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r-kernlab
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Kernel-based machine learning methods for classification, regression, clustering, novelty detection, quantile regression and dimensionality reduction. Among other methods 'kernlab' includes Support Vector Machines, Spectral Clustering, Kernel PCA, Gaussian Processes and a QP solver.
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2023-06-16 |
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r-ape
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Functions for reading, writing, plotting, and manipulating phylogenetic trees, analyses of comparative data in a phylogenetic framework, ancestral character analyses, analyses of diversification and macroevolution, computing distances from DNA sequences, reading and writing nucleotide sequences as well as importing from BioConductor, and several tools such as Mantel's test, generalized skyline plots, graphical exploration of phylogenetic data (alex, trex, kronoviz), estimation of absolute evolutionary rates and clock-like trees using mean path lengths and penalized likelihood, dating trees with non-contemporaneous sequences, translating DNA into AA sequences, and assessing sequence alignments. Phylogeny estimation can be done with the NJ, BIONJ, ME, MVR, SDM, and triangle methods, and several methods handling incomplete distance matrices (NJ*, BIONJ*, MVR*, and the corresponding triangle method). Some functions call external applications (PhyML, Clustal, T-Coffee, Muscle) whose results are returned into R.
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2023-06-16 |
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r-rpart
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Recursive partitioning for classification, regression and survival trees. An implementation of most of the functionality of the 1984 book by Breiman, Friedman, Olshen and Stone.
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2023-06-16 |
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r-curl
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public |
The curl() and curl_download() functions provide highly configurable drop-in replacements for base url() and download.file() with better performance, support for encryption (https, ftps), gzip compression, authentication, and other 'libcurl' goodies. The core of the package implements a framework for performing fully customized requests where data can be processed either in memory, on disk, or streaming via the callback or connection interfaces. Some knowledge of 'libcurl' is recommended; for a more-user-friendly web client see the 'httr' package which builds on this package with http specific tools and logic.
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2023-06-16 |
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r-stringr
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public |
A consistent, simple and easy to use set of wrappers around the fantastic 'stringi' package. All function and argument names (and positions) are consistent, all functions deal with "NA"'s and zero length vectors in the same way, and the output from one function is easy to feed into the input of another.
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2023-06-16 |
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r-sfsmisc
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Useful utilities ['goodies'] from Seminar fuer Statistik ETH Zurich, some of which were ported from S-plus in the 1990's. For graphics, have pretty (Log-scale) axes, an enhanced Tukey-Anscombe plot, combining histogram and boxplot, 2d-residual plots, a 'tachoPlot()', pretty arrows, etc. For robustness, have a robust F test and robust range(). For system support, notably on Linux, provides 'Sys.*()' functions with more access to system and CPU information. Finally, miscellaneous utilities such as simple efficient prime numbers, integer codes, Duplicated(), toLatex.numeric() and is.whole().
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2023-06-16 |
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r-forecast
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Methods and tools for displaying and analysing univariate time series forecasts including exponential smoothing via state space models and automatic ARIMA modelling.
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2023-06-16 |
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r-digest
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public |
Implementation of a function 'digest()' for the creation of hash digests of arbitrary R objects (using the 'md5', 'sha-1', 'sha-256', 'crc32', 'xxhash' and 'murmurhash' algorithms) permitting easy comparison of R language objects, as well as a function 'hmac()' to create hash-based message authentication code. Please note that this package is not meant to be deployed for cryptographic purposes for which more comprehensive (and widely tested) libraries such as 'OpenSSL' should be used.
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2023-06-16 |
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r-dbplyr
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A 'dplyr' back end for databases that allows you to work with remote database tables as if they are in-memory data frames. Basic features works with any database that has a 'DBI' back end; more advanced features require 'SQL' translation to be provided by the package author.
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2023-06-16 |
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r-nlme
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public |
Fit and compare Gaussian linear and nonlinear mixed-effects models.
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2023-06-16 |
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r-zip
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public |
Cross-Platform 'zip' Compression Library. A replacement for the 'zip' function, that does not require any additional external tools on any platform.
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2023-06-16 |
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r-tokenizers
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public |
Convert natural language text into tokens. Includes tokenizers for shingled n-grams, skip n-grams, words, word stems, sentences, paragraphs, characters, shingled characters, lines, tweets, Penn Treebank, regular expressions, as well as functions for counting characters, words, and sentences, and a function for splitting longer texts into separate documents, each with the same number of words. The tokenizers have a consistent interface, and the package is built on the 'stringi' and 'Rcpp' packages for fast yet correct tokenization in 'UTF-8'.
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2023-06-16 |
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r-tfruns
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public |
Create and manage unique directories for each 'TensorFlow' training run. Provides a unique, time stamped directory for each run along with functions to retrieve the directory of the latest run or latest several runs.
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2023-06-16 |
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r-sp
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public |
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.
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2023-06-16 |
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r-reprex
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public |
Convenience wrapper that uses the 'rmarkdown' package to render small snippets of code to target formats that include both code and output. The goal is to encourage the sharing of small, reproducible, and runnable examples on code-oriented websites, such as <http://stackoverflow.com> and <https://github.com>, or in email. 'reprex' also extracts clean, runnable R code from various common formats, such as copy/paste from an R session.
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2023-06-16 |
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r-nmf
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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/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.
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2023-06-16 |
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r-tidyr
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An evolution of 'reshape2'. It's designed specifically for data tidying (not general reshaping or aggregating) and works well with 'dplyr' data pipelines.
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2023-06-16 |
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r-stopwords
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Provides multiple sources of stopwords, for use in text analysis and natural language processing.
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2023-06-16 |
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r-rio
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public |
Streamlined data import and export by making assumptions that the user is probably willing to make: 'import()' and 'export()' determine the data structure from the file extension, reasonable defaults are used for data import and export (e.g., 'stringsAsFactors=FALSE'), web-based import is natively supported (including from SSL/HTTPS), compressed files can be read directly without explicit decompression, and fast import packages are used where appropriate. An additional convenience function, 'convert()', provides a simple method for converting between file types.
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2023-06-16 |
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r-leaflet
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Create and customize interactive maps using the 'Leaflet' JavaScript library and the 'htmlwidgets' package. These maps can be used directly from the R console, from 'RStudio', in Shiny applications and R Markdown documents.
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2023-06-16 |
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r-car
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public |
Functions to Accompany J. Fox and S. Weisberg, An R Companion to Applied Regression, Third Edition, Sage, in press.
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2023-06-16 |
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r-zoo
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public |
An S3 class with methods for totally ordered indexed observations. It is particularly aimed at irregular time series of numeric vectors/matrices and factors. zoo's key design goals are independence of a particular index/date/time class and consistency with ts and base R by providing methods to extend standard generics.
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2023-06-16 |
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r-withr
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A set of functions to run code 'with' safely and temporarily modified global state. Many of these functions were originally a part of the 'devtools' package, this provides a simple package with limited dependencies to provide access to these functions.
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2023-06-16 |
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r-selectr
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public |
Translates a CSS3 selector into an equivalent XPath expression. This allows us to use CSS selectors when working with the XML package as it can only evaluate XPath expressions. Also provided are convenience functions useful for using CSS selectors on XML nodes. This package is a port of the Python package 'cssselect' (<https://cssselect.readthedocs.io/>).
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2023-06-16 |
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r-kohonen
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Functions to train self-organising maps (SOMs). Also interrogation of the maps and prediction using trained maps are supported. The name of the package refers to Teuvo Kohonen, the inventor of the SOM.
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2023-06-16 |
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r-dt
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Data objects in R can be rendered as HTML tables using the JavaScript library 'DataTables' (typically via R Markdown or Shiny). The 'DataTables' library has been included in this R package. The package name 'DT' is an abbreviation of 'DataTables'.
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2023-06-16 |
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r-sparklyr
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R interface to Apache Spark, a fast and general engine for big data processing, see <http://spark.apache.org>. This package supports connecting to local and remote Apache Spark clusters, provides a 'dplyr' compatible back-end, and provides an interface to Spark's built-in machine learning algorithms.
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2023-06-16 |
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r-rngtools
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Provides a set of functions for working with Random Number Generators (RNGs). In particular, a generic S4 framework is defined for getting/setting the current RNG, or RNG data that are embedded into objects for reproducibility. Notably, convenient default methods greatly facilitate the way current RNG settings can be changed.
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2023-06-16 |
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r-rcppeigen
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R and 'Eigen' integration using 'Rcpp'. 'Eigen' is 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. Its performance on many algorithms is comparable with some of the best implementations based on 'Lapack' and level-3 'BLAS'. The 'RcppEigen' package includes the header files from the 'Eigen' C++ template library (currently version 3.3.4). Thus users do not need to install 'Eigen' itself in order to use 'RcppEigen'. Since version 3.1.1, 'Eigen' is licensed under the Mozilla Public License (version 2); earlier version were licensed under the GNU LGPL version 3 or later. 'RcppEigen' (the 'Rcpp' bindings/bridge to 'Eigen') is licensed under the GNU GPL version 2 or later, as is the rest of 'Rcpp'.
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2023-06-16 |
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r-glmnet
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Extremely efficient procedures for fitting the entire lasso or elastic-net regularization path for linear regression, logistic and multinomial regression models, Poisson regression and the Cox model. Two recent additions are the multiple-response Gaussian, and the grouped multinomial regression. The algorithm uses cyclical coordinate descent in a path-wise fashion, as described in the paper linked to via the URL below.
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2023-06-16 |
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r-estimability
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Provides tools for determining estimability of linear functions of regression coefficients, and 'epredict' methods that handle non-estimable cases correctly. Estimability theory is discussed in many linear-models textbooks including Chapter 3 of Monahan, JF (2008), "A Primer on Linear Models", Chapman and Hall (ISBN 978-1-4200-6201-4).
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2023-06-16 |
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r-matrix
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Classes and methods for dense and sparse matrices and operations on them using 'LAPACK' and 'SuiteSparse'.
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2023-06-16 |
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r-foreign
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Reading and writing data stored by some versions of 'Epi Info', 'Minitab', 'S', 'SAS', 'SPSS', 'Stata', 'Systat', 'Weka', and for reading and writing some 'dBase' files.
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2023-06-16 |
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r-squarem
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Algorithms for accelerating the convergence of slow, monotone sequences from smooth, contraction mapping such as the EM algorithm. It can be used to accelerate any smooth, linearly convergent acceleration scheme. A tutorial style introduction to this package is available in a vignette on the CRAN download page or, when the package is loaded in an R session, with vignette("SQUAREM").
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2023-06-16 |
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r-readxl
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Import excel files into R. Supports '.xls' via the embedded 'libxls' C library <https://github.com/evanmiller/libxls> and '.xlsx' via the embedded 'RapidXML' C++ library <https://rapidxml.sourceforge.net>. Works on Windows, Mac and Linux without external dependencies.
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2023-06-16 |
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r-pcapp
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Provides functions for robust PCA by projection pursuit. The methods are described in Croux et al. (2006) <doi:10.2139/ssrn.968376>, Croux et al. (2013) <doi:10.1080/00401706.2012.727746>, Todorov and Filzmoser (2013) <doi:10.1007/978-3-642-33042-1_31>.
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2023-06-16 |
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r-httpuv
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Provides low-level socket and protocol support for handling HTTP and WebSocket requests directly from within R. It is primarily intended as a building block for other packages, rather than making it particularly easy to create complete web applications using httpuv alone. httpuv is built on top of the libuv and http-parser C libraries, both of which were developed by Joyent, Inc. (See LICENSE file for libuv and http-parser license information.)
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2023-06-16 |
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r-bibtex
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Utility to parse a bibtex file.
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2023-06-16 |
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r-iterators
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Support for iterators, which allow a programmer to traverse through all the elements of a vector, list, or other collection of data.
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2023-06-16 |
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r-sourcetools
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Tools for the reading and tokenization of R code. The 'sourcetools' package provides both an R and C++ interface for the tokenization of R code, and helpers for interacting with the tokenized representation of R code.
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2023-06-16 |
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r-quantreg
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Estimation and inference methods for models of conditional quantiles: Linear and nonlinear parametric and non-parametric (total variation penalized) 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.
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2023-06-16 |
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r-stringdist
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Implements an approximate string matching version of R's native 'match' function. Can calculate various string distances based on edits (Damerau-Levenshtein, Hamming, Levenshtein, optimal sting alignment), qgrams (q- gram, cosine, jaccard distance) or heuristic metrics (Jaro, Jaro-Winkler). An implementation of soundex is provided as well. Distances can be computed between character vectors while taking proper care of encoding or between integer vectors representing generic sequences.
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2023-06-16 |
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r-reticulate
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Interface to 'Python' modules, classes, and functions. When calling into 'Python', R data types are automatically converted to their equivalent 'Python' types. When values are returned from 'Python' to R they are converted back to R types. Compatible with all versions of 'Python' >= 2.7.
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2023-06-16 |
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r-rcpparmadillo
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'Armadillo' is a templated C++ linear algebra library (by Conrad Sanderson) 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. The 'RcppArmadillo' package includes the header files from the templated 'Armadillo' library. Thus users do not need to install 'Armadillo' itself in order to use 'RcppArmadillo'. From release 7.800.0 on, 'Armadillo' is licensed under Apache License 2; previous releases were under licensed as MPL 2.0 from version 3.800.0 onwards and LGPL-3 prior to that; 'RcppArmadillo' (the 'Rcpp' bindings/bridge to Armadillo) is licensed under the GNU GPL version 2 or later, as is the rest of 'Rcpp'. Note that Armadillo requires a fairly recent compiler; for the g++ family at least version 4.6.* is required.
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2023-06-16 |
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r-lmertest
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public |
Provides p-values in type I, II or III anova and summary tables for lmer model fits (cf. lme4) via Satterthwaite's degrees of freedom method. A Kenward-Roger method is also available via the pbkrtest package. Model selection methods include step, drop1 and anova-like tables for random effects (ranova). Methods for Least-Square means (LS-means) and tests of linear contrasts of fixed effects are also available.
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2023-06-16 |
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r-lme4
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Fit linear and generalized linear mixed-effects models. The models and their components are represented using S4 classes and methods. The core computational algorithms are implemented using the 'Eigen' C++ library for numerical linear algebra and 'RcppEigen' "glue".
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2023-06-16 |
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r-emmeans
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Obtain estimated marginal means (EMMs) for many linear, generalized linear, and mixed models. Compute contrasts or linear functions of EMMs, trends, and comparisons of slopes. Plots and compact letter displays. Least-squares means are discussed, and the term "estimated marginal means" is suggested, in Searle, Speed, and Milliken (1980) Population marginal means in the linear model: An alternative to least squares means, The American Statistician 34(4), 216-221 <doi:10.1080/00031305.1980.10483031>.
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2023-06-16 |
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r-diagrammer
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Build graph/network structures using functions for stepwise addition and deletion of nodes and edges. Work with data available in tables for bulk addition of nodes, edges, and associated metadata. Use graph selections and traversals to apply changes to specific nodes or edges. A wide selection of graph algorithms allow for the analysis of graphs. Visualize the graphs and take advantage of any aesthetic properties assigned to nodes and edges.
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2023-06-16 |
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r-bcp
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Provides an implementation of the Barry and Hartigan (1993) product partition model for the normal errors change point problem using Markov Chain Monte Carlo. It also extends the methodology to regression models on a connected graph (Wang and Emerson, 2015); this allows estimation of change point models with multivariate responses. Parallel MCMC, previously available in bcp v.3.0.0, is currently not implemented.
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2023-06-16 |
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r-recommended
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R is a free software environment for statistical computing and graphics.
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2023-06-16 |
