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r-urltools
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A toolkit for all URL-handling needs, including encoding and decoding, parsing, parameter extraction and modification. All functions are designed to be both fast and entirely vectorised. It is intended to be useful for people dealing with web-related datasets, such as server-side logs, although may be useful for other situations involving large sets of URLs.
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2025-03-25 |
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r-unrtf
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Wraps the 'unrtf' utility <https://www.gnu.org/software/unrtf/> to extract text from RTF files. Supports document conversion to HTML, LaTeX or plain text. Output in HTML is recommended because 'unrtf' has limited support for converting between character encodings.
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2025-03-25 |
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r-umap
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Uniform manifold approximation and projection is a technique for dimension reduction. The algorithm was described by McInnes and Healy (2018) in <arXiv:1802.03426>. This package provides an interface for two implementations. One is written from scratch, including components for nearest-neighbor search and for embedding. The second implementation is a wrapper for 'python' package 'umap-learn' (requires separate installation, see vignette for more details).
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2025-03-25 |
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r-tuner
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Analyze music and speech, extract features like MFCCs, handle wave files and their representation in various ways, read mp3, read midi, perform steps of a transcription, ... Also contains functions ported from the 'rastamat' 'Matlab' package.
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2025-03-25 |
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r-tsdyn
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Implements nonlinear autoregressive (AR) time series models. For univariate series, a non-parametric approach is available through additive nonlinear AR. Parametric modeling and testing for regime switching dynamics is available when the transition is either direct (TAR: threshold AR) or smooth (STAR: smooth transition AR, LSTAR). For multivariate series, one can estimate a range of TVAR or threshold cointegration TVECM models with two or three regimes. Tests can be conducted for TVAR as well as for TVECM (Hansen and Seo 2002 and Seo 2006).
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2025-03-25 |
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r-tsdist
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A set of commonly used distance measures and some additional functions which, although initially not designed for this purpose, can be used to measure the dissimilarity between time series. These measures can be used to perform clustering, classification or other data mining tasks which require the definition of a distance measure between time series. U. Mori, A. Mendiburu and J.A. Lozano (2016), <doi:10.32614/RJ-2016-058>.
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2025-03-25 |
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r-treetools
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Efficient implementations of functions for the creation, modification and analysis of phylogenetic trees. Applications include: generation of trees with specified shapes; tree rearrangement; analysis of tree shape; rooting of trees and extraction of subtrees; calculation and depiction of split support; plotting the position of rogue taxa (Klopfstein & Spasojevic 2019) <doi:10.1371/journal.pone.0212942>; calculation of ancestor-descendant relationships, of 'stemwardness' (Asher & Smith, 2022) <doi:10.1093/sysbio/syab072>, and of tree balance (Mir et al. 2013) <doi:10.1016/j.mbs.2012.10.005>; artificial extinction (Asher & Smith, 2022) <doi:10.1093/sysbio/syab072>; import and export of trees from Newick, Nexus (Maddison et al. 1997) <doi:10.1093/sysbio/46.4.590>, and TNT <https://www.lillo.org.ar/phylogeny/tnt/> formats; and analysis of splits and cladistic information.
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2025-03-25 |
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r-textshaping
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Provides access to the text shaping functionality in the 'HarfBuzz' library and the bidirectional algorithm in the 'Fribidi' library. 'textshaping' is a low-level utility package mainly for graphic devices that expands upon the font tool-set provided by the 'systemfonts' package.
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2025-03-25 |
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r-texexamrandomizer
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Randomizing exams with 'LaTeX'. If you can compile your main document with 'LaTeX', the program should be able to compile the randomized versions without much extra effort when creating the document.
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2025-03-25 |
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r-testcor
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Different multiple testing procedures for correlation tests are implemented. These procedures were shown to theoretically control asymptotically the Family Wise Error Rate (Roux (2018) <https://tel.archives-ouvertes.fr/tel-01971574v1>) or the False Discovery Rate (Cai & Liu (2016) <doi:10.1080/01621459.2014.999157>). The package gather four test statistics used in correlation testing, four FWER procedures with either single step or stepdown versions, and four FDR procedures.
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2025-03-25 |
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r-tess
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Simulation of reconstructed phylogenetic trees under tree-wide time-heterogeneous birth-death processes and estimation of diversification parameters under the same model. Speciation and extinction rates can be any function of time and mass-extinction events at specific times can be provided. Trees can be simulated either conditioned on the number of species, the time of the process, or both. Additionally, the likelihood equations are implemented for convenience and can be used for Maximum Likelihood (ML) estimation and Bayesian inference.
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2025-03-25 |
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r-terra
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Methods for spatial data analysis with vector (points, lines, polygons) and raster (grid) data. Methods for vector data include geometric operations such as intersect and buffer. Raster methods include local, focal, global, zonal and geometric operations. The predict and interpolate methods facilitate the use of regression type (interpolation, machine learning) models for spatial prediction, including with satellite remote sensing data. Processing of very large files is supported. See the manual and tutorials on <https://rspatial.org/> to get started. 'terra' replaces the 'raster' package ('terra' can do more, and it is faster and easier to use).
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2025-03-25 |
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r-tensora
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Provides convenience functions for advanced linear algebra with tensors and computation with data sets of tensors on a higher level abstraction. It includes Einstein and Riemann summing conventions, dragging, co- and contravariate indices, parallel computations on sequences of tensors.
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2025-03-25 |
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r-teigen
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Fits mixtures of multivariate t-distributions (with eigen-decomposed covariance structure) via the expectation conditional-maximization algorithm under a clustering or classification paradigm.
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2025-03-25 |
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r-tdthap
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Functions and examples are provided for Transmission/disequilibrium tests for extended marker haplotypes, as in Clayton, D. and Jones, H. (1999) "Transmission/disequilibrium tests for extended marker haplotypes". Amer. J. Hum. Genet., 65:1161-1169, <doi:10.1086/302566>.
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2025-03-25 |
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r-tdigest
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The t-Digest construction algorithm, by Dunning et al., (2019) <arXiv:1902.04023v1>, uses a variant of 1-dimensional k-means clustering to produce a very compact data structure that allows accurate estimation of quantiles. This t-Digest data structure can be used to estimate quantiles, compute other rank statistics or even to estimate related measures like trimmed means. The advantage of the t-Digest over previous digests for this purpose is that the t-Digest handles data with full floating point resolution. The accuracy of quantile estimates produced by t-Digests can be orders of magnitude more accurate than those produced by previous digest algorithms. Methods are provided to create and update t-Digests and retrieve quantiles from the accumulated distributions.
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2025-03-25 |
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r-tdboost
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An implementation of a boosted Tweedie compound Poisson model proposed by Yang, Y., Qian, W. and Zou, H. (2018) <doi:10.1080/07350015.2016.1200981>. It is capable of fitting a flexible nonlinear Tweedie compound Poisson model (or a gamma model) and capturing high-order interactions among predictors. This package is based on the 'gbm' package originally developed by Greg Ridgeway.
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2025-03-25 |
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r-tclust
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Provides functions for robust trimmed clustering. The methods are described in Garcia-Escudero (2008) <doi:10.1214/07-AOS515>, Fritz et al. (2012) <doi:10.18637/jss.v047.i12>, Garcia-Escudero et al. (2011) <doi:10.1007/s11222-010-9194-z> and others.
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2025-03-25 |
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r-taustar
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Computes the t* statistic corresponding to the tau* population coefficient introduced by Bergsma and Dassios (2014) <DOI:10.3150/13-BEJ514> and does so in O(n^2) time following the algorithm of Heller and Heller (2016) <arXiv:1605.08732> building off of the work of Weihs, Drton, and Leung (2016) <DOI:10.1007/s00180-015-0639-x>. Also allows for independence testing using the asymptotic distribution of t* as described by Nandy, Weihs, and Drton (2016) <arXiv:1602.04387>.
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2025-03-25 |
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r-tbart
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Solves Teitz and Bart's p-median problem - given a set of points attempts to find subset of size p such that summed distances of any point in the set to the nearest point in p is minimised. Although generally effective, this algorithm does not guarantee that a globally optimal subset is found.
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2025-03-25 |
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r-tau
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Utilities for text analysis.
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2025-03-25 |
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r-taqmngr
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Manager of tick-by-tick transaction data that performs 'cleaning', 'aggregation' and 'import' in an efficient and fast way. The package engine, written in C++, exploits the 'zlib' and 'gzstream' libraries to handle gzipped data without need to uncompress them. 'Cleaning' and 'aggregation' are performed according to Brownlees and Gallo (2006) <DOI:10.1016/j.csda.2006.09.030>. Currently, TAQMNGR processes raw data from WRDS (Wharton Research Data Service, <https://wrds-web.wharton.upenn.edu/wrds/>).
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2025-03-25 |
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r-systemicrisk
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A toolbox for systemic risk based on liabilities matrices. Contains a Gibbs sampler for liabilities matrices where only row and column sums of the liabilities matrix as well as some other fixed entries are observed. Includes models for power law distribution on the degree distribution.
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2025-03-25 |
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r-tagcloud
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Generating Tag and Word Clouds.
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2025-03-25 |
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r-systemfonts
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Provides system native access to the font catalogue. As font handling varies between systems it is difficult to correctly locate installed fonts across different operating systems. The 'systemfonts' package provides bindings to the native libraries on Windows, macOS and Linux for finding font files that can then be used further by e.g. graphic devices. The main use is intended to be from compiled code but 'systemfonts' also provides access from R.
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2025-03-25 |
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r-sysfonts
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Loading system fonts and Google Fonts <https://fonts.google.com/> into R, in order to support other packages such as 'R2SWF' and 'showtext'.
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2025-03-25 |
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r-synlik
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Framework to perform synthetic likelihood inference for models where the likelihood function is unavailable or intractable.
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2025-03-25 |
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r-synthacs
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Provides access to curated American Community Survey (ACS) base tables via a wrapper to library(acs). Builds synthetic micro-datasets at any user-specified geographic level with ten default attributes; and, conducts spatial microsimulation modeling (SMSM) via simulated annealing. SMSM is conducted in parallel by default. Lastly, we provide functionality for data-extensibility of micro-datasets <doi:10.18637/jss.v104.i07>.
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2025-03-25 |
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r-syncrng
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Generate the same random numbers in R and Python.
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2025-03-25 |
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r-synchronicity
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Boost mutex functionality in R.
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2025-03-25 |
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r-symts
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Contains methods for simulation and for evaluating the pdf, cdf, and quantile functions for symmetric stable, symmetric classical tempered stable, and symmetric power tempered stable distributions.
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2025-03-25 |
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r-sylcount
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An English language syllable counter, plus readability score measure-er. For readability, we support 'Flesch' Reading Ease and 'Flesch-Kincaid' Grade Level ('Kincaid' 'et al'. 1975) <https://stars.library.ucf.edu/cgi/viewcontent.cgi?article=1055&context=istlibrary>, Automated Readability Index ('Senter' and Smith 1967) <https://apps.dtic.mil/sti/citations/AD0667273>, Simple Measure of Gobbledygook (McLaughlin 1969) <https://www.semanticscholar.org/paper/SMOG-Grading-A-New-Readability-Formula.-Laughlin/5fccb74c14769762b3de010c5e8a1a7ce700d17a>, and 'Coleman-Liau' (Coleman and 'Liau' 1975) <doi:10.1037/h0076540>. The package has been carefully optimized and should be very efficient, both in terms of run time performance and memory consumption. The main methods are 'vectorized' by document, and scores for multiple documents are computed in parallel via 'OpenMP'.
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2025-03-25 |
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r-swephr
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The Swiss Ephemeris (version 2.10.03) is a high precision ephemeris based upon the DE431 ephemerides from NASA's JPL. It covers the time range 13201 BCE to 17191 CE. This package uses the semi-analytic theory by Steve Moshier. For faster and more accurate calculations, the compressed Swiss Ephemeris data is available in the 'swephRdata' package. To access this data package, run 'install.packages("swephRdata", repos = "https://rstub.r-universe.dev", type = "source")'. The size of the 'swephRdata' package is approximately 115 MB. The user can also use the original JPL DE431 data.
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2025-03-25 |
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r-svglite
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A graphics device for R that produces 'Scalable Vector Graphics'. 'svglite' is a fork of the older 'RSvgDevice' package.
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2025-03-25 |
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r-svmmatch
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Causal effect estimation in observational data often requires identifying a set of untreated observations that are comparable to some treated group of interest. This package provides a suite of functions for identifying such a set of observations and for implementing standard and new diagnostics tools. The primary function, svmmatch(), uses support vector machines to identify a region of common support between treatment and control groups. A sensitivity analysis, balance checking, and assessment of the region of overlap between treated and control groups is included. The Bayesian implementation allows for recovery of uncertainty estimates for the treatment effect and all other parameters.
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2025-03-25 |
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r-svgviewr
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Creates 3D animated, interactive visualizations that can be viewed in a web browser.
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2025-03-25 |
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r-svd
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R bindings to SVD and eigensolvers (PROPACK, nuTRLan).
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2025-03-25 |
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r-survsnp
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Conduct asymptotic and empirical power and sample size calculations for Single-Nucleotide Polymorphism (SNP) association studies with right censored time to event outcomes.
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2025-03-25 |
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r-survpresmooth
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Presmoothed estimators of survival, density, cumulative and non-cumulative hazard functions with right-censored survival data. For details, see Lopez-de-Ullibarri and Jacome (2013) <doi:10.18637/jss.v054.i11>.
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2025-03-25 |
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r-survc1
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Performs inference for C of risk prediction models with censored survival data, using the method proposed by Uno et al. (2011) <doi:10.1002/sim.4154>. Inference for the difference in C between two competing prediction models is also implemented.
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2025-03-25 |
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r-superranker
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Tools for analysing the agreement of two or more rankings of the same items. Examples are importance rankings of predictor variables and risk predictions of subjects. Benchmarks for agreement are computed based on random permutation and bootstrap. See Ekstrøm CT, Gerds TA, Jensen, AK (2018). "Sequential rank agreement methods for comparison of ranked lists." _Biostatistics_, *20*(4), 582-598 <doi:10.1093/biostatistics/kxy017> for more information.
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2025-03-25 |
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r-survauc
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Provides a variety of functions to estimate time-dependent true/false positive rates and AUC curves from a set of censored survival data.
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2025-03-25 |
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r-supergauss
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Likelihood evaluations for stationary Gaussian time series are typically obtained via the Durbin-Levinson algorithm, which scales as O(n^2) in the number of time series observations. This package provides a "superfast" O(n log^2 n) algorithm written in C++, crossing over with Durbin-Levinson around n = 300. Efficient implementations of the score and Hessian functions are also provided, leading to superfast versions of inference algorithms such as Newton-Raphson and Hamiltonian Monte Carlo. The C++ code provides a Toeplitz matrix class packaged as a header-only library, to simplify low-level usage in other packages and outside of R.
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2025-03-25 |
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r-superexacttest
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Identification of sets of objects with shared features is a common operation in all disciplines. Analysis of intersections among multiple sets is fundamental for in-depth understanding of their complex relationships. This package implements a theoretical framework for efficient computation of statistical distributions of multi-set intersections based upon combinatorial theory, and provides multiple scalable techniques for visualizing the intersection statistics. The statistical algorithm behind this package was published in Wang et al. (2015) <doi:10.1038/srep16923>.
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2025-03-25 |
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r-supc
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Implements the self-updating process clustering algorithms proposed in Shiu and Chen (2016) <doi:10.1080/00949655.2015.1049605>.
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2025-03-25 |
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r-sundialr
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Provides a way to call the functions in 'SUNDIALS' C ODE solving library (<https://computing.llnl.gov/projects/sundials>). Currently the serial version of ODE solver, 'CVODE', sensitivity calculator 'CVODES' and differential algebraic solver 'IDA' from the 'SUNDIALS' library are implemented. The package requires ODE to be written as an 'R' or 'Rcpp' function and does not require the 'SUNDIALS' library to be installed on the local machine.
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2025-03-25 |
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r-supclust
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Methodology for supervised grouping aka "clustering" of potentially many predictor variables, such as genes etc, implementing algorithms 'PELORA' and 'WILMA'.
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2025-03-25 |
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r-sunder
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Quantification of the effect of geographic versus environmental isolation on genetic differentiation
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2025-03-25 |
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r-subrank
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Estimation of copula using ranks and subsampling. The main feature of this method is that simulation studies show a low sensitivity to dimension, on realistic cases.
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2025-03-25 |
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r-subtite
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Chooses subgroup specific optimal doses in a phase I dose finding clinical trial allowing for subgroup combination and simulates clinical trials under the subgroup specific time to event continual reassessment method. Chapple, A.G., Thall, P.F. (2018) <doi:10.1002/pst.1891>.
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2025-03-25 |
