colorspace - A Toolbox for Manipulating and Assessing Colors and Palettes

Carries out mapping between assorted color spaces including RGB, HSV, HLS, CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB, and polar CIELAB. Qualitative, sequential, and diverging color palettes based on HCL colors are provided along with corresponding ggplot2 color scales. Color palette choice is aided by an interactive app (with either a Tcl/Tk or a shiny graphical user interface) and shiny apps with an HCL color picker and a color vision deficiency emulator. Plotting functions for displaying and assessing palettes include color swatches, visualizations of the HCL space, and trajectories in HCL and/or RGB spectrum. Color manipulation functions include: desaturation, lightening/darkening, mixing, and simulation of color vision deficiencies (deutanomaly, protanomaly, tritanomaly). Details can be found on the project web page at <https://colorspace.R-Forge.R-project.org/> and in the accompanying scientific paper: Zeileis et al. (2020, Journal of Statistical Software, <doi:10.18637/jss.v096.i01>).

Last updated 13 hours ago

10 stars 18.97 score 0 dependencies 7549 dependents

yaml - Methods to Convert R Data to YAML and Back

Implements the 'libyaml' 'YAML' 1.1 parser and emitter (<https://pyyaml.org/wiki/LibYAML>) for R.

Last updated 14 hours ago

17.27 score 0 dependencies 4775 dependents

polyclip - Polygon Clipping

R port of Angus Johnson's open source library 'Clipper'. Performs polygon clipping operations (intersection, union, set minus, set difference) for polygonal regions of arbitrary complexity, including holes. Computes offset polygons (spatial buffer zones, morphological dilations, Minkowski dilations) for polygonal regions and polygonal lines. Computes Minkowski Sum of general polygons. There is a function for removing self-intersections from polygon data.

Last updated 3 days ago

3 stars 10.11 score 0 dependencies 502 dependents

openxlsx - Read, Write and Edit xlsx Files

Simplifies the creation of Excel .xlsx files by providing a high level interface to writing, styling and editing worksheets. Through the use of 'Rcpp', read/write times are comparable to the 'xlsx' and 'XLConnect' packages with the added benefit of removing the dependency on Java.

Last updated 3 days ago

8.28 score 3 dependencies 250 dependents

xgboost - Extreme Gradient Boosting

Extreme Gradient Boosting, which is an efficient implementation of the gradient boosting framework from Chen & Guestrin (2016) <doi:10.1145/2939672.2939785>. This package is its R interface. The package includes efficient linear model solver and tree learning algorithms. The package can automatically do parallel computation on a single machine which could be more than 10 times faster than existing gradient boosting packages. It supports various objective functions, including regression, classification and ranking. The package is made to be extensible, so that users are also allowed to define their own objectives easily.

Last updated 2 days ago

6 stars 6.19 score 4 dependencies 99 dependents

bayestestR - Understand and Describe Bayesian Models and Posterior Distributions

Provides utilities to describe posterior distributions and Bayesian models. It includes point-estimates such as Maximum A Posteriori (MAP), measures of dispersion (Highest Density Interval - HDI; Kruschke, 2015 <doi:10.1016/C2012-0-00477-2>) and indices used for null-hypothesis testing (such as ROPE percentage, pd and Bayes factors). References: Makowski et al. (2021) <doi:10.21105/joss.01541>.

Last updated 2 days ago

5.56 score 2 dependencies 75 dependents

texreg - Conversion of R Regression Output to LaTeX or HTML Tables

Converts coefficients, standard errors, significance stars, and goodness-of-fit statistics of statistical models into LaTeX tables or HTML tables/MS Word documents or to nicely formatted screen output for the R console for easy model comparison. A list of several models can be combined in a single table. The output is highly customizable. New model types can be easily implemented. Details can be found in Leifeld (2013), JStatSoft <doi:10.18637/jss.v055.i08>.)

Last updated 2 days ago

1 stars 5.37 score 8 dependencies 68 dependents

rio - A Swiss-Army Knife for Data I/O

Streamlined data import and export by making assumptions that the user is probably willing to make: 'import()' and 'export()' determine the data format from the file extension, reasonable defaults are used for data import and export, web-based import is natively supported (including from SSL/HTTPS), compressed files can be read directly, and fast import packages are used where appropriate. An additional convenience function, 'convert()', provides a simple method for converting between file types.

Last updated 2 days ago

5.32 score 38 dependencies 65 dependents

gtsummary - Presentation-Ready Data Summary and Analytic Result Tables

Creates presentation-ready tables summarizing data sets, regression models, and more. The code to create the tables is concise and highly customizable. Data frames can be summarized with any function, e.g. mean(), median(), even user-written functions. Regression models are summarized and include the reference rows for categorical variables. Common regression models, such as logistic regression and Cox proportional hazards regression, are automatically identified and the tables are pre-filled with appropriate column headers.

Last updated 3 days ago

3.06 score 63 dependencies 18 dependents

randomForestSRC - Fast Unified Random Forests for Survival, Regression, and Classification (RF-SRC)

Fast OpenMP parallel computing of Breiman's random forests for univariate, multivariate, unsupervised, survival, competing risks, class imbalanced classification and quantile regression. New Mahalanobis splitting for correlated outcomes. Extreme random forests and randomized splitting. Suite of imputation methods for missing data. Fast random forests using subsampling. Confidence regions and standard errors for variable importance. New improved holdout importance. Case-specific importance. Minimal depth variable importance. Visualize trees on your Safari or Google Chrome browser. Anonymous random forests for data privacy.

Last updated 1 days ago

10 stars 2.97 score 67 dependencies 13 dependents

bbotk - Black-Box Optimization Toolkit

Features highly configurable search spaces via the 'paradox' package and optimizes every user-defined objective function. The package includes several optimization algorithms e.g. Random Search, Iterated Racing, Bayesian Optimization (in 'mlr3mbo') and Hyperband (in 'mlr3hyperband'). bbotk is the base package of 'mlr3tuning', 'mlr3fselect' and 'miesmuschel'.

Last updated 2 days ago

2.70 score 8 dependencies 13 dependents

dtwclust - Time Series Clustering Along with Optimizations for the Dynamic Time Warping Distance

Time series clustering along with optimized techniques related to the Dynamic Time Warping distance and its corresponding lower bounds. Implementations of partitional, hierarchical, fuzzy, k-Shape and TADPole clustering are available. Functionality can be easily extended with custom distance measures and centroid definitions. Implementations of DTW barycenter averaging, a distance based on global alignment kernels, and the soft-DTW distance and centroid routines are also provided. All included distance functions have custom loops optimized for the calculation of cross-distance matrices, including parallelization support. Several cluster validity indices are included.

Last updated 3 days ago

1 stars 2.63 score 75 dependencies 13 dependents

tidycensus - Load US Census Boundary and Attribute Data as 'tidyverse' and 'sf'-Ready Data Frames

An integrated R interface to several United States Census Bureau APIs (<https://www.census.gov/data/developers/data-sets.html>) and the US Census Bureau's geographic boundary files. Allows R users to return Census and ACS data as tidyverse-ready data frames, and optionally returns a list-column with feature geometry for mapping and spatial analysis.

Last updated 1 days ago

2.35 score 56 dependencies 9 dependents

matlib - Matrix Functions for Teaching and Learning Linear Algebra and Multivariate Statistics

A collection of matrix functions for teaching and learning matrix linear algebra as used in multivariate statistical methods. These functions are mainly for tutorial purposes in learning matrix algebra ideas using R. In some cases, functions are provided for concepts available elsewhere in R, but where the function call or name is not obvious. In other cases, functions are provided to show or demonstrate an algorithm. In addition, a collection of functions are provided for drawing vector diagrams in 2D and 3D.

Last updated 1 days ago

2.27 score 83 dependencies 10 dependents

TreeTools - Create, Modify and Analyse Phylogenetic Trees

Efficient implementations of functions for the creation, modification and analysis of phylogenetic trees. Applications include: generation of trees with specified shapes; tree rearrangement; analysis of tree shape; rooting of trees and extraction of subtrees; calculation and depiction of split support; plotting the position of rogue taxa (Klopfstein & Spasojevic 2019) <doi:10.1371/journal.pone.0212942>; calculation of ancestor-descendant relationships, of 'stemwardness' (Asher & Smith, 2022) <doi:10.1093/sysbio/syab072>, and of tree balance (Mir et al. 2013, Lemant et al. 2022) <doi:10.1016/j.mbs.2012.10.005>, <doi:10.1093/sysbio/syac027>; artificial extinction (Asher & Smith, 2022) <doi:10.1093/sysbio/syab072>; import and export of trees from Newick, Nexus (Maddison et al. 1997) <doi:10.1093/sysbio/46.4.590>, and TNT <https://www.lillo.org.ar/phylogeny/tnt/> formats; and analysis of splits and cladistic information.

Last updated 1 days ago

2.22 score 22 dependencies 9 dependents

Ternary - Create Ternary and Holdridge Plots

Plots ternary diagrams (simplex plots / Gibbs triangles) and Holdridge life zone plots <doi:10.1126/science.105.2727.367> using the standard graphics functions. Allows custom annotation, interpolating, contouring and scaling of plotting region. Includes a 'Shiny' user interface for point-and-click ternary plotting. An alternative to 'ggtern', which uses the 'ggplot2' family of plotting functions.

Last updated 1 days ago

1.80 score 35 dependencies 6 dependents

tiledb - Modern Database Engine for Complex Data Based on Multi-Dimensional Arrays

The modern database 'TileDB' introduces a powerful on-disk format for storing and accessing any complex data based on multi-dimensional arrays. It supports dense and sparse arrays, dataframes and key-values stores, cloud storage ('S3', 'GCS', 'Azure'), chunked arrays, multiple compression, encryption and checksum filters, uses a fully multi-threaded implementation, supports parallel I/O, data versioning ('time travel'), metadata and groups. It is implemented as an embeddable cross-platform C++ library with APIs from several languages, and integrations. This package provides the R support.

Last updated 1 days ago

1.75 score 12 dependencies 3 dependents

finbif - Interface for the 'Finnish Biodiversity Information Facility' API

A programmatic interface to the 'Finnish Biodiversity Information Facility' ('FinBIF') API (<https://api.laji.fi>). 'FinBIF' aggregates Finnish biodiversity data from multiple sources in a single open access portal for researchers, citizen scientists, industry and government. 'FinBIF' allows users of biodiversity information to find, access, combine and visualise data on Finnish plants, animals and microorganisms. The 'finbif' package makes the publicly available data in 'FinBIF' easily accessible to programmers. Biodiversity information is available on taxonomy and taxon occurrence. Occurrence data can be filtered by taxon, time, location and other variables. The data accessed are conveniently preformatted for subsequent analyses.

Last updated 3 days ago

apibiodiversitybiodiversity-informaticsbiodiversity-informationfinbiffinbif-accessoccurrencesr-programmingspeciesspecimenstaxontaxonomyweb-services

1.45 score 15 dependencies 3 dependents

nodbi - 'NoSQL' Database Connector

Simplified JSON document database access and manipulation, providing a common API across supported 'NoSQL' databases 'Elasticsearch', 'CouchDB', 'MongoDB' as well as 'SQLite/JSON1', 'PostgreSQL', and 'DuckDB'.

Last updated 1 days ago

databasemongodbelasticsearchcouchdbsqlitepostgresqlduckdbnosqljsondocuments

1.24 score 13 dependencies 1 dependents

RQuantLib - R Interface to the 'QuantLib' Library

The 'RQuantLib' package makes parts of 'QuantLib' accessible from R The 'QuantLib' project aims to provide a comprehensive software framework for quantitative finance. The goal is to provide a standard open source library for quantitative analysis, modeling, trading, and risk management of financial assets.

Last updated 2 days ago

6 stars 1.16 score 3 dependencies

medfate - Mediterranean Forest Simulation

Simulate Mediterranean forest functioning and dynamics using cohort-based description of vegetation [De Caceres et al. (2015) <doi:10.1016/j.agrformet.2015.06.012>; De Caceres et al. (2021) <doi:10.1016/j.agrformet.2020.108233>].

Last updated 3 days ago

2 stars 1.08 score 81 dependencies 1 dependents

cffr - Generate Citation File Format ('cff') Metadata for R Packages

The Citation File Format version 1.2.0 <doi:10.5281/zenodo.5171937> is a human and machine readable file format which provides citation metadata for software. This package provides core utilities to generate and validate this metadata.

Last updated 3 days ago

attributioncitationcreditcitation-filescffmetadata

1.00 score 9 dependencies 2 dependents

YatchewTest - Yatchew (1997), De Chaisemartin & D'Haultfoeuille (2024) Linearity Test

Test of linearity originally proposed by Yatchew (1997) <doi:10.1016/S0165-1765(97)00218-8> and improved by de Chaisemartin & D'Haultfoeuille (2024) <doi:10.2139/ssrn.4284811> to be robust under heteroskedasticity.

Last updated 3 days ago

1.00 score 29 dependencies 2 dependents

syt - Young Tableaux

Deals with Young tableaux (field of combinatorics). For standard Young tabeaux, performs enumeration, counting, random generation, the Robinson-Schensted correspondence, and conversion to and from paths on the Young lattice. Also performs enumeration and counting of semistandard Young tableaux, enumeration of skew semistandard Young tableaux, enumeration of Gelfand-Tsetlin patterns, and computation of Kostka numbers.

Last updated 3 days ago

0.82 score 9 dependencies 1 dependents

knitrProgressBar - Provides Progress Bars in 'knitr'

Provides a progress bar similar to 'dplyr' that can write progress out to a variety of locations, including stdout(), stderr(), or from file(). Useful when using 'knitr' or 'rmarkdown', and you still want to see progress of calculations in the terminal.

Last updated 3 days ago

0.82 score 3 dependencies 2 dependents

frab - How to Add Two R Tables

Methods to "add" two R tables; also an alternative interpretation of named vectors as generalized R tables, so that c(a=1,b=2,c=3) + c(b=3,a=-1) will return c(b=5,c=3). Uses 'disordR' discipline (Hankin, 2022, <doi:10.48550/arXiv.2210.03856>). Extraction and replacement methods are provided. The underlying mathematical structure is the Free Abelian group, hence the name. To cite in publications please use Hankin (2023) <doi:10.48550/arXiv.2307.13184>.

Last updated 2 days ago

0.71 score 5 dependencies 1 dependents

fmri - Analysis of fMRI Experiments

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

Last updated 2 days ago

2 stars 0.71 score 16 dependencies 1 dependents

jagshelper - Extracting and Visualizing Output from 'jagsUI'

Tools are provided to streamline Bayesian analyses in 'JAGS' using the 'jagsUI' package. Included are functions for extracting output in simpler format, functions for streamlining assessment of convergence, and functions for producing summary plots of output. Also included is a function that provides a simple template for running 'JAGS' from 'R'. Referenced materials can be found at <DOI:10.1214/ss/1177011136>.

Last updated 3 days ago

0.71 score 5 dependencies

hicp - Harmonised Index of Consumer Prices

The Harmonised Index of Consumer Prices (HICP) is the key economic figure to measure inflation in the euro area. The methodology underlying the HICP is documented in the HICP Methodological Manual (<https://ec.europa.eu/eurostat/web/products-manuals-and-guidelines/w/ks-gq-24-003>). Based on the manual, this package provides functions to access and work with HICP data from Eurostat's public database (<https://ec.europa.eu/eurostat/data/database>).

Last updated 3 days ago

0.71 score 6 dependencies

glmtoolbox - Set of Tools to Data Analysis using Generalized Linear Models

Set of tools for the statistical analysis of data using: (1) normal linear models; (2) generalized linear models; (3) negative binomial regression models as alternative to the Poisson regression models under the presence of overdispersion; (4) beta-binomial and random-clumped binomial regression models as alternative to the binomial regression models under the presence of overdispersion; (5) Zero-inflated and zero-altered regression models to deal with zero-excess in count data; (6) generalized nonlinear models; (7) generalized estimating equations for cluster correlated data.

Last updated 1 days ago

0.61 score 34 dependencies

KSgeneral - Computing P-Values of the One-Sample K-S Test and the Two-Sample K-S and Kuiper Tests for (Dis)Continuous Null Distribution

Contains functions to compute p-values for the one-sample and two-sample Kolmogorov-Smirnov (KS) tests and the two-sample Kuiper test for any fixed critical level and arbitrary (possibly very large) sample sizes. For the one-sample KS test, this package implements a novel, accurate and efficient method named Exact-KS-FFT, which allows the pre-specified cumulative distribution function under the null hypothesis to be continuous, purely discrete or mixed. In the two-sample case, it is assumed that both samples come from an unspecified (unknown) continuous, purely discrete or mixed distribution, i.e. ties (repeated observations) are allowed, and exact p-values of the KS and the Kuiper tests are computed. Note, the two-sample Kuiper test is often used when data samples are on the line or on the circle (circular data). To cite this package in publication: (for the use of the one-sample KS test) Dimitrina S. Dimitrova, Vladimir K. Kaishev, and Senren Tan. Computing the Kolmogorov-Smirnov Distribution When the Underlying CDF is Purely Discrete, Mixed, or Continuous. Journal of Statistical Software. 2020; 95(10): 1--42. <doi:10.18637/jss.v095.i10>. (for the use of the two-sample KS and Kuiper tests) Dimitrina S. Dimitrova, Yun Jia and Vladimir K. Kaishev (2024). The R functions KS2sample and Kuiper2sample: Efficient Exact Calculation of P-values of the Two-sample Kolmogorov-Smirnov and Kuiper Tests. submitted.

Last updated 1 days ago

0.61 score 3 dependencies

logitr - Logit Models w/Preference & WTP Space Utility Parameterizations

Fast estimation of multinomial (MNL) and mixed logit (MXL) models in R. Models can be estimated using "Preference" space or "Willingness-to-pay" (WTP) space utility parameterizations. Weighted models can also be estimated. An option is available to run a parallelized multistart optimization loop with random starting points in each iteration, which is useful for non-convex problems like MXL models or models with WTP space utility parameterizations. The main optimization loop uses the 'nloptr' package to minimize the negative log-likelihood function. Additional functions are available for computing and comparing WTP from both preference space and WTP space models and for predicting expected choices and choice probabilities for sets of alternatives based on an estimated model. Mixed logit models can include uncorrelated or correlated heterogeneity covariances and are estimated using maximum simulated likelihood based on the algorithms in Train (2009) <doi:10.1017/CBO9780511805271>. More details can be found in Helveston (2023) <doi:10.18637/jss.v105.i10>.

Last updated 2 days ago

0.61 score 16 dependencies 1 dependents

qlcal - R Bindings to the Calendaring Functionality of 'QuantLib'

'QuantLib' bindings are provided for R using 'Rcpp' via an evolved version of the initial header-only 'Quantuccia' project offering an subset of 'QuantLib' (now maintained separately just for the calendaring subset). See the included file 'AUTHORS' for a full list of contributors to 'QuantLib' (and hence also 'Quantuccia').

Last updated 3 days ago

0.61 score 2 dependencies

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

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

Last updated 3 days ago

5 stars 0.61 score 46 dependencies

csquares - Concise Spatial Query and Representation System (c-Squares)

Encode and decode c-squares, from and to simple feature (sf) or spatiotemporal arrays (stars) objects. Use c-squares codes to quickly join or query spatial data.

Last updated 1 days ago

0.49 score 35 dependencies

CRTspat - Workflow for Cluster Randomised Trials with Spillover

Design, workflow and statistical analysis of Cluster Randomised Trials of (health) interventions where there may be spillover between the arms (see <https://thomasasmith.github.io/index.html>).

Last updated 1 days ago

0.49 score 70 dependencies

growthPheno - Functional Analysis of Phenotypic Growth Data to Smooth and Extract Traits

Assists in the plotting and functional smoothing of traits measured over time and the extraction of features from these traits, implementing the SET (Smoothing and Extraction of Traits) method described in Brien et al. (2020) Plant Methods, 16. Smoothing of growth trends for individual plants using natural cubic smoothing splines or P-splines is available for removing transient effects and segmented smoothing is available to deal with discontinuities in growth trends. There are graphical tools for assessing the adequacy of trait smoothing, both when using this and other packages, such as those that fit nonlinear growth models. A range of per-unit (plant, pot, plot) growth traits or features can be extracted from the data, including single time points, interval growth rates and other growth statistics, such as maximum growth or days to maximum growth. The package also has tools adapted to inputting data from high-throughput phenotyping facilities, such from a Lemna-Tec Scananalyzer 3D (see <https://www.youtube.com/watch?v=MRAF_mAEa7E/> for more information). The package 'growthPheno' can also be installed from <http://chris.brien.name/rpackages/>.

Last updated 2 days ago

0.49 score 146 dependencies

MBBEFDLite - Statistical Functions for the Maxwell-Boltzmann-Bose-Einstein-Fermi-Dirac (MBBEFD) Family of Distributions

Provides probability mass, distribution, quantile, random variate generation, and method-of-moments parameter fitting for the MBBEFD family of distributions used in insurance modeling as described in Bernegger (1997) <doi:10.2143/AST.27.1.563208> without any external dependencies.

Last updated 2 days ago

0.49 score 0 dependencies

webmockr - Stubbing and Setting Expectations on 'HTTP' Requests

Stubbing and setting expectations on 'HTTP' requests. Includes tools for stubbing 'HTTP' requests, including expected request conditions and response conditions. Match on 'HTTP' method, query parameters, request body, headers and more. Can be used for unit tests or outside of a testing context.

Last updated 3 days ago

httphttpsapiweb-servicescurlmockmockingfakewebhttp-mockingtestingtesting-toolstdd

0.49 score 13 dependencies 1 dependents

tidyfinance - Tidy Finance Helper Functions

Helper functions for empirical research in financial economics, addressing a variety of topics covered in Scheuch, Voigt, and Weiss (2023) <doi:10.1201/b23237>. The package is designed to provide shortcuts for issues extensively discussed in the book, facilitating easier application of its concepts. For more information and resources related to the book, visit <https://www.tidy-finance.org/r/index.html>.

Last updated 3 days ago

0.49 score 23 dependencies

metatools - Enable the Use of 'metacore' to Help Create and Check Dataset

Uses the metadata information stored in 'metacore' objects to check and build metadata associated columns.

Last updated 3 days ago

0.49 score 30 dependencies 1 dependents

causalweight - Estimation Methods for Causal Inference Based on Inverse Probability Weighting

Various estimators of causal effects based on inverse probability weighting, doubly robust estimation, and double machine learning. Specifically, the package includes methods for estimating average treatment effects, direct and indirect effects in causal mediation analysis, and dynamic treatment effects. The models refer to studies of Froelich (2007) <doi:10.1016/j.jeconom.2006.06.004>, Huber (2012) <doi:10.3102/1076998611411917>, Huber (2014) <doi:10.1080/07474938.2013.806197>, Huber (2014) <doi:10.1002/jae.2341>, Froelich and Huber (2017) <doi:10.1111/rssb.12232>, Hsu, Huber, Lee, and Lettry (2020) <doi:10.1002/jae.2765>, and others.

Last updated 3 days ago

2 stars 0.49 score 74 dependencies

s3fs - 'Amazon Web Service S3' File System

Access 'Amazon Web Service Simple Storage Service' ('S3') <https://aws.amazon.com/s3/> as if it were a file system. Interface based on the R package 'fs'.

Last updated 1 days ago

0.36 score 25 dependencies

digiRhythm - Analyzing Animal's Rhythmicity

Analyze and visualize the rhythmic behavior of animals using the degree of functional coupling (See Scheibe (1999) <doi:10.1076/brhm.30.2.216.1420>), compute and visualize harmonic power, actograms, average activity and diurnality index.

Last updated 1 days ago

0.36 score 51 dependencies

cvasi - Calibration, Validation, and Simulation of TKTD Models

Eases the use of ecotoxicological effect models. Can simulate common toxicokinetic-toxicodynamic (TK/TD) models such as General Unified Threshold models of Survival (GUTS) and Lemna. It can derive effects and effect profiles (EPx) from scenarios. It supports the use of 'tidyr' workflows employing the pipe symbol. Time-consuming tasks can be parallelized.

Last updated 1 days ago

0.36 score 51 dependencies

RALSA - R Analyzer for Large-Scale Assessments

Prepare and analyze data from large-scale assessments and surveys with complex sampling and assessment design (see 'Rutkowski', 2010 <doi:10.3102/0013189X10363170>). Such studies are, for example, international assessments like 'TIMSS', 'PIRLS' and 'PISA'. A graphical interface is available for the non-technical user.The package includes functions to covert the original data from 'SPSS' into 'R' data sets keeping the user-defined missing values, merge data from different respondents and/or countries, generate variable dictionaries, modify data, produce descriptive statistics (percentages, means, percentiles, benchmarks) and multivariate statistics (correlations, linear regression, binary logistic regression). The number of supported studies and analysis types will increase in future. For a general presentation of the package, see 'Mirazchiyski', 2021a (<doi:10.1186/s40536-021-00114-4>). For detailed technical aspects of the package, see 'Mirazchiyski', 2021b (<doi:10.3390/psych3020018>).

Last updated 1 days ago

0.36 score 100 dependencies

stppSim - Spatiotemporal Point Patterns Simulation

Generates artificial point patterns marked by their spatial and temporal signatures. The resulting point cloud may exhibit inherent interactions between both signatures. The simulation integrates microsimulation (Holm, E., (2017)<doi:10.1002/9781118786352.wbieg0320>) and agent-based models (Bonabeau, E., (2002)<doi:10.1073/pnas.082080899>), beginning with the configuration of movement characteristics for the specified agents (referred to as 'walkers') and their interactions within the simulation environment. These interactions (Quaglietta, L. and Porto, M., (2019)<doi:10.1186/s40462-019-0154-8>) result in specific spatiotemporal patterns that can be visualized, analyzed, and used for various analytical purposes. Given the growing scarcity of detailed spatiotemporal data across many domains, this package provides an alternative data source for applications in social and life sciences.

Last updated 2 days ago

0.36 score 131 dependencies

conquestr - An R Package to Extend 'ACER ConQuest'

Extends 'ACER ConQuest' through a family of functions designed to improve graphical outputs and help with advanced analysis (e.g., differential item functioning). Allows R users to call 'ACER ConQuest' from within R and read 'ACER ConQuest' System Files (generated by the command `put` <https://conquestmanual.acer.org/s4-00.html#put>). Requires 'ACER ConQuest' version 5.39 or later. A demonstration version can be downloaded from <https://shop.acer.org/acer-conquest-5.html>.

Last updated 2 days ago

0.36 score 65 dependencies

binsreg - Binscatter Estimation and Inference

Provides tools for statistical analysis using the binscatter methods developed by Cattaneo, Crump, Farrell and Feng (2024a) <doi:10.48550/arXiv.1902.09608>, Cattaneo, Crump, Farrell and Feng (2024b) <https://nppackages.github.io/references/Cattaneo-Crump-Farrell-Feng_2024_NonlinearBinscatter.pdf> and Cattaneo, Crump, Farrell and Feng (2024c) <doi:10.48550/arXiv.1902.09615>. Binscatter provides a flexible way of describing the relationship between two variables based on partitioning/binning of the independent variable of interest. binsreg(), binsqreg() and binsglm() implement binscatter least squares regression, quantile regression and generalized linear regression respectively, with particular focus on constructing binned scatter plots. They also implement robust (pointwise and uniform) inference of regression functions and derivatives thereof. binstest() implements hypothesis testing procedures for parametric functional forms of and nonparametric shape restrictions on the regression function. binspwc() implements hypothesis testing procedures for pairwise group comparison of binscatter estimators. binsregselect() implements data-driven procedures for selecting the number of bins for binscatter estimation. All the commands allow for covariate adjustment, smoothness restrictions and clustering.

Last updated 3 days ago

2 stars 0.36 score 35 dependencies

altdoc - Package Documentation Websites with 'Quarto', 'Docsify', 'Docute', or 'MkDocs'

This is a simple and powerful package to create, render, preview, and deploy documentation websites for 'R' packages. It is a lightweight and flexible alternative to 'pkgdown', with support for many documentation generators, including 'Quarto', 'Docute', 'Docsify', and 'MkDocs'.

Last updated 3 days ago

0.36 score 33 dependencies

PAGFL - Joint Estimation of Latent Groups and Group-Specific Coefficients in Panel Data Models

Latent group structures are a common challenge in panel data analysis. Disregarding group-level heterogeneity can introduce bias. Conversely, estimating individual coefficients for each cross-sectional unit is inefficient and may lead to high uncertainty. This package addresses the issue of unobservable group structures by implementing the pairwise adaptive group fused Lasso (PAGFL) by Mehrabani (2023) <doi:10.1016/j.jeconom.2022.12.002>. PAGFL identifies latent group structures and group-specific coefficients in a single step. On top of that, we extend the PAGFL to time-varying coefficient functions.

Last updated 3 days ago

0.36 score 31 dependencies

scorematchingad - Score Matching Estimation by Automatic Differentiation

Hyvärinen's score matching (Hyvärinen, 2005) <https://jmlr.org/papers/v6/hyvarinen05a.html> is a useful estimation technique when the normalising constant for a probability distribution is difficult to compute. This package implements score matching estimators using automatic differentiation in the 'CppAD' library <https://github.com/coin-or/CppAD> and is designed for quickly implementing score matching estimators for new models. Also available is general robustification (Windham, 1995) <https://www.jstor.org/stable/2346159>. Already in the package are estimators for directional distributions (Mardia, Kent and Laha, 2016) <doi:10.48550/arXiv.1604.08470> and the flexible Polynomially-Tilted Pairwise Interaction model for compositional data. The latter estimators perform well when there are zeros in the compositions (Scealy and Wood, 2023) <doi:10.1080/01621459.2021.2016422>, even many zeros (Scealy, Hingee, Kent, and Wood, 2024) <doi:10.1007/s11222-024-10412-w>.

Last updated 1 days ago

0.23 score 21 dependencies

rdataretriever - R Interface to the Data Retriever

Provides an R interface to the Data Retriever <https://retriever.readthedocs.io/en/latest/> via the Data Retriever's command line interface. The Data Retriever automates the tasks of finding, downloading, and cleaning public datasets, and then stores them in a local database.

Last updated 1 days ago

0.23 score 14 dependencies

rTG - Methods to Analyse Seasonal Radial Tree Growth Data

Methods for comparing different regression algorithms for describing the temporal dynamics of secondary tree growth (xylem and phloem). Users can compare the accuracy of the most common fitting methods usually used to analyse xylem and phloem data, i.e., Gompertz function, Double Gompertz function, General Additive Models (GAMs); and an algorithm newly introduced to the field, i.e., Bayesian Regularised Neural Networks (brnn). The core function of the package is XPSgrowth(), while the results can be interpreted using implemented generic S3 methods, such as plot() and summary().

Last updated 1 days ago

0.23 score 40 dependencies

loggit2 - Easy-to-Use, Dependencyless Logger

An easy-to-use 'ndjson' (newline-delimited 'JSON') logger. It provides a set of wrappers for base R's message(), warning(), and stop() functions that maintain identical functionality, but also log the handler message to an 'ndjson' log file. No change in existing code is necessary to use this package, and only a few additional adjustments are needed to fully utilize its potential.

Last updated 1 days ago

0.23 score 0 dependencies

TensorTest2D - Fitting Second-Order Tensor Data

An implementation of fitting generalized linear models on second-order tensor type data. The functions within this package mainly focus on parameter estimation, including parameter coefficients and standard deviation.

Last updated 1 days ago

1 stars 0.23 score 0 dependencies

ILSM - Analyze Interconnection Structure of Multilayer Interaction Networks

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

Last updated 1 days ago

0.23 score 11 dependencies

AQuality - Water and Measurements Quality

The functions proposed in this package allows to graphically evaluate the process of measurement of the chemical components of water. TSSS() and ICHS functions are useful to control the quality of measurements of chemical components of a sample of water. If one or more measurements include an error, the generated graph will indicate it with a position of the point that represents the sample outside the confidence interval.

Last updated 1 days ago

0.23 score 0 dependencies

psp - Parameter Space Partitioning MCMC for Global Model Evaluation

Implements an n-dimensional parameter space partitioning algorithm for evaluating the global behaviour of formal computational models as described by Pitt, Kim, Navarro and Myung (2006) <doi:10.1037/0033-295X.113.1.57>.

Last updated 2 days ago

0.23 score 3 dependencies

medfateland - Mediterranean Landscape Simulation

Simulate forest hydrology, forest function and dynamics over landscapes [De Caceres et al. (2015) <doi:10.1016/j.agrformet.2015.06.012>]. Parallelization is allowed in several simulation functions and simulations may be conducted including spatial processes such as lateral water transfer and seed dispersal.

Last updated 2 days ago

0.23 score 90 dependencies

dauphin - Compact Standard for Australian Phone Numbers

Phone numbers are often represented as strings because there is no obvious and suitable native representation for them. This leads to high memory use and a lack of standard representation. The package provides integer representation of Australian phone numbers with optional raw vector calling code. The package name is an extension of 'au' and 'ph'.

Last updated 2 days ago

0.23 score 0 dependencies

bayesCureRateModel - Bayesian Cure Rate Modeling for Time-to-Event Data

A fully Bayesian approach in order to estimate a general family of cure rate models under the presence of covariates, see Papastamoulis and Milienos (2023) <doi:10.48550/arXiv.2310.06926>. The promotion time can be modelled (a) parametrically using typical distributional assumptions for time to event data (including the Weibull, Exponential, Gompertz, log-Logistic distributions), or (b) semiparametrically using finite mixtures of Gamma distributions. Posterior inference is carried out by constructing a Metropolis-coupled Markov chain Monte Carlo (MCMC) sampler, which combines Gibbs sampling for the latent cure indicators and Metropolis-Hastings steps with Langevin diffusion dynamics for parameter updates. The main MCMC algorithm is embedded within a parallel tempering scheme by considering heated versions of the target posterior distribution.

Last updated 2 days ago

0.23 score 63 dependencies

StormR - Analyzing the Behaviour of Wind Generated by Tropical Storms and Cyclones

Set of functions to quantify and map the behaviour of winds generated by tropical storms and cyclones in space and time. It includes functions to compute and analyze fields such as the maximum sustained wind field, power dissipation index and duration of exposure to winds above a given threshold. It also includes functions to map the trajectories as well as characteristics of the storms.

Last updated 2 days ago

0.23 score 66 dependencies

isoWater - Discovery, Retrieval, and Analysis of Water Isotope Data

The wiDB...() functions provide an interface to the public API of the wiDB <https://github.com/SPATIAL-Lab/isoWater/blob/master/Protocol.md>: build, check and submit queries, and receive and unpack responses. Data analysis functions support Bayesian inference of the source and source isotope composition of water samples that may have experienced evaporation. Algorithms adapted from Bowen et al. (2018, <doi:10.1007/s00442-018-4192-5>).

Last updated 3 days ago

0.23 score 27 dependencies

bonsai - Model Wrappers for Tree-Based Models

Bindings for additional tree-based model engines for use with the 'parsnip' package. Models include gradient boosted decision trees with 'LightGBM' (Ke et al, 2017.), conditional inference trees and conditional random forests with 'partykit' (Hothorn and Zeileis, 2015. and Hothorn et al, 2006. <doi:10.1198/106186006X133933>), and accelerated oblique random forests with 'aorsf' (Jaeger et al, 2022 <doi:10.5281/zenodo.7116854>).

Last updated 3 days ago

0.23 score 43 dependencies

XiMpLe - A Simple XML Tree Parser and Generator

Provides a simple XML tree parser/generator. It includes functions to read XML files into R objects, get information out of and into nodes, and write R objects back to XML code. It's not as powerful as the 'XML' package and doesn't aim to be, but for simple XML handling it could be useful. It was originally developed for the R GUI and IDE 'RKWard' <https://rkward.kde.org>, to make plugin development easier.

Last updated 3 days ago

0.23 score 0 dependencies

restatis - R Wrapper to Access a Wide Range of Germany's Federal Statistical System Databases Based on the GENESIS Web Service RESTful API of the German Federal Statistical Office (Statistisches Bundesamt/Destatis)

A RESTful API wrapper for accessing the GENESIS database of the German Federal Statistical Office (Destatis) as well as its Census Database and the database of Germany's regional statistics. Supports data search functions, credential management, result caching, and handling remote background jobs for large datasets.

Last updated 1 days ago

0.09 score 35 dependencies

r2pmml - Convert R Models to PMML

R wrapper for the JPMML-R library <https://github.com/jpmml/jpmml-r>, which converts R models to Predictive Model Markup Language (PMML).

Last updated 1 days ago

0.09 score 0 dependencies

gtreg - Regulatory Tables for Clinical Research

Creates tables suitable for regulatory agency submission by leveraging the 'gtsummary' package as the back end. Tables can be exported to HTML, Word, PDF and more. Highly customized outputs are available by utilizing existing styling functions from 'gtsummary' as well as custom options designed for regulatory tables.

Last updated 1 days ago

0.09 score 80 dependencies

cheddar - Analysis and Visualisation of Ecological Communities

Provides a flexible, extendable representation of an ecological community and a range of functions for analysis and visualisation, focusing on food web, body mass and numerical abundance data. Allows inter-web comparisons such as examining changes in community structure over environmental, temporal or spatial gradients.

Last updated 2 days ago

0.09 score 0 dependencies

bartMan - Create Visualisations for BART Models

Investigating and visualising Bayesian Additive Regression Tree (BART) (Chipman, H. A., George, E. I., & McCulloch, R. E. 2010) <doi:10.1214/09-AOAS285> model fits. We construct conventional plots to analyze a model’s performance and stability as well as create new tree-based plots to analyze variable importance, interaction, and tree structure. We employ Value Suppressing Uncertainty Palettes (VSUP) to construct heatmaps that display variable importance and interactions jointly using colour scale to represent posterior uncertainty. Our visualisations are designed to work with the most popular BART R packages available, namely 'BART' Rodney Sparapani and Charles Spanbauer and Robert McCulloch 2021 <doi:10.18637/jss.v097.i01>, 'dbarts' (Vincent Dorie 2023) <https://CRAN.R-project.org/package=dbarts>, and 'bartMachine' (Adam Kapelner and Justin Bleich 2016) <doi:10.18637/jss.v070.i04>.

Last updated 2 days ago

0.09 score 127 dependencies

ROCsurf - ROC Surface Analysis Under the Three-Class Problems

Receiver Operating Characteristic (ROC) analysis is performed assuming samples are from the proposed distributions. In addition, the volume under the ROC surface and true positive fractions values are evaluated by ROC surface analysis.

Last updated 2 days ago

0.09 score 71 dependencies

vcr - Record 'HTTP' Calls to Disk

Record test suite 'HTTP' requests and replays them during future runs. A port of the Ruby gem of the same name (<https://github.com/vcr/vcr/>). Works by hooking into the 'webmockr' R package for matching 'HTTP' requests by various rules ('HTTP' method, 'URL', query parameters, headers, body, etc.), and then caching real 'HTTP' responses on disk in 'cassettes'. Subsequent 'HTTP' requests matching any previous requests in the same 'cassette' use a cached 'HTTP' response.

Last updated 3 days ago

httphttpsapiweb-servicescurlmockmockinghttp-mockingtestingtesting-toolstdd

0.09 score 28 dependencies

simodels - Flexible Framework for Developing Spatial Interaction Models

Develop spatial interaction models (SIMs). SIMs predict the amount of interaction, for example number of trips per day, between geographic entities representing trip origins and destinations. Contains functions for creating origin-destination datasets from geographic input datasets and calculating movement between origin-destination pairs with constrained, production-constrained, and attraction-constrained models (Wilson 1979) <doi:10.1068/a030001>.

Last updated 3 days ago

0.09 score 32 dependencies

ppgam - Generalised Additive Point Process Models

Methods for fitting point processes with parameters of generalised additive model (GAM) form are provided. For an introduction to point processes see Cox, D.R & Isham, V. (Point Processes, 1980, CRC Press), GAMs see Wood, S.N. (2017) <doi:10.1201/9781315370279>, and the fitting approach see Wood, S.N., Pya, N. & Safken, B. (2016) <doi:10.1080/01621459.2016.1180986>.

Last updated 3 days ago

0.09 score 8 dependencies

dcurves - Decision Curve Analysis for Model Evaluation

Diagnostic and prognostic models are typically evaluated with measures of accuracy that do not address clinical consequences. Decision-analytic techniques allow assessment of clinical outcomes, but often require collection of additional information may be cumbersome to apply to models that yield a continuous result. Decision curve analysis is a method for evaluating and comparing prediction models that incorporates clinical consequences, requires only the data set on which the models are tested, and can be applied to models that have either continuous or dichotomous results. See the following references for details on the methods: Vickers (2006) <doi:10.1177/0272989X06295361>, Vickers (2008) <doi:10.1186/1472-6947-8-53>, and Pfeiffer (2020) <doi:10.1002/bimj.201800240>.

Last updated 3 days ago

0.09 score 39 dependencies

Laterality - Functions to Calculate Common Laterality Statistics in Primatology

Calculates and plots Handedness index (HI), absolute HI, mean HI and z-score which are commonly used indexes for the study of hand preference (laterality) in non-human primates.

Last updated 3 days ago

0.09 score 7 dependencies

smdi - Perform Structural Missing Data Investigations

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

Last updated 1 days ago

0.00 score 152 dependencies

htmlTable - Advanced Tables for Markdown/HTML

Tables with state-of-the-art layout elements such as row spanners, column spanners, table spanners, zebra striping, and more. While allowing advanced layout, the underlying css-structure is simple in order to maximize compatibility with common word processors. The package also contains a few text formatting functions that help outputting text compatible with HTML/LaTeX.

Last updated 6 days ago

1 stars 11.16 score 34 dependencies 729 dependents

datawizard - Easy Data Wrangling and Statistical Transformations

A lightweight package to assist in key steps involved in any data analysis workflow: (1) wrangling the raw data to get it in the needed form, (2) applying preprocessing steps and statistical transformations, and (3) compute statistical summaries of data properties and distributions. It is also the data wrangling backend for packages in 'easystats' ecosystem. References: Patil et al. (2022) <doi:10.21105/joss.04684>.

Last updated 5 days ago

6.34 score 1 dependencies 107 dependents

Exact - Unconditional Exact Test

Performs unconditional exact tests and power calculations for 2x2 contingency tables. For comparing two independent proportions, performs Barnard's test (1945) <doi:10.1038/156177a0> using the original CSM test (Barnard, 1947 <doi:10.1093/biomet/34.1-2.123>), using Fisher's p-value referred to as Boschloo's test (1970) <doi:10.1111/j.1467-9574.1970.tb00104.x>, or using a Z-statistic (Suissa and Shuster, 1985, <doi:10.2307/2981892>). For comparing two binary proportions, performs unconditional exact test using McNemar's Z-statistic (Berger and Sidik, 2003, <doi:10.1191/0962280203sm312ra>), using McNemar's conditional p-value, using McNemar's Z-statistic with continuity correction, or using CSM test. Calculates confidence intervals for the difference in proportion. This package interacts with pre-computed data available through the ExactData R package, which is available in a 'drat' repository. Install the ExactData R package from GitHub at <https://pcalhoun1.github.io/drat/>. The ExactData R package is approximately 85 MB.

Last updated 5 days ago

5.86 score 1 dependencies 87 dependents

parameters - Processing of Model Parameters

Utilities for processing the parameters of various statistical models. Beyond computing p values, CIs, and other indices for a wide variety of models (see list of supported models using the function 'insight::supported_models()'), this package implements features like bootstrapping or simulating of parameters and models, feature reduction (feature extraction and variable selection) as well as functions to describe data and variable characteristics (e.g. skewness, kurtosis, smoothness or distribution).

Last updated 5 days ago

5.06 score 3 dependencies 56 dependents

websocket - 'WebSocket' Client Library

Provides a 'WebSocket' client interface for R. 'WebSocket' is a protocol for low-overhead real-time communication: <https://en.wikipedia.org/wiki/WebSocket>.

Last updated 4 days ago

4.40 score 6 dependencies 41 dependents

mlr3 - Machine Learning in R - Next Generation

Efficient, object-oriented programming on the building blocks of machine learning. Provides 'R6' objects for tasks, learners, resamplings, and measures. The package is geared towards scalability and larger datasets by supporting parallelization and out-of-memory data-backends like databases. While 'mlr3' focuses on the core computational operations, add-on packages provide additional functionality.

Last updated 4 days ago

4.23 score 21 dependencies 35 dependents

mlr3measures - Performance Measures for 'mlr3'

Implements multiple performance measures for supervised learning. Includes over 40 measures for regression and classification. Additionally, meta information about the performance measures can be queried, e.g. what the best and worst possible performances scores are.

Last updated 6 days ago

4.18 score 3 dependencies 36 dependents

quarto - R Interface to 'Quarto' Markdown Publishing System

Convert R Markdown documents and 'Jupyter' notebooks to a variety of output formats using 'Quarto'.

Last updated 6 days ago

3.74 score 31 dependencies 27 dependents

WriteXLS - Cross-Platform Perl Based R Function to Create Excel 2003 (XLS) and Excel 2007 (XLSX) Files

Cross-platform Perl based R function to create Excel 2003 (XLS) and Excel 2007 (XLSX) files from one or more data frames. Each data frame will be written to a separate named worksheet in the Excel spreadsheet. The worksheet name will be the name of the data frame it contains or can be specified by the user.

Last updated 6 days ago

1 stars 3.62 score 0 dependencies 25 dependents

secretbase - Cryptographic Hash, Extendable-Output and Base64 Functions

Fast and memory-efficient streaming hash functions and base64 encoding and decoding. Performs direct hashing of strings and raw vectors. Stream hashes files potentially larger than memory, as well as in-memory objects through R's serialization mechanism. Implementations include the SHA-256, SHA-3 and 'Keccak' cryptographic hash functions, SHAKE256 extendable-output function (XOF), and 'SipHash' pseudo-random function.

Last updated 4 days ago

3.16 score 0 dependencies 17 dependents

twang - Toolkit for Weighting and Analysis of Nonequivalent Groups

Provides functions for propensity score estimating and weighting, nonresponse weighting, and diagnosis of the weights.

Last updated 4 days ago

1 stars 2.38 score 48 dependencies 10 dependents

rayvertex - 3D Software Rasterizer

Rasterize images using a 3D software renderer. 3D scenes are created either by importing external files, building scenes out of the included objects, or by constructing meshes manually. Supports point and directional lights, anti-aliased lines, shadow mapping, transparent objects, translucent objects, multiple materials types, reflection, refraction, environment maps, multicore rendering, bloom, tone-mapping, and screen-space ambient occlusion.

Last updated 4 days ago

2.18 score 26 dependencies 9 dependents

ggdag - Analyze and Create Elegant Directed Acyclic Graphs

Tidy, analyze, and plot directed acyclic graphs (DAGs). 'ggdag' is built on top of 'dagitty', an R package that uses the 'DAGitty' web tool (<https://dagitty.net/>) for creating and analyzing DAGs. 'ggdag' makes it easy to tidy and plot 'dagitty' objects using 'ggplot2' and 'ggraph', as well as common analytic and graphical functions, such as determining adjustment sets and node relationships.

Last updated 4 days ago

1.95 score 59 dependencies 7 dependents

wrMisc - Analyze Experimental High-Throughput (Omics) Data

The efficient treatment and convenient analysis of experimental high-throughput (omics) data gets facilitated through this collection of diverse functions. Several functions address advanced object-conversions, like manipulating lists of lists or lists of arrays, reorganizing lists to arrays or into separate vectors, merging of multiple entries, etc. Another set of functions provides speed-optimized calculation of standard deviation (sd), coefficient of variance (CV) or standard error of the mean (SEM) for data in matrixes or means per line with respect to additional grouping (eg n groups of replicates). A group of functions facilitate dealing with non-redundant information, by indexing unique, adding counters to redundant or eliminating lines with respect redundancy in a given reference-column, etc. Help is provided to identify very closely matching numeric values to generate (partial) distance matrixes for very big data in a memory efficient manner or to reduce the complexity of large data-sets by combining very close values. Other functions help aligning a matrix or data.frame to a reference using partial matching or to mine an experimental setup to extract patterns of replicate samples. Many times large experimental datasets need some additional filtering, adequate functions are provided. Convenient data normalization is supported in various different modes, parameter estimation via permutations or boot-strap as well as flexible testing of multiple pair-wise combinations using the framework of 'limma' is provided, too. Batch reading (or writing) of sets of files and combining data to arrays is supported, too.

Last updated 4 days ago

1.45 score 1 dependencies 3 dependents

landscapemetrics - Landscape Metrics for Categorical Map Patterns

Calculates landscape metrics for categorical landscape patterns in a tidy workflow. 'landscapemetrics' reimplements the most common metrics from 'FRAGSTATS' (<https://www.fragstats.org/>) and new ones from the current literature on landscape metrics. This package supports 'terra' SpatRaster objects as input arguments. It further provides utility functions to visualize patches, select metrics and building blocks to develop new metrics.

Last updated 4 days ago

1.45 score 31 dependencies 3 dependents

protr - Generating Various Numerical Representation Schemes for Protein Sequences

Comprehensive toolkit for generating various numerical features of protein sequences described in Xiao et al. (2015) <DOI:10.1093/bioinformatics/btv042>. For full functionality, the software 'ncbi-blast+' is needed, see <https://blast.ncbi.nlm.nih.gov/doc/blast-help/downloadblastdata.html> for more information.

Last updated 5 days ago

1 stars 1.31 score 0 dependencies 3 dependents

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

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

Last updated 3 days ago

1.16 score 112 dependencies 1 dependents

manynet - Many Ways to Make, Modify, Map, Mark, and Measure Myriad Networks

Many tools for making, modifying, mapping, marking, measuring, and motifs and memberships of many different types of networks. All functions operate with matrices, edge lists, and 'igraph', 'network', and 'tidygraph' objects, and on one-mode, two-mode (bipartite), and sometimes three-mode networks. The package includes functions for importing and exporting, creating and generating networks, modifying networks and node and tie attributes, and describing and visualizing networks with sensible defaults.

Last updated 4 days ago

1.16 score 57 dependencies 1 dependents

tinycodet - Functions to Help in your Coding Etiquette

Adds some functions to help in your coding etiquette. 'tinycodet' primarily focuses on 4 aspects. 1) Safer decimal (in)equality testing, standard-evaluated alternatives to with() and aes(), and other functions for safer coding. 2) A new package import system, that attempts to combine the benefits of using a package without attaching it, with the benefits of attaching a package. 3) Extending the string manipulation capabilities of the 'stringi' R package. 4) Reducing repetitive code. Besides linking to 'Rcpp', 'tinycodet' has only one other dependency, namely 'stringi'.

Last updated 5 days ago

1.08 score 2 dependencies

hutilscpp - Miscellaneous Functions in C++

Provides utility functions that are simply, frequently used, but may require higher performance that what can be obtained from base R. Incidentally provides support for 'reverse geocoding', such as matching a point with its nearest neighbour in another array. Used as a complement to package 'hutils' by sacrificing compilation or installation time for higher running speeds. The name is a portmanteau of the author and 'Rcpp'.

Last updated 5 days ago

1.00 score 4 dependencies 2 dependents

nullabor - Tools for Graphical Inference

Tools for visual inference. Generate null data sets and null plots using permutation and simulation. Calculate distance metrics for a lineup, and examine the distributions of metrics.

Last updated 5 days ago

0.91 score 49 dependencies 2 dependents

ChainLadder - Statistical Methods and Models for Claims Reserving in General Insurance

Various statistical methods and models which are typically used for the estimation of outstanding claims reserves in general insurance, including those to estimate the claims development result as required under Solvency II.

Last updated 5 days ago

1 stars 0.91 score 73 dependencies 2 dependents

cards - Analysis Results Data

Construct CDISC (Clinical Data Interchange Standards Consortium) compliant Analysis Results Data objects. These objects are used and re-used to construct summary tables, visualizations, and written reports. The package also exports utilities for working with these objects and creating new Analysis Results Data objects.

Last updated 6 days ago

0.91 score 21 dependencies 2 dependents

sensemakr - Sensitivity Analysis Tools for Regression Models

Implements a suite of sensitivity analysis tools that extends the traditional omitted variable bias framework and makes it easier to understand the impact of omitted variables in regression models, as discussed in Cinelli, C. and Hazlett, C. (2020), "Making Sense of Sensitivity: Extending Omitted Variable Bias." Journal of the Royal Statistical Society, Series B (Statistical Methodology) <doi:10.1111/rssb.12348>.

Last updated 4 days ago

0.82 score 0 dependencies 2 dependents

dsem - Fit Dynamic Structural Equation Models

Applies dynamic structural equation models to time-series data with generic and simplified specification for simultaneous and lagged effects. Methods are described in Thorson et al. (2024) "Dynamic structural equation models synthesize ecosystem dynamics constrained by ecological mechanisms."

Last updated 4 days ago

1 stars 0.82 score 25 dependencies

SEMgraph - Network Analysis and Causal Inference Through Structural Equation Modeling

Estimate networks and causal relationships in complex systems through Structural Equation Modeling. This package also includes functions to import, weight, manipulate, and fit biological network models within the Structural Equation Modeling framework proposed in Grassi M, Palluzzi F, Tarantino B (2022) <doi:10.1093/bioinformatics/btac567>.

Last updated 4 days ago

4 stars 0.82 score 57 dependencies

LadderFuelsR - Automated Tool for Vertical Fuel Continuity Analysis using Airborne Laser Scanning Data

Set of tools for analyzing vertical fuel continuity at the tree level using Airborne Laser Scanning data. The workflow consisted of: 1) calculating the vertical height profiles of each segmented tree; 2) identifying gaps and fuel layers; 3) estimating the distance between fuel layers; and 4) retrieving the fuel layers base height and depth. Additionally, other functions recalculate previous metrics after considering distances greater than certain threshold. Moreover, the package calculates: i) the percentage of Leaf Area Density comprised in each fuel layer, ii) remove fuel layers with Leaf Area Density (LAD) percentage less than 10, and iii) recalculate the distances among the reminder ones. On the other hand, it identifies the crown base height (CBH) based on different criteria: the fuel layer with the highest LAD percentage and the fuel layers located at the largest- and at the last-distance. When there is only one fuel layer, it also identifies the CBH performing a segmented linear regression (breaking points) on the cumulative sum of LAD as a function of height. Finally, a collection of plotting functions is developed to represent: i) the initial gaps and fuel layers; ii) the fuels base height, depths and gaps with distances greater than certain threshold and, iii) the CBH based on different criteria. The methods implemented in this package are original and have not been published elsewhere.

Last updated 6 days ago

0.71 score 39 dependencies

Qval - The Q-Matrix Validation Methods Framework

Provide a variety of Q-matrix validation methods for the generalized cognitive diagnosis models, including the method based on the generalized deterministic input, noisy, and gate model (G-DINA) by de la Torre (2011) <DOI:10.1007/s11336-011-9207-7> discrimination index (the GDI method) by de la Torre and Chiu (2016) <DOI:10.1007/s11336-015-9467-8>, the step-wise Wald test method (the Wald method) by Ma and de la Torre (2020) <DOI:10.1111/bmsp.12156>, the Hull method by Najera et al. (2021) <DOI:10.1111/bmsp.12228>, the multiple logistic regression‑based Q‑matrix validation method (the MLR-B method) by Tu et al. (2022) <DOI:10.3758/s13428-022-01880-x>. Different research methods during Q-matrix validating are available.

Last updated 5 days ago

1 stars 0.61 score 67 dependencies

GSODR - Global Surface Summary of the Day ('GSOD') Weather Data Client

Provides automated downloading, parsing, cleaning, unit conversion and formatting of Global Surface Summary of the Day ('GSOD') weather data from the from the USA National Centers for Environmental Information ('NCEI'). Units are converted from from United States Customary System ('USCS') units to International System of Units ('SI'). Stations may be individually checked for number of missing days defined by the user, where stations with too many missing observations are omitted. Only stations with valid reported latitude and longitude values are permitted in the final data. Additional useful elements, saturation vapour pressure ('es'), actual vapour pressure ('ea') and relative humidity ('RH') are calculated from the original data using the improved August-Roche-Magnus approximation (Alduchov & Eskridge 1996) and included in the final data set. The resulting metadata include station identification information, country, state, latitude, longitude, elevation, weather observations and associated flags. For information on the 'GSOD' data from 'NCEI', please see the 'GSOD' 'readme.txt' file available from, <https://www1.ncdc.noaa.gov/pub/data/gsod/readme.txt>.

Last updated 3 days ago

us-nceimeteorological-dataglobal-weatherweatherweather-datameteorologystation-datasurface-weatherdata-accessus-ncdc

0.49 score 6 dependencies

DIDHAD - Difference-in-Differences in Heterogeneous Adoption Designs with Quasi Stayers

Estimation of Difference-in-Differences (DiD) estimators from de Chaisemartin and D'Haultfoeuille (2024) <doi:10.2139/ssrn.4284811> in Heterogeneous Adoption Designs with no stayers but with quasi stayers.

Last updated 3 days ago

0.49 score 61 dependencies 1 dependents

precommit - Pre-Commit Hooks

Useful git hooks for R building on top of the multi-language framework 'pre-commit' for hook management. This package provides git hooks for common tasks like formatting files with 'styler' or spell checking as well as wrapper functions to access the 'pre-commit' executable.

Last updated 4 days ago

0.49 score 17 dependencies

mlr3fda - Extending 'mlr3' to Functional Data Analysis

Extends the 'mlr3' ecosystem to functional analysis by adding support for irregular and regular functional data as defined in the 'tf' package. The package provides 'PipeOps' for preprocessing functional columns and for extracting scalar features, thereby allowing standard machine learning algorithms to be applied afterwards. Available operations include simple functional features such as the mean or maximum, smoothing, interpolation, flattening, and functional 'PCA'.

Last updated 4 days ago

0.49 score 39 dependencies

easystats - Framework for Easy Statistical Modeling, Visualization, and Reporting

A meta-package that installs and loads a set of packages from 'easystats' ecosystem in a single step. This collection of packages provide a unifying and consistent framework for statistical modeling, visualization, and reporting. Additionally, it provides articles targeted at instructors for teaching 'easystats', and a dashboard targeted at new R users for easily conducting statistical analysis by accessing summary results, model fit indices, and visualizations with minimal programming.

Last updated 4 days ago

0.49 score 38 dependencies

fdaconcur - Concurrent Regression and History Index Models for Functional Data

Provides an implementation of concurrent or varying coefficient regression methods for functional data. The implementations are done for both dense and sparsely observed functional data. Pointwise confidence bands can be constructed for each case. Further, the influence of past predictor values are modeled by a smooth history index function, while the effects on the response are described by smooth varying coefficient functions, which are very useful in analyzing real data such as COVID data. References: Yao, F., Müller, H.G., Wang, J.L. (2005) <doi:10.1214/009053605000000660>. Sentürk, D., Müller, H.G. (2010) <doi:10.1198/jasa.2010.tm09228>.

Last updated 6 days ago

0.49 score 70 dependencies

MethEvolSIM - Simulate DNA Methylation Dynamics on Different Genomic Structures along Genealogies

DNA methylation is an epigenetic modification involved in genomic stability, gene regulation, development and disease. DNA methylation occurs mainly through the addition of a methyl group to cytosines, for example to cytosines in a CpG dinucleotide context (CpG stands for a cytosine followed by a guanine). Tissue-specific methylation patterns lead to genomic regions with different characteristic methylation levels. E.g. in vertebrates CpG islands (regions with high CpG content) that are associated to promoter regions of expressed genes tend to be unmethylated. 'MethEvolSIM' is a model-based simulation software for the generation and modification of cytosine methylation patterns along a given tree, which can be a genealogy of cells within an organism, a coalescent tree of DNA sequences sampled from a population, or a species tree. The simulations are based on an extension of the model of Grosser & Metzler (2020) <doi:10.1186/s12859-020-3438-5> and allows for changes of the methylation states at single cytosine positions as well as simultaneous changes of methylation frequencies in genomic structures like CpG islands.

Last updated 6 days ago

0.49 score 1 dependencies

DiSCos - Distributional Synthetic Controls Estimation

The method of synthetic controls is a widely-adopted tool for evaluating causal effects of policy changes in settings with observational data. In many settings where it is applicable, researchers want to identify causal effects of policy changes on a treated unit at an aggregate level while having access to data at a finer granularity. This package implements a simple extension of the synthetic controls estimator, developed in Gunsilius (2023) <doi:10.3982/ECTA18260>, that takes advantage of this additional structure and provides nonparametric estimates of the heterogeneity within the aggregate unit. The idea is to replicate the quantile function associated with the treated unit by a weighted average of quantile functions of the control units. The package contains tools for aggregating and plotting the resulting distributional estimates, as well as for carrying out inference on them.

Last updated 3 days ago

0.36 score 72 dependencies

stacks - Tidy Model Stacking

Model stacking is an ensemble technique that involves training a model to combine the outputs of many diverse statistical models, and has been shown to improve predictive performance in a variety of settings. 'stacks' implements a grammar for 'tidymodels'-aligned model stacking.

Last updated 4 days ago

0.36 score 88 dependencies

mtarm - Bayesian Estimation of Multivariate Threshold Autoregressive Models

Estimation, inference and forecasting using the Bayesian approach for multivariate threshold autoregressive (TAR) models in which the distribution used to describe the noise process belongs to the class of Gaussian variance mixtures.

Last updated 4 days ago

0.36 score 4 dependencies

UKB.COVID19 - UK Biobank COVID-19 Data Processing and Risk Factor Association Tests

Process UK Biobank COVID-19 test result data for susceptibility, severity and mortality analyses, perform potential non-genetic COVID-19 risk factor and co-morbidity association tests. Wang et al. (2021) <doi:10.5281/zenodo.5174381>.

Last updated 4 days ago

1 stars 0.36 score 129 dependencies

MetaHD - A Multivariate Meta-Analysis Model for Metabolomics Data

Performs multivariate meta-analysis for high-dimensional metabolomics data for integrating and collectively analysing individual-level metabolomics data generated from multiple studies as well as for combining summary estimates. This approach accounts for correlation between metabolites, considers variability within and between studies, handles missing values and uses shrinkage estimation to allow for high dimensionality. A detailed vignette with example datasets and code to prepare data and analyses are available on <https://bookdown.org/a2delivera/MetaHD/>.

Last updated 4 days ago

0.36 score 33 dependencies

HDRFA - High-Dimensional Robust Factor Analysis

Factor models have been widely applied in areas such as economics and finance, and the well-known heavy-tailedness of macroeconomic/financial data should be taken into account when conducting factor analysis. We propose two algorithms to do robust factor analysis by considering the Huber loss. One is based on minimizing the Huber loss of the idiosyncratic error's L2 norm, which turns out to do Principal Component Analysis (PCA) on the weighted sample covariance matrix and thereby named as Huber PCA. The other one is based on minimizing the element-wise Huber loss, which can be solved by an iterative Huber regression algorithm. In this package we also provide the code for traditional PCA, the Robust Two Step (RTS) method by He et al. (2022) and the Quantile Factor Analysis (QFA) method by Chen et al. (2021) and He et al. (2023).

Last updated 4 days ago

0.36 score 8 dependencies

GeneNMF - Non-Negative Matrix Factorization for Single-Cell Omics

A collection of methods to extract gene programs from single-cell gene expression data using non-negative matrix factorization (NMF). 'GeneNMF' contains functions to directly interact with the 'Seurat' toolkit and derive interpretable gene program signatures.

Last updated 4 days ago

1 stars 0.36 score 151 dependencies

r2sundials - Wrapper for 'SUNDIALS' Solving ODE and Sensitivity Problem

Wrapper for widely used 'SUNDIALS' software (SUite of Nonlinear and DIfferential/ALgebraic Equation Solvers) and more precisely to its 'CVODES' solver. It is aiming to solve ordinary differential equations (ODE) and optionally pending forward sensitivity problem. The wrapper is made 'R' friendly by allowing to pass custom parameters to user's callback functions. Such functions can be both written in 'R' and in 'C++' ('RcppArmadillo' flavor). In case of 'C++', performance is greatly improved so this option is highly advisable when performance matters. If provided, Jacobian matrix can be calculated either in dense or sparse format. In the latter case 'rmumps' package is used to solve corresponding linear systems. Root finding and pending event management are optional and can be specified as 'R' or 'C++' functions too. This makes them a very flexible tool for controlling the ODE system during the time course simulation. 'SUNDIALS' library was published in Hindmarsh et al. (2005) <doi:10.1145/1089014.1089020>.

Last updated 4 days ago

0.23 score 3 dependencies

phoenics - Pathways Longitudinal and Differential Analysis in Metabolomics

Perform a differential analysis at pathway level based on metabolite quantifications and information on pathway metabolite composition. The method is based on a Principal Component Analysis step and on a linear mixed model. Automatic query of metabolic pathways is also implemented.

Last updated 4 days ago

0.23 score 111 dependencies

eimpute - Efficiently Impute Large Scale Incomplete Matrix

Efficiently impute large scale matrix with missing values via its unbiased low-rank matrix approximation. Our main approach is Hard-Impute algorithm proposed in <https://www.jmlr.org/papers/v11/mazumder10a.html>, which achieves highly computational advantage by truncated singular-value decomposition.

Last updated 4 days ago

0.23 score 2 dependencies

brea - Bayesian Recurrent Events Analysis

Functions to produce MCMC samples for posterior inference in semiparametric Bayesian discrete time competing risks recurrent events models and multistate models.

Last updated 4 days ago

0.23 score 0 dependencies

wehoop - Access Women's Basketball Play by Play Data

A utility for working with women's basketball data. A scraping and aggregating interface for the WNBA Stats API <https://stats.wnba.com/> and ESPN's <https://www.espn.com> women's college basketball and WNBA statistics. It provides users with the capability to access the game play-by-plays, box scores, standings and results to analyze the data for themselves.

Last updated 5 days ago

0.23 score 58 dependencies

ganDataModel - Build a Metric Subspaces Data Model for a Data Source

Neural networks are applied to create a density value function which approximates density values for a data source. The trained neural network is analyzed for different levels. For each level metric subspaces with density values above a level are determined. The obtained set of metric subspaces and the trained neural network are assembled into a data model. A prerequisite is the definition of a data source, the generation of generative data and the calculation of density values. These tasks are executed using package 'ganGenerativeData' <https://cran.r-project.org/package=ganGenerativeData>.

Last updated 5 days ago

0.23 score 30 dependencies

PMwR - Portfolio Management with R

Tools for the practical management of financial portfolios: backtesting investment and trading strategies, computing profit/loss and returns, analysing trades, handling lists of transactions, reporting, and more. The package provides a small set of reliable, efficient and convenient tools for processing and analysing trade/portfolio data. The Manual provides all the details; it is available from <https://enricoschumann.net/R/packages/PMwR/manual/PMwR.html>. Examples and descriptions of new features are provided at <https://enricoschumann.net/notes/PMwR/>.

Last updated 5 days ago

0.23 score 7 dependencies

czso - Use Open Data from the Czech Statistical Office in R

Get programmatic access to the open data provided by the Czech Statistical Office (CZSO, <https://czso.cz>).

Last updated 6 days ago

0.23 score 35 dependencies

cardx - Extra Analysis Results Data Utilities

Create extra Analysis Results Data (ARD) summary objects. The package supplements the simple ARD functions from the 'cards' package, exporting functions to put statistical results in the ARD format. These objects are used and re-used to construct summary tables, visualizations, and written reports.

Last updated 6 days ago

0.23 score 22 dependencies

finalfit - Quickly Create Elegant Regression Results Tables and Plots when Modelling

Generate regression results tables and plots in final format for publication. Explore models and export directly to PDF and 'Word' using 'RMarkdown'.

Last updated 2 days ago

0.09 score 80 dependencies

wiesbaden - Access Databases from the Federal Statistical Office of Germany

Retrieve and import data from different databases of the Federal Statistical Office of Germany (DESTATIS) using their SOAP XML web service <https://www-genesis.destatis.de/>.

Last updated 4 days ago

0.09 score 41 dependencies

tenm - Temporal Ecological Niche Models

Implements methods and functions to calibrate time-specific niche models (multi-temporal calibration), letting users execute a strict calibration and selection process of niche models based on ellipsoids, as well as functions to project the potential distribution in the present and in global change scenarios.The 'tenm' package has functions to recover information that may be lost or overlooked while applying a data curation protocol. This curation involves preserving occurrences that may appear spatially redundant (occurring in the same pixel) but originate from different time periods. A novel aspect of this package is that it might reconstruct the fundamental niche more accurately than mono-calibrated approaches. The theoretical background of the package can be found in Peterson et al. (2011)<doi:10.5860/CHOICE.49-6266>.

Last updated 4 days ago

0.09 score 65 dependencies

ssdGSA - Single Sample Directional Gene Set Analysis

A method that inherits the standard gene set variation analysis (GSVA) method and also provides the option to use summary statistics from any analysis (disease vs healthy, lesional side vs nonlesional side, etc..) input to define the direction of gene sets used for directional gene set score calculation for a given disease. Hanzelmann, S., Castelo, R., and Guinney, J. (2013) <doi:10.1186/1471-2105-14-7>.

Last updated 4 days ago

0.09 score 152 dependencies

pastboon - Simulation of Parameterized Stochastic Boolean Networks

Applying stochastic noise to Boolean networks is a useful approach for representing the effects of various perturbing stimuli on complex systems. A number of methods have been developed to control noise effects on Boolean networks using parameters integrated into the update rules. This package provides functions to examine three such methods: BNp (Boolean network with perturbations), described by Trairatphisan et al. (2013) <doi:10.1186/1478-811X-11-46>, SDDS (stochastic discrete dynamical systems), proposed by Murrugarra et al. (2012) <doi:10.1186/1687-4153-2012-5>, and PEW (Boolean network with probabilistic edge weights), presented by Deritei et al. (2022) <doi:10.1371/journal.pcbi.1010536>. This package includes source code derived from the 'BoolNet' package, which is licensed under the Artistic License 2.0.

Last updated 4 days ago

0.09 score 0 dependencies

dafishr - Download, Wrangle, and Analyse Vessel Monitoring System Data

Allows to download, clean and analyse raw Vessel Monitoring System, VMS, data from Mexican government. You can use the vms_download() function to download raw data, or you can use the sample_dataset provided within the package. You can follow the tutorial in the vignette available at <https://cbmc-gcmp.github.io/dafishr/index.html>.

Last updated 4 days ago

0.09 score 101 dependencies

bsvarSIGNs - Bayesian SVARs with Sign, Zero, and Narrative Restrictions

Implements state-of-the-art algorithms for the Bayesian analysis of Structural Vector Autoregressions (SVARs) identified by sign, zero, and narrative restrictions. The core model is based on a flexible Vector Autoregression with estimated hyper-parameters of the Minnesota prior and the dummy observation priors as in Giannone, Lenza, Primiceri (2015) <doi:10.1162/REST_a_00483>. The sign restrictions are implemented employing the methods proposed by Rubio-Ramírez, Waggoner & Zha (2010) <doi:10.1111/j.1467-937X.2009.00578.x>, while identification through sign and zero restrictions follows the approach developed by Arias, Rubio-Ramírez, & Waggoner (2018) <doi:10.3982/ECTA14468>. Furthermore, our tool provides algorithms for identification via sign and narrative restrictions, in line with the methods introduced by Antolín-Díaz and Rubio-Ramírez (2018) <doi:10.1257/aer.20161852>. Users can also estimate a model with sign, zero, and narrative restrictions imposed at once. The package facilitates predictive and structural analyses using impulse responses, forecast error variance and historical decompositions, forecasting and conditional forecasting, as well as analyses of structural shocks and fitted values. All this is complemented by colourful plots, user-friendly summary functions, and comprehensive documentation. The 'bsvarSIGNs' package is aligned regarding objects, workflows, and code structure with the R package 'bsvars' by Woźniak (2024) <doi:10.32614/CRAN.package.bsvars>, and they constitute an integrated toolset.

Last updated 4 days ago

0.09 score 10 dependencies

aka - Define Aliases for R Expressions

Create aliases for other R names or arbitrarily complex R expressions. Accessing the alias acts as-if the aliased expression were invoked instead, and continuously reflects the current value of that expression: updates to the original expression will be reflected in the alias; and updates to the alias will automatically be reflected in the original expression.

Last updated 4 days ago

0.09 score 0 dependencies

serocalculator - Estimating Infection Rates from Serological Data

Translates antibody levels measured in cross-sectional population samples into estimates of the frequency with which seroconversions (infections) occur in the sampled populations. Replaces the previous 'seroincidence' package. Methods originally published in Simonsen et al. (2009) <doi:10.1002/sim.3592> and Teunis et al. (2012) <doi:10.1002/sim.5322>, and further developed in subsequent publications by de Graaf et al. (2014) <doi:10.1016/j.epidem.2014.08.002>, Teunis et al. (2016) <doi:10.1016/j.epidem.2016.04.001>, and Teunis et al. (2020) <doi:10.1002/sim.8578>.

Last updated 5 days ago

0.09 score 108 dependencies

poldis - Analyse Political Texts

Wrangle and annotate different types of political texts. It also introduces Urgency Analysis, a new method for the analysis of urgency in political texts.

Last updated 5 days ago

0.09 score 60 dependencies

moc.gapbk - Multi-Objective Clustering Algorithm Guided by a-Priori Biological Knowledge

Implements the Multi-Objective Clustering Algorithm Guided by a-Priori Biological Knowledge (MOC-GaPBK) which was proposed by Parraga-Alava, J. et. al. (2018) <doi:10.1186/s13040-018-0178-4>. It was designed for clustering genes based on co-expression, biological coherence, compactness, and separation criteria. However, its flexible design allows it to be applied to cluster data of various types and domains. The algorithm optimizes object relationships based on two objective functions using cluster quality indexes, incorporating intensification and diversification strategies to enhance the search process.

Last updated 5 days ago

0.09 score 11 dependencies

minimapR - Wrapper for 'minimap2'

Wrapper for 'Minimap2'. 'Minimap2' is a very valuable long read aligner for the Pacbio and Oxford Nanopore Technologies sequencing platforms. 'minimapR' is an R wrapper for 'minimap2' which was developed by Heng Li <[email protected]>. *SPECIAL NOTES 1. Examples can only be run from 'GitHub' installation. 2. If using a Windows operating system, installation of the 'MSYS2' Linux emulator is required. 3. If using a Mac operating system, installation of 'Homebrew' is required. Li, Heng (2018) <doi:10.1093/bioinformatics/bty191> "Minimap2: pairwise alignment for nucleotide sequences".

Last updated 5 days ago

0.09 score 65 dependencies

mimdo - Multivariate Imputation by Mahalanobis Distance Optimization

Imputes missing values of an incomplete data matrix by minimizing the Mahalanobis distance of each sample from the overall mean [Labita, GJ.D. and Tubo, B.F. (2024) <doi:10.24412/1932-2321-2024-278-115-123>].

Last updated 5 days ago

0.09 score 0 dependencies

infiltrodiscR - Minidisc Infiltrometer Data Management

A set of functions for the modeling of data derived from the Minidisc Infiltrometer device. It calculates cumulative infiltration and square root of time. Also, it calculates the A parameter based on soil physical properties.

Last updated 5 days ago

0.09 score 21 dependencies

centr - Weighted and Unweighted Spatial Centers

Generate mean and median weighted or unweighted spatial centers. Functions are analogous to their identically named counterparts within 'ArcGIS Pro'. Median center methodology based off of Kuhn and Kuenne (1962) <doi:10.1111/j.1467-9787.1962.tb00902.x>.

Last updated 5 days ago

0.09 score 13 dependencies

SumcaVer1 - Mean Square Prediction Error Estimation in Small Area Estimation

Estimation of mean squared prediction error of a small area predictor is provided. In particular, the recent method of Simple, Unified, Monte-Carlo Assisted approach for the mean squared prediction error estimation of small area predictor is provided. We also provide other existing methods of mean squared prediction error estimation such as jackknife method for the mixed logistic model.

Last updated 5 days ago

0.09 score 13 dependencies

ResultModelManager - Result Model Manager

Database data model management utilities for R packages in the Observational Health Data Sciences and Informatics program <https://ohdsi.org>. 'ResultModelManager' provides utility functions to allow package maintainers to migrate existing SQL database models, export and import results in consistent patterns.

Last updated 5 days ago

0.09 score 53 dependencies

COMMA - Correcting Misclassified Mediation Analysis

Use three methods to estimate parameters from a mediation analysis with a binary misclassified mediator. These methods correct for the problem of "label switching" using Youden's J criteria. A detailed description of the analysis methods is available in Webb and Wells (2024), "Effect estimation in the presence of a misclassified binary mediator" <doi:10.48550/arXiv.2407.06970>.

Last updated 5 days ago

0.09 score 13 dependencies

OpenRepGrid - Tools to Analyze Repertory Grid Data

Analyze repertory grids, a qualitative-quantitative data collection technique devised by George A. Kelly in the 1950s. Today, grids are used across various domains ranging from clinical psychology to marketing. The package contains functions to quantitatively analyze and visualize repertory grid data (e.g. 'Fransella', 'Bell', & 'Bannister', 2004, ISBN: 978-0-470-09080-0). The package is part of the The package is part of the <https://openrepgrid.org/> project.

Last updated 6 days ago

0.09 score 43 dependencies

OHPL - Ordered Homogeneity Pursuit Lasso for Group Variable Selection

Ordered homogeneity pursuit lasso (OHPL) algorithm for group variable selection proposed in Lin et al. (2017) <DOI:10.1016/j.chemolab.2017.07.004>. The OHPL method exploits the homogeneity structure in high-dimensional data and enjoys the grouping effect to select groups of important variables automatically. This feature makes it particularly useful for high-dimensional datasets with strongly correlated variables, such as spectroscopic data.

Last updated 6 days ago

0.09 score 12 dependencies

NPRED - Predictor Identifier: Nonparametric Prediction

Partial informational correlation (PIC) is used to identify the meaningful predictors to the response from a large set of potential predictors. Details of methodologies used in the package can be found in Sharma, A., Mehrotra, R. (2014). <doi:10.1002/2013WR013845>, Sharma, A., Mehrotra, R., Li, J., & Jha, S. (2016). <doi:10.1016/j.envsoft.2016.05.021>, and Mehrotra, R., & Sharma, A. (2006). <doi:10.1016/j.advwatres.2005.08.007>.

Last updated 1 days ago

0.00 score 0 dependencies

WormTensor - A Clustering Method for Time-Series Whole-Brain Activity Data of 'C. elegans'

A toolkit to detect clusters from distance matrices. The distance matrices are assumed to be calculated between the cells of multiple animals ('Caenorhabditis elegans') from input time-series matrices. Some functions for generating distance matrices, performing clustering, evaluating the clustering, and visualizing the results of clustering and evaluation are available. We're also providing the download function to retrieve the calculated distance matrices from 'figshare' <https://figshare.com>.

Last updated 3 days ago

0.00 score 148 dependencies

trud - Query the 'NHS TRUD API'

A convenient R interface to the 'National Health Service (NHS) Technology Reference Update Distribution (TRUD) API'. Retrieve available releases for items that you are subscribed to and download these with ease. For more information on the API, see <https://isd.digital.nhs.uk/trud/users/guest/filters/0/api>.

Last updated 4 days ago

0.00 score 31 dependencies

pm3 - Propensity Score Matching for Unordered 3-Group Data

You can use this program for 3 sets of categorical data for propensity score matching. Assume that the data has 3 different categorical variables. You can use it to perform propensity matching of baseline indicator groupings. The matching will make the differences in the baseline data smaller. This method was described by Alvaro Fuentes (2022) <doi:10.1080/00273171.2021.1925521>.

Last updated 4 days ago

0.00 score 54 dependencies

StuteTest - Stute (1997) Linearity Test

Non-parametric test, originally proposed by Stute (1997) <https://www.jstor.org/stable/2242560>, that the expectation of a dependent variable Y given an independent variable D is linear in D.

Last updated 4 days ago

0.00 score 34 dependencies

trdist - Univariate Proability Distributions with Truncation

Truncation of univariate probability distributions. The probability distribution can come from other packages so long as the function names follow the standard d, p, q, r naming format. Also other univariate probability distributions are included.

Last updated 5 days ago

0.00 score 0 dependencies

tetRys - Game of 'tetRys'

A game inspired by 'Tetris'. Opens a plot window device and starts a game of 'tetRys' in it. Steer the tetrominos with the arrow keys, press Pause to pause and Esc to end the game.

Last updated 5 days ago

0.00 score 1 dependencies

kpcaIG - Variables Interpretability with Kernel PCA

The kernelized version of principal component analysis (KPCA) has proven to be a valid nonlinear alternative for tackling the nonlinearity of biological sample spaces. However, it poses new challenges in terms of the interpretability of the original variables. 'kpcaIG' aims to provide a tool to select the most relevant variables based on the kernel PCA representation of the data as in Briscik et al. (2023) <doi:10.1186/s12859-023-05404-y>. It also includes functions for 2D and 3D visualization of the original variables (as arrows) into the kernel principal components axes, highlighting the contribution of the most important ones.

Last updated 5 days ago

0.00 score 59 dependencies

geotoolsR - Tools to Improve the Use of Geostatistic

The basic idea of this package is provides some tools to help the researcher to work with geostatistics. Initially, we present a collection of functions that allow the researchers to deal with spatial data using bootstrap procedure. There are five methods available and two ways to display them: bootstrap confidence interval - provides a two-sided bootstrap confidence interval; bootstrap plot - a graphic with the original variogram and each of the B bootstrap variograms.

Last updated 5 days ago

0.00 score 39 dependencies

bodycompref - Reference Values for CT-Assessed Body Composition

Get z-scores, percentiles, absolute values, and percent of predicted of a reference cohort. Functionality requires installing the data packages 'adiposerefdata' and 'musclerefdata'. For more information on the underlying research, please visit our website which also includes a graphical interface. The models and underlying data are described in Marquardt JP et al.(planned publication 2025; reserved doi 10.1097/RLI.0000000000001104), "Subcutaneous and Visceral adipose tissue Reference Values from Framingham Heart Study Thoracic and Abdominal CT", *Investigative Radiology* and Tonnesen PE et al. (2023), "Muscle Reference Values from Thoracic and Abdominal CT for Sarcopenia Assessment [column] The Framingham Heart Study", *Investigative Radiology*, <doi:10.1097/RLI.0000000000001012>.

Last updated 5 days ago

0.00 score 16 dependencies

MLE - Maximum Likelihood Estimation of Various Univariate and Multivariate Distributions

Maximum likelihood estimation of various univariate and multivariate distributions. The list includes univariate continuous and discrete distributions, distributions that lie on the real line, the positive line, interval restricted, circular distributions. Further, multivariate continuous and discrete distributions, distributions for compositional and directional data, etc. Some references include Johnson N. L., Kotz S. and Balakrishnan N. (1994). "Continuous Univariate Distributions, Volume 1" <ISBN:978-0-471-58495-7>, Johnson, Norman L. Kemp, Adrianne W. Kotz, Samuel (2005). "Univariate Discrete Distributions". <ISBN:978-0-471-71580-1> and Mardia, K. V. and Jupp, P. E. (2000). "Directional Statistics". <ISBN:978-0-471-95333-3>.

Last updated 5 days ago

0.00 score 127 dependencies

WASP - Wavelet System Prediction

The wavelet-based variance transformation method is used for system modelling and prediction. It refines predictor spectral representation using Wavelet Theory, which leads to improved model specifications and prediction accuracy. Details of methodologies used in the package can be found in Jiang, Z., Sharma, A., & Johnson, F. (2020) <doi:10.1029/2019WR026962>, Jiang, Z., Rashid, M. M., Johnson, F., & Sharma, A. (2020) <doi:10.1016/j.envsoft.2020.104907>, and Jiang, Z., Sharma, A., & Johnson, F. (2021) <doi:10.1016/J.JHYDROL.2021.126816>.

Last updated 6 days ago

0.00 score 52 dependencies