This package provides functions that solve initial value problems of a system of first-order ordinary differential equations (ODE), of partial differential equations (PDE), of differential algebraic equations (DAE), and of delay differential equations. The functions provide an interface to the FORTRAN functions lsoda, lsodar, lsode, lsodes of the ODEPACK collection, to the FORTRAN functions dvode and daspk and a C-implementation of solvers of the Runge-Kutta family with fixed or variable time steps. The package contains routines designed for solving ODEs resulting from 1-D, 2-D and 3-D partial differential equations that have been converted to ODEs by numerical differencing.

This package provides bindings to the OSQP solver. The OSQP solver is a numerical optimization package or solving convex quadratic programs written in C and based on the alternating direction method of multipliers. See <arXiv:1711.08013> for details.

This is a dedicated package to WELL pseudo random generators, which were introduced in Panneton et al. (2006), ``Improved Long-Period Generators Based on Linear Recurrences Modulo 2'', ACM Transactions on Mathematical Software.

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.

High dimensional interaction search by brute force requires a quadratic computational cost in the number of variables. The xyz algorithm provably finds strong interactions in almost linear time. For details of the algorithm see: G. Thanei, N. Meinshausen and R. Shah (2016). The xyz algorithm for fast interaction search in high-dimensional data.

This is a subset of the spatstat package, containing its functionality for spatial data on a linear network.

This package provides MathJax and macros to enable its use within Rd files for rendering equations in the HTML help files.

This package provides statistical procedures for calculating population-mean cosinor, non-stationary cosinor, estimation of best-fitting period, tests of population rhythm differences and more.

This package provides an implementation of Adaptive Base Error Model in Ultra-deep Sequencing data (ABEMUS), which combines platform-specific genetic knowledge and empirical signal to readily detect and quantify somatic single nucleotide variants (SNVs) in circulating cell free DNA (cfDNA).

The r-nleqslv package solves a system of nonlinear equations using a Broyden or a Newton method with a choice of global strategies such as line search and trust region. There are options for using a numerical or user supplied Jacobian, for specifying a banded numerical Jacobian and for allowing a singular or ill-conditioned Jacobian.

This package provides a set of functions with example data for graphing, pruning, and mapping models. These models are from hierarchical clustering, and classification and regression trees.

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 collection of tools to deal with statistical models. The functionality is experimental and the user interface is likely to change in the future.

Fit linear and generalized linear mixed models with various extensions, including zero-inflation. The models are fitted using maximum likelihood estimation via the Template Model Builder. Random effects are assumed to be Gaussian on the scale of the linear predictor and are integrated out using the Laplace approximation. Gradients are calculated using automatic differentiation.

This is a package for operations on triangular meshes based on VCGLIB. This package integrates nicely with the R-package rgl to render the meshes processed by Rvcg. The Visualization and Computer Graphics Library (VCG for short) is a library for manipulation, processing and displaying with OpenGL of triangle and tetrahedral meshes.

There are a number of binary files associated with the Webdriver/Selenium project (see http://www.seleniumhq.org/download/, https://sites.google.com/a/chromium.org/chromedriver/, https://github.com/mozilla/geckodriver, http://phantomjs.org/download.html, and https://github.com/SeleniumHQ/selenium/wiki/InternetExplorerDriver for more information). This package provides functions to download these binaries and to manage processes involving them.

Users may want to align plots with associated information that requires axes to be exactly matched in subplots, e.g. hierarchical clustering with a heatmap. This package provides utilities to align associated subplots to a main plot at different sides (left, right, top and bottom) with axes exactly matched.

Obtain any major version of jQuery and use it in any webpage generated by htmltools (e.g. shiny, htmlwidgets, and rmarkdown). Most R users don't need to use this package directly, but other R packages (e.g. shiny, rmarkdown, etc.) depend on this package to avoid bundling redundant copies of jQuery.

This is an extension to Shiny that brings interactions and animation effects from the jQuery UI library.

This package performs penalized multivariate analysis: a penalized matrix decomposition, sparse principal components analysis, and sparse canonical correlation analysis.

This package contains functions to compute the nonparametric maximum likelihood estimator (MLE) for the bivariate distribution of (X,Y), when realizations of (X,Y) cannot be observed directly. To be more precise, we consider the situation where we observe a set of rectangles that are known to contain the unobservable realizations of (X,Y). We compute the MLE based on such a set of rectangles. The methods can also be used for univariate censored data (see data set cosmesis), and for censored data with competing risks (see data set menopause). The package also provides functions to visualize the observed data and the MLE.

This package contains routines for logspline density estimation. The function oldlogspline() uses the same algorithm as the logspline package version 1.0.x; i.e., the Kooperberg and Stone (1992) algorithm (with an improved interface). The recommended routine logspline() uses an algorithm from Stone et al (1997).

The TOML configuration format specifies an excellent format suitable for both human editing as well as the common uses of a machine-readable format. This package provides Rcpp bindings to a TOML parser.

This is a pure R implementation of the Covariance Matrix Adaptation Evolution Strategy (CMA-ES) with optional restarts (IPOP-CMA-ES).