Statistical and biological validation of clustering results. This package implements Dunn Index, Silhouette, Connectivity, Stability, BHI and BSI. Further information can be found in Brock, G et al. (2008) <doi: 10.18637/jss.v025.i04>.

This is a package to compare sequence fragment lengths or molecular weights from pairs of lanes. The number of matching bands in the Restriction Fragment Length Polymorphism (RFLP) data is calculated using the align-and-count method.

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 cross-platform solution to open files, directories or URLs with their associated programs.

The ade4 package contains data analysis functions to analyze ecological and environmental data in the framework of Euclidean exploratory methods.

This package provides functionality for random generation of spatial data in the spatstat family of packages. It generates random spatial patterns of points according to many simple rules (complete spatial randomness, Poisson, binomial, random grid, systematic, cell), randomised alteration of patterns (thinning, random shift, jittering), simulated realisations of random point processes (simple sequential inhibition, Matern inhibition models, Matern cluster process, Neyman-Scott cluster processes, log-Gaussian Cox processes, product shot noise cluster processes) and simulation of Gibbs point processes (Metropolis-Hastings birth-death-shift algorithm, alternating Gibbs sampler).

This package provides tools for the visualization of missing and/or imputed values are introduced, which can be used for exploring the data and the structure of the missing and/or imputed values. Depending on this structure of the missing values, the corresponding methods may help to identify the mechanism generating the missing values and explore the data including missing values. In addition, the quality of imputation can be visually explored using various univariate, bivariate, multiple and multivariate plot methods.

This package provides an R interface to the Embedded COnic Solver (ECOS), an efficient and robust C library for convex problems. Conic and equality constraints can be specified in addition to integer and boolean variable constraints for mixed-integer problems. This R interface is inspired by the Python interface and has similar calling conventions.

Content-preserving transformations transformations of PDF files such as split, combine, and compress. This package interfaces directly to the qpdf C++ API and does not require any command line utilities. Note that qpdf does not read actual content from PDF files: to extract text and data you need the pdftools package.

This package provides visualization techniques, data sets, summary and inference procedures aimed particularly at categorical data. Special emphasis is given to highly extensible grid graphics. The package was originally inspired by the book "Visualizing Categorical Data" by Michael Friendly and is now the main support package for a new book, "Discrete Data Analysis with R" by Michael Friendly and David Meyer (2015).

This package provides a fast reimplementation of several density-based algorithms of the DBSCAN family. It includes the clustering algorithms DBSCAN (density-based spatial clustering of applications with noise) and hierarchical DBSCAN (HDBSCAN), the ordering algorithm ordering points to identify the clustering structure (OPTICS), shared nearest neighbor clustering, and the outlier detection algorithms local outlier factor (LOF) and global-local outlier score from hierarchies (GLOSH). The implementations use the kd-tree data structure for faster k-nearest neighbor search. An R interface to fast kNN and fixed-radius NN search is also provided.

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.

This package provides a collection of functions to support matrix calculations for probability, econometric and numerical analysis. There are additional functions that are comparable to APL functions which are useful for actuarial models such as pension mathematics.

This package provides an interface to figshare, a scientific repository to archive and assign DOIs to data, software, figures, and more.

This package provides tools for stochastic fractal and deterministic chaotic time series analysis.

This package provides datasets associated with the gap package. Currently, it includes an example data for regional association plot (CDKN), an example data for a genomewide association meta-analysis (OPG), data in studies of Parkinson's diease (PD), ALHD2 markers and alcoholism (aldh2), APOE/APOC1 markers and Schizophrenia (apoeapoc), cystic fibrosis (cf), a Olink/INF panel (inf1), Manhattan plots with (hr1420, mhtdata) and without (w4) gene annotations.

This package contains utility functions used by the Genome Analysis Toolkit (GATK) to load tables and plot data. The GATK is a toolkit for variant discovery in high-throughput sequencing data.

This package provides an easy to use library to setup, apply and make inference with discrete time and discrete space hidden Markov models.

This package provides a series of additional Tcl commands and Tk widgets with style and various functions to supplement the tcltk package

This package allows the user to specify debug messages as special string constants, and control debugging of packages via environment variables.

This package computes model II simple linear regression using ordinary least squares (OLS), major axis (MA), standard major axis (SMA), and ranged major axis (RMA).

This package provides a suite of elliptic and related functions including Weierstrass and Jacobi forms. It also includes various tools for manipulating and visualizing complex functions.

This package computes spherical trigonometry for geographic applications. That is, compute distances and related measures for angular (longitude/latitude) locations.

Joyplots provide a convenient way of visualizing changes in distributions over time or space. This package enables the creation of such plots in ggplot2.