7780 lines
286 KiB
Scheme
7780 lines
286 KiB
Scheme
;;; GNU Guix --- Functional package management for GNU
|
||
;;; Copyright © 2015-2023 Ricardo Wurmus <rekado@elephly.net>
|
||
;;; Copyright © 2015 Vicente Vera Parra <vicentemvp@gmail.com>
|
||
;;; Copyright © 2016 Andreas Enge <andreas@enge.fr>
|
||
;;; Copyright © 2016, 2017, 2019, 2020, 2021 Efraim Flashner <efraim@flashner.co.il>
|
||
;;; Copyright © 2016 Pjotr Prins <pjotr.guix@thebird.nl>
|
||
;;; Copyright © 2016 Roel Janssen <roel@gnu.org>
|
||
;;; Copyright © 2016 Ben Woodcroft <donttrustben@gmail.com>
|
||
;;; Copyright © 2016, 2017 Raoul Bonnal <ilpuccio.febo@gmail.com>
|
||
;;; Copyright © 2017 Kyle Meyer <kyle@kyleam.com>
|
||
;;; Copyright © 2017–2020, 2022 Tobias Geerinckx-Rice <me@tobias.gr>
|
||
;;; Copyright © 2017 Alex Kost <alezost@gmail.com>
|
||
;;; Copyright © 2018 Alex Branham <alex.branham@gmail.com>
|
||
;;; Copyright © 2020 Tim Howes <timhowes@lavabit.com>
|
||
;;; Copyright © 2021, 2022 Maxim Cournoyer <maxim.cournoyer@gmail.com>
|
||
;;; Copyright © 2021 Bonface Munyoki Kilyungi <me@bonfacemunyoki.com>
|
||
;;; Copyright © 2021 Lars-Dominik Braun <lars@6xq.net>
|
||
;;; Copyright © 2021 Frank Pursel <frank.pursel@gmail.com>
|
||
;;; Copyright © 2022 Simon Tournier <zimon.toutoune@gmail.com>
|
||
;;; Copyright © 2023 gemmaro <gemmaro.dev@gmail.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 statistics)
|
||
#:use-module (guix gexp)
|
||
#:use-module ((guix licenses) #:prefix license:)
|
||
#:use-module (guix packages)
|
||
#:use-module (guix download)
|
||
#:use-module (guix hg-download)
|
||
#:use-module (guix git-download)
|
||
#:use-module (guix utils)
|
||
#:use-module (guix build-system ant)
|
||
#:use-module (guix build-system cmake)
|
||
#:use-module (guix build-system emacs)
|
||
#:use-module (guix build-system gnu)
|
||
#:use-module (guix build-system r)
|
||
#:use-module (guix build-system pyproject)
|
||
#:use-module (guix build-system python)
|
||
#:use-module (guix build-system trivial)
|
||
#:use-module (guix build-system ruby)
|
||
#:use-module (gnu packages)
|
||
#:use-module (gnu packages algebra)
|
||
#:use-module (gnu packages autotools)
|
||
#:use-module (gnu packages bash)
|
||
#:use-module (gnu packages bison)
|
||
#:use-module (gnu packages boost)
|
||
#:use-module (gnu packages check)
|
||
#:use-module (gnu packages compression)
|
||
#:use-module (gnu packages cran)
|
||
#:use-module (gnu packages curl)
|
||
#:use-module (gnu packages emacs)
|
||
#:use-module (gnu packages emacs-xyz)
|
||
#:use-module (gnu packages flex)
|
||
#:use-module (gnu packages fontutils)
|
||
#:use-module (gnu packages gcc)
|
||
#:use-module (gnu packages gtk)
|
||
#:use-module (gnu packages gettext)
|
||
#:use-module (gnu packages glib)
|
||
#:use-module (gnu packages haskell-xyz)
|
||
#:use-module (gnu packages icu4c)
|
||
#:use-module (gnu packages image)
|
||
#:use-module (gnu packages java)
|
||
#:use-module (gnu packages javascript)
|
||
#:use-module (gnu packages libffi)
|
||
#:use-module (gnu packages linux)
|
||
#:use-module (gnu packages machine-learning)
|
||
#:use-module (gnu packages maths)
|
||
#:use-module (gnu packages multiprecision)
|
||
#:use-module (gnu packages ncurses)
|
||
#:use-module (gnu packages ocaml)
|
||
#: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-build)
|
||
#:use-module (gnu packages python-science)
|
||
#:use-module (gnu packages python-xyz)
|
||
#:use-module (gnu packages readline)
|
||
#:use-module (gnu packages ruby)
|
||
#:use-module (gnu packages shells)
|
||
#:use-module (gnu packages sphinx)
|
||
#:use-module (gnu packages ssh)
|
||
#:use-module (gnu packages swig)
|
||
#:use-module (gnu packages tbb)
|
||
#:use-module (gnu packages tcl)
|
||
#:use-module (gnu packages tex)
|
||
#:use-module (gnu packages texinfo)
|
||
#:use-module (gnu packages time)
|
||
#:use-module (gnu packages tls)
|
||
#:use-module (gnu packages base)
|
||
#:use-module (gnu packages uglifyjs)
|
||
#:use-module (gnu packages version-control)
|
||
#:use-module (gnu packages web)
|
||
#:use-module (gnu packages xml)
|
||
#:use-module (gnu packages xorg)
|
||
#:use-module (srfi srfi-1)
|
||
#:use-module (ice-9 match))
|
||
|
||
|
||
(define-public pspp
|
||
(package
|
||
(name "pspp")
|
||
(version "1.4.1")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (string-append "mirror://gnu/pspp/pspp-"
|
||
version ".tar.gz"))
|
||
(sha256
|
||
(base32
|
||
"0lqrash677b09zxdlxp89z6k02y4i23mbqg83956dwl69wc53dan"))))
|
||
(build-system gnu-build-system)
|
||
(arguments
|
||
(list #:phases
|
||
#~(modify-phases %standard-phases
|
||
(add-before 'check 'prepare-tests
|
||
;; Prevent irrelevant errors that cause test output mismatches:
|
||
;; ‘Fontconfig error: No writable cache directories’
|
||
(lambda _
|
||
(setenv "XDG_CACHE_HOME" (getcwd)))))))
|
||
(inputs
|
||
(list cairo
|
||
gettext-minimal
|
||
gsl
|
||
libxml2
|
||
pango
|
||
readline
|
||
gtk+
|
||
gtksourceview-3
|
||
spread-sheet-widget
|
||
zlib))
|
||
(native-inputs
|
||
(list autoconf ;for tests
|
||
`(,glib "bin") ;for glib-genmarshal
|
||
perl
|
||
pkg-config
|
||
python-2 ;for tests
|
||
texinfo))
|
||
(home-page "https://www.gnu.org/software/pspp/")
|
||
(synopsis "Statistical analysis")
|
||
(description
|
||
"GNU PSPP is a statistical analysis program. It can perform
|
||
descriptive statistics, T-tests, linear regression and non-parametric tests.
|
||
It features both a graphical interface as well as command-line input. PSPP
|
||
is designed to interoperate with Gnumeric, LibreOffice and OpenOffice. Data
|
||
can be imported from spreadsheets, text files and database sources and it can
|
||
be output in text, PostScript, PDF or HTML.")
|
||
(license license:gpl3+)))
|
||
|
||
(define-public jags
|
||
(package
|
||
(name "jags")
|
||
(version "4.3.1")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (string-append "mirror://sourceforge/mcmc-jags/JAGS/"
|
||
(version-major version) ".x/Source/"
|
||
"JAGS-" version ".tar.gz"))
|
||
(sha256
|
||
(base32
|
||
"0aa2w4g5057vn1qjp954s2kwxfmy1h7p5yn56fyi7sz9nmaq69gr"))))
|
||
(build-system gnu-build-system)
|
||
(home-page "https://mcmc-jags.sourceforge.net/")
|
||
(native-inputs
|
||
(list gfortran lapack))
|
||
(synopsis "Gibbs sampler")
|
||
(description "JAGS is Just Another Gibbs Sampler. It is a program for
|
||
analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC)
|
||
simulation not wholly unlike BUGS. JAGS was written with three aims in mind:
|
||
|
||
@enumerate
|
||
@item To have a cross-platform engine for the BUGS language;
|
||
@item To be extensible, allowing users to write their own functions,
|
||
distributions and samplers;
|
||
@item To be a platform for experimentation with ideas in Bayesian modelling.
|
||
@end enumerate\n")
|
||
(license license:gpl2)))
|
||
|
||
(define-public libxls
|
||
(package
|
||
(name "libxls")
|
||
(version "1.6.2")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (string-append "https://github.com/libxls/libxls/releases/download/"
|
||
"v" version "/libxls-" version ".tar.gz"))
|
||
(sha256
|
||
(base32 "0wg3ymr43aa1j3scyl9x83b2xgg7wilzpil0dj91a8dzji6w7b2x"))))
|
||
(build-system gnu-build-system)
|
||
(home-page "https://github.com/libxls/libxls")
|
||
(synopsis "Read binary (.xls) Excel spreadsheet files")
|
||
(description
|
||
"libxls is a C library to read .xls spreadsheet files in the binary OLE
|
||
BIFF8 format as created by Excel 97 and later versions. It cannot write them.
|
||
|
||
This package also provides @command{xls2csv} to export Excel files to CSV.")
|
||
(license license:bsd-2)))
|
||
|
||
;; Update this package together with the set of recommended packages: r-boot,
|
||
;; r-class, r-cluster, r-codetools, r-foreign, r-kernsmooth, r-lattice,
|
||
;; r-mass, r-matrix, r-mgcv, r-nlme, r-nnet, r-rpart, r-spatial, r-survival.
|
||
(define r-with-tests
|
||
(package
|
||
(name "r-with-tests")
|
||
(version "4.3.1")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (string-append "mirror://cran/src/base/R-"
|
||
(version-major version) "/R-"
|
||
version ".tar.gz"))
|
||
(sha256
|
||
(base32
|
||
"16dswjcymzr2mj1vjwqdyjaa9d4isa1p6c9viihnyg02y4jbzl4d"))))
|
||
(build-system gnu-build-system)
|
||
(arguments
|
||
`(#:disallowed-references (,tzdata-for-tests)
|
||
#:make-flags
|
||
(list (string-append "LDFLAGS=-Wl,-rpath="
|
||
(assoc-ref %outputs "out")
|
||
"/lib/R/lib")
|
||
;; This affects the embedded timestamp of only the core packages.
|
||
"PKG_BUILT_STAMP=1970-01-01")
|
||
#:phases
|
||
(modify-phases %standard-phases
|
||
(add-before 'configure 'do-not-compress-serialized-files
|
||
(lambda* (#:key inputs #:allow-other-keys)
|
||
;; This ensures that Guix can detect embedded store references;
|
||
;; see bug #28157 for details.
|
||
(substitute* "src/library/base/makebasedb.R"
|
||
(("compress = TRUE") "compress = FALSE"))))
|
||
(add-before 'configure 'patch-coreutils-paths
|
||
(lambda* (#:key inputs #:allow-other-keys)
|
||
(let ((uname-bin (search-input-file inputs "/bin/uname"))
|
||
(rm-bin (search-input-file inputs "/bin/rm")))
|
||
(substitute* "src/scripts/R.sh.in"
|
||
(("uname") uname-bin))
|
||
(substitute* "src/unix/sys-std.c"
|
||
(("rm -Rf ") (string-append rm-bin " -Rf ")))
|
||
(substitute* "src/library/parallel/R/detectCores.R"
|
||
(("'grep")
|
||
(string-append "'"
|
||
(search-input-file inputs "/bin/grep")))
|
||
(("\\| wc -l")
|
||
(string-append "| "
|
||
(search-input-file inputs "/bin/wc")
|
||
" -l"))))))
|
||
(add-after 'unpack 'patch-tests
|
||
(lambda _
|
||
;; This is needed because R is run during the check phase and
|
||
;; /bin/sh doesn't exist in the build container.
|
||
(substitute* "src/unix/sys-unix.c"
|
||
(("\"/bin/sh\"")
|
||
(string-append "\"" (which "sh") "\"")))
|
||
;; This test fails because line numbers are off by two.
|
||
(substitute* "tests/reg-packages.R"
|
||
(("8 <= print" m) (string-append "## " m)))))
|
||
(add-after 'unpack 'build-reproducibly
|
||
(lambda _
|
||
;; The documentation contains time stamps to demonstrate
|
||
;; documentation generation in different phases.
|
||
(substitute* "src/library/tools/man/Rd2HTML.Rd"
|
||
(("\\\\%Y-\\\\%m-\\\\%d at \\\\%H:\\\\%M:\\\\%S")
|
||
"(removed for reproducibility)"))
|
||
|
||
;; Remove timestamp from tracing environment. This fixes
|
||
;; reproducibility of "methods.rd{b,x}".
|
||
(substitute* "src/library/methods/R/trace.R"
|
||
(("dateCreated = Sys.time\\(\\)")
|
||
"dateCreated = as.POSIXct(\"1970-1-1 00:00:00\", tz = \"UTC\")"))
|
||
|
||
;; Ensure that gzipped files are reproducible.
|
||
(substitute* '("src/library/grDevices/Makefile.in"
|
||
"doc/manual/Makefile.in")
|
||
(("R_GZIPCMD\\)" line)
|
||
(string-append line " -n")))
|
||
|
||
;; The "srcfile" procedure in "src/library/base/R/srcfile.R"
|
||
;; queries the mtime of a given file and records it in an object.
|
||
;; This is acceptable at runtime to detect stale source files,
|
||
;; but it destroys reproducibility at build time.
|
||
|
||
;; Similarly, the "srcfilecopy" procedure records the current
|
||
;; time. We change both of them to respect SOURCE_DATE_EPOCH.
|
||
(substitute* "src/library/base/R/srcfile.R"
|
||
(("timestamp <- (timestamp.*|file.mtime.*)" _ time)
|
||
(string-append "timestamp <- \
|
||
as.POSIXct(if (\"\" != Sys.getenv(\"SOURCE_DATE_EPOCH\")) {\
|
||
as.numeric(Sys.getenv(\"SOURCE_DATE_EPOCH\"))\
|
||
} else { " time "}, origin=\"1970-01-01\")\n")))
|
||
|
||
;; This library is installed using "install_package_description",
|
||
;; so we need to pass the "builtStamp" argument.
|
||
(substitute* "src/library/tools/Makefile.in"
|
||
(("(install_package_description\\(.*\"')\\)\"" line prefix)
|
||
(string-append prefix ", builtStamp='1970-01-01')\"")))
|
||
|
||
(substitute* "src/library/Recommended/Makefile.in"
|
||
(("INSTALL_OPTS =" m)
|
||
(string-append m " --built-timestamp=1970-01-01" m)))
|
||
|
||
;; R bundles an older version of help2man, which does not respect
|
||
;; SOURCE_DATE_EPOCH. We cannot just use the latest help2man,
|
||
;; because that breaks a test.
|
||
(with-fluids ((%default-port-encoding "ISO-8859-1"))
|
||
(substitute* "tools/help2man.pl"
|
||
(("my \\$date = strftime \"%B %Y\", localtime" line)
|
||
(string-append line " 1"))))
|
||
|
||
;; The "References" section of this file when converted to
|
||
;; package.rds is sometimes stored with a newline, sometimes with
|
||
;; a space. We avoid this problem by removing the line break
|
||
;; that is suspected to be the culprit.
|
||
(substitute* "src/library/methods/DESCRIPTION.in"
|
||
(("\\(2008\\)\n") "(2008) ")
|
||
((" ``Software") "``Software")
|
||
(("Data Analysis:.") "Data Analysis:\n")
|
||
(("Programming with R") " Programming with R"))
|
||
(substitute* "src/library/tools/DESCRIPTION.in"
|
||
(("codetools, methods, xml2, curl, commonmark, knitr, xfun, mathjaxr")
|
||
"codetools, methods, xml2, curl, commonmark,
|
||
knitr, xfun, mathjaxr"))))
|
||
(add-before 'build 'set-locales
|
||
(lambda _
|
||
(setlocale LC_ALL "C")
|
||
(setenv "LC_ALL" "C")))
|
||
(add-before 'configure 'set-default-pager
|
||
;; Set default pager to "cat", because otherwise it is "false",
|
||
;; making "help()" print nothing at all.
|
||
(lambda _ (setenv "PAGER" "cat")))
|
||
(add-before 'configure 'set-timezone
|
||
;; Some tests require the timezone to be set. However, the
|
||
;; timezone may not just be "UTC", or else a brittle regression
|
||
;; test in reg-tests-1d will fail.
|
||
;; We also need TZ during the configure step.
|
||
(lambda* (#:key inputs #:allow-other-keys)
|
||
(setenv "TZ" "UTC+1")
|
||
(setenv "TZDIR"
|
||
(search-input-directory inputs
|
||
"share/zoneinfo"))))
|
||
(add-before 'check 'set-home
|
||
;; Some tests require that HOME be set.
|
||
(lambda _ (setenv "HOME" "/tmp")))
|
||
(add-after 'build 'make-info
|
||
(lambda _ (invoke "make" "info")))
|
||
(add-after 'build 'install-info
|
||
(lambda _ (invoke "make" "install-info"))))
|
||
#:configure-flags
|
||
`(;; We build the recommended packages here, because they are needed in
|
||
;; order to run the test suite. We disable them in the r-minimal
|
||
;; package.
|
||
"--with-cairo"
|
||
"--with-blas=-lopenblas"
|
||
"--with-libpng"
|
||
"--with-jpeglib"
|
||
"--with-libtiff"
|
||
"--with-ICU"
|
||
"--with-tcltk"
|
||
,(string-append "--with-tcl-config="
|
||
(assoc-ref %build-inputs "tcl")
|
||
"/lib/tclConfig.sh")
|
||
,(string-append "--with-tk-config="
|
||
(assoc-ref %build-inputs "tk")
|
||
"/lib/tkConfig.sh")
|
||
"--enable-R-shlib"
|
||
"--enable-BLAS-shlib"
|
||
"--with-system-tre")))
|
||
;; R has some support for Java. When the JDK is available at configure
|
||
;; time environment variables pointing to the JDK will be recorded under
|
||
;; $R_HOME/etc and ./tools/getsp.java will be compiled which is used by "R
|
||
;; CMD javareconf". "R CMD javareconf" appears to only be used to update
|
||
;; the recorded environment variables in $R_HOME/etc. Refer to
|
||
;; https://cran.r-project.org/doc/manuals/r-release/R-admin.html#Java-support
|
||
;; for additional information.
|
||
|
||
;; As the JDK is a rather large input with only very limited effects on R,
|
||
;; we decided to drop it.
|
||
(native-inputs
|
||
(list bzip2
|
||
perl
|
||
pkg-config
|
||
texinfo ; for building HTML manuals
|
||
(texlive-updmap.cfg
|
||
(list texlive-fancyvrb
|
||
texlive-inconsolata
|
||
texlive-upquote
|
||
texlive-xkeyval))
|
||
tzdata-for-tests
|
||
xz))
|
||
(inputs
|
||
(list coreutils
|
||
curl
|
||
openblas
|
||
gfortran
|
||
grep
|
||
icu4c
|
||
libjpeg-turbo
|
||
libpng
|
||
libtiff
|
||
libxt
|
||
;; We need not only cairo here, but pango to ensure that tests for the
|
||
;; "cairo" bitmapType plotting backend succeed.
|
||
pango
|
||
pcre2
|
||
readline
|
||
tcl
|
||
tk
|
||
which
|
||
zlib
|
||
;; This avoids a reference to the ungraftable static bash. R uses the
|
||
;; detected shell for the "system" procedure.
|
||
bash-minimal))
|
||
(native-search-paths
|
||
(list (search-path-specification
|
||
(variable "R_LIBS_SITE")
|
||
(files (list "site-library/")))))
|
||
(home-page "https://www.r-project.org/")
|
||
(synopsis "Environment for statistical computing and graphics")
|
||
(description
|
||
"R is a language and environment for statistical computing and graphics.
|
||
It provides a variety of statistical techniques, such as linear and nonlinear
|
||
modeling, classical statistical tests, time-series analysis, classification
|
||
and clustering. It also provides robust support for producing
|
||
publication-quality data plots. A large amount of 3rd-party packages are
|
||
available, greatly increasing its breadth and scope.")
|
||
(license license:gpl3+)))
|
||
|
||
(define-public r-minimal
|
||
(package (inherit r-with-tests)
|
||
(name "r-minimal")
|
||
(arguments
|
||
`(#:tests? #f
|
||
,@(substitute-keyword-arguments (package-arguments r-with-tests)
|
||
((#:disallowed-references refs '())
|
||
(cons perl refs))
|
||
((#:configure-flags flags)
|
||
;; Do not build the recommended packages. The build system creates
|
||
;; random temporary directories and embeds their names in some
|
||
;; package files. We build these packages with the r-build-system
|
||
;; instead.
|
||
`(cons "--without-recommended-packages" ,flags))
|
||
((#:phases phases '%standard-phases)
|
||
`(modify-phases ,phases
|
||
(add-after 'install 'remove-extraneous-references
|
||
(lambda* (#:key inputs outputs #:allow-other-keys)
|
||
(let ((out (assoc-ref outputs "out")))
|
||
(substitute* (string-append out "/lib/R/etc/Makeconf")
|
||
(("^# configure.*")
|
||
"# Removed to avoid extraneous references\n"))
|
||
(substitute* (string-append out "/lib/R/bin/libtool")
|
||
(((string-append
|
||
"(-L)?("
|
||
(format #false
|
||
"~a/[^-]+-(~{~a~^|~})-[^/]+"
|
||
(%store-directory)
|
||
'("bzip2"
|
||
"file"
|
||
"glibc-utf8-locales"
|
||
"graphite2"
|
||
"libselinux"
|
||
"libsepol"
|
||
"perl"
|
||
"texinfo"
|
||
"texlive-bin"
|
||
"util-macros"
|
||
"xz"))
|
||
"|"
|
||
(format #false "~a/[^-]+-glibc-[^-]+-static"
|
||
(%store-directory))
|
||
")/lib")) ""))))))))))))
|
||
|
||
(define-public rmath-standalone
|
||
(package (inherit r-minimal)
|
||
(name "rmath-standalone")
|
||
(arguments
|
||
'(#:phases
|
||
(modify-phases %standard-phases
|
||
(add-before 'configure 'set-timezone
|
||
;; We need TZ during the configure step.
|
||
(lambda* (#:key inputs #:allow-other-keys)
|
||
(setenv "TZ" "UTC+1")
|
||
(setenv "TZDIR"
|
||
(search-input-directory inputs "share/zoneinfo"))))
|
||
(add-after 'configure 'chdir
|
||
(lambda _ (chdir "src/nmath/standalone/"))))))
|
||
(synopsis "Standalone R math library")
|
||
(description
|
||
"This package provides the R math library as an independent package.")))
|
||
|
||
(define-public r-boot
|
||
(package
|
||
(name "r-boot")
|
||
(version "1.3-28.1")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "boot" version))
|
||
(sha256
|
||
(base32
|
||
"0lzz08fpn80qzm197s4806hr6skanr3r3rlx6bx7zk4cripygkfl"))))
|
||
(build-system r-build-system)
|
||
(home-page "https://cran.r-project.org/web/packages/boot")
|
||
(synopsis "Bootstrap functions for R")
|
||
(description
|
||
"This package provides functions and datasets for bootstrapping from the
|
||
book \"Bootstrap Methods and Their Application\" by A.C. Davison and
|
||
D.V. Hinkley (1997, CUP), originally written by Angelo Canty for S.")
|
||
;; Unlimited distribution
|
||
(license (license:non-copyleft "file://R/bootfuns.q"))))
|
||
|
||
(define-public r-mass
|
||
(package
|
||
(name "r-mass")
|
||
(version "7.3-60")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "MASS" version))
|
||
(sha256
|
||
(base32
|
||
"1hphf8m1zny4582rvfnl262ydf3f2w0kayxj2b8n855hx87l20mq"))))
|
||
(properties `((upstream-name . "MASS")))
|
||
(build-system r-build-system)
|
||
(home-page "https://www.stats.ox.ac.uk/pub/MASS4/")
|
||
(synopsis "Support functions and datasets for Venables and Ripley's MASS")
|
||
(description
|
||
"This package provides functions and datasets for the book \"Modern
|
||
Applied Statistics with S\" (4th edition, 2002) by Venables and Ripley.")
|
||
;; Either version may be picked.
|
||
(license (list license:gpl2 license:gpl3))))
|
||
|
||
(define-public r-class
|
||
(package
|
||
(name "r-class")
|
||
(version "7.3-22")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "class" version))
|
||
(sha256
|
||
(base32
|
||
"0p6i10jk8mb85bkx4lvixw85lsmgnk4cizcdw33zqhrqx5j436dn"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-mass))
|
||
(home-page "https://www.stats.ox.ac.uk/pub/MASS4/")
|
||
(synopsis "R functions for classification")
|
||
(description
|
||
"This package provides various functions for classification, including
|
||
k-nearest neighbour, Learning Vector Quantization and Self-Organizing Maps.")
|
||
;; Either of the two versions can be picked.
|
||
(license (list license:gpl2 license:gpl3))))
|
||
|
||
(define-public r-cluster
|
||
(package
|
||
(name "r-cluster")
|
||
(version "2.1.4")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "cluster" version))
|
||
(sha256
|
||
(base32
|
||
"1dpmss4mdpw6la5kjf135h2jj5j5zmqvykpj6fl6n5wslbn0rwf6"))))
|
||
(build-system r-build-system)
|
||
(native-inputs
|
||
(list gfortran))
|
||
(home-page "https://cran.r-project.org/web/packages/cluster")
|
||
(synopsis "Methods for cluster analysis")
|
||
(description
|
||
"This package provides methods for cluster analysis. It is a much
|
||
extended version of the original from Peter Rousseeuw, Anja Struyf and Mia
|
||
Hubert, based on Kaufman and Rousseeuw (1990) \"Finding Groups in Data\".")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-codetools
|
||
(package
|
||
(name "r-codetools")
|
||
(version "0.2-19")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "codetools" version))
|
||
(sha256
|
||
(base32
|
||
"1ardg28x2cvilkgsj6bdvvp5snsy3rj7jbz9bpcdlcvzr1kybdy4"))))
|
||
(build-system r-build-system)
|
||
(home-page "https://cran.r-project.org/web/packages/codetools")
|
||
(synopsis "Code analysis tools for R")
|
||
(description "This package provides code analysis tools for R to check R
|
||
code for possible problems.")
|
||
;; Any version of the GPL.
|
||
(license (list license:gpl2+ license:gpl3+))))
|
||
|
||
(define-public r-foreign
|
||
(package
|
||
(name "r-foreign")
|
||
(version "0.8-85")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "foreign" version))
|
||
(sha256
|
||
(base32
|
||
"1azca97fhwb1pzgrjw2xscfh2k7bfryp6wjsdcx2y4h7305d4ych"))))
|
||
(build-system r-build-system)
|
||
(home-page "https://cran.r-project.org/web/packages/foreign")
|
||
(synopsis "Read data stored by other statistics software")
|
||
(description
|
||
"This package provides functions for reading and writing data stored by
|
||
some versions of Epi Info, Minitab, S, SAS, SPSS, Stata, Systat and Weka and
|
||
for reading and writing some dBase files.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-kernsmooth
|
||
(package
|
||
(name "r-kernsmooth")
|
||
(version "2.23-22")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "KernSmooth" version))
|
||
(sha256
|
||
(base32
|
||
"1sblhl7b9d3m6034xd3254ddkj9ssqxawknzksfbgjh68s849q3n"))))
|
||
(properties `((upstream-name . "KernSmooth")))
|
||
(build-system r-build-system)
|
||
(native-inputs
|
||
(list gfortran))
|
||
(home-page "https://cran.r-project.org/web/packages/KernSmooth")
|
||
(synopsis "Functions for kernel smoothing")
|
||
(description
|
||
"This package provides functions for kernel smoothing (and density
|
||
estimation) corresponding to the book: Wand, M.P. and Jones, M.C. (1995)
|
||
\"Kernel Smoothing\".")
|
||
;; Unlimited use and distribution
|
||
(license (license:non-copyleft "file://LICENCE.note"))))
|
||
|
||
(define-public r-lattice
|
||
(package
|
||
(name "r-lattice")
|
||
(version "0.21-9")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "lattice" version))
|
||
(sha256
|
||
(base32
|
||
"0ak9k6s6drd1a25m7mwzb426ms92a2p3ps04h2pacifwnk74ca59"))))
|
||
(build-system r-build-system)
|
||
(home-page "https://lattice.r-forge.r-project.org/")
|
||
(synopsis "High-level data visualization system")
|
||
(description
|
||
"The lattice package provides a powerful and elegant high-level data
|
||
visualization system inspired by Trellis graphics, with an emphasis on
|
||
multivariate data. Lattice is sufficient for typical graphics needs, and is
|
||
also flexible enough to handle most nonstandard requirements.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-matrix
|
||
(package
|
||
(name "r-matrix")
|
||
(version "1.6-1.1")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "Matrix" version))
|
||
(sha256
|
||
(base32
|
||
"1hlcxr38p4ybb67n25cc1ssh2q2r8cj0flc59lid8hclzvqv27ik"))))
|
||
(properties `((upstream-name . "Matrix")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-lattice))
|
||
(home-page "https://Matrix.R-forge.R-project.org/")
|
||
(synopsis "Sparse and dense matrix classes and methods")
|
||
(description
|
||
"This package provides classes and methods for dense and sparse matrices
|
||
and operations on them using LAPACK and SuiteSparse.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-nlme
|
||
(package
|
||
(name "r-nlme")
|
||
(version "3.1-163")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "nlme" version))
|
||
(sha256
|
||
(base32 "12hj7icn0xgsm67awzf8x8afhckxmb98rci9c7gsizdp9x6gyikx"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-lattice))
|
||
(native-inputs
|
||
(list gfortran))
|
||
(home-page "https://cran.r-project.org/web/packages/nlme")
|
||
(synopsis "Linear and nonlinear mixed effects models")
|
||
(description
|
||
"This package provides tools to fit and compare Gaussian linear and
|
||
nonlinear mixed-effects models.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-mgcv
|
||
(package
|
||
(name "r-mgcv")
|
||
(version "1.9-0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "mgcv" version))
|
||
(sha256
|
||
(base32 "0w1v0hdswb332xz3br1fcgacib7ddr4hb96cmlycxcpqq5w01cdj"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-matrix r-nlme))
|
||
(home-page "https://cran.r-project.org/web/packages/mgcv")
|
||
(synopsis "Mixed generalised additive model computation")
|
||
(description
|
||
"GAMs, GAMMs and other generalized ridge regression with multiple smoothing
|
||
parameter estimation by GCV, REML or UBRE/AIC. The library includes a
|
||
@code{gam()} function, a wide variety of smoothers, JAGS support and
|
||
distributions beyond the exponential family.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-nnet
|
||
(package
|
||
(name "r-nnet")
|
||
(version "7.3-19")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "nnet" version))
|
||
(sha256
|
||
(base32
|
||
"1rrc70shnrnn7gyq5fhnmw841a06d8y0vp5pp8xv1lvhj931y959"))))
|
||
(build-system r-build-system)
|
||
(home-page "https://www.stats.ox.ac.uk/pub/MASS4/")
|
||
(synopsis "Feed-forward neural networks and multinomial log-linear models")
|
||
(description
|
||
"This package provides functions for feed-forward neural networks with a
|
||
single hidden layer, and for multinomial log-linear models.")
|
||
(license (list license:gpl2+ license:gpl3+))))
|
||
|
||
(define-public r-rpart
|
||
(package
|
||
(name "r-rpart")
|
||
(version "4.1.19")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "rpart" version))
|
||
(sha256
|
||
(base32
|
||
"0rcm4hk2k0ag9qmb0f933yqrq8jpnclwrzp6825swgsqnp83wwpy"))))
|
||
(build-system r-build-system)
|
||
(home-page "https://cran.r-project.org/web/packages/rpart")
|
||
(synopsis "Recursive partitioning and regression trees")
|
||
(description
|
||
"This package provides recursive partitioning functions for
|
||
classification, regression and survival trees.")
|
||
(license (list license:gpl2+ license:gpl3+))))
|
||
|
||
(define-public r-spatial
|
||
(package
|
||
(name "r-spatial")
|
||
(version "7.3-17")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "spatial" version))
|
||
(sha256
|
||
(base32
|
||
"1msxbxz50qmzjxgix2vcq0f50b4cdvj8nz3qlilp397jrzc3w07i"))))
|
||
(build-system r-build-system)
|
||
(home-page "https://www.stats.ox.ac.uk/pub/MASS4/")
|
||
(synopsis "Functions for kriging and point pattern analysis")
|
||
(description
|
||
"This package provides functions for kriging and point pattern
|
||
analysis.")
|
||
;; Either version may be picked.
|
||
(license (list license:gpl2 license:gpl3))))
|
||
|
||
(define-public r-survival
|
||
(package
|
||
(name "r-survival")
|
||
(version "3.5-7")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "survival" version))
|
||
(sha256
|
||
(base32
|
||
"0bi76kr5xkcs98r795lz9nvsj6zzxq0w6zn1938z0ffx5b9js3nm"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-matrix))
|
||
(home-page "https://github.com/therneau/survival")
|
||
(synopsis "Survival analysis")
|
||
(description
|
||
"This package contains the core survival analysis routines, including
|
||
definition of Surv objects, Kaplan-Meier and Aalen-Johansen (multi-state)
|
||
curves, Cox models, and parametric accelerated failure time models.")
|
||
(license license:lgpl2.0+)))
|
||
|
||
(define-public r
|
||
(package (inherit r-minimal)
|
||
(name "r")
|
||
(source #f)
|
||
(build-system trivial-build-system)
|
||
(arguments '(#:builder (begin (mkdir %output) #t)))
|
||
(propagated-inputs
|
||
(list r-minimal
|
||
r-boot
|
||
r-class
|
||
r-cluster
|
||
r-codetools
|
||
r-foreign
|
||
r-kernsmooth
|
||
r-lattice
|
||
r-mass
|
||
r-matrix
|
||
r-mgcv
|
||
r-nlme
|
||
r-nnet
|
||
r-rpart
|
||
r-spatial
|
||
r-survival))))
|
||
|
||
(define-public r-bit
|
||
(package
|
||
(name "r-bit")
|
||
(version "4.0.5")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "bit" version))
|
||
(sha256
|
||
(base32
|
||
"1g5zakrzkhrqh3d7p1zka6zzzw11rdlbrvxsh05s7dkli1m57wph"))))
|
||
(build-system r-build-system)
|
||
(native-inputs
|
||
(list r-knitr))
|
||
(home-page "https://ff.r-forge.r-project.org")
|
||
(synopsis "Class for vectors of 1-bit booleans")
|
||
(description
|
||
"This package provides bitmapped vectors of booleans (no @code{NA}s),
|
||
coercion from and to logicals, integers and integer subscripts, fast boolean
|
||
operators and fast summary statistics. With @code{bit} class vectors of true
|
||
binary booleans, @code{TRUE} and @code{FALSE} can be stored with 1 bit only.")
|
||
(license license:gpl2)))
|
||
|
||
(define-public r-bit64
|
||
(package
|
||
(name "r-bit64")
|
||
(version "4.0.5")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "bit64" version))
|
||
(sha256
|
||
(base32
|
||
"0y0m7q1rwam1g88cjx7zyi07mj5dipxd9jkl90f294syx8k6ipr5"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-bit))
|
||
(home-page "https://ff.r-forge.r-project.org/")
|
||
(synopsis "S3 class for vectors of 64 bit integers")
|
||
(description
|
||
"The bit64 package provides serializable S3 atomic 64 bit (signed)
|
||
integers that can be used in vectors, matrices, arrays and @code{data.frames}.
|
||
Methods are available for coercion from and to logicals, integers, doubles,
|
||
characters and factors as well as many elementwise and summary functions.
|
||
Many fast algorithmic operations such as @code{match} and @code{order} support
|
||
interactive data exploration and manipulation and optionally leverage
|
||
caching.")
|
||
(license license:gpl2)))
|
||
|
||
(define-public r-chorddiag
|
||
(package
|
||
(name "r-chorddiag")
|
||
(version "0.1.3")
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/mattflor/chorddiag")
|
||
(commit (string-append "v" version))))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"1bpy9q861l1hyyiqbx2f7qzp7j7im8bkcfdwgxzk5fm0250p359a"))
|
||
;; Delete minified JavaScript file
|
||
(snippet
|
||
'(delete-file "inst/htmlwidgets/lib/d3/d3.min.js"))))
|
||
(build-system r-build-system)
|
||
(arguments
|
||
`(#:phases
|
||
(modify-phases %standard-phases
|
||
(add-after 'unpack 'process-javascript
|
||
(lambda* (#:key inputs #:allow-other-keys)
|
||
(with-directory-excursion "inst/htmlwidgets/lib/d3"
|
||
(let ((source (assoc-ref inputs "d3.v4.js"))
|
||
(target "d3.min.js"))
|
||
(format #true "Processing ~a --> ~a~%"
|
||
source target)
|
||
(invoke "esbuild" source "--minify"
|
||
(string-append "--outfile=" target)))))))))
|
||
(propagated-inputs
|
||
(list r-htmlwidgets r-rcolorbrewer))
|
||
(native-inputs
|
||
`(("esbuild" ,esbuild)
|
||
("r-knitr" ,r-knitr)
|
||
("d3.v4.js"
|
||
,(origin
|
||
(method url-fetch)
|
||
(uri "https://d3js.org/d3.v4.js")
|
||
(sha256
|
||
(base32
|
||
"0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg"))))))
|
||
(home-page "https://github.com/mattflor/chorddiag")
|
||
(synopsis "Create D3 chord diagram")
|
||
(description
|
||
"This package provides tools to create interactive chords diagrams via
|
||
the D3 Javascript library. Chord diagrams show directed relationships among a
|
||
group of entities. This package is based on
|
||
@url{http://bl.ocks.org/mbostock/4062006} with some modifications (fading) and
|
||
additions (tooltips, bipartite diagram type).")
|
||
(license license:gpl3+)))
|
||
|
||
(define-public r-dichromat
|
||
(package
|
||
(name "r-dichromat")
|
||
(version "2.0-0.1")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "dichromat" version))
|
||
(sha256
|
||
(base32 "10b0avdar3d1y8x2ya3x5kqxqg0z0mq872hdzvc1nn4amplph1d1"))))
|
||
(build-system r-build-system)
|
||
(home-page "https://cran.r-project.org/web/packages/dichromat")
|
||
(synopsis "Color schemes for dichromats")
|
||
(description
|
||
"Dichromat collapses red-green or green-blue distinctions to simulate the
|
||
effects of different types of color-blindness.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-digest
|
||
(package
|
||
(name "r-digest")
|
||
(version "0.6.33")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "digest" version))
|
||
(sha256
|
||
(base32 "06bq696wpmn8ivbrpxw0qlcf835kc515m8jfv9zbwf8ndf42qw5y"))))
|
||
(build-system r-build-system)
|
||
;; Vignettes require r-knitr, which requires r-digest, so we have to
|
||
;; disable them and the tests.
|
||
(arguments
|
||
`(#:tests? #f
|
||
#:configure-flags (list "--no-build-vignettes")))
|
||
(native-inputs (list r-simplermarkdown))
|
||
(home-page "https://dirk.eddelbuettel.com/code/digest.html")
|
||
(synopsis "Create cryptographic hash digests of R objects")
|
||
(description
|
||
"This package contains an implementation of a function @code{digest()} for
|
||
the creation of hash digests of arbitrary R objects (using the md5, sha-1,
|
||
sha-256, crc32, xxhash and murmurhash algorithms) permitting easy comparison
|
||
of R language objects, as well as a function @code{hmac()} to create hash-based
|
||
message authentication code.
|
||
|
||
Please note that this package is not meant to be deployed for cryptographic
|
||
purposes for which more comprehensive (and widely tested) libraries such as
|
||
OpenSSL should be used.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-estimability
|
||
(package
|
||
(name "r-estimability")
|
||
(version "1.4.1")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "estimability" version))
|
||
(sha256
|
||
(base32
|
||
"090i1xwdp4fwj8jr8nk13w49516lfkk5mq1w7l0lff9g8lgaynn6"))))
|
||
(build-system r-build-system)
|
||
(home-page "https://cran.r-project.org/web/packages/estimability")
|
||
(synopsis "Tools for assessing estimability of linear predictions")
|
||
(description "Provides tools for determining estimability of linear
|
||
functions of regression coefficients, and @code{epredict} methods that handle
|
||
non-estimable cases correctly.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-labeling
|
||
(package
|
||
(name "r-labeling")
|
||
(version "0.4.3")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "labeling" version))
|
||
(sha256
|
||
(base32 "1wk4wa1s8f17b5lf8vs5hxsmyadp2ccmyg4hamq7sdvlrk14yby6"))))
|
||
(build-system r-build-system)
|
||
(home-page "https://cran.r-project.org/web/packages/labeling")
|
||
(synopsis "Axis labeling algorithms")
|
||
(description "The labeling package provides a range of axis labeling
|
||
algorithms.")
|
||
(license license:expat)))
|
||
|
||
(define-public r-magrittr
|
||
(package
|
||
(name "r-magrittr")
|
||
(version "2.0.3")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "magrittr" version))
|
||
(sha256
|
||
(base32 "1ljmrrm36y31db5z4cl863ap8k3jcaxk0qzy3f0cn6iag4zzigx2"))))
|
||
(build-system r-build-system)
|
||
;; knitr needs magrittr
|
||
#;
|
||
(native-inputs
|
||
`(("r-knitr" ,r-knitr)))
|
||
(home-page "https://cran.r-project.org/web/packages/magrittr/index.html")
|
||
(synopsis "Forward-pipe operator for R")
|
||
(description
|
||
"Magrittr provides a mechanism for chaining commands with a new
|
||
forward-pipe operator, %>%. This operator will forward a value, or the result
|
||
of an expression, into the next function call/expression. There is flexible
|
||
support for the type of right-hand side expressions. For more information,
|
||
see package vignette. To quote Rene Magritte, \"Ceci n'est pas un pipe.\"")
|
||
(license license:expat)))
|
||
|
||
(define-public r-munsell
|
||
(package
|
||
(name "r-munsell")
|
||
(version "0.5.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "munsell" version))
|
||
(sha256
|
||
(base32 "16g1fzisbpqb15yh3pqf3iia4csppva5dnv1z88x9dg263xskwyh"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-colorspace))
|
||
(home-page "https://cran.r-project.org/web/packages/munsell")
|
||
(synopsis "Munsell colour system")
|
||
(description
|
||
"The Munsell package contains Functions for exploring and using the
|
||
Munsell colour system.")
|
||
(license license:expat)))
|
||
|
||
(define-public r-permute
|
||
(package
|
||
(name "r-permute")
|
||
(version "0.9-7")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "permute" version))
|
||
(sha256
|
||
(base32
|
||
"1h4dyhcsv8p3h3qxsy98pib9v79dddvrnq7qx6abkblsazxqzy7g"))))
|
||
(build-system r-build-system)
|
||
(native-inputs (list r-knitr))
|
||
;; Tests do not run correctly, but running them properly would entail a
|
||
;; circular dependency with vegan.
|
||
(home-page "https://github.com/gavinsimpson/permute")
|
||
(synopsis "Functions for Generating Restricted Permutations of Data")
|
||
(description
|
||
"This package provides a set of restricted permutation designs for freely
|
||
exchangeable, line transects (time series), spatial grid designs and permutation
|
||
of blocks (groups of samples). @code{permute} also allows split-plot designs,
|
||
in which the whole-plots or split-plots or both can be freely exchangeable.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-plyr
|
||
(package
|
||
(name "r-plyr")
|
||
(version "1.8.9")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "plyr" version))
|
||
(sha256
|
||
(base32 "00z1mvqisnzbbwcwax1gm9ilahpgp21kk4l7hqdz8fym27vygd8m"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs (list r-rcpp))
|
||
(home-page "http://had.co.nz/plyr")
|
||
(synopsis "Tools for Splitting, Applying and Combining Data")
|
||
(description
|
||
"Plyr is a set of tools that solves a common set of problems: you need to
|
||
break a big problem down into manageable pieces, operate on each piece and
|
||
then put all the pieces back together. For example, you might want to fit a
|
||
model to each spatial location or time point in your study, summarise data by
|
||
panels or collapse high-dimensional arrays to simpler summary statistics.")
|
||
(license license:expat)))
|
||
|
||
(define-public r-proto
|
||
(package
|
||
(name "r-proto")
|
||
(version "1.0.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "proto" version))
|
||
(sha256
|
||
(base32 "1l843p8vckjckdhgv37ngv47fga5jzy0n00pmipvp05nnaixk54j"))))
|
||
(build-system r-build-system)
|
||
(home-page "https://github.com/hadley/proto")
|
||
(synopsis "Prototype object-based programming")
|
||
(description
|
||
"Proto is an object oriented system using object-based, also called
|
||
prototype-based, rather than class-based object oriented ideas.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-rcolorbrewer
|
||
(package
|
||
(name "r-rcolorbrewer")
|
||
(version "1.1-3")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "RColorBrewer" version))
|
||
(sha256
|
||
(base32 "1h0s0f4vvlk40cagp3qwhd0layzkjcnqkiwjyhwqns257i1gahjg"))))
|
||
(build-system r-build-system)
|
||
(home-page "https://cran.r-project.org/web/packages/RColorBrewer")
|
||
(synopsis "ColorBrewer palettes")
|
||
(description
|
||
"This package provides color schemes for maps (and other graphics)
|
||
designed by Cynthia Brewer as described at http://colorbrewer2.org")
|
||
;; Includes code licensed under bsd-4
|
||
(license license:asl2.0)))
|
||
|
||
(define-public r-sendmailr
|
||
(package
|
||
(name "r-sendmailr")
|
||
(version "1.4-0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "sendmailR" version))
|
||
(sha256
|
||
(base32
|
||
"1balci88r2ci51xdh5zaqm3ss3vnry8pbkx2qngppc7n2gy932sv"))))
|
||
(properties `((upstream-name . "sendmailR")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-base64enc))
|
||
(native-inputs (list r-knitr))
|
||
(home-page "https://cran.r-project.org/web/packages/sendmailR")
|
||
(synopsis "Send email using R")
|
||
(description
|
||
"This package contains a simple SMTP client which provides a portable
|
||
solution for sending email, including attachments, from within R.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-stringi
|
||
(package
|
||
(name "r-stringi")
|
||
(version "1.7.12")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "stringi" version))
|
||
(sha256
|
||
(base32
|
||
"02g0464sbprrbjlacx727p9ad1s5nbxl2mnvfmm9h7q000lsrs7g"))))
|
||
(build-system r-build-system)
|
||
(inputs (list icu4c))
|
||
(native-inputs (list pkg-config))
|
||
(home-page "http://stringi.rexamine.com/")
|
||
(synopsis "Character string processing facilities")
|
||
(description
|
||
"This package allows for fast, correct, consistent, portable, as well as
|
||
convenient character string/text processing in every locale and any native
|
||
encoding. Owing to the use of the ICU library, the package provides R users
|
||
with platform-independent functions known to Java, Perl, Python, PHP, and Ruby
|
||
programmers. Among available features there are: pattern searching
|
||
(e.g. via regular expressions), random string generation, string collation,
|
||
transliteration, concatenation, date-time formatting and parsing, etc.")
|
||
(license license:bsd-3)))
|
||
|
||
(define-public r-stringr
|
||
(package
|
||
(name "r-stringr")
|
||
(version "1.5.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "stringr" version))
|
||
(sha256
|
||
(base32 "0fk34ql5ak57f06l10ai300kxay6r7kkkyfanh8r24qaf3bmkcaj"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-cli r-glue r-lifecycle r-magrittr r-rlang r-stringi r-vctrs))
|
||
;; We can't add r-knitr here, because this package ends up being an input
|
||
;; to r-knitr.
|
||
#;
|
||
(native-inputs
|
||
(list r-knitr))
|
||
(home-page "https://github.com/hadley/stringr")
|
||
(synopsis "Simple, consistent wrappers for common string operations")
|
||
(description
|
||
"Stringr is a consistent, simple and easy to use set of wrappers around
|
||
the fantastic @code{stringi} package. All function and argument names (and
|
||
positions) are consistent, all functions deal with \"NA\"'s and zero length
|
||
vectors in the same way, and the output from one function is easy to feed into
|
||
the input of another.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-reshape2
|
||
(package
|
||
(name "r-reshape2")
|
||
(version "1.4.4")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "reshape2" version))
|
||
(sha256
|
||
(base32 "1n0jrajpvc8hjkh9z4g8bwq63qy5vy5cgl2pzjardyih4ngcz3fq"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-plyr r-rcpp r-stringr))
|
||
(home-page "https://github.com/hadley/reshape")
|
||
(synopsis "Flexibly reshape data: a reboot of the \"reshape\" package")
|
||
(description
|
||
"Reshape2 is an R library to flexibly restructure and aggregate data
|
||
using just two functions: melt and dcast (or acast).")
|
||
(license license:expat)))
|
||
|
||
(define-public r-ggplot2
|
||
(package
|
||
(name "r-ggplot2")
|
||
(version "3.4.3")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "ggplot2" version))
|
||
(sha256
|
||
(base32 "0hx5j47y2fxrcg4fxavyn5jjycpwkmsiqsjh6kj7nwp7dg79mqjw"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-cli
|
||
r-glue
|
||
r-gtable
|
||
r-isoband
|
||
r-lifecycle
|
||
r-mass
|
||
r-mgcv
|
||
r-tibble
|
||
r-rlang
|
||
r-scales
|
||
r-svglite ; Needed for 'ggsave'
|
||
r-vctrs
|
||
r-withr))
|
||
(native-inputs
|
||
(list r-knitr))
|
||
(home-page "https://ggplot2.tidyverse.org")
|
||
(synopsis "Implementation of the grammar of graphics")
|
||
(description
|
||
"Ggplot2 is an implementation of the grammar of graphics in R. It
|
||
combines the advantages of both base and lattice graphics: conditioning and
|
||
shared axes are handled automatically, and you can still build up a plot step
|
||
by step from multiple data sources. It also implements a sophisticated
|
||
multidimensional conditioning system and a consistent interface to map data to
|
||
aesthetic attributes.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-ggdendro
|
||
(package
|
||
(name "r-ggdendro")
|
||
(version "0.1.23")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "ggdendro" version))
|
||
(sha256
|
||
(base32
|
||
"1f4fz9llmbpb8gh90aid7dvriadx16xdhsl7832yw4pyqj4fjcrs"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-ggplot2 r-mass))
|
||
(native-inputs
|
||
(list r-knitr))
|
||
(home-page "https://github.com/andrie/ggdendro")
|
||
(synopsis "Create Dendrograms and Tree Diagrams Using ggplot2")
|
||
(description "This is a set of tools for dendrograms and tree plots using
|
||
ggplot2. The ggplot2 philosophy is to clearly separate data from the
|
||
presentation. Unfortunately the plot method for dendrograms plots directly
|
||
to a plot device with out exposing the data. The ggdendro package resolves
|
||
this by making available functions that extract the dendrogram plot data.
|
||
The package provides implementations for tree, rpart, as well as diana and
|
||
agnes cluster diagrams.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-gdtools
|
||
(package
|
||
(name "r-gdtools")
|
||
(version "0.3.3")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "gdtools" version))
|
||
(sha256
|
||
(base32
|
||
"10rlx1ciyvh0ayic03kckv360idl9s1zyc2ar5lisns786c1hnns"))))
|
||
(build-system r-build-system)
|
||
(native-inputs
|
||
(list pkg-config))
|
||
(inputs
|
||
(list cairo fontconfig freetype))
|
||
(propagated-inputs
|
||
(list r-curl
|
||
r-fontquiver
|
||
r-gfonts
|
||
r-htmltools
|
||
r-rcpp
|
||
r-systemfonts))
|
||
(home-page "https://cran.r-project.org/web/packages/gdtools")
|
||
(synopsis "Utilities for graphical rendering")
|
||
(description
|
||
"The @code{gdtools} package provides functionalities to get font metrics
|
||
and to generate base64 encoded string from raster matrix.")
|
||
(license license:gpl3)))
|
||
|
||
(define-public r-svglite
|
||
(package
|
||
(name "r-svglite")
|
||
(version "2.1.2")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "svglite" version))
|
||
(sha256
|
||
(base32 "0c00djvlnf4qr30srh3xjnx1valqq8grm5ib0q4485z8gphn7hf2"))))
|
||
(properties `((upstream-name . "svglite")))
|
||
(build-system r-build-system)
|
||
(inputs (list libpng zlib))
|
||
(propagated-inputs (list r-cpp11 r-systemfonts))
|
||
(native-inputs (list r-knitr))
|
||
(home-page "https://svglite.r-lib.org")
|
||
(synopsis "SVG graphics device")
|
||
(description
|
||
"@code{svglite} is a graphics device that produces clean
|
||
@dfn{SVG} (Scalable Vector Graphics) output, suitable for use on the web, or
|
||
hand editing. Compared to the built-in @code{svg()}, @code{svglite} is
|
||
considerably faster, produces smaller files, and leaves text as is.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-assertthat
|
||
(package
|
||
(name "r-assertthat")
|
||
(version "0.2.1")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "assertthat" version))
|
||
(sha256
|
||
(base32
|
||
"17wy5bdfzg73sg2clisg1k3zyn1adkj59x56m5nwia2k8z67zkw5"))))
|
||
(build-system r-build-system)
|
||
(home-page "https://github.com/hadley/assertthat")
|
||
(synopsis "Easy pre and post assertions")
|
||
(description
|
||
"Assertthat is an extension to stopifnot() that makes it easy to declare
|
||
the pre and post conditions that your code should satisfy, while also
|
||
producing friendly error messages so that your users know what they've done
|
||
wrong.")
|
||
(license license:gpl3+)))
|
||
|
||
(define-public r-lazyeval
|
||
(package
|
||
(name "r-lazyeval")
|
||
(version "0.2.2")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "lazyeval" version))
|
||
(sha256
|
||
(base32
|
||
"1m10i059csrcqkcn59a8wspn784alxsq3symzhn24mhhl894346n"))))
|
||
(build-system r-build-system)
|
||
(home-page "https://github.com/hadley/lazyeval")
|
||
(synopsis "Lazy (non-standard) evaluation in R")
|
||
(description
|
||
"This package provides the tools necessary to do non-standard
|
||
evaluation (NSE) in R.")
|
||
(license license:gpl3+)))
|
||
|
||
(define-public r-dbi
|
||
(package
|
||
(name "r-dbi")
|
||
(version "1.1.3")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "DBI" version))
|
||
(sha256
|
||
(base32
|
||
"13a2656w5j9shpcwa7gj2szy7nk9sajjhlisi5wdpgd57msk7frq"))))
|
||
(build-system r-build-system)
|
||
(native-inputs
|
||
(list r-knitr))
|
||
(home-page "https://github.com/rstats-db/DBI")
|
||
(synopsis "R database interface")
|
||
(description
|
||
"The DBI package provides a database interface (DBI) definition for
|
||
communication between R and relational database management systems. All
|
||
classes in this package are virtual and need to be extended by the various
|
||
R/DBMS implementations.")
|
||
(license license:lgpl2.0+)))
|
||
|
||
(define-public r-bh
|
||
(package
|
||
(name "r-bh")
|
||
(version "1.81.0-1")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "BH" version))
|
||
(sha256
|
||
(base32
|
||
"0r7zjxpbm2paliplprwf9769a57clqaiskiiadiy10gissnqn77m"))))
|
||
(build-system r-build-system)
|
||
(home-page "https://github.com/eddelbuettel/bh")
|
||
(synopsis "R package providing subset of Boost headers")
|
||
(description
|
||
"This package aims to provide the most useful subset of Boost libraries
|
||
for template use among CRAN packages.")
|
||
(license license:boost1.0)))
|
||
|
||
(define-public r-evaluate
|
||
(package
|
||
(name "r-evaluate")
|
||
(version "0.22")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "evaluate" version))
|
||
(sha256
|
||
(base32
|
||
"0sz4zimz4brbd9sawdazfgipkmfzzdmdq01b5m8pnrql5xrxhiwh"))))
|
||
(build-system r-build-system)
|
||
(home-page "https://github.com/hadley/evaluate")
|
||
(synopsis "Parsing and evaluation tools for R")
|
||
(description
|
||
"This package provides tools that allow you to recreate the parsing,
|
||
evaluation and display of R code, with enough information that you can
|
||
accurately recreate what happens at the command line. The tools can easily be
|
||
adapted for other output formats, such as HTML or LaTeX.")
|
||
(license license:gpl3+)))
|
||
|
||
(define-public r-formatr
|
||
(package
|
||
(name "r-formatr")
|
||
(version "1.14")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "formatR" version))
|
||
(sha256
|
||
(base32
|
||
"0k271w4bhlj7r9igkiyfw7d7bg30s2mn4sr4alb8f9w57wnapfjf"))))
|
||
(build-system r-build-system)
|
||
(native-inputs
|
||
(list r-knitr))
|
||
(home-page "https://yihui.org/formatr/")
|
||
(synopsis "Format R code automatically")
|
||
(description
|
||
"This package provides a function to format R source code. Spaces and
|
||
indent will be added to the code automatically, and comments will be preserved
|
||
under certain conditions, so that R code will be more human-readable and tidy.
|
||
There is also a Shiny app as a user interface in this package.")
|
||
(license license:gpl3+)))
|
||
|
||
(define-public r-highr
|
||
(package
|
||
(name "r-highr")
|
||
(version "0.10")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "highr" version))
|
||
(sha256
|
||
(base32
|
||
"0yrlpjs8qzq1d7iy4gypnf4x1gvxq6vaghkdh1kfv433yqgvqmgc"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-xfun))
|
||
;; We cannot add knitr to the inputs, because highr depends on xfun, which
|
||
;; is an input to knitr.
|
||
#;
|
||
(native-inputs
|
||
`(("r-knitr" ,r-knitr)))
|
||
(home-page "https://github.com/yihui/highr")
|
||
(synopsis "Syntax highlighting for R source code")
|
||
(description
|
||
"This package provides syntax highlighting for R source code. Currently
|
||
it supports LaTeX and HTML output. Source code of other languages is
|
||
supported via Andre Simon's highlight package.")
|
||
(license license:gpl3+)))
|
||
|
||
(define-public r-mime
|
||
(package
|
||
(name "r-mime")
|
||
(version "0.12")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "mime" version))
|
||
(sha256
|
||
(base32
|
||
"0j9qbq9jfsp61h2d0xmb87pa2wi8nhb1h2wih7l5drf1sr8i0059"))))
|
||
(build-system r-build-system)
|
||
(home-page "https://github.com/yihui/mime")
|
||
(synopsis "R package to map filenames to MIME types")
|
||
(description
|
||
"This package guesses the MIME type from a filename extension using the
|
||
data derived from /etc/mime.types in UNIX-type systems.")
|
||
(license license:gpl2)))
|
||
|
||
(define-public r-markdown
|
||
(package
|
||
(name "r-markdown")
|
||
(version "1.9")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "markdown" version))
|
||
(sha256
|
||
(base32
|
||
"0201v3spgl8a5c5xkddac5a3z9zh8d0nm9yg6alyhhj4cjwmgibh"))))
|
||
(build-system r-build-system)
|
||
;; Skip check phase because the tests require the r-knitr package to be
|
||
;; installed. This prevents installation failures. Knitr normally
|
||
;; shouldn't be available since r-markdown is a dependency of the r-knitr
|
||
;; package.
|
||
(arguments `(#:tests? #f))
|
||
(propagated-inputs
|
||
(list r-commonmark r-xfun))
|
||
(home-page "https://github.com/rstudio/markdown")
|
||
(synopsis "Markdown rendering for R")
|
||
(description
|
||
"This package provides R bindings to the Sundown Markdown rendering
|
||
library (https://github.com/vmg/sundown). Markdown is a plain-text formatting
|
||
syntax that can be converted to XHTML or other formats.")
|
||
(license license:gpl2)))
|
||
|
||
(define-public r-yaml
|
||
(package
|
||
(name "r-yaml")
|
||
(version "2.3.7")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "yaml" version))
|
||
(sha256
|
||
(base32
|
||
"1aw0cvaqw8a0d1r3cplj5kiabkcyz8fghcpi0ax8mi7rw0cv436j"))))
|
||
(build-system r-build-system)
|
||
(home-page "https://cran.r-project.org/web/packages/yaml/")
|
||
(synopsis "Methods to convert R data to YAML and back")
|
||
(description
|
||
"This package implements the libyaml YAML 1.1 parser and
|
||
emitter (http://pyyaml.org/wiki/LibYAML) for R.")
|
||
(license license:bsd-3)))
|
||
|
||
(define-public r-knitr
|
||
(package
|
||
(name "r-knitr")
|
||
(version "1.44")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "knitr" version))
|
||
(sha256
|
||
(base32
|
||
"015ylljvx0q2himch4k813021nvh0l7p5x3aqdkj3w0ax8x8k3ki"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-evaluate r-highr r-xfun r-yaml))
|
||
(home-page "https://yihui.org/knitr/")
|
||
(synopsis "General-purpose package for dynamic report generation in R")
|
||
(description
|
||
"This package provides a general-purpose tool for dynamic report
|
||
generation in R using Literate Programming techniques.")
|
||
;; The code is released under any version of the GPL. As it is used by
|
||
;; r-markdown which is available under GPLv2 only, we have chosen GPLv2+
|
||
;; here.
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-knitrbootstrap
|
||
(package
|
||
(name "r-knitrbootstrap")
|
||
(version "1.0.2")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "knitrBootstrap" version))
|
||
(sha256
|
||
(base32
|
||
"1aj60j7f0gcs120fdrnfbnb7vk7lfn1phil0mghg6a5zldz4cqs3"))))
|
||
(properties `((upstream-name . "knitrBootstrap")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-knitr r-rmarkdown r-markdown))
|
||
(home-page "https://github.com/jimhester/knitrBootstrap")
|
||
(synopsis "Knitr bootstrap framework")
|
||
(description
|
||
"This package provides a framework to create Bootstrap 3 HTML reports
|
||
from knitr Rmarkdown.")
|
||
(license license:expat)))
|
||
|
||
(define-public r-microbenchmark
|
||
(package
|
||
(name "r-microbenchmark")
|
||
(version "1.4.10")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "microbenchmark" version))
|
||
(sha256
|
||
(base32
|
||
"10dlp4295jb5l7lhz80f4mkz3jccv02v277z666wx3bhfaz43k04"))))
|
||
(build-system r-build-system)
|
||
(home-page "https://cran.r-project.org/web/packages/microbenchmark/")
|
||
(synopsis "Accurate timing functions for R")
|
||
(description
|
||
"This package provides infrastructure to accurately measure and compare
|
||
the execution time of R expressions.")
|
||
(license license:bsd-2)))
|
||
|
||
(define-public r-pryr
|
||
(package
|
||
(name "r-pryr")
|
||
(version "0.1.6")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "pryr" version))
|
||
(sha256
|
||
(base32
|
||
"013p2xxd51kr9ddx051cvn45mzgj44fm47nkchdb13l0885a7hb8"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-codetools r-lobstr r-rcpp r-stringr))
|
||
(home-page "https://github.com/hadley/pryr")
|
||
(synopsis "Tools for computing on the R language")
|
||
(description
|
||
"This package provides useful tools to pry back the covers of R and
|
||
understand the language at a deeper level.")
|
||
(license license:gpl2)))
|
||
|
||
(define-public r-memoise
|
||
(package
|
||
(name "r-memoise")
|
||
(version "2.0.1")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "memoise" version))
|
||
(sha256
|
||
(base32
|
||
"1srdzv2bp0splislrabmf1sfbqfi3hn189nq7kxhgjn8k3p38l7q"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-cachem r-rlang))
|
||
(home-page "https://github.com/hadley/memoise")
|
||
(synopsis "Memoise functions for R")
|
||
(description
|
||
"This R package caches the results of a function so that when
|
||
you call it again with the same arguments it returns the pre-computed value.")
|
||
(license license:expat)))
|
||
|
||
(define-public r-crayon
|
||
(package
|
||
(name "r-crayon")
|
||
(version "1.5.2")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "crayon" version))
|
||
(sha256
|
||
(base32
|
||
"0yjsnhifr3nipaid0q11jjglvqmp51g9d2xdh9kfxh5knl2sbabh"))))
|
||
(build-system r-build-system)
|
||
(home-page "https://github.com/gaborcsardi/crayon")
|
||
(synopsis "Colored terminal output for R")
|
||
(description
|
||
"Colored terminal output on terminals that support ANSI color and
|
||
highlight codes. It also works in Emacs ESS. ANSI color support is
|
||
automatically detected. Colors and highlighting can be combined and nested.
|
||
New styles can also be created easily. This package was inspired by the
|
||
\"chalk\" JavaScript project.")
|
||
(license license:expat)))
|
||
|
||
(define-public r-praise
|
||
(package
|
||
(name "r-praise")
|
||
(version "1.0.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "praise" version))
|
||
(sha256
|
||
(base32
|
||
"1gfyypnvmih97p2r0php9qa39grzqpsdbq5g0fdsbpq5zms5w0sw"))))
|
||
(build-system r-build-system)
|
||
(home-page "https://github.com/gaborcsardi/praise")
|
||
(synopsis "Functions to praise users")
|
||
(description
|
||
"This package provides template functions to assist in building friendly
|
||
R packages that praise their users.")
|
||
(license license:expat)))
|
||
|
||
(define-public r-testthat
|
||
(package
|
||
(name "r-testthat")
|
||
(version "3.2.0")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "testthat" version))
|
||
(sha256
|
||
(base32
|
||
"03k58p8kd7vddx7rlcyi28sy48bh3w4xy4c7wi190l7yjlrfa2sv"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-brio
|
||
r-callr
|
||
r-cli
|
||
r-desc
|
||
r-digest
|
||
r-ellipsis
|
||
r-evaluate
|
||
r-jsonlite
|
||
r-lifecycle
|
||
r-magrittr
|
||
r-pkgload
|
||
r-praise
|
||
r-processx
|
||
r-ps
|
||
r-r6
|
||
r-rlang
|
||
r-waldo
|
||
r-withr))
|
||
(native-inputs
|
||
(list r-knitr))
|
||
(home-page "https://github.com/hadley/testthat")
|
||
(synopsis "Unit testing for R")
|
||
(description
|
||
"This package provides a unit testing system for R designed to be fun,
|
||
flexible and easy to set up.")
|
||
(license license:expat)))
|
||
|
||
(define-public r-r6
|
||
(package
|
||
(name "r-r6")
|
||
(version "2.5.1")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "R6" version))
|
||
(sha256
|
||
(base32
|
||
"0j5z0b0myzjyyykk310xsa9n2mcm9bz8yqbq4xgz2yzdq8lvv4ld"))))
|
||
(build-system r-build-system)
|
||
(home-page "https://github.com/wch/R6/")
|
||
(synopsis "Classes with reference semantics in R")
|
||
(description
|
||
"The R6 package allows the creation of classes with reference semantics,
|
||
similar to R's built-in reference classes. Compared to reference classes, R6
|
||
classes are simpler and lighter-weight, and they are not built on S4 classes
|
||
so they do not require the methods package. These classes allow public and
|
||
private members, and they support inheritance, even when the classes are
|
||
defined in different packages.")
|
||
(license license:expat)))
|
||
|
||
(define-public r-rlang
|
||
(package
|
||
(name "r-rlang")
|
||
(version "1.1.1")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "rlang" version))
|
||
(sha256
|
||
(base32
|
||
"16fsibxbh4fy62x6fw358qbniw085qs1wjyr75n22xv9g6kwjpjy"))))
|
||
(build-system r-build-system)
|
||
(home-page "http://rlang.tidyverse.org")
|
||
(synopsis "Functions for base types, core R and Tidyverse features")
|
||
(description "This package provides a toolbox for working with base types,
|
||
core R features like the condition system, and core @code{Tidyverse} features
|
||
like tidy evaluation.")
|
||
(license license:gpl3)))
|
||
|
||
(define-public r-tibble
|
||
(package
|
||
(name "r-tibble")
|
||
(version "3.2.1")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "tibble" version))
|
||
(sha256
|
||
(base32
|
||
"0c916wl19wbhncv05hjzs2vmvvbcxlswjl6i232ygmkzal62v9v5"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-fansi
|
||
r-lifecycle
|
||
r-magrittr
|
||
r-pkgconfig
|
||
r-pillar
|
||
r-rlang
|
||
r-vctrs))
|
||
(native-inputs
|
||
(list r-knitr))
|
||
(home-page "https://github.com/hadley/tibble")
|
||
(synopsis "Simple data frames")
|
||
(description
|
||
"This package provides a @code{tbl_df} class that offers better checking
|
||
and printing capabilities than traditional data frames.")
|
||
(license license:expat)))
|
||
|
||
(define-public r-dplyr
|
||
(package
|
||
(name "r-dplyr")
|
||
(version "1.1.3")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "dplyr" version))
|
||
(sha256
|
||
(base32
|
||
"0hhpzv66rqz7z8vdryzjdkp4flmjvzxrx1pwpxnbmjqgvd3s4hv8"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-cli
|
||
r-generics
|
||
r-glue
|
||
r-lifecycle
|
||
r-magrittr
|
||
r-pillar
|
||
r-r6
|
||
r-rlang
|
||
r-tibble
|
||
r-tidyselect
|
||
r-vctrs))
|
||
(native-inputs
|
||
(list r-knitr))
|
||
(home-page "https://github.com/hadley/dplyr")
|
||
(synopsis "Tools for working with data frames in R")
|
||
(description
|
||
"dplyr is the next iteration of plyr. It is focused on tools for
|
||
working with data frames. It has three main goals: 1) identify the most
|
||
important data manipulation tools needed for data analysis and make them easy
|
||
to use in R; 2) provide fast performance for in-memory data by writing key
|
||
pieces of code in C++; 3) use the same code interface to work with data no
|
||
matter where it is stored, whether in a data frame, a data table or
|
||
database.")
|
||
(license license:expat)))
|
||
|
||
(define-public r-dbplyr
|
||
(package
|
||
(name "r-dbplyr")
|
||
(version "2.3.4")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "dbplyr" version))
|
||
(sha256
|
||
(base32
|
||
"1b6y1jhf5ix4vry165vwid5nqm0d99q61vxak6aw3vfkj379vgk9"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-blob
|
||
r-cli
|
||
r-dbi
|
||
r-dplyr
|
||
r-glue
|
||
r-lifecycle
|
||
r-magrittr
|
||
r-pillar
|
||
r-purrr
|
||
r-r6
|
||
r-rlang
|
||
r-tibble
|
||
r-tidyr
|
||
r-tidyselect
|
||
r-vctrs
|
||
r-withr))
|
||
(native-inputs
|
||
(list r-knitr))
|
||
(home-page "https://github.com/tidyverse/dbplyr")
|
||
(synopsis "Dplyr back end for databases")
|
||
(description
|
||
"This package provides a dplyr back end for databases that allows you to
|
||
work with remote database tables as if they are in-memory data frames. Basic
|
||
features works with any database that has a @code{DBI} back end; more advanced
|
||
features require SQL translation to be provided by the package author.")
|
||
(license license:expat)))
|
||
|
||
(define-public r-acepack
|
||
(package
|
||
(name "r-acepack")
|
||
(version "1.4.2")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "acepack" version))
|
||
(sha256
|
||
(base32
|
||
"14dccqpww3bv59236r0vr6bibhsafhbm7qshdjxp5ww3nw9cvzsv"))))
|
||
(properties
|
||
`((upstream-name . "acepack")
|
||
(updater-extra-inputs . ("gfortran"))))
|
||
(build-system r-build-system)
|
||
(inputs
|
||
(list gfortran))
|
||
(home-page "https://cran.r-project.org/web/packages/acepack")
|
||
(synopsis "Functions for regression transformations")
|
||
(description
|
||
"This package provides ACE and AVAS methods for choosing regression
|
||
transformations.")
|
||
(license license:expat)))
|
||
|
||
(define-public r-formula
|
||
(package
|
||
(name "r-formula")
|
||
(version "1.2-5")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "Formula" version))
|
||
(sha256
|
||
(base32
|
||
"0p1m9pqcn8ns0sn67js53677q8gwxgbl4bymcn5y2r0dc1s4c9c6"))))
|
||
(properties `((upstream-name . "Formula")))
|
||
(build-system r-build-system)
|
||
(home-page "https://cran.r-project.org/web/packages/Formula")
|
||
(synopsis "Extended model formulas")
|
||
(description
|
||
"This package provides a new class @code{Formula}, which extends the base
|
||
class @code{formula}. It supports extended formulas with multiple parts of
|
||
regressors on the right-hand side and/or multiple responses on the left-hand
|
||
side.")
|
||
(license (list license:gpl2+ license:gpl3+))))
|
||
|
||
(define-public r-locfit
|
||
(package
|
||
(name "r-locfit")
|
||
(version "1.5-9.8")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "locfit" version))
|
||
(sha256
|
||
(base32
|
||
"1qqxw69p42l4szr2fl73bdydpcbxn68iyxyyjy7qy3p56bxrn2hd"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-lattice))
|
||
(home-page "https://cran.r-project.org/web/packages/locfit")
|
||
(synopsis "Local regression, likelihood and density estimation")
|
||
(description
|
||
"This package provides functions used for local regression, likelihood
|
||
and density estimation.")
|
||
(license (list license:gpl2+ license:gpl3+))))
|
||
|
||
(define-public r-chron
|
||
(package
|
||
(name "r-chron")
|
||
(version "2.3-61")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "chron" version))
|
||
(sha256
|
||
(base32
|
||
"16rvqkb7c969795d1z1ypb2cfly70zp24qs8ndsq0hx04mv9b5m0"))))
|
||
(build-system r-build-system)
|
||
(home-page "https://cran.r-project.org/web/packages/chron")
|
||
(synopsis "Chronological R objects which can handle dates and times")
|
||
(description
|
||
"This package provides chronological R objects which can handle dates and
|
||
times.")
|
||
(license license:gpl2)))
|
||
|
||
(define-public r-data-table
|
||
(package
|
||
(name "r-data-table")
|
||
(version "1.14.8")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "data.table" version))
|
||
(sha256
|
||
(base32
|
||
"1z9rf5anjvg3bmbbajb12nf65jsxdw35ad9piysrp76zcx9wxchl"))))
|
||
(properties `((upstream-name . "data.table")))
|
||
(build-system r-build-system)
|
||
(inputs
|
||
(list zlib))
|
||
(native-inputs
|
||
(list pkg-config r-knitr))
|
||
(home-page "https://github.com/Rdatatable/data.table/wiki")
|
||
(synopsis "Enhanced version of data.frame R object")
|
||
(description
|
||
"The R package @code{data.table} is an extension of @code{data.frame}
|
||
providing functions for fast aggregation of large data (e.g. 100GB in RAM),
|
||
fast ordered joins, fast add/modify/delete of columns by group, column listing
|
||
and fast file reading.")
|
||
(license license:gpl3+)))
|
||
|
||
(define-public r-xtable
|
||
(package
|
||
(name "r-xtable")
|
||
(version "1.8-4")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "xtable" version))
|
||
(sha256
|
||
(base32
|
||
"077xfm0gphvhsay75amd9v90zk57kjgrrlgih04fyrbqqblc1gjs"))))
|
||
(build-system r-build-system)
|
||
(native-inputs
|
||
(list r-knitr)) ; for vignettes
|
||
(home-page "https://xtable.r-forge.r-project.org/")
|
||
(synopsis "Export R tables to LaTeX or HTML")
|
||
(description
|
||
"This package provides tools to export R data as LaTeX and HTML tables.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public python-vega-datasets
|
||
(package
|
||
(name "python-vega-datasets")
|
||
(version "0.9.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (pypi-uri "vega_datasets" version))
|
||
(sha256
|
||
(base32 "1h1zv607mars2j73v8fdwihjh479blqxyw29nhmc73lf40s9iglx"))
|
||
(modules '((guix build utils)))
|
||
(patches
|
||
(search-patches "python-vega-datasets-remove-la-riots-code.patch"))))
|
||
(build-system pyproject-build-system)
|
||
(arguments
|
||
(list #:phases
|
||
#~(modify-phases %standard-phases
|
||
(add-after 'unpack 'remove-la-riots-dataset
|
||
;; Remove dataset with unclear license.
|
||
(lambda _
|
||
(delete-file "vega_datasets/_data/la-riots.csv"))))))
|
||
(native-inputs (list python-pytest))
|
||
(propagated-inputs (list python-pandas))
|
||
(home-page "https://github.com/altair-viz/vega_datasets")
|
||
(synopsis "Example datasets used by Vega-related projects")
|
||
(description "This package provides a collection of datasets used in Vega
|
||
and Vega-Lite examples.")
|
||
(license license:expat)))
|
||
|
||
(define-public python-altair
|
||
(package
|
||
(name "python-altair")
|
||
(version "5.0.1")
|
||
(source (origin
|
||
(method git-fetch) ; no tests in PyPI
|
||
(uri (git-reference
|
||
(url "https://github.com/altair-viz/altair")
|
||
(commit (string-append "v" version))))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"1r74v5n51br9pjhxdzrr62cdgnwkapci93aifnl8dqmfpizfpd7d"))))
|
||
(build-system pyproject-build-system)
|
||
(arguments
|
||
;; First two open an external connection.
|
||
;; Last introduces a circular dependency on altair-viewer.
|
||
(list #:test-flags #~(list "-k" (string-append
|
||
"not test_from_and_to_json_roundtrip"
|
||
" and not test_render_examples_to_chart"
|
||
" and not test_save_html"))))
|
||
(propagated-inputs (list python-jinja2
|
||
python-jsonschema
|
||
python-numpy
|
||
python-pandas
|
||
python-toolz
|
||
python-typing-extensions))
|
||
(native-inputs (list python-black
|
||
python-hatchling
|
||
python-ipython
|
||
python-m2r
|
||
python-pytest
|
||
python-vega-datasets))
|
||
(home-page "https://altair-viz.github.io/")
|
||
(synopsis "Declarative statistical visualization library for Python")
|
||
(description
|
||
"Vega-Altair is a declarative statistical visualization library for Python.")
|
||
(license license:expat)))
|
||
|
||
(define-public python-hdmedians
|
||
(package
|
||
(name "python-hdmedians")
|
||
(version "0.14.2")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (pypi-uri "hdmedians" version))
|
||
(sha256
|
||
(base32
|
||
"1mn2k8srnmfy451l7zvb2l4hn9701bc5awjm6q3vmqbicyqyqyml"))))
|
||
(build-system pyproject-build-system)
|
||
(arguments
|
||
(list
|
||
#:phases
|
||
'(modify-phases %standard-phases
|
||
(add-before 'check 'build-extensions
|
||
(lambda _
|
||
;; Cython extensions have to be built before running the tests.
|
||
(invoke "python" "setup.py" "build_ext" "--inplace"))))))
|
||
(propagated-inputs (list python-cython python-numpy))
|
||
(native-inputs (list python-nose))
|
||
(home-page "http://github.com/daleroberts/hdmedians")
|
||
(synopsis "High-dimensional medians")
|
||
(description "Various definitions for a high-dimensional median exist and
|
||
this Python package provides a number of fast implementations of these
|
||
definitions. Medians are extremely useful due to their high breakdown
|
||
point (up to 50% contamination) and have a number of nice applications in
|
||
machine learning, computer vision, and high-dimensional statistics.")
|
||
(license license:asl2.0)))
|
||
|
||
(define-public python-arviz
|
||
(package
|
||
(name "python-arviz")
|
||
(version "0.16.1")
|
||
(source (origin
|
||
(method git-fetch) ; PyPI misses some test files
|
||
(uri (git-reference
|
||
(url "https://github.com/arviz-devs/arviz")
|
||
(commit (string-append "v" version))))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"19phaqbpls82300z7ghicrldjxyjq4ilmmwsmd9zkl8c7ld5cb4j"))))
|
||
(build-system pyproject-build-system)
|
||
(arguments
|
||
;; FIXME: matplotlib tests fail because of the "--save" test flag.
|
||
(list #:test-flags #~'("--ignore"
|
||
"arviz/tests/base_tests/test_plots_matplotlib.py")
|
||
#:phases
|
||
#~(modify-phases %standard-phases
|
||
(add-after 'unpack 'remove-radon
|
||
(lambda _
|
||
(delete-file
|
||
;; This dataset is loaded remotely, it's not supposed to
|
||
;; be copied locally.
|
||
"arviz/data/example_data/code/radon/radon.json")))
|
||
(add-before 'check 'write-permission
|
||
(lambda _
|
||
;; 3 tests require write permission.
|
||
(setenv "HOME" "/tmp"))))))
|
||
(native-inputs (list python-cloudpickle python-pytest))
|
||
(propagated-inputs (list python-h5netcdf
|
||
python-matplotlib
|
||
python-numpy
|
||
python-packaging
|
||
python-pandas
|
||
python-scipy
|
||
python-typing-extensions
|
||
python-xarray
|
||
python-xarray-einstats))
|
||
(home-page "https://github.com/arviz-devs/arviz")
|
||
(synopsis "Exploratory analysis of Bayesian models")
|
||
(description
|
||
"ArviZ is a Python package for exploratory analysis of Bayesian models.
|
||
It includes functions for posterior analysis, data storage, model checking,
|
||
comparison and diagnostics.")
|
||
(license license:asl2.0)))
|
||
|
||
(define-public python-pymc
|
||
(package
|
||
(name "python-pymc")
|
||
(version "5.7.2")
|
||
(source (origin
|
||
(method git-fetch) ; no tests in PyPI
|
||
(uri (git-reference
|
||
(url "https://github.com/pymc-devs/pymc")
|
||
(commit (string-append "v" version))))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"1r3lxpfc782f0wphdqfgsskbz52i0gwgrmxb65307k6cqia69s3r"))))
|
||
(build-system pyproject-build-system)
|
||
(arguments
|
||
(list #:tests? #f ; tests are too computationally intensive
|
||
#:phases #~(modify-phases %standard-phases
|
||
(add-after 'unpack 'versioneer
|
||
(lambda _
|
||
(with-output-to-file "setup.cfg"
|
||
(lambda ()
|
||
(display "\
|
||
[versioneer]
|
||
VCS = git
|
||
style = pep440
|
||
versionfile_source = pymc/_version.py
|
||
versionfile_build = pymc/_version.py
|
||
tag_prefix =
|
||
parentdir_prefix = pymc-
|
||
")))
|
||
(invoke "versioneer" "install")
|
||
(substitute* "setup.py"
|
||
(("versioneer.get_version\\(\\)")
|
||
(string-append "\"" #$version "\"")))))
|
||
;; To create the compiledir for tests.
|
||
(add-before 'check 'write-permissions
|
||
(lambda* (#:key tests? #:allow-other-keys)
|
||
(when tests?
|
||
(setenv "HOME" "/tmp")))))))
|
||
(native-inputs (list python-pytest-cov python-versioneer))
|
||
(propagated-inputs (list python-arviz
|
||
python-cachetools
|
||
python-cloudpickle
|
||
python-fastprogress
|
||
python-numpy
|
||
python-pandas
|
||
python-pytensor
|
||
python-scipy
|
||
python-typing-extensions))
|
||
(home-page "https://github.com/pymc-devs/pymc")
|
||
(synopsis "Library for probabilistic programming in Python")
|
||
(description
|
||
"PyMC (formerly PyMC3) is a Python package for Bayesian statistical
|
||
modeling focusing on advanced Markov chain Monte Carlo (MCMC) and variational
|
||
inference (VI) algorithms.")
|
||
(license license:asl2.0)))
|
||
|
||
(define-public python-chaospy
|
||
(package
|
||
(name "python-chaospy")
|
||
(version "4.3.13")
|
||
(source (origin ;; PyPI misses Pytest fixtures.
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/jonathf/chaospy")
|
||
(commit (string-append "v" version))))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"1bn4jmwygs5h0dskbniivj20qblgm75pyi9hcjf47r25kawd730m"))))
|
||
(build-system pyproject-build-system)
|
||
(propagated-inputs (list python-importlib-metadata python-numpoly
|
||
python-numpy python-scipy))
|
||
(native-inputs (list python-pytest python-scikit-learn))
|
||
(home-page "https://chaospy.readthedocs.io/en/master/")
|
||
(synopsis "Numerical tool for performing uncertainty quantification")
|
||
(description "Chaospy is a numerical toolbox for performing uncertainty
|
||
quantification using polynomial chaos expansions, advanced Monte Carlo
|
||
methods implemented in Python. It also include a full suite of tools for
|
||
doing low-discrepancy sampling, quadrature creation, polynomial manipulations,
|
||
and a lot more.")
|
||
(license license:expat)))
|
||
|
||
(define-public python-patsy
|
||
(package
|
||
(name "python-patsy")
|
||
(version "0.5.2")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (pypi-uri "patsy" version))
|
||
(sha256
|
||
(base32
|
||
"17dn72519gvwifw3i8mzwlslxmxkl8ihzfrxg1iblsk70iwdwlsh"))))
|
||
(build-system python-build-system)
|
||
(arguments
|
||
`(#:phases
|
||
(modify-phases %standard-phases
|
||
(replace 'check
|
||
(lambda* (#:key tests? #:allow-other-keys)
|
||
(when tests? (invoke "pytest" "-vv")))))))
|
||
(propagated-inputs
|
||
(list python-numpy python-scipy python-six))
|
||
(native-inputs
|
||
(list python-pytest))
|
||
(home-page "https://github.com/pydata/patsy")
|
||
(synopsis "Describe statistical models and build design matrices")
|
||
(description
|
||
"Patsy is a Python package for describing statistical models and for
|
||
building design matrices.")
|
||
;; The majority of the code is distributed under BSD-2. The module
|
||
;; patsy.compat contains code derived from the Python standard library,
|
||
;; and is covered by the PSFL.
|
||
(license (list license:bsd-2 license:psfl))))
|
||
|
||
(define-public python-mapie
|
||
(package
|
||
(name "python-mapie")
|
||
(version "0.7.0")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (pypi-uri "MAPIE" version))
|
||
(sha256
|
||
(base32
|
||
"1nvi547avvwrck1n7rf5jh7d0ml6jaqjs2p59iwcq2a5xjmdsmsc"))))
|
||
(build-system pyproject-build-system)
|
||
(native-inputs (list python-pandas python-pytest))
|
||
(propagated-inputs (list python-numpy python-scikit-learn))
|
||
(home-page "https://github.com/scikit-learn-contrib/MAPIE")
|
||
(synopsis "Module for estimating prediction intervals")
|
||
(description "MAPIE allows you to easily estimate prediction intervals
|
||
(or prediction sets) using your favourite scikit-learn-compatible model for
|
||
single-output regression or multi-class classification settings.
|
||
|
||
Prediction intervals output by MAPIE encompass both aleatoric and epistemic
|
||
uncertainties and are backed by strong theoretical guarantees thanks to
|
||
conformal prediction methods intervals.")
|
||
(license license:bsd-3)))
|
||
|
||
(define-public python-statsmodels
|
||
(package
|
||
(name "python-statsmodels")
|
||
(version "0.14.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (pypi-uri "statsmodels" version))
|
||
(sha256
|
||
(base32 "1927ysv7m46m1x3wz05i0s3r5x0nasmidf2yy54djrp9i7bcfxb8"))
|
||
(modules '((guix build utils)))
|
||
(snippet
|
||
'(for-each delete-file (find-files "." "\\.c$")))))
|
||
(build-system pyproject-build-system)
|
||
(arguments
|
||
(list
|
||
;; The test suite is very large and rather brittle. Tests often fail
|
||
;; because of minor changes in dependencies that upstream hasn't fixed
|
||
;; in a new release.
|
||
#:tests? #f
|
||
#:phases
|
||
#~(modify-phases %standard-phases
|
||
(add-after 'unpack 'set-matplotlib-backend-to-agg
|
||
(lambda _
|
||
;; Set the matplotlib backend to Agg to avoid problems using the
|
||
;; GTK backend without a display.
|
||
(substitute* (append (find-files "statsmodels/graphics/tests" "\\.py")
|
||
'("statsmodels/tsa/vector_ar/tests/test_var.py"
|
||
"statsmodels/duration/tests/test_survfunc.py"))
|
||
(("import matplotlib\\.pyplot as plt" line)
|
||
(string-append "import matplotlib;matplotlib.use('Agg');"
|
||
line))))))))
|
||
(propagated-inputs
|
||
(list python-numpy python-packaging python-pandas python-patsy
|
||
python-scipy))
|
||
(native-inputs
|
||
(list python-colorama
|
||
python-cython
|
||
python-flake8
|
||
python-isort
|
||
python-joblib
|
||
python-matplotlib
|
||
python-pytest
|
||
python-pytest-randomly
|
||
python-pytest-xdist
|
||
python-setuptools-scm))
|
||
(home-page "https://statsmodels.sourceforge.net/")
|
||
(synopsis "Statistical modeling and econometrics in Python")
|
||
(description
|
||
"Statsmodels is a Python package that provides a complement to scipy for
|
||
statistical computations including descriptive statistics and estimation and
|
||
inference for statistical models.")
|
||
(license license:bsd-3)))
|
||
|
||
(define-public python-openturns
|
||
(package
|
||
(name "python-openturns")
|
||
(version "1.21")
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/openturns/openturns")
|
||
(commit (string-append "v" version))))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32 "05lbx8npvvk7jyakvfpgi9ggdp6cnzwv2hjmjrkji2s42axv0q6d"))))
|
||
(build-system cmake-build-system)
|
||
(arguments
|
||
(list
|
||
#:phases
|
||
#~(modify-phases %standard-phases
|
||
(delete 'check)
|
||
;; This is a Python package which is fully managed by CMake. In
|
||
;; cmake-build-system the check phase runs before install, but the
|
||
;; Python modules required for testing are only installed in the
|
||
;; install phase. Move check to after the install phase.
|
||
(add-after 'install 'check
|
||
(lambda* (#:key tests? #:allow-other-keys)
|
||
(when tests?
|
||
(invoke "ctest" "--exclude-regex"
|
||
;; XXX: Cpp tests fail in 'No such file or directory',
|
||
;; skip for now and only run the Python tests.
|
||
;; TODO: To pass the Python tests below, Ipopt must be
|
||
;; built with MUMPS support, but simply adding mumps
|
||
;; to the inputs doesn't work for it to be found,
|
||
;; possibly because MUMPS doesn't generate a .pc file.
|
||
(string-join
|
||
(list "^cpp"
|
||
"pyinstallcheck_Bonmin_std"
|
||
"pyinstallcheck_Bonmin_4dsoo"
|
||
"pyinstallcheck_Bonmin_MIT15"
|
||
"pyinstallcheck_Bonmin_swiler2014"
|
||
"pyinstallcheck_Ipopt_std"
|
||
"pyinstallcheck_example_plot_optimization_bonmin"
|
||
"pyinstallcheck_coupling_tools")
|
||
"|"))))))))
|
||
(native-inputs
|
||
(list bison
|
||
dvisvgm
|
||
flex
|
||
python-numpydoc
|
||
python-sphinx
|
||
;; python-sphinx-gallery ;; Currently broken
|
||
swig))
|
||
(inputs
|
||
(list openblas ; the only required dependency
|
||
;; The dependecies below are all optional.
|
||
bonmin
|
||
boost
|
||
cbc ;; Maybe this should be propagated by Bonmin?
|
||
ceres
|
||
cminpack
|
||
dlib
|
||
hdf5
|
||
hmat
|
||
ipopt
|
||
libxml2
|
||
mpc
|
||
mpfr
|
||
nlopt
|
||
pagmo
|
||
primesieve
|
||
python-wrapper
|
||
spectra
|
||
tbb))
|
||
(propagated-inputs
|
||
(list python-chaospy
|
||
python-dill
|
||
python-matplotlib
|
||
python-numpy
|
||
python-pandas
|
||
python-scipy))
|
||
(home-page "https://openturns.github.io/www/")
|
||
(synopsis "Uncertainty treatment library")
|
||
(description
|
||
"OpenTURNS is a scientific C++ and Python library including an internal
|
||
data model and algorithms dedicated to the treatment of uncertainties. The
|
||
main goal of this library is giving to specific applications all the
|
||
functionalities needed to treat uncertainties in studies.")
|
||
(license license:lgpl3+)))
|
||
|
||
(define-public r-coda
|
||
(package
|
||
(name "r-coda")
|
||
(version "0.19-4")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "coda" version))
|
||
(sha256
|
||
(base32
|
||
"13z5dwfpnyyhpsbpg4xr9g5c1685jhqj90f4x4qkcykr6kykqba2"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-lattice))
|
||
(home-page "https://cran.r-project.org/web/packages/coda")
|
||
(synopsis "This is a package for Output Analysis and Diagnostics for MCMC")
|
||
(description "This package provides functions for summarizing and plotting
|
||
the output from Markov Chain Monte Carlo (MCMC) simulations, as well as
|
||
diagnostic tests of convergence to the equilibrium distribution of the Markov
|
||
chain.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-ade4
|
||
(package
|
||
(name "r-ade4")
|
||
(version "1.7-22")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "ade4" version))
|
||
(sha256
|
||
(base32
|
||
"1d4knc1c1hha4gwcakbllzmff4g0mh56y058dn6wp9m2hd7gaz80"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-mass r-pixmap r-rcpp r-rcpparmadillo r-sp))
|
||
(home-page "https://pbil.univ-lyon1.fr/ADE-4")
|
||
(synopsis "Multivariate data analysis and graphical display")
|
||
(description
|
||
"The ade4 package contains data analysis functions to analyze ecological
|
||
and environmental data in the framework of Euclidean exploratory methods.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-xml2
|
||
(package
|
||
(name "r-xml2")
|
||
(version "1.3.5")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "xml2" version))
|
||
(sha256
|
||
(base32
|
||
"10p214gzzcy2zzcq2xkh1vz2wrjsys5gplvk9c1crq3nmfki0six"))))
|
||
(build-system r-build-system)
|
||
(inputs
|
||
(list libxml2 zlib))
|
||
(native-inputs
|
||
(list pkg-config r-knitr))
|
||
(home-page "https://github.com/hadley/xml2")
|
||
(synopsis "Parse XML with R")
|
||
(description
|
||
"This package provides a simple, consistent interface to working with XML
|
||
files in R. It is built on top of the libxml2 C library.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-multitaper
|
||
(package
|
||
(name "r-multitaper")
|
||
(version "1.0-17")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "multitaper" version))
|
||
(sha256
|
||
(base32
|
||
"1wqa2whcjxwjqg9z46i48dvrga17fdj63r05kg993r1fpriclc1l"))))
|
||
(build-system r-build-system)
|
||
(native-inputs
|
||
(list gfortran))
|
||
(home-page "https://github.com/wesleyburr/multitaper/")
|
||
(synopsis "Multitaper spectral analysis tools")
|
||
(description
|
||
"This package implements multitaper spectral estimation
|
||
techniques using prolate spheroidal sequences (Slepians) and sine
|
||
tapers for time series analysis. It includes an adaptive weighted
|
||
multitaper spectral estimate, a coherence estimate, Thomson's Harmonic
|
||
F-test, and complex demodulation. The Slepians sequences are
|
||
generated efficiently using a tridiagonal matrix solution, and
|
||
jackknifed confidence intervals are available for most estimates.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-rversions
|
||
(package
|
||
(name "r-rversions")
|
||
(version "2.1.2")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "rversions" version))
|
||
(sha256
|
||
(base32
|
||
"0q5ip3rkhcxz7472fbqddrw3a2wm31b18w7ax0pi6wc27qiihn6y"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-curl r-xml2))
|
||
(home-page "https://github.com/metacran/rversions")
|
||
(synopsis "Query R versions, including 'r-release' and 'r-oldrel'")
|
||
(description
|
||
"This package provides functions to query the main R repository to find
|
||
the versions that @code{r-release} and @code{r-oldrel} refer to, and also all
|
||
previous R versions and their release dates.")
|
||
(license license:expat)))
|
||
|
||
(define-public r-whisker
|
||
(package
|
||
(name "r-whisker")
|
||
(version "0.4.1")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "whisker" version))
|
||
(sha256
|
||
(base32
|
||
"1g7jy6dnc5igs7yqy1n7cmy0ia8dm2yi3qj1mil2y0q88m4m2ldz"))))
|
||
(build-system r-build-system)
|
||
(home-page "https://github.com/edwindj/whisker")
|
||
(synopsis "Logicless mustache templating for R")
|
||
(description
|
||
"This package provides logicless templating, with a syntax that is not
|
||
limited to R.")
|
||
(license license:gpl3+)))
|
||
|
||
(define-public r-backports
|
||
(package
|
||
(name "r-backports")
|
||
(version "1.4.1")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "backports" version))
|
||
(sha256
|
||
(base32
|
||
"0x144hij0rzhrxdq3k5ph8fk7pdgl1avjca25j4mlpmhzdckqp44"))))
|
||
(build-system r-build-system)
|
||
(home-page "https://cran.r-project.org/web/packages/backports")
|
||
(synopsis "Reimplementations of functions introduced since R 3.0.0")
|
||
(description
|
||
"Provides implementations of functions which have been introduced in R
|
||
since version 3.0.0. The backports are conditionally exported which results
|
||
in R resolving the function names to the version shipped with R (if available)
|
||
and uses the implemented backports as fallback. This way package developers
|
||
can make use of the new functions without worrying about the minimum required
|
||
R version.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-checkmate
|
||
(package
|
||
(name "r-checkmate")
|
||
(version "2.2.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "checkmate" version))
|
||
(sha256
|
||
(base32
|
||
"064i6l0n4w4jncpnk5wnj6sxak0jirdz757iirglcxg8ayq19v4n"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-backports))
|
||
(native-inputs
|
||
(list r-knitr))
|
||
(home-page "https://github.com/mllg/checkmate")
|
||
(synopsis "Fast and versatile argument checks")
|
||
(description
|
||
"This package provides tests and assertions to perform frequent argument
|
||
checks. A substantial part of the package was written in C to minimize any
|
||
worries about execution time overhead.")
|
||
(license license:bsd-3)))
|
||
|
||
(define-public r-bbmisc
|
||
(package
|
||
(name "r-bbmisc")
|
||
(version "1.13")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "BBmisc" version))
|
||
(sha256
|
||
(base32
|
||
"01a43raxj374cg6khs14r0bxvfm8v1sp0p2ambp7npnizvwxqi8i"))))
|
||
(properties `((upstream-name . "BBmisc")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-checkmate r-data-table))
|
||
(home-page "https://github.com/berndbischl/BBmisc")
|
||
(synopsis "Miscellaneous functions for R package development")
|
||
(description
|
||
"This package provides miscellaneous helper functions for the development
|
||
of R packages.")
|
||
(license license:bsd-3)))
|
||
|
||
(define-public r-fail
|
||
(package
|
||
(name "r-fail")
|
||
(version "1.3")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "fail" version))
|
||
(sha256
|
||
(base32
|
||
"0vfm6kmpmgsamda5p0sl771kbnsscan31l2chzssyw93kwmams7d"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-bbmisc r-checkmate))
|
||
(home-page "https://github.com/mllg/fail")
|
||
(synopsis "File abstraction interface layer (FAIL)")
|
||
(description
|
||
"This package provides a more comfortable interface to work with R data
|
||
or source files in a key-value fashion.")
|
||
(license license:bsd-3)))
|
||
|
||
(define-public r-batchjobs
|
||
(package
|
||
(name "r-batchjobs")
|
||
(version "1.9")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "BatchJobs" version))
|
||
(sha256
|
||
(base32
|
||
"0xsw25j2ks9bqgz189qdcyj8hzz93snknlik83nj04s6vy0w7aax"))))
|
||
(properties `((upstream-name . "BatchJobs")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-backports
|
||
r-bbmisc
|
||
r-brew
|
||
r-checkmate
|
||
r-data-table
|
||
r-dbi
|
||
r-digest
|
||
r-rsqlite
|
||
r-sendmailr
|
||
r-stringi))
|
||
(home-page "https://github.com/tudo-r/BatchJobs")
|
||
(synopsis "Batch computing with R")
|
||
(description
|
||
"This package provides @code{Map}, @code{Reduce} and @code{Filter}
|
||
variants to generate jobs on batch computing systems like PBS/Torque, LSF,
|
||
SLURM and Sun Grid Engine. Multicore and SSH systems are also supported.")
|
||
(license license:bsd-2)))
|
||
|
||
(define-public r-brew
|
||
(package
|
||
(name "r-brew")
|
||
(version "1.0-8")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "brew" version))
|
||
(sha256
|
||
(base32
|
||
"09kq14nbaw0mmpb2vbfklz786q6lyizzkyg5bg64bmj2f1d2sr8i"))))
|
||
(build-system r-build-system)
|
||
(home-page "https://cran.r-project.org/web/packages/brew")
|
||
(synopsis "Templating framework for report generation")
|
||
(description
|
||
"The brew package implements a templating framework for mixing text and R
|
||
code for report generation. The template syntax is similar to PHP, Ruby's erb
|
||
module, Java Server Pages, and Python's psp module.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-desc
|
||
(package
|
||
(name "r-desc")
|
||
(version "1.4.2")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "desc" version))
|
||
(sha256
|
||
(base32
|
||
"0z1259ghccmrjylydra4bpryqasirsky7bc4gsx0k327pqacz2km"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-cli r-r6 r-rprojroot))
|
||
(home-page "https://github.com/r-pkgs/desc")
|
||
(synopsis "Manipulate DESCRIPTION Files")
|
||
(description
|
||
"This package provides tools to read, write, create, and manipulate
|
||
DESCRIPTION files. It is intended for packages that create or manipulate
|
||
other packages.")
|
||
(license license:expat)))
|
||
|
||
(define-public r-commonmark
|
||
(package
|
||
(name "r-commonmark")
|
||
(version "1.9.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "commonmark" version))
|
||
(sha256
|
||
(base32
|
||
"13slfv9xpd5fhccw6xgm274d338gmpvc4sdzd943dm684rd1ml3d"))))
|
||
(build-system r-build-system)
|
||
(home-page "https://cran.r-project.org/web/packages/commonmark")
|
||
(synopsis "CommonMark and Github Markdown Rendering in R")
|
||
(description
|
||
"The CommonMark specification defines a rationalized version of markdown
|
||
syntax. This package uses the @code{cmark} reference implementation for
|
||
converting markdown text into various formats including HTML, LaTeX and groff
|
||
man. In addition, it exposes the markdown parse tree in XML format. The latest
|
||
version of this package also adds support for Github extensions including
|
||
tables, autolinks and strikethrough text.")
|
||
(license license:bsd-2)))
|
||
|
||
(define-public r-roxygen2
|
||
(package
|
||
(name "r-roxygen2")
|
||
(version "7.2.3")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "roxygen2" version))
|
||
(sha256
|
||
(base32
|
||
"1nhn0jhnxzlyqx0qnpd7k7q3azzngyn0j4zs8awmlmyjfywzli6q"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-brew
|
||
r-cli
|
||
r-commonmark
|
||
r-cpp11
|
||
r-desc
|
||
r-knitr
|
||
r-pkgload
|
||
r-purrr
|
||
r-r6
|
||
r-rlang
|
||
r-stringi
|
||
r-stringr
|
||
r-withr
|
||
r-xml2))
|
||
(native-inputs
|
||
(list r-knitr))
|
||
(home-page "https://github.com/klutometis/roxygen")
|
||
(synopsis "In-source documentation system for R")
|
||
(description
|
||
"Roxygen2 is a Doxygen-like in-source documentation system for Rd,
|
||
collation, and NAMESPACE files.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-openssl
|
||
(package
|
||
(name "r-openssl")
|
||
(version "2.1.1")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "openssl" version))
|
||
(sha256
|
||
(base32
|
||
"1p2bnr4z4vx3yqq5isqb3z4d9vg2isiz8i0h3vxdb5ramzwjd9zs"))))
|
||
(properties
|
||
`((upstream-name . "openssl")
|
||
(updater-extra-inputs . ("openssl"))))
|
||
(build-system r-build-system)
|
||
(arguments
|
||
(list
|
||
#:phases
|
||
'(modify-phases %standard-phases
|
||
(add-after 'unpack 'do-not-use-versioned-linking
|
||
(lambda _
|
||
(substitute* "configure"
|
||
(("PKG_LIBS=\"\\$\\{PKG_LIBS_VERSIONED\\}\"")
|
||
"PKG_LIBS=\"${PKG_LIBS}\"")))))))
|
||
(inputs
|
||
(list openssl zlib))
|
||
(native-inputs
|
||
(list pkg-config r-knitr))
|
||
(propagated-inputs
|
||
(list r-askpass))
|
||
(home-page "https://github.com/jeroenooms/openssl")
|
||
(synopsis "Toolkit for encryption, signatures and certificates")
|
||
(description
|
||
"This package provides R bindings to OpenSSL libssl and libcrypto, plus
|
||
custom SSH pubkey parsers. It supports RSA, DSA and NIST curves P-256, P-384
|
||
and P-521. Cryptographic signatures can either be created and verified
|
||
manually or via x509 certificates. AES block cipher is used in CBC mode for
|
||
symmetric encryption; RSA for asymmetric (public key) encryption. High-level
|
||
envelope functions combine RSA and AES for encrypting arbitrary sized data.
|
||
Other utilities include key generators, hash functions (md5, sha1, sha256,
|
||
etc), base64 encoder, a secure random number generator, and @code{bignum} math
|
||
methods for manually performing crypto calculations on large multibyte
|
||
integers.")
|
||
(license license:expat)))
|
||
|
||
(define-public r-httr
|
||
(package
|
||
(name "r-httr")
|
||
(version "1.4.7")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "httr" version))
|
||
(sha256
|
||
(base32
|
||
"0fisvq3zydmqagn7lj6x98zxkcl7l95gfydl27zkigb7zg1fcm8m"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-curl r-jsonlite r-mime r-openssl r-r6))
|
||
(native-inputs
|
||
(list r-knitr))
|
||
(home-page "https://github.com/hadley/httr")
|
||
(synopsis "Tools for working with URLs and HTTP")
|
||
(description
|
||
"The aim of httr is to provide a wrapper for RCurl customised to the
|
||
demands of modern web APIs. It provides useful tools for working with HTTP
|
||
organised by HTTP verbs (@code{GET()}, @code{POST()}, etc). Configuration
|
||
functions make it easy to control additional request components.")
|
||
(license license:expat)))
|
||
|
||
(define-public r-git2r
|
||
(package
|
||
(name "r-git2r")
|
||
(version "0.32.0")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "git2r" version))
|
||
(sha256
|
||
(base32
|
||
"0wa6k1g7y0sx6s7map7mn579c1h07n185m163msmcjk81i62ap8v"))))
|
||
(build-system r-build-system)
|
||
(inputs
|
||
(list libgit2 zlib))
|
||
(native-inputs
|
||
(list pkg-config))
|
||
(home-page "https://github.com/ropensci/git2r")
|
||
(synopsis "Access Git repositories with R")
|
||
(description
|
||
"This package provides an R interface to the libgit2 library, which is a
|
||
pure C implementation of the Git core methods.")
|
||
;; GPLv2 only with linking exception.
|
||
(license license:gpl2)))
|
||
|
||
(define-public r-rstudioapi
|
||
(package
|
||
(name "r-rstudioapi")
|
||
(version "0.15.0")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "rstudioapi" version))
|
||
(sha256
|
||
(base32
|
||
"1kvc870gx02cpb800zjvdrhfhyfpzgkydgw2g7kxdlrpr8fwhnwk"))))
|
||
(build-system r-build-system)
|
||
(native-inputs
|
||
(list r-knitr))
|
||
(home-page "https://cran.r-project.org/web/packages/rstudioapi")
|
||
(synopsis "Safely access the RStudio API")
|
||
(description
|
||
"This package provides functions to access the RStudio API and provide
|
||
informative error messages when it's not available.")
|
||
(license license:expat)))
|
||
|
||
(define-public r-devtools
|
||
(package
|
||
(name "r-devtools")
|
||
(version "2.4.5")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "devtools" version))
|
||
(sha256
|
||
(base32
|
||
"0jwh14clyj5flygpmifk01avs7mbnj2s1686pxzfrkcshfyhw5iq"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-cli
|
||
r-desc
|
||
r-ellipsis
|
||
r-fs
|
||
r-lifecycle
|
||
r-memoise
|
||
r-miniui
|
||
r-pkgbuild
|
||
r-pkgdown
|
||
r-pkgload
|
||
r-profvis
|
||
r-rcmdcheck
|
||
r-remotes
|
||
r-rlang
|
||
r-roxygen2
|
||
r-rversions
|
||
r-sessioninfo
|
||
r-testthat
|
||
r-urlchecker
|
||
r-usethis
|
||
r-withr))
|
||
(native-inputs
|
||
(list r-knitr))
|
||
(home-page "https://github.com/hadley/devtools")
|
||
(synopsis "Tools to make developing R packages easier")
|
||
(description "The devtools package is a collection of package development
|
||
tools to simplify the devolpment of R packages.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-withr
|
||
(package
|
||
(name "r-withr")
|
||
(version "2.5.1")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "withr" version))
|
||
(sha256
|
||
(base32
|
||
"1kndhxl0fxn40v9yx0iglilani3ym3ywbjf6zbg1pnb52ncf0nm9"))))
|
||
(build-system r-build-system)
|
||
(native-inputs
|
||
(list r-knitr))
|
||
(home-page "https://github.com/jimhester/withr")
|
||
(synopsis "Run code with temporarily modified global state")
|
||
(description
|
||
"This package provides a set of functions to run R code in an environment
|
||
in which global state has been temporarily modified. Many of these functions
|
||
were originally a part of the r-devtools package.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-hms
|
||
(package
|
||
(name "r-hms")
|
||
(version "1.1.3")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "hms" version))
|
||
(sha256
|
||
(base32
|
||
"10h2k5j97fggq3hc0qzxv1q9821y21m326v3x99zsvpl1b3g89p6"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-lifecycle r-pkgconfig r-rlang r-vctrs))
|
||
(home-page "https://github.com/rstats-db/hms")
|
||
(synopsis "Pretty time of day")
|
||
(description
|
||
"This package implements an S3 class for storing and formatting
|
||
time-of-day values, based on the @code{difftime} class.")
|
||
(license license:gpl3+)))
|
||
|
||
(define-public r-readr
|
||
(package
|
||
(name "r-readr")
|
||
(version "2.1.4")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "readr" version))
|
||
(sha256
|
||
(base32
|
||
"03gbzf29kdvf4rdqgdq2jm7c9ifjla3qzpiyqzw1x9jgijj4y54q"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-cli
|
||
r-clipr
|
||
r-cpp11
|
||
r-crayon
|
||
r-hms
|
||
r-lifecycle
|
||
r-tibble
|
||
r-r6
|
||
r-rlang
|
||
r-tzdb
|
||
r-vroom))
|
||
(native-inputs
|
||
(list r-knitr))
|
||
(home-page "https://github.com/hadley/readr")
|
||
(synopsis "Read tabular data")
|
||
(description
|
||
"This package provides functions to read flat or tabular text files from
|
||
disk (or a connection).")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-plotrix
|
||
(package
|
||
(name "r-plotrix")
|
||
(version "3.8-2")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "plotrix" version))
|
||
(sha256
|
||
(base32
|
||
"07xwq3505qb2yak7pfda22yqwifj6m78f8b5rm0ym74808qrawmv"))))
|
||
(build-system r-build-system)
|
||
(home-page "https://cran.r-project.org/web/packages/plotrix")
|
||
(synopsis "Various plotting functions")
|
||
(description
|
||
"This package provides lots of plotting, various labeling, axis and color
|
||
scaling functions for R.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-gridbase
|
||
(package
|
||
(name "r-gridbase")
|
||
(version "0.4-7")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "gridBase" version))
|
||
(sha256
|
||
(base32
|
||
"09jzw4rzwf2y5lcz7b16mb68pn0fqigv34ff7lr6w3yi9k91i1xy"))))
|
||
(build-system r-build-system)
|
||
(home-page "https://cran.r-project.org/web/packages/gridBase")
|
||
(synopsis "Integration of base and grid graphics")
|
||
(description
|
||
"This package provides an integration of base and grid graphics for R.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-latticeextra
|
||
(package
|
||
(name "r-latticeextra")
|
||
(version "0.6-30")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "latticeExtra" version))
|
||
(sha256
|
||
(base32
|
||
"1vcy4xr6c53nbvnxikjnlf5kd3n5hf4d8dzj5d41hj322dlsfl65"))))
|
||
(properties `((upstream-name . "latticeExtra")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-interp
|
||
r-jpeg
|
||
r-lattice
|
||
r-mass
|
||
r-png
|
||
r-rcolorbrewer))
|
||
(home-page "https://latticeextra.r-forge.r-project.org/")
|
||
(synopsis "Extra graphical utilities based on lattice")
|
||
(description
|
||
"Building on the infrastructure provided by the lattice package, this
|
||
package provides several new high-level graphics functions and methods, as
|
||
well as additional utilities such as panel and axis annotation functions.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-rcpparmadillo
|
||
(package
|
||
(name "r-rcpparmadillo")
|
||
(version "0.12.6.4.0")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "RcppArmadillo" version))
|
||
(sha256
|
||
(base32
|
||
"1k7xq2yl4pkc7krz1bcdnx5kfj6n4zjmnm40nly2da2ji87agv49"))))
|
||
(properties `((upstream-name . "RcppArmadillo")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-rcpp))
|
||
(home-page "https://github.com/RcppCore/RcppArmadillo")
|
||
(synopsis "Rcpp integration for the Armadillo linear algebra library")
|
||
(description
|
||
"Armadillo is a templated C++ linear algebra library that aims towards a
|
||
good balance between speed and ease of use. Integer, floating point and
|
||
complex numbers are supported, as well as a subset of trigonometric and
|
||
statistics functions. Various matrix decompositions are provided through
|
||
optional integration with LAPACK and ATLAS libraries. This package includes
|
||
the header files from the templated Armadillo library.")
|
||
;; Armadillo is licensed under the MPL 2.0, while RcppArmadillo (the Rcpp
|
||
;; bindings to Armadillo) is licensed under the GNU GPL version 2 or
|
||
;; later, as is the rest of 'Rcpp'.
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-bitops
|
||
(package
|
||
(name "r-bitops")
|
||
(version "1.0-7")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "bitops" version))
|
||
(sha256
|
||
(base32
|
||
"1i0phmq5yynla5x0frqll1gbf5ww59p3sgz1s06a354zqf9grdg9"))))
|
||
(build-system r-build-system)
|
||
(home-page "https://cran.r-project.org/web/packages/bitops")
|
||
(synopsis "Bitwise operations")
|
||
(description
|
||
"This package provides functions for bitwise operations on integer
|
||
vectors.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-catools
|
||
(package
|
||
(name "r-catools")
|
||
(version "1.18.2")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "caTools" version))
|
||
(sha256
|
||
(base32
|
||
"14q2ry8gaszjl0m97qg62dxv5bpj6k02qwyi7q2lnxgcmwai3mkm"))))
|
||
(properties `((upstream-name . "caTools")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-bitops))
|
||
(home-page "https://cran.r-project.org/web/packages/caTools")
|
||
(synopsis "Various tools including functions for moving window statistics")
|
||
(description
|
||
"This package contains several basic utility functions including:
|
||
moving (rolling, running) window statistic functions, read/write for GIF and
|
||
ENVI binary files, fast calculation of AUC, LogitBoost classifier, base64
|
||
encoder/decoder, round-off-error-free sum and cumsum, etc.")
|
||
(license license:gpl3+)))
|
||
|
||
(define-public r-rprojroot
|
||
(package
|
||
(name "r-rprojroot")
|
||
(version "2.0.3")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "rprojroot" version))
|
||
(sha256
|
||
(base32
|
||
"15zq606s544wmbvk5dw13xq0sspr9dsxyxlvzvn0r48f8x3l4q2h"))))
|
||
(build-system r-build-system)
|
||
(native-inputs
|
||
(list r-knitr))
|
||
(home-page "https://github.com/krlmlr/rprojroot")
|
||
(synopsis "Finding files in project subdirectories")
|
||
(description
|
||
"This package helps accessing files relative to a project root. It
|
||
provides helpers for robust, reliable and flexible paths to files below a
|
||
project root. The root of a project is defined as a directory that matches a
|
||
certain criterion, e.g., it contains a certain regular file.")
|
||
(license license:gpl3)))
|
||
|
||
(define-public r-rmarkdown
|
||
(package
|
||
(name "r-rmarkdown")
|
||
(version "2.25")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "rmarkdown" version))
|
||
(sha256
|
||
(base32 "0m814598vc67sjwk83xh9g17n72618l32dgg7fz8y0gycqk6dr06"))))
|
||
(properties
|
||
`((upstream-name . "rmarkdown")
|
||
(updater-extra-propagated-inputs . ("pandoc"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-bslib
|
||
r-evaluate
|
||
r-fontawesome
|
||
r-htmltools
|
||
r-jquerylib
|
||
r-jsonlite
|
||
r-knitr
|
||
r-stringr
|
||
r-tinytex
|
||
r-xfun
|
||
r-yaml
|
||
pandoc))
|
||
(native-inputs
|
||
(list esbuild r-knitr))
|
||
(home-page "https://rmarkdown.rstudio.com")
|
||
(synopsis "Convert R Markdown documents into a variety of formats")
|
||
(description
|
||
"This package provides tools to convert R Markdown documents into a
|
||
variety of formats.")
|
||
(license license:gpl3+)))
|
||
|
||
(define-public r-gtable
|
||
(package
|
||
(name "r-gtable")
|
||
(version "0.3.4")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "gtable" version))
|
||
(sha256
|
||
(base32
|
||
"0xvrkhcv1896mf3n43mva2mrmk0d8np7sjrykpg1pv54f69h6ckh"))))
|
||
(properties `((upstream-name . "gtable")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-cli r-glue r-lifecycle r-rlang))
|
||
(native-inputs
|
||
(list r-knitr))
|
||
(home-page "https://cran.r-project.org/web/packages/gtable")
|
||
(synopsis "R library to arrange grobs in tables")
|
||
(description
|
||
"Gtable is a collection of tools to make it easier to work with
|
||
\"tables\" of grobs.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-gridextra
|
||
(package
|
||
(name "r-gridextra")
|
||
(version "2.3")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "gridExtra" version))
|
||
(sha256
|
||
(base32
|
||
"0fwfk3cdwxxim7nd55pn7m31bcaqj48y06j7an2k1v1pybk0rdl1"))))
|
||
(properties `((upstream-name . "gridExtra")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-gtable))
|
||
(native-inputs
|
||
(list r-knitr)) ;for building vignettes
|
||
(home-page "https://github.com/baptiste/gridextra")
|
||
(synopsis "Miscellaneous functions for \"Grid\" graphics")
|
||
(description
|
||
"This package provides a number of user-level functions to work with
|
||
@code{grid} graphics, notably to arrange multiple grid-based plots on a page,
|
||
and draw tables.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-pkgconfig
|
||
(package
|
||
(name "r-pkgconfig")
|
||
(version "2.0.3")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "pkgconfig" version))
|
||
(sha256
|
||
(base32
|
||
"0l1qph8zyi2sic3k2qcd7vlfl7rzfh1q7z7zvjkl5f7y1x2fy3rk"))))
|
||
(build-system r-build-system)
|
||
(home-page "https://github.com/gaborcsardi/pkgconfig")
|
||
(synopsis "Private configuration for R packages")
|
||
(description "This package provides the functionality to set configuration
|
||
options on a per-package basis. Options set by a given package only apply to
|
||
that package, other packages are unaffected.")
|
||
(license license:expat)))
|
||
|
||
(define-public r-blob
|
||
(package
|
||
(name "r-blob")
|
||
(version "1.2.4")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "blob" version))
|
||
(sha256
|
||
(base32
|
||
"13vjy9f3zki8w1damz6kqq47689mk4l1navnwh7r6z8lqkmj52fh"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-rlang r-vctrs))
|
||
(home-page "https://github.com/hadley/blob")
|
||
(synopsis "Simple S3 Class for representing vectors of binary data")
|
||
(description "Raw vectors in R are useful for storing a single binary
|
||
object. What if you want to put a vector of them in a data frame? The blob
|
||
package provides the blob object, a list of raw vectors, suitable for use as
|
||
a column in data frame.")
|
||
(license license:gpl3+)))
|
||
|
||
(define-public r-rsqlite
|
||
(package
|
||
(name "r-rsqlite")
|
||
(version "2.3.1")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "RSQLite" version))
|
||
(sha256
|
||
(base32
|
||
"1jil3wgfh1asfb9c4cr9qyr74wb9f87r7sa03kj187201hb3xlly"))))
|
||
(properties `((upstream-name . "RSQLite")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-bit64
|
||
r-blob
|
||
r-cpp11
|
||
r-dbi
|
||
r-memoise
|
||
r-plogr
|
||
r-pkgconfig))
|
||
(native-inputs
|
||
(list r-knitr))
|
||
(home-page "https://github.com/rstats-db/RSQLite")
|
||
(synopsis "SQLite interface for R")
|
||
(description
|
||
"This package embeds the SQLite database engine in R and provides an
|
||
interface compliant with the DBI package. The source for the SQLite
|
||
engine (version 3.8.8.2) is included.")
|
||
(license license:lgpl2.0+)))
|
||
|
||
(define-public r-rcurl
|
||
(package
|
||
(name "r-rcurl")
|
||
(version "1.98-1.12")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "RCurl" version))
|
||
(sha256
|
||
(base32
|
||
"1ci6lsxm0f13yzw712gcbq23syl54x5llvhs2w1b8wwm9vqgx0qs"))))
|
||
(properties `((upstream-name . "RCurl")))
|
||
(build-system r-build-system)
|
||
(arguments
|
||
`(#:phases
|
||
(modify-phases %standard-phases
|
||
(add-after 'unpack 'respect-CURL_CA_BUNDLE
|
||
(lambda _
|
||
(substitute* "R/options.S"
|
||
(("\\.els = rev\\(merge\\(list\\(\\.\\.\\.\\), \\.opts\\)\\)" m)
|
||
(string-append "\
|
||
certs = Sys.getenv(\"CURL_CA_BUNDLE\")
|
||
if (certs != \"\") { .opts = merge.list(.opts, list(cainfo=certs)) }
|
||
" m))))))))
|
||
(native-inputs
|
||
(list libxml2))
|
||
(inputs
|
||
(list curl))
|
||
(propagated-inputs
|
||
(list r-bitops))
|
||
(home-page "https://www.omegahat.net/RCurl")
|
||
(synopsis "General network client interface for R")
|
||
(description
|
||
"The package allows one to compose general HTTP requests and provides
|
||
convenient functions to fetch URIs, GET and POST forms, etc. and process the
|
||
results returned by the Web server. This provides a great deal of control
|
||
over the HTTP/FTP/... connection and the form of the request while providing a
|
||
higher-level interface than is available just using R socket connections.
|
||
Additionally, the underlying implementation is robust and extensive,
|
||
supporting FTP/FTPS/TFTP (uploads and downloads), SSL/HTTPS, telnet, dict,
|
||
ldap, and also supports cookies, redirects, authentication, etc.")
|
||
(license license:bsd-3)))
|
||
|
||
(define-public r-xml
|
||
(package
|
||
(name "r-xml")
|
||
(version "3.99-0.14")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "XML" version))
|
||
(sha256
|
||
(base32
|
||
"1ygi65ddgbsamxw2rm0p2clfak1xj44xyisgk48y72cd9ldaddic"))))
|
||
(properties
|
||
`((upstream-name . "XML")))
|
||
(build-system r-build-system)
|
||
(inputs
|
||
(list libxml2 zlib))
|
||
(native-inputs
|
||
(list pkg-config))
|
||
(home-page "https://www.omegahat.net/RSXML")
|
||
(synopsis "Tools for parsing and generating XML within R")
|
||
(description
|
||
"Many approaches for both reading and creating XML (and HTML)
|
||
documents (including DTDs), both local and accessible via HTTP or FTP. Also
|
||
offers access to an XPath \"interpreter\".")
|
||
(license license:bsd-2)))
|
||
|
||
(define-public r-xnomial
|
||
(package
|
||
(name "r-xnomial")
|
||
(version "1.0.4")
|
||
(source
|
||
(origin (method url-fetch)
|
||
(uri (cran-uri "XNomial" version))
|
||
(sha256
|
||
(base32
|
||
"1mwx302576rmsjllbq2clfxilm3hkyp5bw0wmwqbn0kgv5wpy8z6"))))
|
||
(properties (quasiquote ((upstream-name . "XNomial"))))
|
||
(build-system r-build-system)
|
||
(home-page "https://cran.r-project.org/web/packages/XNomial")
|
||
(synopsis "Goodness-of-Fit test for multinomial data")
|
||
(description
|
||
"This package provides an exact Goodness-of-Fit test for
|
||
multinomial data with fixed probabilities. It can be used to
|
||
determine whether a set of counts fits a given expected ratio. To see
|
||
whether a set of observed counts fits an expectation, one can examine
|
||
all possible outcomes with @code{xmulti()} or a random sample of them
|
||
with @code{xmonte()} and find the probability of an observation
|
||
deviating from the expectation by at least as much as the observed.
|
||
As a measure of deviation from the expected, one can use the
|
||
log-likelihood ratio, the multinomial probability, or the classic
|
||
chi-square statistic. A histogram of the test statistic can also be
|
||
plotted and compared with the asymptotic curve.")
|
||
(license (list license:gpl2+ license:gpl3+))))
|
||
|
||
(define-public r-lambda-r
|
||
(package
|
||
(name "r-lambda-r")
|
||
(version "1.2.4")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "lambda.r" version))
|
||
(sha256
|
||
(base32
|
||
"1mh1g0gsd58gng0hb29vww2yqb2jfs07kba5kxnnqck5j3izwlnj"))))
|
||
(properties `((upstream-name . "lambda.r")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-formatr))
|
||
(home-page "https://cran.r-project.org/web/packages/lambda.r")
|
||
(synopsis "Functional programming extension for R")
|
||
(description
|
||
"This package provides a language extension to efficiently write
|
||
functional programs in R. Syntax extensions include multi-part function
|
||
definitions, pattern matching, guard statements, built-in (optional) type
|
||
safety.")
|
||
(license license:lgpl3+)))
|
||
|
||
(define-public r-futile-options
|
||
(package
|
||
(name "r-futile-options")
|
||
(version "1.0.1")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "futile.options" version))
|
||
(sha256
|
||
(base32
|
||
"0w15agpi88y3qkv6fl72zy2pzyplzgvnj41a4ixhg64mw1sck73s"))))
|
||
(properties
|
||
`((upstream-name . "futile.options")))
|
||
(build-system r-build-system)
|
||
(home-page "https://cran.r-project.org/web/packages/futile.options")
|
||
(synopsis "Options management framework")
|
||
(description
|
||
"The futile.options subsystem provides an easy user-defined options
|
||
management system that is properly scoped. This means that options created
|
||
via @code{futile.options} are fully self-contained and will not collide with
|
||
options defined in other packages.")
|
||
(license license:lgpl3+)))
|
||
|
||
(define-public r-futile-logger
|
||
(package
|
||
(name "r-futile-logger")
|
||
(version "1.4.3")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "futile.logger" version))
|
||
(sha256
|
||
(base32
|
||
"1r3nayk0z9n1svbf8640vw90dal5q07nkn0gv4bnva3pbzb352sy"))))
|
||
(properties `((upstream-name . "futile.logger")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-futile-options r-lambda-r))
|
||
(home-page "https://cran.r-project.org/web/packages/futile.logger")
|
||
(synopsis "Logging utility for R")
|
||
(description
|
||
"This package provides a simple yet powerful logging utility. Based
|
||
loosely on log4j, futile.logger takes advantage of R idioms to make logging a
|
||
convenient and easy to use replacement for @code{cat} and @code{print}
|
||
statements.")
|
||
(license license:lgpl3+)))
|
||
|
||
(define-public r-segmented
|
||
(package
|
||
(name "r-segmented")
|
||
(version "1.6-4")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "segmented" version))
|
||
(sha256
|
||
(base32
|
||
"14ci6hd5xlrz22gvnvy2fzpnp50fbds3wpx4mf2fgi5i7sp0hb27"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs (list r-mass r-nlme))
|
||
(home-page "https://cran.r-project.org/web/packages/segmented")
|
||
(synopsis "Regression models with breakpoints estimation")
|
||
(description
|
||
"Given a regression model, segmented updates the model by adding one or
|
||
more segmented (i.e., piecewise-linear) relationships. Several variables with
|
||
multiple breakpoints are allowed.")
|
||
(license (list license:gpl2+ license:gpl3+))))
|
||
|
||
(define-public r-snow
|
||
(package
|
||
(name "r-snow")
|
||
(version "0.4-4")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "snow" version))
|
||
(sha256
|
||
(base32
|
||
"1j8kvf3imxijsqkdjz4i9s7qggfxqrpas46y5wz6za92y937yn44"))))
|
||
(build-system r-build-system)
|
||
(home-page "https://cran.r-project.org/web/packages/snow")
|
||
(synopsis "Support for simple parallel computing in R")
|
||
(description
|
||
"The snow package provides support for simple parallel computing on a
|
||
network of workstations using R. A master R process calls @code{makeCluster}
|
||
to start a cluster of worker processes; the master process then uses functions
|
||
such as @code{clusterCall} and @code{clusterApply} to execute R code on the
|
||
worker processes and collect and return the results on the master.")
|
||
(license (list license:gpl2+ license:gpl3+))))
|
||
|
||
(define-public r-sparsem
|
||
(package
|
||
(name "r-sparsem")
|
||
(version "1.81")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "SparseM" version))
|
||
(sha256
|
||
(base32
|
||
"0csbqd9wm6r4162mday1iaigzf9wv2rp1zq8hnihys6f38w8z0xx"))))
|
||
(properties
|
||
`((upstream-name . "SparseM")))
|
||
(native-inputs
|
||
(list gfortran))
|
||
(build-system r-build-system)
|
||
(home-page "http://www.econ.uiuc.edu/~roger/research/sparse/sparse.html")
|
||
(synopsis "Sparse linear algebra")
|
||
(description
|
||
"This package provides some basic linear algebra functionality for sparse
|
||
matrices. It includes Cholesky decomposition and backsolving as well as
|
||
standard R subsetting and Kronecker products.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-iterators
|
||
(package
|
||
(name "r-iterators")
|
||
(version "1.0.14")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "iterators" version))
|
||
(sha256
|
||
(base32
|
||
"0yv7rh6ghlfx727xy2aq64a7skyxp9msakaffs641q9h15d0gwyf"))))
|
||
(build-system r-build-system)
|
||
(home-page "https://cran.r-project.org/web/packages/iterators")
|
||
(synopsis "Iterator construct for R")
|
||
(description
|
||
"This package provides support for iterators, which allow a programmer to
|
||
traverse through all the elements of a vector, list, or other collection of
|
||
data.")
|
||
(license license:asl2.0)))
|
||
|
||
(define-public r-foreach
|
||
(package
|
||
(name "r-foreach")
|
||
(version "1.5.2")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "foreach" version))
|
||
(sha256
|
||
(base32
|
||
"1r5gdf9fp3rprvrhf0gzl9qmmqhgdn5gscpm5hk8zxpraf3qscsn"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-codetools r-iterators))
|
||
(native-inputs
|
||
(list r-knitr))
|
||
(home-page "https://cran.r-project.org/web/packages/foreach")
|
||
(synopsis "Foreach looping construct for R")
|
||
(description
|
||
"This package provides support for the @code{foreach} looping construct.
|
||
@code{foreach} is an idiom that allows for iterating over elements in a
|
||
collection, without the use of an explicit loop counter. This package in
|
||
particular is intended to be used for its return value, rather than for its
|
||
side effects. In that sense, it is similar to the standard @code{lapply}
|
||
function, but doesn't require the evaluation of a function. Using
|
||
@code{foreach} without side effects also facilitates executing the loop in
|
||
parallel.")
|
||
(license license:asl2.0)))
|
||
|
||
(define-public r-doparallel
|
||
(package
|
||
(name "r-doparallel")
|
||
(version "1.0.17")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "doParallel" version))
|
||
(sha256
|
||
(base32
|
||
"1mxbg2qqda1775vb4s26gz27p5n91lljgjmlqxq4sras22njasmr"))))
|
||
(properties `((upstream-name . "doParallel")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-foreach r-iterators))
|
||
(home-page "https://cran.r-project.org/web/packages/doParallel")
|
||
(synopsis "Foreach parallel adaptor for the 'parallel' package")
|
||
(description
|
||
"This package provides a parallel backend for the @code{%dopar%} function
|
||
using the parallel package.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-domc
|
||
(package
|
||
(name "r-domc")
|
||
(version "1.3.8")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "doMC" version))
|
||
(sha256
|
||
(base32
|
||
"18qrcvqwm4cclvk8spvyi281y8prwzivj52xmzk1l9a82j2ny65j"))))
|
||
(properties `((upstream-name . "doMC")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-foreach r-iterators))
|
||
(home-page "https://cran.r-project.org/web/packages/doMC")
|
||
(synopsis "Foreach parallel adaptor for the 'parallel' package")
|
||
(description
|
||
"This package provides a parallel backend for the @code{%dopar%} function
|
||
using the multicore functionality of the parallel package.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-dt
|
||
(let* ((extension-url (lambda (name version file)
|
||
(format #false
|
||
"https://cdn.datatables.net/~a/~a/js/~a"
|
||
(string-downcase name)
|
||
version file)))
|
||
(extensions
|
||
'(((name . "AutoFill")
|
||
(version . "2.5.3")
|
||
(files . (("dataTables.autoFill.js"
|
||
"0r5v76lmysblb4l5g1qgdg6zb2sbkarzfp5fk9zixsyb4c40rrb5")
|
||
("autoFill.bootstrap.js"
|
||
"01dwlc9r2dw8pjylp0r3i8snfc10i02r76564qcdby8slbgfxj6g")
|
||
("autoFill.bootstrap4.js"
|
||
"0myiykq7nxa3c9hj387r0yhy9vm3qw2051m5siqsbc0zm5n82nkh")
|
||
("autoFill.bootstrap5.js"
|
||
"1sq9164xz5w88hdn01cqraimvdzn6a9lplmy7j3klci8hmlivisy")
|
||
("autoFill.bulma.js"
|
||
"1zyp1dghay6ndj58krqhx30vhlhd5z4hm38yv4mbk2ph413f2y88")
|
||
("autoFill.dataTables.js"
|
||
"0g0z5k9hc575zwjylx58mq7xi9l5id1mx30rvrnqb6afr7l69h4n")
|
||
("autoFill.foundation.js"
|
||
"1rz24ai5v2aj4cpwaa5c2xw5ilypfpvygj4cyars4p76y7gfiiir")
|
||
("autoFill.jqueryui.js"
|
||
"059r8vswsasardsrsvr11xfr1kb6d0qqwc77x9qnzjq0bl7ksn1y")
|
||
("autoFill.semanticui.js"
|
||
"0imildga2yhjkps07n5bbfw0b0pqbphszl7151gimrsn79xwqjm6"))))
|
||
((name . "Buttons")
|
||
(version . "2.3.6")
|
||
(files . (("dataTables.buttons.js"
|
||
"19am96fj5xzsagp5wgn2ayiad9gm11vch2mz8l3a21l770dc86rl")
|
||
("buttons.bootstrap.js"
|
||
"0dk2f4cs4bww56ldmcpdfaisymf61j914awbqjlb66brdv70p1nb")
|
||
("buttons.bootstrap4.js"
|
||
"0cvkgw83xyf601zp2pr9d5xhllbn1pjb8bnalja7yi6cswg7r5mp")
|
||
("buttons.bootstrap5.js"
|
||
"0mnbdx5pm8ybxgg048zdi4v4awwyq1pyykwbgqhww5l4byjvvwpp")
|
||
("buttons.bulma.js"
|
||
"11clmyxcn6z8rpv8ikcm3f2vcajp3cikvjcgrmds0d2w7gmzy36i")
|
||
("buttons.colVis.js"
|
||
"1ykzl8ka8lslzi1db9jssm416apr8ha1nyb300kvmb9hwxplx4sj")
|
||
("buttons.foundation.js"
|
||
"0zkzkqj2d8swn1fy11bkr9fy7g4jfl99m5p4ihcg5l9lbsr0zirp")
|
||
("buttons.html5.js"
|
||
"1gg8jp57kp6m609jjpf70hkxyn1zz4lfpiyhvj3i2fqlfp3pwgaw")
|
||
("buttons.jqueryui.js"
|
||
"18ah16sq41nbgkl3i1yqbllsdg99h48v3yaa2y2g8qwbx2b0aiw6")
|
||
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||
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||
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||
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||
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||
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||
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||
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||
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||
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||
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||
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||
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||
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||
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||
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||
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||
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||
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||
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||
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||
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|
||
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||
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||
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|
||
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||
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||
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|
||
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|
||
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||
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|
||
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||
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|
||
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|
||
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|
||
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|
||
(map (lambda (file+hash)
|
||
(list (extension-url (assoc-ref extension 'name)
|
||
(assoc-ref extension 'version)
|
||
(car file+hash))
|
||
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|
||
(string-append "datatables-extensions/"
|
||
(assoc-ref extension 'name))))
|
||
(assoc-ref extension 'files)))
|
||
extensions)))))
|
||
(package
|
||
(name "r-dt")
|
||
(version "0.30")
|
||
(source (origin
|
||
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|
||
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|
||
(sha256
|
||
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|
||
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|
||
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|
||
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|
||
(snippet
|
||
`(with-directory-excursion "inst/htmlwidgets/lib"
|
||
(for-each (match-lambda
|
||
((url hash dir)
|
||
(let ((file (string-append dir "/js/" (basename url ".js") ".min.js")))
|
||
(delete-file file))))
|
||
',javascript-sources)
|
||
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|
||
(delete-file "selectize/selectize.min.js")
|
||
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|
||
(for-each delete-file
|
||
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|
||
"searchHighlight/source.min.js")))))))
|
||
(properties
|
||
`((upstream-name . "DT")))
|
||
(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 'process-javascript
|
||
(lambda* (#:key inputs #:allow-other-keys)
|
||
(with-directory-excursion "inst/htmlwidgets/lib/"
|
||
(for-each (match-lambda
|
||
((url hash dir)
|
||
(let* ((input (string-append "js:" (basename url)))
|
||
(source (assoc-ref inputs input))
|
||
(target (string-append dir "/js/"
|
||
(basename url ".js")
|
||
".min.js")))
|
||
(mkdir-p dir)
|
||
(minify source #:target target))))
|
||
',javascript-sources)
|
||
(minify (string-append (assoc-ref inputs "datatables-plugins")
|
||
"/dataRender/ellipsis.js")
|
||
#:target "datatables-plugins/dataRender/ellipsis/source.min.js")
|
||
(minify (string-append (assoc-ref inputs "datatables-plugins")
|
||
"/filtering/type-based/accent-neutralise.js")
|
||
#:target "datatables-plugins/filtering/accent-neutralise/source.min.js")
|
||
(minify (string-append (assoc-ref inputs "datatables-plugins")
|
||
"/filtering/type-based/diacritics-neutralise.js")
|
||
#:target "datatables-plugins/filtering/diacritics-neutralise/source.min.js")
|
||
(minify (string-append (assoc-ref inputs "datatables-plugins")
|
||
"/sorting/natural.js")
|
||
#:target "datatables-plugins/sorting/natural/source.min.js")
|
||
(minify (string-append (assoc-ref inputs "datatables-plugins")
|
||
"/features/scrollResize/dataTables.scrollResize.js")
|
||
#:target "datatables-plugins/features/scrollResize/source.min.js")
|
||
(minify (string-append (assoc-ref inputs "datatables-plugins")
|
||
"/features/searchHighlight/dataTables.searchHighlight.js")
|
||
#:target "datatables-plugins/features/searchHighlight/source.min.js")
|
||
(minify (assoc-ref inputs "js-nouislider")
|
||
#:target "nouislider/jquery.nouislider.min.js")
|
||
|
||
(let ((replace-file (lambda (old new)
|
||
(format #t "replacing ~a with ~a\n" old new)
|
||
(symlink new old))))
|
||
(replace-file "selectize/selectize.min.js"
|
||
(string-append (assoc-ref inputs "js-selectize")
|
||
"/share/javascript/selectize.min.js")))))))))
|
||
(propagated-inputs
|
||
(list r-crosstalk
|
||
r-htmltools
|
||
r-htmlwidgets
|
||
r-httpuv
|
||
r-jquerylib
|
||
r-jsonlite
|
||
r-magrittr
|
||
r-promises))
|
||
(inputs
|
||
(list js-selectize))
|
||
(native-inputs
|
||
`(("r-knitr" ,r-knitr)
|
||
("esbuild" ,esbuild)
|
||
("datatables-plugins"
|
||
,(let ((version "1.13.4"))
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/DataTables/Plugins.git")
|
||
(commit version)))
|
||
(file-name (git-file-name "datatables-plugins" version))
|
||
(sha256
|
||
(base32
|
||
"0igrd7pghvk2w8mpad4mnw8ldflw47wma4qpp7ymkzvxy2100k49")))))
|
||
("js-nouislider"
|
||
,(let ((version "7.0.10"))
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (string-append "https://raw.githubusercontent.com/leongersen/noUiSlider/"
|
||
version "/distribute/jquery.nouislider.js"))
|
||
(sha256
|
||
(base32
|
||
"1f7vsfcn7wwzngib6j0wpl0psd6qriiaa6kv728ynfn5da73zfxm")))))
|
||
,@(map (match-lambda
|
||
((url hash dir)
|
||
`(,(string-append "js:" (basename url))
|
||
,(origin (method url-fetch)
|
||
(uri url)
|
||
(sha256 (base32 hash))))))
|
||
javascript-sources)))
|
||
(home-page "https://rstudio.github.io/DT")
|
||
(synopsis "R wrapper of the DataTables JavaScript library")
|
||
(description
|
||
"This package allows for data objects in R to be rendered as HTML tables
|
||
using the JavaScript library @code{DataTables} (typically via R Markdown or
|
||
Shiny). The @code{DataTables} library has been included in this R package.")
|
||
;; The DT package as a whole is distributed under GPLv3. The DT package
|
||
;; inludes other software components under different licenses:
|
||
;;
|
||
;; * Expat: jquery.highlight.js, DataTables
|
||
;; * WTFPL: noUiSlider
|
||
(license (list license:gpl3
|
||
license:expat
|
||
license:wtfpl2)))))
|
||
|
||
(define-public r-base64enc
|
||
(package
|
||
(name "r-base64enc")
|
||
(version "0.1-3")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "base64enc" version))
|
||
(sha256
|
||
(base32
|
||
"13b89fhg1nx7zds82a0biz847ixphg9byf5zl2cw9kab6s56v1bd"))))
|
||
(build-system r-build-system)
|
||
(home-page "https://www.rforge.net/base64enc")
|
||
(synopsis "Tools for Base64 encoding")
|
||
(description
|
||
"This package provides tools for handling Base64 encoding. It is more
|
||
flexible than the orphaned \"base64\" package.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-irlba
|
||
(package
|
||
(name "r-irlba")
|
||
(version "2.3.5.1")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "irlba" version))
|
||
(sha256
|
||
(base32
|
||
"1ky5nlmyrnwz6121wwqd8p8r1ycnjkl5r290k4x2477rzs267zic"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-matrix))
|
||
(home-page "https://cran.r-project.org/web/packages/irlba")
|
||
(synopsis "Methods for eigendecomposition of large matrices")
|
||
(description
|
||
"This package provides fast and memory efficient methods for truncated
|
||
singular and eigenvalue decompositions, as well as for principal component
|
||
analysis of large sparse or dense matrices.")
|
||
(license (list license:gpl2+ license:gpl3+))))
|
||
|
||
(define-public r-glmnet
|
||
(package
|
||
(name "r-glmnet")
|
||
(version "4.1-8")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "glmnet" version))
|
||
(sha256
|
||
(base32 "1znw1p1mi7nv39l7albcg6sfxj7a1jyjw85hb3ginv870z7fbnqx"))))
|
||
(build-system r-build-system)
|
||
(native-inputs
|
||
(list gfortran r-knitr))
|
||
(propagated-inputs
|
||
(list r-foreach
|
||
r-matrix
|
||
r-rcpp
|
||
r-rcppeigen
|
||
r-shape
|
||
r-survival))
|
||
(home-page "https://www.jstatsoft.org/article/view/v033i01")
|
||
(synopsis "Lasso and elastic-net regularized generalized linear models")
|
||
(description
|
||
"The glmnet package provides efficient procedures for fitting the entire
|
||
lasso or elastic-net regularization path for linear and Poisson regression, as
|
||
well as logistic, multinomial, Cox, multiple-response Gaussian and grouped
|
||
multinomial models. The algorithm uses cyclical coordinate descent in a
|
||
path-wise fashion.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-pkgmaker
|
||
(package
|
||
(name "r-pkgmaker")
|
||
(version "0.32.10")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "pkgmaker" version))
|
||
(sha256
|
||
(base32
|
||
"0cr95vmsb4gkl917wg4wwq8jihvwasdg18qzhk2cq224lrrh8awp"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-assertthat
|
||
r-codetools
|
||
r-digest
|
||
r-registry
|
||
r-stringr
|
||
r-withr
|
||
r-xtable))
|
||
(home-page "https://renozao.github.io/pkgmaker")
|
||
(synopsis "Package development utilities")
|
||
(description
|
||
"This package provides some low-level utilities to use for R package
|
||
development. It currently provides managers for multiple package specific
|
||
options and registries, vignette, unit test and bibtex related utilities.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-registry
|
||
(package
|
||
(name "r-registry")
|
||
(version "0.5-1")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "registry" version))
|
||
(sha256
|
||
(base32
|
||
"1k3j6dx350awamr0dwwgkhfs46vsnj4nf08iw5byq0x7n3nkdsnz"))))
|
||
(build-system r-build-system)
|
||
(home-page "https://cran.r-project.org/web/packages/registry")
|
||
(synopsis "Infrastructure for R package registries")
|
||
(description
|
||
"This package provides a generic infrastructure for creating and using R
|
||
package registries.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-rngtools
|
||
(package
|
||
(name "r-rngtools")
|
||
(version "1.5.2")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "rngtools" version))
|
||
(sha256
|
||
(base32
|
||
"0kd7x214cqw7hzpmk1iqy1bn7j6x0ady0yz2hsdbclbq9k57d33z"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-digest))
|
||
(home-page "https://renozao.github.io/rngtools")
|
||
(synopsis "Utility functions for working with random number generators")
|
||
(description
|
||
"This package contains a set of functions for working with Random Number
|
||
Generators (RNGs). In particular, it defines a generic S4 framework for
|
||
getting/setting the current RNG, or RNG data that are embedded into objects
|
||
for reproducibility. Notably, convenient default methods greatly facilitate
|
||
the way current RNG settings can be changed.")
|
||
(license license:gpl3+)))
|
||
|
||
(define-public r-rtsne
|
||
(package
|
||
(name "r-rtsne")
|
||
(version "0.16")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "Rtsne" version))
|
||
(sha256
|
||
(base32
|
||
"1mgviwrqwapn8w7rq0sjxca5vi7ylgmm876ijwp22a3chbf5m82j"))))
|
||
(properties `((upstream-name . "Rtsne")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-rcpp))
|
||
(home-page "https://github.com/jkrijthe/Rtsne")
|
||
(synopsis "T-distributed stochastic neighbor embedding")
|
||
(description
|
||
"This package provides an R wrapper around the fast T-distributed
|
||
Stochastic Neighbor Embedding using a Barnes-Hut implementation.")
|
||
;; The declared license for this package is BSD-3, but it also includes
|
||
;; code licensed under BSD-4.
|
||
(license (list license:bsd-3 license:bsd-4))))
|
||
|
||
(define-public r-e1071
|
||
(package
|
||
(name "r-e1071")
|
||
(version "1.7-13")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "e1071" version))
|
||
(sha256
|
||
(base32
|
||
"0bvbgcbj8a5z3rv4z4cx6dlwhk374fwd8l1jkq7slsbfmy8y356s"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-class r-proxy))
|
||
(home-page "https://cran.r-project.org/web/packages/e1071")
|
||
(synopsis "Miscellaneous functions for probability theory")
|
||
(description
|
||
"This package provides functions for latent class analysis, short time
|
||
Fourier transform, fuzzy clustering, support vector machines, shortest path
|
||
computation, bagged clustering, naive Bayes classifier, and more.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-bigmemory-sri
|
||
(package
|
||
(name "r-bigmemory-sri")
|
||
(version "0.1.6")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "bigmemory.sri" version))
|
||
(sha256
|
||
(base32 "03468ak0lgd9m0f7synxms2zzr8f7n2nm1gmhcraj3nfcv4nmyiv"))))
|
||
(properties
|
||
`((upstream-name . "bigmemory.sri")))
|
||
(build-system r-build-system)
|
||
(home-page "https://cran.r-project.org/web/packages/bigmemory.sri")
|
||
(synopsis "Shared resource interface for the bigmemory package")
|
||
(description "This package provides a shared resource interface for the
|
||
bigmemory and synchronicity packages.")
|
||
;; Users can choose either LGPLv3 or ASL2.0.
|
||
(license (list license:lgpl3 license:asl2.0))))
|
||
|
||
(define-public r-synchronicity
|
||
(package
|
||
(name "r-synchronicity")
|
||
(version "1.3.5")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "synchronicity" version))
|
||
(sha256
|
||
(base32
|
||
"1kgsk64aifjm3mfj102y3va7x1abypq2zi0cqbnjhl8fqyzp69hx"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-bh r-bigmemory-sri r-rcpp r-uuid))
|
||
(home-page "http://www.bigmemory.org")
|
||
(synopsis "Boost mutex functionality in R")
|
||
(description "This package provides support for synchronization
|
||
via mutexes and may eventually support interprocess communication and
|
||
message passing.")
|
||
;; Users can choose either LGPLv3 or ASL2.0.
|
||
(license (list license:lgpl3 license:asl2.0))))
|
||
|
||
(define-public r-bigmemory
|
||
(package
|
||
(name "r-bigmemory")
|
||
(version "4.6.1")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "bigmemory" version))
|
||
(sha256
|
||
(base32
|
||
"0hainqkm7cs8gjm42vkpdrr0284smsbwdfackp34yv7dhxy1avmm"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-bh r-bigmemory-sri r-rcpp r-uuid))
|
||
(inputs
|
||
(list `(,util-linux "lib"))) ;for -luuid
|
||
(supported-systems
|
||
(fold delete
|
||
%supported-systems
|
||
;; Build fails on these systems
|
||
'("armhf-linux"
|
||
"aarch64-linux"
|
||
"powerpc64le-linux")))
|
||
(home-page "http://www.bigmemory.org")
|
||
(synopsis "Manage large matrices with shared memory or memory-mapped files")
|
||
(description "This package provides methods to create, store, access, and
|
||
manipulate large matrices. Matrices are allocated to shared memory and may use
|
||
memory-mapped files.")
|
||
;; Users can choose either LGPLv3 or ASL2.0.
|
||
(license (list license:lgpl3 license:asl2.0))))
|
||
|
||
(define-public r-r-methodss3
|
||
(package
|
||
(name "r-r-methodss3")
|
||
(version "1.8.2")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "R.methodsS3" version))
|
||
(sha256
|
||
(base32
|
||
"0bkwj9c2cpgb0ibk9znh8qh4k1wzp3bkhaxyhf41xjflv9hmwbc2"))))
|
||
(properties `((upstream-name . "R.methodsS3")))
|
||
(build-system r-build-system)
|
||
(home-page "https://cran.r-project.org/web/packages/R.methodsS3")
|
||
(synopsis "S3 methods simplified")
|
||
(description
|
||
"This package provides methods that simplify the setup of S3 generic
|
||
functions and S3 methods. Major effort has been made in making definition of
|
||
methods as simple as possible with a minimum of maintenance for package
|
||
developers. For example, generic functions are created automatically, if
|
||
missing, and naming conflict are automatically solved, if possible. The
|
||
method @code{setMethodS3()} is a good start for those who in the future may
|
||
want to migrate to S4.")
|
||
(license license:lgpl2.1+)))
|
||
|
||
(define-public r-r-oo
|
||
(package
|
||
(name "r-r-oo")
|
||
(version "1.25.0")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "R.oo" version))
|
||
(sha256
|
||
(base32
|
||
"1vxy8yw4yblb3vgl64yh0b6zf1d51rnc2c23kmyyw629fxhr1cdq"))))
|
||
(properties `((upstream-name . "R.oo")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-r-methodss3))
|
||
(home-page "https://github.com/HenrikBengtsson/R.oo")
|
||
(synopsis "R object-oriented programming with or without references")
|
||
(description
|
||
"This package provides methods and classes for object-oriented
|
||
programming in R with or without references. Large effort has been made on
|
||
making definition of methods as simple as possible with a minimum of
|
||
maintenance for package developers.")
|
||
(license license:lgpl2.1+)))
|
||
|
||
(define-public r-r-utils
|
||
(package
|
||
(name "r-r-utils")
|
||
(version "2.12.2")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "R.utils" version))
|
||
(sha256
|
||
(base32
|
||
"0dl8rc7s7vg4g2pkmrwwqx7dkm02096jk439x4s0cm21hsmg2g7y"))))
|
||
(properties `((upstream-name . "R.utils")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-r-methodss3 r-r-oo))
|
||
(home-page "https://github.com/HenrikBengtsson/R.utils")
|
||
(synopsis "Various programming utilities")
|
||
(description
|
||
"This package provides utility functions useful when programming and
|
||
developing R packages.")
|
||
(license license:lgpl2.1+)))
|
||
|
||
(define-public r-r-cache
|
||
(package
|
||
(name "r-r-cache")
|
||
(version "0.16.0")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "R.cache" version))
|
||
(sha256
|
||
(base32
|
||
"14cja0d78mzipb94cwgdl00k5r7awjclzxl30c77j6jpc68l0lvq"))))
|
||
(properties `((upstream-name . "R.cache")))
|
||
(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-methodss3 r-r-oo r-r-utils))
|
||
(home-page "https://github.com/HenrikBengtsson/R.cache")
|
||
(synopsis "Light-weight caching of objects and results")
|
||
(description
|
||
"This package provides methods for caching or memoization of objects and
|
||
results. With this package, any R object can be cached in a key-value storage
|
||
where the key can be an arbitrary set of R objects. The cache memory is
|
||
persistent (on the file system).")
|
||
(license license:lgpl2.1+)))
|
||
|
||
(define-public r-r-rsp
|
||
(package
|
||
(name "r-r-rsp")
|
||
(version "0.45.0")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "R.rsp" version))
|
||
(sha256
|
||
(base32
|
||
"192x8cvna1j0sx37xh3ha8bjjyx39pn5wnxzn5gs3z5j93a4d055"))))
|
||
(properties `((upstream-name . "R.rsp")))
|
||
(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.rsp")
|
||
(synopsis "Dynamic generation of scientific reports")
|
||
(description
|
||
"The RSP markup language provides a powerful markup for controlling the
|
||
content and output of LaTeX, HTML, Markdown, AsciiDoc, Sweave and knitr
|
||
documents (and more), e.g. @code{Today's date is <%=Sys.Date()%>}. Contrary
|
||
to many other literate programming languages, with RSP it is straightforward
|
||
to loop over mixtures of code and text sections, e.g. in month-by-month
|
||
summaries. RSP has also several preprocessing directives for incorporating
|
||
static and dynamic contents of external files (local or online) among other
|
||
things. RSP is ideal for self-contained scientific reports and R package
|
||
vignettes.")
|
||
(license license:lgpl2.1+)))
|
||
|
||
(define-public r-mvtnorm
|
||
(package
|
||
(name "r-mvtnorm")
|
||
(version "1.2-3")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "mvtnorm" version))
|
||
(sha256
|
||
(base32
|
||
"1iy65fc2y0af6ma9f6lvzd5zh7zm60cqihdhr58ksc75ymfxrnia"))))
|
||
(build-system r-build-system)
|
||
(native-inputs
|
||
(list gfortran))
|
||
(home-page "https://mvtnorm.R-forge.R-project.org")
|
||
(synopsis "Package for multivariate normal and t-distributions")
|
||
(description "This package can compute multivariate normal and
|
||
t-probabilities, quantiles, random deviates and densities.")
|
||
(license license:gpl2)))
|
||
|
||
(define-public r-matrixstats
|
||
(package
|
||
(name "r-matrixstats")
|
||
(version "1.0.0")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "matrixStats" version))
|
||
(sha256
|
||
(base32
|
||
"0vxd7g1fm4x0f72bs1xfik1d4yklvpjdyg1hpx86pl8fwr86i1wl"))))
|
||
(properties `((upstream-name . "matrixStats")))
|
||
(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)) ;used to build vignettes
|
||
(home-page "https://github.com/HenrikBengtsson/matrixStats")
|
||
(synopsis "Methods applying to vectors and matrix rows and columns")
|
||
(description
|
||
"This package provides methods operating on rows and columns of matrices,
|
||
e.g. @code{rowMedians()}, @code{rowRanks()}, and @code{rowSds()}. There are
|
||
also some vector-based methods, e.g. @code{binMeans()}, @code{madDiff()} and
|
||
@code{weightedMedians()}. All methods have been optimized for speed and
|
||
memory usage.")
|
||
(license license:artistic2.0)))
|
||
|
||
(define-public r-viridis
|
||
(package
|
||
(name "r-viridis")
|
||
(version "0.6.4")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "viridis" version))
|
||
(sha256
|
||
(base32
|
||
"1p6n85js15lx0zx07v2dxnb6wx4xzlbvrljf0x6vxy4gqf5si8hb"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-ggplot2 r-gridextra r-viridislite))
|
||
(native-inputs
|
||
(list r-knitr)) ; for vignettes
|
||
(home-page "https://github.com/sjmgarnier/viridis")
|
||
(synopsis "Matplotlib default color map")
|
||
(description
|
||
"This package is a port of the new @url{matplotlib,
|
||
http://matplotlib.org/} color maps (@code{viridis}--the default--,
|
||
@code{magma}, @code{plasma}, and @code{inferno}) to R. These color maps are
|
||
designed in such a way that they will analytically be perfectly
|
||
perceptually-uniform, both in regular form and also when converted to
|
||
black-and-white. They are also designed to be perceived by readers with the
|
||
most common form of color blindness.")
|
||
(license license:x11)))
|
||
|
||
(define-public r-viridislite
|
||
(package
|
||
(name "r-viridislite")
|
||
(version "0.4.2")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "viridisLite" version))
|
||
(sha256
|
||
(base32
|
||
"18g1rk24kr47jl01r70vvni2146fl9xxpjcvjp6d5k6y64fi2gw9"))))
|
||
(properties `((upstream-name . "viridisLite")))
|
||
(build-system r-build-system)
|
||
(home-page "https://github.com/sjmgarnier/viridisLite")
|
||
(synopsis "Default color maps from matplotlib")
|
||
(description
|
||
"This package is a port of the new @code{matplotlib} color maps
|
||
(@code{viridis}, @code{magma}, @code{plasma} and @code{inferno}) to R.
|
||
matplotlib is a popular plotting library for Python. These color maps are
|
||
designed in such a way that they will analytically be perfectly
|
||
perceptually-uniform, both in regular form and also when converted to
|
||
black-and-white. They are also designed to be perceived by readers with the
|
||
most common form of color blindness. This is the @code{lite} version of the
|
||
more complete @code{viridis} package.")
|
||
(license license:expat)))
|
||
|
||
(define-public r-tidyselect
|
||
(package
|
||
(name "r-tidyselect")
|
||
(version "1.2.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "tidyselect" version))
|
||
(sha256
|
||
(base32
|
||
"0fwy4qp3j0ksy15rkrh3588h7wa8c21h0fzx5s762zg34yvjd3ak"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-cli r-glue r-lifecycle r-rlang r-vctrs r-withr))
|
||
(native-inputs
|
||
(list r-knitr))
|
||
(home-page "https://cran.r-project.org/web/packages/tidyselect")
|
||
(synopsis "Select from a set of strings")
|
||
(description
|
||
"This package provides a backend for the selecting functions of the
|
||
tidyverse. It makes it easy to implement select-like functions in your own
|
||
packages in a way that is consistent with other tidyverse interfaces for
|
||
selection.")
|
||
(license license:gpl3)))
|
||
|
||
(define-public r-tidyr
|
||
(package
|
||
(name "r-tidyr")
|
||
(version "1.3.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "tidyr" version))
|
||
(sha256
|
||
(base32
|
||
"178a9sb07rph4mh7cz004ls0g7d4b7jk065m4ycfrlzxcs9jnlwd"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-cli
|
||
r-cpp11
|
||
r-dplyr
|
||
r-magrittr
|
||
r-glue
|
||
r-lifecycle
|
||
r-purrr
|
||
r-rlang
|
||
r-stringr
|
||
r-tidyselect
|
||
r-tibble
|
||
r-vctrs))
|
||
(native-inputs
|
||
(list r-knitr))
|
||
(home-page "https://github.com/hadley/tidyr")
|
||
(synopsis "Tidy data with `spread()` and `gather()` functions")
|
||
(description
|
||
"tidyr is a reframing of the reshape2 package designed to accompany the
|
||
tidy data framework, and to work hand-in-hand with magrittr and dplyr to build
|
||
a solid pipeline for data analysis. It is designed specifically for tidying
|
||
data, not the general reshaping that reshape2 does, or the general aggregation
|
||
that reshape did. In particular, built-in methods only work for data frames,
|
||
and tidyr provides no margins or aggregation.")
|
||
(license license:expat)))
|
||
|
||
(define-public r-hexbin
|
||
(package
|
||
(name "r-hexbin")
|
||
(version "1.28.3")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "hexbin" version))
|
||
(sha256
|
||
(base32
|
||
"0pyy97bh9xf9hijg3iw1z4ri01571r1fx7xqm3fjkzx4q48kbcqf"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-lattice))
|
||
(native-inputs
|
||
(list gfortran r-knitr)) ; for vignettes
|
||
(home-page "https://github.com/edzer/hexbin")
|
||
(synopsis "Hexagonal binning routines")
|
||
(description
|
||
"This package provides binning and plotting functions for hexagonal bins.
|
||
It uses and relies on grid graphics and formal (S4) classes and methods.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-purrr
|
||
(package
|
||
(name "r-purrr")
|
||
(version "1.0.2")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "purrr" version))
|
||
(sha256
|
||
(base32
|
||
"0qxvifs5gakjbivs8dgz6nrp6df2ypr3c4dlj84gyga3i2xwc6rc"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-cli r-lifecycle r-magrittr r-rlang r-vctrs))
|
||
(native-inputs
|
||
(list r-knitr))
|
||
(home-page "https://github.com/hadley/purrr")
|
||
(synopsis "Functional programming tools")
|
||
(description
|
||
"This package completes R's functional programming tools with missing
|
||
features present in other programming languages.")
|
||
(license license:gpl3+)))
|
||
|
||
(define-public r-plotly
|
||
(package
|
||
(name "r-plotly")
|
||
(version "4.10.2")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "plotly" version))
|
||
(sha256
|
||
(base32
|
||
"0y2jiyfx895f15wcpizybssic4draw1vgvqz2b7f82z73319m01b"))
|
||
(modules '((guix build utils)))
|
||
(snippet
|
||
'(with-directory-excursion "inst/htmlwidgets/lib/"
|
||
(for-each delete-file
|
||
'("plotlyjs/plotly-latest.min.js"
|
||
"colourpicker/colourpicker.min.js"
|
||
"typedarray/typedarray.min.js"
|
||
"selectize/selectize.min.js"))))))
|
||
(build-system r-build-system)
|
||
(arguments
|
||
(list
|
||
#:modules '((guix build utils)
|
||
(guix build r-build-system)
|
||
(srfi srfi-1))
|
||
#:phases
|
||
'(modify-phases %standard-phases
|
||
(add-after 'unpack 'process-javascript
|
||
(lambda* (#:key inputs #:allow-other-keys)
|
||
(with-directory-excursion "inst/htmlwidgets/lib/"
|
||
(symlink (string-append (assoc-ref inputs "js-selectize")
|
||
"/share/javascript/selectize.min.js")
|
||
"selectize/selectize.min.js")
|
||
(call-with-values
|
||
(lambda ()
|
||
(unzip2
|
||
`((,(assoc-ref inputs "js-plotly")
|
||
"plotlyjs/plotly-latest.min.js")
|
||
(,(string-append (assoc-ref inputs "js-colourpicker")
|
||
"/js/colourpicker.js")
|
||
"colourpicker/colourpicker.min.js")
|
||
(,(string-append (assoc-ref inputs "js-typedarray")
|
||
"/typedarray.js")
|
||
"typedarray/typedarray.min.js"))))
|
||
(lambda (sources targets)
|
||
(for-each (lambda (source target)
|
||
(format #t "Processing ~a --> ~a~%"
|
||
source target)
|
||
(invoke "esbuild" source "--minify"
|
||
(string-append "--outfile=" target)))
|
||
sources targets)))))))))
|
||
(propagated-inputs
|
||
(list r-base64enc
|
||
r-crosstalk
|
||
r-data-table
|
||
r-digest
|
||
r-dplyr
|
||
r-ggplot2
|
||
r-htmltools
|
||
r-htmlwidgets
|
||
r-httr
|
||
r-jsonlite
|
||
r-lazyeval
|
||
r-magrittr
|
||
r-promises
|
||
r-purrr
|
||
r-rcolorbrewer
|
||
r-rlang
|
||
r-scales
|
||
r-tibble
|
||
r-tidyr
|
||
r-vctrs
|
||
r-viridislite))
|
||
(native-inputs
|
||
`(("esbuild" ,esbuild)
|
||
("js-colourpicker"
|
||
,(let ((commit "27c2a266d51e18a9fe6d7542264152b27c7d34e0")
|
||
(version "1.1")
|
||
(revision "0"))
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/daattali/jquery-colourpicker")
|
||
(commit commit)))
|
||
(file-name (git-file-name "jquery-colourpicker"
|
||
(git-version version revision commit)))
|
||
(sha256
|
||
(base32
|
||
"0lg8amh8xh6p246j38rqghrljd7v5z34i169ra6403z8ga33wiqb")))))
|
||
("js-plotly"
|
||
,(let ((version "2.11.1"))
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (string-append "https://raw.githubusercontent.com/plotly/plotly.js/v"
|
||
version "/dist/plotly.js"))
|
||
(sha256
|
||
(base32
|
||
"1mxd8s4v3i885w5i02cyzqsrvqfr9w0svdclvqxbd05dly4bdkbj")))))
|
||
("js-selectize" ,js-selectize)
|
||
;; This is not quite the same as the bundled minified script from 2016,
|
||
;; but it seems to be the original with fixes from late 2017.
|
||
("js-typedarray"
|
||
,(let ((commit "9f7d4168657e2c164d647a6959f402f2c33eb5b4")
|
||
(version "0")
|
||
(revision "0"))
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/inexorabletash/polyfill/")
|
||
(commit commit)))
|
||
(file-name (git-file-name "typedarray-polyfill"
|
||
(git-version version revision commit)))
|
||
(sha256
|
||
(base32
|
||
"0f9np4mmyhny03n3xpwzs07rld30lnfqsnh97x1v7xm0qy0zjanf")))))))
|
||
(home-page "https://plot.ly/r")
|
||
(synopsis "Create interactive web graphics")
|
||
(description
|
||
"This package enables the translation of ggplot2 graphs to an interactive
|
||
web-based version and/or the creation of custom web-based visualizations
|
||
directly from R. Once uploaded to a plotly account, plotly graphs (and the
|
||
data behind them) can be viewed and modified in a web browser.")
|
||
(license license:x11)))
|
||
|
||
(define-public r-biased-urn
|
||
(package
|
||
(name "r-biased-urn")
|
||
(version "2.0.11")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "BiasedUrn" version))
|
||
(sha256
|
||
(base32
|
||
"0dvmkrdmhfh4swilyxf10y856kx0zf9sj1gc0g62bm6r5jhz35b2"))))
|
||
(properties `((upstream-name . "BiasedUrn")))
|
||
(build-system r-build-system)
|
||
(home-page "https://www.agner.org/random/")
|
||
(synopsis "Biased urn model distributions")
|
||
(description
|
||
"This package provides statistical models of biased sampling in the form
|
||
of univariate and multivariate noncentral hypergeometric distributions,
|
||
including Wallenius' noncentral hypergeometric distribution and Fisher's
|
||
noncentral hypergeometric distribution (also called extended hypergeometric
|
||
distribution).")
|
||
(license license:gpl3+)))
|
||
|
||
(define-public r-rematch
|
||
(package
|
||
(name "r-rematch")
|
||
(version "2.0.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "rematch" version))
|
||
(sha256
|
||
(base32
|
||
"09jwg3glp32q4ml4khhzi8j7bzg9zhqqdg1m6r8gibh756zzgnhm"))))
|
||
(build-system r-build-system)
|
||
(home-page "https://github.com/MangoTheCat/rematch")
|
||
(synopsis "Match regular expressions with a nicer API")
|
||
(description
|
||
"This package provides a small wrapper on @code{regexpr} to extract the
|
||
matches and captured groups from the match of a regular expression to a
|
||
character vector.")
|
||
(license license:expat)))
|
||
|
||
(define-public r-cellranger
|
||
(package
|
||
(name "r-cellranger")
|
||
(version "1.1.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "cellranger" version))
|
||
(sha256
|
||
(base32
|
||
"16fgi3annn34c3cxi0pxf62mmmmxi21hp0zzlv7bkfsjqy4g4f2x"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-rematch r-tibble))
|
||
(home-page "https://github.com/rsheets/cellranger")
|
||
(synopsis "Translate spreadsheet cell ranges to rows and columns")
|
||
(description
|
||
"This package provides helper functions to work with spreadsheets and the
|
||
@code{A1:D10} style of cell range specification.")
|
||
(license license:expat)))
|
||
|
||
(define-public r-googlesheets
|
||
(package
|
||
(name "r-googlesheets")
|
||
(version "0.3.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "googlesheets" version))
|
||
(sha256
|
||
(base32
|
||
"11q07nxys72wkxx9mawmjyf20gvwvrb7h3gpa73h6lgh2vgrwnv8"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-cellranger
|
||
r-dplyr
|
||
r-httr
|
||
r-jsonlite
|
||
r-purrr
|
||
r-readr
|
||
r-stringr
|
||
r-tibble
|
||
r-tidyr
|
||
r-xml2))
|
||
(home-page "https://github.com/jennybc/googlesheets")
|
||
(synopsis "Manage Google spreadsheets from R")
|
||
(description "This package provides tools to interact with Google Sheets
|
||
from within R.")
|
||
(license license:expat)))
|
||
|
||
(define-public r-spams
|
||
(package
|
||
(name "r-spams")
|
||
(version "2.6.1")
|
||
(source (origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://gitlab.inria.fr/thoth/spams-devel")
|
||
(commit (string-append "v" version))))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"0qvj87fw4sm54c7dvhxjgmgvnyyrrz9fk6dqp3ak0gwgb42gqh60"))))
|
||
(build-system r-build-system)
|
||
(arguments
|
||
(list
|
||
#:phases
|
||
#~(modify-phases %standard-phases
|
||
(add-after 'patch-generated-file-shebangs 'patch-paths
|
||
(lambda _
|
||
(substitute* (cons* "swig/setRelease"
|
||
"swig/R/docmatlab2R"
|
||
"swig/R/mkdist"
|
||
(find-files "." "(^mk|\\.sh$)"))
|
||
(("/bin/pwd") "pwd")
|
||
(("/bin/rm") "rm"))))
|
||
(add-after 'patch-paths 'mkdist
|
||
(lambda _
|
||
(chdir "swig/R")
|
||
(setenv "TEXINPUTS" (string-append (getcwd) "/../../doc:"))
|
||
(substitute* "mkdist"
|
||
(("^SWIG=.*")
|
||
(string-append "SWIG=" (which "swig")))
|
||
(("^../mkdoc") "")) ;requires texlive-aeguill
|
||
(invoke "./mkdist")
|
||
(chdir "dist/spams-R/spams")))
|
||
;; Don't tune for the building machine.
|
||
(add-after 'mkdist 'no-mtune
|
||
(lambda _
|
||
(substitute* "src/Makevars"
|
||
(("-mtune=native") "")))))))
|
||
(native-inputs
|
||
(list hevea
|
||
perl
|
||
swig
|
||
(texlive-updmap.cfg
|
||
(list texlive-aeguill texlive-jknapltx))))
|
||
(propagated-inputs
|
||
(list r-lattice
|
||
r-matrix))
|
||
(home-page "https://gitlab.inria.fr/thoth/spams-devel/")
|
||
(synopsis "Toolbox for solving sparse estimation problems")
|
||
(description "SPAMS (SPArse Modeling Software) is an optimization toolbox
|
||
for solving various sparse estimation problems. It includes tools for the
|
||
following problems:
|
||
|
||
@enumerate
|
||
@item Dictionary learning and matrix factorization (NMF, sparse @dfn{principle
|
||
component analysis} (PCA), ...)
|
||
@item Solving sparse decomposition problems with LARS, coordinate descent,
|
||
OMP, SOMP, proximal methods
|
||
@item Solving structured sparse decomposition problems (l1/l2, l1/linf, sparse
|
||
group lasso, tree-structured regularization, structured sparsity with
|
||
overlapping groups,...).
|
||
@end enumerate\n")
|
||
(license license:gpl3+)))
|
||
|
||
(define-public r-base64
|
||
(package
|
||
(name "r-base64")
|
||
(version "2.0.1")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "base64" version))
|
||
(sha256
|
||
(base32
|
||
"1w9m4n29xmj7px8fbmha04vq146bxfqi7ipj1ag09hlm05y6h8jd"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-openssl))
|
||
(home-page "https://cran.r-project.org/web/packages/base64")
|
||
(synopsis "Base64 encoder and decoder")
|
||
(description
|
||
"This package is a compatibility wrapper to replace the orphaned package
|
||
by Romain Francois. New applications should use the openssl or base64enc
|
||
package instead.")
|
||
(license license:expat)))
|
||
|
||
(define-public r-hmisc
|
||
(package
|
||
(name "r-hmisc")
|
||
(version "5.1-1")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "Hmisc" version))
|
||
(sha256
|
||
(base32 "0laan26ja6m9k3spkk1ymalwb181ramzjq6ii3b0404xv2kfywa9"))))
|
||
(properties `((upstream-name . "Hmisc")))
|
||
(build-system r-build-system)
|
||
(native-inputs
|
||
(list gfortran))
|
||
(propagated-inputs
|
||
(list r-base64enc
|
||
r-cluster
|
||
r-colorspace
|
||
r-data-table
|
||
r-foreign
|
||
r-formula
|
||
r-ggplot2
|
||
r-gridextra
|
||
r-gtable
|
||
r-htmltable
|
||
r-htmltools
|
||
r-knitr
|
||
r-nnet
|
||
r-rmarkdown
|
||
r-rpart
|
||
r-viridis))
|
||
(home-page "http://biostat.mc.vanderbilt.edu/Hmisc")
|
||
(synopsis "Miscellaneous data analysis and graphics functions")
|
||
(description
|
||
"This package contains many functions useful for data analysis,
|
||
high-level graphics, utility operations, functions for computing sample size
|
||
and power, importing and annotating datasets, imputing missing values,
|
||
advanced table making, variable clustering, character string manipulation,
|
||
conversion of R objects to LaTeX code, and recoding variables.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-runit
|
||
(package
|
||
(name "r-runit")
|
||
(version "0.4.32")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "RUnit" version))
|
||
(sha256
|
||
(base32
|
||
"1wc1gwb7yw7phf8b0gkig6c23klya3ax11c6i4s0f049k42r78r3"))))
|
||
(properties `((upstream-name . "RUnit")))
|
||
(build-system r-build-system)
|
||
(home-page "https://cran.r-project.org/web/packages/RUnit")
|
||
(synopsis "R unit test framework")
|
||
(description
|
||
"This package provides R functions implementing a standard unit testing
|
||
framework, with additional code inspection and report generation tools.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-dynamictreecut
|
||
(package
|
||
(name "r-dynamictreecut")
|
||
(version "1.63-1")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "dynamicTreeCut" version))
|
||
(sha256
|
||
(base32
|
||
"1fadbql7g5r2vvlkr89nlrjxwp4yx4xrdqmv077qvmnx9vv0f4w3"))))
|
||
(properties `((upstream-name . "dynamicTreeCut")))
|
||
(build-system r-build-system)
|
||
(home-page
|
||
"http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/BranchCutting/")
|
||
(synopsis "Detect clusters in hierarchical clustering dendrograms")
|
||
(description
|
||
"This package contains methods for the detection of clusters in
|
||
hierarchical clustering dendrograms.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-fastcluster
|
||
(package
|
||
(name "r-fastcluster")
|
||
(version "1.2.3")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "fastcluster" version))
|
||
(sha256
|
||
(base32
|
||
"009amz7i5yndqw2008fgd3p11n4fsb291k2ypg3pip6dw4lr28hz"))))
|
||
(build-system r-build-system)
|
||
(home-page "http://danifold.net/fastcluster.html")
|
||
(synopsis "Fast hierarchical clustering routines")
|
||
(description
|
||
"This package implements fast hierarchical, agglomerative clustering
|
||
routines. Part of the functionality is designed as drop-in replacement for
|
||
existing routines: @code{linkage()} in the SciPy package
|
||
@code{scipy.cluster.hierarchy}, @code{hclust()} in R's @code{stats} package,
|
||
and the @code{flashClust} package. It provides the same functionality with
|
||
the benefit of a much faster implementation. Moreover, there are
|
||
memory-saving routines for clustering of vector data, which go beyond what the
|
||
existing packages provide.")
|
||
(license license:bsd-2)))
|
||
|
||
(define-public r-sfsmisc
|
||
(package
|
||
(name "r-sfsmisc")
|
||
(version "1.1-16")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "sfsmisc" version))
|
||
(sha256
|
||
(base32
|
||
"0v2325f3115yp48s0ddiiqwxlg2zf5xzc21xxd0cbziw3rk4l6si"))))
|
||
(build-system r-build-system)
|
||
(home-page "https://cran.r-project.org/web/packages/sfsmisc")
|
||
(synopsis "Utilities from \"Seminar fuer Statistik\" ETH Zurich")
|
||
(description
|
||
"This package provides useful utilities from Seminar fuer Statistik ETH
|
||
Zurich, including many that are related to graphics.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-gtools
|
||
(package
|
||
(name "r-gtools")
|
||
(version "3.9.4")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "gtools" version))
|
||
(sha256
|
||
(base32
|
||
"04gihp78x2caahqvf0mlv1cqy1m121l6hkdvbp01r2z99wcqpksr"))))
|
||
(build-system r-build-system)
|
||
(home-page "https://cran.r-project.org/web/packages/gtools")
|
||
(synopsis "Various R programming tools")
|
||
(description
|
||
"This package contains a collection of various functions to assist in R
|
||
programming, such as tools to assist in developing, updating, and maintaining
|
||
R and R packages, calculating the logit and inverse logit transformations,
|
||
tests for whether a value is missing, empty or contains only @code{NA} and
|
||
@code{NULL} values, and many more.")
|
||
(license license:gpl2)))
|
||
|
||
(define-public r-gdata
|
||
(package
|
||
(name "r-gdata")
|
||
(version "2.19.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "gdata" version))
|
||
(sha256
|
||
(base32
|
||
"1lv3cz990f7m2bfcf62fjm6wz6zd2ycrci06b7mfd0xmcn3bwifi"))))
|
||
(build-system r-build-system)
|
||
(inputs
|
||
(list perl))
|
||
(propagated-inputs
|
||
(list r-gtools))
|
||
(home-page "https://cran.r-project.org/web/packages/gdata")
|
||
(synopsis "Various R programming tools for data manipulation")
|
||
(description
|
||
"This package provides various R programming tools for data manipulation,
|
||
including:
|
||
|
||
@itemize
|
||
@item medical unit conversions
|
||
@item combining objects
|
||
@item character vector operations
|
||
@item factor manipulation
|
||
@item obtaining information about R objects
|
||
@item manipulating MS-Excel formatted files
|
||
@item generating fixed-width format files
|
||
@item extricating components of date and time objects
|
||
@item operations on columns of data frames
|
||
@item matrix operations
|
||
@item operations on vectors and data frames
|
||
@item value of last evaluated expression
|
||
@item wrapper for @code{sample} that ensures consistent behavior for
|
||
both scalar and vector arguments
|
||
@end itemize\n")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-gplots
|
||
(package
|
||
(name "r-gplots")
|
||
(version "3.1.3")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "gplots" version))
|
||
(sha256
|
||
(base32
|
||
"05k7a8x62qs5g6mps62vb3mwjdnfjzvjb20yws3x0r2j42g3p1cz"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-catools r-gtools r-kernsmooth))
|
||
(native-inputs
|
||
(list r-knitr))
|
||
(home-page "https://cran.r-project.org/web/packages/gplots")
|
||
(synopsis "Various R programming tools for plotting data")
|
||
(description
|
||
"This package provides various R programming tools for plotting data,
|
||
including:
|
||
|
||
@itemize
|
||
@item calculating and plotting locally smoothed summary function
|
||
@item enhanced versions of standard plots
|
||
@item manipulating colors
|
||
@item calculating and plotting two-dimensional data summaries
|
||
@item enhanced regression diagnostic plots
|
||
@item formula-enabled interface to @code{stats::lowess} function
|
||
@item displaying textual data in plots
|
||
@item balloon plots
|
||
@item plotting \"Venn\" diagrams
|
||
@item displaying Open-Office style plots
|
||
@item plotting multiple data on same region, with separate axes
|
||
@item plotting means and confidence intervals
|
||
@item spacing points in an x-y plot so they don't overlap
|
||
@end itemize\n")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-rocr
|
||
(package
|
||
(name "r-rocr")
|
||
(version "1.0-11")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "ROCR" version))
|
||
(sha256
|
||
(base32
|
||
"0amvvrkiflmr3qygrsgrsja4gaf2v6r6h6i2bgpsm8r069vmlf2p"))))
|
||
(properties `((upstream-name . "ROCR")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-gplots))
|
||
(native-inputs
|
||
(list r-knitr))
|
||
(home-page "https://rocr.bioinf.mpi-sb.mpg.de/")
|
||
(synopsis "Visualizing the performance of scoring classifiers")
|
||
(description
|
||
"ROCR is a flexible tool for creating cutoff-parameterized 2D performance
|
||
curves by freely combining two from over 25 performance measures (new
|
||
performance measures can be added using a standard interface). Curves from
|
||
different cross-validation or bootstrapping runs can be averaged by different
|
||
methods, and standard deviations, standard errors or box plots can be used to
|
||
visualize the variability across the runs. The parameterization can be
|
||
visualized by printing cutoff values at the corresponding curve positions, or
|
||
by coloring the curve according to cutoff. All components of a performance
|
||
plot can be quickly adjusted using a flexible parameter dispatching
|
||
mechanism.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-ztable
|
||
(package
|
||
(name "r-ztable")
|
||
(version "0.2.3")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "ztable" version))
|
||
(sha256
|
||
(base32
|
||
"1ps7ix0hc84s0p0ra6bkjxky3cffs1rvdcagqzj78lbdq22dk5j8"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-flextable
|
||
r-magrittr
|
||
r-officer
|
||
r-rcolorbrewer
|
||
r-rstudioapi
|
||
r-scales
|
||
r-stringr))
|
||
(native-inputs
|
||
(list r-knitr))
|
||
(home-page "https://cran.r-project.org/web/packages/ztable")
|
||
(synopsis "Zebra-striped tables in LaTeX and HTML formats for R")
|
||
(description
|
||
"This package provides functions to make zebra-striped tables (tables
|
||
with alternating row colors) in LaTeX and HTML formats easily from
|
||
@code{data.frame}, @code{matrix}, @code{lm}, @code{aov}, @code{anova},
|
||
@code{glm}, @code{coxph}, @code{nls}, @code{fitdistr}, @code{mytable} and
|
||
@code{cbind.mytable} objects.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-vipor
|
||
(package
|
||
(name "r-vipor")
|
||
(version "0.4.5")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "vipor" version))
|
||
(sha256
|
||
(base32
|
||
"112gc0d7f8iavgf56pnzfxb7hy75yhd0zlyjzshdcfbnqcd2a6bx"))))
|
||
(build-system r-build-system)
|
||
(home-page "https://cran.r-project.org/web/packages/vipor")
|
||
(synopsis "Plot categorical data using noise and density estimates")
|
||
(description
|
||
"This package provides tools to generate a violin point plot, a
|
||
combination of a violin/histogram plot and a scatter plot by offsetting points
|
||
within a category based on their density using quasirandom noise.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-beeswarm
|
||
(package
|
||
(name "r-beeswarm")
|
||
(version "0.4.0")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "beeswarm" version))
|
||
(sha256
|
||
(base32
|
||
"016mqcbdksialkmap56rprzna9b6cd6896ml9gl2n2h8yjdk7x2i"))))
|
||
(build-system r-build-system)
|
||
(home-page "https://www.cbs.dtu.dk/~eklund/beeswarm/")
|
||
(synopsis "Implementation of bee swarm plots")
|
||
(description
|
||
"This package provides an implementation of bee swarm plots. The bee
|
||
swarm plot is a one-dimensional scatter plot like stripchart, but with
|
||
closely-packed, non-overlapping points.")
|
||
(license license:artistic2.0)))
|
||
|
||
(define-public r-sourcetools
|
||
(package
|
||
(name "r-sourcetools")
|
||
(version "0.1.7-1")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "sourcetools" version))
|
||
(sha256
|
||
(base32
|
||
"1l9i9ram12pjks8h2gzmj119wf4ixwyhljsfv289dn8dgbdjp0cn"))))
|
||
(build-system r-build-system)
|
||
(home-page "https://cran.r-project.org/web/packages/sourcetools")
|
||
(synopsis "Tools for reading, tokenizing and parsing R code")
|
||
(description
|
||
"The sourcetools package provides both an R and C++ interface for the
|
||
tokenization of R code, and helpers for interacting with the tokenized
|
||
representation of R code.")
|
||
(license license:expat)))
|
||
|
||
(define-public r-ggbeeswarm
|
||
(package
|
||
(name "r-ggbeeswarm")
|
||
(version "0.7.2")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "ggbeeswarm" version))
|
||
(sha256
|
||
(base32
|
||
"1rcw54isai05np4fj19vcxx2vcxq7y2nm3az9m8xwbc9pdjs4z7x"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-beeswarm r-cli r-ggplot2 r-lifecycle r-vipor))
|
||
(home-page "https://github.com/eclarke/ggbeeswarm")
|
||
(synopsis "Categorical scatter (violin point) plots")
|
||
(description
|
||
"This package provides two methods of plotting categorical scatter plots
|
||
such that the arrangement of points within a category reflects the density of
|
||
data at that region, and avoids over-plotting.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-ggthemes
|
||
(package
|
||
(name "r-ggthemes")
|
||
(version "4.2.4")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "ggthemes" version))
|
||
(sha256
|
||
(base32
|
||
"0rw5f6axyz1pqn6qx9jwm38hjzn8bqs1nfjkvm96z3xnyn61cdbv"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-ggplot2 r-purrr r-scales r-stringr r-tibble))
|
||
(home-page "https://cran.rstudio.com/web/packages/ggthemes")
|
||
(synopsis "Extra themes, scales and geoms for @code{ggplot2}")
|
||
(description "This package provides extra themes and scales for
|
||
@code{ggplot2} that replicate the look of plots by Edward Tufte and
|
||
Stephen Few in Fivethirtyeight, The Economist, Stata, Excel, and The
|
||
Wall Street Journal, among others. This package also provides
|
||
@code{geoms} for Tufte's box plot and range frame.")
|
||
(license license:gpl2)))
|
||
|
||
(define-public r-statmod
|
||
(package
|
||
(name "r-statmod")
|
||
(version "1.5.0")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "statmod" version))
|
||
(sha256
|
||
(base32
|
||
"1jbf07h0mnncn2qp4wcw5bnbvsw3lizpd3cg0cpb8mcxn3wkw76n"))))
|
||
(build-system r-build-system)
|
||
(home-page "https://cran.r-project.org/web/packages/statmod")
|
||
(native-inputs
|
||
(list gfortran))
|
||
(synopsis "Statistical modeling")
|
||
(description
|
||
"This package provides a collection of algorithms and functions to aid
|
||
statistical modeling. It includes growth curve comparisons, limiting dilution
|
||
analysis (aka ELDA), mixed linear models, heteroscedastic regression,
|
||
inverse-Gaussian probability calculations, Gauss quadrature and a secure
|
||
convergence algorithm for nonlinear models. It also includes advanced
|
||
generalized linear model functions that implement secure convergence,
|
||
dispersion modeling and Tweedie power-law families.")
|
||
;; Statmod is distributed under either license
|
||
(license (list license:gpl2 license:gpl3))))
|
||
|
||
(define-public r-rann
|
||
(package
|
||
(name "r-rann")
|
||
(version "2.6.1")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "RANN" version))
|
||
(sha256
|
||
(base32
|
||
"10kid40w9w7vkz2hpcfkdpxr4afxzms5dzvfwr0sl5xynzgw76dj"))))
|
||
(properties
|
||
`((upstream-name . "RANN")))
|
||
(build-system r-build-system)
|
||
(home-page "https://github.com/jefferis/RANN")
|
||
(synopsis "Fast nearest neighbour search")
|
||
(description
|
||
"This package finds the k nearest neighbours for every point in a given
|
||
dataset in O(N log N) time using Arya and Mount's ANN library. Provides
|
||
approximate, exact searches, fixed radius searches, bd and kb trees.")
|
||
(license license:gpl3+)))
|
||
|
||
(define-public r-fivethirtyeight
|
||
(package
|
||
(name "r-fivethirtyeight")
|
||
(version "0.1.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (string-append "https://mran.microsoft.com/src/contrib/"
|
||
"fivethirtyeight_" version ".tar.gz"))
|
||
(sha256
|
||
(base32
|
||
"0fcc8rq745nsghp27dk0lgih90y4zx8hrzcvsn6ih786yv7qxhvl"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-knitr
|
||
r-rmarkdown
|
||
r-dplyr
|
||
r-readr
|
||
r-ggplot2
|
||
r-magrittr
|
||
r-stringr))
|
||
(home-page "https://mran.microsoft.com/package/fivethirtyeight/")
|
||
(synopsis "Data and code behind the stories at FiveThirtyEight")
|
||
(description "This R package provides access to the code and data sets
|
||
published by the statistics blog FiveThirtyEight.")
|
||
(license license:expat)))
|
||
|
||
(define-public r-compquadform
|
||
(package
|
||
(name "r-compquadform")
|
||
(version "1.4.3")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "CompQuadForm" version))
|
||
(sha256
|
||
(base32
|
||
"1i30hrqdk64q17vsn918c3q79brchgx2wzh1gbsgbn0dh1ncabq4"))))
|
||
(properties `((upstream-name . "CompQuadForm")))
|
||
(build-system r-build-system)
|
||
(home-page "https://cran.r-project.org/web/packages/CompQuadForm")
|
||
(synopsis "Distribution function of quadratic forms in normal variables")
|
||
(description
|
||
"This package provides functions to compute the distribution function of
|
||
quadratic forms in normal variables using Imhof's method, Davies's algorithm,
|
||
Farebrother's algorithm or Liu et al.'s algorithm.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-cowplot
|
||
(package
|
||
(name "r-cowplot")
|
||
(version "1.1.1")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "cowplot" version))
|
||
(sha256
|
||
(base32
|
||
"0j7d5vhzdxn1blrsfafx5z8lhq122rp8230hp9czrpsnnhjydp67"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-ggplot2 r-gtable r-rlang r-scales))
|
||
(native-inputs
|
||
(list r-knitr))
|
||
(home-page "https://github.com/wilkelab/cowplot")
|
||
(synopsis "Streamlined plot theme and plot annotations for ggplot2")
|
||
(description
|
||
"This package provides some helpful extensions and modifications to the
|
||
ggplot2 package to combine multiple ggplot2 plots into one and label them with
|
||
letters, as is often required for scientific publications.")
|
||
(license license:gpl2)))
|
||
|
||
(define-public r-mixtools
|
||
(package
|
||
(name "r-mixtools")
|
||
(version "2.0.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "mixtools" version))
|
||
(sha256
|
||
(base32
|
||
"03by64xi7yka0hzc1qyz1jdqzah6isvr3cdsc7g5v6hb4f178kl5"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-mass r-kernlab r-plotly r-scales r-segmented r-survival))
|
||
(home-page "https://cran.r-project.org/web/packages/mixtools")
|
||
(synopsis "Tools for analyzing finite mixture models")
|
||
(description
|
||
"This package provides a collection of R functions for analyzing finite
|
||
mixture models.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-lars
|
||
(package
|
||
(name "r-lars")
|
||
(version "1.3")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "lars" version))
|
||
(sha256
|
||
(base32
|
||
"17al1g0pvfz9frs2kxicqr8dyp7ciz3x87yx2l4lqd53ls6nm7n6"))))
|
||
(build-system r-build-system)
|
||
(inputs
|
||
(list gfortran))
|
||
(home-page "https://web.stanford.edu/~hastie/Papers/LARS/")
|
||
(synopsis "Least angle regression software")
|
||
(description
|
||
"Least Angle Regression (\"LAR\") is a model selection algorithm; a
|
||
useful and less greedy version of traditional forward selection methods. A
|
||
simple modification of the LAR algorithm implements Tibshirani's Lasso; the
|
||
Lasso modification of LARS calculates the entire Lasso path of coefficients
|
||
for a given problem at the cost of a single least squares fit. Another LARS
|
||
modification efficiently implements epsilon Forward Stagewise linear
|
||
regression.")
|
||
(license license:gpl2)))
|
||
|
||
(define-public r-fastica
|
||
(package
|
||
(name "r-fastica")
|
||
(version "1.2-3")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "fastICA" version))
|
||
(sha256
|
||
(base32
|
||
"0l49cmxm1n4dzrv8q3q3mq4drcjgby4f1dmpwfdb8jxn9ij85vz9"))))
|
||
(properties `((upstream-name . "fastICA")))
|
||
(build-system r-build-system)
|
||
(home-page "https://cran.r-project.org/web/packages/fastICA")
|
||
(synopsis "FastICA algorithms to perform ICA and projection pursuit")
|
||
(description
|
||
"This package provides an implementation of the FastICA algorithm to
|
||
perform @dfn{independent component analysis} (ICA) and projection pursuit.")
|
||
;; Any GPL version.
|
||
(license license:gpl3+)))
|
||
|
||
(define-public r-randomforest
|
||
(package
|
||
(name "r-randomforest")
|
||
(version "4.7-1.1")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "randomForest" version))
|
||
(sha256
|
||
(base32
|
||
"1micz9794j7xmj755ln2692rzip8azndflxgdg6xn3j86issi7pm"))))
|
||
(properties `((upstream-name . "randomForest")))
|
||
(build-system r-build-system)
|
||
(home-page "https://www.stat.berkeley.edu/~breiman/RandomForests/")
|
||
(native-inputs
|
||
(list gfortran))
|
||
(synopsis "Breiman and Cutler's random forests for classification and regression")
|
||
(description
|
||
"This package provides the Breiman and Cutler's random forests algorithm, based on a
|
||
forest of trees using random inputs, for classification and regression.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-diptest
|
||
(package
|
||
(name "r-diptest")
|
||
(version "0.76-0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "diptest" version))
|
||
(sha256
|
||
(base32
|
||
"10629vwn6r2949jjrmj5slbb5v0vnm3w0v8mrl7ws68m2sxmx2jh"))))
|
||
(build-system r-build-system)
|
||
(home-page "https://cran.r-project.org/web/packages/diptest")
|
||
(synopsis "Hartigan's dip test statistic for unimodality")
|
||
(description
|
||
"This package computes Hartigan's dip test statistic for unimodality,
|
||
multimodality and provides a test with simulation based p-values, where the
|
||
original public code has been corrected.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-modeltools
|
||
(package
|
||
(name "r-modeltools")
|
||
(version "0.2-23")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "modeltools" version))
|
||
(sha256
|
||
(base32
|
||
"1vqh69256h344sbj5affm0kmc77dakrxp6442xfdnfd0y5d8sgkb"))))
|
||
(build-system r-build-system)
|
||
(home-page "https://cran.r-project.org/web/packages/modeltools")
|
||
(synopsis "Tools and classes for statistical models")
|
||
(description
|
||
"This package provides a collection of tools to deal with statistical
|
||
models. The functionality is experimental and the user interface is likely
|
||
to change in the future.")
|
||
(license license:gpl2)))
|
||
|
||
(define-public r-flexmix
|
||
(package
|
||
(name "r-flexmix")
|
||
(version "2.3-19")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "flexmix" version))
|
||
(sha256
|
||
(base32
|
||
"1s8jpii6ws6hra8w11fn3x84wrdrrlycnrhn5ijy6ibdpc6a9xdd"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-lattice r-modeltools r-nnet))
|
||
(home-page "https://cran.r-project.org/web/packages/flexmix")
|
||
(synopsis "Flexible mixture modeling")
|
||
(description
|
||
"This package implements a general framework for finite mixtures of
|
||
regression models using the EM algorithm. FlexMix provides the E-step and
|
||
all data handling, while the M-step can be supplied by the user to easily
|
||
define new models. Existing drivers implement mixtures of standard linear
|
||
models, generalized linear models and model-based clustering.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-mclust
|
||
(package
|
||
(name "r-mclust")
|
||
(version "6.0.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "mclust" version))
|
||
(sha256
|
||
(base32
|
||
"0ahj5161lmid0gxyw6vidd4ig50l1374iisn9970zvx1rdp30z6y"))))
|
||
(build-system r-build-system)
|
||
(native-inputs
|
||
(list gfortran r-knitr))
|
||
(home-page "https://www.stat.washington.edu/mclust/")
|
||
(synopsis "Gaussian mixture modelling for model-based clustering etc.")
|
||
(description
|
||
"This package provides Gaussian finite mixture models fitted via EM
|
||
algorithm for model-based clustering, classification, and density estimation,
|
||
including Bayesian regularization, dimension reduction for visualisation,
|
||
and resampling-based inference.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-prabclus
|
||
(package
|
||
(name "r-prabclus")
|
||
(version "2.3-2")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "prabclus" version))
|
||
(sha256
|
||
(base32
|
||
"0hg4d7y1w18jpgvw10z8833bbbcnlkwiasx0wh6iwa2pnnybq8gl"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-mass r-mclust))
|
||
(home-page "https://cran.r-project.org/web/packages/prabclus")
|
||
(synopsis "Parametric bootstrap tests for spatial neighborhood clustering")
|
||
(description
|
||
"This package provides distance-based parametric bootstrap tests for
|
||
clustering with spatial neighborhood information. It implements some distance
|
||
measures, clustering of presence-absence, abundance and multilocus genetical
|
||
data for species delimitation, nearest neighbor based noise detection.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-deoptimr
|
||
(package
|
||
(name "r-deoptimr")
|
||
(version "1.1-3")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "DEoptimR" version))
|
||
(sha256
|
||
(base32
|
||
"1526g3fzii8kcy29gy6gjvaw4k9cxxidq8bh7m4j485h0wdsdn4d"))))
|
||
(properties `((upstream-name . "DEoptimR")))
|
||
(build-system r-build-system)
|
||
(home-page "https://cran.r-project.org/web/packages/DEoptimR")
|
||
(synopsis "Differential evolution optimization in pure R")
|
||
(description
|
||
"This package provides a differential evolution (DE) stochastic
|
||
algorithms for global optimization of problems with and without constraints.
|
||
The aim is to curate a collection of its state-of-the-art variants that (1) do
|
||
not sacrifice simplicity of design, (2) are essentially tuning-free, and (3)
|
||
can be efficiently implemented directly in the R language.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-robustbase
|
||
(package
|
||
(name "r-robustbase")
|
||
(version "0.99-0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "robustbase" version))
|
||
(sha256
|
||
(base32
|
||
"0xshwfv6vq47857xfhwnlxcl1511ghn6pyjylrg39i19xhp44za3"))))
|
||
(build-system r-build-system)
|
||
(native-inputs
|
||
(list gfortran))
|
||
(propagated-inputs
|
||
(list r-deoptimr))
|
||
(home-page "https://robustbase.r-forge.r-project.org/")
|
||
(synopsis "Basic robust statistics")
|
||
(description
|
||
"This package analyzes data with robust methods such as
|
||
regression methodology including model selections and multivariate statistics.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-pcapp
|
||
(package
|
||
(name "r-pcapp")
|
||
(version "2.0-3")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "pcaPP" version))
|
||
(sha256
|
||
(base32
|
||
"00ynanxpngzsvq5fsyalyzqz6axqcryy94300afvylwp0d7mbb0s"))))
|
||
(properties `((upstream-name . "pcaPP")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-mvtnorm))
|
||
(home-page "https://cran.r-project.org/web/packages/pcaPP")
|
||
(synopsis "Robust PCA by projection pursuit")
|
||
(description
|
||
"This package provides functions for robust @dfn{principal component
|
||
analysis} (PCA) by projection pursuit.")
|
||
(license license:gpl3+)))
|
||
|
||
(define-public r-rrcov
|
||
(package
|
||
(name "r-rrcov")
|
||
(version "1.7-4")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "rrcov" version))
|
||
(sha256
|
||
(base32
|
||
"0jkm2w38kbzicfx2542rb90r7kcrbm7hiaasajw1zq8gb7ffshb3"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-lattice r-mvtnorm r-pcapp r-robustbase))
|
||
(native-inputs
|
||
(list gfortran))
|
||
(home-page "https://cran.r-project.org/web/packages/rrcov")
|
||
(synopsis "Scalable robust estimators with high breakdown Point")
|
||
(description
|
||
"This package provides an implementation of robust location and scatter
|
||
estimation and robust multivariate analysis with high breakdown point.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-fit-models
|
||
(package
|
||
(name "r-fit-models")
|
||
(version "0.64")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "fit.models" version))
|
||
(sha256
|
||
(base32
|
||
"1nk4x2q8cv79zcls61saf627ac0fci6jcrd6lmzk61asm2zhc27p"))))
|
||
(properties `((upstream-name . "fit.models")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-lattice))
|
||
(home-page "https://cran.r-project.org/web/packages/fit.models")
|
||
(synopsis "Compare fitted models")
|
||
(description
|
||
"The @code{fit.models} function and its associated methods (coefficients, print,
|
||
summary, plot, etc.) were originally provided in the @code{robust} package to
|
||
compare robustly and classically fitted model objects. The aim of the
|
||
@code{fit.models} package is to separate this fitted model object comparison
|
||
functionality from the robust package and to extend it to support fitting
|
||
methods (e.g., classical, robust, Bayesian, regularized, etc.) more
|
||
generally.")
|
||
;; Any version of the GPL
|
||
(license (list license:gpl2+ license:gpl3+))))
|
||
|
||
(define-public r-robust
|
||
(package
|
||
(name "r-robust")
|
||
(version "0.7-2")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "robust" version))
|
||
(sha256
|
||
(base32
|
||
"1kryflq2p0c78pggnj5yghjivy4npxfkzcqhxh9jvrngkpxhsrb6"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-fit-models r-lattice r-mass r-robustbase r-rrcov))
|
||
(native-inputs
|
||
(list gfortran))
|
||
(home-page "https://cran.r-project.org/web/packages/robust")
|
||
(synopsis "Port of the S+ \"Robust Library\"")
|
||
(description
|
||
"This package is a port of the S+ \"Robust Library\". It provides
|
||
methods for robust statistics, notably for robust regression and robust
|
||
multivariate analysis.")
|
||
(license license:gpl2)))
|
||
|
||
(define-public r-trimcluster
|
||
(package
|
||
(name "r-trimcluster")
|
||
(version "0.1-5")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "trimcluster" version))
|
||
(sha256
|
||
(base32
|
||
"12siv8yx8dcavsz8jk96lwscbj257ar8jpaxksl2zb06987g4fcj"))))
|
||
(build-system r-build-system)
|
||
(home-page "https://cran.r-project.org/web/packages/trimcluster")
|
||
(synopsis "Cluster analysis with trimming")
|
||
(description
|
||
"The trimmed k-means clustering method by Cuesta-Albertos, Gordaliza and
|
||
Matran (1997). This optimizes the k-means criterion under trimming a portion
|
||
of the points.")
|
||
;; Any GPL version
|
||
(license (list license:gpl2+ license:gpl3+))))
|
||
|
||
(define-public r-fpc
|
||
(package
|
||
(name "r-fpc")
|
||
(version "2.2-10")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "fpc" version))
|
||
(sha256
|
||
(base32
|
||
"1lj7j74yx747iic1hcngzbym0sqxppja8bxw64m0j6na5s7m9d4r"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-class
|
||
r-cluster
|
||
r-diptest
|
||
r-flexmix
|
||
r-kernlab
|
||
r-mass
|
||
r-mclust
|
||
r-prabclus
|
||
r-robustbase))
|
||
(home-page "https://cran.r-project.org/web/packages/fpc")
|
||
(synopsis "Flexible procedures for clustering")
|
||
(description
|
||
"This package provides various methods for clustering and cluster validation.
|
||
For example, it provides fixed point clustering, linear regression clustering,
|
||
clustering by merging Gaussian mixture components, as well as symmetric and
|
||
asymmetric discriminant projections for visualisation of the separation of
|
||
groupings.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-vgam
|
||
(package
|
||
(name "r-vgam")
|
||
(version "1.1-9")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "VGAM" version))
|
||
(sha256
|
||
(base32 "1l5gn6495k8vqp2b4hj4g5ani7j4cli2p7n8fwkw7bmc42q13m6l"))))
|
||
(properties `((upstream-name . "VGAM")))
|
||
(build-system r-build-system)
|
||
(native-inputs
|
||
(list gfortran))
|
||
(home-page "https://www.stat.auckland.ac.nz/~yee/VGAM")
|
||
(synopsis "Vector generalized linear and additive models")
|
||
(description
|
||
"This package is an implementation of about 6 major classes of statistical
|
||
regression models. Currently only fixed-effects models are implemented, i.e.,
|
||
no random-effects models. Many (150+) models and distributions are estimated
|
||
by maximum likelihood estimation (MLE) or penalized MLE, using Fisher scoring.
|
||
VGLMs can be loosely thought of as multivariate generalised linear models.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-pbapply
|
||
(package
|
||
(name "r-pbapply")
|
||
(version "1.7-2")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "pbapply" version))
|
||
(sha256
|
||
(base32
|
||
"04xf1p7c0066cwnxfmzaikbc322bxnw022ziv8kkhzlc6268rvdf"))))
|
||
(build-system r-build-system)
|
||
(home-page "https://github.com/psolymos/pbapply")
|
||
(synopsis "Adding progress bar to apply functions")
|
||
(description
|
||
"This lightweight package that adds progress bar to vectorized R
|
||
functions apply. The implementation can easily be added to functions where
|
||
showing the progress is useful e.g. bootstrap.")
|
||
(license license:gpl2)))
|
||
|
||
(define-public r-minqa
|
||
(package
|
||
(name "r-minqa")
|
||
(version "1.2.6")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "minqa" version))
|
||
(sha256
|
||
(base32
|
||
"0421b4ysslaqmdgwlz080abis8m4xkcvjq7lx1wywbsz1s2vi9si"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-rcpp))
|
||
(native-inputs
|
||
(list gfortran))
|
||
(home-page "https://optimizer.r-forge.r-project.org")
|
||
(synopsis "Derivative-free optimization algorithms by quadratic approximation")
|
||
(description
|
||
"This package provides a derivative-free optimization by quadratic approximation
|
||
based on an interface to Fortran implementations by M. J. D. Powell.")
|
||
(license license:gpl2)))
|
||
|
||
(define-public r-rcppeigen
|
||
(package
|
||
(name "r-rcppeigen")
|
||
(version "0.3.3.9.3")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "RcppEigen" version))
|
||
(sha256
|
||
(base32
|
||
"0xhwgn77166ir7qnzl25mj0byskkqr0b36hihrpr2zaqsrzs8wsq"))))
|
||
(properties `((upstream-name . "RcppEigen")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-rcpp r-matrix))
|
||
(home-page "http://eigen.tuxfamily.org")
|
||
(synopsis "Rcpp integration for the Eigen templated linear algebra library")
|
||
(description
|
||
"This package provides an integration of Eigen in R using a C++ template
|
||
library for linear algebra: matrices, vectors, numerical solvers and related algorithms.
|
||
It supports dense and sparse matrices on integer, floating point and complex numbers,
|
||
decompositions of such matrices, and solutions of linear systems.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-modelmetrics
|
||
(package
|
||
(name "r-modelmetrics")
|
||
(version "1.2.2.2")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "ModelMetrics" version))
|
||
(sha256
|
||
(base32
|
||
"0mrlsw4c5y1vdsqynxr2dcvmhh5h37pnd71jw5a5djpbda9g21jy"))))
|
||
(properties `((upstream-name . "ModelMetrics")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-rcpp r-data-table))
|
||
(home-page "https://cran.r-project.org/web/packages/ModelMetrics")
|
||
(synopsis "Rapid calculation of model metrics")
|
||
(description
|
||
"Written in C++ using @code{Rcpp}, this package provides a collection of
|
||
metrics for evaluating models.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-matrixmodels
|
||
(package
|
||
(name "r-matrixmodels")
|
||
(version "0.5-2")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "MatrixModels" version))
|
||
(sha256
|
||
(base32
|
||
"0ap3mfzb2psjwlksfjzs2ycl5598bllwzx5hfmf9db4yjsydn1hw"))))
|
||
(properties `((upstream-name . "MatrixModels")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-matrix))
|
||
(home-page "https://cran.r-project.org/web/packages/MatrixModels")
|
||
(synopsis "Modelling with sparse and dense matrices")
|
||
(description
|
||
"This package models with sparse and dense matrix matrices,
|
||
using modular prediction and response module classes.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-quantreg
|
||
(package
|
||
(name "r-quantreg")
|
||
(version "5.97")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "quantreg" version))
|
||
(sha256
|
||
(base32 "18bdcxm2f8gc2bxdxrk80dcafl8d5snckp0913pkdsfyfrbxxrw7"))))
|
||
(build-system r-build-system)
|
||
(arguments
|
||
(list
|
||
#:phases
|
||
'(modify-phases %standard-phases
|
||
;; This is needed for building vignettes
|
||
(add-after 'unpack 'set-HOME
|
||
(lambda _ (setenv "HOME" "/tmp"))))))
|
||
(native-inputs
|
||
(list gfortran r-r-rsp)) ;for vignettes
|
||
(propagated-inputs
|
||
(list r-mass r-matrix r-matrixmodels r-sparsem r-survival))
|
||
(home-page "https://www.r-project.org")
|
||
(synopsis "Quantile regression")
|
||
(description
|
||
"This package provides an estimation and inference methods for models
|
||
of conditional quantiles: linear and nonlinear parametric and non-parametric
|
||
models for conditional quantiles of a univariate response and several methods
|
||
for handling censored survival data. Portfolio selection methods based on
|
||
expected shortfall risk are also included.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-nloptr
|
||
(package
|
||
(name "r-nloptr")
|
||
(version "2.0.3")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "nloptr" version))
|
||
(sha256
|
||
(base32
|
||
"1mqnjswm0dl6vqc8b2s5k3n1mhanaha3l33vh68dh6zx8q9aq9kv"))))
|
||
(build-system r-build-system)
|
||
(native-inputs
|
||
(list r-knitr ; for building vignettes
|
||
pkg-config gfortran))
|
||
(inputs
|
||
(list nlopt))
|
||
(propagated-inputs (list r-testthat))
|
||
(home-page "https://cran.r-project.org/web/packages/nloptr")
|
||
(synopsis "R interface to NLopt")
|
||
(description
|
||
"This package is interface to NLopt, a library for nonlinear
|
||
optimization. NLopt is a library for nonlinear optimization, providing a
|
||
common interface for a number of different free optimization routines
|
||
available online as well as original implementations of various other
|
||
algorithms.")
|
||
(license license:lgpl3)))
|
||
|
||
(define-public r-lme4
|
||
(package
|
||
(name "r-lme4")
|
||
(version "1.1-34")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "lme4" version))
|
||
(sha256
|
||
(base32
|
||
"1bbaxkrd5m3d40y6jdyrdr4vsjyzkfixbqjwj6c8inmks98f2wp8"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-boot
|
||
r-lattice
|
||
r-mass
|
||
r-matrix
|
||
r-minqa
|
||
r-nlme
|
||
r-nloptr
|
||
r-rcpp
|
||
r-rcppeigen))
|
||
(native-inputs
|
||
(list r-knitr))
|
||
(home-page "https://cran.r-project.org/web/packages/lme4")
|
||
(synopsis "Linear mixed-effects models using eigen and S4")
|
||
(description
|
||
"This package provides fit linear and generalized linear mixed-effects
|
||
models. The models and their components are represented using S4 classes and
|
||
methods. The core computational algorithms are implemented using the Eigen
|
||
C++ library for numerical linear algebra and RcppEigen glue.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-pbkrtest
|
||
(package
|
||
(name "r-pbkrtest")
|
||
(version "0.5.2")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "pbkrtest" version))
|
||
(sha256
|
||
(base32
|
||
"1qxnd4pfpsq762x81s3vkw09wdwpfj25bba5474g7z506pqasycf"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-broom
|
||
r-dplyr
|
||
r-lme4
|
||
r-mass
|
||
r-matrix
|
||
r-numderiv))
|
||
(native-inputs
|
||
(list r-knitr))
|
||
(home-page "https://people.math.aau.dk/~sorenh/software/pbkrtest/")
|
||
(synopsis "Methods for linear mixed model comparison")
|
||
(description
|
||
"This package implements a parametric bootstrap test and a Kenward Roger
|
||
modification of F-tests for linear mixed effects models and a parametric
|
||
bootstrap test for generalized linear mixed models.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-cardata
|
||
(package
|
||
(name "r-cardata")
|
||
(version "3.0-5")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "carData" version))
|
||
(sha256
|
||
(base32 "06j52rpbqi6fj7chfjwjbwbr6slrbb7i3aygv66gnfiyndcp3rq2"))))
|
||
(properties `((upstream-name . "carData")))
|
||
(build-system r-build-system)
|
||
(home-page "https://r-forge.r-project.org/projects/car/")
|
||
(synopsis "Data Sets for the book Companion to Applied Regression")
|
||
(description
|
||
"This package provides datasets to accompany J. Fox and S. Weisberg, An R
|
||
Companion to Applied Regression, Third Edition, Sage.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-car
|
||
(package
|
||
(name "r-car")
|
||
(version "3.1-2")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "car" version))
|
||
(sha256
|
||
(base32 "1j3l8r3j05769gdfrqz0n38xviq6pww1cjrgdd0fkj3sjy8k89l9"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-abind
|
||
r-cardata
|
||
r-lme4
|
||
r-mass
|
||
r-mgcv
|
||
r-nlme
|
||
r-nnet
|
||
r-pbkrtest
|
||
r-quantreg
|
||
r-scales))
|
||
(native-inputs
|
||
(list r-knitr))
|
||
(home-page "https://r-forge.r-project.org/projects/car/")
|
||
(synopsis "Companion to applied regression")
|
||
(description
|
||
"This package provides functions and datasets from book Companion
|
||
to Applied regression, Second Edition, Sage, 2011.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-rcppprogress
|
||
(package
|
||
(name "r-rcppprogress")
|
||
(version "0.4.2")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "RcppProgress" version))
|
||
(sha256
|
||
(base32
|
||
"0j2b37gwjpgmrnr00srdzm751hzlpsjb54ph63xxmcdfnwhlnqmi"))))
|
||
(properties `((upstream-name . "RcppProgress")))
|
||
(build-system r-build-system)
|
||
(home-page "https://github.com/kforner/rcpp_progress")
|
||
(synopsis "Interruptible progress bar for C++ in R packages")
|
||
(description
|
||
"This package displays a progress bar in the R console for long running
|
||
computations taking place in C++ code, and support for interrupting those computations
|
||
even in multithreaded code, typically using OpenMP.")
|
||
(license license:gpl3+)))
|
||
|
||
(define-public r-tmvnsim
|
||
(package
|
||
(name "r-tmvnsim")
|
||
(version "1.0-2")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "tmvnsim" version))
|
||
(sha256
|
||
(base32
|
||
"03xsvsg9bqvgl98ywid3h91mmlhax5s6wvmypp3hq91vmc5kvxlp"))))
|
||
(properties `((upstream-name . "tmvnsim")))
|
||
(build-system r-build-system)
|
||
(native-inputs (list gfortran))
|
||
(home-page "https://www.r-project.org")
|
||
(synopsis "Truncated multivariate normal simulation")
|
||
(description
|
||
"This package implements importance sampling from the truncated
|
||
multivariate normal using the @dfn{Geweke-Hajivassiliou-Keane} (GHK)
|
||
simulator. Unlike Gibbs sampling which can get stuck in one truncation
|
||
sub-region depending on initial values, this package allows truncation based
|
||
on disjoint regions that are created by truncation of absolute values. The
|
||
GHK algorithm uses simple Cholesky transformation followed by recursive
|
||
simulation of univariate truncated normals hence there are also no convergence
|
||
issues. Importance sample is returned along with sampling weights, based on
|
||
which, one can calculate integrals over truncated regions for multivariate
|
||
normals.")
|
||
(license license:gpl2)))
|
||
|
||
(define-public r-mnormt
|
||
(package
|
||
(name "r-mnormt")
|
||
(version "2.1.1")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "mnormt" version))
|
||
(sha256
|
||
(base32
|
||
"020ka48jsxm9l109ksvy2l17xcpm51avm0l971dgs2mgg01sgz4m"))))
|
||
(build-system r-build-system)
|
||
(native-inputs
|
||
(list gfortran))
|
||
(home-page "http://azzalini.stat.unipd.it/SW/Pkg-mnormt")
|
||
(synopsis "Multivariate normal and \"t\" distributions")
|
||
(description
|
||
"This package provides functions for computing the density and the
|
||
distribution function of multivariate normal and \"t\" random variables, and
|
||
for generating random vectors sampled from these distributions. Probabilities
|
||
are computed via non-Monte Carlo methods.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-numderiv
|
||
(package
|
||
(name "r-numderiv")
|
||
(version "2016.8-1.1")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "numDeriv" version))
|
||
(sha256
|
||
(base32
|
||
"0idk02pqkziik932bd8k72d1q775g1is3m4bc861pcxfz6gx3i6q"))))
|
||
(properties `((upstream-name . "numDeriv")))
|
||
(build-system r-build-system)
|
||
(home-page "https://cran.r-project.org/web/packages/numDeriv")
|
||
(synopsis "Accurate numerical derivatives")
|
||
(description
|
||
"This package provides methods for calculating accurate numerical
|
||
first and second order derivatives.")
|
||
(license license:gpl2)))
|
||
|
||
(define-public r-sn
|
||
(package
|
||
(name "r-sn")
|
||
(version "2.1.1")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "sn" version))
|
||
(sha256
|
||
(base32
|
||
"1g92vwbg0kqnqpsgianid2r91334p5shi39hr26v2z6wj5nvbxpr"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-mnormt r-numderiv r-quantreg))
|
||
(native-inputs (list r-r-rsp))
|
||
(home-page "http://azzalini.stat.unipd.it/SN")
|
||
(synopsis "The skew-normal and skew-t distributions")
|
||
(description
|
||
"This package provides functionalities to build and manipulate
|
||
probability distributions of the skew-normal family and some related
|
||
ones, notably the skew-t family, and provides related statistical
|
||
methods for data fitting and diagnostics, in the univariate and the
|
||
multivariate case.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-tclust
|
||
(package
|
||
(name "r-tclust")
|
||
(version "1.5-4")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "tclust" version))
|
||
(sha256
|
||
(base32
|
||
"1a3i6kvfzc2d6rdf75w03n5172jihhqa8mvzcb4m8l0w6mgdlm9b"))))
|
||
(build-system r-build-system)
|
||
;; These are all suggested packages, not build dependencies.
|
||
(propagated-inputs
|
||
(list r-cluster r-mclust r-mvtnorm r-sn))
|
||
(home-page "https://cran.r-project.org/web/packages/tclust")
|
||
(synopsis "Robust trimmed clustering")
|
||
(description
|
||
"This package implements different robust clustering
|
||
algorithms (@code{tclust}) based on trimming and including some graphical
|
||
diagnostic tools (@code{ctlcurves} and @code{DiscrFact}).")
|
||
(license license:gpl3)))
|
||
|
||
(define-public r-ranger
|
||
(package
|
||
(name "r-ranger")
|
||
(version "0.15.1")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "ranger" version))
|
||
(sha256
|
||
(base32
|
||
"0bibv9xf6w8k8nsc13f2yd4kx99aq0i758h3wfh089szgkpdjrad"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-rcpp r-matrix r-rcppeigen))
|
||
(home-page "https://github.com/imbs-hl/ranger")
|
||
(synopsis "Fast implementation of random forests")
|
||
(description
|
||
"This package provides a fast implementation of Random Forests,
|
||
particularly suited for high dimensional data. Ensembles of classification,
|
||
regression, survival and probability prediction trees are supported. Data from
|
||
genome-wide association studies can be analyzed efficiently.")
|
||
(license license:gpl3)))
|
||
|
||
(define-public r-tsne
|
||
(package
|
||
(name "r-tsne")
|
||
(version "0.1-3.1")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "tsne" version))
|
||
(sha256
|
||
(base32
|
||
"126q6ha25wx9mdsfngzkyp8j2fj81ri1knjdq1iyvwx3q1dwdaql"))))
|
||
(build-system r-build-system)
|
||
(home-page "https://github.com/jdonaldson/rtsne/")
|
||
(synopsis "t-Distributed Stochastic Neighbor Embedding for R")
|
||
(description
|
||
"This package provides a pure R implementation of the t-SNE algorithm.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-cairo
|
||
(package
|
||
(name "r-cairo")
|
||
(version "1.6-1")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "Cairo" version))
|
||
(sha256
|
||
(base32
|
||
"051pqbhfsr3dki2wiycbwvka850y4h4gyhvnjjf907q8sz2cykg6"))))
|
||
(properties `((upstream-name . "Cairo")))
|
||
(build-system r-build-system)
|
||
(inputs
|
||
(list cairo harfbuzz icu4c libjpeg-turbo libtiff zlib))
|
||
(native-inputs
|
||
(list pkg-config))
|
||
(home-page "https://www.rforge.net/Cairo/")
|
||
(synopsis "R graphics device using Cairo graphics library")
|
||
(description
|
||
"This package provides a Cairo graphics device that can be use to
|
||
create high-quality vector (PDF, PostScript and SVG) and bitmap
|
||
output (PNG,JPEG,TIFF), and high-quality rendering in displays (X11
|
||
and Win32). Since it uses the same back-end for all output, copying
|
||
across formats is WYSIWYG. Files are created without the dependence
|
||
on X11 or other external programs. This device supports alpha
|
||
channel (semi-transparent drawing) and resulting images can contain
|
||
transparent and semi-transparent regions. It is ideal for use in
|
||
server environments (file output) and as a replacement for other
|
||
devices that don't have Cairo's capabilities such as alpha support or
|
||
anti-aliasing. Backends are modular such that any subset of backends
|
||
is supported.")
|
||
(license license:gpl2)))
|
||
|
||
(define-public r-lubridate
|
||
(package
|
||
(name "r-lubridate")
|
||
(version "1.9.3")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "lubridate" version))
|
||
(sha256
|
||
(base32
|
||
"1zvzycng2hsks9d7552nb93abzjrs43c975rc16s3c1is8318vib"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-generics r-timechange))
|
||
(native-inputs
|
||
(list r-knitr))
|
||
(home-page "https://cran.r-project.org/web/packages/lubridate/")
|
||
(synopsis "Make dealing with dates a little easier")
|
||
(description
|
||
"This package provides functions to work with date-times and time-spans:
|
||
fast and user friendly parsing of date-time data, extraction and updating of
|
||
components of a date-time (years, months, days, hours, minutes, and seconds),
|
||
algebraic manipulation on date-time and time-span objects. The @code{lubridate}
|
||
package has a consistent and memorable syntax that makes working with dates
|
||
easy and fun.")
|
||
(license license:gpl2)))
|
||
|
||
(define-public r-fdrtool
|
||
(package
|
||
(name "r-fdrtool")
|
||
(version "1.2.17")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "fdrtool" version))
|
||
(sha256
|
||
(base32
|
||
"1pf554vb902vavgqc4c0kgghywbgcvr3lkkr414bxngavcd60lil"))))
|
||
(build-system r-build-system)
|
||
(home-page "https://strimmerlab.org/software/fdrtool/")
|
||
(synopsis "Estimation of false discovery rates and higher criticism")
|
||
(description
|
||
"This package provides tools to estimate tail area-based false discovery
|
||
rates as well as local false discovery rates for a variety of null
|
||
models (p-values, z-scores, correlation coefficients, t-scores). The
|
||
proportion of null values and the parameters of the null distribution are
|
||
adaptively estimated from the data. In addition, the package contains
|
||
functions for non-parametric density estimation (Grenander estimator), for
|
||
monotone regression (isotonic regression and antitonic regression with
|
||
weights), for computing the @dfn{greatest convex minorant} (GCM) and the
|
||
@dfn{least concave majorant} (LCM), for the half-normal and correlation
|
||
distributions, and for computing empirical @dfn{higher criticism} (HC) scores
|
||
and the corresponding decision threshold.")
|
||
(license license:gpl3+)))
|
||
|
||
(define-public r-forcats
|
||
(package
|
||
(name "r-forcats")
|
||
(version "1.0.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "forcats" version))
|
||
(sha256
|
||
(base32
|
||
"0ki5c84n7xm4iw4aj629l51hm84f6p5wa3bw88d1wbnr15wibfy5"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-cli
|
||
r-glue
|
||
r-lifecycle
|
||
r-magrittr
|
||
r-tibble
|
||
r-rlang))
|
||
(native-inputs
|
||
(list r-knitr))
|
||
(home-page "https://forcats.tidyverse.org")
|
||
(synopsis "Tools for working with factors")
|
||
(description "This package provides helpers for reordering factor
|
||
levels (including moving specified levels to front, ordering by first
|
||
appearance, reversing, and randomly shuffling), and tools for modifying factor
|
||
levels (including collapsing rare levels into other, \"anonymizing\", and
|
||
manually \"recoding\").")
|
||
(license license:gpl3)))
|
||
|
||
(define-public r-tgconfig
|
||
(let ((commit "15cf199436ae0b2ac0006b2ca7f0aeeb5c9d4445")
|
||
(revision "1"))
|
||
(package
|
||
(name "r-tgconfig")
|
||
(version (git-version "0.1.2" revision commit))
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/tanaylab/tgconfig")
|
||
(commit commit)))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32 "159m8hhbk9ip2fdy6zsa96v0173q1awcrzdz2rr2796awfaxjgx1"))))
|
||
(properties `((upstream-name . "tgconfig")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs (list r-yaml))
|
||
(home-page "https://github.com/tanaylab/tgconfig")
|
||
(synopsis "Infrastructure for managing package parameters")
|
||
(description
|
||
"This is a package to provide infrastructure for managing package parameters.
|
||
Parameters are easy to get in relevant functions within a package,
|
||
and rrror is thrown if a parameter is missing. Developers are able
|
||
to register parameters and set their default value in a config file
|
||
that is part of the package in YAML format, and users are able to
|
||
override parameters using their own YAML. Users get an exception
|
||
when trying to override a parameter that was not registered, and
|
||
can load multiple parameters to the current environment.")
|
||
(license license:gpl3+))))
|
||
|
||
(define-public r-tgutil
|
||
(let ((commit "0e4a2e84e5cf1f74bc66df0a3d8eac89633fd7b1")
|
||
(revision "1"))
|
||
(package
|
||
(name "r-tgutil")
|
||
(version (git-version "0.1.15" revision commit))
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/tanaylab/tgutil")
|
||
(commit commit)))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32 "0pmacpzhrigprlpl8b5j4xz7l110ifw98017xwk569dghbf8zrq1"))))
|
||
(properties `((upstream-name . "tgutil")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs (list r-broom
|
||
r-cowplot
|
||
r-data-table
|
||
r-dplyr
|
||
r-ggplot2
|
||
r-glue
|
||
r-magrittr
|
||
r-matrix
|
||
r-matrixstats
|
||
r-qlcmatrix
|
||
r-readr
|
||
r-rlang
|
||
r-scales
|
||
r-tibble
|
||
r-tidyr))
|
||
(home-page "https://github.com/tanaylab/tgutil")
|
||
(synopsis "Simple utility functions for Tanay lab code")
|
||
(description "Shared utility functions for multiple Tanay lab packages.")
|
||
(license license:gpl3))))
|
||
|
||
(define-public r-catterplots
|
||
(let ((commit "ae17cd5e49ddda4ecfe0eba8a4c21df8c88e72c4")
|
||
(revision "3"))
|
||
(package
|
||
(name "r-catterplots")
|
||
(version (git-version "0" revision commit))
|
||
(source (origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/Gibbsdavidl/CatterPlots")
|
||
(commit commit)))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"0qa8liylffpxgdg8xcgjar5dsvczqhn3akd4w35113hnyg1m4xyg"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-png))
|
||
(home-page "https://github.com/Gibbsdavidl/CatterPlots")
|
||
(synopsis "Scatter plots with cat shaped points")
|
||
(description "Did you ever wish you could make scatter plots with cat
|
||
shaped points? Now you can!")
|
||
(license license:asl2.0))))
|
||
|
||
(define-public r-colorout
|
||
(package
|
||
(name "r-colorout")
|
||
(version "1.2-2")
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/jalvesaq/colorout")
|
||
(commit (string-append "v" version))))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32 "1rsx69wjpa73c6x2hacvvvbzdzxn7wg06gizf97kasjdlb7azmp3"))))
|
||
(build-system r-build-system)
|
||
(home-page "https://github.com/jalvesaq/colorout")
|
||
(synopsis "Colorize output in the R REPL")
|
||
(description "@code{colorout} is an R package that colorizes R output when
|
||
running in terminal emulator.
|
||
|
||
R STDOUT is parsed and numbers, negative numbers, dates in the standard
|
||
format, strings, and R constants are identified and wrapped by special ANSI
|
||
scape codes that are interpreted by terminal emulators as commands to colorize
|
||
the output. R STDERR is also parsed to identify the expressions warning and
|
||
error and their translations to many languages. If these expressions are
|
||
found, the output is colorized accordingly; otherwise, it is colorized as
|
||
STDERROR (blue, by default).
|
||
|
||
You can customize the colors according to your taste, guided by the color
|
||
table made by the command @code{show256Colors()}. You can also set the colors
|
||
to any arbitrary string. In this case, it is up to you to set valid values.")
|
||
(license license:gpl3+)))
|
||
|
||
(define-public r-nnlm
|
||
(let ((commit "4574bca9456fe2285b668b4c22a908cffbad10a0")
|
||
(revision "1"))
|
||
(package
|
||
(name "r-nnlm")
|
||
(version (git-version "0.4.4" revision commit))
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/linxihui/NNLM")
|
||
(commit commit)))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32 "1qzvav4ch0j1k7jcqzk9cvl8dx79fapmvdzmzzyl8smscybhfgba"))))
|
||
(properties `((upstream-name . "NNLM")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs (list r-rcpp r-rcpparmadillo r-rcppprogress))
|
||
(native-inputs (list r-knitr))
|
||
(home-page "https://github.com/linxihui/NNLM")
|
||
(synopsis "Fast and versatile non-negative matrix factorization")
|
||
(description
|
||
"This is a package for @dfn{Non-Negative Linear Models} (NNLM). It
|
||
implements fast sequential coordinate descent algorithms for non-negative
|
||
linear regression and @dfn{non-negative matrix factorization} (NMF). It
|
||
supports mean square error and Kullback-Leibler divergence loss. Many other
|
||
features are also implemented, including missing value imputation, domain
|
||
knowledge integration, designable W and H matrices and multiple forms of
|
||
regularizations.")
|
||
(license license:bsd-2))))
|
||
|
||
(define-public r-swne
|
||
(let ((commit "05fc3ee4e09b2c34d99c69d3b97cece4c1c34143")
|
||
(revision "1"))
|
||
(package
|
||
(name "r-swne")
|
||
(version (git-version "0.6.20" revision commit))
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/yanwu2014/swne")
|
||
(commit commit)))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32 "0crlpg9kclbv4v8250p3086a3lk6f2hcq79psqkdylc1qnrx3kfx"))))
|
||
(properties `((upstream-name . "swne")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-fnn
|
||
r-ggplot2
|
||
r-ggrepel
|
||
r-hash
|
||
r-ica
|
||
r-igraph
|
||
r-irlba
|
||
r-jsonlite
|
||
r-liger
|
||
r-mass
|
||
r-matrix
|
||
r-mgcv
|
||
r-nnlm ;not listed but required at install time
|
||
r-plyr
|
||
r-proxy
|
||
r-rcolorbrewer
|
||
r-rcpp
|
||
r-rcpparmadillo
|
||
r-rcppeigen
|
||
r-reshape
|
||
r-reshape2
|
||
r-snow
|
||
r-umap
|
||
r-usedist))
|
||
(home-page "https://github.com/yanwu2014/swne")
|
||
(synopsis "Visualize high dimensional datasets")
|
||
(description
|
||
"@dfn{Similarity Weighted Nonnegative Embedding} (SWNE) is a method for
|
||
visualizing high dimensional datasets. SWNE uses Nonnegative Matrix
|
||
Factorization to decompose datasets into latent factors, projects those
|
||
factors onto 2 dimensions, and embeds samples and key features in 2 dimensions
|
||
relative to the factors. SWNE can capture both the local and global dataset
|
||
structure, and allows relevant features to be embedded directly onto the
|
||
visualization, facilitating interpretation of the data.")
|
||
(license license:gpl2))))
|
||
|
||
(define-public r-languageserver
|
||
(let ((commit "004da9388f9b19990f031c8dc9b527fb406378ba")
|
||
(revision "1"))
|
||
(package
|
||
(name "r-languageserver")
|
||
(version (git-version "0.3.12" revision commit))
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/REditorSupport/languageserver")
|
||
(commit commit)))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32 "05f22bjpc87fngzq4jsk2q2yb2i3ha03b377r0wx15d0b8xaa1ix"))))
|
||
(properties `((upstream-name . "languageserver")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-callr
|
||
r-collections
|
||
r-fs
|
||
r-jsonlite
|
||
r-lintr
|
||
r-r6
|
||
r-roxygen2
|
||
r-stringi
|
||
r-styler
|
||
r-xml2
|
||
r-xmlparsedata))
|
||
(home-page "https://github.com/REditorSupport/languageserver")
|
||
(synopsis "Language Server for R")
|
||
(description
|
||
"This package provides an implementation of the Language Server
|
||
Protocol for R. The
|
||
@url{https://microsoft.github.io/language-server-protocol/,Language Server
|
||
protocol} is used by an editor client to integrate features like auto
|
||
completion.")
|
||
(license license:expat))))
|
||
|
||
(define-public python-rpy2
|
||
(package
|
||
(name "python-rpy2")
|
||
(version "3.5.5")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (pypi-uri "rpy2" version))
|
||
(sha256
|
||
(base32
|
||
"0dyhb3xn2p6s67yxhgh4qd4hp45mhb5zvgqkdsn26kyg447c8lm2"))))
|
||
(build-system python-build-system)
|
||
(arguments
|
||
'(#:phases
|
||
(modify-phases %standard-phases
|
||
(replace 'check
|
||
(lambda* (#:key tests? #:allow-other-keys)
|
||
(when tests?
|
||
(setenv "TZ" "UTC")
|
||
(invoke "pytest" "-v" "rpy2/tests/")))))))
|
||
(propagated-inputs
|
||
(list python-cffi
|
||
python-six
|
||
python-jinja2
|
||
python-numpy
|
||
python-pandas
|
||
python-pytz
|
||
python-ipython
|
||
python-tzlocal))
|
||
(inputs
|
||
(list readline
|
||
icu4c
|
||
pcre
|
||
r-minimal
|
||
r-survival
|
||
r-ggplot2
|
||
r-rsqlite
|
||
r-dplyr
|
||
r-dbplyr
|
||
python-numpy))
|
||
(native-inputs
|
||
(list zlib python-pytest))
|
||
(home-page "https://rpy2.github.io")
|
||
(synopsis "Python interface to the R language")
|
||
(description "rpy2 is a redesign and rewrite of rpy. It is providing a
|
||
low-level interface to R from Python, a proposed high-level interface,
|
||
including wrappers to graphical libraries, as well as R-like structures and
|
||
functions.")
|
||
;; Any of these licenses can be picked for the R interface. The whole
|
||
;; project is released under GPLv2+ according to the license declaration
|
||
;; in "setup.py".
|
||
(license (list license:mpl2.0 license:gpl2+ license:lgpl2.1+))))
|
||
|
||
(define-public java-jdistlib
|
||
(package
|
||
(name "java-jdistlib")
|
||
(version "0.4.5")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (string-append "mirror://sourceforge/jdistlib/jdistlib-"
|
||
version "-src.jar"))
|
||
(sha256
|
||
(base32
|
||
"1pkj8aahw9ydr1isbaqrkd05nvq98ik5jwwhf3yf3rky3z869v11"))))
|
||
(build-system ant-build-system)
|
||
(arguments
|
||
`(#:jar-name "jdistlib.jar"
|
||
#:jdk ,icedtea-8
|
||
#:tests? #f ; no dedicated test directory
|
||
#:phases
|
||
(modify-phases %standard-phases
|
||
(add-after 'unpack 'fix-broken-encoding
|
||
(lambda _
|
||
(with-fluids ((%default-port-encoding "ISO-8859-1"))
|
||
(substitute* "src/jdistlib/Beta.java"
|
||
(("Scheff.+-Tukey") "Scheffe-Tukey")))
|
||
#t)))))
|
||
(propagated-inputs
|
||
(list java-jtransforms))
|
||
(native-inputs
|
||
(list java-junit))
|
||
(home-page "https://jdistlib.sourceforge.net/")
|
||
(synopsis "Java library of statistical distributions")
|
||
(description "JDistlib is the Java Statistical Distribution Library, a
|
||
Java package that provides routines for various statistical distributions.")
|
||
;; The files that were translated from R code are under GPLv2+; some files
|
||
;; are under the GPLv3, which is a mistake. The author confirmed in an
|
||
;; email that this whole project should be under GPLv2+.
|
||
(license license:gpl2+)))
|
||
|
||
(define-public emacs-ess
|
||
;; Latest release is old. This is not the latest commit either due to bug
|
||
;; reported here: <https://github.com/emacs-ess/ESS/issues/987>.
|
||
(let ((commit "24da603184ce39246611dd5b8602e769d7ebd5bf")
|
||
(version "18.10.2")
|
||
(revision "0"))
|
||
(package
|
||
(name "emacs-ess")
|
||
(version (git-version version revision commit))
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/emacs-ess/ESS")
|
||
(commit commit)))
|
||
(sha256
|
||
(base32 "0j98lv07nzwzd54d4dgcfz01wy5gj48m0mnirxzh5r45ik2myh1r"))
|
||
(file-name (git-file-name name version))
|
||
(modules '((guix build utils)))
|
||
(snippet
|
||
'(begin
|
||
;; Stop ESS from trying to bundle an external julia-mode.el.
|
||
(substitute* "lisp/Makefile"
|
||
((" \\$\\(JULIAS)") "")
|
||
(("\ttest.*julia-mode.*\\.el") ""))
|
||
;; Only build docs in info format.
|
||
(substitute* "doc/Makefile"
|
||
(("all : info text")
|
||
"all : info")
|
||
(("install: install-info install-other-docs")
|
||
"install: install-info"))
|
||
;; Stop install-info from trying to update the info directory.
|
||
(substitute* "doc/Makefile"
|
||
((".*/dir.*") ""))
|
||
;; Fix r-help-mode test.
|
||
(substitute* "test/ess-test-r.el"
|
||
(("\\(equal ess-help-object \"plot.default\")") "t"))
|
||
;; Avoid generating ess-autoloads.el twice.
|
||
(substitute* "Makefile"
|
||
(("all: lisp doc etc autoloads")
|
||
"all: lisp doc etc"))
|
||
;; Install to correct directories.
|
||
(substitute* "Makefile"
|
||
(("mkdir -p \\$\\(ESSDESTDIR)")
|
||
"$(MAKE) -C lisp install; $(MAKE) -C doc install")
|
||
(("\\$\\(INSTALL) -R \\./\\* \\$\\(ESSDESTDIR)/")
|
||
"$(MAKE) -C etc install"))
|
||
#t))
|
||
(patches
|
||
(search-patches "emacs-ess-fix-obsolete-function-alias.patch"))))
|
||
(build-system gnu-build-system)
|
||
(arguments
|
||
(let ((base-directory "/share/emacs/site-lisp"))
|
||
`(#:make-flags (list (string-append "PREFIX=" %output)
|
||
(string-append "ETCDIR=" %output
|
||
,base-directory "/etc")
|
||
(string-append "LISPDIR=" %output
|
||
,base-directory)
|
||
(string-append "INFODIR=" %output
|
||
"/share/info"))
|
||
#:phases
|
||
(modify-phases %standard-phases
|
||
(delete 'configure)
|
||
(replace 'check
|
||
(lambda _ (invoke "make" "test")))))))
|
||
(native-inputs
|
||
(list perl r-roxygen2 texinfo))
|
||
(inputs
|
||
`(("emacs" ,emacs-minimal)
|
||
("r-minimal" ,r-minimal)))
|
||
(propagated-inputs
|
||
(list emacs-julia-mode))
|
||
(home-page "https://ess.r-project.org/")
|
||
(synopsis "Emacs mode for statistical analysis programs")
|
||
(description
|
||
"Emacs Speaks Statistics (ESS) is an add-on package for GNU Emacs. It
|
||
is designed to support editing of scripts and interaction with various
|
||
statistical analysis programs such as R, Julia, and JAGS.")
|
||
(license license:gpl3+))))
|
||
|
||
(define-public emacs-poly-r
|
||
(package
|
||
(name "emacs-poly-r")
|
||
(version "0.2.2")
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/polymode/poly-R")
|
||
(commit (string-append "v" version))))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32 "0a4wx73jkngw5nbq1fa4jfhba6bsmyn6vnsf887x3xhb5v3ykhsg"))))
|
||
(build-system emacs-build-system)
|
||
(propagated-inputs
|
||
(list emacs-ess emacs-poly-noweb emacs-polymode-markdown
|
||
emacs-polymode))
|
||
(properties '((upstream-name . "poly-R")))
|
||
(home-page "https://github.com/polymode/poly-markdown")
|
||
(synopsis "Polymodes for the R language")
|
||
(description
|
||
"This package provides a number of polymodes for working with mixed R
|
||
files, including Rmarkdown files.")
|
||
(license license:gpl3+)))
|
||
|
||
(define-public readstat
|
||
(package
|
||
(name "readstat")
|
||
(version "1.1.9")
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/WizardMac/ReadStat")
|
||
(commit (string-append "v" version))))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32 "0aqalr86d7h9sp9zjkydw3ap4s54qgq2ml6p8gd0gnn1jf0ljm72"))))
|
||
(build-system gnu-build-system)
|
||
(native-inputs
|
||
(list autoconf automake gnu-gettext libtool))
|
||
(inputs
|
||
(list zlib))
|
||
(home-page "https://github.com/WizardMac/ReadStat")
|
||
(synopsis "Convert SAS, Stata, and SPSS files")
|
||
(description "Command-line tool and C library for reading files from
|
||
popular stats packages like SAS, Stata and SPSS.")
|
||
(license license:expat)))
|
||
|
||
(define-public r-quantpsyc
|
||
(package
|
||
(name "r-quantpsyc")
|
||
(version "1.6")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "QuantPsyc" version))
|
||
(sha256
|
||
(base32
|
||
"1dbj830p5837fiwa800nzsaf19lf95vc3n7jmds2q9v06mrz6syq"))))
|
||
(properties `((upstream-name . "QuantPsyc")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-boot
|
||
r-dplyr
|
||
r-mass
|
||
r-purrr))
|
||
(home-page "https://cran.r-project.org/web/packages/QuantPsyc/")
|
||
(synopsis "Quantitative Psychology Tools")
|
||
(description
|
||
"Contains functions useful for data screening, testing moderation,
|
||
mediation and estimating power.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-clubsandwich
|
||
(package
|
||
(name "r-clubsandwich")
|
||
(version "0.5.10")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "clubSandwich" version))
|
||
(sha256
|
||
(base32
|
||
"0qx4qq0k01q06hrs348n417pf338dyfbcy2vsi0y3ap6y1rb7w6s"))))
|
||
(properties `((upstream-name . "clubSandwich")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-sandwich))
|
||
(native-inputs (list r-knitr))
|
||
(home-page "https://github.com/jepusto/clubSandwich")
|
||
(synopsis "Cluster-Robust (Sandwich) Variance Estimators with Small-Sample
|
||
Corrections")
|
||
(description
|
||
"Provides several cluster-robust variance estimators (i.e.,
|
||
sandwich estimators) for ordinary and weighted least squares linear regression
|
||
models, including the bias-reduced linearization estimator introduced by Bell
|
||
and McCaffrey (2002)
|
||
@url{http://www.statcan.gc.ca/pub/12-001-x/2002002/article/9058-eng.pdf} and
|
||
developed further by Pustejovsky and Tipton (2017)
|
||
@url{doi:10.1080/07350015.2016.1247004}. The package includes functions for estimating
|
||
the variance- covariance matrix and for testing single- and multiple-
|
||
contrast hypotheses based on Wald test statistics. Tests of single regression
|
||
coefficients use Satterthwaite or saddle-point corrections. Tests of multiple-
|
||
contrast hypotheses use an approximation to Hotelling's T-squared distribution.
|
||
Methods are provided for a variety of fitted models, including @code{lm()} and
|
||
@code{mlm} objects, @code{glm()}, ivreg (from package @code{AER}), @code{plm()}
|
||
(from package @code{plm}), @code{gls()} and @code{lme()} (from @code{nlme}),
|
||
@code{robu()} (from @code{robumeta}), and @code{rma.uni()} and @code{rma.mv()}
|
||
(from @code{metafor}).")
|
||
(license license:gpl3)))
|
||
|
||
(define-public r-puniform
|
||
(package
|
||
(name "r-puniform")
|
||
(version "0.2.7")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "puniform" version))
|
||
(sha256
|
||
(base32
|
||
"15q5wlcps7387rjz7p1f5kifg1fl5yxxy7gjx6fvspvqwjkjbs4z"))))
|
||
(properties `((upstream-name . "puniform")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-adgoftest r-metafor r-numderiv r-rcpp r-rcpparmadillo))
|
||
(home-page
|
||
"https://github.com/RobbievanAert/puniform")
|
||
(synopsis
|
||
"Meta-Analysis Methods Correcting for Publication Bias")
|
||
(description
|
||
"This package provides meta-analysis methods that correct for publication
|
||
bias and outcome reporting bias. Four methods and a visual tool are currently
|
||
included in the package.
|
||
|
||
@enumerate
|
||
@item The p-uniform method as described in van Assen, van Aert, and Wicherts
|
||
(2015) @url{doi:10.1037/met0000025} can be used for estimating the average
|
||
effect size, testing the null hypothesis of no effect, and testing for
|
||
publication bias using only the statistically significant effect sizes of
|
||
primary studies.
|
||
|
||
@item The p-uniform* method as described in van Aert and van Assen (2019)
|
||
@url{doi:10.31222/osf.io/zqjr9}. This method is an extension of the p-uniform
|
||
method that allows for estimation of the average effect size and the
|
||
between-study variance in a meta-analysis, and uses both the statistically
|
||
significant and nonsignificant effect sizes.
|
||
|
||
@item The hybrid method as described in van Aert and van Assen (2017)
|
||
@url{doi:10.3758/s13428-017-0967-6}. The hybrid method is a meta-analysis
|
||
method for combining an original study and replication and while taking into
|
||
account statistical significance of the original study. The p-uniform and
|
||
hybrid method are based on the statistical theory that the distribution of
|
||
p-values is uniform conditional on the population effect size.
|
||
|
||
@item
|
||
The fourth method in the package is the Snapshot Bayesian Hybrid Meta-Analysis
|
||
Method as described in van Aert and van Assen (2018)
|
||
@url{doi:10.1371/journal.pone.0175302}. This method computes posterior
|
||
probabilities for four true effect sizes (no, small, medium, and large) based
|
||
on an original study and replication while taking into account publication bias
|
||
in the original study. The method can also be used for computing the required
|
||
sample size of the replication akin to power analysis in null hypothesis
|
||
significance testing.
|
||
@end enumerate
|
||
|
||
The meta-plot is a visual tool for meta-analysis that
|
||
provides information on the primary studies in the meta-analysis, the results
|
||
of the meta-analysis, and characteristics of the research on the effect under
|
||
study (van Assen and others, 2020).
|
||
|
||
Helper functions to apply the Correcting for Outcome Reporting Bias (CORB)
|
||
method to correct for outcome reporting bias in a meta-analysis (van Aert &
|
||
Wicherts, 2020).")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-esc
|
||
(package
|
||
(name "r-esc")
|
||
(version "0.5.1")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "esc" version))
|
||
(sha256
|
||
(base32
|
||
"0gns7gz55p6pha05413r3hlvd7f2v1amxkg13d197mab1ypqic7q"))))
|
||
(properties `((upstream-name . "esc")))
|
||
(build-system r-build-system)
|
||
(home-page "https://strengejacke.github.io/esc/")
|
||
(synopsis
|
||
"Effect Size Computation for Meta Analysis")
|
||
(description
|
||
"Implementation of the web-based
|
||
@url{http://www.campbellcollaboration.org/escalc/html/EffectSizeCalculator-Home.php,'Practical
|
||
Meta-Analysis Effect Size Calculator'} from David B. Wilson in R. Based on the
|
||
input, the effect size can be returned as standardized mean difference, Cohen's
|
||
f, Hedges' g, Pearson's r or Fisher's transformation z, odds ratio or log odds,
|
||
or eta squared effect size.")
|
||
(license license:gpl3)))
|
||
|
||
(define-public r-kknn
|
||
(package
|
||
(name "r-kknn")
|
||
(version "1.3.1")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "kknn" version))
|
||
(sha256
|
||
(base32
|
||
"1nzkg3dxaiqp87p56wm895qx5xn86hv5hjr73qvl1yiaxiq0x112"))))
|
||
(properties `((upstream-name . "kknn")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-igraph r-matrix))
|
||
(home-page "https://github.com/KlausVigo/kknn")
|
||
(synopsis "Weighted k-Nearest Neighbors")
|
||
(description
|
||
"Weighted k-Nearest Neighbors for Classification, Regression and Clustering.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-logspline
|
||
(package
|
||
(name "r-logspline")
|
||
(version "2.1.20")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "logspline" version))
|
||
(sha256
|
||
(base32
|
||
"1nsrgz9sh9qg2fj0x7k48lqhpgzq1z78jfz89ckzp5xm4r8lpgcb"))))
|
||
(properties `((upstream-name . "logspline")))
|
||
(build-system r-build-system)
|
||
(native-inputs (list gfortran))
|
||
(home-page
|
||
"https://cran.r-project.org/web/packages/logspline/")
|
||
(synopsis
|
||
"Routines for Logspline Density Estimation")
|
||
(description
|
||
"Contains routines for logspline density estimation. The function
|
||
@code{oldlogspline()} uses the same algorithm as the logspline package version
|
||
1.0.x; i.e., the Kooperberg and Stone (1992) algorithm (with an improved
|
||
interface). The recommended routine @code{logspline()} uses an algorithm from
|
||
@url{doi:10.1214/aos/1031594728,Stone et al (1997)}.")
|
||
(license license:asl2.0)))
|
||
|
||
(define-public r-effects
|
||
(package
|
||
(name "r-effects")
|
||
(version "4.2-2")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "effects" version))
|
||
(sha256
|
||
(base32
|
||
"0nlj79am9a1yg737dhfa8dj1kj2hly9pfknmphsbcvlgxqn35vig"))))
|
||
(properties `((upstream-name . "effects")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-cardata
|
||
r-colorspace
|
||
r-estimability
|
||
r-insight
|
||
r-lattice
|
||
r-lme4
|
||
r-nnet
|
||
r-survey))
|
||
(native-inputs
|
||
(list r-knitr))
|
||
(home-page "https://www.r-project.org")
|
||
(synopsis
|
||
"Effect Displays for Linear, Generalized Linear, and Other Models")
|
||
(description
|
||
"Graphical and tabular effect displays, e.g., of interactions, for
|
||
various statistical models with linear predictors.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-bayesfactor
|
||
(package
|
||
(name "r-bayesfactor")
|
||
(version "0.9.12-4.5")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "BayesFactor" version))
|
||
(sha256
|
||
(base32
|
||
"10bclqzczawpssjwa3b177xpab4mdhczfj1qj23xn2yvrrw1z9mh"))))
|
||
(properties `((upstream-name . "BayesFactor")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-coda
|
||
r-hypergeo
|
||
r-matrix
|
||
r-matrixmodels
|
||
r-mvtnorm
|
||
r-pbapply
|
||
r-rcpp
|
||
r-rcppeigen
|
||
r-stringr))
|
||
(native-inputs (list r-knitr))
|
||
(home-page
|
||
"https://richarddmorey.github.io/BayesFactor/")
|
||
(synopsis
|
||
"Computation of Bayes Factors for Common Designs")
|
||
(description
|
||
"This package provides a suite of functions for computing various Bayes
|
||
factors for simple designs, including contingency tables, one- and two-sample
|
||
designs, one-way designs, general ANOVA designs, and linear regression.")
|
||
(license license:gpl2)))
|
||
|
||
(define-public r-norm
|
||
(package
|
||
(name "r-norm")
|
||
(version "1.0-11.1")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "norm" version))
|
||
(sha256
|
||
(base32
|
||
"1g33g721c0f2b275b334ir6n0h81fh567vs9vrxk60y21z1ydzy2"))))
|
||
(build-system r-build-system)
|
||
(native-inputs
|
||
(list gfortran))
|
||
(home-page "https://cran.r-project.org/web/packages/norm/")
|
||
(synopsis "Analysis of multivariate normal datasets with missing values")
|
||
(description "Multiple imputation of multivariate continuous data under a
|
||
normal model.")
|
||
;; Custom license, see https://cran.r-project.org/web/packages/norm/LICENSE.
|
||
(license (license:non-copyleft "file://LICENSE"))))
|
||
|
||
(define-public r-naniar
|
||
(package
|
||
(name "r-naniar")
|
||
(version "1.0.0")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "naniar" version))
|
||
(sha256
|
||
(base32
|
||
"1x4ljc6yji7312g6cg1shc85jqv5kaf2zlf5q7sdmqh3wryskvf2"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-cli
|
||
r-dplyr
|
||
r-norm
|
||
r-forcats
|
||
r-ggplot2
|
||
r-glue
|
||
r-magrittr
|
||
r-purrr
|
||
r-rlang
|
||
r-tibble
|
||
r-tidyr
|
||
r-upsetr
|
||
r-vctrs
|
||
r-viridis
|
||
r-visdat))
|
||
(native-inputs
|
||
(list r-knitr))
|
||
(home-page "https://github.com/njtierney/naniar")
|
||
(synopsis
|
||
"Data structures, summaries, and visualisations for missing data")
|
||
(description
|
||
"Missing values are ubiquitous in data and need to be explored and
|
||
handled in the initial stages of analysis. The package provides data structures
|
||
and functions that facilitate the plotting of missing values and examination of
|
||
imputations. This allows missing data dependencies to be explored with minimal
|
||
deviation from the common work patterns of @code{ggplot2} and tidy data.")
|
||
(license license:expat)))
|
||
|
||
(define-public r-glinternet
|
||
(package
|
||
(name "r-glinternet")
|
||
(version "1.0.12")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "glinternet" version))
|
||
(sha256
|
||
(base32
|
||
"0aphdscj0s6kqxlkgqkw2d6snrylz6hiis6307pl8ldh7q5cvm33"))))
|
||
(build-system r-build-system)
|
||
(home-page "http://web.stanford.edu/~hastie/Papers/glinternet_jcgs.pdf")
|
||
(synopsis "Learning interactions via hierarchical group-lasso regularization")
|
||
(description "Group-Lasso INTERaction-NET. Fits linear pairwise-interaction
|
||
models that satisfy strong hierarchy: if an interaction coefficient is estimated
|
||
to be nonzero, then its two associated main effects also have nonzero estimated
|
||
coefficients. Accommodates categorical variables (factors) with arbitrary
|
||
numbers of levels, continuous variables, and combinations thereof. Implements
|
||
the machinery described in the paper \"Learning interactions via hierarchical
|
||
group-lasso regularization\" (JCGS 2015, Volume 24, Issue 3).
|
||
Michael Lim & Trevor Hastie (2015)")
|
||
(license license:gpl2)))
|
||
|
||
(define-public r-datasaurus
|
||
(package
|
||
(name "r-datasaurus")
|
||
(version "0.1.6")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "datasauRus" version))
|
||
(sha256
|
||
(base32
|
||
"0vgylf3bab0xcfg08xwvfq9yhxy6w0fxi7wp4kkxfyjb0pw15qxk"))))
|
||
(properties `((upstream-name . "datasauRus")))
|
||
(build-system r-build-system)
|
||
(native-inputs (list r-knitr))
|
||
(home-page
|
||
"https://github.com/lockedata/datasauRus")
|
||
(synopsis "Datasets from the Datasaurus Dozen")
|
||
(description
|
||
"The Datasaurus Dozen is a set of datasets with the same summary
|
||
statistics. They retain the same summary statistics despite having radically
|
||
different distributions. The datasets represent a larger and quirkier object
|
||
lesson that is typically taught via Anscombe's Quartet (available in the
|
||
'datasets' package). Anscombe's Quartet contains four very different
|
||
distributions with the same summary statistics and as such highlights the value
|
||
of visualisation in understanding data, over and above summary statistics. As
|
||
well as being an engaging variant on the Quartet, the data is generated in a
|
||
novel way. The simulated annealing process used to derive datasets from the
|
||
original Datasaurus is detailed in \"Same Stats, Different Graphs: Generating
|
||
Datasets with Varied Appearance and Identical Statistics through Simulated
|
||
Annealing\" @url{doi:10.1145/3025453.3025912}.")
|
||
(license license:expat)))
|
||
|
||
(define-public r-lmom
|
||
(package
|
||
(name "r-lmom")
|
||
(version "3.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "lmom" version))
|
||
(sha256
|
||
(base32 "1482kbb4cm65m2d1xlxml93yjd3d43iiap6nvzg5vd33i9iyh2jb"))))
|
||
(properties `((upstream-name . "lmom")))
|
||
(build-system r-build-system)
|
||
(native-inputs (list gfortran))
|
||
(home-page "https://cran.r-project.org/package=lmom")
|
||
(synopsis "L-Moments for R")
|
||
(description
|
||
"This package provides functions related to L-moments: computation
|
||
of L-moments and trimmed L-moments of distributions and data samples;
|
||
parameter estimation; L-moment ratio diagram; plot vs. quantiles of an
|
||
extreme-value distribution.")
|
||
(license license:cpl1.0)))
|
||
|
||
(define-public r-gld
|
||
(package
|
||
(name "r-gld")
|
||
(version "2.6.6")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "gld" version))
|
||
(sha256
|
||
(base32 "1i7xpyxd7r1fkjy9zkzd3rfsnb35v5c5fkafs1zd9d8729wfj8za"))))
|
||
(properties `((upstream-name . "gld")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs (list r-e1071 r-lmom))
|
||
(home-page
|
||
"https://cran.r-project.org/package=gld")
|
||
(synopsis
|
||
"Estimation and Use of the Generalised (Tukey) Lambda Distribution")
|
||
(description
|
||
"The generalised lambda distribution, or Tukey lambda distribution,
|
||
provides a wide variety of shapes with one functional form. This package
|
||
provides random numbers, quantiles, probabilities, densities and
|
||
density quantiles for four different types of the distribution, the FKML
|
||
(Freimer et al 1988), RS (Ramberg and Schmeiser 1974), GPD (van Staden
|
||
and Loots 2009) and FM5 - see documentation for details. It provides the
|
||
density function, distribution function, and Quantile-Quantile plots.
|
||
It implements a variety of estimation methods for the distribution,
|
||
including diagnostic plots. Estimation methods include the starship (all
|
||
4 types), method of L-Moments for the GPD and FKML types, and a number
|
||
of methods for only the FKML type. These include maximum likelihood,
|
||
maximum product of spacings, Titterington's method, Moments, Trimmed
|
||
L-Moments and Distributional Least Absolutes.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-exact
|
||
(package
|
||
(name "r-exact")
|
||
(version "3.2")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "Exact" version))
|
||
(sha256
|
||
(base32 "0a33gbhzd580i31xxsjxigg0nl8ag1x4xz3jqmq5jqappc6f5d2k"))))
|
||
(properties `((upstream-name . "Exact")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs (list r-rootsolve))
|
||
(home-page "https://cran.r-project.org/package=Exact")
|
||
(synopsis "Unconditional Exact Test")
|
||
(description
|
||
"Performs unconditional exact tests and power calculations for 2x2
|
||
contingency tables. For comparing two independent proportions, performs
|
||
@url{doi:10.1038/156177a0, Barnard's test (1945)} using the original CSM
|
||
test (@url{doi:10.1093/biomet/34.1-2.123, Barnard (1947)}), using Fisher's
|
||
p-value referred to as @url{doi:10.1111/j.1467-9574.1970.tb00104.x,
|
||
Boschloo's test (1970)}, or using a Z-statistic (@url{doi:10.2307/2981892,
|
||
Suissa and Shuster (1985)}). For comparing two binary proportions,
|
||
performs unconditional exact test using McNemar's Z-statistic
|
||
(@url{doi:10.1191/0962280203sm312ra, Berger and Sidik (2003)}), using
|
||
McNemar's Z-statistic with continuity correction, or using CSM test.
|
||
Calculates confidence intervals for the difference in proportion.")
|
||
(license license:gpl2)))
|
||
|
||
(define-public r-desctools
|
||
(package
|
||
(name "r-desctools")
|
||
(version "0.99.50")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "DescTools" version))
|
||
(sha256
|
||
(base32 "1awfhbv7klvkwxki4lvxj086yiwqyys95jnss8q5qqn7wyfz170v"))))
|
||
(properties `((upstream-name . "DescTools")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-bh
|
||
r-boot
|
||
r-data-table
|
||
r-exact
|
||
r-expm
|
||
r-gld
|
||
r-httr
|
||
r-mass
|
||
r-mvtnorm
|
||
r-rcpp
|
||
r-readxl
|
||
r-rstudioapi
|
||
r-withr))
|
||
(native-inputs (list gfortran r-r-rsp))
|
||
(home-page "https://andrisignorell.github.io/DescTools/")
|
||
(synopsis "Tools for Descriptive Statistics")
|
||
(description
|
||
"This package provides a collection of miscellaneous basic statistic
|
||
functions and convenience wrappers for efficiently describing data.
|
||
The author's intention was to create a toolbox, which facilitates the
|
||
(notoriously time consuming) first descriptive tasks in data analysis,
|
||
consisting of calculating descriptive statistics, drawing graphical
|
||
summaries and reporting the results. The package contains furthermore
|
||
functions to produce documents using MS Word (or PowerPoint) and functions
|
||
to import data from Excel. Many of the included functions can be found
|
||
scattered in other packages and other sources written partly by Titans
|
||
of R. The reason for collecting them here, was primarily to have them
|
||
consolidated in ONE instead of dozens of packages (which themselves might
|
||
depend on other packages which are not needed at all), and to provide a
|
||
common and consistent interface as far as function and arguments naming,
|
||
NA handling, recycling rules etc. are concerned. Google style guides
|
||
were used as naming rules (in absence of convincing alternatives).
|
||
The BigCamelCase style was consequently applied to functions borrowed
|
||
from contributed R packages as well.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public xlispstat
|
||
(let ((commit "f1bea6053df658ee48612bf1f63c35de99e2c649")
|
||
(revision "0"))
|
||
(package
|
||
(name "xlispstat")
|
||
(version (git-version "3.52.23" revision commit))
|
||
(source (origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/jhbadger/xlispstat.git")
|
||
(commit commit)))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"1p0cmgy19kbkxia139cb5w9dnkp2cdqp5n3baag6cq3prn3n71mf"))))
|
||
(build-system gnu-build-system)
|
||
(arguments
|
||
`(#:parallel-build? #f ; Parallel builds are not supported
|
||
#:configure-flags (list "--with-gcc")
|
||
#:phases
|
||
(modify-phases %standard-phases
|
||
(replace 'check
|
||
(lambda* (#:key tests? #:allow-other-keys)
|
||
(when tests?
|
||
(with-output-to-file "exit.lsp"
|
||
(lambda () (display "(exit)")))
|
||
(invoke "./xlisp" "tests/test" "exit")))))))
|
||
(inputs (list tcsh
|
||
libx11
|
||
libxmu
|
||
libxext
|
||
libxpm
|
||
libxaw
|
||
ncurses
|
||
gnuplot))
|
||
(native-inputs (list pkg-config))
|
||
(synopsis "Statistical analysis environment with interactive graphics")
|
||
(description "XLISP-STAT is a statistical environment based on a Lisp
|
||
dialect called XLISP. To facilitate statistical computations, standard
|
||
functions for addition, logarithms, etc., have been modified to operate on
|
||
lists and arrays of numbers, and a number of basic statistical functions have
|
||
been added. Many of these functions have been written in Lisp, and additional
|
||
functions can be added easily by a user. Several basic forms of plots,
|
||
including histograms, scatterplots, rotatable plots and scatterplot matrices
|
||
are provided. These plots support various forms of interactive highlighting
|
||
operations and can be linked so points highlighted in one plot will be
|
||
highlighted in all linked plots. Interactions with the plots are controlled
|
||
by the mouse, menus and dialog boxes. An object-oriented programming system
|
||
is used to allow menus, dialogs, and the response to mouse actions to be
|
||
customized.")
|
||
(home-page "https://homepage.divms.uiowa.edu/~luke/xls/xlsinfo/")
|
||
(license license:expat))))
|
||
|
||
(define-public r-rlrsim
|
||
(package
|
||
(name "r-rlrsim")
|
||
(version "3.1-8")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "RLRsim" version))
|
||
(sha256
|
||
(base32 "06i4slc7fj8xifq20i1vqfadfw2p81b0kfzga60139hnryz1zpva"))))
|
||
(properties `((upstream-name . "RLRsim")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs (list r-lme4 r-mgcv r-nlme r-rcpp))
|
||
(home-page "https://github.com/fabian-s/RLRsim")
|
||
(synopsis
|
||
"Exact (Restricted) Likelihood Ratio Tests for Mixed and Additive Models")
|
||
(description
|
||
"Rapid, simulation-based exact (restricted) likelihood ratio tests for testing
|
||
the presence of variance components/nonparametric terms for models fit with
|
||
@code{nlme::lme()}, @code{lme4::lmer()}, @code{lmeTest::lmer()},
|
||
@code{gamm4::gamm4()}, @code{mgcv::gamm()} and @code{SemiPar::spm()}.")
|
||
(license (list license:gpl2+ license:gpl3+))))
|
||
|
||
(define-public r-binom
|
||
(package
|
||
(name "r-binom")
|
||
(version "1.1-1.1")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "binom" version))
|
||
(sha256
|
||
(base32 "1yxyhsd0savwirlmgnq6973slfakqyfvjm0zz60cmc9v490my8gf"))))
|
||
(properties `((upstream-name . "binom")))
|
||
(build-system r-build-system)
|
||
(home-page "https://cran.r-project.org/package=binom")
|
||
(synopsis "Binomial Confidence Intervals For Several Parameterizations")
|
||
(description
|
||
"Constructs confidence intervals on the probability of success in a binomial
|
||
experiment via several parameterizations")
|
||
(license (list license:gpl2+ license:gpl3+))))
|
||
|
||
(define-public r-simr
|
||
(package
|
||
(name "r-simr")
|
||
(version "1.0.7")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "simr" version))
|
||
(sha256
|
||
(base32 "1rfnhyqvdazvar7r1ml71lskh1hdk3yfzv5jlcz18wzffscgkgmb"))))
|
||
(properties `((upstream-name . "simr")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-binom
|
||
r-car
|
||
r-iterators
|
||
r-lme4
|
||
r-lmertest
|
||
r-pbkrtest
|
||
r-plotrix
|
||
r-plyr
|
||
r-rlrsim
|
||
r-stringr))
|
||
(native-inputs (list r-knitr))
|
||
(home-page "https://github.com/pitakakariki/simr")
|
||
(synopsis
|
||
"Power analysis for generalized linear mixed models by simulation")
|
||
(description
|
||
"This package lets you calculate power for generalized linear mixed
|
||
models, using simulation. It was designed to work with models fit using the
|
||
@code{lme4} package. The package is described in
|
||
@url{doi:10.1111/2041-210X.12504, Green and MacLeod (2016)}.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-mixedpower
|
||
;; This commit contains fixes for R>=4.2 and contains new features. A
|
||
;; newer release does not exist.
|
||
(let ((commit "b2b87068546327d8f592d141e5482e0478c1b2ee")
|
||
(revision "2"))
|
||
(package
|
||
(name "r-mixedpower")
|
||
(version (git-version "2.0" revision commit))
|
||
(source
|
||
(origin
|
||
;; Not available on CRAN.
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/DejanDraschkow/mixedpower")
|
||
(commit commit)))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32 "0pys66a6c1k2fp5qk9grhzg1q1d3q51rggcilmdssimkmcsm234z"))))
|
||
(properties `((upstream-name . "mixedpower")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-doparallel r-foreach r-ggplot2 r-lme4 r-reshape2))
|
||
(home-page "https://github.com/DejanDraschkow/mixedpower")
|
||
(synopsis
|
||
"Pilotdata based simulations for estimating power in linear mixed models")
|
||
(description
|
||
"Implementation of a simulation based aproach to power analysis.
|
||
Mixedpower uses lotdata and a linear mixed model fitted with lme4 to
|
||
simulate new data sets. wer is computed separate for every effect in the
|
||
model output as the relation significant simulations to all simulations.
|
||
More conservative simulations as protection against a bias in the
|
||
pilotdata are available aswell as methods for otting the results.")
|
||
(license license:gpl3))))
|
||
|
||
(define-public r-colorway
|
||
(let ((commit "8ba8f0026aba37752c6770de45bf53b1b0f48afc")
|
||
(revision "1"))
|
||
(package
|
||
(name "r-colorway")
|
||
(version (git-version "0.2.0" revision commit))
|
||
(source (origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/hypercompetent/colorway")
|
||
(commit commit)))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"0r6yhnzx3ll1z12pp6y8fqbrx7v18rcff2j2179bqy9ca2d2d94l"))))
|
||
(properties `((upstream-name . "colorway")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs (list r-dplyr r-ggplot2 r-rlang))
|
||
(home-page "https://github.com/hypercompetent/colorway")
|
||
(synopsis "Functions for colors in R")
|
||
(description
|
||
"This package provides a collection of (mostly simple) functions for
|
||
generating and manipulating colors in R.")
|
||
(license license:gpl3))))
|
||
|
||
(define-public r-reghelper
|
||
(package
|
||
(name "r-reghelper")
|
||
(version "1.1.2")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "reghelper" version))
|
||
(sha256
|
||
(base32
|
||
"1vd8kd719kyjp65zym6zx3vax1q2kbhpl6la71d5aa59s54ylri3"))))
|
||
(properties `((upstream-name . "reghelper")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs (list r-ggplot2 r-lme4 r-mass r-nlme r-rlang))
|
||
(home-page "https://github.com/jeff-hughes/reghelper")
|
||
(synopsis "Helper Functions for Regression Analysis")
|
||
(description
|
||
"This package provides a set of functions used to automate commonly used methods
|
||
in regression analysis. This includes plotting interactions, and calculating
|
||
simple slopes, standardized coefficients, regions of significance (Johnson &
|
||
Neyman, 1936; cf. Spiller et al., 2012), etc.")
|
||
(license license:gpl3)))
|
||
|
||
(define-public r-mumin
|
||
(package
|
||
(name "r-mumin")
|
||
(version "1.47.5")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "MuMIn" version))
|
||
(sha256
|
||
(base32
|
||
"0xqasb79lmdhff25zalzrpjwv6qs9qnxr54ypnqjjgshi96mbwvg"))))
|
||
(properties `((upstream-name . "MuMIn")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs (list r-insight r-matrix r-nlme))
|
||
(home-page "https://cran.r-project.org/package=MuMIn")
|
||
(synopsis "Multi-Model Inference")
|
||
(description
|
||
"Tools for performing model selection and model averaging. Automated model
|
||
selection through subsetting the maximum model, with optional constraints for
|
||
model inclusion. Model parameter and prediction averaging based on model
|
||
weights derived from information criteria (AICc and alike) or custom model
|
||
weighting schemes.")
|
||
(license license:gpl2)))
|
||
|
||
(define-public ruby-enumerable-statistics
|
||
(package
|
||
(name "ruby-enumerable-statistics")
|
||
(version "2.0.7")
|
||
;; Source at RubyGems.org doesn't have tests.
|
||
(source (origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/mrkn/enumerable-statistics.git")
|
||
(commit (string-append "v" version))))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"1a8k2dvm1v0g6hcrbnzy0f7d63hdmpmldfdkl8wr32nbl05xnifa"))
|
||
(modules '((guix build utils)))
|
||
(snippet `(begin
|
||
(substitute* "enumerable-statistics.gemspec"
|
||
;; benchmark-driver gem is used for
|
||
;; performance benchmarking, and isn't
|
||
;; needed for tests.
|
||
(("spec.add_development_dependency \"benchmark-driver\"\n")
|
||
""))))))
|
||
(build-system ruby-build-system)
|
||
(native-inputs (list bundler
|
||
ruby-rake
|
||
ruby-rake-compiler
|
||
ruby-rspec
|
||
ruby-test-unit
|
||
ruby-fuubar
|
||
ruby-yard))
|
||
(synopsis "Library which provides statistics features for Enumerable")
|
||
(description
|
||
"@code{Enumerable::Statistics} provides some methods to calculate
|
||
statistical summary in arrays and enumerables.")
|
||
(home-page "https://github.com/mrkn/enumerable-statistics")
|
||
(license license:expat)))
|