This package provides functions for the consistent analysis of compositional data (e.g. portions of substances) and positive numbers (e.g. concentrations).

This tool supports analyses on massive phylogenies comprising up to millions of tips. Functions include pruning, rerooting, calculation of most-recent common ancestors, calculating distances from the tree root and calculating pairwise distances. In addition, this tool takes care of calculation of phylogenetic signal and mean trait depth (trait conservatism), ancestral state reconstruction and hidden character prediction of discrete characters, simulating and fitting models of trait evolution, fitting and simulating diversification models, dating trees, comparing trees, and reading/writing trees in Newick format.

HTML widgets is a framework for creating HTML widgets that render in various contexts including the R console, R Markdown documents, and Shiny web applications.

This light-weight package helps you track and visualize the progress of parallel versions of vectorized R functions of the mc*apply family.

This package provides a collection of helper functions designed to help you to better understand object oriented programming in R, particularly using S3.

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

This package provides a collection of convenient functions for common statistical computations, which are not directly provided by R's base or stats packages. This package aims at providing, first, shortcuts for statistical measures, which otherwise could only be calculated with additional effort. Second, these shortcut functions are generic, and can be applied not only to vectors, but also to other objects as well. The focus of most functions lies on summary statistics or fit measures for regression models, including generalized linear models, mixed effects models and Bayesian models.

The grammar of graphics as implemented in ggplot2 is a poor fit for graph and network visualizations due to its reliance on tabular data input. The ggraph package is an extension of the ggplot2 API tailored to graph visualizations and provides the same flexible approach to building up plots layer by layer.

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 contains a list of functional time series, sliced functional time series, and functional data sets. Functional time series is a special type of functional data observed over time. Sliced functional time series is a special type of functional time series with a time variable observed over time.

This package provides functionality for client-side navigation of the server side file system in shiny apps. In case the app is running locally this gives the user direct access to the file system without the need to "download" files to a temporary location. Both file and folder selection as well as file saving is available.

This tool generates high number of both single- and multi-objective test functions. These functions are frequently used for the benchmarking of (numerical) optimization algorithms. Moreover, it offers a set of convenient functions to generate, plot and work with objective functions.

This package provides flexible parametric models for time-to-event data, including the Royston-Parmar spline model, generalized gamma and generalized F distributions. Any user-defined parametric distribution can be fitted, given at least an R function defining the probability density or hazard. There are also tools for fitting and predicting from fully parametric multi-state models.

This package provides functions for viewing 2D and 3D data, including perspective plots, slice plots, surface plots, scatter plots, etc. It includes data sets from oceanography.

This package carries out a mapping between assorted color spaces including RGB, HSV, HLS, CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB and polar CIELAB. Qualitative, sequential, and diverging color palettes based on HCL colors are provided.

This package is a collection of several algorithms to obtain archetypoids with small and large databases and with both classical multivariate data and functional data (univariate and multivariate). Some of these algorithms also detect anomalies (outliers).

This package provides a basic set of R functions for querying the Cancer Genomics Data Server (CGDS), hosted by the Computational Biology Center at Memorial-Sloan-Kettering Cancer Center (MSKCC).

This package provides a lightweight unit testing framework. Main features:

1. install tests with the package;

2. test results are treated as data that can be stored and manipulated;

3. test files are R scripts interspersed with test commands, that can be programmed over;

4. fully automated build-install-test sequence for packages;

5. skip tests when not run locally (e.g. on CRAN);

6. flexible and configurable output printing;

7. compare computed output with output stored with the package;

8. run tests in parallel;

9. extensible by other packages;

10. report side effects.

This package provides a set of distributions which can be used for modelling the response variables in Generalized Additive Models for Location Scale and Shape. The distributions can be continuous, discrete or mixed distributions. Extra distributions can be created, by transforming, any continuous distribution defined on the real line, to a distribution defined on ranges 0 to infinity or 0 to 1, by using a log or a logit transformation, respectively.

This package provides methods for cluster analysis. It is a much extended version of the original from Peter Rousseeuw, Anja Struyf and Mia Hubert, based on Kaufman and Rousseeuw (1990) "Finding Groups in Data".

Changepoint implements various mainstream and specialised changepoint methods. These methods are suitable for finding single and multiple changepoints within data. Many popular non-parametric and frequentist methods are included as well.

This package provides a simple router for your Shiny apps. The router allows you to create dynamic web applications with a real-time User Interface and easily share url to pages within your Shiny apps.

spacefillr enables generation of random and quasi-random space-filling sequences. It supports the following sequences: Halton, Sobol, Owen-scrambled Sobol, Owen-scrambled Sobol with errors distributed as blue noise, progressive jittered, progressive multi-jittered (PMJ), PMJ with blue noise, PMJ02, and PMJ02 with blue noise. The package also includes a C++ API.

This package helps with quality checks, visualizations and analysis of mass spectrometry data, coming from proteomics experiments. The package is developed, tested and used at the Functional Genomics Center Zurich, where it is used mainly for prototyping, teaching, and having fun with proteomics data. But it can also be used to do data analysis for small scale data sets.