Functions for modelling that help you seamlessly integrate modelling into a pipeline of data manipulation and visualisation.

This package implements a parametric bootstrap test and a Kenward Roger modification of F-tests for linear mixed effects models and a parametric bootstrap test for generalized linear mixed models.

This package provides alluvial plots for ggplot2. Alluvial plots use variable-width ribbons and stacked bar plots to represent multi-dimensional or repeated-measures data with categorical or ordinal variables.

This package provides a simple and flexible way to generate Circos 2D track plot images. The types of plots include: heatmap, histogram, lines, scatterplot, tiles and plot items for further decorations include connector, link (lines and ribbons), and text (gene) label. All functions require only R graphics packages that comes with the base installation.

This package provides functions for simple fixed and random effects meta-analysis for two-sample comparisons and cumulative meta-analyses. It draws standard summary plots, funnel plots, and computes summaries and tests for association and heterogeneity.

This package provides an interface to the C code for Latent Dirichlet Allocation (LDA) models and Correlated Topics Models (CTM) by David M. Blei and co-authors and the C++ code for fitting LDA models using Gibbs sampling by Xuan-Hieu Phan and co-authors.

This package lets you expand factors, characters and other eligible classes into dummy/indicator variables.

This package provides routines for Maximum likelihood, Kalman filtering and smoothing, and Bayesian analysis of Normal linear State Space models, also known as Dynamic Linear Models.

Simultaneous tests and confidence intervals for general linear hypotheses in parametric models, including linear, generalized linear, linear mixed effects, and survival models. The package includes demos reproducing analyzes presented in the book "Multiple Comparisons Using R" (Bretz, Hothorn, Westfall, 2010, CRC Press).

Read and write feather files, a lightweight binary columnar data store designed for maximum speed.

This is a complete suite to estimate models based on moment conditions. It includes the two step Generalized method of moments (Hansen 1982; <doi:10.2307/1912775>), the iterated GMM and continuous updated estimator (Hansen, Eaton and Yaron 1996; <doi:10.2307/1392442>) and several methods that belong to the Generalized Empirical Likelihood family of estimators (Smith 1997; <doi:10.1111/j.0013-0133.1997.174.x>, Kitamura 1997; <doi:10.1214/aos/1069362388>, Newey and Smith 2004; <doi:10.1111/j.1468-0262.2004.00482.x>, and Anatolyev 2005 <doi:10.1111/j.1468-0262.2005.00601.x>).

This package provides tools to compute and represent gene set enrichment or depletion from your data based on pre-saved maps from the Atlas of Cancer Signalling Networks (ACSN) or user imported maps. The gene set enrichment can be run with hypergeometric test or Fisher exact test, and can use multiple corrections. Visualization of data can be done either by barplots or heatmaps.

This package provides a set of tools for post processing the outcomes of species distribution modeling exercises. It includes novel methods for comparing models and tracking changes in distributions through time. It further includes methods for visualizing outcomes, selecting thresholds, calculating measures of accuracy and landscape fragmentation statistics, etc.

Analyze count time series with excess zeros. Two types of statistical models are supported: Markov regression and state-space models. They are also known as observation-driven and parameter-driven models respectively in the time series literature. The functions used for Markov regression or observation-driven models can also be used to fit ordinary regression models with independent data under the zero-inflated Poisson (ZIP) or zero-inflated negative binomial (ZINB) assumption. The package also contains miscellaneous functions to compute density, distribution, quantile, and generate random numbers from ZIP and ZINB distributions.

This package provides miscellaneous functions to help customize ggplot2 objects. High-level functions are provided to post-process ggplot2 layouts and allow alignment between plot panels, as well as setting panel sizes to fixed values. Other functions include a custom geom, and helper functions to enforce symmetric scales or add tags to facetted plots.

Efficient C++ optimized functions for numerical and symbolic calculus. It includes basic symbolic arithmetic, tensor calculus, Einstein summing convention, fast computation of the Levi-Civita symbol and generalized Kronecker delta, Taylor series expansion, multivariate Hermite polynomials, accurate high-order derivatives, differential operators (Gradient, Jacobian, Hessian, Divergence, Curl, Laplacian) and numerical integration in arbitrary orthogonal coordinate systems: cartesian, polar, spherical, cylindrical, parabolic or user defined by custom scale factors.

Reshape2 is an R library to flexibly restructure and aggregate data using just two functions: melt and dcast (or acast).

This package provides a vectorized R function for calculating probabilities from a standard bivariate normal CDF.

Circular layout is an efficient way to visualise huge amounts of information. This package provides an implementation of circular layout generation in R as well as an enhancement of available software. Its flexibility is based on the usage of low-level graphics functions such that self-defined high-level graphics can be easily implemented by users for specific purposes. Together with the seamless connection between the powerful computational and visual environment in R, it gives users more convenience and freedom to design figures for better understanding complex patterns behind multi-dimensional data.

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

This package performs estimation of physical activity and sedentary behavior variables from activPAL events files.

This package provides a collection of libraries for numerical computing (numerical integration, optimization, etc.) and their integration with Rcpp.

How fast can you type R functions on your keyboard? Find out by running a zty.pe game: export R functions as instructions to type to destroy opponents' vessels.

Phangorn is a package for phylogenetic analysis in R. It supports estimation of phylogenetic trees and networks using Maximum Likelihood, Maximum Parsimony, distance methods and Hadamard conjugation.