nlme - Linear and Nonlinear Mixed Effects Models
Fit and compare Gaussian linear and nonlinear mixed-effects models.
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13.25 score 8 stars 4.8k dependents 26k scripts 200k downloadse1071 - 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 ...
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cpp
12.01 score 29 stars 2.4k dependents 71 scripts 344k downloadsnnet - 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.
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11.92 score 6 stars 2.7k dependents 13k scripts 130k downloadsMASS - 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).
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11.44 score 21 stars 7.4k dependents 273 scripts 218k downloadsclass - Functions for Classification
Various functions for classification, including k-nearest neighbour, Learning Vector Quantization and Self-Organizing Maps.
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10.97 score 1 stars 2.7k dependents 9.9k scripts 119k downloadsKernSmooth - 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".
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openblas
10.64 score 2 stars 3.0k dependents 2.1k scripts 115k downloadsRODBC - ODBC Database Access
An ODBC database interface.
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unixodbc
10.47 score 10 stars 36 dependents 4.5k scripts 20k downloadsmgcv - 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, Cross Validation and similar, or using iterated nested Laplace approximation for fully Bayesian inference. See Wood (2025) <doi:10.1146/annurev-statistics-112723-034249> for an overview. Includes a gam() function, a wide variety of smoothers, 'JAGS' support and distributions beyond the exponential family.
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openblasopenmp
10.47 score 34 stars 2.5k dependents 143 scripts 83k downloadstimeDate - 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.
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10.28 score 1 stars 1.8k dependents 942 scripts 381k downloadsflexmix - 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.
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10.24 score 5 stars 102 dependents 880 scripts 32k downloadsproxy - 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.
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10.17 score 3 stars 2.5k dependents 5 scripts 326k downloadssn - 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.
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10.08 score 3 stars 121 dependents 1.6k scripts 16k downloadsmnormt - The Multivariate Normal and t Distributions, and Their Truncated Versions
Functions are provided for computing the density and the distribution function of multi-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.
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glibc
9.86 score 779 dependents 6.0k scripts 173k downloadsboot - Bootstrap Functions
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.
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9.40 score 3 stars 2.7k dependents 123 scripts 85k downloadscaTools - Tools: Moving Window Statistics, GIF, Base64, ROC AUC, etc
Contains several basic utility functions including: moving (rolling, running) window statistic functions, read/write for GIF and ENVI binary files, fast calculation of AUC, LogitBoost classifier, base64 encoder/decoder, round-off-error-free sum and cumsum, etc.
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cpp
9.37 score 8 stars 651 dependents 109 scripts 137k downloadsMuMIn - 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.
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9.19 score 11 stars 30 dependents 6.7k scripts 23k downloadsforeign - 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.
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8.73 score 7 stars 932 dependents 39 scripts 71k downloadsca - Simple, Multiple and Joint Correspondence Analysis
Computation and visualization of simple, multiple and joint correspondence analysis.
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8.49 score 2 stars 114 dependents 743 scripts 61k downloadsvcd - 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).
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8.44 score 5 stars 94 dependents 19 scripts 52k downloadsmc2d - 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).
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8.29 score 2 stars 19 dependents 398 scripts 4.3k downloadsspatial - Functions for Kriging and Point Pattern Analysis
Functions for kriging and point pattern analysis.
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8.21 score 110 dependents 557 scripts 88k downloadsNbClust - 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.
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8.14 score 10 stars 25 dependents 2.4k scripts 7.5k downloadsvipor - 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.
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8.11 score 132 dependents 85 scripts 38k downloadstree - Classification and Regression Trees
Classification and regression trees.
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8.02 score 2 stars 14 dependents 4.7k scripts 13k downloadsepitools - Epidemiology Tools
Tools for training and practicing epidemiologists including methods for two-way and multi-way contingency tables.
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7.95 score 3 stars 12 dependents 8.7k scripts 9.6k downloadssnowfall - 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.
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7.94 score 46 dependents 1.7k scripts 5.1k downloadsfastICA - FastICA Algorithms to Perform ICA and Projection Pursuit
Implementation of FastICA algorithm to perform Independent Component Analysis (ICA) and Projection Pursuit.
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openblas
7.82 score 1 stars 94 dependents 902 scripts 26k downloadsregistry - Infrastructure for R Package Registries
Provides a generic infrastructure for creating and using registries.
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7.81 score 186 dependents 231 scripts 50k downloadsFNN - 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.
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cpp
7.72 score 5 stars 714 dependents 4 scripts 98k downloadsnetwork - 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.
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7.69 score 3 stars 155 dependents 11 scripts 32k downloadsBGLR - Bayesian Generalized Linear Regression
Bayesian Generalized Linear Regression.
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openblas
7.67 score 2 stars 4 dependents 3.5k scripts 5.6k downloadsfutile.options - Futile Options Management
A scoped options management framework. Used in other packages.
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7.66 score 1.4k dependents 18 scripts 121k downloadsgss - General Smoothing Splines
A comprehensive package for structural multivariate function estimation using smoothing splines.
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openblasglibc
7.62 score 3 stars 114 dependents 126 scripts 27k downloadsgee - Generalized Estimation Equation Solver
Generalized Estimation Equation solver.
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openblas
7.38 score 3 stars 17 dependents 1.2k scripts 13k downloadstimeSeries - 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.
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7.35 score 2 stars 121 dependents 1 scripts 31k downloadsgamm4 - 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.
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7.33 score 2 stars 34 dependents 792 scripts 13k downloadsica - Independent Component Analysis
Independent Component Analysis (ICA) using various algorithms: FastICA, Information-Maximization (Infomax), and Joint Approximate Diagonalization of Eigenmatrices (JADE).
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7.25 score 2 stars 126 dependents 103 scripts 29k downloadsfBasics - 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.
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7.11 score 3 stars 107 dependents 1 scripts 27k downloadsRmpi - Interface (Wrapper) to MPI (Message-Passing Interface)
An interface (wrapper) to MPI. It also provides interactive R manager and worker environment.
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openmpi
6.94 score 5 stars 4 dependents 980 scripts 15k downloadscompositions - 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.
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openblas
6.86 score 1 stars 38 dependents 20 scripts 16k downloadsbeanplot - Visualization via Beanplots (Like Boxplot/Stripchart/Violin Plot)
Plots univariate comparison graphs, an alternative to boxplot/stripchart/violin plot.
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6.84 score 1 stars 43 dependents 2 scripts 11k downloadstensorA - 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.
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6.83 score 469 dependents 483k downloadscmprsk - 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>.
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6.80 score 7 stars 86 dependents 12 scripts 29k downloadssna - 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.
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6.76 score 8 stars 92 dependents 2 scripts 26k downloadstrust - Trust Region Optimization
Does local optimization using two derivatives and trust regions. Guaranteed to converge to local minimum of objective function.
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6.71 score 80 dependents 138 scripts 16k downloadscoxme - 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.
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6.67 score 2 stars 13 dependents 7 scripts 15k downloadsspeedglm - 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).
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6.58 score 10 stars 11 dependents 574 scripts 10k downloadslm.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.
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6.57 score 6 dependents 878 scripts 12k downloadscircular - Circular Statistics
Circular Statistics, from "Topics in circular Statistics" (2001) S. Rao Jammalamadaka and A. SenGupta, World Scientific.
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glibc
6.56 score 7 stars 47 dependents 60 scripts 6.1k 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.
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6.42 score 7 dependents 493 scripts 1.3k downloadsrestriktor - 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.
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6.32 score 4 dependents 165 scripts 2.6k downloadsfGarch - Rmetrics - Autoregressive Conditional Heteroskedastic Modelling
Analyze and model heteroskedastic behavior in financial time series.
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glibc
6.29 score 8 stars 54 dependents 1 scripts 10.0k downloadsgaston - 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>.
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zlibcpp
6.19 score 6 stars 13 dependents 5.5k downloadsICS - 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.
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6.19 score 20 dependents 50 scripts 5.2k downloadsbdsmatrix - Routines for Block Diagonal Symmetric Matrices
This is a special case of sparse matrices, used by coxme.
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6.15 score 1 stars 240 dependents 66k downloadsdslabs - 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.
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6.14 score 2 dependents 5.5k scripts 8.3k downloadssae - Small Area Estimation
Functions for small area estimation.
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6.13 score 6 stars 13 dependents 119 scripts 2.4k downloadsPairedData - 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.
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6.13 score 2 stars 8 dependents 1.3k scripts 2.7k downloadsdotCall64 - 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.
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openmp
6.03 score 502 dependents 72k downloadspopbio - 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).
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6.02 score 5 dependents 1.0k scripts 1.4k downloadsglasso - 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.
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fortran
6.01 score 2 stars 118 dependents 10 scripts 14k downloadsrapidjsonr - 'Rapidjson' C++ Header Files
Provides JSON parsing capability through the 'Rapidjson' 'C++' header-only library.
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6.01 score 159 dependents 43k downloadselasticnet - 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.
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5.98 score 1 stars 24 dependents 409 scripts 3.3k downloadstopicmodels - 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.
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gslcpp
5.98 score 8 stars 10 dependents 10 scripts 7.9k downloadsmatlab - 'MATLAB' Emulation Package
Emulate 'MATLAB' code using 'R'.
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5.92 score 22 dependents 593 scripts 2.1k downloadsairGR - 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.
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5.92 score 4 stars 5 dependents 1 scripts 2.3k downloadsFinTS - 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.
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5.91 score 4 stars 6 dependents 1.7k scripts 6.5k 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".
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5.79 score 2 stars 14 dependents 149 scripts 4.9k downloadspolspline - 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.
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openblas
5.77 score 147 dependents 1 scripts 27k downloadsrsatscan - Tools for Running the External 'SaTScan' Software using R Classes and Methods
The 'SaTScan'(TM) <https://www.satscan.org> software uses spatial and space-time scan statistics to detect and evaluate spatial and space-time clusters. With the 'rsatscan' package, you can run the external 'SaTScan' software from within R using R data formats. To successfully select appropriate parameter settings within 'rsatscan', you must first learn 'SaTScan'.
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5.74 score 11 stars 50 scripts 361 downloadslmom - 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.
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glibc
5.74 score 2 stars 179 dependents 51k downloadssets - 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.
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5.71 score 1 stars 115 dependents 15k downloadspso - 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.
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5.70 score 4 stars 34 dependents 182 scripts 3.4k downloadsepiDisplay - 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/>'.
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5.70 score 2 stars 2 dependents 948 scripts 4.4k downloadssurvRM2 - 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.
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5.64 score 3 stars 4 dependents 6 scripts 2.4k downloadstensor - 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.
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5.59 score 1 stars 269 dependents 48k downloadsPresenceAbsence - 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).
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5.56 score 1 stars 9 dependents 276 scripts 4.8k downloadsbigmemory.sri - A Shared Resource Interface for Bigmemory Project Packages
A shared resource interface for the bigmemory and synchronicity packages.
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5.55 score 90 dependents 13k downloadsRVAideMemoire - Testing and Plotting Procedures for Biostatistics
Contains miscellaneous functions useful in biostatistics, mostly univariate and multivariate testing procedures with a special emphasis on permutation tests. Many functions intend to simplify user's life by shortening existing procedures or by implementing plotting functions that can be used with as many methods from different packages as possible.
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5.55 score 8 stars 968 scripts 4.6k downloadsmvnormtest - Normality Test for Multivariate Variables
Generalization of Shapiro-Wilk test for multivariate variables.
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5.54 score 5 dependents 412 scripts 6.3k downloadsorthopolynom - 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.
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5.46 score 43 dependents 262 scripts 8.6k downloadsMetBrewer - 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/>.
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5.39 score 7 dependents 3.8k scripts 3.0k downloadspspline - Penalized Smoothing Splines
Smoothing splines with penalties on order m derivatives.
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5.39 score 1 stars 104 dependents 1 scripts 8.6k downloadsdatarobot - 'DataRobot' Predictive Modeling API
For working with the 'DataRobot' predictive modeling platform's API <https://www.datarobot.com/>.
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5.38 score 2 stars 402 scripts 700 downloadsflexclust - 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.
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5.36 score 3 stars 39 dependents 3 scripts 6.5k downloadstsModel - Time Series Modeling for Air Pollution and Health
Tools for specifying time series regression models.
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5.33 score 1 stars 7 dependents 465 scripts 3.7k downloadsICSNP - 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.
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cpp
5.32 score 17 dependents 208 scripts 3.3k downloadsfossil - 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.
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5.30 score 1 stars 6 dependents 801 scripts 1.4k downloadsISOweek - 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.
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5.24 score 2 stars 14 dependents 354 scripts 5.9k downloadsGenSA - 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.
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openblascpp
5.24 score 4 stars 25 dependents 8.2k downloadssgt - 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.
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5.23 score 1 stars 1 dependents 1.1k scripts 290 downloadsash - David Scott's ASH Routines
David Scott's ASH routines ported from S-PLUS to R.
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5.21 score 187 dependents 14k downloadstruncdist - 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..
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5.19 score 23 dependents 497 scripts 4.5k downloadsJADE - 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>.
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cpp
5.18 score 2 stars 20 dependents 1.3k downloadsgvlma - 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.
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5.11 score 1 stars 1 dependents 1.1k scripts 3.9k downloadsforestmodel - Forest Plots from Regression Models
Produces forest plots using 'ggplot2' from models produced by functions such as stats::lm(), stats::glm() and survival::coxph().
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5.08 score 1 stars 5 dependents 351 scripts 1.5k downloadsSuppDists - 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.
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cpp
5.06 score 84 dependents 6 scripts 15k downloadsBlandAltmanLeh - 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.
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5.06 score 2 dependents 149 scripts 1.3k downloadsHMM - Hidden Markov Models
Easy to use library to setup, apply and make inference with discrete time and discrete space Hidden Markov Models.
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5.04 score 3 stars 3 dependents 403 scripts 915 downloadsmultilevel - 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.
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5.03 score 5 dependents 236 scripts 3.1k downloadsdeming - Deming, Theil-Sen, Passing-Bablock and Total Least Squares Regression
Generalized Deming regression, Theil-Sen regression and Passing-Bablock regression functions.
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5.02 score 4 dependents 137 scripts 1.3k downloadsStatMatch - 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.
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4.98 score 11 dependents 225 scripts 1.3k downloadsNISTunits - 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)
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4.87 score 9 dependents 974 scripts 2.8k 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.
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4.84 score 1 dependents 77 scripts 716 downloadsFlexParamCurve - Tools to Fit Flexible Parametric Curves
Model selection tools and 'selfStart' functions to fit parametric curves in 'nls', 'nlsList' and 'nlme' frameworks.
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4.83 score 11 dependents 19 scripts 13k downloadsrtf - Rich Text Format ('RTF') Output
A set of R functions to output Rich Text Format ('RTF') files with high resolution tables and graphics that may be edited with a standard word processor such as Microsoft Word.
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4.80 score 2 stars 1 dependents 197 scripts 2.2k downloadsfds - Functional Data Sets
Functional data sets.
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4.80 score 1 stars 159 dependents 13k downloadsftsa - Functional Time Series Analysis
Functions for visualizing, modeling, forecasting and hypothesis testing of functional time series.
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4.79 score 6 stars 10 dependents 93 scripts 3.7k downloadspdfCluster - 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.
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4.78 score 5 stars 12 dependents 16 scripts 3.5k downloadssasLM - '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 do not necessarily mean incorrectness. However, many want the same results as 'SAS'. This package aims to achieve that. Reference: Littell RC, Stroup WW, Freund RJ (2002, ISBN:0-471-22174-0).
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4.77 score 4 dependents 41 scripts 794 downloadshsphase - 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.
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openblascppopenmp
4.76 score 2 stars 2 dependents 34 scripts 487 downloadsrainbow - Bagplots, Boxplots and Rainbow Plots for Functional Data
Visualizing functional data and identifying functional outliers.
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4.74 score 158 dependents 12k downloadsrcdd - 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.
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gmp
4.74 score 35 dependents 5.3k downloadspsy - Various Procedures Used in Psychometrics
Kappa, ICC, reliability coefficient, parallel analysis, multi-traits multi-methods, spherical representation of a correlation matrix.
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4.71 score 4 dependents 405 scripts 1.1k downloadsshinycustomloader - 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.
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4.71 score 12 dependents 258 scripts 1.1k downloadsaTSA - 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.
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4.64 score 1 stars 5 dependents 542 scripts 2.7k downloadsPCDimension - 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>.
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clustering
4.60 score 6 dependents 41 scripts 1.3k downloadsVizTest - Optimal Confidence Intervals for Visual Testing
Identifies the optimal confidence level to represent the results of a set of pairwise tests as suggested by Armstrong and Poirier (2025) <doi:10.1017/pan.2024.24>.
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4.58 score 1 stars 1 dependents 17 scripts 371 downloadsasnipe - 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.
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4.58 score 4 stars 2 dependents 158 scripts 680 downloadsoptimbase - 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...
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4.54 score 8 dependents 29 scripts 494 downloadshnp - 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.
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4.52 score 1 stars 6 dependents 144 scripts 1.8k downloadsRfit - 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.
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4.52 score 11 dependents 2.0k 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.
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4.47 score 5 stars 5 dependents 195 scripts 945 downloadsMercator - 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>.
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clustering
4.43 score 1 dependents 30 scripts 532 downloadssom - Self-Organizing Map
Self-Organizing Map (with application in gene clustering).
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cpp
4.42 score 12 dependents 8.2k downloadsCUB - 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.
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4.42 score 1 dependents 87 scripts 363 downloadsCTT - 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.
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4.42 score 1 stars 6 dependents 106 scripts 1.4k downloadsThresher - 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>.
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clustering
4.41 score 5 dependents 43 scripts 374 downloadsevmix - 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.
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4.35 score 2 stars 12 dependents 179 scripts 1.7k downloadsirrCAC - Computing the Extent of Agreement among Raters with Chance-Corrected Agreement Coefficient (CAC)
Contains a series of R functions for calculating various chance-corrected agreement coefficients (CAC) among 2 or more raters. 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. Also included in this package is Bangdiwala's B coefficient.
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4.35 score 1 dependents 2 scripts 1.2k downloadsRSDA - 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.
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4.31 score 1 stars 4 dependents 86 scripts 526 downloadssurvC1 - 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.
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4.31 score 8 dependents 2.1k downloadspbs - Periodic B Splines
Periodic B Splines Basis
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4.29 score 27 dependents 35 scripts 2.3k downloadsSNFtool - 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.
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4.29 score 24 stars 3 dependents 7 scripts 881 downloadsOptimalCutpoints - 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.
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4.27 score 2 stars 2 dependents 156 scripts 546 downloadsrelsurv - 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>.
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openblascpp
4.25 score 5 stars 5 dependents 2.4k downloadsmeboot - 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.
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4.24 score 3 stars 3 dependents 1.6k downloadsNlcOptim - 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.
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4.20 score 4 stars 11 dependents 42 scripts 2.8k downloadslanguageR - Data Sets and Functions with 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.
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4.20 score 687 scripts 2.3k downloadsars - Adaptive Rejection Sampling
Adaptive Rejection Sampling, Original version.
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cpp
4.12 score 7 dependents 65 scripts 9.7k downloadswordbankr - Accessing the 'Wordbank' Database
Connecting to 'Wordbank' <https://wordbank.stanford.edu>, an open repository for developmental vocabulary data from the MacArthur-Bates Communicative Development Inventories (Frank et al. 2017 <doi:10.1017/S0305000916000209>). Data are read from a versioned dataset hosted on 'Redivis', so analyses can be pinned to a specific release.
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4.09 score 245 scripts 56 downloadssgeostat - 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.
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4.02 score 2 stars 42 dependents 4.2k downloadsqrnn - 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>.
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4.01 score 8 stars 1 dependents 86 scripts 527 downloadslogspline - 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>.
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openblas
3.98 score 1 stars 11 dependents 9.7k downloadsGPfit - Gaussian Processes Modeling
A computationally stable approach of fitting a Gaussian Process (GP) model to a deterministic simulator.
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3.96 score 1 stars 4 dependents 147 scripts 5.2k downloadswavemulcor - 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.
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3.94 score 2 dependents 29 scripts 356 downloadsBioVenn - 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>.
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3.94 score 1 stars 1 dependents 29 scripts 465 downloadsSparseGrid - Sparse grid integration in R
SparseGrid is a package to create sparse grids for numerical integration, based on code from www.sparse-grids.de
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3.93 score 8 dependents 12 scripts 3.0k downloadsModeler - 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.
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microarrayclustering
3.89 score 1 dependents 13 scripts 833 downloadsTs - Calculation of the Surface Temperature (Ts) from Geospatial Raster Data
Provides functions to calculate the Surface Temperature (Ts) from geospatial raster data. These functions use albedo, Normalized Difference Vegetation Index (NDVI), and air temperature (Ta) to estimate Ts, facilitating hydrological, ecological, and remote sensing analyses.
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3.87 score 1.5k scripts 629 downloadsdeaR - Conventional and Fuzzy Data Envelopment Analysis
Set of functions for Data Envelopment Analysis, including classical, fuzzy, cross-efficiency, bootstrapping, and Malmquist 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>.
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3.85 score 1 stars 2 dependents 102 scripts 1.4k downloadsisotracer - Isotopic Tracer Analysis Using MCMC
Implements Bayesian models to analyze data from tracer addition experiments. The implemented method was originally described in the article "A New Method to Reconstruct Quantitative Food Webs and Nutrient Flows from Isotope Tracer Addition Experiments" by López-Sepulcre et al. (2020) <doi:10.1086/708546>.
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onetbbcpp
3.85 score 119 downloadseasyNCDF - Tools to Easily Read/Write NetCDF Files into/from Multidimensional R Arrays
Set of wrappers for the 'ncdf4' package to simplify and extend its reading/writing capabilities into/from multidimensional R arrays.
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3.83 score 8 dependents 28 scripts 362 downloadscallback - 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 statistics are computed. This package can also be used for analyzing the results from random experiments.
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3.82 score 330 scripts 241 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.
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3.81 score 3 stars 1 dependents 72 scripts 487 downloadsdiscretization - 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.
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3.81 score 3 stars 5 dependents 119 scripts 1.2k downloadsRcapture - 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.
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3.80 score 1 stars 2 dependents 116 scripts 845 downloadsmix - Estimation/Multiple Imputation for Mixed Categorical and Continuous Data
Estimation/multiple imputation programs for mixed categorical and continuous data.
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3.80 score 2 stars 5 dependents 3.0k downloads
mistr - Mixture and Composite Distributions
A flexible computational framework for mixture distributions with the focus on the composite models.
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3.78 score 1 dependents 100 scripts 338 downloadsCB2 - 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>.
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cpp
3.76 score 58 scripts 523 downloadspks - 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>).
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3.76 score 3 dependents 32 scripts 436 downloadsggenealogy - 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.
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3.76 score 2 stars 57 scripts 446 downloadscyjShiny - 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.
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3.74 score 110 scripts 387 downloadserer - 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.
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3.73 score 3 stars 1 dependents 214 scripts 2.8k downloadsarulesSequences - 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.
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3.72 score 10 stars 5 dependents 1.2k downloadsmultiway - 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.
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3.70 score 3 stars 8 dependents 70 scripts 758 downloadsosdatahub - 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.
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3.70 score 20 scripts 430 downloadsSequential - 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. For regression versions of the methods, Monte Carlo and asymptotic methods are used.
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3.70 score 2 stars 1 dependents 46 scripts 680 downloadsUmpire - 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.
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3.69 score 81 scripts 314 downloadsThreeWay - Three-Way Component Analysis
Component analysis for three-way data arrays by means of Candecomp/Parafac, Tucker3, Tucker2 and Tucker1 models.
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3.64 score 8 dependents 61 scripts 481 downloadscrone - 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>.
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3.63 score 17 scripts 288 downloadskequate - 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.
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3.61 score 3 stars 34 scripts 383 downloadstextreg - 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.
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cpp
3.61 score 1 stars 81 scripts 427 downloadsSAPP - Statistical Analysis of Point Processes
Functions for statistical analysis of point processes.
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glibc
3.60 score 40 scripts 376 downloadsAnthropometry - 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>.
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3.60 score 1 stars 1 dependents 66 scripts 751 downloadsPINSPlus - Clustering Algorithm for Data Integration and Disease Subtyping
Provides a robust approach for omics data integration and disease subtyping. PINSPlus is fast and supports the analysis of large datasets with hundreds of thousands of samples and features. The software automatically determines the optimal number of clusters and then partitions the samples in a way such that the results are robust against noise and data perturbation (Nguyen et al. (2019) <DOI: 10.1093/bioinformatics/bty1049>, Nguyen et al. (2017)<DOI: 10.1101/gr.215129.116>, Nguyen et al. (2021)<DOI: 10.3389/fonc.2021.725133>).
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openblascpp
3.59 score 1 dependents 43 scripts 693 downloadsonlineforecast - Forecast Modelling for Online Applications
A framework for fitting adaptive forecasting models. Provides a way to use forecasts as input to models, e.g. weather forecasts for energy related forecasting. The models can be fitted recursively and can easily be setup for updating parameters when new data arrives. See the included vignettes, the website <https://onlineforecasting.org> and the paper "onlineforecast: An R package for adaptive and recursive forecasting" <https://journal.r-project.org/articles/RJ-2023-031/>.
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openblascpp
3.57 score 3 stars 31 scripts 398 downloadsmhsmm - 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.
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3.56 score 3 stars 2 dependents 608 downloadsconicfit - 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.
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3.53 score 7 dependents 163 scripts 875 downloadsVFP - Variance Function Program
Variance function estimation for models proposed by W. Sadler in his variance function program ('VFP', www.aacb.asn.au/AACB/Resources/Variance-Function-Program). 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.
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3.53 score 1 dependents 19 scripts 421 downloadsscatterPlotMatrix - `htmlwidget` for a Scatter Plot Matrix
Create a scatter plot matrix, using `htmlwidgets` package and `d3.js`.
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3.51 score 65 scripts 409 downloadsprevtoinc - 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.
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3.50 score 1 dependents 21 scripts 302 downloadsconvevol - 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.
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3.49 score 31 scripts 434 downloadscba - Clustering for Business Analytics
Implements clustering techniques such as Proximus and Rock, utility functions for efficient computation of cross distances and data manipulation.
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3.49 score 3 dependents 3.8k downloadsSPAtest - 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>.
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3.48 score 16 dependents 39 scripts 1.6k downloadsmixture - 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>.
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gslopenblascppopenmp
3.48 score 1 stars 25 dependents 894 downloadsicmstate - 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>.
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cpp
3.48 score 20 scripts 249 downloadsfmri - 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>.
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openblas
3.48 score 2 stars 1 dependents 594 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.
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3.47 score 2 stars 37 scripts 503 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.
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glibc
3.43 score 6 stars 1 dependents 669 downloads
mars - Meta Analysis and Research Synthesis
Includes functions for conducting univariate and multivariate meta-analysis. This includes the estimation of the asymptotic variance-covariance matrix of effect sizes. For more details see Becker (1992) <doi:10.2307/1165128>, Cooper, Hedges, and Valentine (2019) <doi:10.7758/9781610448864>, and Schmid, Stijnen, and White (2020) <doi:10.1201/9781315119403>.
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3.41 score 51 scripts 388 downloadsdgof - 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.
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3.40 score 1 stars 6 dependents 1.4k 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.
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openblascppopenmp
3.40 score 25 scripts 393 downloadsRSentiment - 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.
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openjdk
3.40 score 50 scripts 359 downloadsoaxaca - Blinder-Oaxaca Decomposition
An implementation of the Blinder-Oaxaca decomposition for linear regression models.
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3.39 score 3 stars 82 scripts 913 downloadssas7bdat - 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.
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3.39 score 4 stars 12 scripts 1.7k downloadsrandomizeR - 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.
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3.38 score 2 stars 1 dependents 470 downloadsedfReader - 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).
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3.37 score 2 dependents 39 scripts 663 downloadsGmedian - 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.
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cpp
3.36 score 3 stars 9 dependents 2.9k downloadsNBR - 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>.
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3.36 score 23 scripts 291 downloadskendallRandomWalks - 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>.
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3.36 score 23 scripts 284 downloadsglmpath - 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.
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3.35 score 1 dependents 74 scripts 467 downloadsRmosek - 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.
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3.33 score 2 stars 3 dependents 66 scripts 1.8k downloadsgsbm - 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>.
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3.32 score 14 scripts 369 downloadsnpreg - 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.
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3.30 score 4 dependents 168 scripts 631 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.
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3.30 score 9 scripts 428 downloadsmpwR - 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'.
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3.30 score 8 scripts 253 downloadsMLDS - 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.
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3.30 score 40 scripts 551 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>.
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3.28 score 42 scripts 424 downloadsfuser - 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>.
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cpp
3.27 score 37 scripts 377 downloadseegkit - 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.
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3.27 score 6 stars 308 scripts 531 downloadskappaSize - 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.
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3.26 score 4 stars 2 dependents 19 scripts 543 downloadsRCAL - 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>.
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3.26 score 1 dependents 290 downloadschangepoint.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> ).
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3.26 score 2 stars 3 dependents 772 downloadssurvIDINRI - 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).
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3.25 score 1 stars 1 dependents 1.2k downloadsrkt - 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.
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3.25 score 1 stars 1 dependents 74 scripts 482 downloadsGeneNet - 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).
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3.24 score 5 dependents 1.2k downloadsCALIBERrfimpute - 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>.
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3.21 score 2 stars 41 scripts 356 downloadspmsampsize - 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.
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3.21 score 5 stars 1 dependents 2 scripts 1.5k downloadsstpp - 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>.
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3.21 score 2 stars 1 dependents 27 scripts 467 downloadsgaussquad - 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.
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3.21 score 6 dependents 90 scripts 670 downloadstripack - 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.
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3.21 score 1 dependents 217 scripts 1.2k downloadsDCchoice - 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>.
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3.20 score 2 stars 1 dependents 106 scripts 2.5k downloadssplm - Econometric Models for Spatial Panel Data
ML and GM estimation and diagnostic testing of econometric models for spatial panel data.
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3.20 score 10 stars 2 scripts 2.3k downloadsyacca - 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.
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3.19 score 1 stars 1 dependents 52 scripts 595 downloadsrpsftm - 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.
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3.19 score 31 scripts 411 downloadsdeident - 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>.
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3.18 score 17 scripts 471 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.
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3.18 score 1 dependents 283 downloadsairGRdatassim - 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>.
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3.18 score 3 stars 9 scripts 416 downloadsgspcr - Generalized Supervised Principal Component Regression
Generalization of supervised principal component regression (SPCR; Bair et al., 2006, <doi:10.1198/016214505000000628>) to support continuous, binary, and discrete variables as outcomes and predictors (inspired by the 'superpc' R package <https://cran.r-project.org/package=superpc>).
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3.18 score 1 stars 10 scripts 325 downloadsqmrparser - Parser Combinator in R
Basic functions for building parsers, with an application to PC-AXIS format files.
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3.18 score 1 stars 5 dependents 411 downloadsSyScSelection - 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.
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3.18 score 1 stars 1 dependents 268 downloadsKneeArrower - Finds Cutoff Points on Knee Curves
Given a set of points around a knee curve, analyzes first and second derivatives to find knee points.
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3.18 score 1 dependents 296 downloadsGARCHIto - 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.
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3.18 score 3 stars 297 downloadsinterleave - 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.
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cpp
3.14 score 3 dependents 1.5k downloadsGoFKernel - 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>.
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3.14 score 6 dependents 77 scripts 644 downloadscodelist - Working with Code Lists
Functions for working with code lists and vectors with codes. These are an alternative for factor that keep track of both the codes and labels. Methods allow for transforming between codes and labels. Also supports hierarchical code lists.
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3.13 score 27 scripts 310 downloadsEvapotranspiration - 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.
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3.12 score 9 stars 74 scripts 598 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.
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3.11 score 13 scripts 292 downloadsdkanr - 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.
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3.11 score 26 scripts 317 downloadssigclust - 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.
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3.11 score 2 dependents 54 scripts 595 downloadsnephro - Utilities for Nephrology
Set of functions to estimate kidney function and other traits of interest in nephrology.
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3.10 score 4 stars 21 scripts 336 downloadssda - 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.
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3.09 score 2 dependents 2.1k downloadsSpadeR - 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.
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3.08 score 121 scripts 360 downloadsiDINGO - 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>.
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3.08 score 3 stars 20 scripts 343 downloadsspcosa - 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.
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openjdk
3.08 score 2 stars 1 dependents 66 scripts 1.5k downloadsWayFindR - Computing Graph Structures on WikiPathways
Converts pathways from 'WikiPathways' GPML format or 'KEGG' KGML format into 'igraph' objects. Includes tools to find all cycles in the resulting graphs and determine which ones involve negative feedback (inhibition). See <doi:10.1093/nargab/lqag051>.
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3.07 score 13 scripts 454 downloadscausaldrf - 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>.
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3.05 score 4 stars 28 scripts 407 downloadsincidental - Implements Empirical Bayes Incidence Curves
Make empirical Bayes incidence curves from reported case data using a specified delay distribution.
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3.04 score 2 stars 11 scripts 299 downloadsSiFINeT - Single Cell Feature Identification with Network Topology
Cluster-independent method based on topology structure of gene co-expression network for identifying feature gene sets, extracting cellular subpopulations, and elucidating intrinsic relationships among these subpopulations. Without prior cell clustering, SifiNet circumvents potential inaccuracies in clustering that may influence subsequent analyses. This method is introduced in Qi Gao, Zhicheng Ji, Liuyang Wang, Kouros Owzar, Qi-Jing Li, Cliburn Chan, Jichun Xie "SifiNet: a robust and accurate method to identify feature gene sets and annotate cells" (2024) <doi:10.1093/nar/gkae307>.
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openblascppopenmp
3.04 score 1 stars 22 scripts 231 downloadssupport.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.
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3.03 score 3 stars 4 dependents 880 downloadscluster.datasets - Cluster Analysis Data Sets
A collection of data sets for teaching cluster analysis.
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3.03 score 108 scripts 223 downloadsLogicReg - 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>.
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3.02 score 3 dependents 2.3k downloadscentiserve - Find Graph Centrality Indices
Calculates centrality indices additional to the 'igraph' package centrality functions.
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3.01 score 1 stars 1 dependents 85 scripts 454 downloads
HAPTRACE - Haplotype-Based Tracking of Admixed Population for Breed Composition Estimation
Simulate populations and track haplotypes over generations to evaluate population admixture. The 'HAPTRACE' supports customisable population parameters, including size, number of markers, mutation rates and recombination.
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cpp
3.00 score 1 scripts 379 downloads
GridOnClusters - Cluster-Preserving Multivariate Joint Grid Discretization
Discretize multivariate continuous data using a grid to capture the joint distribution that preserves clusters in original data (Wang et al 2020) <doi:10.1145/3388440.3412415>. It can handle both labeled or unlabeled data. Joint grid discretization can prepare data for model-free inference of association, function, or causality.
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cppopenmp
3.00 score 453 downloadsggchord2 - Chord Diagrams with 'ggplot2'
A 'ggplot2' extension that provides functions for drawing chord diagrams for visualising flows between categories. The package extends 'ggplot2' by adding geoms and stats for drawing chord sectors, arcs, and labels.
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3.00 score 5 scripts 366 downloadspoissonsuperlearner - Poisson Super Learner
Provides tools for fitting piecewise-constant hazard models for survival and competing risks data, including ensemble hazard estimation via the Super Learner framework. The package supports estimation of survival functions and absolute risk predictions from fitted cause-specific hazard models. For the Super Learner framework see van der Laan, Polley and Hubbard (2007) <doi:10.2202/1544-6115.1309>.
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cpp
3.00 score 3 scripts 328 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.
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3.00 score 1 scripts 282 downloadsLangevin - 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.
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openblascppopenmp
3.00 score 6 scripts 324 downloadsgmGeostats - 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>.
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openmp
3.00 score 1 stars 8 scripts 340 downloadsparallelPlot - `htmlwidget` for a Parallel Coordinates Plot
Create a parallel coordinates plot, using `htmlwidgets` package and `d3.js`.
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3.00 score 1 scripts 301 downloadstableMatrix - 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.
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3.00 score 20 scripts 203 downloadsadlift - 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>.
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openblas
2.98 score 9 dependents 3.6k downloadsequivalence - 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.
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2.98 score 4 stars 4 dependents 2.0k downloadsHiddenMarkov - 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.
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glibc
2.96 score 3 dependents 2.6k downloadskofnGA - 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.
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2.96 score 2 dependents 151 scripts 387 downloadshouba - Manipulation of (Large) Memory-Mapped Objects (Vectors, Matrices and Arrays)
Manipulate data through memory-mapped files, as vectors, matrices or arrays. Basic arithmetic functions are implemented, but currently no matrix arithmetic. Can write and read descriptor files for compatibility with the 'bigmemory' package.
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cpp
2.95 score 1 dependents 1 scripts 352 downloadsbrnn - Bayesian Regularization for Feed-Forward Neural Networks
Bayesian regularization for feed-forward neural networks.
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openblasopenmp
2.95 score 5 dependents 2.0k downloadsrmcfs - 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>.
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openjdk
2.95 score 1 stars 1 dependents 455 downloadsMultiPhen - 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).
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2.95 score 18 scripts 458 downloadsActivityIndex - 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.
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2.95 score 18 scripts 447 downloadssparcl - 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.
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2.95 score 1 stars 3 dependents 695 downloadsmcclust - 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.
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2.92 score 7 dependents 639 downloadsEntropyEstimation - 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.
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2.91 score 9 dependents 749 downloadsBayesianInference - Bayesian Inference
Beta version of 'Bayesian Inference' (BI) using 'python' and BI. It aims to unify the modeling experience by providing an intuitive model-building syntax together with the flexibility of low-level abstraction coding. It also includes pre-built functions for high-level abstraction and supports hardware-accelerated computation for improved scalability, including parallelization, vectorization, and execution on CPU, GPU, or TPU.
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2.91 score 1 stars 161 scripts 313 downloadsargosfilter - 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.
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2.90 score 79 scripts 467 downloadsyhat - 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.
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2.90 score 1 stars 79 scripts 504 downloadsexpectreg - 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.
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cpp
2.88 score 2 stars 38 scripts 605 downloadsPResiduals - Probability-Scale Residuals and Residual Correlations
Computes probability-scale residuals and residual correlations for continuous, ordinal, binary, count, and time-to-event data Qi Liu, Bryan Shepherd, Chun Li (2020) <doi:10.18637/jss.v094.i12>.
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2.88 score 2 stars 76 scripts 301 downloadsAntibodyForests - Delineating Inter- And Intra-Antibody Repertoire Evolution
The generated wealth of immune repertoire sequencing data requires software to investigate and quantify inter- and intra-antibody repertoire evolution to uncover how B cells evolve during immune responses. Here, we present 'AntibodyForests', a software to investigate and quantify inter- and intra-antibody repertoire evolution.
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2.88 score 15 scripts 322 downloadsrriskDistributions - 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.
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2.88 score 1 dependents 784 downloadsCOUNT - 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).
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2.86 score 2 dependents 12 scripts 615 downloadsMNM - 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>.
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2.86 score 1 dependents 24 scripts 338 downloadsARIbrain - 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>.
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2.86 score 1 stars 2 dependents 12 scripts 399 downloadssiebanxicor - 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/>).
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2.86 score 3 stars 48 scripts 635 downloadsmixsmsn - 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>.
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2.85 score 3 stars 2 dependents 39 scripts 572 downloadsBHSBVAR - 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.
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openblascppopenmp
2.85 score 2 stars 35 scripts 438 downloadsunifed - 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>).
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2.85 score 14 scripts 295 downloadscdparcoord - Top Frequency-Based Parallel Coordinates
Parallel coordinate plotting with resolutions for large data sets and missing values.
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2.85 score 14 scripts 380 downloadstis - Time Indexes and Time Indexed Series
Functions and S3 classes for time indexes and time indexed series, which are compatible with FAME frequencies.
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2.83 score 3 dependents 1 scripts 7.5k downloadssurvPresmooth - 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>.
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2.82 score 5 dependents 4.4k downloadsmAr - Multivariate AutoRegressive Analysis
R functions for the estimation and eigen-decomposition of multivariate autoregressive models.
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2.82 score 1 stars 2 dependents 109 scripts 757 downloadsnormalp - 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).
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2.81 score 8 dependents 27 scripts 555 downloadspspearman - Spearman's Rank Correlation Test
Spearman's rank correlation test with precomputed exact null distribution for n <= 22.
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2.81 score 1 stars 1 dependents 3.1k downloadsRRgeo - Species Distribution Modelling for Rare Species
Performs species distribution modeling for rare species with unprecedented accuracy (Mondanaro et al., 2023 <doi:10.1111/2041-210X.14066>) and finds the area of origin of species and past contact between them taking climatic variability in full consideration (Mondanaro et al., 2025 <doi:10.1111/2041-210X.14478>).
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2.81 score 16 scripts 365 downloadsfclust - Fuzzy Clustering
Algorithms for fuzzy clustering, cluster validity indices and plots for cluster validity and visualizing fuzzy clustering results.
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openblascpp
2.80 score 1 stars 5 dependents 2 scripts 1.0k downloadscapn - Capital Asset Pricing for Nature
Implements the natural capital asset pricing for nature (CAPN) approach, using a collocation or iteration method and associated functions for dynamic programs. Development of this package was supported by the Knobloch Family Foundation and Lenfest Ocean Program Contract ID 00029728.
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2.79 score 31 scripts 347 downloadsNISTnls - Nonlinear least squares examples from NIST
Datasets for testing nonlinear regression routines.
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2.79 score 124 scripts 303 downloadslongitudinal - 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.
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2.78 score 1 stars 8 dependents 22 scripts 1.1k downloadsxlamisc - Helper Functions for 'r-xla'
Frequently used generics and helper functions used in 'anvl' and its companion packages 'stablehlo' and 'pjrt'. Comes with S3 generics to query arrays (shape, data type, device) and to convert them to R arrays and raw vectors, as well as a class for data types.
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2.78 score 4 dependents 1 scriptshglm.data - Data for the 'hglm' Package
This data-only package was created for distributing data used in the examples of the 'hglm' package.
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2.78 score 2 dependents 657 downloadslmomRFA - 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".
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glibc
2.78 score 1 stars 2 dependents 678 downloadsnonmem2R - 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.
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2.78 score 3 stars 1 scripts 417 downloadsseparationplot - 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.
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2.78 score 2 dependents 50 scripts 354 downloadsGenderInfer - 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.
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2.78 score 12 scripts 260 downloadsPoiClaClu - 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.
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2.78 score 1 stars 2 dependents 756 downloadsSmartSVA - 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.
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cpp
2.78 score 2 dependents 1 scripts 538 downloadssds - Spatial Data Sources
Descriptions of spatial data sources that can be read directly with or without download. Most sources are readable by 'GDAL' software. There are functions for imagery, elevation, and a variety of easily accessible data streams including image tile servers, links to online files, and geographic data services.
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2.78 score 2 dependents 20 scriptsgraphicalVAR - 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>.
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openblascpp
2.78 score 2 stars 5 dependents 2.0k downloadsOPTS - 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.
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2.78 score 596 scripts 235 downloadsbios2mds - 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.
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2.77 score 1 stars 74 scripts 539 downloadsFMStable - Finite Moment Stable Distributions
Some basic procedures for dealing with log maximally skew stable distributions, which are also called finite moment log stable distributions.
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2.77 score 9 dependents 2.2k downloadsPCovR - 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.
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2.76 score 4 dependents 12 scripts 353 downloadsrtk - Rarefaction Tool Kit
Rarefy data, calculate diversity and plot the results.
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cpp
2.76 score 23 scripts 289 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".
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2.75 score 56 scripts 247 downloadsES - Edge Selection
Implementation of the Edge Selection Algorithm for undirected graph selection. The least angle regression-based algorithm selects edges of an undirected graph based on the projection of the current residuals on the two dimensional edge-planes. The algorithm selects symmetric adjacency matrix, which many other regression-based undirected graph selection procedures cannot do.
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2.74 score 55 scripts 340 downloadsref.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.
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2.74 score 11 scripts 341 downloadsROCaggregator - 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.
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2.74 score 11 scripts 265 downloadsRecords - Record Values and Record Times
Functions for generating k-record values and k-record times
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2.74 score 137 scripts 204 downloadsjmuOutlier - 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.
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2.73 score 1 dependents 178 scripts 810 downloadsctmcd - 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.
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openblascppopenmp
2.73 score 2 stars 1.3k downloadsSDAResources - 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.
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2.72 score 53 scripts 509 downloadsgamair - 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.
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2.72 score 207 scripts 2.5k downloadsjgd - JSON Graphics Device
A graphics device that translates R plotting operations into JSON and streams them over a local connection to an external display application. The device acts as a pure recorder with no rendering dependencies; all rendering occurs in that application (e.g. a 'VS Code' extension or a web browser). Official display applications are available from the project homepage.
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2.72 score 26 scripts 814 downloadsInterSIM - Simulation of Inter-Related Genomic Datasets
Generates three inter-related genomic datasets: methylation, gene expression and protein expression having user specified cluster patterns. The simulation utilizes the realistic inter- and intra- relationships from real DNA methylation, mRNA expression and protein expression data from the TCGA ovarian cancer study, Chalise (2016) <doi:10.1016/j.cmpb.2016.02.011>.
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2.70 score 2 dependents 28 scripts 573 downloads
minirocketR - 'MiniRocket': A Very Fast (Almost) Deterministic Transform for Time Series Classification
High-performance R and C++ implementation using 'OpenMP' parallelization for the 'MiniRocket' algorithm. Extracts features from univariate time series for downstream classification as described in 'Dempster et al.' (2021) (<doi:10.1145/3447548.3467231>).
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cppopenmp
2.70 score 367 downloadsBuSuCo - Coordinate Survey Samples for Businesses
Contains a number of functions for different business sample coordination algorithms together with a function to generate customizable business data sets. For more details see Straubinger (2025) <https://ubt.opus.hbz-nrw.de/frontdoor/index/index/docId/2785>.
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2.70 score 509 downloadsDACF - Data Analysis with Ceiling and/or Floor Data
An implementation of data analytic methods in R for analyses for data with ceiling/floor effects. The package currently includes functions for mean/variance estimation and mean comparison tests. Implemented methods are from Aitkin (1964) <doi:10.1007/BF02289723> and Liu & Wang (2021) <doi:10.3758/s13428-020-01407-2>.
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2.70 score 1 stars 9 scripts 311 downloadsSNPannotator - Automated Functional Annotation of Genetic Variants and Linked Proxies
To automated functional annotation of genetic variants and linked proxies. Linked SNPs in moderate to high linkage disequilibrium (e.g. r2>0.50) with the corresponding index SNPs will be selected for further analysis.
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2.70 score 3 scripts 359 downloads
vcfheader - Fast Genetic Variant Call Format File Header Intelligence and Audit
Streams and parses variant call format file headers without reading full files. Provides structured metadata, validation, inference, and HTML reporting. For details on the specifications used see Danecek et al. (2021) <doi:10.1093/gigascience/giab008>.
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2.70 score 4 scripts 195 downloadsemcAdr - Evolutionary Version of the Metropolis-Hastings Algorithm
Provides computational methods for detecting adverse high-order drug interactions from individual case safety reports using statistical techniques, allowing the exploration of higher-order interactions among drug cocktails.
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cppopenmp
2.70 score 1 scripts 282 downloadsFGLMtrunc - 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.
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openblascppopenmp
2.70 score 3 scripts 307 downloadstidysummary - An Elegant Approach to Summarizing Clinical Data
Streamlines the analysis of clinical data by automatically selecting appropriate statistical descriptions and inference methods based on variable types. For method details see Motulsky H J (2016) <https://www.graphpad.com/guides/prism/10/statistics/index.htm> and d'Agostino R B (1971) <doi:10.1093/biomet/58.2.341>.
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2.70 score 3 scripts 226 downloadsJustifyAlpha - 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>).
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2.70 score 581 downloadsPepMapViz - 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 peptide clusters in different antibody regions predicting immunogenicity in antibody drug development.
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immunogenicitymassspectrometryproteomicspeptidomicssoftwarevisualization
2.70 score 1 stars 7 scripts 358 downloadsmvs - 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>.
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2.70 score 4 scripts 237 downloadstextanalyzer - 'textanalyzer', an R Package to Analyze Text
It analyzes text to create a count of top n-grams, including tokens (one-word), bigrams(two-word), and trigrams (three-word), while removing all stopwords. It also plots the n-grams and corresponding counts as a bar chart.
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2.70 score 4 scripts 222 downloadsChestVolume - 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>.
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2.70 score 4 scripts 282 downloadsBioPred - 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>.
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2.70 score 1 scripts 378 downloadsatlasapprox - 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>.
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2.70 score 394 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>.
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2.70 score 6 scripts 303 downloadslddmm - 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>.
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openblascppopenmp
2.70 score 5 scripts 308 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>.
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2.70 score 4 scripts 329 downloadsPCObw - 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.
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cpp
2.70 score 3 scripts 288 downloadsAalenJohansen - Conditional Aalen-Johansen Estimation
Provides the conditional Nelson-Aalen and Aalen-Johansen estimators. The methods are based on Bladt & Furrer (2023), in preparation.
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2.70 score 9 scripts 430 downloadsharmonizer - 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.
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2.70 score 10 scripts 329 downloadsMestim - 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>.
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2.70 score 7 scripts 246 downloadsrwarrior - R Warrior - An AI Programming Game
A port of Ruby Warrior. Teaches R programming in a fun and interactive way.
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2.70 score 1 stars 5 scripts 255 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.
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cpp
2.70 score 1 scripts 301 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.
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2.70 score 4 scripts 398 downloadsrlcv - 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>.
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2.70 score 5 scripts 265 downloadsLogRegEquiv - Logistic Regression Equivalence
Tools for assessing equivalence of similar Logistic Regression models.
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2.70 score 242 downloadsMCID - 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>.
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2.70 score 1 stars 1 scripts 207 downloadsIDmeasurer - 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".
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2.70 score 7 scripts 283 downloadsDES - 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>.
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2.70 score 2 scripts 538 downloadsIMTest - Information Matrix Test for Generalized Partial Credit Models
Implementation of the information matrix test for generalized partial credit models.
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2.70 score 5 scripts 877 downloadsBAR - Bayesian Adaptive Randomization
Bayesian adaptive randomization is also called outcome adaptive randomization, which is increasingly used in clinical trials.
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2.68 score 48 scripts 302 downloadsc3net - Inferring Large-Scale Gene Networks with C3NET
Allows inferring gene regulatory networks with direct physical interactions from microarray expression data using C3NET.
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2.68 score 2 stars 1 dependents 591 downloadsCVD - 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.
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2.68 score 80 scripts 343 downloadsfluxweb - 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.
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2.64 score 1 stars 22 scripts 406 downloadsscbursts - 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.
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2.64 score 44 scripts 246 downloadsEQL - 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).
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2.64 score 2 dependents 36 scripts 437 downloadsexcessmort - 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".
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2.63 score 43 scripts 364 downloadsensembleBMA - 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>.
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2.63 score 3 stars 1 dependents 47 scripts 716 downloadsbenthos - 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.
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2.61 score 41 scripts 366 downloadsCADFtest - 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).
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2.61 score 1 stars 41 scripts 875 downloadsBTIME - Bayesian Hierarchical Models for Single-Cell Protein Data
Bayesian Hierarchical beta-binomial models for modeling cell population to predictors/exposures. This package utilizes 'runjags' to run Gibbs sampling, parallelizing the chains. Options for different covariances/relationship structures between parameters of interest.
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jagscpp
2.60 score 1 scripts 328 downloadsMonte.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>.
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2.60 score 238 downloadsmultisensi - Multivariate Sensitivity Analysis
Functions to perform sensitivity analysis on a model with multivariate output.
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2.59 score 1 stars 39 scripts 300 downloadseSIR - 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>.
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jagscpp
2.59 score 1 stars 39 scripts 339 downloadsei - Ecological Inference
Software accompanying Gary King's book: A Solution to the Ecological Inference Problem. (1997). Princeton University Press. ISBN 978-0691012407.
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2.59 score 1 stars 39 scripts 370 downloadsInvariantCausalPrediction - 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.
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2.58 score 4 stars 1 dependents 32 scripts 462 downloadstriplediff - Triple-Difference Estimators
Implements triple-difference (DDD) estimators for both average treatment effects and event-study parameters. Methods include regression adjustment, inverse-probability weighting, and doubly-robust estimators, all of which rely on a conditional DDD parallel-trends assumption and allow covariate adjustment across multiple pre- and post-treatment periods. The methodology is detailed in Ortiz-Villavicencio and Sant'Anna (2025) <doi:10.48550/arXiv.2505.09942>.
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cpp
2.58 score 2 stars 19 scripts 358 downloadsAMModels - 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.
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2.58 score 19 scripts 397 downloadsicd.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.
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2.57 score 74 scripts 388 downloadsCircNNTSR - 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.
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2.56 score 3 dependents 40 scripts 388 downloadsYieldCurve - 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.
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2.56 score 5 stars 72 scripts 520 downloadsMAMS - Designing Multi-Arm Multi-Stage Studies
Designing multi-arm multi-stage studies with (asymptotically) normal endpoints and known variance.
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2.54 score 35 scripts 481 downloadscqrReg - 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).
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openblascpp
2.54 score 5 stars 1 dependents 23 scripts 465 downloadssoilassessment - Soil Health Assessment Models for Assessing Soil Conditions and Suitability
Soil health assessment builds information to improve decision in soil management. It facilitates assessment of soil conditions for crop suitability [such as those given by FAO <https://www.fao.org/land-water/databases-and-software/crop-information/en/>], groundwater recharge, fertility, erosion, salinization [<doi:10.1002/ldr.4211>], carbon sequestration, irrigation potential, and status of soil resources.
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2.54 score 2 stars 43 scripts 412 downloadsREEMtree - 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>.
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2.54 score 2 stars 86 scripts 344 downloadsMCPAN - 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.
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2.53 score 1 stars 3 dependents 38 scripts 467 downloadspointRes - 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.
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2.53 score 1 stars 17 scripts 425 downloadsSSDforR - Functions to Analyze Single System Data
Functions to visually and statistically analyze single system data.
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2.53 score 1 stars 84 scripts 806 downloadsggversa - Conjuntos de Datos para 'Graficas Versatiles con ggplot2'
Una coleccion de conjuntos de datos para el libro "Graficas versatiles con ggplot: Analisis visuales de datos", por Raymond L. Tremblay y Julian Hernandez-Serrano. Incluye datos de ecologia, salud publica, educacion, economia y biodiversidad para la ensenanza de visualizacion de datos con 'ggplot2'.
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2.52 score 66 scripts 350 downloadsoptionstrat - 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.
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2.52 score 1 stars 33 scripts 255 downloadsrasterImage - An Improved Wrapper of image()
This is a wrapper function for image(), which makes reasonable raster plots with nice axis and other useful features.
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2.51 score 4 dependents 27 scripts 541 downloadsaniDom - 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.
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2.51 score 1 stars 1 dependents 27 scripts 457 downloadsCloneSeeker - 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>.
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2.51 score 16 scripts 336 downloadspopReconstruct - 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.
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2.51 score 32 scripts 245 downloadsds - Descriptive Statistics
Performs various analyzes of descriptive statistics, including correlations, graphics and tables.
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2.50 score 63 scripts 272 downloadssynchronicity - Boost Mutex Functionality in R
Boost mutex functionality in R.
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cpp
2.49 score 1 dependents 2.0k downloadsvecsets - 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.
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2.49 score 2 dependents 51 scripts 305 downloadsHDtweedie - 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.
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openblasfortranglibc
2.49 score 3 stars 1 dependents 34 scripts 315 downloadsBimodalIndex - The Bimodality Index
Defines the functions used to compute the bimodal index as defined by Wang et al. (2009) <https://pmc.ncbi.nlm.nih.gov/articles/PMC2730180/>, <doi:10.4137/CIN.S2846>.
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microarray
2.48 score 1 dependents 10 scripts 378 downloadsconfidenceCurves - Frequentist Confidence Analysis for Clinical Trials
Frequentist confidence analysis answers the question: How confident are we in a particular treatment effect? This package calculates the frequentist confidence in a treatment effect of interest given observed data, and returns the family of confidence curves associated with that data.
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2.48 score 1 dependents 2 scripts 348 downloadsGRIDCOPULA - Bivariate Copula Functions Based on Regular Grid
Estimates grid type bivariate copula functions, calculates some association measures and provides several copula graphics.
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2.48 score 1 dependents 3 scripts 345 downloadssorcering - 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'.
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openblascpp
2.48 score 1 stars 387 downloadsSoftBart - 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.
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openblascpp
2.48 score 1 dependents 2 scripts 667 downloadszoib - 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.
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jagscpp
2.48 score 3 stars 50 scripts 377 downloadsSpatialBSS - 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>.
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openblascppopenmp
2.48 score 1 dependents 333 downloadsassortnet - 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.
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2.48 score 60 scripts 415 downloadseatDB - 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.
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2.48 score 2 dependents 5 scripts 501 downloadsREAT - 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.
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2.48 score 3 stars 554 downloadstRnslate - 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.
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2.48 score 1 dependents 5 scripts 250 downloadsCGE - 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.
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2.48 score 1 stars 1 dependents 2 scripts 339 downloadsGSM - 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.
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2.48 score 30 scripts 371 downloadsbinhf - Haar-Fisz Functions for Binomial Data
Binomial Haar-Fisz transforms for Gaussianization as in Nunes and Nason (2009).
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2.47 score 3 dependents 3.3k downloadsFinancialMath - 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.
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2.47 score 4 stars 73 scripts 817 downloadsisodistrreg - Isotonic Distributional Regression (IDR)
Distributional regression under stochastic order restrictions for numeric and binary response variables and partially ordered covariates, including right-censored responses via Survival-IDR. See Henzi, Ziegel, Gneiting (2021) <doi:10.1111/rssb.12450> and Bladt, Henzi, van den Heuvel, Ziegel (2026) <doi:10.48550/arXiv.2608.02914>.
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rustcargo
2.46 score 29 scripts 388 downloadsdagR - 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.
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2.45 score 5 stars 57 scripts 321 downloadspoliscidata - 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.
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2.45 score 282 scripts 830 downloadsairGRdatasets - Hydro-Meteorological Catchments Datasets for the 'airGR' Packages
Sample of hydro-meteorological datasets extracted from the 'CAMELS-FR' French database <doi:10.57745/WH7FJR>. It provides metadata and catchment-scale aggregated hydro-meteorological time series on a pool of French catchments for use by the 'airGR' packages.
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2.45 score 28 scripts 755 downloadsnoweb - The 'noweb' System for R
The noweb system for source code, implemented in R.
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2.45 score 28 scripts 302 downloadspolyapost - 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).
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openblas
2.43 score 27 scripts 355 downloadsevclass - 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.
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2.43 score 1 stars 27 scripts 368 downloadsgeesmv - 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.
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2.43 score 45 scripts 378 downloadspdR - 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>.
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2.41 score 4 stars 65 scripts 741 downloadsssfa - 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.
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2.41 score 2 stars 13 scripts 528 downloadsttutils - Utility Functions
Contains some auxiliary functions.
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2.41 score 5 dependents 17 scripts 388 downloadsvietnamcode - Convert Vietnam Provincial Codes
Converts Vietnam's provinces' names and ID across different formats. Handles diacritics and different spellings.
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2.41 score 51 scripts 232 downloadsFRACTION - Numeric Number into Fraction
Turn numeric,data.frame,matrix into fraction form.
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2.40 score 2 dependents 21 scripts 413 downloadsimpectR - Access Data from the 'Impect' API
Pull data from the 'Impect' Customer API <https://glossary.impect.com/api-design>. The package can retrieve data such as events or match sums.
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2.40 score 4 scripts 321 downloadsMASSTIMATE - Body Mass Estimation Equations for Vertebrates
Estimation equations are from a variety of sources and associated error estimation.
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2.40 score 7 scripts 237 downloadstsBSS - 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>.
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openblascpp
2.38 score 4 stars 2 dependents 484 downloadsclusterSEs - 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, plm (pooling or fixed effects), and mlogit models.
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2.38 score 2 stars 1 dependents 40 scripts 855 downloadsHMR - Flux Estimation with Static Chamber Data
Statistical analysis of static chamber concentration data for trace gas flux estimation.
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2.38 score 1 dependents 355 downloadsdcov - 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>.
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openblascpp
2.38 score 8 dependents 479 downloadsconjoint - An Implementation of Conjoint Analysis Method
This is a simple R package that allows to measure the stated preferences using traditional conjoint analysis method.
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2.37 score 1 stars 112 scripts 1.1k downloadssiland - 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>.
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2.36 score 23 scripts 285 downloadsDAKS - 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.
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2.36 score 23 scripts 353 downloadsnlt - 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.
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2.36 score 4 dependents 19 scripts 342 downloadsammiBayes - Bayesian Ammi Model for Continuous Data with or without Additive and Dominance Effect
Flexible multi-environment trials analysis via MCMC method for Additive Main Effects and Multiplicative Interaction 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.
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2.34 score 11 scripts 576 downloadsrafalib - Convenience Functions for Routine Data Exploration
A series of shortcuts for routine tasks originally developed by Rafael A. Irizarry to facilitate data exploration.
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2.34 score 4 dependents 1 scripts 1.8k downloadsgTests - 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.
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2.33 score 1 stars 2 dependents 36 scripts 371 downloadsRlab - Functions and Datasets Required for ST370 Class
Provides functions and datasets required for the ST 370 course at North Carolina State University.
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2.32 score 7 dependents 871 downloadspgdraw - 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.
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cpp
2.32 score 7 dependents 748 downloadsbshazard - 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>.
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2.32 score 1 stars 1 dependents 1 scripts 545 downloadsCommonDataModel - 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.
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openjdk
2.30 score 1 dependents 12 scripts 1.1k downloadsOrdinalCompositions - Wasserstein-Based Regression for Ordinal Compositional Data
Tools analyzing regression models for ordinal compositional data using Wasserstein-based distances. The package includes linear programming solvers under simplex constraints, tensor product constructions and performance metrics.
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2.30 score 322 downloadscircularEV - 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 <doi:10.1002/env.2667>.
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2.30 score 10 scripts 332 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>.
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2.30 score 1 stars 4 scripts 256 downloadsGTRT - Graph Theoretic Randomness Tests
A collection of functions for testing randomness (or mutual independence) in linear and circular data as proposed in Gehlot and Laha (2025a) <doi:10.48550/arXiv.2506.21157> and Gehlot and Laha (2025b) <doi:10.48550/arXiv.2506.23522>, respectively.
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2.30 score 308 downloadsmvngGrAd - Moving Grid Adjustment in Plant Breeding Field Trials
Package for moving grid adjustment in plant breeding field trials.
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2.30 score 10 scripts 265 downloadsaudiometry - 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>.
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2.30 score 371 downloadsrADA - 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.
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2.30 score 1 stars 5 scripts 245 downloadsvaritas - 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.
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2.30 score 8 scripts 302 downloadsgendist - 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.
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2.30 score 25 scripts 312 downloadsBICORN - 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.
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2.30 score 6 scripts 260 downloadsdecode - 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.
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2.30 score 2 stars 9 scripts 287 downloadsacc - 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.
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openblascpp
2.30 score 1 stars 33 scripts 542 downloadsDTWBI - 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).
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2.29 score 1 dependents 65 scripts 626 downloadsCBCgrps - 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.
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2.28 score 24 scripts 524 downloadsSPlit - 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.
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cppopenmp
2.28 score 3 stars 63 scripts 292 downloadsfTrading - 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.
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2.26 score 3 stars 45 scripts 1.4k downloadsEDISON - 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.
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2.26 score 2 stars 13 scripts 425 downloadsrpnf - 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.
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2.26 score 4 stars 45 scripts 221 downloadsGenAlgo - 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.
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microarrayclustering
2.26 score 18 scripts 557 downloadsmultilevLCA - 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. (2025) <doi:10.1080/00273171.2025.2473935>.
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openblascpp
2.26 score 1 dependents 9 scripts 583 downloadsserial - 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.
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2.26 score 1 dependents 60 scripts 448 downloadsSMASH - Subclone Multiplicity Allocation and Somatic Heterogeneity
Cluster user-supplied somatic read counts with corresponding allele-specific copy number and tumor purity to infer feasible underlying intra-tumor heterogeneity in terms of number of subclones, multiplicity, and allocation (Little et al. (2019) <doi:10.1186/s13073-019-0643-9>).
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openblascppopenmp
2.26 score 18 scripts 245 downloadsSimile - 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.
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2.26 score 18 scripts 214 downloadswbs - 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.
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2.26 score 3 stars 2 dependents 630 downloadscrrSC - 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>.
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2.26 score 1 dependents 530 downloadsbda - Binned Data Analysis
Algorithms developed for binned data analysis, gene expression data analysis and measurement error models for ordinal data analysis.
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2.25 score 88 scripts 689 downloadsgbRd - 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.
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2.24 score 17 scripts 2.1k downloadsdiscSurv - Discrete Time Survival Analysis
Provides data transformations, estimation utilities, predictive evaluation measures and simulation functions for discrete time survival analysis.
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2.24 score 2 stars 87 scripts 618 downloadsnopaco - Non-Parametric Concordance Coefficient
A non-parametric test for multi-observer concordance and differences between concordances in (un)balanced data.
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cpp
2.23 score 17 scripts 238 downloadslm.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>.
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openblascpp
2.23 score 17 scripts 324 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.
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2.23 score 17 scripts 184 downloadsbayesreg - 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>.
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2.23 score 1 stars 2 dependents 28 scripts 544 downloadsCoDiNA - 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>.
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2.23 score 24 scripts 398 downloadsbvls - 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
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2.22 score 3 dependents 1.9k downloadsfImport - Rmetrics - Importing Economic and Financial Data
Provides a collection of utility functions to download and manage data sets from the Internet or from other sources.
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2.21 score 69 scripts 2.4k downloadsinsuranceData - 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.
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2.21 score 1 stars 161 scripts 976 downloadscmaes - Covariance Matrix Adapting Evolutionary Strategy
Single objective optimization using a CMA-ES.
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2.20 score 1 stars 3 dependents 1.8k downloadsCrossValidate - 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.
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microarrayclustering
2.20 score 16 scripts 336 downloadsshinyaframe - '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>.
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2.20 score 1 stars 16 scripts 286 downloadsCovSel - 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.
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2.19 score 1 stars 31 scripts 310 downloadsEBEN - 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.
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openblas
2.19 score 1 stars 31 scripts 439 downloadslunar - Calculate Lunar Phase & Distance, Seasons and Related Environmental Factors
Provides functions to calculate lunar and other related environmental covariates.
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2.19 score 1 dependents 1.7k downloadsaniml - A Collection of ML Tools for Species Detection and Classification in Camera Trap Images and Videos
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.
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2.18 score 10 scripts 523 downloadsisard - Overflow Data for Quantitative Peace Science Research
These are data and functions to support quantitative peace science research. The data are important state-year information on democracy and wealth, which require periodic updates and regular maintenance. The functions permit some exploratory and diagnostic assessment of the kinds of data in demand by the community, but do not impose many dependencies on the user.
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2.18 score 1 dependents 489 downloadsGPArotateDF - 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>.
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2.18 score 15 scripts 391 downloadsaiRthermo - 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.
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2.18 score 1 dependents 50 scripts 538 downloadsSpatialNP - Multivariate Nonparametric Methods Based on Spatial Signs and Ranks
Test and estimates of location, tests of independence, tests of sphericity and several estimates of shape all based on spatial signs, symmetrized signs, ranks and signed ranks. For details, see Oja and Randles (2004) <doi:10.1214/088342304000000558> and Oja (2010) <doi:10.1007/978-1-4419-0468-3>.
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cpp
2.18 score 5 dependents 402 downloadsiso8601 - 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.
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cpp
2.18 score 1 dependents 9 scripts 204 downloadsbiganalytics - 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'.
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cpp
2.18 score 1 stars 5 dependents 2 scripts 909 downloadsfrontiles - 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.
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2.18 score 1 stars 15 scripts 345 downloadsgnrprod - 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.
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2.18 score 3 stars 2 scripts 355 downloadsPEtests - 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>.
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2.18 score 3 stars 219 downloadsGFD - 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>.
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2.18 score 15 scripts 351 downloadsibelief - 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.
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2.18 score 1 stars 1 dependents 372 downloadsrxSeq - 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.
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2.18 score 15 scripts 230 downloadsthreewords - 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.
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2.18 score 1 stars 1 dependents 7 scripts 245 downloadsGNAR - 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>.
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2.16 score 2 stars 72 scripts 422 downloadsbayesmix - Bayesian Mixture Models with JAGS
Fits finite mixture models of univariate Gaussian distributions using JAGS within a Bayesian framework.
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jagscpp
2.15 score 1 dependents 47 scripts 582 downloadsggrcs - 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>.
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2.15 score 1 stars 14 scripts 498 downloadsbdlp - 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.
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2.15 score 14 scripts 357 downloadsMCSim - 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.
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2.15 score 14 scripts 252 downloadsTSCS - Time Series Cointegrated System
A set of functions to implement Time Series Cointegrated System (TSCS) spatial interpolation and relevant data visualization.
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2.15 score 14 scripts 237 downloadsABC.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”.
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2.15 score 14 scripts 418 downloadsexploreR - 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.
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2.15 score 14 scripts 304 downloadsRCPA3 - 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.
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2.14 score 74 scripts 1.9k downloadsPtProcess - 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".
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2.13 score 4 stars 34 scripts 565 downloadsLDRTools - 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>.
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2.13 score 3 dependents 8 scripts 1.5k downloadsfirst - Factor Importance Ranking and Selection using Total Indices
A model-independent factor importance ranking and selection procedure based on total Sobol' indices. Please see Huang and Joseph (2025) <doi:10.1080/00401706.2025.2483531>. This research is supported by U.S. National Science Foundation grants DMS-2310637 and DMREF-1921873.
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2.11 score 1 stars 130 scripts 298 downloadsjointest - 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.
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2.11 score 13 scripts 251 downloadseasynls - Easy Nonlinear Model
Fit and plot some nonlinear models.
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2.11 score 1 stars 16 scripts 280 downloadsIntNMF - Integrative Clustering of Multiple Genomic Dataset
Carries out integrative clustering analysis using multiple types of genomic dataset using integrative Non-negative Matrix factorization.
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2.10 score 3 stars 42 scripts 596 downloadseasyanova - 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.
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2.10 score 1 stars 63 scripts 741 downloadscrossval - Generic Functions for Cross Validation
Contains generic functions for performing cross validation and for computing diagnostic errors.
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2.09 score 1 dependents 1.4k 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. (2025) <doi:10.1371/journal.pcbi.1013293> for method details.
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2.08 score 12 scripts 269 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.
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2.08 score 12 scripts 237 downloadsBSSprep - 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.
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openblascpp
2.08 score 4 dependents 423 downloadsCNLTreg - 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>.
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2.08 score 2 dependents 20 scripts 310 downloadsimp4p - Imputation for Proteomics
Functions to analyse missing value mechanisms and to impute data sets in the context of bottom-up MS-based proteomics.
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cpp
2.08 score 1 stars 1 dependents 40 scripts 560 downloadsYatchewTest - 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.
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cpp
2.07 score 2 dependents 1.9k downloadsfreqdom - 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>.
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2.06 score 1 dependents 38 scripts 378 downloadspgmm - 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>.
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openblas
2.06 score 1 stars 2 dependents 1.9k downloadsoverlapptest - 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>.
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2.04 score 11 scripts 268 downloadssalad - 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.
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2.04 score 11 scripts 199 downloadsLibra - 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.
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gsl
2.04 score 109 scripts 360 downloadsConvergeR - Whitfield Convergence Score and Seurat Metadata Association
Calculates the convergence score defined by Whitfield et al. 2026 <doi:10.1158/0008-5472.CAN-25-4403>. It allows visualization of this score alongside qualitative and quantitative Seurat object metadata via barplots and density curves, and runs appropriate statistical tests for associations.
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softwaresinglecelltranscriptomicsgeneexpression
2.00 scoreSillyPutty - 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.
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clustering
2.00 score 6 scripts 572 downloadsggalttext - Make 'ggplot2' Fully Accessible by Generating Alternative Text
Generates concise alternative text for data visualizations created with 'ggplot2'. Descriptions are produced by inspecting plot layers, labels, scales, and facets, with support for multiple languages and alternative text stored in plot metadata.
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2.00 score 2 scripts 323 downloadsCauMedi - Cell Type-Specific Causal Mediation Models for Single-Cell Data
A causal mediation framework for cell type-specific single-cell data based on joint mediator multilevel models. The framework jointly models overdispersed counts and zero inflation for the mediators.
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2.00 score 1 stars 205 downloadsMLCOPULA - 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>.
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2.00 score 195 downloadsSISIR - 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>.
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2.00 score 8 scripts 277 downloadssvymargins - Predictive Margins for Survey Analyses
Predictive margins like in the 'Stata' procedure 'margins'. This package is based on the survey::svypredmean() function. Supported regression analyses are based on survey::svyglm() and svyVGAM::svy_vglm() functions (for multinomial logistic regression models).
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2.00 score 303 downloadscovercorr - Coverage Correlation Coefficient and Testing for Independence
Computes the coverage correlation coefficient introduced in <doi:10.48550/arXiv.2508.06402> , a statistical measure that quantifies dependence between two random vectors by computing the union volume of data-centered hypercubes in a uniform space.
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2.00 score 407 downloadsstructenforcement - Struct-Like Data Type Checking and Enforcement
Enforcement of field types in lists. A drop-in tool to allow for dynamic input data that might be questionably parsed or cast to be coerced into the specific desired format in a reasonably performant manner.
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2.00 score 1 stars 2 scripts 237 downloadsClimaRep - Estimating Climate Analogue Areas
Offers tools to identify the climate analogues of reference polygons and quantifies their transformation under future climate change scenarios. Approaches described in Mingarro and Lobo (2018) <doi:10.32800/abc.2018.41.0333> and Mingarro and Lobo (2022) <doi:10.1017/S037689292100014X>.
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2.00 score 5 scripts 373 downloadsNPFD - 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.
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2.00 score 195 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.
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2.00 score 407 downloadseasyComment - Generate Comment Boxes with Custom Alignment
Provides a function to generate comment boxes framed with '#' characters, with configurable width and text alignment (left, center, or right). Useful for formatting scripts and improving code readability.
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2.00 score 2 scripts 340 downloadsNScluster - 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>.
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fortranglibcopenmp
2.00 score 1 stars 4 scripts 418 downloadsrGV - 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.
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2.00 score 2 stars 4 scripts 400 downloadspwlmm - 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>.
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cpp
2.00 score 278 downloadsRRmorph - 3D Morphological Analyses with 'RRphylo'
Combined with 'RRphylo', this package provides a powerful tool to analyse and visualise 3d models (surfaces and meshes) in a phylogenetically explicit context (Melchionna et al., 2024 <doi:10.1038/s42003-024-06710-8>).
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2.00 score 3 scripts 352 downloadsrevert - Reversion Mutation Detector for DNA Sequencing Data
Reversion mutations are secondary mutations that reverse the deleterious effects of an original pathogenic mutation, partially or fully restoring the gene's function. The revert package detects reversion mutations for a specific pathogenic mutation from DNA-seq bam files.
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2.00 score 281 downloadsnmaplateplot - 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.
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2.00 score 1 stars 4 scripts 309 downloadstrunmnt - Moments of Truncated Multivariate Normal Distribution
Computes the product moments of the truncated multivariate normal distribution, particularly for cases involving patterned variance-covariance matrices. It also has the capability to calculate these moments with arbitrary positive-definite matrices, although performance may degrade for high-dimensional variables.
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openblascpp
2.00 score 221 downloadsGMC - Generalized Measure of Correlation (GMC)
Provides tools to compute the Generalized Measure of Correlation (GMC), a dependence measure accounting for nonlinearity and asymmetry in the relationship between variables. Based on the method proposed by Zheng, Shi, and Zhang (2012) <doi:10.1080/01621459.2012.710509>.
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2.00 score 1 scripts 235 downloadssamplex - Shiny Tool for Sample Size Calculation
An interactive 'shiny' application to assist in determining sample sizes for common survey designs such as 'simple random sampling', 'stratified sampling', and 'cluster sampling'. It includes formulas, helper calculators, and illustrative examples.
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2.00 score 198 downloadsoptsize - Optimal Plot Size Estimation for Field Experiments
Provides methods for determining optimum plot size and shape in field experiments using Fairfield-Smith's variance law approach. It will evaluate field variability, determine optimum plot size and shape and study fertility trends across the field.
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2.00 score 225 downloadsfdesigns - Optimal Experimental Designs for Dynamic/Functional 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>.
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openblascppopenmp
2.00 score 281 downloadsXDNUTS - Discontinuous Hamiltonian Monte Carlo with Varying Trajectory Length
Hamiltonian Monte Carlo for both continuous and discontinuous posterior distributions with a customizable 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.
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openblascppopenmp
2.00 score 3 scripts 397 downloadseFCM - Exponential Factor Copula Model
Implements the exponential Factor Copula Model (eFCM) of Castro-Camilo, D. and Huser, R. (2020) for spatial extremes, with tools for dependence estimation, tail inference, and visualization. The package supports likelihood-based inference, Gaussian process modeling via Matérn covariance functions, and bootstrap uncertainty quantification. See Castro-Camilo and Huser (2020) <doi:10.1080/01621459.2019.1647842>.
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openblascppopenmp
2.00 score 368 downloadsconfidence - 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.
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2.00 score 7 scripts 313 downloadsNiLeDAM - 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>.
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2.00 score 5 scripts 263 downloadsROCS - Receiver Operating Characteristics Surface
Plots the Receiver Operating Characteristics Surface for high-throughput class-skewed data, calculates the Volume under the Surface (VUS) and the FDR-Controlled Area Under the Curve (FCAUC), and conducts tests to compare two ROC surfaces. Computes eROC curve and the corresponding AUC for imperfect reference standard.
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2.00 score 9 scripts 257 downloadsOptimModel - 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>.
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2.00 score 1 stars 3 scripts 356 downloadsgenset - Generates Multiple Data Sets
Generate multiple data sets 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.
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2.00 score 3 scripts 268 downloadssiren - 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>).
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2.00 score 1 scripts 300 downloadsROKET - Optimal Transport-Based Kernel Regression
Perform optimal transport on somatic point mutations and kernel regression hypothesis testing by integrating pathway level similarities at the gene level (Little et al. (2023) <doi:10.1111/biom.13769>). The software implements balanced and unbalanced optimal transport and omnibus tests with 'C++' across a set of tumor samples and allows for multi-threading to decrease computational runtime.
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openblascppopenmp
2.00 score 271 downloadsUniExactFunTest - 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>.
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cpp
2.00 score 211 downloadsMissCP - 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>.
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openblascpp
2.00 score 3 scripts 254 downloadsCADF - 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.
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2.00 score 1 scripts 403 downloadsHDclust - 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>.
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cppopenmp
2.00 score 228 downloadstRigon - 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.
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2.00 score 3 scripts 250 downloadsStuteTest - 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.
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openblascppopenmp
2.00 score 1 scripts 241 downloadsSNSeg - 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>.
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cpp
2.00 score 1 stars 5 scripts 515 downloadsg.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.
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2.00 score 9 scripts 386 downloadsRFPM - Floating Percentile Model
Floating Percentile Model with additional functions for optimizing inputs and evaluating outputs and assumptions.
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2.00 score 4 scripts 399 downloadsSOHPIE - 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>.
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2.00 score 4 scripts 388 downloadsLabourMarketAreas - 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.
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2.00 score 7 scripts 352 downloadsQuadRoot - Quadratic Root for any Quadratic Equation
It will assist the user to find simple quadratic roots from any quadratic equation.
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2.00 score 4 scripts 287 downloadsTSTutorial - Fitting and Predict Time Series Interactive Laboratory
Interactive laboratory of Time Series based in Box-Jenkins methodology.
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2.00 score 10 scripts 353 downloadsVMDML - 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>.
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2.00 score 4 scripts 263 downloadsHealthCal - 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.
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2.00 score 3 scripts 254 downloadsoptistock - 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.
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2.00 score 1 scripts 220 downloadscoxerr - 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.
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2.00 score 3 scripts 245 downloadsfastAFT - 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>.
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2.00 score 3 scripts 270 downloadsExtremeBounds - 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.
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2.00 score 1 stars 8 scripts 568 downloadsInflectSSP - 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>.
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openjdk
2.00 score 515 downloadsBRACE - 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>.
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2.00 score 239 downloadsforplo - 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.
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2.00 score 5 scripts 378 downloadssiie - 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.
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2.00 score 4 scripts 241 downloadsSIMICO - 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.
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2.00 score 3 scripts 229 downloadsRAT - 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.
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2.00 score 6 scripts 259 downloadsgeno2proteo - 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.
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geneticsproteomicssequencingannotationgenomeannotationgenomeassembly
2.00 score 10 scripts 421 downloadsonlineBcp - 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>.
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2.00 score 1 stars 8 scripts 242 downloadsEUfootball - 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.
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2.00 score 7 scripts 278 downloadsprimate - 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.
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2.00 score 3 scripts 219 downloadssealasso - 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.
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2.00 score 4 scripts 265 downloadscomplexity - 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.
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2.00 score 8 scripts 304 downloadsPHclust - Poisson Hurdle Clustering for Sparse Microbiome Data
Clustering analysis for sparse microbiome data, based on a Poisson hurdle model.
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2.00 score 4 scripts 221 downloadsDCEmgmt - 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'.
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2.00 score 3 scripts 276 downloadssimpleRCache - 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()).
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2.00 score 10 scripts 280 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>.
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jagscpp
2.00 score 250 downloadsrNeighborQTL - 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>.
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2.00 score 4 scripts 479 downloadsSnake - Game of Snake
Implements snake in R as a programming example, see <https://en.wikipedia.org/wiki/Snake_(video_game_genre)>.
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2.00 score 1 scripts 216 downloadsAUtests - 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.
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2.00 score 8 scripts 347 downloadscredsubs - 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>).
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2.00 score 8 scripts 292 downloadsRSqlParser - Parse 'SQL' Statements
Parser for 'SQL' statements. Currently, it supports parsing of only 'SELECT' statements.
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2.00 score 5 scripts 278 downloadssurvCurve - 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.
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2.00 score 4 scripts 225 downloadstukeytrend - 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.
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2.00 score 8 scripts 304 downloadscapitalR - 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.
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2.00 score 10 scripts 362 downloadsggBubbles - 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'.
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2.00 score 8 scripts 330 downloadsBESTree - 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>.
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2.00 score 3 scripts 303 downloadsBALLI - 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.
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2.00 score 284 downloadsCOST - Copula-Based Semiparametric Models for Spatio-Temporal Data
Parameter estimation, one-step ahead forecast and new location prediction methods for spatio-temporal data.
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2.00 score 10 scripts 240 downloadsBPM - 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.
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2.00 score 1 stars 6 scripts 317 downloadsSDT - 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.
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2.00 score 1 stars 8 scripts 190 downloadsrope - 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.
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2.00 score 4 scripts 371 downloadsMGL - 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.
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2.00 score 2 scripts 239 downloadsmltest - Classification Evaluation Metrics
A fast, robust and easy-to-use calculation of multi-class classification evaluation metrics based on confusion matrix.
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2.00 score 33 scripts 261 downloadsNHLData - 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.
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2.00 score 99 scripts 400 downloadsfunFEM - 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.
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2.00 score 1 dependents 33 scripts 414 downloadsFgmutils - 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.
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2.00 score 1 dependents 33 scripts 469 downloadsportes - 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.
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1.99 score 97 scripts 626 downloadsCRTSize - 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).
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1.98 score 16 scripts 349 downloadsGVARX - 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>.
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1.98 score 6 stars 16 scripts 89 downloadsfastGraph - 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.
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1.98 score 96 scripts 969 downloadsBSagri - 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.
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1.98 score 1 stars 32 scripts 335 downloadsglmbb - All Hierarchical or Graphical Generalized Linear Models
Find all hierarchical models of specified generalized linear model with information criterion (AIC, BIC, or AICc) within specified cutoff of minimum value. Alternatively, find all such graphical models. Use branch and bound algorithm so we do not have to fit all models.
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1.97 score 94 scripts 601 downloadseba - 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>).
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1.97 score 1 dependents 31 scripts 533 downloadsbiosignalEMG - 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.
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1.97 score 3 stars 31 scripts 441 downloadsRJSplot - 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.
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1.96 score 4 stars 23 scripts 315 downloadsCEoptim - Cross-Entropy R Package for Optimization
Optimization solver based on the Cross-Entropy method.
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1.95 score 2 stars 15 scripts 387 downloadsEQUIVNONINF - 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).
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1.95 score 45 scripts 345 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.
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cppopenmp
1.95 score 1 stars 3 dependents 449 downloadsACDm - Tools for Autoregressive Conditional Duration Models
Provides tools for autoregressive conditional duration (ACD, Engle and Russell, 1998) models. Functions to create trade, price, or volume durations from transaction data, perform diurnal adjustments, fit various ACD models, and test them.
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cpp
1.95 score 3 stars 1 dependents 579 downloadsmsme - 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.
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1.95 score 1 stars 3 dependents 539 downloadsfICA - Classical, Reloaded and Adaptive FastICA Algorithms
Algorithms for classical symmetric and deflation-based FastICA, reloaded deflation-based FastICA algorithm and an algorithm for adaptive deflation-based FastICA using multiple nonlinearities. For details, see Miettinen et al. (2014) <doi:10.1109/TSP.2014.2356442> and Miettinen et al. (2017) <doi:10.1016/j.sigpro.2016.08.028>. The package is described in Miettinen, Nordhausen and Taskinen (2018) <doi:10.32614/RJ-2018-046>.
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openblascpp
1.95 score 3 dependents 465 downloadssmarter - A Collection of Modified R Functions to Make Basic Coding More Convenient
A collection of recycled and modified R functions to aid in file manipulation, data exploration, wrangling, optimization, and object manipulation. Other functions aid in convenient data visualization, loop progression, software packaging, and installation.
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cppopenmp
1.95 score 3 dependents 281 downloadssupport.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>.
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1.95 score 1 dependents 823 downloadsinteractionTest - 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.
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1.95 score 3 dependents 3 scripts 632 downloadsCBT - 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>.
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1.95 score 1 scripts 244 downloadsscore - 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.
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1.95 score 1 stars 9 scripts 264 downloadsgeoBayes - 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.
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openblasfortranglibc
1.94 score 22 scripts 380 downloadssonar - Fundamental Formulas for Sonar
Formulas for calculating sound velocity, water pressure, depth, density, absorption and sonar equations.
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1.93 score 86 scripts 261 downloadsrankdist - 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.
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cpp
1.92 score 84 scripts 344 downloadsunivOutl - Detection of Univariate Outliers
Provides well-known techniques for detecting univariate outliers. Methods for handling skewed distributions are included. The Hidiroglou-Berthelot (1986) method for detecting outliers in ratios of historical data is also implemented. When available, survey weights can be incorporated in the detection process.
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1.91 score 1 dependents 27 scripts 487 downloadsgie - 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.
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1.90 score 16 scripts 463 downloadsd3plus - Seamless 'D3Plus' Integration
Provides functions that offer seamless 'D3Plus' integration. The examples provided here are taken from the official 'D3Plus' website <http://d3plus.org>.
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1.90 score 16 scripts 401 downloadsBCRA - 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>.
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1.89 score 3 stars 13 scripts 350 downloadsSpatialAcc - 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.
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1.88 score 1 stars 76 scripts 366 downloads
droll - Analyze Roll Distributions
A toolkit for parsing dice notation, analyzing rolls, calculating success probabilities, and plotting outcome distributions.
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1.88 score 15 scripts 284 downloadsDIDHAD - Difference-in-Differences in Heterogeneous Adoption Designs with Quasi Untreated Groups
Estimation of Difference-in-Differences (DiD) estimators from de Chaisemartin et al. (2025) <doi:10.48550/arXiv.2405.04465> in Heterogeneous Adoption Designs with Quasi Untreated Groups.
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1.87 score 1 dependents 4 scripts 2.5k downloadsHUM - 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>).
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cpp
1.86 score 1 stars 12 scripts 313 downloadsWWGbook - Functions and Datasets for WWGbook
Book is "Linear Mixed Models: A Practical Guide Using Statistical Software" published in 2006 by Chapman Hall / CRC Press.
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1.85 score 1 stars 47 scripts 1.5k downloadsnetClust - Model-Based Clustering of Network Data
Clustering unilayer and multilayer network data by means of finite mixtures is the main utility of netClust.
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openblascppopenmp
1.84 score 69 scripts 282 downloadslmf - 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.
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1.84 score 1 dependents 23 scripts 319 downloadsRobustLinearReg - 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>.
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1.84 score 1 dependents 23 scripts 248 downloadsdbstats - 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.
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1.82 score 1 stars 1 dependents 22 scripts 382 downloadstightClust - Tight Clustering
The functions needed to perform tight clustering Algorithm.
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1.82 score 1 dependents 22 scripts 226 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.
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1.80 score 1 dependents 21 scripts 358 downloadsR1magic - 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.
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1.78 score 12 scripts 188 downloadssvmf - The Scaled von Mises-Fisher Distribution
Functions to perform maximum likelihood estimation of and random value simulation from the scaled von Mises-Fisher distribution. The distribution is elliptical symmetric and can be applied to spherical and hyper-spherical data. The reference paper is Scealy J.L. and Wood A.T.A. (2019), <doi:10.1080/01621459.2019.1585249>.
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1.78 score 1 dependents 284 downloadscrops - 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.
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1.78 score 1 dependents 4 scripts 568 downloadsMGBT - 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) and England et al. (2017) <doi:10.3133/tm4B5>. Other utilities for working with peak streamflow are provided.
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1.78 score 1 stars 1 dependents 635 downloadsMN - Matrix Normal Distribution
Density computation, random matrix generation, maximum likelihood estimation, and regression for 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.
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1.78 score 1 dependents 3 scripts 439 downloadsremdata - A Collection of Empirical and Simulated Relational Event Data Sequences
Empirical and simulated data for relational event analyses. Each dataset consists of a relational event sequence and optional actor attributes. Individual datasets are redistributed under their original licenses as documented in inst/DATA_LICENSES.
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1.78 score 1 dependents 2 scripts 303 downloadsNAEPprimer - 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.
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1.78 score 2 dependents 566 downloadsspatialreg.hp - Hierarchical Partitioning of R2 for Spatial Simultaneous Autoregressive Model
Conducts hierarchical partitioning to calculate individual contributions of spatial and predictors (groups) towards total R2 for spatial simultaneous autoregressive model.
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1.78 score 307 downloadsPursuit - 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.
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1.78 score 1 dependents 436 downloadsTSSS - 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).
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fortranglibc
1.78 score 2 stars 1 scripts 484 downloadsOptimalDesign - A Toolbox for Computing Efficient Designs of Experiments
Algorithms for D-, A-, I-, and c-optimal designs. For more details, see the package description. 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.
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1.78 score 1 dependents 332 downloadspycno - 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>.
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1.78 score 3 stars 20 scripts 246 downloadsJFE - Tools for Analyzing Time Series Data of Just Finance and Econometrics
Offer procedures to download financial-economic time series data and enhanced procedures for computing the investment performance indices of Bacon (2004) <DOI:10.1002/9781119206309>.
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1.78 score 2 stars 1 dependents 353 downloadsDWreg - Parametric Regression for Discrete Response
Regression for a discrete response, where the conditional distribution is modelled via a discrete Weibull distribution.
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1.78 score 2 dependents 5 scripts 456 downloadsmultichull - 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.
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1.78 score 2 dependents 4 scripts 405 downloadsadimpro - 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>.
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openblasopenmp
1.78 score 2 dependents 711 downloadsmexhaz - 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>.
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1.78 score 1 dependents 543 downloadsGENLIB - 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>.
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cpp
1.78 score 1 dependents 465 downloadsClickClust - 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.
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1.78 score 2 stars 1 dependents 357 downloadsliftLRD - 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>.
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1.78 score 2 stars 1 dependents 290 downloadsChernoffDist - 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).
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1.78 score 2 dependents 2 scripts 274 downloadsContaminatedMixt - 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>.
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openblas
1.78 score 2 dependents 543 downloadsPTAk - 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.
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1.78 score 1 stars 1 dependents 420 downloadsCPE - 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.
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openblas
1.78 score 2 stars 1 dependents 483 downloadsmvLSW - 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.
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1.78 score 2 dependents 396 downloadsbigsplines - 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.
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1.78 score 2 dependents 507 downloadsfgui - 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.
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1.78 score 2 dependents 10 scripts 426 downloadsOGI - 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>.
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1.78 score 4 scripts 288 downloadscosso - 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.
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1.76 score 1 stars 1 dependents 19 scripts 296 downloadsctrlGene - Assess the Stability of Candidate Housekeeping Genes
A simple way to assess the stability of candidate housekeeping genes is implemented in this package.
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1.76 score 1 dependents 19 scripts 525 downloadsonlinePCA - Online Principal Component Analysis
Online PCA for multivariate and functional data using perturbation methods, low-rank incremental methods, and stochastic optimization methods.
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openblascpp
1.75 score 2 stars 28 scripts 253 downloadsRcmdrPlugin.FactoMineR - Graphical User Interface for FactoMineR
Rcmdr Plugin for the 'FactoMineR' package.
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1.75 score 1 stars 2 scripts 1.1k downloadssimqi - Simulate Quantities of Interest from Regression Models
This is an all-encompassing suite to facilitate the simulation of so-called quantities of interest by way of a multivariate normal distribution of the regression model's coefficients and variance-covariance matrix.
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1.74 score 11 scripts 162 downloadsuniReg - 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.
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1.73 score 1 dependents 18 scripts 338 downloadsVBLPCM - 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>.
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gsl
1.72 score 2 stars 26 scripts 337 downloadsLinkage - 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.
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1.72 score 52 scripts 259 downloadsadamethods - 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>.
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1.71 score 51 scripts 474 downloads
poisFErobust - Poisson Fixed Effects Robust
Computation of robust standard errors of Poisson fixed effects models, following Wooldridge (1999).
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1.70 score 6 scripts 258 downloads
safuzzy - Stability Analysis with Fuzzy Logic
It integrates 'fuzzy logic' into the analysis of genotype adaptability and stability. By classifying genotypes based on degrees of belonging, the package provides a detailed assessment of their behavior in different environmental groups.
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1.70 score 4 scripts 263 downloads
nomads - Nomadic Pectoral Sandpiper Movement Data
Provides satellite tracking data from nomadic pectoral sandpipers published in Kempenaers and Valcu (2017) <doi:10.1038/nature20813>. The data can also serve as benchmark data for clustering movement tracks.
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1.70 score 2 scripts 262 downloadszoteR - R Interface to 'Zotero' via Better BibTeX
Connects R to 'Zotero' through the 'Better BibTeX' for 'Zotero' connector <https://retorque.re/zotero-better-bibtex/>. Provides functions to insert in-text citations and bibliography entries directly into documents, detect citations already present in R Markdown and Quarto files, and synchronise bibliography files. Includes an 'RStudio addin' for interactive use.
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1.70 score 3 scripts 341 downloadsbirdcolors - Create Palettes from the Colors of the World's Birds
Create attractive palettes based on the colors of the world's birds. Palettes are composed of 2 to 9 colors, with options to expand palettes via interpolation. Compatible with the package 'ggplot2' and base R graphics.
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1.70 score 1 scripts 200 downloadsNMAforest - Forest Plots for Network Meta-Analysis with Proportion for Paths and Studies
Provides customized forest plots for network meta-analysis incorporating direct, indirect, and NMA effects. Includes visualizations of evidence contributions through proportion bars based on the hat matrix and evidence flow decomposition.
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1.70 score 1 stars 1 scripts 224 downloadsrsixel - Encoding and Decoding Sixel Images
Provides a native R implementation for encoding and decoding 'sixel' graphics (<https://vt100.net/docs/vt3xx-gp/chapter14.html>), and a dedicated 'sixel' graphics device that allows plots to be rendered directly within compatible terminal emulators.
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1.70 score 1 scripts 177 downloadsbayeslist - 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 (2026) <doi:10.1017/psrm.2025.10084> for examples and details of estimation.
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onetbbcpp
1.70 score 435 downloadsremode - Recursive Mode Detection for Distributions of Ordinal Data
Provides the function remode() for recursive modality detection in ordinal data. 'remode' is an algorithm specifically designed to estimate the number and location of modes in ordinal data while being robust to large sample sizes.
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1.70 score 1 scripts 217 downloadsADSIHT - Adaptive Double Sparse Iterative Hard Thresholding
Solving high-dimensional double sparse linear regression via an iterative hard thresholding algorithm. Furthermore, the method is extended to jointly estimate multiple graphical models. For more details, please see <https://www.jmlr.org/papers/v25/23-0653.html> and <doi:10.48550/arXiv.2503.18722>.
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cpp
1.70 score 5 scripts 287 downloadsloedata - Data Sets from "Lectures on Econometrics" by Chirok Han
Data sets for Chirok Han (2024, ISBN:979-11-303-1964-3, "Lectures on Econometrics"). Students, teachers, and self-learners will find the data sets essential for replicating the results in the book.
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1.70 score 1 scripts 696 downloadsOEFPIL - 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>.
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1.70 score 1 scripts 382 downloadsscitb - 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>.
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1.70 score 1 stars 4 scripts 338 downloadsPANPRSnext - Building PRS Models Based on Summary Statistics of GWAs
Shrinkage estimator for polygenic risk prediction (PRS) models based on summary statistics of genome-wide association (GWA) studies. Based upon the methods and original 'PANPRS' package as found in: Chen, Chatterjee, Landi, and Shi (2020) <doi:10.1080/01621459.2020.1764849>.
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cppopenmp
1.70 score 1 stars 6 scripts 240 downloadsMLBC - Bias Correction Methods for Models Using Synthetic Data
Implements three bias-correction techniques from Battaglia et al. (2025 <doi:10.48550/arXiv.2402.15585>) to improve inference in regression models with covariates generated by AI or machine learning.
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cpp
1.70 score 7 scripts 236 downloadsPolisheR - 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.
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1.70 score 3 scripts 288 downloadsmaxstablePCA - 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.
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1.70 score 3 scripts 198 downloadsfeatForge - Automated Feature Engineering for Credit Scoring
Automated feature engineering functions tailored for credit scoring. It includes utilities for extracting structured features from timestamps, IP addresses, and email addresses, enabling enhanced predictive modeling for financial risk assessment.
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1.70 score 1 scripts 251 downloadsmongopipe - Write MongoDB Queries with R
Translate R code into MongoDB aggregation pipelines.
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1.70 score 3 scripts 302 downloadscbq - 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.
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onetbbcpp
1.70 score 3 scripts 365 downloadssfhelper - Repair Functions for 'sf' Package Objects
A group of functions that support the 'sf' package, focused primarily on repairing polygons that break when re-projected.
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1.70 score 3 scripts 41 downloadsiclogcondist - 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>).
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cpp
1.70 score 2 scripts 445 downloadsroseRF - 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>.
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1.70 score 2 scripts 198 downloadslogconcens - 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>.
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openblas
1.70 score 7 scripts 387 downloadspermutest - 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>.
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1.70 score 2 scripts 146 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.
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1.70 score 5 scripts 241 downloadscryptotrackr - 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>.
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1.70 score 1 stars 2 scripts 252 downloadsclarkeTest - 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>.
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1.70 score 9 scripts 428 downloadsLDAandLDAS - 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>.
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cpp
1.70 score 2 scripts 291 downloadsBayesFluxR - 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.
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1.70 score 4 scripts 277 downloadsexceldata - 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.
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1.70 score 1 stars 1 scripts 359 downloadsnlopt - 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.
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1.70 score 4 scripts 237 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>.
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1.70 score 1 scripts 298 downloadsblsBandit - 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.
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1.70 score 307 downloadspisaRT - 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/>.
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1.70 score 3 scripts 244 downloadsassist - 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.
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openblasglibc
1.70 score 50 scripts 564 downloadsresponsePatterns - 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.
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1.70 score 1 scripts 214 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>.
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1.70 score 1 stars 1 scripts 344 downloadsrfieldclimate - Client for the 'FieldClimate' API
Provides functionality to interact with the 'FieldClimate' API <https://api.fieldclimate.com/v2/docs/>.
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1.70 score 1 scripts 239 downloadsrheroicons - 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.
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1.70 score 1 scripts 220 downloadssurvout - Excel Conversion of R Surival Analysis Output
Simple and quick method of exporting the most often used survival analysis results to an Excel sheet.
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1.70 score 1 scripts 225 downloadsrdaisi - 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.
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1.70 score 3 scripts 210 downloadsgoogleTagManageR - 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.
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1.70 score 4 scripts 362 downloadsfig - A Config Package with No "Con"
Work with configs with a source precedence. Either create own R6 instance or work with convenient functions at a package level.
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1.70 score 1 scripts 337 downloads
sistmr - A Collection of Utility Function from the Inserm/Inria SISTM Team
Functions common to members of the SISTM team.
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1.70 score 230 downloadsleprechaun - 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.
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1.70 score 4 scripts 320 downloadsKingCountyHouses - 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.
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1.70 score 10 scripts 247 downloadsTensorClustering - 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>.
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fortran
1.70 score 1 scripts 261 downloadsdbglm - 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>.
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1.70 score 5 scripts 327 downloadsocd - 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>.
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1.70 score 10 scripts 306 downloadsSphereOptimize - 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>.
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1.70 score 179 downloadslmviz - 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.
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1.70 score 7 scripts 292 downloadsradlibs - 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.
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1.70 score 2 scripts 252 downloadsepxToR - Import 'Epidata' XML Files '.epx'
Import data from 'Epidata' XML files '.epx' and convert it to R data structures.
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1.70 score 3 scripts 269 downloadsnbconvertR - 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.
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1.70 score 8 scripts 218 downloadsmSTEM - 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>.
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1.70 score 210 downloadshans - 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).
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cpp
1.70 score 2 scripts 278 downloadsrapidxmlr - 'Rapidxml' C++ Header Files
Provides XML parsing capability through the 'Rapidxml' 'C++' header-only library.
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1.70 score 180 downloadskernhaz - 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.
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1.70 score 1 stars 4 scripts 196 downloadsIMmailgun - Send Emails using 'Mailgun'
Send emails using the 'mailgun' api. To use this package you will need an account from <https://www.mailgun.com> .
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1.70 score 5 scripts 260 downloadsXKCDdata - Get XKCD Comic Data
Download data from individual XKCD comics, written by Randall Munroe <https://xkcd.com/>.
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1.70 score 7 scripts 261 downloadsSunclarco - Survival Analysis using Copulas
Survival analysis for unbalanced clusters using Archimedean copulas (Prenen et al. (2016) <DOI:10.1111/rssb.12174>).
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1.70 score 1 scripts 176 downloadsSanFranBeachWater - 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>.
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1.70 score 2 scripts 250 downloadsCUMP - Analyze Multivariate Phenotypes by Combining Univariate Results
Combining Univariate Association Test Results of Multiple Phenotypes for Detecting Pleiotropy.
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1.70 score 1 scripts 281 downloadsfavnums - 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).
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1.70 score 1 scripts 271 downloadsspuRs - 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.
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1.69 score 1 stars 49 scripts 582 downloadsastroFns - Astronomy: Time and Position Functions, Misc. Utilities
Miscellaneous astronomy functions, utilities, and data.
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1.69 score 49 scripts 385 downloadsCOINT - Unit Root Tests with Structural Breaks and Fully-Modified Estimators
Procedures include Phillips (1995) FMVAR <doi:10.2307/2171721>, Kitamura and Phillips (1997) FMGMM <doi:10.1016/S0304-4076(97)00004-3>, Park (1992) CCR <doi:10.2307/2951679>, and so on. Tests with 1 or 2 structural breaks include Gregory and Hansen (1996) <doi:10.1016/0304-4076(69)41685-7>, Zivot and Andrews (1992) <doi:10.2307/1391541>, and Kurozumi (2002) <doi:10.1016/S0304-4076(01)00106-3>.
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1.68 score 1 stars 16 scripts 404 downloadsTushare - 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.
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1.66 score 46 scripts 423 downloadsCalibratR - 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.
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1.66 score 2 stars 23 scripts 469 downloadsflexCWM - 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>.
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1.65 score 1 dependents 15 scripts 448 downloadsglobalOptTests - 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
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1.65 score 1 stars 1 dependents 15 scripts 317 downloadsBurStFin - Burns Statistics Financial
A suite of functions for finance, including the estimation of variance matrices via a statistical factor model or Ledoit-Wolf shrinkage.
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1.64 score 2 stars 22 scripts 418 downloadsPermAlgo - 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.
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1.63 score 43 scripts 374 downloadsbdpv - 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.
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1.62 score 21 scripts 261 downloadsSteinIV - 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>.
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1.62 score 2 stars 21 scripts 506 downloadsvartest - Tests for Variance Homogeneity
Performs 18 omnibus tests yielding a total of 28 distinct methodological variations for testing the composite hypothesis of variance homogeneity.
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1.60 score 7 scripts 374 downloadsregressoR - 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.
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1.60 score 2 stars 497 downloadsPOCRE - 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.
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1.60 score 10 scripts 256 downloadswmwpow - 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>.
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1.60 score 9 scripts 240 downloadsBNPTSclust - A Bayesian Nonparametric Algorithm for Time Series Clustering
Performs the algorithm for time series clustering described in Nieto-Barajas and Contreras-Cristan (2014).
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1.60 score 4 stars 10 scripts 381 downloadsZRA - Dynamic Plots for Time Series Forecasting
Combines a forecast of a time series, using the function forecast(), with the dynamic plots from dygraphs.
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1.60 score 4 scripts 309 downloadscenGAM - 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>.
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1.59 score 1 dependents 13 scripts 602 downloadsCreditRisk - 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.
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1.59 score 3 stars 13 scripts 262 downloadsljr - Logistic Joinpoint Regression
Fits and tests logistic joinpoint models.
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openblas
1.59 score 1 stars 13 scripts 290 downloadsmvnTest - 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.
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1.59 score 1 stars 39 scripts 597 downloadsInspectChangepoint - 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.
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1.57 score 1 stars 37 scripts 425 downloadscomato - 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).
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1.57 score 1 stars 37 scripts 320 downloadsIPEC - 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.
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1.56 score 12 scripts 261 downloadssidier - Substitution and Indel Distances to Infer Evolutionary Relationships
Evolutionary reconstruction based on substitutions and insertion-deletion (indels) analyses in a distance-based framework as described in Muñoz-Pajares (2013) <doi:10.1111/2041-210X.12118>.
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1.56 score 36 scripts 340 downloadsflipscores - 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>.
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1.56 score 1 dependents 12 scripts 348 downloadsFAwR - Functions and Datasets for "Forest Analytics with R"
Provides functions and datasets from the book "Forest Analytics with R".
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1.53 score 2 stars 17 scripts 372 downloadsoaPlots - OpenAnalytics Plots Package
Offers a suite of functions for enhancing R plots.
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1.53 score 34 scripts 251 downloadsradar - 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
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1.53 score 1 stars 34 scripts 198 downloadsOBsMD - 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>.
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1.52 score 33 scripts 301 downloadsNeighboot - 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.
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1.52 score 33 scripts 259 downloadsNetCluster - Clustering for networks
Facilitates network clustering and evaluation of cluster configurations.
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1.48 score 2 stars 15 scripts 187 downloadsclogitL1 - 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.
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cpp
1.48 score 1 stars 1 dependents 397 downloadsgSeg - Graph-Based Change-Point Detection (g-Segmentation)
Uses similarity graphs to estimate change-points and their p-values. The default data-level interface constructs a k-MST with k=floor(sqrt(N)) and reports the max-type scan. The generalized, original, and weighted scans remain available explicitly.
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1.48 score 1 stars 30 scripts 531 downloadsLogicForest - Logic Forest
Logic Forest is an ensemble machine learning method that identifies important and interpretable combinations of binary predictors using logic regression trees to model complex relationships with an outcome. Wolf, B.J., Slate, E.H., Hill, E.G. (2010) <doi:10.1093/bioinformatics/btq354>.
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1.48 score 1 stars 371 downloadsdbrobust - Robust Distance-Based Visualization and Analysis of Mixed-Type Data
Robust distance-based methods applied to matrices and data frames, producing distance matrices that can be used as input for various visualization techniques such as graphs, heatmaps, or multidimensional scaling configurations. See Boj and Grané (2024) <doi:10.1016/j.seps.2024.101992>, Boj et al. (2026) <doi:10.1007/s10260-026-00860-1>, and Grané et al. (2026) <doi:10.1007/s10182-026-00565-6>.
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openblascpp
1.48 score 5 scripts 282 downloadsDimodal - Spacing Tests for Multi-Modality
Tests for modality of data using its spacing. The main approach evaluates features (peaks, flats) using a combination of parametric models and non-parametric tests, either after smoothing the spacing by a low-pass filter or by looking over larger intervals.
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1.48 score 306 downloadsCICI - 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>.
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1.48 score 1 stars 2 scripts 414 downloadstimsac - 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>.
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glibc
1.48 score 1 stars 1 dependents 807 downloadsfoldedt - The Folded t Family of Distributions
Maximum likelihood estimation of the folded t and related distributions. The reference paper is: Psarakis and Panaretos (1990). "The folded t distribution". Communications in Statistics--Theory and Methods, 19(7): 2717--2734. <doi:10.1080/03610929008830342>.
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1.48 score 1 dependents 419 downloadspheno - 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.
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1.48 score 1 stars 1 dependents 395 downloadsoceanmap - A Plotting Toolbox for 2D Oceanographic Data
Plotting toolbox for 2D oceanographic data (satellite data, sea surface temperature, chlorophyll, ocean fronts & bathymetry). Recognized classes and formats include netcdf, Raster, '.nc' and '.gz' files.
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1.48 score 1 stars 1 dependents 429 downloadsgor - 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 degree of Data Engineering in Industrial Processes.
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1.48 score 1 dependents 7 scripts 333 downloadsbigBits - 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.
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1.48 score 1 dependents 1 scripts 332 downloadsSMPracticals - 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>.
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1.48 score 1 dependents 559 downloadsTableMonster - Table Monster
Provides a user friendly interface to generation of booktab style tables using 'xtable'.
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1.48 score 1 dependents 380 downloadsdixon - 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.
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1.48 score 1 dependents 427 downloadsecespa - 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>.
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1.48 score 1 dependents 508 downloadstgram - Compute and Plot Tracheidograms
Functions to compute and plot tracheidograms, as in De Soto et al. (2011) <doi:10.1139/x11-045>.
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1.48 score 1 dependents 4 scripts 241 downloadsreadmoRe - 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.
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1.48 score 1 dependents 280 downloadsnpiv - Nonparametric Instrumental Variables Estimation and Inference
Implements methods introduced in Chen, Christensen, and Kankanala (2024) <doi:10.1093/restud/rdae025> for estimating and constructing uniform confidence bands for nonparametric structural functions using instrumental variables, including data-driven choice of tuning parameters. All methods in this package apply to nonparametric regression as a special case.
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1.48 score 1 dependents 537 downloadsCCd - 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>.
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1.48 score 1 dependents 4 scripts 330 downloadsHTMLUtils - Facilitates Automated HTML Report Creation
Facilitates automated HTML report creation, in particular framed HTML pages and dynamically sortable tables.
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1.48 score 1 dependents 476 downloadsRBE3 - 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.
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1.48 score 1 dependents 232 downloadsriskSimul - 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.
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1.48 score 3 stars 2 scripts 368 downloadsgo2bigq - Convert Large Numbers to Bigq Format
This function converts mfpr, numeric, or character strings representing numbers to bigq format without loss of precision.
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1.48 score 1 dependents 327 downloadsrelevent - Relational Event Models
Tools to fit and simulate realizations from relational event models.
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1.48 score 1 stars 1 dependents 449 downloadsTSSVM - 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>.
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1.48 score 1 dependents 269 downloadsdixonTest - 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.
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1.48 score 1 dependents 436 downloadsnilde - 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.
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1.48 score 1 dependents 10 scripts 283 downloadsRockFab - 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.
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1.48 score 1 dependents 305 downloadsProbYX - 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.
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1.48 score 1 dependents 255 downloadseegkitdata - 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.
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1.48 score 1 dependents 8 scripts 489 downloadsbigtabulate - 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.
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cpp
1.48 score 1 dependents 161 downloadsdagwood - 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>.
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1.48 score 1 dependents 309 downloadsmatpow - 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.
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1.48 score 1 dependents 7 scripts 289 downloadsMultiwayRegression - 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.
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1.48 score 1 dependents 263 downloadsSPSL - 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.
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1.48 score 1 dependents 244 downloadspowdist - Power and Reversal Power Distributions
Density, distribution function, quantile function and random generation for the family of power and reversal power distributions.
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1.48 score 1 dependents 247 downloadsthregI - 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.
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1.48 score 1 dependents 8 scripts 296 downloadsMaxSkew - 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.
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1.48 score 1 dependents 211 downloadsRDStreeboot - 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.
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1.48 score 1 dependents 217 downloadsRSKC - Robust Sparse K-Means
This RSKC package contains a function RSKC which runs the robust sparse K-means clustering algorithm.
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1.48 score 1 dependents 372 downloadsoaColors - OpenAnalytics Colors Package
Provides carefully chosen color palettes as used a.o. at OpenAnalytics <http://www.openanalytics.eu>.
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1.48 score 1 dependents 236 downloadsLCFdata - 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.
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1.48 score 1 dependents 434 downloadsfactorplot - 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>.
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1.46 score 29 scripts 399 downloadsfUnitRoots - Rmetrics - Modelling Trends and Unit Roots
Provides four addons for analyzing trends and unit roots in financial time series: (i) functions for the density and probability of the augmented Dickey-Fuller Test, (ii) functions for the density and probability of MacKinnon's unit root test statistics, (iii) reimplementations for the ADF and MacKinnon Test, and (iv) an 'urca' Unit Root Test Interface for Pfaff's unit root test suite.
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1.45 score 1 stars 2 scripts 1.4k downloadsassocInd - 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.
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1.45 score 28 scripts 278 downloadstriangulation - 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.
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1.43 score 27 scripts 145 downloadsbeyondWhittle - 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 (2025) <doi:10.1080/01621459.2025.2594191>. It was supported by DFG grants KI 1443/3-1 and KI 1443/3-2.
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openblascpp
1.41 score 2 stars 13 scripts 575 downloadsHydroMe - Estimating Water Retention and Infiltration Model Parameters using Experimental Data
Estimates the parameters of infiltration and water retention models using the curve-fitting methods as shown in Omuto and Gumbe (2009) <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.
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1.41 score 1 stars 26 scripts 280 downloadsRchivalTag - Analyzing and Interactive Visualization of Archival Tagging Data
A set of functions to generate, access and analyze standard data products from archival tagging data.
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1.41 score 26 scripts 290 downloadsGMMBoost - Likelihood-Based Boosting for Generalized Mixed Models
Likelihood-based boosting approaches for generalized mixed models are provided.
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1.41 score 13 scripts 379 downloadsMultiplierDEA - 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.
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1.41 score 1 stars 26 scripts 244 downloadstropAlgebra - 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>.
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1.41 score 2 stars 13 scripts 208 downloadsGMDH - 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.
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1.41 score 2 stars 13 scripts 325 downloadsmodMax - 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.
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1.41 score 2 stars 13 scripts 217 downloadsivDiag - 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.
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1.40 score 25 scripts 459 downloadsextremogram - 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.
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1.40 score 25 scripts 330 downloadswoe - Computes Weight of Evidence and Information Values
Shows the relationship between an independent and dependent variable through Weight of Evidence and Information Value.
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1.40 score 1 stars 25 scripts 187 downloadsseqmon - 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.
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1.38 score 24 scripts 293 downloadsEvCombR - Evidence Combination in R
Combine pieces of evidence in the form of uncertainty representations.
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1.38 score 24 scripts 325 downloadsphenmod - 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>.
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1.38 score 24 scripts 249 downloadsSQL - Executes 'SQL' Statements
Runs 'SQL' statements on in-memory data frames within a temporary in-memory 'duckdb' data base.
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1.36 score 23 scripts 323 downloadsCNLTtsa - 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>.
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1.36 score 23 scripts 380 downloadsmiLineage - 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).
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1.36 score 23 scripts 254 downloadsalphaOutlier - 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.
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1.34 score 22 scripts 553 downloadsRobustAFT - 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.
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fortranglibc
1.32 score 21 scripts 426 downloadsoptimStrat - Choosing the Sample Strategy
Intended to assist in the choice of the sampling strategy to implement in a survey.
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1.32 score 21 scripts 276 downloadsseqtest - 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.
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1.32 score 21 scripts 149 downloadsCompositionalzerocens - Modelling Zero Values in Compositional Data Using a Censored Model
Modelling structural zeros in compositional data assuming a latent Gaussian model, where MLE is performed via the EM algorithm. The relevant paper is Tsagris and Alharbi (2026) <doi:10.48550/arXiv.2208.13073>.
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1.30 score 237 downloadsmccca - Visualizing Class Specific Heterogeneous Tendencies in Categorical Data
Provides functions for 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 are described in Mariko Takagishi and Michel van de Velden (2022)<doi:10.1080/10618600.2022.2035737>.
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openblascppopenmp
1.30 score 358 downloadscatekappa - Design and Analysis of Consistency Tests Based on Kappa Statistic
Provides a 'Shiny' application and supporting functions for the design and analysis of consistency tests based on Kappa statistic with categorical responses. Wraps 'irr' and 'kappaSize' packages.
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1.30 score 276 downloadsrapidcodeR - Optimized Data Analysis System for AI-Based Text Processing
Extracts machine-readable variables from natural language text using AI APIs. Optimized for speed and cost efficiency through parallel processing and direct CSV-formatted responses from language models. Supports multiple AI providers with robust error handling and automatic retry mechanisms for failed extractions.
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1.30 score 1 stars 3 scripts 341 downloadsccLRforR - Case-Control Likelihood Ratio (ccLR)
Implementation of case-control data analysis using likelihood ratio approaches and logistic regression for the classification of variants of uncertain significance (VUS) in breast, ovarian, or custom cancer susceptibility genes.
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cpp
1.30 score 380 downloadscols - 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>.
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1.30 score 9 scripts 450 downloadsCoImp - Parametric and Nonparametric Copula-Based Imputation Methods
Copula-based imputation methods: parametric and nonparametric algorithms for missing multivariate data through conditional copulas.
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1.30 score 1 stars 8 scripts 506 downloadspsgp - 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>).
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openblascpp
1.30 score 462 downloadscml - Conditional Manifold Learning
Finds a low-dimensional embedding of high-dimensional data, conditioning on available manifold information.
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1.30 score 5 scripts 317 downloadsRwbo - Run the 'Open-WBO' MaxSAT Solver
Provides a wrapper for running the bundled 'Open-WBO' Maximum Satisfiability (MaxSAT) solver (<https://github.com/sat-group/open-wbo>). Users can pass command-line arguments to the solver and capture its output as a character string or file.
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1.30 score 1 scripts 174 downloadsmultipleNCC - 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>.
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1.30 score 9 scripts 382 downloadsMBSP - 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>.
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1.30 score 388 downloadsecipex - 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.
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1.30 score 1 stars 1 scripts 282 downloadsCoClust - A Copula-Based Clustering Algorithm
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. (2019). "Clustering dependent observations with copula functions". Statistical Papers, 60, p.35-51. <doi:10.1007/s00362-016-0822-3>.
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1.30 score 2 stars 10 scripts 339 downloadsRsSimulx - 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.
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1.30 score 2 stars 6 scripts 320 downloadswavScalogram - 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>).
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1.30 score 20 scripts 375 downloadsEnvNicheR - 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.
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1.30 score 3 scripts 251 downloadsOptionPricing - 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.
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1.30 score 2 stars 5 scripts 390 downloadslillies - 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>.
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1.30 score 2 stars 2 scripts 314 downloadsARIMAANN - 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>.
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1.30 score 2 stars 1 scripts 368 downloadsGreyModel - 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>.
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1.30 score 2 stars 4 scripts 244 downloadsnlsmsn - 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>.
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1.30 score 2 stars 3 scripts 232 downloadsspass - Study Planning and Adaptation of Sample Size
Sample size estimation and blinded sample size reestimation in Adaptive Study Design.
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cpp
1.30 score 307 downloadsFHDI - 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>.
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cpp
1.30 score 2 stars 4 scripts 345 downloadsnsROC - 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.
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1.30 score 1 stars 287 downloadsPBNPA - 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.
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1.30 score 4 scripts 233 downloadsSegCorr - Detecting Correlated Genomic Regions
Performs correlation matrix segmentation and applies a test procedure to detect highly correlated regions in gene expression.
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1.30 score 1 stars 7 scripts 266 downloadsConSpline - 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.
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1.30 score 2 stars 5 scripts 333 downloadsGroupTest - 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.
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1.30 score 7 scripts 159 downloadsOptHedging - 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).
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1.30 score 2 stars 3 scripts 332 downloadsbild - 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. (2012) <DOI: 10.18637/jss.v046.i09>.
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glibc
1.28 score 1 stars 19 scripts 365 downloadsglmc - 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.
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1.28 score 1 stars 19 scripts 368 downloadsWCE - 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.
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1.28 score 1 stars 19 scripts 275 downloadsgmDatabase - Accessing a Geometallurgical Database with R
A template for a geometallurgical database and a fast and easy interface for accessing it.
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1.28 score 19 scripts 284 downloadsbqtl - Bayesian QTL Mapping Toolkit
QTL mapping toolkit for inbred crosses and recombinant inbred lines. Includes maximum likelihood and Bayesian tools.
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openblas
1.26 score 18 scripts 655 downloadsfastM - Fast Computation of Multivariate M-Estimators
Implements the new algorithm for fast computation of M-scatter matrices using a partial Newton-Raphson procedure for several estimators. The algorithm is described in Duembgen, Nordhausen and Schuhmacher (2016) <doi:10.1016/j.jmva.2015.11.009>.
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openblascpp
1.26 score 18 scripts 330 downloadsperms - Fast Permutation Computation
Implements the algorithm of Christensen (2024) <doi:10.1214/22-BA1353> for estimating marginal likelihoods via permutation counting.
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1.26 score 18 scripts 228 downloadsNostalgiR - 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.
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1.26 score 1 stars 18 scripts 282 downloadsCliftLRD - 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>.
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1.23 score 17 scripts 297 downloadsreadMLData - 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.
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1.23 score 1 stars 17 scripts 280 downloadsNPHazardRate - Nonparametric Hazard Rate Estimation
Provides functions and examples for histogram, kernel (classical, variable bandwidth and transformations based, see e.g. Bagkavos (2008), <doi:10.1080/10485250802440184>, discrete and semiparametric hazard rate estimators.
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1.20 score 16 scripts 195 downloadsLS2Wstat - 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>.
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1.20 score 1 stars 16 scripts 304 downloadsProbitSpatial - Probit with Spatial Dependence, SAR, SEM and SARAR Models
Fast estimation of binomial spatial probit regression models with spatial autocorrelation for big datasets.
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cpp
1.20 score 16 scripts 321 downloadsserieslcb - 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.
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1.20 score 16 scripts 249 downloadsoptR - 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.
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1.20 score 1 stars 16 scripts 255 downloadsnoaa - Accessing NOAA Climate Data Online
Fetch data from the National Oceanic and Atmospheric Administration Climate Data Online (NOAA CDO) <https://www.ncdc.noaa.gov/cdo-web/webservices/v2> API including daily, monthly, and yearly climate summaries, radar data, climatological averages, precipitation data, annual summaries, storm events, and agricultural meteorology.
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1.18 score 15 scripts 205 downloadsOPDOE - 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).
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1.18 score 15 scripts 307 downloadsStrainRanking - 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.
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1.18 score 15 scripts 195 downloadsMixedPoisson - Mixed Poisson Models
The estimation of the parameters in mixed Poisson models.
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1.18 score 15 scripts 214 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>.
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1.15 score 14 scripts 295 downloadscarSurv - 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>.
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cpp
1.14 score 1.4k downloadsSeleMix - Selective Editing via Mixture Models
Detection of outliers and influential errors using a latent variable model.
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1.11 score 13 scripts 393 downloadscosmoFns - 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.
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1.11 score 13 scripts 320 downloadsSCBmeanfd - 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.
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1.11 score 1 stars 13 scripts 373 downloadsEqualden.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.
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1.11 score 13 scripts 294 downloadsSoftClustering - 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.
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1.11 score 13 scripts 203 downloadsmycobacrvR - 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.
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1.11 score 1 stars 13 scripts 226 downloadsIntegratedJM - 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.
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1.11 score 13 scripts 306 downloadsBurStMisc - Burns Statistics Miscellaneous
Script search, corner, genetic optimization, permutation tests, write expect test.
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1.11 score 13 scripts 372 downloadskriens - Continuation Passing Style Development
Provides basic functions for Continuation-Passing Style development.
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1.11 score 13 scripts 226 downloadsqrjoint - Joint Estimation in Linear Quantile Regression
Joint estimation of quantile specific intercept and slope parameters in a linear regression setting.
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openblascpp
1.08 score 12 scripts 445 downloadsVARtests - Bootstrap Tests for Cointegration and Autocorrelation in VARs
Implements wild bootstrap tests for autocorrelation in Vector Autoregressive (VAR) models based on Ahlgren and Catani (2016) <doi:10.1007/s00362-016-0744-0>, a combined Lagrange Multiplier (LM) test for Autoregressive Conditional Heteroskedasticity (ARCH) in VAR models from Catani and Ahlgren (2016) <doi:10.1016/j.ecosta.2016.10.006>, and bootstrap-based methods for determining the cointegration rank from Cavaliere, Rahbek, and Taylor (2012) <doi:10.3982/ECTA9099> and Cavaliere, Rahbek, and Taylor (2014) <doi:10.1080/07474938.2013.825175>.
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openblascppopenmp
1.08 score 1 stars 12 scripts 248 downloadsmpmcorrelogram - Multivariate Partial Mantel Correlogram
Functions to compute and plot multivariate (partial) Mantel correlograms.
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1.08 score 12 scripts 228 downloadsbetategarch - 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).
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1.08 score 1 stars 12 scripts 493 downloadsrsides - SIDES-Based Subgroup Search Algorithms
R implementation of SIDES-based subgroup search algorithms (Lipkovich et al. (2017) <doi:10.1002/sim.7064>).
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cpp
1.08 score 12 scripts 241 downloadseasyreg - Easy Regression
Performs analysis of regression in simple designs with quantitative treatments, including mixed models and non linear models.
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1.08 score 12 scripts 302 downloadsIndepTest - 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.
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1.08 score 1 stars 12 scripts 301 downloadslongROC - 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>.
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1.08 score 12 scripts 241 downloadsdawai - 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.
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1.04 score 11 scripts 390 downloadsICSShiny - ICS via a Shiny Application
Performs Invariant Coordinate Selection (ICS) (Tyler, Critchley, Duembgen and Oja (2009) <doi:10.1111/j.1467-9868.2009.00706.x>) and especially ICS for multivariate outlier detection with application to quality control (Archimbaud, Nordhausen, Ruiz-Gazen (2018) <doi:10.1016/j.csda.2018.06.011>) using a shiny app.
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1.04 score 11 scripts 297 downloadsGameTheory - Cooperative Game Theory
Implementation of a common set of punctual solutions for Cooperative Game Theory.
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1.04 score 11 scripts 341 downloadsFRCC - 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>.
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1.04 score 11 scripts 312 downloadspogit - 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.
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1.04 score 11 scripts 286 downloadsssmrob - 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>.
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1.04 score 11 scripts 570 downloadswsbackfit - 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>.
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fortran
1.04 score 11 scripts 220 downloadsdadjoke - Displays a Dad Joke
Displays a terrible joke, the kind only dads crack.
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1.04 score 11 scripts 309 downloadsdundermifflin - 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.
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1.04 score 11 scripts 274 downloadsNNMIS - 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.
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1.04 score 1 stars 11 scripts 250 downloadspopulationPDXdesign - 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()'.
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1.04 score 11 scripts 207 downloadsepr - Easy Polynomial Regression
Performs analysis of polynomial regression in simple designs with quantitative treatments.
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1.04 score 11 scripts 320 downloadspAnalysis - 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.
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1.04 score 11 scripts 199 downloadsJPEN - Covariance and Inverse Covariance Matrix Estimation Using Joint Penalty
A Joint PENalty Estimation of Covariance and Inverse Covariance Matrices.
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1.04 score 11 scripts 271 downloadslinearModel - Linear Model Functions
Functions to access and test results from a linear model.
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1.00 score 7 scripts 290 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, Tijana Levajkovic and Michael Messer (2023) <doi:10.1214/22-EJS2101>.
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1.00 score 1 scripts 138 downloadscauchyreg - Cauchy Regression
Cauchy regression modelling and LASSO to perform variable selection are included in this package. Cross-validation is performed to choose the optimal value of the lambda parameter. LASSO is based on the IRLS algorithm. A relevant paper is <doi:10.1109/ICIST.2014.6920341>.
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1.00 score 124 downloadsipr - 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.
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1.00 score 333 downloadsTPEA - 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.
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1.00 score 1 stars 3 scripts 271 downloadsKernelICA - Kernel Independent Component Analysis
The kernel independent component analysis (kernel ICA) method introduced by Bach and Jordan (2002) <doi:10.1162/153244303768966085>. A separate function for the incomplete Cholesky decomposition used in kernel ICA is also provided.
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cppopenmp
1.00 score 1 stars 2 scripts 343 downloadsMVLs - Model Validation Levels
Calculates Model Validation Levels from user provided model data, referent data, and scope files as described by Stafford, Provost, & Jones (2025) <doi:10.1080/17477778.2025.2536096>. Data files must be structured according to one of the accepted Excel templates as shown by Jones, Provost, Stafford, & Young (2026) <https://www.afit.edu/docs/MVL%20User%20Guide%20v4.pdf>.
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1.00 score 1 scripts 243 downloadsiGasso - Statistical Tests and Utilities for Genetic Association
A collection of statistical tests for genetic association studies and summary data based Mendelian randomization.
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1.00 score 6 scripts 328 downloadskernda - Kernel Discriminant Analysis
Functions to perform discriminant analysis using kernel density estimation. For the case of binary classification the package relies on the Nadaraya-Watson estimator. References: Wand M.P. and Jones M.C. (1995). "Kernel smoothing". CRC Press. <ISBN: 0412552701>.
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cpp
1.00 score 198 downloadsrxode2mrgsolvebridge - Convert Models Between 'rxode2' and 'mrgsolve'
Provides an intermediate representation and file-oriented helpers for converting pharmacometric model code between 'rxode2' and 'mrgsolve'. The conversion uses a package-specific intermediate representation described by Hammami F (2026) "rxode2-mrgsolve-bridge" <https://gitlab.com/fiha1/rxode2-mrgsolve-bridge>.
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1.00 score 1 scripts 315 downloadsroundr - Incorporate Rounding for Discrete Data Modeling
Provides density, distribution and random number generator functions to account for discretization in data where recorded values mask the underlying measurement process. Details on methodology are described in Glazer et al. (2026) <doi:10.1080/00031305.2025.2604812>.
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1.00 score 7 scripts 283 downloadsFUNTA - Functional Tangential Angle Pseudo-Depth
Contains functions to compute 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.
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1.00 score 4 scripts 344 downloadsoceanic - 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>.
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1.00 score 404 downloadssymMCD - Symmetrized MCD
Provides implementations of origin-based and symmetrized minimum covariance determinant (MCD) estimators, together with supporting utility functions.
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openblascpp
1.00 score 178 downloadskgen - A Tool for Calculating Stoichiometric Equilibrium Constants (Ks) for Seawater
A unified software package simultaneously implemented in 'Python', 'R', and 'Matlab' providing a uniform and internally-consistent way of calculating stoichiometric equilibrium constants in modern and palaeo seawater as a function of temperature, salinity, pressure and the concentration of magnesium, calcium, sulphate, and fluorine.
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1.00 score 8 scripts 389 downloadsmvhtests - 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.
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1.00 score 1 scripts 344 downloadsCronbach - 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.
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1.00 score 1 scripts 453 downloadscatdap - Categorical Data Analysis Program Package
Categorical data analysis by AIC. The methodology is described in Sakamoto (1992) <ISBN 978-0-7923-1429-5>.
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1.00 score 4 scripts 451 downloadsfertilmodel - 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.
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1.00 score 1 scripts 370 downloadsoutrigger - Outrigger Regression
Performs outrigger local polynomial regression/ distributional adaptation, using a score-matching spline estimator of the conditional score function. Details of the method can be found in Young, Shah and Samworth (2026) <doi:10.48550/arXiv.2603.11282>.
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cpp
1.00 score 309 downloadsGOFclustering - Goodness-of-Fit Testing for Model-Based Clustering
Performs goodness-of-fit tests for model-based clustering based on the methodology developed in <doi:10.48550/arXiv.2511.04206>. It implements a test statistic derived from empirical likelihood to verify the distribution of clusters in multivariate Gaussian mixtures and other latent class models.
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openblascpp
1.00 score 217 downloadsergmclust - Exponential-Family Random Graph Models for Network Clustering
Implements clustering and estimates parameters in Exponential-Family Random Graph Models for static undirected and directed networks, developed in Vu et al. (2013) <https://projecteuclid.org/euclid.aoas/1372338477>.
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cpp
1.00 score 381 downloadsmFDP - Control of the Median of the FDP
Methods for controlling the median of the false discovery proportion (mFDP). Depending on the method, simultaneous or non-simultaneous inference is provided. The methods take a vector of p-values or test statistics as input.
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1.00 score 227 downloadsGFE - Gross Flows Estimation under Complex Surveys
The philosophy in the package is described in Stasny (1988) <doi:10.2307/1391558> and Guti?rrez, 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.
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1.00 score 6 scripts 359 downloadsbdribs - 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).
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jagscpp
1.00 score 3 scripts 295 downloadsPartialTL - Partial Transfer Learning for Causal Estimation
Implements partial transfer learning (PTL) for causal effect estimation using source and target data, with bootstrap-based source detection. Provides data generating processes and nuisance functions for simulation.
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1.00 score 232 downloadsWOAkMedoids - 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>.
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cpp
1.00 score 229 downloadspwrRasch - 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.
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1.00 score 1 stars 9 scripts 303 downloadsiClick - A Button-Based GUI for Financial and Economic Data Analysis
A GUI designed to support the analysis of financial-economic time series data.
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1.00 score 6 scripts 328 downloadsMADtests - Hypothesis Tests and Confidence Intervals for Median Absolute Deviations
Conducts one- and two-sample hypothesis tests for median absolute deviations (mads) for robust inference of dispersion. Comparisons between two samples uses the ratio of mads. Confidence intervals are also computed.
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1.00 score 152 downloadsgek - Gradient-Enhanced Kriging
Gradient-Enhanced Kriging as an emulator for computer experiments based on Maximum-Likelihood estimation.
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1.00 score 221 downloadsNPStability - Rank-Based Stability Index (RSI) for Genotype by Environment Studies
Provides functions to compute the Rank-Based Stability Index (RSI) for genotype by environment interaction data, along with a genotype plus genotype-by-environment (GGE) style biplot visualization of stability.
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1.00 score 320 downloadsCoxLikelihood - Robust Likelihood Ratio Test and Confidence Intervals for the Cox Model
Calculate the likelihood ratio test p-value and likelihood confidence intervals for misspecified Cox models, as described in Shao and Guo (2025) <doi:10.48550/arXiv.2508.11851>.
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1.00 score 226 downloadsmatman - 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.
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1.00 score 294 downloadssyllogi - 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.
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1.00 score 1 scripts 352 downloadsirls - Generalised Linear Models via Iteratively Reweighted Least Squares
Generalised linear models via the iteratively reweighted least squares algorithm. The functions perform logistic, Poisson and Gamma regression (ISBN:9780412317606), either for a single model or many regression models in a column-wise fashion.
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cppopenmp
1.00 score 214 downloadsapor - Assessment of Predictions for an Ordinal Response
Produces several metrics to assess the prediction of ordinal categories based on the estimated probability distribution for each unit of analysis produced by any model returning a matrix with these probabilities.
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1.00 score 202 downloadsTSMCP - Fast Two Stage Multiple Change Point Detection
A novel and fast two stage method for simultaneous multiple change point detection and variable selection for piecewise stationary autoregressive (PSAR) processes and linear regression model. It also simultaneously performs variable selection for each autoregressive model and hence the order selection.
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1.00 score 3 scripts 216 downloadsSEMsensitivity - SEM Sensitivity Analysis
Performs sensitivity analysis for Structural Equation Modeling (SEM). It determines which sample points need to be removed for the sign of a specific path in the SEM model to change, thus assessing the robustness of the model. Methodological manuscript in preparation.
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1.00 score 202 downloadsMLSP - Machine Learning Models for Soil Properties
Creates a spectroscopy guideline with a highly accurate prediction model for soil properties using machine learning or deep learning algorithms such as LASSO, Random Forest, Cubist, etc., and decide which algorithm generates the best model for different soil types.
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1.00 score 225 downloadsRato - Resilience Analysis Toolkit (RATO)
Collection of tools for the analysis of the resilience of dynamic networks. Created as a classroom project.
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1.00 score 219 downloadsEntropicStatistics - Functions Based on Entropic Statistics
Methods for data analysis from an entropic perspective. These methods are nonparametric and perform well on non-ordinal data. Currently includes 'HeatMap()' for visualizing distributional characteristics among multiple populations (groups).
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1.00 score 1 scripts 275 downloadssbde - 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>.
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1.00 score 1 scripts 239 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 (2023) <doi:10.4171/RLM/1026>. 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.
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openblascppopenmp
1.00 score 1 scripts 298 downloadsrFDP - Resampling-Based False Discovery Proportion Control
Methods for Resampling-based False Discovery Proportion control. A function is provided that provides simultaneous, multi-resolution False Discovery Exceedance (FDX) control as described in Hemerik (2025) <doi:10.48550/arXiv.2509.02376>.
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1.00 score 3 scripts 234 downloadsMHDA - Massive Hierarchically Data Analysis
Three main functions about analyzing massive data (missing observations are allowed) considered from multiple layers of categories are demonstrated. Flexible and diverse applications of the function parameters make the data analyses powerful.
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1.00 score 265 downloadsMPDiR - Data Sets and Scripts for Modeling Psychophysical Data in R
Data sets and scripts for Modeling Psychophysical Data in R (Springer).
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1.00 score 424 downloadsLoTTA - Bayesian Inference in Regression Discontinuity Designs
Implementation of the LoTTA (Local Trimmed Taylor Approximation) model described in "Bayesian Regression Discontinuity Design with Unknown Cutoff" by Kowalska, van de Wiel, van der Pas (2024) <doi:10.48550/arXiv.2406.11585>.
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jagscpp
1.00 score 351 downloadsgaussDiff - 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.
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1.00 score 6 scripts 256 downloadsgentransmuted - Estimation and Other Tools for Generalized Transmuted Models
Provide estimation and data generation tools for a generalization of the transmuted distributions discussed in Shaw and Buckley (2007). See <doi:10.48550/arXiv.0901.0434> for more information.
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1.00 score 361 downloadsiForecast - Machine Learning Time Series Forecasting
Compute onestep and multistep time series forecasts for machine learning models.
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1.00 score 1 stars 5 scripts 342 downloadsMCARtest - 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.
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cpp
1.00 score 3 scripts 381 downloadsggmRSCU - Visualizing Multi-Species Relative Synonymous Codon Usage and Extensible Data Exploration
Facilitates efficient visualization of Relative Synonymous Codon Usage patterns across species. Based on analytical outputs from 'codonW', 'MEGA', and 'Phylosuite', it supports multi-species 'RSCU' comparisons and allows users to explore visual analysis of structurally similar datasets.
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1.00 score 2 scripts 229 downloadsextractFAERS - Extract Data from FAERS Database
Provides functions to extract and process data from the FDA Adverse Event Reporting System (FAERS). It facilitates the conversion of raw FAERS data published after 2014Q3 into structured formats for analysis. See Yang et al. (2022) <doi:10.3389/fphar.2021.772768> for related information.
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1.00 score 1 stars 222 downloads
MRQoL - Minimal Clinically Important Difference and Response Shift Effect for Health-Related Quality of Life
To calculate the Minimal Clinically Important Difference by applying the Anchor-based method and the Response shift effect by applying the Then-Test method.
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1.00 score 5 scripts 209 downloadsRcmdrPlugin.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.
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1.00 score 1 stars 2 scripts 863 downloadsHeckmanEM - 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.
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1.00 score 4 scripts 344 downloadsgbm2sas - Convert GBM Object Trees to SAS Code
Writes SAS code to get predicted values from every tree of a gbm.object.
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1.00 score 1 scripts 305 downloadskaraoke - Remove Vocals from a Song
Attempts to remove vocals from a stereo '.wav' recording of a song.
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1.00 score 1 scripts 226 downloadsJUMP - 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), <doi:10.1093/bioinformatics/btad366>].
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cpp
1.00 score 330 downloadsSTAREG - 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., (2024), <doi:10.1371/journal.pgen.1011423>].
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openblascppopenmp
1.00 score 4 scripts 361 downloadsrFocal - Run 'FOCAL' Language Source Code
Execute 'FOCAL' (<https://en.wikipedia.org/wiki/FOCAL_(programming_language)>) source code directly in 'R'. This is achieved by translating 'FOCAL' code into equivalent 'R' commands and controlling the sequence of execution.
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1.00 score 296 downloadsSingleCellStat - A Toolkit for Statistical Analysis of Single-Cell Omics Data
A suite of statistical methods for analysis of single-cell omics data including linear model-based methods for differential abundance analysis for individual level single-cell RNA-seq data. For more details see Zhang, et al. (Submitted to Bioinformatics)<https://github.com/Lujun995/DiSC_Replication_Code>.
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1.00 score 1 stars 1 scripts 232 downloadslogihist - Combined Graphs for Logistic Regression
Provides histograms, boxplots and dotplots as alternatives to scatterplots of data when plotting fitted logistic regressions.
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1.00 score 2 scripts 281 downloadsreplicatedpp2w - 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>.
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1.00 score 2 scripts 291 downloadsRramas - Matrix Population Models
Analyzes and predicts from matrix population models (Caswell 2006) <doi:10.1002/9781118445112.stat07481>.
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1.00 score 4 scripts 269 downloadsselectspm - 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.
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1.00 score 5 scripts 317 downloadsdpcid - Differential Partial Correlation IDentification
Differential partial correlation identification with the ridge and the fusion penalties.
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openblas
1.00 score 6 scripts 400 downloadsVisCov - 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://sites.stat.columbia.edu/gelman/research/unpublished/Visualization.pdf>.
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1.00 score 1 scripts 352 downloadsmixSPE - 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.
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1.00 score 1 scripts 310 downloadsabms - Augmented Bayesian Model Selection for Regression Models
Tools to perform model selection alongside estimation under Linear, Logistic, Negative binomial, Quantile, and Skew-Normal regression. Under the spike-and-slab method, a probability for each possible model is estimated with the posterior mean, credibility interval, and standard deviation of coefficients and parameters under the most probable model.
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1.00 score 1 scripts 356 downloadsLikertEZ - Easy Analysis and Visualization of Likert Scale Data
Provides functions for summarizing, visualizing, and analyzing Likert-scale survey data. Includes support for computing descriptive statistics, Relative Importance Index (RII), reliability analysis (Cronbach's Alpha), and response distribution plots.
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1.00 score 224 downloadscorrRF - Clustered Random Forests for Optimal Prediction and Inference of Clustered Data
A clustered random forest algorithm for fitting random forests for data of independent clusters, that exhibit within cluster dependence. Details of the method can be found in Young and Buehlmann (2025) <doi:10.48550/arXiv.2503.12634>.
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cpp
1.00 score 222 downloadsRcppDPR - 'Rcpp' Implementation of Dirichlet Process Regression
'Rcpp' reimplementation of the the Bayesian non-parametric Dirichlet Process Regression model for penalized regression first published in Zeng and Zhou (2017) <doi:10.1038/s41467-017-00470-2>. A full Bayesian version is implemented with Gibbs sampling, as well as a faster but less accurate variational Bayes approximation.
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openblasgslcpp
1.00 score 237 downloadsStatRec - A Statistical Method for Multi-Item Rating and Recommendation Problems
Implements the methodological developments found in Hermes (2025) <doi:10.48550/arXiv.2503.02786>, and allows for the statistical modeling of data consisting of multiple users that provide an ordinal rating for one or multiple items.
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openblascppopenmp
1.00 score 216 downloadsgolfr - Group Assignment Tool
An efficient algorithm to generate group assignments for classroom settings while minimizing repeated pairings across multiple rounds.
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1.00 score 1 scripts 139 downloadsmetainc - 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.
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1.00 score 239 downloadsCMatching - Matching Algorithms for Causal Inference with Clustered Data
Provides functions to perform matching algorithms for causal inference with clustered data, as described in B. Arpino and M. Cannas (2016) <doi:10.1002/sim.6880>. Pure within-cluster and preferential within-cluster matching are implemented. Both algorithms provide causal estimates with cluster-adjusted estimates of standard errors.
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1.00 score 1 stars 9 scripts 301 downloadsfbati - 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.
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cpp
1.00 score 5 scripts 395 downloadsTailClassifier - 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.
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1.00 score 390 downloadsplattice - 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.
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1.00 score 253 downloadscchs - 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.
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1.00 score 1 stars 2 scripts 427 downloadsMixLFA - 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.
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cpp
1.00 score 318 downloadsSSRA - 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.
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1.00 score 9 scripts 248 downloadsHMMcopula - 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>.
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1.00 score 1 stars 4 scripts 294 downloadsaffluenceIndex - 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.
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1.00 score 9 scripts 390 downloadstwingp - 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.
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cppopenmp
1.00 score 1 stars 8 scripts 340 downloadsR4HCR - R for Health Care Research
A collection of datasets that accompany the forthcoming book "R for Health Care Research".
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1.00 score 320 downloadsSurveyDefense - 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>.
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1.00 score 200 downloadsbexy - 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.
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1.00 score 1 scripts 237 downloadsORIONZ.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.
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1.00 score 187 downloadstrdist - 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.
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1.00 score 196 downloadsEWOC.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.
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jagscpp
1.00 score 249 downloadsltable - 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.
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1.00 score 3 scripts 304 downloadsconvertBCD - 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.
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1.00 score 246 downloadsSpaceTimeBSS - Blind Source Separation for Multivariate Spatio-Temporal Data
Simultaneous/joint diagonalization of local autocovariance matrices to estimate spatio-temporally uncorrelated random fields.
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openblascppopenmp
1.00 score 392 downloadsInquilab - 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.
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1.00 score 180 downloadsrid - 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>.
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cpp
1.00 score 8 scripts 218 downloadsSKFCPD - 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>.
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cpp
1.00 score 5 scripts 273 downloadsSwissAir - 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.
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1.00 score 1 stars 343 downloadsfastliu - 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'.
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openblascppopenmp
1.00 score 256 downloadszfa - Zoom-Focus Algorithm
Performs Zoom-Focus Algorithm (ZFA) to optimize testing regions for rare variant association tests in exome sequencing data.
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1.00 score 1 scripts 210 downloadsBranching - Simulation and Estimation for Branching Processes
Simulation and parameter estimation of multitype Bienayme - Galton - Watson processes.
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cpp
1.00 score 5 scripts 312 downloadsLiftTest - 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>.
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1.00 score 189 downloadsADER - Data Analysis in Ecology
Data sets used in Cayuela and De la Cruz (2022, ISBN:978-84-8476-833-3).
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1.00 score 3 scripts 432 downloadslongclust - 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>.
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openblas
1.00 score 1 stars 4 scripts 339 downloadsnice - Get or Set UNIX Niceness
Get or set UNIX priority (niceness) of running R process.
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1.00 score 6 scripts 116 downloadsInterfaceqPCR - 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.
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openjdk
1.00 score 3 scripts 296 downloadsGammareg - Classic Gamma Regression: Joint Modeling of Mean and Shape Parameters
Performs Gamma regression, where both mean and shape parameters follows lineal regression structures.
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1.00 score 3 scripts 282 downloadspoistweedie - Poisson-Tweedie Exponential Family Models
Simulation of models Poisson-Tweedie.
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1.00 score 279 downloadsrSPARCS - 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>.
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1.00 score 4 scripts 309 downloadsmarradistrees - 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).
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1.00 score 215 downloadspmvalsampsize - 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>.
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1.00 score 9 scripts 484 downloadsbioclim - 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.
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1.00 score 1 scripts 354 downloadsSurvSparse - 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>.
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1.00 score 2 scripts 248 downloadslongitudinalANAL - 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>.
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1.00 score 246 downloadsBosonSampling - 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.
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cpp
1.00 score 3 scripts 287 downloadsAutoTransQF - 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.
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1.00 score 309 downloadsargus - 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.
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1.00 score 10 scripts 354 downloadscrimCV - Group-Based Modelling of Longitudinal Data
A finite mixture of Zero-Inflated Poisson (ZIP) models for analyzing criminal trajectories.
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openblasfortranglibc
1.00 score 388 downloadsIASD - 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.
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1.00 score 2 scripts 246 downloadsGAGBLUP - 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.
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1.00 score 1 stars 242 downloadskerSeg - 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>.
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cpp
1.00 score 3 scripts 243 downloadskerDAA - 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>.
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1.00 score 231 downloadsMKLE - Maximum Kernel Likelihood Estimation
Package for fast computation of the maximum kernel likelihood estimator (mkle).
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1.00 score 6 scripts 216 downloadssaeHB.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).
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jagscpp
1.00 score 1 stars 221 downloadsmrct - 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>.
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1.00 score 235 downloadsStReg - 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>.
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1.00 score 1 scripts 242 downloadstdsc - 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.
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1.00 score 8 scripts 267 downloadsepmrob - 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>.
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1.00 score 287 downloadsOBRE - 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.
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1.00 score 5 scripts 200 downloadsadapt4pv - 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>.
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1.00 score 1 stars 428 downloadslmtestrob - 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>.
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1.00 score 234 downloadsMCPModBC - 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>.
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1.00 score 9 scripts 273 downloadshset - 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>.
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1.00 score 264 downloadsVARSELECTEXPOSURE - Variable Selection Methods Including an Exposure Variable
Utilizes multiple variable selection methods to estimate Average Treatment Effect.
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openblascppopenmp
1.00 score 288 downloadsnlstac - 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>.
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1.00 score 2 scripts 251 downloadsHDCurves - 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.
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1.00 score 1 scripts 239 downloadsmcen - 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.
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1.00 score 1 stars 305 downloadsStatDataML - Read and Write StatDataML Files
Support for reading and writing files in StatDataML---an XML-based data exchange format.
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1.00 score 7 scripts 389 downloadsHYDROCAL - 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>).
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1.00 score 1 scripts 242 downloadsKFPLS - 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().
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1.00 score 234 downloadsnestedpp - Performance Profiles and Nested Performance Profiles
Library to plot performance profiles (Dolan and More (2002) <doi:10.1007/s101070100263>) and nested performance profiles (Hekmati and Mirhajianmoghadam (2019) <doi:10.19139/soic-2310-5070-679>) for a given data frame.
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1.00 score 236 downloadsSLFPCA - 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().
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1.00 score 1 stars 3 scripts 284 downloadsZINAR1 - 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>.
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1.00 score 235 downloadsgllm - 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.
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1.00 score 8 scripts 375 downloadsspcr - Sparse Principal Component Regression
The sparse principal component regression is computed. The regularization parameters are optimized by cross-validation.
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openblas
1.00 score 1 stars 4 scripts 269 downloadsTratamentos.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".
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1.00 score 6 scripts 310 downloadsGiniDistance - 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>.
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cpp
1.00 score 309 downloadsJSparO - 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.
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1.00 score 1 stars 233 downloadsmvLSWimpute - 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>.
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1.00 score 2 scripts 295 downloadsSPB - 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.
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1.00 score 266 downloadsExcessMass - 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.
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1.00 score 6 scripts 285 downloadsgCat - 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.
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cpp
1.00 score 1 stars 3 scripts 284 downloadscpa - Confirmatory Path Analysis Through 'd-sep' Tests
Functions to test and compare causal models using Confirmatory Path Analysis.
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1.00 score 2 scripts 258 downloadsmodesto - 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.
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cpp
1.00 score 6 scripts 284 downloadsOPTtesting - 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.
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1.00 score 191 downloadsSECP - 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>.
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1.00 score 10 scripts 226 downloadsGeneF - 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>.
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1.00 score 2 scripts 193 downloadsZINARp - 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>.
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1.00 score 1 scripts 260 downloadsRIFS - 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>.
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1.00 score 4 scripts 225 downloadsLinCal - Static Univariate Frequentist and Bayesian Linear Calibration
Estimate and confidence/credible intervals for an unknown regressor x0 given an observed y0.
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1.00 score 7 scripts 215 downloadsSPOUSE - 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.
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1.00 score 199 downloadsRivivc - 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.
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1.00 score 3 scripts 227 downloadsmsaeHB - 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>.
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jagscpp
1.00 score 213 downloadsLSWPlib - 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>.
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1.00 score 332 downloadsMultEq - 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.
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1.00 score 5 scripts 248 downloadsBSPADATA - 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.
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1.00 score 7 scripts 327 downloadsDArand - 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>).
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1.00 score 294 downloadsl1spectral - 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).
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openblascpp
1.00 score 309 downloadssupercompress - 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.
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1.00 score 1 stars 4 scripts 182 downloadsmpr - 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>.
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1.00 score 1 scripts 536 downloadsphd - 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>.
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1.00 score 5 scripts 257 downloadsagrifeature - 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>.
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1.00 score 362 downloadsClusPred - 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.
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openblascpp
1.00 score 357 downloadsMNARclust - 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>.
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openblascpp
1.00 score 278 downloadsICglm - Information Criteria for Generalized Linear Regression
Calculate various information criteria in literature for "lm" and "glm" objects.
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1.00 score 6 scripts 279 downloadsCorrectedFDR - 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>.
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bayesian statisticsmathematicalbiology
1.00 score 2 scripts 270 downloadsglvmfit - Methods to Assess Generalized Latent Variable Model Fit
Provides residual global fit indices for generalized latent variable models.
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1.00 score 262 downloadsprimePCA - 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>.
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1.00 score 8 scripts 287 downloadsGIplot - 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.
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1.00 score 253 downloadsgsrs - 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.
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1.00 score 326 downloadsbenford - 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>.
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1.00 score 1 scripts 289 downloadsBioInsight - 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.
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1.00 score 1 scripts 396 downloadsaudit - 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>).
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1.00 score 7 scripts 333 downloadsSportsTour - 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).
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1.00 score 251 downloadsDBfit - 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.
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1.00 score 7 scripts 302 downloadsellipticalsymmetry - 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>.
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1.00 score 3 scripts 306 downloadsrandChecks - 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.
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1.00 score 8 scripts 153 downloadsshapeNA - 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.
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1.00 score 273 downloadscopulareg - 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.
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1.00 score 223 downloadsshutterplot - 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.
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1.00 score 197 downloadsEstimateGroupNetwork - 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.
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1.00 score 1 stars 10 scripts 496 downloadsfdq - 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.
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1.00 score 3 scripts 309 downloadsECTTDNN - 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.
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1.00 score 1 stars 273 downloadsRatingScaleReduction - 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.
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1.00 score 8 scripts 256 downloadsmemify - 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.
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1.00 score 205 downloadsMARSANNhybrid - 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.
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1.00 score 219 downloadsapng - 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.
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1.00 score 1 stars 2 scripts 306 downloadsMARSSVRhybrid - 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.
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1.00 score 250 downloadsRobustBayesianCopas - 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>.
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jagscpp
1.00 score 248 downloadsnlnet - 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>.
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1.00 score 1 stars 9 scripts 273 downloadsBayesBP - 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>.
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1.00 score 3 scripts 330 downloadsnsarfima - 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>.
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1.00 score 1 stars 2 scripts 273 downloadsgridDebug - Debugging 'grid' Graphics
Functions for drawing scene trees representing scenes that have been drawn using grid graphics.
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1.00 score 4 scripts 344 downloadsGMPro - 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>.
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1.00 score 2 scripts 302 downloadsdatasetsICR - 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.
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1.00 score 1 scripts 270 downloadsCeRNASeek - 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.
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competing endogenous rna (cerna)geneexpressiontripletfunctionsoftware
1.00 score 375 downloadsaugSIMEX - 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.
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cpp
1.00 score 1 stars 10 scripts 437 downloadsbivrp - 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.
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1.00 score 3 scripts 329 downloadsTrendInTrend - 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.
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1.00 score 1 stars 3 scripts 310 downloadscdlei - 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>).
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1.00 score 213 downloadsBioProbability - 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.
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1.00 score 2 scripts 262 downloadsRRI - 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.
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openblascpp
1.00 score 229 downloadsGFGM.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.
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1.00 score 8 scripts 279 downloadsBivariate.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.
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1.00 score 8 scripts 333 downloadsHextractoR - 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.
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1.00 score 6 scripts 319 downloadsCautiousLearning - 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.
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cppopenmp
1.00 score 372 downloadsjacpop - 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.
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1.00 score 2 scripts 207 downloadsroccv - 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.
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1.00 score 4 scripts 222 downloadsrobustreg - Robust Regression Functions
Linear regression functions using Huber and bisquare psi functions. Optimal weights are calculated using IRLS algorithm.
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cpp
1.00 score 10 scripts 409 downloadsPlotContour - Plot Contour Line
This function plots a contour line with a user-defined probability and tightness of fit.
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1.00 score 268 downloadsiMediate - Likelihood Methods for Mediation Analysis
Implements likelihood based methods for mediation analysis.
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1.00 score 9 scripts 301 downloadsBalanceCheck - 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.
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1.00 score 1 stars 2 scripts 367 downloadsSPreg - 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>.
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1.00 score 2 scripts 232 downloadsPortfolioOptim - 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.
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1.00 score 9 scripts 414 downloadsbwd - 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.
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1.00 score 2 scripts 282 downloadsmmsample - 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).
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openblascpp
1.00 score 2 scripts 232 downloadskuiper.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>.
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1.00 score 2 scripts 244 downloadsrhmc - 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.
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1.00 score 3 scripts 122 downloadsGroupComparisons - 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>).
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1.00 score 2 scripts 231 downloadsOpt5PL - 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>.
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cpp
1.00 score 6 scripts 249 downloadssym.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.
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1.00 score 9 scripts 249 downloadsHGSL - 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>.
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1.00 score 1 stars 1 scripts 228 downloadsintRegGOF - Integrated Regression Goodness of Fit
Performs Goodness of Fit for regression models using Integrated Regression method. Works for several different fitting techniques.
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1.00 score 3 scripts 263 downloadsminiGUI - 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.
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1.00 score 4 scripts 191 downloadsvitality - Fitting Routines for the Vitality Family of Mortality Models
Provides fitting routines for four versions of the Vitality family of mortality models.
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1.00 score 5 scripts 262 downloadsthgenetics - 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>.
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cpp
1.00 score 1 scripts 197 downloadsNightDay - Night and Day Boundary Plot Function
Computes and plots the boundary between night and day.
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1.00 score 4 scripts 246 downloadsDykstra - 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.
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1.00 score 3 scripts 297 downloadsgLRTH - Genome-Wide Association and Linkage Analysis under Heterogeneity
Likelihood ratio tests for genome-wide association and genome-wide linkage analysis under heterogeneity.
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1.00 score 2 scripts 271 downloadsfactoptd - Factorial Optimal Designs for Two-Colour cDNA Microarray Experiments
Computes factorial A-, D- and E-optimal designs for two-colour cDNA microarray experiments.
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1.00 score 1 scripts 336 downloadsTrioSGL - 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>.
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cpp
1.00 score 1 scripts 171 downloadsfBonds - Rmetrics - Pricing and Evaluating Bonds
It implements the Nelson-Siegel and the Nelson-Siegel-Svensson term structures.
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1.00 score 1 scripts 346 downloadsOptimalTiming - 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>.
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1.00 score 5 scripts 242 downloadsGSMX - 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.
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1.00 score 5 scripts 274 downloadsDoubleCone - 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.
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1.00 score 5 scripts 292 downloadsBayesCR - 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.
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1.00 score 1 scripts 377 downloadscbanalysis - Coffee Break Descriptive Analysis
A set of functions that helps you to generate descriptive statistics based on the variable types.
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1.00 score 2 scripts 314 downloadsCpGFilter - 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.
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1.00 score 6 scripts 272 downloadsFSTpackage - 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.
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1.00 score 5 scripts 310 downloadsMultiSkew - 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.
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1.00 score 8 scripts 220 downloadsfeaturizer - 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.
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1.00 score 4 scripts 277 downloadsRandMeta - 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.
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1.00 score 1 scripts 262 downloadsmro - Multiple Correlation
Computes multiple correlation coefficient when the data matrix is given and tests its significance.
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1.00 score 2 scripts 193 downloadsBLModel - 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.
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1.00 score 6 scripts 520 downloadsprop.comb.RR - Analyzing Combination of Proportions and Relative Risk
Carrying out inferences about any linear combination of proportions and the ratio of two proportions.
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1.00 score 1 stars 4 scripts 356 downloadsotinference - 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.
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1.00 score 3 scripts 332 downloadsVarED - Variance Estimation using Difference-Based Methods
Generating functions for both optimal and ordinary difference sequences, and the difference-based estimation functions.
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1.00 score 3 scripts 331 downloadsCPsurv - Nonparametric Change Point Estimation for Survival Data
Nonparametric change point estimation for survival data based on p-values of exact binomial tests.
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1.00 score 4 scripts 422 downloadsBCC1997 - 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.
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1.00 score 1 scripts 500 downloadsnparsurv - 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.
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1.00 score 1 scripts 224 downloadsQRank - A Novel Quantile Regression Approach for eQTL discovery
A Quantile Rank-score based test for the identification of expression quantitative trait loci.
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1.00 score 5 scripts 245 downloadsphuassess - 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.
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1.00 score 1 scripts 197 downloadsMIDN - 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.
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1.00 score 3 scripts 218 downloadsbacr - Bayesian Adjustment for Confounding
Estimating the average causal effect based on the Bayesian Adjustment for Confounding (BAC) algorithm.
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1.00 score 1 stars 1 scripts 365 downloadsmetafuse - 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.
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1.00 score 4 scripts 312 downloadsmomentchi2 - 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.
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1.00 score 1 stars 331 downloadsspikes - 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.
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1.00 score 8 scripts 274 downloadsspselect - 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.
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1.00 score 8 scripts 242 downloadsmakeFlow - Visualizing Sequential Classifications
A user-friendly tool for visualizing categorical or group movement.
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1.00 score 7 scripts 265 downloadsheatmapFit - 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>.
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1.00 score 10 scripts 291 downloadsuskewFactors - 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.
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1.00 score 2 scripts 252 downloadspRSR - Test of Periodicity using Response Surface Regression
Tests periodicity in short time series using response surface regression.
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1.00 score 9 scripts 303 downloadscrsnls - 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.
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1.00 score 2 scripts 168 downloadscensorcopula - Estimate Parameter of Bivariate Copula
Implement an interval censor method to break ties when using data with ties to fitting a bivariate copula.
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1.00 score 4 scripts 320 downloadstmpm - 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.
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1.00 score 6 scripts 226 downloadssensory - Simultaneous Model-Based Clustering and Imputation via a Progressive Expectation-Maximization Algorithm
Contains the function CUUimpute() which performs model-based clustering and imputation simultaneously.
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1.00 score 1 stars 4 scripts 213 downloadsvudc - Visualization of Univariate Data for Comparison
Contains functions for visualization univariate data: ccdplot and qddplot.
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1.00 score 1 stars 5 scripts 183 downloadspsoptim - Particle Swarm Optimization
Particle swarm optimization - a basic variant.
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1.00 score 4 scripts 263 downloadswildpoker - 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.
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1.00 score 4 scripts 138 downloadsVertexSimilarity - 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>.
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1.00 score 1 scripts 240 downloadsCircOutlier - Detection of Outliers in Circular-Circular Regression
Detection of outliers in circular-circular regression models, modifying its and estimating of models parameters.
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1.00 score 5 scripts 244 downloadsForecastCombinations - 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).
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1.00 score 3 scripts 336 downloadsFACTMLE - Maximum Likelihood Factor Analysis
Perform Maximum Likelihood Factor analysis on a covariance matrix or data matrix.
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1.00 score 2 scripts 211 downloadsSPCALDA - A New Reduced-Rank Linear Discriminant Analysis Method
A new reduced-rank LDA method which works for high dimensional multi-class data.
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1.00 score 1 scripts 187 downloadshotspot - Software Hotspot Analysis
Contains data for software hotspot analysis, along with a function performing the analysis itself.
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1.00 score 1 scripts 217 downloadsSyncMove - 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'.
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1.00 score 2 scripts 188 downloadsHDGLM - Tests for High Dimensional Generalized Linear Models
Test the significance of coefficients in high dimensional generalized linear models.
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1.00 score 2 scripts 190 downloadsLinearRegressionMDE - 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.
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1.00 score 1 scripts 209 downloadsLGRF - 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.
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1.00 score 8 scripts 251 downloadsregRSM - 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.
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1.00 score 1 stars 9 scripts 176 downloadsThreeGroups - 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).
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1.00 score 1 scripts 245 downloadsFastBandChol - 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.
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openblascpp
1.00 score 5 scripts 285 downloadsMDimNormn - 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.
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1.00 score 3 scripts 203 downloadsthreg - 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.
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1.00 score 6 scripts 220 downloadsmmc - 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.
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1.00 score 2 scripts 247 downloadspowerGWASinteraction - 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.
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1.00 score 4 scripts 308 downloadssubgroup - 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.
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1.00 score 3 scripts 150 downloadspartitionMetric - Compute a distance metric between two partitions of a set
partitionMetric computes a distance between two partitions of a set.
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1.00 score 1 scripts 222 downloadsALSCPC - 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.
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1.00 score 1 scripts 284 downloadsFGalgorithm - Flury and Gautschi algorithms
This is a package for implementation of Flury-Gautschi algorithms.
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1.00 score 1 scripts 265 downloadsigraphtosonia - Convert iGraph graps to SoNIA .son files
This program facilitates exporting igraph graphs to the SoNIA file format
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1.00 score 3 scripts 274 downloads