Packages — R (Page 4 of 9)

r-microbenchmark 1.4-4 — Accurate timing functions for R

This package provides infrastructure to accurately measure and compare the execution time of R expressions.

r-mime 0.5 — R package to map filenames to MIME types

This package guesses the MIME type from a filename extension using the data derived from /etc/mime.types in UNIX-type systems.

r-minimal 3.4.4 — Environment for statistical computing and graphics

R is a language and environment for statistical computing and graphics. It provides a variety of statistical techniques, such as linear and nonlinear modeling, classical statistical tests, time-series analysis, classification and clustering. It also provides robust support for producing publication-quality data plots. A large amount of 3rd-party packages are available, greatly increasing its breadth and scope.

r-minqa 1.2.4 — Derivative-free optimization algorithms by quadratic approximation

This package provides a derivative-free optimization by quadratic approximation based on an interface to Fortran implementations by M. J. D. Powell.

r-mixtools 1.1.0 — Tools for analyzing finite mixture models

This package provides a collection of R functions for analyzing finite mixture models.

r-mnormt 1.5-5 — Multivariate normal and "t" distributions

This package provides functions for computing the density and the distribution function of multivariate normal and "t" random variables, and for generating random vectors sampled from these distributions. Probabilities are computed via non-Monte Carlo methods.

r-modelmetrics 1.1.0 — Rapid calculation of model metrics

Written in C++ using Rcpp, this package provides a collection of metrics for evaluating models.

r-modelr 0.1.1 — Helper functions for modelling in pipelines

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

r-modeltools 0.2-21 — Tools and classes for statistical models

This package provides a collection of tools to deal with statistical models. The functionality is experimental and the user interface is likely to change in the future.

r-motifrg 1.22.0 — Discover motifs in high throughput sequencing data

This package provides tools for discriminative motif discovery in high throughput genetic sequencing data sets using regression methods.

r-msnbase 2.4.2 — Base functions and classes for MS-based proteomics

This package provides basic plotting, data manipulation and processing of mass spectrometry based proteomics data.

r-msnid 1.12.1 — Utilities for LC-MSn proteomics identifications

This package extracts tandem mass spectrometry (MS/MS) ID data from mzIdentML (leveraging the mzID package) or text files. After collating the search results from multiple datasets it assesses their identification quality and optimize filtering criteria to achieve the maximum number of identifications while not exceeding a specified false discovery rate. It also contains a number of utilities to explore the MS/MS results and assess missed and irregular enzymatic cleavages, mass measurement accuracy, etc.

r-multitaper 1.0-14 — Multitaper spectral analysis tools

This package implements multitaper spectral estimation techniques using prolate spheroidal sequences (Slepians) and sine tapers for time series analysis. It includes an adaptive weighted multitaper spectral estimate, a coherence estimate, Thomson's Harmonic F-test, and complex demodulation. The Slepians sequences are generated efficiently using a tridiagonal matrix solution, and jackknifed confidence intervals are available for most estimates.

r-munsell 0.4.3 — Munsell colour system

The Munsell package contains Functions for exploring and using the Munsell colour system.

r-mutationalpatterns 1.4.3 — Extract and visualize mutational patterns in genomic data

This package provides an extensive toolset for the characterization and visualization of a wide range of mutational patterns in SNV base substitution data.

r-mvtnorm 1.0-7 — Package for multivariate normal and t-distributions

This package can compute multivariate normal and t-probabilities, quantiles, random deviates and densities.

r-mzid 1.16.0 — Parser for mzIdentML files

This package provides a parser for mzIdentML files implemented using the XML package. The parser tries to be general and able to handle all types of mzIdentML files with the drawback of having less pretty output than a vendor specific parser.

r-mzr 2.12.0 — Parser for mass spectrometry data files

The mzR package provides a unified API to the common file formats and parsers available for mass spectrometry data. It comes with a wrapper for the ISB random access parser for mass spectrometry mzXML, mzData and mzML files. The package contains the original code written by the ISB, and a subset of the proteowizard library for mzML and mzIdentML. The netCDF reading code has previously been used in XCMS.

r-network 1.13.0.1 — Classes for relational data

This package provides tools to create and modify network objects. The network class can represent a range of relational data types, and supports arbitrary vertex/edge/graph attributes.

r-nlme 3.1-137 — Linear and nonlinear mixed effects models

This package provides tools to fit and compare Gaussian linear and nonlinear mixed-effects models.

r-nloptr 1.0.4 — R interface to NLopt

This package is interface to NLopt, a library for nonlinear optimization. NLopt is a library for nonlinear optimization, providing a common interface for a number of different free optimization routines available online as well as original implementations of various other algorithms.

r-nmf 0.21.0 — Algorithms and framework for nonnegative matrix factorization

This package provides a framework to perform Non-negative Matrix Factorization (NMF). The package implements a set of already published algorithms and seeding methods, and provides a framework to test, develop and plug new or custom algorithms. Most of the built-in algorithms have been optimized in C++, and the main interface function provides an easy way of performing parallel computations on multicore machines.

r-nnet 7.3-12 — Feed-forward neural networks and multinomial log-linear models

This package provides functions for feed-forward neural networks with a single hidden layer, and for multinomial log-linear models.

r-np 0.60-6 — Non-parametric kernel smoothing methods for mixed data types

This package provides non-parametric (and semi-parametric) kernel methods that seamlessly handle a mix of continuous, unordered, and ordered factor data types.

r-numderiv 2016.8-1 — Accurate numerical derivatives

This package provides methods for calculating accurate numerical first and second order derivatives.

r-openssl 1.0.1 — Toolkit for encryption, signatures and certificates

This package provides R bindings to OpenSSL libssl and libcrypto, plus custom SSH pubkey parsers. It supports RSA, DSA and NIST curves P-256, P-384 and P-521. Cryptographic signatures can either be created and verified manually or via x509 certificates. AES block cipher is used in CBC mode for symmetric encryption; RSA for asymmetric (public key) encryption. High-level envelope functions combine RSA and AES for encrypting arbitrary sized data. Other utilities include key generators, hash functions (md5, sha1, sha256, etc), base64 encoder, a secure random number generator, and bignum math methods for manually performing crypto calculations on large multibyte integers.

r-openxlsx 4.0.17 — Read, write and edit XLSX files

This package simplifies the creation of Excel .xlsx files by providing a high level interface to writing, styling and editing worksheets. Through the use of Rcpp, read/write times are comparable to the xlsx and XLConnect packages with the added benefit of removing the dependency on Java.

r-optparse 1.4.4 — Command line option parser

This package provides a command line parser inspired by Python's optparse library to be used with Rscript to write shebang scripts that accept short and long options.

r-org-ce-eg-db 3.5.0 — Genome wide annotation for Worm

This package provides mappings from Entrez gene identifiers to various annotations for the genome of the model worm Caenorhabditis elegans.

r-org-dm-eg-db 3.5.0 — Genome wide annotation for Fly

This package provides mappings from Entrez gene identifiers to various annotations for the genome of the model fruit fly Drosophila melanogaster.

r-org-hs-eg-db 3.5.0 — Genome wide annotation for Human

This package contains genome-wide annotations for Human, primarily based on mapping using Entrez Gene identifiers.

r-org-mm-eg-db 3.5.0 — Genome wide annotation for Mouse

This package provides mappings from Entrez gene identifiers to various annotations for the genome of the model mouse Mus musculus.

r-organismdbi 1.20.0 — Software to enable the smooth interfacing of database packages

The package enables a simple unified interface to several annotation packages each of which has its own schema by taking advantage of the fact that each of these packages implements a select methods.

r-parsedate 1.1.3 — Recognize and parse dates in various formats

This package provides three functions for dealing with dates: parse_iso_8601 recognizes and parses all valid ISO 8601 date and time formats, parse_date parses dates in unspecified formats, and format_iso_8601 formats a date in ISO 8601 format.

r-pastecs 1.3.21 — Analysis of space-time ecological series

This package provides functions for regulation, decomposition and analysis of space-time series. The pastecs library is a PNEC-Art4 and IFREMER initiative to bring PASSTEC 2000 functionalities to R.

r-pbapply 1.3-4 — Adding progress bar to apply functions

This lightweight package that adds progress bar to vectorized R functions apply. The implementation can easily be added to functions where showing the progress is useful e.g. bootstrap.

r-pbkrtest 0.4-7 — Methods for linear mixed model comparison

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.

r-pcamethods 1.70.0 — Collection of PCA methods

This package provides Bayesian PCA, Probabilistic PCA, Nipals PCA, Inverse Non-Linear PCA and the conventional SVD PCA. A cluster based method for missing value estimation is included for comparison. BPCA, PPCA and NipalsPCA may be used to perform PCA on incomplete data as well as for accurate missing value estimation. A set of methods for printing and plotting the results is also provided. All PCA methods make use of the same data structure (pcaRes) to provide a common interface to the PCA results.

r-pcapp 1.9-73 — Robust PCA by projection pursuit

This package provides functions for robust principal component analysis (PCA) by projection pursuit.

r-pdist 1.2 — Partitioned distance function

Pdist computes the euclidean distance between rows of a matrix X and rows of another matrix Y. Previously, this could be done by binding the two matrices together and calling dist, but this creates unnecessary computation by computing the distances between a row of X and another row of X, and likewise for Y. Pdist strictly computes distances across the two matrices, not within the same matrix, making computations significantly faster for certain use cases.

r-performanceanalytics 1.5.2 — Econometric tools for performance and risk analysis

This is a collection of econometric functions for performance and risk analysis. This package aims to aid practitioners and researchers in utilizing the latest research in analysis of non-normal return streams. In general, it is most tested on return (rather than price) data on a regular scale, but most functions will work with irregular return data as well, and increasing numbers of functions will work with P&L or price data where possible.

r-permute 0.9-4 — Functions for Generating Restricted Permutations of Data

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.

r-phangorn 2.4.0 — Phylogenetic analysis in R

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.

r-pheatmap 1.0.8 — Pretty heatmaps

This package provides an implementation of heatmaps that offers more control over dimensions and appearance.

r-phontools 0.2-2.1 — Tools for phonetic and acoustic analyses

This package contains tools for the organization, display, and analysis of the sorts of data frequently encountered in phonetics research and experimentation, including the easy creation of IPA vowel plots, and the creation and manipulation of WAVE audio files.

r-pillar 1.2.1 — Coloured formatting for columns

This package provides a pillar generic designed for formatting columns of data using the full range of colours provided by modern terminals.

r-pkgconfig 2.0.1 — Private configuration for R packages

This package provides the functionality to set configuration options on a per-package basis. Options set by a given package only apply to that package, other packages are unaffected.

r-pkgmaker 0.22 — Package development utilities

This package provides some low-level utilities to use for R package development. It currently provides managers for multiple package specific options and registries, vignette, unit test and bibtex related utilities.

r-plogr 0.2.0 — R bindings for the plog C++ logging library

This package provides the header files for a stripped-down version of the plog header-only C++ logging library, and a method to log to R's standard error stream.

r-plotly 4.7.1 — Create interactive web graphics

This package enables the translation of ggplot2 graphs to an interactive web-based version and/or the creation of custom web-based visualizations directly from R. Once uploaded to a plotly account, plotly graphs (and the data behind them) can be viewed and modified in a web browser.

r-plotrix 3.7 — Various plotting functions

This package provides lots of plotting, various labeling, axis and color scaling functions for R.

r-plyr 1.8.4 — Tools for Splitting, Applying and Combining Data

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.

r-png 0.1-7 — Read and write PNG images

This package provides an easy and simple way to read, write and display bitmap images stored in the PNG format. It can read and write both files and in-memory raw vectors.

r-powerlaw 0.70.1 — Tools for the analysis of heavy tailed distributions

This package provides an implementation of maximum likelihood estimators for a variety of heavy tailed distributions, including both the discrete and continuous power law distributions. Additionally, a goodness-of-fit based approach is used to estimate the lower cut-off for the scaling region.

r-powerplus 3.1 — Exponentiation operations

This package provides tools for the computation of matrix and scalar exponentiation.

r-prabclus 2.2-6 — Parametric bootstrap tests for spatial neighborhood clustering

This package provides distance-based parametric bootstrap tests for clustering with spatial neighborhood information. It implements some distance measures, clustering of presence-absence, abundance and multilocus genetical data for species delimitation, nearest neighbor based noise detection.

r-pracma 2.1.4 — Practical numerical math functions

This package provides functions for numerical analysis and linear algebra, numerical optimization, differential equations, plus some special functions. It uses Matlab function names where appropriate to simplify porting.

r-praise 1.0.0 — Functions to praise users

This package provides template functions to assist in building friendly R packages that praise their users.

r-preprocesscore 1.40.0 — Collection of pre-processing functions

This package provides a library of core pre-processing and normalization routines.

r-prettyunits 1.0.2 — Pretty, human readable formatting of quantities

This package provides tools for pretty, human readable formatting of quantities.

r-processx 2.0.0.1 — Execute and control system processes

This package provides portable tools to run system processes in the background. It can check if a background process is running; wait on a background process to finish; get the exit status of finished processes; kill background processes and their children; restart processes. It can read the standard output and error of the processes, using non-blocking connections. processx can poll a process for standard output or error, with a timeout. It can also poll several processes at once.

r-prodlim 2018.04.18 — Product-limit estimation for censored event history analysis

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.

r-progress 1.1.2 — Terminal progress bars

This package provides configurable progress bars. They may include percentage, elapsed time, and/or the estimated completion time. They work in terminals, in Emacs ESS, RStudio, Windows Rgui, and the macOS R.app. The package also provides a C++ API, that works with or without Rcpp.

r-promises 1.0.1 — Abstractions for promise-based asynchronous programming

This package provides fundamental abstractions for doing asynchronous programming in R using promises. Asynchronous programming is useful for allowing a single R process to orchestrate multiple tasks in the background while also attending to something else. Semantics are similar to JavaScript promises, but with a syntax that is idiomatic R.

r-protgenerics 1.10.0 — S4 generic functions for proteomics infrastructure

This package provides S4 generic functions needed by Bioconductor proteomics packages.

r-proto 1.0.0 — Prototype object-based programming

Proto is an object oriented system using object-based, also called prototype-based, rather than class-based object oriented ideas.

r-proxy 0.4-22 — Distance and similarity measures

This package provides an extensible framework for the efficient calculation of auto- and cross-proximities, along with implementations of the most popular ones.

r-prroc 1.3 — Precision-Recall and ROC curves for weighted and unweighted data

This package computes the areas under the precision-recall (PR) and ROC curve for weighted (e.g. soft-labeled) and unweighted data. In contrast to other implementations, the interpolation between points of the PR curve is done by a non-linear piecewise function. In addition to the areas under the curves, the curves themselves can also be computed and plotted by a specific S3-method.

r-pryr 0.1.4 — Tools for computing on the R language

This package provides useful tools to pry back the covers of R and understand the language at a deeper level.

r-psych 1.8.3.3 — Procedures for psychological, psychometric, and personality research

This package provides a general purpose toolbox for personality, psychometric theory and experimental psychology. The functions are primarily for multivariate analysis and scale construction using factor analysis, principal component analysis, cluster analysis and reliability analysis, although others provide basic descriptive statistics. It provides functions for analyzing data at multiple levels within and between group statistics, including correlations and factor analysis; functions for simulating and testing particular item and test structures are included. Several functions serve as a useful front end for structural equation modeling.

r-purrr 0.2.4 — Functional programming tools

This package completes R's functional programming tools with missing features present in other programming languages.

r-qap 0.1-1 — Heuristics for the quadratic assignment problem (QAP)

This package implements heuristics for the quadratic assignment problem (QAP). Currently only a simulated annealing heuristic is available.

r-qtl 1.42-8 — R package for analyzing QTL experiments in genetics

R/qtl is an extension library for the R statistics system. It is used to analyze experimental crosses for identifying genes contributing to variation in quantitative traits (so-called quantitative trait loci, QTLs).

Using a hidden Markov model, R/qtl allows to estimate genetic maps, to identify genotyping errors, and to perform single-QTL and two-QTL, two-dimensional genome scans.

r-quadprog 1.5-5 — Functions to solve quadratic programming problems

This package contains routines and documentation for solving quadratic programming problems.

r-quantmod 0.4-13 — Quantitative financial modelling framework

This package provides a quantitative financial modelling framework to allow users to specify, build, trade, and analyse quantitative financial trading strategies.

r-quantreg 5.35 — Quantile regression

This package provides an estimation and inference methods for models of conditional quantiles: linear and nonlinear parametric and non-parametric models for conditional quantiles of a univariate response and several methods for handling censored survival data. Portfolio selection methods based on expected shortfall risk are also included.

r-qvalue 2.10.0 — Q-value estimation for false discovery rate control

This package takes a list of p-values resulting from the simultaneous testing of many hypotheses and estimates their q-values and local false discovery rate (FDR) values. The q-value of a test measures the proportion of false positives incurred when that particular test is called significant. The local FDR measures the posterior probability the null hypothesis is true given the test's p-value. Various plots are automatically generated, allowing one to make sensible significance cut-offs. The software can be applied to problems in genomics, brain imaging, astrophysics, and data mining.

r-r-cache 0.13.0 — Light-weight caching of objects and results

This package provides methods for caching or memoization of objects and results. With this package, any R object can be cached in a key-value storage where the key can be an arbitrary set of R objects. The cache memory is persistent (on the file system).

r-r-methodss3 1.7.1 — S3 methods simplified

This package provides methods that simplify the setup of S3 generic functions and S3 methods. Major effort has been made in making definition of methods as simple as possible with a minimum of maintenance for package developers. For example, generic functions are created automatically, if missing, and naming conflict are automatically solved, if possible. The method setMethodS3() is a good start for those who in the future may want to migrate to S4.

r-r-oo 1.21.0 — R object-oriented programming with or without references

This package provides methods and classes for object-oriented programming in R with or without references. Large effort has been made on making definition of methods as simple as possible with a minimum of maintenance for package developers.

r-r-rsp 0.42.0 — Dynamic generation of scientific reports

The RSP markup language provides a powerful markup for controlling the content and output of LaTeX, HTML, Markdown, AsciiDoc, Sweave and knitr documents (and more), e.g. Today's date is <%=Sys.Date()%>. Contrary to many other literate programming languages, with RSP it is straightforward to loop over mixtures of code and text sections, e.g. in month-by-month summaries. RSP has also several preprocessing directives for incorporating static and dynamic contents of external files (local or online) among other things. RSP is ideal for self-contained scientific reports and R package vignettes.

r-r-utils 2.6.0 — Various programming utilities

This package provides utility functions useful when programming and developing R packages.

r-r4rna 0.1.4 — Analysis framework for RNA secondary structure

The R4RNA package aims to be a general framework for the analysis of RNA secondary structure and comparative analysis in R.

r-r6 2.2.2 — Classes with reference semantics in R

The R6 package allows the creation of classes with reference semantics, similar to R's built-in reference classes. Compared to reference classes, R6 classes are simpler and lighter-weight, and they are not built on S4 classes so they do not require the methods package. These classes allow public and private members, and they support inheritance, even when the classes are defined in different packages.

r-radiant-data 0.8.1 — Data menu for Radiant: business analytics using R and Shiny

The Radiant Data menu includes interfaces for loading, saving, viewing, visualizing, summarizing, transforming, and combining data. It also contains functionality to generate reproducible reports of the analyses conducted in the application.

r-randomforest 4.6-14 — Breiman and Cutler's random forests for classification and regression

This package provides the Breiman and Cutler's random forests algorithm, based on a forest of trees using random inputs, for classification and regression.

r-ranger 0.9.0 — Fast implementation of random forests

This package provides a fast implementation of Random Forests, particularly suited for high dimensional data. Ensembles of classification, regression, survival and probability prediction trees are supported. Data from genome-wide association studies can be analyzed efficiently.

r-rann 2.5.1 — Fast nearest neighbour search

This package finds the k nearest neighbours for every point in a given dataset in O(N log N) time using Arya and Mount's ANN library. Provides approximate, exact searches, fixed radius searches, bd and kb trees.

r-raremetals2 0.1 — Analyze gene-level association tests for binary trait

The R package rareMETALS2 is an extension of the R package rareMETALS. It was designed to meta-analyze gene-level association tests for binary trait. While rareMETALS offers a near-complete solution for meta-analysis of gene-level tests for quantitative trait, it does not offer the optimal solution for binary trait. The package rareMETALS2 offers improved features for analyzing gene-level association tests in meta-analyses for binary trait.

r-rbgl 1.54.0 — Interface to the Boost graph library

This package provides a fairly extensive and comprehensive interface to the graph algorithms contained in the Boost library.

r-rbiofabric 0.3-1.666c2ae — BioFabric network visualization

This package provides an implementation of the function bioFabric for creating scalable network digrams where nodes are represented by horizontal lines, and edges are represented by vertical lines.

r-rcas 1.3.4 — RNA-centric annotation system

RCAS aims to be a standalone RNA-centric annotation system that provides intuitive reports and publication-ready graphics. This package provides the R library implementing most of the pipeline's features.

r-rcolorbrewer 1.1-2 — ColorBrewer palettes

This package provides color schemes for maps (and other graphics) designed by Cynthia Brewer as described at http://colorbrewer2.org

r-rcpp 0.12.16 — Seamless R and C++ integration

The Rcpp package provides R functions as well as C++ classes which offer a seamless integration of R and C++. Many R data types and objects can be mapped back and forth to C++ equivalents which facilitates both writing of new code as well as easier integration of third-party libraries. Documentation about Rcpp is provided by several vignettes included in this package, via the 'Rcpp Gallery' site at <http://gallery.rcpp.org>, the paper by Eddelbuettel and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see 'citation("Rcpp")' for details on these last two.

r-rcpparmadillo 0.8.400.0.0 — Rcpp integration for the Armadillo linear algebra library

Armadillo is a templated C++ linear algebra library that aims towards a good balance between speed and ease of use. Integer, floating point and complex numbers are supported, as well as a subset of trigonometric and statistics functions. Various matrix decompositions are provided through optional integration with LAPACK and ATLAS libraries. This package includes the header files from the templated Armadillo library.

r-rcppeigen 0.3.3.4.0 — Rcpp integration for the Eigen templated linear algebra library

This package provides an integration of Eigen in R using a C++ template library for linear algebra: matrices, vectors, numerical solvers and related algorithms. It supports dense and sparse matrices on integer, floating point and complex numbers, decompositions of such matrices, and solutions of linear systems.

r-rcppprogress 0.4 — Interruptible progress bar for C++ in R packages

This package allows to display a progress bar in the R console for long running computations taking place in C++ code, and support for interrupting those computations even in multithreaded code, typically using OpenMP.

r-rcpproll 0.2.2 — Efficient rolling and windowed operations

This package provides fast and efficient routines for common rolling / windowed operations. Routines for the efficient computation of windowed mean, median, sum, product, minimum, maximum, standard deviation and variance are provided.

r-rcurl 1.95-0.1.2 — General network client interface for R

The package allows one to compose general HTTP requests and provides convenient functions to fetch URIs, GET and POST forms, etc. and process the results returned by the Web server. This provides a great deal of control over the HTTP/FTP/... connection and the form of the request while providing a higher-level interface than is available just using R socket connections. Additionally, the underlying implementation is robust and extensive, supporting FTP/FTPS/TFTP (uploads and downloads), SSL/HTTPS, telnet, dict, ldap, and also supports cookies, redirects, authentication, etc.

r-readr 1.1.1 — Read tabular data

This package provides functions to read flat or tabular text files from disk (or a connection).