Mirror of GNU Guix
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;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2015 Andreas Enge <andreas@enge.fr>
;;; Copyright © 2016, 2017 Ben Woodcroft <donttrustben@gmail.com>
;;; Copyright © 2016, 2017, 2018, 2020 Roel Janssen <roel@gnu.org>
;;; Copyright © 2017, 2018, 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2017 Raoul Bonnal <ilpuccio.febo@gmail.com>
;;; Copyright © 2018 Vijayalakshmi Vedantham <vijimay12@gmail.com>
;;; Copyright © 2018 Sahithi Yarlagadda <sahi@swecha.net>
;;; Copyright © 2018 Sandeep Subramanian <sandeepsubramanian94@gmail.com>
;;; Copyright © 2018 Charlie Ritter <chewzeirta@posteo.net>
;;; Copyright © 2018 Konrad Hinsen <konrad.hinsen@fastmail.net>
;;; Copyright © 2018, 2020 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
;;; Copyright © 2018 Laura Lazzati <laura.lazzati.15@gmail.com>
;;; Copyright © 2018 Leo Famulari <leo@famulari.name>
;;; Copyright © 2018 Marius Bakke <mbakke@fastmail.com>
;;; Copyright © 2018, 2019 Brett Gilio <brettg@gnu.org>
;;; Copyright © 2019 Nicolò Balzarotti <anothersms@gmail.com>
;;; Copyright © 2019 Wiktor Żelazny <wzelazny@vurv.cz>
;;; Copyright © 2020 Todor Kondić <tk.code@protonmail.com>
;;; Copyright © 2020 Danjela Lura <danielaluraa@gmail.com>
;;; Copyright © 2020 Naga Malleswari <nagamalli@riseup.net>
;;; Copyright © 2020 Eric Brown <ecbrown@ericcbrown.com>
;;;
;;; 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 <http://www.gnu.org/licenses/>.
(define-module (gnu packages cran)
#:use-module ((guix licenses) #:prefix license:)
#:use-module (guix packages)
#:use-module (guix download)
#:use-module (guix git-download)
#:use-module (guix utils)
#:use-module (guix build-system r)
#: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 curl)
#:use-module (gnu packages databases)
#:use-module (gnu packages fontutils)
#: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 lisp-xyz)
#: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 pcre)
#:use-module (gnu packages perl)
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages python)
#:use-module (gnu packages python-xyz)
#:use-module (gnu packages statistics)
#:use-module (gnu packages tcl)
#:use-module (gnu packages tls)
#:use-module (gnu packages web)
#:use-module (gnu packages xorg))
(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-clipr
(package
(name "r-clipr")
(version "0.7.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "clipr" version))
(sha256
(base32
"1qn2p13d0c1bpqss6mv9hk60980rzhznfqpyaf5x0fy65svy9903"))))
(build-system r-build-system)
(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-ggpmisc
(package
(name "r-ggpmisc")
(version "0.3.4")
(source (origin
(method url-fetch)
(uri (cran-uri "ggpmisc" version))
(sha256
(base32
"0xc1yp0kphipq23ri4ij93garx1x2nrf4i0lhs6m10pp9yz7fbmj"))))
(build-system r-build-system)
(propagated-inputs
`(("r-broom" ,r-broom)
("r-dplyr" ,r-dplyr)
("r-ggplot2" ,r-ggplot2)
("r-gridextra" ,r-gridextra)
("r-lubridate" ,r-lubridate)
("r-mass" ,r-mass)
("r-plyr" ,r-plyr)
("r-polynom" ,r-polynom)
("r-splus2r" ,r-splus2r)
("r-tibble" ,r-tibble)
("r-xts" ,r-xts)
("r-zoo" ,r-zoo)))
(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-oenb
(package
(name "r-oenb")
(version "0.0.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "oenb" version))
(sha256
(base32
"1x1jlqp6r27c4gb7wafzpmh5rq6yq61a2d395r5lsmv2g5jb4biz"))))
(properties `((upstream-name . "oenb")))
(build-system r-build-system)
(propagated-inputs
`(("r-dplyr" ,r-dplyr)
("r-xml" ,r-xml)))
(native-inputs `(("r-knitr" ,r-knitr)))
(home-page "https://github.com/franzmohr/oenb")
(synopsis "Tools for the OeNB Data Web Service")
(description
"Tools to access data from the data web service of the
@acronym{OeNB, Oesterreichische Nationalbank},
@url{https://www.oenb.at/en/Statistics/User-Defined-Tables/webservice.html}.")
(license license:gpl2+)))
(define-public r-scales
(package
(name "r-scales")
(version "1.1.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "scales" version))
(sha256
(base32 "00rdbfj5mwc3kr8pskidn3n2zkp4ms6cx36xazz54pxw3pysdr0y"))))
(build-system r-build-system)
(propagated-inputs
`(("r-farver" ,r-farver)
("r-labeling" ,r-labeling)
("r-lifecycle" ,r-lifecycle)
("r-munsell" ,r-munsell)
("r-rcolorbrewer" ,r-rcolorbrewer)
("r-r6" ,r-r6)
("r-viridislite" ,r-viridislite)))
(home-page "https://github.com/hadley/scales")
(synopsis "Scale functions for visualization")
(description
"This package provides graphical scales that map data to aesthetics, and
provides methods for automatically determining breaks and labels for axes and
legends.")
(license license:expat)))
(define-public r-pheatmap
(package
(name "r-pheatmap")
(version "1.0.12")
(source
(origin
(method url-fetch)
(uri (cran-uri "pheatmap" version))
(sha256
(base32
"1hdh74az3vyzz6dqa311rhxdm74n46lyr03p862kn80p0kp9d7ap"))))
(build-system r-build-system)
(propagated-inputs
`(("r-gtable" ,r-gtable)
("r-rcolorbrewer" ,r-rcolorbrewer)
("r-scales" ,r-scales)))
(home-page "https://cran.r-project.org/web/packages/pheatmap")
(synopsis "Pretty heatmaps")
(description
"This package provides an implementation of heatmaps that offers more
control over dimensions and appearance.")
(license license:gpl2+)))
(define-public r-ecp
(package
(name "r-ecp")
(version "3.1.2")
(source (origin
(method url-fetch)
(uri (cran-uri "ecp" version))
(sha256
(base32
"11f9p869xr0zg779i46gmflxlq4xclk9wxbab0nj2fan26pn4sfy"))))
(build-system r-build-system)
(propagated-inputs
`(("r-rcpp" ,r-rcpp)))
(home-page "https://cran.r-project.org/web/packages/ecp/")
(synopsis "Multiple change-point analysis of multivariate data")
(description
"This package implements various procedures for finding multiple
change-points. Two methods make use of dynamic programming and pruning, with
no distributional assumptions other than the existence of certain absolute
moments in one method. Hierarchical and exact search methods are included.
All methods return the set of estimated change-points as well as other summary
information.")
(license license:gpl2+)))
(define-public r-ellipsis
(package
(name "r-ellipsis")
(version "0.3.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "ellipsis" version))
(sha256
(base32
"01z9gq311nzwv3a0sa49jhm5ylqd59srip4vjkrf23hzgb5i9y0b"))))
(build-system r-build-system)
(propagated-inputs
`(("r-rlang" ,r-rlang)))
(home-page "https://github.com/hadley/ellipsis")
(synopsis "Tools for working with additional arguments")
(description
"In S3 generics, it's useful to take @code{...} so that methods can have
additional arguments. But this flexibility comes at a cost: misspelled
arguments will be silently ignored. The @code{ellipsis} package is an
experiment that allows a generic to warn if any arguments passed in @code{...}
are not used.")
(license license:gpl3)))
(define-public r-grr
(package
(name "r-grr")
(version "0.9.5")
(source
(origin
(method url-fetch)
(uri (cran-uri "grr" version))
(sha256
(base32
"0arbcgrvhkwb5xk4nry1ffg2qj0v8ivhjghdr505ib4357g0c9i9"))))
(build-system r-build-system)
(home-page "https://cran.r-project.org/web/packages/grr")
(synopsis "Alternative implementations of base R functions")
(description
"This package provides alternative implementations of some base R
functions, including @code{sort}, @code{order}, and @code{match}. The
functions are simplified but can be faster or have other advantages.")
(license license:gpl3)))
(define-public r-matrix-utils
(package
(name "r-matrix-utils")
(version "0.9.8")
(source
(origin
(method url-fetch)
(uri (cran-uri "Matrix.utils" version))
(sha256
(base32
"0a5fq1scykqk0kc9j051j6fix6j2dqwz5wbgb0amaxsiywz9vigb"))))
(properties `((upstream-name . "Matrix.utils")))
(build-system r-build-system)
(propagated-inputs
`(("r-grr" ,r-grr)
("r-matrix" ,r-matrix)))
(home-page "https://github.com/cvarrichio/Matrix.utils")
(synopsis
"Data.frame-Like Operations on Sparse and Dense Matrix Objects")
(description
"This package implements data manipulation methods such as @code{cast},
@code{aggregate}, and @code{merge}/@code{join} for Matrix and Matrix-like
objects.")
(license license:gpl3)))
(define-public r-sys
(package
(name "r-sys")
(version "3.3")
(source
(origin
(method url-fetch)
(uri (cran-uri "sys" version))
(sha256
(base32
"14wvy46i2iz9jn7lj3cvifmps932s3395wq681hniva0f8m7q8d6"))))
(build-system r-build-system)
(home-page "https://github.com/jeroen/sys")
(synopsis "Powerful and reliable tools for running system commands in R")
(description
"This package provides drop-in replacements for the base @code{system2()}
function with fine control and consistent behavior across platforms. It
supports clean interruption, timeout, background tasks, and streaming STDIN /
STDOUT / STDERR over binary or text connections. The package also provides
functions for evaluating expressions inside a temporary fork. Such
evaluations have no side effects on the main R process, and support reliable
interrupts and timeouts. This provides the basis for a sandboxing
mechanism.")
(license license:expat)))
(define-public r-askpass
(package
(name "r-askpass")
(version "1.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "askpass" version))
(sha256
(base32
"07q0ik8jzk44vpwh48rr3fnpd7dzsdhjjsl4l850rffv3dyq4h6v"))))
(build-system r-build-system)
(propagated-inputs `(("r-sys" ,r-sys)))
(home-page "https://github.com/jeroen/askpass")
(synopsis "Safe password entry for R")
(description
"This package provides cross-platform utilities for prompting the user
for credentials or a passphrase, for example to authenticate with a server or
read a protected key.")
(license license:expat)))
(define-public r-vegan
(package
(name "r-vegan")
(version "2.5-6")
(source
(origin
(method url-fetch)
(uri (cran-uri "vegan" version))
(sha256
(base32
"0g60rgn1i7wqf9pf5m1yki1m45gcp7i5hmjic0ci0f6vng70mh5k"))))
(build-system r-build-system)
(native-inputs
`(("gfortran" ,gfortran)))
(propagated-inputs
`(("r-cluster" ,r-cluster)
("r-knitr" ,r-knitr) ; needed for vignettes
("r-lattice" ,r-lattice)
("r-mass" ,r-mass)
("r-mgcv" ,r-mgcv)
("r-permute" ,r-permute)))
(home-page "https://cran.r-project.org/web/packages/vegan")
(synopsis "Functions for community ecology")
(description
"The vegan package provides tools for descriptive community ecology. It
has most basic functions of diversity analysis, community ordination and
dissimilarity analysis. Most of its multivariate tools can be used for other
data types as well.")
(license license:gpl2+)))
(define-public r-tidyverse
(package
(name "r-tidyverse")
(version "1.3.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "tidyverse" version))
(sha256
(base32
"02gyys08qv2v4cl2d66gml4d31ipxay0iyfwwksvxyclx60wp2kd"))))
(build-system r-build-system)
(propagated-inputs
`(("r-broom" ,r-broom)
("r-cli" ,r-cli)
("r-crayon" ,r-crayon)
("r-dbplyr" ,r-dbplyr)
("r-dplyr" ,r-dplyr)
("r-forcats" ,r-forcats)
("r-ggplot2" ,r-ggplot2)
("r-haven" ,r-haven)
("r-hms" ,r-hms)
("r-httr" ,r-httr)
("r-jsonlite" ,r-jsonlite)
("r-lubridate" ,r-lubridate)
("r-magrittr" ,r-magrittr)
("r-modelr" ,r-modelr)
("r-pillar" ,r-pillar)
("r-purrr" ,r-purrr)
("r-readr" ,r-readr)
("r-readxl" ,r-readxl)
("r-reprex" ,r-reprex)
("r-rlang" ,r-rlang)
("r-rstudioapi" ,r-rstudioapi)
("r-rvest" ,r-rvest)
("r-stringr" ,r-stringr)
("r-tibble" ,r-tibble)
("r-tidyr" ,r-tidyr)
("r-xml2" ,r-xml2)))
(home-page "https://tidyverse.tidyverse.org")
(synopsis "Install and load packages from the \"Tidyverse\"")
(description
"The @code{tidyverse} is a set of packages that work in harmony because
they share common data representations and API design. This package is
designed to make it easy to install and load multiple tidyverse packages in a
single step.")
(license license:gpl3)))
(define-public r-rvest
(package
(name "r-rvest")
(version "0.3.5")
(source
(origin
(method url-fetch)
(uri (cran-uri "rvest" version))
(sha256
(base32 "0r0a5jic09xw5pk0x42pr99r3zab5m9s4x85ymx1sl769jz42zqf"))))
(build-system r-build-system)
(propagated-inputs
`(("r-httr" ,r-httr)
("r-magrittr" ,r-magrittr)
("r-selectr" ,r-selectr)
("r-xml2" ,r-xml2)))
(home-page "https://github.com/hadley/rvest")
(synopsis "Simple web scraping for R")
(description
"@code{r-rvest} helps you scrape information from web pages. It is
designed to work with @code{magrittr} to make it easy to express common web
scraping tasks, inspired by libraries like @code{BeautifulSoup}.")
(license license:gpl3)))
(define-public r-selectr
(package
(name "r-selectr")
(version "0.4-2")
(source
(origin
(method url-fetch)
(uri (cran-uri "selectr" version))
(sha256
(base32 "09y1n3iy297g49xlpl7xrjpwgnm57pskx5991lyfcpizbz8ax22m"))))
(build-system r-build-system)
(propagated-inputs
`(("r-stringr" ,r-stringr)
("r-r6" ,r-r6)))
(home-page "https://sjp.co.nz/projects/selectr/")
(synopsis "Translate CSS selectors to XPath expressions")
(description
"@code{r-selectr} translates a CSS3 selector into an equivalent XPath
expression. This allows you to use CSS selectors when working with the XML
package as it can only evaluate XPath expressions. Also provided are
convenience functions useful for using CSS selectors on XML nodes. This
package is a port of the Python package @code{cssselect}.")
(license license:bsd-3)))
(define-public r-reprex
(package
(name "r-reprex")
(version "0.3.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "reprex" version))
(sha256
(base32
"0v7vxzs8alwz8y1cjicpimp5yimf1g9gb8x5wy3zhvrz6kk2lg10"))))
(build-system r-build-system)
(propagated-inputs
`(("r-callr" ,r-callr)
("r-clipr" ,r-clipr)
("r-fs" ,r-fs)
("r-rlang" ,r-rlang)
("r-rmarkdown" ,r-rmarkdown)
("r-whisker" ,r-whisker)
("r-withr" ,r-withr)))
(home-page "https://github.com/tidyverse/reprex")
(synopsis "Prepare reproducible R code examples for sharing")
(description
"This package provides a convenience wrapper that uses the
@code{rmarkdown} package to render small snippets of code to target formats
that include both code and output. The goal is to encourage the sharing of
small, reproducible, and runnable examples on code-oriented websites or email.
@code{reprex} also extracts clean, runnable R code from various common formats,
such as copy/paste from an R session.")
(license license:expat)))
(define-public r-reordercluster
(package
(name "r-reordercluster")
(version "1.0")
(source (origin
(method url-fetch)
(uri (cran-uri "ReorderCluster" version))
(sha256
(base32
"0ss750frzvj0bm1w7zblmcsjpszhnbffwlkaw31sm003lbx9hy58"))))
(build-system r-build-system)
(propagated-inputs
`(("r-gplots" ,r-gplots)
("r-rcpp" ,r-rcpp)))
(home-page "https://cran.r-project.org/web/packages/ReorderCluster")
(synopsis "Reordering the dendrogram according to the class labels")
(description "This package provides tools for performing the leaf reordering
for the dendrogram that preserves the hierarchical clustering result and at the
same time tries to group instances from the same class together.")
(license license:gpl3+)))
(define-public r-callr
(package
(name "r-callr")
(version "3.4.3")
(source
(origin
(method url-fetch)
(uri (cran-uri "callr" version))
(sha256
(base32
"1dc20gdawy9mhnc452qlshv2p4krs6c2gymvpv365mn141zjgdq1"))))
(build-system r-build-system)
(propagated-inputs
`(("r-r6" ,r-r6)
("r-processx" ,r-processx)))
(home-page "https://github.com/r-lib/callr#readme")
(synopsis "Call R from R")
(description
"It is sometimes useful to perform a computation in a separate R process,
without affecting the current R process at all. This package does exactly
that.")
(license license:expat)))
(define-public r-readxl
(package
(name "r-readxl")
(version "1.3.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "readxl" version))
(sha256
(base32
"15mambxr8c7k2ikdfsl1w3vxvm54dsnk0cl1qvks6iig7rql3d14"))))
(build-system r-build-system)
(propagated-inputs
`(("r-cellranger" ,r-cellranger)
("r-progress" ,r-progress)
("r-rcpp" ,r-rcpp)
("r-tibble" ,r-tibble)))
(home-page "https://readxl.tidyverse.org")
(synopsis "Read Excel files")
(description
"This package lets you import Excel files into R. It supports
@file{.xls} via the embedded @code{libxls} C library and @file{.xlsx} via
the embedded @code{RapidXML} C++ library.")
;; XXX: This package bundles a copy of 'libxsl' which is BSD-2 and
;; 'rapidxml' which is Boost.
(license (list license:gpl3 license:bsd-2 license:boost1.0))))
(define-public r-modelr
(package
(name "r-modelr")
(version "0.1.6")
(source
(origin
(method url-fetch)
(uri (cran-uri "modelr" version))
(sha256
(base32
"1x2m34m4qirb401krmgc5wg3g7ndbcglfab2l0655rmky3fz7rfp"))))
(build-system r-build-system)
(propagated-inputs
`(("r-broom" ,r-broom)
("r-dplyr" ,r-dplyr)
("r-magrittr" ,r-magrittr)
("r-purrr" ,r-purrr)
("r-rlang" ,r-rlang)
("r-tibble" ,r-tibble)
("r-tidyr" ,r-tidyr)
("r-tidyselect" ,r-tidyselect)))
(home-page "https://github.com/tidyverse/modelr")
(synopsis "Helper functions for modelling in pipelines")
(description
"Functions for modelling that help you seamlessly integrate modelling
into a pipeline of data manipulation and visualisation.")
(license license:gpl3)))
(define-public r-httpuv
(package
(name "r-httpuv")
(version "1.5.2")
(source (origin
(method url-fetch)
(uri (cran-uri "httpuv" version))
(sha256
(base32
"13ax0hs2lc39ilznh1zarwqdzahcbhb8adilrfik3xg0fkljpcwk"))))
(build-system r-build-system)
(propagated-inputs
`(("r-bh" ,r-bh)
("r-later" ,r-later)
("r-promises" ,r-promises)
("r-r6" ,r-r6)
("r-rcpp" ,r-rcpp)))
(home-page "https://github.com/rstudio/httpuv")
(synopsis "HTTP and WebSocket server library for R")
(description
"The httpuv package provides low-level socket and protocol support for
handling HTTP and WebSocket requests directly from within R. It is primarily
intended as a building block for other packages, rather than making it
particularly easy to create complete web applications using httpuv alone.")
;; This package includes third-party code that was originally released
;; under various non-copyleft licenses. Full licensing information can be
;; obtained here: https://github.com/rstudio/httpuv/blob/master/LICENSE
(license license:gpl3+)))
(define-public r-jsonlite
(package
(name "r-jsonlite")
(version "1.6.1")
(source (origin
(method url-fetch)
(uri (cran-uri "jsonlite" version))
(sha256
(base32
"0xrki07wc17bkmhz0h7jay784j1sls2i9bf1mfpj6yl59791v4kl"))))
(build-system r-build-system)
(home-page "https://arxiv.org/abs/1403.2805")
(synopsis "Robust, high performance JSON parser and generator for R")
(description
"The jsonlite package provides a fast JSON parser and generator optimized
for statistical data and the web. It offers flexible, robust, high
performance tools for working with JSON in R and is particularly powerful for
building pipelines and interacting with a web API. In addition to converting
JSON data from/to R objects, jsonlite contains functions to stream, validate,
and prettify JSON data. The unit tests included with the package verify that
all edge cases are encoded and decoded consistently for use with dynamic data
in systems and applications.")
(license license:expat)))
(define-public r-servr
(package
(name "r-servr")
(version "0.16")
(source (origin
(method url-fetch)
(uri (cran-uri "servr" version))
(sha256
(base32
"106skz04iq4dkblr17idxsxfcfqic6rcaz8mahydkwjjppnhp5fc"))))
(build-system r-build-system)
(propagated-inputs
`(("r-httpuv" ,r-httpuv)
("r-jsonlite" ,r-jsonlite)
("r-mime" ,r-mime)
("r-xfun" ,r-xfun)))
(home-page "https://github.com/yihui/servr")
(synopsis "Simple HTTP server to serve static files or dynamic documents")
(description
"Servr provides an HTTP server in R to serve static files, or dynamic
documents that can be converted to HTML files (e.g., R Markdown) under a given
directory.")
(license license:expat)))
(define-public r-htmltools
(package
(name "r-htmltools")
(version "0.4.0")
(source (origin
(method url-fetch)
(uri (cran-uri "htmltools" version))
(sha256
(base32
"06l17d8jkf438yk2mchpsp4j90bynnapz3nabh5vkcc324p5a62v"))))
(build-system r-build-system)
(propagated-inputs
`(("r-digest" ,r-digest)
("r-rcpp" ,r-rcpp)
("r-rlang" ,r-rlang)))
(home-page "https://cran.r-project.org/web/packages/htmltools")
(synopsis "R tools for HTML")
(description
"This package provides tools for HTML generation and output in R.")
(license license:expat)))
(define-public r-htmlwidgets
(package
(name "r-htmlwidgets")
(version "1.5.1")
(source (origin
(method url-fetch)
(uri (cran-uri "htmlwidgets" version))
(sha256
(base32
"10fp306l1nybkah6jrlrqwwdb6zvklbddp8i3w9v9naj8la5jbnl"))))
(build-system r-build-system)
(propagated-inputs
`(("r-htmltools" ,r-htmltools)
("r-jsonlite" ,r-jsonlite)
("r-yaml" ,r-yaml)))
(home-page "https://github.com/ramnathv/htmlwidgets")
(synopsis "HTML Widgets for R")
(description
"HTML widgets is a framework for creating HTML widgets that render in
various contexts including the R console, R Markdown documents, and Shiny web
applications.")
(license license:expat)))
(define-public r-htmltable
(package
(name "r-htmltable")
(version "1.13.3")
(source
(origin
(method url-fetch)
(uri (cran-uri "htmlTable" version))
(sha256
(base32
"0g9r156k9yl1f092hfw3b9wjx11akf0shbi3x0d0mvpnflvc8nfl"))))
(properties `((upstream-name . "htmlTable")))
(build-system r-build-system)
(propagated-inputs
`(("r-checkmate" ,r-checkmate)
("r-htmltools" ,r-htmltools)
("r-htmlwidgets" ,r-htmlwidgets)
("r-knitr" ,r-knitr)
("r-magrittr" ,r-magrittr)
("r-rstudioapi" ,r-rstudioapi)
("r-stringr" ,r-stringr)))
(home-page "http://gforge.se/packages/")
(synopsis "Advanced tables for Markdown/HTML")
(description
"This package provides functions to build tables with advanced layout
elements such as row spanners, column spanners, table spanners, zebra
striping, and more. While allowing advanced layout, the underlying
CSS-structure is simple in order to maximize compatibility with word
processors such as LibreOffice. The package also contains a few text
formatting functions that help outputting text compatible with HTML or
LaTeX.")
(license license:gpl3+)))
(define-public r-curl
(package
(name "r-curl")
(version "4.3")
(source (origin
(method url-fetch)
(uri (cran-uri "curl" version))
(sha256
(base32
"1nrf6md41b37j424y6rvifdj9zb3j14f60fj7q71k9jhpf2x81kl"))))
(build-system r-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
;; The environment variable CURL_CA_BUNDLE is only respected when
;; running Windows, so we disable the platform checks.
;; This can be removed once the libcurl has been patched.
(add-after 'unpack 'allow-CURL_CA_BUNDLE
(lambda _
(substitute* "R/onload.R"
(("if \\(!grepl\\(\"mingw\".*")
"if (FALSE)\n"))
(substitute* "src/handle.c"
(("/\\* Only set" m)
(string-append "\
const char *_ca_bundle = getenv(\"CURL_CA_BUNDLE\");
if(_ca_bundle != NULL) { curl_easy_setopt(handle, CURLOPT_CAINFO, _ca_bundle); }
" m)))
#t)))))
(inputs
`(("libcurl" ,curl)
("zlib" ,zlib)))
(native-inputs
`(("pkg-config" ,pkg-config)))
(home-page "https://github.com/jeroenooms/curl")
(synopsis "HTTP client for R")
(description
"The @code{curl()} and @code{curl_download()} functions provide highly
configurable drop-in replacements for base @code{url()} and
@code{download.file()} with better performance, support for encryption, gzip
compression, authentication, and other @code{libcurl} goodies. The core of
the package implements a framework for performing fully customized requests
where data can be processed either in memory, on disk, or streaming via the
callback or connection interfaces.")
(license license:expat)))
(define-public r-hwriter
(package
(name "r-hwriter")
(version "1.3.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "hwriter" version))
(sha256
(base32
"0arjsz854rfkfqhgvpqbm9lfni97dcjs66isdsfvwfd2wz932dbb"))))
(build-system r-build-system)
(home-page "https://cran.r-project.org/web/packages/hwriter")
(synopsis "Output R objects in HTML format")
(description
"This package provides easy-to-use and versatile functions to output R
objects in HTML format.")
(license license:lgpl2.1+)))
(define-public r-rjson
(package
(name "r-rjson")
(version "0.2.20")
(source
(origin
(method url-fetch)
(uri (cran-uri "rjson" version))
(sha256
(base32
"0v1zvdd3svnavklh7y5xbwrrkbvx6053r4c5hgnk7hz7bqg7qa1s"))))
(build-system r-build-system)
(home-page "https://cran.r-project.org/web/packages/rjson")
(synopsis "JSON library for R")
(description
"This package provides functions to convert R objects into JSON objects
and vice-versa.")
(license license:gpl2+)))
(define-public r-fastmap
(package
(name "r-fastmap")
(version "1.0.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "fastmap" version))
(sha256
(base32
"1v7sp56xiha0bh78g3w92k52p9vkp7ryzpw0z66nyddxzrfv0y27"))))
(properties `((upstream-name . "fastmap")))
(build-system r-build-system)
(home-page "https://r-lib.github.io/fastmap/")
(synopsis "Fast implementation of a key-value store")
(description
"This package provides a fast implementation of a key-value store.
Environments are commonly used as key-value stores, but every time a new key
is used, it is added to R's global symbol table, causing a small amount of
memory leakage. This can be problematic in cases where many different keys
are used. Fastmap avoids this memory leak issue by implementing the map using
data structures in C++.")
(license license:expat)))
(define-public r-shiny
(package
(name "r-shiny")
(version "1.4.0.2")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/rstudio/shiny.git")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
"005wgcxq7f2q9g6wvfk29n2nms262w0abpz93sfvx79yv6qxppzs"))))
(build-system r-build-system)
(arguments
`(#:modules ((guix build r-build-system)
(guix build minify-build-system)
(guix build utils)
(ice-9 match))
#:imported-modules (,@%r-build-system-modules
(guix build minify-build-system))
#:phases
(modify-phases (@ (guix build r-build-system) %standard-phases)
(add-after 'unpack 'replace-bundled-minified-JavaScript
(lambda* (#:key inputs #:allow-other-keys)
(let ((replace-file (lambda (old new)
(format #t "replacing ~a with ~a\n" old new)
(delete-file old)
(symlink new old))))
;; NOTE: Files in ./inst/www/shared/datepicker/js/locales/
;; contain just data. They are not minified code, so we don't
;; replace them.
(with-directory-excursion "inst/www/shared"
(replace-file "bootstrap/shim/respond.min.js"
(string-append (assoc-ref inputs "js-respond")
"/share/javascript/respond.min.js"))
(replace-file "bootstrap/shim/html5shiv.min.js"
(string-append (assoc-ref inputs "js-html5shiv")
"/share/javascript/html5shiv.min.js"))
(replace-file "json2-min.js"
(string-append (assoc-ref inputs "js-json2")
"/share/javascript/json2-min.js"))
(replace-file "strftime/strftime-min.js"
(string-append (assoc-ref inputs "js-strftime")
"/share/javascript/strftime.min.js"))
(replace-file "highlight/highlight.pack.js"
(string-append (assoc-ref inputs "js-highlight")
"/share/javascript/highlight.min.js"))
(replace-file "datatables/js/jquery.dataTables.min.js"
(string-append (assoc-ref inputs "js-datatables")
"/share/javascript/jquery.dataTables.min.js"))
(replace-file "selectize/js/selectize.min.js"
(string-append (assoc-ref inputs "js-selectize")
"/share/javascript/selectize.min.js"))
(replace-file "selectize/js/es5-shim.min.js"
(string-append (assoc-ref inputs "js-es5-shim")
"/share/javascript/es5-shim.min.js"))
(for-each (match-lambda
((source . target)
(delete-file 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")
("shiny.js" .
"shiny.min.js")
("jquery.js" .
"jquery.min.js")
("legacy/jquery.js" .
"legacy/jquery.min.js")
("showdown/src/showdown.js" .
"showdown/compressed/showdown.js")))))
#t)))))
(propagated-inputs
`(("r-crayon" ,r-crayon)
("r-digest" ,r-digest)
("r-fastmap" ,r-fastmap)
("r-htmltools" ,r-htmltools)
("r-httpuv" ,r-httpuv)
("r-jsonlite" ,r-jsonlite)
("r-later" ,r-later)
("r-mime" ,r-mime)
("r-promises" ,r-promises)
("r-r6" ,r-r6)
("r-rlang" ,r-rlang)
("r-sourcetools" ,r-sourcetools)
("r-withr" ,r-withr)
("r-xtable" ,r-xtable)))
(inputs
`(("js-datatables" ,js-datatables)
("js-html5shiv" ,js-html5shiv)
("js-json2" ,js-json2)
("js-respond" ,js-respond)
("js-selectize" ,js-selectize)
("js-strftime" ,js-strftime)
("js-highlight" ,js-highlight)
("js-es5-shim" ,js-es5-shim)))
(native-inputs
`(("uglify-js" ,uglify-js)
("gfortran" ,gfortran)))
(home-page "http://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)))
;; 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 (string-append (assoc-ref inputs "js-requirejs")
"/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 "uglify-js" source)))
(call-with-output-file target
(lambda (port)
(dump-port minified port)))))
sources targets))))
#t)))))
(propagated-inputs
`(("r-htmlwidgets" ,r-htmlwidgets)
("r-jsonlite" ,r-jsonlite)
("r-promises" ,r-promises)
("r-shiny" ,r-shiny)
("r-stringr" ,r-stringr)))
(inputs
`(("js-requirejs" ,js-requirejs)))
(native-inputs
`(("uglify-js" ,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 "0.7.1")
(source (origin
(method url-fetch)
(uri (cran-uri "shinydashboard" version))
(sha256
(base32
"0khac8b27q3swdw07kl609hm0fjfjsjv591b388q99mqqr2rk92i"))))
(build-system r-build-system)
;; The directory inst/AdminLTE/ contains a minified JavaScript file.
;; Regenerate it from the included sources.
(arguments
`(#:modules ((guix build utils)
(guix build r-build-system)
(ice-9 popen))
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'generate-minified-javascript
(lambda _
(with-directory-excursion "inst/AdminLTE"
(delete-file "app.min.js")
(let ((minified (open-pipe* OPEN_READ "uglify-js" "app.js")))
(call-with-output-file "app.min.js"
(lambda (port)
(dump-port minified port))))))))))
(propagated-inputs
`(("r-htmltools" ,r-htmltools)
("r-promises" ,r-promises)
("r-shiny" ,r-shiny)))
(native-inputs
`(("uglify-js" ,uglify-js)))
(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 "0.7.5")
(source
(origin
(method url-fetch)
(uri (cran-uri "shinyFiles" version))
(sha256
(base32 "1143m941hma9hc77c3xcw26c0ygfhn9ii2sbp9wrydxv4gc7mr8a"))))
(properties `((upstream-name . "shinyFiles")))
(build-system r-build-system)
(propagated-inputs
`(("r-fs" ,r-fs)
("r-htmltools" ,r-htmltools)
("r-jsonlite" ,r-jsonlite)
("r-shiny" ,r-shiny)
("r-tibble" ,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 "1.1.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "shinythemes" version))
(sha256
(base32
"12miz44n2zxfswnia7p8dirxj3miw0aqn4pkx2111ikz67ax84rf"))))
(properties `((upstream-name . "shinythemes")))
(build-system r-build-system)
(propagated-inputs `(("r-shiny" ,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 "0.8.7")
(source
(origin
(method url-fetch)
(uri (cran-uri "d3r" version))
(sha256
(base32
"0xl3im76lp7pd5lhp8jfyqdm4j4zvjrx5a5fl81xv2cf7x3n4f2a"))))
(build-system r-build-system)
(arguments
`(#:modules ((guix build utils)
(guix build r-build-system)
(srfi srfi-1)
(ice-9 popen))
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'process-javascript
(lambda* (#:key inputs #:allow-other-keys)
(with-directory-excursion "inst/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"))))
(lambda (sources targets)
(for-each (lambda (source target)
(format #t "Processing ~a --> ~a~%"
source target)
(delete-file target)
(let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
(call-with-output-file target
(lambda (port)
(dump-port minified port)))))
sources targets))))
#t)))))
(propagated-inputs
`(("r-dplyr" ,r-dplyr)
("r-htmltools" ,r-htmltools)
("r-tidyr" ,r-tidyr)))
(native-inputs
`(("uglify-js" ,uglify-js)
("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
"0kxvx5pfagxn6nhavdwsdnzyd26g0z5dsfi1pi5dvcmb0c8ipcdn"))))))
(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.git")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32
"0jrcnfax321pszbpjdifnkbrgbjr43bjzvlzv1p5a8wskksqwiyx"))))
(build-system r-build-system)
(propagated-inputs
`(("r-d3r" ,r-d3r)
("r-htmlwidgets" ,r-htmlwidgets)
("r-shiny" ,r-shiny)
("r-magrittr" ,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-crosstalk
(package
(name "r-crosstalk")
(version "1.1.0.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "crosstalk" version))
(sha256
(base32
"03ihj7cimkklrbad9zic78xsrfcisygmgy859hqnx0hiph80p9rn"))))
(build-system r-build-system)
(propagated-inputs
`(("r-htmltools" ,r-htmltools)
("r-jsonlite" ,r-jsonlite)
("r-lazyeval" ,r-lazyeval)
("r-r6" ,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 `(("r-brew" ,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
`(("r-htmltools" ,r-htmltools)
("r-shiny" ,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
`(("r-hms" ,r-hms)
("r-rcpp" ,r-rcpp)
("r-tibble" ,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 "3.3.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "maps" version))
(sha256
(base32
"05i2ppl5z4p8rawgqmy3z4ia05fcblpq1vvrmrkgkkpdlhczx6hr"))))
(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 "1.2.7")
(source
(origin
(method url-fetch)
(uri (cran-uri "mapproj" version))
(sha256
(base32
"0nscsfq8md6ri9258xz57c3dj81wdl6kdwf4a9qcrwwbn20i427h"))))
(build-system r-build-system)
(propagated-inputs `(("r-maps" ,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
`(("r-png" ,r-png)
("r-sp" ,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-geosphere
(package
(name "r-geosphere")
(version "1.5-10")
(source
(origin
(method url-fetch)
(uri (cran-uri "geosphere" version))
(sha256
(base32
"15xlgsmn0vwky1l13n6acdz6jn2b2na3gf6x367y3qh1f5w4zkan"))))
(build-system r-build-system)
(propagated-inputs `(("r-sp" ,r-sp)))
(home-page "https://cran.r-project.org/web/packages/geosphere")
(synopsis "Spherical trigonometry")
(description "This package computes spherical trigonometry for geographic
applications. That is, compute distances and related measures for angular
(longitude/latitude) locations.")
(license license:gpl3+)))
(define-public r-jpeg
(package
(name "r-jpeg")
(version "0.1-8.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "jpeg" version))
(sha256
(base32
"1a8mi70x79a691r40yiw684jkg1mr9n8agkxlcksxcnrdybs9c0x"))))
(build-system r-build-system)
(inputs `(("libjpeg" ,libjpeg)))
(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
`(("r-bitops" ,r-bitops)
("r-digest" ,r-digest)
("r-dplyr" ,r-dplyr)
("r-ggplot2" ,r-ggplot2)
("r-glue" ,r-glue)
("r-httr" ,r-httr)
("r-jpeg" ,r-jpeg)
("r-magrittr" ,r-magrittr)
("r-plyr" ,r-plyr)
("r-png" ,r-png)
("r-purrr" ,r-purrr)
("r-rgooglemaps" ,r-rgooglemaps)
("r-rjson" ,r-rjson)
("r-scales" ,r-scales)
("r-stringr" ,r-stringr)
("r-tibble" ,r-tibble)
("r-tidyr" ,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 "2.2.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "haven" version))
(sha256
(base32
"0g9d6mxqmrw2zdms78jpx2sx73pczlyy771v1h5hmxqz9sqyk7hr"))))
(build-system r-build-system)
(inputs
`(("zlib" ,zlib)))
(propagated-inputs
`(("r-forcats" ,r-forcats)
("r-hms" ,r-hms)
("r-rcpp" ,r-rcpp)
("r-rlang" ,r-rlang)
("r-readr" ,r-readr)
("r-tibble" ,r-tibble)
("r-tidyselect" ,r-tidyselect)))
(home-page "https://haven.tidyverse.org")
(synopsis "Import and Export 'SPSS', 'Stata' and 'SAS' Files")
(description
"This package lets you mport foreign statistical formats into R via the
embedded @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
`(("gfortran" ,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 "5.3")
(source
(origin
(method url-fetch)
(uri (cran-uri "ape" version))
(sha256
(base32
"08wbk1kxhs32bmmvqlqanbdg1w235amd35k8m00fngsj9h9xzc08"))))
(build-system r-build-system)
(propagated-inputs
`(("r-lattice" ,r-lattice)
("r-nlme" ,r-nlme)
("r-rcpp" ,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
`(("r-curl" ,r-curl)
("r-httr" ,r-httr)
("r-plyr" ,r-plyr)
("r-progress" ,r-progress)
("r-readr" ,r-readr)
("r-xml" ,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 "1.4-1")
(source
(origin
(method url-fetch)
(uri (cran-uri "colorspace" version))
(sha256
(base32 "0wyny3ah2d74hqv80s6imrarpna09gq3j9rjnz6zx2qg0lx72gb9"))))
(build-system r-build-system)
(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 "1.4.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "glue" version))
(sha256
(base32
"1hb9j2519jv9zgkgjb25hnqi22i7zxnaksqd16m4nxa1f6gl0v7a"))))
(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-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
`(("r-boot" ,r-boot)))
(home-page "http://www.sciviews.org/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-plogr
(package
(name "r-plogr")
(version "0.2.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "plogr" version))
(sha256
(base32
"0a8dhzlna79ggyhfr0nncgh15a9n6r0dsz664pz0ah323wpblqqf"))))
(build-system r-build-system)
(home-page "https://github.com/krlmlr/plogr")
(synopsis "R bindings for the plog C++ logging library")
(description
"This package provides the header files for a stripped-down version of
the plog header-only C++ logging library, and a method to log to R's standard
error stream.")
(license license:expat)))
(define-public r-pls
(package
(name "r-pls")
(version "2.7-2")
(source
(origin
(method url-fetch)
(uri (cran-uri "pls" version))
(sha256
(base32 "121byimd6bg7jbrq5wz5fpi0vxq0vh8g724vkhnjzszbvcv1xsb7"))))
(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 "1.3.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "ps" version))
(sha256
(base32 "0127q6pw9iw8hhcfp231gmdh29nahh2n5jzc38avrzy7yrm4bwl9"))))
(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 "1.0.6")
(source
(origin
(method url-fetch)
(uri (cran-uri "pkgbuild" version))
(sha256
(base32 "0xnlz6ivhkbmncg9hfw5p69lm4rjy3wn5lyxmygxyf4rrfnnqwxx"))))
(build-system r-build-system)
(propagated-inputs
`(("r-callr" ,r-callr)
("r-cli" ,r-cli)
("r-crayon" ,r-crayon)
("r-desc" ,r-desc)
("r-prettyunits" ,r-prettyunits)
("r-r6" ,r-r6)
("r-rprojroot" ,r-rprojroot)
("r-withr" ,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 "1.0.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "pkgload" version))
(sha256
(base32
"0z7jvharafahi2gv5547mk1n499isjzw06kfwymmxc0gd575d1ii"))))
(build-system r-build-system)
(propagated-inputs
`(("r-desc" ,r-desc)
("r-pkgbuild" ,r-pkgbuild)
("r-rlang" ,r-rlang)
("r-rprojroot" ,r-rprojroot)
("r-rstudioapi" ,r-rstudioapi)
("r-withr" ,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-rcpp
(package
(name "r-rcpp")
(version "1.0.4.6")
(source
(origin
(method url-fetch)
(uri (cran-uri "Rcpp" version))
(sha256
(base32 "00mk23zmrqn1c4mk9d6csjcbnl12wd7yicjk2ikmw5dyvdfngbs5"))))
(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 <http://gallery.rcpp.org>, the paper by Eddelbuettel
and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see
@code{citation(\"Rcpp\")} for details on these last two.")
(license license:gpl2+)))
(define-public r-bindr
(package
(name "r-bindr")
(version "0.1.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "bindr" version))
(sha256
(base32
"1l05fpk2yql3jka321c0bdgx6mqq9pvfrg2844lbjfpbgjkmqy3w"))))
(build-system r-build-system)
(home-page "https://github.com/krlmlr/bindr")
(synopsis "Parametrized active bindings")
(description
"This package provides a simple interface for creating active bindings
where the bound function accepts additional arguments.")
(license license:expat)))
(define-public r-bindrcpp
(package
(name "r-bindrcpp")
(version "0.2.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "bindrcpp" version))
(sha256
(base32
"0rz4ibjdjsxl99ff3ha79z7cnjmilx4rx58fk9kk7ld9xc4hf4s8"))))
(build-system r-build-system)
(propagated-inputs
`(("r-bindr" ,r-bindr)
("r-plogr" ,r-plogr)
("r-rcpp" ,r-rcpp)))
(home-page "https://github.com/krlmlr/bindrcpp")
(synopsis "Rcpp interface to active bindings")
(description
"This package provides an easy way to fill an environment with active
bindings that call a C++ function.")
(license license:expat)))
(define-public r-auc
(package
(name "r-auc")
(version "0.3.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "AUC" version))
(sha256
(base32
"0ripcib2qz0m7rgr1kiz68nx8f6p408l1ww7j78ljqik7p3g41g7"))))
(properties `((upstream-name . "AUC")))
(build-system r-build-system)
(home-page "https://cran.r-project.org/web/packages/AUC")
(synopsis "Compute the area under the curve of selected measures")
(description
"This package includes functions to compute the area under the curve of
selected measures: the area under the sensitivity curve (AUSEC), the area
under the specificity curve (AUSPC), the area under the accuracy
curve (AUACC), and the area under the receiver operating characteristic
curve (AUROC). The curves can also be visualized. Support for partial areas
is provided.")
(license license:gpl2+)))
(define-public r-calibrate
(package
(name "r-calibrate")
(version "1.7.5")
(source
(origin
(method url-fetch)
(uri (cran-uri "calibrate" version))
(sha256
(base32 "1s423nr176l2sc66wp7hzgqkv7c2bq8d2bjrrvrrm5qa9y3zdx1k"))))
(build-system r-build-system)
(propagated-inputs
`(("r-mass" ,r-mass)))
(home-page "https://cran.r-project.org/web/packages/calibrate")
(synopsis "Calibration of scatterplot and biplot axes")
(description
"This is a package for drawing calibrated scales with tick marks
on (non-orthogonal) variable vectors in scatterplots and biplots.")
(license license:gpl2)))
(define-public r-shape
(package
(name "r-shape")
(version "1.4.4")
(source
(origin
(method url-fetch)
(uri (cran-uri "shape" version))
(sha256
(base32
"0hadk3mapkhbh8xjkiz52vxdagmmgvm15xwpzb90ikw4giyipjzl"))))
(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 "0.1.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "GlobalOptions" version))
(sha256
(base32 "0x89hfz80avq4zcskxl71i4zi0mgniqqxfrvz050aa2189wfyja2"))))
(properties `((upstream-name . "GlobalOptions")))
(build-system r-build-system)
(home-page "https://github.com/jokergoo/GlobalOptions")
(synopsis "Generate functions to get or set global options")
(description
"This package provides more controls on the option values such as
validation and filtering on the values, making options invisible or private.")
(license license:gpl2+)))
(define-public r-circlize
(package
(name "r-circlize")
(version "0.4.8")
(source
(origin
(method url-fetch)
(uri (cran-uri "circlize" version))
(sha256
(base32
"0jvr9hmxyhg0zx101iiqkrg8wfaj86kp62xpv42n2j9fkn5r1mi2"))))
(build-system r-build-system)
(propagated-inputs
`(("r-colorspace" ,r-colorspace)
("r-globaloptions" ,r-globaloptions)
("r-shape" ,r-shape)))
(home-page "https://github.com/jokergoo/circlize")
(synopsis "Circular visualization")
(description
"Circular layout is an efficient way to visualise huge amounts of
information. This package provides an implementation of circular layout
generation in R as well as an enhancement of available software. Its
flexibility is based on the usage of low-level graphics functions such that
self-defined high-level graphics can be easily implemented by users for
specific purposes. Together with the seamless connection between the powerful
computational and visual environment in R, it gives users more convenience and
freedom to design figures for better understanding complex patterns behind
multi-dimensional data.")
(license license:gpl2+)))
(define-public r-powerlaw
(package
(name "r-powerlaw")
(version "0.70.4")
(source
(origin
(method url-fetch)
(uri (cran-uri "poweRlaw" version))
(sha256
(base32 "19zah9mx93az5lh9vicn3c8q1xb12g0w46dh5p901fbyimc32vwk"))))
(properties `((upstream-name . "poweRlaw")))
(build-system r-build-system)
(propagated-inputs
`(("r-vgam" ,r-vgam)))
(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 "1.13.4")
(source
(origin
(method url-fetch)
(uri (cran-uri "dendextend" version))
(sha256
(base32
"1pjbz6sb4pgh3d5pm53vmf3q8y6lq3hrgjd6547xxs3m63sb8mn4"))))
(build-system r-build-system)
(propagated-inputs
`(("r-ggplot2" ,r-ggplot2)
("r-magrittr" ,r-magrittr)
("r-viridis" ,r-viridis)))
(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 "0.1.8")
(source
(origin
(method url-fetch)
(uri (cran-uri "GetoptLong" version))
(sha256
(base32
"1l8xkvyl152bsyvxazsvx2sm1vkygn75x0lsg3sbg7xp6drdn3kc"))))
(properties `((upstream-name . "GetoptLong")))
(build-system r-build-system)
(inputs
`(("perl" ,perl)))
(propagated-inputs
`(("r-globaloptions" ,r-globaloptions)
("r-rjson" ,r-rjson)))
(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 "1.1-0")
(source
(origin
(method url-fetch)
(uri (cran-uri "fastmatch" version))
(sha256
(base32
"0z80jxkygmzn11sq0c2iz357s9bpki548lg926g85gldhfj1md90"))))
(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 "2.2-14")
(source
(origin
(method url-fetch)
(uri (cran-uri "ff" version))
(sha256
(base32
"1w724q4jpzbvzpilb2ifviaxkjgk9lzwxz9gksnvicbmfa20fqqw"))))
(build-system r-build-system)
(propagated-inputs `(("r-bit" ,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 "0.12.8")
(source
(origin
(method url-fetch)
(uri (cran-uri "ffbase" version))
(sha256
(base32
"0mjk7dkq1ginqqfvngzny747ggf9a8fd7kblq96n5ys1jrwjyqhq"))))
(build-system r-build-system)
(propagated-inputs
`(("r-bit" ,r-bit)
("r-fastmatch" ,r-fastmatch)
("r-ff" ,r-ff)))
(home-page "http://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-reshape
(package
(name "r-reshape")
(version "0.8.8")
(source
(origin
(method url-fetch)
(uri (cran-uri "reshape" version))
(sha256
(base32
"0s6i0sqxg1vldxs6miv8mi0zydxbqzgpmzfiwkj8y7jix3yrfmad"))))
(build-system r-build-system)
(propagated-inputs
`(("r-plyr" ,r-plyr)
("r-rcpp" ,r-rcpp)))
(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-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
`(("r-crayon" ,r-crayon)
("r-hms" ,r-hms)
("r-prettyunits" ,r-prettyunits)
("r-r6" ,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 "1.5.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "GGally" version))
(sha256
(base32
"082s321zspg5al6acigwrhg4fsrmkkk5caabg662qbcy8v6n34h6"))))
(properties `((upstream-name . "GGally")))
(build-system r-build-system)
(inputs
`(("libressl" ,libressl)))
(propagated-inputs
`(("r-ggplot2" ,r-ggplot2)
("r-gtable" ,r-gtable)
("r-plyr" ,r-plyr)
("r-progress" ,r-progress)
("r-rcolorbrewer" ,r-rcolorbrewer)
("r-reshape" ,r-reshape)
("r-rlang" ,r-rlang)))
(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 "0.4-23")
(source
(origin
(method url-fetch)
(uri (cran-uri "proxy" version))
(sha256
(base32
"17b6qfllqrhzrxqgx7dccffgybnkcria5a68ap5ly3plg04ypm4x"))))
(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 "1.4-1")
(source
(origin
(method url-fetch)
(uri (cran-uri "sp" version))
(sha256
(base32 "0fbh865r4py89g6ln8bslig2vbxxwa642p5k5g02rskyhajg35lg"))))
(build-system r-build-system)
(propagated-inputs
`(("r-lattice" ,r-lattice)))
(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-rmtstat
(package
(name "r-rmtstat")
(version "0.3")
(source
(origin
(method url-fetch)
(uri (cran-uri "RMTstat" version))
(sha256
(base32
"1nn25q4kmh9kj975sxkrpa97vh5irqrlqhwsfinbck6h6ia4rsw1"))))
(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")
(source (origin
(method url-fetch)
(uri (cran-uri "Rmpi" version))
(sha256
(base32
"1rhycla98hxgnnxlxxldr1x51djak7c2jjvlrv3jcsvgwp1ymqdj"))))
(properties `((upstream-name . "Rmpi")))
(build-system r-build-system)
(arguments
`(#:configure-flags '("--configure-args=\"--with-Rmpi-type=OPENMPI\"")
#:phases (modify-phases %standard-phases
(add-before 'install 'mpi-setup
,%openmpi-setup))))
(inputs
`(("openmpi" ,openmpi)))
(native-inputs
`(("pkg-config" ,pkg-config)))
(home-page "http://www.stats.uwo.ca/faculty/yu/Rmpi")
(synopsis "R interface to message-passing interface (MPI)")
(description
"This package provides an interface (wrapper) to MPI APIs. It also
provides an interactive R manager and worker environment.")
(license license:gpl2+)))
(define-public r-lmoments
(package
(name "r-lmoments")
(version "1.3-1")
(source
(origin
(method url-fetch)
(uri (cran-uri "Lmoments" version))
(sha256
(base32
"0pc63bj9a8hzr5m3yssrc4kin39fffwkl8rggs3sagzr12d4i7bw"))))
(properties `((upstream-name . "Lmoments")))
(build-system r-build-system)
(propagated-inputs
`(("r-rcpp" ,r-rcpp)
("r-rcpparmadillo" ,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 "1.0-6")
(source
(origin
(method url-fetch)
(uri (cran-uri "distillery" version))
(sha256
(base32
"1mi3ig9jq0kd7yrwc5m37lmrw04p1b4lirnbsxi10z3n5yay4429"))))
(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-extremes
(package
(name "r-extremes")
(version "2.0-11")
(source
(origin
(method url-fetch)
(uri (cran-uri "extRemes" version))
(sha256
(base32
"0hmgynxhzswqnhwb2sxrkczgam8c17s3vpxqc5bcz0bwczpxxyvm"))))
(properties `((upstream-name . "extRemes")))
(build-system r-build-system)
(propagated-inputs
`(("r-distillery" ,r-distillery)
("r-lmoments" ,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 "0.9-37")
(source
(origin
(method url-fetch)
(uri (cran-uri "lmtest" version))
(sha256
(base32
"02nasm0j2vwkhz11dxqixs23msy1s3yj0jps6949fmgh9gwjkjfx"))))
(build-system r-build-system)
(propagated-inputs
`(("r-zoo" ,r-zoo)))
(native-inputs
`(("gfortran" ,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 "1.2")
(source (origin
(method url-fetch)
(uri (cran-uri "idr" version))
(sha256
(base32
"05nvgw1xdg670bsjjrxkgd1mrdkciccpw4krn0zcgdf2r21dzgwb"))))
(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 "0.3.15")
(source (origin
(method url-fetch)
(uri (cran-uri "inline" version))
(sha256
(base32
"0s4wssvpan189fijahknxq5s22ww9bzmdlmyhnra748r7khky17z"))))
(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 "1.0-1")
(source (origin
(method url-fetch)
(uri (cran-uri "inum" version))
(sha256
(base32
"16d09391l65w557dkzhhx1aqn1ljamcmjj3yh42pwq037k0r8brw"))))
(build-system r-build-system)
(propagated-inputs
`(("r-libcoin" ,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-bdsmatrix
(package
(name "r-bdsmatrix")
(version "1.3-4")
(source
(origin
(method url-fetch)
(uri (cran-uri "bdsmatrix" version))
(sha256
(base32
"1sh6pg43rgqvips4fx0k4vmp5i9lmniix0bqwj2yq5m06gs227i5"))))
(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 "1.0.23.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "bbmle" version))
(sha256
(base32
"0p3l9shbr2846qmw8n0fyzf4j7gmi08aypl82jml3dwh26q1whk0"))))
(build-system r-build-system)
(propagated-inputs
`(("r-bdsmatrix" ,r-bdsmatrix)
("r-lattice" ,r-lattice)
("r-mass" ,r-mass)
("r-matrix" ,r-matrix)
("r-mvtnorm" ,r-mvtnorm)
("r-numderiv" ,r-numderiv)))
(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
`(("r-bbmle" ,r-bbmle)
("r-coda" ,r-coda)
("r-lattice" ,r-lattice)
("r-mass" ,r-mass)
("r-plyr" ,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 "5.6.15")
(source
(origin
(method url-fetch)
(uri (cran-uri "lpSolve" version))
(sha256
(base32
"1fpkyjyqykwa1dxnhiky01pm09syxg169lm7hpy39bdbg10vw9s6"))))
(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
`(("r-lpsolve" ,r-lpsolve)
("r-mass" ,r-mass)
("r-quadprog" ,r-quadprog)))
(native-inputs `(("gfortran" ,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 "1.0-14")
(source
(origin
(method url-fetch)
(uri (cran-uri "fitdistrplus" version))
(sha256
(base32
"10q08wsv8v3w7797jdvvv60bgrf1bi6438wf0jcqv81ays82a245"))))
(build-system r-build-system)
(propagated-inputs
`(("r-mass" ,r-mass)
("r-npsurv" ,r-npsurv)
("r-survival" ,r-survival)))
(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 "1.7-7")
(source
(origin
(method url-fetch)
(uri (cran-uri "energy" version))
(sha256
(base32
"13wnx5nwk7nsv7vf5sxhz4y0rxrnzm76ldgywk1bxrz67srqzf37"))))
(build-system r-build-system)
(propagated-inputs
`(("r-boot" ,r-boot)
("r-rcpp" ,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 "1.1-9.5")
(source
(origin
(method url-fetch)
(uri (cran-uri "SuppDists" version))
(sha256
(base32
"01j6p94m1g363nph2158fq2rmd6z3h5dvcv6aidh2d6syw131xak"))))
(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
`(("r-suppdists" ,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 "0.2-2")
(