This package provides a common interface to specifying clustering models, in the same style as parsnip. It creates a unified interface across different functions and computational engines.

This package provides pure R tools to read BMP format images. It is currently limited to 8 bit greyscale images and 24, 32 bit (A)RGB images.

This package provides R bindings to the Sundown Markdown rendering library (https://github.com/vmg/sundown). Markdown is a plain-text formatting syntax that can be converted to XHTML or other formats.

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

This package holds the database for the extrafont package.

This package provides tools for the comparison of distributions. This includes nonparametric estimation of the relative distribution PDF and CDF and numerical summaries as described in "Relative Distribution Methods in the Social Sciences" by Mark S. Handcock and Martina Morris, Springer-Verlag, 1999, Springer-Verlag, ISBN 0387987789.

This package implements several Approximate Bayesian Computation (ABC) algorithms for performing parameter estimation, model selection, and goodness-of-fit. Cross-validation tools are also available for measuring the accuracy of ABC estimates, and to calculate the misclassification probabilities of different models.

Multivariate data sets often differ in several factors or derived statistical parameters, which have to be selected for a valid interpretation. Basing this selection on traditional statistical limits leads occasionally to the perception of losing information from a data set. This package provides tools to calculate these limits on the basis of the mathematical properties of the distribution of the analyzed items.

This is a package for parameter description and operations in optimization, tuning and machine learning. Parameters can be described (type, constraints, defaults, etc.), combined to parameter sets and can in general be programmed on. A useful OptPath object (archive) to log function evaluations is also provided.

This package contains several basic utility functions including: moving (rolling, running) window statistic functions, read/write for GIF and ENVI binary files, fast calculation of AUC, LogitBoost classifier, base64 encoder/decoder, round-off-error-free sum and cumsum, etc.

This package provides a replacement and extension of the optim function to call to several function minimization codes in R in a single statement. These methods handle smooth, possibly box constrained functions of several or many parameters. Note that the function optimr was prepared to simplify the incorporation of minimization codes going forward. This package also implements some utility codes and some extra solvers, including safeguarded Newton methods. Many methods previously separate are now included here.

This package offers extensive tools for phylogenetic analysis. It focuses on phylogenetic comparative biology but also includes methods for visualizing, analyzing, manipulating, reading, writing, and inferring phylogenetic trees. Functions for comparative biology include ancestral state reconstruction, model fitting, and phylogeny and trait data simulation. A broad range of plotting methods includes mapping trait evolution on trees, projecting trees into phenotype space or geographic maps, and visualizing correlated speciation between trees. Additional functions allow for reading, writing, analyzing, inferring, simulating, and manipulating phylogenetic trees and comparative data. Examples include computing consensus trees, simulating trees and data under various models, and attaching species or clades to a tree either randomly or non-randomly. This package provides numerous tools for tree manipulations and analyses that are valuable for phylogenetic research.

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

This is a package for random number generation for the truncated multivariate normal and Student t distribution. It computes probabilities, quantiles and densities, including one-dimensional and bivariate marginal densities. It computes first and second moments (i.e. mean and covariance matrix) for the double-truncated multinormal case.

Ggfittext is a ggplot2 extension for fitting text into boxes.

This package offers methods for estimating statistical changes in time series. These are used for identifying nearby critical transitions.

In putative Transcription Factor Binding Sites (TFBSs) identification from sequence/alignments, we are interested in the significance of certain match scores. TFMPvalue provides the accurate calculation of a p-value with a score threshold for position weight matrices, or the score with a given p-value. It is an interface to code originally made available by Helene Touzet and Jean-Stephane Varre, 2007, Algorithms Mol Biol:2, 15. Touzet and Varre (2007).

This package supports arithmetic (via S4 classes and methods) for arbitrary precision floating point numbers, including transcendental functions. To this end, the package interfaces with the Multiple Precision Floating-Point Reliable (MPFR) library.

Data exploration and modelling is a process in which a lot of data artifacts are produced. Artifacts like: subsets, data aggregates, plots, statistical models, different versions of data sets and different versions of results. Archivist helps to store and manage artifacts created in R. It allows you to store selected artifacts as binary files together with their metadata and relations. Archivist allows sharing artifacts with others. It can look for already created artifacts by using its class, name, date of the creation or other properties. It also makes it easy to restore such artifacts.

This package provides miscellaneous functions for training and plotting classification and regression models.

This package provides data structures and basic operations for ordinary sets, generalizations such as fuzzy sets, multisets, and fuzzy multisets, customizable sets, and intervals.

This package provides functions that wrap popular phylogenetic software for sequence alignment, masking of sequence alignments, and estimation of phylogenies and ancestral character states.

This package uses both ridge and lasso penalties (and extensions) to penalize specific parameters in structural equation models. The package offers additional cost functions, cross validation, and other extensions beyond traditional structural equation models. It also contains a function to perform exploratory mediation (XMed).

This is a collection of tools for assessment of feature importance and feature effects. Key functions are:

• feature_importance() for assessment of global level feature importance,

• ceteris_paribus() for calculation of the what-if plots,

• partial_dependence() for partial dependence plots,

• conditional_dependence() for conditional dependence plots,

• accumulated_dependence() for accumulated local effects plots,

• aggregate_profiles() and cluster_profiles() for aggregation of ceteris paribus profiles,

• generic print() and plot() for better usability of selected explainers,

• generic plotD3() for interactive, D3 based explanations, and

• generic describe() for explanations in natural language.