using their software of choice. It can also produce a second text file with additional derived data (components of tangent, normal, and binormal vectors), as well as pre-plotted figures if so desired. It is the R version of the Package SPP by Simon Rogers Group for Soft Matter (Simon A. Rogers, Brian M. Erwin, Dimitris Vlassopoulos, Michel Cloitre (2011) <doi:10.1122/1.3544591>).

Last updated 4 years ago

1.00 score 132 downloads

nixmass - Snow Water Equivalent Modeling with the 'Delta.snow' Model and Empirical Regression Models

Snow water equivalent is modeled with the process based 'delta.snow' model and empirical regression models using relationships between density and diverse at-site parameters. The methods are described in Winkler et al. (2021) <doi:10.5194/hess-25-1165-2021>, Guyennon et al. (2019) <doi:10.1016/j.coldregions.2019.102859>, Pistocchi (2016) <doi:10.1016/j.ejrh.2016.03.004>, Jonas et al. (2009) <doi:10.1016/j.jhydrol.2009.09.021> and Sturm et al. (2010) <doi:10.1175/2010JHM1202.1>.

Last updated 4 years ago

1.00 score 3 scripts 141 downloads

TwoArmSurvSim - Simulate Survival Data for Randomized Clinical Trials

A system to simulate clinical trials with time to event endpoints. Event simulation is based on Cox models allowing for covariates in addition to the treatment or group factor. Specific drop-out rates (separate from administrative censoring) can be controlled in the simulation. Other features include stratified randomization, non-proportional hazards, different accrual patterns, and event projection (timing to reach the target event) based on interim data.

Last updated 4 years ago

1.00 score 2 scripts 131 downloads

mscp - Multiscale Change Point Detection via Gradual Bandwidth Adjustment in Moving Sum Processes

Multiscale moving sum procedure for the detection of changes in expectation in univariate sequences. References - Multiscale change point detection via gradual bandwidth adjustment in moving sum processes (2021+), Tijana Levajkovic and Michael Messer.

Last updated 4 years ago

1.00 score 119 downloads

stlTDNN - STL Decomposition and TDNN Hybrid Time Series Forecasting

Implementation of hybrid STL decomposition based time delay neural network model for univariate time series forecasting. For method details see Jha G K, Sinha, K (2014). <doi:10.1007/s00521-012-1264-z>, Xiong T, Li C, Bao Y (2018). <doi:10.1016/j.neucom.2017.11.053>.

Last updated 4 years ago

1.00 score 82 downloads

CoxICPen - Variable Selection for Cox's Model with Interval-Censored Data

Perform variable selection for Cox regression model with interval-censored data. Can deal with both low-dimensional and high-dimensional data. Case-cohort design can be incorporated. Two sets of covariates scenario can also be considered. The references are listed in the URL below.

Last updated 4 years ago

1.00 score 148 downloads

copulareg - Copula Regression

Fits multivariate models in an R-vine pair copula construction framework, in such a way that the conditional copula can be easily evaluated. In addition, the package implements functionality to compute or approximate the conditional expectation via the conditional copula.

Last updated 4 years ago

1.00 score 132 downloads

clusTransition - Monitor Changes in Cluster Solutions of Dynamic Datasets

Monitor and trace changes in clustering solutions of accumulating datasets at successive time points. The clusters can adopt External and Internal transition at succeeding time points. The External transitions comprise of Survived, Merged, Split, Disappeared, and newly Emerged candidates. In contrast, Internal transition includes changes in location and cohesion of the survived clusters. The package uses MONIC framework developed by Spiliopoulou, Ntoutsi, Theodoridis, and Schult (2006)<doi:10.1145/1150402.1150491> .

Last updated 4 years ago

1.00 score 147 downloads

RSmallTelescopes - Empirical Small Telescopes Analysis

We provide functions to perform an empirical small telescopes analysis. This package contains 2 functions, SmallTelescopes() and EstimatePower(). Users only need to call SmallTelescopes() to conduct the analysis. For more information on small telescopes analysis see Uri Simonsohn (2015) <doi:10.1177/0956797614567341>.

Last updated 4 years ago

1.00 score 144 downloads

EcotoneFinder - Characterising and Locating Ecotones and Communities

Analytical methods to locate and characterise ecotones, ecosystems and environmental patchiness along ecological gradients. Methods are implemented for isolated sampling or for space/time series. It includes Detrended Correspondence Analysis (Hill & Gauch (1980) <doi:10.1007/BF00048870>), fuzzy clustering (De Cáceres et al. (2010) <doi:10.1080/01621459.1963.10500845>), biodiversity indices (Jost (2006) <doi:10.1111/j.2006.0030-1299.14714.x>), and network analyses (Epskamp et al. (2012) <doi:10.18637/jss.v048.i04>) - as well as tools to explore the number of clusters in the data. Functions to produce synthetic ecological datasets are also provided.

Last updated 4 years ago

1.00 score 1 scripts 185 downloads

simsl - Single-Index Models with a Surface-Link

An implementation of a single-index regression for optimizing individualized dose rules from an observational study. To model interaction effects between baseline covariates and a treatment variable defined on a continuum, we employ two-dimensional penalized spline regression on an index-treatment domain, where the index is defined as a linear combination of the covariates (a single-index). An unspecified main effect for the covariates is allowed, which can also be modeled through a parametric model. A unique contribution of this work is in the parsimonious single-index parametrization specifically defined for the interaction effect term. We refer to Park, Petkova, Tarpey, and Ogden (2020) <doi:10.1111/biom.13320> (for the case of a discrete treatment) and Park, Petkova, Tarpey, and Ogden (2021) "A single-index model with a surface-link for optimizing individualized dose rules" <arXiv:2006.00267v2> for detail of the method. The model can take a member of the exponential family as a response variable and can also take an ordinal categorical response. The main function of this package is simsl().

Last updated 4 years ago

1.00 score 1 scripts 163 downloads

shutterplot - The R Shutter Plot Package

Shows the scatter plot along with the fitted regression lines. It depicts min, max, the three quartiles, mean, and sd for each variable. It also depicts sd-line, sd-box, r, r-square, prediction boundaries, and regression outliers.

Last updated 4 years ago

1.00 score 119 downloads

EstimateGroupNetwork - Perform the Joint Graphical Lasso and Selects Tuning Parameters

Can be used to simultaneously estimate networks (Gaussian Graphical Models) in data from different groups or classes via Joint Graphical Lasso. Tuning parameters are selected via information criteria (AIC / BIC / extended BIC) or cross validation.

Last updated 4 years ago

1.00 score 1 stars 9 scripts 264 downloads

PHSMM - Penalised Maximum Likelihood Estimation for Hidden Semi-Markov Models

Provides tools for penalised maximum likelihood estimation of hidden semi-Markov models (HSMMs) with flexible state dwell-time distributions. These include functions for model fitting, model checking and state-decoding. The package considers HSMMs for univariate time series with state-dependent gamma, normal, Poisson or Bernoulli distributions. For details, see Pohle, J., Adam, T. and Beumer, L.T. (2021): Flexible estimation of the state dwell-time distribution in hidden semi-Markov models. <arXiv:2101.09197>.

Last updated 4 years ago

openblascpp

1.00 score 3 scripts 197 downloads

FamilyRank - Algorithm for Ranking Predictors Using Graphical Domain Knowledge

Grows families of features by selecting features that maximize a weighted score calculated from empirical feature scores and graphical knowledge. The final weighted score for a feature is determined by summing a feature's family-weighted scores across all families in which the feature appears.

Last updated 4 years ago

1.00 score 8 scripts 734 downloads

essentials - Essential Functions not Included in Base R

Functions for converting objects to scalars (vectors of length 1) and a more inclusive definition of data that can be interpreted as numbers (numeric and complex alike).

Last updated 4 years ago

1.00 score 28 scripts 195 downloads

fdq - Forest Data Quality

Forest data quality is a package containing nine methods of analysis for forest databases, from databases containing inventory data and growth models, the focus of the analyzes is related to the quality of the data present in the database with a focus on consistency , punctuality and completeness of data.

Last updated 4 years ago

1.00 score 3 scripts 253 downloads

ECTTDNN - Cointegration Based Timedelay Neural Network Model

This cointegration based Time Delay Neural Network Model hybrid model allows the researcher to make use of the information extracted by the cointegrating vector as an input in the neural network model.

Last updated 4 years ago

1.00 score 1 stars 112 downloads

RatingScaleReduction - Rating Scale Reduction Procedure

Describes a new procedure of reducing items in a rating scale called Rating Scale Reduction (RSR). The new stop criterion in RSR procedure is added (stop global max). The function order is replaced by sort.list.

Last updated 4 years ago

1.00 score 8 scripts 152 downloads

eemdTDNN - EEMD and Its Variant Based Time Delay Neural Network Model

Forecasting univariate time series with different decomposition based time delay neural network models. For method details see Yu L, Wang S, Lai KK (2008). <doi:10.1016/j.eneco.2008.05.003>.

Last updated 4 years ago

1.00 score 197 downloads

memify - Constructing Functions That Keep State

A simple way to construct and maintain functions that keep state i.e. remember their argument lists. This can be useful when one needs to repeatedly invoke the same function with only a small number of argument changes at each invocation.

Last updated 4 years ago

1.00 score 119 downloads

sparsevb - Spike-and-Slab Variational Bayes for Linear and Logistic Regression

Implements variational Bayesian algorithms to perform scalable variable selection for sparse, high-dimensional linear and logistic regression models. Features include a novel prioritized updating scheme, which uses a preliminary estimator of the variational means during initialization to generate an updating order prioritizing large, more relevant, coefficients. Sparsity is induced via spike-and-slab priors with either Laplace or Gaussian slabs. By default, the heavier-tailed Laplace density is used. Formal derivations of the algorithms and asymptotic consistency results may be found in Kolyan Ray and Botond Szabo (2020) <doi:10.1080/01621459.2020.1847121> and Kolyan Ray, Botond Szabo, and Gabriel Clara (2020) <arXiv:2010.11665>.

Last updated 4 years ago

openblascppopenmp

1.00 score 8 scripts 152 downloads

MARSANNhybrid - MARS Based ANN Hybrid Model

Multivariate Adaptive Regression Spline (MARS) based Artificial Neural Network (ANN) hybrid model is combined Machine learning hybrid approach which selects important variables using MARS and then fits ANN on the extracted important variables.

Last updated 4 years ago

1.00 score 129 downloads

hdpca - Principal Component Analysis in High-Dimensional Data

In high-dimensional settings: Estimate the number of distant spikes based on the Generalized Spiked Population (GSP) model. Estimate the population eigenvalues, angles between the sample and population eigenvectors, correlations between the sample and population PC scores, and the asymptotic shrinkage factors. Adjust the shrinkage bias in the predicted PC scores. Dey, R. and Lee, S. (2019) <doi:10.1016/j.jmva.2019.02.007>.

Last updated 4 years ago

1.00 score 7 scripts 219 downloads

rBMF - Boolean Matrix Factorization

Provides four boolean matrix factorization (BMF) methods. BMF has many applications like data mining and categorical data analysis. BMF is also known as boolean matrix decomposition (BMD) and was found to be an NP-hard (non-deterministic polynomial-time) problem. Currently implemented methods are 'Asso' Miettinen, Pauli and others (2008) <doi:10.1109/TKDE.2008.53>, 'GreConD' R. Belohlavek, V. Vychodil (2010) <doi:10.1016/j.jcss.2009.05.002> , 'GreConDPlus' R. Belohlavek, V. Vychodil (2010) <doi:10.1016/j.jcss.2009.05.002> , 'topFiberM' A. Desouki, M. Roeder, A. Ngonga (2019) <arXiv:1903.10326>.

Last updated 4 years ago

1.00 score 122 downloads

GLMMRR - Generalized Linear Mixed Model (GLMM) for Binary Randomized Response Data

Generalized Linear Mixed Model (GLMM) for Binary Randomized Response Data. Includes Cauchit, Compl. Log-Log, Logistic, and Probit link functions for Bernoulli Distributed RR data. RR Designs: Warner, Forced Response, Unrelated Question, Kuk, Crosswise, and Triangular. Reference: Fox, J-P, Veen, D. and Klotzke, K. (2018). Generalized Linear Mixed Models for Randomized Responses. Methodology. <doi:10.1027/1614-2241/a000153>.

Last updated 4 years ago

1.00 score 7 scripts 190 downloads

apng - Convert Png Files into Animated Png

Convert several png files into an animated png file. This package exports only a single function `apng'. Call the apng function with a vector of file names (which should be png files) to convert them to a single animated png file.

Last updated 4 years ago

1.00 score 1 stars 2 scripts 187 downloads

MARSSVRhybrid - MARS SVR Hybrid

Multivariate Adaptive Regression Spline (MARS) based Support Vector Regression (SVR) hybrid model is combined Machine learning hybrid approach which selects important variables using MARS and then fits SVR on the extracted important variables.

Last updated 4 years ago

1.00 score 97 downloads

RobustBayesianCopas - Robust Bayesian Copas Selection Model

Fits the robust Bayesian Copas (RBC) selection model of Bai et al. (2020) <arXiv:2005.02930> for correcting and quantifying publication bias in univariate meta-analysis. Also fits standard random effects meta-analysis and the Copas-like selection model of Ning et al. (2017) <doi:10.1093/biostatistics/kxx004>.

Last updated 4 years ago

jagscpp

1.00 score 224 downloads

MRmediation - A Causal Mediation Method with Methylated Region (MR) as the Mediator

A causal mediation approach under the counterfactual framework to test the significance of total, direct and indirect effects. In this approach, a group of methylated sites from a predefined region are utilized as the mediator, and the functional transformation is used to reduce the possible high dimension in the region-based methylated sites and account for their location information.

Last updated 4 years ago

1.00 score 171 downloads

MCPtests - Multiples Comparisons Procedures

Performs the execution of the main procedures of multiple comparisons in the literature, Scott-Knott (1974) <http://www.jstor.org/stable/2529204>, Batista (2016) <http://repositorio.ufla.br/jspui/handle/1/11466>, including graphic representations and export to different extensions of its results. An additional part of the package is the presence of the performance evaluation of the tests (Type I error per experiment and the power). This will assist the user in making the decision for the chosen test.

Last updated 4 years ago

1.00 score 10 scripts 158 downloads

pointdensityP - Point Density for Geospatial Data

The function pointdensity returns a density count and the temporal average for every point in the original list. The dataframe returned includes four columns: lat, lon, count, and date_avg. The "lat" column is the original latitude data; the "lon" column is the original longitude data; the "count" is the density count of the number of points within a radius of radius*grid_size (the neighborhood); and the date_avg column includes the average date of each point in the neighborhood.

Last updated 4 years ago

1.00 score 1 stars 20 scripts 211 downloads

sccr - The Self-Consistent, Competing Risks (SC-CR) Algorithms

The SC-SR Algorithm is used to calculate fully non-parametric and self-consistent estimators of the cause-specific failure probabilities in the presence of interval-censoring and possible making of the failure cause in a competing risks environment. In the version 2.0 the function creating the probability matrix from double-censored data is added.

Last updated 4 years ago

1.00 score 140 downloads

latentgraph - Graphical Models with Latent Variables

Three methods are provided to estimate graphical models with latent variables: (1) Jin, Y., Ning, Y., and Tan, K. M. (2020) (preprint available); (2) Chandrasekaran, V., Parrilo, P. A. & Willsky, A. S. (2012) <doi:10.1214/11-AOS949>; (3) Tan, K. M., Ning, Y., Witten, D. M. & Liu, H. (2016) <doi:10.1093/biomet/asw050>.

Last updated 4 years ago

openblascpp

1.00 score 135 downloads

march - Markov Chains

Computation of various Markovian models for categorical data including homogeneous Markov chains of any order, MTD models, Hidden Markov models, and Double Chain Markov Models.

Last updated 4 years ago

1.00 score 1 stars 13 scripts 163 downloads

EwR - Econometrics with R

Function and data sets in the book entitled "R ile Temel Ekonometri", S.Guris, E.C.Akay, B. Guris(2020). The book published in Turkish. It is possible to makes Durbin two stage method for autocorrelation, generalized differencing method for correction autocorrelation, Hausman Test for identification and computes LM, LR and Wald test statistics for redundant variable by using the functions written in this package.

Last updated 4 years ago

1.00 score 1 scripts 164 downloads

mixcure - Mixture Cure Models

Implementation of parametric and semiparametric mixture cure models based on existing R packages. See details of the models in Peng and Yu (2020) <ISBN: 9780367145576>.

Last updated 4 years ago

1.00 score 2 scripts 153 downloads

WinRatio - Win Ratio for Prioritized Outcomes and 95% Confidence Interval

Calculate the win ratio for prioritized outcomes and the 95% confidence interval based on Bebu and Lachin (2016) <doi:10.1093/biostatistics/kxv032>. Three type of outcomes can be analyzed: survival "failure-time" events, repeated survival "failure-time" events and continuous or ordinal "non-failure time" events that are captured at specific time-points in the study.

Last updated 4 years ago

cpp

1.00 score 184 downloads

npsf - Nonparametric and Stochastic Efficiency and Productivity Analysis

Nonparametric efficiency measurement and statistical inference via DEA type estimators (see Färe, Grosskopf, and Lovell (1994) <doi:10.1017/CBO9780511551710>, Kneip, Simar, and Wilson (2008) <doi:10.1017/S0266466608080651> and Badunenko and Mozharovskyi (2020) <doi:10.1080/01605682.2019.1599778>) as well as Stochastic Frontier estimators for both cross-sectional data and 1st, 2nd, and 4th generation models for panel data (see Kumbhakar and Lovell (2003) <doi:10.1017/CBO9781139174411>, Badunenko and Kumbhakar (2016) <doi:10.1016/j.ejor.2016.04.049>). The stochastic frontier estimators can handle both half-normal and truncated normal models with conditional mean and heteroskedasticity. The marginal effects of determinants can be obtained.

Last updated 4 years ago

cpp

1.00 score 14 scripts 293 downloads

Pijavski - Global Univariate Minimization

Global univariate minimization of Lipschitz functions is performed by using Pijavski method, which was published in Pijavski (1972) <DOI:10.1016/0041-5553(72)90115-2>.

Last updated 4 years ago

cpp

1.00 score 1 scripts 149 downloads

nlnet - Nonlinear Network, Clustering, and Variable Selection Based on DCOL

It includes four methods: DCOL-based K-profiles clustering, non-linear network reconstruction, non-linear hierarchical clustering, and variable selection for generalized additive model. References: Tianwei Yu (2018)<DOI: 10.1002/sam.11381>; Haodong Liu and others (2016)<DOI: 10.1371/journal.pone.0158247>; Kai Wang and others (2015)<DOI: 10.1155/2015/918954>; Tianwei Yu and others (2010)<DOI: 10.1109/TCBB.2010.73>.

Last updated 4 years ago

1.00 score 1 stars 8 scripts 124 downloads

TestCor - FWER and FDR Controlling Procedures for Multiple Correlation Tests

Different multiple testing procedures for correlation tests are implemented. These procedures were shown to theoretically control asymptotically the Family Wise Error Rate (Roux (2018) <https://tel.archives-ouvertes.fr/tel-01971574v1>) or the False Discovery Rate (Cai & Liu (2016) <doi:10.1080/01621459.2014.999157>). The package gather four test statistics used in correlation testing, four FWER procedures with either single step or stepdown versions, and four FDR procedures.

Last updated 4 years ago

cpp

1.00 score 1 stars 23 scripts 180 downloads

robustDA - Robust Mixture Discriminant Analysis

Robust mixture discriminant analysis (RMDA), proposed in Bouveyron & Girard, 2009 <doi:10.1016/j.patcog.2009.03.027>, allows to build a robust supervised classifier from learning data with label noise. The idea of the proposed method is to confront an unsupervised modeling of the data with the supervised information carried by the labels of the learning data in order to detect inconsistencies. The method is able afterward to build a robust classifier taking into account the detected inconsistencies into the labels.

Last updated 4 years ago

1.00 score 3 scripts 165 downloads

SE.EQ - SE-Test for Equivalence

Implements the SE-test for equivalence according to Hoffelder et al. (2015) <DOI:10.1080/10543406.2014.920344>. The SE-test for equivalence is a multivariate two-sample equivalence test. Distance measure of the test is the sum of standardized differences between the expected values or in other words: the sum of effect sizes (SE) of all components of the two multivariate samples. The test is an asymptotically valid test for normally distributed data (see Hoffelder et al.,2015). The function SE.EQ() implements the SE-test for equivalence according to Hoffelder et al. (2015). The function SE.EQ.dissolution.profiles() implements a variant of the SE-test for equivalence for similarity analyses of dissolution profiles as mentioned in Suarez-Sharp et al.(2020) <DOI:10.1208/s12248-020-00458-9>). The equivalence margin used in SE.EQ.dissolution.profiles() is analogically defined as for the T2EQ approach according to Hoffelder (2019) <DOI:10.1002/bimj.201700257>) by means of a systematic shift in location of 10 [\% of label claim] of both dissolution profile populations. SE.EQ.dissolution.profiles() checks whether the weighted mean of the differences of the expected values of both dissolution profile populations is statistically significantly smaller than 10 [\% of label claim]. The weights are built up by the inverse variances.

Last updated 4 years ago

1.00 score 93 downloads

MLGdata - Datasets for Use with Salvan, Sartori and Pace (2020)

Contains the datasets for use with the book Salvan, Sartori and Pace (2020, ISBN:978-88-470-4002-1) "Modelli Lineari Generalizzati".

Last updated 4 years ago

1.00 score 1 scripts 285 downloads

FisherEM - The FisherEM Algorithm to Simultaneously Cluster and Visualize High-Dimensional Data

The FisherEM algorithm, proposed by Bouveyron & Brunet (2012) <doi:10.1007/s11222-011-9249-9>, is an efficient method for the clustering of high-dimensional data. FisherEM models and clusters the data in a discriminative and low-dimensional latent subspace. It also provides a low-dimensional representation of the clustered data. A sparse version of Fisher-EM algorithm is also provided.

Last updated 4 years ago

1.00 score 7 scripts 249 downloads

EDNE.EQ - Implements the EDNE-Test for Equivalence

Package implements the EDNE-test for equivalence according to Hoffelder et al. (2015) <DOI:10.1080/10543406.2014.920344>. "EDNE" abbreviates "Euclidean Distance between the Non-standardized Expected values". The EDNE-test for equivalence is a multivariate two-sample equivalence test. Distance measure of the test is the Euclidean distance. The test is an asymptotically valid test for the family of distributions fulfilling the assumptions of the multivariate central limit theorem (see Hoffelder et al.,2015). The function EDNE.EQ() implements the EDNE-test for equivalence according to Hoffelder et al. (2015). The function EDNE.EQ.dissolution.profiles() implements a variant of the EDNE-test for equivalence analyses of dissolution profiles (see Suarez-Sharp et al.,2020 <DOI:10.1208/s12248-020-00458-9>). EDNE.EQ.dissolution.profiles() checks whether the quadratic mean of the differences of the expected values of both dissolution profile populations is statistically significantly smaller than 10 [\% of label claim]. The current regulatory standard approach for equivalence analyses of dissolution profiles is the similarity factor f2. The statistical hypotheses underlying EDNE.EQ.dissolution.profiles() coincide with the hypotheses for f2 (see Hoffelder et al.,2015, Suarez-Sharp et al., 2020).

Last updated 4 years ago

1.00 score 176 downloads

corTest - Robust Tests for Equal Correlation

There are 6 novel robust tests for equal correlation. They are all based on logistic regressions. The score statistic U is proportion to difference of two correlations based on different types of correlation in 6 methods. The ST1() is based on Pearson correlation. ST2() improved ST1() by using median absolute deviation. ST3() utilized type M correlation and ST4() used Spearman correlation. ST5() and ST6() used two different ways to combine ST3() and ST4(). We highly recommend ST5() according to the article titled ''New Statistical Methods for Constructing Robust Differential Correlation Networks to characterize the interactions among microRNAs'' published in Scientific Reports. Please see the reference: Yu et al. (2019) <doi:10.1038/s41598-019-40167-8>.

Last updated 4 years ago

1.00 score 10 scripts 241 downloads

gSeg - Graph-Based Change-Point Detection (g-Segmentation)

Using an approach based on similarity graph to estimate change-point(s) and the corresponding p-values. Can be applied to any type of data (high-dimensional, non-Euclidean, etc.) as long as a reasonable similarity measure is available.

Last updated 4 years ago

1.00 score 1 stars 5 scripts 225 downloads

SailoR - An Extension of the Taylor Diagram to Two-Dimensional Vector Data

A new diagram for the verification of vector variables (wind, current, etc) generated by multiple models against a set of observations is presented in this package. It has been designed as a generalization of the Taylor diagram to two dimensional quantities. It is based on the analysis of the two-dimensional structure of the mean squared error matrix between model and observations. The matrix is divided into the part corresponding to the relative rotation and the bias of the empirical orthogonal functions of the data. The full set of diagnostics produced by the analysis of the errors between model and observational vector datasets comprises the errors in the means, the analysis of the total variance of both datasets, the rotation matrix corresponding to the principal components in observation and model, the angle of rotation of model-derived empirical orthogonal functions respect to the ones from observations, the standard deviation of model and observations, the root mean squared error between both datasets and the squared two-dimensional correlation coefficient. See the output of function UVError() in this package.

Last updated 4 years ago

1.00 score 107 downloads

testtwice - Testing One Hypothesis Twice in Observational Studies

Tests one hypothesis with several test statistics, correcting for multiple testing. The central function in the package is testtwice(). In a sensitivity analysis, the method has the largest design sensitivity of its component tests. The package implements the method and examples in Rosenbaum, P. R. (2012) <doi:10.1093/biomet/ass032> Testing one hypothesis twice in observational studies. Biometrika, 99(4), 763-774.

Last updated 4 years ago

1.00 score 99 downloads

ivitr - Estimate IV-Optimal Individualized Treatment Rules

A method that estimates an IV-optimal individualized treatment rule. An individualized treatment rule is said to be IV-optimal if it minimizes the maximum risk with respect to the putative IV and the set of IV identification assumptions. Please refer to <arXiv:2002.02579> for more details on the methodology and some theory underpinning the method. Function IV-PILE() uses functions in the package 'locClass'. Package 'locClass' can be accessed and installed from the 'R-Forge' repository via the following link: <https://r-forge.r-project.org/projects/locclass/>. Alternatively, one can install the package by entering the following in R: 'install.packages("locClass", repos="<http://R-Forge.R-project.org>")'.

Last updated 4 years ago

1.00 score 135 downloads

PSSIM - Test of Independence & Image Structural Similarity Measure PSSIM

Test-based Image structural similarity measure and test of independence. This package implements the key functions of two tasks: (1) computing image structural similarity measure PSSIM of Wang, Maldonado and Silwal (2011) <DOI:10.1016/j.csda.2011.04.021>; and (2) test of independence between a response and a covariate in presence of heteroscedastic treatment effects proposed by Wang, Tolos, and Wang (2010) <DOI:10.1002/cjs.10068>.

Last updated 4 years ago

1.00 score 118 downloads

spGARCH - Spatial ARCH and GARCH Models (spGARCH)

A collection of functions to deal with spatial and spatiotemporal autoregressive conditional heteroscedasticity (spatial ARCH and GARCH models) by Otto, Schmid, Garthoff (2018, Spatial Statistics) <arXiv:1609.00711>: simulation of spatial ARCH-type processes (spARCH, exponential spARCH, complex spARCH); quasi-maximum-likelihood estimation of the parameters of spARCH models and spatial autoregressive models with spARCH disturbances, diagnostic checks, visualizations.

Last updated 4 years ago

cpp

1.00 score 1 stars 4 scripts 214 downloads

BayesBP - Bayesian Estimation using Bernstein Polynomial Fits Rate Matrix

Smoothed lexis diagrams with Bayesian method specifically tailored to cancer incidence data. Providing to calculating slope and constructing credible interval. LC Chien et al. (2015) <doi:10.1080/01621459.2015.1042106>. LH Chien et al. (2017) <doi:10.1002/cam4.1102>.

Last updated 4 years ago

1.00 score 3 scripts 218 downloads

HeterFunctionalData - Test of No Main and/or Interaction Effects in Functional Data

Distribution free heteroscedastic tests for functional data. The following tests are included in this package: test of no main treatment or contrast effect and no simple treatment effect given in Wang, Higgins, and Blasi (2010) <doi:10.1016/j.spl.2009.11.016>, no main time effect, and no interaction effect based on original observations given in Wang and Akritas (2010a) <doi:10.1080/10485250903171621> and tests based on ranks given in Wang and Akritas (2010b) <doi:10.1016/j.jmva.2010.03.012>.

Last updated 4 years ago

1.00 score 116 downloads

glmglrt - GLRT P-Values in Generalized Linear Models

Provides functions to compute Generalized Likelihood Ratio Tests (GLRT) also known as Likelihood Ratio Tests (LRT) and Rao's score tests of simple and complex contrasts of Generalized Linear Models (GLMs). It provides the same interface as summary.glm(), adding GLRT P-values, less biased than Wald's P-values and consistent with profile-likelihood confidence interval generated by confint(). See Wilks (1938) <doi:10.1214/aoms/1177732360> for the LRT chi-square approximation. See Rao (1948) <doi:10.1017/S0305004100023987> for Rao's score test. See Wald (1943) <doi:10.2307/1990256> for Wald's test.

Last updated 4 years ago

1.00 score 1 scripts 155 downloads

nsarfima - Methods for Fitting and Simulating Non-Stationary ARFIMA Models

Routines for fitting and simulating data under autoregressive fractionally integrated moving average (ARFIMA) models, without the constraint of covariance stationarity. Two fitting methods are implemented, a pseudo-maximum likelihood method and a minimum distance estimator. Mayoral, L. (2007) <doi:10.1111/j.1368-423X.2007.00202.x>. Beran, J. (1995) <doi:10.1111/j.2517-6161.1995.tb02054.x>.

Last updated 4 years ago

1.00 score 1 stars 2 scripts 211 downloads

Phase12Compare - Simulates SPSO and Efftox Phase 12 Trials with Correlated Outcomes

Simulating and conducting four phase 12 clinical trials with correlated binary bivariate outcomes described. Uses the 'Efftox' (efficacy and toxicity tradeoff, <https://biostatistics.mdanderson.org/SoftwareDownload/SingleSoftware/Index/2>) and SPSO (Semi-Parametric Stochastic Ordering) models with Utility and Desirability based objective functions for dose finding.

Last updated 4 years ago

1.00 score 176 downloads

BeyondBenford - Compare the Goodness of Fit of Benford's and Blondeau Da Silva's Digit Distributions to a Given Dataset

Allows to compare the goodness of fit of Benford's and Blondeau Da Silva's digit distributions in a dataset. It is used to check whether the data distribution is consistent with theoretical distributions highlighted by Blondeau Da Silva or not (through the dat.distr() function): this ideal theoretical distribution must be at least approximately followed by the data for the use of Blondeau Da Silva's model to be well-founded. It also enables to plot histograms of digit distributions, both observed in the dataset and given by the two theoretical approaches (with the digit.ditr() function). Finally, it proposes to quantify the goodness of fit via Pearson's chi-squared test (with the chi2() function).

Last updated 4 years ago

1.00 score 9 scripts 311 downloads

l1ball - L1-Ball Prior for Sparse Regression

Provides function for the l1-ball prior on high-dimensional regression. The main function, l1ball(), yields posterior samples for linear regression, as introduced by Xu and Duan (2020) <arXiv:2006.01340>.

Last updated 4 years ago

1.00 score 131 downloads

asymmetry.measures - Asymmetry Measures for Probability Density Functions

Provides functions and examples for the weak and strong density asymmetry measures in the articles: "A measure of asymmetry", Patil, Patil and Bagkavos (2012) <doi:10.1007/s00362-011-0401-6> and "A measure of asymmetry based on a new necessary and sufficient condition for symmetry", Patil, Bagkavos and Wood (2014) <doi:10.1007/s13171-013-0034-z>. The measures provided here are useful for quantifying the asymmetry of the shape of a density of a random variable. The package facilitates implementation of the measures which are applicable in a variety of fields including e.g. probability theory, statistics and economics.

Last updated 4 years ago

1.00 score 202 downloads

ivdesign - Hypothesis Testing in Cluster-Randomized Encouragement Designs

An implementation of randomization-based hypothesis testing for three different estimands in a cluster-randomized encouragement experiment. The three estimands include (1) testing a cluster-level constant proportional treatment effect (Fisher's sharp null hypothesis), (2) pooled effect ratio, and (3) average cluster effect ratio. To test the third estimand, user needs to install 'Gurobi' (>= 9.0.1) optimizer via its R API. Please refer to <https://www.gurobi.com/documentation/9.0/refman/ins_the_r_package.html>.

Last updated 4 years ago

1.00 score 118 downloads

predReliability - Estimates Reliability of Individual Supervised Learning Predictions

An implementation of reliability estimation methods described in the paper (Bosnic, Z., & Kononenko, I. (2008) <doi:10.1007/s10489-007-0084-9>), which allows you to test the reliability of a single predicted instance made by your model and prediction function. It also allows you to make a correlation test to estimate which reliability estimate is the most accurate for your model.

Last updated 4 years ago

1.00 score 127 downloads

regrap - Reverse Graphical Approaches

The graphical approach is proposed as a general framework for clinical trial designs involving multiple hypotheses, where decisions are made only based on the observed marginal p-values. A reverse graphical approach starts from a set of singleton graphs, and gradually add vertices into graphs until rejection of a set of hypotheses is made. See Gou, J. (2020). Reverse graphical approaches for multiple test procedures. Technical Report.

Last updated 4 years ago

1.00 score 1 stars 117 downloads

MCBackscattering - Monte Carlo Simulation for Surface Backscattering

Monte Carlo simulation is a stochastic method computing trajectories of photons in media. Surface backscattering is performing calculations in semi-infinite media and summarizing photon flux leaving the surface. This simulation is modeling the optical measurement of diffuse reflectance using an incident light beam. The semi-infinite media is considered to have flat surface. Media, typically biological tissue, is described by four optical parameters: absorption coefficient, scattering coefficient, anisotropy factor, refractive index. The media is assumed to be homogeneous. Computational parameters of the simulation include: number of photons, radius of incident light beam, lowest photon energy threshold, intensity profile (halo) radius, spatial resolution of intensity profile. You can find more information and validation in the Open Access paper. Laszlo Baranyai (2020) <doi:10.1016/j.mex.2020.100958>.

Last updated 4 years ago

1.00 score 101 downloads

gridDebug - Debugging 'grid' Graphics

Functions for drawing scene trees representing scenes that have been drawn using grid graphics.

Last updated 4 years ago

1.00 score 3 scripts 161 downloads

cspec - Complete Discrete Fourier Transform (DFT) and Periodogram

Calculate the predictive discrete Fourier transform, complete discrete Fourier transform, complete periodogram, and tapered complete periodogram. This algorithm is based on the preprint "Spectral methods for small sample time series: A complete periodogram approach" (2020) by Sourav Das, Suhasini Subba Rao, and Junho Yang.

Last updated 4 years ago

1.00 score 1 scripts 115 downloads

RMPSH - Recursive Modified Pattern Search on Hyper-Rectangle

Optimization of any Black-Box/Non-Convex Function on Hyper-Rectangular Parameter Space. It uses a Variation of Pattern Search Technique. Described in the paper : Das (2016) <arXiv:1604.08616> .

Last updated 4 years ago

cpp

1.00 score 4 scripts 97 downloads

clda - Convolution-Based Linear Discriminant Analysis

Contains a time series classification method that obtains a set of filters that maximize the between-class and minimize the within-class distances.

Last updated 5 years ago

1.00 score 4 scripts 177 downloads

GMPro - Graph Matching with Degree Profiles

Functions for graph matching via nodes' degree profiles are provided in this package. The models we can handle include Erdos-Renyi random graphs and stochastic block models(SBM). More details are in the reference paper: Yaofang Hu, Wanjie Wang and Yi Yu (2020) <arXiv:2006.03284>.

Last updated 5 years ago

1.00 score 1 scripts 127 downloads

fuel - Framework for Unified Estimation in Lognormal Models

Lognormal models have broad applications in various research areas such as economics, actuarial science, biology, environmental science and psychology. The estimation problem in lognormal models has been extensively studied. This R package 'fuel' implements thirty-nine existing and newly proposed estimators. See Zhang, F., and Gou, J. (2020), A unified framework for estimation in lognormal models, Technical report.

Last updated 5 years ago

1.00 score 9 scripts 143 downloads

BreakPoints - Identify Breakpoints in Series of Data

Compute Buishand Range Test, Pettit Test, SNHT, Student t-test, and Mann-Whitney Rank Test, to identify breakpoints in series. For all functions NA is allowed. Since all of the mention methods identify only one breakpoint in a series, a general function to look for N breakpoint is given. Also, the Yamamoto test for climate jump is available. Alexandersson, H. (1986) <doi:10.1002/joc.3370060607>, Buishand, T. (1982) <doi:10.1016/0022-1694(82)90066-X>, Hurtado, S. I., Zaninelli, P. G., & Agosta, E. A. (2020) <doi:10.1016/j.atmosres.2020.104955>, Mann, H. B., Whitney, D. R. (1947) <doi:10.1214/aoms/1177730491>, Pettitt, A. N. (1979) <doi:10.2307/2346729>, Ruxton, G. D., jul (2006) <doi:10.1093/beheco/ark016>, Yamamoto, R., Iwashima, T., Kazadi, S. N., & Hoshiai, M. (1985) <doi:10.2151/jmsj1965.63.6_1157>.

Last updated 5 years ago

1.00 score 6 scripts 193 downloads

raincin - Ranking with Incomplete Information

Various statistical and mathematical ranking and rating methods with incomplete information are included. This package is initially designed for the scoring system in a high school project showcase to rank student research projects, where each judge can only evaluate a set of projects in a limited time period. See Langville, A. N. and Meyer, C. D. (2012), Who is Number 1: The Science of Rating and Ranking, Princeton University Press <doi:10.1515/9781400841677>, and Gou, J. and Wu, S. (2020), A Judging System for Project Showcase: Rating and Ranking with Incomplete Information, Technical Report.

Last updated 5 years ago

1.00 score 105 downloads

datasetsICR - Datasets from the Book "An Introduction to Clustering with R"

Companion to the book "An Introduction to Clustering with R" by P. Giordani, M.B. Ferraro and F. Martella (Springer, Singapore, 2020). The datasets are used in some case studies throughout the text.

Last updated 5 years ago

1.00 score 5 scripts 359 downloads

MetGen - Stochastic Weather Generator

An adaptation of the multi-variable stochastic weather generator proposed in 'Rglimclim' to perform gap-filling and temporal extension at sub-daily resolution. Simulation is performed based on large scale variables and climatic observation data that could be generated from different gauged stations having geographical proximity. SWG relies on reanalyses. Multi-variable dependence is taking into account by using the decomposition of the product rule (in statistics) into conditional probabilities. See <https://hal.archives-ouvertes.fr/hal-02554676>.

Last updated 5 years ago

1.00 score 115 downloads

abcrlda - Asymptotically Bias-Corrected Regularized Linear Discriminant Analysis

Offers methods to perform asymptotically bias-corrected regularized linear discriminant analysis (ABC_RLDA) for cost-sensitive binary classification. The bias-correction is an estimate of the bias term added to regularized discriminant analysis (RLDA) that minimizes the overall risk. The default magnitude of misclassification costs are equal and set to 0.5; however, the package also offers the options to set them to some predetermined values or, alternatively, take them as hyperparameters to tune. A. Zollanvari, M. Abdirash, A. Dadlani and B. Abibullaev (2019) <doi:10.1109/LSP.2019.2918485>.

Last updated 5 years ago

1.00 score 353 downloads

BayesARIMAX - Bayesian Estimation of ARIMAX Model

The Autoregressive Integrated Moving Average (ARIMA) model is very popular univariate time series model. Its application has been widened by the incorporation of exogenous variable(s) (X) in the model and modified as ARIMAX by Bierens (1987) <doi:10.1016/0304-4076(87)90086-8>. In this package we estimate the ARIMAX model using Bayesian framework.

Last updated 5 years ago

1.00 score 1 scripts 262 downloads

wbsd - Wild Bootstrap Size Diagnostics

Implements the diagnostic "theta" developed in Poetscher and Preinerstorfer (2020) "How Reliable are Bootstrap-based Heteroskedasticity Robust Tests?" <arXiv:2005.04089>. This diagnostic can be used to detect and weed out bootstrap-based procedures that provably have size equal to one for a given testing problem. The implementation covers a large variety of bootstrap-based procedures, cf. the above mentioned article for details. A function for computing bootstrap p-values is provided.

Last updated 5 years ago

cppopenmp

1.00 score 88 downloads

LSPFP - Lysate and Secretome Peptide Feature Plotter

Creates plots of peptides from shotgun proteomics analysis of secretome and lysate samples. These plots contain associated protein features and scores for potential secretion and truncation.

Last updated 5 years ago

1.00 score 3 scripts 172 downloads

plothelper - New Plots Based on 'ggplot2' and Functions to Create Regular Shapes

An extension to 'ggplot2' and 'magick'. It contains three groups of functions: Functions in the first group draw 'ggplot2' - based plots: geom_shading_bar() draws barplot with shading colors in each bar. geom_rect_cm(), geom_circle_cm() and geom_ellipse_cm() draw rectangles, circles and ellipses with centimeter as their unit. Thus their sizes do not change when the coordinate system or the aspect ratio changes. annotation_transparent_text() draws labels with transparent texts. annotation_shading_polygon() draws irregular polygons with shading colors. Functions in the second group generate coordinates for regular shapes and make linear transformations. Functions in the third group are 'magick' - based functions facilitating image processing.

Last updated 5 years ago

1.00 score 182 downloads

envoutliers - Methods for Identification of Outliers in Environmental Data

Three semi-parametric methods for detection of outliers in environmental data based on kernel regression and subsequent analysis of smoothing residuals. The first method (Campulova, Michalek, Mikuska and Bokal (2018) <DOI: 10.1002/cem.2997>) analyzes the residuals using changepoint analysis, the second method is based on control charts (Campulova, Veselik and Michalek (2017) <DOI: 10.1016/j.apr.2017.01.004>) and the third method (Holesovsky, Campulova and Michalek (2018) <DOI: 10.1016/j.apr.2017.06.005>) analyzes the residuals using extreme value theory (Holesovsky, Campulova and Michalek (2018) <DOI: 10.1016/j.apr.2017.06.005>).

Last updated 5 years ago

1.00 score 4 scripts 166 downloads

HMB - Hierarchical Model-Based Estimation Approach

For estimation of a variable of interest using two sources of auxiliary information available in a nested structure. For reference see Saarela et al. (2016)<doi:10.1007/s13595-016-0590-1> and Saarela et al. (2018) <doi:10.3390/rs10111832>.

Last updated 5 years ago

openblascppopenmp

1.00 score 7 scripts 123 downloads

MinEDfind - A Bayesian Design for Minimum Effective Dosing-Finding Trial

The nonparametric two-stage Bayesian adaptive design is a novel phase II clinical trial design for finding the minimum effective dose (MinED). This design is motivated by the top priority and concern of clinicians when testing a new drug, which is to effectively treat patients and minimize the chance of exposing them to subtherapeutic or overly toxic doses. It is used to design single-agent trials.

Last updated 5 years ago

1.00 score 106 downloads

pcalls - Pricing of Different Types of Call

Compute the price of different types of call using different methods. The types available are Vanilla European Calls, Vanilla American Calls and American Digital Calls. Available methods are Montecarlo Simulation, Montecarlo Simulation with Antithetic Variates, Black-Scholes and the Binary Tree.

Last updated 5 years ago

1.00 score 102 downloads

CeRNASeek - Identification and Analysis of ceRNA Regulation

Provides several functions to identify and analyse miRNA sponge, including popular methods for identifying miRNA sponge interactions, two types of global ceRNA regulation prediction methods and four types of context-specific prediction methods( Li Y et al.(2017) <doi:10.1093/bib/bbx137>), which are based on miRNA-messenger RNA regulation alone, or by integrating heterogeneous data, respectively. In addition, For predictive ceRNA relationship pairs, this package provides several downstream analysis algorithms, including regulatory network analysis and functional annotation analysis, as well as survival prognosis analysis based on expression of ceRNA ternary pair.

Last updated 5 years ago

competing endogenous rna (cerna)geneexpressiontripletfunctionsoftware

1.00 score 194 downloads

augSIMEX - Analysis of Data with Mixed Measurement Error and Misclassification in Covariates

Implementation of the augmented Simulation-Extrapolation (SIMEX) algorithm proposed by Yi et al. (2015) <doi:10.1080/01621459.2014.922777> for analyzing the data with mixed measurement error and misclassification. The main function provides a similar summary output as that of glm() function. Both parametric and empirical SIMEX are considered in the package.

Last updated 5 years ago

cpp

1.00 score 10 scripts 258 downloads

Diderot - Bibliographic Network Analysis

Enables the user to build a citation network/graph from bibliographic data and, based on modularity and heterocitation metrics, assess the degree of awareness/cross-fertilization between two corpora/communities. This toolset is optimized for Scopus data.

Last updated 5 years ago

1.00 score 22 scripts 215 downloads

FMCCSD - Efficient Estimation of Clustered Current Status Data

Current status data abounds in the field of epidemiology and public health, where the only observable data for a subject is the random inspection time and the event status at inspection. Motivated by such a current status data from a periodontal study where data are inherently clustered, we propose a unified methodology to analyze such complex data.

Last updated 5 years ago

openblascppopenmp

1.00 score 134 downloads

VUROCS - Volume under the ROC Surface for Multi-Class ROC Analysis

Calculates the volume under the ROC surface and its (co)variance for ordered multi-class ROC analysis as well as certain bivariate ordinal measures of association.

Last updated 5 years ago

cpp

1.00 score 1 scripts 108 downloads

DiscreteQvalue - Improved q-Values for Discrete Uniform and Homogeneous Tests

We consider a multiple testing procedure used in many modern applications which is the q-value method proposed by Storey and Tibshirani (2003), <doi:10.1073/pnas.1530509100>. The q-value method is based on the false discovery rate (FDR), hence versions of the q-value method can be defined depending on which estimator of the proportion of true null hypotheses, p0, is plugged in the FDR estimator. We implement the q-value method based on two classical pi0 estimators, and furthermore, we propose and implement three versions of the q-value method for homogeneous discrete uniform P-values based on pi0 estimators which take into account the discrete distribution of the P-values.

Last updated 5 years ago

1.00 score 162 downloads

bivrp - Bivariate Residual Plots with Simulation Polygons

Generates bivariate residual plots with simulation polygons for any diagnostics and bivariate model from which functions to extract the desired diagnostics, simulate new data and refit the models are available.

Last updated 5 years ago

1.00 score 3 scripts 170 downloads

approxmatch - Approximately Optimal Fine Balance Matching with Multiple Groups

Tools for constructing a matched design with multiple comparison groups. Further specifications of refined covariate balance restriction and exact match on covariate can be imposed. Matches are approximately optimal in the sense that the cost of the solution is at most twice the optimal cost, Crama and Spieksma (1992) <doi:10.1016/0377-2217(92)90078-N>, Karmakar, Small and Rosenbaum (2019) <doi:10.1080/10618600.2019.1584900>.

Last updated 5 years ago

1.00 score 5 scripts 189 downloads

eyeTrackR - Organising and Analysing Eye-Tracking Data

A set of functions for organising and analysing datasets from experiments run using 'Eyelink' eye-trackers. Organising functions help to clean and prepare eye-tracking datasets for analysis, and mark up key events such as display changes and responses made by participants. Analysing functions help to create means for a wide range of standard measures (such as 'mean fixation durations'), which can then be fed into the appropriate statistical analyses and graphing packages as necessary.

Last updated 5 years ago

1.00 score 217 downloads

extraterrestrial - Astrobiology Equations Estimating Extraterrestrial Life

Finding life outside the planet Earth several is the ultimate goal of an astrobiologist. Using known astronomical measurements and assumptions the probability of extraterrestrial life existence could be estimated. Equations such as the Drake equation (1961) as stated in the paper of Molina (2019) <arXiv:1912.01783>, Seager (2013) <https://www.space.com/22648-drake-equation-alien-life-seager.html> and Foucher et al, (2017) <doi:10.3390/life7040040> are included in the 'extraterrestrial' package.

Last updated 5 years ago

1.00 score 135 downloads

flexCWM - Flexible Cluster-Weighted Modeling

Allows maximum likelihood fitting of cluster-weighted models, a class of mixtures of regression models with random covariates. Methods are described in Angelo Mazza, Antonio Punzo, Salvatore Ingrassia (2018) <doi:10.18637/jss.v086.i02>.

Last updated 5 years ago

1.00 score 16 scripts 204 downloads

IPCWK - Kendall's Tau Partial Corr. for Survival Trait and Biomarkers

We propose the inverse probability-of-censoring weighted (IPCW) Kendall's tau to measure the association of the survival trait with biomarkers and Kendall's partial correlation to reflect the relationship of the survival trait with interaction variable conditional on main effects, as described in Wang and Chen (2020) <doi:10.1093/bioinformatics/btaa017>.

Last updated 5 years ago

1.00 score 127 downloads

IsoCheck - Isomorphism Check for Multi-Stage Factorial Designs with Randomization Restrictions

Contains functions to check the isomorphism of multi-stage factorial designs with randomisation restrictions based on balanced spreads and balanced covering stars of PG(n-1,2) as described in Spencer, Ranjan and Mendivil (2019) <doi:10.1007/s42519-019-0064-5>.

Last updated 5 years ago

1.00 score 126 downloads

KbMvtSkew - Khattree-Bahuguna's Univariate and Multivariate Skewness

Computes Khattree-Bahuguna's univariate and multivariate skewness, principal-component-based Khattree-Bahuguna's multivariate skewness. It also provides several measures of univariate or multivariate skewnesses including, Pearson’s coefficient of skewness, Bowley’s univariate skewness and Mardia's multivariate skewness. See Khattree, R. and Bahuguna, M. (2019) <doi: 10.1007/s41060-018-0106-1>.

Last updated 5 years ago

1.00 score 139 downloads

NonNorMvtDist - Multivariate Lomax (Pareto Type II) and Its Related Distributions

Implements calculation of probability density function, cumulative distribution function, equicoordinate quantile function and survival function, and random numbers generation for the following multivariate distributions: Lomax (Pareto Type II), generalized Lomax, Mardia’s Pareto of Type I, Logistic, Burr, Cook-Johnson’s uniform, F and Inverted Beta. See Tapan Nayak (1987) <doi:10.2307/3214068>.

Last updated 5 years ago

1.00 score 170 downloads

onlineCOV - Online Change Point Detection in High-Dimensional Covariance Structure

Implement a new stopping rule to detect anomaly in the covariance structure of high-dimensional online data. The detection procedure can be applied to Gaussian or non-Gaussian data with a large number of components. Moreover, it allows both spatial and temporal dependence in data. The dependence can be estimated by a data-driven procedure. The level of threshold in the stopping rule can be determined at a pre-selected average run length. More detail can be seen in Li, L. and Li, J. (2020) "Online Change-Point Detection in High-Dimensional Covariance Structure with Application to Dynamic Networks." <arXiv:1911.07762>.

Last updated 5 years ago

1.00 score 85 downloads

ipr - Iterative Proportional Repartition Algorithm

Let us consider a sample of patients who can suffer from several diseases simultaneously, in a given set of diseases. The goal of the implemented algorithm is to estimate the individual average cost of each disease, starting from the global health costs available for each patient.

Last updated 5 years ago

1.00 score 123 downloads

sdafilter - Symmetrized Data Aggregation

We develop a new class of distribution free multiple testing rules for false discovery rate (FDR) control under general dependence. A key element in our proposal is a symmetrized data aggregation (SDA) approach to incorporating the dependence structure via sample splitting, data screening and information pooling. The proposed SDA filter first constructs a sequence of ranking statistics that fulfill global symmetry properties, and then chooses a data driven threshold along the ranking to control the FDR. For more information, see the website below and the accompanying paper: Du et al. (2020), "False Discovery Rate Control Under General Dependence By Symmetrized Data Aggregation", <arXiv:2002.11992>.

Last updated 5 years ago

1.00 score 1 scripts 121 downloads

TrendInTrend - Odds Ratio Estimation and Power Calculation for the Trend in Trend Model

Estimation of causal odds ratio and power calculation given trends in exposure prevalence and outcome frequencies of stratified data.

Last updated 5 years ago

1.00 score 1 stars 3 scripts 186 downloads

IncomPair - Comparison of Means for the Incomplete Paired Data

Implements a variety of nonparametric and parametric methods that are commonly used when the data set is a mixture of paired observations and independent samples. The package also calculates and returns values of different tests with their corresponding p-values. Bhoj, D. S. (1991) <doi:10.1002/bimj.4710330108> "Testing equality of means in the presence of correlation and missing data". Dubnicka, S. R., Blair, R. C., and Hettmansperger, T. P. (2002) <doi:10.22237/jmasm/1020254460> "Rank-based procedures for mixed paired and two-sample designs". Einsporn, R. L. and Habtzghi, D. (2013) <https://pdfs.semanticscholar.org/89a3/90bafeb2bc41ed4414533cfd5ab84a6b54b6.pdf> "Combining paired and two-sample data using a permutation test". Ekbohm, G. (1976) <doi:10.1093/biomet/63.2.299> "On comparing means in the paired case with incomplete data on both responses". Lin, P. E. and Stivers, L. E. (1974) <doi:10.1093/biomet/61.2.325> On difference of means with incomplete data". Maritz, J. S. (1995) <doi:10.1111/j.1467-842x.1995.tb00649.x> "A permutation paired test allowing for missing values".

Last updated 5 years ago

1.00 score 2 scripts 167 downloads

RBtest - Regression-Based Approach for Testing the Type of Missing Data

The regression-based (RB) approach is a method to test the missing data mechanism. This package contains two functions that test the type of missing data (Missing Completely At Random vs Missing At Random) on the basis of the RB approach. The first function applies the RB approach independently on each variable with missing data, using the completely observed variables only. The second function tests the missing data mechanism globally (on all variables with missing data) with the use of all available information. The algorithm is adapted both to continuous and categorical data.

Last updated 5 years ago

1.00 score 6 scripts 163 downloads

GPL2025 - Convert Chip ID of the GPL2015 into GeneBank Accession and ENTREZID

Convert the chip ID of GPL2025 <https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL2025> to GeneBank Accession and ENTREZID <http://www.ncbi.nlm.nih.gov/gene>.

Last updated 5 years ago

1.00 score 135 downloads

FinePop2 - Fine-Scale Population Analysis (Rewrite for Gene-Trait-Environment Interaction Analysis)

Statistical tool set for population genetics. The package provides following functions: 1) estimators of genetic differentiation (FST), 2) regression analysis of environmental effects on genetic differentiation using generalized least squares (GLS) method, 3) interfaces to read and manipulate 'GENEPOP' format data files). For more information, see Kitada, Nakamichi and Kishino (2020) <doi:10.1101/2020.01.30.927186>.

Last updated 5 years ago

1.00 score 1 scripts 120 downloads

dundermifflin - The Office Quotes on-Demand

Provides functions to randomly select, return, and print quotes or entire scenes from the American version of the show the Office. Receive laughs from one of of the greatest sitcoms of all time on demand. Add these functions to your '.Rprofile' to get a good laugh everytime you start a new R session.

Last updated 5 years ago

1.00 score 10 scripts 138 downloads

TUWmodel - Lumped/Semi-Distributed Hydrological Model for Education Purposes

The model, developed at the Vienna University of Technology, is a lumped conceptual rainfall-runoff model, following the structure of the HBV model. The model can also be run in a semi-distributed fashion and with dual representation of soil layer. The model runs on a daily or shorter time step and consists of a snow routine, a soil moisture routine and a flow routing routine. See Parajka, J., R. Merz, G. Bloeschl (2007) <DOI:10.1002/hyp.6253> Uncertainty and multiple objective calibration in regional water balance modelling: case study in 320 Austrian catchments, Hydrological Processes, 21, 435-446.

Last updated 5 years ago

fortran

1.00 score 1 stars 7 scripts 297 downloads

ricegeneann - Gene Annotation of Rice (Oryza Sativa L.spp.japonica)

Gene annotation of rice (Oryza Sativa L.spp.japonica). The package is based on the annotation file from the website <http://plants.ensembl.org/Oryza_sativa/Info/Index>. Input gene's name then return some information, including the from position, the end position, the position type and the chromosome number.

Last updated 5 years ago

1.00 score 103 downloads

evidenceFactors - Reporting Tools for Sensitivity Analysis of Evidence Factors in Observational Studies

Provides tools for integrated sensitivity analysis of evidence factors in observational studies. When an observational study allows for multiple independent or nearly independent inferences which, if vulnerable, are vulnerable to different biases, we have multiple evidence factors. This package provides methods that respect type I error rate control. Examples are provided of integrated evidence factors analysis in a longitudinal study with continuous outcome and in a case-control study. Karmakar, B., French, B., and Small, D. S. (2019)<DOI:10.1093/biomet/asz003>.

Last updated 5 years ago

1.00 score 5 scripts 154 downloads

PredictionR - Prediction for Future Data from any Continuous Distribution

Functions to get prediction intervals and prediction points of future observations from any continuous distribution.

Last updated 5 years ago

1.00 score 3 scripts 146 downloads

bssn - Birnbaum-Saunders Model

It provides the density, distribution function, quantile function, random number generator, reliability function, failure rate, likelihood function, moments and EM algorithm for Maximum Likelihood estimators, also empirical quantile and generated envelope for a given sample, all this for the three parameter Birnbaum-Saunders model based on Skew-Normal Distribution. Also, it provides the random number generator for the mixture of Birnbaum-Saunders model based on Skew-Normal distribution. Additionally, we incorporate the EM algorithm based on the assumption that the error term follows a finite mixture of Sinh-normal distributions.

Last updated 5 years ago

1.00 score 5 scripts 181 downloads

variosig - Testing Spatial Dependence Using Empirical Variogram

Applying Monte Carlo permutation to generate pointwise variogram envelope and checking for spatial dependence at different scales using permutation test. Empirical Brown's method and Fisher's method are used to compute overall p-value for hypothesis test.

Last updated 5 years ago

1.00 score 7 scripts 134 downloads

cdlei - Cause-Deleted Life Expectancy Improvement Procedure

The concept of cause-deleted life expectancy improvement is statistic designed to quantify the increase in life expectancy if a certain cause of death is removed. See Adamic, P. (2015) (<https://papers.ssrn.com/sol3/papers.cfm?abstract_id=2689352>).

Last updated 5 years ago

1.00 score 133 downloads

factset.analyticsapi.engines - 'FactSet' Engines API Client

Allow clients to fetch 'analytics' through API for Portfolio 'Analytics'('PA'), Style Performance Risk('SPAR') and 'Vault' products of 'FactSet'. Visit <https://github.com/factset/analyticsapi-engines-r-sdk/tree/master/Engines> for more information on the usage of package. Visit <https://developer.factset.com/> for more information on products.

Last updated 5 years ago

1.00 score 25 scripts 141 downloads

BioProbability - Probability in Biostatistics

Several tools for analyzing diagnostic tests and 2x2 contingency tables are provided. In particular, positive and negative predictive values for a diagnostic tests can be calculated from prevalence, sensitivity and specificity values. For contingency tables, relative risk and odds ratio measures are estimated. Furthermore, confidence intervals are provided.

Last updated 5 years ago

1.00 score 3 scripts 494 downloads

Boptbd - Bayesian Optimal Block Designs

Computes Bayesian A- and D-optimal block designs under the linear mixed effects model settings using block/array exchange algorithm of Debusho, Gemechu and Haines (2018) <doi:10.1080/03610918.2018.1429617> where the interest is in a comparison of all possible elementary treatment contrasts. The package also provides an optional method of using the graphical user interface (GUI) R package 'tcltk' to ensure that it is user friendly.

Last updated 5 years ago

1.00 score 178 downloads

SCVA - Single-Case Visual Analysis

Make graphical representations of single case data and transform graphical displays back to raw data, as discussed in Bulte and Onghena (2013) <doi:10.22237/jmasm/1383280020>. The package also includes tools for visually analyzing single-case data, by displaying central location, variability and trend.

Last updated 5 years ago

1.00 score 7 scripts 312 downloads

lcpm - Ordinal Outcomes: Generalized Linear Models with the Log Link

An implementation of the Log Cumulative Probability Model (LCPM) and Proportional Probability Model (PPM) for which the Maximum Likelihood Estimates are determined using constrained optimization. This implementation accounts for the implicit constraints on the parameter space. Other features such as standard errors, z tests and p-values use standard methods adapted from the results based on constrained optimization.

Last updated 5 years ago

1.00 score 2 scripts 117 downloads

olr - Optimal Linear Regression

The optimal linear regression olr(), runs all the possible combinations of linear regression equations. The olr() returns the equation which has the greatest adjusted R-squared term or the greatest R-squared term based on the user's discretion. Essentially, the olr() returns the best fit equation out of all the possible equations. R-squared increases with the addition of an explanatory variable whether it is 'significant' or not, thus this was developed to eliminate that conundrum. Adjusted R-squared is preferred to overcome this phenomenon, but each combination will still produce different results and this will return the best one. Complimentary functions are included which list all of the equations, all of the equations in ascending order, a function to give the user a specific model's summary, and the list of adjusted R-squared terms & R-squared terms. A 'Python' version is available at: <https://pypi.org/project/olr/>.

Last updated 5 years ago

1.00 score 108 downloads

nmadb - Network Meta-Analysis Database API

Set of functions for accessing database of network meta-analyses described in Petropoulou M, et al. Bibliographic study showed improving statistical methodology of network meta-analyses published between 1999 and 2015 <doi:10.1016/j.jclinepi.2016.11.002>. The database is hosted in a REDcap database at the Institute of Social and Preventive Medicine (ISPM) in the University of Bern.

Last updated 5 years ago

1.00 score 10 scripts 158 downloads

RRI - Residual Randomization Inference for Regression Models

Testing and inference for regression models using residual randomization methods. The basis of inference is an invariance assumption on the regression errors, e.g., clustered errors, or doubly-clustered errors.

Last updated 5 years ago

openblascpp

1.00 score 133 downloads

LPower - Calculates Power, Sample Size, or Detectable Effect for Longitudinal Analyses

Computes power, or sample size or the detectable difference for a repeated measures model with attrition. It requires the variance covariance matrix of the observations but can compute this matrix for several common random effects models. See Diggle, P, Liang, KY and Zeger, SL (1994, ISBN:9780198522843).

Last updated 5 years ago

1.00 score 3 scripts 113 downloads

vagam - Variational Approximations for Generalized Additive Models

Fits generalized additive models (GAMs) using a variational approximations (VA) framework. In brief, the VA framework provides a fully or at least closed to fully tractable lower bound approximation to the marginal likelihood of a GAM when it is parameterized as a mixed model (using penalized splines, say). In doing so, the VA framework aims offers both the stability and natural inference tools available in the mixed model approach to GAMs, while achieving computation times comparable to that of using the penalized likelihood approach to GAMs. See Hui et al. (2018) <doi:10.1080/01621459.2018.1518235>.

Last updated 5 years ago

1.00 score 7 scripts 119 downloads

GSelection - Genomic Selection

Genomic selection is a specialized form of marker assisted selection. The package contains functions to select important genetic markers and predict phenotype on the basis of fitted training data using integrated model framework (Guha Majumdar et. al. (2019) <doi:10.1089/cmb.2019.0223>) developed by combining one additive (sparse additive models by Ravikumar et. al. (2009) <doi:10.1111/j.1467-9868.2009.00718.x>) and one non-additive (hsic lasso by Yamada et. al. (2014) <doi:10.1162/NECO_a_00537>) model.

Last updated 5 years ago

1.00 score 20 scripts 131 downloads

cvmdisc - Cramer von Mises Tests for Discrete or Grouped Distributions

Implements Cramer-von Mises Statistics for testing fit to (1) fully specified discrete distributions as described in Choulakian, Lockhart and Stephens (1994) <doi:10.2307/3315828> (2) discrete distributions with unknown parameters that must be estimated from the sample data, see Spinelli & Stephens (1997) <doi:10.2307/3315735> and Lockhart, Spinelli and Stephens (2007) <doi:10.1002/cjs.5550350111> (3) grouped continuous distributions with Unknown Parameters, see Spinelli (2001) <doi:10.2307/3316040>. Maximum likelihood estimation (MLE) is used to estimate the parameters. The package computes the Cramer-von Mises Statistics, Anderson-Darling Statistics and the Watson-Stephens Statistics and their p-values.

Last updated 5 years ago

1.00 score 1 scripts 132 downloads

cotrend - Consistent Co-Trending Rank Selection

Implements cointegration/co-trending rank selection algorithm in Guo and Shintani (2013) "Consistent co-trending rank selection when both stochastic and nonlinear deterministic trends are present". The Econometrics Journal 16: 473-483 <doi:10.1111/j.1368-423X.2012.00392.x>. Numbered examples correspond to Feb 2011 preprint <http://www.fas.nus.edu.sg/ecs/events/seminar/seminar-papers/05Apr11.pdf>.

Last updated 5 years ago

1.00 score 2 scripts 173 downloads

agrostab - Stability Analysis for Agricultural Research

Statistical procedures to perform stability analysis in plant breeding and to identify stable genotypes under diverse environments. It is possible to calculate coefficient of homeostaticity by Khangildin et al. (1979), variance of specific adaptive ability by Kilchevsky&Khotyleva (1989), weighted homeostaticity index by Martynov (1990), steadiness of stability index by Udachin (1990), superiority measure by Lin&Binn (1988) <doi:10.4141/cjps88-018>, regression on environmental index by Erberhart&Rassel (1966) <doi:10.2135/cropsci1966.0011183X000600010011x>, Tai's (1971) stability parameters <doi:10.2135/cropsci1971.0011183X001100020006x>, stability variance by Shukla (1972) <doi:10.1038/hdy.1972.87>, ecovalence by Wricke (1962), nonparametric stability parameters by Nassar&Huehn (1987) <doi:10.2307/2531947>, Francis&Kannenberg's parameters of stability (1978) <doi:10.4141/cjps78-157>.

Last updated 5 years ago

1.00 score 1 scripts 269 downloads

rrat - Robust Regression with Asymmetric Heavy-Tail Noise Distributions

Implementation of Robust Regression tailored to deal with Asymmetric noise Distribution, which was originally proposed by Takeuchi & Bengio & Kanamori (2002) <doi:10.1162/08997660260293300>. In addition, this implementation is extended as introducing potential feature regularization by LASSO etc.

Last updated 5 years ago

1.00 score 95 downloads

BHAI - Estimate the Burden of Healthcare-Associated Infections

Provides an approach which is based on the methodology of the Burden of Communicable Diseases in Europe (BCoDE) and can be used for large and small samples such as individual countries. The Burden of Healthcare-Associated Infections (BHAI) is estimated in disability-adjusted life years, number of infections as well as number of deaths per year. Results can be visualized with various plotting functions and exported into tables.

Last updated 5 years ago

1.00 score 155 downloads

rlmDataDriven - Robust Regression with Data Driven Tuning Parameter

Data driven approach for robust regression estimation in homoscedastic and heteroscedastic context. See Wang et al. (2007), <doi:10.1198/106186007X180156> regarding homoscedastic framework.

Last updated 5 years ago

1.00 score 4 scripts 151 downloads

ccda - Combined Cluster and Discriminant Analysis

Implements the combined cluster and discriminant analysis method for finding homogeneous groups of data with known origin as described in Kovacs et. al (2014): Classification into homogeneous groups using combined cluster and discriminant analysis (CCDA). Environmental Modelling & Software. <doi:10.1016/j.envsoft.2014.01.010>.

Last updated 5 years ago

1.00 score 4 scripts 178 downloads

MLCIRTwithin - Latent Class Item Response Theory (LC-IRT) Models under Within-Item Multidimensionality

Framework for the Item Response Theory analysis of dichotomous and ordinal polytomous outcomes under the assumption of within-item multidimensionality and discreteness of the latent traits. The fitting algorithms allow for missing responses and for different item parametrizations and are based on the Expectation-Maximization paradigm. Individual covariates affecting the class weights may be included in the new version together with possibility of constraints on all model parameters.

Last updated 5 years ago

1.00 score 10 scripts 231 downloads

varEst - Variance Estimation

Error variance estimation in ultrahigh dimensional datasets with four different methods, viz. Refitted cross validation, k-fold refitted cross validation, Bootstrap-refitted cross validation, Ensemble method.

Last updated 5 years ago

1.00 score 1 stars 1 scripts 98 downloads

GLSME - Generalized Least Squares with Measurement Error

Performs linear regression with correlated predictors, responses and correlated measurement errors in predictors and responses, correcting for biased caused by these.

Last updated 5 years ago

1.00 score 4 scripts 183 downloads

ddpca - Diagonally Dominant Principal Component Analysis

Efficient procedures for fitting the DD-PCA (Ke et al., 2019, <arXiv:1906.00051>) by decomposing a large covariance matrix into a low-rank matrix plus a diagonally dominant matrix. The implementation of DD-PCA includes the convex approach using the Alternating Direction Method of Multipliers (ADMM) and the non-convex approach using the iterative projection algorithm. Applications of DD-PCA to large covariance matrix estimation and global multiple testing are also included in this package.

Last updated 5 years ago

1.00 score 132 downloads

DRAYL - Computation of Rayleigh Densities of Arbitrary Dimension

We offer an implementation of the series representation put forth in "A series representation for multidimensional Rayleigh distributions" by Wiegand and Nadarajah <DOI: 10.1002/dac.3510>. Furthermore we have implemented an integration approach proposed by Beaulieu et al. for 3 and 4-dimensional Rayleigh densities (Beaulieu, Zhang, "New simplest exact forms for the 3D and 4D multivariate Rayleigh PDFs with applications to antenna array geometrics", <DOI: 10.1109/TCOMM.2017.2709307>).

Last updated 5 years ago

1.00 score 148 downloads

ClickClustCont - Mixtures of Continuous Time Markov Models

Provides an expectation maximization (EM) algorithm to fit a mixture of continuous time Markov models for use with clickstream or other sequence type data. Gallaugher, M.P.B and McNicholas, P.D. (2018) <arXiv:1802.04849>.

Last updated 5 years ago

1.00 score 154 downloads

MWright - Mainardi-Wright Family of Distributions

Implements random number generation, plotting, and estimation algorithms for the two-parameter one-sided and two-sided M-Wright (Mainardi-Wright) family. The M-Wright distributions naturally generalize the widely used one-sided (Airy and half-normal or half-Gaussian) and symmetric (Airy and Gaussian or normal) models. These are widely studied in time-fractional differential equations. References: Cahoy and Minkabo (2017) <doi:10.3233/MAS-170388>; Cahoy (2012) <doi:10.1007/s00180-011-0269-x>; Cahoy (2012) <doi:10.1080/03610926.2010.543299>; Cahoy (2011); Mainardi, Mura, and Pagnini (2010) <doi:10.1155/2010/104505>.

Last updated 5 years ago

1.00 score 111 downloads

TrendSLR - Estimating Trend, Velocity and Acceleration from Sea Level Records

Analysis of annual average ocean water level time series, providing improved estimates of trend (mean sea level) and associated real-time velocities and accelerations. Improved trend estimates are based on singular spectrum analysis methods. Various gap-filling options are included to accommodate incomplete time series records. The package also includes a range of diagnostic tools to inspect the components comprising the original time series which enables expert interpretation and selection of likely trend components. A wide range of screen and plot to file options are available in the package.

Last updated 5 years ago

1.00 score 91 downloads

HextractoR - Integrated Tool for Hairping Extraction of RNA Sequences

Simple and integrated tool that automatically extracts and folds all hairpin sequences from raw genome-wide data. It predicts the secondary structure of several overlapped segments, with longer length than the mean length of sequences of interest for the species under processing, ensuring that no one is lost nor inappropriately cut.

Last updated 5 years ago

1.00 score 6 scripts 144 downloads

simdistr - Assessment of Data Trial Distributions According to the Carlisle-Stouffer Method

Assessment of the distributions of baseline continuous and categorical variables in randomised trials. This method is based on the Carlisle-Stouffer method with Monte Carlo simulations. It calculates p-values for each trial baseline variable, as well as combined p-values for each trial - these p-values measure how compatible are distributions of trials baseline variables with random sampling. This package also allows for graphically plotting the cumulative frequencies of computed p-values. Please note that code was partly adapted from Carlisle JB, Loadsman JA. (2017) <doi:10.1111/anae.13650>.

Last updated 5 years ago

1.00 score 2 scripts 130 downloads

phenModel - Insect Phenology Model Evaluation Based on Daily Temperatures

Generates predicted stage change days for an insect, based on daily temperatures and development rate parameters, as developed by Pollard (2014) <http://mural.maynoothuniversity.ie/view/ethesisauthor/Pollard=3ACiaran_P=2E=3A=3A.html>. A few example datasets are included and implemented for P. vulgatissima, the blue willow beetle, but the approach can be readily applied to other species that display similar behaviour.

Last updated 5 years ago

1.00 score 130 downloads

MatSkew - Matrix Skew-T Parameter Estimation

Performs matrix skew-t parameter estimation, Gallaugher and McNicholas (2017) <doi: 10.1002/sta4.143>.

Last updated 5 years ago

1.00 score 107 downloads

flexmixNL - Finite Mixture Modeling of Generalized Nonlinear Models

The fitting of mixtures of generalized nonlinear models is implemented as an extension of the existing package 'flexmix'.

Last updated 5 years ago

1.00 score 115 downloads

parade - Pen's Income Parades

Tool for producing Pen's parade graphs, useful for visualizing inequalities in income, wages or other variables, as proposed by Pen (1971, ISBN: 978-0140212594). Income or another economic variable is captured by the vertical axis, while the population is arranged in ascending order of income along the horizontal axis. Pen's income parades provide an easy-to-interpret visualization of economic inequalities.

Last updated 5 years ago

1.00 score 87 downloads

RZigZag - Zig-Zag Sampler

Implements the Zig-Zag algorithm (Bierkens, Fearnhead, Roberts, 2016) <arXiv:1607.03188> applied and Bouncy Particle Sampler <arXiv:1510.02451> for a Gaussian target and Student distribution.

Last updated 5 years ago

cpp

1.00 score 5 scripts 175 downloads

CautiousLearning - Control Charts with Guaranteed In-Control Performance and Cautious Parameters Learning

Design and use of control charts for detecting mean changes based on a delayed updating of the in-control parameter estimates. See Capizzi and Masarotto (2019) <doi:10.1080/00224065.2019.1640096> for the description of the method.

Last updated 5 years ago

cppopenmp

1.00 score 173 downloads

kosel - Variable Selection by Revisited Knockoffs Procedures

Performs variable selection for many types of L1-regularised regressions using the revisited knockoffs procedure. This procedure uses a matrix of knockoffs of the covariates independent from the response variable Y. The idea is to determine if a covariate belongs to the model depending on whether it enters the model before or after its knockoff. The procedure suits for a wide range of regressions with various types of response variables. Regression models available are exported from the R packages 'glmnet' and 'ordinalNet'. Based on the paper linked to via the URL below: Gegout A., Gueudin A., Karmann C. (2019) <arXiv:1907.03153>.

Last updated 5 years ago

1.00 score 124 downloads

intervcomp - Hypothesis Testing Using the Overlapping Interval Estimates

Performs hypothesis testing using the interval estimates (e.g., confidence intervals). The non-overlapping interval estimates indicates the statistical significance. References to these procedures can be found at Noguchi and Marmolejo-Ramos (2016) <doi:10.1080/00031305.2016.1200487>, Bonett and Seier (2003) <doi:10.1198/0003130032323>, and Lemm (2006) <doi:10.1300/J082v51n02_05>.

Last updated 5 years ago

1.00 score 3 scripts 99 downloads

FractalParameterEstimation - Simulation and Parameter Estimation of Randomized Sierpinski Carpets using the p-p-p-q-Model

The parameters p and q are estimated with the aid of a randomized Sierpinski Carpet which is built on a [p-p-p-q]-model. Thereby, for three times a simulation with a p-value and once with a q-value is assumed. Hence, these parameters are estimated and displayed. Moreover, functions for simulating random Sierpinski-Carpets with constant and variable probabilities are included. For more details on the method please see Hermann et al. (2015) <doi:10.1002/sim.6497>.

Last updated 5 years ago

1.00 score 10 scripts 152 downloads

RKHSMetaMod - Ridge Group Sparse Optimization Problem for Estimation of a Meta Model Based on Reproducing Kernel Hilbert Spaces

Estimates the Hoeffding decomposition of an unknown function by solving ridge group sparse optimization problem based on reproducing kernel Hilbert spaces, and approximates its sensitivity indices (see Kamari, H., Huet, S. and Taupin, M.-L. (2019) <arXiv:1905.13695>).

Last updated 5 years ago

gslcpp

1.00 score 1 scripts 140 downloads

StratifiedBalancing - Stratified Covariate Balancing

Performs Stratified Covariate Balancing with Markov blanket feature selection and use of synthetic cases. See Alemi et al. (2016) <DOI:10.1111/1475-6773.12628>.

Last updated 5 years ago

1.00 score 4 scripts 147 downloads

ternvis - Visualisation, Verification and Calibration of Ternary Probabilistic Forecasts

A suite of functions for visualising ternary probabilistic forecasts, as discussed in the paper by Jupp (2012) <doi:10.1098/rsta.2011.0350>.

Last updated 5 years ago

1.00 score 1 stars 127 downloads

TSMSN - Truncated Scale Mixtures of Skew-Normal Distributions

Return the first four moments, estimation of parameters and sample of the TSMSN distributions (Skew Normal, Skew t, Skew Slash or Skew Contaminated Normal).

Last updated 5 years ago

1.00 score 89 downloads

radir - Inverse-Regression Estimation of Radioactive Doses

Radioactive doses estimation using individual chromosomal aberrations information. See Higueras M, Puig P, Ainsbury E, Rothkamm K. (2015) <doi:10.1088/0952-4746/35/3/557>.

Last updated 5 years ago

1.00 score 4 scripts 131 downloads

SemiMarkov - Multi-States Semi-Markov Models

Functions for fitting multi-state semi-Markov models to longitudinal data. A parametric maximum likelihood estimation method adapted to deal with Exponential, Weibull and Exponentiated Weibull distributions is considered. Right-censoring can be taken into account and both constant and time-varying covariates can be included using a Cox proportional model. Reference: A. Krol and P. Saint-Pierre (2015) <doi:10.18637/jss.v066.i06>.

Last updated 5 years ago

1.00 score 8 scripts 263 downloads

QDComparison - Modern Nonparametric Tools for Two-Sample Quantile and Distribution Comparisons

Allows practitioners to determine (i) if two univariate distributions (which can be continuous, discrete, or even mixed) are equal, (ii) how two distributions differ (shape differences, e.g., location, scale, etc.), and (iii) where two distributions differ (at which quantiles), all using nonparametric LP statistics. The primary reference is Jungreis, D. (2019, Technical Report).

Last updated 6 years ago

1.00 score 7 scripts 108 downloads

lvnet - Latent Variable Network Modeling

Estimate, fit and compare Structural Equation Models (SEM) and network models (Gaussian Graphical Models; GGM) using OpenMx. Allows for two possible generalizations to include GGMs in SEM: GGMs can be used between latent variables (latent network modeling; LNM) or between residuals (residual network modeling; RNM). For details, see Epskamp, Rhemtulla and Borsboom (2017) <doi:10.1007/s11336-017-9557-x>.

Last updated 6 years ago

1.00 score 6 scripts 241 downloads

SMITIDstruct - Data Structure and Manipulations Tool for Host and Viral Population

Statistical Methods for Inferring Transmissions of Infectious Diseases from deep sequencing data (SMITID). It allow sequence-space-time host and viral population data storage, indexation and querying.

Last updated 6 years ago

1.00 score 1 scripts 120 downloads

SCCI - Stochastic Complexity-Based Conditional Independence Test for Discrete Data

An efficient implementation of SCCI using 'Rcpp'. SCCI is short for the Stochastic Complexity-based Conditional Independence criterium (Marx and Vreeken, 2019). SCCI is an asymptotically unbiased and L2 consistent estimator of (conditional) mutual information for discrete data.

Last updated 6 years ago

cpp

1.00 score 8 scripts 138 downloads

jacpop - Jaccard Index for Population Structure Identification

Uses the Jaccard similarity index to account for population structure in sequencing studies. This method was specifically designed to detect population stratification based on rare variants, hence it will be especially useful in rare variant analysis.

Last updated 6 years ago

1.00 score 5 scripts 108 downloads

gen2stage - Generalized Two-Stage Designs for Phase II Single-Arm Studies

One can find single-stage and two-stage designs for a phase II single-arm study with either efficacy or safety/toxicity endpoints as described in Kim and Wong (2019) <doi:10.29220/CSAM.2019.26.2.163>.

Last updated 6 years ago

1.00 score 138 downloads

WGScan - A Genome-Wide Scan Statistic Framework for Whole-Genome Sequence Data Analysis

Functions for the analysis of whole-genome sequencing studies to simultaneously detect the existence, and estimate the locations of association signals at genome-wide scale. The functions allow genome-wide association scan, candidate region scan and single window test.

Last updated 6 years ago

1.00 score 4 scripts 147 downloads

vfprogression - Visual Field (VF) Progression Analysis and Plotting Methods

Realization of published methods to analyze visual field (VF) progression. Introduction to the plotting methods (designed by author TE) for VF output visualization. A sample dataset for two eyes, each with 10 follow-ups is included. The VF analysis methods could be found in -- Musch et al. (1999) <doi:10.1016/S0161-6420(99)90147-1>, Nouri-Mahdavi et at. (2012) <doi:10.1167/iovs.11-9021>, Schell et at. (2014) <doi:10.1016/j.ophtha.2014.02.021>, Aptel et al. (2015) <doi:10.1111/aos.12788>.

Last updated 6 years ago

1.00 score 96 downloads

gcerisk - Generalized Competing Event Model

Generalized competing event model based on Cox PH model and Fine-Gray model. This function is designed to develop optimized risk-stratification methods for competing risks data, such as described in: 1. Carmona R, Gulaya S, Murphy JD, Rose BS, Wu J, Noticewala S,McHale MT, Yashar CM, Vaida F, and Mell LK (2014) <DOI:10.1016/j.ijrobp.2014.03.047>. 2. Carmona R, Zakeri K, Green G, Hwang L, Gulaya S, Xu B, Verma R, Williamson CW, Triplett DP, Rose BS, Shen H, Vaida F, Murphy JD, and Mell LK (2016) <DOI:10.1200/JCO.2015.65.0739>. 3. Lunn, Mary, and Don McNeil (1995) <DOI:10.2307/2532940>.

Last updated 6 years ago

1.00 score 1 stars 2 scripts 194 downloads

AFheritability - The Attributable Fraction (AF) Described as a Function of Disease Heritability, Prevalence and Intervention Specific Factors

The AFfunction() is a function which returns an estimate of the Attributable Fraction (AF) and a plot of the AF as a function of heritability, disease prevalence, size of target group and intervention effect. Since the AF is a function of several factors, a shiny app is used to better illustrate how the relationship between the AF and heritability depends on several other factors. The app is ran by the function runShinyApp(). For more information see Dahlqwist E et al. (2019) <doi:10.1007/s00439-019-02006-8>.

Last updated 6 years ago

1.00 score 184 downloads

sparseMatEst - Sparse Matrix Estimation and Inference

The 'sparseMatEst' package provides functions for estimating sparse covariance and precision matrices with error control. A false positive rate is fixed corresponding to the probability of falsely including a matrix entry in the support of the estimator. It uses the binary search method outlined in Kashlak and Kong (2019) <arXiv:1705.02679> and in Kashlak (2019) <arXiv:1903.10988>.

Last updated 6 years ago

1.00 score 1 scripts 94 downloads

MChtest - Monte Carlo Hypothesis Tests with Sequential Stopping

Performs Monte Carlo hypothesis tests, allowing a couple of different sequential stopping boundaries. For example, a truncated sequential probability ratio test boundary (Fay, Kim and Hachey, 2007 <DOI:10.1198/106186007X257025>) and a boundary proposed by Besag and Clifford, 1991 <DOI:10.1093/biomet/78.2.301>. Gives valid p-values and confidence intervals on p-values.

Last updated 6 years ago

1.00 score 129 downloads

roccv - ROC for Cross Validation Results

Cross validate large genetic data while specifying clinical variables that should always be in the model using the function cv(). An ROC plot from the cross validation data with AUC can be obtained using rocplot(), which also can be used to compare different models. Framework was built to handle genetic data, but works for any data.

Last updated 6 years ago

1.00 score 4 scripts 144 downloads

essHist - The Essential Histogram

Provide an optimal histogram, in the sense of probability density estimation and features detection, by means of multiscale variational inference. In other words, the resulting histogram servers as an optimal density estimator, and meanwhile recovers the features, such as increases or modes, with both false positive and false negative controls. Moreover, it provides a parsimonious representation in terms of the number of blocks, which simplifies data interpretation. The only assumption for the method is that data points are independent and identically distributed, so it applies to fairly general situations, including continuous distributions, discrete distributions, and mixtures of both. For details see Li, Munk, Sieling and Walther (2016) <arXiv:1612.07216>.

Last updated 6 years ago

cpp

1.00 score 1 stars 6 scripts 212 downloads

robustreg - Robust Regression Functions

Linear regression functions using Huber and bisquare psi functions. Optimal weights are calculated using IRLS algorithm.

Last updated 6 years ago

cpp

1.00 score 10 scripts 251 downloads

PlotContour - Plot Contour Line

This function plots a contour line with a user-defined probability and tightness of fit.

Last updated 6 years ago

1.00 score 148 downloads

CRWRM - Changing the Reference Group without Re-Running the Model

To re-calculate the coefficients and the standard deviation when changing the reference group.

Last updated 6 years ago

1.00 score 143 downloads

srp - Smooth-Rough Partitioning of the Regression Coefficients

Performs the change-point detection in regression coefficients of linear model by partitioning the regression coefficients into two classes of smoothness. The change-point and the regression coefficients are jointly estimated.

Last updated 6 years ago

1.00 score 9 scripts 105 downloads

Rramas - Matrix Population Models

Analyzes and predicts from matrix population models (Caswell 2006) <doi:10.1002/9781118445112.stat07481>.

Last updated 6 years ago

1.00 score 6 scripts 152 downloads

dstat - Conditional Sensitivity Analysis for Matched Observational Studies

A d-statistic tests the null hypothesis of no treatment effect in a matched, nonrandomized study of the effects caused by treatments. A d-statistic focuses on subsets of matched pairs that demonstrate insensitivity to unmeasured bias in such an observational study, correcting for double-use of the data by conditional inference. This conditional inference can, in favorable circumstances, substantially increase the power of a sensitivity analysis (Rosenbaum (2010) <doi:10.1007/978-1-4419-1213-8_14>). There are two examples, one concerning unemployment from Lalive et al. (2006) <doi:10.1111/j.1467-937X.2006.00406.x>, the other concerning smoking and periodontal disease from Rosenbaum (2017) <doi:10.1214/17-STS621>.

Last updated 6 years ago

1.00 score 170 downloads

word.alignment - Computing Word Alignment Using IBM Model 1 (and Symmetrization) for a Given Parallel Corpus and Its Evaluation

For a given Sentence-Aligned Parallel Corpus, it aligns words for each sentence pair. It considers one-to-many and symmetrization alignments. Moreover, it evaluates the quality of word alignment based on this package and some other software. It also builds an automatic dictionary of two languages based on given parallel corpus.

Last updated 6 years ago

1.00 score 9 scripts 288 downloads

LeArEst - Border and Area Estimation of Data Measured with Additive Error

Provides methods for estimating borders of uniform distribution on the interval (one-dimensional) and on the elliptical domain (two-dimensional) under measurement errors. For one-dimensional case, it also estimates the length of underlying uniform domain and tests the hypothesized length against two-sided or one-sided alternatives. For two-dimensional case, it estimates the area of underlying uniform domain. It works with numerical inputs as well as with pictures in JPG format.

Last updated 6 years ago

1.00 score 6 scripts 135 downloads

iMediate - Likelihood Methods for Mediation Analysis

Implements likelihood based methods for mediation analysis.

Last updated 6 years ago

1.00 score 9 scripts 143 downloads

pmhtutorial - Minimal Working Examples for Particle Metropolis-Hastings

Routines for state estimate in a linear Gaussian state space model and a simple stochastic volatility model using particle filtering. Parameter inference is also carried out in these models using the particle Metropolis-Hastings algorithm that includes the particle filter to provided an unbiased estimator of the likelihood. This package is a collection of minimal working examples of these algorithms and is only meant for educational use and as a start for learning to them on your own.

Last updated 6 years ago

1.00 score 12 scripts 135 downloads

swgee - Simulation Extrapolation Inverse Probability Weighted Generalized Estimating Equations

Simulation extrapolation and inverse probability weighted generalized estimating equations method for longitudinal data with missing observations and measurement error in covariates. References: Yi, G. Y. (2008) <doi:10.1093/biostatistics/kxm054>; Cook, J. R. and Stefanski, L. A. (1994) <doi:10.1080/01621459.1994.10476871>; Little, R. J. A. and Rubin, D. B. (2002, ISBN:978-0-471-18386-0).

Last updated 6 years ago

1.00 score 3 scripts 143 downloads

BalanceCheck - Balance Check for Multiple Covariates in Matched Observational Studies

Two practical tests are provided for assessing whether multiple covariates in a treatment group and a matched control group are balanced in observational studies.

Last updated 6 years ago

1.00 score 1 stars 2 scripts 205 downloads

SPreg - Bias Reduction in the Skew-Probit Model for a Binary Response

Provides a function for the estimation of parameters in a binary regression with the skew-probit link function. Naive MLE, Jeffrey type of prior and Cauchy prior type of penalization are implemented, as described in DongHyuk Lee and Samiran Sinha (2019+) <doi:10.1080/00949655.2019.1590579>.

Last updated 6 years ago

1.00 score 2 scripts 109 downloads

SPCDAnalyze - Design and Analyze Studies using the Sequential Parallel Comparison Design

Programs to find the sample size or power of studies using the Sequential Parallel Comparison Design (SPCD) and programs to analyze such studies. This is a clinical trial design where patients initially on placebo who did not respond are re-randomized between placebo and active drug in a second phase and the results of the two phases are pooled. The method of analyzing binary data with this design is described in Fava,Evins, Dorer and Schoenfeld(2003) <doi:10.1159/000069738>, and the method of analyzing continuous data is described in Chen, Yang, Hung and Wang (2011) <doi:10.1016/j.cct.2011.04.006>.

Last updated 6 years ago

1.00 score 7 scripts 108 downloads

ConfIntVariance - Confidence Interval for the Univariate Population Variance without Normality Assumption

Surrounds the usual sample variance of a univariate numeric sample with a confidence interval for the population variance. This has been done so far only under the assumption that the underlying distribution is normal. Under the hood, this package implements the unique least-variance unbiased estimator of the variance of the sample variance, in a formula that is equivalent to estimating kurtosis and square of the population variance in an unbiased way and combining them according to the classical formula into an estimator of the variance of the sample variance. Both the sample variance and the estimator of its variance are U-statistics. By the theory of U-statistic, the resulting estimator is unique. See Fuchs, Krautenbacher (2016) <doi:10.1080/15598608.2016.1158675> and the references therein for an overview of unbiased estimation of variances of U-statistics.

Last updated 6 years ago

1.00 score 2 scripts 134 downloads

needmining - A Simple Needmining Implementation

Showcasing needmining (the semi-automatic extraction of customer needs from social media data) with Twitter data. It uses the handling of the Twitter API provided by the package 'rtweet' and the textmining algorithms provided by the package 'tm'. Niklas Kuehl (2016) <doi:10.1007/978-3-319-32689-4_14> wrote an introduction to the topic of needmining.

Last updated 6 years ago

1.00 score 7 scripts 107 downloads

glmlep - Fit GLM with LEP-Based Penalized Maximum Likelihood

Efficient algorithms for fitting regularization paths for linear or logistic regression models penalized by LEP.

Last updated 6 years ago

cpp

1.00 score 3 scripts 114 downloads

mimi - Main Effects and Interactions in Mixed and Incomplete Data

Generalized low-rank models for mixed and incomplete data frames. The main function may be used for dimensionality reduction of imputation of numeric, binary and count data (simultaneously). Main effects such as column means, group effects, or effects of row-column side information (e.g. user/item attributes in recommendation system) may also be modelled in addition to the low-rank model. Geneviève Robin, Olga Klopp, Julie Josse, Éric Moulines, Robert Tibshirani (2018) <arXiv:1806.09734>.

Last updated 6 years ago

1.00 score 8 scripts 197 downloads

GPSCDF - Generalized Propensity Score Cumulative Distribution Function

Implements the generalized propensity score cumulative distribution function proposed by Greene (2017) <https://digitalcommons.library.tmc.edu/dissertations/AAI10681743/>. A single scalar balancing score is calculated for any generalized propensity score vector with three or more treatments. This balancing score is used for propensity score matching and stratification in outcome analyses when analyzing either ordinal or multinomial treatments.

Last updated 6 years ago

1.00 score 3 scripts 115 downloads

ccrs - Correct and Cluster Response Style Biased Data

Functions for performing Correcting and Clustering response-style-biased preference data (CCRS). The main functions are correct.RS() for correcting for response styles, and ccrs() for simultaneously correcting and content-based clustering. The procedure begin with making rank-ordered boundary data from the given preference matrix using a function called create.ccrsdata(). Then in correct.RS(), the response style is corrected as follows: the rank-ordered boundary data are smoothed by I-spline functions, the given preference data are transformed by the smoothed functions. The resulting data matrix, which is considered as bias-corrected data, can be used for any data analysis methods. If one wants to cluster respondents based on their indicated preferences (content-based clustering), ccrs() can be applied to the given (response-style-biased) preference data, which simultaneously corrects for response styles and clusters respondents based on the contents. Also, the correction result can be checked by plot.crs() function.

Last updated 6 years ago

1.00 score 4 scripts 145 downloads

UtilityFrailtyPH12 - Implementing EFF-TOX and Monotone Utility Based Phase 12 Trials

Contains functions for simulating phase 12 trial designs described by Chapple and Thall (2019) including simulation and the EFF-TOX trial and simulation and implementation of the U12 trial. Functions for implementing the EFF-TOX trial are found in the package 'Phase123'.

Last updated 6 years ago

1.00 score 6 scripts 126 downloads

kaphom - Test the Homogeneity of Kappa Statistics

Tests the homogeneity of intraclass kappa statistics obtained from independent studies or a stratified study with binary results. It is desired to compare the kappa statistics obtained in multi-center studies or in a single stratified study to give a common or summary kappa using all available information. If the homogeneity test of these kappa statistics is not rejected, then it is possible to make inferences over a single kappa statistic that summarizes all the studies. Muammer Albayrak, Kemal Turhan, Yasemin Yavuz, Zeliha Aydin Kasap (2019) <doi:10.1080/03610918.2018.1538457> Jun-mo Nam (2003) <doi:10.1111/j.0006-341X.2003.00118.x> Jun-mo Nam (2005) <doi:10.1002/sim.2321>Mousumi Banerjee, Michelle Capozzoli, Laura McSweeney,Debajyoti Sinha (1999) <doi:10.2307/3315487> Allan Donner, Michael Eliasziw, Neil Klar (1996) <doi:10.2307/2533154>.

Last updated 6 years ago

1.00 score 11 scripts 117 downloads

PortfolioOptim - Small/Large Sample Portfolio Optimization

Two functions for financial portfolio optimization by linear programming are provided. One function implements Benders decomposition algorithm and can be used for very large data sets. The other, applicable for moderate sample sizes, finds optimal portfolio which has the smallest distance to a given benchmark portfolio.

Last updated 6 years ago

1.00 score 5 scripts 203 downloads

bender - Bender Client

R client for Bender Hyperparameters optimizer : <https://bender.dreem.com> The R client allows you to communicate with the Bender API and therefore submit some new trials within your R script itself.

Last updated 6 years ago

1.00 score 1 scripts 196 downloads

prototest - Inference on Prototypes from Clusters of Features

Procedures for testing for group-wide signal in clusters of variables. Tests can be performed for single groups in isolation (univariate) or multiple groups together (multivariate). Specific tests include the exact and approximate (un)selective likelihood ratio tests described in Reid et al (2015), the selective F test and marginal screening prototype test of Reid and Tibshirani (2015). User may pre-specify columns to be included in prototype formation, or allow the function to select them itself. A mixture of these two is also possible. Any variable selection is accounted for using the selective inference framework. Options for non-sampling and hit-and-run null reference distributions.

Last updated 6 years ago

openblascpp

1.00 score 4 scripts 117 downloads

Semblance - A Data-Driven Similarity Kernel on Probability Spaces

We present a rank-based Mercer kernel to compute a pair-wise similarity metric corresponding to informative representation of data. We tailor the development of a kernel to encode our prior knowledge about the data distribution over a probability space. The philosophical concept behind our construction is that objects whose feature values fall on the extreme of that feature’s probability mass distribution are more similar to each other, than objects whose feature values lie closer to the mean. Semblance emphasizes features whose values lie far away from the mean of their probability distribution. The kernel relies on properties empirically determined from the data and does not assume an underlying distribution. The use of feature ranks on a probability space ensures that Semblance is computational efficacious, robust to outliers, and statistically stable, thus making it widely applicable algorithm for pattern analysis. The output from the kernel is a square, symmetric matrix that gives proximity values between pairs of observations.

Last updated 6 years ago

1.00 score 2 scripts 100 downloads

bspmma - Bayesian Semiparametric Models for Meta-Analysis

The main functions carry out Gibbs' sampler routines for nonparametric and semiparametric Bayesian models for random effects meta-analysis.

Last updated 6 years ago

1.00 score 9 scripts 210 downloads

QHOT - QTL Hotspot Detection

This function produces both the numerical and graphical summaries of the QTL hotspot detection in the genomes that are available on the worldwide web including the flanking markers of QTLs.

Last updated 6 years ago

1.00 score 1 scripts 87 downloads

simexaft - simexaft

Implement of the Simulation-Extrapolation (SIMEX) algorithm for the accelerated failure time (AFT) with covariates subject to measurement error.

Last updated 6 years ago

1.00 score 2 scripts 181 downloads

bwd - Backward Procedure for Change-Point Detection

Implements a backward procedure for single and multiple change point detection proposed by Shin et al. <arXiv:1812.10107>. The backward approach is particularly useful to detect short and sparse signals which is common in copy number variation (CNV) detection.

Last updated 6 years ago

1.00 score 2 scripts 143 downloads

mmsample - Multivariate Matched Sampling

Subset a control group to match an intervention group on a set of features using multivariate matching and propensity score calipers. Based on methods in Rosenbaum and Rubin (1985).

Last updated 6 years ago

openblascpp

1.00 score 2 scripts 97 downloads

Fstability - Calculate Feature Stability

Has two functions to help with calculating feature selection stability. 'Lump' is a function that groups subset vectors into a dataframe, and adds NA to shorter vectors so they all have the same length. 'ASM' is a function that takes a dataframe of subset vectors and the original vector of features as inputs, and calculates the Stability of the feature selection. The calculation for 'asm' uses the Adjusted Stability Measure proposed in: 'Lustgarten', 'Gopalakrishnan', & 'Visweswaran' (2009)<https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2815476/>.

Last updated 6 years ago

1.00 score 2 scripts 98 downloads

GenoScan - A Genome-Wide Scan Statistic Framework for Whole-Genome Sequence Data Analysis

Functions for whole-genome sequencing studies, including genome-wide scan, candidate region scan and single window test.

Last updated 6 years ago

1.00 score 8 scripts 171 downloads

OmnibusFisher - A Modified Fisher’s Method to Test Overall Gene-Level Effect

The separate p-values of SNPs, RNA expressions and DNA methylations are calculated by KM regression. The correlation between different omics data are taken into account. This method can be applied to either samples with all three types of omics data or samples with two types.

Last updated 6 years ago

1.00 score 1 scripts 111 downloads

kuiper.2samp - Two-Sample Kuiper Test

This function performs the two-sample Kuiper test to assess the anomaly of continuous, one-dimensional probability distributions. References used for this method are (1). Kuiper, N. H. (1960). <DOI:10.1016/S1385-7258(60)50006-0> and (2). Paltani, S. (2004). <DOI:10.1051/0004-6361:20034220>.

Last updated 6 years ago

1.00 score 2 scripts 118 downloads

sensitivityCalibration - A Calibrated Sensitivity Analysis for Matched Observational Studies

Implements the calibrated sensitivity analysis approach for matched observational studies. Our sensitivity analysis framework views matched sets as drawn from a super-population. The unmeasured confounder is modeled as a random variable. We combine matching and model-based covariate-adjustment methods to estimate the treatment effect. The hypothesized unmeasured confounder enters the picture as a missing covariate. We adopt a state-of-art Expectation Maximization (EM) algorithm to handle this missing covariate problem in generalized linear models (GLMs). As our method also estimates the effect of each observed covariate on the outcome and treatment assignment, we are able to calibrate the unmeasured confounder to observed covariates. Zhang, B., Small, D. S. (2018). <arXiv:1812.00215>.

Last updated 6 years ago

1.00 score 9 scripts 96 downloads

Partiallyoverlapping - Partially Overlapping Samples Tests

Tests for a comparison of two partially overlapping samples. A comparison of means using the partially overlapping samples t-test: See Derrick, Russ, Toher and White (2017), Test statistics for the comparison of means for two samples which include both paired observations and independent observations, Journal of Modern Applied Statistical Methods, 16(1). A comparison of proportions using the partially overlapping samples z-test: See Derrick, Dobson-Mckittrick, Toher and White (2015), Test statistics for comparing two proportions with partially overlapping samples. Journal of Applied Quantitative Methods, 10(3).

Last updated 6 years ago

1.00 score 9 scripts 163 downloads

multiRDPG - Multiple Random Dot Product Graphs

Fits the Multiple Random Dot Product Graph Model and performs a test for whether two networks come from the same distribution. Both methods are proposed in Nielsen, A.M., Witten, D., (2018) "The Multiple Random Dot Product Graph Model", arXiv preprint <arXiv:1811.12172> (Submitted to Journal of Computational and Graphical Statistics).

Last updated 6 years ago

1.00 score 6 scripts 93 downloads

TeachNet - Fits Neural Networks to Learn About Backpropagation

Can fit neural networks with up to two hidden layer and two different error functions. Also able to handle a weight decay. But just able to compute one output neuron and very slow.

Last updated 6 years ago

1.00 score 1 stars 3 scripts 119 downloads

iClick - A Button-Based GUI for Financial and Economic Data Analysis

A GUI designed to support the analysis of financial-economic time series data.

Last updated 6 years ago

1.00 score 6 scripts 186 downloads

smoothROCtime - Smooth Time-Dependent ROC Curve Estimation

Computes smooth estimations for the Cumulative/Dynamic and Incident/Dynamic ROC curves, in presence of right censorship, based on the bivariate kernel density estimation of the joint distribution function of the Marker and Time-to-event variables.

Last updated 6 years ago

1.00 score 7 scripts 519 downloads

binequality - Methods for Analyzing Binned Income Data

Methods for model selection, model averaging, and calculating metrics, such as the Gini, Theil, Mean Log Deviation, etc, on binned income data where the topmost bin is right-censored. We provide both a non-parametric method, termed the bounded midpoint estimator (BME), which assigns cases to their bin midpoints; except for the censored bins, where cases are assigned to an income estimated by fitting a Pareto distribution. Because the usual Pareto estimate can be inaccurate or undefined, especially in small samples, we implement a bounded Pareto estimate that yields much better results. We also provide a parametric approach, which fits distributions from the generalized beta (GB) family. Because some GB distributions can have poor fit or undefined estimates, we fit 10 GB-family distributions and use multimodel inference to obtain definite estimates from the best-fitting distributions. We also provide binned income data from all United States of America school districts, counties, and states.

Last updated 6 years ago

1.00 score 23 scripts 231 downloads

SAutomata - Inference and Learning in Stochastic Automata

Machine learning provides algorithms that can learn from data and make inferences or predictions. Stochastic automata is a class of input/output devices which can model components. This work provides implementation an inference algorithm for stochastic automata which is similar to the Viterbi algorithm. Moreover, we specify a learning algorithm using the expectation-maximization technique and provide a more efficient implementation of the Baum-Welch algorithm for stochastic automata. This work is based on Inference and learning in stochastic automata was by Karl-Heinz Zimmermann(2017) <doi:10.12732/ijpam.v115i3.15>.

Last updated 6 years ago

1.00 score 6 scripts 85 downloads

RImpact - Calculates Measures of Scholarly Impact

The metrics() function calculates measures of scholarly impact. These include conventional measures, such as the number of publications and the total citations to all publications, as well as modern and robust metrics based on the vector of citations associated with each publication, such as the h index and many of its variants or rivals. These methods are described in Ruscio et al. (2012) <DOI: 10.1080/15366367.2012.711147>.

Last updated 6 years ago

1.00 score 3 scripts 118 downloads

rhmc - Hamiltonian Monte Carlo

Implements simple Hamiltonian Monte Carlo routines in R for sampling from any desired target distribution which is continuous and smooth. See Neal (2017) <arXiv:1701.02434> for further details on Hamiltonian Monte Carlo. Automatic parameter selection is not supported.

Last updated 6 years ago

1.00 score 3 scripts 92 downloads

GroupComparisons - Paired/Unpaired Parametric/Non-Parametric Group Comparisons

Receives two vectors, computes appropriate function for group comparison (i.e., t-test, Mann-Whitney; equality of variances), and reports the findings (mean/median, standard deviation, test statistic, p-value, effect size) in APA format (Fay, M.P., & Proschan, M.A. (2010)<DOI: 10.1214/09-SS051>).

Last updated 6 years ago

1.00 score 2 scripts 135 downloads

DiPhiSeq - Robust Tests for Differential Dispersion and Differential Expression in RNA-Sequencing Data

Implements the algorithm described in Jun Li and Alicia T. Lamere, "DiPhiSeq: Robust comparison of expression levels on RNA-Seq data with large sample sizes" (Unpublished). Detects not only genes that show different average expressions ("differential expression", DE), but also genes that show different diversities of expressions in different groups ("differentially dispersed", DD). DD genes can be important clinical markers. 'DiPhiSeq' uses a redescending penalty on the quasi-likelihood function, and thus has superior robustness against outliers and other noise. Updates from version 0.1.0: (1) Added the option of using adaptive initial value for phi. (2) Added a function for estimating the proportion of outliers in the data. (3) Modified the input parameter names for clarity, and modified the output format for the main function.

Last updated 6 years ago

1.00 score 4 scripts 154 downloads

FourScores - A Game for Human vs. Human or Human vs. AI

A game for two players: Who gets first four in a row (horizontal, vertical or diagonal) wins. As board game published by Milton Bradley, designed by Howard Wexler and Ned Strongin.

Last updated 6 years ago

1.00 score 1 scripts 114 downloads

HSDiC - Homogeneity and Sparsity Detection Incorporating Prior Constraint Information

We explore sparsity and homogeneity of regression coefficients incorporating prior constraint information. A general pairwise fusion approach is proposed to deal with the sparsity and homogeneity detection when combining prior convex constraints. We develop an modified alternating direction method of multipliers algorithm (ADMM) to obtain the estimators.

Last updated 6 years ago

1.00 score 1 stars 1 scripts 134 downloads

Opt5PL - Optimal Designs for the 5-Parameter Logistic Model

Obtain and evaluate various optimal designs for the 3, 4, and 5-parameter logistic models. The optimal designs are obtained based on the numerical algorithm in Hyun, Wong, Yang (2018) <doi:10.18637/jss.v083.i05>.

Last updated 6 years ago

cpp

1.00 score 6 scripts 123 downloads

SpNMF - Supervised NMF

Non-negative Matrix Factorization(NMF) is a powerful tool for identifying the key features of microbial communities and a dimension-reduction method. When we are interested in the differences between the structures of two groups of communities, supervised NMF(Yun Cai, Hong Gu and Tobby Kenney (2017),<doi:10.1186/s40168-017-0323-1>) provides a better way to do this, while retaining all the advantages of NMF -- such as interpretability, and being based on a simple biological intuition.

Last updated 6 years ago

1.00 score 4 scripts 103 downloads

sym.arma - Autoregressive and Moving Average Symmetric Models

Functions for fitting the Autoregressive and Moving Average Symmetric Model for univariate time series introduced by Maior and Cysneiros (2018), <doi:10.1007/s00362-016-0753-z>. Fitting method: conditional maximum likelihood estimation. For details see: Wei (2006), Time Series Analysis: Univariate and Multivariate Methods, Section 7.2.

Last updated 6 years ago

1.00 score 9 scripts 161 downloads

MEPDF - Creation of Empirical Density Functions Based on Multivariate Data

Based on the input data an n-dimensional cube with sub cells of user specified side length is created. The number of sample points which fall in each sub cube is counted, and with the cell volume and overall sample size an empirical probability can be computed. A number of cubes of higher resolution can be superimposed. The basic method stems from J.L. Bentley in "Multidimensional Divide and Conquer". J. L. Bentley (1980) <doi:10.1145/358841.358850>. Furthermore a simple kernel density estimation method is made available, as well as an expansion of Bentleys method, which offers a kernel approach for the grid method.

Last updated 6 years ago

1.00 score 6 scripts 151 downloads

distdichoR - Distributional Method for the Dichotomisation of Continuous Outcomes

Contains a range of functions covering the present development of the distributional method for the dichotomisation of continuous outcomes. The method provides estimates with standard error of a comparison of proportions (difference, odds ratio and risk ratio) derived, with similar precision, from a comparison of means. See the URL below or <arXiv:1809.03279> for more information.

Last updated 6 years ago

1.00 score 5 scripts 147 downloads

DIconvex - Finding Patterns of Monotonicity and Convexity in Data

Given an initial set of points, this package minimizes the number of elements to discard from this set such that there exists at least one monotonic and convex mapping within pre-specified upper and lower bounds.

Last updated 6 years ago

1.00 score 1 scripts 137 downloads

EstMix - Tumor Clones Percentage Estimations

Includes R functions for the estimation of tumor clones percentages for both snp data and (whole) genome sequencing data. See Cheng, Y., Dai, J. Y., Paulson, T. G., Wang, X., Li, X., Reid, B. J., & Kooperberg, C. (2017). Quantification of multiple tumor clones using gene array and sequencing data. The Annals of Applied Statistics, 11(2), 967-991, <doi:10.1214/17-AOAS1026> for more details.

Last updated 6 years ago

cpp

1.00 score 2 scripts 161 downloads

CTTinShiny - Shiny Interface for the CTT Package

A Shiny interface developed in close coordination with the CTT package, providing a GUI that guides the user through CTT analyses.

Last updated 6 years ago

1.00 score 1 scripts 154 downloads

bdribs - Bayesian Detection of Potential Risk Using Inference on Blinded Safety Data

Implements Bayesian inference to detect signal from blinded clinical trial when total number of adverse events of special concerns and total risk exposures from all patients are available in the study. For more details see the article by Mukhopadhyay et. al. (2018) titled 'Bayesian Detection of Potential Risk Using Inference on Blinded Safety Data', in Pharmaceutical Statistics (to appear).

Last updated 6 years ago

jagscpp

1.00 score 3 scripts 197 downloads

HGSL - Heterogeneous Group Square-Root Lasso

Estimation of high-dimensional multi-response regression with heterogeneous noises under Heterogeneous group square-root Lasso penalty. For details see: Ren, Z., Kang, Y., Fan, Y. and Lv, J. (2018)<arXiv:1606.03803>.

Last updated 6 years ago

1.00 score 1 stars 1 scripts 100 downloads

manet - Multiple Allocation Model for Actor-Event Networks

Mixture model with overlapping clusters for binary actor-event data. Parameters are estimated in a Bayesian framework. Model and inference are described in Ranciati, Vinciotti, Wit (2017) Modelling actor-event network data via a mixture model under overlapping clusters. Submitted.

Last updated 6 years ago

1.00 score 6 scripts 106 downloads

IndepTest - Nonparametric Independence Tests Based on Entropy Estimation

Implementations of the weighted Kozachenko-Leonenko entropy estimator and independence tests based on this estimator, (Kozachenko and Leonenko (1987) <http://mi.mathnet.ru/eng/ppi797>). Also includes a goodness-of-fit test for a linear model which is an independence test between covariates and errors.

Last updated 6 years ago

1.00 score 1 stars 7 scripts 136 downloads

EM.Fuzzy - EM Algorithm for Maximum Likelihood Estimation by Non-Precise Information

The EM algorithm is a powerful tool for computing maximum likelihood estimates with incomplete data. This package will help to applying EM algorithm based on triangular and trapezoidal fuzzy numbers (as two kinds of incomplete data). A method is proposed for estimating the unknown parameter in a parametric statistical model when the observations are triangular or trapezoidal fuzzy numbers. This method is based on maximizing the observed-data likelihood defined as the conditional probability of the fuzzy data; for more details and formulas see Denoeux (2011) <doi:10.1016/j.fss.2011.05.022>.

Last updated 6 years ago

1.00 score 3 scripts 128 downloads

NPMLEcmprsk - Type-Specific Failure Rate and Hazard Rate on Competing Risks Data

Given a failure type, the function computes covariate-specific probability of failure over time and covariate-specific conditional hazard rate based on possibly right-censored competing risk data. Specifically, it computes the non-parametric maximum-likelihood estimates of these quantities and their asymptotic variances in a semi-parametric mixture model for competing-risks data, as described in Chang et al. (2007a).

Last updated 6 years ago

1.00 score 1 scripts 146 downloads

rbit - Binary Indexed Tree

A simple implementation of Binary Indexed Tree by R. The BinaryIndexedTree class supports construction of Binary Indexed Tree from a vector, update of a value in the vector and query for the sum of a interval of the vector.

Last updated 6 years ago

1.00 score 1 scripts 94 downloads

happytime - Two Games to Relieve the Boredom

There are two interesting games in this package, one is 2048 games(for windows), using up and down to control the direction until there is a 2048 figure. And the other is 'what to eat today',preparing for people who choose difficulties, including most of the delicious Cantonese cuisine.

Last updated 6 years ago

1.00 score 2 scripts 124 downloads

CliftLRD - Complex-Valued Wavelet Lifting Estimators of the Hurst Exponent for Irregularly Sampled Time Series

Implementation of Hurst exponent estimators based on complex-valued lifting wavelet energy from Knight, M. I and Nunes, M. A. (2018) <doi:10.1007/s11222-018-9820-8>.

Last updated 6 years ago

1.00 score 3 scripts 154 downloads

TangPoemR - Write Chinese Tang Poems

Write Chinese Tang Poems automatically.

Last updated 6 years ago

1.00 score 2 scripts 83 downloads

CNLTtsa - Complex-Valued Wavelet Lifting for Univariate and Bivariate Time Series Analysis

Implementations of recent complex-valued wavelet spectral procedures for analysis of irregularly sampled signals, see Hamilton et al (2018) <doi:10.1080/00401706.2017.1281846>.

Last updated 6 years ago

1.00 score 9 scripts 224 downloads

BioPET - Biomarker Prognostic Enrichment Tool

Prognostic Enrichment is a clinical trial strategy of evaluating an intervention in a patient population with a higher rate of the unwanted event than the broader patient population (R. Temple (2010) <DOI:10.1038/clpt.2010.233>). A higher event rate translates to a lower sample size for the clinical trial, which can have both practical and ethical advantages. This package is a tool to help evaluate biomarkers for prognostic enrichment of clinical trials.

Last updated 6 years ago

1.00 score 3 scripts 214 downloads

DTWUMI - Imputation of Multivariate Time Series Based on Dynamic Time Warping

Functions to impute large gaps within multivariate time series based on Dynamic Time Warping methods. Gaps of size 1 or inferior to a defined threshold are filled using simple average and weighted moving average respectively. Larger gaps are filled using the methodology provided by Phan et al. (2017) <DOI:10.1109/MLSP.2017.8168165>: a query is built immediately before/after a gap and a moving window is used to find the most similar sequence to this query using Dynamic Time Warping. To lower the calculation time, similar sequences are pre-selected using global features. Contrary to the univariate method (package 'DTWBI'), these global features are not estimated over the sequence containing the gap(s), but a feature matrix is built to summarize general features of the whole multivariate signal. Once the most similar sequence to the query has been identified, the adjacent sequence to this window is used to fill the gap considered. This function can deal with multiple gaps over all the sequences componing the input multivariate signal. However, for better consistency, large gaps at the same location over all sequences should be avoided.

Last updated 6 years ago

1.00 score 4 scripts 172 downloads

ExtMallows - An Extended Mallows Model and Its Hierarchical Version for Ranked Data Aggregation

For multiple full/partial ranking lists, R package 'ExtMallows' can (1) detect whether the input ranking lists are over-correlated, and (2) use the Mallows model or extended Mallows model to integrate the ranking lists, and (3) use hierarchical extended Mallows model for rank integration if there are groups of over-correlated ranking lists.

Last updated 6 years ago

1.00 score 8 scripts 117 downloads

scRNAtools - Single Cell RNA Sequencing Data Analysis Tools

We integrated the common analysis methods utilized in single cell RNA sequencing data, which included cluster method, principal components analysis (PCA), the filter of differentially expressed genes, pathway enrichment analysis and correlated analysis methods.

Last updated 6 years ago

1.00 score 9 scripts 153 downloads

mineCitrus - Extract and Analyze Median Molecule Intensity from 'citrus' Output

Citrus is a computational technique developed for the analysis of high dimensional cytometry data sets. This package extracts, statistically analyzes, and visualizes marker expression from 'citrus' data. This code was used to generate data for Figures 3 and 4 in the forthcoming manuscript: Throm et al. “Identification of Enhanced Interferon-Gamma Signaling in Polyarticular Juvenile Idiopathic Arthritis with Mass Cytometry”, JCI-Insight. For more information on Citrus, please see: Bruggner et al. (2014) <doi:10.1073/pnas.1408792111>. To download the 'citrus' package, please see <https://github.com/nolanlab/citrus>.

Last updated 6 years ago

1.00 score 40 scripts 97 downloads

plde - Penalized Log-Density Estimation Using Legendre Polynomials

We present a penalized log-density estimation method using Legendre polynomials with lasso penalty to adjust estimate's smoothness. Re-expressing the logarithm of the density estimator via a linear combination of Legendre polynomials, we can estimate parameters by maximizing the penalized log-likelihood function. Besides, we proposed an implementation strategy that builds on the coordinate decent algorithm, together with the Bayesian information criterion (BIC).

Last updated 6 years ago

1.00 score 7 scripts 106 downloads

GSAfisherCombined - Gene Set Analysis with Fisher Combined Method

Provides the p-value for a joint test of association between a phenotype and a set of genetic variants (SNPs) by combining marginal p-values using the Fisher method. See Fisher, R.A. (1925,ISBN:0-05-002170-2) Statistical Methods for Research Workers.

Last updated 7 years ago

1.00 score 5 scripts 135 downloads

DPtree - Dirichlet-Based Polya Tree

Contains functions to perform copula estimation by the non-parametric Bayesian method, Dirichlet-based Polya Tree. See Ning (2018) <doi:10.1080/00949655.2017.1421194>.

Last updated 7 years ago

1.00 score 9 scripts 142 downloads

metaLik - Likelihood Inference in Meta-Analysis and Meta-Regression Models

First- and higher-order likelihood inference in meta-analysis and meta-regression models.

Last updated 7 years ago

1.00 score 10 scripts 195 downloads

GrimR - Calculate Optical Parameters from Spindle Stage Measurements

Calculates optical parameters of crystals like the optical axes, the axis angle 2V, and the direction of the principal axes of the indicatrix from extinction angles measured on a spindle stage mounted on a polarisation microscope stage. Details of the method can be found in Dufey (2017) <arXiv:1703.00070>.

Last updated 7 years ago

1.00 score 9 scripts 125 downloads

cmce - Computer Model Calibration for Deterministic and Stochastic Simulators

Implements the Bayesian calibration model described in Pratola and Chkrebtii (2018) <DOI:10.5705/ss.202016.0403> for stochastic and deterministic simulators. Additive and multiplicative discrepancy models are currently supported. See <http://www.matthewpratola.com/software> for more information and examples.

Last updated 7 years ago

1.00 score 13 scripts 131 downloads

intRegGOF - Integrated Regression Goodness of Fit

Performs Goodness of Fit for regression models using Integrated Regression method. Works for several different fitting techniques.

Last updated 7 years ago

1.00 score 3 scripts 111 downloads

miniGUI - Tcl/Tk Quick and Simple Function GUI

Quick and simple Tcl/Tk Graphical User Interface to call functions. Also comprises a very simple experimental GUI framework.

Last updated 7 years ago

1.00 score 4 scripts 124 downloads

rsurface - Design of Rotatable Central Composite Experiments and Response Surface Analysis

Produces tables with the level of replication (number of replicates) and the experimental uncoded values of the quantitative factors to be used for rotatable Central Composite Design (CCD) experimentation and a 2-D contour plot of the corresponding variance of the predicted response according to Mead et al. (2012) <doi:10.1017/CBO9781139020879> design_ccd(), and analyzes CCD data with response surface methodology ccd_analysis(). A rotatable CCD provides values of the variance of the predicted response that are concentrically distributed around the average treatment combination used in the experimentation, which with uniform precision (implied by the use of several replicates at the average treatment combination) improves greatly the search and finding of an optimum response. These properties of a rotatable CCD represent undeniable advantages over the classical factorial design, as discussed by Panneton et al. (1999) <doi:10.13031/2013.13267> and Mead et al. (2012) <doi:10.1017/CBO9781139020879.018> among others.

Last updated 7 years ago

1.00 score 2 scripts 150 downloads

sharpr2 - Estimating Regulatory Scores and Identifying ATAC-STARR Data

An algorithm for identifying high-resolution driver elements for datasets from a high-definition reporter assay library. Xinchen Wang, Liang He, Sarah Goggin, Alham Saadat, Li Wang, Melina Claussnitzer, Manolis Kellis (2017) <doi:10.1101/193136>.

Last updated 7 years ago

1.00 score 1 stars 9 scripts 114 downloads

vitality - Fitting Routines for the Vitality Family of Mortality Models

Provides fitting routines for four versions of the Vitality family of mortality models.

Last updated 7 years ago

1.00 score 5 scripts 145 downloads

equalCovs - Testing the Equality of Two Covariance Matrices

Tests the equality of two covariance matrices, used in paper "Two sample tests for high dimensional covariance matrices." Li and Chen (2012) <arXiv:1206.0917>.

Last updated 7 years ago

1.00 score 6 scripts 106 downloads

imdbapi - Get Movie, Television Data from the 'imdb' Database

Provides API access to the <http://imdbapi.net> which maintains metadata about movies, games and television shows through a public API.

Last updated 7 years ago

1.00 score 9 scripts 116 downloads

semsfa - Semiparametric Estimation of Stochastic Frontier Models

Semiparametric Estimation of Stochastic Frontier Models following a two step procedure: in the first step semiparametric or nonparametric regression techniques are used to relax parametric restrictions of the functional form representing technology and in the second step variance parameters are obtained by pseudolikelihood estimators or by method of moments.

Last updated 7 years ago

1.00 score 1 stars 4 scripts 255 downloads

binMto - Many-to-One Comparisons of Proportions

Asymptotic simultaneous confidence intervals for comparison of many treatments with one control, for the difference of binomial proportions, allows for Dunnett-like-adjustment, Bonferroni or unadjusted intervals. Simulation of power of the above interval methods, approximate calculation of any-pair-power, and sample size iteration based on approximate any-pair power. Exact conditional maximum test for many-to-one comparisons to a control.

Last updated 7 years ago

1.00 score 9 scripts 189 downloads

thgenetics - Genetic Rare Variants Tests

A step-up test for genetic rare variants in a gene or in a pathway. The method determines an optimal grouping of rare variants analytically. The method has been described in Hoffmann TJ, Marini NJ, and Witte JS (2010) <doi:10.1371/journal.pone.0013584>.

Last updated 7 years ago

cpp

1.00 score 1 scripts 148 downloads

NightDay - Night and Day Boundary Plot Function

Computes and plots the boundary between night and day.

Last updated 7 years ago

1.00 score 4 scripts 148 downloads

phyreg - The Phylogenetic Regression of Grafen (1989)

Provides general linear model facilities (single y-variable, multiple x-variables with arbitrary mixture of continuous and categorical and arbitrary interactions) for cross-species data. The method is, however, based on the nowadays rather uncommon situation in which uncertainty about a phylogeny is well represented by adopting a single polytomous tree. The theory is in A. Grafen (1989, Proc. R. Soc. B 326, 119-157) and aims to cope with both recognised phylogeny (closely related species tend to be similar) and unrecognised phylogeny (a polytomy usually indicates ignorance about the true sequence of binary splits).

Last updated 7 years ago

1.00 score 2 scripts 131 downloads

mispr - Multiple Imputation with Sequential Penalized Regression

Generates multivariate imputations using sequential regression with L2 penalty. For more details see Zahid and Heumann (2018) <doi:10.1177/0962280218755574>.

Last updated 7 years ago

1.00 score 3 scripts 118 downloads

MultiVarMI - Multiple Imputation for Multivariate Data

Fully parametric Bayesian multiple imputation framework for massive multivariate data of different variable types as seen in Demirtas, H. (2017) <doi:10.1007/978-981-10-3307-0_8>.

Last updated 7 years ago

1.00 score 7 scripts 118 downloads

MargCond - Joint Marginal-Conditional Model

Fits joint marginal conditional models for multivariate longitudinal data, as in Proudfoot, Faig, Natarajan, and Xu (2018) <doi:10.1002/sim.7552>. Development of this package was supported by the UCSD Altman Translational Research Institute, NIH grant UL1TR001442. The content is solely the responsibility of the authors and does not necessarily represent the official views of the NIH.

Last updated 7 years ago

1.00 score 2 scripts 115 downloads

SnakesAndLaddersAnalysis - Play and Analyse the Game of Snakes and Ladders

Plays the game of Snakes and Ladders and has tools for analyses. The tools included allow you to find the average moves to win, frequency of each square, importance of the snakes and the ladders, the most common square and the plotting of the game played.

Last updated 7 years ago

1.00 score 7 scripts 118 downloads

QRegVCM - Quantile Regression in Varying-Coefficient Models

Quantile regression in varying-coefficient models (VCM) using one particular nonparametric technique called P-splines. The functions can be applied on three types of VCM; (1) Homoscedastic VCM, (2) Simple heteroscedastic VCM, and (3) General heteroscedastic VCM.

Last updated 7 years ago

1.00 score 1 stars 11 scripts 136 downloads

depend.truncation - Statistical Methods for the Analysis of Dependently Truncated Data

Estimation and testing methods for dependently truncated data. Semi-parametric methods are based on Emura et al. (2011)<Stat Sinica 21:349-67>, Emura & Wang (2012)<doi:10.1016/j.jmva.2012.03.012>, and Emura & Murotani (2015)<doi:10.1007/s11749-015-0432-8>. Parametric approaches are based on Emura & Konno (2012)<doi:10.1007/s00362-014-0626-2> and Emura & Pan (2017)<doi:10.1007/s00362-017-0947-z>. A regression approach is based on Emura & Wang (2016)<doi:10.1007/s10463-015-0526-9>. Quasi-independence tests are based on Emura & Wang (2010)<doi:10.1016/j.jmva.2009.07.006>. Right-truncated data for Japanese male centenarians are given by Emura & Murotani (2015)<doi:10.1007/s11749-015-0432-8>.

Last updated 7 years ago

1.00 score 15 scripts 236 downloads

icRSF - A Modified Random Survival Forest Algorithm

Implements a modification to the Random Survival Forests algorithm for obtaining variable importance in high dimensional datasets. The proposed algorithm is appropriate for settings in which a silent event is observed through sequentially administered, error-prone self-reports or laboratory based diagnostic tests. The modified algorithm incorporates a formal likelihood framework that accommodates sequentially administered, error-prone self-reports or laboratory based diagnostic tests. The original Random Survival Forests algorithm is modified by the introduction of a new splitting criterion based on a likelihood ratio test statistic.

Last updated 7 years ago

cpp

1.00 score 3 scripts 142 downloads

clespr - Composite Likelihood Estimation for Spatial Data

Composite likelihood approach is implemented to estimating statistical models for spatial ordinal and proportional data based on Feng et al. (2014) <doi:10.1002/env.2306>. Parameter estimates are identified by maximizing composite log-likelihood functions using the limited memory BFGS optimization algorithm with bounding constraints, while standard errors are obtained by estimating the Godambe information matrix.

Last updated 7 years ago

1.00 score 6 scripts 172 downloads

RCRnorm - An Integrated Regression Model for Normalizing 'NanoString nCounter' Data

'NanoString nCounter' is a medium-throughput platform that measures gene or microRNA expression levels. Here is a publication that introduces this platform: Malkov (2009) <doi:10.1186/1756-0500-2-80>. Here is the webpage of 'NanoString nCounter' where you can find detailed information about this platform <https://www.nanostring.com/scientific-content/technology-overview/ncounter-technology>. It has great clinical application, such as diagnosis and prognosis of cancer. Implements integrated system of random-coefficient hierarchical regression model to normalize data from 'NanoString nCounter' platform so that noise from various sources can be removed.

Last updated 7 years ago

1.00 score 1 stars 2 scripts 145 downloads

irtreliability - Item Response Theory Reliability

Estimation of reliability coefficients for ability estimates and sum scores from item response theory models as defined in Cheng, Y., Yuan, K.-H. and Liu, C. (2012) <doi:10.1177/0013164411407315> and Kim, S. and Feldt, L. S. (2010) <doi:10.1007/s12564-009-9062-8>. The package supports the 3-PL and generalized partial credit models and includes estimates of the standard errors of the reliability coefficient estimators, derived in Andersson, B. and Xin, T. (2018) <doi:10.1177/0013164417713570>.

Last updated 7 years ago

1.00 score 2 scripts 106 downloads

ssrm.logmer - Sample Size Determination for Longitudinal Designs with Binary Outcome

Provides the necessary sample size for a longitudinal study with binary outcome in order to attain a pre-specified power while strictly maintaining the Type I error rate. Kapur K, Bhaumik R, Tang XC, Hur K, Reda DJ, Bhaumik D (2014) <doi:10.1002/sim.6203>.

Last updated 7 years ago

1.00 score 1 scripts 118 downloads

Dykstra - Quadratic Programming using Cyclic Projections

Solves quadratic programming problems using Richard L. Dykstra's cyclic projection algorithm. Routine allows for a combination of equality and inequality constraints. See Dykstra (1983) <doi:10.1080/01621459.1983.10477029> for details.

Last updated 7 years ago

1.00 score 3 scripts 141 downloads

bigtcr - Nonparametric Analysis of Bivariate Gap Time with Competing Risks

For studying recurrent disease and death with competing risks, comparisons based on the well-known cumulative incidence function can be confounded by different prevalence rates of the competing events. Alternatively, comparisons of the conditional distribution of the survival time given the failure event type are more relevant for investigating the prognosis of different patterns of recurrence disease. This package implements a nonparametric estimator for the conditional cumulative incidence function and a nonparametric conditional bivariate cumulative incidence function for the bivariate gap times proposed in Huang et al. (2016) <doi:10.1111/biom.12494>.

Last updated 7 years ago

1.00 score 6 scripts 151 downloads

aidar - Tools for Reading AIDA Files

Read objects from the AIDA (<http://aida.freehep.org/>) file and make them available as dataframes in R.

Last updated 7 years ago

1.00 score 13 scripts 245 downloads

gLRTH - Genome-Wide Association and Linkage Analysis under Heterogeneity

Likelihood ratio tests for genome-wide association and genome-wide linkage analysis under heterogeneity.

Last updated 7 years ago

1.00 score 2 scripts 120 downloads

PAmeasures - Prediction and Accuracy Measures for Nonlinear Models and for Right-Censored Time-to-Event Data

We propose a pair of summary measures for the predictive power of a prediction function based on a regression model. The regression model can be linear or nonlinear, parametric, semi-parametric, or nonparametric, and correctly specified or mis-specified. The first measure, R-squared, is an extension of the classical R-squared statistic for a linear model, quantifying the prediction function's ability to capture the variability of the response. The second measure, L-squared, quantifies the prediction function's bias for predicting the mean regression function. When used together, they give a complete summary of the predictive power of a prediction function. Please refer to Gang Li and Xiaoyan Wang (2016) <arXiv:1611.03063> for more details.

Last updated 7 years ago

1.00 score 1 stars 30 scripts 129 downloads

GoogleKnowledgeGraphR - Retrieve Information from 'Google Knowledge Graph' API

Allows you to retrieve information from the 'Google Knowledge Graph' API <https://www.google.com/intl/bn/insidesearch/features/search/knowledge.html> and process it in R in various forms. The 'Knowledge Graph Search' API lets you find entities in the 'Google Knowledge Graph'. The API uses standard 'schema.org' types and is compliant with the 'JSON-LD' specification.

Last updated 7 years ago

1.00 score 2 scripts 110 downloads

factoptd - Factorial Optimal Designs for Two-Colour cDNA Microarray Experiments

Computes factorial A-, D- and E-optimal designs for two-colour cDNA microarray experiments.

Last updated 7 years ago

1.00 score 1 scripts 129 downloads

TrioSGL - Trio Model with a Combination of Lasso and Group Lasso Regularization

Fit a trio model via penalized maximum likelihood. The model is fit for a path of values of the penalty parameter. This package is based on Noah Simon, et al. (2011) <doi:10.1080/10618600.2012.681250>.

Last updated 7 years ago

cpp

1.00 score 1 scripts 97 downloads

PooledMeanGroup - Pooled Mean Group Estimation of Dynamic Heterogenous Panels

Calculates the pooled mean group (PMG) estimator for dynamic panel data models, as described by Pesaran, Shin and Smith (1999) <doi:10.1080/01621459.1999.10474156>.

Last updated 7 years ago

1.00 score 10 scripts 111 downloads

submax - Effect Modification in Observational Studies Using the Submax Method

Effect modification occurs if a treatment effect is larger or more stable in certain subgroups defined by observed covariates. The submax or subgroup-maximum method of Lee et al. (2017) <arXiv:1702.00525> does an overall test and separate tests in subgroups, correcting for multiple testing using the joint distribution.

Last updated 7 years ago

1.00 score 9 scripts 92 downloads

gTests - Graph-Based Two-Sample Tests

Four graph-based tests are provided for testing whether two samples are from the same distribution. It works for both continuous data and discrete data.

Last updated 7 years ago

1.00 score 1 stars 24 scripts 128 downloads

LCF - Linear Combination Fitting

Baseline correction, normalization and linear combination fitting (LCF) of X-ray absorption near edge structure (XANES) spectra. The package includes data loading of .xmu files exported from 'ATHENA' (Ravel and Newville, 2005) <doi:10.1107/S0909049505012719>. Loaded spectra can be background corrected and all standards can be fitted at once. Two linear combination fitting functions can be used: (1) fit_athena(): Simply fitting combinations of standards as in ATHENA, (2) fit_float(): Fitting all standards with changing baseline correction and edge-step normalization parameters.

Last updated 7 years ago

1.00 score 11 scripts 128 downloads

mpmcorrelogram - Multivariate Partial Mantel Correlogram

Functions to compute and plot multivariate (partial) Mantel correlograms.

Last updated 7 years ago

1.00 score 9 scripts 245 downloads

logihist - Combined Graphs for Logistic Regression

Provides histograms, boxplots and dotplots as alternatives to scatterplots of data when plotting fitted logistic regressions.

Last updated 7 years ago

1.00 score 2 scripts 128 downloads

SequentialDesign - Observational Database Study Planning using Exact Sequential Analysis for Poisson and Binomial Data

Functions to be used in conjunction with the 'Sequential' package that allows for planning of observational database studies that will be analyzed with exact sequential analysis. This package supports Poisson- and binomial-based data. The primary function, seq_wrapper(...), accepts parameters for simulation of a simple exposure pattern and for the 'Sequential' package setup and analysis functions. The exposure matrix is used to simulate the true and false positive and negative populations (Green (1983) <doi:10.1093/oxfordjournals.aje.a113521>, Brenner (1993) <doi:10.1093/oxfordjournals.aje.a116805>). Functions are then run from the 'Sequential' package on these populations, which allows for the exploration of outcome misclassification in data.

Last updated 7 years ago

1.00 score 7 scripts 93 downloads

fBonds - Rmetrics - Pricing and Evaluating Bonds

It implements the Nelson-Siegel and the Nelson-Siegel-Svensson term structures.

Last updated 7 years ago

1.00 score 1 scripts 242 downloads

rethinker - RethinkDB Client

Simple, native 'RethinkDB' client.

Last updated 7 years ago

1.00 score 6 scripts 378 downloads

PdPDB - Pattern Discovery in PDB Structures of Metalloproteins

Looks for amino acid and/or nucleotide patterns and/or small ligands coordinated to a given prosthetic centre. Files have to be in the local file system and contain proper extension.

Last updated 7 years ago

1.00 score 1 scripts 126 downloads

DatAssim - Data Assimilation

For estimation of a variable of interest using Kalman filter by incorporating results from previous assessments, i.e. through development weighted estimates where weights are assigned inversely proportional to the variance of existing and new estimates. For reference see Ehlers et al. (2017) <doi:10.20944/preprints201710.0098.v1>.

Last updated 7 years ago

openblascpp

1.00 score 1 scripts 141 downloads

SLDAssay - Software for Analyzing Limiting Dilution Assays

Calculates maximum likelihood estimate, exact and asymptotic confidence intervals, and exact and asymptotic goodness of fit p-values for concentration of infectious units from serial limiting dilution assays. This package uses the likelihood equation, exact goodness of fit p-values, and exact confidence intervals described in Meyers et al. (1994) <http://jcm.asm.org/content/32/3/732.full.pdf>. This software is also implemented as a web application through the Shiny R package <https://iupm.shinyapps.io/sldassay/>.

Last updated 7 years ago

1.00 score 1 scripts 151 downloads

PanJen - A Semi-Parametric Test for Specifying Functional Form

A central decision in a parametric regression is how to specify the relation between an dependent variable and each explanatory variable. This package provides a semi-parametric tool for comparing different transformations of an explanatory variables in a parametric regression. The functions is relevant in a situation, where you would use a box-cox or Box-Tidwell transformations. In contrast to the classic power-transformations, the methods in this package allows for theoretical driven user input and the possibility to compare with a non-parametric transformation.

Last updated 7 years ago

1.00 score 9 scripts 479 downloads

vfcp - Computation of v Values for U and Copula C(U, v)

Computation the value of one of two uniformly distributed marginals if the copula probability value is known and the value of the second marginal is also known. Computation and plotting corresponding cumulative distribution function or survival function. The numerical definition of a common area limited by lines of the cumulative distribution function and survival function. Approximate quantification of the probability of this area. In addition to 'amh', the copula dimension may be larger than 2.

Last updated 7 years ago

1.00 score 11 scripts 124 downloads

XRPython - Structured Interface to 'Python'

A 'Python' interface structured according to the general form described in package 'XR' and in the book "Extending R".

Last updated 7 years ago

1.00 score 9 scripts 132 downloads

swa - Subsampling Winner Algorithm for Classification

This algorithm conducts variable selection in the classification setting. It repeatedly subsamples variables and runs linear discriminant analysis (LDA) on the subsampled variables. Variables are scored based on the AUC and the t-statistics. Variables then enter a competition and the semi-finalist variables will be evaluated in a final round of LDA classification. The algorithm then outputs a list of variable selected. Qiao, Sun and Fan (2017) <http://people.math.binghamton.edu/qiao/swa.html>.

Last updated 7 years ago

1.00 score 1 scripts 115 downloads

GSMX - Multivariate Genomic Selection

Estimating trait heritability and handling overfitting. This package includes a collection of functions for (1) estimating genetic variance-covariances and calculate trait heritability; and (2) handling overfitting by calculating the variance components and the heritability through cross validation.

Last updated 7 years ago

1.00 score 9 scripts 182 downloads

BLRPM - Stochastic Rainfall Generator Bartlett-Lewis Rectangular Pulse Model

Due to a limited availability of observed high-resolution precipitation records with adequate length, simulations with stochastic precipitation models are used to generate series for subsequent studies [e.g. Khaliq and Cunmae, 1996, <doi:10.1016/0022-1694(95)02894-3>, Vandenberghe et al., 2011, <doi:10.1029/2009WR008388>]. This package contains an R implementation of the original Bartlett-Lewis rectangular pulse model (BLRPM), developed by Rodriguez-Iturbe et al. (1987) <doi:10.1098/rspa.1987.0039>. It contains a function for simulating a precipitation time series based on storms and cells generated by the model with given or estimated model parameters. Additionally BLRPM parameters can be estimated from a given or simulated precipitation time series. The model simulations can be plotted in a three-layer plot including an overview of generated storms and cells by the model (which can also be plotted individually), a continuous step-function and a discrete precipitation time series at a chosen aggregation level.

Last updated 7 years ago

1.00 score 8 scripts 157 downloads

INCATome - Internal Control Analysis of Translatome Studies by Microarrays

Data analysis, normalisation and differential expression for Translatome studies by microarrays (T Sbarrato et al. RNA. 2017 Aug 25; <DOI:10.1261/rna.060525.116>).

Last updated 7 years ago

1.00 score 97 downloads

birtr - The R Package for "The Basics of Item Response Theory Using R"

R functions for "The Basics of Item Response Theory Using R" by Frank B. Baker and Seock-Ho Kim (Springer, 2017, ISBN-13: 978-3-319-54204-1) including iccplot(), icccal(), icc(), iccfit(), groupinv(), tcc(), ability(), tif(), and rasch(). For example, iccplot() plots an item characteristic curve under the two-parameter logistic model.

Last updated 7 years ago

1.00 score 10 scripts 204 downloads

DoubleCone - Test Against Parametric Regression Function

Performs hypothesis tests concerning a regression function in a least-squares model, where the null is a parametric function, and the alternative is the union of large-dimensional convex polyhedral cones. See Bodhisattva Sen and Mary C Meyer (2016) <doi:10.1111/rssb.12178> for more details.

Last updated 7 years ago

1.00 score 5 scripts 151 downloads

additiveDEA - Additive Data Envelopment Analysis Models

Provides functions for calculating efficiency with two types of additive Data Envelopment Analysis models: (i) Generalized Efficiency Measures: unweighted additive model (Cooper et al., 2007 <doi:10.1007/978-0-387-45283-8>), Range Adjusted Measure (Cooper et al., 1999, <doi:10.1023/A:1007701304281>), Bounded Adjusted Measure (Cooper et al., 2011 <doi:10.1007/s11123-010-0190-2>), Measure of Inefficiency Proportions (Cooper et al., 1999 <doi:10.1023/A:1007701304281>), and the Lovell-Pastor Measure (Lovell and Pastor, 1995 <doi:10.1016/0167-6377(95)00044-5>); and (ii) the Slacks-Based Measure (Tone, 2001 <doi:10.1016/S0377-2217(99)00407-5>). The functions provide several options: (i) constant and variable returns to scale; (ii) fixed (non-controllable) inputs and/or outputs; (iii) bounding the slacks so that unrealistically large slack values are avoided; and (iv) calculating the efficiency of specific Decision-Making Units (DMUs), rather than of the whole sample. Package additiveDEA also provides a function for reducing computation time when datasets are large.

Last updated 7 years ago

1.00 score 5 scripts 265 downloads

mmpp - Various Similarity and Distance Metrics for Marked Point Processes

Compute similarities and distances between marked point processes.

Last updated 7 years ago

1.00 score 10 scripts 510 downloads

BayesCR - Bayesian Analysis of Censored Regression Models Under Scale Mixture of Skew Normal Distributions

Propose a parametric fit for censored linear regression models based on SMSN distributions, from a Bayesian perspective. Also, generates SMSN random variables.

Last updated 7 years ago

1.00 score 1 scripts 230 downloads

Ohit - OGA+HDIC+Trim and High-Dimensional Linear Regression Models

Ing and Lai (2011) <doi:10.5705/ss.2010.081> proposed a high-dimensional model selection procedure that comprises three steps: orthogonal greedy algorithm (OGA), high-dimensional information criterion (HDIC), and Trim. The first two steps, OGA and HDIC, are used to sequentially select input variables and determine stopping rules, respectively. The third step, Trim, is used to delete irrelevant variables remaining in the second step. This package aims at fitting a high-dimensional linear regression model via OGA+HDIC+Trim.

Last updated 7 years ago

1.00 score 3 scripts 102 downloads

VDSPCalibration - Statistical Methods for Designing and Analyzing a Calibration Study

Provides statistical methods for the design and analysis of a calibration study, which aims for calibrating measurements using two different methods. The package includes sample size calculation, sample selection, regression analysis with error-in measurements and change-point regression. The method is described in Tian, Durazo-Arvizu, Myers, et al. (2014) <DOI:10.1002/sim.6235>.

Last updated 7 years ago

1.00 score 5 scripts 85 downloads

cbanalysis - Coffee Break Descriptive Analysis

A set of functions that helps you to generate descriptive statistics based on the variable types.

Last updated 7 years ago

1.00 score 2 scripts 153 downloads

Fuzzy.p.value - Computing Fuzzy p-Value

The main goal of this package is drawing the membership function of the fuzzy p-value which is defined as a fuzzy set on the unit interval for three following problems: (1) testing crisp hypotheses based on fuzzy data, (2) testing fuzzy hypotheses based on crisp data, and (3) testing fuzzy hypotheses based on fuzzy data. In all cases, the fuzziness of data or/and the fuzziness of the boundary of null fuzzy hypothesis transported via the p-value function and causes to produce the fuzzy p-value. If the p-value is fuzzy, it is more appropriate to consider a fuzzy significance level for the problem. Therefore, the comparison of the fuzzy p-value and the fuzzy significance level is evaluated by a fuzzy ranking method in this package.

Last updated 7 years ago

1.00 score 6 scripts 160 downloads

FPV - Testing Hypotheses via Fuzzy P-Value in Fuzzy Environment

The main goal of this package is drawing the membership function of the fuzzy p-value which is defined as a fuzzy set on the unit interval for three following problems: (1) testing crisp hypotheses based on fuzzy data, see Filzmoser and Viertl (2004) <doi:10.1007/s001840300269>, (2) testing fuzzy hypotheses based on crisp data, see Parchami et al. (2010) <doi:10.1007/s00362-008-0133-4>, and (3) testing fuzzy hypotheses based on fuzzy data, see Parchami et al. (2012) <doi:10.1007/s00362-010-0353-2>. In all cases, the fuzziness of data or / and the fuzziness of the boundary of null fuzzy hypothesis transported via the p-value function and causes to produce the fuzzy p-value. If the p-value is fuzzy, it is more appropriate to consider a fuzzy significance level for the problem. Therefore, the comparison of the fuzzy p-value and the fuzzy significance level is evaluated by a fuzzy ranking method in this package.

Last updated 7 years ago

1.00 score 1 scripts 107 downloads

ccmm - Compositional Mediation Model

Estimate the direct and indirect (mediation) effects of treatment on the outcome when intermediate variables (mediators) are compositional and high-dimensional. Sohn, M.B. and Li, H. (2017). Compositional Mediation Analysis for Microbiome Studies. (AOAS: In revision).

Last updated 7 years ago

1.00 score 9 scripts 135 downloads

CpGFilter - CpG Filtering Method Based on Intra-Class Correlation Coefficients

Filter CpGs based on Intra-class Correlation Coefficients (ICCs) when replicates are available. ICCs are calculated by fitting linear mixed effects models to all samples including the un-replicated samples. Including the large number of un-replicated samples improves ICC estimates dramatically. The method accommodates any replicate design.

Last updated 7 years ago

1.00 score 5 scripts 161 downloads

macc - Mediation Analysis of Causality under Confounding

Performs causal mediation analysis under confounding or correlated errors. This package includes a single level mediation model, a two-level mediation model, and a three-level mediation model for data with hierarchical structures. Under the two/three-level mediation model, the correlation parameter is identifiable and is estimated based on a hierarchical-likelihood, a marginal-likelihood or a two-stage method. See Zhao, Y., & Luo, X. (2014), Estimating Mediation Effects under Correlated Errors with an Application to fMRI, <arXiv:1410.7217> for details.

Last updated 7 years ago

1.00 score 6 scripts 126 downloads

zic - Bayesian Inference for Zero-Inflated Count Models

Provides MCMC algorithms for the analysis of zero-inflated count models. The case of stochastic search variable selection (SVS) is also considered. All MCMC samplers are coded in C++ for improved efficiency. A data set considering the demand for health care is provided.

Last updated 7 years ago

openblascpp

1.00 score 16 scripts 212 downloads

GRCdata - Parameter Inference and Optimal Designs for Grouped and/or Right-Censored Count Data

We implement two main functions. The first function uses a given grouped and/or right-censored grouping scheme and empirical data to infer parameters, and implements chi-square goodness-of-fit tests. The second function searches for the global optimal grouping scheme of grouped and/or right-censored count responses in surveys.

Last updated 7 years ago

1.00 score 2 scripts 134 downloads

CompDist - Multisection Composite Distributions

Computes density function, cumulative distribution function, quantile function and random numbers for a multisection composite distribution specified by the user. Also fits the user specified distribution to a given data set. More details of the package can be found in the following paper submitted to the R journal Wiegand M and Nadarajah S (2017) CompDist: Multisection composite distributions.

Last updated 7 years ago

1.00 score 5 scripts 119 downloads

RkMetrics - Hybrid Mortality Estimation

Hybrid Mortality Modelling (HMM) provides a framework in which mortality around "the accident hump" and at very old ages can be modelled under a single model. The graphics' codes necessary for visualization of the models' output are included here. Specifically, the graphics are based on the assumption that, the mortality rates can be expressed as a function of the area under the curve between the crude mortality rates plots and the tangential transform of the force of mortality.

Last updated 7 years ago

1.00 score 6 scripts 111 downloads

bayeslongitudinal - Adjust Longitudinal Regression Models Using Bayesian Methodology

Adjusts longitudinal regression models using Bayesian methodology for covariance structures of composite symmetry (SC), autoregressive ones of order 1 AR (1) and autoregressive moving average of order (1,1) ARMA (1,1).

Last updated 7 years ago

1.00 score 6 scripts 239 downloads

pcensmix - Model Fitting to Progressively Censored Mixture Data

Functions for generating progressively Type-II censored data in a mixture structure and fitting models using a constrained EM algorithm. It can also create a progressive Type-II censored version of a given real dataset to be considered for model fitting.

Last updated 7 years ago

1.00 score 6 scripts 105 downloads

FastSF - Fast Structural Filtering

An implementation of the fast structural filtering with L0 penalty. It includes an adaptive polynomial estimator by minimizing the least squares error with constraints on the number of breaks in their (k + 1)-st discrete derivative, for a chosen integer k >= 0. It also includes generalized structure sparsity constraint, i.e., graph trend filtering. This package is implemented via the primal dual active set algorithm, which formulates estimates and residuals as primal and dual variables, and utilizes efficient active set selection strategies based on the properties of the primal and dual variables.

Last updated 7 years ago

openblascpp

1.00 score 8 scripts 123 downloads

interfr - Interference Color Charts for Polarized Light Microscopy

Computes interference color tables and plots customized Michel-Levy or Raith-Sorensen charts. Automatic interpretation of polarized-light microscopy images is still under development and will come soon.

Last updated 7 years ago

1.00 score 1 stars 4 scripts 138 downloads

dGAselID - Genetic Algorithm with Incomplete Dominance for Feature Selection

Feature selection from high dimensional data using a diploid genetic algorithm with Incomplete Dominance for genotype to phenotype mapping and Random Assortment of chromosomes approach to recombination.

Last updated 7 years ago

1.00 score 1 stars 1 scripts 164 downloads

correlbinom - Correlated Binomial Probabilities

Calculates the probabilities of k successes given n trials of a binomial random variable with non-negative correlation across trials. The function takes as inputs the scalar values the level of correlation or association between trials, the success probability, the number of trials, an optional input specifying the number of bits of precision used in the calculation, and an optional input specifying whether the calculation approach to be used is from Witt (2014) <doi:10.1080/03610926.2012.725148> or from Kuk (2004) <doi:10.1046/j.1467-9876.2003.05369.x>. The output is a (trials+1)-dimensional vector containing the likelihoods of 0, 1, ..., trials successes.

Last updated 7 years ago

1.00 score 1 scripts 205 downloads

Autoplotprotein - Development of Visualization Tools for Protein Sequence

The image of the amino acid transform on the protein level is drawn, and the automatic routing of the functional elements such as the domain and the mutation site is completed.

Last updated 7 years ago

1.00 score 9 scripts 186 downloads

ExpRep - Experiment Repetitions

Allows to calculate the probabilities of occurrences of an event in a great number of repetitions of Bernoulli experiment, through the application of the local and the integral theorem of De Moivre Laplace, and the theorem of Poisson. Gives the possibility to show the results graphically and analytically, and to compare the results obtained by the application of the above theorems with those calculated by the direct application of the Binomial formula. Is basically useful for educational purposes.

Last updated 7 years ago

1.00 score 9 scripts 128 downloads

FSTpackage - Unified Sequence-Based Association Tests Allowing for Multiple Functional Annotation Scores

Functions for sequencing studies allowing for multiple functional annotation scores. Score type tests and an efficient perturbation method are used for individual gene/large gene-set/genome wide analysis. Only summary statistics are needed.

Last updated 7 years ago

1.00 score 10 scripts 138 downloads

MultiSkew - Measures, Tests and Removes Multivariate Skewness

Computes the third multivariate cumulant of either the raw, centered or standardized data. Computes the main measures of multivariate skewness, together with their bootstrap distributions. Finally, computes the least skewed linear projections of the data.

Last updated 8 years ago

1.00 score 8 scripts 111 downloads

featurizer - Some Helper Functions that Help Create Features from Data

A collection of functions that would help one to build features based on external data. Very useful for Data Scientists in data to day work. Many functions create features using parallel computation. Since the nitty gritty of parallel computation is hidden under the hood, the user need not worry about creating clusters and shutting them down.

Last updated 8 years ago

1.00 score 4 scripts 120 downloads

soptdmaeA - Sequential Optimal Designs for Two-Colour cDNA Microarray Experiments

Computes sequential A-, MV-, D- and E-optimal or near-optimal block and row-column designs for two-colour cDNA microarray experiments using the linear fixed effects and mixed effects models where the interest is in a comparison of all possible elementary treatment contrasts. The package also provides an optional method of using the graphical user interface (GUI) R package 'tcltk' to ensure that it is user friendly.

Last updated 8 years ago

1.00 score 120 downloads

gamlssbssn - Bimodal Skew Symmetric Normal Distribution

Density, distribution function, quantile function and random generation for the bimodal skew symmetric normal distribution of Hassan and El-Bassiouni (2016) <doi:10.1080/03610926.2014.882950>.

Last updated 8 years ago

1.00 score 3 scripts 117 downloads

pencopulaCond - Estimating Non-Simplified Vine Copulas Using Penalized Splines

Estimating Non-Simplified Vine Copulas Using Penalized Splines.

Last updated 8 years ago

1.00 score 1 stars 1 scripts 121 downloads

gomms - GLM-Based Ordination Method

A zero-inflated quasi-Poisson factor model to display similarity between samples visually in a low (2 or 3) dimensional space.

Last updated 8 years ago

1.00 score 1 scripts 100 downloads

plotprotein - Development of Visualization Tools for Protein Sequence

The image of the amino acid transform on the protein level is drawn, and the automatic routing of the functional elements such as the domain and the mutation site is completed.

Last updated 8 years ago

1.00 score 8 scripts 425 downloads

compHclust - Complementary Hierarchical Clustering

Performs the complementary hierarchical clustering procedure and returns X' (the expected residual matrix) and a vector of the relative gene importances.

Last updated 8 years ago

1.00 score 3 scripts 204 downloads

censCov - Linear Regression with a Randomly Censored Covariate

Implementations of threshold regression approaches for linear regression models with a covariate subject to random censoring, including deletion threshold regression and completion threshold regression. Reverse survival regression, which flip the role of response variable and the covariate, is also considered.

Last updated 8 years ago

1.00 score 1 scripts 179 downloads

RandMeta - Efficient Numerical Algorithm for Exact Inference in Meta Analysis

A novel numerical algorithm that provides functionality for estimating the exact 95% confidence interval of the location parameter in the random effects model, and is much faster than the naive method. Works best when the number of studies is between 6-20.

Last updated 8 years ago

1.00 score 1 scripts 137 downloads

TSGSIS - Two Stage-Grouped Sure Independence Screening

To provide a high dimensional grouped variable selection approach for detection of whole-genome SNP effects and SNP-SNP interactions, as described in Fang et al. (2017, under review).

Last updated 8 years ago

1.00 score 1 stars 1 scripts 93 downloads

mro - Multiple Correlation

Computes multiple correlation coefficient when the data matrix is given and tests its significance.

Last updated 8 years ago

1.00 score 2 scripts 123 downloads

optrcdmaeAT - Optimal Row-Column Designs for Two-Colour cDNA Microarray Experiments

Computes A-, MV-, D- and E-optimal or near-optimal row-column designs for two-colour cDNA microarray experiments using the linear fixed effects and mixed effects models where the interest is in a comparison of all pairwise treatment contrasts. The algorithms used in this package are based on the array exchange and treatment exchange algorithms adopted from Debusho, Gemechu and Haines (2016, unpublished) algorithms after adjusting for the row-column designs setup. The package also provides an optional method of using the graphical user interface (GUI) R package tcltk to ensure that it is user friendly.

Last updated 8 years ago

1.00 score 115 downloads

TSMN - Truncated Scale Mixtures of Normal Distributions

Return the first four moments of the SMN distributions (Normal, Student-t, Pearson VII, Slash or Contaminated Normal).

Last updated 8 years ago

1.00 score 3 scripts 444 downloads

BLModel - Black-Litterman Posterior Distribution

Posterior distribution in the Black-Litterman model is computed from a prior distribution given in the form of a time series of asset returns and a continuous distribution of views provided by the user as an external function.

Last updated 8 years ago

1.00 score 6 scripts 535 downloads

hydrogeo - Groundwater Data Presentation and Interpretation

Contains one function for drawing Piper diagrams (also called Piper-Hill diagrams) of water analyses for major ions.

Last updated 8 years ago

1.00 score 17 scripts 613 downloads

Ultimixt - Bayesian Analysis of Location-Scale Mixture Models using a Weakly Informative Prior

A generic reference Bayesian analysis of unidimensional mixture distributions obtained by a location-scale parameterisation of the model is implemented. The including functions simulate and summarize posterior samples for location-scale mixture models using a weakly informative prior. There is no need to define priors for scale-location parameters except two hyperparameters in which are associated with a Dirichlet prior for weights and a simplex.

Last updated 8 years ago

1.00 score 7 scripts 413 downloads

prop.comb.RR - Analyzing Combination of Proportions and Relative Risk

Carrying out inferences about any linear combination of proportions and the ratio of two proportions.

Last updated 8 years ago

1.00 score 1 stars 4 scripts 494 downloads

otinference - Inference for Optimal Transport

Sample from the limiting distributions of empirical Wasserstein distances under the null hypothesis and under the alternative. Perform a two-sample test on multivariate data using these limiting distributions and binning.

Last updated 8 years ago

1.00 score 3 scripts 435 downloads

VarED - Variance Estimation using Difference-Based Methods

Generating functions for both optimal and ordinary difference sequences, and the difference-based estimation functions.

Last updated 8 years ago

1.00 score 3 scripts 454 downloads

CPsurv - Nonparametric Change Point Estimation for Survival Data

Nonparametric change point estimation for survival data based on p-values of exact binomial tests.

Last updated 8 years ago

1.00 score 4 scripts 434 downloads

Dpit - Distribution Pitting

Compares distributions with one another in terms of their fit to each sample in a dataset that contains multiple samples, as described in Joo, Aguinis, and Bradley (in press). Users can examine the fit of seven distributions per sample: pure power law, lognormal, exponential, power law with an exponential cutoff, normal, Poisson, and Weibull. Automation features allow the user to compare all distributions for all samples with a single command line, which creates a separate row containing results for each sample until the entire dataset has been analyzed.

Last updated 8 years ago

1.00 score 2 scripts 436 downloads

WPKDE - Weighted Piecewise Kernel Density Estimation

Weighted Piecewise Kernel Density Estimation for large data.

Last updated 8 years ago

1.00 score 3 scripts 420 downloads

falconx - Finding Allele-Specific Copy Number in Whole-Exome Sequencing Data

This is a method for Allele-specific DNA Copy Number profiling for whole-Exome sequencing data. Given the allele-specific coverage and site biases at the variant loci, this program segments the genome into regions of homogeneous allele-specific copy number. It requires, as input, the read counts for each variant allele in a pair of case and control samples, as well as the site biases. For detection of somatic mutations, the case and control samples can be the tumor and normal sample from the same individual. The implemented method is based on the paper: Chen, H., Jiang, Y., Maxwell, K., Nathanson, K. and Zhang, N. (under review). Allele-specific copy number estimation by whole Exome sequencing.

Last updated 8 years ago

1.00 score 7 scripts 476 downloads

InvasionCorrection - Invasion Correction

The correction is achieved under the assumption that non-migrating cells of the essay approximately form a quadratic flow profile due to frictional effects, compare law of Hagen-Poiseuille for flow in a tube. The script fits a conical plane to give xyz-coordinates of the cells. It outputs the number of migrated cells and the new corrected coordinates.

Last updated 8 years ago

1.00 score 433 downloads

BCC1997 - Calculation of Option Prices Based on a Universal Solution

Calculates the prices of European options based on the universal solution provided by Bakshi, Cao and Chen (1997) <doi:10.1111/j.1540-6261.1997.tb02749.x>. This solution considers stochastic volatility, stochastic interest and random jumps. Please cite their work if this package is used.

Last updated 8 years ago

1.00 score 1 scripts 582 downloads

mdscore - Improved Score Tests for Generalized Linear Models

A set of functions to obtain modified score test for generalized linear models.

Last updated 8 years ago

1.00 score 20 scripts 528 downloads

spdownscale - Spatial Downscaling Using Bias Correction Approach

Spatial downscaling of climate data (Global Circulation Models/Regional Climate Models) using quantile-quantile bias correction technique.

Last updated 8 years ago

1.00 score 1 stars 3 scripts 454 downloads

warpMix - Mixed Effects Modeling with Warping for Functional Data Using B-Spline

Mixed effects modeling with warping for functional data using B- spline. Warping coefficients are considered as random effects, and warping functions are general functions, parameters representing the projection onto B- spline basis of a part of the warping functions. Warped data are modelled by a linear mixed effect functional model, the noise is Gaussian and independent from the warping functions.

Last updated 8 years ago

1.00 score 1 scripts 415 downloads

cope - Coverage Probability Excursion (CoPE) Sets

Provides functions to compute and plot Coverage Probability Excursion (CoPE) sets for real valued functions on a 2-dimensional domain. CoPE sets are obtained from repeated noisy observations of the function on the entire domain. They are designed to bound the excursion set of the target function at a given level from above and below with a predefined probability. The target function can be a parameter in spatially-indexed linear regression. Support by NIH grant R01 CA157528 is gratefully acknowledged.

Last updated 8 years ago

1.00 score 3 scripts 160 downloads

optbdmaeAT - Optimal Block Designs for Two-Colour cDNA Microarray Experiments

Computes A-, MV-, D- and E-optimal or near-optimal block designs for two-colour cDNA microarray experiments using the linear fixed effects and mixed effects models where the interest is in a comparison of all possible elementary treatment contrasts. The algorithms used in this package are based on the treatment exchange and array exchange algorithms of Debusho, Gemechu and Haines (2016, unpublished). The package also provides an optional method of using the graphical user interface (GUI) R package tcltk to ensure that it is user friendly.

Last updated 8 years ago

1.00 score 127 downloads

iosmooth - Functions for Smoothing with Infinite Order Flat-Top Kernels

Density, spectral density, and regression estimation using infinite order flat-top kernels.

Last updated 8 years ago

1.00 score 10 scripts 119 downloads

nparsurv - Nonparametric Tests for Main Effects, Simple Effects and Interaction Effect in a Factorial Design with Censored Data

Nonparametric Tests for Main Effects, Simple Effects and Interaction Effect with Censored Data and Two Factorial Influencing Variables.

Last updated 8 years ago

1.00 score 1 scripts 117 downloads

teda - An Implementation of the Typicality and Eccentricity Data Analysis Framework

The typicality and eccentricity data analysis (TEDA) framework was put forward by Angelov (2013) <DOI:10.14313/JAMRIS_2-2014/16>. It has been further developed into multiple different techniques since, and provides a non-parametric way of determining how similar an observation, from a process that is not purely random, is to other observations generated by the process. This package provides code to use the batch and recursive TEDA methods that have been published.

Last updated 8 years ago

1.00 score 1 stars 5 scripts 101 downloads

SADEG - Stability Analysis in Differentially Expressed Genes

We analyzed the nucleotide composition of genes with a special emphasis on stability of DNA sequences. Besides, in a variety of different organisms unequal use of synonymous codons, or codon usage bias, occurs which also show variation among genes in the same genome. Seemingly, codon usage bias is affected by both selective constraints and mutation bias which allows and enables us to examine and detect changes in these two evolutionary forces between genomes or along one genome. Therefore, we determined the codon adaptation index (CAI), effective number of codons (ENC) and codon usage analysis with calculation of the relative synonymous codon usage (RSCU), and subsequently predicted the translation efficiency and accuracy through GC-rich codon usages. Furthermore, we estimated the relative stability of the DNA sequence following calculation of the average free energy (Delta G) and Dimer base-stacking energy level.

Last updated 8 years ago

1.00 score 14 scripts 92 downloads

QRank - A Novel Quantile Regression Approach for eQTL discovery

A Quantile Rank-score based test for the identification of expression quantitative trait loci.

Last updated 8 years ago

1.00 score 6 scripts 115 downloads

GCPM - Generalized Credit Portfolio Model

Analyze the default risk of credit portfolios. Commonly known models, like CreditRisk+ or the CreditMetrics model are implemented in their very basic settings. The portfolio loss distribution can be achieved either by simulation or analytically in case of the classic CreditRisk+ model. Models are only implemented to respect losses caused by defaults, i.e. migration risk is not included. The package structure is kept flexible especially with respect to distributional assumptions in order to quantify the sensitivity of risk figures with respect to several assumptions. Therefore the package can be used to determine the credit risk of a given portfolio as well as to quantify model sensitivities.

Last updated 8 years ago

cpp

1.00 score 1 stars 7 scripts 221 downloads

SPPcomb - Combining Different Spatial Datasets in Cancer Risk Estimation

We propose a novel two-step procedure to combine epidemiological data obtained from diverse sources with the aim to quantify risk factors affecting the probability that an individual develops certain disease such as cancer. See Hui Huang, Xiaomei Ma, Rasmus Waagepetersen, Theodore R. Holford, Rong Wang, Harvey Risch, Lloyd Mueller & Yongtao Guan (2014) A New Estimation Approach for Combining Epidemiological Data From Multiple Sources, Journal of the American Statistical Association, 109:505, 11-23, <doi:10.1080/01621459.2013.870904>.

Last updated 8 years ago

1.00 score 5 scripts 94 downloads

MTDrh - Mass Transportation Distance Rank Histogram

The Mass Transportation Distance rank histogram was developed to assess the reliability of scenarios with equal or different probabilities of occurrence <doi:10.1002/we.1872>.

Last updated 8 years ago

1.00 score 3 scripts 99 downloads

ampd - An Algorithm for Automatic Peak Detection in Noisy Periodic and Quasi-Periodic Signals

A method for automatic detection of peaks in noisy periodic and quasi-periodic signals. This method, called automatic multiscale-based peak detection (AMPD), is based on the calculation and analysis of the local maxima scalogram, a matrix comprising the scale-dependent occurrences of local maxima. For further information see <doi:10.3390/a5040588>.

Last updated 8 years ago

1.00 score 4 scripts 262 downloads

MixedPoisson - Mixed Poisson Models

The estimation of the parameters in mixed Poisson models.

Last updated 8 years ago

1.00 score 15 scripts 115 downloads

robustsae - Robust Bayesian Small Area Estimation

Functions for Robust Bayesian Small Area Estimation.

Last updated 8 years ago

1.00 score 1 scripts 111 downloads

gafit - Genetic Algorithm for Curve Fitting

A group of sample points are evaluated against a user-defined expression, the sample points are lists of parameters with values that may be substituted into that expression. The genetic algorithm attempts to make the result of the expression as low as possible (usually this would be the sum of residuals squared).

Last updated 8 years ago

1.00 score 2 scripts 210 downloads

phuassess - Proportional Habitat Use Assessment

Assessment of habitat selection by means of the permutation-based combination of sign tests (Fattorini et al., 2014 <DOI:10.1007/s10651-013-0250-7>). To exemplify the application of this procedure, habitat selection is assessed for a population of European Brown Hares settled in central Italy.

Last updated 8 years ago

1.00 score 1 scripts 119 downloads

rhnerm - Random Heteroscedastic Nested Error Regression

Performs the random heteroscedastic nested error regression model described in Kubokawa, Sugasawa, Ghosh and Chaudhuri (2016) <doi:10.5705/ss.202014.0070>.

Last updated 8 years ago

1.00 score 3 scripts 100 downloads

freqdist - Frequency Distribution

Generates a frequency distribution. The frequency distribution includes raw frequencies, percentages in each category, and cumulative frequencies. The frequency distribution can be stored as a data frame.

Last updated 8 years ago

1.00 score 5 scripts 170 downloads

NegBinBetaBinreg - Negative Binomial and Beta Binomial Bayesian Regression Models

The Negative Binomial regression with mean and shape modeling and mean and variance modeling and Beta Binomial regression with mean and dispersion modeling.

Last updated 8 years ago

1.00 score 1 scripts 102 downloads

jointNmix - Joint N-Mixture Models for Site-Associated Species

Fits univariate and joint N-mixture models for data on two unmarked site-associated species. Includes functions to estimate latent abundances through empirical Bayes methods.

Last updated 8 years ago

1.00 score 3 scripts 100 downloads

exteriorMatch - Constructs the Exterior Match from Two Matched Control Groups

If one treated group is matched to one control reservoir in two different ways to produce two sets of treated-control matched pairs, then the two control groups may be entwined, in the sense that some control individuals are in both control groups. The exterior match is used to compare the two control groups.

Last updated 8 years ago

1.00 score 2 scripts 139 downloads

endogenous - Classical Simultaneous Equation Models

Likelihood-based approaches to estimate linear regression parameters and treatment effects in the presence of endogeneity. Specifically, this package includes James Heckman's classical simultaneous equation models-the sample selection model for outcome selection bias and hybrid model with structural shift for endogenous treatment. For more information, see the seminal paper of Heckman (1978) <DOI:10.3386/w0177> in which the details of these models are provided. This package accommodates repeated measures on subjects with a working independence approach. The hybrid model further accommodates treatment effect modification.

Last updated 8 years ago

1.00 score 2 scripts 111 downloads

MIDN - Nearly Exact Sample Size Calculation for Exact Powerful Nonrandomized Tests for Differences Between Binomial Proportions

Implementation of the mid-n algorithms presented in Wellek S (2015) <DOI:10.1111/stan.12063> Statistica Neerlandica 69, 358-373 for exact sample size calculation for superiority trials with binary outcome.

Last updated 8 years ago

1.00 score 3 scripts 99 downloads

fizzbuzzR - Fizz Buzz Implementation

An implementation of the Fizz Buzz algorithm, as defined e.g. in <https://en.wikipedia.org/wiki/Fizz_buzz>. It provides the standard algorithm with 3 replaced by Fizz and 5 replaced by Buzz, with the option of specifying start and end numbers, step size and the numbers being replaced by fizz and buzz, respectively. This package gives interviewers the optional answer of "I use fizzbuzzR::fizzbuzz()" when interviewing rather than having to write an algorithm themselves.

Last updated 8 years ago

1.00 score 4 scripts 121 downloads

bacr - Bayesian Adjustment for Confounding

Estimating the average causal effect based on the Bayesian Adjustment for Confounding (BAC) algorithm.

Last updated 8 years ago

1.00 score 1 stars 1 scripts 169 downloads

metafuse - Fused Lasso Approach in Regression Coefficient Clustering

Fused lasso method to cluster and estimate regression coefficients of the same covariate across different data sets when a large number of independent data sets are combined. Package supports Gaussian, binomial, Poisson and Cox PH models.

Last updated 8 years ago

1.00 score 4 scripts 161 downloads

betategarch - Simulation, Estimation and Forecasting of Beta-Skew-t-EGARCH Models

Simulation, estimation and forecasting of first-order Beta-Skew-t-EGARCH models with leverage (one-component, two-component, skewed versions).

Last updated 8 years ago

1.00 score 1 stars 9 scripts 277 downloads

spikes - Detecting Election Fraud from Irregularities in Vote-Share Distributions

Applies re-sampled kernel density method to detect vote fraud. It estimates the proportion of coarse vote-shares in the observed data relative to the null hypothesis of no fraud.

Last updated 8 years ago

1.00 score 6 scripts 121 downloads

fishkirkko2015 - Dataset of Measurements of Fish Species at Kirkkojarvi Lake, Finland

Dataset of 302 measurements of 11 fish species to accompany the manuscript "Length-weight relationships of six freshwater fish species from lake Kirkkojarvi, Finland".

Last updated 8 years ago

1.00 score 2 scripts 130 downloads

PEGroupTesting - Population Proportion Estimation using Group Testing

The population proportion using group testing can be estimated by different methods. Four functions including p.mle(), p.gart(), p.burrow() and p.order() are provided to implement four estimating methods including the maximum likelihood estimate, Gart's estimate, Burrow's estimate, and order statistic estimate.

Last updated 8 years ago

1.00 score 11 scripts 108 downloads

sonar - Fundamental Formulas for Sonar

Formulas for calculating sound velocity, water pressure, depth, density, absorption and sonar equations.

Last updated 8 years ago

1.00 score 95 scripts 92 downloads

fastcmh - Significant Interval Discovery with Categorical Covariates

A method which uses the Cochran-Mantel-Haenszel test with significant pattern mining to detect intervals in binary genotype data which are significantly associated with a particular phenotype, while accounting for categorical covariates.

Last updated 8 years ago

cpp

1.00 score 4 scripts 181 downloads

alphaOutlier - Obtain Alpha-Outlier Regions for Well-Known Probability Distributions

Given the parameters of a distribution, the package uses the concept of alpha-outliers by Davies and Gather (1993) to flag outliers in a data set. See Davies, L.; Gather, U. (1993): The identification of multiple outliers, JASA, 88 423, 782-792, <doi:10.1080/01621459.1993.10476339> for details.

Last updated 8 years ago

1.00 score 22 scripts 266 downloads

PASenseWear - Summarize Daily Physical Activity from 'SenseWear' Accelerometer Data

Provide summary table of daily physical activity and per-person/grouped heat map for accelerometer data from SenseWear Armband. See <https://templehealthcare.wordpress.com/the-sensewear-armband/> for more information about SenseWear Armband.

Last updated 8 years ago

1.00 score 3 scripts 112 downloads

spselect - Selecting Spatial Scale of Covariates in Regression Models

Fits spatial scale (SS) forward stepwise regression, SS incremental forward stagewise regression, SS least angle regression (LARS), and SS lasso models. All area-level covariates are considered at all available scales to enter a model, but the SS algorithms are constrained to select each area-level covariate at a single spatial scale.

Last updated 8 years ago

1.00 score 8 scripts 142 downloads

makeFlow - Visualizing Sequential Classifications

A user-friendly tool for visualizing categorical or group movement.

Last updated 8 years ago

1.00 score 6 scripts 119 downloads

iRegression - Regression Methods for Interval-Valued Variables

Contains some important regression methods for interval-valued variables. For each method, it is available the fitted values, residuals and some goodness-of-fit measures.

Last updated 8 years ago

1.00 score 1 stars 17 scripts 123 downloads

pfa - Estimates False Discovery Proportion Under Arbitrary Covariance Dependence

Estimate the false discovery proportion (FDP) by Principal Factor Approximation method with general known and unknown covariance dependence.

Last updated 8 years ago

1.00 score 2 scripts 121 downloads

RcmdrPlugin.EcoVirtual - Rcmdr EcoVirtual Plugin

A Rcmdr "plug-in" for the EcoVirtual package, designed primarily for teaching ecological models using simulations.

Last updated 8 years ago

1.00 score 1 scripts 411 downloads

SeqMADE - Network Module-Based Model in the Differential Expression Analysis for RNA-Seq

A network module-based generalized linear model for differential expression analysis with the count-based sequence data from RNA-Seq.

Last updated 8 years ago

1.00 score 8 scripts 107 downloads

IntegrateBs - Integration for B-Spline

Integrated B-spline function.

Last updated 8 years ago

1.00 score 1 scripts 96 downloads

BACCT - Bayesian Augmented Control for Clinical Trials

Implements the Bayesian Augmented Control (BAC, a.k.a. Bayesian historical data borrowing) method under clinical trial setting by calling 'Just Another Gibbs Sampler' ('JAGS') software. In addition, the 'BACCT' package evaluates user-specified decision rules by computing the type-I error/power, or probability of correct go/no-go decision at interim look. The evaluation can be presented numerically or graphically. Users need to have 'JAGS' 4.0.0 or newer installed due to a compatibility issue with 'rjags' package. Currently, the package implements the BAC method for binary outcome only. Support for continuous and survival endpoints will be added in future releases. We would like to thank AbbVie's Statistical Innovation group and Clinical Statistics group for their support in developing the 'BACCT' package.

Last updated 9 years ago

jagscpp

1.00 score 9 scripts 233 downloads

SPIGA - Compute SPI Index using the Methods Genetic Algorithm and Maximum Likelihood

Calculate the Standardized Precipitation Index (SPI) for monitoring drought, using Artificial Intelligence techniques (SPIGA) and traditional numerical technique Maximum Likelihood (SPIML). For more information see: http://drought.unl.edu/monitoringtools/downloadablespiprogram.aspx.

Last updated 9 years ago

1.00 score 3 scripts 97 downloads

HDDesign - Sample Size Calculation for High Dimensional Classification Study

Determine the sample size requirement to achieve the target probability of correct classification (PCC) for studies employing high-dimensional features. The package implements functions to 1) determine the asymptotic feasibility of the classification problem; 2) compute the upper bounds of the PCC for any linear classifier; 3) estimate the PCC of three design methods given design assumptions; 4) determine the sample size requirement to achieve the target PCC for three design methods.

Last updated 9 years ago

1.00 score 15 scripts 106 downloads

heatmapFit - Fit Statistic for Binary Dependent Variable Models

Generates a fit plot for diagnosing misspecification in models of binary dependent variables, and calculates the related heatmap fit statistic described in Esarey and Pierce (2012) <DOI:10.1093/pan/mps026>.

Last updated 9 years ago

1.00 score 13 scripts 166 downloads

DisimForMixed - Calculate Dissimilarity Matrix for Dataset with Mixed Attributes

Implement the methods proposed by Ahmad & Dey (2007) <doi:10.1016/j.datak.2007.03.016> in calculating the dissimilarity matrix at the presence of mixed attributes. This Package includes functions to discretize quantitative variables, calculate conditional probability for each pair of attribute values, distance between every pair of attribute values, significance of attributes, calculate dissimilarity between each pair of objects.

Last updated 9 years ago

1.00 score 6 scripts 151 downloads

fechner - Fechnerian Scaling of Discrete Object Sets

Functions and example datasets for Fechnerian scaling of discrete object sets. User can compute Fechnerian distances among objects representing subjective dissimilarities, and other related information. See package?fechner for an overview.

Last updated 9 years ago

1.00 score 9 scripts 168 downloads

clikcorr - Censoring Data and Likelihood-Based Correlation Estimation

A profile likelihood based method of estimation and inference on the correlation coefficient of bivariate data with different types of censoring and missingness.

Last updated 9 years ago

1.00 score 8 scripts 154 downloads

uskewFactors - Model-Based Clustering via Mixtures of Unrestricted Skew-t Sactor Analyzer Models

Implements mixtures of unrestricted skew-t factor analyzer models via the EM algorithm.

Last updated 9 years ago

1.00 score 2 scripts 128 downloads

pRSR - Test of Periodicity using Response Surface Regression

Tests periodicity in short time series using response surface regression.

Last updated 9 years ago

1.00 score 9 scripts 94 downloads

DiscreteInverseWeibull - Discrete Inverse Weibull Distribution

Probability mass function, distribution function, quantile function, random generation and parameter estimation for the discrete inverse Weibull distribution.

Last updated 9 years ago

1.00 score 9 scripts 197 downloads

StressStrength - Computation and Estimation of Reliability of Stress-Strength Models

Reliability of (normal) stress-strength models and for building two-sided or one-sided confidence intervals according to different approximate procedures.

Last updated 9 years ago

1.00 score 3 scripts 97 downloads

ClusterRankTest - Rank Tests for Clustered Data

Nonparametric rank based tests (rank-sum tests and signed-rank tests) for clustered data, especially useful for clusters having informative cluster size and intra-cluster group size.

Last updated 9 years ago

1.00 score 1 scripts 156 downloads

crsnls - Nonlinear Regression Parameters Estimation by 'CRS4HC' and 'CRS4HCe'

Functions for nonlinear regression parameters estimation by algorithms based on Controlled Random Search algorithm. Both functions (crs4hc(), crs4hce()) adapt current search strategy by four heuristics competition. In addition, crs4hce() improves adaptability by adaptive stopping condition.

Last updated 9 years ago

1.00 score 2 scripts 147 downloads

uHMM - Construct an Unsupervised Hidden Markov Model

Construct a Hidden Markov Model with states learnt by unsupervised classification.

Last updated 9 years ago

1.00 score 98 downloads

decision - Statistical Decision Analysis

Contains a function called dmur() which accepts four parameters like possible values, probabilities of the values, selling cost and preparation cost. The dmur() function generates various numeric decision parameters like MEMV (Maximum (optimum) expected monitory value), best choice, EPPI (Expected profit with perfect information), EVPI (Expected value of the perfect information), EOL (Expected opportunity loss), which facilitate effective decision-making.

Last updated 9 years ago

1.00 score 1 scripts 175 downloads

FUNTA - Functional Tangential Angle Pseudo-Depth

Computes the functional tangential angle pseudo-depth and its robustified version from the paper by Kuhnt and Rehage (2016). See Kuhnt, S.; Rehage, A. (2016): An angle-based multivariate functional pseudo-depth for shape outlier detection, JMVA 146, 325-340, <doi:10.1016/j.jmva.2015.10.016> for details.

Last updated 9 years ago

1.00 score 4 scripts 101 downloads

NEpiC - Network Assisted Algorithm for Epigenetic Studies Using Mean and Variance Combined Signals

Package for a Network assisted algorithm for Epigenetic studies using mean and variance Combined signals: NEpiC. NEpiC combines both signals in mean and variance differences in methylation level between case and control groups searching for differentially methylated sub-networks (modules) using the protein-protein interaction network.

Last updated 9 years ago

1.00 score 4 scripts 129 downloads

censorcopula - Estimate Parameter of Bivariate Copula

Implement an interval censor method to break ties when using data with ties to fitting a bivariate copula.

Last updated 9 years ago

1.00 score 3 scripts 170 downloads

vottrans - Voter Transition Analysis

Calculates voter transitions comparing two elections, using the function solve.QP() in package 'quadprog'.

Last updated 9 years ago

1.00 score 2 scripts 96 downloads

tmpm - Trauma Mortality Prediction Model

Trauma Mortality prediction for ICD-9, ICD-10, and AIS lexicons in long or wide format based on Dr. Alan Cook's tmpm mortality model.

Last updated 9 years ago

1.00 score 6 scripts 94 downloads

sensory - Simultaneous Model-Based Clustering and Imputation via a Progressive Expectation-Maximization Algorithm

Contains the function CUUimpute() which performs model-based clustering and imputation simultaneously.

Last updated 9 years ago

1.00 score 1 stars 4 scripts 130 downloads

linERR - Linear Excess Relative Risk Model

Fits a linear excess relative risk model by maximum likelihood, possibly including several variables and allowing for lagged exposures.

Last updated 9 years ago

1.00 score 2 scripts 89 downloads

vudc - Visualization of Univariate Data for Comparison

Contains functions for visualization univariate data: ccdplot and qddplot.

Last updated 9 years ago

1.00 score 1 stars 5 scripts 101 downloads

WaverR - Data Estimation using Weighted Averages of Multiple Regressions

For multivariate datasets, this function enables the estimation of missing data using the Weighted AVERage of all possible Regressions using the data available.

Last updated 9 years ago

1.00 score 2 scripts 111 downloads

mvnTest - Goodness of Fit Tests for Multivariate Normality

Routines for assessing multivariate normality. Implements three Wald's type chi-squared tests; non-parametric Anderson-Darling and Cramer-von Mises tests; Doornik-Hansen test, Royston test and Henze-Zirkler test.

Last updated 9 years ago

1.00 score 1 stars 18 scripts 536 downloads

TEQR - Target Equivalence Range Design

The TEQR package contains software to calculate the operating characteristics for the TEQR and the ACT designs.The TEQR (toxicity equivalence range) design is a toxicity based cumulative cohort design with added safety rules. The ACT (Activity constrained for toxicity) design is also a cumulative cohort design with additional safety rules. The unique feature of this design is that dose is escalated based on lack of activity rather than on lack of toxicity and is de-escalated only if an unacceptable level of toxicity is experienced.

Last updated 9 years ago

1.00 score 7 scripts 150 downloads

psoptim - Particle Swarm Optimization

Particle swarm optimization - a basic variant.

Last updated 9 years ago

1.00 score 2 scripts 134 downloads

wildpoker - Best Hand Analysis for Poker Variants Including Wildcards

Provides insight into how the best hand for a poker game changes based on the game dealt, players who stay in until the showdown and wildcards added to the base game. At this time the package does not support player tactics, so draw poker variants are not included.

Last updated 9 years ago

1.00 score 4 scripts 99 downloads

sscor - Robust Correlation Estimation and Testing Based on Spatial Signs

Provides the spatial sign correlation and the two-stage spatial sign correlation as well as a one-sample test for the correlation coefficient.

Last updated 9 years ago

1.00 score 6 scripts 130 downloads

VertexSimilarity - Creates Vertex Similarity Matrix for an Undirected Graph

Creates Vertex Similarity matrix of an undirected graph based on the method stated by E. A. Leicht, Petter Holme, AND M. E. J. Newman in their paper <DOI:10.1103/PhysRevE.73.026120>.

Last updated 9 years ago

1.00 score 1 scripts 107 downloads

breakpoint - An R Package for Multiple Break-Point Detection via the Cross-Entropy Method

Implements the Cross-Entropy (CE) method, which is a model based stochastic optimization technique to estimate both the number and their corresponding locations of break-points in continuous and discrete measurements (Priyadarshana and Sofronov (2015), Priyadarshana and Sofronov (2012a), Priyadarshana and Sofronov (2012b)).

Last updated 9 years ago

1.00 score 33 scripts 524 downloads

msltrend - Improved Techniques to Estimate Trend, Velocity and Acceleration from Sea Level Records

Analysis of annual average ocean water level time series from long (minimum length 80 years) individual records, providing improved estimates of trend (mean sea level) and associated real-time velocities and accelerations. Improved trend estimates are based on Singular Spectrum Analysis methods. Various gap-filling options are included to accommodate incomplete time series records. The package also contains a forecasting module to consider the implication of user defined quantum of sea level rise between the end of the available historical record and the year 2100. A wide range of screen and pdf plotting options are available in the package.

Last updated 9 years ago

1.00 score 8 scripts 94 downloads

CircOutlier - Detection of Outliers in Circular-Circular Regression

Detection of outliers in circular-circular regression models, modifying its and estimating of models parameters.

Last updated 9 years ago

1.00 score 5 scripts 166 downloads

acp - Autoregressive Conditional Poisson

Analysis of count data exhibiting autoregressive properties, using the Autoregressive Conditional Poisson model (ACP(p,q)) proposed by Heinen (2003).

Last updated 9 years ago

1.00 score 7 scripts 426 downloads

kriens - Continuation Passing Style Development

Provides basic functions for Continuation-Passing Style development.

Last updated 9 years ago

1.00 score 9 scripts 118 downloads

oaPlots - OpenAnalytics Plots Package

Offers a suite of functions for enhancing R plots.

Last updated 9 years ago

1.00 score 27 scripts 106 downloads

FACTMLE - Maximum Likelihood Factor Analysis

Perform Maximum Likelihood Factor analysis on a covariance matrix or data matrix.

Last updated 9 years ago

1.00 score 2 scripts 161 downloads

ptycho - Bayesian Variable Selection with Hierarchical Priors

Bayesian variable selection for linear regression models using hierarchical priors. There is a prior that combines information across responses and one that combines information across covariates, as well as a standard spike and slab prior for comparison. An MCMC samples from the marginal posterior distribution for the 0-1 variables indicating if each covariate belongs to the model for each response.

Last updated 9 years ago

1.00 score 7 scripts 110 downloads

TRD - Transmission Ratio Distortion

Transmission Ratio Distortion (TRD) is a genetic phenomenon where the two alleles from either parent are not transmitted to the offspring at the expected 1:1 ratio under Mendelian inheritance, leading to spurious signals in genetic association studies. Functions in this package are developed to account for this phenomenon using loglinear model and Transmission Disequilibrium Test (TDT). Some population information can also be calculated.

Last updated 9 years ago

1.00 score 8 scripts 104 downloads

SPCALDA - A New Reduced-Rank Linear Discriminant Analysis Method

A new reduced-rank LDA method which works for high dimensional multi-class data.

Last updated 9 years ago

1.00 score 1 scripts 107 downloads

LRcontrast - Dose Response Signal Detection under Model Uncertainty

Provides functions for calculating test statistics, simulating quantiles and simulating p-values of likelihood ratio contrast tests in regression models with a lack of identifiability.

Last updated 9 years ago

1.00 score 4 scripts 122 downloads

hotspot - Software Hotspot Analysis

Contains data for software hotspot analysis, along with a function performing the analysis itself.

Last updated 9 years ago

1.00 score 1 scripts 129 downloads

GSSE - Genotype-Specific Survival Estimation

We propose a fully efficient sieve maximum likelihood method to estimate genotype-specific distribution of time-to-event outcomes under a nonparametric model. We can handle missing genotypes in pedigrees. We estimate the time-dependent hazard ratio between two genetic mutation groups using B-splines, while applying nonparametric maximum likelihood estimation to the reference baseline hazard function. The estimators are calculated via an expectation-maximization algorithm.

Last updated 9 years ago

1.00 score 8 scripts 136 downloads

ksrlive - Identify Kinase Substrate Relationships Using Dynamic Data

Using this package you can combine known kinase substrate relationships with experimental data and determine active kinases and their substrates.

Last updated 9 years ago

1.00 score 4 scripts 94 downloads

SyncMove - Subsample Temporal Data to Synchronal Events and Compute the MCI

The function 'syncSubsample' subsamples temporal data of different entities so that the result only contains synchronal events. The function 'mci' calculates the Movement Coordination Index (MCI, see reference on help page for function 'mci') of a data set created with the function 'syncSubsample'.

Last updated 9 years ago

1.00 score 2 scripts 98 downloads

HDGLM - Tests for High Dimensional Generalized Linear Models

Test the significance of coefficients in high dimensional generalized linear models.

Last updated 9 years ago

fortran

1.00 score 2 scripts 109 downloads

pwrRasch - Statistical Power Simulation for Testing the Rasch Model

Statistical power simulation for testing the Rasch Model based on a three-way analysis of variance design with mixed classification.

Last updated 9 years ago

1.00 score 1 stars 9 scripts 136 downloads

NostalgiR - Advanced Text-Based Plots

Provides functions to produce advanced ascii graphics, directly to the terminal window. This package utilizes the txtplot() function from the 'txtplot' package, to produce text-based histograms, empirical cumulative distribution function plots, scatterplots with fitted and regression lines, quantile plots, density plots, image plots, and contour plots.

Last updated 9 years ago

1.00 score 1 stars 18 scripts 105 downloads

GRTo - Tools for the Analysis of Gutenberg-Richter Distributions of Earthquake Magnitudes

Offers functions for the comparison of Gutenberg-Richter b-values. Several functions in GRTo are helpful for the assessment of the quality of seismicity catalogs.

Last updated 9 years ago

1.00 score 6 scripts 117 downloads

LinearRegressionMDE - Minimum Distance Estimation in Linear Regression Model

Consider linear regression model Y = Xb + error where the distribution function of errors is unknown, but errors are independent and symmetrically distributed. The package contains a function named LRMDE which takes Y and X as input and returns minimum distance estimator of parameter b in the model.

Last updated 9 years ago

1.00 score 1 scripts 190 downloads

AutoregressionMDE - Minimum Distance Estimation in Autoregressive Model

Consider autoregressive model of order p where the distribution function of innovation is unknown, but innovations are independent and symmetrically distributed. The package contains a function named ARMDE which takes X (vector of n observations) and p (order of the model) as input argument and returns minimum distance estimator of the parameters in the model.

Last updated 9 years ago

1.00 score 1 scripts 177 downloads

regRSM - Random Subspace Method (RSM) for Linear Regression

Performs Random Subspace Method (RSM) for high-dimensional linear regression to obtain variable importance measures. The final model is chosen based on validation set or Generalized Information Criterion.

Last updated 9 years ago

1.00 score 1 stars 8 scripts 127 downloads

ThreeGroups - ML Estimator for Baseline-Placebo-Treatment (Three-Group) Experiments

Implements the Maximum Likelihood estimator for baseline, placebo, and treatment groups (three-group) experiments with non-compliance proposed by Gerber, Green, Kaplan, and Kern (2010).

Last updated 9 years ago

1.00 score 1 scripts 100 downloads

ftsspec - Spectral Density Estimation and Comparison for Functional Time Series

Functions for estimating spectral density operator of functional time series (FTS) and comparing the spectral density operator of two functional time series, in a way that allows detection of differences of the spectral density operator in frequencies and along the curve length.

Last updated 9 years ago

1.00 score 7 scripts 110 downloads

KERE - Expectile Regression in Reproducing Kernel Hilbert Space

An efficient algorithm inspired by majorization-minimization principle for solving the entire solution path of a flexible nonparametric expectile regression estimator constructed in a reproducing kernel Hilbert space.

Last updated 9 years ago

fortran

1.00 score 1 stars 11 scripts 100 downloads

FastBandChol - Fast Estimation of a Covariance Matrix by Banding the Cholesky Factor

Fast and numerically stable estimation of a covariance matrix by banding the Cholesky factor using a modified Gram-Schmidt algorithm implemented in RcppArmadilo. See <http://stat.umn.edu/~molst029> for details on the algorithm.

Last updated 9 years ago

openblascpp

1.00 score 5 scripts 118 downloads

MDimNormn - Multi-Dimensional MA Normalization for Plate Effect

Normalize data to minimize the difference between sample plates (batch effects). For given data in a matrix and grouping variable (or plate), the function 'normn_MA' normalizes the data on MA coordinates. More details are in the citation. The primary method is 'Multi-MA'. Other fitting functions on MA coordinates can also be employed e.g. loess.

Last updated 9 years ago

1.00 score 2 scripts 105 downloads

threg - Threshold Regression

Fit a threshold regression model based on the first-hitting-time of a boundary by the sample path of a Wiener diffusion process. The threshold regression methodology is well suited to applications involving survival and time-to-event data.

Last updated 9 years ago

1.00 score 6 scripts 138 downloads

perspectev - Permutation of Species During Turnover Events

Provides a robust framework for analyzing the extent to which differential survival with respect to higher level trait variation is reducible to lower level variation. In addition to its primary test, it also provides functions for simulation-based power analysis, reading in common data set formats, and visualizing results. Temporarily contains an edited version of function hr.mcp() from package 'wild1', written by Glen Sargeant. For tutorial see: http://evolve.zoo.ox.ac.uk/Evolve/Perspectev.html.

Last updated 9 years ago

1.00 score 1 stars 2 scripts 149 downloads

mmc - Multivariate Measurement Error Correction

Provides routines for multivariate measurement error correction. Includes procedures for linear, logistic and Cox regression models. Bootstrapped standard errors and confidence intervals can be obtained for corrected estimates.

Last updated 9 years ago

1.00 score 3 scripts 91 downloads

Harvest.Tree - Harvest the Classification Tree

Aimed at applying the Harvest classification tree algorithm, modified algorithm of classic classification tree.The harvested tree has advantage of deleting redundant rules in trees, leading to a simplify and more efficient tree model.It was firstly used in drug discovery field, but it also performs well in other kinds of data, especially when the region of a class is disconnected. This package also improves the basic harvest classification tree algorithm by extending the field of data of algorithm to both continuous and categorical variables. To learn more about the harvest classification tree algorithm, you can go to http://www.stat.ubc.ca/Research/TechReports/techreports/220.pdf for more information.

Last updated 9 years ago

1.00 score 1 scripts 152 downloads

MRQoL - Minimal Clinically Important Difference and Response Shift Effect for Health-Related Quality of Life

We can calculate directly used this package the Minimal Clinically Important Difference by applying the Anchor-based method and the Response shift effect by applying the Then-Test method.

Last updated 9 years ago

1.00 score 5 scripts 90 downloads

nordklimdata1 - Dataset for Climate Analysis with Data from the Nordic Region

The Nordklim dataset 1.0 is a unique and useful achievement for climate analysis. It includes observations of twelve different climate elements from more than 100 stations in the Nordic region, in time span over 100 years. The project contractors were NORDKLIM/NORDMET on behalf of the National meteorological services in Denmark (DMI), Finland (FMI), Iceland (VI), Norway (DNMI) and Sweden (SMHI).

Last updated 9 years ago

1.00 score 2 scripts 136 downloads

ORCME - Order Restricted Clustering for Microarray Experiments

Provides clustering of genes with similar dose response (or time course) profiles. It implements the method described by Lin et al. (2012).

Last updated 9 years ago

1.00 score 8 scripts 211 downloads

powerGWASinteraction - Power Calculations for GxE and GxG Interactions for GWAS

Analytical power calculations for GxE and GxG interactions for case-control studies of candidate genes and genome-wide association studies (GWAS). This includes power calculation for four two-step screening and testing procedures. It can also calculate power for GxE and GxG without any screening.

Last updated 9 years ago

1.00 score 4 scripts 148 downloads

csn - Closed Skew-Normal Distribution

Provides functions for computing the density and the log-likelihood function of closed-skew normal variates, and for generating random vectors sampled from this distribution. See Gonzalez-Farias, G., Dominguez-Molina, J., and Gupta, A. (2004). The closed skew normal distribution, Skew-elliptical distributions and their applications: a journey beyond normality, Chapman and Hall/CRC, Boca Raton, FL, pp. 25-42.

Last updated 10 years ago

1.00 score 9 scripts 202 downloads

optifunset - Set Options if Unset

A single function 'options.ifunset(...)' is contained herewith, which allows the user to set a global option ONLY if it is not already set. By this token, for package maintainers this function can be used in preference to the standard 'options(...)' function, making provision for THEIR end user to place 'options(...)' directives within their '.Rprofile' file, which will not be overridden at the point when a package is loaded.

Last updated 10 years ago

1.00 score 2 scripts 109 downloads

readMLData - Reading Machine Learning Benchmark Data Sets in Different Formats

Functions for reading data sets in different formats for testing machine learning tools are provided. This allows to run a loop over several data sets in their original form, for example if they are downloaded from UCI Machine Learning Repository. The data are not part of the package and have to be downloaded separately.

Last updated 10 years ago

1.00 score 1 stars 17 scripts 133 downloads

selfingTree - Genotype Probabilities in Intermediate Generations of Inbreeding Through Selfing

A probability tree allows to compute probabilities of complex events, such as genotype probabilities in intermediate generations of inbreeding through recurrent self-fertilization (selfing). This package implements functionality to compute probability trees for two- and three-marker genotypes in the F2 to F7 selfing generations. The conditional probabilities are derived automatically and in symbolic form. The package also provides functionality to extract and evaluate the relevant probabilities.

Last updated 10 years ago

1.00 score 7 scripts 100 downloads

qdm - Fitting a Quadrilateral Dissimilarity Model to Same-Different Judgments

This package provides different specifications of a Quadrilateral Dissimilarity Model which can be used to fit same-different judgments in order to get a predicted matrix that satisfies regular minimality [Colonius & Dzhafarov, 2006, Measurement and representations of sensations, Erlbaum]. From such a matrix, Fechnerian distances can be computed.

Last updated 10 years ago

1.00 score 4 scripts 113 downloads

propOverlap - Feature (gene) selection based on the Proportional Overlapping Scores

A package for selecting the most relevant features (genes) in the high-dimensional binary classification problems. The discriminative features are identified using analyzing the overlap between the expression values across both classes. The package includes functions for measuring the proportional overlapping score for each gene avoiding the outliers effect. The used measure for the overlap is the one defined in the "Proportional Overlapping Score (POS)" technique for feature selection. A gene mask which represents a gene's classification power can also be produced for each gene (feature). The set size of the selected genes might be set by the user. The minimum set of genes that correctly classify the maximum number of the given tissue samples (observations) can be also produced.

Last updated 10 years ago

1.00 score 1 stars 10 scripts 90 downloads

growthrate - Bayesian reconstruction of growth velocity

A nonparametric empirical Bayes method for recovering gradients (or growth velocities) from observations of smooth functions (e.g., growth curves) at isolated time points.

Last updated 10 years ago

1.00 score 5 scripts 177 downloads

astrodatR - Astronomical Data

A collection of 19 datasets from contemporary astronomical research. They are described the textbook `Modern Statistical Methods for Astronomy with R Applications' by Eric D. Feigelson and G. Jogesh Babu (Cambridge University Press, 2012, Appendix C) or on the website of Penn State's Center for Astrostatistics (http://astrostatistics.psu.edu/datasets). These datasets can be used to exercise methodology involving: density estimation; heteroscedastic measurement errors; contingency tables; two-sample hypothesis tests; spatial point processes; nonlinear regression; mixture models; censoring and truncation; multivariate analysis; classification and clustering; inhomogeneous Poisson processes; periodic and stochastic time series analysis.

Last updated 10 years ago

1.00 score 1 stars 8 scripts 222 downloads

subgroup - Methods for exploring treatment effect heterogeneity in subgroup analysis of clinical trials

Produces various measures of expected treatment effect heterogeneity under an assumption of homogeneity across subgroups. Graphical presentations are created to compare these expected differences with the observed differences.

Last updated 10 years ago

1.00 score 3 scripts 88 downloads

isotonic.pen - Penalized Isotonic Regression in one and two dimensions

Given a response y and a one- or two-dimensional predictor, the isotonic regression estimator is calculated with the usual orderings.

Last updated 11 years ago

1.00 score 2 scripts 101 downloads

LIStest - Tests of independence based on the Longest Increasing Subsequence

Tests for independence between X and Y computed from a paired sample (x1,y1),...(xn,yn) of (X,Y), using one of the following statistics (a) the Longest Increasing Subsequence (Ln), (b) JLn, a Jackknife version of Ln or (c) JLMn, a Jackknife version of the longest monotonic subsequence. This family of tests can be applied under the assumption of continuity of X and Y.

Last updated 11 years ago

1.00 score 5 scripts 107 downloads

partitionMetric - Compute a distance metric between two partitions of a set

partitionMetric computes a distance between two partitions of a set.

Last updated 11 years ago

1.00 score 1 scripts 128 downloads

ALSCPC - Accelerated line search algorithm for simultaneous orthogonal transformation of several positive definite symmetric matrices to nearly diagonal form.

Using of the accelerated line search algorithm for simultaneously diagonalize a set of symmetric positive definite matrices.

Last updated 11 years ago

1.00 score 1 scripts 219 downloads

FGalgorithm - Flury and Gautschi algorithms

This is a package for implementation of Flury-Gautschi algorithms.

Last updated 12 years ago

1.00 score 1 scripts 119 downloads

gaussDiff - Difference measures for multivariate Gaussian probability density functions

A collection difference measures for multivariate Gaussian probability density functions, such as the Euclidea mean, the Mahalanobis distance, the Kullback-Leibler divergence, the J-Coefficient, the Minkowski L2-distance, the Chi-square divergence and the Hellinger Coefficient.

Last updated 12 years ago

1.00 score 7 scripts 136 downloads

makeProject - Creates an empty package framework for the LCFD format

This package creates an empty framework of files and directories for the "Load, Clean, Func, Do" structure described by Josh Reich.

Last updated 13 years ago

1.00 score 1 scripts 113 downloads

rtape - Manage and manipulate large collections of R objects stored as tape-like files

Storing huge data in RData format causes problems because of the necessity to load the whole file to the memory in order to access and manipulate objects inside such file; rtape is a simple solution to this problem. The package contains several wrappers of R built-in serialize/unserialize mechanism allowing user to quickly append objects to a tape-like file and later iterate over them requiring only one copy of each stored object to reside in memory a time.

Last updated 14 years ago

1.00 score 6 scripts 152 downloads

igraphtosonia - Convert iGraph graps to SoNIA .son files

This program facilitates exporting igraph graphs to the SoNIA file format

Last updated 14 years ago

1.00 score 3 scripts 135 downloads

RNCBIEUtilsLibs - EUtils libraries for use in the R environment.

Provides the libraries of the EUtils operations for the RNCBI package.

Last updated 15 years ago

1.00 score 128 downloads

kzs - Kolmogorov-Zurbenko Spatial Smoothing and Applications

A spatial smoothing algorithm based on convolutions of finite rectangular kernels that provides sharp resolution in the presence of high levels of noise.

Last updated 16 years ago

1.00 score 4 scripts 719 downloads