Uniform manifold approximation and projection is a technique for dimension reduction. This package provides an interface to the UMAP algorithm in R, including a translation of the original algorithm into R.

Inference based on models with or without spatially-correlated random effects, multivariate responses, or non-Gaussian random effects (e.g., Beta). Variation in residual variance (heteroscedasticity) can itself be represented by a mixed-effect model. Both classical geostatistical models (Rousset and Ferdy 2014 <doi:10.1111/ecog.00566>), and Markov random field models on irregular grids (as considered in the INLA package, <https://www.r-inla.org>), can be fitted, with distinct computational procedures exploiting the sparse matrix representations for the latter case and other autoregressive models. Laplace approximations are used for likelihood or restricted likelihood. Penalized quasi-likelihood and other variants discussed in the h-likelihood literature (Lee and Nelder 2001 <doi:10.1093/biomet/88.4.987>) are also implemented.

This package provides an R-based solution for symbolic differentiation. It admits user-defined functions as well as function substitution in arguments of functions to be differentiated. Some symbolic simplification is part of the work.

This package lets you plot model surfaces for a wide variety of models using partial dependence plots and other techniques. Also plot model residuals and other information on the model.

This package provides tools for accessing the Botanical Information and Ecology Network (BIEN) database. The BIEN database contains cleaned and standardized botanical data including occurrence, trait, plot and taxonomic data. This package provides functions that query the BIEN database by constructing and executing optimized SQL queries.

This package implements the RUV (Remove Unwanted Variation) algorithms. These algorithms attempt to adjust for systematic errors of unknown origin in high-dimensional data. The algorithms were originally developed for use with genomic data, especially microarray data, but may be useful with other types of high-dimensional data as well. The algorithms require the user to specify a set of negative control variables, as described in the references. The algorithms included in this package are RUV-2, RUV-4, RUV-inv, RUV-rinv, RUV-I, and RUV-III, along with various supporting algorithms.

The fstlib library provides multithreaded serialization of compressed data frames using the fst format. The fst format allows for random access of stored data and compression with the LZ4 and ZSTD compressors.

This package provides code analysis tools for R to check R code for possible problems.

This package provides an R implementation of an extension of the BayeScan software for codominant markers, adding the option to group individual SNPs into pre-defined blocks. A typical application of this new approach is the identification of genomic regions, genes, or gene sets containing one or more SNPs that evolved under directional selection.

This package provides empirical likelihood ratio tests for means/quantiles/hazards from possibly censored and/or truncated data. It also does regression.

This package performs augmented backward elimination and checks the stability of the obtained model. Augmented backward elimination combines significance or information based criteria with the change in estimate to either select the optimal model for prediction purposes or to serve as a tool to obtain a practically sound, highly interpretable model.

This package provides functions related to human natural ordering. It handles adjacent digits in a character sequence as a number so that natural sort function arranges a character vector by their numbers, not digit characters.

This package provides a Wrapper around the SVDLIBC library for (truncated) singular value decomposition of a sparse matrix. Currently, only sparse real matrices in Matrix package format are supported.

This package provides a collection of regular expression tools associated with the qdap package that may be useful outside of the context of discourse analysis. Tools include removal/extraction/replacement of abbreviations, dates, dollar amounts, email addresses, hash tags, numbers, percentages, citations, person tags, phone numbers, times, and zip codes.

This package provides a reticulate wrapper for the Python package anndata. It provides a scalable way of keeping track of data and learned annotations. It is used to read from and write to the h5ad file format.

This package aims to provide easy-to-use, efficient, flexible and scalable statistical tools. It provides and uses file-backed big matrices via memory-mapping. It provides for instance matrix operations, Principal Component Analysis, sparse linear supervised models, utility functions and more.

svglite is a graphics device that produces clean SVG (Scalable Vector Graphics) output, suitable for use on the web, or hand editing. Compared to the built-in svg(), svglite is considerably faster, produces smaller files, and leaves text as is.

This package provides alternative implementations of some base R functions, including sort, order, and match. The functions are simplified but can be faster or have other advantages.

Manipulate and visualize colors in a intuitive, low-dependency and functional way.

This package provides a friendly interface for the construction of regular expressions. Regular expressions are a very powerful feature, however they are often difficult to interpret. Rex allows you to build complex regular expressions from human readable expressions

This package contains R functions and datasets detailed in the book "Time Series Analysis with Applications in R (second edition)" by Jonathan Cryer and Kung-Sik Chan.

This package provides functions to handle basic input output. These functions always read and write UTF-8 (8-bit Unicode Transformation Format) files and provide more explicit control over line endings.

This package provides vector map data from https://www.naturalearthdata.com/. Access functions are provided in the accompanying package rnaturalearth.

This package computes the Kendall rank correlation and Mann-Kendall trend test.