This package is primarily meant as an implementation of generalized blockmodeling for valued networks. In addition, measures of similarity or dissimilarity based on structural equivalence and regular equivalence (REGE algorithms) can be computed and partitioned matrices can be plotted.

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 functions that:

1. find the minimum/maximum of a linear or quadratic function,

2. sample an underdetermined or overdetermined system,

3. solve a linear system Ax=B for the unknown x.

It includes banded and tridiagonal linear systems. The package calls Fortran functions from LINPACK.

This package implements the fast cross-validation via sequential testing (CVST) procedure. CVST is an improved cross-validation procedure which uses non-parametric testing coupled with sequential analysis to determine the best parameter set on linearly increasing subsets of the data. Additionally to the CVST the package contains an implementation of the ordinary k-fold cross-validation with a flexible and powerful set of helper objects and methods to handle the overall model selection process. The implementations of the Cochran's Q test with permutations and the sequential testing framework of Wald are generic and can therefore also be used in other contexts.

This package estimates the parameters in Dirichlet-Multinomial and computes log-likelihoods.

This package lets you manage Google Drive files from R.

The googleVis package provides an interface between R and the Google Charts API. Google Charts offer interactive charts which can be embedded into web pages. The functions of the googleVis package allow the user to visualise data stored in R data frames with Google Charts without uploading the data to Google. The output of a googleVis function is HTML code that contains the data and references to JavaScript functions hosted by Google. googleVis makes use of the internal R HTTP server to display the output locally.

Customize Bootstrap and Bootswatch themes, like colors, fonts, grid layout, to use in Shiny applications, rmarkdown documents and flexdashboard.

This package provides qualitative methods for the validation of dynamic models. It contains

1. an orthogonal set of deviance measures for absolute, relative and ordinal scale and

2. approaches accounting for time shifts.

The first approach transforms time to take time delays and speed differences into account. The second divides the time series into interval units according to their main features and finds the longest common subsequence (LCS) using a dynamic programming algorithm.

Easily and flexibly insert Font Awesome icons into R Markdown documents and Shiny apps. These icons can be inserted into HTML content through inline SVG tags or i tags. There is also a utility function for exporting Font Awesome icons as PNG images for those situations where raster graphics are needed.

This package provides utilities for computation and analysis of correlation/covariation in multiple sequence alignments and in side chain motions during molecular dynamics simulations. Features include the computation of correlation/covariation scores using a variety of scoring functions between either sequence positions in alignments or side chain dihedral angles in molecular dynamics simulations and utilities to analyze the correlation/covariation matrix through a variety of tools including network representation and principal components analysis. In addition, several utility functions are based on the R graphical environment to provide friendly tools for help in data interpretation.

This package provides a collection of tools for building RAxML supermatrix using PHYLIP or aligned FASTA files. These functions will be useful for building large phylogenies using multiple markers.

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 a system for embedded scientific computing and reproducible research with R. The OpenCPU server exposes a simple but powerful HTTP API for RPC and data interchange with R. This provides a reliable and scalable foundation for statistical services or building R web applications. The OpenCPU server runs either as a single-user development server within the interactive R session, or as a multi-user stack based on Apache2.

Dunn's test computes stochastic dominance & reports pairwise comparisons. This is done following a Kruskal-Wallis test (Kruskal and Wallis, 1952). It employs Dunn's z-test-statistic approximations for rank statistics, conducting k(k-1)/2 comparisons. The null hypothesis assumes that the probability of a randomly selected value from the first group being larger than one from the second group is one half, similar to the Wilcoxon-Mann-Whitney test. Dunn's test serves as a test for median difference and takes into account tied ranks.

The vegan package provides tools for descriptive community ecology. It has most basic functions of diversity analysis, community ordination and dissimilarity analysis. Most of its multivariate tools can be used for other data types as well.

This package provides a set of predicates and assertions for checking the properties of models. This is mainly for use by other package developers who want to include run-time testing features in their own packages.

This package implements targeted minimum loss-based estimators of counterfactual means and causal effects that are doubly-robust with respect both to consistency and asymptotic normality.

This package lets you read and write JSON Web Keys (JWK, rfc7517), generate and verify JSON Web Signatures (JWS, rfc7515) and encode/decode JSON Web Tokens (JWT, rfc7519). These standards provide modern signing and encryption formats that are natively supported by browsers via the JavaScript WebCryptoAPI, and used by services like OAuth 2.0, LetsEncrypt, and Github Apps.

This package provides basic classes and methods for Natural Language Processing.

This package implements various estimators of entropy, such as the shrinkage estimator by Hausser and Strimmer, the maximum likelihood and the Millow-Madow estimator, various Bayesian estimators, and the Chao-Shen estimator. It also offers an R interface to the NSB estimator. Furthermore, it provides functions for estimating Kullback-Leibler divergence, chi-squared, mutual information, and chi-squared statistic of independence. In addition there are functions for discretizing continuous random variables.

The base functions for set operations in R can be used for only two sets. This package RVenn provides functions for dealing with multiple sets. It uses purr to find the union, intersection and difference of three or more sets. This package also provides functions for pairwise set operations among several sets. Further, based on ggplot2 and ggforce, a Venn diagram can be drawn for two or three sets. For bigger data sets, a clustered heatmap showing the presence or absence of the elements of the sets can be drawn based on the pheatmap package. Finally, enrichment test can be applied to two sets whether an overlap is statistically significant or not.

This package provides procedures for fitting a principal curve to a data matrix in arbitrary dimensions.

This package provides a set of tools for manipulating and reading geographic data, in particular ESRI Shapefiles. It includes binary access to GSHHG shoreline files. The package also provides interface wrappers for exchanging spatial objects with other R packages.