Equating of multiple forms using Item Response Theory (IRT) methods (Battauz M. (2017) <doi:10.1007/s11336-016-9517-x>, Battauz and Leoncio (2023) <doi:10.1177/01466216231151702>, Haberman S. J. (2009) <doi:10.1002/j.2333-8504.2009.tb02197.x>).

This package provides samplers for various matrix variate distributions: Wishart, inverse-Wishart, normal, t, inverted-t, Beta type I, Beta type II, Gamma, confluent hypergeometric. Allows to simulate the noncentral Wishart distribution without the integer restriction on the degrees of freedom.

This package implements the Bayesian hierarchical model described by Wheldon, Raftery, Clark and Gerland (see: <doi:10.1080/01621459.2012.737729>) for simultaneously estimating age-specific population counts, fertility rates, mortality rates and net international migration flows, at the national level.

Detection of anomalous space-time clusters using the scan statistics methodology. Focuses on prospective surveillance of data streams, scanning for clusters with ongoing anomalies. Hypothesis testing is made possible by Monte Carlo simulation. Allévius (2018) <doi:10.21105/joss.00515>.

The package checks references in a document, looking for numbered but unlabelled equations, for labels which are not used in the text, for unused bibliography references. It can also display label names in text near corresponding numbers of equations and/or bibliography references.

This package provides a set of LaTeX macros that makes it easy to produce linguistic tree diagrams suitable for Role and Reference Grammar (RRG). This package allows the construction of trees with crossing lines, as is required by this theory for many languages.

This package provides a data.frame containing an extended probe manifest for the Illumina Infinium Methylation v2.0 Kit. Contains the complete manifest from the Illumina-provided EPIC-8v2-0_EA.csv, plus additional probewise information described in Peters et al. (2024).

Draw horizontal histograms, color scattered points by 3rd dimension, enhance date- and log-axis plots, zoom in X11 graphics, trace errors and warnings, use the unit hydrograph in a linear storage cascade, convert lists to data.frames and arrays, fit multiple functions.

This package implements a data-augmented block Gibbs sampler for simulating the posterior distribution of concentration matrices for specifying the topology and parameterization of a Gaussian Graphical Model (GGM). This sampler was originally proposed in Wang (2012) <doi:10.1214/12-BA729>.

This package provides an interface to D4Science StorageHub API (<https://dev.d4science.org/>). Allows to get user profile, and perform actions over the StorageHub (workspace) including creation of folders, files management (upload/update/deletion/sharing), and listing of stored resources.

This package creates PRISMA <http://prisma-statement.org/> diagram from a minimal dataset of included and excluded studies and allows for more custom diagrams. PRISMA diagrams are used to track the identification, screening, eligibility, and inclusion of studies in a systematic review.

Imbibition causes seeds to expand, which results in the seed coat or testa being broken. Seed germination begins with imbibition. Imbibition aids in the transport of water into the developing ovules. Imbibition is required during the first stages of root water absorption.

The ReportingTools package enables users to easily display reports of analysis results generated from sources such as microarray and sequencing data. The package allows users to create HTML pages that may be viewed on a web browser, or in other formats. Users can generate tables with sortable and filterable columns, make and display plots, and link table entries to other data sources such as NCBI or larger plots within the HTML page. Using the package, users can also produce a table of contents page to link various reports together for a particular project that can be viewed in a web browser.

This package provides functions and methods for manipulating SNOMED CT concepts. The package contains functions for loading the SNOMED CT release into a convenient R environment, selecting SNOMED CT concepts using regular expressions, and navigating the SNOMED CT ontology. It provides the SNOMEDconcept S3 class for a vector of SNOMED CT concepts (stored as 64-bit integers) and the SNOMEDcodelist S3 class for a table of concepts IDs with descriptions. The package can be used to construct sets of SNOMED CT concepts for research (<doi:10.1093/jamia/ocac158>). For more information about SNOMED CT visit <https://www.snomed.org/>.

This package represents an integrative method of analyzing multi omics data that conducts enrichment analysis of annotated gene sets. ActivePathways uses a statistical data fusion approach, rationalizes contributing evidence and highlights associated genes, improving systems-level understanding of cellular organization in health and disease.

The purpose of the PPIx-Regexp package is to parse regular expressions in a manner similar to the way the PPI package parses Perl. This class forms the root of the parse tree, playing a role similar to PPI::Document.

The package will report number of used registers (counter, dimen, skip, muskip, box, token, input, output, math families, languages, insertions), and will compare the number to the maximum available number of such registers.

This package provides a tool to obtain activity counts, originally a translation of the python package agcounts <https://github.com/actigraph/agcounts>. This tool allows the processing of data from any accelerometer brand, with a more flexible approach to handle different sampling frequencies.

Algorithms for automatically finding appropriate thresholds for numerical data, with special functions for thresholding images. Provides the ImageJ Auto Threshold plugin functionality to R users. See <https://imagej.net/plugins/auto-threshold> and Landini et al. (2017) <DOI:10.1111/jmi.12474>.

This package provides function declarations and inline function definitions that facilitate communication between R and the Armadillo C++ library for linear algebra and scientific computing. This implementation is detailed in Vargas Sepulveda and Schneider Malamud (2024) <doi:10.1016/j.softx.2025.102087>.

This package provides methods for fitting mixture distributions to univariate data using expectation maximization, HWHM and other methods. Supports Gaussian, Cauchy, Student's t and von Mises mixtures. For more details see Merkys (2018) <https://www.lvb.lt/permalink/370LABT_NETWORK/1m6ui06/alma9910036312108451>.

This is the core functions needed by the tsmp package. The low level and carefully checked mathematical functions are here. These are implementations of the Matrix Profile concept that was created by CS-UCR <http://www.cs.ucr.edu/~eamonn/MatrixProfile.html>.

This is a data-only package, containing data needed to run the CRAN package pathfindR', a package for enrichment analysis utilizing active subnetworks. This package contains protein-protein interaction network data, data related to gene sets and example input/output data.

This package provides tools for using the StreamCat and LakeCat API and interacting with the StreamCat and LakeCat database. Convenience functions in the package wrap the API for StreamCat on <https://api.epa.gov/StreamCat/streams/metrics>.