;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2015-2024 Ricardo Wurmus ;;; Copyright © 2015 Andreas Enge ;;; Copyright © 2015, 2016 Pjotr Prins ;;; Copyright © 2016, 2017 Ben Woodcroft ;;; Copyright © 2016, 2017, 2018, 2020, 2021 Roel Janssen ;;; Copyright © 2017, 2018, 2019, 2020 Tobias Geerinckx-Rice ;;; Copyright © 2017 Raoul Bonnal ;;; Copyright © 2018 Vijayalakshmi Vedantham ;;; Copyright © 2018 Sahithi Yarlagadda ;;; Copyright © 2018 Sandeep Subramanian ;;; Copyright © 2018 Charlie Ritter ;;; Copyright © 2018 Konrad Hinsen ;;; Copyright © 2018, 2020-2024 Mădălin Ionel Patrașcu ;;; Copyright © 2018 Laura Lazzati ;;; Copyright © 2018 Leo Famulari ;;; Copyright © 2018 Marius Bakke ;;; Copyright © 2018, 2019 Brett Gilio ;;; Copyright © 2019 Nicolò Balzarotti ;;; Copyright © 2019, 2020, 2021, 2022 Wiktor Żelazny ;;; Copyright © 2019 Arne Babenhauserheide ;;; Copyright © 2019, 2020, 2023 Efraim Flashner ;;; Copyright © 2020 Todor Kondić ;;; Copyright © 2020 Danjela Lura ;;; Copyright © 2020 Naga Malleswari ;;; Copyright © 2020 Eric Brown ;;; Copyright © 2020 Peter Lo ;;; Copyright © 2020 Rafael Luque Leiva ;;; Copyright © 2020, 2021 Lars-Dominik Braun ;;; Copyright © 2020 Vinicius Monego ;;; Copyright © 2020 Antoine Côté ;;; Copyright © 2020 Arun Isaac ;;; Copyright © 2020 Magali Lemes ;;; Copyright © 2020, 2021, 2022, 2023 Simon Tournier ;;; Copyright © 2020 Aniket Patil ;;; Copyright © 2021 Marcel Schilling ;;; Copyright © 2021 Guillaume Le Vaillant ;;; Copyright © 2022-2024 Navid Afkhami ;;; Copyright © 2022 Greg Hogan ;;; ;;; This file is part of GNU Guix. ;;; ;;; GNU Guix is free software; you can redistribute it and/or modify it ;;; under the terms of the GNU General Public License as published by ;;; the Free Software Foundation; either version 3 of the License, or (at ;;; your option) any later version. ;;; ;;; GNU Guix is distributed in the hope that it will be useful, but ;;; WITHOUT ANY WARRANTY; without even the implied warranty of ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the ;;; GNU General Public License for more details. ;;; ;;; You should have received a copy of the GNU General Public License ;;; along with GNU Guix. If not, see . (define-module (gnu packages cran) #:use-module ((guix licenses) #:prefix license:) #:use-module (guix packages) #:use-module (guix download) #:use-module (guix gexp) #:use-module (guix git-download) #:use-module (guix utils) #:use-module (guix build-system gnu) #:use-module (guix build-system r) #:use-module (gnu packages) #:use-module (gnu packages algebra) #:use-module (gnu packages autotools) #:use-module (gnu packages base) #:use-module (gnu packages bioinformatics) #:use-module (gnu packages c) #:use-module (gnu packages compression) #:use-module (gnu packages crypto) #:use-module (gnu packages curl) #:use-module (gnu packages databases) #:use-module (gnu packages fontutils) #:use-module (gnu packages fribidi) #:use-module (gnu packages gcc) #:use-module (gnu packages geo) #:use-module (gnu packages ghostscript) #:use-module (gnu packages gl) #:use-module (gnu packages gnome) #:use-module (gnu packages gtk) #:use-module (gnu packages haskell-xyz) #:use-module (gnu packages icu4c) #:use-module (gnu packages image) #:use-module (gnu packages imagemagick) #:use-module (gnu packages java) #:use-module (gnu packages javascript) #:use-module (gnu packages libevent) #:use-module (gnu packages machine-learning) #:use-module (gnu packages maths) #:use-module (gnu packages mpi) #:use-module (gnu packages multiprecision) #:use-module (gnu packages networking) #:use-module (gnu packages node) #:use-module (gnu packages pcre) #:use-module (gnu packages pdf) #:use-module (gnu packages perl) #:use-module (gnu packages pkg-config) #:use-module (gnu packages pulseaudio) ;libsndfile #:use-module (gnu packages protobuf) #:use-module (gnu packages python) #:use-module (gnu packages python-xyz) #:use-module (gnu packages ssh) #:use-module (gnu packages sqlite) #:use-module (gnu packages statistics) #:use-module (gnu packages tbb) #:use-module (gnu packages tcl) #:use-module (gnu packages tex) #:use-module (gnu packages textutils) #:use-module (gnu packages tls) #:use-module (gnu packages uglifyjs) #:use-module (gnu packages version-control) #:use-module (gnu packages video) #:use-module (gnu packages web) #:use-module (gnu packages xml) #:use-module (gnu packages xorg)) (define-public r-abbreviate (package (name "r-abbreviate") (version "0.1") (source (origin (method url-fetch) (uri (cran-uri "abbreviate" version)) (sha256 (base32 "1cvjdbi17qz8gr5898zchm5fyz4n51z66lwps25v8a9mhwab8imi")))) (properties `((upstream-name . "abbreviate"))) (build-system r-build-system) (home-page "https://github.com/sigbertklinke/abbreviate") (synopsis "Readable string abbreviation") (description "This package abbreviates strings to a specified minimum number of characters, such that the strings remain unique (if they originally were).") (license license:gpl3))) (define-public r-aer (package (name "r-aer") (version "1.2-12") (source (origin (method url-fetch) (uri (cran-uri "AER" version)) (sha256 (base32 "11pas7lglcw1h5649bgab13g8xlnx109pc2aqphwc3fdgvqv1ism")))) (properties `((upstream-name . "AER"))) (build-system r-build-system) (propagated-inputs (list r-car r-formula r-lmtest r-sandwich r-survival r-zoo)) (home-page "https://cran.r-project.org/package=AER") (synopsis "Applied econometrics with R") (description "This package provides functions, data sets, examples, demos, and vignettes for the book Christian Kleiber and Achim Zeileis (2008), Applied Econometrics with R, Springer-Verlag, New York. ISBN 978-0-387-77316-2. (See the vignette \"AER\" for a package overview.)") ;; Either version of the GPL (license (list license:gpl2 license:gpl3)))) (define-public r-afpt (package (name "r-afpt") (version "1.1.0.4") (source (origin (method url-fetch) (uri (cran-uri "afpt" version)) (sha256 (base32 "15pa4p78p6r478l05481lzx6z4ahswj728s1sb3xp3pvn6rv4jfj")))) (properties `((upstream-name . "afpt"))) (build-system r-build-system) (native-inputs (list r-knitr)) (home-page "https://github.com/MarcoKlH/afpt-r/") (synopsis "Tools for modelling of animal flight performance") (description "This package allows estimation and modelling of flight costs in animal (vertebrate) flight, implementing the aerodynamic power model. Flight performance is estimated based on basic morphological measurements such as body mass, wingspan and wing area. @code{Afpt} can be used to make predictions on how animals should adjust their flight behaviour and wingbeat kinematics to varying flight conditions.") 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In addition, this tool takes care of calculation of phylogenetic signal and mean trait depth (trait conservatism), ancestral state reconstruction and hidden character prediction of discrete characters, simulating and fitting models of trait evolution, fitting and simulating diversification models, dating trees, comparing trees, and reading/writing trees in Newick format.") (license license:gpl2+))) (define-public r-changepoint (package (name "r-changepoint") (version "2.2.4") (source (origin (method url-fetch) (uri (cran-uri "changepoint" version)) (sha256 (base32 "16v4p2c9zi2w3anwf5y9snl5dy1g5aidiqz1vn2p64qhfvg6yqxc")))) (properties `((upstream-name . "changepoint"))) (build-system r-build-system) (propagated-inputs (list r-zoo)) (home-page "https://github.com/rkillick/changepoint/") (synopsis "Methods for changepoint detection") (description "Changepoint implements various mainstream and specialised changepoint methods. These methods are suitable for finding single and multiple changepoints within data. Many popular non-parametric and frequentist methods are included as well.") ;; Any version of the GPL. (license license:gpl3+))) (define-public r-celestial (package (name "r-celestial") (version "1.4.6") (source (origin (method url-fetch) (uri (cran-uri "celestial" version)) (sha256 (base32 "1gls0qvr8mxz79lsmk76v253f747g0cqys8p8wjmpijs8r0pyr4z")))) (properties `((upstream-name . "celestial"))) (build-system r-build-system) (propagated-inputs (list r-nistunits r-pracma r-rann)) (home-page "https://cran.r-project.org/package=celestial") (synopsis "Collection of common astronomical conversion routines and functions") (description "This package contains a number of common astronomy conversion routines, particularly the HMS and degrees schemes, which can be fiddly to convert between on mass due to the textural nature of the former. It allows users to coordinate match datasets quickly. It also contains functions for various cosmological calculations.") (license license:gpl3))) (define-public r-cetcolor (package (name "r-cetcolor") (version "0.2.0") (source (origin (method url-fetch) (uri (cran-uri "cetcolor" version)) (sha256 (base32 "0kygdcr9ldanr0z4qpygwh0padki7s2ad0j6myky601g4228z79q")))) (properties `((upstream-name . "cetcolor"))) (build-system r-build-system) (native-inputs (list r-knitr)) (home-page "https://github.com/coatless-rpkg/cetcolor") (synopsis "CET perceptually uniform color maps") (description "This package provides a collection of perceptually uniform color maps made by Peter Kovesi (2015) \"Good Colour Maps: How to Design Them\" at the Centre for Exploration Targeting (CET).") (license license:cc-by-sa4.0))) ;; The package sources include multiple non-minified JavaScript files and the ;; v5.1.0 variant of d3.js. The d3.js file is not minified. (define-public r-chromomap (package (name "r-chromomap") (version "4.1.1") (source (origin (method url-fetch) (uri (cran-uri "chromoMap" version)) (sha256 (base32 "1067h5d6jdbm811n7ayikhqfbcqmxbz5jgp05vf1sbln7qgn9l43")))) (properties `((upstream-name . "chromoMap"))) (build-system r-build-system) (propagated-inputs (list r-htmltools r-htmlwidgets)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/package=chromoMap") (synopsis "Interactive genomic visualization of biological data") (description "This package provides interactive, configurable and graphics visualization of the chromosome regions of any living organism allowing users to map chromosome elements (like genes, SNPs etc.) on the chromosome plot. It introduces a special plot viz. the \"chromosome heatmap\" that, in addition to mapping elements, can visualize the data associated with chromosome elements (like gene expression) in the form of heat colors. Users can investigate the detailed information about the mappings (like gene names or total genes mapped on a location) or can view the magnified single or double stranded view of the chromosome at a location showing each mapped element in sequential order. The package provide multiple features like visualizing multiple sets, chromosome heat-maps, group annotations, adding hyperlinks, and labelling. The plots can be saved as HTML documents that can be customized and shared easily. In addition, you can include them in R Markdown or in R Shiny applications.") (license (list license:gpl3 license:isc)))) ;for bundled d3js (define-public r-consort (package (name "r-consort") (version "1.2.1") (source (origin (method url-fetch) (uri (cran-uri "consort" version)) (sha256 (base32 "03xkypy4r84mdif6m331c27haxnyi1s87vvj2f83xxw0m0s5im5j")))) (properties `((upstream-name . 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It further includes fast functions for common statistical procedures, detailed (grouped, weighted) summary statistics, powerful tools to work with nested data, fast data object conversions, functions for memory efficient R programming, and helpers to effectively deal with variable labels, attributes, and missing data.") (license (list license:gpl2+)))) (define-public r-collections (package (name "r-collections") (version "0.3.7") (source (origin (method url-fetch) (uri (cran-uri "collections" version)) (sha256 (base32 "003zlp5s2ilq3pq0imlp7p46jkfihwzg1hkkgk7378ikcbwnz17z")))) (properties `((upstream-name . "collections"))) (build-system r-build-system) (home-page "https://github.com/randy3k/collections") (synopsis "High performance container data types") (description "This package provides high performance container data types such as queues, stacks, deques, dicts and ordered dicts.") 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It has been applied in a wide range of fields in which continuous data with exact zeros regularly arise. The cplm package provides likelihood based and Bayesian procedures for fitting common Tweedie compound Poisson linear models. In particular, models with hierarchical structures or extra zero inflation can be handled. Further, the package implements the Gini index based on an ordered version of the Lorenz curve as a robust model comparison tool involving zero-inflated and highly skewed distributions.") (license license:gpl2+))) (define-public r-curry (package (name "r-curry") (version "0.1.1") (source (origin (method url-fetch) (uri (cran-uri "curry" version)) (sha256 (base32 "1ps9hvbnb02m0b8hlw4admwbziyjvswj08ldi2dk3ymnrpawcc29")))) (properties `((upstream-name . 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The algorithms included in this package are RUV-2, RUV-4, RUV-inv, RUV-rinv, RUV-I, and RUV-III, along with various supporting algorithms.") ;; Any version of the GPL. (license (list license:gpl2+ license:gpl3+)))) (define-public r-waldo (package (name "r-waldo") (version "0.5.2") (source (origin (method url-fetch) (uri (cran-uri "waldo" version)) (sha256 (base32 "019fvypq36kwvr2znlr0fd9f2ihb08rgigf6ypdybry5n8daxkc2")))) (properties `((upstream-name . "waldo"))) (build-system r-build-system) (propagated-inputs (list r-cli r-diffobj r-fansi r-glue r-rematch2 r-rlang r-tibble)) (home-page "https://github.com/r-lib/waldo") (synopsis "Find differences between R objects") (description "Compare complex R objects and reveal the key differences. This package was designed particularly for use in testing packages where being able to quickly isolate key differences makes understanding test failures much easier.") 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ORQ normalization combines a rank-mapping approach with a shifted logit approximation that allows the transformation to work on data outside the original domain. It is also able to handle new data within the original domain via linear interpolation. The package is built to estimate the best normalizing transformation for a vector consistently and accurately. It implements the Box-Cox transformation, the Yeo-Johnson transformation, three types of Lambert WxF transformations, and the ordered quantile normalization transformation. It estimates the normalization efficacy of other commonly used transformations, and it allows users to specify custom transformations or normalization statistics. Finally, functionality can be integrated into a machine learning workflow via recipes.") 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Currently handlers are provided for CDK, MOE and BCI fingerprint data.") ;; Any version of the GPL (license (list license:gpl2+ license:gpl3+)))) (define-public r-fpeek (package (name "r-fpeek") (version "0.1.2") (source (origin (method url-fetch) (uri (cran-uri "fpeek" version)) (sha256 (base32 "0kv46g21ndxchg3q8ynq7hjjkh6i2zlc21axn5y1jjzigrw047ii")))) (properties `((upstream-name . "fpeek"))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) (home-page "https://github.com/davidgohel/fpeek") (synopsis "Check text files content at a glance") (description "This package provides tools to help working with text files. It can return the number of lines; print the first and last lines; convert encoding. Operations are made without reading the entire file before starting, resulting in good performances with large files.") (license license:expat))) (define-public r-ggalluvial (package (name "r-ggalluvial") (version "0.12.5") (source (origin (method url-fetch) (uri (cran-uri "ggalluvial" version)) (sha256 (base32 "0wax853pi3ghqv5alfkx9rgfb3sm3sqh3miklwvn22bh1s44q14h")))) (properties `((upstream-name . "ggalluvial"))) (build-system r-build-system) (propagated-inputs (list r-dplyr r-ggplot2 r-lazyeval r-rlang r-tidyr r-tidyselect)) (native-inputs (list r-knitr)) (home-page "https://corybrunson.github.io/ggalluvial/") (synopsis "Alluvial plots for ggplot2") (description "This package provides alluvial plots for @code{ggplot2}. Alluvial plots use variable-width ribbons and stacked bar plots to represent multi-dimensional or repeated-measures data with categorical or ordinal variables.") (license license:gpl3))) (define-public r-ggpp (package (name "r-ggpp") (version "0.5.6") (source (origin (method url-fetch) (uri (cran-uri "ggpp" version)) (sha256 (base32 "0xnjbxd1lkg85c2hsx7cgxqsqb3dc0pma8jwdlqfgg7d519d60xa")))) (properties `((upstream-name . 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From version 1.0, it is possible to customize these components as you demand in ordinary @code{ggplot2} grammar.") (license license:gpl3))) (define-public r-lmds (package (name "r-lmds") (version "0.1.0") (source (origin (method url-fetch) (uri (cran-uri "lmds" version)) (sha256 (base32 "130azb0nc2wwxv0qi8v5s4rd02p9lc92zwn634pv7b8awbw81i65")))) (properties `((upstream-name . "lmds"))) (build-system r-build-system) (propagated-inputs (list r-assertthat r-dynutils r-irlba r-matrix)) (home-page "https://github.com/dynverse/lmds") (synopsis "Landmark multi-dimensional scaling") (description "This package provides a fast dimensionality reduction method scalable to large numbers of samples. @dfn{Landmark Multi-Dimensional Scaling} (LMDS) is an extension of classical Torgerson MDS, but rather than calculating a complete distance matrix between all pairs of samples, only the distances between a set of landmarks and the samples are calculated.") (license license:gpl3))) (define-public r-lmodel2 (package (name "r-lmodel2") (version "1.7-3") (source (origin (method url-fetch) (uri (cran-uri "lmodel2" version)) (sha256 (base32 "1fiin2nkffbihz1s8ixmw9lgf8mn3j9krr8iiflizk10mdv54hnb")))) (properties `((upstream-name . "lmodel2"))) (build-system r-build-system) (home-page "https://cran.r-project.org/package=lmodel2") (synopsis "Model II regression") (description "This package computes model II simple linear regression using @dfn{ordinary least squares} (OLS), @dfn{major axis} (MA), @dfn{standard major axis} (SMA), and @dfn{ranged major axis} (RMA).") (license license:gpl2))) (define-public r-ggpmisc (package (name "r-ggpmisc") (version "0.5.5") (source (origin (method url-fetch) (uri (cran-uri "ggpmisc" version)) (sha256 (base32 "1j49q1fbihxir5q5llqwyga111j3lggifzjk3cvq8lphim4c3jia")))) (build-system r-build-system) (propagated-inputs (list r-confintr r-dplyr r-generics r-ggplot2 r-ggpp r-lmodel2 r-lubridate r-mass r-multcomp r-multcompview r-plyr r-polynom r-quantreg r-rlang r-scales r-splus2r r-tibble)) (native-inputs (list r-knitr)) (home-page "https://www.r4photobiology.info/") (synopsis "Miscellaneous Extensions to @code{ggplot2}") (description "This package provides extensions to @code{ggplot2}, respecting the grammar of its graphics paradigm.") (license license:gpl2+))) (define-public r-ggside (package (name "r-ggside") (version "0.3.1") (source (origin (method url-fetch) (uri (cran-uri "ggside" version)) (sha256 (base32 "1r36hsnha9bqzfb3rhpj11zg307wzacnkn4i6hi627xrx4knj5cl")))) (properties `((upstream-name . 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(license license:expat))) (define-public r-gprofiler (package (name "r-gprofiler") (version "0.7.0") (source (origin (method url-fetch) (uri (cran-uri "gProfileR" version)) (sha256 (base32 "1h1v0kgpsn04ald2izznh7fr2riwisj5hcgz4k7h3qc931rf0r4k")))) (properties `((upstream-name . "gProfileR"))) (build-system r-build-system) (propagated-inputs (list r-plyr r-rcurl)) (home-page "https://cran.r-project.org/web/packages/gProfileR/") (synopsis "Interface to the g:Profiler toolkit") (description "This package provides tools for functional enrichment analysis, gene identifier conversion and mapping homologous genes across related organisms via the @code{g:Profiler} toolkit.") (license license:gpl2+))) (define-public r-gprofiler2 (package (name "r-gprofiler2") (version "0.2.3") (source (origin (method url-fetch) (uri (cran-uri "gprofiler2" version)) (sha256 (base32 "1klmg0zj5kr663dzgfzpy1yn161znmjcjq8pl3rahjh2lwaahbmh")))) (properties `((upstream-name . 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The main tools are: @enumerate @item @code{g:GOSt}, functional enrichment analysis and visualization of gene lists; @item @code{g:Convert}, gene/protein/transcript identifier conversion across various namespaces; @item @code{g:Orth}, orthology search across species; @item @code{g:SNPense}, mapping SNP rs identifiers to chromosome positions, genes and variant effects. @end enumerate This package is an R interface corresponding to the 2019 update of @code{g:Profiler} and provides access to versions @code{e94_eg41_p11} and higher.") (license license:gpl2+))) (define-public r-oenb (package (name "r-oenb") (version "0.0.2") (source (origin (method url-fetch) (uri (cran-uri "oenb" version)) (sha256 (base32 "1jgxw7ycx2lcdzglg9nix8k08fs4r6i5jdsjzrd6w1dg6smsinl5")))) (properties `((upstream-name . 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OOMPA uses S4 classes to construct object-oriented tools with a consistent user interface. All higher level analysis tools in OOMPA are compatible with the eSet classes defined in BioConductor. The lower level processing tools offer an alternative to parts of BioConductor, but can also be used to enhance existing BioConductor packages.") (license license:asl2.0))) (define-public r-oompabase (package (name "r-oompabase") (version "3.2.9") (source (origin (method url-fetch) (uri (cran-uri "oompaBase" version)) (sha256 (base32 "1cmw2s5dznmv675484jgvkzgvi6vhg0zbxsq6zhpqsisf672pjhl")))) (properties `((upstream-name . "oompaBase"))) (build-system r-build-system) (propagated-inputs (list r-cluster)) (home-page "https://oompa.r-forge.r-project.org/") (synopsis "Class unions, matrix operations, and color schemes for OOMPA") (description "This package preloads class unions for defining/loading core OOMPA tools. It also includes vectorized operations for row-by-row means, variances, and t-tests. Finally, it provides new colorschemes.") (license license:asl2.0))) (define-public r-orgmassspecr (package (name "r-orgmassspecr") (version "0.5-3") (source (origin (method url-fetch) (uri (cran-uri "OrgMassSpecR" version)) (sha256 (base32 "1dx9d8rb1dfqyhyc26zhfnxiv3rz2ikvs2mwqnsrq3lsjs9dvyc8")))) (properties `((upstream-name . "OrgMassSpecR"))) (build-system r-build-system) (native-inputs (list r-knitr)) (home-page "https://OrgMassSpec.github.io/") (synopsis "Organic or biological mass spectrometry data analysis") (description "This package @code{OrgMassSpecR} is an extension of the @code{R} statistical computing language. It contains functions to assist with organic or biological mass spectrometry data analysis. Mass spectral libraries are available as companion packages.") (license license:bsd-2))) (define-public r-scales (package (name "r-scales") (version "1.3.0") (source (origin (method url-fetch) (uri (cran-uri "scales" version)) (sha256 (base32 "122qyd88qr8cc8h3k46xpygm00inqpm55zdy0b7535958imhygmk")))) (build-system r-build-system) (propagated-inputs (list r-cli r-farver r-glue r-labeling r-lifecycle r-munsell r-r6 r-rcolorbrewer r-rlang r-viridislite)) (home-page "https://github.com/hadley/scales") (synopsis "Scale functions for visualization") (description "This package provides graphical scales that map data to aesthetics, and provides methods for automatically determining breaks and labels for axes and legends.") (license license:expat))) (define-public r-swagger (package (name "r-swagger") (version "3.33.1") (source (origin (method url-fetch) (uri (cran-uri "swagger" version)) (sha256 (base32 "1ldgmy5vjzd11z5yl5a518wkw6y0l469b2zf0lp12hk19jq6k0sj")))) (properties `((upstream-name . 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Pagoda2 primarily performs normalization and differential gene expression analysis, with an interactive application for exploring single-cell RNA-seq datasets. It performs basic tasks such as cell size normalization, gene variance normalization, and can be used to identify subpopulations and run differential expression within individual samples. pagoda2 was written to rapidly process modern large-scale scRNAseq datasets of approximately 1e6 cells. The companion web application allows users to explore which gene expression patterns form the different subpopulations within your data. The package also serves as the primary method for preprocessing data for conos.") (license license:gpl3))) (define-public r-pals (package (name "r-pals") (version "1.8") (source (origin (method url-fetch) (uri (cran-uri "pals" version)) (sha256 (base32 "0z6lkvkq7b3wsxvizljf08sjqrdcj33p5kdx6074pc5jv36dylhb")))) (properties `((upstream-name . 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While allowing advanced layout, the underlying CSS-structure is simple in order to maximize compatibility with word processors such as LibreOffice. The package also contains a few text formatting functions that help outputting text compatible with HTML or LaTeX.") (license license:gpl3+))) (define-public r-curl (package (name "r-curl") (version "5.2.1") (source (origin (method url-fetch) (uri (cran-uri "curl" version)) (sha256 (base32 "147smp4am6z23c3j21bd0zcjxsmhnkkssn4wrlpwl6xa1264syja")))) (properties `((upstream-name . "curl") (updater-extra-inputs . ("curl")))) (build-system r-build-system) (arguments `(#:phases (modify-phases %standard-phases ;; The environment variable CURL_CA_BUNDLE is only respected when ;; running Windows, so we disable the platform checks. ;; This can be removed once the libcurl has been patched. 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(license license:expat))) (define-public r-fastmap (package (name "r-fastmap") (version "1.1.1") (source (origin (method url-fetch) (uri (cran-uri "fastmap" version)) (sha256 (base32 "0wvibiy16i30nzg5k80md68lpz7g6iwbl02j4fyqmbhns2fq08rn")))) (properties `((upstream-name . "fastmap"))) (build-system r-build-system) (home-page "https://r-lib.github.io/fastmap/") (synopsis "Fast implementation of a key-value store") (description "This package provides a fast implementation of a key-value store. Environments are commonly used as key-value stores, but every time a new key is used, it is added to R's global symbol table, causing a small amount of memory leakage. This can be problematic in cases where many different keys are used. Fastmap avoids this memory leak issue by implementing the map using data structures in C++.") 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(define-public r-jquerylib (package (name "r-jquerylib") (version "0.1.4") (source (origin (method url-fetch) (uri (cran-uri "jquerylib" version)) (sha256 (base32 "04a40v4znpj98j7y6009d74a6g9dchj5rr3p08cgz9p3rlfw3g7h")) (snippet '(for-each delete-file '("inst/lib/1.12.4/jquery-1.12.4.min.js" "inst/lib/2.2.4/jquery-2.2.4.min.js" "inst/lib/3.6.0/jquery-3.6.0.min.js"))))) (properties `((upstream-name . 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This leads to unreliable quantification of genes with low or moderate expression, which hinders downstream analysis. This package @dfn{single-cell analysis via expression recovery} (SAVER) implements an expression recovery method for unique molecule index (UMI)-based scRNA-seq data that borrows information across genes and cells to provide accurate expression estimates for all genes.") (license license:gpl2))) ;; This package includes minified JavaScript files. When upgrading please ;; check that there are no new minified JavaScript files. (define-public r-bslib (package (name "r-bslib") (version "0.7.0") (source (origin (method url-fetch) (uri (cran-uri "bslib" version)) (sha256 (base32 "181cfmdvi64j978q8x69bl7wxwpjpx54a52sh4xng0pk3a2djd91")) (snippet '(for-each delete-file '("inst/components/dist/components.min.js" "inst/components/dist/web-components.min.js" "inst/lib/bs-a11y-p/plugins/js/bootstrap-accessibility.min.js" "inst/lib/bs3/assets/javascripts/bootstrap.min.js" "inst/lib/bs4/dist/js/bootstrap.bundle.min.js" "inst/lib/bs5/dist/js/bootstrap.bundle.min.js"))))) (properties `((upstream-name . 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It supports both Bootstrap 3 and 4 as well as their various Bootswatch themes. An interactive widget is also provided for previewing themes in real time.") (license license:expat))) ;; This package includes minified JavaScript files. When upgrading please ;; check that there are no new minified JavaScript files. (define-public r-shiny (package (name "r-shiny") (version "1.8.0") (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/rstudio/shiny") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 (base32 "0rfrch2147yhp2vkr3198gn1ww00ckzcw4i6rywfl38c6fdw9vr1")) (snippet '(for-each delete-file '("inst/www/shared/bootstrap/js/bootstrap.min.js" "inst/www/shared/bootstrap/accessibility/js/bootstrap-accessibility.min.js" ; TODO "inst/www/shared/datatables/js/jquery.dataTables.min.js" "inst/www/shared/datepicker/js/bootstrap-datepicker.min.js" "inst/www/shared/highlight/highlight.pack.js" "inst/www/shared/ionrangeslider/js/ion.rangeSlider.min.js" "inst/www/shared/jquery.min.js" "inst/www/shared/jqueryui/jquery-ui.min.js" "inst/www/shared/legacy/jquery.min.js" "inst/www/shared/selectize/accessibility/js/selectize-plugin-a11y.min.js" "inst/www/shared/selectize/js/selectize.min.js" "inst/www/shared/shiny.min.js" "inst/www/shared/showdown/compressed/showdown.js" "inst/www/shared/strftime/strftime-min.js"))))) (build-system r-build-system) (arguments (list #:modules '((guix build r-build-system) (guix build minify-build-system) (guix build utils) (ice-9 match)) #:imported-modules `(,@%r-build-system-modules (guix build minify-build-system)) #:phases '(modify-phases (@ (guix build r-build-system) %standard-phases) (add-after 'unpack 'replace-bundled-minified-JavaScript (lambda* (#:key inputs #:allow-other-keys) (let ((replace-file (lambda (old new) (format #t "replacing ~a with ~a\n" old new) (symlink new old)))) ;; NOTE: Files in ./inst/www/shared/datepicker/js/locales/ ;; contain just data. 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(license license:gpl3))) ;; This package includes minified JavaScript files. When upgrading please ;; check that there are no new minified JavaScript files. (define-public r-shinytree (package (name "r-shinytree") (version "0.3.1") (source (origin (method url-fetch) (uri (cran-uri "shinyTree" version)) (sha256 (base32 "0krffsgdv99cvyzdspb9l7cdnq1vibsbmpd4w48r5pi4v8jbvfj6")) (snippet ;; Delete minified JavaScript '(for-each delete-file '("inst/www/jsTree-3.3.7/libs/require.js" "inst/www/jsTree-3.3.7/libs/jquery.js" "inst/www/jsTree-3.3.7/jstree.min.js"))))) (properties `((upstream-name . 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(license license:expat))) (define-public r-shinydashboard (package (name "r-shinydashboard") (version "0.7.2") (source (origin (method url-fetch) (uri (cran-uri "shinydashboard" version)) (sha256 (base32 "0hrqkwlpb8rnmp5j74p134g4c4cl16icmwc2ip6k1634fa2y8vm5")))) (build-system r-build-system) ;; The directory inst/AdminLTE/ contains a minified JavaScript file. ;; Regenerate it from the included sources. (arguments `(#:phases (modify-phases %standard-phases (add-after 'unpack 'generate-minified-javascript (lambda _ (with-directory-excursion "inst/AdminLTE" (let ((target "app.min.js") (source "app.js")) (format #t "Processing ~a --> ~a~%" source target) (delete-file target) (invoke "esbuild" source "--minify" (string-append "--outfile=" target))))))))) (propagated-inputs (list r-htmltools r-promises r-shiny)) (native-inputs (list esbuild)) (home-page "https://rstudio.github.io/shinydashboard/") (synopsis "Create dashboards with shiny") (description "This package provides an extension to the Shiny web application framework for R, making it easy to create attractive dashboards.") ;; This package includes software that was released under the Expat ;; license, but the whole package is released under GPL version 2 or ;; later. (license license:gpl2+))) (define-public r-shinyfiles (package (name "r-shinyfiles") (version "0.9.3") (source (origin (method url-fetch) (uri (cran-uri "shinyFiles" version)) (sha256 (base32 "11kjq0vw5c98lzrg80m9w917lkgw5im2h9wgk1b84vlaxrjy2wja")))) (properties `((upstream-name . "shinyFiles"))) (build-system r-build-system) (propagated-inputs (list r-fs r-htmltools r-jsonlite r-shiny r-tibble)) (home-page "https://github.com/thomasp85/shinyFiles") (synopsis "Server-side file system viewer for Shiny") (description "This package provides functionality for client-side navigation of the server side file system in shiny apps. In case the app is running locally this gives the user direct access to the file system without the need to \"download\" files to a temporary location. Both file and folder selection as well as file saving is available.") (license license:gpl2+))) (define-public r-shinythemes (package (name "r-shinythemes") (version "1.2.0") (source (origin (method url-fetch) (uri (cran-uri "shinythemes" version)) (sha256 (base32 "0qr9bfxw8afxns44i2j4msignf6g5qb2nzpay2lpv343rrlqbmip")))) (properties `((upstream-name . "shinythemes"))) (build-system r-build-system) (propagated-inputs (list r-shiny)) (home-page "https://rstudio.github.io/shinythemes/") (synopsis "Themes for Shiny") (description "This package provides themes for use with Shiny. It includes several Bootstrap themes, which are packaged for use with Shiny applications.") ;; The package is released under version 3 of the GPL, but it includes ;; source files that are covered by the Expat license. It also includes ;; fonts under SIL or the ASL. (license (list license:gpl3 license:expat license:silofl1.1 license:asl2.0)))) ;; The package sources include minified variants of d3.js and non-minified ;; source code of d3-jetpack. (define-public r-d3r (package (name "r-d3r") (version "1.1.0") (source (origin (method url-fetch) (uri (cran-uri "d3r" version)) (sha256 (base32 "1dcm53y3jpyswr6y368xhdnn1nkchixf4wkxnsb2mk9lzccb44y4")) (snippet '(for-each delete-file '("inst/www/d3/v3/dist/d3.min.js" "inst/www/d3/v4/dist/d3.min.js" "inst/www/d3/v5/dist/d3.min.js" "inst/www/d3/v6/dist/d3.min.js" "inst/www/d3/v7/dist/d3.min.js"))))) (build-system r-build-system) (arguments `(#:modules ((guix build utils) (guix build r-build-system) (srfi srfi-1)) #:phases (modify-phases %standard-phases (add-after 'unpack 'process-javascript (lambda* (#:key inputs #:allow-other-keys) (with-directory-excursion "inst/www/d3/" (call-with-values (lambda () (unzip2 `((,(assoc-ref inputs "d3.v3.js") "v3/dist/d3.min.js") (,(assoc-ref inputs "d3.v4.js") "v4/dist/d3.min.js") (,(assoc-ref inputs "d3.v5.js") "v5/dist/d3.min.js") (,(assoc-ref inputs "d3.v6.js") "v6/dist/d3.min.js") (,(assoc-ref inputs "d3.v7.js") "v7/dist/d3.min.js")))) (lambda (sources targets) (for-each (lambda (source target) (format #t "Processing ~a --> ~a~%" source target) (invoke "esbuild" source "--minify" (string-append "--outfile=" target))) sources targets))))))))) (propagated-inputs (list r-dplyr r-htmltools r-tidyr)) (native-inputs `(("esbuild" ,esbuild) ("d3.v3.js" ,(origin (method url-fetch) (uri "https://d3js.org/d3.v3.js") (sha256 (base32 "1arr7sr08vy7wh0nvip2mi7dpyjw4576vf3bm45rp4g5lc1k1x41")))) ("d3.v4.js" ,(origin (method url-fetch) (uri "https://d3js.org/d3.v4.js") (sha256 (base32 "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg")))) ("d3.v5.js" ,(origin (method url-fetch) (uri "https://d3js.org/d3.v5.js") (sha256 (base32 "177ypw6mjrp2ch9lj6znibwacwrvm4ypjxflsxsnl2sigx5dcwic")))) ("d3.v6.js" ,(origin (method url-fetch) (uri "https://d3js.org/d3.v6.js") (sha256 (base32 "13hick3glizzm442b9swlwz584rzwwvhpq9qvfbh3m5jay10wxw0")))) ("d3.v7.js" ,(origin (method url-fetch) (uri "https://d3js.org/d3.v7.js") (sha256 (base32 "1m4i3kqzkz7w06sp9zqcy9f88xpdhi7cqih3phdrf4yjmfk1pfjg")))))) (home-page "https://github.com/timelyportfolio/d3r") (synopsis "d3.js utilities for R") (description "This package provides a suite of functions to help ease the use of the d3.js visualization library in R. These helpers include @code{htmltools::htmlDependency} functions, hierarchy builders, and conversion tools for @code{partykit}, @code{igraph}, @code{table}, and @code{data.frame} R objects into the JSON format that the d3.js library expects.") (license license:bsd-3))) ;; We use the latest commit here because the last release was in 2016 while ;; the latest commit was in 2018. (define-public r-sankeyd3 (let ((commit "fd50a74e29056e0d67d75b4d04de47afb2f932bc") (revision "1")) (package (name "r-sankeyd3") (version (git-version "0.3.2" revision commit)) (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/fbreitwieser/sankeyD3") (commit commit))) (file-name (git-file-name name version)) (sha256 (base32 "0jrcnfax321pszbpjdifnkbrgbjr43bjzvlzv1p5a8wskksqwiyx")))) (build-system r-build-system) (propagated-inputs (list r-d3r r-htmlwidgets r-shiny r-magrittr)) (home-page "https://github.com/fbreitwieser/sankeyD3") (synopsis "Sankey network graphs from R") (description "This package provides an R library to generate Sankey network graphs in R and Shiny via the D3 visualization library.") ;; The R code is licensed under GPLv3+. It includes the non-minified ;; JavaScript source code of d3-sankey, which is released under the ;; 3-clause BSD license. (license (list license:gpl3+ license:bsd-3))))) (define-public r-wesanderson (package (name "r-wesanderson") (version "0.3.7") (source (origin (method url-fetch) (uri (cran-uri "wesanderson" version)) (sha256 (base32 "0kjyz5mrkrirg2glf57b0rhxj2fdp1m6q8zx947y0jg1w425cbn9")))) (properties `((upstream-name . "wesanderson"))) (build-system r-build-system) (home-page "https://github.com/karthik/wesanderson") (synopsis "Wes Anderson color palette generator") (description "This package provides color palettes that have been generated mostly from Wes Anderson movies.") (license license:expat))) (define-public r-gg-gap (package (name "r-gg-gap") (version "1.3") (source (origin (method url-fetch) (uri (cran-uri "gg.gap" version)) (sha256 (base32 "0m66050ryn31xmsmmikjsssllasvjdmp9yjbwfdwfpwdv106zn9h")))) (properties `((upstream-name . "gg.gap"))) (build-system r-build-system) (propagated-inputs (list r-cowplot r-ggplot2)) (home-page "https://github.com/ChrisLou-bioinfo/gg.gap") (synopsis "Define segments on the y-axis for ggplot2") (description "The @code{gg.gap} function enables you to define segments for the y-axis in a ggplot2 plot.") (license license:gpl3))) (define-public r-mbess (package (name "r-mbess") (version "4.9.3") (source (origin (method url-fetch) (uri (cran-uri "MBESS" version)) (sha256 (base32 "05ph8dwigwn0c4qg8smqhsjijvsvfawbzvm74mqpasi8qifz8nd3")))) (properties `((upstream-name . "MBESS"))) (build-system r-build-system) (propagated-inputs (list r-boot r-lavaan r-mass r-mnormt r-nlme r-openmx r-sem r-semtools)) (home-page "https://www3.nd.edu/~kkelley/site/MBESS.html") (synopsis "Methods for designing research studies") (description "This package implements methods that are useful in designing research studies and analyzing data, with particular emphasis on methods that are developed for or used within the behavioral, educational, and social sciences (broadly defined). That being said, many of the methods implemented within MBESS are applicable to a wide variety of disciplines. MBESS has a suite of functions for a variety of related topics, such as effect sizes, confidence intervals for effect sizes (including standardized effect sizes and noncentral effect sizes), sample size planning (from the @dfn{accuracy in parameter estimation} (AIPE), power analytic, equivalence, and minimum-risk point estimation perspectives), mediation analysis, various properties of distributions, and a variety of utility functions.") ;; Either version of the GPL. (license (list license:gpl2 license:gpl3)))) (define-public r-homologene (package (name "r-homologene") (version "1.4.68.19.3.27") (source (origin (method url-fetch) (uri (cran-uri "homologene" version)) (sha256 (base32 "0d7wxisk0vqk1n165v1i19bc02zv78h5r5d3jqai5y6nkmwn01sh")))) (properties `((upstream-name . "homologene"))) (build-system r-build-system) (propagated-inputs (list r-dplyr r-magrittr r-purrr r-r-utils r-readr)) (home-page "https://github.com/oganm/homologene") (synopsis "Quick access to homologene and gene annotation updates") (description "This package provides a wrapper for the homologene database by the National Center for Biotechnology Information (NCBI). It allows searching for gene homologs across species. The package also includes an updated version of the homologene database where gene identifiers and symbols are replaced with their latest (at the time of submission) version and functions to fetch latest annotation data to keep updated.") (license license:expat))) (define-public r-ggtern (package (name "r-ggtern") (version "3.5.0") (source (origin (method url-fetch) (uri (cran-uri "ggtern" version)) (sha256 (base32 "0ymly9vdzk7rd4p27m1262bm7fvim989yswgw3mr9y0422dn8awa")))) (properties `((upstream-name . 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There are different layouts available such as a one page dashboard or a multi-page template, where the navigation menu is contained in the navigation bar.") (license license:gpl2+))) (define-public r-spelling (package (name "r-spelling") (version "2.3.0") (source (origin (method url-fetch) (uri (cran-uri "spelling" version)) (sha256 (base32 "0fxa0wpmmx7bal7xb4yy3134s2bskj98kwhqn25bqga3inzqdm6d")))) (properties `((upstream-name . "spelling"))) (build-system r-build-system) (propagated-inputs (list r-commonmark r-hunspell r-knitr r-xml2)) (home-page "https://docs.ropensci.org/spelling/") (synopsis "Tools for spell checking in R") (description "This is an R package for spell checking common document formats including LaTeX, markdown, manual pages, and DESCRIPTION files. It includes utilities to automate checking of documentation and vignettes as a unit test during @code{R CMD check}. Both British and American English are supported out of the box and other languages can be added. In addition, packages may define a wordlist to allow custom terminology without having to abuse punctuation.") (license license:expat))) (define-public r-crosstalk (package (name "r-crosstalk") (version "1.2.1") (source (origin (method url-fetch) (uri (cran-uri "crosstalk" version)) (sha256 (base32 "1w8lc3hcd1nlw541880vs3agk2i6bilyapnq9lcs3mfn2s2g0338")) (snippet '(for-each delete-file (list "inst/lib/jquery/jquery.min.js" "inst/lib/ionrangeslider/js/ion.rangeSlider.min.js" "inst/lib/selectize/js/selectize.min.js" "inst/www/js/crosstalk.min.js"))))) (build-system r-build-system) (arguments (list #:modules '((guix build r-build-system) (guix build minify-build-system) (guix build utils) (ice-9 match)) #:imported-modules `(,@%r-build-system-modules (guix build minify-build-system)) #:phases #~(modify-phases (@ (guix build r-build-system) %standard-phases) (add-after 'unpack 'replace-bundled-minified-JavaScript (lambda* (#:key inputs #:allow-other-keys) (with-directory-excursion "inst/" (copy-file (search-input-file inputs "/share/javascript/selectize.min.js") "lib/selectize/js/selectize.min.js") (for-each (match-lambda ((source . target) (minify source #:target target))) `(("lib/jquery/jquery.js" . 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"GenSA"))) (build-system r-build-system) (home-page "https://cran.r-project.org/package=GenSA") (synopsis "Generalized simulated annealing") (description "This package performs search for the global minimum of a very complex non-linear objective function with a very large number of optima.") (license license:gpl2))) (define-public r-geosphere (package (name "r-geosphere") (version "1.5-18") (source (origin (method url-fetch) (uri (cran-uri "geosphere" version)) (sha256 (base32 "1h6sqvxwxv22js6hz4s8sjk50ygw0y34icbbbdb2v36ca3q6zzwr")))) (build-system r-build-system) (propagated-inputs (list r-rcpp r-sp)) (home-page "https://cran.r-project.org/web/packages/geosphere") (synopsis "Spherical trigonometry") (description "This package computes spherical trigonometry for geographic applications. That is, compute distances and related measures for angular (longitude/latitude) locations.") (license license:gpl3+))) (define-public r-jpeg (package (name "r-jpeg") (version "0.1-10") (source (origin (method url-fetch) (uri (cran-uri "jpeg" version)) (sha256 (base32 "1jkqj58hj33ar9wyl7c1cnj3h42icq7crmjk93n933q8qc4zdnf8")))) (build-system r-build-system) (inputs (list libjpeg-turbo)) (home-page "https://www.rforge.net/jpeg/") (synopsis "Read and write JPEG images with R") (description "This package provides a way to read, write and display bitmap images stored in the JPEG format with R. It can read and write both files and in-memory raw vectors.") (license license:gpl2+))) (define-public r-ggmap (package (name "r-ggmap") (version "4.0.0") (source (origin (method url-fetch) (uri (cran-uri "ggmap" version)) (sha256 (base32 "1x9lqx0mizqiyxzgg8pgkbi8qmbn2a0zsq5r5riknvh6ghskkrhd")))) (build-system r-build-system) (propagated-inputs (list r-bitops r-cli r-digest r-dplyr r-ggplot2 r-glue r-httr r-jpeg r-magrittr r-plyr r-png r-purrr r-rlang r-scales r-stringr r-tibble r-tidyr)) (home-page "https://github.com/dkahle/ggmap") (synopsis "Spatial visualization with ggplot2") (description "This package provides a collection of functions to visualize spatial data and models on top of static maps from various online sources (e.g Google Maps and Stamen Maps). It includes tools common to those tasks, including functions for geolocation and routing.") (license license:gpl2))) (define-public r-ggmosaic (package (name "r-ggmosaic") (version "0.3.3") (source (origin (method url-fetch) (uri (cran-uri "ggmosaic" version)) (sha256 (base32 "1zm1zfbd0qk6icw65m9hz1hgyqj632ibq3qilidvx5jy7jh8nbpy")))) (properties `((upstream-name . "ggmosaic"))) (build-system r-build-system) (propagated-inputs (list r-dplyr r-ggplot2 r-ggrepel r-plotly r-productplots r-purrr r-rlang r-scales r-tidyr)) (native-inputs (list r-knitr)) (home-page "https://github.com/haleyjeppson/ggmosaic") (synopsis "Mosaic plots in the ggplot2 framework") (description "This package provides mosaic plots for the ggplot2 framework. Mosaic plot functionality is provided in a single ggplot2 layer by calling the @code{geom} @code{mosaic}.") (license license:gpl2+))) (define-public r-haven (package (name "r-haven") (version "2.5.4") (source (origin (method url-fetch) (uri (cran-uri "haven" version)) (sha256 (base32 "0dd83v3bfs7and9ydx35m8zw0md3wgchwpnvj6yllixa6yxk25cy")) (modules '((guix build utils))) (snippet ;; unvendor readstat '(delete-file-recursively "src/readstat")))) (build-system r-build-system) (properties '((updater-extra-inputs . ("readstat")))) (arguments '(#:phases (modify-phases %standard-phases (add-after 'unpack 'unbundle-readstat (lambda _ ;; We’re not building readstat. (substitute* "configure" (("^PKG_CONFIG_NAME=\"zlib\"") "PKG_CONFIG_NAME=\"readstat zlib\"") (("^PKG_LIBS=\"-lz\"") "PKG_LIBS=\"-lz -lreadstat\"\n") (("exit 1") ""))))))) ;don't be so dramatic! (inputs (list readstat zlib)) (native-inputs (list pkg-config r-knitr)) (propagated-inputs (list r-cli r-cpp11 r-forcats r-hms r-lifecycle r-readr r-rlang r-tibble r-tidyselect r-vctrs)) (home-page "https://haven.tidyverse.org") (synopsis "Import and export SPSS, Stata and SAS files") (description "This package lets you import foreign statistical formats into R via the @url{https://github.com/WizardMac/ReadStat,ReadStat} C library.") (license license:expat))) (define-public r-amap (package (name "r-amap") (version "0.8-19") (source (origin (method url-fetch) (uri (cran-uri "amap" version)) (sha256 (base32 "000r5705lq2mc15skin07dfxjf5816nbfy4gqkya1sv99dlfljbk")))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "http://mulcyber.toulouse.inra.fr/projects/amap/") (synopsis "Another multidimensional analysis package") (description "This package provides tools for clustering and principal component analysis (with robust methods, and parallelized functions).") (license license:gpl2+))) (define-public r-ape (package (name "r-ape") (version "5.8") (source (origin (method url-fetch) (uri (cran-uri "ape" version)) (sha256 (base32 "092dx0x763r6ch6pp4c4fkmnq5alrq0527p72w1wdg71g6cp5ki4")))) (build-system r-build-system) (propagated-inputs (list r-digest r-lattice r-nlme r-rcpp)) (home-page "http://ape-package.ird.fr/") (synopsis "Analyses of phylogenetics and evolution") (description "This package provides 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, and several other tools.") (license license:gpl2+))) (define-public r-abbyyr (package (name "r-abbyyr") (version "0.5.5") (source (origin (method url-fetch) (uri (cran-uri "abbyyR" version)) (sha256 (base32 "1vldnd3dg89aj6a73nhirirqddbfdrnzhb5m3679i60sark8nk6r")))) (properties `((upstream-name . "abbyyR"))) (build-system r-build-system) (propagated-inputs (list r-curl r-httr r-plyr r-progress r-readr r-xml)) (home-page "https://github.com/soodoku/abbyyR") (synopsis "Access to Abbyy Optical Character Recognition (OCR) API") (description "This package provides tools to get text from images of text using Abbyy Cloud Optical Character Recognition (OCR) API. With abbyyyR, one can easily OCR images, barcodes, forms, documents with machine readable zones, e.g. passports and get the results in a variety of formats including plain text and XML. To learn more about the Abbyy OCR API, see @url{http://ocrsdk.com/}.") (license license:expat))) (define-public r-colorspace (package (name "r-colorspace") (version "2.1-0") (source (origin (method url-fetch) (uri (cran-uri "colorspace" version)) (sha256 (base32 "0k31hazd2rq5lyg3y89y2v5jqadz2qlxd1bhvj89q4aldfxql1q4")))) (build-system r-build-system) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/colorspace") (synopsis "Color space manipulation") (description "This package carries out a mapping between assorted color spaces including RGB, HSV, HLS, CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB and polar CIELAB. Qualitative, sequential, and diverging color palettes based on HCL colors are provided.") (license license:bsd-3))) (define-public r-glue (package (name "r-glue") (version "1.7.0") (source (origin (method url-fetch) (uri (cran-uri "glue" version)) (sha256 (base32 "1p4699p68k9f8d76bmgx5xabay6xjrcgajckzqxyn6icym8ipx8s")))) (build-system r-build-system) (properties ;; knitr depends on glue, so we can't add knitr here to build the ;; vignettes. '((updater-ignored-native-inputs . ("r-knitr")))) (home-page "https://github.com/tidyverse/glue") (synopsis "Interpreted string literals") (description "This package provides an implementation of interpreted string literals, inspired by Python's Literal String Interpolation (PEP-0498) and Docstrings (PEP-0257) and Julia's Triple-Quoted String Literals.") (license license:expat))) (define-public r-glmnetutils (package (name "r-glmnetutils") (version "1.1.9") (source (origin (method url-fetch) (uri (cran-uri "glmnetUtils" version)) (sha256 (base32 "0rh07i9j6bxiqcl84d8jnn7dzqdwfdzak7w8bf4j4521r24mwm01")))) (properties `((upstream-name . "glmnetUtils"))) (build-system r-build-system) (propagated-inputs (list r-glmnet r-matrix)) (native-inputs (list r-knitr)) (home-page "https://github.com/hongooi73/glmnetUtils") (synopsis "Streamline the process of fitting elastic net models with glmnet") (description "This package provides a collection of tools to streamline the process of fitting elastic net models with @code{glmnet}. In addition to providing a formula interface, it also features a function @code{cva.glmnet} to do crossvalidation for both α and λ, as well as some utility functions.") (license license:gpl2))) (define-public r-paletteer (package (name "r-paletteer") (version "1.6.0") (source (origin (method url-fetch) (uri (cran-uri "paletteer" version)) (sha256 (base32 "1n4jim2fgyff6c5mjridq92jgvr5m2qgwfsgvhyj1pwk1hq21pmm")))) (properties `((upstream-name . "paletteer"))) (build-system r-build-system) (propagated-inputs (list r-prismatic r-rematch2 r-rlang r-rstudioapi)) (home-page "https://github.com/EmilHvitfeldt/paletteer") (synopsis "Comprehensive collection of color palettes") (description "The choices of color palettes in R can be quite overwhelming with palettes spread over many packages with many different API's. This package aims to collect all color palettes across the R ecosystem under the same package with a streamlined API.") (license license:gpl3))) (define-public r-palmerpenguins (package (name "r-palmerpenguins") (version "0.1.1") (source (origin (method url-fetch) (uri (cran-uri "palmerpenguins" version)) (sha256 (base32 "1d1h3bfx750is4qqj4w00rcigk9rrdy69bvd5bgqz5y7ls5x8h1a")))) (properties `((upstream-name . "palmerpenguins"))) (build-system r-build-system) (home-page "https://allisonhorst.github.io/palmerpenguins/") (synopsis "Palmer Archipelago (Antarctica) penguin data") (description "This package includes size measurements, clutch observations, and blood isotope ratios for adult foraging Adélie, Chinstrap, and Gentoo penguins observed on islands in the Palmer Archipelago near Palmer Station, Antarctica. Data were collected and made available by Dr. Kristen Gorman and the Palmer Station Long Term Ecological Research (LTER) Program.") (license license:cc0))) (define-public r-pastecs (package (name "r-pastecs") (version "1.4.2") (source (origin (method url-fetch) (uri (cran-uri "pastecs" version)) (sha256 (base32 "1y3nngdmslbs1rls0n2nbx8jpp9z3nvv11w1z6rff6v0ky05ddj3")))) (build-system r-build-system) (propagated-inputs (list r-boot)) (native-inputs (list r-knitr)) (home-page "https://github.com/phgrosjean/pastecs") (synopsis "Analysis of space-time ecological series") (description "This package provides functions for regulation, decomposition and analysis of space-time series. The @code{pastecs} library is a PNEC-Art4 and IFREMER initiative to bring PASSTEC 2000 functionalities to R.") (license license:gpl2+))) (define-public r-partykit (package (name "r-partykit") (version "1.2-20") (source (origin (method url-fetch) (uri (cran-uri "partykit" version)) (sha256 (base32 "1np0sa7fx7wvwxbpk5lpgbdpz0xwcvppq0sc52nifx1dxnirll33")))) (build-system r-build-system) (propagated-inputs (list r-formula r-inum r-libcoin r-mvtnorm r-rpart r-survival)) (home-page "https://partykit.R-Forge.R-project.org/partykit") (synopsis "Toolkit for recursive partytioning") (description "This package provides a toolkit with infrastructure for representing, summarizing, and visualizing tree-structured regression and classification models.") (license license:gpl2+))) (define-public r-plogr (package (name "r-plogr") (version "0.2.0") (source (origin (method url-fetch) (uri (cran-uri "plogr" version)) (sha256 (base32 "0a8dhzlna79ggyhfr0nncgh15a9n6r0dsz664pz0ah323wpblqqf")))) (build-system r-build-system) (home-page "https://github.com/krlmlr/plogr") (synopsis "R bindings for the plog C++ logging library") (description "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.") (license license:expat))) (define-public r-pls (package (name "r-pls") (version "2.8-3") (source (origin (method url-fetch) (uri (cran-uri "pls" version)) (sha256 (base32 "1qvbwr567vxywpfsl7cb15lpwxpd04kf01nzk1v8dm4csf6p5sz6")))) (build-system r-build-system) (home-page "https://mevik.net/work/software/pls.html") (synopsis "Partial Least Squares and Principal Component Regression") (description "The pls package implements multivariate regression methods: Partial Least Squares Regression (@dfn{PLSR}), Principal Component Regression (@dfn{PCR}), and Canonical Powered Partial Least Squares (@dfn{CPPLS}). It supports: @itemize @item several algorithms: the traditional orthogonal scores (@dfn{NIPALS}) PLS algorithm, kernel PLS, wide kernel PLS, Simpls, and PCR through @code{svd} @item multi-response models (or @dfn{PLS2}) @item flexible cross-validation @item Jackknife variance estimates of regression coefficients @item extensive and flexible plots: scores, loadings, predictions, coefficients, (R)MSEP, R², and correlation loadings @item formula interface, modelled after @code{lm()}, with methods for predict, print, summary, plot, update, etc. @item extraction functions for coefficients, scores, and loadings @item MSEP, RMSEP, and R² estimates @item multiplicative scatter correction (@dfn{MSC}) @end itemize\n") (license license:gpl2))) (define-public r-ps (package (name "r-ps") (version "1.7.6") (source (origin (method url-fetch) (uri (cran-uri "ps" version)) (sha256 (base32 "1lkd0mxr65sfh47dig0ck530kmsaxxqxdfy7ji59h78y7py5zhsj")))) (build-system r-build-system) (home-page "https://ps.r-lib.org") (synopsis "List, query, and manipulate system processes") (description "The ps package implements an API to list, query, and manipulate system processes. Most of its code is based on the @code{psutil} Python package.") (license license:bsd-3))) (define-public r-pkgbuild (package (name "r-pkgbuild") (version "1.4.4") (source (origin (method url-fetch) (uri (cran-uri "pkgbuild" version)) (sha256 (base32 "1a72s2gg7ddjj94naiii44f3vyhky05gaa6xvdf72m1nshy88wjr")))) (build-system r-build-system) (propagated-inputs (list r-callr r-cli r-desc r-processx r-r6)) (home-page "https://github.com/r-pkgs/pkgbuild") (synopsis "Find tools needed to build R packages") (description "This package provides functions used to build R packages. It locates compilers needed to build R packages on various platforms and ensures the PATH is configured appropriately so R can use them.") (license license:gpl3))) (define-public r-pkgload (package (name "r-pkgload") (version "1.3.4") (source (origin (method url-fetch) (uri (cran-uri "pkgload" version)) (sha256 (base32 "1ki6k7l7dpb6bncvvcndrv5764jb1adrzs5iaxicakfsija4pc30")))) (build-system r-build-system) (propagated-inputs (list r-cli r-crayon r-desc r-fs r-glue r-pkgbuild r-rlang r-rprojroot r-withr)) (home-page "https://github.com/r-lib/pkgload") (synopsis "Simulate package installation and attach") (description "This package simulates the process of installing a package and then attaching it. This is a key part of the @code{devtools} package as it allows you to rapidly iterate while developing a package.") (license license:gpl3))) (define-public r-pki (package (name "r-pki") (version "0.1-12") (source (origin (method url-fetch) (uri (cran-uri "PKI" version)) (sha256 (base32 "0nidg6l9nrmpyimi502fydy22r247w9i4ngb2xdbxjvfhr17m0xd")))) (properties `((upstream-name . "PKI"))) (build-system r-build-system) (inputs (list openssl zlib)) (propagated-inputs (list r-base64enc)) (native-inputs (list pkg-config)) (home-page "http://www.rforge.net/PKI") (synopsis "Public Key Infrastucture for R based on the X.509 standard") (description "This is a package containing Public Key Infrastucture functions such as verifying certificates, RSA encryption and signing, which can be used to build PKI infrastructure and perform cryptographic tasks.") ;; Either of these licenses. (license (list license:gpl2 license:gpl3)))) (define-public r-pvclust (package (name "r-pvclust") (version "2.2-0") (source (origin (method url-fetch) (uri (cran-uri "pvclust" version)) (sha256 (base32 "0082icm54k2yq60k06qpr92a626k39j2jr0046lva4ylmhxqb4kq")))) (build-system r-build-system) (home-page "https://github.com/shimo-lab/pvclust") (synopsis "Hierarchical clustering with P-values via multiscale bootstrap resampling") (description "This package provides an implementation of multiscale bootstrap resampling for assessing the uncertainty in hierarchical cluster analysis. It provides an AU (approximately unbiased) P-value as well as a BP (bootstrap probability) value for each cluster in a dendrogram.") (license license:gpl2+))) (define-public r-rcpp (package (name "r-rcpp") (version "1.0.12") (source (origin (method url-fetch) (uri (cran-uri "Rcpp" version)) (sha256 (base32 "1l1b0q2r6q2bjr4wvj98kp9844fyrsn2ppx339v05vmy8g65jwqc")))) (build-system r-build-system) (home-page "https://www.rcpp.org") (synopsis "Seamless R and C++ integration") (description "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 @code{Rcpp Gallery} site at , the paper by Eddelbuettel and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see @code{citation(\"Rcpp\")} for details on these last two.") (license license:gpl2+))) (define-public r-rcppde (package (name "r-rcppde") (version "0.1.7") (source (origin (method url-fetch) (uri (cran-uri "RcppDE" version)) (sha256 (base32 "1846pl9gxikycdvwfgy1gw41z0fx4ycjp5p4295v8k2pgvlqw8sa")))) (properties `((upstream-name . "RcppDE"))) (build-system r-build-system) (propagated-inputs (list r-rcpp r-rcpparmadillo)) (home-page "https://cran.r-project.org/package=RcppDE") (synopsis "Global optimization by differential evolution in C++") (description "This package provides an iteration of the @code{DEoptim} function. It performs global optimization by differential evolution.") (license license:gpl2+))) (define-public r-rcppdist (package (name "r-rcppdist") (version "0.1.1") (source (origin (method url-fetch) (uri (cran-uri "RcppDist" version)) (sha256 (base32 "02g57xwfipdcljv06krhm02dbqn9kfyj2km6rdg0a7vq9prwdz1x")))) (properties `((upstream-name . "RcppDist"))) (build-system r-build-system) (propagated-inputs (list r-rcpp r-rcpparmadillo)) (native-inputs (list r-knitr)) (home-page "https://github.com/duckmayr/RcppDist") (synopsis "Integration of additional probability distributions") (description "RcppDist provides a header-only C++ library with functions for additional statistical distributions that can be called from C++ when writing code using Rcpp or RcppArmadillo. Functions are available that return a @code{NumericVector} as well as doubles, and for multivariate or matrix distributions, Armadillo vectors and matrices.") (license license:gpl2+))) (define-public r-rcppml (package (name "r-rcppml") (version "0.3.7") (source (origin (method url-fetch) (uri (cran-uri "RcppML" version)) (sha256 (base32 "1ih8i7i6m221iw227mnl3rvnaw2l53h8fpnc4f8yn9sm10anap1j")))) (properties `((upstream-name . "RcppML"))) (build-system r-build-system) (propagated-inputs (list r-matrix r-rcpp r-rcppeigen)) (native-inputs (list r-knitr)) (home-page "https://github.com/zdebruine/RcppML") (synopsis "Rcpp machine learning library") (description "This package provides fast machine learning algorithms including matrix factorization and divisive clustering for large sparse and dense matrices.") (license license:gpl2+))) (define-public r-rcppspdlog (package (name "r-rcppspdlog") (version "0.0.16") (source (origin (method url-fetch) (uri (cran-uri "RcppSpdlog" version)) (sha256 (base32 "12xryg2mp00nxmpchf0lki43c13c1vsda14pcc4dcfplamwkhlza")))) (properties `((upstream-name . "RcppSpdlog"))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) (native-inputs (list r-simplermarkdown)) (home-page "https://github.com/eddelbuettel/rcppspdlog") (synopsis "R and C++ interfaces to spdlog C++ header library for logging") (description "The spdlog library is a widely-used and very capable header-only C++ library for logging. This package includes its headers as an R package to permit other R packages to deploy it via a simple @code{LinkingTo: RcppSpdlog}. As of version 0.0.9, it also provides both simple R logging functions and compiled functions callable by other packages.") (license license:gpl2+))) (define-public r-rcppthread (package (name "r-rcppthread") (version "2.1.7") (source (origin (method url-fetch) (uri (cran-uri "RcppThread" version)) (sha256 (base32 "1s5v4fa59gmjcd0cn7q7zy67ww9zwnly4apbgr87x9qkzgzbmpl8")))) (properties `((upstream-name . "RcppThread"))) (build-system r-build-system) (native-inputs (list r-r-rsp)) (home-page "https://github.com/tnagler/RcppThread") (synopsis "R threading in C++") (description "This package provides a C++11-style thread class and thread pool that can safely be interrupted from R.") (license license:expat))) (define-public r-rcppnumerical (package (name "r-rcppnumerical") (version "0.6-0") (source (origin (method url-fetch) (uri (cran-uri "RcppNumerical" version)) (sha256 (base32 "11nph9fz1bzb0pcvh6xx4cb94090ahwpj21zmbi06m4pibb1a1rg")))) (build-system r-build-system) (propagated-inputs (list r-rcpp r-rcppeigen)) (native-inputs (list r-knitr r-rmarkdown)) (home-page "https://github.com/yixuan/RcppNumerical") (synopsis"Numerical computing libraries integration with @code{Rcpp}") (description "This package provides a collection of libraries for numerical computing (numerical integration, optimization, etc.) and their integration with @code{Rcpp}.") (license license:gpl2+))) (define-public r-rcppxptrutils (package (name "r-rcppxptrutils") (version "0.1.2") (source (origin (method url-fetch) (uri (cran-uri "RcppXPtrUtils" version)) (sha256 (base32 "0hm57nf4dzgsmg4hjj6wikwjx93fgfwkmybw6ly4b58wi6qwml1l")))) (properties `((upstream-name . "RcppXPtrUtils"))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) (home-page "https://github.com/Enchufa2/RcppXPtrUtils") (synopsis "XPtr add-ons for Rcpp") (description "This package provides the means to compile user-supplied C++ functions with Rcpp and retrieve an @code{XPtr} that can be passed to other C++ components.") (license license:expat))) (define-public r-bb (package (name "r-bb") (version "2019.10-1") (source (origin (method url-fetch) (uri (cran-uri "BB" version)) (sha256 (base32 "0kf9sfsm3n036a8a8gjfpc9qdryvadb019kqjh80n1szdv7bdl04")))) (properties `((upstream-name . "BB"))) (build-system r-build-system) (propagated-inputs (list r-quadprog)) (home-page "https://publichealth.jhu.edu/") (synopsis "Solving and optimizing large-scale nonlinear systems") (description "This package implements Barzilai-Borwein spectral methods for solving nonlinear system of equations, and for optimizing nonlinear objective functions subject to simple constraints.") (license license:gpl3))) (define-public r-bindr (package (name "r-bindr") (version "0.1.1") (source (origin (method url-fetch) (uri (cran-uri "bindr" version)) (sha256 (base32 "1l05fpk2yql3jka321c0bdgx6mqq9pvfrg2844lbjfpbgjkmqy3w")))) (build-system r-build-system) (home-page "https://github.com/krlmlr/bindr") (synopsis "Parametrized active bindings") (description "This package provides a simple interface for creating active bindings where the bound function accepts additional arguments.") (license license:expat))) (define-public r-bindrcpp (package (name "r-bindrcpp") (version "0.2.3") (source (origin (method url-fetch) (uri (cran-uri "bindrcpp" version)) (sha256 (base32 "1yn9is89r76ay314s216whr0igych4r78kjz85amhwgfb9wawbb6")))) (build-system r-build-system) (propagated-inputs (list r-bindr r-plogr r-rcpp)) (home-page "https://github.com/krlmlr/bindrcpp") (synopsis "Rcpp interface to active bindings") (description "This package provides an easy way to fill an environment with active bindings that call a C++ function.") (license license:expat))) (define-public r-auc (package (name "r-auc") (version "0.3.2") (source (origin (method url-fetch) (uri (cran-uri "AUC" version)) (sha256 (base32 "07xf47kypqbsg2mixmq6mnh4s89aqan9bgl6kfv6lbx8ajv2asw3")))) (properties `((upstream-name . "AUC"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/AUC") (synopsis "Compute the area under the curve of selected measures") (description "This package includes functions to compute the area under the curve of selected measures: the area under the sensitivity curve (AUSEC), the area under the specificity curve (AUSPC), the area under the accuracy curve (AUACC), and the area under the receiver operating characteristic curve (AUROC). The curves can also be visualized. Support for partial areas is provided.") (license license:gpl2+))) (define-public r-calibrate (package (name "r-calibrate") (version "1.7.7") (source (origin (method url-fetch) (uri (cran-uri "calibrate" version)) (sha256 (base32 "19kgrnsyq67iqv1biyssqi30a6v2836ql20nabpy2m692ns0jfvi")))) (build-system r-build-system) (propagated-inputs (list r-mass)) (home-page "https://cran.r-project.org/web/packages/calibrate") (synopsis "Calibration of scatterplot and biplot axes") (description "This is a package for drawing calibrated scales with tick marks on (non-orthogonal) variable vectors in scatterplots and biplots.") (license license:gpl2))) (define-public r-shape (package (name "r-shape") (version "1.4.6.1") (source (origin (method url-fetch) (uri (cran-uri "shape" version)) (sha256 (base32 "1912znpk85j8c01s4m2f7x8rcqwski8b5n7g70cczmkzk47vvya3")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/shape") (synopsis "Functions for plotting graphical shapes") (description "This package provides functions for plotting graphical shapes such as ellipses, circles, cylinders, arrows, ...") (license license:gpl3+))) (define-public r-globaloptions (package (name "r-globaloptions") (version "0.1.2") (source (origin (method url-fetch) (uri (cran-uri "GlobalOptions" version)) (sha256 (base32 "0gkm77w6db9ajyncy1xdcivplap06a51zi99m009kylccschd2a7")))) (properties `((upstream-name . "GlobalOptions"))) (build-system r-build-system) (native-inputs (list r-knitr)) (home-page "https://github.com/jokergoo/GlobalOptions") (synopsis "Generate functions to get or set global options") (description "This package provides more controls on the option values such as validation and filtering on the values, making options invisible or private.") (license license:gpl2+))) (define-public r-circlize (package (name "r-circlize") (version "0.4.16") (source (origin (method url-fetch) (uri (cran-uri "circlize" version)) (sha256 (base32 "0rqbcmmp4h1jjl0y59bzn6k8kywjdqwvp0ajkqxd21j9f33k5p0n")))) (build-system r-build-system) (propagated-inputs (list r-colorspace r-globaloptions r-shape)) (native-inputs (list r-knitr)) (home-page "https://github.com/jokergoo/circlize") (synopsis "Circular visualization") (description "Circular layout is an efficient way to visualise huge amounts of information. This package provides an implementation of circular layout generation in R as well as an enhancement of available software. Its flexibility is based on the usage of low-level graphics functions such that self-defined high-level graphics can be easily implemented by users for specific purposes. Together with the seamless connection between the powerful computational and visual environment in R, it gives users more convenience and freedom to design figures for better understanding complex patterns behind multi-dimensional data.") (license license:gpl2+))) (define-public r-rcircos (package (name "r-rcircos") (version "1.2.2") (source (origin (method url-fetch) (uri (cran-uri "RCircos" version)) (sha256 (base32 "1z0aam60p1b6q7csn50rrwdilm07myr05bw54s9ah8idzyxc7gav")))) (properties `((upstream-name . "RCircos"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/RCircos/") (synopsis "Circos 2D track plot") (description "This package provides a simple and flexible way to generate Circos 2D track plot images. The types of plots include: heatmap, histogram, lines, scatterplot, tiles and plot items for further decorations include connector, link (lines and ribbons), and text (gene) label. All functions require only R graphics packages that comes with the base installation.") (license license:gpl2+))) (define-public r-ctrdata (package (name "r-ctrdata") (version "1.17.2") (source (origin (method url-fetch) (uri (cran-uri "ctrdata" version)) (sha256 (base32 "0xsi3yc08gg9h5zh9h9r2d2ixv36f6wblmkcv51h9nfmawjyd8f8")))) (properties `((upstream-name . "ctrdata"))) (build-system r-build-system) (propagated-inputs (list r-clipr r-curl r-digest r-dplyr r-httr r-jqr r-jsonlite r-lubridate r-nodbi r-readr r-stringi r-tibble r-v8 r-xml2 r-zip)) (native-inputs (list r-r-rsp)) (home-page "https://cran.r-project.org/package=ctrdata") (synopsis "Retrieve and analyze clinical trials in public registers") (description "This package provides a system for querying, retrieving and analyzing protocol- and results-related information on clinical trials from three public registers, the European Union Clinical Trials Register (EUCTR), ClinicalTrials.gov (CTGOV) and the ISRCTN. Trial information is downloaded, converted and stored in a database. Functions are included to identify deduplicated records, to easily find and extract variables (fields) of interest even from complex nesting as used by the registers, and to update previous queries. The package can be used for meta-analysis and trend-analysis of the design and conduct as well as for results of clinical trials.") (license license:expat))) (define-public r-ctrialsgov (package (name "r-ctrialsgov") (version "0.2.5") (source (origin (method url-fetch) (uri (cran-uri "ctrialsgov" version)) (sha256 (base32 "0hdh1fdfaja8amf7fkvk1c6yif703132bvacq0j9pk5jr97czgpw")))) (properties `((upstream-name . "ctrialsgov"))) (build-system r-build-system) (propagated-inputs (list r-dbi r-dplyr r-ggplot2 r-htmlwidgets r-lubridate r-matrix r-plotly r-purrr r-rlang r-stringi r-tibble)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/package=ctrialsgov") (synopsis "Query data from U.S. National Library of Medicine's Clinical Trials Database") (description "This package provides tools to query the U.S. National Library of Medicine's Clinical Trials database. Functions are provided for a variety of techniques for searching the data using range queries, categorical filtering, and by searching for full-text keywords. Minimal graphical tools are also provided for interactively exploring the constructed data.") (license license:expat))) (define-public r-powerlaw (package (name "r-powerlaw") (version "0.80.0") (source (origin (method url-fetch) (uri (cran-uri "poweRlaw" version)) (sha256 (base32 "1jvj2x22h6px1rcxmpz9h3x8r4486sb8zl3hjrsdxqa73ypmcdbi")))) (properties `((upstream-name . "poweRlaw"))) (build-system r-build-system) (propagated-inputs (list r-pracma)) (native-inputs (list r-knitr)) (home-page "https://github.com/csgillespie/poweRlaw") (synopsis "Tools for the analysis of heavy tailed distributions") (description "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.") ;; Any of these GPL versions. (license (list license:gpl2 license:gpl3)))) (define-public r-ptw (package (name "r-ptw") (version "1.9-16") (source (origin (method url-fetch) (uri (cran-uri "ptw" version)) (sha256 (base32 "0rma3h9ksc5qigdvk5vappb4ipd4rpk64wckzcxvxspakr5w71vy")))) (properties `((upstream-name . "ptw"))) (build-system r-build-system) (propagated-inputs (list r-rcppde)) (home-page "https://github.com/rwehrens/ptw") (synopsis "Parametric time warping") (description "Parametric time warping aligns patterns. It aims to put corresponding features at the same locations. The algorithm searches for an optimal polynomial describing the warping. It is possible to align one sample to a reference, several samples to the same reference, or several samples to several references. One can choose between calculating individual warpings, or one global warping for a set of samples and one reference. Two optimization criteria are implemented: @acronym{RMS, Root Mean Square} error and @acronym{WCC, Weighted Cross Correlation}. Both warping of peak profiles and of peak lists are supported.") (license license:gpl2+))) (define-public r-compare (package (name "r-compare") (version "0.2-6") (source (origin (method url-fetch) (uri (cran-uri "compare" version)) (sha256 (base32 "0k9zms930b5dz9gy8414li21wy0zg9x9vp7301v5cvyfi0g7xzgw")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/compare") (synopsis "Comparing objects for differences") (description "This package provides functions to compare a model object to a comparison object. If the objects are not identical, the functions can be instructed to explore various modifications of the objects (e.g., sorting rows, dropping names) to see if the modified versions are identical.") (license license:gpl2+))) (define-public r-dendextend (package (name "r-dendextend") (version "1.17.1") (source (origin (method url-fetch) (uri (cran-uri "dendextend" version)) (sha256 (base32 "08g5z5qyrn2nkw1jw5520sval4jf9l6invqwvzsv8dkjkq8nxsc7")))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-magrittr r-viridis)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/dendextend") (synopsis "Extending 'dendrogram' functionality in R") (description "This package offers a set of functions for extending @code{dendrogram} objects in R, letting you visualize and compare trees of hierarchical clusterings. You can adjust a tree's graphical parameters (the color, size, type, etc of its branches, nodes and labels) and visually and statistically compare different dendrograms to one another.") ;; Any of these versions (license (list license:gpl2 license:gpl3)))) (define-public r-dendsort (package (name "r-dendsort") (version "0.3.4") (source (origin (method url-fetch) (uri (cran-uri "dendsort" version)) (sha256 (base32 "0rs7y471wrhkgibxdmfh5xhp3pa004rrlm2w08b6qli5gq4im5d2")))) (properties `((upstream-name . "dendsort"))) (build-system r-build-system) (native-inputs (list r-knitr)) (home-page "https://github.com/evanbiederstedt/dendsort") (synopsis "Modular leaf ordering methods for dendrogram nodes") (description "This package represents an implementation of functions to optimize ordering of nodes in a dendrogram, without affecting the meaning of the dendrogram. A dendrogram can be sorted based on the average distance of subtrees, or based on the smallest distance value. These sorting methods improve readability and interpretability of tree structure, especially for tasks such as comparison of different distance measures or linkage types and identification of tight clusters and outliers. As a result, it also introduces more meaningful reordering for a coupled heatmap visualization.") ;; Any of these versions (license (list license:gpl2 license:gpl3)))) (define-public r-getoptlong (package (name "r-getoptlong") (version "1.0.5") (source (origin (method url-fetch) (uri (cran-uri "GetoptLong" version)) (sha256 (base32 "00fpm6nd3kqa2ikasxa62jzywi46fvvmx1mdavcp5yrxxn37j8wc")))) (properties `((upstream-name . "GetoptLong"))) (build-system r-build-system) (inputs (list perl)) (propagated-inputs (list r-crayon r-globaloptions r-rjson)) (native-inputs (list r-knitr)) (home-page "https://github.com/jokergoo/GetoptLong") (synopsis "Parsing command-line arguments and variable interpolation") (description "This is yet another command-line argument parser which wraps the powerful Perl module @code{Getopt::Long} and with some adaptation for easier use in R. It also provides a simple way for variable interpolation in R.") (license license:gpl2+))) (define-public r-fastmatch (package (name "r-fastmatch") (version "1.1-4") (source (origin (method url-fetch) (uri (cran-uri "fastmatch" version)) (sha256 (base32 "0symkcmyrqvz6hkawr40ga808rb3w4hy9ssfsi5ri8hykjn4r4cs")))) (build-system r-build-system) (home-page "https://www.rforge.net/fastmatch") (synopsis "Fast match function") (description "This package provides a fast @code{match} replacement for cases that require repeated look-ups. It is slightly faster that R's built-in @code{match} function on first match against a table, but extremely fast on any subsequent lookup as it keeps the hash table in memory.") (license license:gpl2))) (define-public r-ff (package (name "r-ff") (version "4.0.12") (source (origin (method url-fetch) (uri (cran-uri "ff" version)) (sha256 (base32 "1gs1zf3x0clnim7qlrkhlsjf2xgry5ybqnh8ipa2kzhhk9d3bbq8")))) (build-system r-build-system) (propagated-inputs (list r-bit)) (home-page "https://ff.r-forge.r-project.org/") (synopsis "Memory-efficient storage of large data on disk and access functions") (description "This package provides data structures that are stored on disk but behave (almost) as if they were in RAM by transparently mapping only a section in main memory.") ;; error Architecture not supported. (supported-systems (delete "aarch64-linux" %supported-systems)) (license license:gpl2))) (define-public r-ffbase (package (name "r-ffbase") (version "0.13.3") (source (origin (method url-fetch) (uri (cran-uri "ffbase" version)) (sha256 (base32 "1dp6lblfq2j7r1b4b8ls47jlx8j27n88d5vp8w116lb8pa01zxmk")))) (build-system r-build-system) (arguments (list #:phases '(modify-phases %standard-phases ;; R 4.3.0 removed the typedef for Sint, which used to be just int. (add-after 'unpack 'r-compatibility (lambda _ (substitute* '("src/grouprunningcumsum.c" "src/grouprunningcumsumindex.c") (("\\bSint ") "int "))))))) (propagated-inputs (list r-bit r-fastmatch r-ff)) (home-page "https://github.com/edwindj/ffbase") (synopsis "Basic statistical functions for package 'ff'") (description "This package extends the out of memory vectors of @code{ff} with statistical functions and other utilities to ease their usage.") (license license:gpl3))) (define-public r-prettyunits (package (name "r-prettyunits") (version "1.2.0") (source (origin (method url-fetch) (uri (cran-uri "prettyunits" version)) (sha256 (base32 "1smcxrfsz6cxym9h8iaiqrrw5bzp2bbpmf05zr8y70jw59zg4ngh")))) (build-system r-build-system) (home-page "https://github.com/gaborcsardi/prettyunits") (synopsis "Pretty, human readable formatting of quantities") (description "This package provides tools for pretty, human readable formatting of quantities.") (license license:expat))) (define-public r-princurve (package (name "r-princurve") (version "2.1.6") (source (origin (method url-fetch) (uri (cran-uri "princurve" version)) (sha256 (base32 "0wzk329bxljkzz57y220lsfckpsn45w348m6dcxh29zbj0ik65h2")))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) (home-page "https://github.com/rcannood/princurve") (synopsis "Fit a principal curve in arbitrary dimension") (description "This package provides procedures for fitting a principal curve to a data matrix in arbitrary dimensions.") (license license:gpl2))) (define-public r-prismatic (package (name "r-prismatic") (version "1.1.2") (source (origin (method url-fetch) (uri (cran-uri "prismatic" version)) (sha256 (base32 "0qg2f5d7sz6q0ijrrdmjhp1msx9n77wndphrqqhjkdf9six5pgxs")))) (properties `((upstream-name . "prismatic"))) (build-system r-build-system) (propagated-inputs (list r-farver)) (home-page "https://github.com/EmilHvitfeldt/prismatic") (synopsis "Color manipulation tools") (description "Manipulate and visualize colors in a intuitive, low-dependency and functional way.") (license license:expat))) (define-public r-reshape (package (name "r-reshape") (version "0.8.9") (source (origin (method url-fetch) (uri (cran-uri "reshape" version)) (sha256 (base32 "0j203qmc076x5lp6q2xi4dq4xdb73jmsa42rpxp1c37knnrph4br")))) (build-system r-build-system) (propagated-inputs (list r-plyr)) (home-page "http://had.co.nz/reshape") (synopsis "Flexibly reshape data") (description "Flexibly restructure and aggregate data using just two functions: @code{melt} and @code{cast}. This package provides them.") (license license:expat))) (define-public r-restrserve (package (name "r-restrserve") (version "1.2.2") (source (origin (method url-fetch) (uri (cran-uri "RestRserve" version)) (sha256 (base32 "0jbzalk17jg4qm99005q69pyk76c0wjvdwzjp25npzcvlbsxa194")))) (build-system r-build-system) (propagated-inputs (list r-checkmate r-digest r-jsonlite r-mime r-r6 r-rcpp r-rserve r-uuid)) (native-inputs (list r-knitr)) (home-page "https://restrserve.org") (synopsis "R web API framework") (description "RestRserve is an R web API framework for building high-performance AND robust microservices and app backends. With Rserve backend on UNIX-like systems it is parallel by design. It will handle incoming requests in parallel - each request in a separate fork.") (license license:gpl2+))) (define-public r-progress (package (name "r-progress") (version "1.2.3") (source (origin (method url-fetch) (uri (cran-uri "progress" version)) (sha256 (base32 "0xljky4ad2jbbcfrcyh48li461pc5b2wk210n4x5rs2di6dhfaza")))) (build-system r-build-system) (propagated-inputs (list r-crayon r-hms r-prettyunits r-r6)) (home-page "https://github.com/gaborcsardi/progress") (synopsis "Terminal progress bars") (description "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.") (license license:expat))) (define-public r-ggally (package (name "r-ggally") (version "2.2.1") (source (origin (method url-fetch) (uri (cran-uri "GGally" version)) (sha256 (base32 "1il6yphqxcyj1039imi8pn6ygyni24daz8ljxxp3z9inb5k2dcwb")))) (properties `((upstream-name . "GGally"))) (build-system r-build-system) (inputs (list openssl)) (propagated-inputs (list r-dplyr r-ggplot2 r-ggstats r-gtable r-lifecycle r-magrittr r-plyr r-progress r-rcolorbrewer r-rlang r-scales r-tidyr)) (home-page "https://ggobi.github.io/ggally") (synopsis "Extension to ggplot2") (description "The R package ggplot2 is a plotting system based on the grammar of graphics. GGally extends ggplot2 by adding several functions to reduce the complexity of combining geometric objects with transformed data. Some of these functions include a pairwise plot matrix, a two group pairwise plot matrix, a parallel coordinates plot, a survival plot, and several functions to plot networks.") (license license:gpl2+))) (define-public r-proxy (package (name "r-proxy") (version "0.4-27") (source (origin (method url-fetch) (uri (cran-uri "proxy" version)) (sha256 (base32 "0gsng2aggnljl4z82la9hpnd26hngzhj8fizx4wx22npqjj93694")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/proxy") (synopsis "Distance and similarity measures") (description "This package provides an extensible framework for the efficient calculation of auto- and cross-proximities, along with implementations of the most popular ones.") (license license:gpl2))) (define-public r-sp (package (name "r-sp") (version "2.1-3") (source (origin (method url-fetch) (uri (cran-uri "sp" version)) (sha256 (base32 "0m44qr2l8xmqbgi95h200bwy9ca8jihiqzfarws1p09lwmr954zs")))) (build-system r-build-system) (propagated-inputs (list r-lattice)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/sp") (synopsis "Classes and methods for spatial data") (description "This package provides classes and methods for spatial data; the classes document where the spatial location information resides, for 2D or 3D data. Utility functions are provided, e.g. for plotting data as maps, spatial selection, as well as methods for retrieving coordinates, for subsetting, print, summary, etc.") (license license:gpl2+))) (define-public r-lambertw (package (name "r-lambertw") (version "0.6.9-1") (source (origin (method url-fetch) (uri (cran-uri "LambertW" version)) (sha256 (base32 "19j6vjhywyzmrf7rsrx5kf0hg8cpk1gn8al24q813jzp0vsv9ljj")))) (properties `((upstream-name . "LambertW"))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-lamw r-mass r-rcolorbrewer r-rcpp r-reshape2)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/package=LambertW") (synopsis "Probabilistic models to analyze and Gaussianize heavy-tailed, skewed data") (description "Lambert W x F distributions are a generalized framework to analyze skewed, heavy-tailed data. It is based on an input/output system, where the output random variable (RV) Y is a non-linearly transformed version of an input RV X ~ F with similar properties as X, but slightly skewed (heavy-tailed). The transformed RV Y has a Lambert W x F distribution. This package contains functions to model and analyze skewed, heavy-tailed data the Lambert Way: simulate random samples, estimate parameters, compute quantiles, and plot/ print results nicely. The most useful function is @code{Gaussianize}, which works similarly to @code{scale}, but actually makes the data Gaussian. A do-it-yourself toolkit allows users to define their own Lambert W x @code{MyFavoriteDistribution} and use it in their analysis right away.") (license license:gpl2+))) (define-public r-lamw (package (name "r-lamw") (version "2.2.3") (source (origin (method url-fetch) (uri (cran-uri "lamW" version)) (sha256 (base32 "0jq3xq2ll4lpj8f5aqwazqlb978nzyk7hln4iwlzrlkkcqc35qm1")))) (properties `((upstream-name . "lamW"))) (build-system r-build-system) (propagated-inputs (list r-rcpp r-rcppparallel)) (home-page "https://github.com/aadler/lamW") (synopsis "Lambert-W function") (description "This package implements both real-valued branches of the Lambert-W function (Corless et al, 1996) without the need for installing the entire GSL.") (license license:bsd-2))) (define-public r-laplacesdemon (package (name "r-laplacesdemon") (version "16.1.6") (source (origin (method url-fetch) (uri (cran-uri "LaplacesDemon" version)) (sha256 (base32 "1dsfp65cg06f25zjzd5ib4qyn1alfhbhpgyvpcw5n6bszn13idap")))) (properties `((upstream-name . "LaplacesDemon"))) (build-system r-build-system) (home-page "https://github.com/LaplacesDemonR/LaplacesDemon") (synopsis "Complete environment for Bayesian inference") (description "This package provides a complete environment for Bayesian inference using a variety of different samplers.") (license license:expat))) (define-public r-rmdfiltr (package (name "r-rmdfiltr") (version "0.1.3") (source (origin (method url-fetch) (uri (cran-uri "rmdfiltr" version)) (sha256 (base32 "0llnn4pdfznidalm4f7fpyxbhzsqv1096fkbsl1pgf4f7ll6w7a7")))) (properties `((upstream-name . "rmdfiltr"))) (build-system r-build-system) (inputs (list pandoc)) (propagated-inputs (list r-assertthat r-rmarkdown)) (native-inputs (list r-knitr)) (home-page "https://github.com/crsh/rmdfiltr") (synopsis "Lua filters for R Markdown") (description "This package provides a collection of Lua filters that extend the functionality of R Markdown templates (e.g., count words or post-process citations).") (license license:expat))) (define-public r-rmtstat (package (name "r-rmtstat") (version "0.3.1") (source (origin (method url-fetch) (uri (cran-uri "RMTstat" version)) (sha256 (base32 "1r1a2sdqv64m9cpm2pz6r8abf7l810126ayd8iq3gx86c7bjfj5v")))) (properties `((upstream-name . "RMTstat"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/RMTstat") (synopsis "Distributions, statistics and tests derived from random matrix theory") (description "This package provides functions for working with the Tracy-Widom laws and other distributions related to the eigenvalues of large Wishart matrices.") (license license:bsd-3))) (define-public r-rmpi (package (name "r-rmpi") (version "0.7-2") (source (origin (method url-fetch) (uri (cran-uri "Rmpi" version)) (sha256 (base32 "1vrf6bakx9i73sdgggpxzl1lxjn68b8pwvmk69d56lnya2gzm4c5")))) (properties `((upstream-name . "Rmpi") (updater-extra-inputs . 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(license license:gpl2))) (define-public r-distillery (package (name "r-distillery") (version "1.2-1") (source (origin (method url-fetch) (uri (cran-uri "distillery" version)) (sha256 (base32 "1ymmxyamkq0zbz2m4gllln1ihks2hcib6gs0mls92as79srz122b")))) (build-system r-build-system) (home-page "https://ral.ucar.edu/staff/ericg/") (synopsis "Functions for confidence intervals and object information") (description "This package provides some very simple method functions for confidence interval calculation and to distill pertinent information from a potentially complex object; primarily used in common with the packages extRemes and SpatialVx.") (license license:gpl2+))) (define-public r-etrunct (package (name "r-etrunct") (version "0.1") (source (origin (method url-fetch) (uri (cran-uri "etrunct" version)) (sha256 (base32 "0ayazgyqlc8jcqr03cwfmfhm4pck6xri1r6vkgqy4arqkrrnrcqr")))) (properties `((upstream-name . 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"evd"))) (build-system r-build-system) (home-page "https://cran.r-project.org/package=evd") (synopsis "Functions for extreme value distributions") (description "This package extends simulation, distribution, quantile and density functions to univariate and multivariate parametric extreme value distributions, and provides fitting functions which calculate maximum likelihood estimates for univariate and bivariate maxima models, and for univariate and bivariate threshold models.") (license license:gpl3))) (define-public r-evmix (package (name "r-evmix") (version "2.12") (source (origin (method url-fetch) (uri (cran-uri "evmix" version)) (sha256 (base32 "02rabc9snci00s1x7h0svfr66lmw1wjcdg0149wc52mnccsdaivf")))) (properties `((upstream-name . "evmix"))) (build-system r-build-system) (propagated-inputs (list r-gsl r-mass r-sparsem)) (home-page "http://www.math.canterbury.ac.nz/~c.scarrott/evmix.shtml") (synopsis "Extreme value threshold estimation and uncertainty quantification") (description "This package provides the usual distribution functions, maximum likelihood inference and model diagnostics for univariate stationary extreme value mixture models. Also, there are provided kernel density estimation including various boundary corrected kernel density estimation methods and a wide choice of kernels, with cross-validation likelihood based bandwidth estimator. Reasonable consistency with the base functions in the evd package is provided, so that users can safely interchange most code.") (license license:gpl3))) ;; This package contains minified JavaScript: jExcel CE Spreadsheet, ;; version 3.9.1. It is not clear how to obtain this particular ;; version as there is no tag for 3.9.1. There only is 3.6.1 and ;; 4.2.0 at https://github.com/jspreadsheet/ce. (define-public r-excelr (package (name "r-excelr") (version "0.4.0") (source (origin (method url-fetch) (uri (cran-uri "excelR" version)) (sha256 (base32 "1pb4sy54zjv5vrh7gjjv7qlpab74km6mfsmfyl0yhmr0jx01hrw0")) (snippet '(delete-file "inst/htmlwidgets/lib/jexcel/js/jexcel.min.js")))) (properties `((upstream-name . 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(let* ((commit "8af1960f76e6803bebc5750013d2ebe95354e88a") (version (git-version "3.9.1" "0" commit))) (origin (method git-fetch) (uri (git-reference (url "https://github.com/jspreadsheet/ce") (commit commit))) (file-name (git-file-name "jexcel" version)) (sha256 (base32 "1zk0wc4h0vax7zgimhwqq2icrvjr84agm3qv42l16gim7gq7fqfq")))))) (home-page "https://github.com/Swechhya/excelR") (synopsis "Wrapper of the JavaScript library jExcel") (description "This package provides an R interface to the jExcel library to create web-based interactive tables and spreadsheets compatible with spreadsheet software.") (license license:expat))) (define-public r-extremes (package (name "r-extremes") (version "2.1-4") (source (origin (method url-fetch) (uri (cran-uri "extRemes" version)) (sha256 (base32 "12mphdq9zi0r07x3gpj5dg4687hwnjx42d9a392rjbbsgvv2r96f")))) (properties `((upstream-name . "extRemes"))) (build-system r-build-system) (propagated-inputs (list r-distillery r-lmoments)) (home-page "https://www.assessment.ucar.edu/toolkit/") (synopsis "Extreme value analysis") (description "ExtRemes is a suite of functions for carrying out analyses on the extreme values of a process of interest; be they block maxima over long blocks or excesses over a high threshold.") (license license:gpl2+))) (define-public r-lmtest (package (name "r-lmtest") (version "0.9-40") (source (origin (method url-fetch) (uri (cran-uri "lmtest" version)) (sha256 (base32 "15yr2kx08wy085bnziqmj1p6hf9mg3qp2a8465jk2df6di6hsh34")))) (build-system r-build-system) (propagated-inputs (list r-zoo)) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/lmtest") (synopsis "Testing linear regression models") (description "This package provides a collection of tests, data sets, and examples for diagnostic checking in linear regression models. Furthermore, some generic tools for inference in parametric models are provided.") ;; Either version is okay (license (list license:gpl2 license:gpl3)))) (define-public r-idr (package (name "r-idr") (version "1.3") (source (origin (method url-fetch) (uri (cran-uri "idr" version)) (sha256 (base32 "1r6icxf0c0y9wvihwmkk5xqscr1qhacqk3w2076kjm2993f10fbb")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/idr/") (synopsis "Irreproducible discovery rate") (description "This is a package for estimating the copula mixture model and plotting correspondence curves in \"Measuring reproducibility of high-throughput experiments\" (2011), Annals of Applied Statistics, Vol. 5, No. 3, 1752-1779, by Li, Brown, Huang, and Bickel") (license license:gpl2+))) (define-public r-inext (package (name "r-inext") (version "3.0.1") (source (origin (method url-fetch) (uri (cran-uri "iNEXT" version)) (sha256 (base32 "1nf4jhwqx5im966qzq7si78c5q4jgsa73d74ya8q8aj02n49jcyy")))) (properties `((upstream-name . 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(license license:gpl3+))) (define-public r-inline (package (name "r-inline") (version "0.3.19") (source (origin (method url-fetch) (uri (cran-uri "inline" version)) (sha256 (base32 "1mcr9hgq6kkq03n7pkcccxa7vg8jma0q7lfxc5vvkc6snydk1s8f")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/inline") (synopsis "Functions to inline C, C++, Fortran function calls from R") (description "This package provides functionality to dynamically define R functions and S4 methods with inlined C, C++ or Fortran code supporting @code{.C} and @code{.Call} calling conventions.") ;; Any version of the LGPL. (license license:lgpl3+))) (define-public r-inum (package (name "r-inum") (version "1.0-5") (source (origin (method url-fetch) (uri (cran-uri "inum" version)) (sha256 (base32 "1gbbsffbzxjrgi8yw21fl35fsbx7ns8hdrhja50byfqvnghbg5p6")))) (build-system r-build-system) (propagated-inputs (list r-libcoin)) (home-page "https://cran.r-project.org/web/packages/inum/") (synopsis "Interval and enum-type representation of vectors") (description "This package provides an enum-type representation of vectors and representation of intervals, including a method of coercing variables in data frames.") (license license:gpl2))) (define-public r-invgamma (package (name "r-invgamma") (version "1.1") (source (origin (method url-fetch) (uri (cran-uri "invgamma" version)) (sha256 (base32 "12ga2y4wc9bc5zz6vimvxwgjpsx3ys3209nq63gscbw559ydxa5a")))) (properties `((upstream-name . 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This package modifies and extends the @code{mle} classes in the @code{stats4} package.") ;; Any version of the GPL (license license:gpl2+))) (define-public r-emdbook (package (name "r-emdbook") (version "1.3.13") (source (origin (method url-fetch) (uri (cran-uri "emdbook" version)) (sha256 (base32 "069w10i1590bcyzv4kfsg7wsr1yl9nlsyj6yvys088xll5z4n116")))) (build-system r-build-system) (propagated-inputs (list r-bbmle r-coda r-lattice r-mass r-plyr)) (home-page "https://www.math.mcmaster.ca/bolker/emdbook") (synopsis "Support functions and data for \"Ecological Models and Data\"") (description "This package provides auxiliary functions and data sets for \"Ecological Models and Data\", a book presenting maximum likelihood estimation and related topics for ecologists (ISBN 978-0-691-12522-0).") ;; Any GPL version (license (list license:gpl2 license:gpl3)))) (define-public r-lpsolve (package (name "r-lpsolve") (version "5.6.20") (source (origin (method url-fetch) (uri (cran-uri "lpSolve" version)) (sha256 (base32 "1nr1vjz6ma42kxbcay4g9j30r9srkbw79f06sdnc68sid2h0dziz")))) (properties `((upstream-name . 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("icu4c" "zlib")))) (build-system r-build-system) (arguments (list #:phases #~(modify-phases %standard-phases (add-after 'install 'install-executable (lambda _ (install-file "inst/bin/r" (string-append #$output "/bin"))))))) (inputs (list icu4c zlib)) (native-inputs (list r-simplermarkdown)) (home-page "https://github.com/eddelbuettel/littler") (synopsis "R at the command-line via r") (description "This package provides a scripting and command-line front-end is provided by r (aka littler) as a lightweight binary wrapper around the GNU R language and environment for statistical computing and graphics. While R can be used in batch mode, the r binary adds full support for both shebang-style scripting (i.e. using a hash-mark-exclamation-path expression as the first line in scripts) as well as command-line use in standard pipelines. In other words, r provides the R language without the environment.") (license license:gpl2+))) (define-public r-fitdistrplus (package (name "r-fitdistrplus") (version "1.1-11") (source (origin (method url-fetch) (uri (cran-uri "fitdistrplus" version)) (sha256 (base32 "0gdm06anjmihfj1d0yiqy36d887kmc0d8553pjl1f90bf4mly9r6")))) (build-system r-build-system) (propagated-inputs (list r-mass r-survival)) (native-inputs (list r-knitr)) (home-page "https://riskassessment.r-forge.r-project.org") (synopsis "Fitting a parametric distribution from data") (description "This package extends the @code{fitdistr} function of the MASS package with several functions to help the fit of a parametric distribution to non-censored or censored data. Censored data may contain left-censored, right-censored and interval-censored values, with several lower and upper bounds. In addition to @dfn{maximum likelihood estimation} (MLE), the package provides moment matching (MME), quantile matching (QME) and maximum goodness-of-fit estimation (MGE) methods (available only for non-censored data). Weighted versions of MLE, MME and QME are available.") (license license:gpl2+))) (define-public r-energy (package (name "r-energy") (version "1.7-11") (source (origin (method url-fetch) (uri (cran-uri "energy" version)) (sha256 (base32 "04b55ckmaqbnlpifg4w7smvly03kqycklvbg9x8d4yf902q8z7y2")))) (build-system r-build-system) (propagated-inputs (list r-boot r-gsl r-rcpp)) (home-page "https://cran.r-project.org/web/packages/energy") (synopsis "Multivariate inference via the energy of data") (description "This package provides e-statistics (energy) tests and statistics for multivariate and univariate inference, including distance correlation, one-sample, two-sample, and multi-sample tests for comparing multivariate distributions, are implemented. Measuring and testing multivariate independence based on distance correlation, partial distance correlation, multivariate goodness-of-fit tests, clustering based on energy distance, testing for multivariate normality, distance components (disco) for non-parametric analysis of structured data, and other energy statistics/methods are implemented.") (license license:gpl2+))) (define-public r-envstats (package (name "r-envstats") (version "2.8.1") (source (origin (method url-fetch) (uri (cran-uri "EnvStats" version)) (sha256 (base32 "19nnab201yalxbgpvpp5lkgqs0m17b5plsswmaxbvdv4mag2p58j")))) (properties `((upstream-name . 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It includes scripts reproducing analyses presented in the book \"EnvStats: An R Package for Environmental Statistics\" (Millard, 2013, Springer, ISBN 978-1-4614-8455-4, @url{https://link.springer.com/book/10.1007/978-1-4614-8456-1}).") (license license:gpl3+))) (define-public r-suntools (package (name "r-suntools") (version "1.0.0") (source (origin (method url-fetch) (uri (cran-uri "suntools" version)) (sha256 (base32 "1qlp0q2ckqg5v3yvbr98k3nr9awgg7ks0l1103nqvm1ssadv7ds2")))) (properties `((upstream-name . "suntools"))) (build-system r-build-system) (propagated-inputs (list r-sf)) (home-page "https://github.com/adokter/suntools/") (synopsis "Calculate sun position, sunrise, sunset, solar noon and twilight") (description "This package provides a set of convenient functions for calculating sun-related information, including the sun's position (elevation and azimuth), and the times of sunrise, sunset, solar noon, and twilight for any given geographical location on Earth. These calculations are based on equations provided by the National Oceanic & Atmospheric Administration (NOAA) as described in \"Astronomical Algorithms\" by Jean Meeus (1991). A resource for researchers and professionals working in fields such as climatology, biology, and renewable energy.") (license license:gpl3+))) (define-public r-suppdists (package (name "r-suppdists") (version "1.1-9.7") (source (origin (method url-fetch) (uri (cran-uri "SuppDists" version)) (sha256 (base32 "025b9nlxz62wk84295csyzbncpn80i3iby3sxdigf3swcgi2fmbb")))) (properties `((upstream-name . "SuppDists"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/SuppDists") (synopsis "Supplementary distributions") (description "This package provides ten distributions supplementing those built into R. Inverse Gauss, Kruskal-Wallis, Kendall's Tau, Friedman's chi squared, Spearman's rho, maximum F ratio, the Pearson product moment correlation coefficient, Johnson distributions, normal scores and generalized hypergeometric distributions. In addition two random number generators of George Marsaglia are included.") (license license:gpl2+))) (define-public r-kpmt (package (name "r-kpmt") (version "0.1.0") (source (origin (method url-fetch) (uri (cran-uri "kpmt" version)) (sha256 (base32 "15d26khc0v3kc1c7l1avqp48pfqmc6xj32029mv7myivr41ashk3")))) (properties `((upstream-name . "kpmt"))) (build-system r-build-system) (propagated-inputs (list r-matrixstats)) (home-page "https://cran.r-project.org/package=kpmt") (synopsis "Known population median test") (description "This package provides functions that implement the known population median test.") (license license:expat))) (define-public r-ksamples (package (name "r-ksamples") (version "1.2-10") (source (origin (method url-fetch) (uri (cran-uri "kSamples" version)) (sha256 (base32 "13ap5ggid3w3s3k5mzz1ir31j96hjg6msa2s1hcy66zv242wqrid")))) (properties `((upstream-name . "kSamples"))) (build-system r-build-system) (propagated-inputs (list r-suppdists)) (home-page "https://cran.r-project.org/web/packages/kSamples") (synopsis "K-Sample rank tests and their combinations") (description "This package provides tools to compares k samples using the Anderson-Darling test, Kruskal-Wallis type tests with different rank score criteria, Steel's multiple comparison test, and the Jonckheere-Terpstra (JT) test. It computes asymptotic, simulated or (limited) exact P-values, all valid under randomization, with or without ties, or conditionally under random sampling from populations, given the observed tie pattern. Except for Steel's test and the JT test it also combines these tests across several blocks of samples.") (license license:gpl2+))) (define-public r-cvst (package (name "r-cvst") (version "0.2-3") (source (origin (method url-fetch) (uri (cran-uri "CVST" version)) (sha256 (base32 "0bgk0d6w3dyhb5s30idnp6jpb3m8wf3b79wqlg127wwm0cird8pg")))) (properties `((upstream-name . "CVST"))) (build-system r-build-system) (propagated-inputs (list r-kernlab r-matrix)) (home-page "https://cran.r-project.org/web/packages/CVST") (synopsis "Fast cross-validation via sequential testing") (description "This package implements the fast cross-validation via sequential testing (CVST) procedure. CVST is an improved cross-validation procedure which uses non-parametric testing coupled with sequential analysis to determine the best parameter set on linearly increasing subsets of the data. Additionally to the CVST the package contains an implementation of the ordinary k-fold cross-validation with a flexible and powerful set of helper objects and methods to handle the overall model selection process. The implementations of the Cochran's Q test with permutations and the sequential testing framework of Wald are generic and can therefore also be used in other contexts.") (license license:gpl2+))) (define-public r-cvxr (package (name "r-cvxr") (version "1.0-12") (source (origin (method url-fetch) (uri (cran-uri "CVXR" version)) (sha256 (base32 "1igzi231rkqi7pc5ak8b29a8x7fry0yqs8vg2m4i5ab9jdm8fsp7")))) (properties `((upstream-name . 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Qhull does not support constrained Delaunay triangulations, or mesh generation of non-convex objects, but the package does include some R functions that allow for this. Currently the package only gives access to Delaunay triangulation and convex hull computation.") ;; The Qhull sources are included and are distributed under a custom ;; non-copyleft license. The R sources are released under GPL version 2. 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"statsExpressions"))) (build-system r-build-system) (propagated-inputs (list r-afex r-bayesfactor r-correlation r-datawizard r-dplyr r-effectsize r-glue r-insight r-magrittr r-parameters r-performance r-pmcmrplus r-purrr r-rlang r-tibble r-tidyr r-withr r-wrs2 r-zeallot)) (native-inputs (list r-knitr)) (home-page "https://indrajeetpatil.github.io/statsExpressions/") (synopsis "Dataframes and expressions with statistical details") (description "This package provides tools for creating detailed dataframes for common statistical approaches and tests. These include parametric, nonparametric, robust, and Bayesian t-test, one-way ANOVA, correlation analyses, contingency table analyses, and meta-analyses. The functions are pipe-friendly and provide a consistent syntax to work with tidy data. These dataframes additionally contain expressions with statistical details, and can be used in graphing packages. This package also forms the statistical processing backend for ggstatsplot.") (license license:gpl3))) (define-public r-strawr (package (name "r-strawr") (version "0.0.91") (source (origin (method url-fetch) (uri (cran-uri "strawr" version)) (sha256 (base32 "1nbcn20g3f3f5x9sscj3020n5h4iaphr70s90n2fz31vc4snzq2m")))) (properties `((upstream-name . "strawr"))) (build-system r-build-system) (inputs (list curl zlib)) (propagated-inputs (list r-rcpp)) (home-page "https://github.com/aidenlab/straw/tree/master/R") (synopsis "Fast implementation of reading / dumping of .hic files") (description "This package provides an API for efficient @file{.hic} file data extraction with programmatic matrix access. It doesn't store the pointer data for all the matrices, only the one queried, and currently it only supports matrices.") (license license:expat))) (define-public r-stringdist (package (name "r-stringdist") (version "0.9.12") (source (origin (method url-fetch) (uri (cran-uri "stringdist" version)) (sha256 (base32 "1i365vwjx8kk47wzry8d3zhzrlv51hn76s2ipk9vi121zx939171")))) (build-system r-build-system) (home-page "https://github.com/markvanderloo/stringdist") (synopsis "Approximate string matching and string distance functions") (description "This package implements an approximate string matching version of R's native @code{match} function. It can calculate various string distances based on edits (Damerau-Levenshtein, Hamming, Levenshtein, optimal string 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.") (license license:gpl3+))) (define-public r-uchardet (package (name "r-uchardet") (version "1.1.1") (source (origin (method url-fetch) (uri (cran-uri "uchardet" version)) (sha256 (base32 "0m3xy807smqdxhkhd9cwrcf3ljlyvfmnkd7831qzpgcadam2jcdj")))) (properties `((upstream-name . "uchardet"))) (build-system r-build-system) (native-inputs (list r-knitr)) (home-page "https://artemklevtsov.gitlab.io/uchardet") (synopsis "Universal character encoding detector") (description "This package provides R bindings to the uchardet encoding detector library from Mozilla. It takes a sequence of bytes in an unknown character encoding without any additional information, and attempts to get the encoding of the text. All return names of the encodings are iconv-compatible.") (license license:gpl2))) (define-public r-ucminf (package (name "r-ucminf") (version "1.2.1") (source (origin (method url-fetch) (uri (cran-uri "ucminf" version)) (sha256 (base32 "10ycpzxx73div9vpzmkhy524yd47kzmpl7ajpm248clsv6ivngpd")))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/ucminf/") (synopsis "General-purpose unconstrained non-linear optimization") (description "This package provides an implementation of an algorithm for general-purpose unconstrained non-linear optimization. The algorithm is of quasi-Newton type with BFGS updating of the inverse Hessian and soft line search with a trust region type monitoring of the input to the line search algorithm. The interface of @code{ucminf} is designed for easy interchange with the package @code{optim}.") (license license:gpl2+))) (define-public r-usedist (package (name "r-usedist") (version "0.4.0") (source (origin (method url-fetch) (uri (cran-uri "usedist" version)) (sha256 (base32 "0ddf1zcalbrn293qmr9kdzz3x16fzc4k1bwb1pjmwnspisqfi8kj")))) (properties `((upstream-name . "usedist"))) (build-system r-build-system) (home-page "https://cran.r-project.org/package=usedist") (synopsis "Distance matrix utilities") (description "This package provides functions to re-arrange, extract, and work with distances.") (license license:gpl3))) (define-public r-useful (package (name "r-useful") (version "1.2.6.1") (source (origin (method url-fetch) (uri (cran-uri "useful" version)) (sha256 (base32 "1gb9hqvbm6pr56dfqlsgz26lan7xargfsm8jpdja18mpgli2gyvc")))) (properties `((upstream-name . "useful"))) (build-system r-build-system) (propagated-inputs (list r-assertthat r-dplyr r-ggplot2 r-magrittr r-matrix r-plyr r-purrr r-scales)) (home-page "https://github.com/jaredlander/useful") (synopsis "Collection of handy, useful functions") (description "This package provides a set of little functions that have been found useful to do little odds and ends such as plotting the results of K-means clustering, substituting special text characters, viewing parts of a @code{data.frame}, constructing formulas from text and building design and response matrices.") (license license:bsd-3))) (define-public r-ordinal (package (name "r-ordinal") (version "2023.12-4") (source (origin (method url-fetch) (uri (cran-uri "ordinal" version)) (sha256 (base32 "18lzpmf36vvc3krk7jqz7naikhrcdyplj2z9y6xgzlnzhgcjln7m")))) (build-system r-build-system) (propagated-inputs (list r-mass r-matrix r-nlme r-numderiv r-ucminf)) (home-page "https://github.com/runehaubo/ordinal") (synopsis "Regression models for ordinal data") (description "This package provides an implementation of cumulative link (mixed) models also known as ordered regression models, proportional odds models, proportional hazards models for grouped survival times and ordered models. Estimation is via maximum likelihood and mixed models are fitted with the Laplace approximation and adaptive Gauss-Hermite quadrature.") (license license:gpl2+))) (define-public r-jomo (package (name "r-jomo") (version "2.7-6") (source (origin (method url-fetch) (uri (cran-uri "jomo" version)) (sha256 (base32 "1np2sw0kq21kdhkv227pz2rqvpxg06r3mk93ggkrz5nl45ajmyiz")))) (build-system r-build-system) (propagated-inputs (list r-lme4 r-mass r-ordinal r-survival r-tibble)) (home-page "https://cran.r-project.org/web/packages/jomo/") (synopsis "Multilevel Joint Modelling Multiple Imputation") (description "Similarly to Schafer's package pan, jomo is a package for multilevel joint modelling multiple imputation @url{Carpenter and Kenward (2013), http://doi.org/10.1002/9781119942283}. Novel aspects of jomo are the possibility of handling binary and categorical data through latent normal variables, the option to use cluster-specific covariance matrices and to impute compatibly with the substantive model.") (license license:gpl2))) (define-public r-pan (package (name "r-pan") (version "1.9") (source (origin (method url-fetch) (uri (cran-uri "pan" version)) (sha256 (base32 "0liwcym035174h6c4b9ddmqxa3vkpkk3alyr9psk8yhv7i61hzp3")))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/pan/") (synopsis "Multiple imputation for multivariate panel or clustered data") (description "This package implements multiple imputation for multivariate panel or clustered data.") (license license:gpl3))) (define-public r-mitml (package (name "r-mitml") (version "0.4-5") (source (origin (method url-fetch) (uri (cran-uri "mitml" version)) (sha256 (base32 "1szfw993ma4qn377bab08bkvm4s0sxs5x2hdcj9kgk47661fqsh5")))) (build-system r-build-system) (propagated-inputs (list r-haven r-jomo r-pan)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/mitml/") (synopsis "Tools for multiple imputation in multilevel modeling") (description "This package provides tools for multiple imputation of missing data in multilevel modeling. It includes a user-friendly interface to the packages pan and jomo, and several functions for visualization, data management and the analysis of multiply imputed data sets.") (license license:gpl2+))) (define-public r-mice (package (name "r-mice") (version "3.16.0") (source (origin (method url-fetch) (uri (cran-uri "mice" version)) (sha256 (base32 "0h20lirk2257y3i1ww5y2pqp9lc21ilmf8yykmz36h55hm8jiw19")))) (build-system r-build-system) (propagated-inputs (list r-broom r-cpp11 r-dplyr r-generics r-glmnet r-lattice r-mitml r-nnet r-rcpp r-rlang r-rpart r-tidyr)) (home-page "https://cran.r-project.org/web/packages/mice/") (synopsis "Multivariate imputation by chained equations") (description "Multiple imputation using @dfn{Fully Conditional Specification} (FCS) implemented by the MICE algorithm as described in @url{Van Buuren and Groothuis-Oudshoorn (2011), http://doi.org/10.18637/jss.v045.i03}. Each variable has its own imputation model. Built-in imputation models are provided for continuous data (predictive mean matching, normal), binary data (logistic regression), unordered categorical data (polytomous logistic regression) and ordered categorical data (proportional odds). MICE can also impute continuous two-level data (normal model, pan, second-level variables). Passive imputation can be used to maintain consistency between variables. Various diagnostic plots are available to inspect the quality of the imputations.") ;; Any of these two versions. (license (list license:gpl2 license:gpl3)))) (define-public r-transformr (package (name "r-transformr") (version "0.1.5") (source (origin (method url-fetch) (uri (cran-uri "transformr" version)) (sha256 (base32 "125y99wpgvp92qsg7934nzjqy6irjzaj21c0dcq7apqd2hqamfxw")))) (properties `((upstream-name . "transformr"))) (build-system r-build-system) (propagated-inputs (list r-cpp11 r-lpsolve r-rlang r-sf r-tweenr r-vctrs)) (home-page "https://github.com/thomasp85/transformr") (synopsis "Polygon and path transformations") (description "In order to smoothly animate the transformation of polygons and paths, many aspects needs to be taken into account, such as differing number of control points, changing center of rotation, etc. The transformr package provides an extensive framework for manipulating the shapes of polygons and paths and can be seen as the spatial brother to the tweenr package.") (license license:expat))) (define-public r-truncnorm (package (name "r-truncnorm") (version "1.0-9") (source (origin (method url-fetch) (uri (cran-uri "truncnorm" version)) (sha256 (base32 "0267gvcg6mmf28x26z6njw373prwpaq8aqkd6aavyhrjsv2aqmji")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/truncnorm/") (synopsis "Truncated normal distribution") (description "This package provides functions for the truncated normal distribution with mean equal to @code{mean} and standard deviation equal to @code{sd}. It includes density, distribution, quantile, and expected value functions, as well as a random generation function.") (license license:gpl2))) (define-public r-truncdist (package (name "r-truncdist") (version "1.0-2") (source (origin (method url-fetch) (uri (cran-uri "truncdist" version)) (sha256 (base32 "02ihw4ixhadwr3sqm6r264i8vpcaz8pn69vkzabd8fwqvn5vcj5q")))) (properties `((upstream-name . "truncdist"))) (build-system r-build-system) (propagated-inputs (list r-evd)) (home-page "https://cran.r-project.org/package=truncdist") (synopsis "Truncated random variables") (description "This package provides a collection of tools to evaluate probability density functions, cumulative distribution functions, quantile functions and random numbers for truncated random variables. These functions are provided to also compute the expected value and variance. @acronym{Q-Q, quantile–quantile} plots can be produced. All the probability functions in the stats, stats4 and evd packages are automatically available for truncation.") (license license:gpl2+))) (define-public r-trycatchlog (package (name "r-trycatchlog") (version "1.3.1") (source (origin (method url-fetch) (uri (cran-uri "tryCatchLog" version)) (sha256 (base32 "0k40a48qzwmardjnkf0h5s5zryivzvdanz61kxdqdfqlil19ma0d")))) (properties `((upstream-name . "tryCatchLog"))) (build-system r-build-system) (native-inputs (list r-knitr)) (home-page "https://github.com/aryoda/tryCatchLog") (synopsis "Advanced tryCatch and try functions") (description "This package provides advanced @code{tryCatch} and @code{try} functions for better error handling (logging, stack trace with source code references and support for post-mortem analysis via dump files).") (license license:gpl3))) (define-public r-rsolnp (package (name "r-rsolnp") (version "1.16") (source (origin (method url-fetch) (uri (cran-uri "Rsolnp" version)) (sha256 (base32 "0w7nkj6igr0gi7r7jg950lsx7dj6aipgxi6vbjsf5f5yc9h7fhii")))) (properties `((upstream-name . "Rsolnp"))) (build-system r-build-system) (propagated-inputs (list r-truncnorm)) (home-page "https://cran.r-project.org/web/packages/Rsolnp/") (synopsis "General non-linear optimization") (description "The Rsolnp package implements a general non-linear augmented Lagrange multiplier method solver, a @dfn{sequential quadratic programming} (SQP) based solver).") ;; Any version of the GPL. (license license:gpl2+))) (define-public r-hardyweinberg (package (name "r-hardyweinberg") (version "1.7.8") (source (origin (method url-fetch) (uri (cran-uri "HardyWeinberg" version)) (sha256 (base32 "1wddy32zljyya37isqb54sqhpp07s2kizjl36i08pj37bbza7yac")))) (properties `((upstream-name . "HardyWeinberg"))) (build-system r-build-system) (propagated-inputs (list r-mice r-nnet r-rcpp r-rsolnp r-shape)) (native-inputs (list r-knitr r-rmarkdown)) (home-page "https://cran.r-project.org/package=HardyWeinberg") (synopsis "Statistical tests and graphics for Hardy-Weinberg equilibrium") (description "This package contains tools for exploring Hardy-Weinberg equilibrium for diallelic genetic marker data. All classical tests (chi-square, exact, likelihood-ratio and permutation tests) for Hardy-Weinberg equilibrium are included in the package, as well as functions for power computation and for the simulation of marker data under equilibrium and disequilibrium. Routines for dealing with markers on the X-chromosome are included. Functions for testing equilibrium in the presence of missing data by using multiple imputation are also provided. Implements several graphics for exploring the equilibrium status of a large set of diallelic markers: ternary plots with acceptance regions, log-ratio plots and Q-Q plots.") (license license:gpl2+))) (define-public r-sm (package (name "r-sm") (version "2.2-6.0") (source (origin (method url-fetch) (uri (cran-uri "sm" version)) (sha256 (base32 "0q8xav1alammiyiw2p8y0qq94ag5rln910jry8q3sb2p38ly79i7")))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "http://www.stats.gla.ac.uk/~adrian/sm/") (synopsis "Smoothing methods for nonparametric regression and density estimation") (description "This is software accompanying the book 'Applied Smoothing Techniques for Data Analysis---The Kernel Approach with S-Plus Illustrations', Oxford University Press. It provides smoothing methods for nonparametric regression and density estimation") (license license:gpl2+))) (define-public r-smoof (package (name "r-smoof") (version "1.6.0.3") (source (origin (method url-fetch) (uri (cran-uri "smoof" version)) (sha256 (base32 "1cazhnd0m5jjzixaqgqh2h3rsa2sw3k8slj5cmgm8v47aaqn91mg")))) (properties `((upstream-name . "smoof"))) (build-system r-build-system) (propagated-inputs (list r-bbmisc r-checkmate r-ggplot2 r-paramhelpers r-rcpp r-rcpparmadillo)) (home-page "https://jakobbossek.github.io/smoof/") (synopsis "Single and multi-objective optimization test functions") (description "This tool generates high number of both single- and multi-objective test functions. These functions are frequently used for the benchmarking of (numerical) optimization algorithms. Moreover, it offers a set of convenient functions to generate, plot and work with objective functions.") (license license:bsd-2))) (define-public r-smurf (package (name "r-smurf") (version "1.1.5") (source (origin (method url-fetch) (uri (cran-uri "smurf" version)) (sha256 (base32 "1gpzzj67x0i70vw1x4rv56mhk2b74ynvdsy93rzmdk6b2h3dvv46")))) (properties `((upstream-name . "smurf"))) (build-system r-build-system) (propagated-inputs (list r-catdata r-glmnet r-mass r-matrix r-mgcv r-rcolorbrewer r-rcpp r-rcpparmadillo)) (native-inputs (list r-knitr)) (home-page "https://gitlab.com/TReynkens/smurf") (synopsis "Sparse multi-type regularized feature modeling") (description "The @code{smurf} package contains the implementation of the @dfn{Sparse Multi-type Regularized Feature} (SMuRF) modeling algorithm to fit @dfn{generalized linear models} (GLMs) with multiple types of predictors via regularized maximum likelihood. Next to the fitting procedure, following functionality is available: @itemize @item Selection of the regularization tuning parameter lambda using three different approaches: in-sample, out-of-sample or using cross-validation. @item S3 methods to handle the fitted object including visualization of the coefficients and a model summary. @end itemize") (license license:gpl2+))) (define-public r-venndiagram (package (name "r-venndiagram") (version "1.7.3") (source (origin (method url-fetch) (uri (cran-uri "VennDiagram" version)) (sha256 (base32 "0ilcxcp8qskmb5cp7fyb7i0qizg42lrx0ny8ws3if90kfrglghp7")))) (properties `((upstream-name . "VennDiagram"))) (build-system r-build-system) (propagated-inputs (list r-futile-logger)) (home-page "https://cran.r-project.org/web/packages/VennDiagram/") (synopsis "Generate High-Resolution Venn and Euler Plots") (description "This package provides a set of functions to generate high-resolution Venn and Euler plots. It includes handling for several special cases, including two-case scaling, and extensive customization of plot shape and structure.") (license license:gpl2+))) (define-public r-vioplot (package (name "r-vioplot") (version "0.4.0") (source (origin (method url-fetch) (uri (cran-uri "vioplot" version)) (sha256 (base32 "1db7g0378jbcd6ssb7afff4y4r0v472qnb625hfwixx4wf1v8aap")))) (build-system r-build-system) (propagated-inputs (list r-sm r-zoo)) (native-inputs (list r-knitr)) (home-page "http://wsopuppenkiste.wiso.uni-goettingen.de/~dadler") (synopsis "Violin plot") (description "This package provides a violin plot, which is a combination of a box plot and a kernel density plot.") (license license:bsd-3))) (define-public r-rsofia (package (name "r-rsofia") (version "1.1") (source (origin (method url-fetch) ;; This package has been removed from CRAN, so we can ;; only fetch it from the archives. (uri (string-append "https://cran.r-project.org/src/" "contrib/Archive/RSofia/RSofia_" version ".tar.gz")) (sha256 (base32 "0q931y9rcf6slb0s2lsxhgqrzy4yqwh8hb1124nxg0bjbxvjbihn")))) (properties `((upstream-name . "RSofia"))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) (home-page "https://cran.r-project.org/src/contrib/Archive/RSofia") (synopsis "Port of sofia-ml to R") (description "This package is a port of sofia-ml to R. Sofia-ml is a suite of fast incremental algorithms for machine learning that can be used for training models for classification or ranking.") (license license:asl2.0))) (define-public r-xts (package (name "r-xts") (version "0.13.2") (source (origin (method url-fetch) (uri (cran-uri "xts" version)) (sha256 (base32 "1yqx1x395hvdav1fvmpwrfm8sir398ky1bi0x5zsm7acbkv91maa")))) (build-system r-build-system) (propagated-inputs (list r-zoo)) (home-page "https://github.com/joshuaulrich/xts") (synopsis "Extensible time series") (description "This package provides for uniform handling of R's different time-based data classes by extending @code{zoo}, maximizing native format information preservation and allowing for user-level customization and extension, while simplifying cross-class interoperability.") (license license:gpl2+))) (define-public r-performanceanalytics (package (name "r-performanceanalytics") (version "2.0.4") (source (origin (method url-fetch) (uri (cran-uri "PerformanceAnalytics" version)) (sha256 (base32 "0ci26hsj4wnw9g0mh4vrn0cg986cpcpx169rvw6v6rbnjxq718bq")))) (properties `((upstream-name . "PerformanceAnalytics"))) (build-system r-build-system) (propagated-inputs (list r-quadprog r-xts r-zoo)) (home-page "https://r-forge.r-project.org/projects/returnanalytics/") (synopsis "Econometric tools for performance and risk analysis") (description "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.") ;; Either version may be picked. (license (list license:gpl2 license:gpl3)))) (define-public r-laeken (package (name "r-laeken") (version "0.5.3") (source (origin (method url-fetch) (uri (cran-uri "laeken" version)) (sha256 (base32 "02z8jyya6xv0pyfqaalbry174fw44h13s7p1jk5b4h9a9x4myjb0")))) (build-system r-build-system) (propagated-inputs (list r-boot r-mass)) (home-page "https://cran.r-project.org/web/packages/laeken/") (synopsis "Estimation of indicators on social exclusion and poverty") (description "This package provides tools for the estimation of indicators on social exclusion and poverty, as well as an implementation of Pareto tail modeling for empirical income distributions.") (license license:gpl2+))) (define-public r-vcd (package (name "r-vcd") (version "1.4-12") (source (origin (method url-fetch) (uri (cran-uri "vcd" version)) (sha256 (base32 "127dkln826ah5ydp3pmd5bqyns9m9m6yrjnmn7fir4r9al8yycf9")))) (build-system r-build-system) (propagated-inputs (list r-colorspace r-lmtest r-mass)) (home-page "https://cran.r-project.org/web/packages/vcd/") (synopsis "Visualizing categorical data") (description "This package provides visualization techniques, data sets, summary and inference procedures aimed particularly at categorical data. Special emphasis is given to highly extensible grid graphics. The package was originally inspired by the book \"Visualizing Categorical Data\" by Michael Friendly and is now the main support package for a new book, \"Discrete Data Analysis with R\" by Michael Friendly and David Meyer (2015).") (license license:gpl2))) (define-public r-vcfr (package (name "r-vcfr") (version "1.15.0") (source (origin (method url-fetch) (uri (cran-uri "vcfR" version)) (sha256 (base32 "1yj91cphin232m09wrpj8l27vxblyryh658siakz55hxjs5y85yz")))) (build-system r-build-system) (native-inputs (list r-knitr)) (inputs (list zlib)) (propagated-inputs (list r-ape r-dplyr r-magrittr r-memuse r-pinfsc50 r-rcpp r-stringr r-tibble r-vegan r-viridislite)) (home-page "https://github.com/knausb/vcfR") (synopsis "Manipulate and visualize VCF data") (description "This package facilitates easy manipulation of variant call format (VCF) data. Functions are provided to rapidly read from and write to VCF files. Once VCF data is read into R, a parser function extracts matrices of data. This information can then be used for quality control or other purposes. Additional functions provide visualization of genomic data. Once processing is complete data may be written to a VCF file. It also may be converted into other popular R objects. This package provides a link between VCF data and familiar R software.") (license license:gpl3))) (define-public r-rvcg (package (name "r-rvcg") (version "0.22.2") (source (origin (method url-fetch) (uri (cran-uri "Rvcg" version)) (sha256 (base32 "077p4c16nqi6ayxv1i31cr6sw9fwnxpmfkmrrhzh02khpi2c2jg5")))) (properties `((upstream-name . "Rvcg"))) (build-system r-build-system) (propagated-inputs (list r-rcpp r-rcpparmadillo r-rcppeigen)) (home-page "https://github.com/zarquon42b/Rvcg") (synopsis "Manipulations of triangular meshes based on the VCGLIB API") (description "This is a package for operations on triangular meshes based on VCGLIB. This package integrates nicely with the R-package rgl to render the meshes processed by Rvcg. The Visualization and Computer Graphics Library (VCG for short) is a library for manipulation, processing and displaying with OpenGL of triangle and tetrahedral meshes.") 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DTW computes the optimal (least cumulative distance) alignment between points of two time series. Common DTW variants covered include local (slope) and global (window) constraints, subsequence matches, arbitrary distance definitions, normalizations, minimum variance matching, and so on.") (license license:gpl2+))) (define-public r-sdmtools (package (name "r-sdmtools") (version "1.1-221.2") (source (origin (method url-fetch) (uri (cran-uri "SDMTools" version)) (sha256 (base32 "1xvcd97ikqsfdpk2fddy3k0z1ajqga7nv9bgac9c1wnjk1gqrpgh")))) (properties `((upstream-name . "SDMTools"))) (build-system r-build-system) (propagated-inputs (list r-r-utils)) (home-page "https://www.rforge.net/SDMTools/") (synopsis "Species distribution modelling tools") (description "This package provides a set of tools for post processing the outcomes of species distribution modeling exercises. It includes novel methods for comparing models and tracking changes in distributions through time. It further includes methods for visualizing outcomes, selecting thresholds, calculating measures of accuracy and landscape fragmentation statistics, etc.") (license license:gpl3+))) (define-public r-scatterplot3d (package (name "r-scatterplot3d") (version "0.3-44") (source (origin (method url-fetch) (uri (cran-uri "scatterplot3d" version)) (sha256 (base32 "1hkfislhzx05y5qqa7pvrils3qf9rhxbf37lkpsjbn9yihs0i70w")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/scatterplot3d/") (synopsis "3D scatter plot") (description "This package provides an implementation of scatter plots for plotting. a three dimensional point cloud.") 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(license license:gpl2))) (define-public r-ggjoy (package (name "r-ggjoy") (version "0.4.1") (source (origin (method url-fetch) (uri (cran-uri "ggjoy" version)) (sha256 (base32 "012md2m0jqfcccb933j423m3ck31v3p0pd41gjxpyg9082y7ixyj")))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-ggridges)) (home-page "https://github.com/clauswilke/ggjoy") (synopsis "Joyplots in ggplot2") (description "Joyplots provide a convenient way of visualizing changes in distributions over time or space. This package enables the creation of such plots in @code{ggplot2}.") (license license:gpl2))) (define-public r-gss (package (name "r-gss") (version "2.2-7") (source (origin (method url-fetch) (uri (cran-uri "gss" version)) (sha256 (base32 "0siz9xmfiirkg8sb0amzyp7k1mjbgz8jmsmlc8schw65093i84rv")))) (properties `((upstream-name . 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(license license:expat))) (define-public r-argparser (package (name "r-argparser") (version "0.7.2") (source (origin (method url-fetch) (uri (cran-uri "argparser" version)) (sha256 (base32 "0j9hnbyzbyzclgm4qwyqqkrqcrblxfm190489sgcvr5i7vg2smr8")))) (build-system r-build-system) (home-page "https://bitbucket.org/djhshih/argparser") (synopsis "Command-line argument parser") (description "This package provides a cross-platform command-line argument parser written purely in R with no external dependencies. It is useful with the Rscript front-end and facilitates turning an R script into an executable script.") (license license:gpl3+))) (define-public r-aricode (package (name "r-aricode") (version "1.0.3") (source (origin (method url-fetch) (uri (cran-uri "aricode" version)) (sha256 (base32 "02nrw66jfpzf6dy0zy21sbdjxjc8c11iv9fkjqj5akzb7wskk9qh")))) (properties `((upstream-name . 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(license license:expat))) (define-public r-processx (package (name "r-processx") (version "3.8.4") (source (origin (method url-fetch) (uri (cran-uri "processx" version)) (sha256 (base32 "02z7n59pglz6jw1vyyl0mkc7mz2c7y8yzsnhq5yz62digwnnf9v6")))) (build-system r-build-system) (propagated-inputs (list r-ps r-r6)) (home-page "https://github.com/r-lib/processx3") (synopsis "Execute and control system processes") (description "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. @code{processx} can poll a process for standard output or error, with a timeout. It can also poll several processes at once.") (license license:expat))) (define-public r-timeseries (package (name "r-timeseries") (version "4032.109") (source (origin (method url-fetch) (uri (cran-uri "timeSeries" version)) (sha256 (base32 "07vkppp9azbrn0lv1xhi4s3vpy4mglhysp7d250fl08b9rc4f32y")))) (properties `((upstream-name . "timeSeries"))) (build-system r-build-system) (propagated-inputs (list r-timedate)) (home-page "https://r-forge.r-project.org/scm/viewvc.php/pkg/timeSeries/?root=rmetrics") (synopsis "Metrics for financial time series objects") (description "This package implements S4 classes and various tools for financial time series. Basic functions such as scaling and sorting, subsetting, mathematical operations and statistical functions are provided.") (license license:gpl2+))) (define-public r-tsp (package (name "r-tsp") (version "1.2-4") (source (origin (method url-fetch) (uri (cran-uri "TSP" version)) (sha256 (base32 "1263ay3dar2mzm89nf31gl7n8d983qjiy4qwz7sgv8vwkbz0pg9h")))) (properties `((upstream-name . "TSP"))) (build-system r-build-system) (propagated-inputs (list r-foreach)) (home-page "https://cran.r-project.org/web/packages/TSP/") (synopsis "Traveling salesperson problem (TSP)") (description "This package provides basic infrastructure and some algorithms for the @dfn{traveling salesperson problem}(TSP) (also known as the traveling salesman problem).") (license license:gpl3))) (define-public r-qap (package (name "r-qap") (version "0.1-2") (source (origin (method url-fetch) (uri (cran-uri "qap" version)) (sha256 (base32 "19adb1bw46pcnmmhqz2jklr0vmma3llxajqp0j9mqfksmsisv927")))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/qap/") (synopsis "Heuristics for the quadratic assignment problem (QAP)") (description "This package implements heuristics for the @dfn{quadratic assignment problem} (QAP). Currently only a simulated annealing heuristic is available.") (license license:gpl3))) (define-public r-gclus (package (name "r-gclus") (version "1.3.2") (source (origin (method url-fetch) (uri (cran-uri "gclus" version)) (sha256 (base32 "1cz0g0i972955hhaji30rx8448x7f3as7z1sww9i5h86ybgirilw")))) (build-system r-build-system) (propagated-inputs (list r-cluster)) (home-page "https://cran.r-project.org/web/packages/gclus/") (synopsis "Clustering graphics") (description "This package orders panels in scatterplot matrices and parallel coordinate displays by some merit index. It contains various indices of merit, ordering functions, and enhanced versions of @code{pairs} and @code{parcoord} which color panels according to their merit level.") (license license:gpl2+))) (define-public r-webchem (package (name "r-webchem") (version "1.3.0") (source (origin (method url-fetch) (uri (cran-uri "webchem" version)) (sha256 (base32 "06b9i9jipg564zyw4gkgiidz7501rlp40hxm4z3k5mzy148lr5vq")))) (properties `((upstream-name . "webchem"))) (build-system r-build-system) (propagated-inputs (list r-base64enc r-data-tree r-dplyr r-httr r-jsonlite r-purrr r-rlang r-rvest r-stringr r-tibble r-xml2)) (native-inputs (list r-knitr)) (home-page "https://docs.ropensci.org/webchem/") (synopsis "Chemical information from the web") (description "This package interacts with a suite of web services for chemical information. Sources include: Alan Wood's Compendium of Pesticide Common Names, Chemical Identifier Resolver, ChEBI, Chemical Translation Service, ChemSpider, ETOX, Flavornet, NIST Chemistry WebBook, OPSIN, PubChem, SRS, Wikidata.") (license license:expat))) (define-public r-webshot (package (name "r-webshot") (version "0.5.5") (source (origin (method url-fetch) (uri (cran-uri "webshot" version)) (sha256 (base32 "04xrrf72323sgzsdkbl05p2fdsi486i9avrrxvw0l3n8r8y92xfn")))) (build-system r-build-system) (propagated-inputs (list r-callr r-jsonlite r-magrittr)) (home-page "https://github.com/wch/webshot/") (synopsis "Take screenshots of web pages") (description "Webshot makes it easy to take screenshots of web pages from within R. It can also run Shiny applications locally and take screenshots of the application; and it can render and screenshot static as well as interactive R Markdown documents.") (license license:gpl2))) (define-public r-seriation (package (name "r-seriation") (version "1.5.4") (source (origin (method url-fetch) (uri (cran-uri "seriation" version)) (sha256 (base32 "17rk4674r5knfgqyik9gbz6yj42qv6h79j2prw79glc1ym99qcyj")))) (build-system r-build-system) (propagated-inputs (list r-ca r-cluster r-colorspace r-foreach r-gclus r-mass r-qap r-registry r-tsp r-vegan)) (native-inputs (list gfortran)) (home-page "https://s2.smu.edu/IDA/seriation/") (synopsis "Infrastructure for ordering objects using seriation") (description "This package provides infrastructure for seriation with an implementation of several seriation/sequencing techniques to reorder matrices, dissimilarity matrices, and dendrograms. It also provides (optimally) reordered heatmaps, color images and clustering visualizations like dissimilarity plots, and visual assessment of cluster tendency plots (VAT and iVAT).") (license license:gpl3))) (define-public r-xfun (package (name "r-xfun") (version "0.43") (source (origin (method url-fetch) (uri (cran-uri "xfun" version)) (sha256 (base32 "1hqn9r4xk0jjm1kafn7r8jbpciqciw8gh1vqch0wlvzda8m4dbar")))) (build-system r-build-system) (properties ;; knitr itself depends on xfun '((updater-ignored-native-inputs . ("r-knitr")))) (home-page "https://github.com/yihui/xfun") (synopsis "Miscellaneous functions") (description "This package provides miscellaneous functions commonly used in other packages maintained by Yihui Xie.") 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(license license:asl2.0))) (define-public r-zeallot (package (name "r-zeallot") (version "0.1.0") (source (origin (method url-fetch) (uri (cran-uri "zeallot" version)) (sha256 (base32 "1sd1igcfnv27pa3bqxlbyxchi562h7grnjg1l7wxx3bwr49i57s3")))) (build-system r-build-system) (home-page "https://github.com/nteetor/zeallot") (synopsis "Multiple, unpacking, and destructuring assignment") (description "This package provides a @code{%<-%} operator to perform multiple, unpacking, and destructuring assignment in R. The operator unpacks the right-hand side of an assignment into multiple values and assigns these values to variables on the left-hand side of the assignment.") (license license:expat))) (define-public r-zlog (package (name "r-zlog") (version "1.0.2") (source (origin (method url-fetch) (uri (cran-uri "zlog" version)) (sha256 (base32 "0fi9aqrmikdg5ibwhn82kslj4lxih03vm27jmi14m73h09yy4in5")))) (properties `((upstream-name . 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("r-knitr")))) (home-page "https://github.com/r-lib/vctrs") (synopsis "Vector helpers") (description "There are three main goals to the @code{vctrs} package: @enumerate @item To propose @code{vec_size()} and @code{vec_type()} as alternatives to @code{length()} and @code{class()}. These definitions are paired with a framework for type-coercion and size-recycling. @item To define type- and size-stability as desirable function properties, use them to analyse existing base function, and to propose better alternatives. This work has been particularly motivated by thinking about the ideal properties of @code{c()}, @code{ifelse()}, and @code{rbind()}. @item To provide a new @code{vctr} base class that makes it easy to create new S3 vectors. @code{vctrs} provides methods for many base generics in terms of a few new @code{vctrs} generics, making implementation considerably simpler and more robust. @end enumerate\n") (license license:gpl3))) (define-public r-pillar (package (name "r-pillar") (version "1.9.0") (source (origin (method url-fetch) (uri (cran-uri "pillar" version)) (sha256 (base32 "1k3sp37dpn46d2xbq621alpvzgnm06x5qb87nk169y47q23b8gpj")))) (build-system r-build-system) (propagated-inputs (list r-cli r-fansi r-glue r-lifecycle r-rlang r-utf8 r-vctrs)) (native-inputs (list r-knitr)) (home-page "https://github.com/r-lib/pillar") (synopsis "Coloured formatting for columns") (description "This package provides a @code{pillar} generic designed for formatting columns of data using the full range of colours provided by modern terminals.") (license license:gpl3))) (define-public r-pinfsc50 (package (name "r-pinfsc50") (version "1.3.0") (source (origin (method url-fetch) (uri (cran-uri "pinfsc50" version)) (sha256 (base32 "1gs9x328qqvqwx3k4z9jgzq5zb6g8kdz4430n96v7zb78p7jf5lp")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/pinfsc50/") (synopsis "Genomic data for the plant pathogen Phytophthora infestans") (description "This package contains genomic data for the plant pathogen Phytophthora infestans. It includes a variant file, a sequence file and an annotation file. This package is intended to be used as example data for packages that work with genomic data.") (license license:gpl2+))) (define-public r-piton (package (name "r-piton") (version "1.0.0") (source (origin (method url-fetch) (uri (cran-uri "piton" version)) (sha256 (base32 "1krf6zi238m275nxjlpyayv8y2drbgs2kg19dpkqm0lmlz5y5ar8")))) (properties `((upstream-name . "piton"))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) (home-page "https://github.com/Ironholds/piton") (synopsis "Parsing expression grammars in Rcpp") (description "This package provides a wrapper around the Parsing Expression Grammar Template Library, a C++11 library for generating parsing expression grammars, that makes it accessible within Rcpp. With this, developers can implement their own grammars and easily expose them in R packages.") (license license:expat))) (define-public r-uuid (package (name "r-uuid") (version "1.2-0") (source (origin (method url-fetch) (uri (cran-uri "uuid" version)) (sha256 (base32 "1z9a4b7hkymkwjq69d00myy5xw8kl9g99f4m2y4lxqqjz0a0lwbk")))) (build-system r-build-system) (home-page "https://www.rforge.net/uuid") (synopsis "Tools for generating and handling of UUIDs") (description "This package provides tools for generating and handling of @dfn{Universally Unique Identifiers} (UUIDs).") (license license:expat))) (define-public r-tinylabels (package (name "r-tinylabels") (version "0.2.4") (source (origin (method url-fetch) (uri (cran-uri "tinylabels" version)) (sha256 (base32 "01pvnirma3wzfqnnz8zvyqajjyysjm3sd6813bgdhz199lcg7hhz")))) (properties `((upstream-name . "tinylabels"))) (build-system r-build-system) (native-inputs (list r-knitr)) (home-page "https://github.com/mariusbarth/tinylabels") (synopsis "Lightweight variable labels") (description "This package lets you assign, extract, or remove variable labels from R vectors.") 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The @code{sqldf} or @code{read.csv.sql} functions can also be used to read filtered files into R even if the original files are larger than R itself can handle.") (license license:gpl2))) (define-public r-abind (package (name "r-abind") (version "1.4-5") (source (origin (method url-fetch) (uri (cran-uri "abind" version)) (sha256 (base32 "0b1zd8jbnl6l292cr9rb50m09fy3ylxvzkpgi5lfb1nbzddcwfis")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/abind/") (synopsis "Combine multidimensional arrays") (description "This package provides tools to combine multidimensional arrays into a single array. This is a generalization of @code{cbind} and @code{rbind}. It works with vectors, matrices, and higher-dimensional arrays. It also provides the functions @code{adrop}, @code{asub}, and @code{afill} for manipulating, extracting and replacing data in arrays.") 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In addition, the quality of imputation can be visually explored using various univariate, bivariate, multiple and multivariate plot methods.") (license license:gpl2+))) (define-public r-fnn (package (name "r-fnn") (version "1.1.4") (source (origin (method url-fetch) (uri (cran-uri "FNN" version)) (sha256 (base32 "09zwlblkb7wkyk6azq2iizv3kj2wdqmjhg0r8zjiy1f692ivakfv")))) (properties `((upstream-name . "FNN"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/FNN") (synopsis "Fast nearest neighbor search algorithms and applications") (description "This package provides cover-tree and kd-tree fast k-nearest neighbor search algorithms. Related applications including KNN classification, regression and information measures are implemented.") ;; The DESCRIPTION file erroneously states that GPL version 2.1 or ;; later can be used. (license license:gpl2+))) (define-public r-smoother (package (name "r-smoother") (version "1.3") (source (origin (method url-fetch) (uri (cran-uri "smoother" version)) (sha256 (base32 "0xw28qv8f5i05ajx32njnql6hql5njqyc47wcq6c75cxiv44ppz8")))) (build-system r-build-system) (propagated-inputs (list r-ttr)) (home-page "https://cran.r-project.org/web/packages/smoother") (synopsis "Functions relating to the smoothing of numerical data") (description "This package provides a collection of methods for smoothing numerical data, commencing with a port of the Matlab gaussian window smoothing function. In addition, several functions typically used in smoothing of financial data are included.") 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The fst format allows for random access of stored data and compression with the LZ4 and ZSTD compressors.") (license license:mpl2.0))) (define-public r-fst (package (name "r-fst") (version "0.9.8") (source (origin (method url-fetch) (uri (cran-uri "fst" version)) (sha256 (base32 "0r96inwrr960m7wmc80603bw2vvvwab225bh9dq3lalwhy4yiis4")))) (properties `((upstream-name . "fst"))) (build-system r-build-system) (propagated-inputs (list r-fstcore r-rcpp)) (home-page "https://www.fstpackage.org") (synopsis "Fast serialization of data frames") (description "The fst package for R provides a fast, easy and flexible way to serialize data frames. With access speeds of multiple GB/s, fst is specifically designed to unlock the potential of high speed solid state disks. Data frames stored in the fst format have full random access, both in column and rows. The fst format allows for random access of stored data and compression with the LZ4 and ZSTD compressors.") (license license:agpl3))) (define-public r-snftool (package (name "r-snftool") (version "2.3.1") (source (origin (method url-fetch) (uri (cran-uri "SNFtool" version)) (sha256 (base32 "05hz230aq5wbzhknxzr4iqv3nqjhbpf66n6bp1rc5h2jgz2yfbwq")))) (properties `((upstream-name . "SNFtool"))) (build-system r-build-system) (propagated-inputs (list r-alluvial r-exposition)) (home-page "https://cran.r-project.org/package=SNFtool") (synopsis "Similarity network fusion") (description "Similarity Network Fusion takes multiple views of a network and fuses them together to construct an overall status matrix. The input to our algorithm can be feature vectors, pairwise distances, or pairwise similarities. The learned status matrix can then be used for retrieval, clustering, and classification.") ;; Any version of the GPL (license license:gpl3+))) (define-public r-snowfall (package (name "r-snowfall") (version "1.84-6.3") (source (origin (method url-fetch) (uri (cran-uri "snowfall" version)) (sha256 (base32 "0hxip3rzv7slxvif1000avbcid2mjxj1y9mimyvk87h404mr6h96")))) (build-system r-build-system) (propagated-inputs (list r-snow)) (home-page "https://cran.r-project.org/web/packages/snowfall/") (synopsis "Easier cluster computing") (description "This package is a usability wrapper around snow for easier development of parallel R programs. This package offers e.g. extended error checks, and additional functions. All functions work in sequential mode, too, if no cluster is present or wished. The package is also designed as connector to the cluster management tool @code{sfCluster}, but can also used without it.") (license license:gpl2+))) (define-public r-rgexf (package (name "r-rgexf") (version "0.16.2") (source (origin (method url-fetch) (uri (cran-uri "rgexf" version)) (sha256 (base32 "00c2zka1n3k7p1l0mlchr063s6x58p9r3fb64d4wgl4rvsq55q3f")) ;; Delete minified JavaScript files (snippet '(for-each delete-file '("inst/gexf-js/js/jquery-2.0.2.min.js" "inst/gexf-js/js/jquery-ui-1.10.3.custom.min.js" "inst/gexf-js/js/jquery.mousewheel.min.js"))))) (properties `((upstream-name . 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It allows the user to easily build/read graph files including attributes, GEXF visual attributes (such as color, size, and position), network dynamics (for both edges and nodes) and edge weighting. Users can build/handle graphs element-by-element or massively through data-frames, visualize the graph on a web browser through gexf-js (a JavaScript library) and interact with the igraph package.") (license license:expat))) (define-public r-data-tree (package (name "r-data-tree") (version "1.1.0") (source (origin (method url-fetch) (uri (cran-uri "data.tree" version)) (sha256 (base32 "0qxd1g159phc6f18iddjljdg96sh09w63xqawjwbwyhg4blm9ddh")))) (properties `((upstream-name . "data.tree"))) (build-system r-build-system) (propagated-inputs (list r-r6 r-stringi)) (native-inputs (list r-knitr r-rmarkdown)) (home-page "https://github.com/gluc/data.tree") (synopsis "General purpose hierarchical data structure") (description "Create tree structures from hierarchical data, and traverse the tree in various orders. Aggregate, cumulate, print, plot, convert to and from data.frame and more. This is useful for decision trees, machine learning, finance, conversion from and to JSON, and many other applications.") (license license:gpl2+))) (define-public r-dtplyr (package (name "r-dtplyr") (version "1.3.1") (source (origin (method url-fetch) (uri (cran-uri "dtplyr" version)) (sha256 (base32 "1rfnr1f3dzzivzmw9jjaclckkany6c625bqr8lkx32qbcjd6iad5")))) (properties `((upstream-name . "dtplyr"))) (build-system r-build-system) (propagated-inputs (list r-cli r-data-table r-dplyr r-glue r-lifecycle r-rlang r-tibble r-tidyselect r-vctrs)) (native-inputs (list r-knitr)) (home-page "https://github.com/tidyverse/dtplyr") (synopsis "Data Table back-end for dplyr") (description "This package provides a @code{data.table} backend for @code{dplyr}. The goal of @code{dtplyr} is to allow you to write @code{dplyr} code that is automatically translated to the equivalent, but usually much faster, @code{data.table} code.") (license license:expat))) (define-public r-collapsibletree (package (name "r-collapsibletree") (version "0.1.8") (source (origin (method url-fetch) (uri (cran-uri "collapsibleTree" version)) (sha256 (base32 "1i5nmw5w7m8xdgxzim8z8n4w321f42isxbvvajl8ii59pg7drilq")) (snippet '(begin ;; Delete minified JavaScript file (delete-file "inst/htmlwidgets/lib/d3-4.10.2/d3.min.js") #true)))) (properties `((upstream-name . "collapsibleTree"))) (build-system r-build-system) (arguments `(#:phases (modify-phases %standard-phases (add-after 'unpack 'process-javascript (lambda* (#:key inputs #:allow-other-keys) (with-directory-excursion "inst/htmlwidgets/lib/d3-4.10.2/" (let ((source (assoc-ref inputs "d3.v4.js")) (target "d3.min.js")) (format #t "Processing ~a --> ~a~%" source target) (invoke "esbuild" source "--minify" (string-append "--outfile=" target))))))))) (propagated-inputs (list r-data-tree r-htmlwidgets)) (native-inputs `(("esbuild" ,esbuild) ("d3.v4.js" ,(origin (method url-fetch) (uri "https://d3js.org/d3.v4.js") (sha256 (base32 "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg")))))) (home-page "https://github.com/AdeelK93/collapsibleTree") (synopsis "Interactive collapsible tree diagrams using D3.js") (description "This is a package for interactive Reingold-Tilford tree diagrams created using D3.js, where every node can be expanded and collapsed by clicking on it. Tooltips and color gradients can be mapped to nodes using a numeric column in the source data frame.") (license license:gpl3+))) (define-public r-rapiclient (package (name "r-rapiclient") (version "0.1.3") (source (origin (method url-fetch) (uri (cran-uri "rapiclient" version)) (sha256 (base32 "1pm4kdga2nz1cpmchdb0ad8gr3bqfm84b1kl32cyc0x3x5rr2syz")))) (properties `((upstream-name . "rapiclient"))) (build-system r-build-system) (propagated-inputs (list r-httr r-jsonlite r-yaml)) (home-page "https://github.com/bergant/rapiclient") (synopsis "Dynamic OpenAPI/Swagger client") (description "This package lets you access services specified in OpenAPI (formerly Swagger) format. It is not a code generator. The client is generated dynamically as a list of R functions.") (license license:expat))) (define-public r-rappdirs (package (name "r-rappdirs") (version "0.3.3") (source (origin (method url-fetch) (uri (cran-uri "rappdirs" version)) (sha256 (base32 "1161i3jgjvzjv4p8qbz9r976fnggkcrw3mlj4yd1h2svnijrz5a9")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/rappdirs/") (synopsis "Determine where to save data, caches, and logs") (description "This package provides an easy way to determine which directories on the user's computer should be used to save data, caches and logs. It is a port of Python's @url{https://github.com/ActiveState/appdirs,Appdirs} to R.") (license license:expat))) (define-public r-rastervis (package (name "r-rastervis") (version "0.51.6") (source (origin (method url-fetch) (uri (cran-uri "rasterVis" version)) (sha256 (base32 "12cl201gwah0bn14ji4nbygayd77w5fck9zkcikhrda5s0chvgb1")))) (properties `((upstream-name . "rasterVis"))) (build-system r-build-system) (propagated-inputs (list r-hexbin r-lattice r-latticeextra r-raster r-rcolorbrewer r-sp r-terra r-viridislite r-zoo)) (home-page "https://oscarperpinan.github.io/rastervis/") (synopsis "Visualization methods for raster data") (description "This package provides methods for enhanced visualization and interaction with raster data. It implements visualization methods for quantitative data and categorical data, both for univariate and multivariate rasters. It also provides methods to display spatiotemporal rasters, and vector fields.") (license license:gpl3))) (define-public r-rentrez (package (name "r-rentrez") (version "1.2.3") (source (origin (method url-fetch) (uri (cran-uri "rentrez" version)) (sha256 (base32 "0x1g2f6hvkqqlb39z8m5qxhcvsizddic5i7rpqw0wy77xfbna9gv")))) (properties `((upstream-name . "rentrez"))) (build-system r-build-system) (propagated-inputs (list r-httr r-jsonlite r-xml)) (native-inputs (list r-knitr)) (home-page "https://docs.ropensci.org/rentrez/") (synopsis "Entrez in R") (description "This package provides an R interface to the NCBI's EUtils API, allowing users to search databases like GenBank PubMed, process the results of those searches and pull data into their R sessions.") (license license:expat))) (define-public r-renv (package (name "r-renv") (version "1.0.7") (source (origin (method url-fetch) (uri (cran-uri "renv" version)) (sha256 (base32 "01s5g4w96s0jz9xa1gdj8y4pfvz8cf3gg0kz2smh6f3l4f5baq3v")))) (properties `((upstream-name . "renv"))) (build-system r-build-system) (native-inputs (list r-knitr)) (home-page "https://rstudio.github.io/renv") (synopsis "Project environments") (description "This package provides a dependency management toolkit for R. Using renv, you can create and manage project-local R libraries, save the state of these libraries to a lockfile, and later restore your library as required. Together, these tools can help make your projects more isolated, portable, and reproducible.") (license license:expat))) ;; TODO: esbuild (define-public r-learnr (package (name "r-learnr") (version "0.11.5") (source (origin (method url-fetch) (uri (cran-uri "learnr" version)) (sha256 (base32 "01xig6ijsjnkwdjh03zdp86mqm5pjlqp9br34pn644rf98qg8k2y")))) (build-system r-build-system) (native-inputs (list esbuild r-knitr)) (propagated-inputs (list r-checkmate r-digest r-ellipsis r-evaluate r-htmltools r-htmlwidgets r-jsonlite r-knitr r-lifecycle r-markdown r-promises r-rappdirs r-renv r-rlang r-rmarkdown r-rprojroot r-shiny r-withr)) (home-page "https://rstudio.github.io/learnr/") (synopsis "Interactive tutorials for R") (description "This package provides tools to create interactive tutorials using R Markdown. Use a combination of narrative, figures, videos, exercises, and quizzes to create self-paced tutorials for learning about R and R packages.") (license license:asl2.0))) (define-public r-analytics (package (name "r-analytics") (version "3.0") (source (origin (method url-fetch) (uri (cran-uri "analytics" version)) (sha256 (base32 "0js3c8lwj3knccb55nq03cbjlf4w390p9aid2mi5x80l3ayd9in1")))) (build-system r-build-system) (propagated-inputs (list r-car r-cluster r-fractal r-lmtest r-mass r-np r-powerplus r-robust r-trend r-tsa r-urca r-vim)) (home-page "https://cran.r-project.org/web/packages/analytics/") (synopsis "Collection of data analysis tools") (description "This package is a collection of data analysis tools. It includes tools for regression outlier detection in a fitted linear model, stationary bootstrap using a truncated geometric distribution, a comprehensive test for weak stationarity, column means by group, weighted biplots, and a heuristic to obtain a better initial configuration in non-metric MDS.") (license license:gpl2))) (define-public r-here (package (name "r-here") (version "1.0.1") (source (origin (method url-fetch) (uri (cran-uri "here" version)) (sha256 (base32 "0srlr8h8qmr0wrmp7gs4g2ry5dni2hx8n947bik3s3a26f091v88")))) (properties `((upstream-name . "here"))) (build-system r-build-system) (propagated-inputs (list r-rprojroot)) (native-inputs (list r-knitr)) (home-page "https://here.r-lib.org/") (synopsis "Simpler way to find files") (description "This package lets you construct paths to your project's files. Use the @code{here} function as a drop-in replacement for @code{file.path}, it will always locate the files relative to your project root.") (license license:expat))) (define-public r-reticulate (package (name "r-reticulate") (version "1.36.0") (source (origin (method url-fetch) (uri (cran-uri "reticulate" version)) (sha256 (base32 "0bxxdcinpw76pwnx3a3hcqhq7gjvs4sxcza464vz333xq9s2337l")))) (build-system r-build-system) (arguments (list #:phases '(modify-phases %standard-phases (add-after 'unpack 'build-reproducibly (lambda _ (setenv "PYTHONHASHSEED" "0") (setenv "PYTHONDONTWRITEBYTECODE" "1")))))) (inputs (list python)) (propagated-inputs (list r-here r-jsonlite r-matrix r-png r-rappdirs r-rcpp r-rcpptoml r-rlang r-withr)) (native-inputs (list r-knitr)) (home-page "https://github.com/rstudio/reticulate") (synopsis "R interface to Python") (description "This package provides an interface from R 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.") (license license:asl2.0))) (define-public r-bibtex (package (name "r-bibtex") (version "0.5.1") (source (origin (method url-fetch) (uri (cran-uri "bibtex" version)) (sha256 (base32 "1l9y945qmpla68rx6dnaxc83vmvkw26cw4zzfgfsvi36wsja1hgk")))) (build-system r-build-system) (propagated-inputs (list r-backports)) (home-page "https://github.com/romainfrancois/bibtex") (synopsis "Bibtex parser") (description "This package provides a utility for R to parse a bibtex file.") (license license:gpl2+))) (define-public r-billboarder (package (name "r-billboarder") (version "0.4.1") (source (origin (method url-fetch) (uri (cran-uri "billboarder" version)) (sha256 (base32 "0byj1ilwnmq9n9gswsnj17r8pzhm4fp6567nbz1xfmlvl3402qkn")) (snippet '(delete-file "inst/htmlwidgets/lib/billboard/billboard.pkgd.min.js")))) (properties `((upstream-name . "billboarder"))) (build-system r-build-system) (arguments `(#:phases (modify-phases %standard-phases (add-after 'unpack 'process-javascript (lambda* (#:key inputs #:allow-other-keys) (with-directory-excursion "inst/htmlwidgets/lib/billboard/" (let ((source (assoc-ref inputs "js-billboard")) (target "billboard.pkgd.min.js")) (format #true "Processing ~a --> ~a~%" source target) (invoke "esbuild" source "--minify" (string-append "--outfile=" target))))))))) (propagated-inputs (list r-ggplot2 r-htmltools r-htmlwidgets r-jsonlite r-magrittr r-rlang r-scales r-shiny)) (native-inputs `(("r-knitr" ,r-knitr) ("esbuild" ,esbuild) ;; It is not ideal to use this concatenated (but not minified) ;; JavaScript file, as the original source is written in TypeScript. ;; However, this can still be considered source code as it is readable ;; and can be modified. ("js-billboard" ,(origin (method url-fetch) (uri "https://unpkg.com/billboard.js@3.6.3/dist/billboard.js") (sha256 (base32 "1lyj4yl95qgh06iygb2y2mdg1zxijzxi5h85z7kp8ngm825z6rpi")))))) (home-page "https://github.com/dreamRs/billboarder") (synopsis "Create interactive charts with the JavaScript Billboard library") (description "This package provides an @code{htmlwidgets} interface to billboard.js, a re-usable easy interface JavaScript chart library, based on D3 v4+. Chart types include line charts, scatterplots, bar/lollipop charts, histogram/density plots, pie/donut charts and gauge charts. All charts are interactive, and a proxy method is implemented to smoothly update a chart without rendering it again in shiny apps.") (license license:expat))) (define-public r-ggseqlogo (package (name "r-ggseqlogo") (version "0.2") (source (origin (method url-fetch) (uri (cran-uri "ggseqlogo" version)) (sha256 (base32 "1drncw73950dzjx3lyyfqrxm3rdbrp44n27sl4b17m9d0crdbgqw")))) (build-system r-build-system) (propagated-inputs (list r-ggplot2)) (native-inputs (list r-knitr)) (home-page "https://github.com/omarwagih/ggseqlogo") (synopsis "ggplot2 extension for drawing genetic sequence logos") (description "The range of functions provided by this package makes it possible to draw highly versatile genomic sequence logos. Features include, but are not limited to, modifying colour schemes and fonts used to draw the logo, generating multiple logo plots, and aiding the visualisation with annotations. Sequence logos can easily be combined with other ggplot2 plots.") ;; Unspecified version of the LGPL. (license license:lgpl3+))) (define-public r-ggsci (package (name "r-ggsci") (version "3.0.3") (source (origin (method url-fetch) (uri (cran-uri "ggsci" version)) (sha256 (base32 "1m806aqp97pp57i6dl5ykmfhd4lvd1gpamzghks8fx1nksh935mx")))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-scales)) (native-inputs (list r-knitr)) (home-page "https://nanx.me/ggsci/") (synopsis "Scientific journal and sci-fi themed color palettes for ggplot2") (description "This package provides a collection of ggplot2 color palettes inspired by plots in scientific journals, data visualization libraries, science fiction movies, and TV shows.") (license license:gpl3))) (define-public r-ggsignif (package (name "r-ggsignif") (version "0.6.4") (source (origin (method url-fetch) (uri (cran-uri "ggsignif" version)) (sha256 (base32 "02mjailzyqkdnzky60dgampw2sq6mnn7s66fk0lhy32s8apm280i")))) (build-system r-build-system) (native-inputs (list r-knitr)) (propagated-inputs (list r-ggplot2)) (home-page "https://github.com/const-ae/ggsignif") (synopsis "Significance brackets for ggplot2") (description "Enrich your ggplots with group-wise comparisons. This package provides an easy way to indicate if two groups are significantly different. Commonly this is shown by a bracket on top connecting the groups of interest which itself is annotated with the level of significance. The package provides a single layer that takes the groups for comparison and the test as arguments and adds the annotation to the plot.") (license license:gpl3))) (define-public r-rstatix (package (name "r-rstatix") (version "0.7.2") (source (origin (method url-fetch) (uri (cran-uri "rstatix" version)) (sha256 (base32 "1891a976k2qjrh1vkzfg8icxblxa978wbazg7mqq8pcw3nmzbip0")))) (properties `((upstream-name . "rstatix"))) (build-system r-build-system) (propagated-inputs (list r-broom r-car r-corrplot r-dplyr r-generics r-magrittr r-purrr r-rlang r-tibble r-tidyr r-tidyselect)) (home-page "https://rpkgs.datanovia.com/rstatix/") (synopsis "Pipe-friendly framework for basic statistical tests") (description "This package provides a simple and intuitive pipe-friendly framework, coherent with the @code{tidyverse} design philosophy, for performing basic statistical tests, including t-test, Wilcoxon test, ANOVA, Kruskal-Wallis and correlation analyses. The output of each test is automatically transformed into a tidy data frame to facilitate visualization. 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(license license:gpl2))) (define-public r-flextable (package (name "r-flextable") (version "0.9.5") (source (origin (method url-fetch) (uri (cran-uri "flextable" version)) (sha256 (base32 "14mq27k7998405qwpdpxa1csbf5pdgzj9s892xm95bd4chnshdvw")))) (build-system r-build-system) (propagated-inputs (list r-data-table r-gdtools r-htmltools r-knitr r-officer r-ragg r-rlang r-rmarkdown r-uuid r-xml2)) (native-inputs (list r-knitr)) (home-page "https://davidgohel.github.io/flextable") (synopsis "Functions for tabular reporting") (description "This package provides tools to create pretty tables for HTML documents and other formats. Functions are provided to let users create tables, modify and format their content. It extends the @code{officer} package and can be used within R markdown documents when rendering to HTML and to Word documents.") (license license:gpl3))) (define-public r-writexl (package (name "r-writexl") (version "1.5.0") (source (origin (method url-fetch) (uri (cran-uri "writexl" version)) (sha256 (base32 "1kkd17xw7giy1k2azw1xnagka7ihicp17bi7nzlm3gqay1cdqlz2")))) (build-system r-build-system) (inputs (list zlib)) (home-page "https://github.com/ropensci/writexl") (synopsis "Export data frames to xlsx format") (description "This package provides a data frame to xlsx exporter based on libxlsxwriter.") (license license:bsd-2))) (define-public r-writexls (package (name "r-writexls") (version "6.5.0") (source (origin (method url-fetch) (uri (cran-uri "WriteXLS" version)) (sha256 (base32 "1rkc0r6l7cfz7h83i7gw6g0nlyy347mdh6bj73j0f8mdv3nmwwn4")))) (properties `((upstream-name . "WriteXLS"))) (build-system r-build-system) (inputs (list perl)) (home-page "https://github.com/marcschwartz/WriteXLS") (synopsis "Create Excel 2003 (XLS) and Excel 2007 (XLSX) files") (description "This package provides a cross-platform Perl-based R function to create Excel 2003 (XLS) and Excel 2007 (XLSX) files from one or more data frames. Each data frame will be written to a separate named worksheet in the Excel spreadsheet. The worksheet name will be the name of the data frame it contains or can be specified by the user.") (license license:gpl2+))) (define-public r-wrs2 (package (name "r-wrs2") (version "1.1-6") (source (origin (method url-fetch) (uri (cran-uri "WRS2" version)) (sha256 (base32 "1wsnsl4gy1hbgxfzzhfybak0jqmxq9fsh3scqyxydd7ia9r2n52k")))) (properties `((upstream-name . "WRS2"))) (build-system r-build-system) (propagated-inputs (list r-mass r-plyr r-reshape)) (native-inputs (list r-knitr)) (home-page "https://r-forge.r-project.org/projects/psychor/") (synopsis "Collection of robust statistical methods") (description "R-wrs2 offers a range of strong stats methods from Wilcox WRS functions. It implements robust t-tests, both independent and dependent, robust ANOVA, including designs with between-within subjects, quantile ANOVA, robust correlation, robust mediation, and nonparametric ANCOVA models using robust location measures.") (license license:gpl3))) (define-public r-biasedurn (package (name "r-biasedurn") (version "2.0.11") (source (origin (method url-fetch) (uri (cran-uri "BiasedUrn" version)) (sha256 (base32 "0dvmkrdmhfh4swilyxf10y856kx0zf9sj1gc0g62bm6r5jhz35b2")))) (properties `((upstream-name . "BiasedUrn"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/BiasedUrn/") (synopsis "Biased Urn model distributions") (description "This package provides statistical models of biased sampling in the form of univariate and multivariate noncentral hypergeometric distributions, including Wallenius' noncentral hypergeometric distribution and Fisher's noncentral hypergeometric distribution (also called extended hypergeometric distribution).") (license license:gpl3))) (define-public r-golem (package (name "r-golem") (version "0.4.1") (source (origin (method url-fetch) (uri (cran-uri "golem" version)) (sha256 (base32 "0pcvp2rmwzvl0wi73fp9pmjq1rrknq2h45sfvbjhmbz8ilvr8zpa")))) (properties `((upstream-name . "golem"))) (build-system r-build-system) (propagated-inputs (list r-attempt r-config r-here r-htmltools r-rlang r-shiny r-yaml)) (native-inputs (list r-knitr)) (home-page "https://github.com/ThinkR-open/golem") (synopsis "Framework for robust Shiny applications") (description "This package implements an opinionated framework for building a production- ready Shiny application. Golem contains a series of tools like dependency management, version management, easy installation and deployment or documentation management.") (license license:expat))) (define-public r-goplot (package (name "r-goplot") (version "1.0.2") (source (origin (method url-fetch) (uri (cran-uri "GOplot" version)) (sha256 (base32 "1y8dv0kbzpr9za91njw0x233vx5d13vqml9hmpddcyi9s6va5nix")))) (properties `((upstream-name . "GOplot"))) (build-system r-build-system) (propagated-inputs (list r-ggdendro r-ggplot2 r-gridextra r-rcolorbrewer)) (home-page "https://github.com/wencke/wencke.github.io") (synopsis "Visualization of functional analysis data") (description "This package provides an implementation of multilayered visualizations for enhanced graphical representation of functional analysis data. It combines and integrates omics data derived from expression and functional annotation enrichment analyses. Its plotting functions have been developed with an hierarchical structure in mind: starting from a general overview to identify the most enriched categories (modified bar plot, bubble plot) to a more detailed one displaying different types of relevant information for the molecules in a given set of categories (circle plot, chord plot, cluster plot, Venn diagram, heatmap).") (license license:gpl2))) (define-public r-getopt (package (name "r-getopt") (version "1.20.4") (source (origin (method url-fetch) (uri (cran-uri "getopt" version)) (sha256 (base32 "12qy48adnibfi9rpv5qd8k3hipbc4q85514dsz0xnhdsdnz6rlw7")))) (build-system r-build-system) (home-page "https://github.com/trevorld/getopt") (synopsis "Command-line option processor for R") (description "This package is designed to be used with Rscript to write shebang scripts that accept short and long options. Many users will prefer to use the packages @code{optparse} or @code{argparse} which add extra features like automatically generated help options and usage texts, support for default values, positional argument support, etc.") (license license:gpl2+))) (define-public r-findpython (package (name "r-findpython") (version "1.0.8") (source (origin (method url-fetch) (uri (cran-uri "findpython" version)) (sha256 (base32 "1dydchid5mc79253v5b86bnbg3rm78w0hs586c1rr56lmz5r12hg")))) (build-system r-build-system) (home-page "https://github.com/trevorld/findpython") (synopsis "Functions to find an acceptable Python binary") (description "This package was designed to find an acceptable Python binary that matches version and feature constraints.") (license license:expat))) ;; This in not the same as "r-argparser" (define-public r-argparse (package (name "r-argparse") (version "2.2.3") (source (origin (method url-fetch) (uri (cran-uri "argparse" version)) (sha256 (base32 "0x16zp6jh9asyval1kwkxzavwjhx3a47xzlc593kw1hz4bhw8355")))) (build-system r-build-system) (inputs (list python)) (propagated-inputs (list r-findpython r-jsonlite r-r6)) (native-inputs (list r-knitr)) (home-page "https://github.com/trevorld/argparse") (synopsis "Command line optional and positional argument parser") (description "This package provides a command line parser to be used with Rscript to write shebang scripts that gracefully accept positional and optional arguments and automatically generate usage notices.") (license license:gpl2+))) (define-public r-hash (package (name "r-hash") (version "2.2.6.3") (source (origin (method url-fetch) (uri (cran-uri "hash" version)) (sha256 (base32 "044ifii4gpinzi9vbv5aw0da956ccslxg34xmx24njf6x5dhn0wa")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/hash/") (synopsis "Implementation of hash/associated arrays/dictionaries") (description "This package implements a data structure similar to hashes in Perl and dictionaries in Python but with a purposefully R flavor. For objects of appreciable size, access using hashes outperforms native named lists and vectors.") (license license:gpl2+))) (define-public r-orddom (package (name "r-orddom") (version "3.1") (source (origin (method url-fetch) (uri (cran-uri "orddom" version)) (sha256 (base32 "165axs15fvwhrp89xd87l81q3h2qjll1vrwcsap645cwvb85nwsh")))) (build-system r-build-system) (propagated-inputs (list r-psych)) (home-page "https://cran.r-project.org/web/packages/orddom/") (synopsis "Ordinal dominance statistics") (description "This package provides tools to compute ordinal, statistics and effect sizes as an alternative to mean comparison: Cliff's delta or success rate difference (SRD), Vargha and Delaney's A or the Area Under a Receiver Operating Characteristic Curve (AUC), the discrete type of McGraw & Wong's Common Language Effect Size (CLES) or Grissom & Kim's Probability of Superiority (PS), and the Number needed to treat (NNT) effect size. Moreover, comparisons to Cohen's d are offered based on Huberty & Lowman's Percentage of Group (Non-)Overlap considerations.") (license license:gpl2))) (define-public r-deriv (package (name "r-deriv") (version "4.1.3") (source (origin (method url-fetch) (uri (cran-uri "Deriv" version)) (sha256 (base32 "130g3mv0z9sqs6y23a0a94512iiw05yr6fp378vhdxxbignzbnyv")))) (properties `((upstream-name . "Deriv"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/Deriv") (synopsis "Symbolic differentiation") (description "This package provides an R-based solution for symbolic differentiation. It admits user-defined functions as well as function substitution in arguments of functions to be differentiated. Some symbolic simplification is part of the work.") (license license:gpl3+))) (define-public r-doby (package (name "r-doby") (version "4.6.20") (source (origin (method url-fetch) (uri (cran-uri "doBy" version)) (sha256 (base32 "08nsl9xzyi2k7xkwa9mn91fn77ji0z9z5lm388pfdmydbfmpy2ks")))) (properties `((upstream-name . "doBy"))) (build-system r-build-system) (propagated-inputs (list r-broom r-deriv r-dplyr r-ggplot2 r-magrittr r-mass r-matrix r-microbenchmark r-pbkrtest r-tibble)) (native-inputs (list r-knitr)) (home-page "https://people.math.aau.dk/~sorenh/software/doBy/") (synopsis "Groupwise statistics, LSmeans, linear contrasts, and utilities") (description "This package contains: @itemize @item facilities for working with grouped data: @code{do} something to data stratified @code{by} some variables. @item implementations of least-squares means, general linear contrasts, and @item miscellaneous other utilities. @end itemize\n") (license license:gpl2+))) (define-public r-refgenome (package (name "r-refgenome") (version "1.7.7") (source (origin (method url-fetch) (uri (cran-uri "refGenome" version)) (sha256 (base32 "1za89bn3am1zgvm641qi1ab6kaqpll4rb9p9f1sjwvcgqq6065g5")))) (properties `((upstream-name . "refGenome"))) (build-system r-build-system) (propagated-inputs (list r-dbi r-doby r-rsqlite)) (home-page "https://cran.r-project.org/web/packages/refGenome/") (synopsis "Gene and splice site annotation using annotation data from Ensembl and UCSC") (description "This package contains functionality for importing and managing of downloaded genome annotation data from the Ensembl genome browser (European Bioinformatics Institute) and from the UCSC genome browser (University of California, Santa Cruz) and annotation routines for genomic positions and splice site positions.") (license license:gpl2))) (define-public r-basix (package (name "r-basix") (version "1.1") (source (origin (method url-fetch) (uri (cran-uri "BASIX" version)) (sha256 (base32 "18dkvv1iwskfnlpl6xridcgqpalbbpm2616mvc3hfrc0b26v01id")))) (properties `((upstream-name . "BASIX"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/BASIX/") (synopsis "Efficient C/C++ toolset for R") (description "BASIX provides some efficient C/C++ implementations of native R procedures to speed up calculations in R.") (license license:gpl2))) (define-public r-blockfest (package (name "r-blockfest") (version "2.0") (source (origin (method url-fetch) (uri (cran-uri "BlockFeST" version)) (sha256 (base32 "1fcl3yc1cf09znqbj787d3fd2kl5rp63la7pxawsgmap7nxwkp65")))) (properties `((upstream-name . "BlockFeST"))) (build-system r-build-system) (propagated-inputs (list r-basix)) (home-page "https://cran.r-project.org/web/packages/BlockFeST/") (synopsis "Bayesian calculation of region-specific fixation index") (description "This package provides an R implementation of an extension of the BayeScan software for codominant markers, adding the option to group individual SNPs into pre-defined blocks. A typical application of this new approach is the identification of genomic regions, genes, or gene sets containing one or more SNPs that evolved under directional selection.") (license license:gpl2))) (define-public r-proc (package (name "r-proc") (version "1.18.5") (source (origin (method url-fetch) (uri (cran-uri "pROC" version)) (sha256 (base32 "129cnh3kh9sr42nc7n9f14kr9svi3501834x40njynnzlr0wi4sm")))) (properties `((upstream-name . "pROC"))) (build-system r-build-system) (propagated-inputs (list r-plyr r-rcpp)) (home-page "https://web.expasy.org/pROC/") (synopsis "Display and analyze ROC curves") (description "This package provides tools for visualizing, smoothing and comparing receiver operating characteristic (ROC curves). The area under the curve (AUC) can be compared with statistical tests based on U-statistics or bootstrap. Confidence intervals can be computed for (p)AUC or ROC curves.") (license license:gpl3+))) (define-public r-rootsolve (package (name "r-rootsolve") (version "1.8.2.4") (source (origin (method url-fetch) (uri (cran-uri "rootSolve" version)) (sha256 (base32 "0p9qmn82bg0ks9hmh2dkygnzhxcnp5z8z8b8aq52w6clliz32sp1")))) (properties `((upstream-name . "rootSolve"))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/rootSolve/") (synopsis "Tools for the analysis of ordinary differential equations") (description "This package provides routines to find the root of nonlinear functions, and to perform steady-state and equilibrium analysis of @dfn{ordinary differential equations} (ODE). It includes routines that: @enumerate @item generate gradient and jacobian matrices (full and banded), @item find roots of non-linear equations by the Newton-Raphson method, @item estimate steady-state conditions of a system of (differential) equations in full, banded or sparse form, using the Newton-Raphson method, or by dynamically running, @item solve the steady-state conditions for uni- and multicomponent 1-D, 2-D, and 3-D partial differential equations, that have been converted to ordinary differential equations by numerical differencing (using the method-of-lines approach). @end enumerate\n") (license license:gpl2+))) (define-public r-abcanalysis (package (name "r-abcanalysis") (version "1.2.1") (source (origin (method url-fetch) (uri (cran-uri "ABCanalysis" version)) (sha256 (base32 "0wac1ksmnxa36v99ca4hv8k0rsh3igwpcllmlv9wf7i9kgqviqwi")))) (properties `((upstream-name . 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(license license:gpl3))) (define-public r-slam (package (name "r-slam") (version "0.1-50") (source (origin (method url-fetch) (uri (cran-uri "slam" version)) (sha256 (base32 "1ggqcf8l1z2hpi7qy4mg0d2ps48bjjb8z1y1xz6fq162cqrbz6bq")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/slam/") (synopsis "Sparse lightweight arrays and matrices") (description "This package contains data structures and algorithms for sparse arrays and matrices, based on index arrays and simple triplet representations, respectively.") (license license:gpl2))) (define-public r-manipulatewidget (package (name "r-manipulatewidget") (version "0.11.1") (source (origin (method url-fetch) (uri (cran-uri "manipulateWidget" version)) (sha256 (base32 "1dpgzmiv08afm57yxr017b014lfn9h3pa4w65prk5k3dgn6p4wsv")))) (properties `((upstream-name . "manipulateWidget"))) (build-system r-build-system) (propagated-inputs (list r-base64enc r-codetools r-htmltools r-htmlwidgets r-knitr r-miniui r-shiny r-shinyjs r-webshot)) (native-inputs (list r-knitr)) (home-page "https://github.com/rte-antares-rpackage/manipulateWidget/") (synopsis "Add even more interactivity to interactive charts") (description "This package lets you create in just a few lines of R code a nice user interface to modify the data or the graphical parameters of one or multiple interactive charts. It is useful to quickly explore visually some data or for package developers to generate user interfaces easy to maintain.") (license license:gpl2+))) (define-public r-a3 (package (name "r-a3") (version "1.0.0") (source (origin (method url-fetch) (uri (cran-uri "A3" version)) (sha256 (base32 "017hq9pjsv1h9i7cqk5cfx27as54shlhdsdvr6jkhb8jfkpdb6cw")))) (properties `((upstream-name . "A3"))) (build-system r-build-system) (propagated-inputs (list r-pbapply r-xtable)) (home-page "https://cran.r-project.org/web/packages/A3/") (synopsis "Error metrics for predictive models") (description "This package supplies tools for tabulating and analyzing the results of predictive models. The methods employed are applicable to virtually any predictive model and make comparisons between different methodologies straightforward.") (license license:gpl2+))) (define-public r-infotheo (package (name "r-infotheo") (version "1.2.0.1") (source (origin (method url-fetch) (uri (cran-uri "infotheo" version)) (sha256 (base32 "1m1979vf8rvq3534mp1hihfadikhxrg3p6ac3hirz96kgb4qxyy0")))) (build-system r-build-system) (home-page "http://homepage.meyerp.com/software") (synopsis "Information-theoretic measures") (description "This package implements various measures of information theory based on several entropy estimators.") (license license:gpl3+))) (define-public r-nsprcomp (package (name "r-nsprcomp") (version "0.5.1-2") (source (origin (method url-fetch) (uri (cran-uri "nsprcomp" version)) (sha256 (base32 "1zlc1ximx96f235c0l8qfs6vbp1kpnbf943wxsfahnnlnxvwi59f")))) (properties `((upstream-name . "nsprcomp"))) (build-system r-build-system) (home-page "https://sigg-iten.ch/research/") (synopsis "Non-negative and sparse PCA") (description "This package implements two methods for performing a constrained principal component analysis (PCA), where non-negativity and/or sparsity constraints are enforced on the principal axes (PAs). The function @code{nsprcomp} computes one principal component (PC) after the other. Each PA is optimized such that the corresponding PC has maximum additional variance not explained by the previous components. In contrast, the function @code{nscumcomp} jointly computes all PCs such that the cumulative variance is maximal. Both functions have the same interface as the @code{prcomp} function from the @code{stats} package (plus some extra parameters).") (license license:gpl2+))) (define-public r-cmplot (package (name "r-cmplot") (version "4.5.1") (source (origin (method url-fetch) (uri (cran-uri "CMplot" version)) (sha256 (base32 "0ml6n1wjxrnq13042jihpjlmm6vmkaiks9n49qp7v7rg47gn2ik8")))) (properties `((upstream-name . "CMplot"))) (build-system r-build-system) (home-page "https://github.com/YinLiLin/CMplot") (synopsis "Circle Manhattan plot") (description "Circle Manhattan Plot is an R package that can lay out genome-wide association study P-value results in both traditional rectangular patterns, QQ-plot and novel circular ones. United in only one bull's eye style plot, association results from multiple traits can be compared interactively, thereby to reveal both similarities and differences between signals. Additional functions include: highlight signals, a group of SNPs, chromosome visualization and candidate genes around SNPs.") (license license:gpl2+))) (define-public r-precrec (package (name "r-precrec") (version "0.14.4") (source (origin (method url-fetch) (uri (cran-uri "precrec" version)) (sha256 (base32 "03hvp5h7fz4v2aswxim0mqgj9rdrhnk5xqz212161kpcrw6m67z8")))) (properties `((upstream-name . "precrec"))) (build-system r-build-system) (propagated-inputs (list r-assertthat r-data-table r-ggplot2 r-gridextra r-rcpp r-rlang r-withr)) (native-inputs (list r-knitr)) (home-page "https://evalclass.github.io/precrec/") (synopsis "Calculate accurate precision-recall and ROC curves") (description "This package provides tools for accurate calculations and visualization of precision-recall and ROC (Receiver Operator Characteristics) curves.") (license license:gpl3))) (define-public r-netrep (package (name "r-netrep") (version "1.2.7") (source (origin (method url-fetch) (uri (cran-uri "NetRep" version)) (sha256 (base32 "02ss45giv30pi31b5rysa36bn5c4fs5x58g4vb0arz9cnicznv97")))) (properties `((upstream-name . "NetRep"))) (build-system r-build-system) (propagated-inputs (list r-abind r-bh r-foreach r-rcolorbrewer r-rcpp r-rcpparmadillo r-rhpcblasctl r-statmod)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/package=NetRep") (synopsis "Permutation testing network module preservation across datasets") (description "This package provides functions for assessing the replication/preservation of a network module's topology across datasets through permutation testing.") (license license:gpl2))) (define-public r-intergraph (package (name "r-intergraph") (version "2.0-4") (source (origin (method url-fetch) (uri (cran-uri "intergraph" version)) (sha256 (base32 "1jarzhrgm5g8z2h10h8x7jk9q2al6rx5kgnwvwi2199am6gjypsq")))) (properties `((upstream-name . "intergraph"))) (build-system r-build-system) (propagated-inputs (list r-igraph r-network)) (native-inputs (list r-knitr)) (home-page "https://mbojan.github.io/intergraph") (synopsis "Coercion routines for network data objects") (description "Functions implemented in this package allow coercing (i.e. convert) network data between classes provided by other R packages. Currently supported classes are those defined in packages @code{network} and @code{igraph}.") 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(license license:gpl2+))) (define-public r-abcoptim (package (name "r-abcoptim") (version "0.15.0") (source (origin (method url-fetch) (uri (cran-uri "ABCoptim" version)) (sha256 (base32 "1ih0xk88qhsmpvnxf56041wx5sk8as2f4f2gdnpnwdym9mbr9n4b")))) (properties `((upstream-name . "ABCoptim"))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) (home-page "https://github.com/gvegayon/ABCoptim/") (synopsis "Optimization of Artificial Bee Colony algorithm") (description "Artificial Bee Colony (ABC) is one of the most recently defined algorithms by Dervis Karaboga in 2005, motivated by the intelligent behavior of honey bees. It is as simple as Particle Swarm Optimization (PSO) and Differential Evolution (DE) algorithms, and uses only common control parameters such as colony size and maximum cycle number. The @code{r-abcoptim} implements the Artificial bee colony optimization algorithm @url{http://mf.erciyes.edu.tr/abc/pub/tr06_2005.pdf}. This version is a work-in-progress and is written in R code.") (license license:expat))) (define-public r-abcp2 (package (name "r-abcp2") (version "1.2") (source (origin (method url-fetch) (uri (cran-uri "ABCp2" version)) (sha256 (base32 "1s2skkxpzss7c29i8600psgrp0hl46jcrxqrmy2b4db8hc0kcnbx")))) (properties `((upstream-name . "ABCp2"))) (build-system r-build-system) (propagated-inputs (list r-mass)) (home-page "https://cran.r-project.org/web/packages/ABCp2/") (synopsis "Approximate Bayesian Computational Model for Estimating P2") (description "This package tests the goodness of fit of a distribution of offspring to the Normal, Poisson, and Gamma distribution and estimates the proportional paternity of the second male (P2) based on the best fit distribution.") 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(license license:gpl3))) (define-public r-furrr (package (name "r-furrr") (version "0.3.1") (source (origin (method url-fetch) (uri (cran-uri "furrr" version)) (sha256 (base32 "12z4q0fn7asxis17hisi82bvfabl5if1338lmfqmkrwv5rg7748d")))) (build-system r-build-system) (propagated-inputs (list r-future r-globals r-lifecycle r-purrr r-rlang r-vctrs)) (home-page "https://github.com/DavisVaughan/furrr") (synopsis "Apply mapping functions in parallel using futures") (description "This package provides implementations of the family of @code{map()} functions from the @code{purrr} package that can be resolved using any @code{future}-supported backend, e.g. parallel on the local machine or distributed on a compute cluster.") 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(license license:gpl2+))) (define-public r-pscl (package (name "r-pscl") (version "1.5.9") (source (origin (method url-fetch) (uri (cran-uri "pscl" version)) (sha256 (base32 "1zkfzrc1cr3f5dlz0mv45ym0as1yp9gicds6lhxpj13qk38zz1c0")))) (build-system r-build-system) (propagated-inputs (list r-mass)) (home-page "https://github.com/atahk/pscl/") (synopsis "Political science computational laboratory") (description "The @code{pscl} is an R package providing classes and methods for: @enumerate @item Bayesian analysis of roll call data (item-response models); @item elementary Bayesian statistics; @item maximum likelihood estimation of zero-inflated and hurdle models for count data; @item utility functions. @end enumerate") (license license:gpl2))) (define-public r-accelmissing (package (name "r-accelmissing") (version "1.4") (source (origin (method url-fetch) (uri (cran-uri "accelmissing" version)) (sha256 (base32 "1nql9inx6azdzi3z4sfm2vdml2mms6krl8wzlf1dn1c97ahn57fy")))) (build-system r-build-system) (propagated-inputs (list r-mice r-pscl)) (home-page "https://cran.r-project.org/web/packages/accelmissing/") (synopsis "Missing value imputation for accelerometer data") (description "This package provides a statistical method to impute the missing values in accelerometer data. The methodology includes both parametric and semi-parametric multiple imputations under the zero-inflated Poisson lognormal model. It also provides multiple functions to preprocess the accelerometer data previous to the missing data imputation. These include detecting the wearing and the non-wearing time, selecting valid days and subjects, and creating plots.") (license license:gpl2+))) (define-public r-mhsmm (package (name "r-mhsmm") (version "0.4.21") (source (origin (method url-fetch) (uri (cran-uri "mhsmm" version)) (sha256 (base32 "1fibgpl65bl3rwlf9dhlams3gxbjqgwcd26gb0flp4wln6pl8d99")))) (build-system r-build-system) (propagated-inputs (list r-mvtnorm)) (home-page "https://github.com/jaredo/mhsmm/") (synopsis "Inference for hidden Markov and semi-Markov models") (description "The @code{r-mhsmm} package implements estimation and prediction methods for hidden Markov and semi-Markov models for multiple observation sequences. Such techniques are of interest when observed data is thought to be dependent on some unobserved (or hidden) state. Also, this package is suitable for equidistant time series data, with multivariate and/or missing data. Allows user defined emission distributions.") (license license:gpl2+))) (define-public r-nleqslv (package (name "r-nleqslv") (version "3.3.5") (source (origin (method url-fetch) (uri (cran-uri "nleqslv" version)) (sha256 (base32 "0fjby0qva2lp2i7x752wva0z15xqys9fgrrcfimqszg65wnig60j")))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/nleqslv/") (synopsis "Solve systems of nonlinear equations") (description "The @code{r-nleqslv} package solves a system of nonlinear equations using a Broyden or a Newton method with a choice of global strategies such as line search and trust region. There are options for using a numerical or user supplied Jacobian, for specifying a banded numerical Jacobian and for allowing a singular or ill-conditioned Jacobian.") (license license:gpl2+))) (define-public r-phyclust (package (name "r-phyclust") (version "0.1-34") (source (origin (method url-fetch) (uri (cran-uri "phyclust" version)) (sha256 (base32 "1wzmd02ng7zphn97xdra3hgivrxqpizqcy5kpg45sk7jx4q7016j")))) (properties `((upstream-name . "phyclust"))) (build-system r-build-system) (propagated-inputs (list r-ape)) (home-page "https://snoweye.github.io/phyclust/") (synopsis "Studying phyloclustering and exploring DNA sequence data") (description "@dfn{Phylogenetic clustering} (phyloclustering) is an evolutionary continuous time Markov Chain model-based approach to identify population structure from molecular data without assuming linkage equilibrium. The package @code{phyclust} provides a convenient implementation of phyloclustering for DNA and SNP data, capable of clustering individuals into subpopulations and identifying molecular sequences representative of those subpopulations. It is designed in @code{C} for performance and interfaced with @code{R} for visualization.") (license license:gpl2+))) (define-public r-physicalactivity (package (name "r-physicalactivity") (version "0.2-4") (source (origin (method url-fetch) (uri (cran-uri "PhysicalActivity" version)) (sha256 (base32 "0b27prkv3x6v2afz0y53ccs9scibpc7nj54n0hpd9fgn1wyg4c40")))) (properties `((upstream-name . "PhysicalActivity"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/PhysicalActivity/") (synopsis "Processing accelerometer data for physical activity measurement") (description "This @code{r-physicalactivity} package provides a function @code{wearingMarking} for classification of monitored wear and nonwear time intervals in accelerometer data collected to assess physical activity. The package also contains functions for making plots of accelerometer data and obtaining the summary of various information including daily monitor wear time and the mean monitor wear time during valid days. The revised package version 0.2-1 improved the functions regarding speed, robustness and add better support for time zones and daylight saving. In addition, several functions were added: @enumerate @item the @code{markDelivery} can classify days for ActiGraph delivery by mail; @item the @code{markPAI} can categorize physical activity intensity level based on user-defined cut-points of accelerometer counts. @end enumerate It also supports importing ActiGraph (AGD) files with @code{readActigraph} and @code{queryActigraph} functions.") (license license:gpl3+))) (define-public r-acc (package (name "r-acc") (version "1.3.3") (source (origin (method url-fetch) (uri (cran-uri "acc" version)) (sha256 (base32 "1ii2vm47djxbixa75h690q1s2f9m9x6i8nkygik93j6dayr6kr1m")))) (build-system r-build-system) (propagated-inputs (list r-circlize r-dbi r-ggplot2 r-iterators r-mhsmm r-nleqslv r-physicalactivity r-plyr r-r-utils r-rcpp r-rcpparmadillo r-rsqlite r-zoo)) (home-page "https://cran.r-project.org/web/packages/acc/") (synopsis "Exploring accelerometer data") (description "This package processes accelerometer data from uni-axial and tri-axial devices and generates data summaries. Also, includes functions to plot, analyze, and simulate accelerometer data.") (license license:gpl2+))) (define-public r-rbenchmark (package (name "r-rbenchmark") (version "1.0.0") (source (origin (method url-fetch) (uri (cran-uri "rbenchmark" version)) (sha256 (base32 "010fn3qwnk2k411cbqyvra1d12c3bhhl3spzm8kxffmirj4p2al9")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/rbenchmark/") (synopsis "Benchmarking routine for R") (description "This @code{r-rbenchmark} package is inspired by the Perl module Benchmark, and is intended to facilitate benchmarking of arbitrary R code. The library consists of just one function, benchmark, which is a simple wrapper around system.time. Given a specification of the benchmarking process (counts of replications, evaluation environment) and an arbitrary number of expressions, benchmark evaluates each of the expressions in the specified environment, replicating the evaluation as many times as specified, and returning the results conveniently wrapped into a data frame.") (license license:gpl2+))) (define-public r-mitools (package (name "r-mitools") (version "2.4") (source (origin (method url-fetch) (uri (cran-uri "mitools" version)) (sha256 (base32 "0c2x2n1p53lcw0vx4vmy5j7m2f95i7g2iwbryl89imr99rvz617j")))) (build-system r-build-system) (propagated-inputs (list r-dbi)) (home-page "https://cran.r-project.org/web/packages/mitools/") (synopsis "Tools for multiple imputation of missing data") (description "This package provides tools to perform analyses and combine results from multiple-imputation datasets.") (license license:gpl2))) (define-public r-mixsqp (package (name "r-mixsqp") (version "0.3-54") (source (origin (method url-fetch) (uri (cran-uri "mixsqp" version)) (sha256 (base32 "13pv3mmz514kl4svxqwyk5b241dy1q52khwdc6rmh712ia8xxl7p")))) (properties `((upstream-name . "mixsqp"))) (build-system r-build-system) (propagated-inputs (list r-irlba r-rcpp r-rcpparmadillo)) (native-inputs (list r-knitr)) (home-page "https://github.com/stephenslab/mixsqp") (synopsis "Sequential quadratic programming for maximum-likelihood estimation") (description "This package provides an optimization method based on sequential quadratic programming for maximum likelihood estimation of the mixture proportions in a finite mixture model where the component densities are known. The algorithm is expected to obtain solutions that are at least as accurate as the state-of-the-art MOSEK interior-point solver, and they are expected to arrive at solutions more quickly when the number of samples is large and the number of mixture components is not too large.") (license license:expat))) (define-public r-magick (package (name "r-magick") (version "2.8.3") (source (origin (method url-fetch) (uri (cran-uri "magick" version)) (sha256 (base32 "0yf08ns5qgqi2bzvxvawip521ji2rgvvfrhj747zb6ci5qnm4awk")))) (properties '((updater-extra-inputs . ("imagemagick")))) (build-system r-build-system) (inputs (list imagemagick pcre2 zlib)) (propagated-inputs (list r-curl r-magrittr r-rcpp)) (native-inputs (list pkg-config r-knitr)) (home-page "https://github.com/ropensci/magick") (synopsis "Advanced graphics and image-processing in R") (description "This package provides bindings to ImageMagick, a comprehensive image processing library. It supports many common formats (PNG, JPEG, TIFF, PDF, etc.) and manipulations (rotate, scale, crop, trim, flip, blur, etc). All operations are vectorized via the Magick++ STL meaning they operate either on a single frame or a series of frames for working with layers, collages, or animation. In RStudio, images are automatically previewed when printed to the console, resulting in an interactive editing environment.") (license license:expat))) (define-public r-survey (package (name "r-survey") (version "4.4-2") (source (origin (method url-fetch) (uri (cran-uri "survey" version)) (sha256 (base32 "1ggisal5g16p3n03bch7ymawd4hig3fmm02nhxy1z5zh48qhyjla")))) (build-system r-build-system) (propagated-inputs (list r-lattice r-matrix r-minqa r-mitools r-numderiv r-rcpp r-rcpparmadillo r-survival)) (native-inputs (list r-r-rsp)) (home-page "https://r-survey.r-forge.r-project.org/survey/") (synopsis "Analysis of complex survey samples") (description "This package provides tools for the analysis of complex survey samples. The provided features include: summary statistics, two-sample tests, rank tests, generalised linear models, cumulative link models, Cox models, loglinear models, and general maximum pseudolikelihood estimation for multistage stratified, cluster-sampled, unequally weighted survey samples; variances by Taylor series linearisation or replicate weights; post-stratification, calibration, and raking; two-phase subsampling designs; graphics; PPS sampling without replacement; principal components, and factor analysis.") ;; Either version of the GPL. (license (list license:gpl2 license:gpl3)))) (define-public r-gee (package (name "r-gee") (version "4.13-26") (source (origin (method url-fetch) (uri (cran-uri "gee" version)) (sha256 (base32 "1323qv2hiinixmwcb8rfvf5qmkffnnq9f1g8kj9amwsimfsm71cs")))) (properties `((upstream-name . "gee"))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/gee/") (synopsis "Generalized estimation equation solver") (description "This package provides a solver for generalized estimation equations.") (license license:gpl2))) (define-public r-tab (package (name "r-tab") (version "5.1.1") (source (origin (method url-fetch) (uri (cran-uri "tab" version)) (sha256 (base32 "1kg8c1safi9klkx2mdkmsf5dn9piy4jljwd4ma7g4jz2rwl4jzhv")))) (properties `((upstream-name . "tab"))) (build-system r-build-system) (propagated-inputs (list r-dplyr r-kableextra r-knitr r-mass r-survey)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/tab/") (synopsis "Create summary tables for statistical reports") (description "This package contains functions for creating various types of summary tables, e.g. comparing characteristics across levels of a categorical variable and summarizing fitted generalized linear models, generalized estimating equations, and Cox proportional hazards models. Functions are available to handle data from simple random samples as well as complex surveys.") (license license:gpl3+))) (define-public r-tarchetypes (package (name "r-tarchetypes") (version "0.8.0") (source (origin (method url-fetch) (uri (cran-uri "tarchetypes" version)) (sha256 (base32 "18vn2mx5nqlib0by5v7493g8gsbzcdbg0dn92cpbf713r69v1lbk")))) (properties `((upstream-name . "tarchetypes"))) (build-system r-build-system) (propagated-inputs (list r-digest r-dplyr r-fs r-rlang r-targets r-tibble r-tidyselect r-vctrs r-withr)) (home-page "https://docs.ropensci.org/tarchetypes/") (synopsis "Archetypes for Targets") (description "Function-oriented Make-like declarative pipelines for statistics and data science are supported in the targets R package. As an extension to targets, the tarchetypes package provides convenient user-side functions to make targets easier to use. By establishing reusable archetypes for common kinds of targets and pipelines, these functions help express complicated reproducible pipelines concisely and compactly. The methods in this package were influenced by the drake R package by Will Landau (2018) .") (license license:expat))) (define-public r-targets (package (name "r-targets") (version "1.6.0") (source (origin (method url-fetch) (uri (cran-uri "targets" version)) (sha256 (base32 "1ddpbhvdydxm62k6ay7hpqjh8kh2isjpcdh3gygzcdrghx6d7x65")))) (properties `((upstream-name . "targets"))) (build-system r-build-system) (propagated-inputs (list r-base64url r-callr r-cli r-codetools r-data-table r-digest r-igraph r-knitr r-ps r-r6 r-rlang r-secretbase r-tibble r-tidyselect r-vctrs r-yaml)) (native-inputs (list r-knitr)) (home-page "https://docs.ropensci.org/targets/") (synopsis "Dynamic function-oriented Make-like declarative pipelines") (description "This package provides a pipeline toolkit for statistics and data science in R; the @code{targets} package brings function-oriented programming to Make-like declarative pipelines. It orchestrates a pipeline as a graph of dependencies, skips steps that are already up to date, runs the necessary computation with optional parallel workers, abstracts files as R objects, and provides tangible evidence that the results are reproducible given the underlying code and data. The methodology in this package borrows from GNU Make (2015, ISBN:978-9881443519) and drake (2018, ).") (license license:expat))) (define-public r-tidygeocoder (package (name "r-tidygeocoder") (version "1.0.5") (source (origin (method url-fetch) (uri (cran-uri "tidygeocoder" version)) (sha256 (base32 "1ffj8ka5miv3jnds7fdrkcqdc3m2w1ab724z9m10biky213skqka")))) (properties `((upstream-name . "tidygeocoder"))) (build-system r-build-system) (propagated-inputs (list r-dplyr r-httr r-jsonlite r-lifecycle r-progress r-tibble)) (native-inputs (list r-knitr)) (home-page "https://jessecambon.github.io/tidygeocoder/") (synopsis "Intuitive interface for getting data from geocoding services") (description "Tidygeocoder makes getting data from geocoding services easy. A unified high-level interface is provided for a selection of supported geocoding services and results are returned in tibble format.") (license license:expat))) (define-public r-dvmisc (package (name "r-dvmisc") (version "1.1.4") (source (origin (method url-fetch) (uri (cran-uri "dvmisc" version)) (sha256 (base32 "01v6sixx0f3nrn6ymfifb3pvd2msfrwm21kmdv38laxq29vc4rsi")))) (build-system r-build-system) (propagated-inputs (list r-cubature r-data-table r-dplyr r-ggplot2 r-mass r-mvtnorm r-pracma r-rbenchmark r-rcpp r-survey r-tab)) (home-page "https://cran.r-project.org/web/packages/dvmisc/") (synopsis "Faster computation of common statistics and miscellaneous functions") (description "This package implements faster versions of base R functions (e.g. mean, standard deviation, covariance, weighted mean), mostly written in C++, along with miscellaneous functions for various purposes (e.g. create the histogram with fitted probability density function or probability mass function curve, create the body mass index groups, assess the linearity assumption in logistic regression).") (license license:gpl2))) (define-public r-accelerometry (package (name "r-accelerometry") (version "3.1.2") (source (origin (method url-fetch) (uri (cran-uri "accelerometry" version)) (sha256 (base32 "13xzrwhr4i1nj9c8vrmfdg2rmrc8n446iihcyxmy99sm99hpzyip")))) (build-system r-build-system) (propagated-inputs (list r-dvmisc r-rcpp)) (home-page "https://cran.r-project.org/web/packages/accelerometry/") (synopsis "Functions for processing accelerometer data") (description "This package provides a collection of functions that perform operations on time-series accelerometer data, such as identify the non-wear time, flag minutes that are part of an activity bout, and find the maximum 10-minute average count value. The functions are generally very flexible, allowing for a variety of algorithms to be implemented.") (license license:gpl3))) (define-public r-absim (package (name "r-absim") (version "0.2.6") (source (origin (method url-fetch) (uri (cran-uri "AbSim" version)) (sha256 (base32 "16ddjk8b6xw80ch4jis1y751i9561wdxh0gifbf15qiz3vjckq8m")))) (properties `((upstream-name . "AbSim"))) (build-system r-build-system) (propagated-inputs (list r-ape r-powerlaw)) (home-page "https://cran.r-project.org/web/packages/AbSim/") (synopsis "Time resolved simulations of antibody repertoires") (description "This package provides simulation methods for the evolution of antibody repertoires. The heavy and light chain variable region of both human and C57BL/6 mice can be simulated in a time-dependent fashion. Both single lineages using one set of V-, D-, and J-genes or full repertoires can be simulated. The algorithm begins with an initial V-D-J recombination event, starting the first phylogenetic tree. Upon completion, the main loop of the algorithm begins, with each iteration representing one simulated time step. Various mutation events are possible at each time step, contributing to a diverse final repertoire.") (license license:gpl2))) (define-public r-quic (package (name "r-quic") (version "1.1") (source (origin (method url-fetch) (uri (cran-uri "QUIC" version)) (sha256 (base32 "021bp9xbaih60qmss015ycblbv6d1dvb1z89y93zpqqnc2qhpv3c")))) (properties `((upstream-name . "QUIC"))) (build-system r-build-system) (home-page "https://www.cs.utexas.edu/users/sustik/QUIC/") (synopsis "Regularized sparse inverse covariance matrix estimation") (description "This package implements the regularized Gaussian maximum likelihood estimation of the inverse of a covariance matrix. It uses Newton's method and coordinate descent to solve the regularized inverse covariance matrix estimation problem.") ;; The project home page states that the release is under GPLv3 or later. ;; The CRAN page only says GPL-3. (license license:gpl3+))) (define-public r-quickjsr (package (name "r-quickjsr") (version "1.1.3") (source (origin (method url-fetch) (uri (cran-uri "QuickJSR" version)) (sha256 (base32 "0ccp7dx2jhlarfn48jc0mhci5kkj0r3ibh6rjnxswvp3yg2x2bgd")))) (properties `((upstream-name . "QuickJSR"))) (build-system r-build-system) (propagated-inputs (list r-jsonlite r-r6 r-rcpp)) (home-page "https://cran.r-project.org/package=QuickJSR") (synopsis "Interface for the QuickJS lightweight JavaScript engine") (description "This package provides an R interface to the @code{QuickJS} portable @code{JavaScript} engine. The engine is bundled entirely within the package, requiring no external system dependencies beyond a C compiler.") (license license:expat))) (define-public r-abundant (package (name "r-abundant") (version "1.2") (source (origin (method url-fetch) (uri (cran-uri "abundant" version)) (sha256 (base32 "15m3ngj5aipjg961yy5kvdg9xlfcpliw30dq6gchzxabhnfzcipd")))) (build-system r-build-system) (propagated-inputs (list r-glasso)) (home-page "https://cran.r-project.org/web/packages/abundant/") (synopsis "Abundant regression and high-dimensional principal fitted components") (description "This package provides tools to fit and predict with the high-dimensional principal fitted components model. This model is described by Cook, Forzani, and Rothman (2012) @url{doi:10.1214/11-AOS962}.") ;; The DESCRIPTION file states GPL-2, but since it directly depends on a ;; GPLv3+ package (QUIC) this likely means GPLv2+. (license license:gpl2+))) (define-public r-ac3net (package (name "r-ac3net") (version "1.2.2") (source (origin (method url-fetch) (uri (cran-uri "Ac3net" version)) (sha256 (base32 "1ns4n0xxz6p34c11bj0k7nzgmyqr9mis2b0g5nfz37dbikndyqyz")))) (properties `((upstream-name . "Ac3net"))) (build-system r-build-system) (propagated-inputs (list r-data-table)) (home-page "https://cran.r-project.org/web/packages/Ac3net/") (synopsis "Inferring directional conservative causal core gene networks") (description "This package infers directional Conservative causal core (gene) networks (C3NET). This is a version of the algorithm C3NET with directional network.") (license license:gpl3+))) (define-public r-aca (package (name "r-aca") (version "1.1") (source (origin (method url-fetch) (uri (cran-uri "ACA" version)) (sha256 (base32 "1i3hm27nvnkvc39xlh0d1blq8q0q02czmvgi3cazmjx3jvxay0vq")))) (properties `((upstream-name . 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Acceptance sampling is a methodology commonly used in quality control and improvement. International standards of acceptance sampling provide sampling plans for specific circumstances. The aim of this package is to provide an easy-to-use interface to visualize single, double or multiple sampling plans. In addition, methods have been provided to enable the user to assess sampling plans against pre-specified levels of performance, as measured by the probability of acceptance for a given level of quality in the lot.") (license license:gpl3+))) (define-public r-acclma (package (name "r-acclma") (version "1.0") (source (origin (method url-fetch) (uri (cran-uri "ACCLMA" version)) (sha256 (base32 "1na27sp18fq12gp6vxgqw1ffsz2yi1d8xvrxbrzx5g1kqxrayy0v")))) (properties `((upstream-name . "ACCLMA"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/ACCLMA/") (synopsis "ACC & LMA graph plotting") (description "This package contains a function that imports data from a @acronym{CSV, Comma-Separated Values} file, or uses manually entered data from the format (x, y, weight) and plots the appropriate @acronym{ACC, Absolute Concentration Curve} vs @acronym{LOI, Line of Independence} graph and @acronym{LMA, @acronym{LOI} Minus @acronym{ACC}} graph. The main function is @code{plotLMA} (source file, header) that takes a data set and plots the appropriate @acronym{LMA} and @acronym{ACC} graphs. If no source file (a string) was passed, a manual data entry window is opened. The header parameter indicates by TRUE/FALSE (false by default) if the source @acronym{CSV} file has a header row or not. The dataset should contain only one independent variable (x) and one dependent variable (y) and can contain a weight for each observation.") (license license:gpl2))) (define-public r-aspi (package (name "r-aspi") (version "0.2.0") (source (origin (method url-fetch) (uri (cran-uri "aspi" version)) (sha256 (base32 "0rhvxw243vvdv3hxa6pi343gcjc2cbxq1jzqirl9k1l4i3897l87")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/aspi/") (synopsis "Analysis of symmetry of parasitic infections") (description "This package provides tools for the analysis and visualization of bilateral asymmetry in parasitic infections.") (license license:gpl3+))) (define-public r-sandwich (package (name "r-sandwich") (version "3.1-0") (source (origin (method url-fetch) (uri (cran-uri "sandwich" version)) (sha256 (base32 "1yi3l2q63j0vlaqqh1x3bxb0i7v6lrmmbsc6s8gilfahxq2y3c4n")) (modules '((guix build utils))) (snippet '(with-directory-excursion "inst/doc" ;; These files are generated from Rnw files. (for-each delete-file (list "sandwich-OOP.pdf" "sandwich-OOP.R" "sandwich-OOP.Rnw" "sandwich-CL.R" "sandwich-CL.Rnw" "sandwich-CL.pdf" "sim-CL.rda" "sim-CL.R" "sandwich.pdf" "sandwich.R")))))) (build-system r-build-system) (propagated-inputs (list r-zoo)) (home-page "https://cran.r-project.org/web/packages/sandwich/") (synopsis "Robust Covariance Matrix Estimators") (description "This package provides model-robust standard error estimators for cross-sectional, time series, clustered, panel, and longitudinal data.") ;; Either version of the license. (license (list license:gpl2 license:gpl3)))) (define-public r-th-data (package (name "r-th-data") (version "1.1-2") (source (origin (method url-fetch) (uri (cran-uri "TH.data" version)) (sha256 (base32 "0wyyvm6l6yvqvfnd1c4l9ff5445zaq9lr0ihz8pg9kkggfslxya7")))) (properties `((upstream-name . "TH.data"))) (build-system r-build-system) (propagated-inputs (list r-mass r-survival)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/TH.data/") (synopsis "Shared data sets") (description "This package contains supporting data sets that are used in other packages maintained by Torsten Hothorn.") (license license:gpl3))) (define-public r-multcomp (package (name "r-multcomp") (version "1.4-25") (source (origin (method url-fetch) (uri (cran-uri "multcomp" version)) (sha256 (base32 "10njzzxdi3jw5f419s7chcynxkzyqmmvzf7jk7ybdrwrlqhpiylx")))) (build-system r-build-system) (propagated-inputs (list r-codetools r-mvtnorm r-sandwich r-survival r-th-data)) (home-page "https://cran.r-project.org/web/packages/multcomp/") (synopsis "Simultaneous inference in general parametric models") (description "Simultaneous tests and confidence intervals for general linear hypotheses in parametric models, including linear, generalized linear, linear mixed effects, and survival models. The package includes demos reproducing analyzes presented in the book \"Multiple Comparisons Using R\" (Bretz, Hothorn, Westfall, 2010, CRC Press).") 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(license license:gpl3+))) (define-public r-emmeans (package (name "r-emmeans") (version "1.10.1") (source (origin (method url-fetch) (uri (cran-uri "emmeans" version)) (sha256 (base32 "175az87aj2zrjsi94vvca612krbhry7yqq6l03ybq31jhj7vc2fa")))) (build-system r-build-system) (propagated-inputs (list r-estimability r-mvtnorm r-numderiv)) (native-inputs (list r-knitr)) (home-page "https://github.com/rvlenth/emmeans") (synopsis "Estimated marginal means, aka least-squares means") (description "This package provides tools to obtain @dfn{estimated marginal means} (EMMs) for many linear, generalized linear, and mixed models. It can be used to compute contrasts or linear functions of EMMs, trends, and comparisons of slopes.") ;; Either version of the license. (license (list license:gpl2 license:gpl3)))) (define-public r-pwr (package (name "r-pwr") (version "1.3-0") (source (origin (method url-fetch) (uri (cran-uri "pwr" version)) (sha256 (base32 "1kfzy73v3z6ipc3kdfkcjrp4b4p5k54nwk796gqi36srm93hgc2v")))) (build-system r-build-system) (native-inputs (list r-knitr)) (home-page "https://github.com/heliosdrm/pwr") (synopsis "Basic functions for power analysis") (description "This package provides power analysis functions along the lines of Cohen (1988).") 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(license license:gpl2))) (define-public r-coin (package (name "r-coin") (version "1.4-3") (source (origin (method url-fetch) (uri (cran-uri "coin" version)) (sha256 (base32 "0x5rh002w4xgczbvnh7qfv3qv4iv7p6vdrwwyvchqmzgygdh4qwa")))) (build-system r-build-system) (arguments (list #:phases '(modify-phases %standard-phases ;; This test fails because the file has an invalid encoding (add-after 'unpack 'remove-test-file-with-latin-encoding (lambda _ (delete-file "tests/regtest_size.R")))))) (propagated-inputs (list r-libcoin r-matrixstats r-modeltools r-multcomp r-mvtnorm r-survival)) (home-page "https://coin.r-forge.r-project.org") (synopsis "Conditional inference procedures in a permutation test framework") (description "This package provides conditional inference procedures for the general independence problem including two-sample, K-sample (non-parametric ANOVA), correlation, censored, ordered and multivariate problems.") (license license:gpl2))) (define-public r-bayesplot (package (name "r-bayesplot") (version "1.11.1") (source (origin (method url-fetch) (uri (cran-uri "bayesplot" version)) (sha256 (base32 "0c1q1znp9vd0w6l35xa208bgiwr5f2w8j2c97v6ml4z0j5rycwag")))) (build-system r-build-system) (inputs (list pandoc)) (native-inputs (list r-knitr)) (propagated-inputs (list r-dplyr r-ggplot2 r-ggridges r-glue r-posterior r-reshape2 r-rlang r-tibble r-tidyselect)) (home-page "https://mc-stan.org/bayesplot") (synopsis "Plotting for Bayesian models") (description "This package provides plotting functions for posterior analysis, model checking, and MCMC diagnostics. The package is designed not only to provide convenient functionality for users, but also a common set of functions that can be easily used by developers working on a variety of R packages for Bayesian modeling.") 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(license license:gpl2))) (define-public r-sjstats (package (name "r-sjstats") (version "0.18.2") (source (origin (method url-fetch) (uri (cran-uri "sjstats" version)) (sha256 (base32 "0a1y6bqyvgs0avzasr8g6vwcxcnj4d9g0rfz2qiznwadpjzqw66h")))) (build-system r-build-system) (propagated-inputs (list r-bayestestr r-broom r-datawizard r-dplyr r-effectsize r-emmeans r-insight r-lme4 r-magrittr r-mass r-modelr r-parameters r-performance r-purrr r-rlang r-sjlabelled r-sjmisc r-tidyr)) (home-page "https://github.com/strengejacke/sjstats") (synopsis "Functions for common statistical computations") (description "This package provides a collection of convenient functions for common statistical computations, which are not directly provided by R's @code{base} or @code{stats} packages. This package aims at providing, first, shortcuts for statistical measures, which otherwise could only be calculated with additional effort. Second, these shortcut functions are generic, and can be applied not only to vectors, but also to other objects as well. The focus of most functions lies on summary statistics or fit measures for regression models, including generalized linear models, mixed effects models and Bayesian models.") (license license:gpl3))) (define-public r-glmmtmb (package (name "r-glmmtmb") (version "1.1.9") (source (origin (method url-fetch) (uri (cran-uri "glmmTMB" version)) (sha256 (base32 "0qw9ww3l506vivs6k8v5cdiv6lf9a32f0d1iq6bizxxh0ywsdmck")))) (properties `((upstream-name . "glmmTMB"))) (build-system r-build-system) (propagated-inputs (list r-lme4 r-matrix r-mgcv r-nlme r-numderiv r-rcppeigen r-tmb)) (native-inputs (list r-knitr r-rmarkdown)) ; for vignettes (home-page "https://github.com/glmmTMB") (synopsis "Generalized linear mixed models") (description "Fit linear and generalized linear mixed models with various extensions, including zero-inflation. The models are fitted using maximum likelihood estimation via the Template Model Builder. Random effects are assumed to be Gaussian on the scale of the linear predictor and are integrated out using the Laplace approximation. Gradients are calculated using automatic differentiation.") (license license:agpl3+))) (define-public r-bayestestr (package (name "r-bayestestr") (version "0.13.2") (source (origin (method url-fetch) (uri (cran-uri "bayestestR" version)) (sha256 (base32 "15xnmjay0s9kgaj25z43cxky4qcjn3gv8yd1x548jzbxzxxma07n")))) (properties `((upstream-name . "bayestestR"))) (build-system r-build-system) (propagated-inputs (list r-datawizard r-insight)) (native-inputs (list r-knitr)) (home-page "https://github.com/easystats/bayestestR") (synopsis "Describe Bayesian models and posterior distributions") (description "This package provides utilities to understand and describe posterior distributions and Bayesian models. It includes point-estimates such as @dfn{Maximum A Posteriori} (MAP), measures of dispersion such as @dfn{Highest Density Interval} (HDI), and indices used for null-hypothesis testing (such as ROPE percentage and pd).") (license license:gpl3))) (define-public r-performance (package (name "r-performance") (version "0.11.0") (source (origin (method url-fetch) (uri (cran-uri "performance" version)) (sha256 (base32 "03zs162lah8yv2x2q829ifc3jwy7m89r6md4ildjz8qmfjf0js82")))) (build-system r-build-system) (propagated-inputs (list r-bayestestr r-datawizard r-insight)) (home-page "https://easystats.github.io/performance/") (synopsis "Assessment of regression models performance") (description "This package provides utilities for computing measures to assess model quality, which are not directly provided by R's @code{base} or @code{stats} packages. These include e.g. measures like r-squared, intraclass correlation coefficient, root mean squared error or functions to check models for overdispersion, singularity or zero-inflation and more. Functions apply to a large variety of regression models, including generalized linear models, mixed effects models and Bayesian models.") (license license:gpl3))) (define-public r-ggeffects (package (name "r-ggeffects") (version "1.5.2") (source (origin (method url-fetch) (uri (cran-uri "ggeffects" version)) (sha256 (base32 "1f5ralb5fkcv2rflsl0y9lgwdmx6zzv3s1087lql9x5vjd1hkvcg")))) (build-system r-build-system) (propagated-inputs (list r-insight)) (native-inputs (list r-knitr)) (home-page "https://github.com/strengejacke/ggeffects") (synopsis "Create tidy data frames of marginal effects for ggplot") (description "This package provides tools to compute marginal effects from statistical models and return the result as tidy data frames. These data frames are ready to use with the @code{ggplot2} package. Marginal effects can be calculated for many different models. Interaction terms, splines and polynomial terms are also supported. The two main functions are @code{ggpredict()} and @code{ggeffect()}. There is a generic @code{plot()} method to plot the results using @code{ggplot2}.") (license license:gpl3))) (define-public r-effectsize (package (name "r-effectsize") (version "0.8.7") (source (origin (method url-fetch) (uri (cran-uri "effectsize" version)) (sha256 (base32 "07lfa0pvqhanjyyx9hs6gdqw1zyi1y21k539jgvgnrvixfilfkb2")))) (properties `((upstream-name . 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"effsize"))) (build-system r-build-system) (home-page "https://github.com/mtorchiano/effsize/") (synopsis "Efficient effect size computation") (description "This package provides a collection of functions to compute the standardized effect sizes for experiments (Cohen d, Hedges g, Cliff delta, Vargha-Delaney A). The computation algorithms have been optimized to allow efficient computation even with very large data sets.") (license license:gpl2))) (define-public r-sjplot (package (name "r-sjplot") (version "2.8.15") (source (origin (method url-fetch) (uri (cran-uri "sjPlot" version)) (sha256 (base32 "10lvn8dnckpjjpapmf0d2zwjkzjvs4iiswd3rmijzviz4ichhxjs")))) (properties `((upstream-name . 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(license license:gpl3))) (define-public r-ini (package (name "r-ini") (version "0.3.1") (source (origin (method url-fetch) (uri (cran-uri "ini" version)) (sha256 (base32 "04yqij344dwm0xqgara8xia42mlmij3i8711qbb5534w05a1l6bv")))) (build-system r-build-system) (home-page "https://github.com/dvdscripter/ini") (synopsis "Read and write configuration files") (description "This package provides tools to parse simple @code{.ini} configuration files to an structured list. Users can manipulate this resulting list with @code{lapply()} functions. This same structured list can be used to write back to file after modifications.") (license license:gpl3))) (define-public r-gillespiessa2 (package (name "r-gillespiessa2") (version "0.3.0") (source (origin (method url-fetch) (uri (cran-uri "GillespieSSA2" version)) (sha256 (base32 "0wjz0fh9cwvaw6n7hs2lkh818jzbjl11ps5gxnjqizz8gfp9fr10")))) (properties `((upstream-name . "GillespieSSA2"))) (build-system r-build-system) (propagated-inputs (list r-assertthat r-dplyr r-dynutils r-matrix r-purrr r-rcpp r-rcppxptrutils r-readr r-rlang r-stringr r-tidyr)) (native-inputs (list r-knitr)) (home-page "https://github.com/rcannood/GillespieSSA2") (synopsis "Gillespie's stochastic simulation algorithm") (description "This package provides a fast, scalable, and versatile framework for simulating large systems with Gillespie's @dfn{Stochastic Simulation Algorithm} (SSA). This package is the spiritual successor to the GillespieSSA package. Benefits of this package include major speed improvements (>100x), easier to understand documentation, and many unit tests that try to ensure the package works as intended.") 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The package both helps the user to setup a local git installation, and also provides a back-end for git/ssh client libraries to authenticate with existing user credentials.") (license license:expat))) (define-public r-gert (package (name "r-gert") (version "2.0.1") (source (origin (method url-fetch) (uri (cran-uri "gert" version)) (sha256 (base32 "14nh7j0xz1s4ngsd5n3hixr534z843a38y57grwqkkh9g21q9mqf")))) (properties `((upstream-name . "gert"))) (build-system r-build-system) (inputs (list libgit2 openssh openssl zlib)) (propagated-inputs (list r-askpass r-credentials r-openssl r-rstudioapi r-sys r-zip)) (native-inputs (list pkg-config r-knitr)) (home-page "https://docs.ropensci.org/gert/") (synopsis "Simple Git client for R") (description "This package provides a simple git client for R based on libgit2 with support for SSH and HTTPS remotes. All functions in gert use basic R data types (such as vectors and data-frames) for their arguments and return values. User credentials are shared with command line git through the @code{git-credential} store and SSH keys stored on disk or ssh-agent.") (license license:expat))) (define-public r-usethis (package (name "r-usethis") (version "2.2.3") (source (origin (method url-fetch) (uri (cran-uri "usethis" version)) (sha256 (base32 "1cyy1k5iansg63ziph4w76kzl59dgmam7m2wp6sz9d93bjcrh34d")))) (build-system r-build-system) (propagated-inputs (list r-cli r-clipr r-crayon r-curl r-desc r-fs r-gert r-gh r-glue r-jsonlite r-lifecycle r-purrr r-rappdirs r-rlang r-rprojroot r-rstudioapi r-whisker r-withr r-yaml)) (home-page "https://github.com/r-lib/usethis") (synopsis "Automate R package and project setup") (description "This package helps you to automate R package and project setup tasks that are otherwise performed manually. This includes setting up unit testing, test coverage, continuous integration, Git, GitHub integration, licenses, Rcpp, RStudio projects, and more.") 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(license license:gpl2))) (define-public r-remotes (package (name "r-remotes") (version "2.5.0") (source (origin (method url-fetch) (uri (cran-uri "remotes" version)) (sha256 (base32 "0345s9q0fyv0wrxkklcy97h7bi85jfb3vwkh80px926d4qa3yrjd")))) (build-system r-build-system) (native-inputs (list r-knitr)) (home-page "https://github.com/r-lib/remotes#readme") (synopsis "R package installation from remote repositories") (description "Download and install R packages stored in GitHub, BitBucket, or plain subversion or git repositories. This package is a lightweight replacement of the @code{install_*} functions in the @code{devtools} package. Indeed most of the code was copied over from @code{devtools}.") (license license:gpl2+))) (define-public r-xopen (package (name "r-xopen") (version "1.0.0") (source (origin (method url-fetch) (uri (cran-uri "xopen" version)) (sha256 (base32 "1vrvgdika1d63dwygynbv2wmd87ll8dji5dy89hj576n8hw601z2")))) (build-system r-build-system) (propagated-inputs (list r-processx)) (home-page "https://github.com/r-lib/xopen#readme") (synopsis "Open system files, URLs, anything") (description "This package provides a cross-platform solution to open files, directories or URLs with their associated programs.") (license license:expat))) (define-public r-rcmdcheck (package (name "r-rcmdcheck") (version "1.4.0") (source (origin (method url-fetch) (uri (cran-uri "rcmdcheck" version)) (sha256 (base32 "1l696byn3kjq2xvz4wxybzaj6ink85h4lz3a35v2132ba5yyzm5v")))) (build-system r-build-system) (propagated-inputs (list r-callr r-cli r-curl r-desc r-digest r-pkgbuild r-prettyunits r-r6 r-rprojroot r-sessioninfo r-withr r-xopen)) (home-page "https://github.com/r-Lib/rcmdcheck#readme") (synopsis "Run R CMD check from R and capture results") (description "Run @code{R CMD check} from R programmatically, and capture the results of the individual checks.") (license license:expat))) (define-public r-rapportools (package (name "r-rapportools") (version "1.1") (source (origin (method url-fetch) (uri (cran-uri "rapportools" version)) (sha256 (base32 "0qr86idng12g6hdd764j0wmli700v7rjhw7jdjxj0ka8xm5v7ymm")))) (build-system r-build-system) (propagated-inputs (list r-mass r-pander r-plyr r-reshape2)) (home-page "https://cran.r-project.org/web/packages/rapportools/") (synopsis "Miscellaneous helper functions with sane defaults for reporting") (description "This package provides helper functions that act as wrappers to more advanced statistical methods with the advantage of having sane defaults for quick reporting.") (license license:agpl3+))) (define-public r-pander (package (name "r-pander") (version "0.6.5") (source (origin (method url-fetch) (uri (cran-uri "pander" version)) (sha256 (base32 "144zkq5w7v6fpzk3x40i0baybbp0y6x2ckh4b9qljryas9mhgp9a")))) (build-system r-build-system) (propagated-inputs (list r-digest r-rcpp)) (native-inputs (list r-knitr)) (home-page "https://rapporter.github.io/pander") (synopsis "Render R objects into Pandoc's markdown") (description "The main aim of the pander R package is to provide a minimal and easy tool for rendering R objects into Pandoc's markdown. The package is also capable of exporting/converting complex Pandoc documents (reports) in various ways.") ;; This package is licensed under either the AGPLv3+ or the very rarely ;; used OSL 3.0. (license license:agpl3+))) (define-public r-summarytools (package (name "r-summarytools") (version "1.0.1") (source (origin (method url-fetch) (uri (cran-uri "summarytools" version)) (sha256 (base32 "0gr95cd1ja8di6s0xghk6w7nj3bh3z4g7j7ixdy7f88q681aixgx")))) (build-system r-build-system) (propagated-inputs (list r-base64enc r-checkmate r-dplyr r-htmltools r-lubridate r-magick r-matrixstats r-pander r-pryr r-rapportools r-tibble r-tidyr)) (native-inputs (list r-knitr)) (home-page "https://github.com/dcomtois/summarytools") (synopsis "Tools to quickly and neatly summarize data") (description "This package provides tools for data frame summaries, cross-tabulations, weight-enabled frequency tables and common univariate statistics in concise tables available in a variety of formats (plain ASCII, Markdown and HTML). A good point-of-entry for exploring data, both for experienced and new R users.") (license license:gpl2))) (define-public r-lsei (package (name "r-lsei") (version "1.3-0") (source (origin (method url-fetch) (uri (cran-uri "lsei" version)) (sha256 (base32 "1dka0rigfw4vj809qma2dkiwjb3nw5635ynnba5cm299cn7hb2b2")))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "https://www.stat.auckland.ac.nz/~yongwang") (synopsis "Solve regression problems under equality/inequality constraints") (description "It contains functions that solve least squares linear regression problems under linear equality/inequality constraints. Functions for solving quadratic programming problems are also available, which transform such problems into least squares ones first.") (license license:gpl2+))) (define-public r-npsurv (package (name "r-npsurv") (version "0.5-0") (source (origin (method url-fetch) (uri (cran-uri "npsurv" version)) (sha256 (base32 "1ihxhb42cga1hssj2jv4ah0f4hlwsky899ij5261fzh1wxvdp1xw")))) (build-system r-build-system) (propagated-inputs (list r-lsei)) (home-page "https://www.stat.auckland.ac.nz/~yongwang") (synopsis "Nonparametric survival analysis") (description "This package contains functions for non-parametric survival analysis of exact and interval-censored observations.") (license license:gpl2+))) (define-public r-clustercrit (package (name "r-clustercrit") (version "1.3.0") (source (origin (method url-fetch) (uri (cran-uri "clusterCrit" version)) (sha256 (base32 "0raxlyvr3kr8c8bzjgs7hb9n76m314vzvfiz7c74v6cqpkmh6dkx")))) (properties `((upstream-name . "clusterCrit"))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "https://www.r-project.org/") (synopsis "Computing clustering validation indices") (description "The @code{clusterCrit} package provides an implementation of the following indices: Czekanowski-Dice, Folkes-Mallows, Hubert Γ, Jaccard, McNemar, Kulczynski, Phi, Rand, Rogers-Tanimoto, Russel-Rao or Sokal-Sneath. ClusterCrit defines several functions which compute internal quality indices or external comparison indices. The partitions are specified as an integer vector giving the index of the cluster each observation belongs to.") (license license:gpl2+))) (define-public r-clusteval (package (name "r-clusteval") (version "0.1") (source (origin (method url-fetch) (uri (cran-uri "clusteval" version)) (sha256 (base32 "1ld0bdl4fy8dsfzm3k7a37cyxc6pfc9qs31x4pxd3z5rslghz7rj")))) (build-system r-build-system) (propagated-inputs (list r-mvtnorm r-rcpp)) (home-page "https://cran.r-project.org/web/packages/clusteval/") (synopsis "Evaluation of clustering algorithms") (description "This R package provides a suite of tools to evaluate clustering algorithms, clusterings, and individual clusters.") (license license:expat))) (define-public r-clustergeneration (package (name "r-clustergeneration") (version "1.3.8") (source (origin (method url-fetch) (uri (cran-uri "clusterGeneration" version)) (sha256 (base32 "0w1sywv9cgl78wrsamh1zrig67r3grnyl27f036ipd1ab1b2510g")))) (properties `((upstream-name . "clusterGeneration"))) (build-system r-build-system) (propagated-inputs (list r-mass)) (home-page "https://cran.r-project.org/package=clusterGeneration") (synopsis "Random cluster generation (with specified degree of separation)") (description "The clusterGeneration package provides functions for generating random clusters, generating random covariance/correlation matrices, calculating a separation index (data and population version) for pairs of clusters or cluster distributions, and 1-D and 2-D projection plots to visualize clusters. The package also contains a function to generate random clusters based on factorial designs with factors such as degree of separation, number of clusters, number of variables, number of noisy variables.") (license license:gpl2+))) (define-public r-tweedie (package (name "r-tweedie") (version "2.3.5") (source (origin (method url-fetch) (uri (cran-uri "tweedie" version)) (sha256 (base32 "0ghwggdx6d391m7nay9n5li2xjqh3kmw416xx130sy2sxrgp8g4q")))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/tweedie/") (synopsis "Evaluation of Tweedie exponential family models") (description "Maximum likelihood computations for Tweedie families, including the series expansion (Dunn and Smyth, 2005; ) and the Fourier inversion (Dunn and Smyth, 2008; ), and related methods.") (license license:gpl2+))) (define-public r-rcppgsl (package (name "r-rcppgsl") (version "0.3.13") (source (origin (method url-fetch) (uri (cran-uri "RcppGSL" version)) (sha256 (base32 "1rwkin79ppkdz1y9pghxx29vlyvs84bylvqblkhj8r4w26y76ppy")))) (properties `((upstream-name . "RcppGSL"))) (build-system r-build-system) (propagated-inputs (list r-rcpp gsl)) (home-page "https://cran.r-project.org/web/packages/RcppGSL/") (synopsis "Rcpp integration for GSL vectors and matrices") (description "The GNU Scientific Library (or GSL) is a collection of numerical routines for scientific computing. It is particularly useful for C and C++ programs as it provides a standard C interface to a wide range of mathematical routines. There are over 1000 functions in total with an extensive test suite. The RcppGSL package provides an easy-to-use interface between GSL data structures and R using concepts from Rcpp which is itself a package that eases the interfaces between R and C++.") (license license:gpl2+))) (define-public r-mvabund (package (name "r-mvabund") (version "4.2.1") (source (origin (method url-fetch) (uri (cran-uri "mvabund" version)) (sha256 (base32 "01kss9dx4an1ir5zs46jypvhj8sdc8wcs00i1223ai09av4lcsgd")))) (build-system r-build-system) (propagated-inputs (list r-mass r-rcpp r-rcppgsl r-statmod r-tweedie)) (home-page "https://cran.r-project.org/web/packages/mvabund/") (synopsis "Statistical methods for analysing multivariate abundance data") (description "This package provides a set of tools for displaying, modeling and analysing multivariate abundance data in community ecology.") (license license:lgpl2.1+))) (define-public r-mvnfast (package (name "r-mvnfast") (version "0.2.8") (source (origin (method url-fetch) (uri (cran-uri "mvnfast" version)) (sha256 (base32 "1869xqq2wd7yw23q4ma5qawcnbdp7myafk6rdxazqymqak7f0wc8")))) (properties `((upstream-name . "mvnfast"))) (build-system r-build-system) (propagated-inputs (list r-bh r-rcpp r-rcpparmadillo)) (native-inputs (list r-knitr)) (home-page "https://github.com/mfasiolo/mvnfast/") (synopsis "Fast multivariate normal and Student's t methods") (description "This package provides computationally efficient tools related to the multivariate normal and Student's t distributions. The main functionalities are: simulating multivariate random vectors, evaluating multivariate normal or Student's t densities and Mahalanobis distances. These tools are developed using C++ code and of the OpenMP API.") (license license:gpl2+))) (define-public r-afex (package (name "r-afex") (version "1.3-1") (source (origin (method url-fetch) (uri (cran-uri "afex" version)) (sha256 (base32 "1a1ilqn5xz7kkiwwaqi911b1cf9zc78l9my0fvjq3l73hrzgnr2a")))) (build-system r-build-system) ;; This is needed for the vignette builder (arguments '(#:phases (modify-phases %standard-phases (add-after 'unpack 'set-HOME (lambda _ (setenv "HOME" "/tmp")))))) (propagated-inputs (list r-car r-lme4 r-lmertest r-pbkrtest r-reshape2)) (native-inputs (list r-knitr r-r-rsp)) ;vignette builder (home-page "https://afex.singmann.science/") (synopsis "Analysis of factorial experiments") (description "This package provides convenience functions for analyzing factorial experiments using ANOVA or mixed models.") (license license:gpl2+))) (define-public r-lmertest (package (name "r-lmertest") (version "3.1-3") (source (origin (method url-fetch) (uri (cran-uri "lmerTest" version)) (sha256 (base32 "1zd8gqjkazhxgpnnr484xwsq30p62fq8592nzyc171zjyplpbaim")))) (properties `((upstream-name . "lmerTest"))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-lme4 r-mass r-numderiv)) (home-page "https://github.com/runehaubo/lmerTestR") (synopsis "Tests in linear mixed effects models") (description "This package provides p-values in type I, II or III anova and summary tables for @code{lmer} model fits via Satterthwaite's degrees of freedom method. A Kenward-Roger method is also available via the @code{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.") (license license:gpl2+))) (define-public r-r2glmm (package (name "r-r2glmm") (version "0.1.2") (source (origin (method url-fetch) (uri (cran-uri "r2glmm" version)) (sha256 (base32 "0iim92blpa59vgz97c2pi05yhbjjmaffdbkbmk5kplfb2vmazgiy")))) (build-system r-build-system) (propagated-inputs (list r-afex r-data-table r-dplyr r-ggplot2 r-gridextra r-lmertest r-mass r-matrix r-mgcv r-pbkrtest)) (home-page "https://github.com/bcjaeger/r2glmm") (synopsis "Compute R squared for mixed (multilevel) models") (description "This package computes model and semi partial R squared with confidence limits for the linear and generalized linear mixed model (LMM and GLMM). The R squared measure from L. J. Edwards et al. (2008) is extended to the GLMM using @dfn{penalized quasi-likelihood} (PQL) estimation (see Jaeger et al. (2016)).") (license license:gpl2))) (define-public r-cmdfun (package (name "r-cmdfun") (version "1.0.2") (source (origin (method url-fetch) (uri (cran-uri "cmdfun" version)) (sha256 (base32 "1pbcq7hi2lcmqnghmy3q2fsk0c9fy5m0637acyzmc096fxbx723j")))) (properties `((upstream-name . "cmdfun"))) (build-system r-build-system) (propagated-inputs (list r-magrittr r-purrr r-r-utils r-rlang r-testthat r-usethis)) (native-inputs (list r-knitr)) (home-page "https://snystrom.github.io/cmdfun/") (synopsis "Framework for building interfaces to shell commands") (description "Writing interfaces to command line software is cumbersome. The cmdfun package provides a framework for building function calls to seamlessly interface with shell commands by allowing lazy evaluation of command line arguments. It also provides methods for handling user-specific paths to tool installs or secrets like API keys. Its focus is to equally serve package builders who wish to wrap command line software, and to help analysts stay inside R when they might usually leave to execute non-R software.") (license license:expat))) (define-public r-rslurm (package (name "r-rslurm") (version "0.6.2") (source (origin (method url-fetch) (uri (cran-uri "rslurm" version)) (sha256 (base32 "0z5lyrkvfh2201sc772gzbz3hc1mc04pxww611iwjf6qwzn5h0al")))) (properties `((upstream-name . "rslurm"))) (build-system r-build-system) (propagated-inputs (list r-whisker)) (native-inputs (list r-knitr)) (home-page "http://cyberhelp.sesync.org/rslurm/") (synopsis "Submit R calculations to a Slurm cluster") (description "This package provides functions that simplify submitting R scripts to a Slurm workload manager, in part by automating the division of embarrassingly parallel calculations across cluster nodes.") (license license:gpl3))) (define-public r-chk (package (name "r-chk") (version "0.9.1") (source (origin (method url-fetch) (uri (cran-uri "chk" version)) (sha256 (base32 "19q5ylkgrkdmnzg2df1lnrp2arbfzwfz4rbrr16j9ih2237kvd7r")))) (properties `((upstream-name . "chk"))) (build-system r-build-system) (propagated-inputs (list r-lifecycle r-rlang)) (native-inputs (list r-knitr)) (home-page "https://github.com/poissonconsulting/chk") (synopsis "Check user-supplied function arguments") (description "This is a package for developers to check user-supplied function arguments. It is designed to be simple, fast and customizable. Error messages follow the tidyverse style guide.") (license license:expat))) (define-public r-weights (package (name "r-weights") (version "1.0.4") (source (origin (method url-fetch) (uri (cran-uri "weights" version)) (sha256 (base32 "1fnchf7f0hyl514bk8sc3l884kg25kb5xm4mc2l28n6hm7l6bgpg")))) (build-system r-build-system) (propagated-inputs (list r-gdata r-hmisc r-lme4 r-mice)) (home-page "https://cran.r-project.org/web/packages/weights/") (synopsis "Weighting and weighted statistics") (description "This package Provides a variety of functions for producing simple weighted statistics, such as weighted Pearson's correlations, partial correlations, Chi-Squared statistics, histograms, and t-tests. Also now includes some software for quickly recoding survey data and plotting point estimates from interaction terms in regressions (and multiply imputed regressions). NOTE: Weighted partial correlation calculations pulled to address a bug.") (license license:gpl2+))) (define-public r-rcppalgos (package (name "r-rcppalgos") (version "2.8.3") (source (origin (method url-fetch) (uri (cran-uri "RcppAlgos" version)) (sha256 (base32 "0ppix426yg8rnh07z2clv634ynvvwmjlsjnsxh3srss6xa8yfrb0")))) (properties `((upstream-name . "RcppAlgos"))) (build-system r-build-system) (inputs (list gmp)) (propagated-inputs (list r-cpp11 r-gmp)) (native-inputs (list r-knitr)) (home-page "https://github.com/jwood000/RcppAlgos") (synopsis "High performance tools for combinatorics and computational mathematics") (description "This package provides optimized functions and flexible combinatorial iterators implemented in C++ for solving problems in combinatorics and computational mathematics. It utilizes the @code{RMatrix} class from @code{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. It is capable of generating specific combinations/permutations which sets up nicely for parallelization as well as random sampling. Gmp support permits exploration where the total number of results is large. Additionally, there are several high performance number theoretic functions that are useful for problems common in computational mathematics.") (license license:gpl2+))) (define-public r-rcppannoy (package (name "r-rcppannoy") (version "0.0.22") (source (origin (method url-fetch) (uri (cran-uri "RcppAnnoy" version)) (sha256 (base32 "0rcgvmlp3by57k562pbxsncirww1vv8zarfxrjzfgly4hzbj28cz")))) (properties `((upstream-name . "RcppAnnoy"))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) (home-page "https://cran.r-project.org/web/packages/RcppAnnoy/") (synopsis "Rcpp bindings for Annoy, a library for Approximate Nearest Neighbors") (description "Annoy is a small C++ library for Approximate Nearest Neighbors written for efficient memory usage as well an ability to load from and save to disk. This package provides an R interface.") ;; Annoy is released under ASL 2.0, but this wrapper is released under ;; GPLv2+. (license (list license:gpl2+ license:asl2.0)))) (define-public r-rcpphnsw (package (name "r-rcpphnsw") (version "0.6.0") (source (origin (method url-fetch) (uri (cran-uri "RcppHNSW" version)) (sha256 (base32 "03sqzz1993jsjm5vpyd1n1fpsrdfrky6dpv7m9ialhs1m00fv9m5")))) (properties `((upstream-name . "RcppHNSW"))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) (home-page "https://cran.r-project.org/web/packages/RcppHNSW/") (synopsis "Rcpp bindings for hnswlib, a library for approximate nearest neighbors") (description "Hnswlib is a C++ library for approximate nearest neighbors. This package provides a minimal R interface by relying on the Rcpp package.") ;; hnswlib is released under Version 2.0 of the Apache License. (license (list license:gpl3 license:asl2.0)))) (define-public r-rcppparallel (package (name "r-rcppparallel") (version "5.1.7") (source (origin (method url-fetch) (uri (cran-uri "RcppParallel" version)) (sha256 (base32 "175j0plh9gzy45sxsck0wdqfkjwdsbb17m9511czrgqsrswhxhzr")) (modules '((guix build utils))) (snippet '(delete-file-recursively "src/tbb/")))) (properties `((upstream-name . "RcppParallel"))) (build-system r-build-system) (arguments (list #:phases '(modify-phases %standard-phases (add-after 'unpack 'use-system-tbb (lambda* (#:key inputs #:allow-other-keys) (setenv "TBB_ROOT" (assoc-ref inputs "tbb"))))))) (inputs (list tbb-2020)) (home-page "https://rcppcore.github.io/RcppParallel/") (synopsis "Parallel programming tools for Rcpp") (description "This package provides high level functions for parallel programming with Rcpp. For example, the @code{parallelFor()} function can be used to convert the work of a standard serial @code{for} loop into a parallel one and the @code{parallelReduce()} function can be used for accumulating aggregates or other values.") (license license:gpl2))) (define-public r-ncdf4 (package (name "r-ncdf4") (version "1.22") (source (origin (method url-fetch) (uri (cran-uri "ncdf4" version)) (sha256 (base32 "040jpcgsb98s6knch0z3f3f5fpmlwks1grpvb9k8s02c9w0a5adr")))) (build-system r-build-system) (inputs (list netcdf zlib)) (home-page "https://cran.r-project.org/web/packages/ncdf4/index.html") (synopsis "R interface to Unidata netCDF format data files") (description "This package provides a high-level R interface to data files written using Unidata's netCDF library (version 4 or earlier), which are binary data files that are portable across platforms and include metadata information in addition to the data sets. Using this package, netCDF files can be opened and data sets read in easily. It is also easy to create new netCDF dimensions, variables, and files, in either version 3 or 4 format, and manipulate existing netCDF files.") (license license:gpl3+))) (define-public r-ncmisc (package (name "r-ncmisc") (version "1.2.0") (source (origin (method url-fetch) (uri (cran-uri "NCmisc" version)) (sha256 (base32 "10wzznqa26fxyj6bl979qmq29p3dkr8yap4s70l3mwhhk33zpz16")))) (properties `((upstream-name . "NCmisc"))) (build-system r-build-system) (home-page "https://cran.r-project.org/package=NCmisc") (synopsis "Functions for creating adaptive functions and scripts") (description "This package provides a set of handy functions. It includes a versatile one line progress bar, one line function timer with detailed output, time delay function, text histogram, object preview, CRAN package search, simpler package installer, Linux command install check, a flexible Mode function, top function, simulation of correlated data, and more.") (license license:gpl2+))) (define-public r-biocmanager (package (name "r-biocmanager") (version "1.30.22") (source (origin (method url-fetch) (uri (cran-uri "BiocManager" version)) (sha256 (base32 "0dg86nbh9h77ypaarsd79df24j0vnlm2df4zcmbhfasnsv0ck2ak")))) (properties `((upstream-name . "BiocManager"))) (build-system r-build-system) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/BiocManager/") (synopsis "Access the Bioconductor project package repository") (description "This package provides a convenient tool to install and update Bioconductor packages.") (license license:artistic2.0))) ;; TODO: one more minified JavaScript files is included that should be built ;; from the included .src.js files, but it is not entirely clear how. The ;; file is inst/htmlwidgets/lib/rglClass/rglClass.min.js. (define-public r-rgl (package (name "r-rgl") (version "1.3.1") (source (origin (method url-fetch) (uri (cran-uri "rgl" version)) (sha256 (base32 "0jbda1b4lrkcpdld369687pm7isy69l5sx1wg2yrpvvzvmcppslz")) (snippet '(delete-file "inst/htmlwidgets/lib/CanvasMatrix/CanvasMatrix.min.js")))) ;; For OpenGL and X11 support (properties '((updater-extra-inputs . ("glu" "libx11")))) (build-system r-build-system) (arguments (list #:phases '(modify-phases %standard-phases (add-after 'unpack 'process-javascript (lambda* (#:key inputs #:allow-other-keys) (with-directory-excursion "inst/htmlwidgets/lib/" (let ((source "CanvasMatrix/CanvasMatrix.src.js") (target "CanvasMatrix/CanvasMatrix.min.js")) (invoke "esbuild" source "--minify" (string-append "--outfile=" target))))))))) (native-inputs (list esbuild pkg-config r-knitr r-rmarkdown)) ;for vignettes (inputs (list freetype glu libpng libx11 zlib zlib)) (propagated-inputs (list r-base64enc r-htmltools r-htmlwidgets r-jsonlite r-knitr r-magrittr r-mime r-r6)) (home-page "https://r-forge.r-project.org/projects/rgl/") (synopsis "3D visualization using OpenGL") (description "This package provides medium to high level functions for 3D interactive graphics, including functions modelled on base graphics (@code{plot3d()}, etc.) as well as functions for constructing representations of geometric objects (@code{cube3d()}, etc.). Output may be on screen using OpenGL, or to various standard 3D file formats including WebGL, PLY, OBJ, STL as well as 2D image formats, including PNG, Postscript, SVG, PGF.") ;; Any version of the GPL. (license (list license:gpl2+ license:gpl3+)))) (define-public r-multicool (package (name "r-multicool") (version "1.0.1") (source (origin (method url-fetch) (uri (cran-uri "multicool" version)) (sha256 (base32 "07vcyp7yd1rzlldxzpzrdgifnw88z0maq2dgsqc218vyplgxwwmx")))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) (home-page "https://cran.r-project.org/web/packages/multicool/") (synopsis "Permutations of multisets in cool-lex order") (description "This package provides a set of tools to permute multisets without loops or hash tables and to generate integer partitions. Cool-lex order is similar to colexicographical order.") (license license:gpl2))) (define-public r-multidplyr (package (name "r-multidplyr") (version "0.1.3") (source (origin (method url-fetch) (uri (cran-uri "multidplyr" version)) (sha256 (base32 "18yl24s1g8wf3xi6f0k7jhs99ka4dslxf5p9ax9m5l1rbva5xdwj")))) (properties `((upstream-name . "multidplyr"))) (build-system r-build-system) (propagated-inputs (list r-callr r-cli r-crayon r-dplyr r-magrittr r-qs r-r6 r-rlang r-tibble r-tidyselect r-vctrs)) (native-inputs (list r-knitr)) (home-page "https://multidplyr.tidyverse.org") (synopsis "Multi-process dplyr backend") (description "Partition a data frame across multiple worker processes to provide simple multicore parallelism.") (license license:expat))) (define-public r-misc3d (package (name "r-misc3d") (version "0.9-1") (source (origin (method url-fetch) (uri (cran-uri "misc3d" version)) (sha256 (base32 "0r9x57s63kx9f6dgam2nhbziq8nrs9wd8pk7g76hds2kw46vnyx0")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/misc3d/") (synopsis "Miscellaneous 3D Plots") (description "This package provides a collection of miscellaneous 3d plots, including isosurfaces.") ;; Any version of the GPL. (license (list license:gpl2+ license:gpl3+)))) (define-public r-missforest (package (name "r-missforest") (version "1.5") (source (origin (method url-fetch) (uri (cran-uri "missForest" version)) (sha256 (base32 "13c38hpl60ca1kwyv61cxsla6ccmsj4qzp0vrxcq7b827fh5aw21")))) (properties `((upstream-name . "missForest"))) (build-system r-build-system) (propagated-inputs (list r-dorng r-foreach r-iterators r-itertools r-randomforest)) (home-page "https://github.com/stekhoven/missForest") (synopsis "Nonparametric missing value imputation using Random Forest") (description "The function @code{missForest} in this package is used to impute missing values, particularly in the case of mixed-type data. It uses a random forest trained on the observed values of a data matrix to predict the missing values. It can be used to impute continuous and/or categorical data, including complex interactions and non-linear relations. It yields an @acronym{OOB, out-of-bag} imputation error estimate without the need of a test set or elaborate cross- validation. It can be run in parallel to save computation time.") (license license:gpl2+))) (define-public r-ks (package (name "r-ks") (version "1.14.2") (source (origin (method url-fetch) (uri (cran-uri "ks" version)) (sha256 (base32 "1jrzh1syq6jdqpp5xmb25hqsk07bpbn6caqhp9mw5zpsdi3k14gi")))) (build-system r-build-system) (propagated-inputs (list r-fnn r-kernlab r-kernsmooth r-matrix r-mclust r-mgcv r-multicool r-mvtnorm r-pracma)) (home-page "https://www.mvstat.net/tduong/") (synopsis "Kernel smoothing") (description "This package provides kernel smoothers for univariate and multivariate data, including density functions, density derivatives, cumulative distributions, modal clustering, discriminant analysis, and two-sample hypothesis testing.") ;; Either version of the GPL. (license (list license:gpl2 license:gpl3)))) (define-public r-feature (package (name "r-feature") (version "1.2.15") (source (origin (method url-fetch) (uri (cran-uri "feature" version)) (sha256 (base32 "0yzn1w1sasilcp8v0pcjnxjv9l6lspkskqi412i6h040gqmjjf6y")))) (build-system r-build-system) (propagated-inputs (list r-ks r-plot3d)) (native-inputs (list r-knitr)) (home-page "https://www.mvstat.net/tduong/") (synopsis "Inferential feature significance for kernel density estimation") (description "The feature package contains functions to display and compute kernel density estimates, significant gradient and significant curvature regions. Significant gradient and/or curvature regions often correspond to significant features (e.g. local modes).") ;; Either version of the GPL. (license (list license:gpl2 license:gpl3)))) (define-public r-arm (package (name "r-arm") (version "1.14-4") (source (origin (method url-fetch) (uri (cran-uri "arm" version)) (sha256 (base32 "1g8732naydqyv5pq1fkyb1i6qddv62jdmn2ys5lbdvx2zq5cnns2")))) (build-system r-build-system) (propagated-inputs (list r-abind r-coda r-lme4 r-mass r-matrix r-nlme)) (home-page "https://cran.r-project.org/web/packages/arm/") (synopsis "Data analysis using regression and multilevel/hierarchical models") (description "This package provides functions to accompany A. Gelman and J. Hill, Data Analysis Using Regression and Multilevel/Hierarchical Models, Cambridge University Press, 2007.") (license license:gpl3+))) (define-public r-circular (package (name "r-circular") (version "0.5-0") (source (origin (method url-fetch) (uri (cran-uri "circular" version)) (sha256 (base32 "14kvkbmvdfzh8j4hgw93qkjkg86xlpw69sp7g8d5smcyw9fxmx2b")))) (build-system r-build-system) (propagated-inputs (list r-boot r-mvtnorm)) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/circular/") (synopsis "Circular statistics") (description "This package provides tools for circular statistics, from \"Topics in circular Statistics\" (2001) S. Rao Jammalamadaka and A. SenGupta, World Scientific.") (license license:gpl2+))) (define-public r-activity (package (name "r-activity") (version "1.3.4") (source (origin (method url-fetch) (uri (cran-uri "activity" version)) (sha256 (base32 "10gp2yvqxz5ysmh5z8qvrpli8kc2kn2z3nd2llfabpyh21476in2")))) (build-system r-build-system) (propagated-inputs (list r-pbapply)) (home-page "https://cran.r-project.org/web/packages/activity/") (synopsis "Animal activity statistics") (description "This package provides functions to fit kernel density functions to animal activity time data; plot activity distributions; quantify overall levels of activity; statistically compare activity metrics through bootstrapping; and evaluate variation in linear variables with time (or other circular variables).") (license license:gpl3))) (define-public r-ouch (package (name "r-ouch") (version "2.19") (source (origin (method url-fetch) (uri (cran-uri "ouch" version)) (sha256 (base32 "15ryd76max77zwjlbijj4v7h42mscr4zqg8b01cq3gsr51l8bwkf")))) (build-system r-build-system) (propagated-inputs (list r-subplex)) (home-page "https://kingaa.github.io/ouch/") (synopsis "Ornstein-Uhlenbeck models for phylogenetic comparative hypotheses") (description "This package provides tools to fit and compare Ornstein-Uhlenbeck models for evolution along a phylogenetic tree.") (license license:gpl2+))) (define-public r-fmri (package (name "r-fmri") (version "1.9.12") (source (origin (method url-fetch) (uri (cran-uri "fmri" version)) (sha256 (base32 "1cv5mxcdpyf05n5pcjdawl59j7f4k40386r4m38qf15vcy45zdfq")))) (properties `((upstream-name . "fmri"))) (build-system r-build-system) (propagated-inputs (list r-aws r-metafor r-nlme r-oro-nifti)) (native-inputs (list gfortran)) (home-page "http://www.wias-berlin.de/software/imaging/") (synopsis "Analysis of fMRI experiments") (description "This package contains R-functions to perform an fMRI analysis as described in Polzehl and Tabelow (2019) , Tabelow et al. (2006) , Polzehl et al. (2010) , Tabelow and Polzehl (2011) .") (license license:gpl2+))) (define-public r-fmsb (package (name "r-fmsb") (version "0.7.6") (source (origin (method url-fetch) (uri (cran-uri "fmsb" version)) (sha256 (base32 "1cnkg4njb432p05j8hdwfa2swiynwm864yixgfbyr26r8jfz4zg5")))) (build-system r-build-system) (home-page "https://minato.sip21c.org/msb/") (synopsis "Functions for medical statistics book with demographic data") (description "This package provides several utility functions for the book entitled \"Practices of Medical and Health Data Analysis using R\" (Pearson Education Japan, 2007) with Japanese demographic data and some demographic analysis related functions.") (license license:gpl2+))) (define-public r-stabledist (package (name "r-stabledist") (version "0.7-1") (source (origin (method url-fetch) (uri (cran-uri "stabledist" version)) (sha256 (base32 "0scar396wiq6wkbkvwp4qrxqc1m075y56p37i6iry5rw796p1i86")))) (build-system r-build-system) (home-page "https://www.rmetrics.org") (synopsis "Stable distribution functions") (description "This package provides density, probability and quantile functions, and random number generation for (skew) stable distributions, using the parametrizations of Nolan.") 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"ADGofTest"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/ADGofTest") (synopsis "Anderson-Darling GoF test") (description "This package provides an implementation of the Anderson-Darling GoF test with p-value calculation based on Marsaglia's 2004 paper \"Evaluating the Anderson-Darling Distribution\".") ;; Any version of the GPL. (license license:gpl3+))) (define-public r-adimpro (package (name "r-adimpro") (version "0.9.6") (source (origin (method url-fetch) (uri (cran-uri "adimpro" version)) (sha256 (base32 "0d5viz9ayywpp1pas1yzmhllzn9rjrl8a3k7bj7h46f95l5x1586")))) (properties `((upstream-name . "adimpro"))) (build-system r-build-system) (propagated-inputs (list r-awsmethods imagemagick)) (native-inputs (list gfortran)) (home-page "https://www.wias-berlin.de/software/imaging/") (synopsis "Adaptive smoothing of digital images") (description "This package implements tools for manipulation of digital images and the Propagation Separation approach by Polzehl and Spokoiny (2006) for smoothing digital images, see Polzehl and Tabelow (2007) .") (license license:gpl2+))) (define-public r-admisc (package (name "r-admisc") (version "0.35") (source (origin (method url-fetch) (uri (cran-uri "admisc" version)) (sha256 (base32 "0gzdb9dm34qfkjqgfrd3wm96dzhcps4xayyrhp80mzgh14zmnjyg")))) (properties `((upstream-name . "admisc"))) (build-system r-build-system) (home-page "https://github.com/dusadrian/admisc") (synopsis "Adrian Dusa's miscellaneous") (description "This package contains miscellaneous functions used to interpret and translate, factorize and negate Sum of Products expressions, for both binary and multi-value crisp sets, and to extract information (set names, set values) from those expressions. Other functions perform various other checks if possibly numeric (even if all numbers reside in a character vector) and coerce to numeric, or check if the numbers are whole. It also offers, among many others, a highly flexible recoding routine and a more flexible alternative to the base function @code{with()}.") (license license:gpl3+))) (define-public r-oro-nifti (package (name "r-oro-nifti") (version "0.11.4") (source (origin (method url-fetch) (uri (cran-uri "oro.nifti" version)) (sha256 (base32 "01mn90qxb7i15zr83xrl2cn4akayfzpm83r5x71zczz3qb9gbr7g")))) (properties `((upstream-name . "oro.nifti"))) (build-system r-build-system) (propagated-inputs (list r-abind r-bitops r-rnifti)) (home-page "https://rigorousanalytics.blogspot.com") (synopsis "Vizualization of medical imaging data") (description "This package provides functions for the input/output and visualization of medical imaging data that follow either the ANALYZE, NIfTI or AFNI formats. This package is part of the Rigorous Analytics bundle.") (license license:bsd-3))) (define-public r-mritc (package (name "r-mritc") (version "0.5-3") (source (origin (method url-fetch) (uri (cran-uri "mritc" version)) (sha256 (base32 "1bpnm2qzq67dgjxsa4wxn51f4a4cxal5r6abgs3m7p5a9a16jmjp")))) (properties `((upstream-name . "mritc"))) (build-system r-build-system) (propagated-inputs (list r-lattice r-misc3d r-oro-nifti)) (home-page "https://cran.r-project.org/package=mritc") (synopsis "MRI tissue classification") (description "This package provides various methods for MRI tissue classification.") ;; Any version of the GPL. (license license:gpl3+))) (define-public r-sodium (package (name "r-sodium") (version "1.3.1") (source (origin (method url-fetch) (uri (cran-uri "sodium" version)) (sha256 (base32 "0cbj7mgchi42ri6h1fc24asj7lkcn9n3l0zbabrx89s9zi4im0gx")))) (properties `((upstream-name . "sodium"))) (build-system r-build-system) (inputs (list libsodium)) (native-inputs (list pkg-config r-knitr)) (home-page "https://github.com/jeroen/sodium") (synopsis "R bindings to the libsodium crypto library") (description "This package provides bindings to libsodium: a library for encryption, decryption, signatures, password hashing and more. Sodium uses curve25519, a Diffie-Hellman function by Daniel Bernstein, which has become very popular after it was discovered that the NSA had backdoored Dual EC DRBG.") (license license:expat))) (define-public r-softimpute (package (name "r-softimpute") (version "1.4-1") (source (origin (method url-fetch) (uri (cran-uri "softImpute" version)) (sha256 (base32 "1v2a4d688ij5zcvkzpra9yx40xckdfnllnfnyq2450zf3n1kjk7a")))) (properties `((upstream-name . "softImpute"))) (build-system r-build-system) (propagated-inputs (list r-matrix)) (native-inputs (list gfortran r-knitr)) (home-page "https://cran.r-project.org/web/packages/softImpute") (synopsis "Matrix completion via iterative soft-thresholded SVD") (description "This package provides iterative methods for matrix completion that use nuclear-norm regularization. The package includes procedures for centering and scaling rows, columns or both, and for computing low-rank @dfn{single value decompositions} (SVDs) on large sparse centered matrices (i.e. principal components).") (license license:gpl2))) (define-public r-som (package (name "r-som") (version "0.3-5.1") (source (origin (method url-fetch) (uri (cran-uri "som" version)) (sha256 (base32 "1fbza1jxvwrkf5x3inkj36vshhkn7mz0ajqlxalbfmk6ngjw1x56")))) (properties `((upstream-name . "som"))) (build-system r-build-system) (home-page "https://cran.r-project.org/package=som") (synopsis "Self-organizing map") (description "This package implements a self-organizing map which has application in gene clustering. It provides functions like: @itemize @item filtering data by certain floor, ceiling, max/min ratio, and max - min difference; @item normalization of the data; @item get the average distortion measure; @item train a self-organizing map; @item summarize a som object; @item yeast cell cycle. @end itemize") (license license:gpl3+))) (define-public r-fftwtools (package (name "r-fftwtools") (version "0.9-11") (source (origin (method url-fetch) (uri (cran-uri "fftwtools" version)) (sha256 (base32 "0zrchp4l0jdbir2gibjf00x225y9giqk80zvqmr2yyvc12lwkw7i")))) (build-system r-build-system) (inputs (list fftw)) (native-inputs (list pkg-config)) (home-page "https://github.com/krahim/fftwtools") (synopsis "Wrapper for FFTW3") (description "This package provides a wrapper for several FFTW functions. It provides access to the two-dimensional FFT, the multivariate FFT, and the one-dimensional real to complex FFT using the FFTW3 library. The package includes the functions @code{fftw()} and @code{mvfftw()} which are designed to mimic the functionality of the R functions @code{fft()} and @code{mvfft()}. The FFT functions have a parameter that allows them to not return the redundant complex conjugate when the input is real data.") (license license:gpl2+))) (define-public r-tiff (package (name "r-tiff") (version "0.1-12") (source (origin (method url-fetch) (uri (cran-uri "tiff" version)) (sha256 (base32 "0p41irri0nxg9mm06g8jp5zqssv80g5zg0iifrr7ancjkxqww46z")))) (build-system r-build-system) (inputs (list libtiff libjpeg-turbo zlib)) (native-inputs (list pkg-config)) (home-page "https://www.rforge.net/tiff/") (synopsis "Read and write TIFF images") (description "This package provides an easy and simple way to read, write and display bitmap images stored in the TIFF format. It can read and write both files and in-memory raw vectors.") ;; Either of these two license versions. (license (list license:gpl2 license:gpl3)))) (define-public r-nlp (package (name "r-nlp") (version "0.2-1") (source (origin (method url-fetch) (uri (cran-uri "NLP" version)) (sha256 (base32 "1dpj04fmld2lnhg072ahgjbhmciqqy9h1lrz0wf32mr7mm9s9sh5")))) (properties `((upstream-name . "NLP"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/NLP/") (synopsis "Natural language processing infrastructure") (description "This package provides basic classes and methods for Natural Language Processing.") (license license:gpl3))) (define-public r-tm (package (name "r-tm") (version "0.7-12") (source (origin (method url-fetch) (uri (cran-uri "tm" version)) (sha256 (base32 "1z0zpz6jgzg34cz07cdpya2zwwsvywrd8xgwahhlz15vnaij7j3y")))) (properties `((upstream-name . "tm"))) (build-system r-build-system) (propagated-inputs (list r-bh r-nlp r-rcpp r-slam r-xml2)) (home-page "https://tm.r-forge.r-project.org/") (synopsis "Text mining package") (description "This package provides a framework for text mining applications within R.") (license license:gpl3))) (define-public r-waffle (package (name "r-waffle") (version "1.0.2") (source (origin (method url-fetch) (uri (cran-uri "waffle" version)) (sha256 (base32 "17z05mlnp2k9dywr0bbqz633sq1xs8q9879bl2na1in39qxq0l76")))) (properties `((upstream-name . "waffle"))) (build-system r-build-system) (propagated-inputs (list r-curl r-dt r-extrafont r-ggplot2 r-gridextra r-gtable r-htmlwidgets r-plyr r-rcolorbrewer r-rlang r-stringr)) (home-page "https://github.com/hrbrmstr/waffle/tree/cran") (synopsis "Creating waffle chart visualizations in R") (description "This package creates square pie charts also known as waffle charts. These can be used to communicate parts of a whole for categorical quantities. To emulate the percentage view of a pie chart, a 10x10 grid should be used. In this way each square is representing 1% of the total. Waffle provides tools to create charts as well as stitch them together. Isotype pictograms can be made by using glyphs.") (license license:gpl2+))) (define-public r-waveslim (package (name "r-waveslim") (version "1.8.4") (source (origin (method url-fetch) (uri (cran-uri "waveslim" version)) (sha256 (base32 "1510xpkgrhdw394m5anxccdczjikcxazyd09ix2z73i15akyx3j0")))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "http://waveslim.blogspot.com") (synopsis "Basic wavelet routines for signal processing") (description "This package provides basic wavelet routines for time series (1D), image (2D) and array (3D) analysis. The code provided here is based on wavelet methodology developed in Percival and Walden (2000); Gencay, Selcuk and Whitcher (2001); the dual-tree complex wavelet transform (DTCWT) from Kingsbury (1999, 2001) as implemented by Selesnick; and Hilbert wavelet pairs (Selesnick 2001, 2002).") (license license:bsd-3))) (define-public r-word2vec (package (name "r-word2vec") (version "0.4.0") (source (origin (method url-fetch) (uri (cran-uri "word2vec" version)) (sha256 (base32 "14ba0cj430d02bd6fay3nl4ldwqyj77iwjm4gzgdc0f6sx597iiq")))) (properties `((upstream-name . "word2vec"))) (build-system r-build-system) (propagated-inputs (list r-rcpp r-rcppprogress)) (home-page "https://github.com/bnosac/word2vec") (synopsis "Distributed representations of words") (description "Learn vector representations of words by continuous bag of words and skip-gram implementations of the word2vec algorithm. The techniques are detailed in the paper \"Distributed Representations of Words and Phrases and their Compositionality\" by Mikolov et al. (2013), available at .") (license license:asl2.0))) (define-public r-wordcloud (package (name "r-wordcloud") (version "2.6") (source (origin (method url-fetch) (uri (cran-uri "wordcloud" version)) (sha256 (base32 "0j96yyvm6bcrrpbdx4w26piqx44a0vbsr3px9cb4zk8a8da6jwak")))) (build-system r-build-system) (propagated-inputs (list r-rcolorbrewer r-rcpp ;; The "tm" package is only "suggested" according to CRAN, but the ;; wordcloud package cannot be loaded without it. r-tm)) (home-page "https://cran.r-project.org/web/packages/wordcloud") (synopsis "Word clouds") (description "This package provides functionality to create pretty word clouds, visualize differences and similarity between documents, and avoid over-plotting in scatter plots with text.") (license license:lgpl2.1))) (define-public r-colorramps (package (name "r-colorramps") (version "2.3.4") (source (origin (method url-fetch) (uri (cran-uri "colorRamps" version)) (sha256 (base32 "1y4gn6v8wmwq3wcfgdnx1ah2qa53gayvbfa62kp286ga4c8k3prw")))) (properties `((upstream-name . "colorRamps"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/colorRamps") (synopsis "Build color tables") (description "This package provides features to build gradient color maps.") ;; Any version of the GPL (license license:gpl3+))) (define-public r-tidytree (package (name "r-tidytree") (version "0.4.6") (source (origin (method url-fetch) (uri (cran-uri "tidytree" version)) (sha256 (base32 "14i2v6ryqw4cd74n8kz4qwwx730wzx4f0rssg5vgm0vjfsx0kafv")))) (build-system r-build-system) (propagated-inputs (list r-ape r-cli r-dplyr r-lazyeval r-magrittr r-pillar r-rlang r-tibble r-tidyr r-tidyselect r-yulab-utils)) (native-inputs (list r-knitr)) (home-page "https://github.com/GuangchuangYu/tidytree") (synopsis "Tidy tool for phylogenetic tree data manipulation") (description "Phylogenetic trees generally contain multiple components including nodes, edges, branches and associated data. This package provides an approach to convert tree objects to tidy data frames. It also provides tidy interfaces to manipulate tree data.") (license license:artistic2.0))) (define-public r-rvcheck (package (name "r-rvcheck") (version "0.2.1") (source (origin (method url-fetch) (uri (cran-uri "rvcheck" version)) (sha256 (base32 "09khjklvzbafd7r55496by01a9g3y291d87hpy43w44dmz9fzn9a")))) (build-system r-build-system) (propagated-inputs (list r-biocmanager r-yulab-utils)) (home-page "https://cran.r-project.org/web/packages/rvcheck") (synopsis "R package version check") (description "This package provides tools to check the latest release version of R and R packages (on CRAN, Bioconductor or Github).") (license license:artistic2.0))) (define-public r-doc2vec (package (name "r-doc2vec") (version "0.2.0") (source (origin (method url-fetch) (uri (cran-uri "doc2vec" version)) (sha256 (base32 "0249hm0103kxxsi4gks4h20wf6p00gbrk9jf8c148mbja1l56f6v")))) (properties `((upstream-name . 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These dense areas are the topic clusters which can be represented by the corresponding topic vector which is an aggregate of the document embeddings of the documents which are part of that topic cluster. In the same semantic space similar words can be found which are representative of the topic.") (license license:expat))) (define-public r-docopt (package (name "r-docopt") (version "0.7.1") (source (origin (method url-fetch) (uri (cran-uri "docopt" version)) (sha256 (base32 "1zxhwizs916qm5by7nfslqnarl2q5202xc2azlhrnzk0wj3khiwz")))) (build-system r-build-system) (home-page "https://github.com/docopt/docopt.R") (synopsis "Command-line interface specification language") (description "This package enables you to define a command-line interface by just giving it a description in the specific format.") 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(license (list license:bsd-3 license:bsd-2)))) (define-public r-speedglm (package (name "r-speedglm") (version "0.3-5") (source (origin (method url-fetch) (uri (cran-uri "speedglm" version)) (sha256 (base32 "0jxvh9gbhip1hj7hzjs5fj8iw6ibvl6hc0llcg2j9wqgq5vkcrpq")))) (build-system r-build-system) (propagated-inputs (list r-biglm r-mass r-matrix)) (home-page "https://cran.r-project.org/web/packages/speedglm") (synopsis "Fit linear and generalized linear models to large data sets") (description "This package provides tools for fitting linear models and generalized linear models to large data sets by updating algorithms.") ;; Any version of the GPL (license license:gpl2+))) (define-public r-densityclust (package (name "r-densityclust") (version "0.3.3") (source (origin (method url-fetch) (uri (cran-uri "densityClust" version)) (sha256 (base32 "0iiq2zal792741z1a23h7cy9jp4hsc7513dxain132526f1yrzsl")))) (properties `((upstream-name . 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(license license:gpl2+))) (define-public r-combinat (package (name "r-combinat") (version "0.0-8") (source (origin (method url-fetch) (uri (cran-uri "combinat" version)) (sha256 (base32 "1h9hr88gigihc4na7lb5i7rn4az1xa7sb34zvnznaj6pdrmwy4qm")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/combinat") (synopsis "Combinatorics utilities") (description "This package provides assorted routines for combinatorics.") (license license:gpl2))) (define-public r-qlcmatrix (package (name "r-qlcmatrix") (version "0.9.7") (source (origin (method url-fetch) (uri (cran-uri "qlcMatrix" version)) (sha256 (base32 "0iqkcvvy8rxlk0s83sjq57dd6fadb18p5z31lzy0gnzv1hsy1x8y")))) (properties `((upstream-name . 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(license license:gpl2+))) (define-public r-ddrtree (package (name "r-ddrtree") (version "0.1.5") (source (origin (method url-fetch) (uri (cran-uri "DDRTree" version)) (sha256 (base32 "16s5fjw7kwlxhrkzdny62sx32fvmg3rxjc3wrh6krd31jh1fqlfk")))) (properties `((upstream-name . "DDRTree"))) (build-system r-build-system) (propagated-inputs (list r-bh r-irlba r-rcpp r-rcppeigen)) (home-page "https://cran.r-project.org/web/packages/DDRTree") (synopsis "Learning principal graphs with DDRTree") (description "This package provides an implementation of the framework of @dfn{reversed graph embedding} (RGE) which projects data into a reduced dimensional space while constructs a principal tree which passes through the middle of the data simultaneously. DDRTree shows superiority to alternatives (Wishbone, DPT) for inferring the ordering as well as the intrinsic structure of single cell genomics data. In general, it could be used to reconstruct the temporal progression as well as the bifurcation structure of any data type.") (license license:asl2.0))) (define-public r-corpcor (package (name "r-corpcor") (version "1.6.10") (source (origin (method url-fetch) (uri (cran-uri "corpcor" version)) (sha256 (base32 "028fw61n61i79fhnaqx7gmdifdpbvp3yiaq9vvfrbv4k7i84r83i")))) (build-system r-build-system) (home-page "https://strimmerlab.org/software/corpcor/") (synopsis "Efficient estimation of covariance and (partial) correlation") (description "This package implements a James-Stein-type shrinkage estimator for the covariance matrix, with separate shrinkage for variances and correlations. Furthermore, functions are available for fast singular value decomposition, for computing the pseudoinverse, and for checking the rank and positive definiteness of a matrix.") (license license:gpl3+))) (define-public r-rspectra (package (name "r-rspectra") (version "0.16-1") (source (origin (method url-fetch) (uri (cran-uri "RSpectra" version)) (sha256 (base32 "16ij84wgpsmqmnxqiii8dgihy3bfxazry9znmckhwzba7m0d79fb")))) (properties `((upstream-name . "RSpectra"))) (build-system r-build-system) (propagated-inputs (list r-matrix r-rcpp r-rcppeigen)) (native-inputs (list r-knitr)) (home-page "https://github.com/yixuan/RSpectra") (synopsis "Solvers for large-scale Eigenvalue and SVD problems") (description "This package provides an R interface to the Spectra library for large-scale eigenvalue and SVD problems. It is typically used to compute a few eigenvalues/vectors of an n by n matrix, e.g., the k largest eigenvalues, which is usually more efficient than @code{eigen()} if k << n.") ;; MPL 2 or later. (license license:mpl2.0))) (define-public r-vbsr (package (name "r-vbsr") (version "0.0.5") (source (origin (method url-fetch) (uri (cran-uri "vbsr" version)) (sha256 (base32 "1avskbxxyinjjdga4rnghcfvd4sypv4m39ysfaij5avvmi89bx3b")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/vbsr") (synopsis "Variational Bayes spike regression regularized linear models") (description "This package provides an efficient algorithm for solving ultra-sparse regularized regression models using a variational Bayes algorithm with a spike prior. The algorithm is solved on a path, with coordinate updates, and is capable of generating very sparse models. Very general model diagnostics for controlling type-1 errors are also provided.") (license license:gpl2))) (define-public r-flare (package (name "r-flare") (version "1.7.0.1") (source (origin (method url-fetch) (uri (cran-uri "flare" version)) (sha256 (base32 "1xvrbvq2y7zfp98ijal3z8y1w2xbzfcdykzw4pqc3mnh0qrhq2d5")))) (build-system r-build-system) (propagated-inputs (list r-igraph r-lattice r-mass r-matrix)) (home-page "https://cran.r-project.org/web/packages/flare") (synopsis "Family of Lasso regression implementations") (description "This package provides implementations of a family of Lasso variants including Dantzig Selector, LAD Lasso, SQRT Lasso, Lq Lasso for estimating high dimensional sparse linear models.") (license license:gpl2))) (define-public r-lassopv (package (name "r-lassopv") (version "0.2.0") (source (origin (method url-fetch) (uri (cran-uri "lassopv" version)) (sha256 (base32 "0yawnjw063jypk3riy9xab9cmliv6c9dnabi18670khd3gzb2r9z")))) (build-system r-build-system) (propagated-inputs (list r-lars)) (home-page "https://github.com/lingfeiwang/lassopv") (synopsis "Non-parametric p-value estimation for predictors in Lasso") (description "This package enables you to estimate the p-values for predictors x against target variable y in Lasso regression, using the regularization strength when each predictor enters the active set of regularization path for the first time as the statistic.") (license license:gpl3))) (define-public r-splitstackshape (package (name "r-splitstackshape") (version "1.4.8") (source (origin (method url-fetch) (uri (cran-uri "splitstackshape" version)) (sha256 (base32 "0mpyf2kkfdl69pdc6brl1r6101vyc6pgr7z17s55ppg3y71k4q35")))) (build-system r-build-system) (propagated-inputs (list r-data-table)) (home-page "https://github.com/mrdwab/splitstackshape") (synopsis "Stack and reshape datasets after splitting concatenated values") (description "Online data collection tools like Google Forms often export multiple-response questions with data concatenated in cells. The @code{concat.split} (cSplit) family of functions provided by this package splits such data into separate cells. This package also includes functions to stack groups of columns and to reshape wide data, even when the data are \"unbalanced\"---something which @code{reshape} (from base R) does not handle, and which @code{melt} and @code{dcast} from @code{reshape2} do not easily handle.") (license license:gpl3))) (define-public r-tfmpvalue (package (name "r-tfmpvalue") (version "0.0.9") (source (origin (method url-fetch) (uri (cran-uri "TFMPvalue" version)) (sha256 (base32 "1rsxqvq1nkyhwmhm7mf7rd02rvh7xinnhqbqic6q9vicbvkmdnxr")))) (properties `((upstream-name . "TFMPvalue"))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) (home-page "https://github.com/ge11232002/TFMPvalue") (synopsis "P-value computation for position weight matrices") (description "In putative @dfn{Transcription Factor Binding Sites} (TFBSs) identification from sequence/alignments, we are interested in the significance of certain match scores. TFMPvalue provides the accurate calculation of a p-value with a score threshold for position weight matrices, or the score with a given p-value. It is an interface to code originally made available by Helene Touzet and Jean-Stephane Varre, 2007, Algorithms Mol Biol:2, 15. Touzet and Varre (2007).") (license license:gpl2))) (define-public r-rnaturalearth (package (name "r-rnaturalearth") (version "1.0.1") (source (origin (method url-fetch) (uri (cran-uri "rnaturalearth" version)) (sha256 (base32 "1vfkn4bf77mr2n7dhmnl55ma4cvwy2nazhizmdqd98w2ydl13z3p")))) (properties `((upstream-name . "rnaturalearth"))) (build-system r-build-system) (propagated-inputs (list r-httr r-jsonlite r-sf r-terra)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/package=rnaturalearth") (synopsis "World map data from Natural Earth") (description "This package facilitates mapping by making natural earth map data from @url{https://www.naturalearthdata.com/} more easily available to R users.") 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(license license:cc0))) (define-public r-rncl (package (name "r-rncl") (version "0.8.7") (source (origin (method url-fetch) (uri (cran-uri "rncl" version)) (sha256 (base32 "0flrqz7pansy11ds23qv06bcmh6vxqljq0517v6292ibbx7nx1qx")))) (build-system r-build-system) (propagated-inputs (list r-progress r-rcpp)) (home-page "https://github.com/fmichonneau/rncl") (synopsis "Interface to the Nexus class library") (description "This package provides an interface to the Nexus class library which allows parsing of NEXUS, Newick and other phylogenetic tree file formats. It provides elements of the file that can be used to build phylogenetic objects such as @code{ape}'s @code{phylo} or @code{phylobase}'s @code{phylo4(d)}. This functionality is demonstrated with @code{read_newick_phylo()} and @code{read_nexus_phylo()}.") 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(license license:gpl2))) (define-public r-rnexml (package (name "r-rnexml") (version "2.4.11") (source (origin (method url-fetch) (uri (cran-uri "RNeXML" version)) (sha256 (base32 "0ipxdhfzccpqmnfrqdy8bizm80k2chhdlzg3p0dl05p8n35i6s94")))) (build-system r-build-system) (propagated-inputs (list r-ape r-dplyr r-httr r-plyr r-reshape2 r-rlang r-stringi r-stringr r-tidyr r-uuid r-xml r-xml2)) (native-inputs (list r-knitr)) (home-page "https://docs.ropensci.org/RNeXML/") (synopsis "Semantically rich I/O for the NeXML Format") (description "This package provides access to phyloinformatic data in NeXML format. The package should add new functionality to R such as the possibility to manipulate NeXML objects in more various and refined way and compatibility with @code{ape} objects.") 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(license license:gpl2))) (define-public r-tractor-base (package (name "r-tractor-base") (version "3.4.2") (source (origin (method url-fetch) (uri (cran-uri "tractor.base" version)) (sha256 (base32 "12mp5x6c7c82a4z7p39cb478kwwf6lkrgbis6ak00yibsd3n6na3")))) (properties `((upstream-name . "tractor.base"))) (build-system r-build-system) (propagated-inputs (list r-ore r-reportr r-rnifti r-shades)) (home-page "https://www.tractor-mri.org.uk") (synopsis "Read, manipulate and visualize magnetic resonance images") (description "This package provides functions for working with magnetic resonance images. It supports reading and writing of popular file formats (DICOM, Analyze, NIfTI-1, NIfTI-2, MGH); interactive and non-interactive visualization; flexible image manipulation; metadata and sparse image handling.") (license license:gpl2))) (define-public r-gridpattern (package (name "r-gridpattern") (version "1.1.1") (source (origin (method url-fetch) (uri (cran-uri "gridpattern" version)) (sha256 (base32 "1v7xfgbnrr4v3arr7nm0663aywn47xb89sd0rn9s9dcz7r50aa2i")))) (properties `((upstream-name . "gridpattern"))) (build-system r-build-system) (propagated-inputs (list r-glue r-memoise r-png r-rlang r-sf)) (native-inputs (list r-knitr r-rmarkdown)) (home-page "https://trevorldavis.com/R/gridpattern/") (synopsis "Grid pattern grobs") (description "This package provides grid grobs that fill in a user-defined area with various patterns. It includes enhanced versions of the geometric and image-based patterns originally contained in the ggpattern package as well as original @code{pch}, @code{polygon_tiling}, @code{regular_polygon}, @code{rose}, @code{text}, @code{wave}, and @code{weave} patterns plus support for custom user-defined patterns.") (license license:expat))) (define-public r-gridsvg (package (name "r-gridsvg") (version "1.7-5") (source (origin (method url-fetch) (uri (cran-uri "gridSVG" version)) (sha256 (base32 "1p8qnx9q96bni39x44l40rgcdi9r440zbipdfvkbs2paysx6mkr5")))) (properties `((upstream-name . "gridSVG"))) (build-system r-build-system) (propagated-inputs (list r-jsonlite r-xml)) (home-page "https://cran.r-project.org/package=gridSVG") (synopsis "Export grid gaphics as SVG") (description "This package provides functions to export graphics drawn with package grid to SVG format. Extra functions provide access to SVG features that are not available in standard R graphics, such as hyperlinks, animation, filters, masks, clipping paths, and gradient and pattern fills.") ;; Any version of the GPL. (license (list license:gpl2 license:gpl3)))) (define-public r-grimport (package (name "r-grimport") (version "0.9-7") (source (origin (method url-fetch) (uri (cran-uri "grImport" version)) (sha256 (base32 "196h7i4y1gzkwlybml9iz78p5xsx7y22nk5pmzibryn5amdbdy05")))) (properties `((upstream-name . "grImport"))) (build-system r-build-system) (inputs (list ghostscript)) (propagated-inputs (list r-xml)) (home-page "https://cran.r-project.org/web/packages/grImport") (synopsis "Convert, import, and draw PostScript pictures") (description "This package provides functions for converting, importing, and drawing PostScript pictures in R plots.") (license license:gpl2+))) (define-public r-grimport2 (package (name "r-grimport2") (version "0.3-1") (source (origin (method url-fetch) (uri (cran-uri "grImport2" version)) (sha256 (base32 "1lj58z6yc2p6ns27fkgh11ac90bcihi65hf62gxpsylcn5dilsi1")))) (properties `((upstream-name . 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(license license:gpl2+))) (define-public r-kohonen (package (name "r-kohonen") (version "3.0.12") (source (origin (method url-fetch) (uri (cran-uri "kohonen" version)) (sha256 (base32 "188cxw2fvpfr3dyi8g52igcyc8d5jffyn6rhc84dja52da8lp520")))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) (home-page "https://cran.r-project.org/web/packages/kohonen") (synopsis "Supervised and unsupervised self-organising maps") (description "This package provides functions to train @dfn{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.") (license license:gpl2+))) (define-public r-nnls (package (name "r-nnls") (version "1.5") (source (origin (method url-fetch) (uri (cran-uri "nnls" version)) (sha256 (base32 "0lilga63p7k5mkkfcf5p3swx76vwysl979jxszm6svzqhsrgww6d")))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/nnls") (synopsis "Lawson-Hanson algorithm for non-negative least squares") (description "This package provides an R interface to the Lawson-Hanson implementation of an algorithm for @dfn{non-negative least squares} (NNLS). It also allows the combination of non-negative and non-positive constraints.") (license license:gpl2+))) (define-public r-iso (package (name "r-iso") (version "0.0-21") (source (origin (method url-fetch) (uri (cran-uri "Iso" version)) (sha256 (base32 "19lgwbfbca30mh3hhnarzab5cvnrwnr0pxam6fvfnadnqzhjm15n")))) (properties `((upstream-name . 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It was designed as a R companion to the book \"Introduction to Multivariate Statistical Analysis in Chemometrics\" written by K. Varmuza and P. Filzmoser (2009).") (license license:gpl3+))) (define-public r-chemometricswithr (package (name "r-chemometricswithr") (version "0.1.13") (source (origin (method url-fetch) (uri (cran-uri "ChemometricsWithR" version)) (sha256 (base32 "166va1g3m1wv21qkmw4wpz0bsrclh3jih8smxphdc13l9pqgclpq")))) (properties `((upstream-name . "ChemometricsWithR"))) (build-system r-build-system) (propagated-inputs (list r-devtools r-kohonen r-mass r-pls)) (home-page "https://github.com/rwehrens/CWR") (synopsis "Chemometrics with R") (description "This package provides functions and scripts used in the book \"Chemometrics with R - Multivariate Data Analysis in the Natural Sciences and Life Sciences\" by Ron Wehrens, Springer (2011).") (license license:gpl2+))) (define-public r-als (package (name "r-als") (version "0.0.7") (source (origin (method url-fetch) (uri (cran-uri "ALS" version)) (sha256 (base32 "184d6xr4mgs78jvi7xa4njrq6p625i9sx69wak6mdn53qpl9b8ap")))) (properties `((upstream-name . "ALS"))) (build-system r-build-system) (propagated-inputs (list r-iso r-nnls)) (home-page "https://cran.r-project.org/web/packages/ALS") (synopsis "Multivariate curve resolution alternating least squares") (description "Alternating least squares is often used to resolve components contributing to data with a bilinear structure; the basic technique may be extended to alternating constrained least squares. This package provides an implementation of @dfn{multivariate curve resolution alternating least squares} (MCR-ALS). Commonly applied constraints include unimodality, non-negativity, and normalization of components. Several data matrices may be decomposed simultaneously by assuming that one of the two matrices in the bilinear decomposition is shared between datasets.") (license license:gpl2+))) (define-public r-strucchange (package (name "r-strucchange") (version "1.5-3") (source (origin (method url-fetch) (uri (cran-uri "strucchange" version)) (sha256 (base32 "11hgz64snlwhfqsmqajmkciflwkz1wficxr340wqvk38iw1b9ina")))) (build-system r-build-system) (propagated-inputs (list r-sandwich r-zoo)) (home-page "https://cran.r-project.org/web/packages/strucchange") (synopsis "Testing, monitoring, and dating structural changes") (description "This package provides tools for testing, monitoring and dating structural changes in (linear) regression models. It features tests/methods from the generalized fluctuation test framework as well as from the F test (Chow test) framework. This includes methods to fit, plot and test fluctuation processes (e.g., CUSUM, MOSUM, recursive/moving estimates) and F statistics, respectively. It is possible to monitor incoming data online using fluctuation processes. Finally, the breakpoints in regression models with structural changes can be estimated together with confidence intervals. Emphasis is always given to methods for visualizing the data.") ;; Either of these two GPL versions (license (list license:gpl2 license:gpl3)))) (define-public r-pixmap (package (name "r-pixmap") (version "0.4-12") (source (origin (method url-fetch) (uri (cran-uri "pixmap" version)) (sha256 (base32 "1v1a1adsgh5jlvvi98j4nhb1h681s97ip76zdrga12rlsjaahfw9")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/pixmap") (synopsis "Tools for bitmap images") (description "This package provides functions for importing, exporting, plotting and other manipulations of bitmapped images.") 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(license license:gpl3+))) (define-public r-assertive (package (name "r-assertive") (version "0.3-6") (source (origin (method url-fetch) (uri (cran-uri "assertive" version)) (sha256 (base32 "02palil82idqhhshcdjsfsja9qkqnd0dczqzj5gbccy4hfg1c0y4")))) (build-system r-build-system) (propagated-inputs (list r-assertive-base r-assertive-code r-assertive-data r-assertive-data-uk r-assertive-data-us r-assertive-datetimes r-assertive-files r-assertive-matrices r-assertive-models r-assertive-numbers r-assertive-properties r-assertive-reflection r-assertive-sets r-assertive-strings r-assertive-types r-knitr)) (native-inputs (list r-knitr)) (home-page "https://bitbucket.org/richierocks/assertive") (synopsis "Readable check functions to ensure code integrity") (description "This package provides lots of predicates (@code{is_*} functions) to check the state of your variables, and assertions (@code{assert_*} functions) to throw errors if they aren't in the right form.") (license license:gpl3+))) (define-public r-dotcall64 (package (name "r-dotcall64") (version "1.1-1") (source (origin (method url-fetch) (uri (cran-uri "dotCall64" version)) (sha256 (base32 "06y9y9m5prjvqlprqpanbamgr6jkw27wj7nnha5ayyn08zbxgf11")))) (properties `((upstream-name . "dotCall64"))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "https://git.math.uzh.ch/reinhard.furrer/dotCall64") (synopsis "Enhanced foreign function interface supporting long vectors") (description "This package provides @code{.C64()}, an enhanced version of @code{.C()} and @code{.Fortran()} from the R foreign function interface. @code{.C64()} supports long vectors, arguments of type 64-bit integer, and provides a mechanism to avoid unnecessary copies of read-only and write-only arguments. This makes it a convenient and fast interface to C/C++ and Fortran code.") (license license:gpl2+))) (define-public r-spam (package (name "r-spam") (version "2.10-0") (source (origin (method url-fetch) (uri (cran-uri "spam" version)) (sha256 (base32 "0ydc513jg7phzdqg8jp7210ayrrmxq91jafqzx8z1v0172i8d73i")))) (build-system r-build-system) (propagated-inputs (list r-dotcall64 r-rcpp)) (native-inputs (list gfortran r-knitr r-r-rsp)) (home-page "https://www.math.uzh.ch/pages/spam/") (synopsis "Sparse matrix algebra") (description "This package provides a set of functions for sparse matrix algebra. Differences with other sparse matrix packages are: @enumerate @item it only supports (essentially) one sparse matrix format; @item it is based on transparent and simple structure(s); @item it is tailored for MCMC calculations within G(M)RF; @item and it is fast and scalable (with the extension package @code{spam64}). @end enumerate\n") ;; Either of these licenses (license (list license:bsd-3 license:lgpl2.0)))) (define-public r-fields (package (name "r-fields") (version "15.2") (source (origin (method url-fetch) (uri (cran-uri "fields" version)) (sha256 (base32 "0gdddigzbzlhrbp6h2ma5b05m68pmggrkcd80hzgjbjj64ihy9qz")))) (build-system r-build-system) (propagated-inputs (list r-maps r-spam r-viridislite)) (native-inputs (list gfortran)) (home-page "https://www.image.ucar.edu/fields") (synopsis "Tools for spatial data") (description "This is a package for curve, surface and function fitting with an emphasis on splines, spatial data and spatial statistics. The major methods include cubic, and thin plate splines, Kriging, and compactly supported covariance functions for large data sets.") (license license:gpl2+))) (define-public r-spatialextremes (package (name "r-spatialextremes") (version "2.1-0") (source (origin (method url-fetch) (uri (cran-uri "SpatialExtremes" version)) (sha256 (base32 "0z1swxp1syz8hdskarjxx4sdd7wx835kcnb783bwqm235yh991j3")))) (properties `((upstream-name . "SpatialExtremes"))) (build-system r-build-system) (propagated-inputs (list r-fields r-maps)) (home-page "https://spatialextremes.r-forge.r-project.org/") (synopsis "Modelling spatial extremes") (description "This package provides tools for the statistical modelling of spatial extremes using max-stable processes, copula or Bayesian hierarchical models. More precisely, this package allows (conditional) simulations from various parametric max-stable models, analysis of the extremal spatial dependence, the fitting of such processes using composite likelihoods or least square (simple max-stable processes only), model checking and selection and prediction.") (license license:gpl2+))) (define-public r-drc (package (name "r-drc") (version "3.0-1") (source (origin (method url-fetch) (uri (cran-uri "drc" version)) (sha256 (base32 "0c8xn8ripzq270hy8d16fcnx02l02alddznd7fqwk3jyi6113h1y")))) (build-system r-build-system) (propagated-inputs (list r-car r-gtools r-mass r-multcomp r-plotrix r-scales)) (home-page "https://cran.r-project.org/web/packages/drc") (synopsis "Analysis of dose-response curves") (description "This package provides a suite of flexible and versatile model fitting and after-fitting functions for the analysis of dose-response data.") (license license:gpl2+))) (define-public r-rmeta (package (name "r-rmeta") (version "3.0") (source (origin (method url-fetch) (uri (cran-uri "rmeta" version)) (sha256 (base32 "0vkbnxp579v8zmcv1isdbzj5swpr6fq17zwparxcvzswjc2x9ydr")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/rmeta") (synopsis "Tools for meta-analysis") (description "This package provides functions for simple fixed and random effects meta-analysis for two-sample comparisons and cumulative meta-analyses. It draws standard summary plots, funnel plots, and computes summaries and tests for association and heterogeneity.") (license license:gpl2))) (define-public r-bootstrap (package (name "r-bootstrap") (version "2019.6") (source (origin (method url-fetch) (uri (cran-uri "bootstrap" version)) (sha256 (base32 "1546jqhhw5h177ii8jkdikyd26rv6gwkav816np1zks4p7zgsljj")))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/bootstrap") (synopsis "Functions for the book \"An Introduction to the Bootstrap\"") (description "This package provides software and data for the book \"An Introduction to the Bootstrap\" by B. Efron and R. Tibshirani, 1993, Chapman and Hall. This package is primarily provided for projects already based on it, and for support of the book. New projects should preferentially use the recommended package \"boot\".") (license license:bsd-3))) (define-public r-survivalroc (package (name "r-survivalroc") (version "1.0.3.1") (source (origin (method url-fetch) (uri (cran-uri "survivalROC" version)) (sha256 (base32 "0p6irjs8a9xxgxwax0y9fzapcib237if3iy8g6lzv793mzmsyx41")))) (properties `((upstream-name . "survivalROC"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/survivalROC") (synopsis "Time-dependent ROC curve estimation from censored survival data") (description "Compute time-dependent ROC curve from censored survival data using Kaplan-Meier (KM) or Nearest Neighbor Estimation (NNE) method of Heagerty, Lumley & Pepe (Biometrics, Vol 56 No 2, 2000, PP 337-344)") (license license:gpl2+))) (define-public r-locfdr (package (name "r-locfdr") (version "1.1-8") (source (origin (method url-fetch) (uri (cran-uri "locfdr" version)) (sha256 (base32 "1falkbp2xz07am8jlhwlvyqvxnli4nwl188kd0g58vdfjcjy3mj2")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/locfdr/") (synopsis "Computes local false discovery rates") (description "This package can be used to compute local false discovery rates.") (license license:gpl2))) (define-public r-logging (package (name "r-logging") (version "0.10-108") (source (origin (method url-fetch) (uri (cran-uri "logging" version)) (sha256 (base32 "13gd40ygx586vs6xcp6clg69a92aj8zxlk1rn3xzkx8klfjimjc5")))) (properties `((upstream-name . "logging"))) (build-system r-build-system) (home-page "https://github.com/WLOGSolutions/r-logging") (synopsis "R logging implementation of log4j") (description "This package implements the R version of the @code{log4j} package. It offers hierarchic loggers, multiple handlers per logger, level based filtering, space handling in messages and custom formatting.") (license license:gpl3))) (define-public r-logistf (package (name "r-logistf") (version "1.26.0") (source (origin (method url-fetch) (uri (cran-uri "logistf" version)) (sha256 (base32 "02qrh07c13khlpz3z3f6qq827h37j91i88n7jn3c8ky6r1lfa5pr")))) (properties `((upstream-name . "logistf"))) (build-system r-build-system) (propagated-inputs (list r-formula-tools r-matrix r-mgcv r-mice)) (home-page "https://cemsiis.meduniwien.ac.at/en/kb/science-research\ /software/statistical-software/firth-correction/") (synopsis "Firth's bias-reduced logistic regression") (description "Fit a logistic regression model using Firth's bias reduction method, equivalent to penalization of the log-likelihood by the Jeffreys prior. Confidence intervals for regression coefficients can be computed by penalized profile likelihood. Firth's method was proposed as ideal solution to the problem of separation in logistic regression, see Heinze and Schemper (2002) . If needed, the bias reduction can be turned off such that ordinary maximum likelihood logistic regression is obtained. Two new modifications of Firth's method, FLIC and FLAC, lead to unbiased predictions and are now available in the package as well, see Puhr et al (2017) .") ;; Any version of the GPL (license license:gpl3+))) (define-public r-longdat (package (name "r-longdat") (version "1.1.2") (source (origin (method url-fetch) (uri (cran-uri "LongDat" version)) (sha256 (base32 "1rzkb7byd32jqvhf75zyvy0dlkq79aicz8j0x7lk821qiq4dfv6l")))) (properties `((upstream-name . "LongDat"))) (build-system r-build-system) (propagated-inputs (list r-bestnormalize r-car r-dplyr r-effsize r-emmeans r-ggplot2 r-glmmtmb r-lme4 r-magrittr r-mass r-patchwork r-reshape2 r-rlang r-rstatix r-stringr r-tibble r-tidyr)) (native-inputs (list r-knitr)) (home-page "https://github.com/CCY-dev/LongDat") (synopsis "Tool for covariate-sensitive longitudinal analysis on omics data") (description "This tool takes longitudinal dataset as input and analyzes if there is significant change of the features over time (a proxy for treatments), while detects and controls for covariates simultaneously. LongDat is able to take in several data types as input, including count, proportion, binary, ordinal and continuous data. The output table contains p values, effect sizes and covariates of each feature, making the downstream analysis easy.") (license license:gpl2))) (define-public r-longitudinal (package (name "r-longitudinal") (version "1.1.13") (source (origin (method url-fetch) (uri (cran-uri "longitudinal" version)) (sha256 (base32 "046w3xbr535c5jyd68adv42a7limxp1mv57b5w6w673w707lmw2p")))) (build-system r-build-system) (propagated-inputs (list r-corpcor)) (home-page "https://strimmerlab.org/software/longitudinal/") (synopsis "Analysis of multiple time course data") (description "This package contains general data structures and functions for longitudinal data with multiple variables, repeated measurements, and irregularly spaced time points. It also implements a shrinkage estimator of dynamical correlation and dynamical covariance.") (license license:gpl3+))) (define-public r-genenet (package (name "r-genenet") (version "1.2.16") (source (origin (method url-fetch) (uri (cran-uri "GeneNet" version)) (sha256 (base32 "1r1khga3nxxjghs4vnbymzp0cwb1q17zw2v3a94qz8fsrirq1sf1")))) (properties `((upstream-name . "GeneNet"))) (build-system r-build-system) (propagated-inputs (list r-corpcor r-fdrtool r-longitudinal)) (home-page "https://strimmerlab.org/software/genenet/") (synopsis "Modeling and inferring gene networks") (description "This package analyzes gene expression (time series) data with focus on the inference of gene networks. In particular, GeneNet implements the methods of Schaefer and Strimmer (2005a,b,c) and Opgen-Rhein and Strimmer (2006, 2007) for learning large-scale gene association networks (including assignment of putative directions).") (license license:gpl3+))) (define-public r-rbamtools (package (name "r-rbamtools") (version "2.16.17") (source (origin (method url-fetch) (uri (cran-uri "rbamtools" version)) (sha256 (base32 "0qj37ljdva3v29s01dkrbg31mcfzy3bl145cp40d54v4h9xhcghc")))) (build-system r-build-system) (inputs (list zlib)) (propagated-inputs (list r-refgenome)) (home-page "https://cran.r-project.org/web/packages/rbamtools") (synopsis "Read and write BAM (binary alignment) files") (description "This package provides an R interface to functions of the SAMtools library.") (license license:artistic2.0))) (define-public r-profvis (package (name "r-profvis") (version "0.3.8") (source (origin (method url-fetch) (uri (cran-uri "profvis" version)) (sha256 (base32 "1cmlcp91q8v0550iay9vsw5wllb6w2ldy6k99rb76ylhr5dwf0pc")) (modules '((guix build utils))) (snippet '(with-directory-excursion "inst/htmlwidgets/lib" (for-each delete-file (list "highlight/highlight.js" ;from rmarkdown "jquery/jquery.min.js" ;version 1.12.4 "d3/d3.min.js")))))) ;version 3.5.6 (properties `((upstream-name . "profvis"))) (build-system r-build-system) (arguments `(#:phases (modify-phases %standard-phases (add-after 'unpack 'process-javascript (lambda* (#:key inputs #:allow-other-keys) (with-directory-excursion "inst/htmlwidgets/lib/" (copy-file (search-input-file inputs "/site-library/rmarkdown/rmd/h/highlightjs/highlight.js") "highlight/highlight.js") (let ((mapping `((,(assoc-ref inputs "js-jquery") . "jquery/jquery.min.js") (,(assoc-ref inputs "js-d3") . "d3/d3.min.js")))) (for-each (lambda (source target) (format #true "Processing ~a --> ~a~%" source target) (invoke "esbuild" source "--minify" (string-append "--outfile=" target))) (map car mapping) (map cdr mapping))))))))) (native-inputs `(("esbuild" ,esbuild) ("r-rmarkdown" ,r-rmarkdown) ("js-d3" ,(origin (method url-fetch) (uri "https://raw.githubusercontent.com/d3/d3/v3.5.6/d3.js") (sha256 (base32 "17qlbwn7vgx335gciq6zp2ib6zg1r9lfa6p1bd9g0ds0xbcsbvgd")))) ("js-jquery" ,(origin (method url-fetch) (uri "https://code.jquery.com/jquery-1.12.4.js") (sha256 (base32 "0x9mrc1668icvhpwzvgafm8xm11x9lfai9nwr66aw6pjnpwkc3s3")))))) (propagated-inputs (list r-htmlwidgets r-purrr r-rlang r-stringr r-vctrs)) (home-page "https://rstudio.github.io/profvis/") (synopsis "Interactive visualizations for profiling R code") (description "This package provides interactive visualizations for profiling R code.") (license license:gpl3))) (define-public r-prospectr (package (name "r-prospectr") (version "0.2.7") (source (origin (method url-fetch) (uri (cran-uri "prospectr" version)) (sha256 (base32 "0hg2afw5aixx0xdwwr6g0wi8sksn7r21hz8diyqxg2345rwnzbg4")))) (properties `((upstream-name . "prospectr"))) (build-system r-build-system) (propagated-inputs (list r-foreach r-iterators r-lifecycle r-mathjaxr r-rcpp r-rcpparmadillo)) (native-inputs (list r-knitr)) (home-page "https://github.com/l-ramirez-lopez/prospectr") (synopsis "Functions for processing and sample selection of spectroscopic data") (description "@code{prospectr} provides miscellaneous functions to preprocess spectroscopic data and conduct representative sample selection, or calibration sampling.") (license license:expat))) (define-public r-protviz (package (name "r-protviz") (version "0.7.9") (source (origin (method url-fetch) (uri (cran-uri "protViz" version)) (sha256 (base32 "1wsjr4asjsknv8fkfv15xqnl67zfv8d2xmvw1i2l0wflxbps3af7")))) (properties `((upstream-name . "protViz"))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) (home-page "https://github.com/protViz/protViz/") (synopsis "Visualizing and analyzing mass spectrometry data in proteomics") (description "This package helps with quality checks, visualizations and analysis of mass spectrometry data, coming from proteomics experiments. The package is developed, tested and used at the Functional Genomics Center Zurich, where it is used mainly for prototyping, teaching, and having fun with proteomics data. But it can also be used to do data analysis for small scale data sets.") (license license:gpl3))) (define-public r-cmprsk (package (name "r-cmprsk") (version "2.2-11") (source (origin (method url-fetch) (uri (cran-uri "cmprsk" version)) (sha256 (base32 "050f24l5ab1ds9824c7yjahimf6pg8ih2k83jzpzfb0n5k5jfh44")))) (build-system r-build-system) (propagated-inputs (list r-survival)) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/cmprsk") (synopsis "Subdistribution analysis of competing risks") (description "This package provides tool for estimation, testing and regression modeling of subdistribution functions in competing risks, as described in Gray (1988), A class of K-sample tests for comparing the cumulative incidence of a competing risk, Ann. Stat. 16:1141-1154, and Fine JP and Gray RJ (1999), A proportional hazards model for the subdistribution of a competing risk, JASA, 94:496-509.") (license license:gpl2+))) (define-public r-etm (package (name "r-etm") (version "1.1.1") (source (origin (method url-fetch) (uri (cran-uri "etm" version)) (sha256 (base32 "1hvrplmdpjjpjji663rw0vjbbrzj2nvr04d1nkc8bf46p4ixyxgy")))) (build-system r-build-system) (propagated-inputs (list r-data-table r-lattice r-rcpp r-rcpparmadillo r-survival)) (home-page "https://cran.r-project.org/web/packages/etm") (synopsis "Empirical transition matrix") (description "The @dfn{empirical transition matrix} (etm) package estimates the matrix of transition probabilities for any time-inhomogeneous multistate model with finite state space using the Aalen-Johansen estimator.") (license license:expat))) (define-public r-epi (package (name "r-epi") (version "2.48") (source (origin (method url-fetch) (uri (cran-uri "Epi" version)) (sha256 (base32 "06965d2x47hb1c7dbqyhhywgr7k9xdcms1v08m2cx52qg6cdkiyp")))) (properties `((upstream-name . "Epi"))) (build-system r-build-system) (propagated-inputs (list r-cmprsk r-data-table r-dplyr r-etm r-magrittr r-mass r-matrix r-mgcv r-numderiv r-plyr r-survival r-zoo)) (home-page "https://BendixCarstensen.com/Epi/") (synopsis "Statistical analysis in epidemiology") (description "This package provides functions for demographic and epidemiological analysis in the Lexis diagram, i.e. register and cohort follow-up data, in particular representation, manipulation and simulation of multistate data - the Lexis suite of functions, which includes interfaces to the @code{mstate}, @code{etm} and @code{cmprsk} packages. It also contains functions for Age-Period-Cohort and Lee-Carter modeling and a function for interval censored data and some useful functions for tabulation and plotting, as well as a number of epidemiological data sets.") (license license:gpl2))) (define-public r-ppls (package (name "r-ppls") (version "1.6-1.1") (source (origin (method url-fetch) (uri (cran-uri "ppls" version)) (sha256 (base32 "1zyrisy3c4cz896j1bjh61sf57wdl9p8ywdq268cl819szfq78mx")))) (build-system r-build-system) (propagated-inputs (list r-mass)) (home-page "https://cran.r-project.org/web/packages/ppls") (synopsis "Penalized partial least squares") (description "This package contains linear and nonlinear regression methods based on partial least squares and penalization techniques. Model parameters are selected via cross-validation, and confidence intervals ans tests for the regression coefficients can be conducted via jackknifing.") (license license:gpl2+))) (define-public r-huge (package (name "r-huge") (version "1.3.5") (source (origin (method url-fetch) (uri (cran-uri "huge" version)) (sha256 (base32 "1sl457a1lndrx98y2j9a2smanawx2iqlhl82iand0g3p5xp8ch4j")))) (build-system r-build-system) (propagated-inputs (list r-igraph r-mass r-matrix r-rcpp r-rcppeigen)) (home-page "https://cran.r-project.org/web/packages/huge") (synopsis "High-dimensional undirected graph estimation") (description "This package provides a general framework for high-dimensional undirected graph estimation. It integrates data preprocessing, neighborhood screening, graph estimation, and model selection techniques into a pipeline.") (license license:gpl2))) (define-public r-parcor (package (name "r-parcor") (version "0.2-6") (source (origin (method url-fetch) (uri (cran-uri "parcor" version)) (sha256 (base32 "0vgs6k92vdr0cmb8cwbv2ff6qavw30agskfd8bfh17hsskrisvx0")))) (build-system r-build-system) (propagated-inputs (list r-epi r-genenet r-glmnet r-mass r-ppls)) (home-page "https://cran.r-project.org/web/packages/parcor") (synopsis "Regularized estimation of partial correlation matrices") (description "This package estimates the matrix of partial correlations based on different regularized regression methods: lasso, adaptive lasso, PLS, and Ridge Regression. In addition, the package provides model selection for lasso, adaptive lasso and Ridge regression based on cross-validation.") (license license:gpl2+))) (define-public r-mcmc (package (name "r-mcmc") (version "0.9-8") (source (origin (method url-fetch) (uri (cran-uri "mcmc" version)) (sha256 (base32 "19vfh868lr4a491gc2x2b2xs83gldw294zbl4bqsgs2q9c6l81ka")))) (build-system r-build-system) (home-page "https://www.stat.umn.edu/geyer/mcmc/") (synopsis "Markov chain Monte Carlo") (description "This package simulates continuous distributions of random vectors using @dfn{Markov chain Monte Carlo} (MCMC). Users specify the distribution by an R function that evaluates the log unnormalized density. Algorithms are random walk Metropolis algorithm (function @code{metrop}), simulated tempering (function @code{temper}), and morphometric random walk Metropolis (function @code{morph.metrop}), which achieves geometric ergodicity by change of variable.") (license license:expat))) (define-public r-listenv (package (name "r-listenv") (version "0.9.1") (source (origin (method url-fetch) (uri (cran-uri "listenv" version)) (sha256 (base32 "0fqwikd3z6n5mia55s3fn5wxnmf2vbw3cmf0hcmm3iligd4ayaj2")))) (build-system r-build-system) (arguments `(#:phases (modify-phases %standard-phases (add-after 'unpack 'set-HOME (lambda _ (setenv "HOME" "/tmp")))))) (native-inputs (list r-r-rsp)) ; vignette builder (home-page "https://github.com/HenrikBengtsson/listenv") (synopsis "Environments behaving (almost) as lists") (description "This package implements list environments. List environments are environments that have list-like properties. For instance, the elements of a list environment are ordered and can be accessed and iterated over using index subsetting.") (license license:lgpl2.1+))) (define-public r-globals (package (name "r-globals") (version "0.16.3") (source (origin (method url-fetch) (uri (cran-uri "globals" version)) (sha256 (base32 "0nwcl40sbmmf812di9c3lryls9wn2k2dyjvpkp9832wd4jafsg6p")))) (build-system r-build-system) (propagated-inputs (list r-codetools)) (home-page "https://github.com/HenrikBengtsson/globals") (synopsis "Identify global objects in R expressions") (description "This package provides tools to identify global (\"unknown\" or \"free\") objects in R expressions by code inspection using various strategies, e.g. conservative or liberal. The objective of this package is to make it as simple as possible to identify global objects for the purpose of exporting them in distributed compute environments.") (license license:lgpl2.1+))) (define-public r-parallelly (package (name "r-parallelly") (version "1.37.1") (source (origin (method url-fetch) (uri (cran-uri "parallelly" version)) (sha256 (base32 "189ngbh9i6mqmfn4z6446in7687ddlpdq6v5rj3hr8zqinqlwznz")))) (properties `((upstream-name . "parallelly"))) (build-system r-build-system) (home-page "https://github.com/HenrikBengtsson/parallelly") (synopsis "Enhancements of the parallel package") (description "This package provides utility functions that enhance the @code{parallel} package and support the built-in parallel backends of the @code{future} package. For example, @code{availableCores} gives the number of CPU cores available to your R process as given by R options and environment variables, including those set by job schedulers on high-performance compute clusters. If none is set, it will fall back to @code{parallel::detectCores}. Another example is @code{makeClusterPSOCK}, which is backward compatible with @code{parallel::makePSOCKcluster} while doing a better job in setting up remote cluster workers without the need for configuring the firewall to do port-forwarding to your local computer.") (license license:lgpl2.1+))) (define-public r-future (package (name "r-future") (version "1.33.2") (source (origin (method url-fetch) (uri (cran-uri "future" version)) (sha256 (base32 "0rma4h9rjy28n7csn748v9b83m2v5hyh0hgwwckfpbnd5331m9xm")))) (build-system r-build-system) (arguments `(#:phases (modify-phases %standard-phases (add-after 'unpack 'set-HOME (lambda _ (setenv "HOME" "/tmp")))))) (propagated-inputs (list r-digest r-globals r-listenv r-parallelly)) (native-inputs (list r-r-rsp)) ; vignette builder (home-page "https://github.com/HenrikBengtsson/future") (synopsis "Unified parallel and distributed processing in R") (description "The purpose of this package is to provide a lightweight and unified Future API for sequential and parallel processing of R expression via futures. This package implements sequential, multicore, multisession, and cluster futures. With these, R expressions can be evaluated on the local machine, in parallel a set of local machines, or distributed on a mix of local and remote machines. Extensions to this package implement additional backends for processing futures via compute cluster schedulers etc. Because of its unified API, there is no need to modify any code in order to switch from sequential on the local machine to, say, distributed processing on a remote compute cluster.") (license license:lgpl2.1+))) (define-public r-future-apply (package (name "r-future-apply") (version "1.11.2") (source (origin (method url-fetch) (uri (cran-uri "future.apply" version)) (sha256 (base32 "11qkv2r8ml1i95j5ra191ij5w1dvllgvr9ld5xnq43ayzaq3b9pl")))) (properties `((upstream-name . "future.apply"))) (build-system r-build-system) (arguments `(#:phases (modify-phases %standard-phases (add-after 'unpack 'set-HOME (lambda _ (setenv "HOME" "/tmp")))))) (propagated-inputs (list r-future r-globals)) (native-inputs (list r-r-rsp)) ; vignette builder (home-page "https://github.com/HenrikBengtsson/future.apply") (synopsis "Apply function to elements in parallel using futures") (description "This package provides implementations of @code{apply()}, @code{eapply()}, @code{lapply()}, @code{Map()}, @code{mapply()}, @code{replicate()}, @code{sapply()}, @code{tapply()}, and @code{vapply()} that can be resolved using any future-supported backend, e.g. parallel on the local machine or distributed on a compute cluster.") (license license:gpl2+))) (define-public r-future-callr (package (name "r-future-callr") (version "0.8.2") (source (origin (method url-fetch) (uri (cran-uri "future.callr" version)) (sha256 (base32 "14hq53cam65ff25l6y17zv37448ls90sa0w51f13199m1kffaaqb")))) (properties '((upstream-name . "future.callr") (updater-extra-native-inputs . ("r-markdown")))) (build-system r-build-system) ;; This is needed for the vignette builder R.rsp. (arguments (list #:phases #~(modify-phases %standard-phases (add-after 'unpack 'set-HOME (lambda _ (setenv "HOME" "/tmp")))))) (propagated-inputs (list r-callr r-future)) (native-inputs (list r-markdown r-r-rsp)) (home-page "https://future.callr.futureverse.org") (synopsis "Future API for Parallel Processing using 'callr'") (description "This is an implementation of the Future API on top of the callr package. This allows you to process futures, as defined by the future package, in parallel out of the box, on your local machine. Contrary to backends relying on the parallel package (e.g. @code{future::multisession}) and socket connections, the callr backend provided here can run more than 125 parallel R processes.") (license license:lgpl2.1+))) (define-public r-rsvd (package (name "r-rsvd") (version "1.0.5") (source (origin (method url-fetch) (uri (cran-uri "rsvd" version)) (sha256 (base32 "07p2hjmpcwcsang8z9sjkpy94rydcin7m3hyvcgzgm5cd6w8c1p4")))) (build-system r-build-system) (propagated-inputs (list r-matrix)) (home-page "https://github.com/erichson/rSVD") (synopsis "Randomized singular value decomposition") (description "Low-rank matrix decompositions are fundamental tools and widely used for data analysis, dimension reduction, and data compression. Classically, highly accurate deterministic matrix algorithms are used for this task. However, the emergence of large-scale data has severely challenged our computational ability to analyze big data. The concept of randomness has been demonstrated as an effective strategy to quickly produce approximate answers to familiar problems such as the @dfn{singular value decomposition} (SVD). This package provides several randomized matrix algorithms such as the randomized singular value decomposition (@code{rsvd}), randomized principal component analysis (@code{rpca}), randomized robust principal component analysis (@code{rrpca}), randomized interpolative decomposition (@code{rid}), and the randomized CUR decomposition (@code{rcur}). In addition several plot functions are provided.") (license license:gpl3+))) (define-public r-sloop (package (name "r-sloop") (version "1.0.1") (source (origin (method url-fetch) (uri (cran-uri "sloop" version)) (sha256 (base32 "00fk5fr5zsk2qxc1kfhmshhjxgnamm3401089sx8m2l529zd6r8j")))) (build-system r-build-system) (propagated-inputs (list r-codetools r-crayon r-purrr r-rlang r-tibble)) (home-page "https://github.com/r-lib/sloop") (synopsis "Helpers for object-oriented programming in R") (description "This package provides a collection of helper functions designed to help you to better understand object oriented programming in R, particularly using @code{S3}.") (license license:gpl3))) (define-public r-capushe (package (name "r-capushe") (version "1.1.2") (source (origin (method url-fetch) (uri (cran-uri "capushe" version)) (sha256 (base32 "1mazsfdiqmhy0ywahqw49qql899ph0l6jllriz2spyp1bs98q9b7")))) (build-system r-build-system) (propagated-inputs (list r-mass)) (home-page "https://cran.r-project.org/web/packages/capushe/index.html") (synopsis "Calibrating penalties using slope heuristics") (description "This package provides tools for the calibration of penalized criteria for model selection. The calibration methods available are based on the slope heuristics.") (license license:gpl2+))) (define-public r-dorng (package (name "r-dorng") (version "1.8.6") (source (origin (method url-fetch) (uri (cran-uri "doRNG" version)) (sha256 (base32 "1qkxa3jxpnn5anhqycqcbk18kw87m9pl5m78q8d89ygihghascjh")))) (properties `((upstream-name . "doRNG"))) (build-system r-build-system) (propagated-inputs (list r-foreach r-iterators r-rngtools)) (native-inputs (list r-knitr)) (home-page "https://renozao.github.io/doRNG/") (synopsis "Generic reproducible parallel backend for foreach loops") (description "This package provides functions to perform reproducible parallel @code{foreach} loops, using independent random streams as generated by L'Ecuyer's combined multiple-recursive generator. It enables to easily convert standard @code{%dopar%} loops into fully reproducible loops, independently of the number of workers, the task scheduling strategy, or the chosen parallel environment and associated foreach backend.") (license license:gpl2+))) (define-public r-blockmodeling (package (name "r-blockmodeling") (version "1.1.5") (source (origin (method url-fetch) (uri (cran-uri "blockmodeling" version)) (sha256 (base32 "00qmpf0jdc8vl76rzfg12z2mdr215q8qd9p3a4b816y2g0092vrv")))) (build-system r-build-system) (propagated-inputs (list r-matrix)) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/blockmodeling") (synopsis "Generalized and classical blockmodeling of valued networks") (description "This package is primarily meant as an implementation of generalized blockmodeling for valued networks. In addition, measures of similarity or dissimilarity based on structural equivalence and regular equivalence (REGE algorithms) can be computed and partitioned matrices can be plotted.") (license license:gpl2+))) (define-public r-upsetr (package (name "r-upsetr") (version "1.4.0") (source (origin (method url-fetch) (uri (cran-uri "UpSetR" version)) (sha256 (base32 "007i0njnjjy7vbrxabwav7a1kk2n0hn2mkvqsdzzfk10ckp5y7im")))) (properties `((upstream-name . "UpSetR"))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-gridextra r-plyr r-scales)) (home-page "https://github.com/hms-dbmi/UpSetR") (synopsis "Visualize intersecting sets") (description "This package provides a more scalable alternative to Venn and Euler diagrams for visualizing intersecting sets. Create visualizations of intersecting sets using a novel matrix design, along with visualizations of several common set, element and attribute related tasks.") (license license:expat))) (define-public r-shinycustomloader (package (name "r-shinycustomloader") (version "0.9.0") (source (origin (method url-fetch) (uri (cran-uri "shinycustomloader" version)) (sha256 (base32 "1klx71vr26g0gjf6hbiia1qidqii5d467i1sdjvlrg1hxdcggqff")))) (properties `((upstream-name . "shinycustomloader"))) (build-system r-build-system) (propagated-inputs (list r-glue r-shiny)) (home-page "https://cran.r-project.org/package=shinycustomloader") (synopsis "Custom loader for Shiny outputs") (description "This package provides a custom @code{CSS/HTML} or @code{GIF/image} file for the loading screen in R @code{Shiny}. It also can use the marquee to have a custom text loading screen.") (license license:gpl3))) ;; This package includes a JavaScript file, which is not minified. When ;; upgrading please check that there are no new minified JavaScript files. (define-public r-shinybs (package (name "r-shinybs") (version "0.61.1") (source (origin (method url-fetch) (uri (cran-uri "shinyBS" version)) (sha256 (base32 "0h51685a9qll4agayldjyryi60ih969219ibg071slv0613p5v8a")))) (properties `((upstream-name . "shinyBS"))) (build-system r-build-system) ;; The tests spawn Shiny browser apps. They cannot be run ;; non-interactively. (arguments '(#:tests? #f)) (propagated-inputs (list r-htmltools r-shiny)) (home-page "https://ebailey78.github.io/shinyBS/") (synopsis "Twitter Bootstrap components for Shiny") (description "This package adds additional Twitter Bootstrap components to Shiny.") (license license:gpl3))) (define-public r-shinyjqui (package (name "r-shinyjqui") (version "0.4.1") (source (origin (method url-fetch) (uri (cran-uri "shinyjqui" version)) (sha256 (base32 "135gwz7syyb6pbn0lkvmq0v1c6r1zivavnqhi1rnzbbzlysi27v1")) (snippet '(for-each delete-file (list "inst/www/shinyjqui.min.js" "inst/www/jquery.ui.touch-punch.min.js"))))) (properties `((upstream-name . "shinyjqui"))) (build-system r-build-system) (arguments `(#:phases (modify-phases %standard-phases (add-after 'unpack 'process-javascript (lambda* (#:key inputs #:allow-other-keys) (with-directory-excursion "inst/www" (let ((mapping `((,(string-append (assoc-ref inputs "js-jquery.ui.touch-punch") "/jquery.ui.touch-punch.js") . "jquery.ui.touch-punch.min.js") ("shinyjqui.js" . "shinyjqui.min.js")))) (for-each (lambda (source target) (format #true "Processing ~a --> ~a~%" source target) (invoke "esbuild" source "--minify" (string-append "--outfile=" target))) (map car mapping) (map cdr mapping))))))))) (propagated-inputs (list r-htmltools r-htmlwidgets r-jsonlite r-rlang r-shiny)) (native-inputs `(("r-knitr" ,r-knitr) ("esbuild" ,esbuild) ("js-jquery.ui.touch-punch" ,(origin (method git-fetch) (uri (git-reference (url "https://github.com/furf/jquery-ui-touch-punch") (commit "8f7559b6e65cdc3ee3648d5fe76d38c653f87ff5"))) (sha256 (base32 "1lzywp2q9hwx6d5fqjla95vp7ra2lahr5dam7lsqjmch9d98r48q")))))) (home-page "https://github.com/yang-tang/shinyjqui") (synopsis "jQuery UI interactions and effects for Shiny") (description "This is an extension to Shiny that brings interactions and animation effects from the jQuery UI library.") (license license:expat))) (define-public r-shinymanager (package (name "r-shinymanager") (version "1.0.410") (source (origin (method url-fetch) (uri (cran-uri "shinymanager" version)) (sha256 (base32 "0nl672dgwj34wm4i3pxk28lv6qw9xsgg3hm0h78q3zdgk8a33kdn")))) (properties `((upstream-name . "shinymanager"))) (build-system r-build-system) (propagated-inputs (list r-billboarder r-dbi r-dt r-htmltools r-openssl r-r-utils r-r6 r-rsqlite r-scrypt r-shiny)) (native-inputs (list r-knitr)) (home-page "https://github.com/datastorm-open/shinymanager") (synopsis "Authentication management for Shiny applications") (description "This package provides simple and secure authentication mechanism for single Shiny applications. Credentials are stored in an encrypted SQLite database.") (license license:gpl3))) (define-public r-outliers (package (name "r-outliers") (version "0.15") (source (origin (method url-fetch) (uri (cran-uri "outliers" version)) (sha256 (base32 "1yrmwvjjb0a6sbx940k9svf23cykcxz8rrwcgyic7lpgzbrdfcfc")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/outliers/index.html") (synopsis "Tests for outliers") (description "This package provides a collection of some tests commonly used for identifying outliers.") (license license:gpl2+))) (define-public r-bayesm (package (name "r-bayesm") (version "3.1-6") (source (origin (method url-fetch) (uri (cran-uri "bayesm" version)) (sha256 (base32 "1d9wp7yr5hadyv48f51xqa5yzfnhh01n813sivwla209vjf2pmqp")))) (build-system r-build-system) (propagated-inputs (list r-rcpp r-rcpparmadillo)) (native-inputs (list r-knitr)) (home-page "https://www.perossi.org/home/bsm-1") (synopsis "Bayesian inference for marketing/micro-econometrics") (description "This package covers many important models used in marketing and micro-econometrics applications, including Bayes Regression (univariate or multivariate dep var), Bayes Seemingly Unrelated Regression (SUR), Binary and Ordinal Probit, Multinomial Logit (MNL) and Multinomial Probit (MNP), Multivariate Probit, Negative Binomial (Poisson) Regression, Multivariate Mixtures of Normals (including clustering), Dirichlet Process Prior Density Estimation with normal base, Hierarchical Linear Models with normal prior and covariates, Hierarchical Linear Models with a mixture of normals prior and covariates, Hierarchical Multinomial Logits with a mixture of normals prior and covariates, Hierarchical Multinomial Logits with a Dirichlet Process prior and covariates, Hierarchical Negative Binomial Regression Models, Bayesian analysis of choice-based conjoint data, Bayesian treatment of linear instrumental variables models, Analysis of Multivariate Ordinal survey data with scale usage heterogeneity, and Bayesian Analysis of Aggregate Random Coefficient Logit Models.") (license license:gpl2+))) (define-public r-tensora (package (name "r-tensora") (version "0.36.2.1") (source (origin (method url-fetch) (uri (cran-uri "tensorA" version)) (sha256 (base32 "1dvxc4d5c8k3mqkx6bjgfmnb98rrdd1rsazyva76mzvxzrhq4n06")))) (properties `((upstream-name . "tensorA"))) (build-system r-build-system) (home-page "http://www.stat.boogaart.de/tensorA") (synopsis "Advanced tensor arithmetic with named indices") (description "This package provides convenience functions for advanced linear algebra with tensors and computation with datasets of tensors on a higher level abstraction. It includes Einstein and Riemann summing conventions, dragging, co- and contravariate indices, and parallel computations on sequences of tensors.") (license license:gpl2+))) (define-public r-rarpack (package (name "r-rarpack") (version "0.11-0") (source (origin (method url-fetch) (uri (cran-uri "rARPACK" version)) (sha256 (base32 "12h2y46xcfldhjdmm960swgn9b23zvkj5vg2bi42s9qxwgi02d63")))) (properties `((upstream-name . "rARPACK"))) (build-system r-build-system) (propagated-inputs (list r-rspectra)) (home-page "https://github.com/yixuan/rARPACK") (synopsis "Solvers for large scale eigenvalue and SVD problems") (description "This package was previously an R wrapper of the ARPACK library, and now a shell of the R package RSpectra, an R interface to the Spectra library for solving large scale eigenvalue/vector problems. The current version of rARPACK simply imports and exports the functions provided by RSpectra. New users of rARPACK are advised to switch to the RSpectra package.") (license license:bsd-3))) (define-public r-compositions (package (name "r-compositions") (version "2.0-8") (source (origin (method url-fetch) (uri (cran-uri "compositions" version)) (sha256 (base32 "147j3sbqcy3hfja1zs8s8p9zzp9a68vk52s545c2p6anyj4381n5")))) (build-system r-build-system) (propagated-inputs (list r-bayesm r-mass r-robustbase r-tensora)) (native-inputs (list r-knitr)) (home-page "http://www.stat.boogaart.de/compositions") (synopsis "Compositional data analysis") (description "This package provides functions for the consistent analysis of compositional data (e.g. portions of substances) and positive numbers (e.g. concentrations).") (license license:gpl2+))) (define-public r-cobs (package (name "r-cobs") (version "1.3-8") (source (origin (method url-fetch) (uri (cran-uri "cobs" version)) (sha256 (base32 "08cqpiylbfy5j5xxajpngqaycmmciwhyf3sk3972x2l6rg3lj81c")))) (build-system r-build-system) (propagated-inputs (list r-quantreg r-sparsem)) (home-page "https://cran.r-project.org/web/packages/cobs") (synopsis "Constrained B-Splines (sparse matrix based)") (description "This package provides qualitatively constrained (regression) smoothing splines via linear programming and sparse matrices.") (license license:gpl2+))) (define-public r-drimpute (package (name "r-drimpute") (version "1.0") (source (origin (method url-fetch) (uri (cran-uri "DrImpute" version)) (sha256 (base32 "1adzarrwqb282pqgx2yqswp9rpwd1naxsmar54kddr6qyd6b923b")))) (properties `((upstream-name . "DrImpute"))) (build-system r-build-system) (propagated-inputs (list r-rcpp r-rcpparmadillo)) (home-page "https://github.com/ikwak2/DrImpute") (synopsis "Imputing dropout events in single-cell RNA-Seq data") (description "This is an R package for imputing dropout events. Many statistical methods in cell type identification, visualization and lineage reconstruction do not account for dropout events. DrImpute can improve the performance of such software by imputing dropout events.") (license license:gpl3))) (define-public r-gamlss-dist (package (name "r-gamlss-dist") (version "6.1-1") (source (origin (method url-fetch) (uri (cran-uri "gamlss.dist" version)) (sha256 (base32 "0sch2bh1mchl7kfdy4wcmwzzgx7cldswn65a2br2x73rb1v3mnyj")))) (properties `((upstream-name . "gamlss.dist"))) (build-system r-build-system) (propagated-inputs (list r-mass)) (home-page "http://www.gamlss.org/") (synopsis "Distributions for Generalized Additive Models for location scale and shape") (description "This package provides a set of distributions which can be used for modelling the response variables in Generalized Additive Models for Location Scale and Shape. The distributions can be continuous, discrete or mixed distributions. Extra distributions can be created, by transforming, any continuous distribution defined on the real line, to a distribution defined on ranges 0 to infinity or 0 to 1, by using a @code{log} or a @code{logit} transformation, respectively.") ;; Either version of the GPL. (license (list license:gpl2 license:gpl3)))) ;; This package includes JavaScript files, which are not minified. When ;; upgrading please check that there are no new minified JavaScript files. (define-public r-shinyjs (package (name "r-shinyjs") (version "2.1.0") (source (origin (method url-fetch) (uri (cran-uri "shinyjs" version)) (sha256 (base32 "1id9gsrkr28xl80a8794in17rxmmz06zqvd5hlns7mqz3fzhrhky")))) (build-system r-build-system) (propagated-inputs (list r-digest r-jsonlite r-shiny)) (native-inputs (list r-knitr)) (home-page "https://deanattali.com/shinyjs") (synopsis "Improve the user experience of your Shiny apps") (description "Perform common useful JavaScript operations in Shiny apps that will greatly improve your apps without having to know any JavaScript. Examples include: hiding an element, disabling an input, resetting an input back to its original value, delaying code execution by a few seconds, and many more useful functions for both the end user and the developer. Shinyjs can also be used to easily call your own custom JavaScript functions from R.") (license license:agpl3+))) ;; This package includes minified JavaScript files. When upgrading please ;; check that there are no new minified JavaScript files. (define-public r-colourpicker (package (name "r-colourpicker") (version "1.3.0") (source (origin (method url-fetch) (uri (cran-uri "colourpicker" version)) (sha256 (base32 "0415238r7a8xrp3kvq8lczzxz534irj2q1zfbb0pl7xfs6663wn7")) (snippet '(for-each delete-file (list "inst/examples/colourInput/www/salvattore.min.js" "inst/htmlwidgets/lib/jquery/jquery.min.js" "inst/www/shared/colourpicker/js/colourpicker.min.js"))))) (build-system r-build-system) (arguments (list #:phases '(modify-phases %standard-phases (add-after 'unpack 'process-javascript (lambda* (#:key inputs #:allow-other-keys) (with-directory-excursion "inst" (let ((mapping `((,(assoc-ref inputs "js-salvattore") . "examples/colourInput/www/salvattore.min.js") (,(assoc-ref inputs "js-jquery") . "htmlwidgets/lib/jquery/jquery.min.js") ("www/shared/colourpicker/js/colourpicker.js" . "www/shared/colourpicker/js/colourpicker.min.js")))) (for-each (lambda (source target) (format #true "Processing ~a --> ~a~%" source target) (invoke "esbuild" source "--minify" (string-append "--outfile=" target))) (map car mapping) (map cdr mapping))))))))) (propagated-inputs (list r-ggplot2 r-htmltools r-htmlwidgets r-jsonlite r-miniui r-shiny r-shinyjs)) (native-inputs `(("esbuild" ,esbuild) ("js-jquery" ,(origin (method url-fetch) (uri "https://code.jquery.com/jquery-3.6.1.js") (sha256 (base32 "1lm4zcpvqdi7qi2s7bgci2z74wazq0z0bdvjmlrqbhmfrpk42ffz")))) ("js-salvattore" ,(origin (method url-fetch) (uri "https://raw.githubusercontent.com/rnmp/salvattore/v1.0.9/dist/salvattore.js") (sha256 (base32 "0lfrbx7l9w5x89jpc6njmd0pk7h8fpvg537vklai2vf7b1r2nnk5")))))) (home-page "https://github.com/daattali/colourpicker") (synopsis "Color picker tool for Shiny and for selecting colors in plots") (description "This package provides a color picker that can be used as an input in Shiny apps or Rmarkdown documents. The color picker supports alpha opacity, custom color palettes, and many more options. A plot color helper tool is available as an RStudio Addin, which helps you pick colors to use in your plots. A more generic color picker RStudio Addin is also provided to let you select colors to use in your R code.") (license license:expat))) (define-public r-ggextra (package (name "r-ggextra") (version "0.10.1") (source (origin (method url-fetch) (uri (cran-uri "ggExtra" version)) (sha256 (base32 "0b78bnkhjlfa2h3f5iib0hqas8r289vqglfbk71a419rivzfsyb8")))) (properties `((upstream-name . "ggExtra"))) (build-system r-build-system) (propagated-inputs (list r-colourpicker r-ggplot2 r-gtable r-miniui r-r6 r-scales r-shiny r-shinyjs)) (native-inputs (list r-knitr)) (home-page "https://github.com/daattali/ggExtra") (synopsis "Marginal histograms for ggplot2 and other enhancements") (description "This package is a collection of functions and layers to enhance ggplot2. The flagship function is @code{ggMarginal()}, which can be used to add marginal histograms/boxplots/density plots to ggplot2 scatterplots.") (license license:expat))) (define-public r-ggpattern (package (name "r-ggpattern") (version "1.0.1") (source (origin (method url-fetch) (uri (cran-uri "ggpattern" version)) (sha256 (base32 "1b9bfxlg64gr39bz58fp6jmg4nziwk8rk94rzpjsqhfhpwi2lrgr")))) (properties `((upstream-name . "ggpattern"))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-glue r-gridpattern r-rlang r-scales)) (native-inputs (list r-knitr r-ragg r-rmarkdown)) (home-page "https://github.com/coolbutuseless/ggpattern") (synopsis "Ggplot2 pattern geoms") (description "This package provides ggplot2 geoms filled with various patterns. It includes a patterned version of every ggplot2 geom that has a region that can be filled with a pattern. It provides a suite of ggplot2 aesthetics and scales for controlling pattern appearances. It supports over a dozen builtin patterns (every pattern implemented by gridpattern) as well as allowing custom user-defined patterns.") (license license:expat))) (define-public r-minpack-lm (package (name "r-minpack-lm") (version "1.2-4") (source (origin (method url-fetch) (uri (cran-uri "minpack.lm" version)) (sha256 (base32 "0cg7arnmb7x6v5x487gkc2k4i5gchgdwblrrd0k0vw1w6pza83z3")))) (properties `((upstream-name . "minpack.lm"))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/minpack.lm") (synopsis "Levenberg-Marquardt Nonlinear Least-Squares algorithm") (description "The @code{nls.lm} function provides an R interface to @code{lmder} and @code{lmdif} from the MINPACK library, for solving nonlinear least-squares problems by a modification of the Levenberg-Marquardt algorithm, with support for lower and upper parameter bounds. The implementation can be used via @code{nls}-like calls using the @code{nlsLM} function.") (license license:gpl3))) (define-public r-moments (package (name "r-moments") (version "0.14.1") (source (origin (method url-fetch) (uri (cran-uri "moments" version)) (sha256 (base32 "0r6qf3i1rzh2822bx1p0h8mh91gsbgg6asl2rzh2l4ys094bilif")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/moments") (synopsis "Moments, cumulants, skewness, kurtosis and related tests") (description "This package provides functions to calculate: moments, Pearson's kurtosis, Geary's kurtosis and skewness; it also includes tests related to them (Anscombe-Glynn, D'Agostino, Bonett-Seier).") (license license:gpl2+))) (define-public r-msir (package (name "r-msir") (version "1.3.3") (source (origin (method url-fetch) (uri (cran-uri "msir" version)) (sha256 (base32 "1wm83m3cqd6llxb9p2jwim0wb81v84pgdmgcznygzaaq6kbn3n84")))) (build-system r-build-system) (propagated-inputs (list r-mclust)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/msir") (synopsis "Model-based sliced inverse regression") (description "This is an R package for dimension reduction based on finite Gaussian mixture modeling of inverse regression.") (license license:gpl2+))) (define-public r-pbivnorm (package (name "r-pbivnorm") (version "0.6.0") (source (origin (method url-fetch) (uri (cran-uri "pbivnorm" version)) (sha256 (base32 "05jzrjqxzbcf6z245hlk7sjxiszv9paadaaimvcx5y5qgi87vhq7")))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "https://github.com/brentonk/pbivnorm") (synopsis "Vectorized bivariate normal CDF") (description "This package provides a vectorized R function for calculating probabilities from a standard bivariate normal CDF.") (license license:gpl2+))) (define-public r-lavaan (package (name "r-lavaan") (version "0.6-17") (source (origin (method url-fetch) (uri (cran-uri "lavaan" version)) (sha256 (base32 "1bppbv17b35h48vfci6zplix9zb5isi210za52cs9yyc68g2acwj")))) (build-system r-build-system) (propagated-inputs (list r-mass r-mnormt r-numderiv r-pbivnorm r-quadprog)) (home-page "https://lavaan.ugent.be") (synopsis "Latent variable analysis") (description "This package provides tools to fit a variety of latent variable models, including confirmatory factor analysis, structural equation modeling and latent growth curve models.") (license license:gpl2+))) (define-public r-nonnest2 (package (name "r-nonnest2") (version "0.5-6") (source (origin (method url-fetch) (uri (cran-uri "nonnest2" version)) (sha256 (base32 "1s31a03c148azvc20ihmz8vhzgs7a3r0nxzf806zsr5j1zsl94dm")))) (build-system r-build-system) (propagated-inputs (list r-compquadform r-lavaan r-mvtnorm r-sandwich)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/nonnest2/") (synopsis "Tests of non-nested models") (description "This package allows for testing of non-nested models. It includes tests of model distinguishability and of model fit that can be applied to both nested and non-nested models. The package also includes functionality to obtain confidence intervals associated with AIC and BIC.") ;; Either version of the GPL. (license (list license:gpl2 license:gpl3)))) (define-public r-penalized (package (name "r-penalized") (version "0.9-52") (source (origin (method url-fetch) (uri (cran-uri "penalized" version)) (sha256 (base32 "08badmgygppbqzay20qijyww028yw6s8dyd8ijcp8g4r9rn8xqyq")))) (build-system r-build-system) (propagated-inputs (list r-rcpp r-rcpparmadillo r-survival)) (home-page "https://cran.r-project.org/web/packages/penalized/") (synopsis "Penalized estimation in GLMs and in the Cox model") (description "This package provides tools for fitting possibly high dimensional penalized regression models. The penalty structure can be any combination of an L1 penalty (lasso and fused lasso), an L2 penalty (ridge) and a positivity constraint on the regression coefficients. The supported regression models are linear, logistic and Poisson regression and the Cox Proportional Hazards model. Cross-validation routines allow optimization of the tuning parameters.") (license license:gpl2+))) (define-public r-zim (package (name "r-zim") (version "1.1.0") (source (origin (method url-fetch) (uri (cran-uri "ZIM" version)) (sha256 (base32 "0scyfjn4ilsvha3x41c3b8bcfi31hlhwm77wn2a8hj5dsvnnmzig")))) (properties `((upstream-name . "ZIM"))) (build-system r-build-system) (propagated-inputs (list r-mass)) (home-page "https://github.com/biostatstudio/ZIM") (synopsis "Zero-inflated models (ZIM) for count time series with excess zeros") (description "Analyze count time series with excess zeros. Two types of statistical models are supported: Markov regression and state-space models. They are also known as observation-driven and parameter-driven models respectively in the time series literature. The functions used for Markov regression or observation-driven models can also be used to fit ordinary regression models with independent data under the zero-inflated Poisson (ZIP) or zero-inflated negative binomial (ZINB) assumption. The package also contains miscellaneous functions to compute density, distribution, quantile, and generate random numbers from ZIP and ZINB distributions.") (license license:gpl3))) (define-public r-nor1mix (package (name "r-nor1mix") (version "1.3-3") (source (origin (method url-fetch) (uri (cran-uri "nor1mix" version)) (sha256 (base32 "0vh7vlvijska09rm0cb2lakwhjm38mc4daksc2zniyj7r3wd1gwp")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/nor1mix/") (synopsis "Normal (1-d) mixture models") (description "This package provides S3 classes and methods for one-dimensional normal mixture models, for, e.g., density estimation or clustering algorithms research and teaching; it provides the widely used Marron-Wand densities. It also provides tools for efficient random number generation and graphics.") (license license:gpl2+))) (define-public r-beanplot (package (name "r-beanplot") (version "1.3.1") (source (origin (method url-fetch) (uri (cran-uri "beanplot" version)) (sha256 (base32 "1b8mvlcsv5l9g08ag92hndsvk8jmgxvznhzgazc8y4296kp8l5a9")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/beanplot/") (synopsis "Visualization via beanplots") (description "This package provides beanplots, an alternative to boxplot/stripchart/violin plots. It can be used to plot univariate comparison graphs.") (license license:gpl2))) (define-public r-pbdzmq (package (name "r-pbdzmq") (version "0.3-11") (source (origin (method url-fetch) (uri (cran-uri "pbdZMQ" version)) (sha256 (base32 "0ns0fpfsbx28iyxmas691i29sh1gia0bspx0flgj0w3khm6j0zns")))) (properties `((upstream-name . "pbdZMQ"))) (build-system r-build-system) (inputs (list zeromq zlib)) (native-inputs (list pkg-config)) (home-page "https://pbdr.org/") (synopsis "R interface to ZeroMQ") (description "ZeroMQ is a well-known library for high-performance asynchronous messaging in scalable, distributed applications. This package provides high level R wrapper functions to easily utilize ZeroMQ. The main focus is on interactive client/server programming frameworks. A few wrapper functions compatible with @code{rzmq} are also provided.") (license license:gpl3))) (define-public r-repr (package (name "r-repr") (version "1.1.7") (source (origin (method url-fetch) (uri (cran-uri "repr" version)) (sha256 (base32 "06q2xmg27w1hhapcf320zz92f5arwrf2sf0y1mp0j4a29mmnkgbk")))) (build-system r-build-system) (propagated-inputs (list r-base64enc r-htmltools r-jsonlite r-pillar)) (home-page "https://cran.r-project.org/web/packages/repr/") (synopsis "Serializable representations") (description "This package provides string and binary representations of objects for several formats and MIME types.") (license license:gpl3))) (define-public r-irdisplay (package (name "r-irdisplay") (version "1.1") (source (origin (method url-fetch) (uri (cran-uri "IRdisplay" version)) (sha256 (base32 "0awdiv4rr93y8jb1d64sm1iy37ywyniqm7w98yv6qm0zz47h7sw3")))) (properties `((upstream-name . "IRdisplay"))) (build-system r-build-system) (propagated-inputs (list r-repr)) (home-page "https://cran.r-project.org/web/packages/IRdisplay/") (synopsis "Jupyter display machinery") (description "This package provides an interface to the rich display capabilities of Jupyter front-ends (e.g. Jupyter Notebook). It is designed to be used from a running IRkernel session.") (license license:expat))) (define-public r-irkernel (package (name "r-irkernel") (version "1.3.2") (source (origin (method url-fetch) (uri (cran-uri "IRkernel" version)) (sha256 (base32 "19i4wj5cb62n6j83nxgv500dcdzrf6rzwdy5v6fh7r93vjyxiip1")))) (properties `((upstream-name . "IRkernel"))) (build-system r-build-system) (arguments `(#:phases (modify-phases %standard-phases (add-after 'install 'install-kernelspec (lambda* (#:key outputs #:allow-other-keys) (let ((out (assoc-ref outputs "out"))) (setenv "HOME" "/tmp") (invoke "jupyter" "kernelspec" "install" "--name" "ir" "--prefix" out (string-append out "/site-library/IRkernel/kernelspec")) ;; Record the absolute file name of the 'R' executable in ;; 'kernel.json'. (substitute* (string-append out "/share/jupyter" "/kernels/ir/kernel.json") (("\\[\"R\",") (string-append "[\"" (which "R") "\","))) #t)))))) (inputs (list jupyter)) (propagated-inputs (list r-crayon r-digest r-evaluate r-irdisplay r-jsonlite ;; sets R_LIBS_SITE, so R can actually find this package (IRkernel) r-minimal r-pbdzmq r-repr r-uuid)) (home-page "https://cran.r-project.org/web/packages/IRkernel/") (synopsis "Native R kernel for Jupyter") (description "The R kernel for the Jupyter environment executes R code which the front-end (Jupyter Notebook or other front-ends) submits to the kernel via the network.") (license license:expat))) (define-public r-gmodels (package (name "r-gmodels") (version "2.19.1") (source (origin (method url-fetch) (uri (cran-uri "gmodels" version)) (sha256 (base32 "13c8x7iwyz36qir3ikbvjb5dl6gdh4fh82qdxcpcdinwfhrbhmxv")))) (build-system r-build-system) (propagated-inputs (list r-gdata r-mass)) (home-page "https://cran.r-project.org/web/packages/gmodels/") (synopsis "Various R programming tools for model fitting") (description "This package provides various R programming tools for model fitting.") (license license:gpl2))) (define-public r-apcluster (package (name "r-apcluster") (version "1.4.11") (source (origin (method url-fetch) (uri (cran-uri "apcluster" version)) (sha256 (base32 "0crk7skivcmlvr0njsbd8dksj5wa6qlvdp99ay5b2b40cs3xm5s4")))) (build-system r-build-system) (propagated-inputs (list r-matrix r-rcpp)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/apcluster/") (synopsis "Affinity propagation clustering") (description "This package implements affinity propagation clustering introduced by Frey and Dueck (2007). The package further provides leveraged affinity propagation and an algorithm for exemplar-based agglomerative clustering that can also be used to join clusters obtained from affinity propagation. Various plotting functions are available for analyzing clustering results.") (license license:gpl2+))) (define-public r-remacor (package (name "r-remacor") (version "0.0.18") (source (origin (method url-fetch) (uri (cran-uri "remaCor" version)) (sha256 (base32 "0c8n2zj84m2z0vznx81qrspnyyj38imb73di4l2k0brr8jxgzr2p")))) (properties `((upstream-name . "remaCor"))) (build-system r-build-system) (propagated-inputs (list r-envstats r-ggplot2 r-mvtnorm r-rcpp r-rcpparmadillo r-rdpack r-reshape2)) (native-inputs (list r-knitr)) (home-page "https://diseaseneurogenomics.github.io/remaCor/") (synopsis "Random effects meta-analysis for correlated test statistics") (description "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.") (license license:artistic2.0))) (define-public r-rematch2 (package (name "r-rematch2") (version "2.1.2") (source (origin (method url-fetch) (uri (cran-uri "rematch2" version)) (sha256 (base32 "1fzpz8vhghw8ygwg6rsvfy3783pqk7ch029i5851lwypkplvz77y")))) (build-system r-build-system) (propagated-inputs (list r-tibble)) (home-page "https://github.com/r-lib/rematch2") (synopsis "Tidy output from regular expression matching") (description "This package provides wrappers on @code{regexpr} and @code{gregexpr} to return the match results in tidy data frames.") (license license:expat))) (define-public r-picante (package (name "r-picante") (version "1.8.2") (source (origin (method url-fetch) (uri (cran-uri "picante" version)) (sha256 (base32 "19savjzj44b7ifdxcp02ynj22z4n4ikq2aipc74ljzy3yykmqmjn")))) (build-system r-build-system) (propagated-inputs (list r-ape r-nlme r-vegan)) (home-page "https://cran.r-project.org/web/packages/picante/") (synopsis "Integrating phylogenies and ecology") (description "This package provides functions for phylocom integration, community analyses, null-models, traits and evolution. It implements numerous ecophylogenetic approaches including measures of community phylogenetic and trait diversity, phylogenetic signal, estimation of trait values for unobserved taxa, null models for community and phylogeny randomizations, and utility functions for data input/output and phylogeny plotting. A full description of package functionality and methods are provided by Kembel et al. (2010).") (license license:gpl2))) (define-public r-reinforcelearn (package (name "r-reinforcelearn") (version "0.2.1") (source (origin (method url-fetch) (uri (cran-uri "reinforcelearn" version)) (sha256 (base32 "176z2q69p24i29a8sh19xxn2zl3h1z2ixdssr5i6m4yvkvdrvv3b")))) (build-system r-build-system) (propagated-inputs (list r-checkmate r-nnet r-purrr r-r6)) (home-page "https://markusdumke.github.io/reinforcelearn") (synopsis "Reinforcement learning") (description "This package implements reinforcement learning environments and algorithms as described in Sutton & Barto (1998). The Q-Learning algorithm can be used with function approximation, eligibility traces (Singh & Sutton, 1996) and experience replay (Mnih et al., 2013).") (license license:expat))) (define-public r-lemon (package (name "r-lemon") (version "0.4.9") (source (origin (method url-fetch) (uri (cran-uri "lemon" version)) (sha256 (base32 "1yjam478s6sz1spggybb34akpmpgq8ybyrhzy3b1v9s1j81b6k87")))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-gridextra r-gtable r-knitr r-lattice r-plyr r-scales)) (native-inputs (list r-knitr)) (home-page "https://github.com/stefanedwards/lemon") (synopsis "Freshen up your ggplot2 plots") (description "This package provides functions for working with legends and axis lines of ggplot2, facets that repeat axis lines on all panels, and some knitr extensions.") (license license:gpl3))) (define-public r-wgaim (package (name "r-wgaim") (version "2.0-1") (source (origin (method url-fetch) (uri (cran-uri "wgaim" version)) (sha256 (base32 "1qiyfkpsbzjr9xsq5kqq6rlqpndngkn2irdfh3gyi45h6hn118j4")))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-qtl)) (home-page "https://cran.r-project.org/web/packages/wgaim") (synopsis "Whole genome average interval mapping for QTL detection") (description "This package integrates sophisticated mixed modelling methods with a whole genome approach to detecting significant QTL in linkage maps.") (license license:gpl2+))) (define-public r-bedr (package (name "r-bedr") (version "1.0.7") (source (origin (method url-fetch) (uri (cran-uri "bedr" version)) (sha256 (base32 "0zpqvyjgwyqawxm8qrhcv8zq2b3yxgcqkkc87br29yrl7sjb8h6j")))) (build-system r-build-system) (propagated-inputs (list r-data-table r-r-utils r-testthat r-venndiagram r-yaml bedops bedtools htslib)) ; for tabix (native-inputs (list r-knitr)) ; for vignettes (home-page "https://cran.r-project.org/web/packages/bedr") (synopsis "Genomic region processing") (description "This package is for genomic regions processing using command line tools such as BEDTools, BEDOPS and Tabix. These tools offer scalable and efficient utilities to perform genome arithmetic e.g indexing, formatting and merging. The bedr package's API enhances access to these tools as well as offers additional utilities for genomic regions processing.") (license license:gpl2))) (define-public r-setrng (package (name "r-setrng") (version "2024.2-1") (source (origin (method url-fetch) (uri (cran-uri "setRNG" version)) (sha256 (base32 "0h2wbpsi07c48h72zjglvp9b58hq3j77289sah32qg6vnw41pcp3")))) (properties `((upstream-name . "setRNG"))) (build-system r-build-system) (home-page "https://distr.r-forge.r-project.org/") (synopsis "Set (normal) random number generator and seed") (description "This package provides utilities to help set and record the setting of the seed and the uniform and normal generators used when a random experiment is run. The utilities can be used in other functions that do random experiments to simplify recording and/or setting all the necessary information for reproducibility. See the vignette and reference manual for examples.") (license license:gpl2))) (define-public r-sets (package (name "r-sets") (version "1.0-25") (source (origin (method url-fetch) (uri (cran-uri "sets" version)) (sha256 (base32 "1x14q29jjmrs5ldbjc7pxp5pr52j3dw6zr9k5qvz4ycniwhnk92w")))) (properties `((upstream-name . "sets"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/sets") (synopsis "Sets, generalized sets, customizable sets and intervals") (description "This package provides data structures and basic operations for ordinary sets, generalizations such as fuzzy sets, multisets, and fuzzy multisets, customizable sets, and intervals.") (license license:gpl2))) (define-public r-partitions (package (name "r-partitions") (version "1.10-7") (source (origin (method url-fetch) (uri (cran-uri "partitions" version)) (sha256 (base32 "1kxiy1wl7dr39kyfg2y9hd67s32knd83r2jsb7j9p3vg8iqq7yqb")))) (build-system r-build-system) (propagated-inputs (list r-gmp r-mathjaxr r-polynom r-rdpack r-sets)) (home-page "https://cran.r-project.org/web/packages/partitions") (synopsis "Additive partitions of integers") (description "This package provides tools to enumerates the partitions, unequal partitions, and restricted partitions of an integer; the three corresponding partition functions are also given.") ;; Any version of the GPL (license license:gpl2+))) (define-public r-brobdingnag (package (name "r-brobdingnag") (version "1.2-9") (source (origin (method url-fetch) (uri (cran-uri "Brobdingnag" version)) (sha256 (base32 "07p9416rdzfyiigbglxjpbcg7pfly9nw19yn2mwg98621cjjs0gr")))) (properties `((upstream-name . "Brobdingnag"))) (build-system r-build-system) (propagated-inputs (list r-matrix)) (home-page "https://github.com/RobinHankin/Brobdingnag.git") (synopsis "Very large numbers in R") (description "This package handles very large numbers in R. Real numbers are held using their natural logarithms, plus a logical flag indicating sign. The package includes a vignette that gives a step-by-step introduction to using S4 methods.") ;; Any version of the GPL (license license:gpl2+))) (define-public r-unglue (package (name "r-unglue") (version "0.1.0") (source (origin (method url-fetch) (uri (cran-uri "unglue" version)) (sha256 (base32 "0w8ld4xllx0lj1jz8i2sj92f8136hlwri1d8ldpg1ymxj7aw93vg")))) (properties `((upstream-name . 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(license license:gpl2+))) (define-public r-stepwise (package (name "r-stepwise") (version "0.3") (source (origin (method url-fetch) (uri (cran-uri "stepwise" version)) (sha256 (base32 "1lbx1bxwkf9dw6q46w40pp7h5nkxgghmx8rkpaymm6iybc7gyir2")))) (build-system r-build-system) (home-page "https://stat.sfu.ca/statgen/research/stepwise.html") (synopsis "Stepwise detection of recombination breakpoints") (description "This package provides a stepwise approach to identifying recombination breakpoints in a genomic sequence alignment.") (license license:gpl2+))) (define-public r-snpmaxsel (package (name "r-snpmaxsel") (version "1.0-3") (source (origin (method url-fetch) (uri (cran-uri "SNPmaxsel" version)) (sha256 (base32 "0pjvixwqzjd3jwccc8yqq9c76afvbmfq0z1w0cwyj8bblrjpx13z")))) (properties `((upstream-name . "SNPmaxsel"))) (build-system r-build-system) (propagated-inputs (list r-combinat r-mvtnorm)) (home-page "https://cran.r-project.org/web/packages/SNPmaxsel/index.html") (synopsis "Maximally selected statistics for SNP data") (description "This package implements asymptotic methods related to maximally selected statistics, with applications to @dfn{single-nucleotide polymorphism} (SNP) data.") (license license:gpl2+))) (define-public r-acsnminer (package (name "r-acsnminer") (version "0.16.8.25") (source (origin (method url-fetch) (uri (cran-uri "ACSNMineR" version)) (sha256 (base32 "0gh604s8qall6zfjlwcg2ilxjvz08dplf9k5g47idhv43scm748l")))) (properties `((upstream-name . 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(license license:gpl2+))) (define-public r-seqinr (package (name "r-seqinr") (version "4.2-36") (source (origin (method url-fetch) (uri (cran-uri "seqinr" version)) (sha256 (base32 "09dj2k5mi6xylsihnwbmdd8f4qg855gyh7yvz9gamam7j6h646lk")))) (build-system r-build-system) (propagated-inputs (list r-ade4 r-segmented)) (inputs (list zlib)) (home-page "https://seqinr.r-forge.r-project.org/") (synopsis "Biological sequences retrieval and analysis") (description "This package provides tools for exploratory data analysis and data visualization of biological sequence (DNA and protein) data. It also includes utilities for sequence data management under the ACNUC system.") (license license:gpl2+))) (define-public r-unigd (package (name "r-unigd") (version "0.1.1") (source (origin (method url-fetch) (uri (cran-uri "unigd" version)) (sha256 (base32 "0q6nix6pqjg7adfyisg6zn7hzwkdmz1dhd34c6a58dsg2yq1qh1a")))) (properties `((upstream-name . "unigd"))) (build-system r-build-system) (inputs (list cairo fontconfig freetype libpng zlib)) (propagated-inputs (list r-cpp11 r-systemfonts)) (native-inputs (list pkg-config r-knitr)) (home-page "https://github.com/nx10/unigd") (synopsis "Universal graphics device") (description "This package provides a unified R graphics backend. Render R graphics fast and easy to many common file formats. It provides a thread safe C interface for asynchronous rendering of R graphics.") (license license:gpl2+))) (define-public r-units (package (name "r-units") (version "0.8-5") (source (origin (method url-fetch) (uri (cran-uri "units" version)) (sha256 (base32 "1c836qazrs8z9p1xkcfl9gl882i8q7qf2g73l483w18bfspq0pnr")))) (build-system r-build-system) (inputs (list udunits)) (propagated-inputs (list r-rcpp)) (native-inputs (list r-knitr)) (home-page "https://github.com/r-quantities/units/") (synopsis "Measurement Units for R Vectors") (description "This package provides support for measurement units in R vectors, matrices and arrays: automatic propagation, conversion, derivation and simplification of units; raising errors in case of unit incompatibility. It is compatible with the @code{POSIXct}, @code{Date} and @code{difftime} classes.") (license license:gpl2))) (define-public r-udunits2 (package (name "r-udunits2") (version "0.13.2.1") (source (origin (method url-fetch) (uri (cran-uri "udunits2" version)) (sha256 (base32 "00prsy8m41v1camcsz94d7gm8qab2mdnwl3x0dyhz4r49b02jm4z")))) (properties `((upstream-name . "udunits2"))) (build-system r-build-system) (inputs (list udunits)) (home-page "https://cran.r-project.org/package=udunits2") (synopsis "Udunits-2 bindings for R") (description "This package provides simple bindings to Unidata's udunits library.") (license license:gpl2))) (define-public r-classint (package (name "r-classint") (version "0.4-10") (source (origin (method url-fetch) (uri (cran-uri "classInt" version)) (sha256 (base32 "12rbwh7g0a6abvy423xjiv53gx1f9lg4y78r80lc0fj9pjpiwmn3")))) (properties `((upstream-name . "classInt"))) (build-system r-build-system) (propagated-inputs (list r-class r-e1071 r-kernsmooth)) (native-inputs (list gfortran r-knitr)) (home-page "https://github.com/r-spatial/classInt/") (synopsis "Choose univariate class intervals") (description "This package provides selected commonly used methods for choosing univariate class intervals for mapping or other graphics purposes.") (license license:gpl2+))) (define-public r-spdata (package (name "r-spdata") (version "2.3.0") (source (origin (method url-fetch) (uri (cran-uri "spData" version)) (sha256 (base32 "12w4chk71vqy1chij79928ppxdg2cz03hx9bgs5cgwj9f1ciyb2b")))) (properties `((upstream-name . "spData"))) (build-system r-build-system) (propagated-inputs (list r-sp)) (home-page "https://github.com/Nowosad/spData") (synopsis "Datasets for spatial analysis") (description "This a package containing diverse spatial datasets for demonstrating, benchmarking and teaching spatial data analysis. It includes R data of class @code{sf}, @code{Spatial}, and @code{nb}. It also contains data stored in a range of file formats including GeoJSON, ESRI Shapefile and GeoPackage. Some of the datasets are designed to illustrate specific analysis techniques. @code{cycle_hire()} and @code{cycle_hire_osm()}, for example, are designed to illustrate point pattern analysis techniques.") (license license:cc0))) (define-public r-learnbayes (package (name "r-learnbayes") (version "2.15.1") (source (origin (method url-fetch) (uri (cran-uri "LearnBayes" version)) (sha256 (base32 "0ch54v2zz2yyyk0lvn5rfikdmyz1qh9j1wk3585wl8v58mc0h4cv")))) (properties `((upstream-name . "LearnBayes"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/LearnBayes") (synopsis "Functions for learning Bayesian inference") (description "This package provides a collection of functions helpful in learning the basic tenets of Bayesian statistical inference. It contains functions for summarizing basic one and two parameter posterior distributions and predictive distributions. It contains MCMC algorithms for summarizing posterior distributions defined by the user. It also contains functions for regression models, hierarchical models, Bayesian tests, and illustrations of Gibbs sampling.") (license license:gpl2+))) (define-public r-deldir (package (name "r-deldir") (version "2.0-4") (source (origin (method url-fetch) (uri (cran-uri "deldir" version)) (sha256 (base32 "0ls69b9yynvsiy6madvzafcb0jdvxw66sin7cinpnw63israq66l")))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/deldir") (synopsis "Delaunay triangulation and Dirichlet (Voronoi) tessellation") (description "This package provides tools for calculating the Delaunay triangulation and the Dirichlet or Voronoi tessellation (with respect to the entire plane) of a planar point set. It plots triangulations and tessellations in various ways, clips tessellations to sub-windows, calculates perimeters of tessellations, and summarizes information about the tiles of the tessellation.") (license license:gpl2+))) (define-public r-wk (package (name "r-wk") (version "0.9.1") (source (origin (method url-fetch) (uri (cran-uri "wk" version)) (sha256 (base32 "0yxzyb09by9winspdn0585xhjmdcablb07wx6pf7ahg0q18sz85p")))) (properties `((upstream-name . "wk"))) (build-system r-build-system) (home-page "https://paleolimbot.github.io/wk/") (synopsis "Lightweight well-known geometry parsing") (description "This package provides a minimal R and C++ API for parsing well-known binary and well-known text representation of geometries to and from R-native formats. Well-known binary is compact and fast to parse; well-known text is human-readable and is useful for writing tests. These formats are only useful in R if the information they contain can be accessed in R, for which high-performance functions are provided here.") (license license:expat))) (define-public r-s2 (package (name "r-s2") (version "1.1.6") (source (origin (method url-fetch) (uri (cran-uri "s2" version)) (sha256 (base32 "0rm0jd5k5w725v1bnn6ix8vic40grdh61y6qdy8jy4lhg1mjx78x")))) (properties `((upstream-name . "s2"))) (build-system r-build-system) (arguments (list #:phases `(modify-phases %standard-phases ;; We don't want to convert -lssl to -l:libssl.so.1.1; there is only ;; one libssl.so anyway and the -l:* thing breaks linking. (add-after 'unpack 'undo-library-versioning (lambda _ (substitute* "configure" (("PKG_LIBS_VERSIONED=.*") "PKG_LIBS_VERSIONED=\"${PKG_LIBS}\"\n"))))))) (propagated-inputs (list r-rcpp r-wk)) (inputs (list openssl)) (native-inputs (list pkg-config)) (home-page "https://r-spatial.github.io/s2/") (synopsis "Spherical geometry operators using the S2 geometry library") (description "This package provides R bindings for Google's s2 library for geometric calculations on the sphere. High-performance constructors and exporters provide high compatibility with existing spatial packages, transformers construct new geometries from existing geometries, predicates provide a means to select geometries based on spatial relationships, and accessors extract information about geometries.") (license license:asl2.0))) (define-public r-sf (package (name "r-sf") (version "1.0-16") (source (origin (method url-fetch) (uri (cran-uri "sf" version)) (sha256 (base32 "11wrbaj5s0dqbnh1mfm03l7xi9flzx8grgbkqxrs1wnd2481jvp9")))) (build-system r-build-system) (inputs (list curl gdal geos openssh openssl pcre2 proj sqlite zlib)) (propagated-inputs (list r-classint r-dbi r-magrittr r-rcpp r-s2 r-units)) (native-inputs (list pkg-config r-knitr)) (home-page "https://github.com/r-spatial/sf/") (synopsis "Simple features for R") (description "This package provides support for simple features, a standardized way to encode spatial vector data. It binds to GDAL for reading and writing data, to GEOS for geometrical operations, and to PROJ for projection conversions and datum transformations.") ;; Either of these licenses (license (list license:gpl2 license:expat)))) (define-public r-sftime (package (name "r-sftime") (version "0.2-0") (source (origin (method url-fetch) (uri (cran-uri "sftime" version)) (sha256 (base32 "1ymi60ag8kqb3293bdcvb83zwsgrz000ylifjvlpzzmh1xsisanq")))) (properties `((upstream-name . "sftime"))) (build-system r-build-system) (propagated-inputs (list r-sf)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/package=sftime") (synopsis "Simple feature objects that have a time column") (description "This package provides classes and methods for spatial objects that have a registered time column, in particular for irregular spatiotemporal data. The @code{time} column can be of any type, but needs to be ordinal. Regularly laid out spatiotemporal data (vector or raster data cubes) are handled by package stars'.") (license license:asl2.0))) (define-public r-spdep (package (name "r-spdep") (version "1.3-3") (source (origin (method url-fetch) (uri (cran-uri "spdep" version)) (sha256 (base32 "06j26v0w33vyh5ilq1cn0rh8z0lrr3n0lxwxc7bsk2w524d3v6yw")) (snippet '(for-each delete-file '("inst/doc/CO69.html" "inst/doc/CO69.R" "inst/doc/nb.html" "inst/doc/nb.R" "inst/doc/nb_sf.html" "inst/doc/nb_sf.R" "inst/doc/nb_sf.Rmd" "inst/doc/sids.html" "inst/doc/sids.R"))))) (build-system r-build-system) (propagated-inputs (list r-boot r-deldir r-e1071 r-s2 r-sf r-sp r-spdata r-units)) (native-inputs (list r-knitr)) (home-page "https://github.com/r-spatial/spdep/") (synopsis "Spatial dependence: weighting schemes, statistics and models") (description "This package provides a collection of functions to create spatial weights matrix objects from polygon contiguities, from point patterns by distance and tessellations, for summarizing these objects, and for permitting their use in spatial data analysis, including regional aggregation by minimum spanning tree.") (license license:gpl2+))) (define-public r-adegenet (package (name "r-adegenet") (version "2.1.10") (source (origin (method url-fetch) (uri (cran-uri "adegenet" version)) (sha256 (base32 "0qxig2jyj1q0a8pwpv5f5v5b4x4af8s9p1p0yc0msmyxq457hqmb")))) (build-system r-build-system) (propagated-inputs (list r-ade4 r-ape r-boot r-dplyr r-ggplot2 r-igraph r-mass r-reshape2 r-seqinr r-shiny r-vegan)) (home-page "https://github.com/thibautjombart/adegenet") (synopsis "Exploratory analysis of genetic and genomic data") (description "This package provides a toolset for the exploration of genetic and genomic data. Adegenet provides formal (S4) classes for storing and handling various genetic data, including genetic markers with varying ploidy and hierarchical population structure (@code{genind} class), alleles counts by populations (@code{genpop}), and genome-wide SNP data (@code{genlight}). It also implements original multivariate methods (DAPC, sPCA), graphics, statistical tests, simulation tools, distance and similarity measures, and several spatial methods. A range of both empirical and simulated datasets is also provided to illustrate various methods.") (license license:gpl2+))) (define-public r-pegas (package (name "r-pegas") (version "1.3") (source (origin (method url-fetch) (uri (cran-uri "pegas" version)) (sha256 (base32 "1j1xrnwi80ycwziwcsb48sfdm2ifdzgsn8clh0ai7rvhknrb4ghh")))) (build-system r-build-system) (propagated-inputs (list r-ape)) (home-page "http://ape-package.ird.fr/pegas.html") (synopsis "Population and evolutionary genetics analysis system") (description "This package provides functions for reading, writing, plotting, analysing, and manipulating allelic and haplotypic data, including from VCF files, and for the analysis of population nucleotide sequences and micro-satellites including coalescent analyses, linkage disequilibrium, population structure (Fst, Amova) and equilibrium (HWE), haplotype networks, minimum spanning tree and network, and median-joining networks.") (license license:gpl2+))) (define-public r-genetics (package (name "r-genetics") (version "1.3.8.1.3") (source (origin (method url-fetch) (uri (cran-uri "genetics" version)) (sha256 (base32 "0lljxvz7nc6y2z303icphar2niir0i407w5cyhy2pwspd9gwkwpy")))) (build-system r-build-system) (propagated-inputs (list r-combinat r-gdata r-gtools r-mass r-mvtnorm)) (home-page "https://cran.r-project.org/web/packages/genetics/") (synopsis "Population genetics") (description "This package provides classes and methods for handling genetic data. It includes classes to represent genotypes and haplotypes at single markers up to multiple markers on multiple chromosomes. Function include allele frequencies, flagging homo/heterozygotes, flagging carriers of certain alleles, estimating and testing for Hardy-Weinberg disequilibrium, estimating and testing for linkage disequilibrium, ...") ;; Any GPL version. (license license:gpl2+))) (define-public r-snp-plotter (package (name "r-snp-plotter") (version "0.5.1") (source (origin (method url-fetch) (uri (cran-uri "snp.plotter" version)) (sha256 (base32 "16apsqvkah5l0d5qcwp3lq2jspkb6n62wzr0wskmj84jblx483vv")))) (properties `((upstream-name . "snp.plotter"))) (build-system r-build-system) (propagated-inputs (list r-genetics)) (home-page "https://cran.r-project.org/web/packages/snp.plotter/") (synopsis "Plot p-values using single SNP and/or haplotype data") (description "This package helps you create plots of p-values using single SNP and/or haplotype data. Main features of the package include options to display a @dfn{linkage disequilibrium} (LD) plot and the ability to plot multiple datasets simultaneously. Plots can be created using global and/or individual haplotype p-values along with single SNP p-values. Images are created as either PDF/EPS files.") (license license:gpl2+))) (define-public r-polspline (package (name "r-polspline") (version "1.1.24") (source (origin (method url-fetch) (uri (cran-uri "polspline" version)) (sha256 (base32 "0mal78f79jl6cj02xabv9vqf88m4iiadmgiv3qliv117cxkc6hb6")))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/polspline/") (synopsis "Polynomial spline routines") (description "This package provides routines for the polynomial spline fitting routines hazard regression, hazard estimation with flexible tails, logspline, lspec, polyclass, and polymars.") (license license:gpl2+))) (define-public r-rms (package (name "r-rms") (version "6.8-0") (source (origin (method url-fetch) (uri (cran-uri "rms" version)) (sha256 (base32 "1cd6m6i2ild2f2x9rkyd2aqb33q3xy0596bs3dnvr2mnh5fcar5d")))) (build-system r-build-system) (propagated-inputs (list r-cluster r-colorspace r-digest r-ggplot2 r-hmisc r-htmltable r-htmltools r-knitr r-mass r-multcomp r-nlme r-polspline r-quantreg r-rpart r-sparsem r-survival)) (native-inputs (list gfortran)) (home-page "http://biostat.mc.vanderbilt.edu/rms") (synopsis "Regression modeling strategies") (description "This is a package for regression modeling, testing, estimation, validation, graphics, prediction, and typesetting by storing enhanced model design attributes in the fit. The rms package is a collection of functions that assist with and streamline modeling. It also contains functions for binary and ordinal logistic regression models, ordinal models for continuous Y with a variety of distribution families, and the Buckley-James multiple regression model for right-censored responses, and implements penalized maximum likelihood estimation for logistic and ordinary linear models. The package works with almost any regression model, but it was especially written to work with binary or ordinal regression models, Cox regression, accelerated failure time models, ordinary linear models, the Buckley-James model, generalized least squares for serially or spatially correlated observations, generalized linear models, and quantile regression.") (license license:gpl2+))) (define-public r-arsenal (package (name "r-arsenal") (version "3.6.3") (source (origin (method url-fetch) (uri (cran-uri "arsenal" version)) (sha256 (base32 "0qvs3ld28djnjnggdhqjwq8sbv8zz322qahlvf7dnx35yqf6xkms")))) (properties `((upstream-name . "arsenal"))) (build-system r-build-system) (propagated-inputs (list r-knitr)) (native-inputs (list r-knitr)) (home-page "https://github.com/mayoverse/arsenal") (synopsis "Functions for large-scale statistical summaries") (description "This package provides an arsenal of R functions for large-scale statistical summaries, which are streamlined to work within the latest reporting tools in R and RStudio and which use formulas and versatile summary statistics for summary tables and models. The primary functions include @enumerate @item @code{tableby}, a Table-1-like summary of multiple variable types by the levels of one or more categorical variables; @item @code{paired}, a Table-1-like summary of multiple variable types paired across two time points; @item @code{modelsum}, which performs simple model fits on one or more endpoints for many variables (univariate or adjusted for covariates); @item @code{freqlist}, a powerful frequency table across many categorical variables; @item @code{comparedf}, a function for comparing @code{data.frames}; and @item @code{write2}, a function to output tables to a document. @end enumerate ") (license license:gpl2+))) (define-public r-haplo-stats (package (name "r-haplo-stats") (version "1.9.5.1") (source (origin (method url-fetch) (uri (cran-uri "haplo.stats" version)) (sha256 (base32 "1fcnyglmz9ia6zpk0vvmjqiwxlpal58rksgb1yvrajqgylw3kbsy")))) (properties `((upstream-name . "haplo.stats"))) (build-system r-build-system) (propagated-inputs (list r-arsenal r-rms)) (native-inputs (list r-r-rsp)) ; for vignettes (home-page "https://www.mayo.edu/research/labs/statistical-genetics-genetic-epidemiology/software") (synopsis "Analysis of haplotypes when linkage phase is ambiguous") (description "This package provides routines for the analysis of indirectly measured haplotypes. The statistical methods assume that all subjects are unrelated and that haplotypes are ambiguous (due to unknown linkage phase of the genetic markers). The main functions are: @code{haplo.em()}, @code{haplo.glm()}, @code{haplo.score()}, and @code{haplo.power()}; all of which have detailed examples in the vignette.") (license license:gpl2+))) (define-public r-bqtl (package (name "r-bqtl") (version "1.0-36") (source (origin (method url-fetch) (uri (cran-uri "bqtl" version)) (sha256 (base32 "18fwg52j6dv1v1pcc4997j2f5vlfmcvqqdg0618fq9zaq8j4cz6h")))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "http://famprevmed.ucsd.edu/faculty/cberry/bqtl/") (synopsis "Bayesian QTL mapping toolkit") (description "This is a QTL mapping toolkit for inbred crosses and recombinant inbred lines. It includes maximum likelihood and Bayesian tools.") (license license:gpl2+))) (define-public r-ibdreg (package (name "r-ibdreg") (version "0.3.8") (source (origin (method url-fetch) (uri (cran-uri "ibdreg" version)) (sha256 (base32 "0c4svyfd7xjx9k6pl40l7y9rc67zschs0nz1l386xi1m7arsp44n")))) (build-system r-build-system) (home-page "https://www.mayo.edu/research/labs/\ statistical-genetics-genetic-epidemiology/software") (synopsis "Regression methods for IBD linkage with covariates") (description "This package provides a method to test genetic linkage with covariates by regression methods with response IBD sharing for relative pairs. Account for correlations of IBD statistics and covariates for relative pairs within the same pedigree.") (license license:gpl2+))) (define-public r-dlmap (package (name "r-dlmap") (version "1.13") (source (origin (method url-fetch) (uri (cran-uri "dlmap" version)) (sha256 (base32 "0s6wlkggkm3qndwyvw72xv1n0mcjb7ss3ajbq2ll6rv30splq0db")))) (build-system r-build-system) (propagated-inputs (list r-ibdreg r-mgcv r-nlme r-qtl r-wgaim)) (home-page "https://cran.r-project.org/web/packages/dlmap/") (synopsis "Detection localization mapping for QTL") (description "This is package for QTL mapping in a mixed model framework with separate detection and localization stages. The first stage detects the number of QTL on each chromosome based on the genetic variation due to grouped markers on the chromosome; the second stage uses this information to determine the most likely QTL positions. The mixed model can accommodate general fixed and random effects, including spatial effects in field trials and pedigree effects. It is applicable to backcrosses, doubled haploids, recombinant inbred lines, F2 intercrosses, and association mapping populations.") (license license:gpl2))) (define-public r-hwde (package (name "r-hwde") (version "0.67-3") (source (origin (method url-fetch) (uri (cran-uri "hwde" version)) (sha256 (base32 "0kj3vf4pmcvxy95hx1d0q6c626y8d0ljj3r76y5hd90a6v75b5xa")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/hwde/") (synopsis "Models and tests for departure from Hardy-Weinberg equilibrium") (description "This package fits models for genotypic disequilibria, as described in Huttley and Wilson (2000), Weir (1996) and Weir and Wilson (1986). Contrast terms are available that account for first order interactions between loci. It also implements, for a single locus in a single population, a conditional exact test for Hardy-Weinberg equilibrium.") (license license:gpl2+))) (define-public r-tdthap (package (name "r-tdthap") (version "1.3") (source (origin (method url-fetch) (uri (cran-uri "tdthap" version)) (sha256 (base32 "05yj7jwwd0q2yk8gpp44fhh3sknvw3g6p9glj6z6rz46p9xf31kr")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/tdthap/") (synopsis "TDT tests for extended haplotypes") (description "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\".") (license license:artistic2.0))) (define-public r-sparql (package (name "r-sparql") (version "1.16") (source (origin (method url-fetch) (uri (cran-uri "SPARQL" version)) (sha256 (base32 "0gak1q06yyhdmcxb2n3v0h9gr1vqd0viqji52wpw211qp6r6dcrc")))) (properties `((upstream-name . "SPARQL"))) (build-system r-build-system) (propagated-inputs (list r-rcurl r-xml)) (home-page "https://cran.r-project.org/web/packages/SPARQL") (synopsis "SPARQL client for R") (description "This package provides an interface to use SPARQL to pose SELECT or UPDATE queries to an end-point.") ;; The only license indication is found in the DESCRIPTION file, ;; which states GPL-3. So we cannot assume GPLv3+. (license license:gpl3))) (define-public r-bookdown (package (name "r-bookdown") (version "0.39") (source (origin (method url-fetch) (uri (cran-uri "bookdown" version)) (sha256 (base32 "1brfv50lq92m7d4d18n92ywhfr28lrbq02naf0bwdsmd0ngasxrm")) ;; TODO: there is one more file to replace: ;; inst/resources/gitbook/js/app.min.js (snippet '(for-each delete-file '("inst/resources/gitbook/js/clipboard.min.js" "inst/resources/gitbook/js/lunr.js" "inst/resources/mathquill/mathquill.min.js"))))) (properties `((upstream-name . "bookdown") ;; We cannot add knitr because this package depends on xfun, which is ;; an input to knitr. (updater-ignored-native-inputs . ("r-knitr")))) (build-system r-build-system) (arguments (list #:modules '((guix build r-build-system) (guix build minify-build-system) (guix build utils) (ice-9 match)) #:imported-modules `(,@%r-build-system-modules (guix build minify-build-system)) #:phases #~(modify-phases (@ (guix build r-build-system) %standard-phases) (add-after 'unpack 'process-javascript (lambda* (#:key inputs #:allow-other-keys) (with-directory-excursion "inst/resources" (invoke "tar" "-xf" (assoc-ref inputs "js-mathquill") "-C" "/tmp" "--strip-components=2") (for-each (match-lambda ((source . target) (minify source #:target target))) `((,(search-input-file inputs "/dist/clipboard.js") . "gitbook/js/clipboard.min.js") (,(search-input-file inputs "/lunr.js") . "gitbook/js/lunr.js") ("/tmp/mathquill.js" . "mathquill/mathquill.min.js"))))))))) (propagated-inputs (list r-htmltools r-jquerylib r-knitr r-rmarkdown r-tinytex r-xfun r-yaml pandoc)) (native-inputs `(("esbuild" ,esbuild) ("js-clipboard" ,(let ((version "2.0.4")) (origin (method git-fetch) (uri (git-reference (url "https://github.com/zenorocha/clipboard.js") (commit (string-append "v" version)))) (file-name (git-file-name "clipboard.js" version)) (sha256 (base32 "02zzirnddf4kcqdiqb2i7a7yki3rwgscca388qhy3namkw793x4z"))))) ("js-lunarjs" ,(let ((version "0.5.12")) (origin (method git-fetch) (uri (git-reference (url "https://github.com/olivernn/lunr.js") (commit (string-append "v" version)))) (file-name (git-file-name "lunr.js" version)) (sha256 (base32 "1xwdymcnc75b22bb95hq7ijcf7agf47g2fnqzzj09aihx2c5r430"))))) ("js-mathquill" ,(origin (method url-fetch) (uri "https://github.com/mathquill/mathquill/\ releases/download/v0.10.1/mathquill-0.10.1.tgz") (sha256 (base32 "1159l2fi7k3wyclp0pksc0qng291glb8qpa67bvcxwyb9dfiwav7")))))) (home-page "https://github.com/rstudio/bookdown") (synopsis "Authoring books and technical documents with R markdown") (description "This package provides output formats and utilities for authoring books and technical documents with R Markdown.") (license license:gpl3))) (define-public r-options (package (name "r-options") (version "0.1.0") (source (origin (method url-fetch) (uri (cran-uri "options" version)) (sha256 (base32 "0pprbp2pxvgh120f8dahswws44gpdm4f4nlq3h3nvqrlhnspwnb8")))) (properties `((upstream-name . "options"))) (build-system r-build-system) (native-inputs (list r-knitr)) (home-page "https://dgkf.github.io/options/") (synopsis "Simple, consistent package options") (description "This package provides simple mechanisms for defining and interpreting package options. It provides helpers for interpreting environment variables, global options, defining default values and more.") (license license:expat))) (define-public r-optparse (package (name "r-optparse") (version "1.7.5") (source (origin (method url-fetch) (uri (cran-uri "optparse" version)) (sha256 (base32 "04jp85jik1zkbb08w44m2h0hqyzd80w4pjnfp1lnwy40ax81gj8c")))) (build-system r-build-system) (propagated-inputs (list r-getopt)) (native-inputs (list r-knitr)) (home-page "https://github.com/trevorld/optparse") (synopsis "Command line option parser") (description "This package provides a command line parser inspired by Python's @code{optparse} library to be used with Rscript to write shebang scripts that accept short and long options.") (license license:gpl2+))) (define-public r-osqp (package (name "r-osqp") (version "0.6.3.2") (source (origin (method url-fetch) (uri (cran-uri "osqp" version)) (sha256 (base32 "0i1jh3fr8d45b7inq9s6iyqszhh18hps8jpzkm0hzgj2k8r3nm0q")))) (properties `((upstream-name . 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(license (list license:asl2.0)))) (define-public r-kernlab (package (name "r-kernlab") (version "0.9-32") (source (origin (method url-fetch) (uri (cran-uri "kernlab" version)) (sha256 (base32 "1p3gbn9qgc6yqx9irkl8c23khvkx77jl96hk9hn4vsrx6i7g6kk5")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/kernlab") (synopsis "Kernel-based machine learning tools") (description "This package provides kernel-based machine learning methods for classification, regression, clustering, novelty detection, quantile regression and dimensionality reduction. Among other methods @code{kernlab} includes Support Vector Machines, Spectral Clustering, Kernel PCA, Gaussian Processes and a QP solver.") (license license:gpl2))) (define-public r-hierfstat (package (name "r-hierfstat") (version "0.5-11") (source (origin (method url-fetch) (uri (cran-uri "hierfstat" version)) (sha256 (base32 "0nyb5091lr8ma9vydbssyx9503601rynlrbldv98mmrmh74h6v41")))) (build-system r-build-system) (propagated-inputs (list r-ade4 r-adegenet r-gaston r-gtools)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/hierfstat/") (synopsis "Estimation and tests of hierarchical F-statistics") (description "This package allows the estimation of hierarchical F-statistics from haploid or diploid genetic data with any numbers of levels in the hierarchy, following the algorithm of Yang (Evolution, 1998, 52(4):950-956). Functions are also given to test via randomisations the significance of each F and variance components, using the likelihood-ratio statistics G.") (license license:gpl2+))) (define-public r-hapassoc (package (name "r-hapassoc") (version "1.2-9") (source (origin (method url-fetch) (uri (cran-uri "hapassoc" version)) (sha256 (base32 "09ijc4sbw743z74fzklmvig11ndkycg6j86k4214wfsj1yj6j9x6")))) (build-system r-build-system) (home-page "https://stat.sfu.ca/statgen/research/hapassoc.html") (synopsis "Inference of trait associations with SNP haplotypes") (description "Hapassoc performs likelihood inference of trait associations with haplotypes and other covariates in @dfn{generalized linear models} (GLMs). The functions are developed primarily for data collected in cohort or cross-sectional studies. They can accommodate uncertain haplotype phase and handle missing genotypes at some SNPs.") (license license:gpl2))) (define-public r-sampling (package (name "r-sampling") (version "2.10") (source (origin (method url-fetch) (uri (cran-uri "sampling" version)) (sha256 (base32 "0x976wblv663aidqmcif1rjv72nbxf4nzms901lmryxbq1p9gv7x")))) (build-system r-build-system) (propagated-inputs (list r-lpsolve r-mass)) (home-page "https://cran.r-project.org/web/packages/sampling/") (synopsis "Survey sampling") (description "This package provides functions for drawing and calibrating samples.") (license license:gpl2+))) (define-public r-r2html (package (name "r-r2html") (version "2.3.3") (source (origin (method url-fetch) (uri (cran-uri "R2HTML" version)) (sha256 (base32 "12qg9rp1j26h2f48dfg5k9jds26ycacv3f3ymk686ks43hd1hzja")))) (properties `((upstream-name . "R2HTML"))) (build-system r-build-system) (home-page "https://github.com/nalimilan/R2HTML") (synopsis "HTML export for R objects") (description "This package includes HTML functions and methods to write in an HTML file. Thus, making HTML reports is easy. It includes a function that allows redirection on the fly, which appears to be very useful for teaching purposes, as the student can keep a copy of the produced output to keep all that they did during the course. The package comes with a vignette describing how to write HTML reports for statistical analysis. Finally, a driver for Sweave parses HTML flat files containing R code and to automatically write the corresponding outputs (tables and graphs).") (license license:gpl2+))) (define-public r-rjava (package (name "r-rjava") (version "1.0-11") (source (origin (method url-fetch) (uri (cran-uri "rJava" version)) (sha256 (base32 "05v4k0vzv1yx80b5dgmp6l7q3w64cr3k5a29hvggg1ixapswr84y")))) (properties `((upstream-name . "rJava"))) (build-system r-build-system) (arguments (list #:phases #~(modify-phases %standard-phases (add-after 'unpack 'set-JAVA_HOME (lambda* (#:key inputs #:allow-other-keys) (let ((jdk (assoc-ref inputs "jdk"))) (setenv "JAVA_HOME" jdk) (setenv "JAVA" (which "java")) (setenv "JAR" (which "jar")) (setenv "JAVAC" (which "javac")) (setenv "JAVAH" (which "javah")) (setenv "JAVA_CPPFLAGS" (string-append "-I" jdk "/include " "-I" jdk "/include/linux")) (setenv "JAVA_LIBS" (search-input-file inputs "/lib/libjvm.so")))))))) (inputs `(("icu4c" ,icu4c) ("jdk" ,openjdk11 "jdk") ("zlib" ,zlib))) (home-page "https://www.rforge.net/rJava/") (synopsis "Low-Level R to Java interface") (description "This package provides a low-level interface to the Java VM very much like .C/.Call and friends. It allows the creation of objects, calling methods and accessing fields.") (license license:gpl2))) (define-public r-svmisc (package (name "r-svmisc") (version "1.2.3") (source (origin (method url-fetch) (uri (cran-uri "svMisc" version)) (sha256 (base32 "1r3kih5bnr4plnzdn5f2gg3xl3krgyl7gkdlf58a2l8vk13j3m9d")))) (properties `((upstream-name . "svMisc"))) (build-system r-build-system) (native-inputs (list r-knitr)) (home-page "https://github.com/SciViews/svMisc") (synopsis "Miscellaneous functions for SciViews") (description "This package provides miscellaneous functions for SciViews or general use, including tools to manage a temporary environment attached to the search path for temporary variables you do not want to @code{save()} or @code{load()}; test the current platform; showing progress bars, etc.") (license license:gpl2))) (define-public r-xyz (package (name "r-xyz") (version "0.2") (source (origin (method url-fetch) (uri (cran-uri "xyz" version)) (sha256 (base32 "13w4sb4pvgciwr8wsz785dafj2k2kpx7znz46r5d32wx88vkycp4")))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) (home-page "https://cran.r-project.org/web/packages/xyz/") (synopsis "Algorithm for fast interaction search in high-dimensional data") (description "High dimensional interaction search by brute force requires a quadratic computational cost in the number of variables. The xyz algorithm provably finds strong interactions in almost linear time. For details of the algorithm see: G. Thanei, N. Meinshausen and R. Shah (2016). The xyz algorithm for fast interaction search in high-dimensional data.") ;; Any version of the GPL. (license license:gpl2+))) (define-public r-rttf2pt1 (package (name "r-rttf2pt1") (version "1.3.12") (source (origin (method url-fetch) (uri (cran-uri "Rttf2pt1" version)) (sha256 (base32 "10x580dnzddm9z045gya5ya01d10s9mpp0fy8ilrldlh74q7ljqb")))) (properties `((upstream-name . "Rttf2pt1"))) (build-system r-build-system) (home-page "https://github.com/wch/Rttf2pt1") (synopsis "Font conversion utility") (description "This package contains the program @code{ttf2pt1}, for use with the @code{extrafont} package.") ;; Most of the files are covered under the Expat license. Some files are ;; covered under BSD-3. Deviations for individual files are recorded in ;; the LICENSE file. (license (list license:bsd-3 license:expat (license:non-copyleft "file://LICENSE"))))) (define-public r-extrafontdb (package (name "r-extrafontdb") (version "1.0") (source (origin (method url-fetch) (uri (cran-uri "extrafontdb" version)) (sha256 (base32 "115n42hfvv5h4nn4cfkfmkmn968py4lpy8zd0d6w5yylwpzbm8gs")))) (build-system r-build-system) (home-page "https://github.com/wch/extrafontdb") (synopsis "Database for the extrafont package") (description "This package holds the database for the @code{extrafont} package.") (license license:gpl2))) (define-public r-extrafont (package (name "r-extrafont") (version "0.19") (source (origin (method url-fetch) (uri (cran-uri "extrafont" version)) (sha256 (base32 "13dbrlf54nbyfz3z2snz7x4m6rfnnhk2l8kkwpgcagzi5lar13sf")))) (build-system r-build-system) (propagated-inputs (list r-extrafontdb r-rttf2pt1)) (home-page "https://github.com/wch/extrafont") (synopsis "Tools for using fonts in R") (description "The extrafont package makes it easier to use fonts other than the basic PostScript fonts that R uses. Fonts that are imported into extrafont can be used with PDF or PostScript output files. There are two hurdles for using fonts in PDF (or Postscript) output files: @enumerate @item Making R aware of the font and the dimensions of the characters. @item Embedding the fonts in the PDF file so that the PDF can be displayed properly on a device that doesn't have the font. This is usually needed if you want to print the PDF file or share it with others. @end enumerate The extrafont package makes both of these things easier.") (license license:gpl2))) (define-public r-xkcd (package (name "r-xkcd") (version "0.0.6") (source (origin (method url-fetch) (uri (cran-uri "xkcd" version)) (sha256 (base32 "1z2y0ihn68ppay7xkglhw7djki5654g6z4bbpyy41if57z9q554f")))) (build-system r-build-system) (propagated-inputs (list r-extrafont r-ggplot2 r-hmisc)) (home-page "https://cran.r-project.org/web/packages/xkcd/") (synopsis "Plot ggplot2 graphics in the XKCD style") (description "This package provides the means to plot ggplot2 graphs in the style of the XKCD web comic.") (license license:gpl3))) (define-public r-babelgene (package (name "r-babelgene") (version "22.9") (source (origin (method url-fetch) (uri (cran-uri "babelgene" version)) (sha256 (base32 "1ql5r1chl5ajzy9ppcnk755ia3m2a8n08m837dnm2ll3nzf02rnf")))) (properties `((upstream-name . 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(license license:expat))) (define-public r-msigdbr (package (name "r-msigdbr") (version "7.5.1") (source (origin (method url-fetch) (uri (cran-uri "msigdbr" version)) (sha256 (base32 "1jna9bkq0a7r6f8nhxziyiw75kfhsyh1rv7sx5d4551mvxxlhc6w")))) (build-system r-build-system) (propagated-inputs (list r-babelgene r-dplyr r-magrittr r-rlang r-tibble r-tidyselect)) (native-inputs (list r-knitr)) (home-page "https://github.com/igordot/msigdbr") (synopsis "MSigDB gene sets for multiple organisms") (description "This package provides the @dfn{Molecular Signatures Database} (MSigDB) gene sets typically used with the @dfn{Gene Set Enrichment Analysis} (GSEA) software in a standard R data frame with key-value pairs. Included are the original human gene symbols and Entrez IDs as well as the equivalents for various frequently studied model organisms such as mouse, rat, pig, fly, and yeast.") ;; The package is covered under the Expat license, but the upstream MSigDB ;; files are made available under the Creative Commons Attribution 4.0 ;; International license. (license (list license:expat license:cc-by4.0)))) (define-public r-gridgraphics (package (name "r-gridgraphics") (version "0.5-1") (source (origin (method url-fetch) (uri (cran-uri "gridGraphics" version)) (sha256 (base32 "12yswy02j3h5wir7m5jnkhpjmb0sa4snn61vjd68i49qwsa6w219")))) (properties `((upstream-name . "gridGraphics"))) (build-system r-build-system) (home-page "https://github.com/pmur002/gridgraphics") (synopsis "Redraw base graphics using @code{grid} graphics") (description "This package provides functions to convert a page of plots drawn with the @code{graphics} package into identical output drawn with the @code{grid} package. The result looks like the original @code{graphics}-based plot, but consists of @code{grid} grobs and viewports that can then be manipulated with @code{grid} functions (e.g., edit grobs and revisit viewports).") (license license:gpl2+))) (define-public r-farver (package (name "r-farver") (version "2.1.1") (source (origin (method url-fetch) (uri (cran-uri "farver" version)) (sha256 (base32 "1klnr73fhm7n46q85in1v9gi99y6rcdzzg4h4wvnbx23lxndmkqd")))) (build-system r-build-system) (home-page "https://github.com/thomasp85/farver") (synopsis "Vectorized color conversion and comparison") (description "The encoding of color can be handled in many different ways, using different color spaces. As different color spaces have different uses, efficient conversion between these representations are important. This package provides a set of functions that gives access to very fast color space conversion and comparisons implemented in C++, and offers 100-fold speed improvements over the @code{convertColor} function in the @code{grDevices} package.") (license license:expat))) (define-public r-yulab-utils (package (name "r-yulab-utils") (version "0.1.4") (source (origin (method url-fetch) (uri (cran-uri "yulab.utils" version)) (sha256 (base32 "0m1iip6w711z92y6qw0rc0flxl9bzj85vrhm2q2rqjz9pyqf3m1j")))) (properties `((upstream-name . "yulab.utils"))) (build-system r-build-system) (propagated-inputs (list r-cli r-digest r-fs r-memoise r-rlang)) (home-page "https://cran.r-project.org/package=yulab.utils") (synopsis "Supporting functions for packages maintained by YuLab-SMU") (description "Miscellaneous functions commonly used by YuLab-SMU, such as @code{install_zip_gh} to install R packages from Github ZIP files.") (license license:artistic2.0))) (define-public r-ggplotify (package (name "r-ggplotify") (version "0.1.2") (source (origin (method url-fetch) (uri (cran-uri "ggplotify" version)) (sha256 (base32 "11qfk4pj0bb013m9964q2fsrj4x39c4kwh84vfyi3qhlkrsybfh1")))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-gridgraphics r-yulab-utils)) (native-inputs (list r-knitr)) (home-page "https://github.com/GuangchuangYu/ggplotify") (synopsis "Convert plots to @code{grob} or @code{ggplot} object") (description "This package provides tools to convert plot function calls (using expression or formula) to @code{grob} or @code{ggplot} objects that are compatible with the @code{grid} and @code{ggplot2} environment. With this package, we are able to e.g. use @code{cowplot} to align plots produced by @code{base} graphics, @code{grid}, @code{lattice}, @code{vcd} etc. by converting them to @code{ggplot} objects.") (license license:artistic2.0))) (define-public r-triebeard (package (name "r-triebeard") (version "0.4.1") (source (origin (method url-fetch) (uri (cran-uri "triebeard" version)) (sha256 (base32 "1xz0xwq9c986as6g7z2g1ycvw1ryh4g89ygldvakpr21cgpjybqr")))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) (native-inputs (list r-knitr)) (home-page "https://github.com/Ironholds/triebeard/") (synopsis "Radix trees in Rcpp") (description "Radix trees, or tries, are key-value data structures optimized for efficient lookups, similar in purpose to hash tables. This package provides an implementation of radix trees for use in R programming and in developing packages with Rcpp.") (license license:expat))) (define-public r-tweenr (package (name "r-tweenr") (version "2.0.3") (source (origin (method url-fetch) (uri (cran-uri "tweenr" version)) (sha256 (base32 "1glc7ks5yymcm4pi0fjpi1zh7m5d4cz7zy20pa3kfraxlh9fbazg")))) (build-system r-build-system) (arguments (list #:phases '(modify-phases %standard-phases (add-after 'unpack 'build-reproducibly (lambda _ (substitute* "R/aaa.R" (("BASEDATETIME <- Sys.time.*") "BASEDATETIME <- structure(0, class = c(\"POSIXct\", \"POSIXt\"))\n"))))))) (propagated-inputs (list r-cpp11 r-farver r-magrittr r-rlang r-vctrs)) (home-page "https://github.com/thomasp85/tweenr") (synopsis "Interpolate data for smooth animations") (description "In order to create smooth animation between states of data, tweening is necessary. This package provides a range of functions for creating tweened data that can be used as basis for animation. Furthermore it adds a number of vectorized interpolaters for common R data types such as numeric, date and color.") (license license:expat))) (define-public r-polyclip (package (name "r-polyclip") (version "1.10-6") (source (origin (method url-fetch) (uri (cran-uri "polyclip" version)) (sha256 (base32 "0qwb5w1ishbhg1nhdp8985ddvcs7ljdyrbv059hx576xmgni6brw")))) (build-system r-build-system) (native-inputs (list pkg-config)) (home-page "http://www.angusj.com/delphi/clipper.php") (synopsis "Polygon clipping") (description "This package provides an R port of the library Clipper. It performs polygon clipping operations (intersection, union, set minus, set difference) for polygonal regions of arbitrary complexity, including holes. It computes offset polygons (spatial buffer zones, morphological dilations, Minkowski dilations) for polygonal regions and polygonal lines. It computes the Minkowski Sum of general polygons. There is a function for removing self-intersections from polygon data.") (license license:boost1.0))) (define-public r-urlchecker (package (name "r-urlchecker") (version "1.0.1") (source (origin (method url-fetch) (uri (cran-uri "urlchecker" version)) (sha256 (base32 "06034lb94krbzawqg5xklwcksvyyzl3qy355f66baj5pw7dms5k2")))) (properties `((upstream-name . "urlchecker"))) (build-system r-build-system) (propagated-inputs (list r-cli r-curl r-xml2)) (home-page "https://github.com/r-lib/urlchecker") (synopsis "Run CRAN URL checks from older R versions") (description "This package provides the URL checking tools available in R 4.1+ as a package for earlier versions of R. It also uses concurrent requests so can be much faster than the serial versions.") 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(license license:gpl2+))) (define-public r-pamr (package (name "r-pamr") (version "1.56.1") (source (origin (method url-fetch) (uri (cran-uri "pamr" version)) (sha256 (base32 "0ycpgkk23y3zzkb42n2skcyl35ps1n7jmyzfj7pbxr3f6gr2grfh")))) (build-system r-build-system) (propagated-inputs (list r-cluster r-survival)) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/pamr/") (synopsis "Prediction Analysis for Microarrays") (description "This package provides some functions for sample classification in microarrays.") 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(license license:gpl2))) (define-public r-gbm (package (name "r-gbm") (version "2.1.9") (source (origin (method url-fetch) (uri (cran-uri "gbm" version)) (sha256 (base32 "1r5d8mkg4z14l3743h39r35r0qqjx5p40ixdkcc5iyjab0fzm24x")))) (build-system r-build-system) (propagated-inputs (list r-lattice r-survival)) (native-inputs (list r-knitr)) (home-page "https://github.com/gbm-developers/gbm") (synopsis "Generalized boosted regression models") (description "This package is an implementation of extensions to Freund and Schapire's AdaBoost algorithm and Friedman's gradient boosting machine. It includes regression methods for least squares, absolute loss, t-distribution loss, quantile regression, logistic, multinomial logistic, Poisson, Cox proportional hazards partial likelihood, AdaBoost exponential loss, Huberized hinge loss, and Learning to Rank measures (LambdaMart).") 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This is useful to visualize the 2D-distribution of points in case of overplotting.") (license license:gpl3))) (define-public r-arrow (package (name "r-arrow") (version "15.0.1") (source (origin (method url-fetch) (uri (cran-uri "arrow" version)) (sha256 (base32 "070pp0p5h1ij7pg34l5grrx4vwfihagnvnk4kj7l3w0gh8y88ibz")))) (properties `((upstream-name . "arrow"))) (build-system r-build-system) (inputs (list `(,apache-arrow "lib") zlib)) (propagated-inputs (list r-assertthat r-bit64 r-cpp11 r-glue r-purrr r-r6 r-rlang r-tidyselect r-vctrs)) (native-inputs (list pkg-config)) (home-page "https://github.com/apache/arrow/") (synopsis "R integration to Apache Arrow") (description "Apache Arrow is a cross-language development platform for in-memory data. It specifies a standardized language-independent columnar memory format for flat and hierarchical data, organized for efficient analytic operations on modern hardware. This package provides an R interface to the Arrow C++ library.") (license license:asl2.0))) (define-public r-rex (package (name "r-rex") (version "1.2.1") (source (origin (method url-fetch) (uri (cran-uri "rex" version)) (sha256 (base32 "1mmzlc3j7xa0rbjxa369f4sr0iw3gq58g8fmjjxbsjvfq14ychmg")))) (build-system r-build-system) (propagated-inputs (list r-lazyeval)) (native-inputs (list r-knitr)) (home-page "https://github.com/kevinushey/rex") (synopsis "Friendly regular expressions") (description "This package provides a friendly interface for the construction of regular expressions. Regular expressions are a very powerful feature, however they are often difficult to interpret. Rex allows you to build complex regular expressions from human readable expressions") (license license:expat))) (define-public r-mlapi (package (name "r-mlapi") (version "0.1.1") (source (origin (method url-fetch) (uri (cran-uri "mlapi" version)) (sha256 (base32 "1qyiii6x9b89i4pd4yi2zd23aabpmnpj18gqi5va0zy0l8r7kknr")))) (properties `((upstream-name . 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"rsparse"))) (build-system r-build-system) (propagated-inputs (list r-data-table r-float r-lgr r-matrix r-matrixextra r-rcpp r-rcpparmadillo r-rhpcblasctl)) (home-page "https://github.com/rexyai/rsparse") (synopsis "Statistical learning on sparse matrices") (description "This package implements many algorithms for statistical learning on sparse matrices: matrix factorizations, matrix completion, elastic net regressions, factorization machines. The rsparse package also enhances the Matrix package by providing methods for multithreaded matrix products and native slicing of the sparse matrices in @dfn{Compressed Sparse Row} (CSR) format.") (license license:gpl2+))) (define-public r-text2vec (package (name "r-text2vec") (version "0.6.4") (source (origin (method url-fetch) (uri (cran-uri "text2vec" version)) (sha256 (base32 "0sjlvp4zhzwc0ai7626fpw3ws8xv0xhl8gv8mrk24lrpk5nhin2h")))) (properties `((upstream-name . 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"MCMCpack"))) (build-system r-build-system) (propagated-inputs (list r-coda r-lattice r-mass r-mcmc r-quantreg)) (home-page "https://cran.r-project.org/package=MCMCpack") (synopsis "Markov Chain Monte Carlo (MCMC) package") (description "This package contains functions to perform Bayesian inference using posterior simulation for a number of statistical models. Most simulation is done in compiled C++ written in the Scythe Statistical Library. All models return @code{coda} @code{mcmc} objects that can then be summarized using the @code{coda} package. Some useful utility functions such as density functions, pseudo-random number generators for statistical distributions, a general purpose Metropolis sampling algorithm, and tools for visualization are provided.") (license license:gpl3))) (define-public r-xmlparsedata (package (name "r-xmlparsedata") (version "1.0.5") (source (origin (method url-fetch) (uri (cran-uri "xmlparsedata" version)) (sha256 (base32 "1c6bnz3ng1qw7sfip8wq3a4dn36a4d6rbja0sadn0a4pbsmk8q3n")))) (properties `((upstream-name . "xmlparsedata"))) (build-system r-build-system) (home-page "https://github.com/r-lib/xmlparsedata#readme") (synopsis "Parse data of @code{R} code as an @code{XML} tree") (description "This package provides tools to convert the output of @code{utils::getParseData()} to an @code{XML} tree, that one can search via @code{XPath}, and is easier to manipulate in general.") (license license:expat))) (define-public r-cyclocomp (package (name "r-cyclocomp") (version "1.1.1") (source (origin (method url-fetch) (uri (cran-uri "cyclocomp" version)) (sha256 (base32 "0kdinnn6cgkfc94japyyp5qr7imjxddajds3qqxf4q5higahdzws")))) (properties `((upstream-name . "cyclocomp"))) (build-system r-build-system) (propagated-inputs (list r-callr r-crayon r-desc r-remotes r-withr)) (home-page "https://github.com/MangoTheCat/cyclocomp") (synopsis "Cyclomatic complexity of R code") (description "Cyclomatic complexity is a software metric, used to indicate the complexity of a program. It is a quantitative measure of the number of linearly independent paths through a program's source code. This package provides tools to compute this metric.") (license license:expat))) (define-public r-lintr (package (name "r-lintr") (version "3.1.2") (source (origin (method url-fetch) (uri (cran-uri "lintr" version)) (sha256 (base32 "0xska080wnifvibywmwalmp4a0xdnsgpn0k3m5ahjbqckfcpklrm")))) (properties `((upstream-name . "lintr"))) (build-system r-build-system) (propagated-inputs (list r-backports r-codetools r-cyclocomp r-digest r-glue r-knitr r-rex r-xml2 r-xmlparsedata)) (native-inputs (list r-knitr)) (home-page "https://github.com/jimhester/lintr") (synopsis "Linter for R code") (description "This package checks adherence to a given style, syntax errors and possible semantic issues. It supports on the fly checking of R code edited with @code{RStudio IDE}, @code{Emacs} and @code{Vim}.") (license license:expat))) (define-public r-sccore (package (name "r-sccore") (version "1.0.5") (source (origin (method url-fetch) (uri (cran-uri "sccore" version)) (sha256 (base32 "12jljngm0v75zp0zka1zdrn6pvxvqy7qpakr7vzazvq1vvjd5qlg")))) (properties `((upstream-name . "sccore"))) (build-system r-build-system) (propagated-inputs (list r-dplyr r-ggplot2 r-ggrepel r-igraph r-irlba r-magrittr r-matrix r-pbmcapply r-proc r-rcpp r-rcpparmadillo r-rcppeigen r-rcppprogress r-rlang r-scales r-tibble r-uwot r-withr)) (home-page "https://github.com/kharchenkolab/sccore") (synopsis "Core utilities for single-cell RNA-Seq") (description "This package implements core utilities for single-cell RNA-seq data analysis. Contained within are utility functions for working with @acronym{DE, differential expression} matrices and count matrices, a collection of functions for manipulating and plotting data via ggplot2, and functions to work with cell graphs and cell embeddings. Graph-based methods include embedding kNN cell graphs into a UMAP, collapsing vertices of each cluster in the graph, and propagating graph labels.") (license license:gpl3))) (define-public r-scs (package (name "r-scs") (version "3.2.4") (source (origin (method url-fetch) (uri (cran-uri "scs" version)) (sha256 (base32 "13r944b9ip078hqwdpzn3jv21zm47d9l2b1f5y6glcj5pxs9iwy3")))) (properties `((upstream-name . "scs"))) (build-system r-build-system) (home-page "https://github.com/FlorianSchwendinger/scs") (synopsis "Splitting conic solver") (description "This package solves convex cone programs via operator splitting. It can solve: linear programs, second-order cone programs, semidefinite programs, exponential cone programs, and power cone programs, or problems with any combination of those cones. SCS uses AMD (a set of routines for permuting sparse matrices prior to factorization) and LDL (a sparse LDL factorization and solve package) from SuiteSparse.") (license license:gpl3))) (define-public r-sctransform (package (name "r-sctransform") (version "0.4.1") (source (origin (method url-fetch) (uri (cran-uri "sctransform" version)) (sha256 (base32 "0wgimf7qqgnnmyspn2rpb4a8hl570fv0fwh0r0r4qgjlpvwffssz")))) (build-system r-build-system) (propagated-inputs (list r-dplyr r-future r-future-apply r-ggplot2 r-gridextra r-magrittr r-mass r-matrix r-matrixstats r-rcpp r-rcpparmadillo r-reshape2 r-rlang)) (home-page "https://github.com/ChristophH/sctransform") (synopsis "Variance stabilizing transformations for Single Cell UMI Data") (description "This package provides a normalization method for single-cell UMI count data using a variance stabilizing transformation. The transformation is based on a negative binomial regression model with regularized parameters. As part of the same regression framework, this package also provides functions for batch correction, and data correction.") (license license:gpl3))) (define-public r-styler (package (name "r-styler") (version "1.10.3") (source (origin (method url-fetch) (uri (cran-uri "styler" version)) (sha256 (base32 "0hfspw1q40jqla238dw86iyf0lyk1agc19flwvf9nrm824hw5fdd")))) (build-system r-build-system) ;; This is needed by R.cache. (arguments `(#:phases (modify-phases %standard-phases (add-after 'unpack 'set-HOME (lambda _ (setenv "HOME" "/tmp")))))) (propagated-inputs (list r-cli r-magrittr r-purrr r-r-cache r-rlang r-rprojroot r-vctrs r-withr)) (native-inputs (list r-knitr)) (home-page "https://github.com/r-lib/styler") (synopsis "Non-invasive pretty printing of R code") (description "This is a package for pretty-printing R code without changing the user's formatting intent.") (license license:gpl3))) (define-public r-scrime (package (name "r-scrime") (version "1.3.5") (source (origin (method url-fetch) (uri (cran-uri "scrime" version)) (sha256 (base32 "0y2mh9fsffjf3i15bafpasa17z99c1s75r8g6h4hgcwfgpjx75sx")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/scrime/") (synopsis "Analysis of high-dimensional categorical data such as SNP data") (description "This package provides tools for the analysis of high-dimensional data developed/implemented at the group \"Statistical Complexity Reduction In Molecular Epidemiology\" (SCRIME). The main focus is on SNP data, but most of the functions can also be applied to other types of categorical data.") (license license:gpl2))) (define-public r-pbmcapply (package (name "r-pbmcapply") (version "1.5.1") (source (origin (method url-fetch) (uri (cran-uri "pbmcapply" version)) (sha256 (base32 "1p8jf7c4k45482w72sr0jw4jkz787krrxai3sl6jz5l4lda2iz3z")))) (build-system r-build-system) (home-page "https://github.com/kvnkuang/pbmcapply") (synopsis "Track the progress of apply procedures with a progress bar") (description "This light-weight package helps you track and visualize the progress of parallel versions of vectorized R functions of the @code{mc*apply} family.") (license license:expat))) (define-public r-blme (package (name "r-blme") (version "1.0-5") (source (origin (method url-fetch) (uri (cran-uri "blme" version)) (sha256 (base32 "0413j7gwr5yj14jamkizj55q7xii1a0kgazzj0ilqn2ascclz6k7")))) (build-system r-build-system) (propagated-inputs (list r-lme4)) (home-page "https://github.com/vdorie/blme") (synopsis "Bayesian linear mixed-effects models") (description "This package provides tools for maximum a posteriori estimation for linear and generalized linear mixed-effects models in a Bayesian setting. It extends the lme4 package.") (license license:gpl2+))) (define-public r-batchtools (package (name "r-batchtools") (version "0.9.17") (source (origin (method url-fetch) (uri (cran-uri "batchtools" version)) (sha256 (base32 "1rlvfk0279saf930z48g230p9z30dd7qil9aiprjn35px1advqdn")))) (build-system r-build-system) (propagated-inputs (list r-backports r-base64url r-brew r-checkmate r-data-table r-digest r-fs r-progress r-r6 r-rappdirs r-stringi r-withr)) (native-inputs (list r-knitr)) (home-page "https://github.com/mllg/batchtools") (synopsis "Tools for computation on batch systems") (description "As a successor of the packages BatchJobs and BatchExperiments, this package provides a parallel implementation of the Map function for high performance computing systems managed by various schedulers. A multicore and socket mode allow the parallelization on a local machines, and multiple machines can be hooked up via SSH to create a makeshift cluster. Moreover, the package provides an abstraction mechanism to define large-scale computer experiments in a well-organized and reproducible way.") (license license:lgpl3))) (define-public r-clue (package (name "r-clue") (version "0.3-65") (source (origin (method url-fetch) (uri (cran-uri "clue" version)) (sha256 (base32 "1y1ycb5yw034ccxz15x41ah699hgjffsfvbn15fwdcdjbz9zvy5x")))) (build-system r-build-system) (propagated-inputs (list r-cluster)) (home-page "https://cran.r-project.org/web/packages/clue/") (synopsis "Tools for analyzing cluster ensembles") (description "Cluster ensembles are collections of individual solutions to a given clustering problem which are useful or necessary to consider in a wide range of applications. This R package provides an extensible computational environment for creating and analyzing cluster ensembles, with basic data structures for representing partitions and hierarchies, and facilities for computing on them, including methods for measuring proximity and obtaining consensus and secondary clusterings.") (license license:gpl2))) (define-public r-sitmo (package (name "r-sitmo") (version "2.0.2") (source (origin (method url-fetch) (uri (cran-uri "sitmo" version)) (sha256 (base32 "1hm89zi38ldgbskyx1cn7gm87yqy7zrxli8q05a36y1ndvazi3j4")))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) (native-inputs (list r-knitr)) (home-page "https://github.com/coatless/sitmo/") (synopsis "Parallel pseudo random number generator header files") (description "This package provides two high quality and fast PPRNGs that may be used in an OpenMP parallel environment. In addition, there is a generator for one dimensional low-discrepancy sequence.") (license license:expat))) (define-public r-dqrng (package (name "r-dqrng") (version "0.3.2") (source (origin (method url-fetch) (uri (cran-uri "dqrng" version)) (sha256 (base32 "171y7487flla0vqxmzvf9nls7vn046vplcgzvyiva3d418hwl0nd")))) (build-system r-build-system) (propagated-inputs (list r-bh r-rcpp r-sitmo)) (native-inputs (list r-knitr)) (home-page "https://www.daqana.org/dqrng") (synopsis "Fast pseudo random number generators") (description "Several fast random number generators are provided as C++ header-only libraries: the PCG family as well as Xoroshiro128+ and Xoshiro256+. Additionally, fast functions for generating random numbers according to a uniform, normal and exponential distribution are included. The latter two use the Ziggurat algorithm originally proposed by Marsaglia and Tsang. These functions are exported to R and as a C++ interface and are enabled for use with the default 64 bit generator from the PCG family, Xoroshiro128+ and Xoshiro256+ as well as the 64 bit version of the 20 rounds Threefry engine (Salmon et al., 2011) as provided by the package @code{sitmo}.") ;; This package includes code under CC0 and Apache 2.0 or Expat, but as a ;; whole is distributed under the terms of the AGPL 3. (license license:agpl3))) (define-public r-ingredients (package (name "r-ingredients") (version "2.3.0") (source (origin (method url-fetch) (uri (cran-uri "ingredients" version)) (sha256 (base32 "0jvxkdhbc28a096hi0y6519cj4im4mnl1vz9s563dvb5g4vb7r7b")))) (properties `((upstream-name . "ingredients"))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-gridextra r-scales)) (native-inputs (list r-knitr)) (home-page "https://ModelOriented.github.io/ingredients/") (synopsis "Effects and importances of model ingredients") (description "This is a collection of tools for assessment of feature importance and feature effects. Key functions are: @itemize @item @code{feature_importance()} for assessment of global level feature importance, @item @code{ceteris_paribus()} for calculation of the what-if plots, @item @code{partial_dependence()} for partial dependence plots, @item @code{conditional_dependence()} for conditional dependence plots, @item @code{accumulated_dependence()} for accumulated local effects plots, @item @code{aggregate_profiles()} and @code{cluster_profiles()} for aggregation of ceteris paribus profiles, @item generic @code{print()} and @code{plot()} for better usability of selected explainers, @item generic @code{plotD3()} for interactive, D3 based explanations, and @item generic @code{describe()} for explanations in natural language. @end itemize\n") (license license:gpl3))) (define-public r-ibreakdown (package (name "r-ibreakdown") (version "2.1.2") (source (origin (method url-fetch) (uri (cran-uri "iBreakDown" version)) (sha256 (base32 "1qacvfzknchfm27mhl7a357fnb6lzjkj4vh8lch5aljz82sdmdaf")))) (properties `((upstream-name . 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(license license:gpl3))) (define-public r-dae (package (name "r-dae") (version "3.2.25") (source (origin (method url-fetch) (uri (cran-uri "dae" version)) (sha256 (base32 "168kisjgfc8cp7j6frgpci7qxw548rynpi9wv008k8hfszkfkgny")))) (build-system r-build-system) (arguments '(#:phases (modify-phases %standard-phases (add-after 'unpack 'set-HOME ;; Needed for vignette builder (lambda _ (setenv "HOME" "/tmp")))))) (propagated-inputs (list r-ggplot2 r-ggpubr r-plyr r-trycatchlog)) (native-inputs (list r-r-rsp)) ; vignette builder (home-page "http://chris.brien.name") (synopsis "Functions useful in the design and ANOVA of experiments") (description "This package provides functions useful in the design and ANOVA of experiments. The content falls into the following groupings: @enumerate @item data, @item factor manipulation functions, @item design functions, @item ANOVA functions, @item matrix functions, @item projector and canonical efficiency functions, and @item miscellaneous functions. @end enumerate There is a vignette called @code{DesignNotes} describing how to use the design functions for randomizing and assessing designs. The ANOVA functions facilitate the extraction of information when the @code{Error} function has been used in the call to @code{aov}.") (license license:gpl2))) (define-public r-dalex (package (name "r-dalex") (version "2.4.3") (source (origin (method url-fetch) (uri (cran-uri "DALEX" version)) (sha256 (base32 "08cd5nhgd6vaazcqq985kwivg99v6ily4idhgkpz8l9ffl3lavm0")))) (properties `((upstream-name . "DALEX"))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-ibreakdown r-ingredients)) (home-page "https://pbiecek.github.io/DALEX/") (synopsis "Descriptive machine learning explanations") (description "Machine Learning models are widely used and have various applications in classification or regression. Models created with boosting, bagging, stacking or similar techniques are often used due to their high performance, but such black-box models usually lack interpretability. The DALEX package contains various explainers that help to understand the link between input variables and model output.") ;; Any version of the GPL (license license:gpl3+))) (define-public r-enrichr (package (name "r-enrichr") (version "3.2") (source (origin (method url-fetch) (uri (cran-uri "enrichR" version)) (sha256 (base32 "1g97q6vqwvb2l02y61343sblarqi433gjl3qmlyxjxq2lnjrnak1")))) (properties `((upstream-name . "enrichR"))) (build-system r-build-system) (propagated-inputs (list r-curl r-ggplot2 r-httr r-rjson r-writexls)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/enrichR/") (synopsis "R Interface to Enrichr database for analyzing gene sets") (description "This package provides an R interface to all Enrichr databases, a web-based tool for analyzing gene sets and returns any enrichment of common annotated biological functions.") (license license:gpl2+))) (define-public r-plot3d (package (name "r-plot3d") (version "1.4.1") (source (origin (method url-fetch) (uri (cran-uri "plot3D" version)) (sha256 (base32 "1x6ian6hfkaih2aa11z92qlihqqf5wmpc9705dzigafx8i4gfvfv")))) (properties `((upstream-name . "plot3D"))) (build-system r-build-system) (propagated-inputs (list r-misc3d)) (home-page "https://cran.r-project.org/web/packages/plot3D") (synopsis "Plot multi-dimensional data") (description "This package provides functions for viewing 2D and 3D data, including perspective plots, slice plots, surface plots, scatter plots, etc. It includes data sets from oceanography.") (license license:gpl3+))) (define-public r-plotroc (package (name "r-plotroc") (version "2.3.1") (source (origin (method url-fetch) (uri (cran-uri "plotROC" version)) (sha256 (base32 "15jvn1dlx8qh5ghnkhqyc49frw6rp58ikpjs3ga8mjxrqyz7wb1g")) (snippet '(delete-file "inst/d3.v3.min.js")))) (properties `((upstream-name . "plotROC"))) (build-system r-build-system) (arguments (list #:phases '(modify-phases %standard-phases (add-after 'unpack 'process-javascript (lambda* (#:key inputs #:allow-other-keys) (let ((source (assoc-ref inputs "d3.v3.js")) (target "inst/d3.v3.min.js")) (invoke "esbuild" source "--minify" (string-append "--outfile=" target)))))))) (propagated-inputs (list r-ggplot2 r-gridsvg r-plyr r-rlang r-shiny)) (native-inputs `(("r-knitr" ,r-knitr) ("esbuild" ,esbuild) ("d3.v3.js" ,(origin (method url-fetch) (uri "https://d3js.org/d3.v3.js") (sha256 (base32 "1arr7sr08vy7wh0nvip2mi7dpyjw4576vf3bm45rp4g5lc1k1x41")))))) (home-page "https://sachsmc.github.io/plotROC/") (synopsis "Generating useful receiver operating characteristic curve charts") (description "This package generates @acronym{ROC, receiver operating characteristic} plots. Most ROC curve plots obscure the cutoff values and inhibit interpretation and comparison of multiple curves. This attempts to address those shortcomings by providing plotting and interactive tools. Functions are provided to generate an interactive ROC curve plot for web use, and print versions. A Shiny application implementing the functions is also included.") (license license:expat))) (define-public r-ggfortify (package (name "r-ggfortify") (version "0.4.17") (source (origin (method url-fetch) (uri (cran-uri "ggfortify" version)) (sha256 (base32 "1ygbvk3b99mabwqc9hh5lz3adj1i05ym7i8b6kbgid8cgrbaaxag")))) (build-system r-build-system) (propagated-inputs (list r-dplyr r-ggplot2 r-gridextra r-scales r-stringr r-tibble r-tidyr)) (native-inputs (list r-knitr)) (home-page "https://github.com/sinhrks/ggfortify") (synopsis "Data visualization tools for statistical analysis results") (description "This package provides unified plotting tools for statistics commonly used, such as GLM, time series, PCA families, clustering and survival analysis. The package offers a single plotting interface for these analysis results and plots in a unified style using the @code{ggplot2} package.") (license license:gpl2))) (define-public r-refmanager (package (name "r-refmanager") (version "1.4.0") (source (origin (method url-fetch) (uri (cran-uri "RefManageR" version)) (sha256 (base32 "1kjd66gp2z9fzrnyr1bqfd9p58q0bin3a187z9b56hiqmdjhyc78")))) (properties `((upstream-name . "RefManageR"))) (build-system r-build-system) (propagated-inputs (list r-bibtex r-httr r-jsonlite r-lubridate r-plyr r-stringr r-xml2)) (native-inputs (list r-knitr)) (home-page "https://github.com/ropensci/RefManageR/") (synopsis "Straightforward BibTeX and BibLaTeX bibliography management") (description "This package provides tools for importing and working with bibliographic references. It greatly enhances the @code{bibentry} class by providing a class @code{BibEntry} which stores BibTeX and BibLaTeX references, supports UTF-8 encoding, and can be easily searched by any field, by date ranges, and by various formats for name lists (author by last names, translator by full names, etc.). Entries can be updated, combined, sorted, printed in a number of styles, and exported. BibTeX and BibLaTeX @code{.bib} files can be read into R and converted to @code{BibEntry} objects.") ;; Any of these licenses may be picked. (license (list license:gpl2 license:gpl3 license:bsd-3)))) (define-public r-citr (package (name "r-citr") (version "0.3.2") (source (origin (method url-fetch) (uri (cran-uri "citr" version)) (sha256 (base32 "1qbarvafjb8jgkrnrhh6jw7mcglmjwf7dpdiibxf39jkmlhf7las")))) (build-system r-build-system) (propagated-inputs (list r-assertthat r-curl r-httr r-miniui r-refmanager r-rstudioapi r-shiny r-shinyjs r-yaml)) (home-page "https://github.com/crsh/citr") (synopsis "RStudio add-in to insert Markdown citations") (description "This package provides functions and an RStudio add-in that search a BibTeX or BibLaTeX file to create and insert formatted Markdown citations into the current document.") (license license:expat))) (define-public r-xgboost (package (name "r-xgboost") (version "1.7.7.1") (source (origin (method url-fetch) (uri (cran-uri "xgboost" version)) (sha256 (base32 "08wpxr8jkzsqb5zaw43bmq5r7k3jnb1ibjkliwh2ffjq7b7jr4gp")))) (build-system r-build-system) (propagated-inputs (list r-data-table r-jsonlite r-matrix)) (native-inputs (list r-knitr)) (home-page "https://github.com/dmlc/xgboost") (synopsis "Extreme gradient boosting") (description "This package provides an R interface to Extreme Gradient Boosting, which is an efficient implementation of the gradient boosting framework from Chen and Guestrin (2016). The package includes efficient linear model solver and tree learning algorithms. The package can automatically do parallel computation on a single machine. It supports various objective functions, including regression, classification and ranking. The package is made to be extensible, so that users are also allowed to define their own objectives easily.") (license license:asl2.0))) (define-public r-umap (package (name "r-umap") (version "0.2.10.0") (source (origin (method url-fetch) (uri (cran-uri "umap" version)) (sha256 (base32 "1abfddi0rq75b7nlx6550fx9nrqa62vb92xyp05ris25jf98ciwd")))) (build-system r-build-system) (propagated-inputs (list r-matrix r-openssl r-rcpp r-reticulate r-rspectra)) (native-inputs (list r-knitr)) (home-page "https://github.com/tkonopka/umap") (synopsis "Uniform manifold approximation and projection") (description "Uniform manifold approximation and projection is a technique for dimension reduction. This package provides an interface to the UMAP algorithm in R, including a translation of the original algorithm into R.") (license license:expat))) (define-public r-uwot (package (name "r-uwot") (version "0.2.1") (source (origin (method url-fetch) (uri (cran-uri "uwot" version)) (sha256 (base32 "1gg21kxm4qq0i0gc6jg5k37nnyxj8652zf4jp95ffb9xsn22gpvc")))) (build-system r-build-system) (propagated-inputs (list r-dqrng r-fnn r-irlba r-matrix r-rcpp r-rcppannoy r-rcppprogress)) (native-inputs (list r-knitr)) (home-page "https://github.com/jlmelville/uwot") (synopsis "Uniform manifold approximation and projection") (description "This package provides an implementation of the Uniform Manifold Approximation and Projection dimensionality reduction by McInnes et al. (2018). It also provides means to transform new data and to carry out supervised dimensionality reduction. An implementation of the related LargeVis method of Tang et al. (2016) is also provided.") (license license:gpl3))) (define-public r-kableextra (package (name "r-kableextra") (version "1.4.0") (source (origin (method url-fetch) (uri (cran-uri "kableExtra" version)) (sha256 (base32 "02blaamz6xkdwgyvw6akjhn5fvwy8l24k7nwqj2id6g8qagwrqlg")))) (properties `((upstream-name . "kableExtra"))) (build-system r-build-system) (propagated-inputs (list r-digest r-htmltools r-knitr r-magrittr r-rmarkdown r-rstudioapi r-scales r-stringr r-svglite r-viridislite r-xml2)) (native-inputs (list r-knitr)) (home-page "https://haozhu233.github.io/kableExtra/") (synopsis "Construct complex tables with pipe syntax") (description "Build complex HTML or LaTeX tables using @code{kable()} from @code{knitr} and the piping syntax from @code{magrittr}. The function @code{kable()} is a light weight table generator coming from @code{knitr}. This package simplifies the way to manipulate the HTML or LaTeX codes generated by @code{kable()} and allows users to construct complex tables and customize styles using a readable syntax.") (license license:expat))) (define-public r-glasso (package (name "r-glasso") (version "1.11") (source (origin (method url-fetch) (uri (cran-uri "glasso" version)) (sha256 (base32 "02p3612rpydk195n2qr77lp1j2w8zsw1ckkk98c8angm4r5q8dsc")))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "https://statweb.stanford.edu/~tibs/glasso/") (synopsis "Graphical Lasso: estimation of Gaussian graphical models") (description "This is a package for estimation of a sparse inverse covariance matrix using a lasso (L1) penalty. Facilities are provided for estimates along a path of values for the regularization parameter.") (license license:gpl2))) (define-public r-glassofast (package (name "r-glassofast") (version "1.0.1") (source (origin (method url-fetch) (uri (cran-uri "glassoFast" version)) (sha256 (base32 "0nyvmmrw6cr5j1mkf1qv6hn3q24kyn6gn48q6r7az4vn1m141hzz")))) (properties `((upstream-name . "glassoFast"))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/package=glassoFast") (synopsis "Fast graphical LASSO") (description "This package provides a fast and improved implementation of the graphical LASSO.") (license license:gpl3+))) (define-public r-gldex (package (name "r-gldex") (version "2.0.0.9.3") (source (origin (method url-fetch) (uri (cran-uri "GLDEX" version)) (sha256 (base32 "0xv9w4kmivmmcnn19a6s6d1ilhi1misdgrp07ks7rbd177zjy5vs")))) (properties `((upstream-name . "GLDEX"))) (build-system r-build-system) (propagated-inputs (list r-cluster r-spacefillr)) (home-page "https://cran.r-project.org/package=GLDEX") (synopsis "Fitting single and mixture of generalised lambda distributions") (description "@code{GLDEX} offers fitting algorithms corresponding to two major objectives. One is to provide a smoothing device to fit distributions to data using the weighted and unweighted discretised approach based on the bin width of the histogram. The other is to provide a definitive fit to the data set using the maximum likelihood and quantile matching estimation. Other methods such as moment matching, starship method, and L moment matching are also provided. Diagnostics on goodness of fit can be done via qqplots, KS-resample tests and comparing mean, variance, skewness and kurtosis of the data with the fitted distribution.") (license license:gpl3+))) (define-public r-rhandsontable (package (name "r-rhandsontable") (version "0.3.8") (source (origin (method url-fetch) (uri (cran-uri "rhandsontable" version)) (sha256 (base32 "07fj6npq65pq836vdwblkhprdaq4i4f13cwdmm9gmxrnk72xj7lh")) (modules '((guix build utils))) (snippet '(with-directory-excursion "inst/htmlwidgets/lib" (for-each delete-file '("chroma/chroma.min.js" "handsontable/all.min.js" "handsontable/handsontable.full.min.js" "jquery/jquery.min.js" "numbro/languages.min.js" "sparkline/jquery.sparkline.min.js")))))) (properties `((upstream-name . "rhandsontable"))) (build-system r-build-system) (arguments (list #:modules '((guix build utils) (guix build r-build-system) (srfi srfi-1)) #:phases '(modify-phases %standard-phases (add-after 'unpack 'process-javascript (lambda* (#:key inputs #:allow-other-keys) (with-directory-excursion "inst/htmlwidgets/lib" ;; Generate languages.js by importing all numbro language ;; files. (with-output-to-file "/tmp/languages.js" (lambda () (for-each (lambda (file) (format (current-output-port) "require(\"~a/~a\")~%" (dirname file) (basename file ".js"))) (find-files (string-append (assoc-ref inputs "js-numbro") "/languages/") "\\.js$")))) ;; Then bundle and minify it. (invoke "esbuild" "/tmp/languages.js" "--bundle" "--minify" "--outfile=numbro/languages.min.js") ;; Minify the other source files. (call-with-values (lambda () (unzip2 `((,(search-input-file inputs "/chroma.js") "chroma/chroma.min.js") (,(search-input-file inputs "/dist/languages/all.js") "handsontable/all.min.js") (,(search-input-file inputs "/dist/handsontable.full.js") "handsontable/handsontable.full.min.js") (,(assoc-ref inputs "js-jquery-sparkline") "sparkline/jquery.sparkline.min.js") (,(assoc-ref inputs "js-jquery") "jquery/jquery.min.js")))) (lambda (sources targets) (for-each (lambda (source target) (format #true "Processing ~a --> ~a~%" source target) (invoke "esbuild" source "--minify" (string-append "--outfile=" target))) sources targets))))))))) (propagated-inputs (list r-htmlwidgets r-jsonlite r-magrittr)) (native-inputs `(("esbuild" ,esbuild) ("r-knitr" ,r-knitr) ("js-chroma" ,(origin (method git-fetch) (uri (git-reference (url "https://github.com/gka/chroma.js") (commit "v1.3.3"))) (file-name (git-file-name "chroma" "1.3.3")) (sha256 (base32 "091xn40n868pgb76gdl5jpg5gqqqzhykgxsslni230jzgc0hh1vm")))) ("js-handsontable" ,(origin (method git-fetch) (uri (git-reference (url "https://github.com/handsontable/handsontable") (commit "6.2.2"))) (file-name (git-file-name "handsontable" "6.2.2")) (sha256 (base32 "1rq4l24m9yz5r4sagdhq78jcjxlyh0ngryp43p5k33q2l77l4cp8")))) ("js-jquery-sparkline" ,(origin (method url-fetch) (uri "https://omnipotent.net/jquery.sparkline/2.1.2/jquery.sparkline.js") (sha256 (base32 "0d28qg5wlv44l02xafla6h6fvl3a71r5w7k0xhadagighh5wnarg")))) ("js-jquery" ,(origin (method url-fetch) (uri "https://code.jquery.com/jquery-3.2.1.js") (sha256 (base32 "08dv528xy8ksrg5qqw73bvpjrzxv66xq41sfidn9ypgskwl2g40d")))) ;; We guessed the version based on ;; 62993ac9be3a1a4188150f7a6502b48b899f075e in ;; https://github.com/jrowen/rhandsontable, which added numbro's ;; languages.min.js. This was committed in Nov 2018, so the most ;; recent release of numbro at that time would have been 2.0.6 from May ;; 2018. ("js-numbro" ,(origin (method git-fetch) (uri (git-reference (url "https://github.com/BenjaminVanRyseghem/numbro") (commit "2.0.6"))) (file-name (git-file-name "numbro" "2.0.6")) (sha256 (base32 "1gsswkd482p0id00yx4q67ay0jvvwwidj71v41mq1cws8v2jjywx")))))) (home-page "https://jrowen.github.io/rhandsontable/") (synopsis "Htmlwidget based on the handsontable.js library") (description "Handsontable is a data grid component with an Excel like appearance. Built in JavaScript, it integrates with any data source with peak efficiency. It comes with powerful features like data validation, sorting, grouping, data binding, formula support or column ordering.") (license license:expat))) (define-public r-rhpcblasctl (package (name "r-rhpcblasctl") (version "0.23-42") (source (origin (method url-fetch) (uri (cran-uri "RhpcBLASctl" version)) (sha256 (base32 "05b6jhmxdr1rdpbvf5gwi9dqb57m8z2860qzkw5hcr72d5drv22w")))) (properties `((upstream-name . "RhpcBLASctl"))) (build-system r-build-system) (home-page "https://prs.ism.ac.jp/~nakama/Rhpc/") (synopsis "Control the number of threads on BLAS") (description "This package allows you to control the number of threads the BLAS library uses. It is also possible to control the number of threads in OpenMP.") (license license:agpl3+))) (define-public r-lda (package (name "r-lda") (version "1.4.2") (source (origin (method url-fetch) (uri (cran-uri "lda" version)) (sha256 (base32 "03r4h5kgr8mfy44p66mfj5bp4k00g8zh4a1mhn46jw14pkhs21jn")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/lda/") (synopsis "Collapsed Gibbs sampling methods for topic models") (description "This package implements @dfn{latent Dirichlet allocation} (LDA) and related models. This includes (but is not limited to) sLDA, corrLDA, and the mixed-membership stochastic blockmodel. Inference for all of these models is implemented via a fast collapsed Gibbs sampler written in C. Utility functions for reading/writing data typically used in topic models, as well as tools for examining posterior distributions are also included.") ;; Any version of the LGPL (license license:lgpl3+))) (define-public r-rann-l1 (package (name "r-rann-l1") (version "2.5.2") (source (origin (method url-fetch) (uri (cran-uri "RANN.L1" version)) (sha256 (base32 "1hanh3my84mdr5wy6b89fawqzfc184vff1y65wy4l5ld9qza1n44")))) (properties `((upstream-name . "RANN.L1"))) (build-system r-build-system) (home-page "https://github.com/jefferis/RANN/tree/master-L1") (synopsis "Fast nearest neighbour search using L1 metric") (description "This package provides tools to find the k nearest neighbours for every point in a given dataset in O(N log N) time using Arya and Mount's ANN library. There is support for approximate as well as exact searches, fixed radius searches and @code{bd} as well as @code{kd} trees. The distance is computed using the L1 (Manhattan, taxicab) metric.") (license license:gpl3+))) (define-public r-leiden (package (name "r-leiden") (version "0.4.3.1") (source (origin (method url-fetch) (uri (cran-uri "leiden" version)) (sha256 (base32 "1qihzjrwcb09aga27frcdrdv4dp0g295dbrk07fqykbjlb7vpv59")))) (properties `((upstream-name . "leiden"))) (build-system r-build-system) (propagated-inputs (list r-igraph r-matrix r-reticulate)) (native-inputs (list r-knitr)) (home-page "https://github.com/TomKellyGenetics/leiden") (synopsis "R implementation of Leiden clustering algorithm") (description "This package implements the Python @code{leidenalg} module to be called in R. It enables clustering using the Leiden algorithm for partitioning a graph into communities. See also Traag et al (2018) \"From Louvain to Leiden: guaranteeing well-connected communities.\" .") (license license:gpl3))) (define-public r-leidenalg (package (name "r-leidenalg") (version "1.1.3") (source (origin (method url-fetch) (uri (cran-uri "leidenAlg" version)) (sha256 (base32 "0g4gs6rrz3wn97ag7wsfr6qa4zgb75i0k9jc1siii4pf6h689d1x")))) (properties `((upstream-name . "leidenAlg") (updater-extra-inputs . ("gmp")))) (build-system r-build-system) (inputs (list glpk gmp libxml2)) (propagated-inputs (list r-igraph r-matrix r-rcpp r-rcpparmadillo r-rcppeigen r-sccore)) (native-inputs (list gfortran)) (home-page "https://github.com/kharchenkolab/leidenAlg") (synopsis "Leiden algorithm via an R interface") (description "This package implements an R interface to the Leiden algorithm, an iterative community detection algorithm on networks. The algorithm is designed to converge to a partition in which all subsets of all communities are locally optimally assigned, yielding communities guaranteed to be connected. The implementation proves to be fast, scales well, and can be run on graphs of millions of nodes (as long as they can fit in memory).") ;; The DESCRIPTION file says GPL-3, but the code was copied from ;; https://github.com/vtraag/leidenalg, which is under GPLv3+. (license license:gpl3+))) (define-public r-patchwork (package (name "r-patchwork") (version "1.2.0") (source (origin (method url-fetch) (uri (cran-uri "patchwork" version)) (sha256 (base32 "18b83gsv8idi5d062m9dvb46r7kxda97sa72pzllshhcaq9ylcfc")))) (build-system r-build-system) (propagated-inputs (list r-cli r-ggplot2 r-gtable r-rlang)) (native-inputs (list r-knitr)) (home-page "https://github.com/thomasp85/patchwork") (synopsis "Compose ggplot2 plots") (description "The @code{ggplot2} package provides a strong API for sequentially building up a plot, but does not concern itself with composition of multiple plots. Patchwork is a package that expands the API to allow for arbitrarily complex composition of plots by providing mathematical operators for combining multiple plots.") (license license:expat))) (define-public r-rliger (package (name "r-rliger") (version "0.4.2") (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/MacoskoLab/liger") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 (base32 "16dzwwcpw6n78pxlc5w3kraigki35ix7zhd2cbx5f3y60bbkhlmx")) (modules '((guix build utils))) (snippet '(delete-file "inst/java/ModularityOptimizer.jar")))) (build-system r-build-system) (arguments (list #:modules '((guix build r-build-system) ((guix build ant-build-system) #:prefix ant:) (guix build utils)) #:imported-modules `((guix build ant-build-system) ,@%r-build-system-modules) #:phases '(modify-phases %standard-phases (add-after 'unpack 'build-java-part (lambda* (#:key inputs #:allow-other-keys) (invoke "unzip" (assoc-ref inputs "optimizer-src")) (for-each (lambda (file) (invoke "javac" file)) (find-files "." "\\.java$")) (apply invoke "jar" "cf" "inst/java/ModularityOptimizer.jar" (find-files "." "\\.class$")))) (add-after 'install 'strip-jar-timestamps (assoc-ref ant:%standard-phases 'strip-jar-timestamps))))) (propagated-inputs (list r-cowplot r-dosnow r-dplyr r-fnn r-foreach r-ggplot2 r-ggrepel r-hmisc r-ica r-irlba r-matrix r-mclust r-patchwork r-plyr r-rann-l1 r-rcpp r-rcpparmadillo r-riverplot r-rtsne r-snow)) (native-inputs `(("jdk" ,icedtea "jdk") ;; See https://github.com/MacoskoLab/liger/issues/96 ;; The optimizer is released under the Expat license. ("optimizer-src" ,(origin (method url-fetch) (uri "http://www.ludowaltman.nl/slm/modularity_optimizer_source.zip") (sha256 (base32 "01hmm6sapcmldvayknqx2w4cav3qv71mwwkdkwj4qgq6dss09g18")))) ("unzip" ,unzip) ("zip" ,zip) ("r-knitr" ,r-knitr))) ; for vignettes (home-page "https://github.com/MacoskoLab/liger") (synopsis "Integrate and analyze multiple single-cell datasets") (description "LIGER is a package for integrating and analyzing multiple single-cell datasets, developed and maintained by the Macosko lab. It relies on integrative non-negative matrix factorization to identify shared and dataset-specific factors.") (license license:gpl3))) (define-public r-liger (deprecated-package "r-liger" r-rliger)) (define-public r-harmony (package (name "r-harmony") (version "1.2.0") (source (origin (method url-fetch) (uri (cran-uri "harmony" version)) (sha256 (base32 "1df7bb9ba3m0c44fhmh8cs4hlkh4fffjwm8rz7l87lf5pdy7sg56")))) (properties `((upstream-name . "harmony"))) (build-system r-build-system) (propagated-inputs (list r-cowplot r-dplyr r-ggplot2 r-matrix r-rcpp r-rcpparmadillo r-rcppprogress r-rhpcblasctl r-rlang r-tibble)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/harmony/index.html") (synopsis "Integration of single cell sequencing data") (description "This package provides an implementation of the Harmony algorithm for single cell integration. This package includes a standalone Harmony function and interfaces to external frameworks.") (license license:gpl3))) (define-public r-covr (package (name "r-covr") (version "3.6.4") (source (origin (method url-fetch) (uri (cran-uri "covr" version)) (sha256 (base32 "0al6n4gnnvgxk968skqnajpqpqyl6kpam3fmn782kihhcl1h8qib")) (modules '((guix build utils))) ;; TODO: still need to replace highlight.js/highlight.pack.js (snippet '(with-directory-excursion "inst/www/shared" (for-each delete-file '("bootstrap/js/bootstrap.min.js" "bootstrap/shim/html5shiv.min.js" "bootstrap/shim/respond.min.js")))))) (properties `((upstream-name . "covr"))) (build-system r-build-system) (arguments (list #:modules '((guix build utils) (guix build r-build-system) (srfi srfi-1)) #:phases #~(modify-phases %standard-phases (add-after 'unpack 'process-javascript (lambda* (#:key inputs #:allow-other-keys) (with-directory-excursion "inst/www/shared" (call-with-values (lambda () (unzip2 `((,(search-input-file inputs "/dist/js/bootstrap.js") "bootstrap/js/bootstrap.min.js") (,(search-input-file inputs "/dist/html5shiv.js") "bootstrap/shim/html5shiv.min.js") (,(search-input-file inputs "/dest/respond.src.js") "bootstrap/shim/respond.min.js")))) (lambda (sources targets) (for-each (lambda (source target) (format #true "Processing ~a --> ~a~%" source target) (invoke "esbuild" source "--minify" (string-append "--outfile=" target))) sources targets))))))))) (propagated-inputs (list r-crayon r-digest r-httr r-jsonlite r-rex r-withr r-yaml)) (native-inputs (list esbuild r-knitr ;for vignettes (let ((version "3.3.5")) (origin (method git-fetch) (uri (git-reference (url "https://github.com/twbs/bootstrap") (commit (string-append "v" version)))) (file-name (git-file-name "js-bootstrap" version)) (sha256 (base32 "1zxrjhnnd594rflnwzqhbx3rx0gjlh6hgx9v2nppgkmrkqb7y1a4")))) (let ((version "3.7.2")) (origin (method git-fetch) (uri (git-reference (url "https://github.com/aFarkas/html5shiv") (commit version))) (file-name (git-file-name "js-html5shiv" version)) (sha256 (base32 "0mw4bbl9a9d1ibywscjgmbky0jkj4081l1yd4x3ss0flwaa3fwsk")))) (let ((version "1.4.2")) (origin (method git-fetch) (uri (git-reference (url "https://github.com/scottjehl/Respond") (commit version))) (file-name (git-file-name "js-respond" version)) (sha256 (base32 "00xid731rirc7sdy1gc8qal3v9g0agr2qx15hm4x97l1lcbylyn2")))))) (home-page "https://github.com/r-lib/covr") (synopsis "Test coverage for R packages") (description "Thisp package enables you to track and report code coverage for your package and (optionally) upload the results to a coverage service. Code coverage is a measure of the amount of code being exercised by a set of tests. It is an indirect measure of test quality and completeness. This package is compatible with any testing methodology or framework and tracks coverage of both R code and compiled C/C++/FORTRAN code.") (license license:gpl3))) (define-public r-systemfonts (package (name "r-systemfonts") (version "1.0.6") (source (origin (method url-fetch) (uri (cran-uri "systemfonts" version)) (sha256 (base32 "1mqxb2njfnk5rfwkqc940xbpwd3dh25zac4sapv5mjyddrxnwn6i")))) (properties `((upstream-name . "systemfonts"))) (build-system r-build-system) (propagated-inputs (list r-cpp11)) (inputs (list fontconfig freetype zlib)) (native-inputs (list pkg-config r-knitr)) (home-page "https://github.com/r-lib/systemfonts") (synopsis "System native font finding") (description "This package 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 for finding font files that can then be used further by e.g. graphic devices.") (license license:expat))) (define-public r-graphlayouts (package (name "r-graphlayouts") (version "1.1.1") (source (origin (method url-fetch) (uri (cran-uri "graphlayouts" version)) (sha256 (base32 "009q5y46lbizdabbb6a61xlfa3g5lf3nd9w42709lcxi0ad4bhkv")))) (properties `((upstream-name . "graphlayouts"))) (build-system r-build-system) (propagated-inputs (list r-igraph r-rcpp r-rcpparmadillo)) (native-inputs (list r-knitr)) (home-page "https://github.com/schochastics/graphlayouts") (synopsis "Additional layout algorithms for network visualizations") (description "This package provides several layout algorithms to visualize networks which are not part of the igraph library. Most are based on the concept of stress majorization by Gansner et al. (2004) . Some more specific algorithms emphasize hidden group structures in networks or focus on specific nodes.") (license license:expat))) (define-public r-terra (package (name "r-terra") (version "1.7-71") (source (origin (method url-fetch) (uri (cran-uri "terra" version)) (sha256 (base32 "0dq47d5irkplgxcv0h0xgawwf9cc48vygg94zdiqppg5cspz7dqx")))) (properties `((upstream-name . "terra"))) (build-system r-build-system) (inputs (list curl gdal geos openssh openssl pcre2 proj sqlite zlib)) (propagated-inputs (list r-rcpp)) (native-inputs (list pkg-config)) (home-page "https://rspatial.org/terra") (synopsis "Spatial data analysis") (description "This package provides methods for spatial data analysis, especially raster data. The included methods allow for low-level data manipulation as well as high-level global, local, zonal, and focal computation. The predict and interpolate methods facilitate the use of regression type (interpolation, machine learning) models for spatial prediction. Processing of very large files is supported.") (license license:gpl3+))) (define-public r-tidygraph (package (name "r-tidygraph") (version "1.3.1") (source (origin (method url-fetch) (uri (cran-uri "tidygraph" version)) (sha256 (base32 "06mc31yb771midi8lq0zdfymcsm2s4y1mqdxxjz1n24njfxx9hda")))) (properties `((upstream-name . "tidygraph"))) (build-system r-build-system) (propagated-inputs (list r-cli r-cpp11 r-dplyr r-igraph r-lifecycle r-magrittr r-pillar r-r6 r-rlang r-tibble r-tidyr)) (home-page "https://github.com/thomasp85/tidygraph") (synopsis "Tidy API for graph manipulation") (description "This package provides a graph implementation that can be thought of as two tidy data frames describing node and edge data respectively. It provides an approach to manipulate these two virtual data frames using the API defined in the @code{dplyr} package, and it also provides tidy interfaces to a lot of common graph algorithms.") (license license:expat))) (define-public r-soupx (let ((commit "a3354be76fb52fd795be6ddf163cf056c05c6cb8") (revision "1")) (package (name "r-soupx") (version (git-version "0.3.1" revision commit)) (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/constantAmateur/SoupX") (commit commit))) (file-name (git-file-name name version)) (sha256 (base32 "1zmlyzrl0fz6l79gn2wswid670p88mm3y292is89sa5p3h7frr99")))) (properties `((upstream-name . "SoupX"))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-matrix r-seurat)) (home-page "https://github.com/constantAmateur/SoupX") (synopsis "Single cell mRNA Soup eXterminator") (description "This package provides a package for quantifying, profiling and removing cell free mRNA contamination (the \"soup\") from droplet based single cell RNA-seq experiments.") (license license:gpl2)))) (define-public r-assertr (package (name "r-assertr") (version "3.0.1") (source (origin (method url-fetch) (uri (cran-uri "assertr" version)) (sha256 (base32 "0g7h88kkls6v1nfzbar40y56yv3lkqb7vrcy63xqgc99zcf8k4bc")))) (build-system r-build-system) (propagated-inputs (list r-dplyr r-mass r-rlang)) (native-inputs (list r-knitr)) ; needed for vignette (home-page "https://github.com/ropensci/assertr") (synopsis "Assertive programming for R analysis pipelines") (description "This package provides functionality to assert conditions that have to be met so that errors in data used in analysis pipelines can fail quickly. It is similar to @code{stopifnot()} but more powerful, friendly, and easier for use in pipelines.") (license license:expat))) (define-public r-parameters (package (name "r-parameters") (version "0.21.6") (source (origin (method url-fetch) (uri (cran-uri "parameters" version)) (sha256 (base32 "004ld3m9qdq3bwl8qmp3h700kzqlgbmgz739d7fpiqgrs0s2gv83")))) (properties `((upstream-name . "parameters"))) (build-system r-build-system) (propagated-inputs (list r-bayestestr r-datawizard r-insight)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/parameters") (synopsis "Processing of model parameters") (description "This package provides utilities for processing the parameters of various statistical models. Beyond computing p values, CIs, and other indices for a wide variety of models, this package implements features like standardization or bootstrapping of parameters and models, feature reduction (feature extraction and variable selection) as well as conversion between indices of effect size.") (license license:gpl3))) (define-public r-rgdal (package (name "r-rgdal") (version "1.6-7") (source (origin (method url-fetch) (uri (cran-uri "rgdal" version)) (sha256 (base32 "0cxfmm7niixw3dnbqm7a00603dyqjrphajqx0q5vjpdhmpyysp2m")))) (properties `((upstream-name . "rgdal") (updater-extra-inputs . ("gdal" "proj")) ;; These are only needed for Windows (updater-ignored-inputs . ("curl" "openssl" "openssh" "pcre2")))) (build-system r-build-system) (inputs (list gdal proj zlib)) (propagated-inputs (list r-sp)) (native-inputs (list pkg-config r-knitr)) (home-page "https://rgdal.r-forge.r-project.org") (synopsis "Bindings for the Geospatial Data Abstraction Library") (description "This package provides bindings to the Geospatial Data Abstraction Library (GDAL) and access to projection/transformation operations from the PROJ.4 library.") (license license:gpl2+))) (define-public r-insol (package (name "r-insol") (version "1.2.2") (source (origin (method url-fetch) (uri (cran-uri "insol" version)) (sha256 (base32 "166kgxgzbh55y2qqya6c2si22x0v7asi70im054g6xxwc5187kh3")))) (properties `((upstream-name . "insol"))) (build-system r-build-system) (propagated-inputs (list r-raster)) (native-inputs (list gfortran)) (home-page "https://meteoexploration.com/R/insol/index.html") (synopsis "Tools for calculating solar radiation") (description "This package provides functions to compute insolation on tilted surfaces, computes atmospheric transmittance and related parameters such as: Earth radius vector, declination, sunset and sunrise, daylength, equation of time, vector in the direction of the sun, vector normal to surface, and some atmospheric physics.") (license license:gpl2+))) (define-public r-lifecycle (package (name "r-lifecycle") (version "1.0.4") (source (origin (method url-fetch) (uri (cran-uri "lifecycle" version)) (sha256 (base32 "1k4ibf2x90xgmzaq47vf9wrsh6a2fp2lg1l8bq89632bx33x795d")))) (build-system r-build-system) (propagated-inputs (list r-cli r-glue r-rlang)) (properties ;; We can't add this here because via r-stringr this package ends up ;; being an input to r-knitr. '((updater-ignored-native-inputs . ("r-knitr")) (upstream-name . "lifecycle"))) (home-page "https://github.com/r-lib/lifecycle") (synopsis "Manage the life cycle of your package functions") (description "Manage the life cycle of your exported functions with shared conventions, documentation badges, and non-invasive deprecation warnings. The lifecycle package defines four development stages (experimental, maturing, stable, and questioning) and three deprecation stages (soft-deprecated, deprecated, and defunct). It makes it easy to insert badges corresponding to these stages in your documentation. Usage of deprecated functions are signalled with increasing levels of non-invasive verbosity.") (license license:gpl3))) (define-public r-assertable (package (name "r-assertable") (version "0.2.8") (source (origin (method url-fetch) (uri (cran-uri "assertable" version)) (sha256 (base32 "1cciil1nzxd8gbj49w99jiv077lbpb59vx7bmb4p218aj2h5hqq4")))) (build-system r-build-system) (propagated-inputs (list r-data-table)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/assertable/") (synopsis "Verbose assertions for tabular data (data.frames and data.tables)") (description "This package provides simple, flexible assertions on data.frame or data.table objects with verbose output for vetting. While other assertion packages apply towards more general use-cases, @code{assertable} is tailored towards tabular data. It includes functions to check variable names and values, whether the dataset contains all combinations of a given set of unique identifiers, and whether it is a certain length. In addition, @code{assertable} includes utility functions to check the existence of target files and to efficiently import multiple tabular data files into one data.table.") (license license:gpl3))) (define-public r-quadprog (package (name "r-quadprog") (version "1.5-8") (source (origin (method url-fetch) (uri (cran-uri "quadprog" version)) (sha256 (base32 "1ka9g8zak8sg4y2xbz93dfrldznlk9qpd4pq9z21cdcdn3b8s4i2")))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/quadprog") (synopsis "Functions to solve quadratic programming problems") (description "This package contains routines and documentation for solving quadratic programming problems.") (license license:gpl3+))) (define-public r-desolve (package (name "r-desolve") (version "1.40") (source (origin (method url-fetch) (uri (cran-uri "deSolve" version)) (sha256 (base32 "1vq0yli1pkk3z92x1jgm4z19zwwhnwqdxvj4k2dmcnw7nrmsw2cc")))) (properties `((upstream-name . "deSolve"))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "https://desolve.r-forge.r-project.org/") (synopsis "Solvers for initial value problems of differential equations") (description "This package provides functions that solve initial value problems of a system of first-order @dfn{ordinary differential equations} (ODE), of @dfn{partial differential equations} (PDE), of @dfn{differential algebraic equations} (DAE), and of delay differential equations. The functions provide an interface to the FORTRAN functions @code{lsoda}, @code{lsodar}, @code{lsode}, @code{lsodes} of the ODEPACK collection, to the FORTRAN functions @code{dvode} and @code{daspk} and a C-implementation of solvers of the Runge-Kutta family with fixed or variable time steps. The package contains routines designed for solving ODEs resulting from 1-D, 2-D and 3-D partial differential equations that have been converted to ODEs by numerical differencing.") (license license:gpl2+))) (define-public r-pmcmrplus (package (name "r-pmcmrplus") (version "1.9.10") (source (origin (method url-fetch) (uri (cran-uri "PMCMRplus" version)) (sha256 (base32 "0w0zxlq80n673zlrfw46qzidwshc6rxsqka6pahbr816zabzi0yq")))) (properties `((upstream-name . "PMCMRplus"))) (build-system r-build-system) (inputs (list gmp)) (propagated-inputs (list r-bwstest r-gmp r-ksamples r-mass r-multcompview r-mvtnorm r-rmpfr r-suppdists)) (native-inputs (list gfortran r-knitr r-rmarkdown)) (home-page "https://cran.r-project.org/package=PMCMRplus") (synopsis "Calculate pairwise multiple comparisons of mean rank sums extended") (description "This package provides multiple pairwise tests.") (license license:gpl3+))) (define-public r-pracma (package (name "r-pracma") (version "2.4.4") (source (origin (method url-fetch) (uri (cran-uri "pracma" version)) (sha256 (base32 "0zxsqr7f4pcr1nmbbzliihyldv091ykzajv1mbdrkycp46pz6khs")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/pracma/") (synopsis "Practical numerical math functions") (description "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.") (license license:gpl3+))) (define-public r-subplex (package (name "r-subplex") (version "1.8") (source (origin (method url-fetch) (uri (cran-uri "subplex" version)) (sha256 (base32 "19g5bd39gmcn27xdsklkzxg99x1r5v5q8zcw1iwry31qj24ivhrv")))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/subplex") (synopsis "Unconstrained optimization using the subplex algorithm") (description "This package implements the Subplex optimization algorithm. It solves unconstrained optimization problems using a simplex method on subspaces. The method is well suited for optimizing objective functions that are noisy or are discontinuous at the solution.") (license license:gpl3+))) (define-public r-txtplot (package (name "r-txtplot") (version "1.0-4") (source (origin (method url-fetch) (uri (cran-uri "txtplot" version)) (sha256 (base32 "00sriml48y70j18jz235dsfm5x3a81bnzskfp3hnv6cbjwwsmca4")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/txtplot/") (synopsis "Text-based plotting") (description "This package provides functions to produce rudimentary ASCII graphics directly in the terminal window. This package provides a basic plotting function (and equivalents of curve, density, acf and barplot) as well as a boxplot function.") (license license:lgpl3+))) (define-public r-bio3d (package (name "r-bio3d") (version "2.4-4") (source (origin (method url-fetch) (uri (cran-uri "bio3d" version)) (sha256 (base32 "1scxzmh22ca0nmpkvapsdcmq3n06j2wy74ljz1g27r1k1p0ylm2n")))) (properties `((upstream-name . "bio3d"))) (build-system r-build-system) (inputs (list zlib)) (propagated-inputs (list r-rcpp)) (native-inputs (list r-knitr)) (home-page "http://thegrantlab.org/bio3d/") (synopsis "Biological structure analysis") (description "This package provides utilities to process, organize and explore protein structure, sequence and dynamics data. Features include the ability to read and write structure, sequence and dynamic trajectory data, perform sequence and structure database searches, data summaries, atom selection, alignment, superposition, rigid core identification, clustering, torsion analysis, distance matrix analysis, structure and sequence conservation analysis, normal mode analysis, principal component analysis of heterogeneous structure data, and correlation network analysis from normal mode and molecular dynamics data. In addition, various utility functions are provided to enable the statistical and graphical power of the R environment to work with biological sequence and structural data.") (license license:gpl2+))) (define-public r-bios2cor (package (name "r-bios2cor") (version "2.2.1") (source (origin (method url-fetch) (uri (cran-uri "Bios2cor" version)) (sha256 (base32 "0xj7ab9a463p4a67y0hlv6mfd08xf8didkn2mwrfa7gxjqqvix4z")))) (properties `((upstream-name . "Bios2cor"))) (build-system r-build-system) (propagated-inputs (list r-bigmemory r-bio3d r-circular r-igraph)) (home-page "https://cran.r-project.org/web/packages/Bios2cor/") (synopsis "From biological sequences and simulations to correlation analysis") (description "This package provides utilities for computation and analysis of correlation/covariation in multiple sequence alignments and in side chain motions during molecular dynamics simulations. Features include the computation of correlation/covariation scores using a variety of scoring functions between either sequence positions in alignments or side chain dihedral angles in molecular dynamics simulations and utilities to analyze the correlation/covariation matrix through a variety of tools including network representation and principal components analysis. In addition, several utility functions are based on the R graphical environment to provide friendly tools for help in data interpretation.") (license license:gpl2+))) ;; This package includes minified JavaScript files. When upgrading please ;; check that there are no new minified JavaScript files. (define-public r-networkd3 (package (name "r-networkd3") (version "0.4") (source (origin (method url-fetch) (uri (cran-uri "networkD3" version)) (sha256 (base32 "02wxki67drppgfka1is1ykg1f2rxf0x0657c0crj7ipfy62jbf1k")) (snippet '(begin (delete-file "inst/htmlwidgets/lib/d3-4.5.0/d3.min.js") #t)))) (properties `((upstream-name . "networkD3"))) (build-system r-build-system) (arguments `(#:modules ((guix build utils) (guix build r-build-system) (srfi srfi-1) (ice-9 popen)) #:phases (modify-phases %standard-phases (add-after 'unpack 'process-javascript (lambda* (#:key inputs #:allow-other-keys) (with-directory-excursion "inst/htmlwidgets/lib/" (call-with-values (lambda () (unzip2 `((,(assoc-ref inputs "d3.v4.js") "d3-4.5.0/d3.min.js")))) (lambda (sources targets) (for-each (lambda (source target) (format #t "Processing ~a --> ~a~%" source target) (let ((minified (open-pipe* OPEN_READ "uglifyjs" source))) (call-with-output-file target (lambda (port) (dump-port minified port))))) sources targets)))) #t))))) (native-inputs `(("uglifyjs" ,node-uglify-js) ;; NOTE: Make sure that this version of d3 is still valid when ;; upgrading the package. 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(2006), ``Improved Long-Period Generators Based on Linear Recurrences Modulo 2'', ACM Transactions on Mathematical Software.") (license license:bsd-3))) (define-public r-rnmf (package (name "r-rnmf") (version "0.5.0") (source (origin (method url-fetch) (uri (cran-uri "rNMF" version)) (sha256 (base32 "1nz6h0j5ywdh48m0swmhp34hbkycd7n13rclrxaw85qi9wc42597")))) (build-system r-build-system) (propagated-inputs (list r-knitr r-nnls)) (home-page "https://cran.r-project.org/web/packages/rNMF/") (synopsis "Robust nonnegative matrix factorization") (description "This package provides an implementation of robust nonnegative matrix factorization (rNMF). The rNMF algorithm decomposes a nonnegative high dimension data matrix into the product of two low rank nonnegative matrices, while detecting and trimming outliers. The main function is @code{rnmf()}. The package also includes a visualization tool, @code{see()}, that arranges and prints vectorized images.") (license license:gpl2+))) (define-public r-randtoolbox (package (name "r-randtoolbox") (version "2.0.4") (source (origin (method url-fetch) (uri (cran-uri "randtoolbox" version)) (sha256 (base32 "0jwylffr8zajgd1x24nrv4xxlkic10i8cfd9sy0pkz2g7sai9nll")))) (properties `((upstream-name . "randtoolbox"))) (build-system r-build-system) (propagated-inputs (list r-rngwell)) (home-page "https://cran.r-project.org/web/packages/randtoolbox/") (synopsis "Toolbox for pseudo and quasi random number generation") (description "This package provides @enumerate @item pseudo random generators, such as general linear congruential generators, multiple recursive generators and generalized feedback shift register (SF-Mersenne Twister algorithm and WELL generators) @item quasi random generators, such as the Torus algorithm, the Sobol sequence, the Halton sequence (including the Van der Corput sequence), and @item some generator tests: the gap test, the serial test, the poker test. @end enumerate See e.g. Gentle (2003) @url{doi:10.1007/b97336}.") (license license:bsd-3))) (define-public r-lhs (package (name "r-lhs") (version "1.1.6") (source (origin (method url-fetch) (uri (cran-uri "lhs" version)) (sha256 (base32 "0gyjdic714pqvq2jv1v0vh7hl9s83sg2zxx2gdkp38z6xx2cwzz3")))) (properties `((upstream-name . "lhs"))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) (native-inputs (list r-knitr)) (home-page "https://github.com/bertcarnell/lhs") (synopsis "Latin Hypercube Samples") (description "This package provides a number of methods for creating and augmenting Latin Hypercube Samples.") (license license:gpl3))) (define-public r-acebayes (package (name "r-acebayes") (version "1.10") (source (origin (method url-fetch) (uri (cran-uri "acebayes" version)) (sha256 (base32 "11bffz430gdfdaxjx3simig66vhynmx6l1ylac4q2shcmj52nx73")))) (properties `((upstream-name . "acebayes"))) (build-system r-build-system) (propagated-inputs (list r-compare r-lhs r-randtoolbox r-rcpp r-rcpparmadillo)) (home-page "https://cran.r-project.org/web/packages/acebayes/") (synopsis "Optimal Bayesian experimental design using the ACE algorithm") (description "Finding an optimal Bayesian experimental design involves maximizing an objective function given by the expectation of some appropriately chosen utility function with respect to the joint distribution of unknown quantities (including responses). This objective function is usually not available in closed form and the design space can be continuous and of high dimensionality. This package uses @dfn{Approximate Coordinate Exchange} (ACE) to maximise an approximation to the expectation of the utility function.") (license license:gpl2))) (define-public r-acet (package (name "r-acet") (version "1.9.0") (source (origin (method url-fetch) (uri (cran-uri "ACEt" version)) (sha256 (base32 "1071d75sw5bcfw1acjsg6bn81sapb5hkwrxjfrfxlz5r83w6213f")))) (properties `((upstream-name . "ACEt"))) (build-system r-build-system) (propagated-inputs (list r-bh r-mass r-rcpp r-rcpparmadillo)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/ACEt/") (synopsis "Estimating dynamic heritability and twin model comparison") (description "This package supports twin models that are able to estimate the dynamic behaviour of the variance components in the classical twin models with respect to age using B-splines and P-splines.") (license license:gpl2+))) (define-public r-acfmperiod (package (name "r-acfmperiod") (version "1.0.0") (source (origin (method url-fetch) (uri (cran-uri "acfMPeriod" version)) (sha256 (base32 "1yww8isfrbs2v9s94hx7p2imyszcgadwafdgpj438n2ik0q6p9d5")))) (properties `((upstream-name . "acfMPeriod"))) (build-system r-build-system) (propagated-inputs (list r-mass)) (home-page "https://cran.r-project.org/web/packages/acfMPeriod/") (synopsis "Estimation of the ACF from the M-periodogram") (description "This package support non-robust and robust computations of the sample autocovariance (ACOVF) and sample autocorrelation functions (ACF) of univariate and multivariate processes. The methodology consists in reversing the diagonalization procedure involving the periodogram or the cross-periodogram and the Fourier transform vectors, and, thus, obtaining the ACOVF or the ACF as discussed in Fuller (1995) @url{doi:10.1002/9780470316917}. The robust version is obtained by fitting robust M-regressors to obtain the M-periodogram or M-cross-periodogram as discussed in Reisen et al. (2017) @url{doi:10.1016/j.jspi.2017.02.008}.") (license license:gpl2+))) (define-public r-gamlss-data (package (name "r-gamlss-data") (version "6.0-6") (source (origin (method url-fetch) (uri (cran-uri "gamlss.data" version)) (sha256 (base32 "08mb154mz1kk19zb414i5mg1q1yv7nylwpc5kzsb602mv4cxpq5s")))) (properties `((upstream-name . "gamlss.data"))) (build-system r-build-system) (home-page "http://www.gamlss.org/") (synopsis "GAMLSS data") (description "This package provides data used as examples to demonstrate GAMLSS models.") ;; Either version of the license (license (list license:gpl2 license:gpl3)))) (define-public r-gamlss (package (name "r-gamlss") (version "5.4-22") (source (origin (method url-fetch) (uri (cran-uri "gamlss" version)) (sha256 (base32 "0bgya6jb462ggqnmlpwdymxqvqbkah15i3aai1xi9496z66r1rh1")))) (properties `((upstream-name . "gamlss"))) (build-system r-build-system) (propagated-inputs (list r-gamlss-data r-gamlss-dist r-mass r-nlme r-survival)) (home-page "http://www.gamlss.org/") (synopsis "Generalized additive models for location scale and shape") (description "This package provides functions for fitting the generalized additive models for location scale and shape introduced by Rigby and Stasinopoulos (2005), @url{doi:10.1111/j.1467-9876.2005.00510.x}. The models use a distributional regression approach where all the parameters of the conditional distribution of the response variable are modelled using explanatory variables.") ;; Either version of the license (license (list license:gpl2 license:gpl3)))) (define-public r-acid (package (name "r-acid") (version "1.1") (source (origin (method url-fetch) (uri (cran-uri "acid" version)) (sha256 (base32 "030i0y8s283ivbsmjccpbv9v7mgbcg2jk9df7vgcbbns74swf9hd")))) (properties `((upstream-name . "acid"))) (build-system r-build-system) (propagated-inputs (list r-gamlss r-gamlss-dist r-hmisc)) (home-page "https://cran.r-project.org/web/packages/acid/") (synopsis "Analysing conditional income distributions") (description "This package provides functions for the analysis of income distributions for subgroups of the population as defined by a set of variables like age, gender, region, etc. This entails a Kolmogorov-Smirnov test for a mixture distribution as well as functions for moments, inequality measures, entropy measures and polarisation measures of income distributions. This package thus aides the analysis of income inequality by offering tools for the exploratory analysis of income distributions at the disaggregated level.") (license license:gpl3))) (define-public r-acm4r (package (name "r-acm4r") (version "1.0") (source (origin (method url-fetch) (uri (cran-uri "acm4r" version)) (sha256 (base32 "1wqzc35i1rshx0zlmas8y4qkkvy6h9r4i4apscjjv1xg2wjflzxa")))) (properties `((upstream-name . "acm4r"))) (build-system r-build-system) (propagated-inputs (list r-mass)) (home-page "https://cran.r-project.org/web/packages/acm4r/") (synopsis "Align-and-count method comparisons of RFLP data") (description "This is a package to compare sequence fragment lengths or molecular weights from pairs of lanes. The number of matching bands in the @dfn{Restriction Fragment Length Polymorphism} (RFLP) data is calculated using the align-and-count method.") ;; Any version of the GPL (license (list license:gpl2+ license:gpl3+)))) (define-public r-filelock (package (name "r-filelock") (version "1.0.3") (source (origin (method url-fetch) (uri (cran-uri "filelock" version)) (sha256 (base32 "0dqi0w92zq1f9542ma2nk5gkqzfmd4jlf34vysb4vv7mag20xk9d")))) (properties `((upstream-name . "filelock"))) (build-system r-build-system) (home-page "https://github.com/r-lib/filelock") (synopsis "Portable file locking") (description "This library lets you place an exclusive or shared lock on a file using the appropriate system call provided by the underlying operating system.") (license license:expat))) (define-public r-filematrix (package (name "r-filematrix") (version "1.3") (source (origin (method url-fetch) (uri (cran-uri "filematrix" version)) (sha256 (base32 "1v3aj1ng742msb0sfdnjsbqb508mqjf8jlq2v33vxldhradw5w0b")))) (properties `((upstream-name . "filematrix"))) (build-system r-build-system) ;; These inputs are needed for vignettes (native-inputs (list r-knitr r-rmarkdown)) (home-page "https://github.com/andreyshabalin/filematrix") (synopsis "File-backed matrix class with convenient read and write access") (description "This package provides an interface for working with large matrices stored in files, not in computer memory. It supports multiple non-character data types (double, integer, logical and raw) of various sizes (e.g. 8 and 4 byte real values). Access to parts of the matrix is done by indexing, exactly as with usual R matrices. It supports very large matrices; the package has been tested on multi-terabyte matrices. It allows for more than 2^32 rows or columns, ad allows for quick addition of extra columns to a filematrix.") (license license:lgpl3))) (define-public r-filesstrings (package (name "r-filesstrings") (version "3.4.0") (source (origin (method url-fetch) (uri (cran-uri "filesstrings" version)) (sha256 (base32 "0p5vgrzbvipja9lgarygqphnr1z8vy9kl9n83jnfyvf0gp4ansl2")))) (properties `((upstream-name . "filesstrings"))) (build-system r-build-system) (propagated-inputs (list r-checkmate r-magrittr r-purrr r-rlang r-strex r-stringi r-stringr r-withr)) (native-inputs (list r-knitr)) (home-page "https://github.com/rorynolan/filesstrings") (synopsis "Handy file and string manipulation") (description "This started out as a package for file and string manipulation. Since then, the @code{fs} and @code{strex} packages emerged, offering functionality previously given by this package. Those packages have hence almost pushed filesstrings into extinction. However, it still has a small number of unique, handy file manipulation functions which can be seen in the vignette. One example is a function to remove spaces from all file names in a directory.") (license license:gpl3))) (define-public r-acmeeqtl (package (name "r-acmeeqtl") (version "1.6") (source (origin (method url-fetch) (uri (cran-uri "ACMEeqtl" version)) (sha256 (base32 "049xjv2ym35bbn43zwi68cq27fwdh404vp0r2ca5gxgmmx8kj1cz")))) (properties `((upstream-name . "ACMEeqtl"))) (build-system r-build-system) (propagated-inputs (list r-filematrix)) (home-page "https://github.com/andreyshabalin/ACMEeqtl") (synopsis "Estimation of interpretable eQTL effect sizes") (description "This package provides a non-linear model, termed ACME, that reflects a parsimonious biological model for allelic contributions of cis-acting eQTLs. With non-linear least-squares algorithm the maximum likelihood parameters can be estimated. The ACME model provides interpretable effect size estimates and p-values with well controlled Type-I error.") (license license:lgpl3))) (define-public r-acmer (package (name "r-acmer") (version "1.1.0") (source (origin (method url-fetch) (uri (cran-uri "acmeR" version)) (sha256 (base32 "000b2hqlhj93958nddw0fqb15ahigs08najv2miivym046x04mf7")))) (properties `((upstream-name . "acmeR"))) (build-system r-build-system) (propagated-inputs (list r-foreign)) (home-page "https://cran.r-project.org/web/packages/acmeR/") (synopsis "ACME estimator of bird and bat mortality by wind turbines") (description "This package provides an implementation of the ACME estimator, described in Wolpert (2015), ACME: A Partially Periodic Estimator of Avian & Chiropteran Mortality at Wind Turbines. Unlike most other models, this estimator supports decreasing-hazard Weibull model for persistence; decreasing search proficiency as carcasses age; variable bleed-through at successive searches; and interval mortality estimates. The package provides, based on search data, functions for estimating the mortality inflation factor in Frequentist and Bayesian settings.") (license license:expat))) (define-public r-r-huge (package (name "r-r-huge") (version "0.10.1") (source (origin (method url-fetch) (uri (cran-uri "R.huge" version)) (sha256 (base32 "1s3cg0kjaici6chgy21zhxwag9ldiif4103ajk121l8ambd1xjq5")))) (properties `((upstream-name . "R.huge"))) (build-system r-build-system) (propagated-inputs (list r-r-methodss3 r-r-oo r-r-utils)) (home-page "https://github.com/HenrikBengtsson/R.huge") (synopsis "Methods for accessing huge amounts of data") (description "This is a deprecated package for accessing huge amounts of data. Cross-platform alternatives are the following packages: bigmemory (CRAN), ff (CRAN), or BufferedMatrix (Bioconductor). The main usage of it was inside the @code{aroma.affymetrix} package.") (license license:lgpl2.1+))) (define-public r-r-filesets (package (name "r-r-filesets") (version "2.15.1") (source (origin (method url-fetch) (uri (cran-uri "R.filesets" version)) (sha256 (base32 "1qwxk3p56yq06nsdl0jwbw6j8r6qjakznsd3z63gnpsgkckfkx88")))) (properties `((upstream-name . "R.filesets"))) (build-system r-build-system) (arguments '(#:phases (modify-phases %standard-phases (add-after 'unpack 'set-HOME (lambda _ (setenv "HOME" "/tmp")))))) (propagated-inputs (list r-digest r-r-cache r-r-methodss3 r-r-oo r-r-utils)) (home-page "https://github.com/HenrikBengtsson/R.filesets") (synopsis "Easy handling of and access to files") (description "This package provides classes and methods to locate, setup, subset, navigate and iterate file sets, i.e. sets of files located in one or more directories on the file system. The API is designed such that these classes can be extended via inheritance to provide a richer API for special file formats. Moreover, a specific name format is defined such that filenames and directories can be considered to have full names which consists of a name followed by comma-separated tags. This adds additional flexibility to identify file sets and individual files.") (license license:lgpl2.1+))) (define-public r-r-devices (package (name "r-r-devices") (version "2.17.2") (source (origin (method url-fetch) (uri (cran-uri "R.devices" version)) (sha256 (base32 "15gcvhmqwqyl3n299l9znwcjri8d8vixwwv915162sfxabsylgj0")))) (properties `((upstream-name . "R.devices"))) (build-system r-build-system) (arguments (list #:phases '(modify-phases %standard-phases ;; This is needed for the vignette builder (add-after 'unpack 'set-HOME (lambda _ (setenv "HOME" "/tmp")))))) (propagated-inputs (list r-base64enc r-r-methodss3 r-r-oo r-r-utils)) (native-inputs (list r-r-rsp)) (home-page "https://github.com/HenrikBengtsson/R.devices") (synopsis "Unified handling of graphics devices") (description "This package provides functions for creating plots and image files in a unified way regardless of output format (EPS, PDF, PNG, SVG, TIFF, WMF, etc.). Default device options as well as scales and aspect ratios are controlled in a uniform way across all device types. Switching output format requires minimal changes in code. This package is ideal for large-scale batch processing, because it will never leave open graphics devices or incomplete image files behind, even on errors or user interrupts.") (license license:lgpl2.1+))) (define-public r-acnr (package (name "r-acnr") (version "1.0.0") (source (origin (method url-fetch) (uri (cran-uri "acnr" version)) (sha256 (base32 "087hq4i7jp67ba2finzsqjfnqbiprl33na6ryjv9zqzsdawj9cym")))) (properties `((upstream-name . "acnr"))) (build-system r-build-system) (home-page "https://github.com/mpierrejean/acnr") (synopsis "Annotated copy-number regions") (description "This package provides SNP array data from different types of copy-number regions. These regions were identified manually by the authors of the package and may be used to generate realistic data sets with known truth.") (license license:lgpl2.1+))) (define-public r-acopula (package (name "r-acopula") (version "0.9.4") (source (origin (method url-fetch) (uri (cran-uri "acopula" version)) (sha256 (base32 "0asxfcjrsr9d7ab59pdajs0zvdjgwfswk9rdlpfdr51535wpjrfy")))) (properties `((upstream-name . "acopula"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/acopula/") (synopsis "Modelling dependence with multivariate Archimax copulas") (description "Archimax copulas are a mixture of Archimedean and EV copulas. This package provides definitions of several parametric families of generator and dependence function, computes CDF and PDF, estimates parameters, tests for goodness of fit, generates random sample and checks copula properties for custom constructs. In the 2-dimensional case explicit formulas for density are used, contrary to higher dimensions when all derivatives are linearly approximated. Several non-archimax families (normal, FGM, Plackett) are provided as well.") (license license:gpl2))) (define-public r-tuner (package (name "r-tuner") (version "1.4.7") (source (origin (method url-fetch) (uri (cran-uri "tuneR" version)) (sha256 (base32 "02lnnsh2r22qg54ygdjjpd6986gqr5r3qbzxxrz34lq98jh58h9n")))) (properties `((upstream-name . "tuneR"))) (build-system r-build-system) (propagated-inputs (list r-signal)) (home-page "https://cran.r-project.org/web/packages/tuneR/") (synopsis "Analysis of music and speech") (description "This is a package for the analysis of music and speech. 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, ...") ;; Either of these versions. (license (list license:gpl2 license:gpl3)))) (define-public r-seewave (package (name "r-seewave") (version "2.2.3") (source (origin (method url-fetch) (uri (cran-uri "seewave" version)) (sha256 (base32 "13c48sn453yp4j0ap8slnnr2gfhlxasz926p2pazkrg817w7m28z")))) (properties `((upstream-name . "seewave"))) (build-system r-build-system) (inputs (list libsndfile)) (propagated-inputs (list r-tuner)) (home-page "https://rug.mnhn.fr/seewave") (synopsis "Sound analysis and synthesis") (description "This package provides functions for analysing, manipulating, displaying, editing and synthesizing time waves (particularly sound). This package processes time analysis (oscillograms and envelopes), spectral content, resonance quality factor, entropy, cross correlation and autocorrelation, zero-crossing, dominant frequency, analytic signal, frequency coherence, 2D and 3D spectrograms and many other analyses.") (license license:gpl2+))) (define-public r-acousticndlcoder (package (name "r-acousticndlcoder") (version "1.0.2") (source (origin (method url-fetch) (uri (cran-uri "AcousticNDLCodeR" version)) (sha256 (base32 "1fgzgwanpv2pzy74xdk3hamc44p8qch467wh163dxby8jr9ik0sb")))) (properties `((upstream-name . "AcousticNDLCodeR"))) (build-system r-build-system) (propagated-inputs (list r-seewave r-tuner r-zoo)) (home-page "https://cran.r-project.org/web/packages/AcousticNDLCodeR/") (synopsis "Coding sound files for use with NDL") (description "Make acoustic cues to use with the R package @code{ndl}. The package implements functions used in the PLoS ONE paper \"Words from spontaneous conversational speech can be recognized with human-like accuracy by an error-driven learning algorithm that discriminates between meanings straight from smart acoustic features, bypassing the phoneme as recognition unit.\" @url{doi:10.1371/journal.pone.0174623}") (license license:gpl2+))) (define-public r-acp (package (name "r-acp") (version "2.1") (source (origin (method url-fetch) (uri (cran-uri "acp" version)) (sha256 (base32 "0lcwbjcyyr32m6qjmjqh25qjwrbyqj1n092xhgbhxzd8fslppnmn")))) (properties `((upstream-name . "acp"))) (build-system r-build-system) (propagated-inputs (list r-quantmod r-tseries)) (home-page "https://cran.r-project.org/web/packages/acp/") (synopsis "Autoregressive conditional Poisson") (description "This package supports the analysis of count data exhibiting autoregressive properties, using the @dfn{Autoregressive Conditional Poisson} model (ACP(p,q)) proposed by Heinen (2003).") (license license:gpl2))) (define-public r-ada (package (name "r-ada") (version "2.0-5") (source (origin (method url-fetch) (uri (cran-uri "ada" version)) (sha256 (base32 "1h3a07czp0w3hrhjcg1fz721y8vsfclzqi3rq8qfzgpfb4h1f06r")))) (properties `((upstream-name . "ada"))) (build-system r-build-system) (propagated-inputs (list r-rpart)) (home-page "https://cran.r-project.org/web/packages/ada/") (synopsis "Stochastic boosting") (description "This package provides a straightforward, well-documented, and broad boosting routine for classification, ideally suited for small to moderate-sized data sets. It performs discrete, real, and gentle boost under both exponential and logistic loss on a given data set.") ;; Any version of the GPL. (license (list license:gpl2+ license:gpl3+)))) (define-public r-genalg (package (name "r-genalg") (version "0.2.1") (source (origin (method url-fetch) (uri (cran-uri "genalg" version)) (sha256 (base32 "1y4qz1s85zpd1r3259gr542arssf2vpd4drhy0wnq5q47ignrvna")))) (properties `((upstream-name . "genalg"))) (build-system r-build-system) (home-page "https://github.com/egonw/genalg") (synopsis "R based genetic algorithm") (description "This package provides an R based genetic algorithm for binary and floating point chromosomes.") (license license:gpl2))) (define-public r-kernelfactory (package (name "r-kernelfactory") (version "0.3.0") (source (origin (method url-fetch) (uri (cran-uri "kernelFactory" version)) (sha256 (base32 "001kw9k3ivd4drd4mwqapkkk3f4jgljiaprhg2630hmll064s89j")))) (properties `((upstream-name . "kernelFactory"))) (build-system r-build-system) (propagated-inputs (list r-auc r-genalg r-kernlab r-randomforest)) (home-page "https://cran.r-project.org/web/packages/kernelFactory/") (synopsis "Ensemble of kernel machines") (description "Kernel factory is an ensemble method where each base classifier (random forest) is fit on the kernel matrix of a subset of the training data.") (license license:gpl2+))) (define-public r-dummies (package (name "r-dummies") (version "1.5.6") (source (origin (method url-fetch) (uri (cran-uri "dummies" version)) (sha256 (base32 "01f84crqx17xd6xy55qxlvsj3knm8lhw7jl26p2rh2w3y0nvqlbm")))) (properties `((upstream-name . "dummies"))) (build-system r-build-system) (home-page "https://decisionpatterns.com") (synopsis "Create dummy/indicator variables flexibly and efficiently") (description "This package lets you expand factors, characters and other eligible classes into dummy/indicator variables.") (license license:gpl2+))) (define-public r-dunn-test (package (name "r-dunn-test") (version "1.3.6") (source (origin (method url-fetch) (uri (cran-uri "dunn.test" version)) (sha256 (base32 "0z3qyq0lnflmsx41dbkr5lwgiqf3z8rn5wy54c93fwmahva0lqs9")))) (properties `((upstream-name . "dunn.test"))) (build-system r-build-system) (home-page "https://cran.r-project.org/package=dunn.test") (synopsis "Dunn's test of multiple comparisons using rank sums") (description "Dunn's test computes stochastic dominance & reports pairwise comparisons. This is done following a Kruskal-Wallis test (Kruskal and Wallis, 1952). It employs Dunn's z-test-statistic approximations for rank statistics, conducting k(k-1)/2 comparisons. The null hypothesis assumes that the probability of a randomly selected value from the first group being larger than one from the second group is one half, similar to the Wilcoxon-Mann-Whitney test. Dunn's test serves as a test for median difference and takes into account tied ranks.") (license license:gpl2))) (define-public r-acrm (package (name "r-acrm") (version "0.1.1") (source (origin (method url-fetch) (uri (cran-uri "aCRM" version)) (sha256 (base32 "0kzp568hd9c9a9qgniia5s5gv0q5f89xfvvwpzb197gqhs3x092v")))) (properties `((upstream-name . "aCRM"))) (build-system r-build-system) (propagated-inputs (list r-ada r-dummies r-kernelfactory r-randomforest)) (home-page "https://cran.r-project.org/web/packages/aCRM/") (synopsis "Convenience functions for analytical customer relationship management") (description "This package provides convenience functions for data preparation and modeling often used in @dfn{analytical customer relationship management} (aCRM).") (license license:gpl2+))) (define-public r-tree (package (name "r-tree") (version "1.0-43") (source (origin (method url-fetch) (uri (cran-uri "tree" version)) (sha256 (base32 "11sjkm89ql1576jy0cqbxzjdpx7qs95wbgdxg92lzkiw05nrj2lv")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/tree/") (synopsis "Classification and regression trees") (description "This package provides procedures to work with classification and regression trees.") (license license:gpl2+))) (define-public r-treeclust (package (name "r-treeclust") (version "1.1-7") (source (origin (method url-fetch) (uri (cran-uri "treeClust" version)) (sha256 (base32 "1s7kh6q0bkixsygrip95zf1bi10ihddsa5lq9dfxd68yh8rsby6z")))) (properties `((upstream-name . "treeClust"))) (build-system r-build-system) (propagated-inputs (list r-cluster r-rpart)) (home-page "https://cran.r-project.org/web/packages/treeClust/") (synopsis "Cluster distances through trees") (description "This package provides tools to create a measure of inter-point dissimilarity useful for clustering mixed data, and, optionally, perform the clustering.") (license license:gpl2+))) (define-public r-treemap (package (name "r-treemap") (version "2.4-4") (source (origin (method url-fetch) (uri (cran-uri "treemap" version)) (sha256 (base32 "1h3pas3kn8zrpdpvp9vs745q94kixw5lxkbq74l5lh0n3wkqnnn5")))) (properties `((upstream-name . "treemap"))) (build-system r-build-system) (propagated-inputs (list r-colorspace r-data-table r-ggplot2 r-gridbase r-igraph r-rcolorbrewer r-shiny)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/package=treemap") (synopsis "Treemap visualization") (description "A treemap is a space-filling visualization of hierarchical structures. This package offers great flexibility to draw treemaps.") (license license:gpl3+))) (define-public r-acrosstic (package (name "r-acrosstic") (version "1.0-3") (source (origin (method url-fetch) (uri (cran-uri "AcrossTic" version)) (sha256 (base32 "03180h79jhjd66ibrnsfp3yyp2jlfysp7cymw46phzj2palghsc0")))) (properties `((upstream-name . "AcrossTic"))) (build-system r-build-system) (propagated-inputs (list r-lpsolve r-treeclust)) (home-page "https://cran.r-project.org/web/packages/AcrossTic/") (synopsis "Cost-minimal regular spanning subgraph with TreeClust") (description "This is a package for constructing minimum-cost regular spanning subgraph as part of a non-parametric two-sample test for equality of distribution.") (license license:gpl2+))) (define-public r-acrt (package (name "r-acrt") (version "1.0.1") (source (origin (method url-fetch) (uri (cran-uri "acrt" version)) (sha256 (base32 "0y9ndcq8ffpfrv7w9rikm4zn68jpsj6baqisq9kp2433xrwzdb6s")))) (properties `((upstream-name . "acrt"))) (build-system r-build-system) (propagated-inputs (list r-rcpp r-rcppeigen r-sandwich)) (home-page "https://cran.r-project.org/web/packages/acrt/") (synopsis "Autocorrelation robust testing") (description "This package provides functions for testing affine hypotheses on the regression coefficient vector in regression models with autocorrelated errors.") (license license:gpl2))) (define-public r-acs (package (name "r-acs") (version "2.1.4") (source (origin (method url-fetch) (uri (cran-uri "acs" version)) (sha256 (base32 "0ajw9rf8l8akcvgqvbxjvryc6wjx74521xyxswz2b0bky3m6kah5")))) (properties `((upstream-name . "acs"))) (build-system r-build-system) (propagated-inputs (list r-httr r-plyr r-rcpp r-stringr r-xml)) (home-page "https://dusp.mit.edu/faculty/ezra-haber-glenn") (synopsis "Work with data from the US Census") (description "This package provides a general toolkit for downloading, managing, analyzing, and presenting data from the @url{https://www.census.gov/data/developers/data-sets.html, U.S. Census}, including SF1 (Decennial short-form), SF3 (Decennial long-form), and the American Community Survey (ACS). Confidence intervals provided with ACS data are converted to standard errors to be bundled with estimates in complex @code{acs} objects. The package provides new methods to conduct standard operations on @code{acs} objects and present/plot data in statistically appropriate ways.") (license license:gpl3))) (define-public r-acss-data (package (name "r-acss-data") (version "1.0") (source (origin (method url-fetch) (uri (cran-uri "acss.data" version)) (sha256 (base32 "09kl4179ipr8bq19g89xcdi1xxs397zcx5cvgp6viy8gn687ilgv")))) (properties `((upstream-name . "acss.data"))) (build-system r-build-system) (home-page "http://complexitycalculator.com/methodology.html") (synopsis "Data for algorithmic complexity of short strings") (description "This is a data only package providing the algorithmic complexity of short strings, computed using the coding theorem method. For a given set of symbols in a string, all possible or a large number of random samples of Turing machines with a given number of states (e.g., 5) and number of symbols corresponding to the number of symbols in the strings were simulated until they reached a halting state or failed to end. This package contains data on 4.5 million strings from length 1 to 12 simulated on Turing machines with 2, 4, 5, 6, and 9 symbols. The complexity of the string corresponds to the distribution of the halting states.") (license license:gpl2+))) (define-public r-acss (package (name "r-acss") (version "0.2-5") (source (origin (method url-fetch) (uri (cran-uri "acss" version)) (sha256 (base32 "0cqa60544f58l5qd7h6xmsir40b9hqnq6pqgd5hfx2j2l5n7qhmk")))) (properties `((upstream-name . "acss"))) (build-system r-build-system) (propagated-inputs (list r-acss-data r-zoo)) (home-page "http://complexitycalculator.com/methodology.html") (synopsis "Algorithmic complexity for short strings") (description "The main purpose of this package is to provide the algorithmic complexity for short strings, an approximation of the Kolmogorov Complexity of a short string using the coding theorem method. While the database containing the complexity is provided in the data only package @code{acss.data}, this package provides functions accessing the data such as @code{prob_random} returning the posterior probability that a given string was produced by a random process. In addition, two traditional (but problematic) measures of complexity are also provided: entropy and change complexity.") (license license:gpl2+))) (define-public r-acswr (package (name "r-acswr") (version "1.0") (source (origin (method url-fetch) (uri (cran-uri "ACSWR" version)) (sha256 (base32 "195vjrkang5cl7gwsna0aq4p0h4jym9xg9yh94bnf8vq6wf8j83n")))) (properties `((upstream-name . "ACSWR"))) (build-system r-build-system) (propagated-inputs (list r-mass)) (home-page "https://cran.r-project.org/web/packages/ACSWR/") (synopsis "Companion package for the book \"A Course in Statistics with R\"") (description "This is a companion package for the book \"A Course in Statistics with R\" (ISBN 978-1-119-15272-9.)") (license license:gpl2))) (define-public r-alabama (package (name "r-alabama") (version "2023.1.0") (source (origin (method url-fetch) (uri (cran-uri "alabama" version)) (sha256 (base32 "075zqyarb970d4zpxsivaxhnmdg916ypfxrp0mqngnww5p3nfpwj")))) (properties `((upstream-name . "alabama"))) (build-system r-build-system) (propagated-inputs (list r-numderiv)) (home-page "https://cran.r-project.org/web/packages/alabama/") (synopsis "Constrained nonlinear optimization") (description "Alabama stands for Augmented Lagrangian Adaptive Barrier Minimization Algorithm; it is used for optimizing smooth nonlinear objective functions with constraints. Linear or nonlinear equality and inequality constraints are allowed.") (license license:gpl2+))) (define-public r-gdina (package (name "r-gdina") (version "2.9.4") (source (origin (method url-fetch) (uri (cran-uri "GDINA" version)) (sha256 (base32 "10bbwr4q6cp36dnwhddviqg7f00h92gdmvblw0lxn72v4869vhn1")))) (properties `((upstream-name . "GDINA"))) (build-system r-build-system) (propagated-inputs (list r-alabama r-ggplot2 r-mass r-nloptr r-numderiv r-rcpp r-rcpparmadillo r-rsolnp r-shiny r-shinydashboard)) (native-inputs (list r-knitr)) (home-page "https://github.com/Wenchao-Ma/GDINA") (synopsis "Generalized DINA model framework") (description "This package provides a set of psychometric tools for cognitive diagnosis modeling based on the generalized deterministic inputs, noisy and gate (G-DINA) model by de la Torre (2011) @url{doi:10.1007/s11336-011-9207-7} and its extensions, including the sequential G-DINA model by Ma and de la Torre (2016) @url{doi:10.1111/bmsp.12070} for polytomous responses, and the polytomous G-DINA model by Chen and de la Torre @url{doi:10.1177/0146621613479818} for polytomous attributes. Joint attribute distribution can be independent, saturated, higher-order, loglinear smoothed or structured. Q-matrix validation, item and model fit statistics, model comparison at test and item level and differential item functioning can also be conducted. A graphical user interface is also provided.") (license license:gpl3))) (define-public r-actcd (package (name "r-actcd") (version "1.3-0") (source (origin (method url-fetch) (uri (cran-uri "ACTCD" version)) (sha256 (base32 "1a0gsznca5fv7i29xpcns4rkas5q88wv01rxvd4j66n64gw0ri4j")))) (properties `((upstream-name . "ACTCD"))) (build-system r-build-system) (propagated-inputs (list r-gdina r-r-methodss3)) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/ACTCD/") (synopsis "Asymptotic classification theory for cognitive diagnosis") (description "This is a package supporting cluster analysis for cognitive diagnosis based on the Asymptotic Classification Theory (Chiu, Douglas & Li, 2009; @url{doi:10.1007/s11336-009-9125-0}). Given the sample statistic of sum-scores, cluster analysis techniques can be used to classify examinees into latent classes based on their attribute patterns. In addition to the algorithms used to classify data, three labeling approaches are proposed to label clusters so that examinees' attribute profiles can be obtained.") (license license:gpl2+))) (define-public r-ineq (package (name "r-ineq") (version "0.2-13") (source (origin (method url-fetch) (uri (cran-uri "ineq" version)) (sha256 (base32 "09fsxyrh0j7mwmb5hkhmrzgcy7kf85jxkh7zlwpgqgcsyl1n91z0")))) (properties `((upstream-name . "ineq"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/ineq/") (synopsis "Measuring inequality, concentration, and poverty") (description "This package provides tools for measuring inequality, concentration, and poverty measures. It provides both empirical and theoretical Lorenz curves.") ;; Either of these two versions. (license (list license:gpl2 license:gpl3)))) (define-public r-actfrag (package (name "r-actfrag") (version "0.1.1") (source (origin (method url-fetch) (uri (cran-uri "ActFrag" version)) (sha256 (base32 "08r3gwjz4fkyy85dxqix0ffm5xyq45032qv3snnzxnlqxslxbqn1")))) (properties `((upstream-name . "ActFrag"))) (build-system r-build-system) (propagated-inputs (list r-accelerometry r-dplyr r-ineq r-survival r-tidyr)) (home-page "https://github.com/junruidi/ActFrag") (synopsis "Activity fragmentation metrics extraction") (description "This package provides functions to extract commonly used fragmentation metrics to quantify time accumulation strategies based on minute level actigraphy-measured activity counts data.") (license license:gpl3))) (define-public r-ash (package (name "r-ash") (version "1.0-15") (source (origin (method url-fetch) (uri (cran-uri "ash" version)) (sha256 (base32 "1ay2a2agdmiz7zzvn26mli0x0iwk09g5pp4yy1r23knhkp1pn2lb")))) (properties `((upstream-name . "ash"))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/ash/") (synopsis "David Scott's ASH routines") (description "This package provides David Scott's ASH routines ported from S-PLUS to R.") (license license:gpl2+))) (define-public r-hdrcde (package (name "r-hdrcde") (version "3.4") (source (origin (method url-fetch) (uri (cran-uri "hdrcde" version)) (sha256 (base32 "16qlk44cjvn2s0vzaf915df65ksdx20dbxhy7fpdqins46hccha3")))) (properties `((upstream-name . "hdrcde"))) (build-system r-build-system) (propagated-inputs (list r-ash r-ggplot2 r-kernsmooth r-ks r-locfit r-rcolorbrewer)) (native-inputs (list gfortran)) (home-page "https://pkg.robjhyndman.com/hdrcde") (synopsis "Highest density regions and conditional density estimation") (description "This is a package for the computation of highest density regions in one and two dimensions, kernel estimation of univariate density functions conditional on one covariate, and multimodal regression.") (license license:gpl3))) (define-public r-rainbow (package (name "r-rainbow") (version "3.8") (source (origin (method url-fetch) (uri (cran-uri "rainbow" version)) (sha256 (base32 "0gc25napmcgg1qr17z4zixzxcdiv9midi1x5fin4pzkhicl5d97c")))) (properties `((upstream-name . "rainbow"))) (build-system r-build-system) (propagated-inputs (list r-cluster r-colorspace r-hdrcde r-ks r-mass r-pcapp)) (home-page "https://cran.r-project.org/web/packages/rainbow/") (synopsis "Bagplots, boxplots and rainbow plots for functional data") (description "This is a package for visualizing functional data and identifying functional outliers with bagplots, boxplots and rainbow plots.") (license license:gpl3))) (define-public r-fds (package (name "r-fds") (version "1.8") (source (origin (method url-fetch) (uri (cran-uri "fds" version)) (sha256 (base32 "1284vncixrzrz9x6b52gslrbrbia07sd0xac7nwdqhp5f5v5wfi0")))) (properties `((upstream-name . "fds"))) (build-system r-build-system) (propagated-inputs (list r-rainbow r-rcurl)) (home-page "https://cran.r-project.org/web/packages/fds/") (synopsis "Functional data sets") (description "This package contains a list of functional time series, sliced functional time series, and functional data sets. Functional time series is a special type of functional data observed over time. Sliced functional time series is a special type of functional time series with a time variable observed over time.") (license license:gpl2+))) (define-public r-fda (package (name "r-fda") (version "6.1.8") (source (origin (method url-fetch) (uri (cran-uri "fda" version)) (sha256 (base32 "01y488zviaj9z8h88vnia9wg4as62jx73la1qji1ljbr5258b3gg")))) (properties `((upstream-name . "fda"))) (build-system r-build-system) (propagated-inputs (list r-desolve r-fds)) (native-inputs (list r-knitr)) (home-page "https://www.functionaldata.org") (synopsis "Functional data analysis") (description "These functions were developed to support functional data analysis as described in Ramsay, J. O. and Silverman, B. W. (2005) Functional Data Analysis. The package includes data sets and script files working many examples.") (license license:gpl2+))) (define-public r-actigraphy (package (name "r-actigraphy") (version "1.4.0") (source (origin (method url-fetch) (uri (cran-uri "Actigraphy" version)) (sha256 (base32 "0bpmvszzv5fm72nar3wgnmfl5am7znqfajmlbv38ihkbi7jbwk20")))) (properties `((upstream-name . "Actigraphy"))) (build-system r-build-system) (propagated-inputs (list r-fda)) (home-page "https://cran.r-project.org/web/packages/Actigraphy/") (synopsis "Actigraphy data analysis") (description "This package provides tools for functional linear modeling and analysis of actigraphy data.") (license license:asl2.0))) (define-public r-activedriver (package (name "r-activedriver") (version "1.0.0") (source (origin (method url-fetch) (uri (cran-uri "ActiveDriver" version)) (sha256 (base32 "10c7ga48fwvpd5mc4dqiyw4kc2l0iz5qn4hg7xk15r1qmm5rsipa")))) (properties `((upstream-name . "ActiveDriver"))) (build-system r-build-system) (propagated-inputs (list r-mass)) (home-page "https://cran.r-project.org/web/packages/ActiveDriver/") (synopsis "Tools for finding cancer driver proteins") (description "This package provides a mutation analysis tool that discovers cancer driver genes with frequent mutations in protein signalling sites such as post-translational modifications (phosphorylation, ubiquitination, etc). The Poisson generalized linear regression model identifies genes where cancer mutations in signalling sites are more frequent than expected from the sequence of the entire gene. Integration of mutations with signalling information helps find new driver genes and propose candidate mechanisms to known drivers.") (license license:gpl2+))) (define-public r-activitycounts (package (name "r-activitycounts") (version "0.1.2") (source (origin (method url-fetch) (uri (cran-uri "activityCounts" version)) (sha256 (base32 "0zgxr2sk3a8kmygfxx1p5hnrfwdkxx7php6jlrhm8wv6052ck8jz")))) (properties `((upstream-name . "activityCounts"))) (build-system r-build-system) (propagated-inputs (list r-lubridate r-magrittr r-seewave r-signal r-tibble)) (home-page "https://github.com/walkabillylab/activityCounts") (synopsis "Generate ActiLife counts") (description "ActiLife generates activity counts from data collected by Actigraph accelerometers. Actigraph is one of the most common research-grade accelerometers. There is considerable research validating and developing algorithms for human activity using ActiLife counts. Unfortunately, ActiLife counts are proprietary and difficult to implement if researchers use different accelerometer brands. The code creates ActiLife counts from raw acceleration data for different accelerometer brands.") (license license:gpl3))) (define-public r-activityindex (package (name "r-activityindex") (version "0.3.7") (source (origin (method url-fetch) (uri (cran-uri "ActivityIndex" version)) (sha256 (base32 "1zj2b6x31a1kxl80rarmkrlm7ack4154mrkbqs3fpi48zpmjbgd5")))) (properties `((upstream-name . "ActivityIndex"))) (build-system r-build-system) (propagated-inputs (list r-data-table r-matrixstats r-r-utils)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/ActivityIndex/") (synopsis "Activity Index calculation using raw accelerometry data") (description "This is a package to read raw accelerometry from GT3X+ accelerometry data and plain table data to calculate the Activity Index from Bai et al. (2016) @url{doi:10.1371/journal.pone.0160644}.") (license license:gpl3))) (define-public r-activpal (package (name "r-activpal") (version "0.1.3") (source (origin (method url-fetch) (uri (cran-uri "activPAL" version)) (sha256 (base32 "1h6hp5z89ji73gdzxy1dgbfwjysiy5lvcqh90xagpb7sa7ahs3na")))) (properties `((upstream-name . "activPAL"))) (build-system r-build-system) (propagated-inputs (list r-devtools r-dplyr r-ggplot2 r-lubridate r-magrittr r-tidyr)) (home-page "https://cran.r-project.org/web/packages/activPAL") (synopsis "Processing and chart generation from activPAL events files") (description "This package contains functions to generate pre-defined summary statistics from activPAL events files. The package also contains functions to produce informative graphics that visualize physical activity behaviour and trends. This includes generating graphs that align physical activity behaviour with additional time based observations described by other data sets, such as sleep diaries and continuous glucose monitoring data.") (license license:gpl3))) (define-public r-activpalprocessing (package (name "r-activpalprocessing") (version "1.0.2") (source (origin (method url-fetch) (uri (cran-uri "activpalProcessing" version)) (sha256 (base32 "1y0bjx2qx53iy930y9iww4q1yzjj8y16cwgixk1mq3w4g1f116d1")))) (properties `((upstream-name . "activpalProcessing"))) (build-system r-build-system) (propagated-inputs (list r-chron)) (home-page "https://cran.r-project.org/web/packages/activpalProcessing/") (synopsis "Process activPAL events files") (description "This package performs estimation of physical activity and sedentary behavior variables from activPAL events files.") ;; Either version of the GPL. (license (list license:gpl2 license:gpl3)))) (define-public r-actogrammr (package (name "r-actogrammr") (version "0.2.3") (source (origin (method url-fetch) (uri (cran-uri "actogrammr" version)) (sha256 (base32 "1jzvarmd41yqlrkagzlc8m19n5mn0w0b36fy50lyvgrfsafjfbqa")))) (properties `((upstream-name . "actogrammr"))) (build-system r-build-system) (propagated-inputs (list r-dplyr r-ggplot2 r-lubridate r-readr r-tidyr)) (home-page "https://cran.r-project.org/web/packages/actogrammr/") (synopsis "Read in activity data and plot actograms") (description "Read in activity measurements from standard file formats used by circadian rhythm researchers, currently only ClockLab format, and process and plot the data. The central type of plot is the actogram, as first described in \"Activity and distribution of certain wild mice in relation to biotic communities\" by MS Johnson (1926) @url{doi:10.2307/1373575}.") (license license:gpl3))) (define-public r-expint (package (name "r-expint") (version "0.1-8") (source (origin (method url-fetch) (uri (cran-uri "expint" version)) (sha256 (base32 "1cn6c84pqf8bgk109qm4znn186h6s6cpll3d11cw144h0vh4yr8j")))) (properties `((upstream-name . "expint"))) (build-system r-build-system) (home-page "https://gitlab.com/vigou3/expint") (synopsis "Exponential integral and incomplete Gamma function") (description "This package provides the exponential integrals @code{E_1(x)}, @code{E_2(x)}, @code{E_n(x)} and @code{Ei(x)}, and the incomplete gamma function @code{G(a, x)} defined for negative values of its first argument. The package also gives easy access to the underlying C routines through an API; see the package vignette for details.") (license license:gpl2+))) (define-public r-actuar (package (name "r-actuar") (version "3.3-4") (source (origin (method url-fetch) (uri (cran-uri "actuar" version)) (sha256 (base32 "06693w4cwcchi0z64vgg7khc4k4209nw6m2x441nwix4x6rk1zjs")))) (properties `((upstream-name . "actuar"))) (build-system r-build-system) (propagated-inputs (list r-expint)) (home-page "https://gitlab.com/vigou3/actuar") (synopsis "Actuarial functions and heavy tailed distributions") (description "This package provides functions and data sets for actuarial science: modeling of loss distributions; risk theory and ruin theory; simulation of compound models, discrete mixtures and compound hierarchical models; credibility theory. It boasts support for many additional probability distributions to model insurance loss amounts and loss frequency: 19 continuous heavy tailed distributions; the Poisson-inverse Gaussian discrete distribution; zero-truncated and zero-modified extensions of the standard discrete distributions. It also supports phase-type distributions commonly used to compute ruin probabilities.") (license license:gpl2+))) (define-public r-bmp (package (name "r-bmp") (version "0.3") (source (origin (method url-fetch) (uri (cran-uri "bmp" version)) (sha256 (base32 "0jd67r11bn98hjwgyr6gas423787xy7ji2hq7ay80blkkcj91xxx")))) (properties `((upstream-name . "bmp"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/bmp/") (synopsis "Read Bitmap (BMP) images") (description "This package provides pure R tools to read BMP format images. It is currently limited to 8 bit greyscale images and 24, 32 bit (A)RGB images.") (license license:gpl2+))) (define-public r-readbitmap (package (name "r-readbitmap") (version "0.1.5") (source (origin (method url-fetch) (uri (cran-uri "readbitmap" version)) (sha256 (base32 "14825906l326w59g6apy00j55jg3h5kx2r6s031f4gdkbrc7szbk")))) (properties `((upstream-name . "readbitmap"))) (build-system r-build-system) (inputs (list libjpeg-turbo libpng)) (propagated-inputs (list r-bmp r-jpeg r-png r-tiff)) (home-page "https://github.com/jefferis/readbitmap") (synopsis "Unified interface to read bitmap images (BMP, JPEG, PNG, TIFF)") (description "This package provides tools to identify and read BMP, JPEG, PNG, and TIFF format bitmap images. Identification defaults to the use of the magic number embedded in the file rather than the file extension.") (license license:gpl2+))) (define-public r-imager (package (name "r-imager") (version "0.45.8") (source (origin (method url-fetch) (uri (cran-uri "imager" version)) (sha256 (base32 "0vrv7m9b9w8xjqa9w17xvrmpl403476zr0l9wqdp9ir6ssvnaf2f")))) (properties `((upstream-name . 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(license license:gpl2))) (define-public r-cdm (package (name "r-cdm") (version "8.2-6") (source (origin (method url-fetch) (uri (cran-uri "CDM" version)) (sha256 (base32 "1lcq3i5rlyqkc12c26kj0x4fm2gh1jsisp6kbf59y3hjdkiqajhl")))) (properties `((upstream-name . "CDM"))) (build-system r-build-system) (propagated-inputs (list r-mvtnorm r-polycor r-rcpp r-rcpparmadillo)) (home-page "https://github.com/alexanderrobitzsch/CDM") (synopsis "Cognitive diagnosis modeling") (description "This package provides functions for cognitive diagnosis modeling and multidimensional item response modeling for dichotomous and polytomous item responses. It enables the estimation of the DINA and DINO model, the multiple group (polytomous) GDINA model, the multiple choice DINA model, the general diagnostic model (GDM), the structured latent class model (SLCA), and regularized latent class analysis. 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In addition, a sequential testing procedure for GPD-GoF-tests is also implemented here.") (license license:gpl3))) (define-public r-awsmethods (package (name "r-awsmethods") (version "1.1-1") (source (origin (method url-fetch) (uri (cran-uri "awsMethods" version)) (sha256 (base32 "0hbmrcpdyg15zg4rysscsmxpxlpy0dkxx2aa63qibq7l1k14v4sh")))) (properties `((upstream-name . "awsMethods"))) (build-system r-build-system) (home-page "http://www.wias-berlin.de/software/imaging/") (synopsis "Class and methods definitions") (description "This package defines the generic method @code{extract} and provides @code{openMP} support as needed in several packages like @code{aws}, @code{adimpro}, @code{fmri}, and @code{dwi}.") (license license:gpl2+))) (define-public r-aws (package (name "r-aws") (version "2.5-5") (source (origin (method url-fetch) (uri (cran-uri "aws" version)) (sha256 (base32 "0nsc7fakwcppav2h2kys0j28ga2p2si4kbygfka955dmbiwv4z5j")))) (properties `((upstream-name . 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(lambda* (#:key outputs #:allow-other-keys) (let* ((out (assoc-ref outputs "out")) (bin (string-append out "/bin"))) (substitute* "src/Makevars.in" (("\\$\\(R_HOME\\)") out)) (mkdir-p bin))))))) (propagated-inputs (list r-checkmate r-mime r-jsonlite r-knitr r-r6 r-rcpp r-uuid)) (inputs (list openssl zlib)) (home-page "https://github.com/s-u/Rserve") (synopsis "Server providing access to R from many languages and systems") (description "Rserve acts as a socket server (TCP/IP or local sockets) which allows binary requests to be sent to R. Every connection has a separate workspace and working directory. Client-side implementations are available for popular languages such as C/C++ and Java, allowing any application to use facilities of R without the need of linking to R code. Rserve supports remote connection, user authentication and file transfer. A simple R client is included in this package as well.") (license license:gpl2))) (define-public r-gamm4 (package (name "r-gamm4") (version "0.2-6") (source (origin (method url-fetch) (uri (cran-uri "gamm4" version)) (sha256 (base32 "128c725y9s07c1m9cvd9hgi9hldrymcs5divd8pw7bdjh9jvdiap")))) (properties `((upstream-name . "gamm4"))) (build-system r-build-system) (propagated-inputs (list r-lme4 r-matrix r-mgcv)) (home-page "https://cran.r-project.org/web/packages/gamm4/") (synopsis "Generalized additive mixed models using mgcv and lme4") (description "Estimate generalized additive mixed models via a version of function @code{gamm} from the @code{mgcv} package, using the @code{lme4} packagefor estimation.") (license license:gpl2+))) (define-public r-optimx (package (name "r-optimx") (version "2023-10.21") (source (origin (method url-fetch) (uri (cran-uri "optimx" version)) (sha256 (base32 "1da4daxgk4kbq1n2mn72482c3j96wba0xf4mzffgasn20ib2swqd")))) (properties `((upstream-name . 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(license license:gpl2))) (define-public r-projpred (package (name "r-projpred") (version "2.8.0") (source (origin (method url-fetch) (uri (cran-uri "projpred" version)) (sha256 (base32 "1xm1444qv0pkxdf2nacxnb2apx5lar1f3qz4jrxp6xd2xk2xv0xk")))) (properties `((upstream-name . "projpred"))) (build-system r-build-system) (propagated-inputs (list r-abind r-gamm4 r-ggplot2 r-gtools r-lme4 r-loo r-mass r-mclogit r-mgcv r-mvtnorm r-nnet r-ordinal r-rcpp r-rcpparmadillo r-rstantools r-scales)) (native-inputs (list r-knitr r-rmarkdown)) (home-page "https://mc-stan.org/projpred/") (synopsis "Projection predictive feature selection") (description "This package performs projection predictive feature selection for generalized linear models and generalized linear and additive multilevel models. The package is compatible with the @code{rstanarm} and @code{brms} packages, but other reference models can also be used. See the package vignette for more information and examples.") 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In addition to providing generic replacements for p/d/q/r functions, other useful statistics can be computed including means, variances, intervals, and highest density regions.") (license license:gpl3))) (define-public r-posterior (package (name "r-posterior") (version "1.5.0") (source (origin (method url-fetch) (uri (cran-uri "posterior" version)) (sha256 (base32 "1pp233ddrs116w1rmp3khhmibjf6l021b1x79k6z48g3r9zk042a")))) (properties `((upstream-name . "posterior"))) (build-system r-build-system) (propagated-inputs (list r-abind r-checkmate r-distributional r-matrixstats r-pillar r-rlang r-tensora r-tibble r-vctrs)) (native-inputs (list r-knitr)) (home-page "https://mc-stan.org/posterior/") (synopsis "Tools for working with posterior distributions") (description "This package provides useful tools for both users and developers of packages for fitting Bayesian models or working with output from Bayesian models. The primary goals of the package are to: @enumerate @item Efficiently convert between many different useful formats of draws (samples) from posterior or prior distributions. @item Provide consistent methods for operations commonly performed on draws, for example, subsetting, binding, or mutating draws. @item Provide various summaries of draws in convenient formats. @item Provide lightweight implementations of state of the art posterior inference diagnostics. @end enumerate ") (license license:bsd-3))) (define-public r-brms (package (name "r-brms") (version "2.21.0") (source (origin (method url-fetch) (uri (cran-uri "brms" version)) (sha256 (base32 "0n2xxiibypfazcbx8rx4h5c4pl9zlmm0mkpyny23bf54q8rzz2bj")))) (properties `((upstream-name . 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In addition, all parameters of the response distribution can be predicted in order to perform distributional regression. Prior specifications are flexible and explicitly encourage users to apply prior distributions that actually reflect their beliefs. Model fit can easily be assessed and compared with posterior predictive checks and leave-one-out cross-validation.") (license license:gpl2))) (define-public r-mstate (package (name "r-mstate") (version "0.3.2") (source (origin (method url-fetch) (uri (cran-uri "mstate" version)) (sha256 (base32 "054dzrd5b0xjjjl7862q3aq1jwgrxbkqz7zpvbdirqsld3zksirw")))) (properties `((upstream-name . 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The algorithm was specifically designed to make it costly to perform large-scale custom hardware attacks by requiring large amounts of memory.") (license license:bsd-2))) (define-public r-boruta (package (name "r-boruta") (version "8.0.0") (source (origin (method url-fetch) (uri (cran-uri "Boruta" version)) (sha256 (base32 "1irx7qg1sw69ggsk4jgxfd3pp741kd944fipnda1qbcbphg5prrq")))) (properties `((upstream-name . "Boruta"))) (build-system r-build-system) (propagated-inputs (list r-ranger)) (home-page "https://gitlab.com/mbq/Boruta/") (synopsis "Wrapper algorithm for all relevant feature selection") (description "This package provides an all relevant feature selection wrapper algorithm. It finds relevant features by comparing original attributes' importance with importance achievable at random, estimated using their permuted copies (shadows).") 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It is designed to be distributed and efficient with the following goals: @enumerate @item Faster training speed and higher efficiency; @item lower memory usage; @item better accuracy; @item parallel learning supported; and @item capable of handling large-scale data. @end enumerate ") (license license:expat))) (define-public r-shapforxgboost (package (name "r-shapforxgboost") (version "0.1.3") (source (origin (method url-fetch) (uri (cran-uri "SHAPforxgboost" version)) (sha256 (base32 "0b3h6py80a0dmb8f8j4h7a7d0k6ld8l0qr24r8pxxy7dbqbyxh5x")))) (properties `((upstream-name . 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"semver"))) (build-system r-build-system) (propagated-inputs (list r-assertthat r-rcpp)) (native-inputs (list r-knitr)) (home-page "https://github.com/johndharrison/semver") (synopsis "Parser for Semantic Versioning 2.0.0") (description "This package provides tools and functions for parsing, rendering and operating on semantic version strings. Semantic versioning is a simple set of rules and requirements that dictate how version numbers are assigned and incremented as outlined at @url{http://semver.org}.") (license license:expat))) (define-public r-binman (package (name "r-binman") (version "0.1.3") (source (origin (method url-fetch) (uri (cran-uri "binman" version)) (sha256 (base32 "1xz9ky3axidm0fp518rj80ma6q14ybyvashil79hhkk3iqmx0lhw")))) (properties `((upstream-name . "binman"))) (build-system r-build-system) (propagated-inputs (list r-assertthat r-httr r-jsonlite r-rappdirs r-semver r-xml2 r-yaml)) (native-inputs (list r-knitr)) (home-page "https://github.com/ropensci/binman") (synopsis "Binary download manager") (description "This package provides tools and functions for managing the download of binary files. Binary repositories are defined in the YAML format. Defining new pre-download, download and post-download templates allow additional repositories to be added.") (license license:expat))) (define-public r-wdman (package (name "r-wdman") (version "0.2.6") (source (origin (method url-fetch) (uri (cran-uri "wdman" version)) (sha256 (base32 "0n0wwb9ip6qc8qzdxn4dsqfbc8b3f607n8l6jigryd7g83ibnbp6")))) (properties `((upstream-name . "wdman"))) (build-system r-build-system) (propagated-inputs (list r-assertthat r-binman r-processx r-semver r-yaml)) (native-inputs (list r-knitr)) (home-page "https://docs.ropensci.org/wdman/") (synopsis "Webdriver/Selenium binary manager") (description "There are a number of binary files associated with the Webdriver/Selenium project (see @url{http://www.seleniumhq.org/download/}, @url{https://sites.google.com/a/chromium.org/chromedriver/}, @url{https://github.com/mozilla/geckodriver}, @url{http://phantomjs.org/download.html}, and @url{https://github.com/SeleniumHQ/selenium/wiki/InternetExplorerDriver} for more information). This package provides functions to download these binaries and to manage processes involving them.") (license license:expat))) (define-public r-rselenium (package (name "r-rselenium") (version "1.7.9") (source (origin (method url-fetch) (uri (cran-uri "RSelenium" version)) (sha256 (base32 "18hd0gfpblg9ij99ik7ccc60q9dxha89n5rrwrrzx498c5sscjg2")))) (properties `((upstream-name . "RSelenium"))) (build-system r-build-system) (propagated-inputs (list r-catools r-httr r-wdman)) (native-inputs (list r-knitr)) (home-page "https://docs.ropensci.org/RSelenium/") (synopsis "R bindings for Selenium WebDriver") (description "This package provides a set of R bindings for the Selenium 2.0 WebDriver (see @url{https://selenium.dev/documentation/en/} for more information) using the @code{JsonWireProtocol} (see @url{https://github.com/SeleniumHQ/selenium/wiki/JsonWireProtocol} for more information). Selenium 2.0 WebDriver allows driving a web browser natively as a user would either locally or on a remote machine using the Selenium server it marks a leap forward in terms of web browser automation. Selenium automates web browsers (commonly referred to as browsers). Using RSelenium you can automate browsers locally or remotely.") (license license:agpl3+))) (define-public r-conquer (package (name "r-conquer") (version "1.3.3") (source (origin (method url-fetch) (uri (cran-uri "conquer" version)) (sha256 (base32 "1fnyjym21i9hw2d1c9da0wvjzbi9abn46n0lg6if5w2asxg1bim2")))) (properties `((upstream-name . "conquer"))) (build-system r-build-system) (propagated-inputs (list r-matrix r-matrixstats r-rcpp r-rcpparmadillo)) (home-page "https://github.com/XiaoouPan/conquer") (synopsis "Convolution-type smoothed quantile regression") (description "This package provides fast and accurate convolution-type smoothed quantile regression, implemented using Barzilai-Borwein gradient descent with a Huber regression warm start. Confidence intervals for regression coefficients are constructed using multiplier bootstrap.") (license license:gpl3))) (define-public r-consrank (package (name "r-consrank") (version "2.1.4") (source (origin (method url-fetch) (uri (cran-uri "ConsRank" version)) (sha256 (base32 "001hmiii7khh1q2wav38737svzr0anr42nyp8hhplqfbiw0cc4y2")))) (properties `((upstream-name . "ConsRank"))) (build-system r-build-system) (propagated-inputs (list r-gtools r-proxy r-rgl r-rlist r-tidyr)) (home-page "https://www.r-project.org/") (synopsis "Compute median rankings according to Kemeny's axiomatic approach") (description "This package lets you compute the median ranking according to Kemeny's axiomatic approach. Rankings can or cannot contain ties, rankings can be both complete or incomplete. The package contains both branch-and-bound algorithms and heuristic solutions recently proposed. The searching space of the solution can either be restricted to the universe of the permutations or unrestricted to all possible ties. The package also provides some useful utilities for deal with preference rankings, including both element-weight Kemeny distance and correlation coefficient.") (license license:gpl3))) (define-public r-fastshap (package (name "r-fastshap") (version "0.1.1") (source (origin (method url-fetch) (uri (cran-uri "fastshap" version)) (sha256 (base32 "1j6bnkv4q8n85xlvzm5p6p4yg8wdp6an6skbvdif5g9c376hzqb2")))) (properties `((upstream-name . "fastshap"))) (build-system r-build-system) (propagated-inputs (list r-foreach r-rcpp r-rcpparmadillo)) (native-inputs (list r-knitr)) (home-page "https://github.com/bgreenwell/fastshap") (synopsis "Fast approximate Shapley values") (description "This package computes fast (relative to other implementations) approximate Shapley values for any supervised learning model. Shapley values help to explain the predictions from any black box model using ideas from game theory; see @url{Strumbel and Kononenko (2014), doi.org/10.1007/s10115-013-0679-x} for details.") (license license:gpl2+))) (define-public r-memisc (package (name "r-memisc") (version "0.99.31.7") (source (origin (method url-fetch) (uri (cran-uri "memisc" version)) (sha256 (base32 "0drn923y8bwwwk2csa7l9b3fd06zfrfgi3b0pn7b23aja1c1h0xl")))) (properties `((upstream-name . "memisc"))) (build-system r-build-system) (propagated-inputs (list r-data-table r-jsonlite r-lattice r-mass r-yaml)) (native-inputs (list r-knitr)) (home-page "https://www.elff.eu/software/memisc/") (synopsis "Management of survey data and presentation of analysis results") (description "This package provides infrastructure for the management of survey data including value labels, definable missing values, recoding of variables, production of code books, and import of (subsets of) SPSS and Stata files is provided. Further, the package allows to produce tables and data frames of arbitrary descriptive statistics and (almost) publication-ready tables of regression model estimates, which can be exported to LaTeX and HTML.") ;; Either of these two version. (license (list license:gpl2 license:gpl3)))) (define-public r-memuse (package (name "r-memuse") (version "4.2-3") (source (origin (method url-fetch) (uri (cran-uri "memuse" version)) (sha256 (base32 "0816s6airiqmn8faprpwmchxaay6llri4673ivlx1bp2cpvdyvwh")))) (properties `((upstream-name . "memuse"))) (build-system r-build-system) (home-page "https://github.com/shinra-dev/memuse") (synopsis "Memory Estimation Utilities") (description "This package provides procedures to answer the following questions: How much ram do you need to store a 100,000 by 100,000 matrix? How much ram is your current R session using? How much ram do you even have?") 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(license license:bsd-3))) (define-public r-iml (package (name "r-iml") (version "0.11.2") (source (origin (method url-fetch) (uri (cran-uri "iml" version)) (sha256 (base32 "1sjv0cj50iivjlb2hri401z78rmidxxh6q5akscd42k98jyw2r30")))) (properties `((upstream-name . "iml"))) (build-system r-build-system) (propagated-inputs (list r-checkmate r-data-table r-formula r-future r-future-apply r-ggplot2 r-metrics r-r6)) (native-inputs (list r-knitr)) (home-page "https://github.com/christophM/iml") (synopsis "Interpretable machine learning") (description "This package provides interpretability methods to analyze the behavior and predictions of any machine learning model. Implemented methods are: @itemize @item Feature importance described by Fisher et al. (2018), @item accumulated local effects plots described by Apley (2018), @item partial dependence plots described by Friedman (2001), @item individual conditional expectation ('ice') plots described by Goldstein et al. (2013) @url{https://doi.org/10.1080/10618600.2014.907095}, @item local models (variant of 'lime') described by Ribeiro et. al (2016), @item the Shapley Value described by Strumbelj et. al (2014) @url{https://doi.org/10.1007/s10115-013-0679-x}, @item feature interactions described by Friedman et. al @url{https://doi.org/10.1214/07-AOAS148} and tree surrogate models. @end itemize ") (license license:expat))) (define-public r-goftest (package (name "r-goftest") (version "1.2-3") (source (origin (method url-fetch) (uri (cran-uri "goftest" version)) (sha256 (base32 "06bz6k7smr4jbvzmb73qc5fkf4my59w5gbl18wlmpkkymsv78prs")))) (properties `((upstream-name . "goftest"))) (build-system r-build-system) (home-page "https://github.com/baddstats/goftest") (synopsis "Classical Goodness-of-Fit tests for univariate distributions") (description "This package provides Cramer-Von Mises and Anderson-Darling tests of goodness-of-fit for continuous univariate distributions, using efficient algorithms.") (license license:gpl2+))) (define-public r-tensor (package (name "r-tensor") (version "1.5") (source (origin (method url-fetch) (uri (cran-uri "tensor" version)) (sha256 (base32 "19mfsgr6vz4lgwidm80i4yw0y1dr3n8i6qz7g4n2xa0k74zc5pp1")))) (properties `((upstream-name . "tensor"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/tensor/") (synopsis "Tensor product of arrays") (description "The tensor product of two arrays is notionally an outer product of the arrays collapsed in specific extents by summing along the appropriate diagonals. This package allows you to compute the tensor product of arrays.") (license license:gpl2+))) (define-public r-spatstat-explore (package (name "r-spatstat-explore") (version "3.2-7") (source (origin (method url-fetch) (uri (cran-uri "spatstat.explore" version)) (sha256 (base32 "08740yclqv86mnds0a8xhn6r2qdqhw4qgkbrb2cl93crqwcdkr2f")))) (properties `((upstream-name . "spatstat.explore"))) (build-system r-build-system) (propagated-inputs (list r-abind r-goftest r-matrix r-nlme r-spatstat-data r-spatstat-geom r-spatstat-random r-spatstat-sparse r-spatstat-utils)) (home-page "https://spatstat.org/") (synopsis "Exploratory data analysis for the spatstat family") (description "This package implements functionality for exploratory data analysis and nonparametric analysis of spatial data, mainly spatial point patterns, in the @code{spatstat} family of packages. Methods include quadrat counts, K-functions and their simulation envelopes, nearest neighbour distance and empty space statistics, Fry plots, pair correlation function, kernel smoothed intensity, relative risk estimation with cross-validated bandwidth selection, mark correlation functions, segregation indices, mark dependence diagnostics, and kernel estimates of covariate effects. Formal hypothesis tests of random pattern (chi-squared, Kolmogorov-Smirnov, Monte Carlo, Diggle-Cressie-Loosmore-Ford, Dao-Genton, two-stage Monte Carlo) and tests for covariate effects (Cox-Berman-Waller-Lawson, Kolmogorov-Smirnov, ANOVA) are also supported.") (license license:gpl2+))) (define-public r-spatstat-model (package (name "r-spatstat-model") (version "3.2-11") (source (origin (method url-fetch) (uri (cran-uri "spatstat.model" version)) (sha256 (base32 "0hvnqig6cdrp8hk2fkcajag3hrqsamfr6h66wn4cs30iblic23bh")))) (properties `((upstream-name . 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Formal hypothesis tests of random pattern (chi-squared, Kolmogorov-Smirnov, Monte Carlo, Diggle-Cressie-Loosmore-Ford, Dao-Genton, two-stage Monte Carlo) and tests for covariate effects (Cox-Berman-Waller-Lawson, Kolmogorov-Smirnov, ANOVA) are also supported.") (license license:gpl2+))) (define-public r-spatstat-utils (package (name "r-spatstat-utils") (version "3.0-4") (source (origin (method url-fetch) (uri (cran-uri "spatstat.utils" version)) (sha256 (base32 "1i1w1ys29s22jfjvliqnbw3zi6zar8bxxz3r8za182p2w0wqwhax")))) (properties `((upstream-name . "spatstat.utils"))) (build-system r-build-system) (home-page "https://www.spatstat.org") (synopsis "Utility functions for spatstat") (description "This package contains utility functions for the @code{spatstat} package which may also be useful for other purposes.") 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(license license:gpl2+))) (define-public r-spatstat (package (name "r-spatstat") (version "3.0-8") (source (origin (method url-fetch) (uri (cran-uri "spatstat" version)) (sha256 (base32 "0ghhj161n7bxd6hpk3hz6lq2gv8bwx5clrdp729lfyi9d1xjw162")))) (properties `((upstream-name . "spatstat"))) (build-system r-build-system) (propagated-inputs (list r-spatstat-data r-spatstat-explore r-spatstat-geom r-spatstat-linnet r-spatstat-model r-spatstat-random r-spatstat-utils)) (home-page "https://www.spatstat.org") (synopsis "Spatial Point Pattern analysis, model-fitting, simulation, tests") (description "This package provides a comprehensive toolbox for analysing Spatial Point Patterns. It is focused mainly on two-dimensional point patterns, including multitype/marked points, in any spatial region. It also supports three-dimensional point patterns, space-time point patterns in any number of dimensions, point patterns on a linear network, and patterns of other geometrical objects. It supports spatial covariate data such as pixel images and contains over 2000 functions for plotting spatial data, exploratory data analysis, model-fitting, simulation, spatial sampling, model diagnostics, and formal inference.") (license license:gpl2+))) (define-public r-gaston (package (name "r-gaston") (version "1.6") (source (origin (method url-fetch) (uri (cran-uri "gaston" version)) (sha256 (base32 "1knjyw2dsarljj2zsqp3hi6hk6m90sfqp2l535h3arj70l3rq9x4")))) (properties `((upstream-name . "gaston"))) (build-system r-build-system) (inputs (list zlib)) (propagated-inputs (list r-rcpp r-rcppeigen r-rcppparallel)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/gaston/") (synopsis "Genetic data handling (QC, GRM, LD, PCA) and linear mixed models") (description "This is a package for the manipulation of genetic data (SNPs). Computation of @dfn{genetic relationship matrix} (GRM) and dominance matrix, @dfn{linkage disequilibrium} (LD), and heritability with efficient algorithms for linear mixed models (AIREML).") (license license:gpl3))) (define-public r-cpp11 (package (name "r-cpp11") (version "0.4.7") (source (origin (method url-fetch) (uri (cran-uri "cpp11" version)) (sha256 (base32 "0i234s1g1vc6m2sqxia5r1gaca05znjv4bff5dj74fach9k147c0")))) (properties `((upstream-name . "cpp11"))) (build-system r-build-system) (native-inputs (list r-knitr)) (home-page "https://github.com/r-lib/cpp11") (synopsis "C++11 Interface for R's C Interface") (description "This package provides a header only, C++11 interface to R's C interface. Compared to other approaches @code{cpp11} strives to be safe against long jumps from the C API as well as C++ exceptions, conform to normal R function semantics and supports interaction with @code{ALTREP} vectors.") 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"RcppZiggurat"))) (build-system r-build-system) (propagated-inputs (list r-rcpp r-rcppgsl)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/RcppZiggurat/") (synopsis "Rcpp integration of different \"Ziggurat\" normal RNG implementations") (description "The Ziggurat generator for normally distributed random numbers, originally proposed by Marsaglia and Tsang (2000, @url{https://doi.org/10.18637/jss.v005.i08}) has been improved upon a few times starting with Leong et al (2005, @url{https://doi.org/10.18637/jss.v012.i07}). This package provides an aggregation for comparing different implementations in order to provide a 'faster but good enough' alternative for use with R and C++ code.") (license license:gpl2+))) (define-public r-rfast (package (name "r-rfast") (version "2.1.0") (source (origin (method url-fetch) (uri (cran-uri "Rfast" version)) (sha256 (base32 "1zqq4k85i0nbzndkh0iiq3k83ly0mpl3pn4wkka6qxfvk6n6rr7r")))) (properties `((upstream-name . 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(license license:gpl2+))) (define-public r-rffc (package (name "r-rffc") (version "1.0") (source (origin (method url-fetch) (uri (string-append "https://download.r-forge.r-project.org/src/contrib/" "rfFC_" version ".tar.gz")) (sha256 (base32 "05x9wgzsmx4vb12lmcspymgmpb2xw8bwryb8ysg7vzg2nkh0ma3g")))) (build-system r-build-system) (propagated-inputs (list r-randomforest)) (home-page "https://r-forge.r-project.org/projects/rffc/") (synopsis "Random Forest Feature Contributions") (description "This package provides functions for extracting feature contributions from a random forest model from package @code{randomForest}. Feature contributions provide detailed information about the relationship between data variables and the predicted value returned by random forest model.") (license license:gpl2))) (define-public r-clusterr (package (name "r-clusterr") (version "1.3.2") (source (origin (method url-fetch) (uri (cran-uri "ClusterR" version)) (sha256 (base32 "1bs1sl3yy90zx4ni0lhvdivzfas6i4v9203m59njvk5df9x82ffp")))) (properties `((upstream-name . "ClusterR"))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-gmp r-lifecycle r-rcpp r-rcpparmadillo)) (native-inputs (list r-knitr)) (home-page "https://github.com/mlampros/ClusterR") (synopsis "Clustering") (description "This package provides Gaussian mixture models, k-means, mini-batch-kmeans, k-medoids and affinity propagation clustering with the option to plot, validate, predict (new data) and estimate the optimal number of clusters. The package takes advantage of @code{RcppArmadillo} to speed up the computationally intensive parts of the functions. For more information, see @enumerate @item \"Clustering in an Object-Oriented Environment\" by Anja Struyf, Mia Hubert, Peter Rousseeuw (1997), Journal of Statistical Software, @url{https://doi.org/10.18637/jss.v001.i04}; @item \"Web-scale k-means clustering\" by D. Sculley (2010), ACM Digital Library, @url{https://doi.org/10.1145/1772690.1772862}; @item \"Armadillo: a template-based C++ library for linear algebra\" by Sanderson et al (2016), The Journal of Open Source Software, @url{https://doi.org/10.21105/joss.00026}; @item \"Clustering by Passing Messages Between Data Points\" by Brendan J. Frey and Delbert Dueck, Science 16 Feb 2007: Vol. 315, Issue 5814, pp. 972-976, @url{https://doi.org/10.1126/science.1136800}. @end enumerate ") (license license:gpl3))) (define-public r-spectrum (package (name "r-spectrum") (version "1.1") (source (origin (method url-fetch) (uri (cran-uri "Spectrum" version)) (sha256 (base32 "0n38d360azkck6vvhr771zsh0gbvd9qsf9ygg5r18vhz0pb1xcfw")))) (properties `((upstream-name . "Spectrum"))) (build-system r-build-system) (propagated-inputs (list r-clusterr r-diptest r-ggplot2 r-rfast)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/Spectrum/") (synopsis "Fast adaptive spectral clustering for single and multi-view data") (description "This package provides a self-tuning spectral clustering method for single or multi-view data. Spectrum uses a new type of adaptive density aware kernel that strengthens connections in the graph based on common nearest neighbours. 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(license license:gpl2+))) (define-public r-transphylo (package (name "r-transphylo") (version "1.4.5") (source (origin (method url-fetch) (uri (cran-uri "TransPhylo" version)) (sha256 (base32 "0g92kwi1nlmpc8m4pc9kv9xhczryr2kn9icfr3js7da7vy8g50xy")))) (properties `((upstream-name . "TransPhylo"))) (build-system r-build-system) (propagated-inputs (list r-ape r-rcpp)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/TransPhylo/") (synopsis "Inference of transmission tree from a dated phylogeny") (description "This is a package to infer transmission trees from a dated phylogeny. It includes methods to simulate and analyze outbreaks. The methodology is described in @url{https://doi.org/10.1093/molbev/msu121,Didelot et al. (2014)} and @url{https://doi.org/10.1093/molbev/msw275,Didelot et al. (2017)}.") (license license:gpl2+))) (define-public r-km-ci (package (name "r-km-ci") (version "0.5-6") (source (origin (method url-fetch) (uri (cran-uri "km.ci" version)) (sha256 (base32 "18sc9vhbdgks8lhk2nfxkkayh8j4j227hl63fm5p04f7z4wm6wc1")))) (properties `((upstream-name . "km.ci"))) (build-system r-build-system) (propagated-inputs (list r-survival)) (home-page "https://cran.r-project.org/web/packages/km.ci/") (synopsis "Confidence intervals for the Kaplan-Meier estimator") (description "This package computes various @dfn{confidence intervals} (CI) for the Kaplan-Meier estimator, namely: Petos CI, Rothman CI, CIs based on Greenwoods variance, Thomas and Grunkemeier CI and the simultaneous confidence bands by Nair and Hall and Wellner.") (license license:gpl2+))) (define-public r-kmsurv (package (name "r-kmsurv") (version "0.1-5") (source (origin (method url-fetch) (uri (cran-uri "KMsurv" version)) (sha256 (base32 "0hi5vvk584rl70gbrr75w9hc775xmbxnaig0dd6hlpi4071pnqjm")))) (properties `((upstream-name . "KMsurv"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/KMsurv/") (synopsis "Data sets from Klein and Moeschberger (1997), Survival Analysis") (description "This package provides data sets and functions for Klein and Moeschberger (1997), \"Survival Analysis, Techniques for Censored and Truncated Data\", Springer.") (license license:gpl3+))) (define-public r-survmisc (package (name "r-survmisc") (version "0.5.6") (source (origin (method url-fetch) (uri (cran-uri "survMisc" version)) (sha256 (base32 "014cf7sfndmib9jmj0p3h67sr750k2pvw7m865zwdpvlqddi44fr")))) (properties `((upstream-name . 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(license license:gpl2+))) (define-public r-survminer (package (name "r-survminer") (version "0.4.9") (source (origin (method url-fetch) (uri (cran-uri "survminer" version)) (sha256 (base32 "0byh0wxdbjfwdrzsnqv4xlmnik6lj0vkkzfxy7lssk8dv5zmj7nz")))) (properties `((upstream-name . "survminer"))) (build-system r-build-system) (propagated-inputs (list r-broom r-dplyr r-ggplot2 r-ggpubr r-ggtext r-gridextra r-magrittr r-maxstat r-purrr r-rlang r-scales r-survival r-survmisc r-tibble r-tidyr)) (native-inputs (list r-knitr)) (home-page "https://rpkgs.datanovia.com/survminer/index.html") (synopsis "Drawing survival curves using ggplot2") (description "This package contains the function @code{ggsurvplot()} for easily drawing beautiful and 'ready-to-publish' survival curves with the 'number at risk' table and 'censoring count plot'. Other functions are also available to plot adjusted curves for Cox model and to visually examine Cox model assumptions.") (license license:gpl2))) (define-public r-forge (package (name "r-forge") (version "0.2.0") (source (origin (method url-fetch) (uri (cran-uri "forge" version)) (sha256 (base32 "0pjfzsc35agkh0zfw2czwajkbsyn6liys5irl5bhz5r1vim3jmwa")))) (properties `((upstream-name . "forge"))) (build-system r-build-system) (propagated-inputs (list r-magrittr r-rlang)) (home-page "https://cran.r-project.org/web/packages/forge/") (synopsis "Cast values into shape") (description "This package provides helper functions with a consistent interface to coerce and verify the types and shapes of values for input checking.") (license license:asl2.0))) (define-public r-config (package (name "r-config") (version "0.3.2") (source (origin (method url-fetch) (uri (cran-uri "config" version)) (sha256 (base32 "0r8hjg7jrhr9lncb82xmq2slygv3slacd2w8ds6shnvdp3122p3v")))) (properties `((upstream-name . 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(license license:gpl2+))) (define-public r-metafor (package (name "r-metafor") (version "4.6-0") (source (origin (method url-fetch) (uri (cran-uri "metafor" version)) (sha256 (base32 "0rl6w4j1fqvr7vn0dbzmir28xbi2wdn9m3lrxwjvvf47pp1lqd07")))) (properties `((upstream-name . "metafor"))) (build-system r-build-system) (propagated-inputs (list r-mathjaxr r-matrix r-metadat r-nlme r-numderiv r-pbapply)) (native-inputs (list r-r-rsp)) (home-page "https://cran.r-project.org/web/packages/metafor/") (synopsis "Meta-analysis package for R") (description "This package provides a comprehensive collection of functions for conducting meta-analyses in R. The package includes functions to calculate various effect sizes or outcome measures, fit fixed-, random-, and mixed-effects models to such data, carry out moderator and meta-regression analyses, and create various types of meta-analytical plots (e.g., forest, funnel, radial, L'Abbe, Baujat, GOSH plots). For meta-analyses of binomial and person-time data, the package also provides functions that implement specialized methods, including the Mantel-Haenszel method, Peto's method, and a variety of suitable generalized linear (mixed-effects) models (i.e. mixed-effects logistic and Poisson regression models). Finally, the package provides functionality for fitting meta-analytic multivariate/multilevel models that account for non-independent sampling errors and/or true effects (e.g. due to the inclusion of multiple treatment studies, multiple endpoints, or other forms of clustering). Network meta-analyses and meta-analyses accounting for known correlation structures (e.g. due to phylogenetic relatedness) can also be conducted.") 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"perm"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/perm/") (synopsis "Exact or asymptotic permutation tests") (description "This package provides several methods for performing permutation tests. It has three main functions, to perform linear permutation tests. These tests are tests where the test statistic is the sum of the product of a covariate (usually group indicator) and the scores.") ;; Any version of the GPL (license license:gpl2+))) (define-public r-qtl (package (name "r-qtl") (version "1.66") (source (origin (method url-fetch) (uri (cran-uri "qtl" version)) (sha256 (base32 "10fnc3ms97rdqsqxz5jpvg2cmrwmz69wjxxs3h65r1yhy94pssnl")))) (build-system r-build-system) (home-page "https://rqtl.org/") (synopsis "R package for analyzing QTL experiments in genetics") (description "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 estimates genetic maps, to identify genotyping errors, and to perform single-QTL and two-QTL, two-dimensional genome scans.") (license license:gpl3))) (define-public r-qtl2 (package (name "r-qtl2") (version "0.34") (source (origin (method url-fetch) (uri (cran-uri "qtl2" version)) (sha256 (base32 "1h3wim850b2xk09z9vgnyfp20k7vg94zf7szcrlw5nf1w9gn4wzy")))) (build-system r-build-system) (propagated-inputs (list r-data-table r-jsonlite r-rcpp r-rcppeigen r-rsqlite r-yaml)) (home-page "https://kbroman.org/qtl2/") (synopsis "Quantitative Trait Locus Mapping in Experimental Crosses") (description "This package provides a set of tools to perform @dfn{Quantitative Trait Locus} (QTL) analysis in experimental crosses. It is a reimplementation of the @code{R/qtl} package to better handle high-dimensional data and complex cross designs. Broman et al. (2018) .") (license license:gpl3))) (define-public r-seqminer (package (name "r-seqminer") (version "9.4") (source (origin (method url-fetch) (uri (cran-uri "seqminer" version)) (sha256 (base32 "0m9ysdq4ch4c2i3d86gd32rbi0v637djvr295wzzwgkflk66sz5c")))) (build-system r-build-system) (inputs (list zlib)) (home-page "http://seqminer.genomic.codes") (synopsis "Read nucleotide sequence data (VCF, BCF, and METAL formats)") (description "This package provides tools to integrate nucleotide sequencing data (variant call format, e.g. VCF or BCF) or meta-analysis results in R.") ;; Any version of the GPL is acceptable (license (list license:gpl2+ license:gpl3+)))) (define-public r-maldiquant (package (name "r-maldiquant") (version "1.22.2") (source (origin (method url-fetch) (uri (cran-uri "MALDIquant" version)) (sha256 (base32 "1zygmn8cny5r4s0ni2kgqbg2xzjvjh9rzmqnw256jg0035qb0lb0")))) (properties `((upstream-name . "MALDIquant"))) (build-system r-build-system) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/MALDIquant") (synopsis "Quantitative analysis of mass spectrometry data") (description "This package provides a complete analysis pipeline for matrix-assisted laser desorption/ionization-time-of-flight (MALDI-TOF) and other two-dimensional mass spectrometry data. In addition to commonly used plotting and processing methods it includes distinctive features, namely baseline subtraction methods such as morphological filters (TopHat) or the statistics-sensitive non-linear iterative peak-clipping algorithm (SNIP), peak alignment using warping functions, handling of replicated measurements as well as allowing spectra with different resolutions.") (license license:gpl3+))) (define-public r-scattermore (package (name "r-scattermore") (version "1.2") (source (origin (method url-fetch) (uri (cran-uri "scattermore" version)) (sha256 (base32 "1l820rc4ncmqd5sacdc420xf6r5dh34sbhgzzgq7a4yx1dxshd2m")))) (properties `((upstream-name . "scattermore"))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-scales)) (native-inputs (list r-knitr)) (home-page "https://github.com/exaexa/scattermore") (synopsis "Scatterplots with more points") (description "This package provides C-based tools for converting large scatterplot data to rasters. It speeds up plotting of data with millions of points.") (license license:gpl3+))) (define-public r-seuratobject (package (name "r-seuratobject") (version "5.0.1") (source (origin (method url-fetch) (uri (cran-uri "SeuratObject" version)) (sha256 (base32 "0hgrymldcqja40prr23gwx1c7lvwjjwcla3dld6x8wzkzqh1gkjs")))) (properties `((upstream-name . "SeuratObject"))) (build-system r-build-system) (propagated-inputs (list r-future r-future-apply r-generics r-lifecycle r-matrix r-progressr r-rcpp r-rcppeigen r-rlang r-sp r-spam)) (home-page "https://satijalab.org/seurat") (synopsis "Data structures for single cell data") (description "This package defines S4 classes for single-cell genomic data and associated information, such as dimensionality reduction embeddings, nearest-neighbor graphs, and spatially-resolved coordinates. It provides data access methods and R-native hooks to ensure the Seurat object is familiar to other R users.") (license license:gpl3))) ;; This is for r-seurat5 (define-public r-seurat5object (let ((commit "185884ae527d6ce71cb51d2e84a630030e8439a3") (revision "1")) (package (inherit r-seuratobject) (name "r-seurat5object") (version (git-version "4.9.9.9084" revision commit)) (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/mojaveazure/seurat-object") (commit commit))) (file-name (git-file-name name version)) (sha256 (base32 "1nbai31gjsgiaazb4jhpqw8h04nm8xd131fng7zcw11kspj54n9z")) ;; This file triggers renv, which we don't want to use. (snippet '(delete-file ".Rprofile")))) (propagated-inputs (list r-future r-future-apply r-generics r-lifecycle r-matrix r-progressr r-rcpp r-rcppeigen r-rlang r-sp r-spam))))) (define-public r-seurat (package (name "r-seurat") (version "5.0.3") (source (origin (method url-fetch) (uri (cran-uri "Seurat" version)) (sha256 (base32 "08r5l6sk8i134izd29ydfm7hva7a9b3lfglmgngc9w73qs9dzwz4")))) (properties `((upstream-name . "Seurat"))) (build-system r-build-system) (propagated-inputs (list r-cluster r-cowplot r-fastdummies r-fitdistrplus r-future r-future-apply r-generics r-ggplot2 r-ggrepel r-ggridges r-httr r-ica r-igraph r-irlba r-jsonlite r-kernsmooth r-leiden r-lifecycle r-lmtest r-mass r-matrix r-matrixstats r-miniui r-patchwork r-pbapply r-plotly r-png r-progressr r-purrr r-rann r-rcolorbrewer r-rcpp r-rcppannoy r-rcppeigen r-rcpphnsw r-rcppprogress r-reticulate r-rlang r-rocr r-rspectra r-rtsne r-scales r-scattermore r-sctransform r-seuratobject r-shiny r-spatstat-explore r-spatstat-geom r-tibble r-uwot)) (home-page "https://www.satijalab.org/seurat") (synopsis "Seurat is an R toolkit for single cell genomics") (description "This package is an R package designed for QC, analysis, and exploration of single cell RNA-seq data. It easily enables widely-used analytical techniques, including the identification of highly variable genes, dimensionality reduction; PCA, ICA, t-SNE, standard unsupervised clustering algorithms; density clustering, hierarchical clustering, k-means, and the discovery of differentially expressed genes and markers.") (license license:gpl3))) ;; Seurat5 is only available via the seurat5 branch. It will replace r-seurat ;; eventually once it has been released to CRAN. (define-public r-seurat5 (let ((commit "9d59c02042b9ae4f182fbde84cc8b18c0873ef4d") (revision "1")) (package (inherit r-seurat) (name "r-seurat5") (version (git-version "4.9.9.9044" revision commit)) (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/satijalab/seurat") (commit commit))) (file-name (git-file-name name version)) (sha256 (base32 "0y4wl6aanq9scn2clazlxsar35g64v4sfy561j43fq1i85na7m4i")))) (propagated-inputs (list r-cluster r-cowplot r-fastdummies r-fitdistrplus r-future r-future-apply r-generics r-ggplot2 r-ggrepel r-ggridges r-httr r-ica r-igraph r-irlba r-jsonlite r-kernsmooth r-leiden r-lifecycle r-lmtest r-mass r-matrix r-matrixstats r-miniui r-patchwork r-pbapply r-plotly r-png r-progressr r-rann r-rcolorbrewer r-rcpp r-rcppannoy r-rcppeigen r-rcpphnsw r-rcppprogress r-reticulate r-rlang r-rocr r-rspectra r-rtsne r-scales r-scattermore r-sctransform r-seurat5object r-shiny r-spatstat-explore r-spatstat-geom r-tibble r-uwot))))) (define-public r-seuratdisk (let ((commit "877d4e18ab38c686f5db54f8cd290274ccdbe295") (revision "1")) (package (name "r-seuratdisk") (version (git-version "0.0.0.9021" revision commit)) (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/mojaveazure/seurat-disk") (commit commit))) (file-name (git-file-name name version)) (sha256 (base32 "0ma9qk95symk95slp8klriqg64d8klqf1634y93ml74icarxw1dm")))) (properties `((upstream-name . "SeuratDisk"))) (build-system r-build-system) (propagated-inputs (list r-cli r-crayon r-hdf5r r-matrix r-r6 r-rlang r-seurat r-seuratobject r-stringi r-withr)) (native-inputs (list r-knitr)) (home-page "https://github.com/mojaveazure/seurat-disk") (synopsis "Interfaces for HDF5-based single cell file formats") (description "The h5Seurat file format is specifically designed for the storage and analysis of multi-modal single-cell and spatially-resolved expression experiments, for example, from CITE-seq or 10X Visium technologies. It holds all molecular information and associated metadata, including (for example) nearest-neighbor graphs, dimensional reduction information, spatial coordinates and image data, and cluster labels. This package also supports rapid and on-disk conversion between h5Seurat and AnnData objects, with the goal of enhancing interoperability between Seurat and Scanpy.") (license license:gpl3)))) (define-public r-seuratdata (let ((commit "4dc08e022f51c324bc7bf785b1b5771d2742701d") (revision "1")) (package (name "r-seuratdata") (version (git-version "0.2.2.9001" revision commit)) (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/satijalab/seurat-data") (commit commit))) (file-name (git-file-name name version)) (sha256 (base32 "1wac1jqh42nbaikkd8v3apr1lwqcn1ppprfkwqfnqs6mvavgqavp")))) (properties `((upstream-name . "SeuratData"))) (build-system r-build-system) (arguments `(#:phases (modify-phases %standard-phases ;; When there is no HOME directory, this package will fail to load ;; the included list of packages. (add-after 'unpack 'set-HOME (lambda _ (setenv "HOME" "/tmp")))))) (propagated-inputs (list r-cli r-crayon r-rappdirs r-seurat r-seuratobject)) (home-page "https://github.com/satijalab/seurat-data") (synopsis "Install and manage Seurat datasets") (description "Single cell RNA sequencing datasets can be large, consisting of matrices that contain expression data for several thousand features across several thousand cells. This package is designed to easily install, manage, and learn about various single-cell datasets, provided Seurat objects and distributed as independent packages.") (license license:gpl3)))) (define-public r-phangorn (package (name "r-phangorn") (version "2.11.1") (source (origin (method url-fetch) (uri (cran-uri "phangorn" version)) (sha256 (base32 "086lxqzqx1n3237h9q28r54libaz2xk9h3f6vfj8l49yw356w28h")))) (build-system r-build-system) (propagated-inputs (list r-ape r-digest r-fastmatch r-generics r-igraph r-matrix r-quadprog r-rcpp)) (native-inputs (list r-knitr)) (home-page "https://github.com/KlausVigo/phangorn") (synopsis "Phylogenetic analysis in R") (description "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.") (license license:gpl2+))) (define-public r-diversitree (package (name "r-diversitree") (version "0.10-0") (source (origin (method url-fetch) (uri (cran-uri "diversitree" version)) (sha256 (base32 "1xl2swbmgpni2y2divl29xh702b88kxgcswa47g62ny59gh2fdn1")))) (build-system r-build-system) (inputs (list fftw gsl)) (propagated-inputs (list r-ape r-desolve r-rcpp r-subplex)) (home-page "https://www.zoology.ubc.ca/prog/diversitree") (synopsis "Comparative 'phylogenetic' analyses of diversification") (description "This package contains a number of comparative \"phylogenetic\" methods, mostly focusing on analysing diversification and character evolution. Contains implementations of \"BiSSE\" (Binary State Speciation and Extinction) and its unresolved tree extensions, \"MuSSE\" (Multiple State Speciation and Extinction), \"QuaSSE\", \"GeoSSE\", and \"BiSSE-ness\" Other included methods include Markov models of discrete and continuous trait evolution and constant rate speciation and extinction.") (license license:gpl2+))) (define-public r-calculus (package (name "r-calculus") (version "1.0.1") (source (origin (method url-fetch) (uri (cran-uri "calculus" version)) (sha256 (base32 "1p80bgg6896z798cx7nwqbwd0rxdv27kamaw1gw0hv4lpqsr7q10")))) (properties `((upstream-name . "calculus"))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) (native-inputs (list r-knitr)) (home-page "https://github.com/eguidotti/calculus") (synopsis "High dimensional numerical and symbolic calculus") (description "Efficient C++ optimized functions for numerical and symbolic calculus. It includes basic symbolic arithmetic, tensor calculus, Einstein summing convention, fast computation of the Levi-Civita symbol and generalized Kronecker delta, Taylor series expansion, multivariate Hermite polynomials, accurate high-order derivatives, differential operators (Gradient, Jacobian, Hessian, Divergence, Curl, Laplacian) and numerical integration in arbitrary orthogonal coordinate systems: cartesian, polar, spherical, cylindrical, parabolic or user defined by custom scale factors.") (license license:gpl3))) (define-public r-decon (package (name "r-decon") (version "1.3-4") (source (origin (method url-fetch) (uri (cran-uri "decon" version)) (sha256 (base32 "036cv56wf42q2p3d5h15hbrp5rc29xxy20qwv4k1qzhkq6hmw0qs")))) (properties `((upstream-name . "decon"))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/decon/") (synopsis "Deconvolution Estimation in Measurement Error Models") (description "This package contains a collection of functions to deal with nonparametric measurement error problems using deconvolution kernel methods. We focus two measurement error models in the package: (1) an additive measurement error model, where the goal is to estimate the density or distribution function from contaminated data; (2) nonparametric regression model with errors-in-variables. The R functions allow the measurement errors to be either homoscedastic or heteroscedastic. To make the deconvolution estimators computationally more efficient in R, we adapt the \"Fast Fourier Transform\" (FFT) algorithm for density estimation with error-free data to the deconvolution kernel estimation. Several methods for the selection of the data-driven smoothing parameter are also provided in the package. See details in: Wang, X.F. and Wang, B. (2011). Deconvolution estimation in measurement error models: The R package decon. Journal of Statistical Software, 39(10), 1-24.") (license license:gpl3+))) (define-public r-densestbayes (package (name "r-densestbayes") (version "1.0-2.2") (source (origin (method url-fetch) (uri (cran-uri "densEstBayes" version)) (sha256 (base32 "0ydnjyprv8fz037nkfvjd8w6hg4a19lbnq4kl7yankxksjfdyqc3")))) (properties `((upstream-name . 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Bandwidth selection is also provided for each method.") (license license:gpl2+))) (define-public r-aws-signature (package (name "r-aws-signature") (version "0.6.0") (source (origin (method url-fetch) (uri (cran-uri "aws.signature" version)) (sha256 (base32 "15llpcnrdq4y6jsn7079yjmgbr5d1wgy2ymsm3jj3gkrd5l4zzpp")))) (properties `((upstream-name . "aws.signature"))) (build-system r-build-system) (propagated-inputs (list r-base64enc r-digest)) (home-page "https://github.com/cloudyr/aws.signature") (synopsis "Amazon Web Services Request Signatures") (description "This package generates version 2 and 4 request signatures for Amazon Web Services (AWS) and provides a mechanism for retrieving credentials from environment variables, AWS credentials files, and EC2 instance metadata. For use on EC2 instances, the package 'aws.ec2metadata' is suggested.") (license license:gpl2+))) (define-public r-aws-s3 (package (name "r-aws-s3") (version "0.3.21") (source (origin (method url-fetch) (uri (cran-uri "aws.s3" version)) (sha256 (base32 "132cczq0ml7lpp2yl6l4p99dn1zihrncnpa6wyad4m9mnr50a8dx")))) (properties `((upstream-name . "aws.s3"))) (build-system r-build-system) (propagated-inputs (list r-aws-signature r-base64enc r-curl r-digest r-httr r-xml2)) (home-page "https://github.com/cloudyr/aws.s3") (synopsis "AWS S3 Client Package") (description "This package provides a simple client package for the Amazon Web Services (AWS) Simple Storage Service (S3) REST API.") (license license:gpl2+))) (define-public r-lgr (package (name "r-lgr") (version "0.4.4") (source (origin (method url-fetch) (uri (cran-uri "lgr" version)) (sha256 (base32 "09x1vw6cnc1c0p0ylcz1q1vcxyaf1kljhh7ni3gl5jm19zii2h4c")))) (build-system r-build-system) (propagated-inputs (list r-r6)) (native-inputs (list r-knitr)) (home-page "https://s-fleck.github.io/lgr/") (synopsis "Fully featured logging framework") (description "This package offers a flexible, feature-rich yet light-weight logging framework based on @code{R6} classes. It supports hierarchical loggers, custom log levels, arbitrary data fields in log events, logging to plaintext, JSON, (rotating) files, memory buffers, and databases, as well as email and push notifications.") (license license:expat))) (define-public r-mhg (package (name "r-mhg") (version "1.1") (source (origin (method url-fetch) (uri (cran-uri "mHG" version)) (sha256 (base32 "1rz5ncrvvv9h9grls15apa63v2nh9j87fmp4mwjjil37jx6a5zki")))) (properties `((upstream-name . "mHG"))) (build-system r-build-system) (home-page "https://cran.r-project.org/package=mHG") (synopsis "Minimum-hypergeometric test") (description "This package runs a minimum-hypergeometric (mHG) test as described in \"Discovering Motifs in Ranked Lists of DNA Sequences\" by Eran Eden.") (license license:gpl2))) (define-public r-mlr (package (name "r-mlr") (version "2.19.1") (source (origin (method url-fetch) (uri (cran-uri "mlr" version)) (sha256 (base32 "00jjhvaqifj6glqsyzixlp56bvlch5smck8kk3klcmwx9pasyllx")))) (properties `((upstream-name . "mlr"))) (build-system r-build-system) (inputs (list gdal geos glu gmp gsl jags mpfr openmpi proj udunits)) (propagated-inputs (list r-backports r-bbmisc r-checkmate r-data-table r-ggplot2 r-parallelmap r-paramhelpers r-stringi r-survival r-xml)) (native-inputs (list r-knitr)) (home-page "https://mlr.mlr-org.com") (synopsis "Machine learning in R") (description "This package provides an interface to a large number of classification and regression techniques. These techniques include machine-readable parameter descriptions. There is also an experimental extension for survival analysis, clustering and general, example-specific cost-sensitive learning. Also included: @itemize @item Generic resampling, including cross-validation, bootstrapping and subsampling; @item Hyperparameter tuning with modern optimization techniques, for single- and multi-objective problems; @item Filter and wrapper methods for feature selection; @item Extension of basic learners with additional operations common in machine learning, also allowing for easy nested resampling. @end itemize Most operations can be parallelized.") (license license:bsd-2))) (define-public r-mlrmbo (package (name "r-mlrmbo") (version "1.1.5.1") (source (origin (method url-fetch) (uri (cran-uri "mlrMBO" version)) (sha256 (base32 "16fwj7m28g4km7yalqppxmh3lw2jln0z072l6awia38qkdg6xwhc")))) (properties `((upstream-name . "mlrMBO"))) (build-system r-build-system) (propagated-inputs (list r-backports r-bbmisc r-checkmate r-data-table r-lhs r-mlr r-parallelmap r-paramhelpers r-smoof)) (native-inputs (list r-knitr)) (home-page "https://github.com/mlr-org/mlrMBO") (synopsis "Model-based optimization with mlr") (description "This package is a flexible and comprehensive R toolbox for model-based optimization. It implements Efficient Global Optimization Algorithm for single- and multi-objective optimization. It supports mixed parameters. The machine learning toolbox mlr offers regression learners. It provides various infill criteria and features batch proposal, parallel execution, visualization, and logging. Its modular implementation allows easy customization by the user.") (license license:bsd-2))) (define-public r-mlr3measures (package (name "r-mlr3measures") (version "0.5.0") (source (origin (method url-fetch) (uri (cran-uri "mlr3measures" version)) (sha256 (base32 "0k0i1xx63lds1870p2ljy1dlp2i376gdd0sq9s4xiqljqjb8va57")))) (build-system r-build-system) (propagated-inputs (list r-checkmate r-prroc)) (home-page "https://mlr3measures.mlr-org.com/") (synopsis "Performance measures for mlr3") (description "This package implements multiple performance measures for supervised learning. It includes over 40 measures for regression and classification. Additionally, meta information about the performance measures can be queried, e.g. what the best and worst possible performances scores are.") (license license:lgpl3))) (define-public r-mlr3misc (package (name "r-mlr3misc") (version "0.15.0") (source (origin (method url-fetch) (uri (cran-uri "mlr3misc" version)) (sha256 (base32 "1l40l0sx1dgs2rdblx7pd9nk93flad6y1mvppzg7qf4cyn8gfc3x")))) (build-system r-build-system) (propagated-inputs (list r-backports r-checkmate r-data-table r-digest r-r6)) (home-page "https://mlr3misc.mlr-org.com/") (synopsis "Helper functions for mlr3") (description "@code{mlr3misc} provides frequently used helper functions and assertions used in @code{mlr3} and its companion packages. It comes with helper functions for functional programming, for printing, to work with @code{data.table}, as well as some generally useful @code{R6} classes. This package also supersedes the package @code{BBmisc}.") (license license:lgpl3))) (define-public r-mlr3pipelines (package (name "r-mlr3pipelines") (version "0.5.1") (source (origin (method url-fetch) (uri (cran-uri "mlr3pipelines" version)) (sha256 (base32 "1brsvzn519yc5vq2sax0q5xwvs0180ykn6ljk2wy502aabrcxzmg")))) (build-system r-build-system) (propagated-inputs (list r-backports r-checkmate r-data-table r-digest r-lgr r-mlr3 r-mlr3misc r-paradox r-r6 r-withr)) (native-inputs (list r-knitr)) (home-page "https://mlr3pipelines.mlr-org.com/") (synopsis "Preprocessing Operators and Pipelines for @code{mlr3}") (description "@code{mlr3pipelines} enriches @code{mlr3} with a diverse set of pipelining operators (PipeOps) that can be composed into graphs. Operations exist for data preprocessing, model fitting, and ensemble learning. Graphs can themselves be treated as @code{mlr3} Learners and can therefore be resampled, benchmarked, and tuned.") (license license:lgpl3))) (define-public r-mlr3ordinal (let ((commit "736e3a39be6b7088b650297cc6d90208ec58c0d7") (revision "1")) (package (name "r-mlr3ordinal") (version (git-version "0.1.0-9000" revision commit)) (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/mlr-org/mlr3ordinal") (commit commit))) (file-name (git-file-name name version)) (sha256 (base32 "0ipf6n4m6giicn0x7f3lrfmbqkhw8zkz32hzq2xf209wndkqhqm1")))) (build-system r-build-system) (propagated-inputs (list r-checkmate r-data-table r-mlr3 r-mlr3misc r-mlr3pipelines r-nloptr r-ordinal r-paradox r-r6)) (home-page "https://mlr3ordinal.mlr-org.com/") (synopsis "Ordinal Regression for mlr3") (description "This package extends @code{mlr3} with support for performing ordinal regression.") (license license:expat)))) (define-public r-paradox (package (name "r-paradox") (version "0.11.1") (source (origin (method url-fetch) (uri (cran-uri "paradox" version)) (sha256 (base32 "0igza40ycirnf5chs7z2nnh0w6d48v4wv102zn2vnvh0kkvgv3hd")))) (build-system r-build-system) (propagated-inputs (list r-backports r-checkmate r-data-table r-mlr3misc r-r6)) (home-page "https://paradox.mlr-org.com/") (synopsis "Define and work with parameter spaces for complex algorithms") (description "With this package it is possible to define parameter spaces, constraints and dependencies for arbitrary algorithms, and to program on such spaces. It also includes statistical designs and random samplers. Objects are implemented as @code{R6} classes.") (license license:lgpl3))) (define-public r-mlr3 (package (name "r-mlr3") (version "0.18.0") (source (origin (method url-fetch) (uri (cran-uri "mlr3" version)) (sha256 (base32 "0v83lwigpm227dqr8hz5x1khcjqf3q0glqvz812sckbcf74ibhdz")))) (build-system r-build-system) (propagated-inputs (list r-backports r-checkmate r-data-table r-evaluate r-future r-future-apply r-lgr r-mlbench r-mlr3measures r-mlr3misc r-palmerpenguins r-paradox r-parallelly r-r6 r-rhpcblasctl r-uuid)) (home-page "https://mlr3.mlr-org.com/") (synopsis "Machine Learning in R - Next Generation") (description "@code{mlr3} enables efficient, object-oriented programming on the building blocks of machine learning. It provides @code{R6} objects for tasks, learners, resamplings, and measures. The package is geared towards scalability and larger datasets by supporting parallelization and out-of-memory data-backends like databases. While @code{mlr3} focuses on the core computational operations, add-on packages provide additional functionality.") (license license:lgpl3))) (define-public r-mlr3learners (package (name "r-mlr3learners") (version "0.6.0") (source (origin (method url-fetch) (uri (cran-uri "mlr3learners" version)) (sha256 (base32 "06gz6h19cnb62js1b35nddy453dyj64mr788p8ww56kgfk6yzxr8")))) (build-system r-build-system) (propagated-inputs (list r-checkmate r-data-table r-mlr3 r-mlr3misc r-paradox r-r6)) (home-page "https://mlr3learners.mlr-org.com/") (synopsis "Recommended Learners for @code{mlr3}") (description "@code{mlr3learners} extends @code{mlr3} and @code{mlr3proba} with interfaces to essential machine learning packages on CRAN. This includes, but is not limited to: (penalized) linear and logistic regression, linear and quadratic discriminant analysis, k-nearest neighbors, naive Bayes, support vector machines, and gradient boosting.") (license license:lgpl3))) (define-public r-bbotk (package (name "r-bbotk") (version "0.8.0") (source (origin (method url-fetch) (uri (cran-uri "bbotk" version)) (sha256 (base32 "1ggfl1lhvjnnkxib4svqd82agrvjcg1101cbf4g2c0kzgzm1jaj6")))) (properties `((upstream-name . "bbotk"))) (build-system r-build-system) (propagated-inputs (list r-checkmate r-data-table r-lgr r-mlr3misc r-paradox r-r6)) (native-inputs (list r-knitr)) (home-page "https://bbotk.mlr-org.com") (synopsis "Black-Box Optimization Toolkit") (description "This package provides a common framework for optimization of black-box functions for other packages, e.g. @code{mlr3}. It offers various optimization methods e.g. grid search, random search and generalized simulated annealing.") (license license:lgpl3))) (define-public r-mlr3tuning (package (name "r-mlr3tuning") (version "0.20.0") (source (origin (method url-fetch) (uri (cran-uri "mlr3tuning" version)) (sha256 (base32 "1y1cqfqdx9v0lfb4619y2hw6clhhjzi7hjwrpwzdpd7ymcx3dgi3")))) (build-system r-build-system) (propagated-inputs (list r-bbotk r-checkmate r-data-table r-lgr r-mlr3 r-mlr3misc r-paradox r-r6)) (native-inputs (list r-knitr)) (home-page "https://mlr3tuning.mlr-org.com/") (synopsis "Tuning for @code{mlr3}") (description "@code{mlr3tuning} implements methods for hyperparameter tuning, e.g. Grid Search, Random Search, or Simulated Annealing. Various termination criteria can be set and combined. The class @code{AutoTuner} provides a convenient way to perform nested resampling in combination with @code{mlr3}.") (license license:lgpl3))) (define-public r-fontliberation (package (name "r-fontliberation") (version "0.1.0") (source (origin (method url-fetch) (uri (cran-uri "fontLiberation" version)) (sha256 (base32 "1w1rl0g4ayyp8lwppmz9yzj9cizg7i50g07216jkm1q5w0is9pmc")))) (properties `((upstream-name . "fontLiberation"))) (build-system r-build-system) (home-page "https://cran.r-project.org/package=fontLiberation") (synopsis "Liberation fonts") (description "This package provides a placeholder for the Liberation fontset intended for the fontquiver package. This fontset covers the 12 combinations of families (sans, serif, mono) and faces (plain, bold, italic, bold italic) supported in R graphics devices.") (license license:silofl1.1))) (define-public r-fontbitstreamvera (package (name "r-fontbitstreamvera") (version "0.1.1") (source (origin (method url-fetch) (uri (cran-uri "fontBitstreamVera" version)) (sha256 (base32 "0nipdlmhjv1wr3aidcl97nk6mppdkd65krgwqnhdsnv0jpfv761j")))) (properties `((upstream-name . "fontBitstreamVera"))) (build-system r-build-system) (home-page "https://cran.r-project.org/package=fontBitstreamVera") (synopsis "Fonts for fontquiver") (description "This package is a placeholder for the Bitstream Vera font. It is intended for the fontquiver package.") (license (license:fsdg-compatible "https://www.gnome.org/fonts/#Final_Bitstream_Vera_Fonts" "The Font Software may be sold as part of a larger software package but no copy of one or more of the Font Software typefaces may be sold by itself.")))) (define-public r-fontquiver (package (name "r-fontquiver") (version "0.2.1") (source (origin (method url-fetch) (uri (cran-uri "fontquiver" version)) (sha256 (base32 "0qv3i9hch7cygl9983s3w68wfh5qvym2jkm52pp06p6mq8a1i1wm")))) (properties `((upstream-name . "fontquiver"))) (build-system r-build-system) (propagated-inputs (list r-fontbitstreamvera r-fontliberation)) (home-page "https://cran.r-project.org/package=fontquiver") (synopsis "Set of installed fonts") (description "This package provides a set of fonts. This is useful when you want to avoid system fonts to make sure your outputs are reproducible.") (license license:gpl3))) (define-public r-freetypeharfbuzz (package (name "r-freetypeharfbuzz") (version "0.2.6") (source (origin (method url-fetch) (uri (cran-uri "freetypeharfbuzz" version)) (sha256 (base32 "0r3icgnq3jk4fm6z92cmhzdmflbk5df8zsmjg0dzpc4y48xafnk7")))) (properties `((upstream-name . "freetypeharfbuzz"))) (build-system r-build-system) (arguments `(#:phases (modify-phases %standard-phases (add-after 'unpack 'prepare-static-libraries (lambda* (#:key inputs #:allow-other-keys) (mkdir-p "src/target/include") (let ((freetype (assoc-ref inputs "static-freetype")) (harfbuzz (assoc-ref inputs "static-harfbuzz"))) (substitute* "src/Makevars.in" (("include @MK_FILE@") "") ; do not build static libs (("^HB_STATIC_LIB =.*") (string-append "HB_STATIC_LIB = " harfbuzz "/lib/libharfbuzz.a\n")) (("^FT_STATIC_LIB =.*") (string-append "FT_STATIC_LIB = " freetype "/lib/libfreetype.a\n"))) (copy-recursively (string-append freetype "/include") "src/target/include") (copy-recursively (string-append harfbuzz "/include") "src/target/include"))))))) (propagated-inputs (list r-fontquiver)) ;; This may defeat the purpose of this package as our versions of freetype ;; and harfbuzz obviously differ from the tarballs offered by this ;; project. On the other hand, Guix arguably does a better job at ;; "ensur[ing] deterministic computation". (native-inputs `(("static-freetype" ,(package (inherit (static-package freetype)) (arguments `(#:configure-flags (list "--enable-static=yes" "--with-pic=yes" "--without-zlib" "--without-bzip2" "--without-png" "--without-harfbuzz"))))) ("static-harfbuzz" ,(package (inherit (static-package harfbuzz)) (arguments `(#:tests? #false ; fail because shared library is disabled #:configure-flags (list "--enable-static=yes" "--enable-shared=no" "--with-pic=yes" "--with-freetype=yes" "--without-icu" "--without-cairo" "--without-fontconfig" "--without-glib"))))))) (inputs (list zlib)) (home-page "https://cran.r-project.org/package=freetypeharfbuzz") (synopsis "Deterministic computation of text box metrics") (description "Unlike other tools that dynamically link to the Cairo stack, freetypeharfbuzz is statically linked to specific versions of the FreeType and harfbuzz libraries. This ensures deterministic computation of text box extents for situations where reproducible results are crucial (for instance unit tests of graphics).") (license license:gpl3))) (define-public r-vdiffr (package (name "r-vdiffr") (version "1.0.7") (source (origin (method url-fetch) (uri (cran-uri "vdiffr" version)) (sha256 (base32 "1ljj94swqgs8pvicdrlals6pckm7knwfvxxmmbhhi2zfcxdjwhzd")))) (properties `((upstream-name . "vdiffr"))) (build-system r-build-system) (inputs (list libpng zlib)) (propagated-inputs (list r-cpp11 r-diffobj r-glue r-htmltools r-lifecycle r-rlang r-testthat r-xml2)) (home-page "https://github.com/r-lib/vdiffr") (synopsis "Visual regression testing and graphical diffing") (description "This package is an extension to the testthat package that makes it easy to add graphical unit tests. It provides a Shiny application to manage the test cases.") (license license:gpl3))) (define-public r-highlight (package (name "r-highlight") (version "0.5.1") (source (origin (method url-fetch) (uri (cran-uri "highlight" version)) (sha256 (base32 "06sirfmkdl355rfr5bb475829v7zx1spkz82vi31vl55jzijq54m")))) (properties `((upstream-name . "highlight"))) (build-system r-build-system) (home-page "https://github.com/hadley/highlight") (synopsis "Syntax highlighter for R code") (description "This package provides a syntax highlighter for R code based on the results of the R parser. It supports rendering in HTML and LaTeX markup. It includes a custom Sweave driver performing syntax highlighting of R code chunks.") (license license:gpl3+))) (define-public r-clustree (package (name "r-clustree") (version "0.5.1") (source (origin (method url-fetch) (uri (cran-uri "clustree" version)) (sha256 (base32 "05yizn8hcf4nsibypxahp2mz64sy10vli776mi0d2gvfb5p4kwmm")))) (properties `((upstream-name . "clustree"))) (build-system r-build-system) (propagated-inputs (list r-checkmate r-dplyr r-ggplot2 r-ggraph r-ggrepel r-igraph r-rlang r-tidygraph r-viridis)) (native-inputs (list r-knitr)) (home-page "https://github.com/lazappi/clustree") (synopsis "Visualize clusterings at different resolutions") (description "Deciding what resolution to use can be a difficult question when approaching a clustering analysis. One way to approach this problem is to look at how samples move as the number of clusters increases. This package allows you to produce clustering trees, a visualization for interrogating clusterings as resolution increases.") (license license:gpl3))) (define-public r-textshaping (package (name "r-textshaping") (version "0.3.7") (source (origin (method url-fetch) (uri (cran-uri "textshaping" version)) (sha256 (base32 "0hpcjz66ykji89g2lzpp6hfkz10388py8vn2ss08n4xl3yz4v4ps")))) (properties `((upstream-name . 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"pkgdown"))) (build-system r-build-system) (inputs (list pandoc)) (propagated-inputs (list r-bslib r-callr r-cli r-desc r-digest r-downlit r-fs r-httr r-jsonlite r-magrittr r-memoise r-purrr r-ragg r-rlang r-rmarkdown r-tibble r-whisker r-withr r-xml2 r-yaml)) (native-inputs (list r-knitr)) (home-page "https://pkgdown.r-lib.org") (synopsis "Make static HTML documentation for an R package") (description "The goal of this package is to generate an attractive and useful website from a source package. @code{pkgdown} converts your documentation, vignettes, README file, and more to HTML making it easy to share information about your package online.") (license license:expat))) (define-public r-prereg (package (name "r-prereg") (version "0.6.0") (source (origin (method url-fetch) (uri (cran-uri "prereg" version)) (sha256 (base32 "039nrl5cirsx1ysh214dr6xnn1h6h3f90im6k9dgmzfksxdqigpw")))) (properties `((upstream-name . "prereg"))) (build-system r-build-system) (propagated-inputs (list r-rmarkdown ;; The package provides a custom LaTex template in ;; inst/rmd/prereg_form.tex, which depends on these packages: texlive-amsmath texlive-booktabs texlive-etoolbox texlive-fancyhdr texlive-fancyvrb texlive-geometry texlive-graphics texlive-iftex texlive-listings texlive-polyglossia texlive-threeparttable texlive-titlesec texlive-titling texlive-tools texlive-ulem texlive-upquote (texlive-updmap.cfg (list texlive-lm)))) (home-page "https://github.com/crsh/prereg") (synopsis "R Markdown Templates to preregister Scientific Studies") (description "This package provides a collection of templates to author preregistration documents for scientific studies in PDF format.") (license license:gpl3))) (define-public r-ez (package (name "r-ez") (version "4.4-0") (source (origin (method url-fetch) (uri (cran-uri "ez" version)) (sha256 (base32 "0a58s94x576dfz7wcbivrr2hmdh5x1vy16zwkqp9fmdzqx38pagq")))) (properties `((upstream-name . "ez"))) (build-system r-build-system) (propagated-inputs (list r-car r-ggplot2 r-lme4 r-mass r-matrix r-mgcv r-plyr r-reshape2 r-scales r-stringr)) (home-page "https://github.com/mike-lawrence/ez") (synopsis "Easy Analysis and Visualization of Factorial Experiments") (description "Facilitates easy analysis of factorial experiments, including purely within-Ss designs (a.k.a. \"repeated measures\"), purely between-Ss designs, and mixed within-and-between-Ss designs. The functions in this package aim to provide simple, intuitive and consistent specification of data analysis and visualization. Visualization functions also include design visualization for pre-analysis data auditing, and correlation matrix visualization. Finally, this package includes functions for non-parametric analysis, including permutation tests and bootstrap resampling. The bootstrap function obtains predictions either by cell means or by more advanced/powerful mixed effects models, yielding predictions and confidence intervals that may be easily visualized at any level of the experiment's design.") (license license:gpl2+))) (define-public r-qdapregex (package (name "r-qdapregex") (version "0.7.8") (source (origin (method url-fetch) (uri (cran-uri "qdapRegex" version)) (sha256 (base32 "1pf1cz03i6sn83d1aaj4cv4jfavs6k81nn5sy7b0aw4i1hpkyiwz")))) (properties `((upstream-name . "qdapRegex"))) (build-system r-build-system) (propagated-inputs (list r-stringi)) (home-page "https://trinker.github.com/qdapRegex/") (synopsis "Regular Expression Removal, Extraction, and Replacement Tools") (description "This package provides a collection of regular expression tools associated with the @code{qdap} package that may be useful outside of the context of discourse analysis. Tools include removal/extraction/replacement of abbreviations, dates, dollar amounts, email addresses, hash tags, numbers, percentages, citations, person tags, phone numbers, times, and zip codes.") (license license:gpl2))) (define-public r-mgsub (package (name "r-mgsub") (version "1.7.3") (source (origin (method url-fetch) (uri (cran-uri "mgsub" version)) (sha256 (base32 "1mci6x65h94qiz9cwikx2inbrwkykv43zbs8abfbx416zrh2bbn9")))) (properties `((upstream-name . "mgsub"))) (build-system r-build-system) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/package=mgsub") (synopsis "Safe, Multiple, Simultaneous String Substitution") (description "Designed to enable simultaneous substitution in strings in a safe fashion. Safe means it does not rely on placeholders (which can cause errors in same length matches).") (license license:expat))) (define-public r-textshape (package (name "r-textshape") (version "1.7.5") (source (origin (method url-fetch) (uri (cran-uri "textshape" version)) (sha256 (base32 "1g193dg4rhw8a1iwkyqsswlj95h9irm9xziclwc1mhd3jm5wyify")))) (properties `((upstream-name . "textshape"))) (build-system r-build-system) (propagated-inputs (list r-data-table r-slam r-stringi)) (home-page "https://github.com/trinker/textshape") (synopsis "Tools for Reshaping Text") (description "Tools that can be used to reshape and restructure text data.") (license license:gpl2))) (define-public r-syuzhet (package (name "r-syuzhet") (version "1.0.7") (source (origin (method url-fetch) (uri (cran-uri "syuzhet" version)) (sha256 (base32 "0cpjg16hwn6843jdxp4h94qjw1wwwblvjzg30w54rac08m62nkxg")))) (properties `((upstream-name . "syuzhet"))) (build-system r-build-system) (propagated-inputs (list r-dplyr r-dtt r-nlp r-rlang r-textshape r-tidyr r-zoo)) (native-inputs (list r-knitr)) (home-page "https://github.com/mjockers/syuzhet") (synopsis "Extracts Sentiment and Sentiment-Derived Plot Arcs from Text") (description "Extracts sentiment and sentiment-derived plot arcs from text using a variety of sentiment dictionaries conveniently packaged for consumption by R users. Implemented dictionaries include @dfn{syuzhet} (default) developed in the Nebraska Literary Lab, @dfn{afinn} developed by Finn Arup Nielsen, @dfn{bing} developed by Minqing Hu and Bing Liu, and @dfn{nrc} developed by Mohammad, Saif M. and Turney, Peter D. Applicable references are available in @file{README.md} and in the documentation for the @code{get_sentiment} function. The package also provides a hack for implementing Stanford's coreNLP sentiment parser. The package provides several methods for plot arc normalization.") (license license:gpl3))) (define-public r-lexicon (package (name "r-lexicon") (version "1.2.1") (source (origin (method url-fetch) (uri (cran-uri "lexicon" version)) (sha256 (base32 "0x7rscsh6par2lj11sby7bmz41cxn63iiw51lgh29z09cg8j606c")))) (properties `((upstream-name . "lexicon"))) (build-system r-build-system) (propagated-inputs (list r-data-table r-syuzhet)) (home-page "https://github.com/trinker/lexicon") (synopsis "Lexicons for Text Analysis") (description "This package provides a collection of lexical hash tables, dictionaries, and word lists.") (license license:gpl3))) (define-public r-english (package (name "r-english") (version "1.2-6") (source (origin (method url-fetch) (uri (cran-uri "english" version)) (sha256 (base32 "1g3nmy5p8wj3ix1vp1qmkmy3dyqisrw0md8cjrx4klqkp0wqlms9")))) (properties `((upstream-name . "english"))) (build-system r-build-system) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/package=english") (synopsis "Translate Integers into English") (description "Allow numbers to be presented in an English language version, one, two, three, ... Ordinals are also available, first, second, third, ... and indefinite article choice, \"a\" or \"an\".") (license license:gpl2))) (define-public r-textclean (package (name "r-textclean") (version "0.9.3") (source (origin (method url-fetch) (uri (cran-uri "textclean" version)) (sha256 (base32 "0kgjh6c4f14qkjc4fds7q7rpf4nkma3p0igm54fplmm3p853nvrz")))) (properties `((upstream-name . "textclean"))) (build-system r-build-system) (propagated-inputs (list r-data-table r-english r-glue r-lexicon r-mgsub r-qdapregex r-stringi r-textshape)) (home-page "https://github.com/trinker/textclean") (synopsis "Text Cleaning Tools") (description "Tools to clean and process text. Tools are geared at checking for substrings that are not optimal for analysis and replacing or removing them (normalizing) with more analysis friendly substrings (see Sproat, Black, Chen, Kumar, Ostendorf, & Richards (2001) @url{doi:10.1006/csla.2001.0169}) or extracting them into new variables. For example, emoticons are often used in text but not always easily handled by analysis algorithms. The @code{replace_emoticon()} function replaces emoticons with word equivalents.") (license license:gpl2))) (define-public r-striprtf (package (name "r-striprtf") (version "0.6.0") (source (origin (method url-fetch) (uri (cran-uri "striprtf" version)) (sha256 (base32 "1c8z2qf1kp43ir4dmyxq6hc46dclq8vx3ggkj02p8j1icjswm9bh")))) (properties `((upstream-name . "striprtf"))) (build-system r-build-system) (propagated-inputs (list r-magrittr r-rcpp r-stringr)) (home-page "https://github.com/kota7/striprtf") (synopsis "Extract Text from RTF File") (description "Extracts plain text from @dfn{Rich Text Format} (RTF) file.") (license license:expat))) (define-public r-ndjson (package (name "r-ndjson") (version "0.9.0") (source (origin (method url-fetch) (uri (cran-uri "ndjson" version)) (sha256 (base32 "18j5bibranvbv84hvbsg6glmvhfancdsf2w6j99n3nw53bcgb12d")) (modules '((guix build utils))) (snippet '(begin ;; unvendor gzstream (for-each delete-file '("src/gzstream.cpp" "src/gzstream.h")) #t)))) (properties `((upstream-name . "ndjson"))) (build-system r-build-system) (arguments '(#:phases (modify-phases %standard-phases (add-after 'unpack 'use-system-gzstream (lambda* (#:key inputs #:allow-other-keys) (substitute* "src/Makevars" (("PKG_LIBS = " all) (string-append all "-lgzstream "))) #t))))) (inputs (list zlib gzstream)) (propagated-inputs (list r-data-table r-rcpp r-tibble)) (home-page "https://gitlab.com/hrbrmstr/ndjson") (synopsis "Wicked-Fast @dfn{Streaming JSON} (ndjson) Reader") (description "@dfn{Streaming JSON} (ndjson) has one JSON record per-line and many modern ndjson files contain large numbers of records. These constructs may not be columnar in nature, but it is often useful to read in these files and \"flatten\" the structure out to enable working with the data in an R @code{data.frame}-like context. Functions are provided that make it possible to read in plain ndjson files or compressed (@code{gz}) ndjson files and either validate the format of the records or create \"flat\" @code{data.table} structures from them.") (license license:expat))) (define-public r-streamr (package (name "r-streamr") (version "0.4.5") (source (origin (method url-fetch) (uri (cran-uri "streamR" version)) (sha256 (base32 "1clx3b0j2515r1nmnl6ki7qw5n54q3x2jvqv3zrc00kq71mlj7ix")))) (properties `((upstream-name . "streamR"))) (build-system r-build-system) (propagated-inputs (list r-ndjson r-rcurl r-rjson)) (home-page "https://cran.r-project.org/package=streamR") (synopsis "Access to Twitter Streaming API via R") (description "This package provides functions to access Twitter's filter, sample, and user streams, and to parse the output into data frames.") (license license:gpl2))) (define-public r-strex (package (name "r-strex") (version "2.0.0") (source (origin (method url-fetch) (uri (cran-uri "strex" version)) (sha256 (base32 "1cxkpqwnpsqkg0i6n6bkkgbf3jkbgff5s8db95rz57lki8xwlqp9")))) (properties `((upstream-name . "strex"))) (build-system r-build-system) (propagated-inputs (list r-checkmate r-lifecycle r-magrittr r-rlang r-stringi r-stringr)) (native-inputs (list r-knitr)) (home-page "https://rorynolan.github.io/strex/") (synopsis "Extra string manipulation functions") (description "Strex is a collection of string manipulation functions not provided by the @code{stringi} or @code{stringr} packages. The foremost of these is the extraction of numbers from strings. There are many other handy functionalities in strex.") (license license:gpl3))) (define-public r-readods (package (name "r-readods") (version "2.2.0") (source (origin (method url-fetch) (uri (cran-uri "readODS" version)) (sha256 (base32 "1f87bnvjxalr0gp651axpyq4abzirxq7l3mirbak0c4b4l2phb1n")))) (properties `((upstream-name . "readODS"))) (build-system r-build-system) (propagated-inputs (list r-cellranger r-cpp11 r-readr r-stringi r-tibble r-vctrs r-zip)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/package=readODS") (synopsis "Read and Write ODS Files") (description "This package lets you import @dfn{OpenDocument Spreadsheet} (ODS) into R as a data frame. It also supports writing data frames to an ODS file.") (license license:gpl3))) (define-public r-qpdf (package (name "r-qpdf") (version "1.3.3") (source (origin (method url-fetch) (uri (cran-uri "qpdf" version)) (sha256 (base32 "0lzyc1g7q809h047il5nkizv124j13m1zf3j32in0gx7dyz10mj1")) (modules '((guix build utils))) (snippet '(begin ;; unvendor libqpdf (delete-file-recursively "src/libqpdf") (delete-file-recursively "src/include/qpdf"))))) (properties `((upstream-name . "qpdf") (updater-extra-inputs . ("qpdf")))) (build-system r-build-system) (arguments '(#:phases (modify-phases %standard-phases (add-after 'unpack 'configure (lambda _ (setenv "EXTERNAL_QPDF" "1")))))) (inputs (list libjpeg-turbo qpdf zlib)) (propagated-inputs (list r-askpass r-curl r-rcpp)) (native-inputs (list pkg-config)) (home-page "https://github.com/ropensci/qpdf") (synopsis "Split, Combine and Compress PDF Files") (description "Content-preserving transformations transformations of PDF files such as split, combine, and compress. This package interfaces directly to the @code{qpdf} C++ API and does not require any command line utilities. Note that @code{qpdf} does not read actual content from PDF files: to extract text and data you need the @code{pdftools} package.") (license license:asl2.0))) (define-public r-pbdmpi (package (name "r-pbdmpi") (version "0.5-1") (source (origin (method url-fetch) (uri (cran-uri "pbdMPI" version)) (sha256 (base32 "047pxra6n3pacyqg5qdg8dbz32s8bq8z9dyi5rvs0ax76vr1v8v4")))) (properties `((upstream-name . "pbdMPI"))) (build-system r-build-system) (arguments `(#:phases (modify-phases %standard-phases (add-before 'install 'mpi-setup ,%openmpi-setup)))) (inputs (list openmpi)) (propagated-inputs (list r-float)) (native-inputs (list pkg-config)) (home-page "https://pbdr.org/") (synopsis "Programming with Big Data -- Interface to MPI") (description "This package provides an efficient interface to MPI by utilizing S4 classes and methods with a focus on @dfn{Single Program/Multiple Data} (SPMD) parallel programming style, which is intended for batch parallel execution.") (license license:mpl2.0))) (define-public r-pdftools (package (name "r-pdftools") (version "3.4.0") (source (origin (method url-fetch) (uri (cran-uri "pdftools" version)) (sha256 (base32 "0r1c91qrva8lz0gs717llzs6zjiqjrdjhi71asf9bmx600hpp78b")))) (properties `((upstream-name . "pdftools"))) (build-system r-build-system) (inputs (list zlib poppler)) (propagated-inputs (list r-qpdf r-rcpp)) (native-inputs (list pkg-config)) (home-page "https://docs.ropensci.org/pdftools/") (synopsis "Text Extraction, Rendering and Converting of PDF Documents") (description "This package provides utilities based on @code{libpoppler} for extracting text, fonts, attachments and metadata from a PDF file. It also supports high quality rendering of PDF documents into PNG, JPEG, TIFF format, or into raw bitmap vectors for further processing in R.") (license license:expat))) (define-public r-antiword (package (name "r-antiword") (version "1.3.3") (source (origin (method url-fetch) (uri (cran-uri "antiword" version)) (sha256 (base32 "1cc355sldhsbpx9wl5hkx0ydkgd3racxhkrriv58yw5xbb3b18ff")) (modules '((guix build utils))) ;; unvendor libantiword (snippet '(delete-file-recursively "src")))) (properties `((upstream-name . "antiword") (updater-extra-inputs . ("antiword")))) (build-system r-build-system) (arguments (list #:phases #~(modify-phases %standard-phases (add-after 'unpack 'use-system-antiword (lambda _ (substitute* "R/antiword.R" (("system.file\\(\"bin\", package = \"antiword\"\\)") (string-append "\"" #$(this-package-input "antiword") "/bin\"")))))))) (inputs (list antiword)) (propagated-inputs (list r-sys)) (home-page "https://github.com/ropensci/antiword#readme") (synopsis "Extract text from Microsoft Word documents") (description "This package wraps the @code{AntiWord} utility to extract text from Microsoft Word documents. The utility only supports the old @code{doc} format, not the new XML based @code{docx} format. Use the @code{xml2} package to read the latter.") (license license:gpl2))) (define-public r-readtext (package (name "r-readtext") (version "0.91") (source (origin (method url-fetch) (uri (cran-uri "readtext" version)) (sha256 (base32 "0bzaq0vx6c83i4xf7p9zwka7h7jbv1qfy6w4v3kljx30hl048dpn")))) (properties `((upstream-name . "readtext"))) (build-system r-build-system) (propagated-inputs (list r-antiword r-data-table r-digest r-httr r-jsonlite r-pdftools r-pillar r-readods r-readxl r-streamr r-stringi r-striprtf r-xml2)) (native-inputs (list r-knitr)) (home-page "https://github.com/quanteda/readtext") (synopsis "Import and Handling for Plain and Formatted Text Files") (description "This package provides functions for importing and handling text files and formatted text files with additional meta-data, such including @code{.csv}, @code{.tab}, @code{.json}, @code{.xml}, @code{.html}, @code{.pdf}, @code{.doc}, @code{.docx}, @code{.rtf}, @code{.xls}, @code{.xlsx}, and others.") (license license:gpl3))) (define-public r-packcircles (package (name "r-packcircles") (version "0.3.6") (source (origin (method url-fetch) (uri (cran-uri "packcircles" version)) (sha256 (base32 "0fjc575i1vxjp2v4niv2syqqk0d609wm86gkq9rvgmch841x40ps")))) (properties `((upstream-name . "packcircles"))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) (native-inputs (list r-knitr)) (home-page "https://github.com/mbedward/packcircles") (synopsis "Circle Packing") (description "Algorithms to find arrangements of non-overlapping circles.") (license license:expat))) ;; Cannot unbundle liblwgeom, because PostGIS does not support building it on ;; its own. (define-public r-lwgeom (package (name "r-lwgeom") (version "0.2-14") (source (origin (method url-fetch) (uri (cran-uri "lwgeom" version)) (sha256 (base32 "174jpsri9xpr9zb5hvzqhbhnajqw3aa38ajy1skl7ky8vgvnrnr6")))) (properties `((upstream-name . "lwgeom"))) (build-system r-build-system) (inputs (list geos proj sqlite zlib)) (propagated-inputs (list r-rcpp r-sf r-units)) (native-inputs (list pkg-config)) (home-page "https://github.com/r-spatial/lwgeom/") (synopsis "Bindings to Selected 'liblwgeom' Functions for Simple Features") (description "Access to selected functions found in @url{https://github.com/postgis/postgis/tree/master/liblwgeom,liblwgeom}, the light-weight geometry library used by @url{http://postgis.net/,PostGIS}.") (license license:gpl2))) (define-public r-stars (package (name "r-stars") (version "0.6-5") (source (origin (method url-fetch) (uri (cran-uri "stars" version)) (sha256 (base32 "1b5gs0qa8097f2mvz4rgl46wrvk1rbbbi2a4s901hdg4bkr15jsg")))) (properties `((upstream-name . "stars"))) (build-system r-build-system) (propagated-inputs (list r-abind r-classint r-rlang r-sf r-units)) (native-inputs (list r-knitr)) (home-page "https://r-spatial.github.io/stars/") (synopsis "Spatiotemporal Arrays, Raster and Vector Data Cubes") (description "Reading, manipulating, writing and plotting spatiotemporal arrays (raster and vector data cubes) in @code{R}, using @code{GDAL} bindings provided by @code{sf}, and @code{NetCDF} bindings by @code{ncmeta} and @code{RNetCDF}.") (license license:asl2.0))) (define-public r-tmaptools (package (name "r-tmaptools") (version "3.1-1") (source (origin (method url-fetch) (uri (cran-uri "tmaptools" version)) (sha256 (base32 "0bal3czrdr93qig8s5cf5szld5vjbbks67rismfhlkmlgw6wp2gx")))) (properties `((upstream-name . "tmaptools"))) (build-system r-build-system) (propagated-inputs (list r-dichromat r-lwgeom r-magrittr r-rcolorbrewer r-sf r-stars r-units r-viridislite r-xml)) (home-page "https://github.com/mtennekes/tmaptools") (synopsis "Thematic Map Tools") (description "Set of tools for reading and processing spatial data. The aim is to supply the workflow to create thematic maps. This package also facilitates @code{tmap}, the package for visualizing thematic maps.") (license license:gpl3))) (define-public r-rworldmap (package (name "r-rworldmap") (version "1.3-8") (source (origin (method url-fetch) (uri (cran-uri "rworldmap" version)) (sha256 (base32 "007avjl7jhllybp82illrn8v38a85j6xbzk5pvykfx8ayx4wc3m6")))) (properties `((upstream-name . "rworldmap"))) (build-system r-build-system) (propagated-inputs (list r-fields r-raster r-sp r-terra)) (home-page "https://github.com/AndySouth/rworldmap/") (synopsis "Mapping Global Data") (description "Enables mapping of country level and gridded user datasets.") (license license:gpl2+))) (define-public r-rtweet (package (name "r-rtweet") (version "2.0.0") (source (origin (method url-fetch) (uri (cran-uri "rtweet" version)) (sha256 (base32 "1w41a1a5mgg06gvs468vrg9pax2nrnkiqhwllxmkk0i7s15gvi42")))) (properties `((upstream-name . "rtweet"))) (build-system r-build-system) (propagated-inputs (list r-bit64 r-curl r-httr r-httr2 r-jsonlite r-lifecycle r-progress r-rlang r-tibble r-withr)) (native-inputs (list r-knitr)) (home-page "https://docs.ropensci.org/rtweet/") (synopsis "Collect Twitter data") (description "This package implements tools designed to collect and organize Twitter data via @url{https://developer.twitter.com/en/docs,Twitter's REST and stream Application Program Interfaces (API)}.") (license license:expat))) (define-public r-intervals (package (name "r-intervals") (version "0.15.4") (source (origin (method url-fetch) (uri (cran-uri "intervals" version)) (sha256 (base32 "13wzwg5yc1wr8ww8bhv9x5ha78yajsfmb9phq4nbgrxkmbiy3h2h")))) (properties `((upstream-name . "intervals"))) (build-system r-build-system) (home-page "https://github.com/edzer/intervals") (synopsis "Tools for Working with Points and Intervals") (description "Tools for working with and comparing sets of points and intervals.") (license license:artistic2.0))) (define-public r-eyelinker (package (name "r-eyelinker") (version "0.2.1") (source (origin (method url-fetch) (uri (cran-uri "eyelinker" version)) (sha256 (base32 "0wijd45p6j2qal6wnj7zywks8p9v3m9cmyp7axmk44mrjdjx2i71")))) (properties `((upstream-name . "eyelinker"))) (build-system r-build-system) (propagated-inputs (list r-intervals r-readr r-stringi r-stringr r-tibble)) (native-inputs (list r-knitr)) (home-page "https://github.com/a-hurst/eyelinker") (synopsis "Import ASC Files from EyeLink Eye Trackers") (description "Imports plain-text ASC data files from EyeLink eye trackers into (relatively) tidy data frames for analysis and visualization.") (license license:gpl3))) (define-public r-btm (package (name "r-btm") (version "0.3.7") (source (origin (method url-fetch) (uri (cran-uri "BTM" version)) (sha256 (base32 "0lal2fr2lpaky03hrc1gb15kky3s5sr9rbkmrp3v9g2iksd7b5yb")))) (properties `((upstream-name . "BTM"))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) (home-page "https://github.com/bnosac/BTM") (synopsis "Biterm Topic Models for Short Text") (description "Biterm Topic Models find topics in collections of short texts. It is a word co-occurrence based topic model that learns topics by modeling word-word co-occurrences patterns which are called biterms. This in contrast to traditional topic models like Latent Dirichlet Allocation and Probabilistic Latent Semantic Analysis which are word-document co-occurrence topic models. A biterm consists of two words co-occurring in the same short text window. This context window can for example be a twitter message, a short answer on a survey, a sentence of a text or a document identifier. The techniques are explained in detail in the paper 'A Biterm Topic Model For Short Text' by Xiaohui Yan, Jiafeng Guo, Yanyan Lan, Xueqi Cheng (2013) @url{https://github.com/xiaohuiyan/xiaohuiyan.github.io/blob/master/paper/\ BTM-WWW13.pdf}.") (license license:asl2.0))) (define-public r-delaporte (package (name "r-delaporte") (version "8.4.0") (source (origin (method url-fetch) (uri (cran-uri "Delaporte" version)) (sha256 (base32 "1jqz2qxig35rhmwvazmsl3a081dylfq2jfz3bjpj61y4c55mnwar")))) (properties `((upstream-name . "Delaporte"))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "https://github.com/aadler/Delaporte") (synopsis "Statistical functions for the Delaporte distribution") (description "This package provides probability mass, distribution, quantile, random-variate generation, and method-of-moments parameter-estimation functions for the Delaporte distribution with parameterization based on Vose (2008). The Delaporte is a discrete probability distribution which can be considered the convolution of a negative binomial distribution with a Poisson distribution. Alternatively, it can be considered a counting distribution with both Poisson and negative binomial components. It has been studied in actuarial science as a frequency distribution which has more variability than the Poisson, but less than the negative binomial.") (license license:bsd-2))) (define-public r-rjsonio (package (name "r-rjsonio") (version "1.3-1.9") (source (origin (method url-fetch) (uri (cran-uri "RJSONIO" version)) (sha256 (base32 "1kiy36hjzh5if5npqv5mdvkr5pdfg3ibj178gr0kz1r81i5h6wzi")))) (properties `((upstream-name . "RJSONIO"))) (build-system r-build-system) (home-page "https://cran.r-project.org/package=RJSONIO") (synopsis "Serialize R objects to JSON") (description "This is a package that allows conversion to and from data in JavaScript Object Notation (JSON) format. This allows R objects to be inserted into Javascript/ECMAScript/ActionScript code and allows R programmers to read and convert JSON content to R objects. This is an alternative to the @code{rjson} package.") (license license:bsd-3))) (define-public r-revgeo (package (name "r-revgeo") (version "0.15") (source (origin (method url-fetch) (uri (cran-uri "revgeo" version)) (sha256 (base32 "1ns7d1817475lriss6wwgvdm6lj760p40yxqaifla13c2xb73a55")))) (properties `((upstream-name . "revgeo"))) (build-system r-build-system) (propagated-inputs (list r-rcurl r-rjsonio)) (home-page "https://cran.r-project.org/package=revgeo") (synopsis "Reverse geocoding") (description "The @code{revgeo} procedure allows you to use the Photon geocoder for OpenStreetMap, Google Maps, and Bing to reverse geocode coordinate pairs with minimal hassle.") (license license:gpl3+))) (define-public r-qpcr (package (name "r-qpcr") (version "1.4-1") (source (origin (method url-fetch) (uri (cran-uri "qpcR" version)) (sha256 (base32 "1r01q7jv3w59yx1gc0qw91rq7rvdhqsi8y57sqqkmwyqfw2x2vsv")))) (properties `((upstream-name . "qpcR"))) (build-system r-build-system) (propagated-inputs (list r-mass r-matrix r-minpack-lm r-rgl r-robustbase)) (home-page "https://cran.r-project.org/package=qpcR") (synopsis "Modelling and analysis of real-time PCR data") (description "This is a package for model fitting, optimal model selection and calculation of various features that are essential in the analysis of quantitative real-time polymerase chain reaction (qPCR).") (license license:gpl2+))) (define-public r-textplot (package (name "r-textplot") (version "0.2.2") (source (origin (method url-fetch) (uri (cran-uri "textplot" version)) (sha256 (base32 "1ag2h365zsx0fxbl05s2yfhf1q13p40akvbqg4qwsb5ynh2a56bf")))) (properties `((upstream-name . "textplot"))) (build-system r-build-system) (propagated-inputs (list r-data-table r-lattice r-matrix)) (native-inputs (list r-knitr)) (home-page "https://github.com/bnosac/textplot") (synopsis "Text Plots") (description "Visualise complex relations in texts. This is done by providing functionalities for displaying text co-occurrence networks, text correlation networks, dependency relationships as well as text clustering. Feel free to join the effort of providing interesting text visualisations.") (license license:gpl2))) (define-public r-gsa (package (name "r-gsa") (version "1.03.2") (source (origin (method url-fetch) (uri (cran-uri "GSA" version)) (sha256 (base32 "1f1mrxxdbdlnibgav6nsvbpniz2x3km2svc0hf43spb4zicn0z8p")))) (properties `((upstream-name . 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(license license:expat))) (define-public r-randomforestsrc (package (name "r-randomforestsrc") (version "2.9.3") (source (origin (method url-fetch) (uri (cran-uri "randomForestSRC" version)) (sha256 (base32 "05ifvj49jv0n5p6k46milpgj9r10sc5aw23fypyyibdgwpwvwixw")))) (properties `((upstream-name . "randomForestSRC"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/randomForestSRC/") (synopsis "Random forests for survival, regression, and classification") (description "This package implements fast OpenMP parallel computing of Breiman's random forests for survival, competing risks, regression and classification based on Ishwaran and Kogalur's popular random survival forests (RSF) package. It handles missing data and now includes multivariate, unsupervised forests, quantile regression and solutions for class imbalanced data. It provides a fast interface using subsampling and confidence regions for variable importance.") (license license:gpl3+))) (define-public r-contfrac (package (name "r-contfrac") (version "1.1-12") (source (origin (method url-fetch) (uri (cran-uri "contfrac" version)) (sha256 (base32 "0sq5c7ny235yrkv2xc4insgxby6rvzc1qsj8h301cd2if3lwbgwm")))) (properties `((upstream-name . "contfrac"))) (build-system r-build-system) (home-page "https://github.com/RobinHankin/contfrac") (synopsis "Continued Fractions") (description "Various utilities for evaluating continued fractions.") (license license:gpl2))) (define-public r-elliptic (package (name "r-elliptic") (version "1.4-0") (source (origin (method url-fetch) (uri (cran-uri "elliptic" version)) (sha256 (base32 "1dhba0yfxjd5rlqsxp5a7s2hclfkla9wigsr39dlma67l6qjjmxn")))) (properties `((upstream-name . 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(license license:gpl2))) (define-public r-gganimate (package (name "r-gganimate") (version "1.0.9") (source (origin (method url-fetch) (uri (cran-uri "gganimate" version)) (sha256 (base32 "016nky797h4093qrpynq5rr1p7h4chpv1hyngpcs2csr1064rjmz")))) (properties `((upstream-name . "gganimate"))) (build-system r-build-system) (arguments `(#:phases (modify-phases %standard-phases (add-after 'unpack 'absolute-paths (lambda* (#:key inputs #:allow-other-keys) (substitute* "R/renderers.R" (("'ffmpeg'") (string-append "'" (assoc-ref inputs "ffmpeg") "/bin/ffmpeg'")))))))) (inputs ;; For video output. (list ffmpeg)) (propagated-inputs (list r-cli r-ggplot2 r-glue r-lifecycle r-progress r-rlang r-scales r-stringi r-transformr r-tweenr r-vctrs ;; For GIF/SVG output. gifski is faster, but depends on Rust. r-magick ;; For HTML output. r-base64enc r-htmltools)) (native-inputs (list r-knitr)) (home-page "https://gganimate.com") (synopsis "Grammar of Animated Graphics") (description "This package extends the grammar of graphics as implemented by @code{ggplot2} to include the description of animation. It does this by providing a range of new grammar classes that can be added to the plot object in order to customise how it should change with time.") (license license:expat))) ;; This library bundles ‘date’ from (gnu packages calendar). We cannot unbundle ;; it, because its C++ libtz.so is built with different compiler flags than ;; ours. (define-public r-tzdb (package (name "r-tzdb") (version "0.4.0") (source (origin (method url-fetch) (uri (cran-uri "tzdb" version)) (sha256 (base32 "08rskp7kv2w5pfnrxzswgkdsrg1g0pq3n64q7i3gvpdx85hccls2")))) (properties `((upstream-name . "tzdb"))) (build-system r-build-system) (propagated-inputs (list r-cpp11)) (home-page "https://github.com/r-lib/tzdb") (synopsis "Time Zone Database Information") (description "This package provides an up-to-date copy of the Internet Assigned Numbers Authority (IANA) Time Zone Database. It is updated periodically to reflect changes made by political bodies to time zone boundaries, UTC offsets, and daylight saving time rules. Additionally, this package provides a C++ interface for working with the @code{date} library. @code{date} provides comprehensive support for working with dates and date-times, which this package exposes to make it easier for other R packages to utilize. Headers are provided for calendar specific calculations, along with a limited interface for time zone manipulations.") (license license:expat))) (define-public r-vroom (package (name "r-vroom") (version "1.6.5") (source (origin (method url-fetch) (uri (cran-uri "vroom" version)) (sha256 (base32 "0qapkgn5k9g07l48scgln8y1k6fkkzsq5la5fjfh9if9b0ga5p3v")))) (properties `((upstream-name . "vroom"))) (build-system r-build-system) (propagated-inputs (list r-bit64 r-cli r-cpp11 r-crayon r-glue r-hms r-lifecycle r-progress r-rlang r-tibble r-tidyselect r-tzdb r-vctrs r-withr)) (native-inputs (list r-knitr)) (home-page "https://vroom.r-lib.org") (synopsis "Read and Write Rectangular Text Data") (description "This package reads and writes data files like @acronym{CSV}, @acronym{TSV} and @acronym{FWF}. When reading it uses a quick initial indexing step, then reads the values lazily, so only the data you actually use needs to be read. The writer formats the data in parallel and writes to disk asynchronously from formatting.") (license license:expat))) (define-public r-rmisc (package (name "r-rmisc") (version "1.5.1") (source (origin (method url-fetch) (uri (cran-uri "Rmisc" version)) (sha256 (base32 "1h6jb0xwkyhm9lwm7nj9bhrb5dhrsifvkpqkrd594j1lz74dar8x")))) (build-system r-build-system) (propagated-inputs (list r-plyr r-lattice)) (home-page "https://cran.r-project.org/web/packages/Rmisc/") (synopsis "Ryan Miscellaneous") (description "The Rmisc library contains functions for data analysis and utility operations.") (license license:gpl3))) (define-public r-rsq (package (name "r-rsq") (version "2.6") (source (origin (method url-fetch) (uri (cran-uri "rsq" version)) (sha256 (base32 "01b9rl2ng1sq0ibpfsf50agkwh01pfpw354vvgdjd0lzh9dxmsgp")))) (properties `((upstream-name . 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(license license:expat))) (define-public r-opencpu (package (name "r-opencpu") (version "2.2.11") (source (origin (method url-fetch) (uri (cran-uri "opencpu" version)) (sha256 (base32 "1hdvfbzc8xmv8hrmchad590f91s4vq1nq83wi2ffh4n7q6ixr03s")) (snippet '(for-each delete-file '("inst/test/jquery-1.10.2.min.js" "inst/test/bootstrap/js/bootstrap.min.js"))))) (properties `((upstream-name . "opencpu") (updater-ignored-inputs . ("apparmor")) (updater-extra-native-inputs . 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The OpenCPU server exposes a simple but powerful HTTP API for RPC and data interchange with R. This provides a reliable and scalable foundation for statistical services or building R web applications. The OpenCPU server runs either as a single-user development server within the interactive R session, or as a multi-user stack based on Apache2.") (license license:asl2.0))) (define-public r-exactextractr (package (name "r-exactextractr") (version "0.10.0") (source (origin (method url-fetch) (uri (cran-uri "exactextractr" version)) (sha256 (base32 "1pj3145c20r4hnyyrynzmps96a4fpgn408lrl6b9bs79y33c6zwv")))) (properties `((upstream-name . 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Log ratios are used to compare the relative (rather than the absolute) dimensions of animals from archaeological contexts. The zoolog package is also able to seamlessly integrate data and references with heterogeneous nomenclature, which is internally managed by a zoolog thesaurus.") (license license:gpl3))) (define-public r-filehash (package (name "r-filehash") (version "2.4-5") (source (origin (method url-fetch) (uri (cran-uri "filehash" version)) (sha256 (base32 "0b52bnsqp65s3r4aw9mvfwfnjmsrqq8ndcadwig547nn9mwy47iv")))) (properties `((upstream-name . "filehash"))) (build-system r-build-system) (propagated-inputs (list r-digest)) (home-page "http://github.com/rdpeng/filehash") (synopsis "Simple key-value database") (description "This package implements a simple key-value style database where character string keys are associated with data values that are stored on the disk. A simple interface is provided for inserting, retrieving, and deleting data from the database. 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(license license:gpl2+))) (define-public r-zonebuilder (package (name "r-zonebuilder") (version "0.0.2") (source (origin (method url-fetch) (uri (cran-uri "zonebuilder" version)) (sha256 (base32 "0mxf3dz0d6bi5wwjilqivdxhy5ypnq5svky8zygha0clv45l4dmn")))) (properties `((upstream-name . "zonebuilder"))) (build-system r-build-system) (propagated-inputs (list r-rcolorbrewer r-sf)) (native-inputs (list r-knitr)) (home-page "https://github.com/zonebuilders/zonebuilder") (synopsis "Create and explore geographic zoning systems") (description "This package provides functions, documentation and example data to help divide geographic space into discrete polygons (zones). The functions are motivated by research into the merits of different zoning systems. A flexible @code{ClockBoard} zoning system is provided, which breaks-up space by concentric rings and radial lines emanating from a central point.") 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"cccd"))) (build-system r-build-system) (propagated-inputs (list r-deldir r-fnn r-igraph r-proxy)) (home-page "https://cran.r-project.org/package=cccd") (synopsis "Class cover catch digraphs") (description "This package provides tools to create Class Cover Catch Digraphs, neighborhood graphs, and relatives.") (license license:gpl2+))) (define-public r-crul (package (name "r-crul") (version "1.4.2") (source (origin (method url-fetch) (uri (cran-uri "crul" version)) (sha256 (base32 "0is164bbdk5zy1gxrliiqzlmj47nvzsjym05ijzzs3zkj7qpfp20")))) (properties `((upstream-name . "crul"))) (build-system r-build-system) (propagated-inputs (list r-curl r-httpcode r-jsonlite r-mime r-r6 r-urltools)) (native-inputs (list r-knitr)) (home-page "https://github.com/ropensci/crul") (synopsis "HTTP client") (description "This package provides a simple HTTP client, with tools for making HTTP requests, and mocking HTTP requests. The package is built on R6, and takes inspiration from Ruby's @code{faraday} gem.") (license license:expat))) (define-public r-gistr (package (name "r-gistr") (version "0.9.0") (source (origin (method url-fetch) (uri (cran-uri "gistr" version)) (sha256 (base32 "0ac9ikrdg6i8xvlma0gizvsdva46408lk7hvsgkqirhy2ljy02hp")))) (properties `((upstream-name . "gistr"))) (build-system r-build-system) (propagated-inputs (list r-assertthat r-crul r-dplyr r-httr r-jsonlite r-knitr r-magrittr r-rmarkdown)) (native-inputs (list r-knitr)) (home-page "https://github.com/ropensci/gistr") (synopsis "Work with Gists in browser") (description "This package allows the user to create new Github gists, update gists with new files, rename files, delete files, get and delete gists, star and un-star them, fork them, open a gist in your default browser, get an embed code for a gist, list gist commits, and get rate limit information when authenticated.") (license license:expat))) (define-public r-rbokeh (package (name "r-rbokeh") (version "0.5.2") (source (origin (method url-fetch) (uri (cran-uri "rbokeh" version)) (sha256 (base32 "1h2fpzqf17pw9d09r1g1iyxsj5qma4fsk8vnar7f1z4fjyypvi6q")) (snippet '(for-each delete-file '("inst/htmlwidgets/lib/bokehjs/bokeh-widgets.min.js" "inst/htmlwidgets/lib/bokehjs/bokeh.min.js"))))) (properties `((upstream-name . "rbokeh"))) (build-system r-build-system) (arguments `(#:phases (modify-phases %standard-phases (add-after 'unpack 'process-javascript (lambda* (#:key inputs #:allow-other-keys) (with-directory-excursion "inst/htmlwidgets/lib/bokehjs" (let ((mapping `((,(assoc-ref inputs "js-bokeh-widgets") . "bokeh-widgets.min.js") (,(assoc-ref inputs "js-bokeh") . "bokeh.min.js")))) (for-each (lambda (source target) (format #true "Processing ~a --> ~a~%" source target) (invoke "esbuild" source "--minify" (string-append "--outfile=" target))) (map car mapping) (map cdr mapping))))))))) (propagated-inputs (list r-digest r-gistr r-hexbin r-htmlwidgets r-jsonlite r-lazyeval r-magrittr r-maps r-pryr r-scales)) ;; Version 0.12.15 is mentioned in lib/htmlwidgets/rbokeh.yaml. (native-inputs `(("esbuild" ,esbuild) ("js-bokeh-widgets" ,(origin (method url-fetch) (uri "https://unpkg.com/bokehjs@0.12.15/build/js/bokeh-widgets.js") (sha256 (base32 "07v9lrkfcbdznpb10qqwi4m660zp65g85vlnfw7kn83zmkxkhhxy")))) ("js-bokeh" ,(origin (method url-fetch) (uri "https://unpkg.com/bokehjs@0.12.15/build/js/bokeh.js") (sha256 (base32 "1pq0059aad7d2jv50nv9449p3w0gbkxkl0mhblc76m5d9qjqav2q")))) ("r-knitr" ,r-knitr))) (home-page "https://cran.r-project.org/web/packages/rbokeh/") (synopsis "R interface for the Bokeh visualization library") (description "This package provides a native R plotting library that provides a flexible declarative interface for creating interactive web-based graphics, backed by the @url{https://bokeh.pydata.org/, Bokeh visualization library}.") (license license:expat))) (define-public r-fauxpas (package (name "r-fauxpas") (version "0.5.2") (source (origin (method url-fetch) (uri (cran-uri "fauxpas" version)) (sha256 (base32 "1xhyws6nr9ayir4sykvhyaf1aprx9rjm2xyb3p5ikd26l5hp7l44")))) (properties `((upstream-name . "fauxpas"))) (build-system r-build-system) (propagated-inputs (list r-httpcode r-r6 r-whisker)) (native-inputs (list r-knitr)) (home-page "https://docs.ropensci.org/fauxpas") (synopsis "HTTP error helpers") (description "This package provides HTTP error helpers. Methods are included for general purpose HTTP error handling, as well as individual methods for every HTTP status code, both via status code numbers as well as their descriptive names. It supports the ability to adjust behavior to stop, message or warning. It includes the ability to use a custom whisker template to have any configuration of status code, short description, and verbose message.") (license license:expat))) (define-public r-webmockr (package (name "r-webmockr") (version "0.9.0") (source (origin (method url-fetch) (uri (cran-uri "webmockr" version)) (sha256 (base32 "1a590fyzmag1p6c9a82yp93wd1s4jdznk0416i0pv8r5jwarkdv7")))) (properties `((upstream-name . "webmockr"))) (build-system r-build-system) (propagated-inputs (list r-base64enc r-crul r-curl r-fauxpas r-jsonlite r-magrittr r-r6 r-urltools)) (home-page "https://github.com/ropensci/webmockr") (synopsis "Stubbing and setting expectations on HTTP Requests") (description "This is a package for stubbing and setting expectations on HTTP requests. It includes tools for stubbing HTTP requests, including expected request conditions and response conditions. You can match on HTTP method, query parameters, request body, headers and more. It can be used for unit tests or outside of a testing context.") (license license:expat))) (define-public r-iotools (package (name "r-iotools") (version "0.3-5") (source (origin (method url-fetch) (uri (cran-uri "iotools" version)) (sha256 (base32 "12xlf31aawj5sxanb2m63r665a9x5v87q4ig8qkvaygpdg51gycw")))) (properties `((upstream-name . "iotools"))) (build-system r-build-system) (home-page "https://www.rforge.net/iotools") (synopsis "I/O tools for streaming") (description "This package provides basic I/O tools for streaming and data parsing.") ;; GPL 2 or GPL 3. (license license:gpl3))) (define-public r-wordspace (package (name "r-wordspace") (version "0.2-8") (source (origin (method url-fetch) (uri (cran-uri "wordspace" version)) (sha256 (base32 "17fqd4zrsklv2ik3lg00x66yasfh1kyhs3k9ri6lrk56wwv6hzb2")))) (properties `((upstream-name . 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(license license:gpl3))) (define-public r-zoib (package (name "r-zoib") (version "1.6") (source (origin (method url-fetch) (uri (cran-uri "zoib" version)) (sha256 (base32 "1px4jjjpn6ikngzlxz1i6fgld9cy5lv6nqn1bjin4q6sqqixyx2j")))) (properties `((upstream-name . "zoib"))) (build-system r-build-system) (propagated-inputs (list r-abind r-coda r-formula r-rjags)) (home-page "https://www.r-project.org") (synopsis "Bayesian inference for beta regression") (description "This package lets you fit beta regression and zero-or-one inflated beta regression and obtain Bayesian inference of the model via the Markov Chain Monte Carlo approach implemented in JAGS.") (license license:gpl3+))) (define-public r-logger (package (name "r-logger") (version "0.3.0") (source (origin (method url-fetch) (uri (cran-uri "logger" version)) (sha256 (base32 "0ivhrmq408pb7gx7yhmrn6mjkx15dvkb4bpk4z5y642l3j2vv9vd")))) (properties `((upstream-name . 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Think half boxplot and half jitterplot, or half violinplot and half dotplot.") (license license:expat))) (define-public r-zoeppritz (package (name "r-zoeppritz") (version "1.0-9") (source (origin (method url-fetch) (uri (cran-uri "zoeppritz" version)) (sha256 (base32 "0bl1hrghyv5vjs02r2f5k9p7l4ialwdpl7si14lz8lbb0r1a6fwq")))) (properties `((upstream-name . "zoeppritz"))) (build-system r-build-system) (home-page "https://cran.r-project.org/package=zoeppritz") (synopsis "Seismic reflection and scattering coefficients for waves") (description "The @code{r-zoeppritz} package calculates and plots scattering matrix coefficients or scattering amplitudes, for seismological P and S-waves at an interface.") (license license:gpl2+))) (define-public r-metadat (package (name "r-metadat") (version "1.2-0") (source (origin (method url-fetch) (uri (cran-uri "metadat" version)) (sha256 (base32 "1f7mb3pw5d0akr09jjva06ay223izhpzbr21bapnw99x1kiybk7h")))) (properties `((upstream-name . 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"spacetime"))) (build-system r-build-system) (propagated-inputs (list r-intervals r-lattice r-sp r-xts r-zoo)) (native-inputs (list r-knitr)) (home-page "https://github.com/edzer/spacetime/") (synopsis "Classes and methods for spatio-temporal data") (description "@command{spacetime} provides classes and methods for spatio-temporal data, including space-time regular lattices, sparse lattices, irregular data, and trajectories; utility functions for plotting data as map sequences (lattice or animation) or multiple time series; methods for spatial and temporal matching or aggregation, retrieving coordinates, print, summary, etc.") (license license:gpl2+))) (define-public r-gstat (package (name "r-gstat") (version "2.1-1") (source (origin (method url-fetch) (uri (cran-uri "gstat" version)) (sha256 (base32 "09ax28di93r4r334qwdp84i95809lkr6587w4xlgpvsma7k0bcj8")))) (properties `((upstream-name . "gstat"))) (build-system r-build-system) (propagated-inputs (list r-fnn r-lattice r-sp r-sf r-sftime r-spacetime r-stars r-zoo)) (home-page "https://github.com/r-spatial/gstat/") (synopsis "Spatial and spatio-temporal geostatistical modelling, prediction and simulation") (description "This package enables variogram modelling, including: simple, ordinary and universal point or block (co)kriging; spatio-temporal kriging; and sequential Gaussian or indicator (co)simulation. It includes variogram and variogram map plotting utility functions, and supports @command{sf} and @command{stars}.") (license license:gpl2+))) (define-public r-automap (package (name "r-automap") (version "1.1-9") (source (origin (method url-fetch) (uri (cran-uri "automap" version)) (sha256 (base32 "0hrsdynjxv0n5n1pbdk05rgrcwfd0g5p9pgdbicx4ljk73nhl1zk")))) (properties `((upstream-name . "automap"))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-gstat r-lattice r-reshape r-sf r-sp r-stars)) (home-page "https://cran.r-project.org/package=automap") (synopsis "Automatic interpolation package") (description "@command{automap} performs an automatic interpolation by automatically estimating the variogram and then calling @command{gstat}.") (license (list license:gpl2+ license:gpl3+)))) (define-public r-cartogram (package (name "r-cartogram") (version "0.3.0") (source (origin (method url-fetch) (uri (cran-uri "cartogram" version)) (sha256 (base32 "1vkcp8k9ajrnm14p2fqrcb4vk67503zd0w51h8amcljg3p21wzkl")))) (properties `((upstream-name . "cartogram"))) (build-system r-build-system) (propagated-inputs (list r-packcircles r-sf)) (home-page "https://github.com/sjewo/cartogram/") (synopsis "Create cartograms with R") (description "This package enables construction of continuous and non-contiguous area cartograms.") (license license:gpl3))) (define-public r-measurements (package (name "r-measurements") (version "1.5.1") (source (origin (method url-fetch) (uri (cran-uri "measurements" version)) (sha256 (base32 "061xjwsacsk8vblva4s09xdrvd7kfgxydnpgr7imigyny01c5bh9")))) (properties `((upstream-name . "measurements"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/measurements/") (synopsis "Tools for units of measurement") (description "This package provides a collection of tools to make working with physical measurements easier. One can convert between metric and imperial units, or calculate a dimension's unknown value from other dimensions' measurements.") (license license:gpl3))) (define-public r-sungeo (package (name "r-sungeo") (version "1.1.1") (source (origin (method url-fetch) (uri (cran-uri "SUNGEO" version)) (sha256 (base32 "1sy9kw3nr69jf33034kcnv418lqyz6sfrd01646i7dfsm64aydp2")) (modules '((guix build utils))) (snippet '(begin ;; Fortunately, the package does not actually use ;; rmapshaper, which has got a js/node dependency. ;; The only occurrence is in R/point2poly_tess.R, ;; where it is commented out. (substitute* "DESCRIPTION" (("rmapshaper,") "")) (substitute* "NAMESPACE" (("importFrom\\(rmapshaper,ms_dissolve\\) ") "")))))) (properties `((upstream-name . "SUNGEO"))) (build-system r-build-system) (propagated-inputs (list r-automap r-cartogram r-data-table r-dplyr r-httr r-jsonlite r-measurements r-packcircles r-purrr r-rann r-raster r-rcpp r-rcurl r-rlang r-sf r-sp r-spdep r-stringr r-terra)) (home-page "https://github.com/zhukovyuri/SUNGEO/") (synopsis "Sub-National Geospatial Data Archive: Geoprocessing Toolkit") (description "Tools for integrating spatially-misaligned GIS datasets. Part of the Sub-National Geospatial Data Archive System.") (license license:gpl2))) ;;; ;;; Avoid adding new packages to the end of this file. To reduce the chances ;;; of a merge conflict, place them above by existing packages with similar ;;; functionality or similar names. ;;;