This package provides a stepwise approach to identifying recombination breakpoints in a genomic sequence alignment.

The snow package provides support for simple parallel computing on a network of workstations using R. A master R process calls makeCluster to start a cluster of worker processes; the master process then uses functions such as clusterCall and clusterApply to execute R code on the worker processes and collect and return the results on the master.

This package contains data which are used by functions of the abc package which implements several Approximate Bayesian Computation (ABC) algorithms for performing parameter estimation, model selection, and goodness-of-fit.

This package can be used to compute local false discovery rates.

The sourcetools package provides both an R and C++ interface for the tokenization of R code, and helpers for interacting with the tokenized representation of R code.

This package provides several layout algorithms to visualize networks which are not part of the igraph library. Most are based on the concept of stress majorization by Gansner et al. (2004) <doi:10.1007/978-3-540-31843-9_25>. Some more specific algorithms emphasize hidden group structures in networks or focus on specific nodes.

iheatmapr is an R package for building complex, interactive heatmaps using modular building blocks. "Complex" heatmaps are heatmaps in which subplots along the rows or columns of the main heatmap add more information about each row or column. For example, a one column additional heatmap may indicate what group a particular row or column belongs to. Complex heatmaps may also include multiple side by side heatmaps which show different types of data for the same conditions. Interactivity can improve complex heatmaps by providing tooltips with information about each cell and enabling zooming into interesting features. iheatmapr uses the plotly library for interactivity.

This package provides fast and memory efficient methods for truncated singular and eigenvalue decompositions, as well as for principal component analysis of large sparse or dense matrices.

This package provides a simple interface for creating active bindings where the bound function accepts additional arguments.

This package provides ggplot2 geoms filled with various patterns. It includes a patterned version of every ggplot2 geom that has a region that can be filled with a pattern. It provides a suite of ggplot2 aesthetics and scales for controlling pattern appearances. It supports over a dozen builtin patterns (every pattern implemented by gridpattern) as well as allowing custom user-defined patterns.

This package provides number-theoretic functions for factorization, prime numbers, twin primes, primitive roots, modular logarithm and inverses, extended GCD, Farey series and continued fractions. It includes Legendre and Jacobi symbols, some divisor functions, Euler's Phi function, etc.

This package provides routines for simple graphs and network analysis. It can handle large graphs very well and provides functions for generating random and regular graphs, graph visualization, centrality methods and much more.

This package provides a utility for R to parse a bibtex file.

Run R CMD check from R programmatically, and capture the results of the individual checks.

Efficient C++ optimized functions for numerical and symbolic calculus. It includes basic symbolic arithmetic, tensor calculus, Einstein summing convention, fast computation of the Levi-Civita symbol and generalized Kronecker delta, Taylor series expansion, multivariate Hermite polynomials, accurate high-order derivatives, differential operators (Gradient, Jacobian, Hessian, Divergence, Curl, Laplacian) and numerical integration in arbitrary orthogonal coordinate systems: cartesian, polar, spherical, cylindrical, parabolic or user defined by custom scale factors.

This package provides a suite of elliptic and related functions including Weierstrass and Jacobi forms. It also includes various tools for manipulating and visualizing complex functions.

There are three main goals to the vctrs package:

1. To propose vec_size() and vec_type() as alternatives to length() and class(). These definitions are paired with a framework for type-coercion and size-recycling.

2. To define type- and size-stability as desirable function properties, use them to analyse existing base function, and to propose better alternatives. This work has been particularly motivated by thinking about the ideal properties of c(), ifelse(), and rbind().

3. To provide a new vctr base class that makes it easy to create new S3 vectors. vctrs provides methods for many base generics in terms of a few new vctrs generics, making implementation considerably simpler and more robust.

This package provides an R to C/C++ interface that runs the Leiden community detection algorithm to find a basic partition. It runs the equivalent of the leidenalg find_partition() function. This package includes the required source code files from the official leidenalg distribution and functions from the R igraph package.

This package provides a DBI interface to MySQL / MariaDB. The RMySQL package contains an old implementation based on legacy code from S-PLUS which is being phased out. A modern MySQL client based on Rcpp is available from the RMariaDB package.

This package provides exploratory data analysis methods to summarize, visualize and describe datasets. The main principal component methods are available, those with the largest potential in terms of applications: principal component analysis (PCA) when variables are quantitative, correspondence analysis (CA) and multiple correspondence analysis (MCA) when variables are categorical, Multiple Factor Analysis when variables are structured in groups, etc. and hierarchical cluster analysis.

This package performs approximate bayesian computation (ABC) model choice and parameter inference via random forests. This machine learning tool named random forests (RF) can conduct selection among the highly complex models covered by ABC algorithms.

This package provides a function to format R source code. Spaces and indent will be added to the code automatically, and comments will be preserved under certain conditions, so that R code will be more human-readable and tidy. There is also a Shiny app as a user interface in this package.

This package provides a collection of tools for building RAxML supermatrix using PHYLIP or aligned FASTA files. These functions will be useful for building large phylogenies using multiple markers.

This package OrgMassSpecR is an extension of the R statistical computing language. It contains functions to assist with organic or biological mass spectrometry data analysis. Mass spectral libraries are available as companion packages.