Package for Breed Wheat Genomic Selection Pipeline. The R package BWGS is developed by Louis Gautier Tran <louis.gautier.tran@gmail.com> and Gilles Charmet <gilles.charmet@inra.fr>. This repository is forked from original repository <https://forgemia.inra.fr/umr-gdec/bwgs> and modified as a R package.

This package implements a wide variety of one- and two-parameter Bayesian CRM designs. The program can run interactively, allowing the user to enter outcomes after each cohort has been recruited, or via simulation to assess operating characteristics. See Sweeting et al. (2013): <doi:10.18637/jss.v054.i13>.

Implementation of algorithms for cutting numerical values exhibiting a potentially highly skewed distribution into evenly distributed groups (bins). This functionality can be applied for binning discrete values, such as counts, as well as for discretization of continuous values, for example, during generation of features used in machine learning algorithms.

This package provides a Bayesian model averaging approach to causal effect estimation based on the BCEE algorithm. Currently supports binary or continuous exposures and outcomes. For more details, see Talbot et al. (2015) <doi:10.1515/jci-2014-0035> Talbot and Beaudoin (2022) <doi:10.1515/jci-2021-0023>.

Converts customer transaction data (ID, purchase date) into a R6 class called customer. The class stores various customer analytics calculations at the customer level. The package also contains functionality to convert data in the R6 class to data.frames that can serve as inputs for various customer analytics models.

Partition data points (variables) into communities/clusters, similar to clustering algorithms, such as k-means and hierarchical clustering. This package implements a clustering algorithm based on a new metric CORD, defined for high dimensional parametric or semi-parametric distributions. Read http://arxiv.org/abs/1508.01939 for more details.

Discover causality for bivariate categorical data. This package aims to enable users to discover causality for bivariate observational categorical data. See Ni, Y. (2022) <arXiv:2209.08579> "Bivariate Causal Discovery for Categorical Data via Classification with Optimal Label Permutation. Advances in Neural Information Processing Systems 35 (in press)".

This package contains a function, also called cchs', that calculates Estimator III of Borgan et al (2000), <DOI:10.1023/A:1009661900674>. This estimator is for fitting a Cox proportional hazards model to data from a case-cohort study where the subcohort was selected by stratified simple random sampling.

Diff, patch and merge for data frames. Document changes in data sets and use them to apply patches. Changes to data can be made visible by using render_diff(). The V8 package is used to wrap the daff.js JavaScript library which is included in the package.

This package provides a collection of functions to perform Detrended Fluctuation Analysis (DFA) and Detrended Cross-Correlation Analysis (DCCA). This package implements the results presented in Prass, T.S. and Pumi, G. (2019). "On the behavior of the DFA and DCCA in trend-stationary processes" <arXiv:1910.10589>.

Feature Ordering by Integrated R square Dependence (FORD) is a variable selection algorithm based on the new measure of dependence: Integrated R2 Dependence Coefficient (IRDC). For more information, see the paper: Azadkia and Roudaki (2025),"A New Measure Of Dependence: Integrated R2" <doi:10.48550/arXiv.2505.18146>.

This package provides a set of functions that facilitate basic data manipulation and cleaning for statistical analysis including functions for finding and fixing duplicate rows and columns, missing values, outliers, and special characters in column and row names and functions for checking data consistency, distribution, quality, reliability, and structure.

Some methods for the inference and clustering of univariate and multivariate functional data, using a generalization of Mahalanobis distance, along with some functions useful for the analysis of functional data. For further details, see Martino A., Ghiglietti, A., Ieva, F. and Paganoni A. M. (2017) <arXiv:1708.00386>.

Computes measures of multivariate kurtosis, matrices of fourth-order moments and cumulants, kurtosis-based projection pursuit. Franceschini, C. and Loperfido, N. (2018, ISBN:978-3-319-73905-2). "An Algorithm for Finding Projections with Extreme Kurtosis". Loperfido, N. (2017,ISSN:0024-3795). "A New Kurtosis Matrix, with Statistical Applications".

Spatial and spatio-temporal modelling of point patterns using the log-Gaussian Cox process. Bayesian inference for spatial, spatiotemporal, multivariate and aggregated point processes using Markov chain Monte Carlo. See Benjamin M. Taylor, Tilman M. Davies, Barry S. Rowlingson, Peter J. Diggle (2015) <doi:10.18637/jss.v063.i07>.

Multivariate Analysis methods and data sets used in John Marden's book Multivariate Statistics: Old School (2015) <ISBN:978-1456538835>. This also serves as a companion package for the STAT 571: Multivariate Analysis course offered by the Department of Statistics at the University of Illinois at Urbana-Champaign ('UIUC').

This package provides functions for MultiDimensional Feature Selection (MDFS): calculating multidimensional information gains, scoring variables, finding important variables, plotting selection results. This package includes an optional CUDA implementation that speeds up information gain calculation using NVIDIA GPGPUs. R. Piliszek et al. (2019) <doi:10.32614/RJ-2019-019>.

This package provides methods for detecting signals related to (adverse event, medical product e.g. drugs, vaccines) pairs, a data generation function for simulating pharmacovigilance datasets, and various utility functions. For more details please see Liu A., Mukhopadhyay R., and Markatou M. <doi:10.48550/arXiv.2410.01168>.

Compute and select tuning parameters for the MRCE estimator proposed by Rothman, Levina, and Zhu (2010) <doi:10.1198/jcgs.2010.09188>. This estimator fits the multiple output linear regression model with a sparse estimator of the error precision matrix and a sparse estimator of the regression coefficient matrix.

Facilitates the automatic detection of acoustic signals, providing functions to diagnose and optimize the performance of detection routines. Detections from other software can also be explored and optimized. This package has been peer-reviewed by rOpenSci. Araya-Salas et al. (2022) <doi:10.1101/2022.12.13.520253>.

Principal component of explained variance (PCEV) is a statistical tool for the analysis of a multivariate response vector. It is a dimension- reduction technique, similar to Principal component analysis (PCA), that seeks to maximize the proportion of variance (in the response vector) being explained by a set of covariates.

This package provides a tool for automatic generation of sibling items from a parent item model defined by the user. It is an implementation of the process automatic item generation (AIG) focused on generating quantitative multiple-choice type of items (see Embretson, Kingston (2018) <doi:10.1111/jedm.12166>).

This package provides methods and feature set definitions for feature or gene set enrichment analysis in transcriptional and metabolic profiling data. Package includes tests for enrichment based on ranked lists of features, functions for visualisation and multivariate functional analysis. See Zyla et al (2019) <doi:10.1093/bioinformatics/btz447>.

Calculate optimal Zhong's two-/three-stage Phase II designs (see Zhong (2012) <doi:10.1016/j.cct.2012.07.006>). Generate Target Toxicity decision table for Phase I dose-finding (two-/three-stage). This package also allows users to run dose-finding simulations based on customized decision table.