This package provides subsets with reference semantics, i.e. subsets which automatically reflect changes in the original object, and which optionally update the original object when they are changed.

Estimation of Bayes and local Bayes false discovery rates for replicability analysis (Heller & Yekutieli, 2014 <doi:10.1214/13-AOAS697> ; Heller at al., 2015 <doi: 10.1093/bioinformatics/btu434>).

This package makes GREAT (Genomic Regions Enrichment of Annotations Tool) analysis automatic by constructing a HTTP POST request according to user's input and automatically retrieving results from GREAT web server.

This package performs Random Subspace Method (RSM) for high-dimensional linear regression to obtain variable importance measures. The final model is chosen based on validation set or Generalized Information Criterion.

This package provides methods for regression for functional data, including function-on-scalar, scalar-on-function, and function-on-function regression. Some of the functions are applicable to image data.

RT provides a framework for writing regression test suites.

This Common Lisp package provides a regular expression engine.

Library to connect and control a running dune instance.

Nucleosome positioning for Tiling Arrays and NGS experiments.

Estimates VAR and VARX models with Structured Penalties.

Dynamic simulations and graphical depictions of autoregressive relationships.

Probability distributions that are sometimes useful in hydrology.

Tabulate and plot directional and other multivariate histograms.

Generalise the starting point of the array index.

This tool provides an algorithm to identify rare cell types in single-cell data. It also identifies abundant cell types. The method is based on transcript counts obtained with unique molecular identifies.

Non-inferiority test and diagnostic test are very important in clinical trails. This package is to get a p value from the non-inferiority test for ROC curves from diagnostic test.

This package provides a tool to exchange data between R and Raven sound analysis software (Cornell Lab of Ornithology). Functions work on data formats compatible with the R package warbleR'.

Eprime is a set of programs for administering psychological experiments by computer. This package provides functions for loading, parsing, filtering and exporting data in the text files produced by Eprime experiments.

An implementation of algorithms for estimation of the graphical lasso regularization parameter described in Pedro Cisneros-Velarde, Alexander Petersen and Sang-Yun Oh (2020) <http://proceedings.mlr.press/v108/cisneros20a.html>.

Perform derivative-free optimization algorithms in R using C++. A wrapper interface is provided to call C function of the bobyqa implementation (See <https://github.com/emmt/Algorithms/tree/master/bobyqa>).

This package is a port of sofia-ml to R. Sofia-ml is a suite of fast incremental algorithms for machine learning that can be used for training models for classification or ranking.

An extremely simple stack data type, implemented with R6 classes. The size of the stack increases as needed, and the amortized time complexity is O(1). The stack may contain arbitrary objects.

This package implements diversification analyses using the phylogenetic birth-death-shift model. It leverages belief propagation techniques to calculate branch-specific diversification rates, see Kopperud & Hoehna (2025) <doi:10.1093/sysbio/syaf041>.

This package performs regularization of differential item functioning (DIF) parameters in item response theory (IRT) models (Belzak & Bauer, 2020) <https://pubmed.ncbi.nlm.nih.gov/31916799/> using a penalized expectation-maximization algorithm.