Facilities for working with Atlantis box-geometry model (BGM) files. Atlantis is a deterministic, biogeochemical, whole-of-ecosystem model. Functions are provided to read from BGM files directly, preserving their internal topology, as well as helper functions to generate spatial data from these mesh forms. This functionality aims to simplify the creation and modification of box and geometry as well as the ability to integrate with other data sources.

Interface to the ReebGraphPairing program to compute critical points of Reeb graphs following Tu, Hajij, & Rosen (2019) <doi:10.1007/978-3-030-33720-9_8> via the rJava package. Also store Reeb graphs in a minimal S3 class, convert between other network data structures, and post-process pairing data to obtain extended persistent homology following Carrière & Oudot (2018) <doi:10.1007/s10208-017-9370-z>.

Efficient algorithms for generating ensembles of robust, sparse and diverse models via robust multi-model subset selection (RMSS). The robust ensembles are generated by minimizing the sum of the least trimmed square loss of the models in the ensembles under constraints for the size of the models and the sharing of the predictors. Tuning parameters for the robustness, sparsity and diversity of the robust ensemble are selected by cross-validation.

r-kmer is an R package for rapidly computing distance matrices and clustering large sequence datasets using fast alignment-free k-mer counting and recursive k-means partitioning.

This package provides an implementation of interpreted string literals, inspired by Python's Literal String Interpolation (PEP-0498) and Docstrings (PEP-0257) and Julia's Triple-Quoted String Literals.

This package proposes a new file format named gson for storing gene set and related information, and provides read, write and other utilities to process this file format.

This package provides an integrated set of functions for the analysis of multivariate normal datasets with missing values, including implementation of the EM algorithm, data augmentation, and multiple imputation.

This is a package for model fitting, optimal model selection and calculation of various features that are essential in the analysis of quantitative real-time polymerase chain reaction (qPCR).

This package provides the Rakarrack effects as LV2 plugins. The ports are done such that hopefully when Rakarrack gets an active maintainer these will get merged into the original project.

Computationally efficient method to estimate orthant probabilities of high-dimensional Gaussian vectors. Further implements a function to compute conservative estimates of excursion sets under Gaussian random field priors.

This package implements Bayesian response-adaptive randomization methods based on Bayesian hypothesis testing for multi-arm settings (Pawel and Held, 2025, <doi:10.48550/arXiv.2510.01734>).

This package implements the Cross-contribution Compensating Multiple standard Normalization (CCMN) method described in Redestig et al. (2009) Analytical Chemistry <doi:10.1021/ac901143w> and other normalization algorithms.

This package provides analytical methods for analyzing CRISPR screen data at different levels of gene expression. Multi-component normal mixture models and EM algorithms are used for modeling.

This package provides functions to check whether a vector of p-values respects the assumptions of FDR (false discovery rate) control procedures and to compute adjusted p-values.

Fixation and saccade detection in eye movement recordings. This package implements a dispersion-based algorithm (I-DT) proposed by Salvucci & Goldberg (2000) which detects fixation duration and position.

Real capture frequencies will be fitted to various distributions which provide the basis of estimating population sizes, their standard error, and symmetric as well as asymmetric confidence intervalls.

Perform gene set enrichment analyses using the Gene set Ordinal Association Test (GOAT) algorithm and visualize your results. Koopmans, F. (2024) <doi:10.1038/s42003-024-06454-5>.

Enables calculation of image textures (Haralick 1973) <doi:10.1109/TSMC.1973.4309314> from grey-level co-occurrence matrices (GLCMs). Supports processing images that cannot fit in memory.

Providing various equations to calculate Gini coefficients. The methods used in this package can be referenced from Brown MC (1994) <doi: 10.1016/0277-9536(94)90189-9>.

Providing a method for Local Discrimination via Latent Class Models. The approach is described in <https://www.r-project.org/conferences/useR-2009/abstracts/pdf/Bucker.pdf>.

This package provides functions for simulating missing morphometric data randomly, with taxonomic bias and with anatomical bias. LOST also includes functions for estimating linear and geometric morphometric data.

Fits semi-confirmatory structural equation modeling (SEM) via penalized likelihood (PL) or penalized least squares (PLS). For details, please see Huang (2020) <doi:10.18637/jss.v093.i07>.

Model evaluation based on a modified version of the recursive feature elimination algorithm. This package is designed to determine the optimal model(s) by leveraging all available features.

This package provides routines to compute normalised prediction distribution errors, a metric designed to evaluate non-linear mixed effect models such as those used in pharmacokinetics and pharmacodynamics.