Analyzing pedigree data of wild populations. While primarily designed to process outputs from the COLONY (Jones & Wang (2010) <doi:10.1111/j.1755-0998.2009.02787.x>) pedigree reconstruction software, it can also accommodate data from other sources. By linking reconstructed pedigrees with genetic sample metadata, wpeR produces spatial and temporal visualizations as well as tabular summaries that support interpretation of family structures and dynamics. The main goal of the package is to provide a solution for the analysis of complex wild pedigree data and to help the user to gain insights into genetic relationships within wild animal populations.

Download and plot education specific demographic data from the Wittgenstein Centre for Demography and Human Capital Data Explorer <https://dataexplorer.wittgensteincentre.org/>.

This package provides a comprehensive data analysis framework for NIH-funded research that streamlines workflows for both data cleaning and preparing NIH Data Archive ('NDA') submission templates. Provides unified access to multiple data sources ('REDCap', MongoDB', Qualtrics', SQL', ORACLE') through interfaces to their APIs, with specialized functions for data cleaning, filtering, merging, and parsing. Features automatic validation, field harmonization, and memory-aware processing to enhance reproducibility in multi-site collaborative research as described in Mittal et al. (2021) <doi:10.20900/jpbs.20210011>.

This package provides survival analysis functions with support for time-dependent and subject-specific (e.g., propensity score) weighting. Implements weighted estimation for Cox models, Kaplan-Meier survival curves, and treatment differences with point-wise and simultaneous confidence bands. Includes restricted mean survival time (RMST) comparisons evaluated across all potential truncation times with both point-wise and simultaneous confidence bands. See Cole, S. R. & Hernán, M. A. (2004) <doi:10.1016/j.cmpb.2003.10.004> for methodological background.

This package provides tools for fitting and simulating mixtures of Watson distributions. The package is described in Sablica, Hornik and Leydold (2026) <doi:10.18637/jss.v115.i04>. The random sampling scheme of the package offers two sampling algorithms that are based of the results of Sablica, Hornik and Leydold (2022) <doi:10.1080/10618600.2024.2416521>. What is more, the package offers a smart tool to combine these two methods, and based on the selected parameters, it approximates the relative sampling speed for both methods and picks the faster one. In addition, the package offers a fitting function for the mixtures of Watson distribution, that uses the expectation-maximization (EM) algorithm. Special features are the possibility to use multiple variants of the E-step and M-step, sparse matrices for the data representation and state of the art methods for numerical evaluation of needed special functions using the results of Sablica and Hornik (2022) <doi:10.1090/mcom/3690> and Sablica and Hornik (2024) <doi:10.1016/j.jmaa.2024.128262>.

This package provides a wrapper around Michel Scheffers's libassp (<https://libassp.sourceforge.net/>). The libassp (Advanced Speech Signal Processor) library aims at providing functionality for handling speech signal files in most common audio formats and for performing analyses common in phonetic science/speech science. This includes the calculation of formants, fundamental frequency, root mean square, auto correlation, a variety of spectral analyses, zero crossing rate, filtering etc. This wrapper provides R with a large subset of libassp's signal processing functions and provides them to the user in a (hopefully) user-friendly manner.

This package provides 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>.

Retrieval the leaf area index (LAI) and soil moisture (SM) from microwave backscattering data using water cloud model (WCM) model . The WCM algorithm attributed to Pervot et al.(1993) <doi:10.1016/0034-4257(93)90053-Z>. The authors are grateful to SAC, ISRO, Ahmedabad for providing financial support to Dr. Prashant K Srivastava to conduct this research work.

Estimates the standard and weighted Elo (WElo, Angelini et al., 2022 <doi:10.1016/j.ejor.2021.04.011>) rates. The current version provides Elo and WElo rates for tennis, according to different systems of weights (games or sets) and scale factors (constant, proportional to the number of matches, with more weight on Grand Slam matches or matches played on a specific surface). Moreover, the package gives the possibility of estimating the (bootstrap) standard errors for the rates. Finally, the package includes betting functions that automatically select the matches on which place a bet.

The weighted scores method and composite likelihood information criteria as an intermediate step for variable/correlation selection for longitudinal ordinal and count data in Nikoloulopoulos, Joe and Chaganty (2011) <doi:10.1093/biostatistics/kxr005>, Nikoloulopoulos (2016) <doi:10.1002/sim.6871> and Nikoloulopoulos (2017) <arXiv:1510.07376>.

This package provides a set of functions devoted to multivariate exploratory statistics on textual data. Classical methods such as correspondence analysis and agglomerative hierarchical clustering are available. Chronologically constrained agglomerative hierarchical clustering enriched with labelled-by-words trees is offered. Given a division of the corpus into parts, their characteristic words and documents are identified. Further, accessing to FactoMineR functions is very easy. Two of them are relevant in textual domain. MFA() addresses multiple lexical table allowing applications such as dealing with multilingual corpora as well as simultaneously analyzing both open-ended and closed questions in surveys. See <http://xplortext.unileon.es> for examples.

This package implements a probabilistic approach to time series forecasting combining XGBoost regression with conformal inference methods. The package provides functionality for generating predictive distributions, evaluating uncertainty, and optimizing hyperparameters using Bayesian, coarse-to-fine, or random search strategies.

An R interface to the OpenPyXL Python library to create native Excel charts and work with Microsoft Excel files.

Read and write XES Files to create event log objects used by the bupaR framework. XES (Extensible Event Stream) is the `IEEE` standard for storing and sharing event data (see <http://standards.ieee.org/findstds/standard/1849-2016.html> for more info).

This tool enables in-database scoring of XGBoost models built in R, by translating trained model objects into SQL query. XGBoost <https://github.com/dmlc/xgboost> provides parallel tree boosting (also known as gradient boosting machine, or GBM) algorithms in a highly efficient, flexible and portable way. GBM algorithm is introduced by Friedman (2001) <doi:10.1214/aos/1013203451>, and more details on XGBoost can be found in Chen & Guestrin (2016) <doi:10.1145/2939672.2939785>.

This package implements the recursively detrended panel unit root tests proposed by Westerlund (2015) <doi:10.1016/j.jeconom.2014.09.013>. Two variants are provided: the basic t-REC test assuming iid errors, and the robust t-RREC test that accounts for serial correlation, cross-sectional dependence, and heteroskedasticity via defactoring and BIC-selected lag augmentation. Both tests have a standard normal null distribution requiring no mean or variance correction. The panel must be strongly balanced.

This package provides functions for Estimating a (c)DCC-GARCH Model in large dimensions based on a publication by Engle et,al (2017) <doi:10.1080/07350015.2017.1345683> and Nakagawa et,al (2018) <doi:10.3390/ijfs6020052>. This estimation method is consist of composite likelihood method by Pakel et al. (2014) <http://paneldataconference2015.ceu.hu/Program/Cavit-Pakel.pdf> and (Non-)linear shrinkage estimation of covariance matrices by Ledoit and Wolf (2004,2015,2016). (<doi:10.1016/S0047-259X(03)00096-4>, <doi:10.1214/12-AOS989>, <doi:10.1016/j.jmva.2015.04.006>).

This package provides tools to download and merge data files on sub-national conflict, violence and protests from <http://www.x-sub.org>.

Grammatical evolution (see O'Neil, M. and Ryan, C. (2003,ISBN:1-4020-7444-1)) uses decoders to convert linear (binary or integer genes) into programs. In addition, automatic determination of codon precision with a limited rule choice bias is provided. For a recent survey of grammatical evolution, see Ryan, C., O'Neill, M., and Collins, J. J. (2018) <doi:10.1007/978-3-319-78717-6>.

This package provides tools to analyze sex differences in omics data for complex diseases. It includes functions for differential expression analysis using the limma method <doi:10.1093/nar/gkv007>, interaction testing between sex and disease, pathway enrichment with clusterProfiler <doi:10.1089/omi.2011.0118>, and gene regulatory network (GRN) construction and analysis using igraph'. The package enables a reproducible workflow from raw data processing to biological interpretation.

Helpers for transforming XML content into number of tables while preserving parent to child relationships.

This package implements an iterative mean-variance panel regression estimator that allows both the mean and variance of the dependent variable to be functions of covariates. The method alternates between estimating a mean equation (using generalized linear models with Gaussian family) and a variance equation (using generalized linear models with Gamma family on squared within-group residuals) until convergence. Based on the methodology in Mooi-Reci and Liao (2025) <doi:10.1093/esr/jcae052>.

Provide R functions to read/write/format Excel 2007 and Excel 97/2000/XP/2003 file formats.

Reading and writing sheets of a single Excel file into and from a list of data frames. Eases I/O of tabular data in bioinformatics while keeping them in a human readable format.