This package provides tools to visualize simple graphs (networks) based on a transition matrix, utilities to plot flow diagrams, visualizing webs, electrical networks, etc. It also includes supporting material for the book "A practical guide to ecological modelling - using R as a simulation platform" by Karline Soetaert and Peter M.J. Herman (2009) and the book "Solving Differential Equations in R" by Karline Soetaert, Jeff Cash and Francesca Mazzia (2012).

tidyr is a reframing of the reshape2 package designed to accompany the tidy data framework, and to work hand-in-hand with magrittr and dplyr to build a solid pipeline for data analysis. It is designed specifically for tidying data, not the general reshaping that reshape2 does, or the general aggregation that reshape did. In particular, built-in methods only work for data frames, and tidyr provides no margins or aggregation.

This package provides a C++11-style thread class and thread pool that can safely be interrupted from R.

This package simulates continuous distributions of random vectors using Markov chain Monte Carlo (MCMC). Users specify the distribution by an R function that evaluates the log unnormalized density. Algorithms are random walk Metropolis algorithm (function metrop), simulated tempering (function temper), and morphometric random walk Metropolis (function morph.metrop), which achieves geometric ergodicity by change of variable.

This package provides functions to perform reproducible parallel foreach loops, using independent random streams as generated by L'Ecuyer's combined multiple-recursive generator. It enables to easily convert standard %dopar% loops into fully reproducible loops, independently of the number of workers, the task scheduling strategy, or the chosen parallel environment and associated foreach backend.

This package provides enhanced message functions (cat() / message() / warning() / error()) using wrappers around sprintf(). It also provides multiple assertion functions (e.g. to check class, length, values, files, arguments, etc.).

This package provides utility functions that enhance the parallel package and support the built-in parallel backends of the future package. For example, availableCores gives the number of CPU cores available to your R process as given by R options and environment variables, including those set by job schedulers on high-performance compute clusters. If none is set, it will fall back to parallel::detectCores. Another example is makeClusterPSOCK, which is backward compatible with parallel::makePSOCKcluster while doing a better job in setting up remote cluster workers without the need for configuring the firewall to do port-forwarding to your local computer.

This package provides functions for the input/output and visualization of medical imaging data that follow either the ANALYZE, NIfTI or AFNI formats. This package is part of the Rigorous Analytics bundle.

This package offers an easy to use way to draw a Venn diagram with ggplot2.

Asio is a cross-platform C++ library for network and low-level I/O programming that provides developers with a consistent asynchronous model using a modern C++ approach. It is also included in Boost but requires linking when used with Boost. Standalone it can be used header-only (provided a recent compiler). Asio is written and maintained by Christopher M. Kohlhoff, and released under the Boost Software License', Version 1.0.

This package lets you import OpenDocument Spreadsheet (ODS) into R as a data frame. It also supports writing data frames to an ODS file.

This package contains miscellaneous functions used to interpret and translate, factorize and negate Sum of Products expressions, for both binary and multi-value crisp sets, and to extract information (set names, set values) from those expressions. Other functions perform various other checks if possibly numeric (even if all numbers reside in a character vector) and coerce to numeric, or check if the numbers are whole. It also offers, among many others, a highly flexible recoding routine and a more flexible alternative to the base function with().

This package contains genomic data for the plant pathogen Phytophthora infestans. It includes a variant file, a sequence file and an annotation file. This package is intended to be used as example data for packages that work with genomic data.

Extracts plain text from Rich Text Format (RTF) file.

This package provides an R Client for the Europe PubMed Central RESTful Web Service. It gives access to both metadata on life science literature and open access full texts. Europe PMC indexes all PubMed content and other literature sources including Agricola, a bibliographic database of citations to the agricultural literature, or Biological Patents. In addition to bibliographic metadata, the client allows users to fetch citations and reference lists. Links between life-science literature and other EBI databases, including ENA, PDB or ChEMBL are also accessible.

The ROI is a framework for handling optimization problems in R.

This package provides tools to convert R Markdown documents into a variety of formats.

This package is designed as an integrated package for genetic data analysis of both population and family data. Currently, it contains functions for sample size calculations of both population-based and family-based designs, probability of familial disease aggregation, kinship calculation, statistics in linkage analysis, and association analysis involving genetic markers including haplotype analysis with or without environmental covariates. Over years, the package has been developed in-between many projects hence also in line with the name (gap).

This package provides a placeholder for the Liberation fontset intended for the fontquiver package. This fontset covers the 12 combinations of families (sans, serif, mono) and faces (plain, bold, italic, bold italic) supported in R graphics devices.

This package provides tools for the estimation and simulation of latent variable models.

This package extends the fitdistr function of the MASS package with several functions to help the fit of a parametric distribution to non-censored or censored data. Censored data may contain left-censored, right-censored and interval-censored values, with several lower and upper bounds. In addition to maximum likelihood estimation (MLE), the package provides moment matching (MME), quantile matching (QME) and maximum goodness-of-fit estimation (MGE) methods (available only for non-censored data). Weighted versions of MLE, MME and QME are available.

This package provides fit linear and generalized linear mixed-effects models. The models and their components are represented using S4 classes and methods. The core computational algorithms are implemented using the Eigen C++ library for numerical linear algebra and RcppEigen glue.

This is a package for graphical and statistical analyses of environmental data, with a focus on analyzing chemical concentrations and physical parameters, usually in the context of mandated environmental monitoring. It provides major environmental statistical methods found in the literature and regulatory guidance documents, with extensive help that explains what these methods do, how to use them, and where to find them in the literature. It comes with numerous built-in data sets from regulatory guidance documents and environmental statistics literature. It includes scripts reproducing analyses presented in the book "EnvStats: An R Package for Environmental Statistics" (Millard, 2013, Springer, ISBN 978-1-4614-8455-4, https://link.springer.com/book/10.1007/978-1-4614-8456-1).

RestRserve is an R web API framework for building high-performance AND robust microservices and app backends. With Rserve backend on UNIX-like systems it is parallel by design. It will handle incoming requests in parallel - each request in a separate fork.