This package provides support for simple features, a standardized way to encode spatial vector data. It binds to GDAL for reading and writing data, to GEOS for geometrical operations, and to PROJ for projection conversions and datum transformations.

runc is a command line client for running applications packaged according to the Open Container Initiative (OCI) format and is a compliant implementation of the Open Container Initiative specification.

This package provides functionalities to build and manipulate probability distributions of the skew-normal family and some related ones, notably the skew-t family, and provides related statistical methods for data fitting and diagnostics, in the univariate and the multivariate case.

ROOT is a data analysis framework developed by CERN for tasks such as data storage, processing, and visualization. It provides tools for histograms, statistical tests, fitting, simulations, and machine learning. It can handle large datasets and uses a specialized file format.

Rdup is a utility inspired by rsync and the plan9 way of doing backups. Rdup itself does not backup anything, it only print a list of absolute file names to standard output. Auxiliary scripts are needed that act on this list and implement the backup strategy.

This package provides classes and methods for spatial data; the classes document where the spatial location information resides, for 2D or 3D data. Utility functions are provided, e.g. for plotting data as maps, spatial selection, as well as methods for retrieving coordinates, for subsetting, print, summary, etc.

GNU Rush is a restricted user shell, for systems on which users are to be provided with only limited functionality or resources. Administrators set user rights via a configuration file which can be used to limit, for example, the commands that can be executed, CPU time, or virtual memory usage.

This package provides R bindings for Google's s2 library for geometric calculations on the sphere. High-performance constructors and exporters provide high compatibility with existing spatial packages, transformers construct new geometries from existing geometries, predicates provide a means to select geometries based on spatial relationships, and accessors extract information about geometries.

This package provides functions for data manipulation, imputing missing values in an approximate Bayesian framework, diagnostics of the models used to generate the imputations, confidence-building mechanisms to validate some of the assumptions of the imputation algorithm, and functions to analyze multiply imputed data sets with the appropriate degree of sampling uncertainty.

RVVM is a RISC-V CPU and system software implementation written in C. It supports the entire RV64GC ISA, and it passes compliance tests for both RV64 and RV32. OpenSBI, U-Boot, and custom firmwares boot and execute properly. It is capable of running Linux, FreeBSD, OpenBSD, Haiku, and other OSes. Furthermore, it emulates a variety of hardware and peripherals.

This package provides a new object oriented programming system designed to be a successor to S3 and S4. It includes formal class, generic, and method specification, and a limited form of multiple dispatch. It has been designed and implemented collaboratively by the R Consortium Object-Oriented Programming Working Group, which includes representatives from R-Core, Bioconductor, Posit/tidyverse, and the wider R community.

re2c generates minimalistic hard-coded state machine (as opposed to full-featured table-based lexers). A flexible API allows generated code to be wired into virtually any environment. Instead of exposing a traditional yylex() style API, re2c exposes its internals. Be sure to take a look at the examples, as they cover a lot of real-world cases and shed some light on dark corners of the re2c API.

This package provides a minimal R and C++ API for parsing well-known binary and well-known text representation of geometries to and from R-native formats. Well-known binary is compact and fast to parse; well-known text is human-readable and is useful for writing tests. These formats are only useful in R if the information they contain can be accessed in R, for which high-performance functions are provided here.

RSEM is a software package for estimating gene and isoform expression levels from RNA-Seq data. The RSEM package provides a user-friendly interface, supports threads for parallel computation of the EM algorithm, single-end and paired-end read data, quality scores, variable-length reads and RSPD estimation. In addition, it provides posterior mean and 95% credibility interval estimates for expression levels. For visualization, it can generate BAM and Wiggle files in both transcript-coordinate and genomic-coordinate.

RCCL (pronounced "Rickle") is a stand-alone library of standard collective communication routines for GPUs, implementing all-reduce, all-gather, reduce, broadcast, reduce-scatter, gather, scatter, and all-to-all. There is also initial support for direct GPU-to-GPU send and receive operations. It has been optimized to achieve high bandwidth on platforms using PCIe, xGMI as well as networking using InfiniBand Verbs or TCP/IP sockets. RCCL supports an arbitrary number of GPUs installed in a single node or multiple nodes, and can be used in either single- or multi-process (e.g., MPI) applications.

Flexible general-purpose toolbox implementing genetic algorithms (GAs) for stochastic optimisation. Binary, real-valued, and permutation representations are available to optimize a fitness function, i.e., a function provided by users depending on their objective function. Several genetic operators are available and can be combined to explore the best settings for the current task. Furthermore, users can define new genetic operators and easily evaluate their performances. Local search using general-purpose optimisation algorithms can be applied stochastically to exploit interesting regions. GAs can be run sequentially or in parallel, using an explicit master-slave parallelisation or a coarse-grain islands approach.

Facilitates easy analysis of factorial experiments, including purely within-Ss designs (a.k.a. "repeated measures"), purely between-Ss designs, and mixed within-and-between-Ss designs. The functions in this package aim to provide simple, intuitive and consistent specification of data analysis and visualization. Visualization functions also include design visualization for pre-analysis data auditing, and correlation matrix visualization. Finally, this package includes functions for non-parametric analysis, including permutation tests and bootstrap resampling. The bootstrap function obtains predictions either by cell means or by more advanced/powerful mixed effects models, yielding predictions and confidence intervals that may be easily visualized at any level of the experiment's design.

This package provides support software for Statistical Analysis and Data Display (Second Edition, Springer, ISBN 978-1-4939-2121-8, 2015) and (First Edition, Springer, ISBN 0-387-40270-5, 2004) by Richard M. Heiberger and Burt Holland. This contemporary presentation of statistical methods features extensive use of graphical displays for exploring data and for displaying the analysis. The second edition includes redesigned graphics and additional chapters. The authors emphasize how to construct and interpret graphs, discuss principles of graphical design, and show how accompanying traditional tabular results are used to confirm the visual impressions derived directly from the graphs. Many of the graphical formats are novel and appear here for the first time in print. All chapters have exercises. All functions introduced in the book are in the package. R code for all examples, both graphs and tables, in the book is included in the scripts directory of the package.

This package lets you rarefy data, calculate diversity and plot the results.

Probabilistic analysis of probe reliability and differential gene expression on short oligonucleotide arrays.

The rpx package implements an interface to proteomics data submitted to the ProteomeXchange consortium.

The ROI is a framework for handling optimization problems in R.

This package provides utilities for Receiver Operating Characteristic (ROC) curves, with a focus on micro arrays.

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