This package lets you fit generalized linear mixed models for a single grouping factor under maximum likelihood approximating the integrals over the random effects with an adaptive Gaussian quadrature rule; Jose C. Pinheiro and Douglas M. Bates (1995) <doi:10.1080/10618600.1995.10474663>.

This package provides simple and secure authentication mechanism for single Shiny applications. Credentials are stored in an encrypted SQLite database.

This package provides a syntax highlighter for R code based on the results of the R parser. It supports rendering in HTML and LaTeX markup. It includes a custom Sweave driver performing syntax highlighting of R code chunks.

This package arranges data by a set of methods. It uses rearrangers to reorder data points and mutators to change their values. From basic utilities, to centering the greatest value, to swirling in 3-dimensional space, rearrr enables creativity when plotting and experimenting with data.

This package facilitates RNA secondary structure plotting.

This package lets you analyze response times and accuracies from psychological experiments with the linear ballistic accumulator (LBA) model from Brown and Heathcote (2008). The LBA model is optionally fitted with explanatory variables on the parameters such as the drift rate, the boundary and the starting point parameters. A log-link function on the linear predictors can be used to ensure that parameters remain positive when needed.

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 defines S4 classes for single-cell genomic data and associated information, such as dimensionality reduction embeddings, nearest-neighbor graphs, and spatially-resolved coordinates. It provides data access methods and R-native hooks to ensure the Seurat object is familiar to other R users.

This package provides R6 abstract classes for building machine learning models with a scikit-learn like API. Scikit-learn is a popular module for the Python programming language whose design became a de facto standard in industry for machine learning tasks.

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

This package provides tools for shrunken centroids regularized discriminant analysis for the purpose of classifying high dimensional data.

This package provides functions and vignettes to update data sets in Ecdat and to create, manipulate, plot, and analyze those and similar data sets.

This package provides interactive, configurable and graphics visualization of the chromosome regions of any living organism allowing users to map chromosome elements (like genes, SNPs etc.) on the chromosome plot. It introduces a special plot viz. the "chromosome heatmap" that, in addition to mapping elements, can visualize the data associated with chromosome elements (like gene expression) in the form of heat colors. Users can investigate the detailed information about the mappings (like gene names or total genes mapped on a location) or can view the magnified single or double stranded view of the chromosome at a location showing each mapped element in sequential order. The package provide multiple features like visualizing multiple sets, chromosome heat-maps, group annotations, adding hyperlinks, and labelling. The plots can be saved as HTML documents that can be customized and shared easily. In addition, you can include them in R Markdown or in R Shiny applications.

GAMs, GAMMs and other generalized ridge regression with multiple smoothing parameter estimation by GCV, REML or UBRE/AIC. The library includes a gam() function, a wide variety of smoothers, JAGS support and distributions beyond the exponential family.

This package provides software for the book Spectral Analysis for Physical Applications, Donald B. Percival and Andrew T. Walden, Cambridge University Press, 1993.

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

This package provides a collection of templates to author preregistration documents for scientific studies in PDF format.

Intense parallel workloads can be difficult to monitor. Packages crew.cluster, clustermq, and future.batchtools distribute hundreds of worker processes over multiple computers. If a worker process exhausts its available memory, it may terminate silently, leaving the underlying problem difficult to detect or troubleshoot. Using the autometric package, a worker can proactively monitor itself in a detached background thread. The worker process itself runs normally, and the thread writes to a log every few seconds. If the worker terminates unexpectedly, autometric can read and visualize the log file to reveal potential resource-related reasons for the crash. The autometric package borrows heavily from the methods of packages ps and psutil.

Webshot makes it easy to take screenshots of web pages from within R. It can also run Shiny applications locally and take screenshots of the application; and it can render and screenshot static as well as interactive R Markdown documents.

Some basic features of MUMPS are wrapped in a class whose methods can be used for sequentially solving a sparse linear system (symmetric or not) with one or many right hand sides (dense or sparse). There is a possibility to do separately symbolic analysis, LU (or LDL^t) factorization and system solving. Third part ordering libraries are included and can be used: PORD, METIS, SCOTCH.

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

This package was previously an R wrapper of the ARPACK library, and now a shell of the R package RSpectra, an R interface to the Spectra library for solving large scale eigenvalue/vector problems. The current version of rARPACK simply imports and exports the functions provided by RSpectra. New users of rARPACK are advised to switch to the RSpectra package.

This is a package for variable elimination (Gaussian elimination, Fourier-Motzkin elimination), Moore-Penrose pseudoinverse, reduction to reduced row echelon form, value substitution, projecting a vector on the convex polytope described by a system of (in)equations, simplify systems by removing spurious columns and rows and collapse implied equalities, test if a matrix is totally unimodular, compute variable ranges implied by linear (in)equalities.