This package provides a command line parser to be used with Rscript to write shebang scripts that gracefully accept positional and optional arguments and automatically generate usage notices.

R-tgb provides Bayesian nonstationary regression and treed Gaussian processes. In addition, it provides visualization functions, tree drawing, sensitivity analysis, multi-resolution models, and sequential experimental design tools, including ALM, ALC, and expected improvement for optimizing noisy black-box functions.

This package provides tools for shrunken centroids regularized discriminant analysis for the purpose of classifying high dimensional data.

This package provides a minor collection of HTTP wrappers for the Zamzar file conversion API. The wrappers makes it easy to utilize the API and thus convert between more than 100 different file formats (ranging from audio files, images, movie formats, etc., etc.) through an R session.

The grammar of graphics as shown in ggplot2 has provided an expressive API for users to build plots. This package ggside extends ggplot2 by allowing users to add graphical information about one of the main panel's axis using a familiar ggplot2 style API with tidy data. This package is particularly useful for visualizing metadata on a discrete axis, or summary graphics on a continuous axis such as a boxplot or a density distribution.

This package provides implementations of the family of map() functions from the purrr package that can be resolved using any future-supported backend, e.g. parallel on the local machine or distributed on a compute cluster.

This package adds additional Twitter Bootstrap components to Shiny.

This package provides methods for fast access to large ASCII files. Currently the following file formats are supported: comma separated format (CSV) and fixed width format. It is assumed that the files are too large to fit into memory, although the package can also be used to efficiently access files that do fit into memory. Methods are provided to access and process files blockwise. Furthermore, an opened file can be accessed as one would an ordinary data.frame. The LaF vignette gives an overview of the functionality provided.

This package provides functions for quickly writing and reading any R object to and from disk.

This package provides functions to fit kernel density functions to data on temporal activity patterns of animals; estimate coefficients of overlapping of densities for two species; and calculate bootstrap estimates of confidence intervals.

This package provides a fast and user-friendly implementation of nonparametric estimators for censored event history (survival) analysis with the Kaplan-Meier and Aalen-Johansen methods.

dplyr is the next iteration of plyr. It is focused on tools for working with data frames. It has three main goals: 1) identify the most important data manipulation tools needed for data analysis and make them easy to use in R; 2) provide fast performance for in-memory data by writing key pieces of code in C++; 3) use the same code interface to work with data no matter where it is stored, whether in a data frame, a data table or database.

This package provides common base and stats methods for rle objects, aiming to make it possible to treat them transparently as vectors.

This is package for QTL mapping in a mixed model framework with separate detection and localization stages. The first stage detects the number of QTL on each chromosome based on the genetic variation due to grouped markers on the chromosome; the second stage uses this information to determine the most likely QTL positions. The mixed model can accommodate general fixed and random effects, including spatial effects in field trials and pedigree effects. It is applicable to backcrosses, doubled haploids, recombinant inbred lines, F2 intercrosses, and association mapping populations.

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.

Rserve acts as a socket server (TCP/IP or local sockets) which allows binary requests to be sent to R. Every connection has a separate workspace and working directory. Client-side implementations are available for popular languages such as C/C++ and Java, allowing any application to use facilities of R without the need of linking to R code. Rserve supports remote connection, user authentication and file transfer. A simple R client is included in this package as well.

This package provides probability mass, distribution, quantile, random-variate generation, and method-of-moments parameter-estimation functions for the Delaporte distribution with parameterization based on Vose (2008). The Delaporte is a discrete probability distribution which can be considered the convolution of a negative binomial distribution with a Poisson distribution. Alternatively, it can be considered a counting distribution with both Poisson and negative binomial components. It has been studied in actuarial science as a frequency distribution which has more variability than the Poisson, but less than the negative binomial.

This package provides a minimal R client to access the GitHub API.

r-kmer is an R package for rapidly computing distance matrices and clustering large sequence datasets using fast alignment-free k-mer counting and recursive k-means partitioning.

This package fits multivariate generalized linear mixed models and related models. This is done using Markov chain Monte Carlo techniques.

This is an R package for the imputation of left-censored data under a compositional approach. The implemented methods consider aspects of relevance for a compositional approach such as scale invariance, subcompositional coherence or preserving the multivariate relative structure of the data. Based on solid statistical frameworks, it comprises the ability to deal with single and varying censoring thresholds, consistent treatment of closed and non-closed data, exploratory tools, multiple imputation, Markov Chain Monte Carlo (MCMC), robust and non-parametric alternatives, and recent proposals for count data.

This package provides several utility functions for the book entitled "Practices of Medical and Health Data Analysis using R" (Pearson Education Japan, 2007) with Japanese demographic data and some demographic analysis related functions.

This package provides tools for handling Base64 encoding. It is more flexible than the orphaned "base64" package.

Full 64-bit resolution date and time functionality with nanosecond granularity is provided, with easy transition to and from the standard POSIXct type. Three additional classes offer interval, period and duration functionality for nanosecond-resolution timestamps.