This package defines sparse three-dimensional arrays and supports standard operations on them. The package also includes utility functions for matrix calculations that are common in statistics, such as quadratic forms.

This package provides infrastructure for seriation with an implementation of several seriation/sequencing techniques to reorder matrices, dissimilarity matrices, and dendrograms. It also provides (optimally) reordered heatmaps, color images and clustering visualizations like dissimilarity plots, and visual assessment of cluster tendency plots (VAT and iVAT).

The h5Seurat file format is specifically designed for the storage and analysis of multi-modal single-cell and spatially-resolved expression experiments, for example, from CITE-seq or 10X Visium technologies. It holds all molecular information and associated metadata, including (for example) nearest-neighbor graphs, dimensional reduction information, spatial coordinates and image data, and cluster labels. This package also supports rapid and on-disk conversion between h5Seurat and AnnData objects, with the goal of enhancing interoperability between Seurat and Scanpy.

This package provides tools to calculate the Earth Mover's Distance (EMD).

Stringr is a consistent, simple and easy to use set of wrappers around the fantastic stringi package. All function and argument names (and positions) are consistent, all functions deal with "NA"'s and zero length vectors in the same way, and the output from one function is easy to feed into the input of another.

This package provides HTTP error helpers. Methods are included for general purpose HTTP error handling, as well as individual methods for every HTTP status code, both via status code numbers as well as their descriptive names. It supports the ability to adjust behavior to stop, message or warning. It includes the ability to use a custom whisker template to have any configuration of status code, short description, and verbose message.

This package provides a complete unit test system and functions to implement its GUI part.

This package provides a set of simple functions that transforms longitudinal data to estimate the cosinor linear model as described in Tong (1976). Methods are given to summarize the mean, amplitude and acrophase, to predict the mean annual outcome value, and to test the coefficients.

This package provides drop-in replacements for the base system2() function with fine control and consistent behavior across platforms. It supports clean interruption, timeout, background tasks, and streaming STDIN / STDOUT / STDERR over binary or text connections. The package also provides functions for evaluating expressions inside a temporary fork. Such evaluations have no side effects on the main R process, and support reliable interrupts and timeouts. This provides the basis for a sandboxing mechanism.

Function-oriented Make-like declarative pipelines for statistics and data science are supported in the targets R package. As an extension to targets, the tarchetypes package provides convenient user-side functions to make targets easier to use. By establishing reusable archetypes for common kinds of targets and pipelines, these functions help express complicated reproducible pipelines concisely and compactly. The methods in this package were influenced by the drake R package by Will Landau (2018) <doi:10.21105/joss.00550>.

This package support non-robust and robust computations of the sample autocovariance (ACOVF) and sample autocorrelation functions (ACF) of univariate and multivariate processes. The methodology consists in reversing the diagonalization procedure involving the periodogram or the cross-periodogram and the Fourier transform vectors, and, thus, obtaining the ACOVF or the ACF as discussed in Fuller (1995) doi:10.1002/9780470316917. The robust version is obtained by fitting robust M-regressors to obtain the M-periodogram or M-cross-periodogram as discussed in Reisen et al. (2017) doi:10.1016/j.jspi.2017.02.008.

This package contains an implementation of a function digest() for the creation of hash digests of arbitrary R objects (using the md5, sha-1, sha-256, crc32, xxhash and murmurhash algorithms) permitting easy comparison of R language objects, as well as a function hmac() to create hash-based message authentication code.

Please note that this package is not meant to be deployed for cryptographic purposes for which more comprehensive (and widely tested) libraries such as OpenSSL should be used.

The GNU Scientific Library (or GSL) is a collection of numerical routines for scientific computing. It is particularly useful for C and C++ programs as it provides a standard C interface to a wide range of mathematical routines. There are over 1000 functions in total with an extensive test suite. The RcppGSL package provides an easy-to-use interface between GSL data structures and R using concepts from Rcpp which is itself a package that eases the interfaces between R and C++.

Alabama stands for Augmented Lagrangian Adaptive Barrier Minimization Algorithm; it is used for optimizing smooth nonlinear objective functions with constraints. Linear or nonlinear equality and inequality constraints are allowed.

The aim of httr is to provide a wrapper for RCurl customised to the demands of modern web APIs. It provides useful tools for working with HTTP organised by HTTP verbs (GET(), POST(), etc). Configuration functions make it easy to control additional request components.

This package provides an extension of the functionality of the Matrix package for using sparse matrices. Some of the functions are very general, while other are highly specific for the special data format used for quantitative language comparison (QLC).

This package provides tools to infer the code style (which style rules are followed and which ones are not) from one package and use it to check another. This makes it easier to find and correct the most important problems first.

This package provides an R interface to the NCBI's EUtils API, allowing users to search databases like GenBank PubMed, process the results of those searches and pull data into their R sessions.

This package provides tools to create pretty tables for HTML documents and other formats. Functions are provided to let users create tables, modify and format their content. It extends the officer package and can be used within R markdown documents when rendering to HTML and to Word documents.

This package provides a self-tuning spectral clustering method for single or multi-view data. Spectrum uses a new type of adaptive density aware kernel that strengthens connections in the graph based on common nearest neighbours. It uses a tensor product graph data integration and diffusion procedure to integrate different data sources and reduce noise. Spectrum uses either the eigengap or multimodality gap heuristics to determine the number of clusters. The method is sufficiently flexible so that a wide range of Gaussian and non-Gaussian structures can be clustered with automatic selection of K.

This package provides string and binary representations of objects for several formats and MIME types.

This package provides functions for easily manipulating colors, creating color scales and calculating color distances.

This package provides tools to compares k samples using the Anderson-Darling test, Kruskal-Wallis type tests with different rank score criteria, Steel's multiple comparison test, and the Jonckheere-Terpstra (JT) test. It computes asymptotic, simulated or (limited) exact P-values, all valid under randomization, with or without ties, or conditionally under random sampling from populations, given the observed tie pattern. Except for Steel's test and the JT test it also combines these tests across several blocks of samples.

The Munsell package contains functions for exploring and using the Munsell colour system.