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r-rrcovhd
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public |
Robust multivariate methods for high dimensional data including outlier detection (Filzmoser and Todorov (2013) <doi:10.1016/j.ins.2012.10.017>), robust sparse PCA (Croux et al. (2013) <doi:10.1080/00401706.2012.727746>, Todorov and Filzmoser (2013) <doi:10.1007/978-3-642-33042-1_31>), robust PLS (Todorov and Filzmoser (2014) <doi:10.17713/ajs.v43i4.44>), and robust sparse classification (Ortner et al. (2020) <doi:10.1007/s10618-019-00666-8>).
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2025-03-25 |
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r-rqpen
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public |
Performs penalized quantile regression with LASSO, elastic net, SCAD and MCP penalty functions including group penalties. Provides a function that automatically generates lambdas and evaluates different models with cross validation or BIC, including a large p version of BIC. Below URL provides a link to a work in progress vignette.
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2025-03-25 |
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r-round
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public |
Decimal rounding is non-trivial in binary arithmetic. ISO standard round to even is more rare than typically assumed as most decimal fractions are not exactly representable in binary. Our 'roundX()' versions explore differences between current and potential future versions of round() in R. Further, provides (some partly related) C99 math lib functions not in base R.
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2025-03-25 |
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r-rpeglmen
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Implements the fast iterative shrinkage-thresholding algorithm (FISTA) algorithm to fit a Gamma distribution with an elastic net penalty as described in Chen, Arakvin and Martin (2018) <arxiv:1804.07780>. An implementation for the case of the exponential distribution is also available, with details available in Chen and Martin (2018) <https://papers.ssrn.com/abstract_id=3085672>.
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2025-03-25 |
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r-roll
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public |
Fast and efficient computation of rolling and expanding statistics for time-series data.
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2025-03-25 |
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r-roi.plugin.qpoases
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public |
Enhances the 'R' Optimization Infrastructure ('ROI') package with the quadratic solver 'qpOASES'. More information about 'qpOASES' can be found at <https://github.com/coin-or/qpOASES>.
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2025-03-25 |
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r-robustvarcomp
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public |
Robust Estimation of Variance Component Models by classic and composite robust procedures. The composite procedures are robust against outliers generated by the Independent Contamination Model.
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2025-03-25 |
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r-robustlmm
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public |
Implements the Robust Scoring Equations estimator to fit linear mixed effects models robustly. Robustness is achieved by modification of the scoring equations combined with the Design Adaptive Scale approach.
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2025-03-25 |
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r-robusthd
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public |
Robust methods for high-dimensional data, in particular linear model selection techniques based on least angle regression and sparse regression. Specifically, the package implements robust least angle regression (Khan, Van Aelst & Zamar, 2007; <doi:10.1198/016214507000000950>), (robust) groupwise least angle regression (Alfons, Croux & Gelper, 2016; <doi:10.1016/j.csda.2015.02.007>), and sparse least trimmed squares regression (Alfons, Croux & Gelper, 2013; <doi:10.1214/12-AOAS575>).
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2025-03-25 |
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r-robstattm
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public |
Companion package for the book: "Robust Statistics: Theory and Methods, second edition", <http://www.wiley.com/go/maronna/robust>. This package contains code that implements the robust estimators discussed in the recent second edition of the book above, as well as the scripts reproducing all the examples in the book.
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2025-03-25 |
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r-robust
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public |
Methods for robust statistics, a state of the art in the early 2000s, notably for robust regression and robust multivariate analysis.
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2025-03-25 |
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r-robslopes
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public |
Fast algorithms for the Theil-Sen estimator, Siegel's repeated median slope estimator, and Passing-Bablok regression. The implementation is based on algorithms by Dillencourt et. al (1992) <doi:10.1142/S0218195992000020> and Matousek et. al (1998) <doi:10.1007/PL00009190>. The implementations are detailed in Raymaekers (2023) <doi:10.32614/RJ-2023-012> and Raymaekers J., Dufey F. (2022) <arXiv:2202.08060>. All algorithms run in quasilinear time.
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2025-03-25 |
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r-rniftyreg
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public |
Provides an 'R' interface to the 'NiftyReg' image registration tools <https://github.com/KCL-BMEIS/niftyreg>. Linear and nonlinear registration are supported, in two and three dimensions.
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2025-03-25 |
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r-robcompositions
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Methods for analysis of compositional data including robust methods (<doi:10.1007/978-3-319-96422-5>), imputation of missing values (<doi:10.1016/j.csda.2009.11.023>), methods to replace rounded zeros (<doi:10.1080/02664763.2017.1410524>, <doi:10.1016/j.chemolab.2016.04.011>, <doi:10.1016/j.csda.2012.02.012>), count zeros (<doi:10.1177/1471082X14535524>), methods to deal with essential zeros (<doi:10.1080/02664763.2016.1182135>), (robust) outlier detection for compositional data, (robust) principal component analysis for compositional data, (robust) factor analysis for compositional data, (robust) discriminant analysis for compositional data (Fisher rule), robust regression with compositional predictors, functional data analysis (<doi:10.1016/j.csda.2015.07.007>) and p-splines (<doi:10.1016/j.csda.2015.07.007>), contingency (<doi:10.1080/03610926.2013.824980>) and compositional tables (<doi:10.1111/sjos.12326>, <doi:10.1111/sjos.12223>, <doi:10.1080/02664763.2013.856871>) and (robust) Anderson-Darling normality tests for compositional data as well as popular log-ratio transformations (addLR, cenLR, isomLR, and their inverse transformations). In addition, visualisation and diagnostic tools are implemented as well as high and low-level plot functions for the ternary diagram.
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2025-03-25 |
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r-rnewsflow
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public |
A collection of tools for measuring the similarity of text messages and tracing the flow of messages over time and across media.
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2025-03-25 |
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r-rmvl
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public |
Mappable vector library provides convenient way to access large datasets. Use all of your data at once, with few limits. Memory mapped data can be shared between multiple R processes. Access speed depends on storage medium, so solid state drive is recommended, preferably with PCI Express (or M.2 nvme) interface or a fast network file system. The data is memory mapped into R and then accessed using usual R list and array subscription operators. Convenience functions are provided for merging, grouping and indexing large vectors and data.frames. The layout of underlying MVL files is optimized for large datasets. The vectors are stored to guarantee alignment for vector intrinsics after memory map. The package is built on top of libMVL, which can be used as a standalone C library. libMVL has simple C API making it easy to interchange datasets with outside programs.
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2025-03-25 |
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r-rmgarch
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public |
Feasible multivariate GARCH models including DCC, GO-GARCH and Copula-GARCH.
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2025-03-25 |
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r-rle
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public |
Common 'base' and 'stats' methods for 'rle' objects, aiming to make it possible to treat them transparently as vectors.
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2025-03-25 |
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r-rkeops
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public |
The 'KeOps' library lets you compute generic reductions of very large arrays whose entries are given by a mathematical formula with CPU and GPU computing support. It combines a tiled reduction scheme with an automatic differentiation engine. It is perfectly suited to the efficient computation of Kernel dot products and the associated gradients, even when the full kernel matrix does not fit into the GPU memory.
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2025-03-25 |
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r-rioja
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public |
Constrained clustering, transfer functions, and other methods for analysing Quaternary science data.
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2025-03-25 |
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r-rhrv
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public |
Allows users to import data files containing heartbeat positions in the most broadly used formats, to remove outliers or points with unacceptable physiological values present in the time series, to plot HRV data, and to perform time domain, frequency domain and nonlinear HRV analysis. See Garcia et al. (2017) <DOI:10.1007/978-3-319-65355-6>.
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2025-03-25 |
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r-rgeoda
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Provides spatial data analysis functionalities including Exploratory Spatial Data Analysis, Spatial Cluster Detection and Clustering Analysis, Regionalization, etc. based on the C++ source code of 'GeoDa', which is an open-source software tool that serves as an introduction to spatial data analysis. The 'GeoDa' software and its documentation are available at <https://geodacenter.github.io>.
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2025-03-25 |
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r-revdbayes
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Provides functions for the Bayesian analysis of extreme value models. The 'rust' package <https://cran.r-project.org/package=rust> is used to simulate a random sample from the required posterior distribution. The functionality of 'revdbayes' is similar to the 'evdbayes' package <https://cran.r-project.org/package=evdbayes>, which uses Markov Chain Monte Carlo ('MCMC') methods for posterior simulation. In addition, there are functions for making inferences about the extremal index, using the models for threshold inter-exceedance times of Suveges and Davison (2010) <doi:10.1214/09-AOAS292> and Holesovsky and Fusek (2020) <doi:10.1007/s10687-020-00374-3>. Also provided are d,p,q,r functions for the Generalised Extreme Value ('GEV') and Generalised Pareto ('GP') distributions that deal appropriately with cases where the shape parameter is very close to zero.
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2025-03-25 |
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r-restrserve
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public |
Allows to easily create high-performance full featured HTTP APIs from R functions. Provides high-level classes such as 'Request', 'Response', 'Application', 'Middleware' in order to streamline server side application development. Out of the box allows to serve requests using 'Rserve' package, but flexible enough to integrate with other HTTP servers such as 'httpuv'.
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2025-03-25 |
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r-remote
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public |
Empirical orthogonal teleconnections in R. 'remote' is short for 'R(-based) EMpirical Orthogonal TEleconnections'. It implements a collection of functions to facilitate empirical orthogonal teleconnection analysis. Empirical Orthogonal Teleconnections (EOTs) denote a regression based approach to decompose spatio-temporal fields into a set of independent orthogonal patterns. They are quite similar to Empirical Orthogonal Functions (EOFs) with EOTs producing less abstract results. In contrast to EOFs, which are orthogonal in both space and time, EOT analysis produces patterns that are orthogonal in either space or time.
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2025-03-25 |
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r-remacor
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Meta-analysis is widely used to summarize estimated effects sizes across multiple statistical tests. Standard fixed and random effect meta-analysis methods assume that the estimated of the effect sizes are statistically independent. Here we relax this assumption and enable meta-analysis when the correlation matrix between effect size estimates is known. Fixed effect meta-analysis uses the method of Lin and Sullivan (2009) <doi:10.1016/j.ajhg.2009.11.001>, and random effects meta-analysis uses the method of Han, et al. <doi:10.1093/hmg/ddw049>.
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2025-03-25 |
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r-rehh
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Population genetic data such as 'Single Nucleotide Polymorphisms' (SNPs) is often used to identify genomic regions that have been under recent natural or artificial selection and might provide clues about the molecular mechanisms of adaptation. One approach, the concept of an 'Extended Haplotype Homozygosity' (EHH), introduced by (Sabeti 2002) <doi:10.1038/nature01140>, has given rise to several statistics designed for whole genome scans. The package provides functions to compute three of these, namely: 'iHS' (Voight 2006) <doi:10.1371/journal.pbio.0040072> for detecting positive or 'Darwinian' selection within a single population as well as 'Rsb' (Tang 2007) <doi:10.1371/journal.pbio.0050171> and 'XP-EHH' (Sabeti 2007) <doi:10.1038/nature06250>, targeted at differential selection between two populations. Various plotting functions are included to facilitate visualization and interpretation of these statistics.
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2025-03-25 |
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r-regsem
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Uses both ridge and lasso penalties (and extensions) to penalize specific parameters in structural equation models. The package offers additional cost functions, cross validation, and other extensions beyond traditional structural equation models. Also contains a function to perform exploratory mediation (XMed).
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2025-03-25 |
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r-readxlsb
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public |
Import data from 'Excel' binary (.xlsb) workbooks into R.
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2025-03-25 |
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r-reddyproc
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Standard and extensible Eddy-Covariance data post-processing (Wutzler et al. (2018) <doi:10.5194/bg-15-5015-2018>) includes uStar-filtering, gap-filling, and flux-partitioning. The Eddy-Covariance (EC) micrometeorological technique quantifies continuous exchange fluxes of gases, energy, and momentum between an ecosystem and the atmosphere. It is important for understanding ecosystem dynamics and upscaling exchange fluxes. (Aubinet et al. (2012) <doi:10.1007/978-94-007-2351-1>). This package inputs pre-processed (half-)hourly data and supports further processing. First, a quality-check and filtering is performed based on the relationship between measured flux and friction velocity (uStar) to discard biased data (Papale et al. (2006) <doi:10.5194/bg-3-571-2006>). Second, gaps in the data are filled based on information from environmental conditions (Reichstein et al. (2005) <doi:10.1111/j.1365-2486.2005.001002.x>). Third, the net flux of carbon dioxide is partitioned into its gross fluxes in and out of the ecosystem by night-time based and day-time based approaches (Lasslop et al. (2010) <doi:10.1111/j.1365-2486.2009.02041.x>).
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2025-03-25 |
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r-recordlinkage
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Provides functions for linking and deduplicating data sets. Methods based on a stochastic approach are implemented as well as classification algorithms from the machine learning domain. For details, see our paper "The RecordLinkage Package: Detecting Errors in Data" Sariyar M / Borg A (2010) <doi:10.32614/RJ-2010-017>.
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2025-03-25 |
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r-readods
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public |
Read ODS (OpenDocument Spreadsheet) into R as data frame. Also support writing data frame into ODS file.
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2025-03-25 |
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r-rcppsimdjson
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public |
The 'JSON' format is ubiquitous for data interchange, and the 'simdjson' library written by Daniel Lemire (and many contributors) provides a high-performance parser for these files which by relying on parallel 'SIMD' instruction manages to parse these files as faster than disk speed. See the <arXiv:1902.08318> paper for more details about 'simdjson'. This package parses 'JSON' from string, file, or remote URLs under a variety of settings.
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2025-03-25 |
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r-rcppspdlog
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The mature and widely-used C++ logging library 'spdlog' by Gabi Melman provides many desirable features. This package bundles these header files for easy use by R packages from both their R and C or C++ code. Explicit use via 'LinkingTo:' is also supported. Also see the 'spdl' package which enhanced this package with a consistent R and C++ interface.
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2025-03-25 |
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r-rcppint64
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'Int64' values can be created and accessed via the 'bit64' package and its 'integer64' class which package the 'int64' representation cleverly into a 'double'. The 'nanotime' packages builds on this to support nanosecond-resolution timestamps. This packages helps conversions between 'R' and 'C++' via several helper functions provided via a single header file. A complete example client package is included as an illustration.
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2025-03-25 |
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r-rcppml
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Fast machine learning algorithms including matrix factorization and divisive clustering for large sparse and dense matrices.
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2025-03-25 |
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r-rcppalgos
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public |
Provides optimized functions and flexible combinatorial iterators implemented in C++ for solving problems in combinatorics and computational mathematics. Utilizes the RMatrix class from 'RcppParallel' for thread safety. There are combination/permutation functions with constraint parameters that allow for generation of all results of a vector meeting specific criteria (e.g. generating integer partitions/compositions or finding all combinations such that the sum is between two bounds). Capable of generating specific combinations/permutations (e.g. retrieve only the nth lexicographical result) which sets up nicely for parallelization as well as random sampling. Gmp support permits exploration where the total number of results is large (e.g. comboSample(10000, 500, n = 4)). Additionally, there are several high performance number theoretic functions that are useful for problems common in computational mathematics. Some of these functions make use of the fast integer division library 'libdivide'. The primeSieve function is based on the segmented sieve of Eratosthenes implementation by Kim Walisch. It is also efficient for large numbers by using the cache friendly improvements originally developed by Tomás Oliveira. Finally, there is a prime counting function that implements Legendre's formula based on the work of Kim Walisch.
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2025-03-25 |
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r-rcatch22
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Calculate 22 summary statistics coded in C on time-series vectors to enable pattern detection, classification, and regression applications in the feature space as proposed by Lubba et al. (2019) <doi:10.1007/s10618-019-00647-x>.
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2025-03-25 |
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r-rayimage
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Uses convolution-based techniques to generate simulated camera bokeh, depth of field, and other camera effects, using an image and an optional depth map. Accepts both filename inputs and in-memory array representations of images and matrices. Includes functions to perform 2D convolutions, reorient and resize images/matrices, add image overlays, generate camera vignette effects, and add titles to images.
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2025-03-25 |
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r-rayvertex
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Rasterize images using a 3D software renderer. 3D scenes are created either by importing external files, building scenes out of the included objects, or by constructing meshes manually. Supports point and directional lights, anti-aliased lines, shadow mapping, transparent objects, translucent objects, multiple materials types, reflection, refraction, environment maps, multicore rendering, bloom, tone-mapping, and screen-space ambient occlusion.
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2025-03-25 |
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r-raptr
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Biodiversity is in crisis. The overarching aim of conservation is to preserve biodiversity patterns and processes. To this end, protected areas are established to buffer species and preserve biodiversity processes. But resources are limited and so protected areas must be cost-effective. This package contains tools to generate plans for protected areas (prioritizations), using spatially explicit targets for biodiversity patterns and processes. To obtain solutions in a feasible amount of time, this package uses the commercial 'Gurobi' software (obtained from <https://www.gurobi.com/>). For more information on using this package, see Hanson et al. (2018) <doi:10.1111/2041-210X.12862>.
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2025-03-25 |
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r-randomlca
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Fits standard and random effects latent class models. The single level random effects model is described in Qu et al <doi:10.2307/2533043> and the two level random effects model in Beath and Heller <doi:10.1177/1471082X0800900302>. Examples are given for their use in diagnostic testing.
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2025-03-25 |
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r-quickmatch
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public |
Provides functions for constructing near-optimal generalized full matching. Generalized full matching is an extension of the original full matching method to situations with more intricate study designs. The package is made with large data sets in mind and derives matches more than an order of magnitude quicker than other methods.
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2025-03-25 |
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r-qwraps2
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A collection of (wrapper) functions the creator found useful for quickly placing data summaries and formatted regression results into '.Rnw' or '.Rmd' files. Functions for generating commonly used graphics, such as receiver operating curves or Bland-Altman plots, are also provided by 'qwraps2'. 'qwraps2' is a updated version of a package 'qwraps'. The original version 'qwraps' was never submitted to CRAN but can be found at <https://github.com/dewittpe/qwraps/>. The implementation and limited scope of the functions within 'qwraps2' <https://github.com/dewittpe/qwraps2/> is fundamentally different from 'qwraps'.
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2025-03-25 |
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r-quickjsr
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An 'R' interface to the 'QuickJS' portable 'JavaScript' engine. The engine is bundled entirely within the package, requiring no external system dependencies beyond a 'C' compiler.
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2025-03-25 |
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r-quanteda.textstats
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public |
Textual statistics functions formerly in the 'quanteda' package. Textual statistics for characterizing and comparing textual data. Includes functions for measuring term and document frequency, the co-occurrence of words, similarity and distance between features and documents, feature entropy, keyword occurrence, readability, and lexical diversity. These functions extend the 'quanteda' package and are specially designed for sparse textual data.
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2025-03-25 |
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r-quanteda.textmodels
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Scaling models and classifiers for sparse matrix objects representing textual data in the form of a document-feature matrix. Includes original implementations of 'Laver', 'Benoit', and Garry's (2003) <doi:10.1017/S0003055403000698>, 'Wordscores' model, the Perry and 'Benoit' (2017) <arXiv:1710.08963> class affinity scaling model, and the 'Slapin' and 'Proksch' (2008) <doi:10.1111/j.1540-5907.2008.00338.x> 'wordfish' model, as well as methods for correspondence analysis, latent semantic analysis, and fast Naive Bayes and linear 'SVMs' specially designed for sparse textual data.
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2025-03-25 |
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r-quanteda.textplots
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public |
Plotting functions for visualising textual data. Extends 'quanteda' and related packages with plot methods designed specifically for text data, textual statistics, and models fit to textual data. Plot types include word clouds, lexical dispersion plots, scaling plots, network visualisations, and word 'keyness' plots.
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2025-03-25 |
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r-quanteda
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public |
A fast, flexible, and comprehensive framework for quantitative text analysis in R. Provides functionality for corpus management, creating and manipulating tokens and n-grams, exploring keywords in context, forming and manipulating sparse matrices of documents by features and feature co-occurrences, analyzing keywords, computing feature similarities and distances, applying content dictionaries, applying supervised and unsupervised machine learning, visually representing text and text analyses, and more.
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2025-03-25 |
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r-qtools
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public |
Functions for unconditional and conditional quantiles. These include methods for transformation-based quantile regression, quantile-based measures of location, scale and shape, methods for quantiles of discrete variables, quantile-based multiple imputation, restricted quantile regression, directional quantile classification, and quantile ratio regression. A vignette is given in Geraci (2016, The R Journal) <doi:10.32614/RJ-2016-037> and included in the package.
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2025-03-25 |
