This package provides tools to create a measure of inter-point dissimilarity useful for clustering mixed data, and, optionally, perform the clustering.

This package provides a unit testing system for R designed to be fun, flexible and easy to set up.

Tools for integrating spatially-misaligned GIS datasets. Part of the Sub-National Geospatial Data Archive System.

This package supports the analysis of count data exhibiting autoregressive properties, using the Autoregressive Conditional Poisson model (ACP(p,q)) proposed by Heinen (2003).

This is a package for estimating the copula mixture model and plotting correspondence curves in "Measuring reproducibility of high-throughput experiments" (2011), Annals of Applied Statistics, Vol. 5, No. 3, 1752-1779, by Li, Brown, Huang, and Bickel

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

This is an extension of the testthat package that lets you add parameters to your unit tests. Parameterized unit tests are often easier to read and more reliable, since they follow the DNRY (do not repeat yourself) rule.

This package provides utilities to process, organize and explore protein structure, sequence and dynamics data. Features include the ability to read and write structure, sequence and dynamic trajectory data, perform sequence and structure database searches, data summaries, atom selection, alignment, superposition, rigid core identification, clustering, torsion analysis, distance matrix analysis, structure and sequence conservation analysis, normal mode analysis, principal component analysis of heterogeneous structure data, and correlation network analysis from normal mode and molecular dynamics data. In addition, various utility functions are provided to enable the statistical and graphical power of the R environment to work with biological sequence and structural data.

This package provides a suite of methods for powerful and robust microbiome data analysis, including data normalization, data simulation, community-level association testing and differential abundance analysis. It implements generalized UniFrac distances, Geometric Mean of Pairwise Ratios (GMPR) normalization, semiparametric data simulator, distance-based statistical methods, and feature- based statistical methods. The distance-based statistical methods include three extensions of PERMANOVA:

• PERMANOVA using the Freedman-Lane permutation scheme,

• PERMANOVA omnibus test using multiple matrices, and

• analytical approach to approximating PERMANOVA p-value.

Feature-based statistical methods include linear model-based methods for differential abundance analysis of zero-inflated high-dimensional compositional data.

Zoltar is a website that provides a repository of model forecast results in a standardized format and a central location. It supports storing, retrieving, comparing, and analyzing time series forecasts for prediction challenges of interest to the modeling community. This package provides functions for working with the Zoltar API, including connecting and authenticating, getting information about projects, models, and forecasts, deleting and uploading forecast data, and downloading scores.

This package lets you edit and simplify geojson, Spatial, and sf objects. This is a wrapper around the mapshaper JavaScript library to perform topologically-aware polygon simplification, as well as other operations such as clipping, erasing, dissolving, and converting multi-part to single-part geometries.

This is a package for estimation and inference from generalized linear models based on various methods for bias reduction and maximum penalized likelihood with powers of the Jeffreys prior as penalty. The brglmFit fitting method can achieve reduction of estimation bias by solving either the mean bias-reducing adjusted score equations in Firth (1993) <doi:10.1093/biomet/80.1.27> and Kosmidis and Firth (2009) <doi:10.1093/biomet/asp055>, or the median bias-reduction adjusted score equations in Kenne et al. (2017) <doi:10.1093/biomet/asx046>, or through the direct subtraction of an estimate of the bias of the maximum likelihood estimator from the maximum likelihood estimates as in Cordeiro and McCullagh (1991) <https://www.jstor.org/stable/2345592>.

The futile.options subsystem provides an easy user-defined options management system that is properly scoped. This means that options created via futile.options are fully self-contained and will not collide with options defined in other packages.

The empirical transition matrix (etm) package estimates the matrix of transition probabilities for any time-inhomogeneous multistate model with finite state space using the Aalen-Johansen estimator.

This package provides a developer-facing interface to Arrow Database Connectivity (ADBC) for the purposes of driver development, driver testing, and building high-level database interfaces for users. ADBC is an API standard for database access libraries that uses Arrow for result sets and query parameters.

This package contains all the datasets for the spatstat package.

Create interactive 3D scatter plots, network plots, and globes in R using the three.js visualization library.

This package provides an implementation of the Tukey, Mandel, Johnson-Graybill, LBI, Tusell and modified Tukey non-additivity tests.

This package offers an implementation of the Abnormal blood profile score (ABPS). The ABPS is a part of the Athlete biological passport program of the World anti-doping agency, which combines several blood parameters into a single score in order to detect blood doping. The package also contains functions to calculate other scores used in anti-doping programs, such as the ratio of hemoglobin to reticulocytes (OFF-score), as well as example data.

The package implements basic and high-level functions for reading, writing, manipulating, analyzing and modeling of gridded spatial data. Processing of very large files is supported.

This package provides tools to read, write, create, and manipulate DESCRIPTION files. It is intended for packages that create or manipulate other packages.

The Tweedie compound Poisson distribution is a mixture of a degenerate distribution at the origin and a continuous distribution on the positive real line. It has been applied in a wide range of fields in which continuous data with exact zeros regularly arise. The cplm package provides likelihood based and Bayesian procedures for fitting common Tweedie compound Poisson linear models. In particular, models with hierarchical structures or extra zero inflation can be handled. Further, the package implements the Gini index based on an ordered version of the Lorenz curve as a robust model comparison tool involving zero-inflated and highly skewed distributions.

This package provides the header files for a stripped-down version of the plog header-only C++ logging library, and a method to log to R's standard error stream.

This package lets you import foreign statistical formats into R via the ReadStat C library.