;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022 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, 2021, 2022 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 Wiktor Żelazny ;;; Copyright © 2019 Arne Babenhauserheide ;;; Copyright © 2019, 2020 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 Simon Tournier ;;; Copyright © 2020 Aniket Patil ;;; Copyright © 2021 Marcel Schilling ;;; Copyright © 2021 Guillaume Le Vaillant ;;; Copyright © 2022 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 graph) #: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 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-aer (package (name "r-aer") (version "1.2-10") (source (origin (method url-fetch) (uri (cran-uri "AER" version)) (sha256 (base32 "1p6vxr0220lim5i4gwsvphqrfd65zbs8h3qydz4gipca9asmy2k5")))) (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 "1.1.0.2") (source (origin (method url-fetch) (uri (cran-uri "afpt" version)) (sha256 (base32 "1z0r4r7prxbhadmkdg6345g0b5vq9dqyyw9hh3fpad9zkc7k6xbc")))) (properties `((upstream-name . 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Compared to other implementations such a @code{purrr::partial()} the operators in @code{curry} composes functions with named arguments, aiding in autocomplete etc.") (license license:gpl2+))) (define-public r-datawizard (package (name "r-datawizard") (version "0.6.0") (source (origin (method url-fetch) (uri (cran-uri "datawizard" version)) (sha256 (base32 "1r89h5npv8iwsvylkpazfpcadgh55zd336rz8hndbzp0w9dcmpli")))) (properties `((upstream-name . "datawizard"))) (build-system r-build-system) (propagated-inputs (list r-insight)) (native-inputs (list r-knitr)) (home-page "https://easystats.github.io/datawizard/") (synopsis "Easy data wrangling") (description "This package provides a lightweight package to easily manipulate, clean, transform, and prepare your data for analysis. It also forms the data wrangling backend for the packages in the @code{easystats} ecosystem.") (license license:gpl3))) (define-public r-dbscan (package (name "r-dbscan") (version "1.1-10") (source (origin (method url-fetch) (uri (cran-uri "dbscan" version)) (sha256 (base32 "1h8x1v9kk5zmw5qd575cyr16yz8l226lsaq71n079l4i8crcrzg1")))) (properties `((upstream-name . "dbscan"))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) (native-inputs (list r-knitr)) (home-page "https://github.com/mhahsler/dbscan") (synopsis "Density-based spatial clustering of applications with noise") (description "This package provides a fast reimplementation of several density-based algorithms of the DBSCAN family. It includes the clustering algorithms DBSCAN (density-based spatial clustering of applications with noise) and @dfn{hierarchical DBSCAN} (HDBSCAN), the ordering algorithm @dfn{ordering points to identify the clustering structure} (OPTICS), shared nearest neighbor clustering, and the outlier detection algorithms @dfn{local outlier factor} (LOF) and @dfn{global-local outlier score from hierarchies} (GLOSH). The implementations use the kd-tree data structure for faster k-nearest neighbor search. An R interface to fast kNN and fixed-radius NN search is also provided.") (license license:gpl2+))) (define-public r-diffobj (package (name "r-diffobj") (version "0.3.5") (source (origin (method url-fetch) (uri (cran-uri "diffobj" version)) (sha256 (base32 "0q6gwd9pqh41f6j5p9jl92aji4p8kx9inffpha93d7jc3ndsfq6q")))) (properties `((upstream-name . 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Further new functionality includes lollipop charts, dumbbell charts, the ability to encircle points and coordinate-system-based text annotations.") (license license:agpl3))) (define-public r-glmpca (package (name "r-glmpca") (version "0.2.0") (source (origin (method url-fetch) (uri (cran-uri "glmpca" version)) (sha256 (base32 "02xjf0gg52925hw9nw2j0znfmzfzfwbv0fxjl9d2fy9j63drr2h4")))) (properties `((upstream-name . "glmpca"))) (build-system r-build-system) (propagated-inputs (list r-mass)) (native-inputs (list r-knitr)) (home-page "https://github.com/willtownes/glmpca") (synopsis "Dimension Reduction of Non-Normally Distributed Data") (description "This package implements a generalized version of principal components analysis (GLM-PCA) for dimension reduction of non-normally distributed data such as counts or binary matrices.") 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You can execute a command inside a container, mount a volume or copy a file.") (license license:expat))) (define-public r-benchmarkmedata (package (name "r-benchmarkmedata") (version "1.0.4") (source (origin (method url-fetch) (uri (cran-uri "benchmarkmeData" version)) (sha256 (base32 "1n4vjkagqlm6kw2hilf4gjfcdjad0bcg652j9nl2ygbq3kdnh1vf")))) (build-system r-build-system) (propagated-inputs (list r-dplyr r-tibble)) (home-page "https://github.com/csgillespie/benchmarkme-data") (synopsis "Data set for the @code{benchmarkme} package") (description "This package contains the data set for the crowd-sourced benchmarks from running the @code{benchmarkme} package.") 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(license license:gpl2+))) (define-public r-bezier (package (name "r-bezier") (version "1.1.2") (source (origin (method url-fetch) (uri (cran-uri "bezier" version)) (sha256 (base32 "1vw5128v8h973xwa1fdm9cw2jvrldj87nd55lddlp3qsz3ag4br6")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/bezier/") (synopsis "Bezier curve and spline toolkit") (description "This package is a toolkit for working with Bezier curves and splines. The package provides functions for point generation, arc length estimation, degree elevation and curve fitting.") (license license:gpl2+))) (define-public r-bwstest (package (name "r-bwstest") (version "0.2.2") (source (origin (method url-fetch) (uri (cran-uri "BWStest" version)) (sha256 (base32 "02amzlfprmw5pyis0dg0kg0x8xqh50a4vfdcxxmklrzik3b1vzzs")))) (properties `((upstream-name . "BWStest"))) (build-system r-build-system) (propagated-inputs (list r-memoise r-rcpp)) (home-page "https://github.com/shabbychef/BWStest") (synopsis "Baumgartner Weiss Schindler Test of equal distributions") (description "This package performs the Baumgartner-Weiss-Schindler two-sample test of equal probability distributions (doi:10.2307/2533862). It also performs similar rank-based tests for equal probability distributions due to Neuhauser (doi:10.1080/10485250108832874) and Murakami (doi:10.1080/00949655.2010.551516).") (license license:lgpl3))) (define-public r-v8 (package (name "r-v8") (version "4.2.1") (source (origin (method url-fetch) (uri (cran-uri "V8" version)) (sha256 (base32 "1w1zihmhrygn2i674wimbv7xqjnwlld4x3ndvh5dl4cdg7s1m24r")))) (properties `((upstream-name . "V8"))) (build-system r-build-system) (arguments `(#:phases (modify-phases %standard-phases (add-after 'unpack 'find-v8 (lambda* (#:key inputs #:allow-other-keys) (substitute* "configure" (("^PKG_LIBS=.*") (string-append "PKG_LIBS=" (assoc-ref inputs "libnode") "/lib/libnode.so.64\n"))) (setenv "INCLUDE_DIR" (string-append (assoc-ref inputs "libnode") "/include/node")) (setenv "LIB_DIR" (string-append (assoc-ref inputs "libnode") "/lib"))))))) (inputs (list libnode zlib)) (propagated-inputs (list r-curl r-jsonlite r-rcpp)) (native-inputs (list r-knitr)) (home-page "https://jeroen.cran.dev/V8") (synopsis "Embedded JavaScript and WebAssembly engine for R") (description "This package provides an R interface to V8: Google's JavaScript and WebAssembly engine.") (license license:expat))) (define-public r-rvenn (package (name "r-rvenn") (version "1.1.0") (source (origin (method url-fetch) (uri (cran-uri "RVenn" version)) (sha256 (base32 "016m00xv59lkwm2is32v5nr4lw5a1ymdnz34r3ffflcv9bfrc6n4")))) (properties `((upstream-name . "RVenn"))) (build-system r-build-system) (propagated-inputs (list r-ggforce r-ggplot2 r-magrittr r-pheatmap r-purrr r-rlang r-vegan)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/package=RVenn") (synopsis "Set operations for many sets") (description "The base functions for set operations in @code{R} can be used for only two sets. This package @code{RVenn} provides functions for dealing with multiple sets. It uses @code{purr} to find the union, intersection and difference of three or more sets. This package also provides functions for pairwise set operations among several sets. Further, based on @code{ggplot2} and @code{ggforce}, a Venn diagram can be drawn for two or three sets. For bigger data sets, a clustered heatmap showing the presence or absence of the elements of the sets can be drawn based on the @code{pheatmap} package. Finally, enrichment test can be applied to two sets whether an overlap is statistically significant or not.") (license license:gpl3))) (define-public r-dot (package (name "r-dot") (version "0.1") (source (origin (method url-fetch) (uri (cran-uri "DOT" version)) (sha256 (base32 "0qh5n57cp9c2n5yn59q4wggz82943pwfanp3kx869aba2x3sj30i")))) (properties `((upstream-name . "DOT"))) (build-system r-build-system) (propagated-inputs (list r-v8)) (home-page "http://haghish.com/dot") (synopsis "Render and Export DOT Graphs in R") (description "This package provides tools to render DOT diagram markup language in R and also provides the possibility to export the graphs in PostScript and SVG (Scalable Vector Graphics) formats. In addition, it supports literate programming packages such as @code{knitr} and @code{rmarkdown}.") (license license:expat))) (define-public r-carrier (package (name "r-carrier") (version "0.1.0") (source (origin (method url-fetch) (uri (cran-uri "carrier" version)) (sha256 (base32 "0bqnwnnjqjk9q0lxq6kkz9s75ss10lfyyywyyi24m8wppxpw1vqc")))) (properties `((upstream-name . "carrier"))) (build-system r-build-system) (propagated-inputs (list r-pryr r-rlang)) (home-page "https://github.com/r-lib/carrier") (synopsis "Isolate functions for remote execution") (description "Sending functions to remote processes can be wasteful of resources because they carry their environments with them. With this package, it is easy to create functions that are isolated from their environment. These isolated functions, also called crates, print to the console with their total size and can be easily tested locally before being sent to a remote.") (license license:gpl3))) (define-public r-clipr (package (name "r-clipr") (version "0.8.0") (source (origin (method url-fetch) (uri (cran-uri "clipr" version)) (sha256 (base32 "1s9vvv3cxnz8w11gsi8z9ddv9jzib5qf5qqxnwqrrv7vj8cr7hij")))) (build-system r-build-system) (native-inputs (list r-knitr)) (home-page "https://github.com/mdlincoln/clipr") (synopsis "Read and write from the system clipboard") (description "This package provides simple utility functions to read from and write to the system clipboards.") (license license:gpl3))) (define-public r-clvalid (package (name "r-clvalid") (version "0.7") (source (origin (method url-fetch) (uri (cran-uri "clValid" version)) (sha256 (base32 "18aiyjhnh5mfdxbzns4cy0r8bymfikhwkybpn4g04qhli5ls8z83")))) (properties `((upstream-name . "clValid"))) (build-system r-build-system) (propagated-inputs (list r-class r-cluster)) (home-page "https://cran.r-project.org/package=clValid") (synopsis "Validation of clustering results") (description "Statistical and biological validation of clustering results. This package implements Dunn Index, Silhouette, Connectivity, Stability, BHI and BSI. Further information can be found in Brock, G et al. (2008) .") (license license:lgpl3))) (define-public r-dlm (package (name "r-dlm") (version "1.1-5") (source (origin (method url-fetch) (uri (cran-uri "dlm" version)) (sha256 (base32 "1aksm66sfa7ipl5xgs4j5giac7q2m744wjl40mva56xn6i674h4r")))) (properties `((upstream-name . "dlm"))) (build-system r-build-system) (home-page "https://cran.r-project.org/package=dlm") (synopsis "Bayesian and Likelihood Analysis of Dynamic Linear Models") (description "This package provides routines for Maximum likelihood, Kalman filtering and smoothing, and Bayesian analysis of Normal linear State Space models, also known as Dynamic Linear Models.") (license license:gpl2+))) (define-public r-zoo (package (name "r-zoo") (version "1.8-11") (source (origin (method url-fetch) (uri (cran-uri "zoo" version)) (sha256 (base32 "19cw09bhwj2qyd72765ym1cm2wmhh801ccif889nzq5gfpw513l4")))) (build-system r-build-system) (propagated-inputs (list r-lattice)) (home-page "http://zoo.R-Forge.R-project.org/") (synopsis "S3 infrastructure for regular and irregular time series") (description "This package contains an S3 class with methods for totally ordered indexed observations. It is particularly aimed at irregular time series of numeric vectors/matrices and factors.") (license license:gpl2+))) (define-public r-fontawesome (package (name "r-fontawesome") (version "0.3.0") (source (origin (method url-fetch) (uri (cran-uri "fontawesome" version)) (sha256 (base32 "0c8sb8isiyn2gr3xfql75yyssf9wlb152cw67whq83aqsksgrvjd")))) (properties `((upstream-name . "fontawesome"))) (build-system r-build-system) (propagated-inputs (list r-htmltools r-rlang)) (home-page "https://github.com/rstudio/fontawesome") (synopsis "Easily work with Font Awesome icons") (description "Easily and flexibly insert Font Awesome icons into R Markdown documents and Shiny apps. These icons can be inserted into HTML content through inline SVG tags or @code{i} tags. There is also a utility function for exporting Font Awesome icons as PNG images for those situations where raster graphics are needed.") (license license:expat))) (define-public r-fingerprint (package (name "r-fingerprint") (version "3.5.7") (source (origin (method url-fetch) (uri (cran-uri "fingerprint" version)) (sha256 (base32 "04jcwkydjrs31pia6kq8z2n9s54im950q08hs2ay15xjxxkmb8ic")))) (properties `((upstream-name . "fingerprint"))) (build-system r-build-system) (home-page "https://cran.r-project.org/package=fingerprint") (synopsis "Functions to Operate on Binary Fingerprint Data") (description "This package provides functions to manipulate binary fingerprints of arbitrary length. A fingerprint is represented by an object of S4 class @code{fingerprint}. The bitwise logical functions in R are overridden so that they can be used directly with @code{fingerprint} objects. A number of distance metrics are also available. Fingerprints can be converted to Euclidean vectors (i.e., points on the unit hypersphere) and can also be folded. Arbitrary fingerprint formats can be handled via line handlers. 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 "0.12.3") (source (origin (method url-fetch) (uri (cran-uri "ggalluvial" version)) (sha256 (base32 "0mkan9gxg3yxjism22yxbhvlh2lh7wpbrqpb355za790prcmjbh3")))) (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 "http://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 "0.4.4") (source (origin (method url-fetch) (uri (cran-uri "ggpp" version)) (sha256 (base32 "0wcaczxjav5yg8h2197cf288mqk13p3iq675q0x0di9g8lnblvk1")))) (properties `((upstream-name . "ggpp"))) (build-system r-build-system) (propagated-inputs (list r-dplyr r-ggplot2 r-glue r-gridextra r-lubridate r-magrittr r-mass r-polynom r-rlang r-scales r-stringr r-tibble r-xts r-zoo)) (native-inputs (list r-knitr)) (home-page "https://docs.r4photobiology.info/ggpp/") (synopsis "Grammar extensions to ggplot2") (description "This package contains extensions to ggplot2. @enumerate @item Geomas: @code{geom_table}, @code{geom_plot} and @code{geom_grob} add insets to plots using native data coordinates, while @code{geom_table_npc}, @code{geom_plot_npc} and @code{geom_grob_npc} do the same using @code{npc} coordinates through new aesthetics @code{npcx} and @code{npcy}. @item Statistics: select observations based on 2D density. @item Positions: radial nudging away from a center point and nudging away from a line or curve. @end enumerate ") (license license:gpl2+))) (define-public r-ggprism (package (name "r-ggprism") (version "1.0.3") (source (origin (method url-fetch) (uri (cran-uri "ggprism" version)) (sha256 (base32 "09dh0r8r5s61i5dbk6rswajc2vm7k8wvlqyvzq8wr160676lycjp")))) (properties `((upstream-name . "ggprism"))) (build-system r-build-system) (propagated-inputs (list r-digest r-ggplot2 r-glue r-gtable r-rlang r-scales r-tibble)) (native-inputs (list r-knitr)) (home-page "https://csdaw.github.io/ggprism/") (synopsis "ggplot2 extension inspired by GraphPad Prism") (description "This package provides various themes, palettes, and other functions that are used to customise ggplots to look like they were made in GraphPad Prism. The Prism-look is achieved with @code{theme_prism()} and @code{scale_fill|colour_prism()}, axes can be changed with custom guides like @code{guide_prism_minor()}, and significance indicators added with @code{add_pvalue()}.") (license license:gpl3+))) (define-public r-ggrastr (package (name "r-ggrastr") (version "1.0.1") (source (origin (method url-fetch) (uri (cran-uri "ggrastr" version)) (sha256 (base32 "07sx5wlawfyb0zy5am2q1ajhkdym5r9ih47p57l8bv4dlc7ykml2")))) (properties `((upstream-name . "ggrastr"))) (build-system r-build-system) (propagated-inputs (list r-cairo r-ggbeeswarm r-ggplot2 r-png r-ragg)) (native-inputs (list r-knitr)) (home-page "https://github.com/VPetukhov/ggrastr") (synopsis "Rasterize layers for ggplot2") (description "Rasterize only specific layers of a ggplot2 plot while simultaneously keeping all labels and text in vector format. This allows users to keep plots within the reasonable size limit without losing vector properties of the scale-sensitive information.") (license license:expat))) (define-public r-ggvenn (package (name "r-ggvenn") (version "0.1.9") (source (origin (method url-fetch) (uri (cran-uri "ggvenn" version)) (sha256 (base32 "0bm52j3idchignp6nrw7c76jlbfkjf5zng258957vq019vx9qxrq")))) (properties `((upstream-name . "ggvenn"))) (build-system r-build-system) (propagated-inputs (list r-dplyr r-ggplot2)) (home-page "https://cran.r-project.org/package=ggvenn") (synopsis "Draw Venn diagram with ggplot2") (description "This package offers an easy to use way to draw a Venn diagram with @code{ggplot2}.") (license license:expat))) (define-public r-ggvenndiagram (package (name "r-ggvenndiagram") (version "1.2.2") (source (origin (method url-fetch) (uri (cran-uri "ggVennDiagram" version)) (sha256 (base32 "1l4cincm7c2q9x3djiv1lm9bvivaqk7kincx19b8f760wz9hp74k")))) (properties `((upstream-name . "ggVennDiagram"))) (build-system r-build-system) (propagated-inputs (list r-dplyr r-ggplot2 r-magrittr r-plotly r-purrr r-rvenn r-sf r-tibble r-yulab-utils)) (native-inputs (list r-knitr)) (home-page "https://github.com/gaospecial/ggVennDiagram") (synopsis "Implementention of the Venn diagram using ggplot2") (description "This package implements easy-to-use functions to generate 2-7 sets Venn plot in publication quality. @code{ggVennDiagram} plot Venn using well-defined geometry dataset and @code{ggplot2}. The shapes of 2-4 sets Venn use circles and ellipses, while the shapes of 4-7 sets Venn use irregular polygons (4 has both forms), which are developed and imported from another package @code{venn}. We provide internal functions to integrate shape data with user provided sets data, and calculated the geometry of every regions/intersections of them, then separately plot Venn in three components: set edges, set labels, and regions. 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 "0.5.0") (source (origin (method url-fetch) (uri (cran-uri "ggpmisc" version)) (sha256 (base32 "1i7cfmhmgih3hn0zr5yn33ziznfa3a4j8hkn237bv7jckwzpklxw")))) (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-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 "0.2.1") (source (origin (method url-fetch) (uri (cran-uri "ggside" version)) (sha256 (base32 "1vl7kzgmi5xxxsqvyg4cm4xwd3lfjgysay1lw6hri5vj22mnga5h")))) (properties `((upstream-name . "ggside"))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-glue r-gtable r-rlang r-scales r-tibble)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/package=ggside") (synopsis "Side grammar graphics that extends @code{ggplot2}") (description "The grammar of graphics as shown in @code{ggplot2} has provided an expressive API for users to build plots. This package @{ggside} extends @code{ggplot2} by allowing users to add graphical information about one of the main panel's axis using a familiar @code{ggplot2} style API with tidy data. This package is particularly useful for visualizing metadata on a discrete axis, or summary graphics on a continuous axis such as a boxplot or a density distribution.") (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 "0.2.1") (source (origin (method url-fetch) (uri (cran-uri "gprofiler2" version)) (sha256 (base32 "0r0h34b35xzgd9rh55yndn0anxy0z45zdlqa6qfmpn91b6v1bb1g")))) (properties `((upstream-name . "gprofiler2"))) (build-system r-build-system) (propagated-inputs (list r-crosstalk r-dplyr r-ggplot2 r-gridextra r-jsonlite r-plotly r-rcurl r-tidyr r-viridislite)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/gprofiler2/") (synopsis "Interface to the g:Profiler toolset") (description "This package provides a toolset for functional enrichment analysis and visualization, gene/protein/SNP identifier conversion and mapping orthologous genes across species via @url{https://biit.cs.ut.ee/gprofiler,g:Profiler}. 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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They are not minified code, so we don't ;; replace them. (with-directory-excursion "inst/www/shared" (replace-file "strftime/strftime-min.js" (search-input-file inputs "/share/javascript/strftime.min.js")) (replace-file "highlight/highlight.pack.js" (search-input-file inputs "/share/javascript/highlight.min.js")) (replace-file "datatables/js/jquery.dataTables.min.js" (search-input-file inputs "/share/javascript/jquery.dataTables.min.js")) (replace-file "selectize/js/selectize.min.js" (search-input-file inputs "/share/javascript/selectize.min.js")) (for-each (match-lambda ((source . target) (minify source #:target target))) `(("jqueryui/jquery-ui.js" . "jqueryui/jquery-ui.min.js") ("datepicker/js/bootstrap-datepicker.js" . "datepicker/js/bootstrap-datepicker.min.js") ("ionrangeslider/js/ion.rangeSlider.js" . "ionrangeslider/js/ion.rangeSlider.min.js") ("bootstrap/js/bootstrap.js" . "bootstrap/js/bootstrap.min.js") (,(assoc-ref inputs "js-bootstrap-accessibility") . 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"showdown/compressed/showdown.js")))))))))) (propagated-inputs (list r-bslib r-cachem r-commonmark r-crayon r-ellipsis r-fastmap r-fontawesome r-glue r-htmltools r-httpuv r-jsonlite r-later r-lifecycle r-mime r-promises r-r6 r-rlang r-sourcetools r-withr r-xtable)) (inputs (list js-datatables js-selectize js-strftime js-highlight)) (native-inputs `(("uglifyjs" ,node-uglify-js) ("gfortran" ,gfortran) ("js-bootstrap-accessibility" ,(origin (method url-fetch) (uri "https://raw.githubusercontent.com/paypal/bootstrap-accessibility-plugin/\ v1.0.7/_site/plugins/js/bootstrap-accessibility.js") (sha256 (base32 "1489wyzwrpf86y7vhc13n4v3mszmsfybhd3f75jkpnbvyp5sncm8")))))) (home-page "https://shiny.rstudio.com") (synopsis "Easy interactive web applications with R") (description "Makes it incredibly easy to build interactive web applications with R. Automatic \"reactive\" binding between inputs and outputs and extensive prebuilt widgets make it possible to build beautiful, responsive, and powerful applications with minimal effort.") (license license:artistic2.0))) (define-public r-shinyhelper (package (name "r-shinyhelper") (version "0.3.2") (source (origin (method url-fetch) (uri (cran-uri "shinyhelper" version)) (sha256 (base32 "1c4hvf19j3yyh8r12nx85ldkxs89g98q74csnqs5ml5l79a65vgp")))) (properties `((upstream-name . "shinyhelper"))) (build-system r-build-system) (propagated-inputs (list r-markdown r-shiny)) (home-page "https://cran.r-project.org/package=shinyhelper") (synopsis "Easily add Markdown help files to shiny app elements") (description "This package creates a lightweight way to add markdown helpfiles to Shiny apps, using modal dialog boxes, with no need to observe each help button separately.") (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 "0.2.7") (source (origin (method url-fetch) (uri (cran-uri "shinyTree" version)) (sha256 (base32 "0jfx2capckv7hf2yx3fn8i4rcmhi222ah91jnmhg497x8wgz31s3")) (modules '((guix build utils))) (snippet '(begin ;; 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")) #t)))) (properties `((upstream-name . "shinyTree"))) (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 'replace-minified-javascript (lambda* (#:key inputs #:allow-other-keys) (with-directory-excursion "inst/www/jsTree-3.3.7/" (symlink (search-input-file inputs "/share/javascript/require.min.js") "libs/require.js") (call-with-values (lambda () (unzip2 `((,(assoc-ref inputs "js-jquery") "libs/jquery.js") ("jstree.js" "jstree.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))))) (propagated-inputs (list r-htmlwidgets r-jsonlite r-promises r-shiny r-stringr)) (inputs (list js-requirejs)) (native-inputs `(("uglifyjs" ,node-uglify-js) ("js-jquery" ,(origin (method url-fetch) (uri "https://code.jquery.com/jquery-3.3.1.js") (sha256 (base32 "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq")))))) (home-page "https://cran.r-project.org/web/packages/shinyTree/") (synopsis "jsTree bindings for Shiny") (description "This package exposes R bindings to jsTree, a JavaScript library that supports interactive trees, to enable rich, editable trees in Shiny.") (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 "1.0.0") (source (origin (method url-fetch) (uri (cran-uri "d3r" version)) (sha256 (base32 "1qijkllfaaw0lb29j8mappm8jz9kg8gkihxq5wqhb4gabsazdwva")))) (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) (delete-file target) (invoke "esbuild" source "--minify" (string-append "--outfile=" target))) sources targets))))))))) (propagated-inputs (list r-dplyr r-htmltools r-rlang 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 "1hif1phswlkkpvcf1hbqmfsxdb5s5gr5g2frcwbh0rh8g6nbkyqi")))))) (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 "0.3.6") (source (origin (method url-fetch) (uri (cran-uri "wesanderson" version)) (sha256 (base32 "09mr6p2jmqdjq27cz974w5hyxgn929zp9z3inhxqmmh1582fmdi2")))) (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 "4.9.1") (source (origin (method url-fetch) (uri (cran-uri "MBESS" version)) (sha256 (base32 "18klyyjvmwggv4ma2x77jac3640yxbsbinl3s2rp1ik4n9phnjd0")))) (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 "3.3.5") (source (origin (method url-fetch) (uri (cran-uri "ggtern" version)) (sha256 (base32 "15hhn8msy0l8zbq8ms0zvg1iajn1c28gd77v3hp6dvwwsla8zzbd")))) (properties `((upstream-name . "ggtern"))) (build-system r-build-system) (propagated-inputs (list r-compositions r-ggplot2 r-gridextra r-gtable r-hexbin r-latex2exp r-lattice r-mass r-plyr r-proto r-scales)) (home-page "http://www.ggtern.com") (synopsis "Extension to ggplot2 for ternary diagrams") (description "This package extends the functionality of ggplot2, providing the capability to plot ternary diagrams for (a subset of) the ggplot2 geometries. Additionally, ggtern has implemented several new geometries which are unavailable to the standard ggplot2 release.") (license license:gpl2))) (define-public r-tablerdash (package (name "r-tablerdash") (version "0.1.0") (source (origin (method url-fetch) (uri (cran-uri "tablerDash" version)) (sha256 (base32 "1mnp6lxa7d669r325aynq1n3f35r9sy4v1fvdh4cymbf33s8mkmm")) (snippet '(begin ;; Delete minified JavaScript (for-each delete-file '("inst/tablerDash-0.1.0/require.min.js" "inst/bootstrap-4.0.0/bootstrap.bundle.min.js")) #true)))) (properties `((upstream-name . "tablerDash"))) (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" (call-with-values (lambda () (unzip2 `((,(assoc-ref inputs "js-requirejs") "tablerDash-0.1.0/require.min.js") (,(assoc-ref inputs "js-bootstrap") "bootstrap-4.0.0/bootstrap.bundle.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)))) #t))))) (propagated-inputs (list r-htmltools r-knitr r-shiny)) (native-inputs `(("esbuild" ,esbuild) ("js-requirejs" ,(origin (method url-fetch) (uri "https://raw.githubusercontent.com/requirejs/requirejs/2.3.5/require.js") (sha256 (base32 "06w32mwqii9cx409ivda88z58qbkcdb4p6hf6jawchsgagaziyds")))) ("js-bootstrap" ,(origin (method url-fetch) (uri "https://raw.githubusercontent.com/twbs/bootstrap/\ v4.0.0/dist/js/bootstrap.bundle.js") (sha256 (base32 "0cvfqffn45vfbj3fk6wmrhkyndhk4id89vgydssbbzxjkfwprfrj")))))) (home-page "https://rinterface.github.io/tablerDash/") (synopsis "Tabler API for Shiny") (description "This package provides an R interface to the @url{https://tabler.io,Tabler} HTML template. tablerDash is a light Bootstrap 4 dashboard template. 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 "2.2") (source (origin (method url-fetch) (uri (cran-uri "spelling" version)) (sha256 (base32 "179nj9w1v27qq9q5240ddvggp0795998sxyqjvbqjvq9dmach3bl")))) (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 "1.2.0") (source (origin (method url-fetch) (uri (cran-uri "crosstalk" version)) (sha256 (base32 "180y7mhpj17axpadwhh7s0qvrpdnag7g977vk256l96d6nmvlds2")))) (build-system r-build-system) (propagated-inputs (list r-htmltools r-jsonlite r-lazyeval r-r6)) (home-page "https://rstudio.github.io/crosstalk/") (synopsis "Inter-widget interactivity for HTML widgets") (description "This package provides building blocks for allowing HTML widgets to communicate with each other, with Shiny or without (i.e., static @code{.html} files). It currently supports linked brushing and filtering.") (license license:expat))) (define-public r-rook (package (name "r-rook") (version "1.1-1") (source (origin (method url-fetch) (uri (cran-uri "Rook" version)) (sha256 (base32 "00s9a0kr9rwxvlq433daxjk4ji8m0w60hjdprf502msw9kxfrx00")))) (properties `((upstream-name . "Rook"))) (build-system r-build-system) (propagated-inputs (list r-brew)) (home-page "https://cran.r-project.org/web/packages/Rook") (synopsis "Web server interface for R") (description "This package contains the Rook specification and convenience software for building and running Rook applications. A Rook application is an R reference class object that implements a @code{call} method or an R closure that takes exactly one argument, an environment, and returns a list with three named elements: the @code{status}, the @code{headers}, and the @code{body}.") (license license:gpl2))) (define-public r-miniui (package (name "r-miniui") (version "0.1.1.1") (source (origin (method url-fetch) (uri (cran-uri "miniUI" version)) (sha256 (base32 "1h5h2sc57h95d6bsgs95l26911g38hvjc1v50bc31xl9689l2as5")))) (properties `((upstream-name . "miniUI"))) (build-system r-build-system) (propagated-inputs (list r-htmltools r-shiny)) (home-page "https://cran.r-project.org/web/packages/miniUI/") (synopsis "Shiny UI widgets for small screens") (description "This package provides UI widget and layout functions for writing Shiny apps that work well on small screens.") (license license:gpl3))) (define-public r-feather (package (name "r-feather") (version "0.3.5") (source (origin (method url-fetch) (uri (cran-uri "feather" version)) (sha256 (base32 "1gxd0h2m56sjjlzn4dry6s13nddxc4l5i11gsvavaf2dwbahdzsh")))) (build-system r-build-system) (propagated-inputs (list r-hms r-rcpp r-tibble)) (home-page "https://github.com/wesm/feather") (synopsis "R Bindings to the Feather API") (description "Read and write feather files, a lightweight binary columnar data store designed for maximum speed.") (license license:asl2.0))) (define-public r-maps (package (name "r-maps") (version "3.4.0") (source (origin (method url-fetch) (uri (cran-uri "maps" version)) (sha256 (base32 "0ispkx1szgwxhr0zzhdzgqqwcgc6psg7vry4sj4rb89w76rcq63r")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/maps") (synopsis "Draw geographical maps") (description "This package provides an R module for display of maps. Projection code and larger maps are in separate packages (@code{mapproj} and @code{mapdata}).") (license license:gpl2))) (define-public r-mapproj (package (name "r-mapproj") (version "1.2.8") (source (origin (method url-fetch) (uri (cran-uri "mapproj" version)) (sha256 (base32 "10bpib827011fpgvzsmlv4j3i41s0r3cv1hvawwdlk753s7i0pw6")))) (build-system r-build-system) (propagated-inputs (list r-maps)) (home-page "https://cran.r-project.org/web/packages/mapproj") (synopsis "Map projection in R") (description "This package converts latitude/longitude into projected coordinates.") (license (list license:gpl2 ; The R interface (license:non-copyleft ; The C code "https://www.gnu.org/licenses/license-list.en.html#lucent102" "Lucent Public License Version 1.02"))))) (define-public r-rgooglemaps (package (name "r-rgooglemaps") (version "1.4.5.3") (source (origin (method url-fetch) (uri (cran-uri "RgoogleMaps" version)) (sha256 (base32 "02v8k0bw70q4qwx4lcdy8p25q7n3ql2ll46lfpqllxa1p26svmfi")))) (properties `((upstream-name . "RgoogleMaps"))) (build-system r-build-system) (propagated-inputs (list r-png r-sp)) (home-page "https://cran.r-project.org/web/packages/RgoogleMaps") (synopsis "Use Google Maps in R") (description "This package serves two purposes: @enumerate @item Provide a comfortable R interface to query the Google server for static maps, and @item Use the map as a background image to overlay plots within R. This requires proper coordinate scaling. @end enumerate\n") (license license:gpl2+))) (define-public r-gensa (package (name "r-gensa") (version "1.1.7") (source (origin (method url-fetch) (uri (cran-uri "GenSA" version)) (sha256 (base32 "03xqwxm7v7rnihx730a4p65dfwhjh4345r3d78y0qxxplk8d76cx")))) (properties `((upstream-name . "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.") 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(license license:gpl3+))) (define-public r-jpeg (package (name "r-jpeg") (version "0.1-9") (source (origin (method url-fetch) (uri (cran-uri "jpeg" version)) (sha256 (base32 "0wihj538wdnr71wdldym83qadb4kh68a6rkallwbh2f25r27b881")))) (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 "3.0.0") (source (origin (method url-fetch) (uri (cran-uri "ggmap" version)) (sha256 (base32 "13dmzl6z62pzjiffilarkji46vy0sacxa8a7mhrhc3biq3ylzhln")))) (build-system r-build-system) (propagated-inputs (list r-bitops r-digest r-dplyr r-ggplot2 r-glue r-httr r-jpeg r-magrittr r-plyr r-png r-purrr r-rgooglemaps r-rjson 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-haven (package (name "r-haven") (version "2.5.1") (source (origin (method url-fetch) (uri (cran-uri "haven" version)) (sha256 (base32 "0w0aqm0z4h0rm1f7fylm1mbv79p43y2r795w64wczcd0jwh4ch4z")) (modules '((guix build utils))) (snippet ;; unvendor readstat '(delete-file-recursively "src/readstat")))) (build-system r-build-system) (arguments '(#:phases (modify-phases %standard-phases (add-after 'unpack 'unbundle-readstat (lambda _ ;; We’re not building readstat. (substitute* "configure" (("exit 1") "")) ;don't be so dramatic! (substitute* '("src/Makevars.in" "configure") (("^PKG_LIBS=.*") "PKG_LIBS=\"-lreadstat\"\n"))))))) (inputs (list readstat)) (native-inputs (list r-knitr)) (propagated-inputs (list r-cli r-cpp11 r-forcats r-hms r-lifecycle r-rlang r-readr 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 "0.8-18") (source (origin (method url-fetch) (uri (cran-uri "amap" version)) (sha256 (base32 "0zpcb73w413na23f6giml9311jh0j0y766w2fh9i40d2h7bbvyvs")))) (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 "5.6-2") (source (origin (method url-fetch) (uri (cran-uri "ape" version)) (sha256 (base32 "0mqjsh7maczd02iwa4fb896q3kgd9jnlilq7y1yz18ch0c54aqlv")))) (build-system r-build-system) (propagated-inputs (list 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 "2.0-3") (source (origin (method url-fetch) (uri (cran-uri "colorspace" version)) (sha256 (base32 "0zw52s8g2gxp8i1ax96azxmxqrbhb7aad5px0c1vgr6n9p682mp7")))) (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 "1.6.2") (source (origin (method url-fetch) (uri (cran-uri "glue" version)) (sha256 (base32 "1gzxk5jgdh2xq9r7z09xs306ygzf27vhg3pyfl7ck1755gqii9cx")))) (build-system r-build-system) ;; knitr depends on glue, so we can't add knitr here to build the ;; vignettes. #; (native-inputs `(("r-knitr" ,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-paletteer (package (name "r-paletteer") (version "1.4.1") (source (origin (method url-fetch) (uri (cran-uri "paletteer" version)) (sha256 (base32 "0vj945cgpfhmbd98mcj167mgshghv32dxh8m4ngxs6i4q4y5blm7")))) (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 "1.3.21") (source (origin (method url-fetch) (uri (cran-uri "pastecs" version)) (sha256 (base32 "0z4dic94ar646w7zc2ggi5hgvf2qnznsani94c5pyql8zspz47lc")))) (build-system r-build-system) (propagated-inputs (list r-boot)) (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 "1.2-16") (source (origin (method url-fetch) (uri (cran-uri "partykit" version)) (sha256 (base32 "1cnx6qbw5svwh3nq40n5vr20179ihd3jgznm7mz4k50qkkid8hz6")))) (build-system r-build-system) (propagated-inputs (list r-formula r-inum r-libcoin r-mvtnorm r-rpart r-survival)) (home-page "http://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.") 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(license license:expat))) (define-public r-pls (package (name "r-pls") (version "2.8-1") (source (origin (method url-fetch) (uri (cran-uri "pls" version)) (sha256 (base32 "137jg3x7aqwyki29i4kzp8d6imn17nq6wzzfjw5q19pixvmpybp2")))) (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 "1.7.1") (source (origin (method url-fetch) (uri (cran-uri "ps" version)) (sha256 (base32 "1waylmbrl23j62010r12c8xwzlvs1dys3cnh7hnrgk27glvqlicw")))) (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 "1.3.1") (source (origin (method url-fetch) (uri (cran-uri "pkgbuild" version)) (sha256 (base32 "0j6v5nbp8kg1m3j999gd1qsbdmqcqm1mf28ngmm177miwv8q4skw")))) (build-system r-build-system) (propagated-inputs (list r-callr r-cli r-crayon r-desc r-prettyunits r-r6 r-rprojroot r-withr)) (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 "1.3.0") (source (origin (method url-fetch) (uri (cran-uri "pkgload" version)) (sha256 (base32 "0a22kxgm9a8ax1dw2q9v3338qhjmhfbcqw8r4b6608k6074m7xjs")))) (build-system r-build-system) (propagated-inputs (list r-cli r-crayon r-desc r-fs r-glue 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-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 "1.0.9") (source (origin (method url-fetch) (uri (cran-uri "Rcpp" version)) (sha256 (base32 "0xli48y9nsj8x8p5vkhisiz4l23g8r2623rn0i4xb5javh3fqz40")))) (build-system r-build-system) (home-page "http://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.") 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(license license:expat))) (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.") 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(license license:gpl2))) (define-public r-shape (package (name "r-shape") (version "1.4.6") (source (origin (method url-fetch) (uri (cran-uri "shape" version)) (sha256 (base32 "0yqbrrx2ywmfl99s6d1n6jblc63k1mxbiqyv8y0kq8jws1g3w45r")))) (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 . 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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-powerlaw (package (name "r-powerlaw") (version "0.70.6") (source (origin (method url-fetch) (uri (cran-uri "poweRlaw" version)) (sha256 (base32 "14d1myxllvm1grnfiszzzxaiqpb2jpmsi19wq70r8r2wki293h7g")))) (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-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 "1.16.0") (source (origin (method url-fetch) (uri (cran-uri "dendextend" version)) (sha256 (base32 "0rl4f0b73s1gdjfxgpnz87lhv131qazxb6vsv2935ad266fd0bzc")))) (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-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 "1.1-3") (source (origin (method url-fetch) (uri (cran-uri "fastmatch" version)) (sha256 (base32 "0qcq1gwl9pijgp34giyq5y9rk0ly3d7xza2b7r68xx63ifqa1vqx")))) (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 "4.0.7") (source (origin (method url-fetch) (uri (cran-uri "ff" version)) (sha256 (base32 "1yl3ipzz9bjkfy9bbna7xz5n7iz4lchnw5l7agww7by764yk6iqa")))) (build-system r-build-system) (propagated-inputs (list r-bit)) (home-page "http://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) (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 "1.1.1") (source (origin (method url-fetch) (uri (cran-uri "prettyunits" version)) (sha256 (base32 "1ibmzgknw5896q2i6r59jz2izblxwgb29ivvjzx50pkd1jl9l6cs")))) (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 "1.1.1") (source (origin (method url-fetch) (uri (cran-uri "prismatic" version)) (sha256 (base32 "013i0mq4n8s2zbzvfrz1vjcn2a6l98bamslkcv1a3cn70gpphja9")))) (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 "1.2.1") (source (origin (method url-fetch) (uri (cran-uri "RestRserve" version)) (sha256 (base32 "1xfcp0y9l31815g1jk33mnkb6z68qpjl0gb4fj7f4578kx3v1c8p")))) (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 "1.2.2") (source (origin (method url-fetch) (uri (cran-uri "progress" version)) (sha256 (base32 "0dgzb362641aqm8xd88iqa8jmpdm43xs0aba0d5kk6fvapnxi95l")))) (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 "2.1.2") (source (origin (method url-fetch) (uri (cran-uri "GGally" version)) (sha256 (base32 "1r98zgh2grn8330cf26r1c20gl131zm778szvn5wj6q6pwv2yd9h")))) (properties `((upstream-name . "GGally"))) (build-system r-build-system) (inputs (list openssl)) (propagated-inputs (list r-dplyr r-forcats r-ggplot2 r-gtable r-lifecycle r-plyr r-progress r-rcolorbrewer r-reshape 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 "1.5-0") (source (origin (method url-fetch) (uri (cran-uri "sp" version)) (sha256 (base32 "077q1wh9ihhcn1338xspnd90hy16ljxsav1xcrxdxj4fyynhd6lk")))) (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-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-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 "0.6-9.2") (source (origin (method url-fetch) (uri (cran-uri "Rmpi" version)) (sha256 (base32 "06mxqgrimhfsag5giv810c7ycdbaycqs4qcj41pnfbj0jypw32im")))) (properties `((upstream-name . 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"Lmoments"))) (build-system r-build-system) (propagated-inputs (list r-rcpp r-rcpparmadillo)) (home-page "http://www.tilastotiede.fi/juha_karvanen.html") (synopsis "L-moments and quantile mixtures") (description "This package contains functions to estimate L-moments and trimmed L-moments from the data. It also contains functions to estimate the parameters of the normal polynomial quantile mixture and the Cauchy polynomial quantile mixture from L-moments and trimmed L-moments.") (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 . "etrunct"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/etrunct") (synopsis "Computes moments of univariate truncated T distribution") (description "This package computes moments of univariate truncated T distribution. There is only one exported function, @code{e_trunct}, which should be seen for details.") (license license:expat))) (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 . "excelR"))) (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/jexcel/js/" (let ((source (assoc-ref inputs "js-jexcel")) (target "jexcel.min.js")) (format #true "Processing ~a --> ~a~%" source target) (invoke "esbuild" source "--minify" (string-append "--outfile=" target))))))))) (native-inputs `(("esbuild" ,esbuild) ;; There is no tag for this particular commit, but comparison of the ;; contents of the JavaScript files point to this commit as the most ;; likely source. ("js-jexcel" ,(origin (method url-fetch) (uri (string-append "https://raw.githubusercontent.com/jspreadsheet/ce/" "8af1960f76e6803bebc5750013d2ebe95354e88a/dist/jexcel.js")) (sha256 (base32 "0y88hsr9d8cpnvdmbm17m328pc4kc5wbcv02kzmhm0bryzhviw7h")))))) (propagated-inputs (list r-htmlwidgets r-jsonlite)) (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 "2.1-2") (source (origin (method url-fetch) (uri (cran-uri "extRemes" version)) (sha256 (base32 "19q560prq02h3bwk01jb68693qb5bhsv8wiqhia7v5knm34qv8x7")))) (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-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 "1.0-4") (source (origin (method url-fetch) (uri (cran-uri "inum" version)) (sha256 (base32 "1khkzja8lwn9075864vbyajqina9m588ahf1fsrrajrsqilyzssz")))) (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 . "invgamma"))) (build-system r-build-system) (home-page "https://github.com/dkahle/invgamma") (synopsis "Inverse gamma distribution") (description "This package provides a light weight implementation of the standard distribution functions for the inverse gamma distribution, wrapping those for the gamma distribution in the @code{stats} package.") (license license:gpl2))) (define-public r-bdsmatrix (package (name "r-bdsmatrix") (version "1.3-6") (source (origin (method url-fetch) (uri (cran-uri "bdsmatrix" version)) (sha256 (base32 "1g300x11rv56f826mbv7mbb67a5xz3dv74hpjc18jh3q8gap3j7r")))) (properties `((upstream-name . "bdsmatrix"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/bdsmatrix/") (synopsis "Routines for block diagonal symmetric matrices") (description "This package provides procedures to work with block diagonal symmetric matrices, a special case of sparse matrices.") (license license:lgpl2.0))) (define-public r-bbmle (package (name "r-bbmle") (version "1.0.25") (source (origin (method url-fetch) (uri (cran-uri "bbmle" version)) (sha256 (base32 "0mdj21q7k0fp4cj7la14vmcjmp49zqm57g7r6zrwmxpv0acwda46")))) (build-system r-build-system) (propagated-inputs (list r-bdsmatrix r-lattice r-mass r-matrix r-mvtnorm r-numderiv)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/bbmle") (synopsis "Tools for General Maximum Likelihood Estimation") (description "This package provides methods and functions for fitting maximum likelihood models in R. 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 "1.3.12") (source (origin (method url-fetch) (uri (cran-uri "emdbook" version)) (sha256 (base32 "0ls3zxxlwmdv7zn1v9i1y9zc2sn0hbgmyjvsj7zn3ajsw7wwlih6")))) (build-system r-build-system) (propagated-inputs (list r-bbmle r-coda r-lattice r-mass r-plyr)) (home-page "http://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 "5.6.16") (source (origin (method url-fetch) (uri (cran-uri "lpSolve" version)) (sha256 (base32 "0amvxki4l2sp60adcc6ra7kbqjrfv55gbn6kasq04klihi8ix88q")))) (properties `((upstream-name . "lpSolve"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/lpSolve") (synopsis "R interface to Lp_solve to solve linear/integer programs") (description "Lp_solve is software for solving linear, integer and mixed integer programs. This implementation supplies a \"wrapper\" function in C and some R functions that solve general linear/integer problems, assignment problems, and transportation problems.") (license license:lgpl2.0))) (define-public r-limsolve (package (name "r-limsolve") (version "1.5.6") (source (origin (method url-fetch) (uri (cran-uri "limSolve" version)) (sha256 (base32 "1829rd2cnd8qj80z9a7sgc7gx4sf3kvl5g6d2a0lqqw30f9sjzmr")))) (properties `((upstream-name . "limSolve"))) (build-system r-build-system) (propagated-inputs (list r-lpsolve r-mass r-quadprog)) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/limSolve") (synopsis "Solving linear inverse models") (description "This package provides functions that: @enumerate @item find the minimum/maximum of a linear or quadratic function, @item sample an underdetermined or overdetermined system, @item solve a linear system Ax=B for the unknown x. @end enumerate It includes banded and tridiagonal linear systems. The package calls Fortran functions from LINPACK.") ;; Any GPL version. (license (list license:gpl2+ license:gpl3+)))) (define-public r-fitdistrplus (package (name "r-fitdistrplus") (version "1.1-8") (source (origin (method url-fetch) (uri (cran-uri "fitdistrplus" version)) (sha256 (base32 "0nhgjvwya95v6b9khbsgp44lw10xg35w61lmka1v6wq7yh827izk")))) (build-system r-build-system) (propagated-inputs (list r-mass r-survival)) (native-inputs (list r-knitr)) (home-page "http://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 "1.7-10") (source (origin (method url-fetch) (uri (cran-uri "energy" version)) (sha256 (base32 "19xyw5bkyzfk22gly2ca2nsznqnrhaq4a77727kr1k26bj3y8gal")))) (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-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-ksamples (package (name "r-ksamples") (version "1.2-9") (source (origin (method url-fetch) (uri (cran-uri "kSamples" version)) (sha256 (base32 "1zs22p68d6320kcylisnk0b5wmpapxkyz15py09czxzw7npw8gms")))) (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-squarem (package (name "r-squarem") (version "2021.1") (source (origin (method url-fetch) (uri (cran-uri "SQUAREM" version)) (sha256 (base32 "0n1s32l9p4vdm3h5q6g43s0qbpzry08difsh0yay80wrla6f3rb6")))) (properties `((upstream-name . "SQUAREM"))) (build-system r-build-system) (home-page "https://coah.jhu.edu/people/Faculty_personal_Pages/Varadhan.html") (synopsis "Squared Extrapolation Methods for Accelerating EM-Like Monotone Algorithms") (description "This package provides algorithms for accelerating the convergence of slow, monotone sequences from smooth, contraction mapping such as the EM algorithm. It can be used to accelerate any smooth, linearly convergent acceleration scheme. A tutorial style introduction to this package is available in a vignette.") (license license:gpl2+))) (define-public r-progressr (package (name "r-progressr") (version "0.11.0") (source (origin (method url-fetch) (uri (cran-uri "progressr" version)) (sha256 (base32 "1nbc6vvsyqa1gvh1a1m4prnvng88wsa0r35i9fiwq84a6j18qrnq")))) (properties `((upstream-name . "progressr"))) (build-system r-build-system) (propagated-inputs (list r-digest)) (home-page "https://progressr.futureverse.org") (synopsis "Inclusive, unifying API for progress updates") (description "This package provides a minimal, unifying API for scripts and packages to report progress updates from anywhere including when using parallel processing. The package is designed such that the developer can to focus on what progress should be reported on without having to worry about how to present it. The end user has full control of how, where, and when to render these progress updates.") (license license:gpl3+))) (define-public r-lava (package (name "r-lava") (version "1.6.10") (source (origin (method url-fetch) (uri (cran-uri "lava" version)) (sha256 (base32 "0bi3c1aqwlq7jbz4raz6vga4r264w7lldi0i62xjlbl7hnlgi23s")))) (build-system r-build-system) (propagated-inputs (list r-future-apply r-numderiv r-progressr r-squarem r-survival)) (native-inputs (list r-knitr)) (home-page "https://github.com/kkholst/lava") (synopsis "Latent variable models") (description "This package provides tools for the estimation and simulation of latent variable models.") (license license:gpl3))) (define-public r-drr (package (name "r-drr") (version "0.0.4") (source (origin (method url-fetch) (uri (cran-uri "DRR" version)) (sha256 (base32 "1y70si1gig4l7jx5jiqsqliyywfsvimkx53x3zh1lc3yj2j6bqwk")))) (properties `((upstream-name . "DRR"))) (build-system r-build-system) (propagated-inputs (list r-cvst r-kernlab r-matrix)) (home-page "https://cran.r-project.org/web/packages/DRR") (synopsis "Dimensionality reduction via regression") (description "This package provides an implementation of dimensionality reduction via regression using Kernel Ridge Regression.") (license license:gpl3))) (define-public r-prodlim (package (name "r-prodlim") (version "2019.11.13") (source (origin (method url-fetch) (uri (cran-uri "prodlim" version)) (sha256 (base32 "03wvh3kirp1prac5nky6a5whs97rvaf4hc27x0fnh51sa17r42b8")))) (build-system r-build-system) (propagated-inputs (list r-kernsmooth r-lava r-rcpp r-survival)) (home-page "https://cran.r-project.org/web/packages/prodlim") (synopsis "Product-limit estimation for censored event history analysis") (description "This package provides a fast and user-friendly implementation of nonparametric estimators for censored event history (survival) analysis with the Kaplan-Meier and Aalen-Johansen methods.") (license license:gpl2+))) (define-public r-dimred (package (name "r-dimred") (version "0.2.6") (source (origin (method url-fetch) (uri (cran-uri "dimRed" version)) (sha256 (base32 "05zlkf6hjdqqr1sgw7ww9f17vjnsiqfaj9kvdvi146phh53v2zls")))) (properties `((upstream-name . "dimRed"))) (build-system r-build-system) (propagated-inputs (list r-drr r-magrittr)) (native-inputs (list r-knitr)) (home-page "https://github.com/gdkrmr/dimRed") (synopsis "Framework for dimensionality reduction") (description "This package provides a collection of dimensionality reduction techniques from R packages and provides a common interface for calling the methods.") (license license:gpl3))) (define-public r-timedate (package (name "r-timedate") (version "4021.104") (source (origin (method url-fetch) (uri (cran-uri "timeDate" version)) (sha256 (base32 "03ncgbc9igiwl4s8pa94nj2v7aw3gw8ay51pwvv9gkv2f7l7dvh3")))) (properties `((upstream-name . "timeDate"))) (build-system r-build-system) (home-page "https://www.rmetrics.org") (synopsis "Chronological and calendar objects") (description "This package provides an environment for teaching \"Financial Engineering and Computational Finance\" and for managing chronological and calendar objects.") (license license:gpl2+))) (define-public r-magic (package (name "r-magic") (version "1.6-0") (source (origin (method url-fetch) (uri (cran-uri "magic" version)) (sha256 (base32 "1gybia2aq80ldk1d845y5srncfzbbmpqhgl7vfaz7qqqjs6d85j5")))) (build-system r-build-system) (propagated-inputs (list r-abind)) (home-page "https://github.com/RobinHankin/magic.git") (synopsis "Create and investigate magic squares") (description "This package provides a collection of efficient, vectorized algorithms for the creation and investigation of magic squares and hypercubes, including a variety of functions for the manipulation and analysis of arbitrarily dimensioned arrays.") (license license:gpl2))) (define-public r-rmysql (package (name "r-rmysql") (version "0.10.23") (source (origin (method url-fetch) (uri (cran-uri "RMySQL" version)) (sha256 (base32 "05aavyggyjv46awa7ggbxlfcy9707vak5kh7kj0ljdx8zga7xb7l")))) (properties `((upstream-name . "RMySQL"))) (build-system r-build-system) (inputs (list `(,mariadb "dev") zlib)) (propagated-inputs (list r-dbi)) (home-page "https://github.com/r-dbi/RMySQL") (synopsis "Database interface and MySQL driver for R") (description "This package provides a DBI interface to MySQL / MariaDB. The RMySQL package contains an old implementation based on legacy code from S-PLUS which is being phased out. A modern MySQL client based on Rcpp is available from the RMariaDB package.") (license license:gpl2))) (define-public r-rpostgresql (package (name "r-rpostgresql") (version "0.7-4") (source (origin (method url-fetch) (uri (cran-uri "RPostgreSQL" version)) (sha256 (base32 "1ijnsly8wgy6cfib4xvdaz2g9hk1gzg7q52r37zkvc7jjh0gdbdn")))) (properties `((upstream-name . "RPostgreSQL"))) (build-system r-build-system) (inputs (list postgresql)) (propagated-inputs (list r-dbi)) (home-page "https://github.com/tomoakin/RPostgreSQL") (synopsis "R interface to the PostgreSQL database system") (description "This package provides a Database Interface (DBI) compliant driver for R to access PostgreSQL database systems.") ;; The whole package is released under GPL version 2. It includes code ;; under the PostgreSQL license. (license license:gpl2))) (define-public r-linprog (package (name "r-linprog") (version "0.9-4") (source (origin (method url-fetch) (uri (cran-uri "linprog" version)) (sha256 (base32 "1d34m2nyk7m6j2dci69bhy5mlw479xax1517j7f14pq7vhpsm9l1")))) (build-system r-build-system) (propagated-inputs (list r-lpsolve)) (home-page "http://linprog.r-forge.r-project.org/") (synopsis "Linear programming and optimization") (description "This package can be used to solve Linear Programming / Linear Optimization problems by using the simplex algorithm.") (license license:gpl2+))) (define-public r-geometry (package (name "r-geometry") (version "0.4.6.1") (source (origin (method url-fetch) (uri (cran-uri "geometry" version)) (sha256 (base32 "0wplszaxi6phxffp3zww5alwnfbh9521qi43h65w057lrm1pmj2j")))) (build-system r-build-system) (propagated-inputs (list r-magic r-linprog r-lpsolve r-rcpp r-rcppprogress)) (home-page "http://geometry.r-forge.r-project.org/") (synopsis "Mesh generator and surface tessellator") (description "This package makes the qhull library available in R, in a similar manner as in Octave. Qhull computes convex hulls, Delaunay triangulations, halfspace intersections about a point, Voronoi diagrams, furthest-site Delaunay triangulations, and furthest-site Voronoi diagrams. It runs in 2-d, 3-d, 4-d, and higher dimensions. It implements the Quickhull algorithm for computing the convex hull. 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. (license (list license:gpl2 (license:non-copyleft "http://www.qhull.org/COPYING.txt"))))) (define-public r-ddalpha (package (name "r-ddalpha") (version "1.3.13") (source (origin (method url-fetch) (uri (cran-uri "ddalpha" version)) (sha256 (base32 "1bjfgb3lbzhjb5wx9hzp90jppq7vnj59bmd2n9ymi8sh1570m9p4")))) (build-system r-build-system) (propagated-inputs (list r-bh r-class r-geometry r-mass r-rcpp r-robustbase r-sfsmisc)) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/ddalpha") (synopsis "Depth-Based classification and calculation of data depth") (description "This package contains procedures for depth-based supervised learning, which are entirely non-parametric, in particular the DDalpha-procedure (Lange, Mosler and Mozharovskyi, 2014). The training data sample is transformed by a statistical depth function to a compact low-dimensional space, where the final classification is done. It also offers an extension to functional data and routines for calculating certain notions of statistical depth functions. 50 multivariate and 5 functional classification problems are included.") (license license:gpl2))) (define-public r-gower (package (name "r-gower") (version "1.0.0") (source (origin (method url-fetch) (uri (cran-uri "gower" version)) (sha256 (base32 "0p9qx9aafkdm7wibfwk59jzw6vspsff6zwp84bc40lg0myxbf737")))) (build-system r-build-system) (home-page "https://github.com/markvanderloo/gower") (synopsis "Gower's distance") (description "This package provides tools to compute Gower's distance (or similarity) coefficient between records, and to compute the top-n matches between records. Core algorithms are executed in parallel on systems supporting OpenMP.") (license license:gpl3))) (define-public r-rcpproll (package (name "r-rcpproll") (version "0.3.0") (source (origin (method url-fetch) (uri (cran-uri "RcppRoll" version)) (sha256 (base32 "0srzfhzkk42kzrdjnhbb37946jp1p688rgysy6k3i2is8jb21zyb")))) (properties `((upstream-name . "RcppRoll"))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) (home-page "https://cran.r-project.org/web/packages/RcppRoll") (synopsis "Efficient rolling and windowed operations") (description "This package provides fast and efficient routines for common rolling / windowed operations. Routines for the efficient computation of windowed mean, median, sum, product, minimum, maximum, standard deviation and variance are provided.") 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(license license:gpl2+))) (define-public r-psych (package (name "r-psych") (version "2.2.5") (source (origin (method url-fetch) (uri (cran-uri "psych" version)) (sha256 (base32 "08f3byqwabgkqcxwpjbsxdcjkdg012iraqinw0fzskfl1srzkhyw")))) (build-system r-build-system) (propagated-inputs (list r-lattice r-mnormt r-nlme)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/psych/") (synopsis "Procedures for psychological, psychometric, and personality research") (description "This package provides a general purpose toolbox for personality, psychometric theory and experimental psychology. Functions are primarily for multivariate analysis and scale construction using factor analysis, principal component analysis, cluster analysis and reliability analysis, although others provide basic descriptive statistics. Item Response Theory is done using factor analysis of tetrachoric and polychoric correlations. Functions for analyzing data at multiple levels include within and between group statistics, including correlations and factor analysis. Functions for simulating and testing particular item and test structures are included. Several functions serve as a useful front end for structural equation modeling. Graphical displays of path diagrams, factor analysis and structural equation models are created using basic graphics.") (license license:gpl2+))) (define-public r-generics (package (name "r-generics") (version "0.1.3") (source (origin (method url-fetch) (uri (cran-uri "generics" version)) (sha256 (base32 "0lyhhwik0w7m5h3fbwl2f52gc1v2g6g6h6sc47sa9f58pxin213m")))) (build-system r-build-system) (home-page "https://github.com/r-lib/generics") (synopsis "Common S3 generics not provided by base R methods") (description "In order to reduce potential package dependencies and conflicts, generics provides a number of commonly used S3 generics that are not provided by base R methods related to model fitting.") (license license:gpl2))) (define-public r-broom (package (name "r-broom") (version "1.0.1") (source (origin (method url-fetch) (uri (cran-uri "broom" version)) (sha256 (base32 "14i8729m38nxf5q344isgq4006p3b50wi3q8jgckxqphhnj5lpjb")))) (build-system r-build-system) (propagated-inputs (list r-backports r-dplyr r-ellipsis r-generics r-ggplot2 r-glue r-purrr r-rlang r-stringr r-tibble r-tidyr)) (native-inputs (list r-knitr)) (home-page "https://github.com/tidyverse/broom") (synopsis "Convert statistical analysis objects into tidy data frames") (description "This package provides tools to convert statistical analysis objects from R into tidy data frames, so that they can more easily be combined, reshaped and otherwise processed with tools like @code{dplyr}, @code{tidyr} and @code{ggplot2}. The package provides three S3 generics: @code{tidy}, which summarizes a model's statistical findings such as coefficients of a regression; @code{augment}, which adds columns to the original data such as predictions, residuals and cluster assignments; and @code{glance}, which provides a one-row summary of model-level statistics.") (license license:expat))) (define-public r-recipes (package (name "r-recipes") (version "1.0.1") (source (origin (method url-fetch) (uri (cran-uri "recipes" version)) (sha256 (base32 "1jav29biq13xf0vg9kj3k6khqb71hqak26kxxi0vy29l849f4fly")))) (build-system r-build-system) (propagated-inputs (list r-cli r-dplyr r-ellipsis r-generics r-glue r-gower r-hardhat r-ipred r-lifecycle r-lubridate r-magrittr r-matrix r-purrr r-rlang r-tibble r-tidyr r-tidyselect r-timedate r-vctrs r-withr)) (native-inputs (list r-knitr)) (home-page "https://github.com/topepo/recipes") (synopsis "Preprocessing tools to create design matrices") (description "Recipes is an extensible framework to create and preprocess design matrices. Recipes consist of one or more data manipulation and analysis \"steps\". Statistical parameters for the steps can be estimated from an initial data set and then applied to other data sets. The resulting design matrices can then be used as inputs into statistical or machine learning models.") (license license:gpl2))) (define-public r-pdist (package (name "r-pdist") (version "1.2.1") (source (origin (method url-fetch) (uri (cran-uri "pdist" version)) (sha256 (base32 "0bvg8si81hs79v39d7svv4zbv2p0sk2r6m9vamibvkh9qvl4x406")))) (build-system r-build-system) (home-page "https://github.com/jeffwong/pdist") (synopsis "Partitioned distance function") (description "Pdist computes the euclidean distance between rows of a matrix X and rows of another matrix Y. Previously, this could be done by binding the two matrices together and calling @code{dist}, but this creates unnecessary computation by computing the distances between a row of X and another row of X, and likewise for Y. Pdist strictly computes distances across the two matrices, not within the same matrix, making computations significantly faster for certain use cases.") (license license:gpl3+))) (define-public r-ggrepel (package (name "r-ggrepel") (version "0.9.1") (source (origin (method url-fetch) (uri (cran-uri "ggrepel" version)) (sha256 (base32 "1z5xyr5f4aryy0v1gzz9m8m4s5fzzwbrf0fxll1nbflr8xnr3yr9")))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-rcpp r-rlang r-scales)) (native-inputs (list r-knitr)) ; for vignettes (home-page "https://github.com/slowkow/ggrepel") (synopsis "Repulsive text and label geometries for ggplot2") (description "This package provides text and label geometries for ggplot2 that help to avoid overlapping text labels. Labels repel away from each other and away from the data points.") (license license:gpl3))) (define-public r-coro (package (name "r-coro") (version "1.0.3") (source (origin (method url-fetch) (uri (cran-uri "coro" version)) (sha256 (base32 "0wvxdpdh3xrskz5s5wfkva856x849knx1jigbf0ff6s6n6qjjxsf")))) (properties `((upstream-name . 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(license license:expat))) (define-public r-corrplot (package (name "r-corrplot") (version "0.92") (source (origin (method url-fetch) (uri (cran-uri "corrplot" version)) (sha256 (base32 "1g98jk6xsl08z4n6sy5vriif99m31zhbz7j3dh1kfj4w7yb9zh78")))) (build-system r-build-system) (native-inputs (list r-knitr)) (home-page "https://github.com/taiyun/corrplot") (synopsis "Visualization of a correlation matrix") (description "This package provides a graphical display of a correlation matrix or general matrix. It also contains some algorithms to do matrix reordering. In addition, corrplot is good at details, including choosing color, text labels, color labels, layout, etc.") ;; Any version of the GPL (license license:gpl2+))) (define-public r-stringdist (package (name "r-stringdist") (version "0.9.8") (source (origin (method url-fetch) (uri (cran-uri "stringdist" version)) (sha256 (base32 "1fv1hbdlm8qwx57b2aj50mw0say5k48awzavx65mfk67qp6ddk7g")))) (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-ucminf (package (name "r-ucminf") (version "1.1-4") (source (origin (method url-fetch) (uri (cran-uri "ucminf" version)) (sha256 (base32 "01vggwg1w71k98qs6fhb0x1843vi322mf4g3hbclks94kcpkisx2")))) (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") (source (origin (method url-fetch) (uri (cran-uri "useful" version)) (sha256 (base32 "0n50v1q75k518sq23id14jphwla35q4sasahrnrnllwrachl67v1")))) (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 "2019.12-10") (source (origin (method url-fetch) (uri (cran-uri "ordinal" version)) (sha256 (base32 "09bpmjmbf4x82kgf6bm4bkncq2apdv9mk20zj4zgma2jx2vyfhbs")))) (build-system r-build-system) (propagated-inputs (list r-mass r-matrix 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 "2.7-4") (source (origin (method url-fetch) (uri (cran-uri "jomo" version)) (sha256 (base32 "1zck7p872k080hyfs0hibq7v13zmsry1jdlnq7k33ff1iljbq99d")))) (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 "1.6") (source (origin (method url-fetch) (uri (cran-uri "pan" version)) (sha256 (base32 "1dk3jjj826p7xrz10qz04vyc068xnypg7bp0pj4c32z3da0xzh5d")))) (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 "0.4-3") (source (origin (method url-fetch) (uri (cran-uri "mitml" version)) (sha256 (base32 "00i18nnvrdrg91crgcp2a431xs71cawaip3xkqk2myv0iav3xga9")))) (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 "3.14.0") (source (origin (method url-fetch) (uri (cran-uri "mice" version)) (sha256 (base32 "01fnfrr7adp29s5kic95r9q0rdznkz2pjmziyimnrqzyicyvfyzq")))) (build-system r-build-system) (propagated-inputs (list r-broom r-cpp11 r-dplyr r-generics r-lattice r-rcpp r-rlang r-tidyr r-withr)) (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-truncnorm (package (name "r-truncnorm") (version "1.0-8") (source (origin (method url-fetch) (uri (cran-uri "truncnorm" version)) (sha256 (base32 "0zn88wdd58223kibk085rhsikl4yhlrwiyq109hzjg06hy6lwmj9")))) (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-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 "1.7.5") (source (origin (method url-fetch) (uri (cran-uri "HardyWeinberg" version)) (sha256 (base32 "0b3szw090dsc3bkas2kvx787ww2i6zzg2qmdyivmqc8amx5arn6g")))) (properties `((upstream-name . "HardyWeinberg"))) (build-system r-build-system) (propagated-inputs (list r-mice r-nnet r-rcpp r-rsolnp)) (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 "2.2-5.7.1") (source (origin (method url-fetch) (uri (cran-uri "sm" version)) (sha256 (base32 "0mql7rlm8wkdwmx1lv7pscdk9ibvsdpfdv8bpaz1hv2gn4pc637a")))) (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-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 "0.3.7") (source (origin (method url-fetch) (uri (cran-uri "vioplot" version)) (sha256 (base32 "1dmdasp3jldc41233z6r08w3j76vyyp9m3jrj7n4ahk48yd5siq6")))) (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 "0.12.1") (source (origin (method url-fetch) (uri (cran-uri "xts" version)) (sha256 (base32 "0b6a7mpyk9aw6axas7nz01gadczprwwfhii01fz31z26z555i06n")))) (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 "0.5.2") (source (origin (method url-fetch) (uri (cran-uri "laeken" version)) (sha256 (base32 "1p3ccbaydlr52p8qmgmm2l6kryvq6jjjx7mqn2vv0gpjaxqhyy92")))) (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 "1.4-10") (source (origin (method url-fetch) (uri (cran-uri "vcd" version)) (sha256 (base32 "0nxkl1x39xf8l0apgvlbr30i8lasix7hyyc93g6514r8z8m1k23i")))) (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 "1.13.0") (source (origin (method url-fetch) (uri (cran-uri "vcfR" version)) (sha256 (base32 "1g4y11vpr3wrvf5prj7y33c2bah6rn4xfb4a1y7n7niafd2yhg3l")))) (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-ica (package (name "r-ica") (version "1.0-3") (source (origin (method url-fetch) (uri (cran-uri "ica" version)) (sha256 (base32 "0rdqd3kz2cv3xvf6yz55bwhsg3k7j90d450i3azs2xkbn4q3aka7")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/ica/") (synopsis "Independent component analysis") (description "This package provides tools for @dfn{Independent Component Analysis} (ICA) using various algorithms: FastICA, Information-Maximization (Infomax), and @dfn{Joint Approximate Diagonalization of Eigenmatrices} (JADE).") (license license:gpl2+))) (define-public r-ips (package (name "r-ips") (version "0.0.11") (source (origin (method url-fetch) (uri (cran-uri "ips" version)) (sha256 (base32 "02jxanfhsjrabj33nwjv71vdc87hiyzikyqrfdj9ix6dky6lm199")))) (properties `((upstream-name . 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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 "0.3-42") (source (origin (method url-fetch) (uri (cran-uri "scatterplot3d" version)) (sha256 (base32 "05jjdiam5w0znb114vc90zahclj22pqj1zzvr96nr10s1vkxvzm9")))) (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.") (license license:gpl2))) (define-public r-ggridges (package (name "r-ggridges") (version "0.5.3") (source (origin (method url-fetch) (uri (cran-uri "ggridges" version)) (sha256 (base32 "0bmlqy1p6rac90af97ffpdi6php7dblx66l2hcm8ljidgyqzmspm")))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-plyr r-scales r-withr)) (native-inputs (list r-knitr)) (home-page "https://github.com/clauswilke/ggridges") (synopsis "Ridgeline plots in ggplot2") (description "Ridgeline plots 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-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}.") 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(license license:expat))) (define-public r-tsp (package (name "r-tsp") (version "1.2-1") (source (origin (method url-fetch) (uri (cran-uri "TSP" version)) (sha256 (base32 "1pa6pb4qrh2iybpjzjiny6hshj0shjdm0pxqnidcrg5hyfzzxd9b")))) (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-webshot (package (name "r-webshot") (version "0.5.3") (source (origin (method url-fetch) (uri (cran-uri "webshot" version)) (sha256 (base32 "1h6v94zwq0ypgi4vf8xlhp5k13j7f9061hx908177i68c6zg5i5p")))) (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 "1.3.6") (source (origin (method url-fetch) (uri (cran-uri "seriation" version)) (sha256 (base32 "1i0bbfxbvzy2lwprliqrn97ww8lqr2s9klg0g3qqjyr8cdxs5fyc")))) (build-system r-build-system) (propagated-inputs (list r-cluster r-colorspace r-gclus r-mass r-qap r-registry r-tsp)) (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 "0.33") (source (origin (method url-fetch) (uri (cran-uri "xfun" version)) (sha256 (base32 "0v7f84gqsb94zff4x64478fssjg0sbis9m34vsxnjyw6ab9c5ys5")))) (build-system r-build-system) ;; knitr itself depends on xfun #; (native-inputs `(("r-knitr" ,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.") (license license:expat))) (define-public r-utf8 (package (name "r-utf8") (version "1.2.2") (source (origin (method url-fetch) (uri (cran-uri "utf8" version)) (sha256 (base32 "1x6qg19z4qih9lk3mvnmx0vailm1khp5lylw4hlwz6rssj3yw6m7")))) (build-system r-build-system) (native-inputs (list r-knitr r-rmarkdown)) ; for vignettes (home-page "https://github.com/patperry/r-utf8") (synopsis "Unicode text processing") (description "This package provides tools to process and print UTF-8 encoded international text (Unicode). Input, validate, normalize, encode, format, and display.") (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 "1.0.0") (source (origin (method url-fetch) (uri (cran-uri "zlog" version)) (sha256 (base32 "1d5j31p0h3rrn230087h3ngpvwknlisjv0f1qdbicdj9m177spci")))) (properties `((upstream-name . "zlog"))) (build-system r-build-system) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/package=zlog") (synopsis "Transformation for laboratory easurements") (description "The @code{zlog} package offers functions to transform laboratory measurements into standardised z or @math{z(log)-values}. Therefore the lower and upper reference limits are needed. If these are not known they could be estimated from a given sample.") (license license:gpl3+))) (define-public r-vctrs (package (name "r-vctrs") (version "0.4.1") (source (origin (method url-fetch) (uri (cran-uri "vctrs" version)) (sha256 (base32 "1pb0wjpwix29q8d8p3wi72a9mp9mif7369pk31w238cs00g8hxln")))) (build-system r-build-system) (propagated-inputs (list r-cli r-glue r-rlang)) (native-inputs (list 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 "1.8.1") (source (origin (method url-fetch) (uri (cran-uri "pillar" version)) (sha256 (base32 "1v47dm2v4nlswd1gmgcx5c7yrgn1ksdfr9lqkc63jf2nkv6af1ig")))) (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 "1.2.0") (source (origin (method url-fetch) (uri (cran-uri "pinfsc50" version)) (sha256 (base32 "1547xyxmfb7zi8h9bsm6k67dcw4hpp129xzvmgwfw7r6p4af47zd")))) (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-uuid (package (name "r-uuid") (version "1.1-0") (source (origin (method url-fetch) (uri (cran-uri "uuid" version)) (sha256 (base32 "0bzlc2knmr338h4ykx8v8c2a1inizxafj8rh13kwii68gpp50nz7")))) (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-tinytex (package (name "r-tinytex") (version "0.41") (source (origin (method url-fetch) (uri (cran-uri "tinytex" version)) (sha256 (base32 "1fhnh53fg8l4qyignvgz0nk5nqmljyykn8gpvq82nr7c051rfqaz")))) (build-system r-build-system) (propagated-inputs (list r-xfun)) (home-page "https://github.com/yihui/tinytex") (synopsis "Helper functions for TeX Live and compiling LaTeX documents") (description "This package provides helper functions to install and maintain the LaTeX distribution named TinyTeX, a lightweight, cross-platform, portable, and easy-to-maintain version of TeX Live. This package also contains helper functions to compile LaTeX documents, and install missing LaTeX packages automatically.") 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Main features: @enumerate @item install tests with the package; @item test results are treated as data that can be stored and manipulated; @item test files are R scripts interspersed with test commands, that can be programmed over; @item fully automated build-install-test sequence for packages; @item skip tests when not run locally (e.g. on CRAN); @item flexible and configurable output printing; @item compare computed output with output stored with the package; @item run tests in parallel; @item extensible by other packages; @item report side effects. @end enumerate ") (license license:gpl3))) (define-public r-network (package (name "r-network") (version "1.17.2") (source (origin (method url-fetch) (uri (cran-uri "network" version)) (sha256 (base32 "1xrhzbci7ls4h05skdlirxl49jsvmylrqivz2kd6i33wh2ca324m")))) (build-system r-build-system) (propagated-inputs (list r-magrittr r-statnet-common r-tibble)) (home-page "https://statnet.org/") (synopsis "Classes for relational data") (description "This package provides tools to create and modify network objects. The @code{network} class can represent a range of relational data types, and supports arbitrary vertex/edge/graph attributes.") (license license:gpl2+))) (define-public r-stabs (package (name "r-stabs") (version "0.6-4") (source (origin (method url-fetch) (uri (cran-uri "stabs" version)) (sha256 (base32 "1nf1yg14cgxrs4np1yghpzw1nczaslfv3rvf3918wrlzg0vp6l7q")))) (build-system r-build-system) (native-inputs (list r-knitr)) (home-page "https://github.com/hofnerb/stabs") (synopsis "Stability selection with error control") (description "This package provides resampling procedures to assess the stability of selected variables with additional finite sample error control for high-dimensional variable selection procedures such as Lasso or boosting. Both, standard stability selection (Meinshausen & Buhlmann, 2010) and complementary pairs stability selection with improved error bounds (Shah & Samworth, 2013) are implemented. The package can be combined with arbitrary user specified variable selection approaches.") (license license:gpl2))) (define-public r-rle (package (name "r-rle") (version "0.9.2") (source (origin (method url-fetch) (uri (cran-uri "rle" version)) (sha256 (base32 "0sagl0jggg40lihzy7pfq4593rfvc3b3f7g6ggi85s7n18qvwg40")))) (properties `((upstream-name . "rle"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/rle/") (synopsis "Common functions for run-length encoded vectors") (description "This package provides common @code{base} and @code{stats} methods for @code{rle} objects, aiming to make it possible to treat them transparently as vectors.") (license license:gpl3))) (define-public r-statnet-common (package (name "r-statnet-common") (version "4.7.0") (source (origin (method url-fetch) (uri (cran-uri "statnet.common" version)) (sha256 (base32 "1cx1h1yzs8jjxk10y2h0wl69caspzgx5wdqp36dp4sxm0sk335xn")))) (properties `((upstream-name . 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(license license:gpl3))) (define-public r-statcheck (package (name "r-statcheck") (version "1.3.0") (source (origin (method url-fetch) (uri (cran-uri "statcheck" version)) (sha256 (base32 "0ivybdcrymlsfv6pg6p5bv70qdvgxf2vgp0kf4r0pf2fcvav1mcp")))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-plyr r-rmarkdown)) (home-page "https://cran.r-project.org/web/packages/statcheck/") (synopsis "Extract statistics from articles and recompute p-values") (description "This package can automatically extract statistical null-hypothesis significant testing (NHST) results from articles and recompute the p-values based on the reported test statistic and degrees of freedom to detect possible inconsistencies.") (license license:gpl2))) (define-public r-sna (package (name "r-sna") (version "2.7") (source (origin (method url-fetch) (uri (cran-uri "sna" version)) (sha256 (base32 "0ka319s1w857fj28ja1i1ljgv2h6ji4d69riqy9pwhvvghsa83s4")))) (build-system r-build-system) (propagated-inputs (list r-network r-statnet-common)) (home-page "https://statnet.org") (synopsis "Tools for social network analysis") (description "This package provides a range of tools for social network analysis, including node and graph-level indices, structural distance and covariance methods, structural equivalence detection, network regression, random graph generation, and 2D/3D network visualization.") (license license:gpl2+))) (define-public r-tfisher (package (name "r-tfisher") (version "0.2.0") (source (origin (method url-fetch) (uri (cran-uri "TFisher" version)) (sha256 (base32 "0vz74ww1lf1prfwz74hfsi3a8nzq8ss7aqjr85c1d87vss2796xx")))) (properties `((upstream-name . 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(substitute* "inst/include/ut_RS.h" (("#include \"R.h\"" m) (string-append "\ #define R_PROBLEM_BUFSIZE 4096 #define PROBLEM {char R_problem_buf[R_PROBLEM_BUFSIZE];(sprintf)(R_problem_buf, #define MESSAGE {char R_problem_buf[R_PROBLEM_BUFSIZE];(sprintf)(R_problem_buf, #define ERROR ),error(R_problem_buf);} #define WARNING(x) ),warning(R_problem_buf);} #define WARN WARNING(NULL) " m)))))))) (propagated-inputs (list r-mass r-splus2r)) (home-page "https://cran.r-project.org/web/packages/ifultools/") (synopsis "Insightful research tools") (description "This package provides C code used by the wmtsa, fractal, and sapa R packages.") 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(license license:gpl3))) (define-public r-quantmod (package (name "r-quantmod") (version "0.4.20") (source (origin (method url-fetch) (uri (cran-uri "quantmod" version)) (sha256 (base32 "154fqhw46kc7r08zsj5fsg97hg93phsli3z14xwmz22xb50xymzp")))) (build-system r-build-system) (propagated-inputs (list r-curl r-ttr r-xts r-zoo)) (home-page "https://cran.r-project.org/web/packages/quantmod/") (synopsis "Quantitative financial modelling framework") (description "This package provides a quantitative financial modelling framework to allow users to specify, build, trade, and analyse quantitative financial trading strategies.") (license license:gpl3))) (define-public r-tseries (package (name "r-tseries") (version "0.10-51") (source (origin (method url-fetch) (uri (cran-uri "tseries" version)) (sha256 (base32 "0zr09ikaz96djcvnjbr8ah6waqzjy06f4yd4isshlwc391q20px5")))) (build-system r-build-system) (propagated-inputs (list r-quadprog r-quantmod r-zoo)) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/tseries/") (synopsis "Time series analysis and computational finance") (description "This package provides functions relating to time series analysis and computational finance.") (license license:gpl2))) (define-public r-wmtsa (package (name "r-wmtsa") (version "2.0-3") (source (origin (method url-fetch) (uri (cran-uri "wmtsa" version)) (sha256 (base32 "1q436krz5p1f4a7a7sya6a9rh9x9mi8zzcgq66gbk9w9w4hcqcj6")))) (build-system r-build-system) (propagated-inputs (list r-ifultools r-mass r-splus2r)) (home-page "https://cran.r-project.org/web/packages/wmtsa/") (synopsis "Wavelet methods for time series analysis") (description "This package provides software to accompany the book \"Wavelet Methods for Time Series Analysis\", Donald B. Percival and Andrew T. Walden, Cambridge University Press, 2000.") (license license:gpl2))) (define-public r-tsa (package (name "r-tsa") (version "1.3.1") (source (origin (method url-fetch) (uri (cran-uri "TSA" version)) (sha256 (base32 "14g58s2w7wma1fgcg3b51267b3676zrv0w8v4hpypxygz023d9bx")))) (properties `((upstream-name . 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"extraDistr"))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) (home-page "https://github.com/twolodzko/extraDistr") (synopsis "Additional univariate and multivariate distributions") (description "This package implements density, distribution functions, quantile functions and random generation functions for a large number of univariate and multivariate distributions.") (license license:gpl2))) (define-public r-fractal (package (name "r-fractal") (version "2.0-4") (source (origin (method url-fetch) (uri (cran-uri "fractal" version)) (sha256 (base32 "18lr9z0gslvfc3z8vyj3krqj3bfhg60zv1fzinrwwkc4cpk1w7mp")))) (build-system r-build-system) (propagated-inputs (list r-ifultools r-mass r-sapa r-scatterplot3d r-splus2r r-wmtsa)) (home-page "https://cran.r-project.org/web/packages/fractal/") (synopsis "Fractal time series modeling and analysis") (description "This package provides tools for stochastic fractal and deterministic chaotic time series analysis.") (license license:gpl2))) (define-public r-urca (package (name "r-urca") (version "1.3-3") (source (origin (method url-fetch) (uri (cran-uri "urca" version)) (sha256 (base32 "1wg9f691pif59xds43gnnw77mmzc9xpnhhvaksk2b0szffvaifj3")))) (build-system r-build-system) (propagated-inputs (list r-nlme)) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/urca/") (synopsis "Unit root and cointegration tests for time series data") (description "This package provides unit root and cointegration tests encountered in applied econometric analysis.") (license license:gpl2+))) (define-public r-cubature (package (name "r-cubature") (version "2.0.4.5") (source (origin (method url-fetch) (uri (cran-uri "cubature" version)) (sha256 (base32 "08whkhvn218089r930spn97m91vv1njgh2amksia8l3rbf7127x8")))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) (native-inputs (list r-knitr)) (home-page "https://github.com/bnaras/cubature") (synopsis "Adaptive multivariate integration over hypercubes") (description "This package is an R wrapper around the cubature C library for adaptive multivariate integration over hypercubes. This version provides both @code{hcubature} and @code{pcubature} routines in addition to a vector interface.") ;; The included cubature C library is released under GPLv2+, but the ;; wrapper declares the license to be GPLv3+. (license (list license:gpl2+ license:gpl3+)))) (define-public r-trend (package (name "r-trend") (version "1.1.4") (source (origin (method url-fetch) (uri (cran-uri "trend" version)) (sha256 (base32 "1mr5g5gaxiqj6x83ngcbwwh57vhrhcz0x9dh0rmvs9y2ivk29ccs")))) (build-system r-build-system) (propagated-inputs (list r-extradistr)) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/trend/") (synopsis "Non-parametric trend tests and change-point detection") (description "The analysis of environmental data often requires the detection of trends and change-points. This package includes tests for trend detection (Cox-Stuart Trend Test, Mann-Kendall Trend Test, (correlated) Hirsch-Slack Test, partial Mann-Kendall Trend Test, multivariate (multisite) Mann-Kendall Trend Test, (Seasonal) Sen's slope, partial Pearson and Spearman correlation trend test), change-point detection (Lanzante's test procedures, Pettitt's test, Buishand Range Test, Buishand U Test, Standard Normal Homogeinity Test), detection of non-randomness (Wallis-Moore Phase Frequency Test, Bartels rank von Neumann's ratio test, Wald-Wolfowitz Test) and the two sample Robust Rank-Order Distributional Test.") (license license:gpl3))) (define-public r-expm (package (name "r-expm") (version "0.999-6") (source (origin (method url-fetch) (uri (cran-uri "expm" version)) (sha256 (base32 "1p5dapwv8ycxaysgi6imnby04i4kh1c5a2czqa4wygz0s8pr2y9c")))) (build-system r-build-system) (propagated-inputs (list r-matrix)) (native-inputs (list gfortran)) (home-page "https://r-forge.r-project.org/projects/expm/") (synopsis "Tools for matrix exponentials and related quantities") (description "This package provides tools for the computation of the matrix exponential, logarithm, square root, and related quantities.") (license license:gpl2+))) (define-public r-exposition (package (name "r-exposition") (version "2.8.23") (source (origin (method url-fetch) (uri (cran-uri "ExPosition" version)) (sha256 (base32 "0x9400ggmgrnaish0cfgnyvw549g4ibfv9aj6vzq7j68n58vq405")))) (properties `((upstream-name . 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(license license:gpl2))) (define-public r-complexplus (package (name "r-complexplus") (version "2.1") (source (origin (method url-fetch) (uri (cran-uri "complexplus" version)) (sha256 (base32 "16w9v7d1ckavqmr86l34frr37pkvdn0iqnb17ssb8xaggns5lgqx")))) (build-system r-build-system) (propagated-inputs (list r-expm r-matrix)) (home-page "https://cran.r-project.org/web/packages/complexplus/") (synopsis "Functions of complex or real variables") (description "This package extends several functions to the complex domain, including the matrix exponential and logarithm, and the determinant.") (license license:gpl2))) (define-public r-phontools (package (name "r-phontools") (version "0.2-2.1") (source (origin (method url-fetch) (uri (cran-uri "phonTools" version)) (sha256 (base32 "01i481mhswsys3gpasw9gn6nxkfmi7bz46g5c84m13pg0cv8hxc7")))) (properties `((upstream-name . 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(license license:bsd-2))) (define-public r-np (package (name "r-np") (version "0.60-14") (source (origin (method url-fetch) (uri (cran-uri "np" version)) (sha256 (base32 "0v6mhcwdnqj5kjxwrzcqlff021ih2jdarwmikdm5bvjfwi8pyarl")))) (build-system r-build-system) (propagated-inputs (list r-boot r-cubature r-quadprog r-quantreg)) (home-page "https://github.com/JeffreyRacine/R-Package-np") (synopsis "Non-parametric kernel smoothing methods for mixed data types") (description "This package provides non-parametric (and semi-parametric) kernel methods that seamlessly handle a mix of continuous, unordered, and ordered factor data types.") ;; Any version of the GPL. (license license:gpl3+))) (define-public r-powerplus (package (name "r-powerplus") (version "3.1") (source (origin (method url-fetch) (uri (cran-uri "powerplus" version)) (sha256 (base32 "0ayp6x34hkzgris4j3zbbs0r23n81bhww3wgfyy630ri4sk6brrn")))) (build-system r-build-system) (propagated-inputs (list r-complexplus r-expm r-mass r-matrix r-phontools)) (home-page "https://cran.r-project.org/web/packages/powerplus/") (synopsis "Exponentiation operations") (description "This package provides tools for the computation of matrix and scalar exponentiation.") (license license:gpl2))) (define-public r-egg (package (name "r-egg") (version "0.4.5") (source (origin (method url-fetch) (uri (cran-uri "egg" version)) (sha256 (base32 "1fy7srpiavfn8kyrr1m84an7acgwi6ydzrg71m3b0vk7y9ybmj0m")))) (properties `((upstream-name . 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(license license:gpl3))) (define-public r-heatmap3 (package (name "r-heatmap3") (version "1.1.9") (source (origin (method url-fetch) (uri (cran-uri "heatmap3" version)) (sha256 (base32 "0sfvizmmwfk1bjhn6zfx5a4qqfgj1ldg8x90b65crqibgfa36k2r")))) (build-system r-build-system) (propagated-inputs (list r-fastcluster)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/heatmap3/") (synopsis "Improved heatmap package") (description "This package provides an improved heatmap package. It is completely compatible with the original R function @code{heatmap}, and provides more powerful and convenient features.") 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A heatmap is a popular graphical method for visualizing high-dimensional data, in which a table of numbers is encoded as a grid of colored cells. The rows and columns of the matrix are ordered to highlight patterns and are often accompanied by dendrograms.") ;; Either version of the license. (license (list license:gpl2 license:gpl3)))) (define-public r-h5 (package (name "r-h5") (version "0.9.9") (source (origin (method url-fetch) (uri (cran-uri "h5" version)) (sha256 (base32 "14p7i1sj24ky87kd7qr3n9fc9l64s0bp0rwbyl6i2x69xn75gpsx")))) (build-system r-build-system) (inputs (list zlib hdf5)) (native-inputs (list which)) (propagated-inputs (list r-rcpp)) (home-page "https://github.com/mannau/h5") (synopsis "Interface to the HDF5 Library") (description "This package provides an S4 interface to the HDF5 library supporting fast storage and retrieval of R-objects like vectors, matrices and arrays to binary files in a language independent format. The HDF5 format can therefore be used as an alternative to R's save/load mechanism. Since h5 is able to access only subsets of stored data it can also handle data sets which do not fit into memory.") (license license:bsd-2))) (define-public r-cgdsr (package (name "r-cgdsr") (version "1.3.0") (source (origin (method url-fetch) (uri (cran-uri "cgdsr" version)) (sha256 (base32 "07yc819hkabpzzh0g0cbqza6bcfy67b2marrzz1lj97f9iba78ja")))) (build-system r-build-system) (propagated-inputs (list r-httr r-r-methodss3 r-r-oo)) (home-page "https://github.com/cBioPortal/cgdsr") (synopsis "R-based API for accessing the MSKCC Cancer Genomics Data Server") (description "This package provides a basic set of R functions for querying the Cancer Genomics Data Server (CGDS), hosted by the Computational Biology Center at Memorial-Sloan-Kettering Cancer Center (MSKCC).") 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(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 "1.26") (source (origin (method url-fetch) (uri (cran-uri "reticulate" version)) (sha256 (base32 "1ibliic3qp597nskak2bfa6iyl721ssgcavwvfaf1c71plilimrz")))) (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-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.") 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("js-billboard" ,(origin (method url-fetch) (uri "https://unpkg.com/billboard.js@3.2.0/dist/billboard.js") (sha256 (base32 "1kx5rqmn87pgal2cwmcij2rrnwa0fgcsw6y99m4i0l2sdm0qffv2")))))) (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.") 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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 "1.0.7") (source (origin (method url-fetch) (uri (cran-uri "findpython" version)) (sha256 (base32 "0jf10jpqla90x03kl3k77gnd255zmw9rvr8d724vb17cqawh9yar")))) (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 "2.1.6") (source (origin (method url-fetch) (uri (cran-uri "argparse" version)) (sha256 (base32 "14p57nm0w3siqd473snzhpmnvsgl72x92pdcd64vhy2qg6nzmmra")))) (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.") 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(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 "4.6.13") (source (origin (method url-fetch) (uri (cran-uri "doBy" version)) (sha256 (base32 "0qnfcw4rg5kd1mll3rq6vchz3lgdqfif9469p8x6ixsgrxxpivbz")))) (properties `((upstream-name . 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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 "1.18.0") (source (origin (method url-fetch) (uri (cran-uri "pROC" version)) (sha256 (base32 "1abvbzdss12n64pp9vlgnn0q3abh0nj4n0a8cinwwvhphjrm9vym")))) (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.") 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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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"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 . 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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 "4.1.0") (source (origin (method url-fetch) (uri (cran-uri "CMplot" version)) (sha256 (base32 "1h09prpiw7l32mr7jarp8ddrddg1431nfn4kw3bznfnv0sr78zfg")))) (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 "0.12.9") (source (origin (method url-fetch) (uri (cran-uri "precrec" version)) (sha256 (base32 "1dfz2rqx2ww2l5r40ahg0qdj3rjrwiwh427mw7j5ynhpcj21j2qm")))) (properties `((upstream-name . "precrec"))) (build-system r-build-system) (propagated-inputs (list r-assertthat r-data-table r-ggplot2 r-gridextra r-rcpp 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 "1.2.4") (source (origin (method url-fetch) (uri (cran-uri "NetRep" version)) (sha256 (base32 "1swlb2k9bc7whvslxbklz864j9ynvna73hvq5rhv61cv5vy05ksd")))) (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 "2.0-2") (source (origin (method url-fetch) (uri (cran-uri "intergraph" version)) (sha256 (base32 "18a7xgb2rp0w9jl2rkh8nzyjprrs5w7h2iidvc8c38bzx3qpggkc")))) (properties `((upstream-name . "intergraph"))) (build-system r-build-system) (propagated-inputs (list r-igraph r-network)) (native-inputs (list r-knitr)) (home-page "http://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}.") (license license:gpl3))) (define-public r-interp (package (name "r-interp") (version "1.1-3") (source (origin (method url-fetch) (uri (cran-uri "interp" version)) (sha256 (base32 "0gzsnlg8f7knb100n6vv6307c3v2jd8f9qzrq62jkc6g71mn0kmp")))) (properties `((upstream-name . "interp"))) (build-system r-build-system) (propagated-inputs (list r-deldir r-rcpp r-rcppeigen)) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/package=interp") (synopsis "Interpolation methods") (description "Bivariate data interpolation on regular and irregular grids, either linear or using splines are the main part of this package. It is intended to provide replacement functions for the ACM licensed @code{akima::interp} and @code{tripack::tri.mesh} functions.") (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.") (license license:gpl2))) (define-public r-abcrf (package (name "r-abcrf") (version "1.9") (source (origin (method url-fetch) (uri (cran-uri "abcrf" version)) (sha256 (base32 "08mh1a6gxp0mfx6qnp1qzcrfx7xp64qj9kad4ziyswfx22ykdsxi")))) (build-system r-build-system) (propagated-inputs (list r-doparallel r-foreach r-mass r-matrixstats r-ranger r-rcpp r-rcpparmadillo r-readr r-stringr)) (home-page "https://cran.r-project.org/web/packages/abcrf/") (synopsis "Approximate bayesian computation via random forests") (description "This package performs approximate bayesian computation (ABC) model choice and parameter inference via random forests. This machine learning tool named random forests (RF) can conduct selection among the highly complex models covered by ABC algorithms.") 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(license license:expat))) (define-public r-mosaicdata (package (name "r-mosaicdata") (version "0.20.3") (source (origin (method url-fetch) (uri (cran-uri "mosaicData" version)) (sha256 (base32 "1s97yq24z7yhzmx0dpspfadpd8hndyhn7aiw0nslwrhvilhwa409")))) (properties `((upstream-name . "mosaicData"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/mosaicData/") (synopsis "Data sets for project Mosaic") (description "This package provides data sets from project Mosaic @url{http://mosaic-web.org} used to teach mathematics, statistics, computation and modeling.") 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(license license:gpl2+))) (define-public r-abd (package (name "r-abd") (version "0.2-8") (source (origin (method url-fetch) (uri (cran-uri "abd" version)) (sha256 (base32 "191gspqzdv573vaw624ri0f5cm6v4j524bjs74d4a1hn3kn6r9b7")))) (build-system r-build-system) (propagated-inputs (list r-lattice r-mosaic r-nlme)) (home-page "https://cran.r-project.org/web/packages/abd/") (synopsis "Analysis of biological data") (description "The @code{r-abd} package contains data sets and sample code for the Analysis of biological data by Michael Whitlock and Dolph Schluter.") (license license:gpl2))) (define-public r-svgui (package (name "r-svgui") (version "1.0.1") (source (origin (method url-fetch) (uri (cran-uri "svGUI" version)) (sha256 (base32 "0ch5gdfk834xj9w3vxpm3x4770fz3nnlyn8b0jsw9f3n2as7g979")))) (properties `((upstream-name . 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(license license:gpl2+))) (define-public r-abf2 (package (name "r-abf2") (version "0.7-1") (source (origin (method url-fetch) (uri (cran-uri "abf2" version)) (sha256 (base32 "0d65mc1w4pbiv7xaqzdlw1bfsxf25587rv597hh41vs0j0zlfpxx")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/abf2/") (synopsis "Load gap-free axon @code{r-abf2} files") (description "This package loads electrophysiology data from ABF2 files, as created by Axon Instruments/Molecular Devices software. Only files recorded in gap-free mode are currently supported.") (license license:artistic2.0))) (define-public r-abhgenotyper (package (name "r-abhgenotyper") (version "1.0.1") (source (origin (method url-fetch) (uri (cran-uri "ABHgenotypeR" version)) (sha256 (base32 "08cpmnaaxsm5c5bjifnfxdlvg5inrf13biqpcl2yq5zpqjmiki0l")))) (properties `((upstream-name . 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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.") (license license:lgpl2.1+))) (define-public r-abjutils (package (name "r-abjutils") (version "0.3.2") (source (origin (method url-fetch) (uri (cran-uri "abjutils" version)) (sha256 (base32 "0lmf4va8qnzwg698i2h4fcwvd6dhsgdkqsfh41aa3wg1flimhsr7")))) (build-system r-build-system) (propagated-inputs (list r-dplyr r-magrittr r-purrr r-rlang r-rstudioapi r-stringi r-stringr r-tidyr)) (home-page "https://github.com/abjur/abjutils/") (synopsis "Collection of tools for jurimetrical analysis") (description "This package implements general purpose tools, such as functions for sampling and basic manipulation of Brazilian lawsuits identification number. It also implements functions for text cleaning, such as accentuation removal.") (license license:expat))) (define-public r-abnormality (package (name "r-abnormality") (version "0.1.0") (source (origin (method url-fetch) (uri (cran-uri "abnormality" version)) (sha256 (base32 "1fzfskl9akl06nliy8hkv2a0pznpj8pwcypg3gj5r2nzvr3kan9v")))) (build-system r-build-system) (propagated-inputs (list r-mass r-matrix)) (home-page "https://cran.r-project.org/web/packages/abnormality/") (synopsis "Measure a subject's abnormality with respect to a reference population") (description "This package contains functions to implement the methodology and considerations laid out by Marks et al. in the article \"Measuring abnormality in high dimensional spaces: applications in biomechanical gait analysis\". Using high-dimensional datasets to measure a subject's overall level of abnormality as compared to a reference population is often needed in outcomes research.") (license license:expat))) (define-public r-abodoutlier (package (name "r-abodoutlier") (version "0.1") (source (origin (method url-fetch) (uri (cran-uri "abodOutlier" version)) (sha256 (base32 "1pvhgxmh23br84r0fbmv7g53z2427birdja96a67vqgz18r3fdvj")))) (properties `((upstream-name . "abodOutlier"))) (build-system r-build-system) (propagated-inputs (list r-cluster)) (home-page "https://cran.r-project.org/web/packages/abodOutlier/") (synopsis "Angle-based outlier detection") (description "This package performs angle-based outlier detection on a given data frame. It offers three methods to process data: @enumerate @item full but slow implementation using all the data that has cubic complexity; @item a fully randomized method; @item a method using k-nearest neighbours. @end enumerate These algorithms are well suited for high dimensional data outlier detection.") (license license:expat))) (define-public r-abps (package (name "r-abps") (version "0.3") (source (origin (method url-fetch) (uri (cran-uri "ABPS" version)) (sha256 (base32 "0n3f66nmfi5v94il1mxy026mi84w01ph2aljk60vn3mrz8kwf2ll")))) (properties `((upstream-name . "ABPS"))) (build-system r-build-system) (propagated-inputs (list r-kernlab)) (home-page "https://cran.r-project.org/web/packages/ABPS/") (synopsis "Abnormal blood profile score to detect blood doping") (description "This package offers an implementation of the @dfn{Abnormal blood profile score} (ABPS). The ABPS is a part of the Athlete biological passport program of the World anti-doping agency, which combines several blood parameters into a single score in order to detect blood doping. The package also contains functions to calculate other scores used in anti-doping programs, such as the ratio of hemoglobin to reticulocytes (OFF-score), as well as example data.") (license license:gpl2+))) (define-public r-parmigene (package (name "r-parmigene") (version "1.1.0") (source (origin (method url-fetch) (uri (cran-uri "parmigene" version)) (sha256 (base32 "067rqxqyzy1fsjj0s1g7af4527whwdhzjzc5b8a8n7683na59ns4")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/parmigene/") (synopsis "Mutual information estimation for gene network reconstruction") (description "This package provides a parallel estimation of the mutual information based on entropy estimates from k-nearest neighbors distances and algorithms for the reconstruction of gene regulatory networks.") (license license:agpl3+))) (define-public r-pscl (package (name "r-pscl") (version "1.5.5") (source (origin (method url-fetch) (uri (cran-uri "pscl" version)) (sha256 (base32 "0vzf5wazs92bhqhqd66v3vwmbfmnh67gb2466g1xxawim649nk05")))) (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 "0.4.16") (source (origin (method url-fetch) (uri (cran-uri "mhsmm" version)) (sha256 (base32 "009dj0zkj1zry7jr9hf4cknb686z50a2l967if64xm0dvjmp7dgs")))) (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 "3.3.3") (source (origin (method url-fetch) (uri (cran-uri "nleqslv" version)) (sha256 (base32 "0cy65bqkmnnr8v0x1cag84caxwdxyr0yw4w443apxzfxjp7dyiif")))) (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 "0.1-30") (source (origin (method url-fetch) (uri (cran-uri "phyclust" version)) (sha256 (base32 "0fy9q95vmlm9idpax7alhpfwn30gflnc9md72g91jypyxkx5nr7p")))) (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 . 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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.") 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(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 "0.3-43") (source (origin (method url-fetch) (uri (cran-uri "mixsqp" version)) (sha256 (base32 "1qics04w0swyp216d6g8dmsph8q2kpadpacp66h2qih3521js12q")))) (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 "2.7.3") (source (origin (method url-fetch) (uri (cran-uri "magick" version)) (sha256 (base32 "0h942bn7wfnzbbgq9hrs75c7igmg5r1c5sad2v0znhza4cp7p1w3")))) (build-system r-build-system) (inputs (list imagemagick 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 "4.1-1") (source (origin (method url-fetch) (uri (cran-uri "survey" version)) (sha256 (base32 "0ljsszybzri531q6xab04r6zq11vchfs7y0snjzk57m3g0b9ms05")))) (build-system r-build-system) (propagated-inputs (list r-lattice r-matrix r-minqa r-mitools r-numderiv r-survival)) (home-page "http://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 "4.13-23") (source (origin (method url-fetch) (uri (cran-uri "gee" version)) (sha256 (base32 "0v0fam678pqqkxmj95f1pwsi08y1rbz1wxnp1ig81jvpn0xpq8gq")))) (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-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-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 . "ACA"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/ACA/") (synopsis "Abrupt change-point or aberration detection in point series") (description "This package offers an interactive function for the detection of breakpoints in series.") ;; Any version of the GPL (license (list license:gpl2+ license:gpl3+)))) (define-public r-acceptancesampling (package (name "r-acceptancesampling") (version "1.0-8") (source (origin (method url-fetch) (uri (cran-uri "AcceptanceSampling" version)) (sha256 (base32 "1ja1g0v8qvf7yj81x37wc6i7fkwpc573756jgvazazi8yf1gm12p")))) (properties `((upstream-name . "AcceptanceSampling"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/AcceptanceSampling/") (synopsis "Creation and evaluation of acceptance sampling plans") (description "This @code{r-acceptancesampling} provides functionality for creating and evaluating acceptance sampling plans. 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 "3.0-2") (source (origin (method url-fetch) (uri (cran-uri "sandwich" version)) (sha256 (base32 "1d72vwxidsyac9mbyxrm06qds63rzcr82nn4c05466gbajsvcc3f")) (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 "1.1-1") (source (origin (method url-fetch) (uri (cran-uri "TH.data" version)) (sha256 (base32 "0ynxacnz002bjsp2ybql7rdqw4zd14af8r7w44nwbx22n4bapwzd")))) (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 "1.4-20") (source (origin (method url-fetch) (uri (cran-uri "multcomp" version)) (sha256 (base32 "1z1cqklahnp4qi48r335xlqvw7h7xbjrlpb4pjky9gc987xf92rj")))) (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).") (license license:gpl2))) (define-public r-multcompview (package (name "r-multcompview") (version "0.1-8") (source (origin (method url-fetch) (uri (cran-uri "multcompView" version)) (sha256 (base32 "1rfq9wvvrghq0542ff40wy8vdmsyd8spzz6ihcywcvxdfa8m6g8j")))) (properties `((upstream-name . "multcompView"))) (build-system r-build-system) (home-page "https://cran.r-project.org/package=multcompView") (synopsis "Visualizations of paired comparisons") (description "Convert a logical vector or a vector of p-values or a correlation, difference, or distance matrix into a display identifying the pairs for which the differences were not significantly different.") ;; Any version of the GPL. (license license:gpl3+))) (define-public r-emmeans (package (name "r-emmeans") (version "1.8.1-1") (source (origin (method url-fetch) (uri (cran-uri "emmeans" version)) (sha256 (base32 "0xv55v50v3fdg289mfqirfm4p644gn4ckqnvs0wb09sl4m25xz3r")))) (build-system r-build-system) (propagated-inputs (list r-estimability r-mvtnorm r-numderiv r-xtable)) (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).") (license license:gpl3+))) (define-public r-libcoin (package (name "r-libcoin") (version "1.0-9") (source (origin (method url-fetch) (uri (cran-uri "libcoin" version)) (sha256 (base32 "1syrcdj5qg5m3zd3dlxgpfklswbalfg42w058dr09hnzqsvx0z9d")))) (build-system r-build-system) (propagated-inputs (list r-mvtnorm)) (home-page "https://cran.r-project.org/web/packages/libcoin") (synopsis "Linear test statistics for permutation inference") (description "This package provides basic infrastructure for linear test statistics and permutation inference in the framework of Strasser and Weber (1999).") (license license:gpl2))) (define-public r-coin (package (name "r-coin") (version "1.4-2") (source (origin (method url-fetch) (uri (cran-uri "coin" version)) (sha256 (base32 "1cpv7jx840inzg98bkhrb5yscx0gpag6br237r5qpnc2gbrd2ikm")))) (build-system r-build-system) (propagated-inputs (list r-libcoin r-matrixstats r-modeltools r-multcomp r-mvtnorm r-survival)) (home-page "http://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 "1.9.0") (source (origin (method url-fetch) (uri (cran-uri "bayesplot" version)) (sha256 (base32 "0hqy597ang53phxnl084hak35ffqz9lw9hygax7370gpkjws908a")))) (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.") (license license:gpl3+))) (define-public r-tmb (package (name "r-tmb") (version "1.9.1") (source (origin (method url-fetch) (uri (cran-uri "TMB" version)) (sha256 (base32 "03zv38gig31ir5gdhgw5j6j8xn1f4y91j2r87fv31gywmg1bhzl9")))) (properties `((upstream-name . "TMB"))) (build-system r-build-system) (propagated-inputs (list r-matrix r-rcppeigen)) (home-page "http://tmb-project.org") (synopsis "Template model builder: a general random effect tool") (description "With this tool, a user should be able to quickly implement complex random effect models through simple C++ templates. The package combines @code{CppAD} (C++ automatic differentiation), @code{Eigen} (templated matrix-vector library) and @code{CHOLMOD} (sparse matrix routines available from R) to obtain an efficient implementation of the applied Laplace approximation with exact derivatives. Key features are: Automatic sparseness detection, parallelism through BLAS and parallel user templates.") (license license:gpl2))) (define-public r-sjstats (package (name "r-sjstats") (version "0.18.1") (source (origin (method url-fetch) (uri (cran-uri "sjstats" version)) (sha256 (base32 "1cv80yjnyh6qihxf57zivihhia20gibr5f03x8aspy6382wnwlka")))) (build-system r-build-system) (propagated-inputs (list r-bayestestr r-broom 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 "1.1.4") (source (origin (method url-fetch) (uri (cran-uri "glmmTMB" version)) (sha256 (base32 "1ldly6qn8iwqr41ndqlwsdz4v2n36giavsmx33vybn9g7r2fq4m7")))) (properties `((upstream-name . "glmmTMB"))) (build-system r-build-system) (propagated-inputs (list r-lme4 r-matrix 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. 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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 "0.9.2") (source (origin (method url-fetch) (uri (cran-uri "performance" version)) (sha256 (base32 "0fdszf1dngqlbwcp7ynfdkzjgg0lang4d3b53ygjwsq7ph20xsw6")))) (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. 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(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 "0.6.1") (source (origin (method url-fetch) (uri (cran-uri "rslurm" version)) (sha256 (base32 "19451icfh7snjbbmpzpr1hrdf52q8ijv0ag1di3y55r2la3jxxcf")))) (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 "0.8.1") (source (origin (method url-fetch) (uri (cran-uri "chk" version)) (sha256 (base32 "0nw3aj8sbd2x8rsvpglsiavk7kivd330mgx676k46m7lhhj7nmpw")))) (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 "2.6.0") (source (origin (method url-fetch) (uri (cran-uri "RcppAlgos" version)) (sha256 (base32 "11dvh0ba3chsqf3vw8g9h1754arxgwqryayavx3n6vm5daz2krqa")))) (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 "0.0.19") (source (origin (method url-fetch) (uri (cran-uri "RcppAnnoy" version)) (sha256 (base32 "12k8ny981dmky5js8yl6bih5r5mq3w43f2f9admhkwqn0n80kcl9")))) (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 "0.4.1") (source (origin (method url-fetch) (uri (cran-uri "RcppHNSW" version)) (sha256 (base32 "0x3w14cz6hkrl8hi6217j0dl65l3yphbzka1dmsvgp3p9waq402g")))) (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 "5.1.5") (source (origin (method url-fetch) (uri (cran-uri "RcppParallel" version)) (sha256 (base32 "1sn211ajlb1p12sglxqns175rg078yvww268m8cp0vvd7cmk55k3")) (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 "1.19") (source (origin (method url-fetch) (uri (cran-uri "ncdf4" version)) (sha256 (base32 "0qzvin2fjzcb7h2knlnw14s6043pwi1nm7yf6p27ax7w269173fb")))) (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-biocmanager (package (name "r-biocmanager") (version "1.30.18") (source (origin (method url-fetch) (uri (cran-uri "BiocManager" version)) (sha256 (base32 "0dawbd546rznllpw5wq282r0viga4cck398d4s1inkk18mmi4qzp")))) (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))) (define-public r-rgl (package (name "r-rgl") (version "0.109.6") (source (origin (method url-fetch) (uri (cran-uri "rgl" version)) (sha256 (base32 "1jl89v2gwk1d4q3vn7kx8x7abjbgiisfiyrs4d40qixr6iil8hrz")))) (build-system r-build-system) (native-inputs (list pkg-config r-knitr r-rmarkdown)) ;for vignettes (inputs (list freetype libpng glu libx11 pandoc 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 "0.1-12") (source (origin (method url-fetch) (uri (cran-uri "multicool" version)) (sha256 (base32 "0djacq0irfqz4nlnx238kja73yvr1n5qybbfyl6bw1n6qgcjhza8")))) (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-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-ks (package (name "r-ks") (version "1.13.5") (source (origin (method url-fetch) (uri (cran-uri "ks" version)) (sha256 (base32 "05bqrjkbx2kn5aax0hy3xd6pf7nxka9bm1sp8ll1cc2gf1nx1i6i")))) (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-plot3d 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 "1.13-1") (source (origin (method url-fetch) (uri (cran-uri "arm" version)) (sha256 (base32 "0dz9dnsky77da2mc198dr3600kz9vk75z1iihjarnsdrq68a4bf0")))) (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 "0.4-95") (source (origin (method url-fetch) (uri (cran-uri "circular" version)) (sha256 (base32 "1qmwj1pf37lc2s5r83y7nqckscznqhbsv66bdfgfbby7x4qkwga8")))) (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 "1.3.2") (source (origin (method url-fetch) (uri (cran-uri "activity" version)) (sha256 (base32 "11n6wmqz7p3428rr615f92m61a5gb908xpn4l8q484h61bwg38c3")))) (build-system r-build-system) (propagated-inputs (list r-insol 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 "2.18") (source (origin (method url-fetch) (uri (cran-uri "ouch" version)) (sha256 (base32 "119s9llpjy0b4q830xig2xr66fq6izp6mr2k4k79ggmf3gxww8as")))) (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 "1.9.6") (source (origin (method url-fetch) (uri (cran-uri "fmri" version)) (sha256 (base32 "1wh77xwpm8f9d9vky3r7vfmkik3hls008ifk8hkm2rq6i06jj53n")))) (properties `((upstream-name . "fmri"))) (build-system r-build-system) (propagated-inputs (list r-aws r-metafor r-nlme)) (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 "0.7.3") (source (origin (method url-fetch) (uri (cran-uri "fmsb" version)) (sha256 (base32 "1gi94xr0b1yk9xzwfprfafxi25yic1lcivd66p73n6iqfzdaimbk")))) (build-system r-build-system) (home-page "http://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.") (license license:gpl2+))) (define-public r-gsl (package (name "r-gsl") (version "2.1-7.1") (source (origin (method url-fetch) (uri (cran-uri "gsl" version)) (sha256 (base32 "118rj9kjx9rzlynvhrly19qz3yxg8jzws35971ssgzrp5lwd367f")))) (build-system r-build-system) (inputs (list gsl)) (home-page "https://cran.r-project.org/web/packages/gsl") (synopsis "Wrapper for the GNU Scientific Library") (description "This package provides an R wrapper for the special functions and quasi random number generators of the GNU Scientific Library.") (license license:gpl2+))) (define-public r-adgoftest (package (name "r-adgoftest") (version "0.3") (source (origin (method url-fetch) (uri (cran-uri "ADGofTest" version)) (sha256 (base32 "0ik817qzqp6kfbckjp1z7srlma0w6z2zcwykh0jdiv7nahwk3ncw")))) (properties `((upstream-name . "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 "0.9.3") (source (origin (method url-fetch) (uri (cran-uri "adimpro" version)) (sha256 (base32 "0njw38vcdm02sni193nj10mpv7hiklpamrkjlz5bnhjxx9mvf4cl")))) (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 "0.30") (source (origin (method url-fetch) (uri (cran-uri "admisc" version)) (sha256 (base32 "01b2qjxz0qicqjm1swvm04qkiwhr7zjn7lhqv26l6rj4yb43y339")))) (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 "0.5-2") (source (origin (method url-fetch) (uri (cran-uri "mritc" version)) (sha256 (base32 "07b1b2k1ka43ikj2mhwnazw3ig7w10bf759fimxpksvk5k6wanx2")))) (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 "1.2.1") (source (origin (method url-fetch) (uri (cran-uri "sodium" version)) (sha256 (base32 "1a03z2asvmalnmsn89lapzp8a4fr0qvzdv3xgin8pbqhjyb9hvpp")))) (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-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 "0.1-11") (source (origin (method url-fetch) (uri (cran-uri "tiff" version)) (sha256 (base32 "0xgc7vyndxxahfhc2qqzmwi56bnfyl0pn72l820jz5sd24aymhxq")))) (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 "0.7-8") (source (origin (method url-fetch) (uri (cran-uri "tm" version)) (sha256 (base32 "0mk2lsplynms15nw92vbdgsafg4bw1m0ik31gch1mnsnv61idsxi")))) (properties `((upstream-name . "tm"))) (build-system r-build-system) (propagated-inputs (list r-bh r-nlp r-rcpp r-slam r-xml2)) (home-page "http://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-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-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 "2.3.1") (source (origin (method url-fetch) (uri (cran-uri "colorRamps" version)) (sha256 (base32 "12jnkj50yh2hc5l7j56lrrrmn58akrj9dwj98vzf42iq4h42kwb1")))) (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 "0.4.0") (source (origin (method url-fetch) (uri (cran-uri "tidytree" version)) (sha256 (base32 "0dm71zdrb1qwaja23jlzjpraa609b6yxl8bhksz8slgpfm1jgs00")))) (build-system r-build-system) (propagated-inputs (list r-ape 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-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.") (license license:expat))) (define-public r-sparsesvd (package (name "r-sparsesvd") (version "0.2-1") (source (origin (method url-fetch) (uri (cran-uri "sparsesvd" version)) (sha256 (base32 "0yz0mgayxriyrz6bbrd41cck0s56b916xvyh13hw86gydd6kpl5k")))) (build-system r-build-system) (propagated-inputs (list r-matrix)) (home-page "http://tedlab.mit.edu/~dr/SVDLIBC/") (synopsis "Sparse truncated singular value decomposition") (description "This package provides a Wrapper around the SVDLIBC library for (truncated) singular value decomposition of a sparse matrix. Currently, only sparse real matrices in Matrix package format are supported.") ;; SVDLIBC is released under BSD-2. The R interface is released under ;; BSD-3. (license (list license:bsd-3 license:bsd-2)))) (define-public r-speedglm (package (name "r-speedglm") (version "0.3-4") (source (origin (method url-fetch) (uri (cran-uri "speedglm" version)) (sha256 (base32 "1kj662nfkfhvx37jrbvxd4dyjclz5cm3xh50z7s5rbzapiyxn4hs")))) (build-system r-build-system) (propagated-inputs (list 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 "0.3.2") (source (origin (method url-fetch) (uri (cran-uri "densityClust" version)) (sha256 (base32 "05x2fi1zdnkrg2nimf8k904j3lpyw0f7nmk6ax5p7x7a98wb2iqs")))) (properties `((upstream-name . "densityClust"))) (build-system r-build-system) (propagated-inputs (list r-fnn r-ggplot2 r-ggrepel r-gridextra r-rcolorbrewer r-rcpp r-rtsne)) (home-page "https://cran.r-project.org/web/packages/densityClust") (synopsis "Clustering by fast search and find of density peaks") (description "This package provides an improved implementation (based on k-nearest neighbors) of the density peak clustering algorithm, originally described by Alex Rodriguez and Alessandro Laio (Science, 2014 vol. 344). It can handle large datasets (> 100,000 samples) very efficiently.") (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 "http://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 "0.0.8") (source (origin (method url-fetch) (uri (cran-uri "TFMPvalue" version)) (sha256 (base32 "0h9qkl15k8v17v3g9bdnfwvh2s04ywjgg5y0xn2077dmywlja1bd")))) (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-rncl (package (name "r-rncl") (version "0.8.6") (source (origin (method url-fetch) (uri (cran-uri "rncl" version)) (sha256 (base32 "1ywgwqn82z8h6zpcxxq4hgngdpfa6dj0lr7bfq4cwfml9z075jgw")))) (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()}.") (license license:bsd-2))) (define-public r-phylobase (package (name "r-phylobase") (version "0.8.10") (source (origin (method url-fetch) (uri (cran-uri "phylobase" version)) (sha256 (base32 "0jzr1gdvmi4l640hwwzh9bxqmpja69bn3ygnaqx37awvyh7khi2s")))) (build-system r-build-system) (propagated-inputs (list r-ade4 r-ape r-rcpp r-rncl r-rnexml)) (native-inputs (list r-knitr)) (home-page "https://github.com/fmichonneau/phylobase") (synopsis "Base package for phylogenetic structures and comparative data") (description "This package provides a base @code{S4} class for comparative methods, incorporating one or more trees and trait data.") (license license:gpl2+))) (define-public r-phylotools (package (name "r-phylotools") (version "0.2.2") (source (origin (method url-fetch) (uri (cran-uri "phylotools" version)) (sha256 (base32 "1dhk1ncp5zi4zl1xfnjz64v983dm7bq7iimfjin80j0bdcpps44w")))) (properties `((upstream-name . 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(license license:gpl2))) (define-public r-rnexml (package (name "r-rnexml") (version "2.4.7") (source (origin (method url-fetch) (uri (cran-uri "RNeXML" version)) (sha256 (base32 "1zp6pijsc73jx8cmxb1hng36nvaf5wnhldnzlqhmba9kv9niscfb")))) (build-system r-build-system) (propagated-inputs (list r-ape r-dplyr r-httr r-lazyeval 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.") (license license:bsd-3))) (define-public r-rnifti (package (name "r-rnifti") (version "1.4.1") (source (origin (method url-fetch) (uri (cran-uri "RNifti" version)) (sha256 (base32 "058jzhw91wd4hb9l06mn0ihf1yp2fapz1fyb32w9bjwxq7qxvii2")))) (properties `((upstream-name . "RNifti"))) (build-system r-build-system) (inputs (list zlib)) (propagated-inputs (list r-rcpp)) (home-page "https://github.com/jonclayden/RNifti") (synopsis "Fast R and C++ access to NIfTI images") (description "This package provides very fast read and write access to images stored in the NIfTI-1 and ANALYZE-7.5 formats, with seamless synchronisation between compiled C and interpreted R code. It also provides a C/C++ API that can be used by other packages.") (license license:gpl2))) (define-public r-shades (package (name "r-shades") (version "1.4.0") (source (origin (method url-fetch) (uri (cran-uri "shades" version)) (sha256 (base32 "1zg95sjhrfvbdlfc387g9p0vnb8nb6agdk1mb3wq3kwkm2da0bqj")))) (build-system r-build-system) (home-page "https://github.com/jonclayden/shades") (synopsis "Simple color manipulation") (description "This package provides functions for easily manipulating colors, creating color scales and calculating color distances.") (license license:bsd-3))) (define-public r-ore (package (name "r-ore") (version "1.7.1.1") (source (origin (method url-fetch) (uri (cran-uri "ore" version)) (sha256 (base32 "0rs5r5h11x4l4nsbl4xqzbl4ahajd5374fq05abcmfjnjr9j64w5")))) (build-system r-build-system) (home-page "https://github.com/jonclayden/ore") (synopsis "R interface to the Onigmo regular expression library") (description "This package provides an alternative to R's built-in functionality for handling regular expressions, based on the Onigmo library. It offers first-class compiled regex objects, partial matching and function-based substitutions, amongst other features.") (license license:bsd-3))) (define-public r-reportr (package (name "r-reportr") (version "1.3.0") (source (origin (method url-fetch) (uri (cran-uri "reportr" version)) (sha256 (base32 "0zynplxqvbmf23cm2rsz3wz2jx6mv55z94mn1k44ny3lx625cnpw")))) (build-system r-build-system) (propagated-inputs (list r-ore)) (home-page "https://github.com/jonclayden/reportr") (synopsis "General message and error reporting system") (description "This package provides a system for reporting messages, which offers certain useful features over the standard R system, such as the incorporation of output consolidation, message filtering, assertions, expression substitution, automatic generation of stack traces for debugging, and conditional reporting based on the current \"output level\".") (license license:gpl2))) (define-public r-tractor-base (package (name "r-tractor-base") (version "3.3.5.1") (source (origin (method url-fetch) (uri (cran-uri "tractor.base" version)) (sha256 (base32 "0fxbzbhpi6l55m14nmww8y3kdxgchzj4mw1yf4xkm2y6s68phvgc")))) (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-grimport (package (name "r-grimport") (version "0.9-5") (source (origin (method url-fetch) (uri (cran-uri "grImport" version)) (sha256 (base32 "0pbzc45wgp0cpycnw0bzn65ckdszzay0zrp7c7ssxdkifp8bai3a")))) (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 "0.2-0") (source (origin (method url-fetch) (uri (cran-uri "grImport2" version)) (sha256 (base32 "19q0dd8fpp1g4xf6sg5f8dxybwxjfw553ra6wgjd8b74fzca40m1")))) (properties `((upstream-name . 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(license license:gpl2+))) (define-public r-kohonen (package (name "r-kohonen") (version "3.0.11") (source (origin (method url-fetch) (uri (cran-uri "kohonen" version)) (sha256 (base32 "1bk3j0n8w4fhffv89rgyn4n21c0wcx6lr8jv4wbagpxprl585381")))) (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 "1.4") (source (origin (method url-fetch) (uri (cran-uri "nnls" version)) (sha256 (base32 "07vcrrxvswrvfiha6f3ikn640yg0m2b4yd9lkmim1g0jmsmpfp8f")))) (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 "0.0-18.1") (source (origin (method url-fetch) (uri (cran-uri "Iso" version)) (sha256 (base32 "0vy6jdyvp751430sf2f690yhasjr70cpk3p3lnaaxjq3fs5gg99g")))) (properties `((upstream-name . "Iso"))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "https://www.stat.auckland.ac.nz/~rolf/") (synopsis "Functions to perform isotonic regression") (description "This package provides support for linear order and unimodal order (univariate) isotonic regression and bivariate isotonic regression with linear order on both variables.") (license license:gpl2+))) (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.") (license license:gpl2))) (define-public r-rapidjsonr (package (name "r-rapidjsonr") (version "1.2.0") (source (origin (method url-fetch) (uri (cran-uri "rapidjsonr" version)) (sha256 (base32 "07zdirhbzmvq3cp4xn8ngk1lgxbbabzays315zxbs3sxrz6lzjb2")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/rapidjsonr") (synopsis "JSON parser") (description "This package provides JSON parsing capability through the Rapidjson library.") (license license:expat))) (define-public r-ontologyindex (package (name "r-ontologyindex") (version "2.10") (source (origin (method url-fetch) (uri (cran-uri "ontologyIndex" version)) (sha256 (base32 "0hisb9scxyyqkxhxhvgsgwix54pkq0zma3xq3ywczyazvzcxd5f9")))) (properties `((upstream-name . 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This includes functions and classes for handling common credential types and for preparing, executing, and processing HTTP requests.") (license license:expat))) (define-public r-bigrquery (package (name "r-bigrquery") (version "1.4.0") (source (origin (method url-fetch) (uri (cran-uri "bigrquery" version)) (sha256 (base32 "02msq61l7vamzpvbhvalh3qil1aa7pr68pwpsivbb6pvz6p4zyns")))) (build-system r-build-system) (propagated-inputs (list r-assertthat r-bit64 r-curl r-dbi r-gargle r-glue r-httr r-jsonlite r-lifecycle r-prettyunits r-progress r-rapidjsonr r-rcpp r-rlang r-tibble)) (home-page "https://github.com/rstats-db/bigrquery") (synopsis "R interface to Google's BigQuery API") (description "This package provides an R interface to Google's BigQuery database.") (license license:gpl3))) (define-public r-gmp (package (name "r-gmp") (version "0.6-6") (source (origin (method url-fetch) (uri (cran-uri "gmp" version)) (sha256 (base32 "14r7xlxjrwww6l726sispq6jhxy2yfwbcqrqgc9x4ma812l9byl7")))) (build-system r-build-system) (arguments '(#:phases (modify-phases %standard-phases (add-after 'unpack 'set-CC (lambda _ (setenv "CC" "gcc") #t))))) (inputs (list gmp)) (home-page "https://cran.r-project.org/web/packages/gmp") (synopsis "Multiple precision arithmetic") (description "This package supports multiple precision arithmetic (big integers and rationals, prime number tests, matrix computation), \"arithmetic without limitations\" using the GNU Multiple Precision library.") ;; Any version of the GPL. (license license:gpl3+))) (define-public r-rmpfr (package (name "r-rmpfr") (version "0.8-9") (source (origin (method url-fetch) (uri (cran-uri "Rmpfr" version)) (sha256 (base32 "12mwvgyalzh4zf5d002fm1hpr3wwhiypy9ia6wy47ij9gns5mvng")))) (properties `((upstream-name . "Rmpfr"))) (build-system r-build-system) (inputs (list mpfr gmp)) (propagated-inputs (list r-gmp)) (native-inputs (list pkg-config)) (home-page "http://rmpfr.r-forge.r-project.org/") (synopsis "R bindings to the MPFR library") (description "This package supports arithmetic (via S4 classes and methods) for arbitrary precision floating point numbers, including transcendental functions. To this end, the package interfaces with the @dfn{Multiple Precision Floating-Point Reliable} (MPFR) library.") 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(license license:gpl3+))) (define-public r-dotcall64 (package (name "r-dotcall64") (version "1.0-1") (source (origin (method url-fetch) (uri (cran-uri "dotCall64" version)) (sha256 (base32 "1im5k8jbviwj2i42mq1kmjskh80isa7jr9w8i0fknidrzzy2h2zi")))) (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.") 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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 "14.1") (source (origin (method url-fetch) (uri (cran-uri "fields" version)) (sha256 (base32 "0d2lm4s9p3rv676z291fynpx3vdmi6cikcqlj23fxlj34icwbi2p")))) (build-system r-build-system) (propagated-inputs (list r-maps r-spam r-viridis)) (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 "http://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") (source (origin (method url-fetch) (uri (cran-uri "survivalROC" version)) (sha256 (base32 "0wnd65ff5w679hxa1zrpfrx9qg47q21pjxppsga6m3h4iq1yfj8l")))) (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-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 "http://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 "http://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 "0.3.7") (source (origin (method url-fetch) (uri (cran-uri "profvis" version)) (sha256 (base32 "1f86m426pcf90l29hf4hkirzf8f38dihk52bxbdq2gvrrdili5s3")) (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-stringr)) (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-protviz (package (name "r-protviz") (version "0.7.3") (source (origin (method url-fetch) (uri (cran-uri "protViz" version)) (sha256 (base32 "0f6jwzcqi0w37hvg3i5dlk0c3anpkqh54ibf94vaf17r8sykr4nw")))) (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 "2.47") (source (origin (method url-fetch) (uri (cran-uri "Epi" version)) (sha256 (base32 "1dkdx000cvy2rgxq3w6ppl3j9h7mwmcqg5xqsqh5hr3aks845pwx")))) (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 "0.9-7") (source (origin (method url-fetch) (uri (cran-uri "mcmc" version)) (sha256 (base32 "0q42m8ab7b6bxhns494ksjdss5f3c5m2jjfdlfj6fk1nz7ax7i5p")))) (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 "0.8.0") (source (origin (method url-fetch) (uri (cran-uri "listenv" version)) (sha256 (base32 "0ps8bk7zlhbviawrw7vw25skjq81hkk3ijyi6g74dmfqy8zsyapx")))) (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 "0.16.1") (source (origin (method url-fetch) (uri (cran-uri "globals" version)) (sha256 (base32 "158y39qv99f1kc2i7w8d4lm2ls96plb43fzamz31im9xb9bkmxpp")))) (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 "1.32.1") (source (origin (method url-fetch) (uri (cran-uri "parallelly" version)) (sha256 (base32 "146a9i999vrflr4g1fph1pgkl4bq0dw102bjw8pp1zy7kbsqbiii")))) (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 "1.28.0") (source (origin (method url-fetch) (uri (cran-uri "future" version)) (sha256 (base32 "1xhv0nf97yxxxsmxczyqqbnb4yn5sfn5vzvhm9dmw9csrmmadpbg")))) (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 "1.9.1") (source (origin (method url-fetch) (uri (cran-uri "future.apply" version)) (sha256 (base32 "0cr141mamjxby79sww02493yal9lahslvp3a3ic7f856rbawq8jg")))) (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-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 "1.1.1") (source (origin (method url-fetch) (uri (cran-uri "capushe" version)) (sha256 (base32 "1aa76ir1kp67hiz7dr60azyc71yzslshyc640fjh0fpw0sp5kwbc")))) (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 "1.8.2") (source (origin (method url-fetch) (uri (cran-uri "doRNG" version)) (sha256 (base32 "1jff27zzrvd1fd61x2m9468h8xn3s1c9f6wibviy5zdhj5dx9s9k")))) (properties `((upstream-name . "doRNG"))) (build-system r-build-system) (propagated-inputs (list r-foreach r-iterators r-rngtools)) (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 "1.1.3") (source (origin (method url-fetch) (uri (cran-uri "blockmodeling" version)) (sha256 (base32 "19mxmxsnl6rrh85p0sak91vcaw4dz2cnm70hdzfwnvdrr695yw2z")))) (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))) ;; 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 "1.0.400") (source (origin (method url-fetch) (uri (cran-uri "shinymanager" version)) (sha256 (base32 "1np2yp5pn8g9i4jhysfgprmdn13cpw4vaaagrd72rnk2r4hpmyx4")))) (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 "3.1-4") (source (origin (method url-fetch) (uri (cran-uri "bayesm" version)) (sha256 (base32 "154glks7rsjkza0sfi1kj7wj727py9sl1ba6sswflwmwc9n226q6")))) (build-system r-build-system) (propagated-inputs (list r-rcpp r-rcpparmadillo)) (home-page "http://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") (source (origin (method url-fetch) (uri (cran-uri "tensorA" version)) (sha256 (base32 "19wwh654qlja4z1n7afjpzsrrm53p8ddysa2vra5mdnkddb4g2cf")))) (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 "2.0-4") (source (origin (method url-fetch) (uri (cran-uri "compositions" version)) (sha256 (base32 "1bqg0qqzsf92q0jb7hdjycr54bwv8rk7ajhvxgch5yslyqxpm73v")))) (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 "1.3-5") (source (origin (method url-fetch) (uri (cran-uri "cobs" version)) (sha256 (base32 "04f6a6gp11p93j2k35mbrfqgjx5qsgi3dj1085a5v5s0z6l7vbkz")))) (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 "6.0-5") (source (origin (method url-fetch) (uri (cran-uri "gamlss.dist" version)) (sha256 (base32 "03m275qvrmpzmc10hs48277kxp503riz8sz6xk9pkpj8n7gsz20g")))) (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 "1.1.1") (source (origin (method url-fetch) (uri (cran-uri "colourpicker" version)) (sha256 (base32 "1q1wi3g403fbzp4ys3gsjbwdc86x770cx323qgi47ca8n219kl50")))) (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" (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) (delete-file 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-1.11.3.js") (sha256 (base32 "1v956yf5spw0156rni5z77hzqwmby7ajwdcd6mkhb6zvl36awr90")))) ("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 "0.10.0") (source (origin (method url-fetch) (uri (cran-uri "ggExtra" version)) (sha256 (base32 "1rd3qv6ah3zphr1jicjhgxms73vi496mjnxnsrcgl7z8nyxmas6w")))) (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-minpack-lm (package (name "r-minpack-lm") (version "1.2-2") (source (origin (method url-fetch) (uri (cran-uri "minpack.lm" version)) (sha256 (base32 "11yz6hk2r33571d16kq01cb1x6sgdzi6jmksqlrm8mr84l95c2f7")))) (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 "0.6-12") (source (origin (method url-fetch) (uri (cran-uri "lavaan" version)) (sha256 (base32 "17h79pnww1mihvlp6ap0r6d8wnly9bwszj13l5dkby0284z2fj40")))) (build-system r-build-system) (propagated-inputs (list r-mass r-mnormt r-numderiv r-pbivnorm)) (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 "0.5-5") (source (origin (method url-fetch) (uri (cran-uri "nonnest2" version)) (sha256 (base32 "1ddaqwx8i3ygwvxf11mc8xhgk4nkvnail99nr5szq8i168752zq2")))) (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 "1.3-0") (source (origin (method url-fetch) (uri (cran-uri "nor1mix" version)) (sha256 (base32 "1817wcvlmxs70vs4db0jkxd7i037744zz8ay3c2a9949z29fxr4w")))) (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 "0.3-7") (source (origin (method url-fetch) (uri (cran-uri "pbdZMQ" version)) (sha256 (base32 "020qy6fq8w8wq0j3bii14ahrlg8wzl0lrnndfr6scmrg9ghjnbfz")))) (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 "1.1.4") (source (origin (method url-fetch) (uri (cran-uri "repr" version)) (sha256 (base32 "0h3h14ybamcbwmm31ib66fx13v75vkzn4bn2v26n2h097sl9qybg")))) (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") (source (origin (method url-fetch) (uri (cran-uri "IRkernel" version)) (sha256 (base32 "00qrmsywpzw2hfp88020zjaijma7q4hqm9h2cz53rywdjzywnzss")))) (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 "2.18.1.1") (source (origin (method url-fetch) (uri (cran-uri "gmodels" version)) (sha256 (base32 "158y7yh4maawn9vki8cq4sil48xib2bbpl6qgj5gvlkw3c14hzfs")))) (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 "1.4.10") (source (origin (method url-fetch) (uri (cran-uri "apcluster" version)) (sha256 (base32 "1820j1xjlbmw6j2fwwv2g806dqpk5qrbbaqsrbrn6igql8pzf552")))) (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-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 "0.4.5") (source (origin (method url-fetch) (uri (cran-uri "lemon" version)) (sha256 (base32 "1y3ljidhqdakxlya2npj2w0az820g8kw6gl1cfm4f0cxvzgd1ly4")))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-gridextra r-gtable r-knitr r-lattice r-plyr r-rlang 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-sets (package (name "r-sets") (version "1.0-21") (source (origin (method url-fetch) (uri (cran-uri "sets" version)) (sha256 (base32 "1h1a03b1850kh5hd3gxbspx2nxqxvk2gb0wm0s60b70qb6zg0csp")))) (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 "1.2-7") (source (origin (method url-fetch) (uri (cran-uri "Brobdingnag" version)) (sha256 (base32 "0hnp5nrpnscykvgrrbgp7987660hcbv92zc2q8lmpnin4ws399vk")))) (properties `((upstream-name . "Brobdingnag"))) (build-system r-build-system) (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-untb (package (name "r-untb") (version "1.7-4") (source (origin (method url-fetch) (uri (cran-uri "untb" version)) (sha256 (base32 "1i7m4vfslsix98dwx4jlrsldm7fhhfp25gr7aapcxqxms7ryaby6")))) (build-system r-build-system) (propagated-inputs (list r-brobdingnag r-partitions r-polynom)) (home-page "https://github.com/RobinHankin/untb.git") (synopsis "Ecological drift under the UNTB") (description "This package provides numerical simulations, and visualizations, of Hubbell's @dfn{Unified Neutral Theory of Biodiversity} (UNTB).") (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 . "ACSNMineR"))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-gridextra)) (home-page "https://cran.r-project.org/web/packages/ACSNMineR") (synopsis "Gene enrichment analysis") (description "This package provides tools to compute and represent gene set enrichment or depletion from your data based on pre-saved maps from the @dfn{Atlas of Cancer Signalling Networks} (ACSN) or user imported maps. The gene set enrichment can be run with hypergeometric test or Fisher exact test, and can use multiple corrections. Visualization of data can be done either by barplots or heatmaps.") (license license:gpl2+))) (define-public r-seqinr (package (name "r-seqinr") (version "4.2-16") (source (origin (method url-fetch) (uri (cran-uri "seqinr" version)) (sha256 (base32 "0cj07b7km5mla63qhbkxg1mnqq6vh79lsyyfpnbm29gw68w2bwy4")))) (build-system r-build-system) (propagated-inputs (list r-ade4 r-segmented)) (inputs (list zlib)) (home-page "http://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-units (package (name "r-units") (version "0.8-0") (source (origin (method url-fetch) (uri (cran-uri "units" version)) (sha256 (base32 "06mjprqi06xprj6185k5cmrrdl025x0pd1r6a4x3s74ciq9zwilw")))) (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 "0.4-7") (source (origin (method url-fetch) (uri (cran-uri "classInt" version)) (sha256 (base32 "0vk06k10mxcm6wn4b74njzc1kc1ividsn03ii523j4yfhy4kl3m3")))) (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 "2.2.0") (source (origin (method url-fetch) (uri (cran-uri "spData" version)) (sha256 (base32 "07whxr039cxvk2nn65jada3i8vqqw34lgca9j17ah8chy9r0m73f")))) (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 "1.0-6") (source (origin (method url-fetch) (uri (cran-uri "deldir" version)) (sha256 (base32 "1igq0l2knsbhizncgydcsidgkvvlwwlkrifbcdyhnzk0bhrdixkd")))) (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 "0.6.0") (source (origin (method url-fetch) (uri (cran-uri "wk" version)) (sha256 (base32 "1xga4rrqsr190g55by39az4nimnn06bf5b6mcjgwqvba0lvjhb5g")))) (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 "1.1.0") (source (origin (method url-fetch) (uri (cran-uri "s2" version)) (sha256 (base32 "05n459rp5b1wk826sq3c5d2z1xwgkpfp8m1jnfshvs4gadlfkap3")))) (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 "1.0-8") (source (origin (method url-fetch) (uri (cran-uri "sf" version)) (sha256 (base32 "0cl7m47ar3iw95rpwpmjl23frdbscxa15q39mlzmwswxwy871p1x")))) (build-system r-build-system) (inputs (list gdal geos 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-spdep (package (name "r-spdep") (version "1.2-5") (source (origin (method url-fetch) (uri (cran-uri "spdep" version)) (sha256 (base32 "1ib5jgahjgjpj2ajp5g71r4fw0q1zkddixgmywi1n73nqr39qwp2")) (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 "2.1.7") (source (origin (method url-fetch) (uri (cran-uri "adegenet" version)) (sha256 (base32 "0zkbxw9w0fcb4s3zv2a8nxcsihzkfz49psaipxw99nwgm7l9jrh9")))) (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 "1.1") (source (origin (method url-fetch) (uri (cran-uri "pegas" version)) (sha256 (base32 "0ngd0laqbs139ji9hm9kwsm9rm56agw2yyfcplxgqva936l93fl7")))) (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-rmetasim (package (name "r-rmetasim") (version "3.1.14") (source (origin (method url-fetch) (uri (cran-uri "rmetasim" version)) (sha256 (base32 "0rdkhfgyr97r2d1kd9g8ipb2pn563qxm1y4m9z678q0kqan2ddl0")))) (build-system r-build-system) (propagated-inputs (list r-ade4 r-adegenet r-gtools r-pegas)) (home-page "https://cran.r-project.org/web/packages/rmetasim") (synopsis "Individual-based population genetic simulation environment") (description "This package provides an interface between R and the metasim simulation engine. The simulation environment is documented in: Strand, A.(2002), Metasim 1.0: an individual-based environment for simulating population genetics of complex population dynamics.") ;; Any GPL version (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 "1.1.20") (source (origin (method url-fetch) (uri (cran-uri "polspline" version)) (sha256 (base32 "1dd1jwiaglkkhajzvqfkd1x5r3wzjlk5ww0yxzmns0s1kr74i4k9")))) (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 "6.3-0") (source (origin (method url-fetch) (uri (cran-uri "rms" version)) (sha256 (base32 "1yfk800q4mgmrjkh0hqjkiv907sr1bi1jaigrj8l6pmg1mkynhbc")))) (build-system r-build-system) (propagated-inputs (list r-cluster r-digest r-ggplot2 r-hmisc r-htmltable r-htmltools r-lattice 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 "1.8.9") (source (origin (method url-fetch) (uri (cran-uri "haplo.stats" version)) (sha256 (base32 "0np9kw4f30xbvwr4f79g909ilis5n273ridmlwyzjxiskiry6mx0")))) (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 "1.0-33") (source (origin (method url-fetch) (uri (cran-uri "bqtl" version)) (sha256 (base32 "1sbzpi9z94f010lw2y1gmifjrvpmiqs4m26za7vr1xz72azrqvs9")))) (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 "0.3.6") (source (origin (method url-fetch) (uri (cran-uri "ibdreg" version)) (sha256 (base32 "1x8z0vr2cmdks12hxfm0wwxskb0cr669w5j5rpa2ln8q704yy41g")))) (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") (source (origin (method url-fetch) (uri (cran-uri "hwde" version)) (sha256 (base32 "0wb2f9i5qi7w77ygh8bvydfpr7j5x8dyvnnhdkajaz0wdcpkyaqy")))) (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 "1.1-11") (source (origin (method url-fetch) (uri (cran-uri "tdthap" version)) (sha256 (base32 "15qlj2bivvz3pizd8dq34wczbkbxhzqh3cqp1ixkdkprlyvcxj5k")))) (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 "0.29") (source (origin (method url-fetch) (uri (cran-uri "bookdown" version)) (sha256 (base32 "08zpky94bdbjsbhi90pymxpczpfkjxwbx7p1v7ip8raw9b23skjv")))) (build-system r-build-system) (propagated-inputs (list r-htmltools r-jquerylib r-knitr r-rmarkdown r-tinytex r-xfun r-yaml pandoc)) ;; We cannot add knitr because this package depends on xfun, which is an ;; input to knitr. #; (native-inputs (list r-knitr)) (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-optparse (package (name "r-optparse") (version "1.7.3") (source (origin (method url-fetch) (uri (cran-uri "optparse" version)) (sha256 (base32 "1v87db7fm494dwxvdsnl1m2kj84nplq7pkh0g41najhx0npy31v2")))) (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-kernlab (package (name "r-kernlab") (version "0.9-31") (source (origin (method url-fetch) (uri (cran-uri "kernlab" version)) (sha256 (base32 "12i7ffc1aacyy7bpjc0w60wwivn88wri8jz43h77irn5q5jwcnbk")))) (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 "2.9") (source (origin (method url-fetch) (uri (cran-uri "sampling" version)) (sha256 (base32 "11xis4vzn2ga8ml9xrgfgqzccvwbnabq35aidzdvpnvciybsanvz")))) (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 "1.0-6") (source (origin (method url-fetch) (uri (cran-uri "rJava" version)) (sha256 (base32 "1ijqhvnb8ab38cp9pwdf7zq7xqqlm6x94gkrab2dd98p6d4x1472")))) (properties `((upstream-name . "rJava"))) (build-system r-build-system) (arguments `(#:modules ((guix build utils) (guix build r-build-system) (ice-9 match)) #: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")) (match (find-files (string-append jdk "/jre/lib/") "libjvm.so") ((lib) (setenv "JAVA_LIBS" lib)) (_ (error "Could not find libjvm.so")))) #t))))) (inputs `(("icu4c" ,icu4c) ("jdk" ,icedtea-8 "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 "1.3.10") (source (origin (method url-fetch) (uri (cran-uri "Rttf2pt1" version)) (sha256 (base32 "1fp1y0kxa5xg8w0dplm12wfm8h78az4k6ql1758wwhb3d17np241")))) (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 "0.18") (source (origin (method url-fetch) (uri (cran-uri "extrafont" version)) (sha256 (base32 "0mx810mld67vb1w3wkl4fhpjmkq32lgpq5x1c0a9rf8li5wskrj4")))) (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 "22.3") (source (origin (method url-fetch) (uri (cran-uri "babelgene" version)) (sha256 (base32 "1735h4s2vahv55pmq65zkgxq8d5x71i1is03rf17dric8yynjjhg")))) (properties `((upstream-name . "babelgene"))) (build-system r-build-system) (propagated-inputs (list r-dplyr r-rlang)) (native-inputs (list r-knitr)) (home-page "https://igordot.github.io/babelgene/") (synopsis "Gene orthologs for model organisms in a Tidy data format") (description "Genomic analysis of model organisms often requires the use of databases based on human data or making comparisons to patient-derived resources. This requires converting genes between human and non-human analogues. The babelgene R package provides predicted gene orthologs/homologs for frequently studied model organisms in an R-friendly tidy/long format. The package integrates orthology assertion predictions sourced from multiple databases as compiled by the HGNC Comparison of Orthology Predictions (HCOP).") (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 "0.0.5") (source (origin (method url-fetch) (uri (cran-uri "yulab.utils" version)) (sha256 (base32 "0sq5wc0mp84h6fs4wa2smvf7dcn0p0xarzb2ljvqc3p4vb2lvkbf")))) (properties `((upstream-name . "yulab.utils"))) (build-system r-build-system) (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 "0.1.0") (source (origin (method url-fetch) (uri (cran-uri "ggplotify" version)) (sha256 (base32 "12mk3fa8fdjxj7xxz21jkr7h91w5wdgwjqhszcz1qffwsgb773qp")))) (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.") 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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 "0.3-61") (source (origin (method url-fetch) (uri (cran-uri "clue" version)) (sha256 (base32 "0cfw2k1kh4a8imdv7b5qw977xd6indampsabhfldj3rqrqb1ncbi")))) (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 "0.3.0") (source (origin (method url-fetch) (uri (cran-uri "dqrng" version)) (sha256 (base32 "1fwsldqcri2lccna4icbmmlqic3w4xyjm7rn0xmikrsw4kzapvjb")))) (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 "2.2.0") (source (origin (method url-fetch) (uri (cran-uri "ingredients" version)) (sha256 (base32 "11bv4l4fn9kr7y2nfzrwnaya8fi9w3nwcm9vzlqb7dva83rkqbsc")))) (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 "2.0.1") (source (origin (method url-fetch) (uri (cran-uri "iBreakDown" version)) (sha256 (base32 "00jzrndb3ahsv6ihp2pvs732n9cc944m83vdinrl9v1pxd82prkh")))) (properties `((upstream-name . "iBreakDown"))) (build-system r-build-system) (propagated-inputs (list r-ggplot2)) (native-inputs (list r-knitr)) (home-page "https://ModelOriented.github.io/iBreakDown/") (synopsis "Model agnostic instance level variable attributions") (description "This package provides a model agnostic tool for decomposition of predictions from black boxes. It supports additive attributions and attributions with interactions. The Break Down Table shows contributions of every variable to a final prediction. The Break Down Plot presents variable contributions in a concise graphical way. This package works for classification and regression models.") (license license:gpl3))) (define-public r-dae (package (name "r-dae") (version "3.2-13") (source (origin (method url-fetch) (uri (cran-uri "dae" version)) (sha256 (base32 "0mq94ah21p1glvsbvdmi2p7nlgz1bvq7w3rz2z3mdqq18kz6nkjw")))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-plyr)) (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 "2.4.2") (source (origin (method url-fetch) (uri (cran-uri "DALEX" version)) (sha256 (base32 "1m19ibv8rpghqm4vr8nrvarrjkm9rxw6jx8xl3hzrqnnmf2xifqr")))) (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 "3.1") (source (origin (method url-fetch) (uri (cran-uri "enrichR" version)) (sha256 (base32 "0ad7jp398prvmm2fym07268qhv40mg67dx55ml4ayqkwxwffr1i9")))) (properties `((upstream-name . "enrichR"))) (build-system r-build-system) (propagated-inputs (list r-curl r-ggplot2 r-httr r-rjson)) (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") (source (origin (method url-fetch) (uri (cran-uri "plot3D" version)) (sha256 (base32 "1h59zlsyzbjylaziwavppl9bjmnba4iiq34772y3dys6fqclajnh")))) (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-ggfortify (package (name "r-ggfortify") (version "0.4.14") (source (origin (method url-fetch) (uri (cran-uri "ggfortify" version)) (sha256 (base32 "038m74azpy43869ax1yi6wxbl1kr59iaxl8raiikjg749vcx6njw")))) (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 "1.3.0") (source (origin (method url-fetch) (uri (cran-uri "RefManageR" version)) (sha256 (base32 "1spzdp5ni52dybcaxqnhwdphh27wjyrsfy4hsxsplpg9rqwfqfps")))) (properties `((upstream-name . "RefManageR"))) (build-system r-build-system) (propagated-inputs (list 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 "1.6.0.1") (source (origin (method url-fetch) (uri (cran-uri "xgboost" version)) (sha256 (base32 "1gafjv6vcpny03lqw8s68xszalsylniavaqwsbzh46vyk4h9mscs")))) (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 "0.2.9.0") (source (origin (method url-fetch) (uri (cran-uri "umap" version)) (sha256 (base32 "1282v09kpds83mlr7kz06k8a40ji15hw85p30vrnp1g6w64w26sm")))) (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 "0.1.14") (source (origin (method url-fetch) (uri (cran-uri "uwot" version)) (sha256 (base32 "1q4z98w3pkc51vrcpmwaibnwmlm17zjcnh0qlx660wky5ccyh5l0")))) (build-system r-build-system) (propagated-inputs (list r-dqrng r-fnn r-irlba r-matrix r-rcpp r-rcppannoy r-rcppprogress)) (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 "1.3.4") (source (origin (method url-fetch) (uri (cran-uri "kableExtra" version)) (sha256 (base32 "1c5vzy95cbz36jwyssr927qicrayifinv861rvnmg4nghb1gl7q9")))) (properties `((upstream-name . "kableExtra"))) (build-system r-build-system) (propagated-inputs (list r-digest r-glue r-htmltools r-knitr r-magrittr r-rmarkdown r-rstudioapi r-rvest r-scales r-stringr r-svglite r-viridislite r-webshot 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-gldex (package (name "r-gldex") (version "2.0.0.9") (source (origin (method url-fetch) (uri (cran-uri "GLDEX" version)) (sha256 (base32 "1g0wg6z4ba1n6p2nw3kr734wlgmq0aw1a4spr6xw6djj7idsfi61")))) (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-rhpcblasctl (package (name "r-rhpcblasctl") (version "0.21-247.1") (source (origin (method url-fetch) (uri (cran-uri "RhpcBLASctl" version)) (sha256 (base32 "0scpr6jq25xx7wmqyc380ann4h536ll0g7wblikk25yqvpamzrav")))) (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") (source (origin (method url-fetch) (uri (cran-uri "leiden" version)) (sha256 (base32 "0f09k3mhb0di2cz1q95y6qd3rqh7xdybn0dpnd4ifqhfhr5lnika")))) (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-patchwork (package (name "r-patchwork") (version "1.1.2") (source (origin (method url-fetch) (uri (cran-uri "patchwork" version)) (sha256 (base32 "0xw9mh1qakj131nw98icxrxwvdlwy2ngwvmagrqr3m84sz9dbffs")))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-gtable)) (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-liger (package (name "r-liger") (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 '(begin (delete-file "inst/java/ModularityOptimizer.jar") #t)))) (build-system r-build-system) (arguments `(#: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$")) #t))))) (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) ("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-harmony (package (name "r-harmony") (version "0.1") (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/immunogenomics/harmony") (commit version))) (file-name (git-file-name name version)) (sha256 (base32 "05r401q09rbr6fqhb9mbd95082cjdi3nag1cv6zn96xkr0f6imq9")) (modules '((guix build utils))) (snippet '(begin (for-each delete-file '("config.status" "configure")) #t)))) (build-system r-build-system) (propagated-inputs (list r-cowplot r-dplyr r-ggplot2 r-irlba r-matrix r-rcpp r-rcpparmadillo r-rcppprogress r-rlang r-tibble r-tidyr)) (native-inputs (list autoconf)) (home-page "https://github.com/immunogenomics/harmony") (synopsis "Integration of single cell sequencing data") (description "This package provides an implementation of the Harmony algorithm for single cell integration, described in Korsunsky et al @url{doi.org/10.1101/461954}. The package includes a standalone Harmony function and interfaces to external frameworks.") (license license:gpl3))) (define-public r-covr (package (name "r-covr") (version "3.6.1") (source (origin (method url-fetch) (uri (cran-uri "covr" version)) (sha256 (base32 "0mqiqmbwq5f083lda208nqd4ya0f912bkkya2i62fkqsii1ibgpz")))) (properties `((upstream-name . "covr"))) (build-system r-build-system) (propagated-inputs (list r-crayon r-digest r-httr r-jsonlite r-rex r-withr r-yaml)) (native-inputs (list r-knitr)) ; for vignettes (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 "1.0.4") (source (origin (method url-fetch) (uri (cran-uri "systemfonts" version)) (sha256 (base32 "1h44bal845jp7ya8i7ff1kz1n3wklkb00jk6hb9lgwa2p5snqxpg")))) (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 "0.8.1") (source (origin (method url-fetch) (uri (cran-uri "graphlayouts" version)) (sha256 (base32 "0yhg42p3jlz78kd712jd5525zm1h3n5gmjplfscjkgn342r3w92v")))) (properties `((upstream-name . "graphlayouts"))) (build-system r-build-system) (propagated-inputs (list r-igraph r-rcpp r-rcpparmadillo)) (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 "1.6-17") (source (origin (method url-fetch) (uri (cran-uri "terra" version)) (sha256 (base32 "00mwigymvsqf7r3swbkdw8fwqzr05ddk84fhyhr16lfa4118z26v")))) (properties `((upstream-name . "terra"))) (build-system r-build-system) (inputs (list gdal geos proj sqlite ; needed for proj 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 "1.2.2") (source (origin (method url-fetch) (uri (cran-uri "tidygraph" version)) (sha256 (base32 "0w34jfldjkynbkyinmi1vdrfjhjrs47hm599mbnx4sxmnpbclmfm")))) (properties `((upstream-name . "tidygraph"))) (build-system r-build-system) (propagated-inputs (list r-cli r-cpp11 r-dplyr r-igraph 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 "2.8") (source (origin (method url-fetch) (uri (cran-uri "assertr" version)) (sha256 (base32 "00764vv86r3bn4r85in4w637harffyw605fgq0dj6mrbrwcfb650")))) (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 "0.18.2") (source (origin (method url-fetch) (uri (cran-uri "parameters" version)) (sha256 (base32 "04swg19zb34y3nmclf94v19yskqlb2diqg93jflhgagrv9550az9")))) (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 "1.5-32") (source (origin (method url-fetch) (uri (cran-uri "rgdal" version)) (sha256 (base32 "1vbkyhw8nd7dw1r53qisphav31x6zvpbzilvnlvbjbj9hzhs90s5")))) (properties `((upstream-name . "rgdal"))) (build-system r-build-system) (inputs (list gdal proj zlib)) (propagated-inputs (list r-sp)) (native-inputs (list pkg-config r-knitr)) (home-page "http://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 "1.0.2") (source (origin (method url-fetch) (uri (cran-uri "lifecycle" version)) (sha256 (base32 "0qssl9lmfn94kmvcg1xpd4md17jx31i3sdbb77dwas60z673qgvv")))) (properties `((upstream-name . "lifecycle"))) (build-system r-build-system) (propagated-inputs (list r-glue r-rlang)) (native-inputs (list r-knitr)) ; for vignettes (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 "1.33") (source (origin (method url-fetch) (uri (cran-uri "deSolve" version)) (sha256 (base32 "115nr3j1zp2016qpk9ab6r8n15zygvlihlmc10ilfznf0ng9gpki")))) (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 "1.9.6") (source (origin (method url-fetch) (uri (cran-uri "PMCMRplus" version)) (sha256 (base32 "1mvj3cwrdkl3frk7fvh6l7v7yya5p3xm4z0qhc4fvykxdmb92ivz")))) (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)) (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 "2.3.8") (source (origin (method url-fetch) (uri (cran-uri "pracma" version)) (sha256 (base32 "0r17siivm37k4gp253v9mlg5m7cwqp85h9kk2hbp2wkf81ad80i3")))) (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 "2.4-3") (source (origin (method url-fetch) (uri (cran-uri "bio3d" version)) (sha256 (base32 "0x3apqxbk4lvvcnvvdsyjd9f6qh9f9qgml3ih69hl9ikj06iy0y6")))) (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 . 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("d3.v4.js" ,(origin (method url-fetch) (uri "https://d3js.org/d3.v4.js") (sha256 (base32 "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg")))))) (propagated-inputs (list r-htmlwidgets r-igraph r-magrittr)) (home-page "https://cran.r-project.org/package=networkD3") (synopsis "D3 JavaScript network graphs from R") (description "This package creates D3 JavaScript network, tree, dendrogram, and Sankey graphs from R.") (license license:gpl3+))) (define-public r-aasea (package (name "r-aasea") (version "1.1.0") (source (origin (method url-fetch) (uri (cran-uri "aaSEA" version)) (sha256 (base32 "0him4r8qyp0xssgrmdxjs45yn4d28h5anv4jyxxbbs9phb0m6j3h")))) (properties `((upstream-name . "aaSEA"))) (build-system r-build-system) (propagated-inputs (list r-bios2cor r-dt r-hmisc r-magrittr r-networkd3 r-plotly r-seqinr r-shiny r-shinydashboard)) (home-page "https://cran.r-project.org/web/packages/aaSEA/") (synopsis "Amino acid substitution effect analyzer") (description "Given a protein multiple sequence alignment, it is a daunting task to assess the effects of substitutions along sequence length. The aaSEA package is intended to help researchers to rapidly analyze property changes caused by single, multiple and correlated amino acid substitutions in proteins.") (license license:gpl3))) (define-public r-abacus (package (name "r-abacus") (version "1.0.0") (source (origin (method url-fetch) (uri (cran-uri "ABACUS" version)) (sha256 (base32 "0m1dnkwjr1522l9ddbzzx7ayxvli17sbmk6s28adpmzzjwh2kd1i")))) (properties `((upstream-name . 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(define-public r-rintrojs (package (name "r-rintrojs") (version "0.3.2") (source (origin (method url-fetch) (uri (cran-uri "rintrojs" version)) (sha256 (base32 "19lpq421hrs1wc9bnimbwxx35p8bbzil3x1h9l28gjayn4djmjsh")) (snippet '(delete-file "inst/javascript/introjs/intro.min.js")))) (properties `((upstream-name . "rintrojs"))) (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/javascript/introjs/" (let ((source (assoc-ref inputs "intro.js")) (target "intro.min.js")) (format #true "Processing ~a --> ~a~%" source target) (invoke "esbuild" source "--minify" (string-append "--outfile=" target))))))))) (native-inputs `(("esbuild" ,esbuild) ("intro.js" ,(origin (method url-fetch) (uri "https://cdn.jsdelivr.net/npm/intro.js@3.2.1/intro.js") (sha256 (base32 "0vh5n7hqqyx2pdvlqq6xadfqibcn78h5961rwhpf817kpxfzv8v7")))))) (propagated-inputs (list r-jsonlite r-shiny)) (home-page "https://github.com/carlganz/rintrojs") (synopsis "Wrapper for the Intro.js library") (description "This package provides a wrapper for the @url{http://www.introjs.com, Intro.js} library. This package makes it easy to include step-by-step introductions, and clickable hints in a Shiny application. It supports both static introductions in the UI, and programmatic introductions from the server-side.") ;; The intro.js library is licensed under Expat. (license (list license:agpl3+ license:expat)))) (define-public r-sysfonts (package (name "r-sysfonts") (version "0.8.8") (source (origin (method url-fetch) (uri (cran-uri "sysfonts" version)) (sha256 (base32 "1fq5dn4l09sgrbznfz9cakf4vgc3761zwicvqaazh0s8mzbaicpn")))) (properties `((upstream-name . "sysfonts"))) (build-system r-build-system) (inputs (list freetype libpng zlib)) (native-inputs (list pkg-config)) (home-page "https://github.com/yixuan/sysfonts") (synopsis "Loading fonts into R") (description "This is a package to simplify loading of system fonts and Google Fonts into R, in order to support other packages.") (license license:gpl2))) (define-public r-showtextdb (package (name "r-showtextdb") (version "3.0") (source (origin (method url-fetch) (uri (cran-uri "showtextdb" version)) (sha256 (base32 "0hlnc3fhgrdkd46n7hb6id0gg1v0bf8s4679nrr7rchyp455szq2")))) (properties `((upstream-name . "showtextdb"))) (build-system r-build-system) (propagated-inputs (list r-sysfonts)) (home-page "https://cran.r-project.org/web/packages/showtextdb/") (synopsis "Font files for the 'showtext' package") (description "This package provides font files that can be used by the @code{showtext} package.") (license license:asl2.0))) (define-public r-showtext (package (name "r-showtext") (version "0.9-5") (source (origin (method url-fetch) (uri (cran-uri "showtext" version)) (sha256 (base32 "1larnqxn9nanbqiadm35ah5hh89xrzm4fdj9pfc93zzzhlfrvhb3")))) (properties `((upstream-name . "showtext"))) (build-system r-build-system) (inputs (list freetype libpng zlib)) (propagated-inputs (list r-showtextdb r-sysfonts)) (native-inputs (list pkg-config r-knitr)) (home-page "https://github.com/yixuan/showtext") (synopsis "Using fonts more easily in R graphs") (description "This package aims to make it easy to use various types of fonts (TrueType, OpenType, Type 1, web fonts, etc.) in R graphs, and supports most output formats of R graphics including PNG, PDF and SVG. Text glyphs will be converted into polygons or raster images, hence after the plot has been created, it no longer relies on the font files. No external software such as Ghostscript is needed to use this package.") (license license:asl2.0))) (define-public r-emojifont (package (name "r-emojifont") (version "0.5.5") (source (origin (method url-fetch) (uri (cran-uri "emojifont" version)) (sha256 (base32 "1hhrwilv36hd9gs1kcl2zsi6519md0h9aixjrm6lfclxvz8r6k1i")))) (properties `((upstream-name . "emojifont"))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-proto r-showtext r-sysfonts)) (native-inputs (list r-knitr)) (home-page "https://guangchuangyu.github.io/emojifont") (synopsis "Emoji and Font Awesome in R graphics") (description "This package enables the use of emoji and the Font Awesome glyphs in both base and ggplot2 graphics.") (license license:artistic2.0))) (define-public r-abstractr (package (name "r-abstractr") (version "0.1.0") (source (origin (method url-fetch) (uri (cran-uri "abstractr" version)) (sha256 (base32 "1ymwp7syrynwd4i8aj2x5n8jdi9d96fjzl6jb09n0bnr5fgl7vig")))) (properties `((upstream-name . "abstractr"))) (build-system r-build-system) (propagated-inputs (list r-colourpicker r-emojifont r-ggplot2 r-gridextra r-rintrojs r-shiny r-shinythemes)) (home-page "https://matt-kumar.shinyapps.io/portfolio") (synopsis "R-Shiny application for creating visual abstracts") (description "This package provides an R Shiny application to create visual abstracts for original research. A variety of user defined options and formatting are included.") (license license:gpl3))) (define-public r-qgam (package (name "r-qgam") (version "1.3.4") (source (origin (method url-fetch) (uri (cran-uri "qgam" version)) (sha256 (base32 "1jyamamdffaks89rspyhmg18b4iik0nb1j0vgqzvfnm890514cvn")))) (properties `((upstream-name . "qgam"))) (build-system r-build-system) (propagated-inputs (list r-doparallel r-mgcv r-plyr r-shiny)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/qgam/") (synopsis "Smooth additive quantile regression models") (description "This package provides smooth additive quantile regression models, fitted using the methods of Fasiolo et al. (2017). Differently from @code{quantreg}, the smoothing parameters are estimated automatically by marginal loss minimization, while the regression coefficients are estimated using either PIRLS or Newton algorithm. The learning rate is determined so that the Bayesian credible intervals of the estimated effects have approximately the correct coverage. The main function is @code{qgam()} which is similar to @code{gam()} in the @code{mgcv} package, but fits non-parametric quantile regression models.") (license license:gpl2+))) (define-public r-abtest (package (name "r-abtest") (version "1.0.1") (source (origin (method url-fetch) (uri (cran-uri "abtest" version)) (sha256 (base32 "0jz2ry5364p8h8xlk5a5sycn8xlpxd1iasfg99bcr4jqzd92jfqg")))) (properties `((upstream-name . "abtest"))) (build-system r-build-system) (propagated-inputs (list r-matrix r-mvtnorm r-plotrix r-qgam r-rcolorbrewer r-rcpp r-sn r-truncnorm)) (home-page "https://cran.r-project.org/web/packages/abtest/") (synopsis "Bayesian A/B testing") (description "This package provides functions for Bayesian A/B testing including prior elicitation options based on Kass and Vaidyanathan (1992) @url{doi:10.1111/j.2517-6161.1992.tb01868.x}.") (license license:gpl2+))) (define-public r-reldist (package (name "r-reldist") (version "1.7-1") (source (origin (method url-fetch) (uri (cran-uri "reldist" version)) (sha256 (base32 "17kbqqapqmckghv7jizibmicv3bzbycfr3mz4xg3yjp3c2bap4r6")))) (properties `((upstream-name . "reldist"))) (build-system r-build-system) (propagated-inputs (list r-densestbayes r-mgcv)) (home-page "http://www.stat.ucla.edu/~handcock/RelDist") (synopsis "Relative distribution methods") (description "This package provides tools for the comparison of distributions. This includes nonparametric estimation of the relative distribution PDF and CDF and numerical summaries as described in \"Relative Distribution Methods in the Social Sciences\" by Mark S. Handcock and Martina Morris, Springer-Verlag, 1999, Springer-Verlag, ISBN 0387987789.") ;; See also https://cran.r-project.org/web/packages/reldist/LICENSE for ;; attribution requirements. (license license:gpl3))) (define-public r-accept (package (name "r-accept") (version "0.9.1") (source (origin (method url-fetch) (uri (cran-uri "accept" version)) (sha256 (base32 "0risdxw17jk3d56q40a78slb1rcj93b6kz71hn5hbwr0iih722gr")))) (properties `((upstream-name . "accept"))) (build-system r-build-system) (propagated-inputs (list r-dplyr r-reldist)) (home-page "https://cran.r-project.org/web/packages/accept/") (synopsis "Acute COPD Exacerbation Prediction Tool (ACCEPT)") (description "This package allows clinicians to predict the rate and severity of future acute exacerbation in @dfn{Chronic Obstructive Pulmonary Disease} (COPD) patients, based on the clinical prediction model published in Adibi et al. (2019) @url{doi:10.1101/651901}.") (license license:gpl3))) (define-public r-smpracticals (package (name "r-smpracticals") (version "1.4-3") (source (origin (method url-fetch) (uri (cran-uri "SMPracticals" version)) (sha256 (base32 "0zxq84f9i3b86xx6msb25b61gyj9k09iab2b7wg4d93yas9qzayf")))) (properties `((upstream-name . "SMPracticals"))) (build-system r-build-system) (propagated-inputs (list r-ellipse r-mass r-nlme r-survival)) (home-page "http://statwww.epfl.ch/davison/SM/") (synopsis "Practicals for use with Davison (2003) Statistical Models") (description "This package contains the datasets and a few functions for use with the practicals outlined in Appendix A of the book Statistical Models (Davison, 2003, Cambridge University Press). The practicals themselves can be found at @url{http://statwww.epfl.ch/davison/SM/}.") (license license:gpl2+))) (define-public r-fgui (package (name "r-fgui") (version "1.0-8") (source (origin (method url-fetch) (uri (cran-uri "fgui" version)) (sha256 (base32 "024fzd1c7iwqprn26hwjb9l2qlvvyzl449d7iixy0x69djwsrysv")))) (properties `((upstream-name . "fgui"))) (build-system r-build-system) (home-page "https://sites.google.com/site/thomashoffmannproject/software/fgui") (synopsis "Create GUI for R functions") (description "Rapidly create a GUI for a function you created by automatically creating widgets for arguments of the function. This package automatically parses help routines for context-sensitive help to these arguments. The interface is essentially a wrapper to some Tcl/Tk routines to both simplify and facilitate GUI creation. More advanced Tcl/Tk routines/GUI objects can be incorporated into the interface for greater customization for the more experienced.") ;; Any version of the GPL. (license (list license:gpl2+ license:gpl3+)))) (define-public r-tcltk2 (package (name "r-tcltk2") (version "1.2-11") (source (origin (method url-fetch) (uri (cran-uri "tcltk2" version)) (sha256 (base32 "1ibxld379600xx7kiqq3fck083s8psry12859980218rnzikl65d")))) (properties `((upstream-name . "tcltk2"))) (build-system r-build-system) (inputs (list tcl tk)) (home-page "https://www.sciviews.org/SciViews-R") (synopsis "Tcl/Tk additions") (description "This package provides a series of additional Tcl commands and Tk widgets with style and various functions to supplement the tcltk package") (license license:lgpl3))) (define-public r-accrual (package (name "r-accrual") (version "1.3") (source (origin (method url-fetch) (uri (cran-uri "accrual" version)) (sha256 (base32 "11clm9s5c5518nmp6hd6pjnp0s28y92b2i2x0xgj4j5g816p4j3z")))) (properties `((upstream-name . "accrual"))) (build-system r-build-system) (propagated-inputs (list r-fgui r-smpracticals r-tcltk2)) (home-page "https://cran.r-project.org/web/packages/accrual/") (synopsis "Bayesian accrual prediction") (description "Subject recruitment for medical research is challenging. Slow patient accrual leads to delay in research. Accrual monitoring during the process of recruitment is critical. Researchers need reliable tools to manage the accrual rate. This package provides an implementation of a Bayesian method that integrates researcher's experience on previous trials and data from the current study, providing reliable prediction on accrual rate for clinical studies. It provides functions for Bayesian accrual prediction which can be easily used by statisticians and clinical researchers.") (license license:gpl2))) (define-public r-accrued (package (name "r-accrued") (version "1.4.1") (source (origin (method url-fetch) (uri (cran-uri "accrued" version)) (sha256 (base32 "05g1jb5914z18rcai1ahn7nihn27vr2rnadwv94gc1j7ivvikvs5")))) (properties `((upstream-name . "accrued"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/accrued/") (synopsis "Data quality visualization tools for partially accruing data") (description "This is a package for visualizing data quality of partially accruing data.") (license license:gpl3))) (define-public r-mda (package (name "r-mda") (version "0.5-3") (source (origin (method url-fetch) (uri (cran-uri "mda" version)) (sha256 (base32 "0qw4scc2w7jmnxssj5w2mdxb9rrl4dscqn54gplzm1gk2yf419mx")))) (properties `((upstream-name . "mda"))) (build-system r-build-system) (propagated-inputs (list r-class)) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/mda/") (synopsis "Mixture and flexible discriminant analysis") (description "This is a package for mixture and flexible discriminant analysis, @dfn{multivariate adaptive regression splines} (MARS), BRUTO, and so on.") (license license:gpl2))) (define-public r-elasticnet (package (name "r-elasticnet") (version "1.3") (source (origin (method url-fetch) (uri (cran-uri "elasticnet" version)) (sha256 (base32 "0nxcw06d0cp2mbqzg2fm9yys5xm6xx7bfcfvr0avcs8afkvz29j8")))) (properties `((upstream-name . "elasticnet"))) (build-system r-build-system) (propagated-inputs (list r-lars)) (home-page "http://users.stat.umn.edu/~zouxx019/") (synopsis "Elastic-Net for sparse estimation and sparse PCA") (description "This package provides functions for fitting the entire solution path of the Elastic-Net and also provides functions for estimating sparse Principal Components. The Lasso solution paths can be computed by the same function.") (license license:gpl2+))) (define-public r-sparselda (package (name "r-sparselda") (version "0.1-9") (source (origin (method url-fetch) (uri (cran-uri "sparseLDA" version)) (sha256 (base32 "1k3sw9kc40yxnfss4vrsx34qxmv8ssddyhbfjhxrdldvblhbwchb")))) (properties `((upstream-name . "sparseLDA"))) (build-system r-build-system) (propagated-inputs (list r-elasticnet r-mass r-mda)) (home-page "https://www.imm.dtu.dk/~lkhc/") (synopsis "Sparse discriminant analysis") (description "This package performs sparse linear discriminant analysis for Gaussians and mixture of Gaussian models.") (license license:gpl2+))) (define-public r-accsda (package (name "r-accsda") (version "1.1.2") (source (origin (method url-fetch) (uri (cran-uri "accSDA" version)) (sha256 (base32 "0jf4x5j9y7a3mvf2ghjp6bxdq1s5jh2sx3x3ar6f3lyzzvrnls4v")))) (properties `((upstream-name . "accSDA"))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-ggthemes r-gridextra r-mass)) (home-page "https://github.com/gumeo/accSDA/wiki") (synopsis "Accelerated sparse discriminant analysis") (description "This package provides an implementation of sparse linear discriminant analysis, which is a supervised classification method for multiple classes. Various novel optimization approaches to this problem are implemented including @dfn{alternating direction method of multipliers} (ADMM), @dfn{proximal gradient} (PG) and @dfn{accelerated proximal gradient} (APG). Functions for performing cross validation are also supplied along with basic prediction and plotting functions. @dfn{Sparse zero variance discriminant} (SZVD) analysis is also included in the package.") (license license:gpl2+))) (define-public r-ace2fastq (package (name "r-ace2fastq") (version "0.6.0") (source (origin (method url-fetch) (uri (cran-uri "ace2fastq" version)) (sha256 (base32 "09kk3yyqnr2xp820g0p3aai9a21figigjr9lxkr3zjq2d8gzwfic")))) (properties `((upstream-name . "ace2fastq"))) (build-system r-build-system) (propagated-inputs (list r-stringr)) (home-page "https://github.com/c5sire/ace2fastq") (synopsis "ACE file to FASTQ converter") (description "The ACE file format is used in genomics to store contigs from sequencing machines. This tools converts it into FASTQ format. Both formats contain the sequence characters and their corresponding quality information. Unlike the FASTQ file, the ACE file stores the quality values numerically. The conversion algorithm uses the standard Sanger formula. The package facilitates insertion into pipelines, and content inspection.") (license license:gpl3))) (define-public r-rngwell (package (name "r-rngwell") (version "0.10-7") (source (origin (method url-fetch) (uri (cran-uri "rngWELL" version)) (sha256 (base32 "0f1dxxaimfb0fww8ym9ciqf6q760ai46wxldl37m5mfpd57ca00c")))) (properties `((upstream-name . "rngWELL"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/rngWELL/") (synopsis "Toolbox for WELL random number generators") (description "This is a dedicated package to WELL pseudo random generators, which were introduced in Panneton et al. (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 "2.0.2") (source (origin (method url-fetch) (uri (cran-uri "randtoolbox" version)) (sha256 (base32 "0mvafd2gm1jpg19gdn6bw8668pqghi0xmcb56rl4fwamg8jg09xn")))) (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 "1.1.5") (source (origin (method url-fetch) (uri (cran-uri "lhs" version)) (sha256 (base32 "0fb3bc3s5pbwg92qkjbg7v8ah36wm6qs05vf098hwjakr7f6yg3s")))) (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 "1.8.1") (source (origin (method url-fetch) (uri (cran-uri "ACEt" version)) (sha256 (base32 "0b5lfpnppyk0237phr2aybhx29nhm8ngwk2qa1y4lshrvsw97wg4")))) (properties `((upstream-name . "ACEt"))) (build-system r-build-system) (propagated-inputs (list r-bh r-mass r-rcpp r-rcpparmadillo)) (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}.") 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"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 "1.0.2") (source (origin (method url-fetch) (uri (cran-uri "filelock" version)) (sha256 (base32 "00ql5fw1hidpfnm0szaavf43ahmsnvdbi8i5lr1nrcc90yaiaadc")))) (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-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 "0.9.0") (source (origin (method url-fetch) (uri (cran-uri "R.huge" version)) (sha256 (base32 "13p558qalv60pgr24nsm6mi92ryj65rsbqa6pgdwy0snjqx12bgi")))) (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 "2.15.0") (source (origin (method url-fetch) (uri (cran-uri "R.filesets" version)) (sha256 (base32 "14dngx6ffhfvlaixpvlq890nwgil6zyaw8wy3dlcrv001wynzmms")))) (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 "2.17.1") (source (origin (method url-fetch) (uri (cran-uri "R.devices" version)) (sha256 (base32 "02cwdhb9m97gxi4pki4kasc5j3a12r7yzsychzzk9h0ijc1mfziv")))) (properties `((upstream-name . "R.devices"))) (build-system r-build-system) (propagated-inputs (list r-base64enc r-r-methodss3 r-r-oo r-r-utils)) (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 "0.9.3") (source (origin (method url-fetch) (uri (cran-uri "acopula" version)) (sha256 (base32 "0vvbbw8pfs9jwfz5c57lw48pr0qj661r0ys007q6zf9jmlrhx1ln")))) (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 "1.4.0") (source (origin (method url-fetch) (uri (cran-uri "tuneR" version)) (sha256 (base32 "1sd0drxzbdy71bh35fccg9ajhpdhdpy0m9nja2lw82p1pzhyl7jn")))) (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 "2.2.0") (source (origin (method url-fetch) (uri (cran-uri "seewave" version)) (sha256 (base32 "0bi1l47l3846c18k6h2vrv0xp9xh00n544a578jrndahzrj1hfwl")))) (properties `((upstream-name . "seewave"))) (build-system r-build-system) (inputs (list libsndfile)) (propagated-inputs (list r-tuner)) (home-page "http://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-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 "1.0-42") (source (origin (method url-fetch) (uri (cran-uri "tree" version)) (sha256 (base32 "1q3jgkhl5d4d8c396cyvkw60094p0z0a3x7xwhdbi8gl4c2c65ss")))) (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-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 "2022.4-1") (source (origin (method url-fetch) (uri (cran-uri "alabama" version)) (sha256 (base32 "0v6kl6ndm8wvp9xzya3x4gj5kh03qgx13x5vyzn410wsndcjiim8")))) (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 "2.9.3") (source (origin (method url-fetch) (uri (cran-uri "GDINA" version)) (sha256 (base32 "0bwg9sfsqs5nsqwhjnbb631fbhj0mx2dc4c185qkym9cjb5lfkm9")))) (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 "1.2-0") (source (origin (method url-fetch) (uri (cran-uri "ACTCD" version)) (sha256 (base32 "0mzjxxr2zfdidw8ibh6w8mvpkw3q3nvngqi05g9ind26ckvk053p")))) (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 "http://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 "3.6") (source (origin (method url-fetch) (uri (cran-uri "rainbow" version)) (sha256 (base32 "11vfcck17d2xjc049ci5i8l1nqv345anmd110gdz7654i1pj9lb3")))) (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 "6.0.5") (source (origin (method url-fetch) (uri (cran-uri "fda" version)) (sha256 (base32 "1wdq35acxavarh7qrxxmdpcjc9jcs56mp3p9rbb4qa35ziv5fi0l")))) (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 "0.1-7") (source (origin (method url-fetch) (uri (cran-uri "expint" version)) (sha256 (base32 "01d0a7pc4qx7044a0cymnv5ld88r90vdvlqjbnzg9qlfbizdgyvw")))) (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 "3.3-0") (source (origin (method url-fetch) (uri (cran-uri "actuar" version)) (sha256 (base32 "1qi9y2x93pxxbynwl06rbiasm86vb0jh7sckw1dw3s21rsx1f5c5")))) (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 "0.42.13") (source (origin (method url-fetch) (uri (cran-uri "imager" version)) (sha256 (base32 "0zygnmxwbbmj5i2l2affzdz90xvsa7b5pbkzkhjbm40is69rh2nr")))) (properties `((upstream-name . "imager"))) (build-system r-build-system) (inputs (list fftw libtiff libx11 zlib)) (propagated-inputs (list r-downloader r-igraph r-jpeg r-magrittr r-png r-purrr r-rcpp r-readbitmap r-stringr)) (native-inputs (list pkg-config r-knitr)) (home-page "https://dahtah.github.io/imager/") (synopsis "Image processing library") (description "This is a package for fast image processing for images in up to 4 dimensions (two spatial dimensions, one time/depth dimension, one color dimension). It provides most traditional image processing tools (filtering, morphology, transformations, etc.) as well as various functions for easily analyzing image data using R. The package wraps @url{http://cimg.eu, CImg}, a simple, modern C++ library for image processing.") (license license:lgpl3))) (define-public r-acuityview (package (name "r-acuityview") (version "0.1") (source (origin (method url-fetch) (uri (cran-uri "AcuityView" version)) (sha256 (base32 "0f0iclmnwdc8ixiiai4svk4x1g3pjy7dhm3cm58fv6ckx12d3d2l")))) (properties `((upstream-name . "AcuityView"))) (build-system r-build-system) (propagated-inputs (list r-fftwtools r-imager r-plotrix)) (home-page "https://cran.r-project.org/web/packages/AcuityView/") (synopsis "Display scenes as seen by an animal with less acute vision") (description "This package provides a simple method for representing a visual scene as it may be seen by an animal with less acute vision.") (license license:gpl2+))) (define-public r-caret (package (name "r-caret") (version "6.0-93") (source (origin (method url-fetch) (uri (cran-uri "caret" version)) (sha256 (base32 "01sa1h9pc3a062pwm0rxadvg9qxszwcylya7llv08fcxhy46n5ac")))) (build-system r-build-system) (propagated-inputs (list r-e1071 r-foreach r-ggplot2 r-lattice r-modelmetrics r-nlme r-plyr r-proc r-recipes r-reshape2 r-withr)) (native-inputs (list r-knitr)) (home-page "https://github.com/topepo/caret") (synopsis "Classification and regression training") (description "This package provides miscellaneous functions for training and plotting classification and regression models.") (license license:gpl2+))) (define-public r-adabag (package (name "r-adabag") (version "4.2") (source (origin (method url-fetch) (uri (cran-uri "adabag" version)) (sha256 (base32 "109wrl1pwvmyv2l909hrvk7dg4aa9pv449mvdycp50zwrsw9w0a7")))) (properties `((upstream-name . "adabag"))) (build-system r-build-system) (propagated-inputs (list r-caret r-doparallel r-foreach r-rpart)) (home-page "https://cran.r-project.org/web/packages/adabag/") (synopsis "Multiclass AdaBoost.M1, SAMME and Bagging") (description "This package implements Freund and Schapire's Adaboost.M1 algorithm and Breiman's Bagging algorithm using classification trees as individual classifiers. Once these classifiers have been trained, they can be used to predict on new data. Also, cross validation estimation of the error can be done.") (license license:gpl2+))) (define-public r-adagio (package (name "r-adagio") (version "0.8.4") (source (origin (method url-fetch) (uri (cran-uri "adagio" version)) (sha256 (base32 "0ihv05402iq003m0338f85pnqnlnrmx0pf1mg8cz9sgi5h98mbnl")))) (properties `((upstream-name . "adagio"))) (build-system r-build-system) (propagated-inputs (list r-lpsolve)) (home-page "https://cran.r-project.org/web/packages/adagio/") (synopsis "Discrete and global optimization routines") (description "This package provides methods and algorithms for discrete optimization, e.g. knapsack and subset sum procedures, derivative-free Nelder-Mead and Hooke-Jeeves minimization, and some (evolutionary) global optimization functions.") (license license:gpl3+))) (define-public r-univoutl (package (name "r-univoutl") (version "0.4") (source (origin (method url-fetch) (uri (cran-uri "univOutl" version)) (sha256 (base32 "1kp014bhs8v02fp7misrj4fpfp2na9lg45p5zqvlfaypnm5imsr9")))) (properties `((upstream-name . "univOutl"))) (build-system r-build-system) (propagated-inputs (list r-hmisc r-robustbase)) (home-page "https://github.com/marcellodo/univOutl") (synopsis "Detection of univariate outliers") (description "This package provides well-known outlier detection techniques in the univariate case. Methods to deal with skewed distribution are included too. The Hidiroglou-Berthelot (1986) method to search for outliers in ratios of historical data is implemented as well. When available, survey weights can be used in outliers detection.") (license license:gpl2+))) (define-public r-tolerance (package (name "r-tolerance") (version "2.0.0") (source (origin (method url-fetch) (uri (cran-uri "tolerance" version)) (sha256 (base32 "001snzr2ipag3zprynydlbi9prkjzrllc054qh7m0qwkb3r19jjd")))) (properties `((upstream-name . "tolerance"))) (build-system r-build-system) (propagated-inputs (list r-mass r-rgl)) (home-page "https://cran.r-project.org/web/packages/tolerance/") (synopsis "Statistical tolerance intervals and regions") (description "This package provides functions for estimating tolerance limits (intervals) for various univariate distributions (binomial, Cauchy, discrete Pareto, exponential, two-parameter exponential, extreme value, hypergeometric, Laplace, logistic, negative binomial, negative hypergeometric, normal, Pareto, Poisson-Lindley, Poisson, uniform, and Zipf-Mandelbrot), Bayesian normal tolerance limits, multivariate normal tolerance regions, nonparametric tolerance intervals, tolerance bands for regression settings (linear regression, nonlinear regression, nonparametric regression, and multivariate regression), and analysis of variance tolerance intervals. Visualizations are also available for most of these settings.") (license license:gpl2+))) ;; Keep this in sync with the liblantern package. (define-public r-torch (package (name "r-torch") (version "0.8.1") (source (origin (method url-fetch) (uri (cran-uri "torch" version)) (sha256 (base32 "1dncf5njdzw1hf98knlv94rxcxnc5gl3cmk2cvlbn1z8mri86rlc")))) (properties `((upstream-name . "torch"))) (build-system r-build-system) (arguments (list #:phases (let ((python-version (version-major+minor (package-version python)))) #~(modify-phases %standard-phases (add-after 'install 'link-libraries (lambda* (#:key inputs #:allow-other-keys) (let ((deps (string-append #$output "/site-library/torch/deps")) (site-packages (string-append "/lib/python" #$python-version "/site-packages"))) (mkdir-p deps) (symlink (search-input-file inputs (string-append site-packages "/torch/lib/libtorch.so")) (string-append deps "/libtorch.so")) (symlink (search-input-file inputs "/lib/liblantern.so") (string-append deps "/liblantern.so"))))))))) (inputs (list python-pytorch-for-r-torch liblantern)) (propagated-inputs (list r-bit64 r-callr r-cli r-coro r-ellipsis r-magrittr r-r6 r-rcpp r-rlang r-withr)) (native-inputs (list r-knitr)) (home-page "https://torch.mlverse.org/docs") (synopsis "Tensors and neural networks with GPU acceleration") (description "This package provides functionality to define and train neural networks similar to PyTorch but written entirely in R using the libtorch library. It also supports low-level tensor operations and GPU acceleration.") (license license:expat))) (define-public r-additivitytests (package (name "r-additivitytests") (version "1.1-4.1") (source (origin (method url-fetch) (uri (cran-uri "additivityTests" version)) (sha256 (base32 "00kzfv86z6kk0gvbz9mg3p6xi5fb8cn74rhslr17rdpd02md0884")))) (properties `((upstream-name . "additivityTests"))) (build-system r-build-system) (native-inputs (list r-knitr)) (home-page "https://github.com/simecek/additivityTests") (synopsis "Additivity tests in the two way Anova with single sub-class numbers") (description "This package provides an implementation of the Tukey, Mandel, Johnson-Graybill, LBI, Tusell and modified Tukey non-additivity tests.") (license license:gpl3))) (define-public r-flexclust (package (name "r-flexclust") (version "1.4-1") (source (origin (method url-fetch) (uri (cran-uri "flexclust" version)) (sha256 (base32 "13akk3w6a76jpws5v9108c3hdmb8i6gm0sc06lr2hqly0pgpfyfn")))) (properties `((upstream-name . "flexclust"))) (build-system r-build-system) (propagated-inputs (list r-class r-lattice r-modeltools)) (home-page "https://cran.r-project.org/web/packages/flexclust/") (synopsis "Flexible cluster algorithms") (description "The main function @code{kcca} implements a general framework for k-centroids cluster analysis supporting arbitrary distance measures and centroid computation. Further cluster methods include hard competitive learning, neural gas, and QT clustering. There are numerous visualization methods for cluster results (neighborhood graphs, convex cluster hulls, barcharts of centroids, ...), and bootstrap methods for the analysis of cluster stability.") 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Functions are optimised for large sparse matrices using the Armadillo and Intel TBB libraries. Among several built-in similarity/distance measures, computation of correlation, cosine similarity and Euclidean distance is particularly fast.") (license license:gpl3))) (define-public r-isocodes (package (name "r-isocodes") (version "2022.01.10") (source (origin (method url-fetch) (uri (cran-uri "ISOcodes" version)) (sha256 (base32 "0gy7n5bgxnl4rawry0pg078bkks9lzsbsrwjq8q5cvxl4k3dwpdj")))) (properties `((upstream-name . "ISOcodes"))) (build-system r-build-system) (home-page "https://cran.r-project.org/package=ISOcodes") (synopsis "Selected ISO codes") (description "This package provides ISO language, territory, currency, script and character codes. It provides ISO 639 language codes, ISO 3166 territory codes, ISO 4217 currency codes, ISO 15924 script codes, and the ISO 8859 character codes as well as the UN M.49 area codes.") (license license:gpl2))) (define-public r-stopwords (package (name "r-stopwords") (version "2.3") (source (origin (method url-fetch) (uri (cran-uri "stopwords" version)) (sha256 (base32 "1ci1cgxrcvlhhplximsfv0plvjdbcd5kv0nphxnpildsn5m1rv65")))) (properties `((upstream-name . "stopwords"))) (build-system r-build-system) (propagated-inputs (list r-isocodes)) (home-page "https://github.com/quanteda/stopwords") (synopsis "Multilingual stopword lists") (description "This package provides multiple sources of stopwords, for use in text analysis and natural language processing.") (license license:expat))) (define-public r-spacyr (package (name "r-spacyr") (version "1.2.1") (source (origin (method url-fetch) (uri (cran-uri "spacyr" version)) (sha256 (base32 "1b2ccgwsiqkvp7w37x8k7699c676q16vfrybkrfvyczyhki4s6nw")))) (properties `((upstream-name . "spacyr"))) (build-system r-build-system) (propagated-inputs (list r-data-table r-reticulate)) (home-page "https://spacyr.quanteda.io") (synopsis "R wrapper for the spaCy NLP library") (description "This package provides an R wrapper to the Python @dfn{natural language processing} (NLP) library @code{spaCy}, from @url{http://spacy.io}.") (license license:gpl3))) (define-public r-snowballc (package (name "r-snowballc") (version "0.7.0") (source (origin (method url-fetch) (uri (cran-uri "SnowballC" version)) (sha256 (base32 "1wwm71mp4b2mjb5985x782p6xj519dfrpd40qli7lmig6afyw3xi")))) (properties `((upstream-name . 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(license license:gpl2+))) (define-public r-stanheaders (package (name "r-stanheaders") (version "2.21.0-7") (source (origin (method url-fetch) (uri (cran-uri "StanHeaders" version)) (sha256 (base32 "0srkyawyiykn3p5lw1z3zf18s4ax4iasv1ci3l1px40f9w36wm17")))) (properties `((upstream-name . "StanHeaders"))) (build-system r-build-system) (inputs (list pandoc)) (propagated-inputs (list r-rcppeigen r-rcppparallel)) (native-inputs (list gfortran r-knitr)) ; for vignettes (home-page "https://mc-stan.org/") (synopsis "C++ header files for Stan") (description "The C++ header files of the Stan project are provided by this package. There is a shared object containing part of the @code{CVODES} library, but it is not accessible from R. @code{r-stanheaders} is only useful for developers who want to utilize the @code{LinkingTo} directive of their package's DESCRIPTION file to build on the Stan library without incurring unnecessary dependencies. 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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 "1.5.7") (source (origin (method url-fetch) (uri (cran-uri "gaston" version)) (sha256 (base32 "14z94dpln4dvgrv2w7w9ik7h6rpvbf02qhq1hqzx8c2cndzxr21i")))) (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). 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(license license:gpl2))) (define-public r-clusterr (package (name "r-clusterr") (version "1.2.6") (source (origin (method url-fetch) (uri (cran-uri "ClusterR" version)) (sha256 (base32 "00mha8madcba83ix4fc04rb7sagfm0lxlh1wvs7dvjdrngps41jr")))) (properties `((upstream-name . "ClusterR"))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-gmp r-gtools 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-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 "0.3.1") (source (origin (method url-fetch) (uri (cran-uri "config" version)) (sha256 (base32 "0l2zp7v6qaz72dclcbjrlis633zlwp8rsi5azr7iw127iyz7i26l")))) (properties `((upstream-name . 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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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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 "0.28") (source (origin (method url-fetch) (uri (cran-uri "qtl2" version)) (sha256 (base32 "0ppc6dzlq77mppxc6bczai9gi40jrbxd1466y2cn2s8a4ah1jg9y")))) (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. 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(license license:gpl3)))) (define-public r-phangorn (package (name "r-phangorn") (version "2.10.0") (source (origin (method url-fetch) (uri (cran-uri "phangorn" version)) (sha256 (base32 "1kjxp352jdk1amxpk9jrql490d0qy79zm65y8szyxrm1adqghlyi")))) (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.") 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(license license:lgpl3))) (define-public r-mlr3pipelines (package (name "r-mlr3pipelines") (version "0.4.1") (source (origin (method url-fetch) (uri (cran-uri "mlr3pipelines" version)) (sha256 (base32 "1zz55i8c08znxpcs6gp5inaw96c6la9wnsla0972ankvj1hsrcr2")))) (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)) (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 "0.10.0") (source (origin (method url-fetch) (uri (cran-uri "paradox" version)) (sha256 (base32 "08h92wk8splf0w3rach9zbk3xz13phgcd1yybmgbs0sj4vx93whd")))) (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 "0.14.0") (source (origin (method url-fetch) (uri (cran-uri "mlr3" version)) (sha256 (base32 "0cnyby4947g1w0h45nd3ld5zr4k19xrwp565mq1hnqkjwmyjsgdj")))) (build-system r-build-system) (propagated-inputs (list r-r6 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-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 "0.5.4") (source (origin (method url-fetch) (uri (cran-uri "mlr3learners" version)) (sha256 (base32 "0sa2qjvhvjzsfssln9ah08zknzdcps1z28xzgkdfgi6dj25a0y3k")))) (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 "0.5.4") (source (origin (method url-fetch) (uri (cran-uri "bbotk" version)) (sha256 (base32 "02dp0b62dv02rvxsgj63mkmmcdzrlf06vxjr5gqy9rhq5s2mg4fa")))) (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 "0.14.0") (source (origin (method url-fetch) (uri (cran-uri "mlr3tuning" version)) (sha256 (base32 "10q4m37sg79y1v0gwk7bjrnc5b0a6sb80ramnza93mx9gx3vl99m")))) (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)) (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 "1.0.4") (source (origin (method url-fetch) (uri (cran-uri "vdiffr" version)) (sha256 (base32 "1z8nn8yh6jfzb9r7ylmigwh1p30lrclqm6khmp323qqphzmzfdwy")))) (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 "0.5.0") (source (origin (method url-fetch) (uri (cran-uri "highlight" version)) (sha256 (base32 "1shar4y07wyixg0ichdrn2xhgwkl3mv2pxkalqzisc69w605b3hf")))) (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 "0.5.0") (source (origin (method url-fetch) (uri (cran-uri "clustree" version)) (sha256 (base32 "1haam13aifak8fladyxwa0gz56anj1zfczfjgs07gbw90kf6azx8")))) (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 "0.3.6") (source (origin (method url-fetch) (uri (cran-uri "textshaping" version)) (sha256 (base32 "1niaj1dh09rqrg9hrh98ddnc0f2nkyq9iizv24lcwm9gjs3w1ql0")))) (properties `((upstream-name . "textshaping"))) (build-system r-build-system) (inputs (list freetype fribidi harfbuzz zlib)) (propagated-inputs (list r-cpp11 r-systemfonts)) (native-inputs (list pkg-config r-knitr)) (home-page "https://github.com/r-lib/textshaping") (synopsis "Bindings to the HarfBuzz and Fribidi libraries for text shaping") (description "This package provides access to the text shaping functionality in the HarfBuzz library and the bidirectional algorithm in the Fribidi library. This is a low-level utility package mainly for graphic devices that expands upon the font tool-set provided by the @code{systemfonts} package.") (license license:expat))) (define-public r-ragg (package (name "r-ragg") (version "1.2.2") (source (origin (method url-fetch) (uri (cran-uri "ragg" version)) (sha256 (base32 "1q43pwmljsqgrikkh2g1n7bpz9c8py5dnj44cfg3y2br7b4m2q9v")))) (properties `((upstream-name . "ragg"))) (build-system r-build-system) (inputs (list freetype libjpeg-turbo libpng libtiff zlib)) (propagated-inputs (list r-systemfonts r-textshaping)) (native-inputs (list pkg-config)) (home-page "https://ragg.r-lib.org") (synopsis "Graphic devices based on AGG") (description "Anti-Grain Geometry (AGG) is a high-quality and high-performance 2D drawing library. The ragg package provides a set of graphic devices based on AGG to use as alternative to the raster devices provided through the @code{grDevices} package.") (license license:expat))) (define-public r-downlit (package (name "r-downlit") (version "0.4.2") (source (origin (method url-fetch) (uri (cran-uri "downlit" version)) (sha256 (base32 "0g3yncj3gmaqsc6cw7g9slgvd0kfk2414yz5m1dilk8h15lzdprk")))) (properties `((upstream-name . "downlit"))) (build-system r-build-system) (propagated-inputs (list r-brio r-desc r-digest r-evaluate r-fansi r-memoise r-rlang r-vctrs r-withr r-yaml)) (home-page "https://downlit.r-lib.org/") (synopsis "Syntax highlighting and automatic linking") (description "This package provides syntax highlighting of R code, specifically designed for the needs of RMarkdown packages like @code{pkgdown}, @code{hugodown}, and @code{bookdown}. It includes linking of function calls to their documentation on the web, and automatic translation of ANSI escapes in output to the equivalent HTML.") (license license:expat))) (define-public r-pkgdown (package (name "r-pkgdown") (version "2.0.6") (source (origin (method url-fetch) (uri (cran-uri "pkgdown" version)) (sha256 (base32 "0sbz3kzd0hbdnszylsb281arldn2z1c9yxifhj4zv2dilp46b6nj")))) (properties `((upstream-name . "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-generic-iftex texlive-latex-fancyhdr texlive-latex-fancyvrb texlive-latex-geometry texlive-latex-graphics texlive-latex-threeparttable texlive-latex-titlesec texlive-latex-upquote texlive-listings texlive-polyglossia texlive-titling texlive-tools texlive-ulem (texlive-updmap.cfg (list texlive-amsfonts 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 "0.7.5") (source (origin (method url-fetch) (uri (cran-uri "qdapRegex" version)) (sha256 (base32 "1hdilycwrvi0q6cx7k8vg87bamm2xsafjkya5x4smxysm5k1r4qb")))) (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 "1.7.3") (source (origin (method url-fetch) (uri (cran-uri "textshape" version)) (sha256 (base32 "0k9injxykgj2qprc7dygd7gafvcbh3r9x84qzaa1al21pk0dz7ds")))) (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 "1.0.6") (source (origin (method url-fetch) (uri (cran-uri "syuzhet" version)) (sha256 (base32 "16iccqdbw02iw82nah6kwz3gwfghi864j2y698n4b9dyc386ijzv")))) (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 "0.5.3") (source (origin (method url-fetch) (uri (cran-uri "striprtf" version)) (sha256 (base32 "0dqcsh3fb8j0mmmxvxjl77rryhmrjm7a3scqvk2xkgxk4xq6q316")))) (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 "0.8.0") (source (origin (method url-fetch) (uri (cran-uri "ndjson" version)) (sha256 (base32 "0lvzbgfi1sg4kya1mvv67z14qk3vz9q57x22qh57xq8ampdkg812")) (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-readods (package (name "r-readods") (version "1.7.0") (source (origin (method url-fetch) (uri (cran-uri "readODS" version)) (sha256 (base32 "1hi217ab7hp15jsbzi5ak57cqf8jn2rv78bnn74q72gn9mrfra7n")))) (properties `((upstream-name . "readODS"))) (build-system r-build-system) (propagated-inputs (list r-cellranger r-readr r-stringi r-xml2)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/package=readODS") (synopsis "Read and Write ODS Files") (description "Import @dfn{OpenDocument Spreadsheet} (ODS) into R as a data frame. Also support writing data frame into ODS file.") (license license:gpl3))) (define-public r-qpdf (package (name "r-qpdf") (version "1.2.0") (source (origin (method url-fetch) (uri (cran-uri "qpdf" version)) (sha256 (base32 "1a1d7zad2l94z068mic6dg9wr9bq8mlmqszrj8vxps1441mb6gfh")) (modules '((guix build utils))) (snippet '(begin ;; unvendor libqpdf (delete-file-recursively "src/libqpdf") (delete-file-recursively "src/include/qpdf"))))) (properties `((upstream-name . "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 "0.4-4") (source (origin (method url-fetch) (uri (cran-uri "pbdMPI" version)) (sha256 (base32 "006pm2yn4mdrpwhfflqcybzv41lz7zssrjrcpq5g98zf60p9c07a")))) (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 r-rlecuyer)) (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 "3.3.0") (source (origin (method url-fetch) (uri (cran-uri "pdftools" version)) (sha256 (base32 "151f7vaznxigwka4qhp17v4gnahm245rfgcvb8j132vix7md44q9")))) (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 "1.3.1") (source (origin (method url-fetch) (uri (cran-uri "antiword" version)) (sha256 (base32 "123v8zlczwh6fr1v3x7dl3885xlmddq1bqlcxih8zh07w0hlk1k2")) (modules '((guix build utils))) (snippet '(begin ;; unvendor libantiword (delete-file-recursively "src") #t)))) (properties `((upstream-name . "antiword"))) (build-system r-build-system) (arguments '(#:phases (modify-phases %standard-phases (add-after 'unpack 'use-system-antiword (lambda* (#:key inputs #:allow-other-keys) (substitute* "R/antiword.R" (("system.file\\(\"bin\", package = \"antiword\"\\)") (string-append "\"" (assoc-ref inputs "antiword") "/bin\""))) #t))))) (inputs (list antiword)) (propagated-inputs (list r-sys)) (home-page "https://github.com/ropensci/antiword#readme") (synopsis "Extract Text from Microsoft Word Documents") (description "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 "0.81") (source (origin (method url-fetch) (uri (cran-uri "readtext" version)) (sha256 (base32 "0k782h5hns5v5h8a6qyfqck2hc15nq0awg8bsp196q4zviv5jw3c")))) (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-readods r-readxl r-streamr r-stringi r-striprtf r-tibble 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 "0.3.4") (source (origin (method url-fetch) (uri (cran-uri "packcircles" version)) (sha256 (base32 "05pv5c4k4njkr0xw6i6ksiy34hcyx2lbiqpv5gxw81yrkm0rxfyk")))) (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 "0.2-8") (source (origin (method url-fetch) (uri (cran-uri "lwgeom" version)) (sha256 (base32 "0d4b1djwrzla91mmyya2m1250mb44fzmq3d36w5mk81d4bg952pl")))) (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 "0.5-6") (source (origin (method url-fetch) (uri (cran-uri "stars" version)) (sha256 (base32 "0qcli9bangpym4yp96yfibd5f4li5qw1622jnbvzfd9n8aakqhg0")))) (properties `((upstream-name . "stars"))) (build-system r-build-system) (propagated-inputs (list r-abind r-classint r-lwgeom 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 "1.3-6") (source (origin (method url-fetch) (uri (cran-uri "rworldmap" version)) (sha256 (base32 "1q1h0n9qr0m5pdx10swrh9ddsvdj8kv5nqngrf3lnx9rg9iwivjk")))) (properties `((upstream-name . "rworldmap"))) (build-system r-build-system) (propagated-inputs (list r-fields r-maptools r-sp)) (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 "1.0.2") (source (origin (method url-fetch) (uri (cran-uri "rtweet" version)) (sha256 (base32 "1dhdq2c2zl88h29caqpm7zh2i5970q7rfg98zf2xb7x4zak7bq9x")))) (properties `((upstream-name . "rtweet"))) (build-system r-build-system) (propagated-inputs (list r-bit64 r-curl r-httr 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 "0.15.2") (source (origin (method url-fetch) (uri (cran-uri "intervals" version)) (sha256 (base32 "0mvwfwc03ifb30a3dzbmkv9adwqb8ajxhcw24d8xip8px063plhb")))) (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 "0.3.6") (source (origin (method url-fetch) (uri (cran-uri "BTM" version)) (sha256 (base32 "0ab0wr8nbwn1w1j9hpwfz52lm1sw0qk93713y9k0hpm3pw9dq4jr")))) (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 "8.0.3") (source (origin (method url-fetch) (uri (cran-uri "Delaporte" version)) (sha256 (base32 "1d1jkbxlwnqznh9pkjpkr7np2nmqzjvrdmlb210y1lb08mqmb73w")))) (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 "1.3-1.6") (source (origin (method url-fetch) (uri (cran-uri "RJSONIO" version)) (sha256 (base32 "17x0ayk7daprbc8w2hvb2jl9mfnw4dic9yc3sr5adcjqfzmcklc2")))) (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 . "GSA"))) (build-system r-build-system) (home-page "https://statweb.stanford.edu/~tibs/GSA/") (synopsis "Gene set analysis") (description "This package lets you determine the significance of pre-defined sets of genes with respect to an outcome variable, such as a group indicator, a quantitative variable or a survival time.") ;; Any version of the LGPL (license license:lgpl3+))) (define-public r-gsalib (package (name "r-gsalib") (version "2.1") (source (origin (method url-fetch) (uri (cran-uri "gsalib" version)) (sha256 (base32 "1k3zjdydzb0dfh1ihih08d4cw6rdamgb97cdqna9mf0qdjc3pcp1")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/gsalib") (synopsis "Utility functions for GATK") (description "This package contains utility functions used by the Genome Analysis Toolkit (GATK) to load tables and plot data. The GATK is a toolkit for variant discovery in high-throughput sequencing data.") (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 "1.0.8") (source (origin (method url-fetch) (uri (cran-uri "gganimate" version)) (sha256 (base32 "1jabs9qr0319w508kdsk5nmzfhl6nzykpp1by7l639yfvrfqcbd1")))) (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-ggplot2 r-glue r-progress r-rlang r-scales r-stringi r-tweenr ;; 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 "0.3.0") (source (origin (method url-fetch) (uri (cran-uri "tzdb" version)) (sha256 (base32 "0f3h4zaf9f4l371k6nc1mq6z2f9aj1vaf2inni8jnsds3zng16b0")))) (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 "1.5.7") (source (origin (method url-fetch) (uri (cran-uri "vroom" version)) (sha256 (base32 "1plz20x6s01gkkcac51lhx4r2s024pgh778ri7y25hkiiwacp1yh")))) (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. 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(license license:expat))) (define-public r-opencpu (package (name "r-opencpu") (version "2.2.8") (source (origin (method url-fetch) (uri (cran-uri "opencpu" version)) (sha256 (base32 "1h0s7fbifyf4h1296sdk3amij0m6s12wq32mbky7xg4nz8wj29ni")))) (properties `((upstream-name . "opencpu"))) (build-system r-build-system) (inputs (list pandoc)) (propagated-inputs (list r-brew r-curl r-evaluate r-httpuv r-jsonlite r-knitr r-mime r-openssl r-protolite r-rappdirs r-remotes r-sys r-webutils r-zip)) (native-inputs (list r-knitr)) (home-page "https://www.opencpu.org") (synopsis "API for embedded scientific computing") (description "This package provides a system for embedded scientific computing and reproducible research with R. 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. 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(license license:asl2.0))) (define-public r-paws-compute (package (name "r-paws-compute") (version "0.1.13") (source (origin (method url-fetch) (uri (cran-uri "paws.compute" version)) (sha256 (base32 "1s7g4y2h763xf32p08drs3ygkfqb2zjikkgxb7yl91gk13zp7kjm")))) (properties `((upstream-name . "paws.compute"))) (build-system r-build-system) (propagated-inputs (list r-paws-common)) (home-page "https://github.com/paws-r/paws") (synopsis "Amazon Web Services compute services") (description "This package provides an interface to Amazon Web Services compute services, including Elastic Compute Cloud (EC2), Lambda functions-as-a-service, containers, batch processing, and more.") (license license:asl2.0))) (define-public r-paws (package (name "r-paws") (version "0.1.12") (source (origin (method url-fetch) (uri (cran-uri "paws" version)) (sha256 (base32 "0kn1z045r106fwqcaz52hb02bhrcblh479cajfjiq480s1iljcw6")))) (properties `((upstream-name . "paws"))) (build-system r-build-system) (propagated-inputs (list r-paws-analytics r-paws-application-integration r-paws-compute r-paws-cost-management r-paws-customer-engagement r-paws-database r-paws-developer-tools r-paws-end-user-computing r-paws-machine-learning r-paws-management r-paws-networking r-paws-security-identity r-paws-storage)) (home-page "https://github.com/paws-r/paws") (synopsis "Amazon Web Services software development kit") (description "This package provides an interface to Amazon Web Services, including storage, database, and compute services, such as Simple Storage Service (S3), DynamoDB NoSQL database, and Lambda functions-as-a-service.") (license license:asl2.0))) (define-public r-zoomgroupstats (package (name "r-zoomgroupstats") (version "0.1.0") (source (origin (method url-fetch) (uri (cran-uri "zoomGroupStats" version)) (sha256 (base32 "0gndiq92cy6gi7f833hdjvqii3cn83wz5rjvygcvjl3dw4pwv966")))) (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 "2.4-3") (source (origin (method url-fetch) (uri (cran-uri "filehash" version)) (sha256 (base32 "1ga17smgjd4qsnf5a7qk0giwhpc5969ylqj520favs1k6b4y557k")))) (properties `((upstream-name . "filehash"))) (build-system r-build-system) (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. Utilities are provided that allow filehash databases to be treated much like environments and lists are already used in R. These utilities are provided to encourage interactive and exploratory analysis on large datasets.") (license license:gpl2+))) (define-public r-mlearning (package (name "r-mlearning") (version "1.1.1") (source (origin (method url-fetch) (uri (cran-uri "mlearning" version)) (sha256 (base32 "1zjnh4gcw068li1bks60gazn3205xhmqz67hbkb1san33lmlxya3")))) (properties `((upstream-name . "mlearning"))) (build-system r-build-system) (propagated-inputs (list r-class r-e1071 r-ipred r-mass r-nnet r-randomforest)) (home-page "http://www.sciviews.org/zooimage") (synopsis "Machine learning algorithms with unified interface") (description "This package provides a unified interface to various machine learning algorithms. Confusion matrices are provided too.") (license license:gpl2+))) (define-public r-zooimage (package (name "r-zooimage") (version "5.5.2") (source (origin (method url-fetch) (uri (cran-uri "zooimage" version)) (sha256 (base32 "0ck8w0zb9l1n9xvjwqshq9q9l8pigy3yslq2hnfbgcwk17kk9mp8")))) (properties `((upstream-name . "zooimage"))) (build-system r-build-system) (propagated-inputs (list r-digest r-dt r-filehash r-jpeg r-mass r-mda r-mlearning r-png r-shiny r-svdialogs r-svmisc r-tiff)) (home-page "http://www.sciviews.org/zooimage") (synopsis "Analysis of numerical plankton images") (description "This package provides a solution for analyzing digital images of plankton. In combination with ImageJ, an image analysis system, it processes digital images, measures individuals, trains for automatic classification of taxa, and finally, measures plankton samples (abundances, total and partial size spectra or biomasses, etc.).") (license license:gpl2+))) (define-public r-zooarch (package (name "r-zooarch") (version "1.2") (source (origin (method url-fetch) (uri (cran-uri "zooaRch" version)) (sha256 (base32 "0grc378xppv0303sf4flfqz5002vq5a23nzbq4bsff41rww7dihc")))) (properties `((upstream-name . "zooaRch"))) (build-system r-build-system) (propagated-inputs (list r-ggplot2)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/package=zooaRch") (synopsis "Analytical Tools for Zooarchaeological Data") (description "The analysis and inference of faunal remains recovered from archaeological sites concerns the field of zooarchaeology. The zooaRch package provides analytical tools to make inferences on zooarchaeological data. Functions in this package allow users to read, manipulate, visualize, and analyze zooarchaeological data.") 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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 "1.0-8") (source (origin (method url-fetch) (uri (cran-uri "zoeppritz" version)) (sha256 (base32 "1711szx9zz17q6pfinyzlyrw7m9772c8ywlixqar2l165bkjalgm")))) (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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(license (list license:asl2.0 license:gpl3)))) (define-public r-spacefillr (package (name "r-spacefillr") (version "0.3.0") (source (origin (method url-fetch) (uri (cran-uri "spacefillr" version)) (sha256 (base32 "0c4yasc1zizjmhd2ciyz86lg76fsrxvl19yjkb2fmkda9rmnc0bf")))) (properties `((upstream-name . "spacefillr"))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) (home-page "https://github.com/tylermorganwall/spacefillr") (synopsis "Space-Filling Random and Quasi-Random Sequences") (description "@code{spacefillr} enables generation of random and quasi-random space-filling sequences. It supports the following sequences: Halton, Sobol, Owen-scrambled Sobol, Owen-scrambled Sobol with errors distributed as blue noise, progressive jittered, progressive multi-jittered (PMJ), PMJ with blue noise, PMJ02, and PMJ02 with blue noise. The package also includes a C++ API.") 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