This package carries out a mapping between assorted color spaces including RGB, HSV, HLS, CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB and polar CIELAB. Qualitative, sequential, and diverging color palettes based on HCL colors are provided.

This package provides a new object oriented programming system designed to be a successor to S3 and S4. It includes formal class, generic, and method specification, and a limited form of multiple dispatch. It has been designed and implemented collaboratively by the R Consortium Object-Oriented Programming Working Group, which includes representatives from R-Core, Bioconductor, Posit/tidyverse, and the wider R community.

This package provides a set of handy functions. It includes a versatile one line progress bar, one line function timer with detailed output, time delay function, text histogram, object preview, CRAN package search, simpler package installer, Linux command install check, a flexible Mode function, top function, simulation of correlated data, and more.

This package enables the use of emoji and the Font Awesome glyphs in both base and ggplot2 graphics.

This package provides an improved heatmap package. It is completely compatible with the original R function heatmap, and provides more powerful and convenient features.

The DHARMa package uses a simulation-based approach to create readily interpretable scaled (quantile) residuals for fitted (generalized) linear mixed models. Moreover, externally created simulations, e.g. posterior predictive simulations from Bayesian software such as JAGS, STAN, or BUGS can be processed as well. The resulting residuals are standardized to values between 0 and 1 and can be interpreted as intuitively as residuals from a linear regression. The package also provides a number of plot and test functions for typical model misspecification problems, such as over/underdispersion, zero-inflation, and residual spatial, phylogenetic and temporal autocorrelation.

This package provides simple bindings to Unidata's udunits library.

This package provides utilities based on libpoppler for extracting text, fonts, attachments and metadata from a PDF file. It also supports high quality rendering of PDF documents into PNG, JPEG, TIFF format, or into raw bitmap vectors for further processing in R.

This package provides functions for performing phylogenetic comparative analyses.

This package provides utilities for working with Google APIs. This includes functions and classes for handling common credential types and for preparing, executing, and processing HTTP requests.

The tkrplot package lets you place R graphics in a Tk, cross-platform graphical user interface toolkit widget.

This package provides mosaic plots for the ggplot2 framework. Mosaic plot functionality is provided in a single ggplot2 layer by calling the geom mosaic.

This package extends the ggplot2 plotting system to support network visualization. Inspired by ggtree, ggtangle is designed to work with network associated data.

This package provides functions to compare a model object to a comparison object. If the objects are not identical, the functions can be instructed to explore various modifications of the objects (e.g., sorting rows, dropping names) to see if the modified versions are identical.

This package provides tools to find the k nearest neighbours for every point in a given dataset in O(N log N) time using Arya and Mount's ANN library. There is support for approximate as well as exact searches, fixed radius searches and bd as well as kd trees. The distance is computed using the L1 (Manhattan, taxicab) metric.

This package computes model II simple linear regression using ordinary least squares (OLS), major axis (MA), standard major axis (SMA), and ranged major axis (RMA).

This package provides methods for manipulating regression models and for describing these in a style adapted for medical journals. It contains functions for generating an HTML table with crude and adjusted estimates, plotting hazard ratio, plotting model estimates and confidence intervals using forest plots, extending this to comparing multiple models in a single forest plots. In addition to the descriptive methods, there are functions for the robust covariance matrix provided by the sandwich package, a function for adding non-linearities to a model, and a wrapper around the Epi package's Lexis() functions for time-splitting a dataset when modeling non-proportional hazards in Cox regressions.

This package provides functionality to compute various node centrality measures on networks. Included are functions to compute betweenness centrality (by utilizing Madduri and Bader's SNAP library), implementations of Burt's constraint and effective network size (ENS) metrics, Borgatti's algorithm to identify key players, and Valente's bridging metric. The betweenness, Key Players, and bridging implementations are parallelized with OpenMP.

LIGER is a package for integrating and analyzing multiple single-cell datasets, developed and maintained by the Macosko lab. It relies on integrative non-negative matrix factorization to identify shared and dataset-specific factors.

This package provides a command line parser to be used with Rscript to write shebang scripts that gracefully accept positional and optional arguments and automatically generate usage notices.

This package provides Map, Reduce and Filter variants to generate jobs on batch computing systems like PBS/Torque, LSF, SLURM and Sun Grid Engine. Multicore and SSH systems are also supported.

This package interacts with a suite of web services for chemical information. Sources include: Alan Wood's Compendium of Pesticide Common Names, Chemical Identifier Resolver, ChEBI, Chemical Translation Service, ChemSpider, ETOX, Flavornet, NIST Chemistry WebBook, OPSIN, PubChem, SRS, Wikidata.

The range of functions provided by this package makes it possible to draw highly versatile genomic sequence logos. Features include, but are not limited to, modifying colour schemes and fonts used to draw the logo, generating multiple logo plots, and aiding the visualisation with annotations. Sequence logos can easily be combined with other ggplot2 plots.

Logging functions in RcppSpdlog provide access to the logging functionality from the spdlog C++ library. This package offers shorter convenience wrappers for the R functions which match the C++ functions, namely via, say, spdl::debug() at the debug level. The actual formatting is done by the fmt::format() function from the fmtlib library (that is also std::format() in C++20 or later).