This package contains extensions to ggplot2.

1. Geomas: geom_table, geom_plot and geom_grob add insets to plots using native data coordinates, while geom_table_npc, geom_plot_npc and geom_grob_npc do the same using npc coordinates through new aesthetics npcx and npcy.

2. Statistics: select observations based on 2D density.

3. Positions: radial nudging away from a center point and nudging away from a line or curve.

This package provides an R based genetic algorithm for binary and floating point chromosomes.

This package provides functions for drawing and calibrating samples.

This package provides implementations of the SHA-3 cryptographic hash and SHAKE256 extendable-output functions (XOF).

This package provides a suite of tools designed to build attractive command line interfaces (CLIs). It includes tools for drawing rules, boxes, trees, and Unicode symbols with ASCII alternatives.

This package provides an implementation of dimensionality reduction via regression using Kernel Ridge Regression.

This package proposes a new file format named gson for storing gene set and related information, and provides read, write and other utilities to process this file format.

This package provides geometries to plot network objects with the ggplot2 package.

This package creates a lightweight way to add markdown helpfiles to Shiny apps, using modal dialog boxes, with no need to observe each help button separately.

This package abbreviates strings to a specified minimum number of characters, such that the strings remain unique (if they originally were).

This package contains the datasets and a few functions for use with the practicals outlined in Appendix A of the book Statistical Models (Davison, 2003, Cambridge University Press). The practicals themselves can be found at http://statwww.epfl.ch/davison/SM/.

Functions and examples are provided for transmission/disequilibrium tests for extended marker haplotypes, as in Clayton, D. and Jones, H. (1999) "Transmission/disequilibrium tests for extended marker haplotypes".

Raw vectors in R are useful for storing a single binary object. What if you want to put a vector of them in a data frame? The blob package provides the blob object, a list of raw vectors, suitable for use as a column in data frame.

This package provides a set of restricted permutation designs for freely exchangeable, line transects (time series), spatial grid designs and permutation of blocks (groups of samples). permute also allows split-plot designs, in which the whole-plots or split-plots or both can be freely exchangeable.

Plyr is a set of tools that solves a common set of problems: you need to break a big problem down into manageable pieces, operate on each piece and then put all the pieces back together. For example, you might want to fit a model to each spatial location or time point in your study, summarise data by panels or collapse high-dimensional arrays to simpler summary statistics.

This is a package to infer transmission trees from a dated phylogeny. It includes methods to simulate and analyze outbreaks. The methodology is described in Didelot et al. (2014) and Didelot et al. (2017).

This package contains utility functions for the spatstat package which may also be useful for other purposes.

This package OrgMassSpecR is an extension of the R statistical computing language. It contains functions to assist with organic or biological mass spectrometry data analysis. Mass spectral libraries are available as companion packages.

This package provides an implementation of many measures for the assessment of the stability of feature selection. Both simple measures and measures which take into account the similarities between features are available.

This package implements Freund and Schapire's Adaboost.M1 algorithm and Breiman's Bagging algorithm using classification trees as individual classifiers. Once these classifiers have been trained, they can be used to predict on new data. Also, cross validation estimation of the error can be done.

This package computes fast (relative to other implementations) approximate Shapley values for any supervised learning model. Shapley values help to explain the predictions from any black box model using ideas from game theory; see doi.org/10.1007/s10115-013-0679-x for details.

This package is a port of sofia-ml to R. Sofia-ml is a suite of fast incremental algorithms for machine learning that can be used for training models for classification or ranking.

This package provides the header files of mio, a cross-platform C++11 header-only library for memory mapped file IO.

This package performs 2D Delaunay triangulation, constrained or unconstrained, with the help of the C++ library CDT. A function to plot the triangulation is provided. The constrained Delaunay triangulation has applications in geographic information systems.