mirror of
https://git.in.rschanz.org/ryan77627/guix.git
synced 2024-12-29 07:42:23 -05:00
9cf5f134d5
* gnu/packages/audio.scm (ardour)[arguments]: Switch to using version-major. (hmmer)[source]: Switch to using version-major. (pidgin)[native-search-paths]: Switch to using version-major. (r-minimal)[source]: Switch to using version-major.
5505 lines
192 KiB
Scheme
5505 lines
192 KiB
Scheme
;;; GNU Guix --- Functional package management for GNU
|
|
;;; Copyright © 2015, 2016, 2017 Ricardo Wurmus <rekado@elephly.net>
|
|
;;; Copyright © 2015 Vicente Vera Parra <vicentemvp@gmail.com>
|
|
;;; Copyright © 2016 Andreas Enge <andreas@enge.fr>
|
|
;;; Copyright © 2016, 2017 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>
|
|
;;;
|
|
;;; 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 licenses) #:prefix license:)
|
|
#:use-module (guix packages)
|
|
#:use-module (guix download)
|
|
#:use-module (guix hg-download)
|
|
#:use-module (guix utils)
|
|
#:use-module (guix build-system gnu)
|
|
#:use-module (guix build-system r)
|
|
#:use-module (guix build-system python)
|
|
#:use-module (guix build-system trivial)
|
|
#:use-module (gnu packages)
|
|
#:use-module (gnu packages check)
|
|
#:use-module (gnu packages compression)
|
|
#:use-module (gnu packages cran)
|
|
#:use-module (gnu packages curl)
|
|
#: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)
|
|
#:use-module (gnu packages icu4c)
|
|
#:use-module (gnu packages image)
|
|
#:use-module (gnu packages java)
|
|
#:use-module (gnu packages machine-learning)
|
|
#:use-module (gnu packages maths)
|
|
#:use-module (gnu packages multiprecision)
|
|
#: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 readline)
|
|
#:use-module (gnu packages ssh)
|
|
#:use-module (gnu packages texinfo)
|
|
#:use-module (gnu packages time)
|
|
#:use-module (gnu packages tls)
|
|
#:use-module (gnu packages base)
|
|
#:use-module (gnu packages web)
|
|
#:use-module (gnu packages xml)
|
|
#:use-module (gnu packages xorg)
|
|
#:use-module (srfi srfi-1))
|
|
|
|
|
|
(define-public pspp
|
|
(package
|
|
(name "pspp")
|
|
(version "1.0.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (string-append "mirror://gnu/pspp/pspp-"
|
|
version ".tar.gz"))
|
|
(sha256
|
|
(base32
|
|
"1r8smr5057993h90nx0mdnff8nxw9x546zzh6qpy4h3xblp1la5s"))))
|
|
(build-system gnu-build-system)
|
|
(inputs
|
|
`(("cairo" ,cairo)
|
|
("gettext" ,gettext-minimal)
|
|
("gsl" ,gsl)
|
|
("libxml2" ,libxml2)
|
|
("pango" ,pango)
|
|
("readline" ,readline)
|
|
("gtk" ,gtk+)
|
|
("gtksourceview" ,gtksourceview)
|
|
("zlib" ,zlib)))
|
|
(native-inputs
|
|
`(("glib" ,glib "bin") ;for glib-genmarshal
|
|
("perl" ,perl)
|
|
("pkg-config" ,pkg-config)))
|
|
(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+)))
|
|
|
|
;; 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-public r-minimal
|
|
(package
|
|
(name "r-minimal")
|
|
(version "3.4.3")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (string-append "mirror://cran/src/base/R-"
|
|
(version-major version) "/R-"
|
|
version ".tar.gz"))
|
|
(sha256
|
|
(base32
|
|
"09pl0w01fr09bsrwd7nz2r5psysj0z93w4chz3hm2havvqqvhg3s"))))
|
|
(build-system gnu-build-system)
|
|
(arguments
|
|
`(#:disallowed-references (,tzdata-2017a)
|
|
#: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"))
|
|
#t))
|
|
(add-before 'configure 'patch-uname
|
|
(lambda* (#:key inputs #:allow-other-keys)
|
|
(let ((uname-bin (string-append (assoc-ref inputs "coreutils")
|
|
"/bin/uname")))
|
|
(substitute* "src/scripts/R.sh.in"
|
|
(("uname") uname-bin)))
|
|
#t))
|
|
(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.
|
|
;;
|
|
;; Instead of disabling this feature, which may have unexpected
|
|
;; consequences, we reset the mtime of generated files before
|
|
;; passing them to the "srcfile" procedure.
|
|
(substitute* "src/library/Makefile.in"
|
|
(("@\\(cd base && \\$\\(MAKE\\) mkdesc\\)" line)
|
|
(string-append line "\n find $(top_builddir)/library/tools | xargs touch -d '1970-01-01'; \n"))
|
|
(("@\\$\\(MAKE\\) Rdobjects" line)
|
|
(string-append "@find $(srcdir)/tools | xargs touch -d '1970-01-01'; \n "
|
|
line)))
|
|
(substitute* "src/library/tools/Makefile.in"
|
|
(("@\\$\\(INSTALL_DATA\\) all.R \\$\\(top_builddir\\)/library/\\$\\(pkg\\)/R/\\$\\(pkg\\)" line)
|
|
(string-append
|
|
line
|
|
"\n find $(srcdir)/$(pkg) $(top_builddir)/library/$(pkg) | xargs touch -d \"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')\"")))
|
|
|
|
;; 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"))))
|
|
#t))
|
|
(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") #t))
|
|
(add-before 'check '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.
|
|
(lambda* (#:key inputs #:allow-other-keys)
|
|
(setenv "TZ" "UTC+1")
|
|
(setenv "TZDIR"
|
|
(string-append (assoc-ref inputs "tzdata")
|
|
"/share/zoneinfo"))
|
|
#t))
|
|
(add-after 'build 'make-info
|
|
(lambda _ (zero? (system* "make" "info"))))
|
|
(add-after 'build 'install-info
|
|
(lambda _ (zero? (system* "make" "install-info")))))
|
|
#:configure-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.
|
|
"--without-recommended-packages"
|
|
"--with-cairo"
|
|
"--with-blas=-lopenblas"
|
|
"--with-libpng"
|
|
"--with-jpeglib"
|
|
"--with-libtiff"
|
|
"--with-ICU"
|
|
"--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
|
|
`(("bzip2" ,bzip2)
|
|
("perl" ,perl)
|
|
("pkg-config" ,pkg-config)
|
|
("texinfo" ,texinfo) ; for building HTML manuals
|
|
("tzdata" ,tzdata-2017a)
|
|
("xz" ,xz)))
|
|
(inputs
|
|
`(;; We need not only cairo here, but pango to ensure that tests for the
|
|
;; "cairo" bitmapType plotting backend succeed.
|
|
("pango" ,pango)
|
|
("coreutils" ,coreutils)
|
|
("curl" ,curl)
|
|
("openblas" ,openblas)
|
|
("gfortran" ,gfortran)
|
|
("icu4c" ,icu4c)
|
|
("libjpeg" ,libjpeg)
|
|
("libpng" ,libpng)
|
|
("libtiff" ,libtiff)
|
|
("libxt" ,libxt)
|
|
("pcre" ,pcre)
|
|
("readline" ,readline)
|
|
("which" ,which)
|
|
("zlib" ,zlib)))
|
|
(native-search-paths
|
|
(list (search-path-specification
|
|
(variable "R_LIBS_SITE")
|
|
(files (list "site-library/")))))
|
|
(home-page "http://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 rmath-standalone
|
|
(package (inherit r-minimal)
|
|
(name "rmath-standalone")
|
|
(arguments
|
|
'(#:phases
|
|
(modify-phases %standard-phases
|
|
(add-after 'configure 'chdir
|
|
(lambda _ (chdir "src/nmath/standalone/") #t)))))
|
|
(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 "1.3-20")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "boot" version))
|
|
(sha256
|
|
(base32
|
|
"0ai1qpm0p4z07xr0dvag8sdn9jrxcwanrsk9khzmww094jvr1jxd"))))
|
|
(build-system r-build-system)
|
|
(home-page "http://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 "7.3-47")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "MASS" version))
|
|
(sha256
|
|
(base32
|
|
"1gy6z7ly9wn86rfn9xrmqiqq1ijw3pkasrr2299kbzsgx2mwsi7d"))))
|
|
(properties `((upstream-name . "MASS")))
|
|
(build-system r-build-system)
|
|
(home-page "http://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 "7.3-14")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "class" version))
|
|
(sha256
|
|
(base32
|
|
"173b8a16lh1i0zjmr784l0xr0azp9v8bgslh12hfdswbq7dpdf0q"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-mass" ,r-mass)))
|
|
(home-page "http://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 "2.0.6")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "cluster" version))
|
|
(sha256
|
|
(base32
|
|
"1z4gbz7chxxi4ly6c0yjlikwgf8aa8dlg05cn5cd6pjr21zvh97l"))))
|
|
(build-system r-build-system)
|
|
(inputs
|
|
`(("gfortran" ,gfortran)))
|
|
(home-page "http://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 "0.2-15")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "codetools" version))
|
|
(sha256
|
|
(base32
|
|
"0h7sjmvvsi35041jp47cxhsqzgf1y8jrw6fxii7n26i8g7nrh1sf"))))
|
|
(build-system r-build-system)
|
|
(home-page "http://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 "0.8-69")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "foreign" version))
|
|
(sha256
|
|
(base32
|
|
"0s1lxmd85dd0kxx8hwk02w9l7pmpk4bpy7787fbyh2dbq5g9ys0k"))))
|
|
(build-system r-build-system)
|
|
(home-page "http://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 "2.23-15")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "KernSmooth" version))
|
|
(sha256
|
|
(base32
|
|
"1xhha8kw10jv8pv8b61hb5in9qiw3r2a9kdji3qlm991s4zd4wlb"))))
|
|
(properties `((upstream-name . "KernSmooth")))
|
|
(build-system r-build-system)
|
|
(inputs
|
|
`(("gfortran" ,gfortran)))
|
|
(home-page "http://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 "0.20-35")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "lattice" version))
|
|
(sha256
|
|
(base32
|
|
"0pcnmaz3lr62ly0dcy5hnnqxshc4yqd43hrvlz3almgc9l7sna88"))))
|
|
(build-system r-build-system)
|
|
(home-page "http://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 "1.2-12")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "Matrix" version))
|
|
(sha256
|
|
(base32
|
|
"1wm45hg4x5ay15y03k6rmgkd1n9r01da72mszk24vafwd7pimr8n"))))
|
|
(properties `((upstream-name . "Matrix")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-lattice" ,r-lattice)))
|
|
(home-page "http://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 "3.1-131")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "nlme" version))
|
|
(sha256
|
|
(base32
|
|
"0k2nvdzhic6bzhfsbq6la6q6a1i5nlj4pnh6lpdxiiwvxdks3nkr"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-lattice" ,r-lattice)))
|
|
(native-inputs
|
|
`(("gfortran" ,gfortran)))
|
|
(home-page "http://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 "1.8-22")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "mgcv" version))
|
|
(sha256
|
|
(base32
|
|
"1546p6aflg3z6xl2mns1n2c3j8q2spr9cjggj9rn33vrrhsv4fss"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-matrix" ,r-matrix)
|
|
("r-nlme" ,r-nlme)))
|
|
(home-page "http://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 "7.3-12")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "nnet" version))
|
|
(sha256
|
|
(base32
|
|
"17amqnw9dpap2w8ivx53hxha2xrm0drwfnj32li0xk41hlz548r7"))))
|
|
(build-system r-build-system)
|
|
(home-page "http://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 "4.1-11")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "rpart" version))
|
|
(sha256
|
|
(base32
|
|
"165djqj7lk81jr7z5fwccq3h7ayys26hx1kj9hndvg2rkyaq1arq"))))
|
|
(build-system r-build-system)
|
|
(home-page "http://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 "7.3-11")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "spatial" version))
|
|
(sha256
|
|
(base32
|
|
"04aw8j533sn63ybyrf4hyhrqm4058vfcb7yhjy07kq92mk94hi32"))))
|
|
(build-system r-build-system)
|
|
(home-page "http://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 "2.41-3")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "survival" version))
|
|
(sha256
|
|
(base32
|
|
"07cnr0hnki6ybbjll54l4s5lllhk19vni5f8m0mvsfp99ls7qygk"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-matrix" ,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 (mkdir %output)))
|
|
(propagated-inputs
|
|
`(("r-minimal" ,r-minimal)
|
|
("r-boot" ,r-boot)
|
|
("r-class" ,r-class)
|
|
("r-cluster" ,r-cluster)
|
|
("r-codetools" ,r-codetools)
|
|
("r-foreign" ,r-foreign)
|
|
("r-kernsmooth" ,r-kernsmooth)
|
|
("r-lattice" ,r-lattice)
|
|
("r-mass" ,r-mass)
|
|
("r-matrix" ,r-matrix)
|
|
("r-mgcv" ,r-mgcv)
|
|
("r-nlme" ,r-nlme)
|
|
("r-nnet" ,r-nnet)
|
|
("r-rpart" ,r-rpart)
|
|
("r-spatial" ,r-spatial)
|
|
("r-survival" ,r-survival)))))
|
|
|
|
(define-public r-bit
|
|
(package
|
|
(name "r-bit")
|
|
(version "1.1-12")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "bit" version))
|
|
(sha256
|
|
(base32
|
|
"0a6ig6nnjzq80r2ll4hc74za3xwzbzig6wlyb4dby0knzf3iqa6f"))))
|
|
(build-system r-build-system)
|
|
(home-page "http://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 "0.9-7")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "bit64" version))
|
|
(sha256
|
|
(base32
|
|
"07znvz9vp1nz1y5ljng4qyskvm943cdbmy996s67560ijxzsm6kv"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-bit" ,r-bit)))
|
|
(home-page "http://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-dichromat
|
|
(package
|
|
(name "r-dichromat")
|
|
(version "2.0-0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "dichromat" version))
|
|
(sha256
|
|
(base32 "1l8db1nk29ccqg3mkbafvfiw0775iq4gapysf88xq2zp6spiw59i"))))
|
|
(build-system r-build-system)
|
|
(home-page "http://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 "0.6.12")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "digest" version))
|
|
(sha256
|
|
(base32 "1awy9phxdvqnadby7rvwy2hkbrj210bqf4xvi27asdq028zlcyd4"))))
|
|
(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")))
|
|
(home-page "http://dirk.eddelbuettel.com/code/digest.html")
|
|
(synopsis "Create cryptographic hash digests of R objects")
|
|
(description
|
|
"This package contains an implementation of a function '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 '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 "1.2")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "estimability" version))
|
|
(sha256
|
|
(base32
|
|
"13b80bpnbrarazjvnpnk91ljjsqgfm2fm3gy66aj09cmmsmv199h"))))
|
|
(build-system r-build-system)
|
|
(home-page "http://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 'epredict' methods that handle
|
|
non-estimable cases correctly.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-pheatmap
|
|
(package
|
|
(name "r-pheatmap")
|
|
(version "1.0.8")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "pheatmap" version))
|
|
(sha256
|
|
(base32
|
|
"1ik0k69kb4n7xl3bkx4p09kw08ri93855zcsxq1c668171jqfiji"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-gtable" ,r-gtable)
|
|
("r-rcolorbrewer" ,r-rcolorbrewer)
|
|
("r-scales" ,r-scales)))
|
|
(home-page
|
|
"http://cran.r-project.org/web/packages/pheatmap")
|
|
(synopsis "Pretty heatmaps")
|
|
(description
|
|
"This package provides an implementation of heatmaps that offers more
|
|
control over dimensions and appearance.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-labeling
|
|
(package
|
|
(name "r-labeling")
|
|
(version "0.3")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "labeling" version))
|
|
(sha256
|
|
(base32 "13sk7zrrrzry6ky1bp8mmnzcl9jhvkig8j4id9nny7z993mnk00d"))))
|
|
(build-system r-build-system)
|
|
(home-page "http://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 "1.5")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "magrittr" version))
|
|
(sha256
|
|
(base32 "1s1ar6rag8m277qcqmdp02gn4awn9bdj9ax0r8s32i59mm1mki05"))))
|
|
(build-system r-build-system)
|
|
(home-page "http://cran.r-project.org/web/packages/magrittr/index.html")
|
|
(synopsis "A 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 "0.4.3")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "munsell" version))
|
|
(sha256
|
|
(base32 "0jdxlbjslkzaqgp058da1cgm85qvqi09wpcgpvp4hvwnmy83qz1r"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-colorspace" ,r-colorspace)))
|
|
(home-page "http://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 "0.9-4")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "permute" version))
|
|
(sha256
|
|
(base32
|
|
"1w8wzk1fg9q7wvisnfp2js70dg0m9wi12gkdhpyngpbdcgssahd5"))))
|
|
(build-system r-build-system)
|
|
;; 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 "1.8.4")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "plyr" version))
|
|
(sha256
|
|
(base32 "1igar5pcjqh0jyxv0z3jah8rz617vfa86vw0r5c7c031b7bj5db0"))))
|
|
(build-system r-build-system)
|
|
(native-inputs `(("r-rcpp" ,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 "1.1-2")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "RColorBrewer" version))
|
|
(sha256
|
|
(base32 "1pfcl8z1pnsssfaaz9dvdckyfnnc6rcq56dhislbf571hhg7isgk"))))
|
|
(build-system r-build-system)
|
|
(home-page "http://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 "1.2-1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "sendmailR" version))
|
|
(sha256
|
|
(base32
|
|
"0z7ipywnzgkhfvl4zb2fjwl1xq7b5wib296vn9c9qgbndj6b1zh4"))))
|
|
(properties `((upstream-name . "sendmailR")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-base64enc" ,r-base64enc)))
|
|
(home-page
|
|
"http://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 "1.1.6")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "stringi" version))
|
|
(sha256
|
|
(base32
|
|
"122im5m8x9bqpahc0hbxmvdq6hnsmgnxwwyjpvbihyv2jq5kd44m"))))
|
|
(build-system r-build-system)
|
|
(inputs `(("icu4c" ,icu4c)))
|
|
(native-inputs `(("pkg-config" ,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 "1.2.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "stringr" version))
|
|
(sha256
|
|
(base32 "16hj2rmv8x03lp6cp2jk0k2plibvbggf444kp05przdvd03v7l31"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-magrittr" ,r-magrittr)
|
|
("r-stringi" ,r-stringi)))
|
|
(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 '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 "1.4.2")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "reshape2" version))
|
|
(sha256
|
|
(base32 "0swvjmc9f8cvkrsz463cp6snd8bncbv6q8yrfrb4rgkr0dhq6dvd"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-plyr" ,r-plyr)
|
|
("r-rcpp" ,r-rcpp)
|
|
("r-stringr" ,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-scales
|
|
(package
|
|
(name "r-scales")
|
|
(version "0.5.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "scales" version))
|
|
(sha256
|
|
(base32 "0zg9wfzmsdjxpbld0nzv7hcpq5r0wazqxmn7grvvif2agj0w1z6v"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-dichromat" ,r-dichromat)
|
|
("r-labeling" ,r-labeling)
|
|
("r-munsell" ,r-munsell)
|
|
("r-plyr" ,r-plyr)
|
|
("r-rcolorbrewer" ,r-rcolorbrewer)
|
|
("r-rcpp" ,r-rcpp)
|
|
("r-r6" ,r-r6)
|
|
("r-viridislite" ,r-viridislite)))
|
|
(home-page "https://github.com/hadley/scales")
|
|
(synopsis "Scale functions for visualization")
|
|
(description
|
|
"This package provides graphical scales that map data to aesthetics, and
|
|
provides methods for automatically determining breaks and labels for axes and
|
|
legends.")
|
|
(license license:expat)))
|
|
|
|
(define-public r-ggplot2
|
|
(package
|
|
(name "r-ggplot2")
|
|
(version "2.2.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "ggplot2" version))
|
|
(sha256
|
|
(base32 "0543782ddv2hp6s0l702mnxfg8n7a6qlbm8bm55x22hnqgz8kg2z"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-digest" ,r-digest)
|
|
("r-gtable" ,r-gtable)
|
|
("r-plyr" ,r-plyr)
|
|
("r-lazyeval" ,r-lazyeval)
|
|
("r-mass" ,r-mass)
|
|
("r-tibble" ,r-tibble)
|
|
("r-reshape2" ,r-reshape2)
|
|
("r-scales" ,r-scales)
|
|
("r-svglite" ,r-svglite))) ; Needed for 'ggsave'
|
|
(home-page "http://ggplot2.org")
|
|
(synopsis "An 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 "0.1-20")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "ggdendro" version))
|
|
(sha256
|
|
(base32
|
|
"1zzq1hxd0d1qa5hrzwfkdw6fzscpcafbwbpkrb62dm559y8awp0j"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-ggplot2" ,r-ggplot2)
|
|
("r-mass" ,r-mass)
|
|
("r-knitr" ,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 "0.1.6")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "gdtools" version))
|
|
(sha256
|
|
(base32
|
|
"103wnc8sq0iwcnj4j14hd420d2dqdyf13s3f25icsznrlyzdkhf5"))))
|
|
(build-system r-build-system)
|
|
(native-inputs
|
|
`(("r-rcpp" ,r-rcpp)
|
|
("pkg-config" ,pkg-config)))
|
|
(inputs
|
|
`(("cairo" ,cairo)))
|
|
(propagated-inputs
|
|
`(("r-withr" ,r-withr)))
|
|
(home-page "http://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 "1.2.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "svglite" version))
|
|
(sha256
|
|
(base32
|
|
"1bws3lc4hlhln11zd7lalhiyc43yk6c6vrzy41fkxk1dkjazfx51"))))
|
|
(build-system r-build-system)
|
|
(native-inputs `(("r-rcpp" ,r-rcpp)))
|
|
(propagated-inputs
|
|
`(("r-bh" ,r-bh)
|
|
("r-gdtools" ,r-gdtools)))
|
|
(home-page "https://github.com/hadley/svglite")
|
|
(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 "0.2.0")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "assertthat" version))
|
|
(sha256
|
|
(base32
|
|
"1wp5znk3xy338x6hknppk702jn596yr735d9i7c3wabm3sdzfgnp"))))
|
|
(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 "0.2.1")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "lazyeval" version))
|
|
(sha256
|
|
(base32
|
|
"0q9zx78ncy2ffzrf9sh053069kd3w1xn1ss3gsbyf3y4jhza9cw3"))))
|
|
(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 "0.7")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "DBI" version))
|
|
(sha256
|
|
(base32
|
|
"04fyrxdpqcygg5wviy637y6lgk64xqjjq31lvv4hwqj5kbaxamr5"))))
|
|
(build-system r-build-system)
|
|
(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 "1.65.0-1")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "BH" version))
|
|
(sha256
|
|
(base32
|
|
"0n6byzrvl1w4hjdxz479q4a7w1118f9ckqc4gqydq7lgzs5agfl2"))))
|
|
(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 "0.10.1")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "evaluate" version))
|
|
(sha256
|
|
(base32
|
|
"070vvmnbdlp7sz2zhza7fhd2a6mlwiln8fn4hyzhsiizbn4n79y9"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-stringr" ,r-stringr)))
|
|
(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 "1.5")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "formatR" version))
|
|
(sha256
|
|
(base32
|
|
"19sd23vgs4ac0fwlw40j3676k6mramb0ajlq8hdw23kjwdx1jk47"))))
|
|
(build-system r-build-system)
|
|
(home-page "http://yihui.name/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 "0.6")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "highr" version))
|
|
(sha256
|
|
(base32
|
|
"0n9v44dxdy5fhkdmpbpa2p78whyd9z3rhhy42ipdz5m5vsr55qa3"))))
|
|
(build-system r-build-system)
|
|
(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 "0.5")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "mime" version))
|
|
(sha256
|
|
(base32
|
|
"0i91m3ivaja1k33jwcvz16pfjypkci27awm8glil7sxhmwaj3izw"))))
|
|
(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 "0.8")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "markdown" version))
|
|
(sha256
|
|
(base32
|
|
"1vcgsh2m2f5kfgappgg71nbf04ff0j1sbk668krjs3r2n89dk3sk"))))
|
|
(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
|
|
`(("r-mime" ,r-mime)))
|
|
(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 "2.1.14")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "yaml" version))
|
|
(sha256
|
|
(base32
|
|
"0x88xicrf7vwp77xgan27mnpdljhpkn0pz5kphnwqi3ddy25k9a1"))))
|
|
(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 "1.17")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "knitr" version))
|
|
(sha256
|
|
(base32
|
|
"00gljbz57n9lkvbd6az4n37gpbs8vg3fxx5p9biamhmhqyra514l"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-evaluate" ,r-evaluate)
|
|
("r-digest" ,r-digest)
|
|
("r-highr" ,r-highr)
|
|
("r-markdown" ,r-markdown)
|
|
("r-stringr" ,r-stringr)
|
|
("r-yaml" ,r-yaml)))
|
|
(home-page "http://yihui.name/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 "1.0.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "knitrBootstrap" version))
|
|
(sha256
|
|
(base32
|
|
"089147g7nqp99rwdxxsfmklsrwc8aia09sr8ndmrc335r33v6r6p"))))
|
|
(properties `((upstream-name . "knitrBootstrap")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-knitr" ,r-knitr)
|
|
("r-rmarkdown" ,r-rmarkdown)))
|
|
(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 "1.4-2.1")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "microbenchmark" version))
|
|
(sha256
|
|
(base32
|
|
"0qn5r1a6qidghcisc2hpbdmj62pnixc3zz6p4ipk8mvakf0hdsvg"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-ggplot2" ,r-ggplot2)))
|
|
(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 "0.1.3")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "pryr" version))
|
|
(sha256
|
|
(base32
|
|
"1b1rcywq9sqzgjsnh3ynnx16gp41n94kkzfalm3y4kyy3ls8ikba"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-stringr" ,r-stringr)
|
|
("r-codetools" ,r-codetools)))
|
|
(native-inputs
|
|
`(("r-rcpp" ,r-rcpp)))
|
|
(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 "1.1.0")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "memoise" version))
|
|
(sha256
|
|
(base32
|
|
"034qfc2xlh30x1q2vya239w34a3ir3y2fwnx2agbgbi6592zjxmj"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-digest" ,r-digest)))
|
|
(home-page "https://github.com/hadley/memoise")
|
|
(synopsis "Memoise functions for R")
|
|
(description
|
|
"This R package allows to cache 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 "1.3.4")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "crayon" version))
|
|
(sha256
|
|
(base32
|
|
"0s7s6vc3ww8pzanpjisym4jjvwcc5pi2qg8srx7jqlz9j3wrnvpw"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-memoise" ,r-memoise)))
|
|
(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 "1.0.2")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "testthat" version))
|
|
(sha256
|
|
(base32
|
|
"0pj1r01x4ny4capr83dfa19hi5i2sjjxky99schzip8zrq5dzxqf"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-digest" ,r-digest)
|
|
("r-crayon" ,r-crayon)
|
|
("r-magrittr" ,r-magrittr)
|
|
("r-praise" ,r-praise)
|
|
("r-r6" ,r-r6)))
|
|
(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 "2.2.2")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "R6" version))
|
|
(sha256
|
|
(base32
|
|
"13xfdr19ca7ymisidsanm6w7hsk3qmy5l8c0mlz3nk48f7s5cxq8"))))
|
|
(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 "0.1.4")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "rlang" version))
|
|
(sha256
|
|
(base32
|
|
"1x5rwwsx7xrlyspy41yl5nhyvfgzl73195nsdb4rc6z85ab6r6wd"))))
|
|
(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 "1.3.4")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "tibble" version))
|
|
(sha256
|
|
(base32
|
|
"02vn6yqzcvmazy5jaqar3wwbrmh83a1bfgsqgk0hgz38i80zgvm7"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-rlang" ,r-rlang)
|
|
("r-rcpp" ,r-rcpp)))
|
|
(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 "0.7.4")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "dplyr" version))
|
|
(sha256
|
|
(base32
|
|
"1hm8ml7yaraag1ak6kvz2mxx6if568c759ix8a1n9d7va03wj7vv"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-assertthat" ,r-assertthat)
|
|
("r-r6" ,r-r6)
|
|
("r-magrittr" ,r-magrittr)
|
|
("r-rlang" ,r-rlang)
|
|
("r-plogr" ,r-plogr)
|
|
("r-glue" ,r-glue)
|
|
("r-pkgconfig" ,r-pkgconfig)
|
|
("r-bindrcpp" ,r-bindrcpp)
|
|
("r-tibble" ,r-tibble)))
|
|
(native-inputs
|
|
`(("r-rcpp" ,r-rcpp)
|
|
("r-bh" ,r-bh)))
|
|
(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 focussed 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 "1.1.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "dbplyr" version))
|
|
(sha256
|
|
(base32
|
|
"17gn8vr4a6m9ynarjbm9xsrhcvgn5lnxhb2qhiiglmhh5mm4a7kv"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-assertthat" ,r-assertthat)
|
|
("r-dbi" ,r-dbi)
|
|
("r-dplyr" ,r-dplyr)
|
|
("r-glue" ,r-glue)
|
|
("r-purrr" ,r-purrr)
|
|
("r-r6" ,r-r6)
|
|
("r-rlang" ,r-rlang)
|
|
("r-tibble" ,r-tibble)))
|
|
(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 "1.4.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "acepack" version))
|
|
(sha256
|
|
(base32
|
|
"1f98rpfjmhd92rdc3j004plyfpjailz6j0ycysbac0kgj83haxc2"))))
|
|
(build-system r-build-system)
|
|
(inputs
|
|
`(("gfortran" ,gfortran)))
|
|
(home-page "http://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 "1.2-2")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "Formula" version))
|
|
(sha256
|
|
(base32
|
|
"0ad49bzip1zqmpj1d8jajwl4bd81fm3k6dq8p26x6mvlzc04dvwd"))))
|
|
(properties `((upstream-name . "Formula")))
|
|
(build-system r-build-system)
|
|
(home-page "http://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 "1.5-9.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "locfit" version))
|
|
(sha256
|
|
(base32
|
|
"0lafrmq1q7x026m92h01hc9cjjiximqqi3v1g2hw7ai9vf7i897m"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-lattice" ,r-lattice)))
|
|
(home-page "http://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 "2.3-51")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "chron" version))
|
|
(sha256
|
|
(base32
|
|
"05aznigw9nwv3hbwjnjbvqhfjqkwsw2csgrjx8500gzr2fvla5w8"))))
|
|
(build-system r-build-system)
|
|
(home-page "http://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 "1.10.4-3")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "data.table" version))
|
|
(sha256
|
|
(base32
|
|
"12caklgr19vy9wprdks6zh825vr1iw1cajgwcnbpyvmijqdlz2xs"))))
|
|
(build-system r-build-system)
|
|
(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 "1.8-2")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "xtable" version))
|
|
(sha256
|
|
(base32
|
|
"0398qkpvlw3dv0myz4mjcyqwpwc2m31l127r8vdzwc71wb6s28qn"))))
|
|
(build-system r-build-system)
|
|
(native-inputs
|
|
`(("r-knitr" ,r-knitr)))
|
|
(home-page "http://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-patsy
|
|
(package
|
|
(name "python-patsy")
|
|
(version "0.4.1")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (pypi-uri "patsy" version ".zip"))
|
|
(sha256
|
|
(base32
|
|
"1m6knyq8hbqlx242y4da02j0x86j4qggs1j7q186w3jv0j0c476w"))))
|
|
(build-system python-build-system)
|
|
(arguments
|
|
`(#:phases
|
|
(modify-phases %standard-phases
|
|
(replace 'check (lambda _ (zero? (system* "nosetests" "-v")))))))
|
|
(propagated-inputs
|
|
`(("python-numpy" ,python-numpy)
|
|
("python-scipy" ,python-scipy)
|
|
("python-six" ,python-six)))
|
|
(native-inputs
|
|
`(("python-nose" ,python-nose)
|
|
("unzip" ,unzip)))
|
|
(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 python2-patsy
|
|
(package-with-python2 python-patsy))
|
|
|
|
(define-public python-statsmodels
|
|
(package
|
|
(name "python-statsmodels")
|
|
(version "0.8.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (pypi-uri "statsmodels" version))
|
|
(sha256
|
|
(base32
|
|
"0j30v3932shnj9368c9jr3svkyrvfj90h2l7nxnqkbpv0svilhr6"))
|
|
(patches (search-patches "python-statsmodels-fix-tests.patch"))))
|
|
(build-system python-build-system)
|
|
(arguments
|
|
`(#:phases
|
|
(modify-phases %standard-phases
|
|
;; tests must be run after installation
|
|
(delete 'check)
|
|
(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)))
|
|
#t))
|
|
(add-after 'install 'check
|
|
(lambda* (#:key inputs outputs #:allow-other-keys)
|
|
;; Make installed package available for running the tests
|
|
(add-installed-pythonpath inputs outputs)
|
|
(with-directory-excursion "/tmp"
|
|
(zero? (system* "nosetests"
|
|
"--stop"
|
|
"-v" "statsmodels"))))))))
|
|
(propagated-inputs
|
|
`(("python-numpy" ,python-numpy)
|
|
("python-scipy" ,python-scipy)
|
|
("python-pandas" ,python-pandas)
|
|
("python-patsy" ,python-patsy)
|
|
("python-matplotlib" ,python-matplotlib)))
|
|
(native-inputs
|
|
`(("python-cython" ,python-cython)
|
|
("python-nose" ,python-nose)
|
|
("python-sphinx" ,python-sphinx)))
|
|
(home-page "http://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 python2-statsmodels
|
|
(let ((stats (package-with-python2 python-statsmodels)))
|
|
(package (inherit stats)
|
|
(propagated-inputs
|
|
`(("python2-pytz" ,python2-pytz)
|
|
("python2-numpy" ,python2-numpy)
|
|
("python2-scipy" ,python2-scipy)
|
|
("python2-pandas" ,python2-pandas)
|
|
("python2-patsy" ,python2-patsy)
|
|
("python2-matplotlib" ,python2-matplotlib))))))
|
|
|
|
(define-public r-coda
|
|
(package
|
|
(name "r-coda")
|
|
(version "0.19-1")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "coda" version))
|
|
(sha256
|
|
(base32
|
|
"14a4a8df4ygj05h37chmdn8kzcqs07fpbflxfrq530563mrza7yl"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-lattice" ,r-lattice)))
|
|
(home-page "http://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 "1.7-8")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "ade4" version))
|
|
(sha256
|
|
(base32
|
|
"1a5p3wf8l9cp1bjp57b1pc5bqs39kw1v21i4waj9j18wawzlmpb6"))))
|
|
(build-system r-build-system)
|
|
(home-page "http://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 "1.1.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "xml2" version))
|
|
(sha256
|
|
(base32
|
|
"05iifrcgzx53w5ciw8bbm4vdwc3giv4xsvazv8chqxkndfvf7wq0"))))
|
|
(build-system r-build-system)
|
|
(inputs
|
|
`(("libxml2" ,libxml2)))
|
|
(propagated-inputs
|
|
`(("r-rcpp" ,r-rcpp)
|
|
("r-bh" ,r-bh)))
|
|
(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 "1.0-14")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "multitaper" version))
|
|
(sha256
|
|
(base32
|
|
"04wd9bbhyx7697pfy0fpj02v1csr48hkpqj62h9p8a6w84ji4k68"))))
|
|
(build-system r-build-system)
|
|
(native-inputs
|
|
`(("gfortran" ,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 "1.0.3")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "rversions" version))
|
|
(sha256
|
|
(base32
|
|
"0i2gi05nrvknr7g89rbppkswyfcwwd4r9gp75fdfhpah8sgq1l11"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-curl" ,r-curl)
|
|
("r-xml2" ,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 "0.3-2")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "whisker" version))
|
|
(sha256
|
|
(base32
|
|
"0z4cn115gxcl086d6bnqr8afi67b6a7xqg6ivmk3l4ng1x8kcj28"))))
|
|
(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 "1.1.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "backports" version))
|
|
(sha256
|
|
(base32
|
|
"15w8psmv203wzijrk4hvwaw3i4byh2m5s09yrkqwhfckhaj82kj9"))))
|
|
(build-system r-build-system)
|
|
(home-page "http://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 "1.8.5")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "checkmate" version))
|
|
(sha256
|
|
(base32
|
|
"1q6igk50lq4fp5d3imgcn1j063h3gsp214ra4nlf534hf4wjlkg9"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-backports" ,r-backports)))
|
|
(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 "1.11")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "BBmisc" version))
|
|
(sha256
|
|
(base32
|
|
"1lh1n4bvxzivb5rbz69mvd8xdgr3gr2bnqd68a39sd1530l8r90y"))))
|
|
(properties `((upstream-name . "BBmisc")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-checkmate" ,r-checkmate)))
|
|
(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
|
|
`(("r-bbmisc" ,r-bbmisc)
|
|
("r-checkmate" ,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 "1.7")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "BatchJobs" version))
|
|
(sha256
|
|
(base32
|
|
"035658marnw57p4f38g99rwmvmb6hpbq0fhlxp3qbw22zfnnkvs9"))))
|
|
(properties `((upstream-name . "BatchJobs")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-backports" ,r-backports)
|
|
("r-bbmisc" ,r-bbmisc)
|
|
("r-brew" ,r-brew)
|
|
("r-checkmate" ,r-checkmate)
|
|
("r-data-table" ,r-data-table)
|
|
("r-dbi" ,r-dbi)
|
|
("r-digest" ,r-digest)
|
|
("r-rsqlite" ,r-rsqlite)
|
|
("r-sendmailr" ,r-sendmailr)
|
|
("r-stringi" ,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 "1.0-6")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "brew" version))
|
|
(sha256
|
|
(base32
|
|
"1vghazbcha8gvkwwcdagjvzx6yl8zm7kgr0i9wxr4jng06d1l3fp"))))
|
|
(build-system r-build-system)
|
|
(home-page "http://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 "1.1.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "desc" version))
|
|
(sha256
|
|
(base32
|
|
"0k07qighac1xzmm8k988zi7i88a0yfvia3gk5hbz0fyvb2v9kzrj"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-assertthat" ,r-assertthat)
|
|
("r-crayon" ,r-crayon)
|
|
("r-r6" ,r-r6)
|
|
("r-rprojroot" ,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 "1.4")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "commonmark" version))
|
|
(sha256
|
|
(base32
|
|
"1vb8r9khpvcf0q7acv8rsplfjjwcll302bg5kp596cvn6aacypl6"))))
|
|
(build-system r-build-system)
|
|
(home-page "http://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 '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 "6.0.1")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "roxygen2" version))
|
|
(sha256
|
|
(base32
|
|
"0xpzziminf225kjwhyl51kgkzhplyzhk5farhf5s822krl2xqbfj"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-brew" ,r-brew)
|
|
("r-commonmark" ,r-commonmark)
|
|
("r-desc" ,r-desc)
|
|
("r-digest" ,r-digest)
|
|
("r-r6" ,r-r6)
|
|
("r-rcpp" ,r-rcpp)
|
|
("r-stringi" ,r-stringi)
|
|
("r-stringr" ,r-stringr)
|
|
("r-xml2" ,r-xml2)))
|
|
(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 "0.9.9")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "openssl" version))
|
|
(sha256
|
|
(base32
|
|
"1ir7ggs0rxgn83h40r6jg9dzhb7hbcwhkcj5nsdzj7jz61sfgv77"))))
|
|
(build-system r-build-system)
|
|
(inputs
|
|
`(("libressl" ,libressl)))
|
|
(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 "1.3.1")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "httr" version))
|
|
(sha256
|
|
(base32
|
|
"0n7jz2digbgv48rbr9vmzv4vmf4rahl9jjy31izs7sxj4rs4s4r2"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-curl" ,r-curl)
|
|
("r-jsonlite" ,r-jsonlite)
|
|
("r-openssl" ,r-openssl)
|
|
("r-mime" ,r-mime)
|
|
("r-r6" ,r-r6)))
|
|
(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 "0.19.0")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "git2r" version))
|
|
(sha256
|
|
(base32
|
|
"0ws6fbndmaafk2am4dwnz24qizxhld0yh54hgx0z6lzv3p1j209q"))))
|
|
(build-system r-build-system)
|
|
;; This R package contains modified sources of libgit2. This modified
|
|
;; version of libgit2 is built as the package is built. Hence libgit2 is
|
|
;; not among the inputs of this package.
|
|
(inputs
|
|
`(("libssh2" ,libssh2)
|
|
("openssl" ,openssl)
|
|
("zlib" ,zlib)))
|
|
(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 "0.7")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "rstudioapi" version))
|
|
(sha256
|
|
(base32
|
|
"133s75q2hr6jg28m1wvs96qrbc9c4vw87migwhkjqb88xxvbqhd5"))))
|
|
(build-system r-build-system)
|
|
(home-page "http://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 "1.13.4")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "devtools" version))
|
|
(sha256
|
|
(base32
|
|
"1az1qf50vyhm4w6k2a6wqw3pqc8jv2iqzdhs36cg079hx9swm0mb"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-digest" ,r-digest)
|
|
("r-git2r" ,r-git2r)
|
|
("r-httr" ,r-httr)
|
|
("r-jsonlite" ,r-jsonlite)
|
|
("r-memoise" ,r-memoise)
|
|
("r-rstudioapi" ,r-rstudioapi)
|
|
("r-whisker" ,r-whisker)
|
|
("r-withr" ,r-withr)))
|
|
(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 "2.1.0")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "withr" version))
|
|
(sha256
|
|
(base32
|
|
"12v263fj6l3ds9nrsj6q7h6zhbivp3w2jk7w9dpk1610d3nx9gf8"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-lattice" ,r-lattice)))
|
|
(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 "0.4.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "hms" version))
|
|
(sha256
|
|
(base32
|
|
"07sh75flp15lx2b00s3nxh04xr9gk4qhlbh125qx25isf71zw6zl"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-rlang" ,r-rlang)
|
|
("r-pkgconfig" ,r-pkgconfig)))
|
|
(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 "1.1.1")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "readr" version))
|
|
(sha256
|
|
(base32
|
|
"1cvw5wdcqk88cp5fyv678mnmp66l3whcd2yh33p2qvx0168bja8s"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-rcpp" ,r-rcpp)
|
|
("r-hms" ,r-hms)
|
|
("r-tibble" ,r-tibble)
|
|
("r-r6" ,r-r6)
|
|
("r-bh" ,r-bh)))
|
|
(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 "3.6-6")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "plotrix" version))
|
|
(sha256
|
|
(base32
|
|
"07hywp3ym0gbpqdj3f4vhr0bhmynhby8vh6p1b9cm2hv26pzs9q4"))))
|
|
(build-system r-build-system)
|
|
(home-page "http://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 "http://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 "0.6-28")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "latticeExtra" version))
|
|
(sha256
|
|
(base32
|
|
"1hkyqsa7klk5glj9y1hg3rxr5qilqw8h0017zc4c3nps7lr9a1kq"))))
|
|
(properties `((upstream-name . "latticeExtra")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-lattice" ,r-lattice)
|
|
("r-rcolorbrewer" ,r-rcolorbrewer)))
|
|
(home-page "http://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 "0.8.100.1.0")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "RcppArmadillo" version))
|
|
(sha256
|
|
(base32
|
|
"19sghlkslz6llcrjk5pd8c6dsb338jsi4dnwrbbrjkfq6jdr5jlp"))))
|
|
(properties `((upstream-name . "RcppArmadillo")))
|
|
(build-system r-build-system)
|
|
(native-inputs
|
|
`(("r-knitr" ,r-knitr))) ; needed for vignettes
|
|
(propagated-inputs
|
|
`(("r-rcpp" ,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 "1.0-6")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "bitops" version))
|
|
(sha256
|
|
(base32
|
|
"176nr5wpnkavn5z0yy9f7d47l37ndnn2w3gv854xav8nnybi6wwv"))))
|
|
(build-system r-build-system)
|
|
(home-page "http://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 "1.17.1")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "caTools" version))
|
|
(sha256
|
|
(base32
|
|
"1x4szsn2qmbzpyjfdaiz2q7jwhap2gky9wq0riah74q0pzz76ank"))))
|
|
(properties `((upstream-name . "caTools")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-bitops" ,r-bitops)))
|
|
(home-page "http://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 "1.2")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "rprojroot" version))
|
|
(sha256
|
|
(base32
|
|
"1fgyxv1zv04sllcclzz089xl6hpdzac7xk61l0l4acb7rqsx5d18"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-backports" ,r-backports)))
|
|
(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 "1.8")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "rmarkdown" version))
|
|
(sha256
|
|
(base32
|
|
"0q1y1qx87xp6vf9h7mfl77rqhmd01xl53l9ap9qj99bfvpabb572"))))
|
|
(properties `((upstream-name . "rmarkdown")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-base64enc" ,r-base64enc)
|
|
("r-evaluate" ,r-evaluate)
|
|
("r-htmltools" ,r-htmltools)
|
|
("r-jsonlite" ,r-jsonlite)
|
|
("r-knitr" ,r-knitr)
|
|
("r-mime" ,r-mime)
|
|
("r-rprojroot" ,r-rprojroot)
|
|
("r-stringr" ,r-stringr)
|
|
("r-yaml" ,r-yaml)
|
|
("ghc-pandoc" ,ghc-pandoc)))
|
|
(home-page "http://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 "0.2.0")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "gtable" version))
|
|
(sha256
|
|
(base32
|
|
"0vz7073m0a2q12qzzihrfh5c2kx5jqi5l7z470fxmwqghdllh7l0"))))
|
|
(properties `((upstream-name . "gtable")))
|
|
(build-system r-build-system)
|
|
(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
|
|
`(("r-gtable" ,r-gtable)))
|
|
(native-inputs
|
|
`(("r-knitr" ,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 "2.0.1")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "pkgconfig" version))
|
|
(sha256
|
|
(base32
|
|
"0h2sp93fqqjbfqgq82a3i94ybnndx6ghaal8pbf99firnsjb40mb"))))
|
|
(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 "1.1.0")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "blob" version))
|
|
(sha256
|
|
(base32
|
|
"05pazzcyz3c3vd2l70zq9cf172cgjff4dnf419zigfnxycyn1mhn"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-tibble" ,r-tibble)))
|
|
(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 "2.0")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "RSQLite" version))
|
|
(sha256
|
|
(base32
|
|
"1xpg1i1jkzkzv44k512k90c2vvl960pl2d4a3spwcha6yclyc3vz"))))
|
|
(properties `((upstream-name . "RSQLite")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-dbi" ,r-dbi)
|
|
("r-bh" ,r-bh)
|
|
("r-memoise" ,r-memoise)
|
|
("r-plogr" ,r-plogr)
|
|
("r-rcpp" ,r-rcpp)
|
|
("r-bit64" ,r-bit64)
|
|
("r-blob" ,r-blob)
|
|
("r-pkgconfig" ,r-pkgconfig)))
|
|
(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 "1.95-0.1.2")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (string-append "https://www.bioconductor.org/packages/"
|
|
"release/extra/src/"
|
|
"contrib/RCurl_" version ".tar.gz"))
|
|
(sha256
|
|
(base32
|
|
"0l7qi45jxlf898n0jazabnam1yyczvqfdknd00bdirhhiplpd1sc"))))
|
|
(properties `((upstream-name . "RCurl")))
|
|
(build-system r-build-system)
|
|
(inputs
|
|
`(("libcurl" ,curl)))
|
|
(propagated-inputs
|
|
`(("r-bitops" ,r-bitops)))
|
|
(home-page "http://www.omegahat.org/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 "3.98-1.9")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "XML" version))
|
|
(sha256
|
|
(base32
|
|
"1hzkdkgs0nzmfg9wm7kyh1j9i0i2g7925whzlihqvg9grdlh3dx3"))))
|
|
(properties
|
|
`((upstream-name . "XML")))
|
|
(build-system r-build-system)
|
|
(inputs
|
|
`(("libxml2" ,libxml2)))
|
|
(home-page "http://www.omegahat.org/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 "http://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")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "lambda.r" version))
|
|
(sha256
|
|
(base32
|
|
"0vql32np716dpd0kjn7s7wgawd02ysgp2a5il4kb19nlw661ii3x"))))
|
|
(properties `((upstream-name . "lambda.r")))
|
|
(build-system r-build-system)
|
|
(home-page "http://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 "1.0.0")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "futile.options" version))
|
|
(sha256
|
|
(base32
|
|
"1hp82h6xqq5cck67h7lpf22n3j7mg3v1mla5y5ivnzrrb7iyr17f"))))
|
|
(properties
|
|
`((upstream-name . "futile.options")))
|
|
(build-system r-build-system)
|
|
(home-page "http://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
|
|
`(("r-futile-options" ,r-futile-options)
|
|
("r-lambda-r" ,r-lambda-r)))
|
|
(home-page "http://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 "0.5-2.2")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "segmented" version))
|
|
(sha256
|
|
(base32
|
|
"1wdjxkgqjqw5q2nywmgkf6y21lb0alhvaqg0m0dr2xyxf1ii79rs"))))
|
|
(build-system r-build-system)
|
|
(home-page "http://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 "0.4-2")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "snow" version))
|
|
(sha256
|
|
(base32
|
|
"1mxbrkpnmq32x4wd0194d541661yvfrrjlr3lsf7qq53ms3h21zf"))))
|
|
(build-system r-build-system)
|
|
(home-page "http://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 "1.77")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "SparseM" version))
|
|
(sha256
|
|
(base32
|
|
"0p6ljma2h12cq1xmy0cxb48ih8dhxxbnwkqzvx3cckxf2kprycm9"))))
|
|
(properties
|
|
`((upstream-name . "SparseM")))
|
|
(inputs
|
|
`(("gfortran" ,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 "1.0.8")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "iterators" version))
|
|
(sha256
|
|
(base32
|
|
"1f057pabs7ss9h1n244can26qsi5n2k3salrdk0b0vkphlrs4kmf"))))
|
|
(build-system r-build-system)
|
|
(home-page "http://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 "1.4.3")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "foreach" version))
|
|
(sha256
|
|
(base32
|
|
"10aqsd3rxz03s1qdb6gsb1cj89mj4vmh491zfpin4skj1xvkzw0y"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-codetools" ,r-codetools)
|
|
("r-iterators" ,r-iterators)))
|
|
(home-page "http://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 "1.0.11")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "doParallel" version))
|
|
(sha256
|
|
(base32
|
|
"0sppgxk3d8mfsrb3cjdyn0mv0s4i7pcy8g8c3cjzbr6k8vmx5jsc"))))
|
|
(properties `((upstream-name . "doParallel")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-foreach" ,r-foreach)
|
|
("r-iterators" ,r-iterators)))
|
|
(home-page "http://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 "1.3.4")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "doMC" version))
|
|
(sha256
|
|
(base32
|
|
"0y47jl6g4f83r14pj8bafdzq1phj7bxy5dwyz3k43d2rr8phk8bn"))))
|
|
(properties `((upstream-name . "doMC")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-foreach" ,r-foreach)
|
|
("r-iterators" ,r-iterators)))
|
|
(home-page "http://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
|
|
(package
|
|
(name "r-dt")
|
|
(version "0.2")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "DT" version))
|
|
(sha256
|
|
(base32
|
|
"1g86p0jcjqi2ph5rhm45jkzibsa6yfcj8n5cg3giy90sqgjzkdx1"))))
|
|
(properties
|
|
`((upstream-name . "DT")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-htmltools" ,r-htmltools)
|
|
("r-htmlwidgets" ,r-htmlwidgets)
|
|
("r-magrittr" ,r-magrittr)))
|
|
(home-page "http://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 'DataTables' (typically via R Markdown or Shiny).
|
|
The '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, jquery.highlight.js, DataTables
|
|
;; * ASL2.0: selectize.js
|
|
;; * WTFPL: noUiSlider
|
|
(license (list license:gpl3
|
|
license:expat
|
|
license:asl2.0
|
|
(license:non-copyleft "http://www.wtfpl.net/txt/copying/")))))
|
|
|
|
(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 "http://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 "2.3.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "irlba" version))
|
|
(sha256
|
|
(base32
|
|
"1dclzzkm75sbbqda5scj2hlqnw2sksgxbiqagxs4359fwfszi0k0"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-matrix" ,r-matrix)))
|
|
(home-page "http://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 "2.0-13")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "glmnet" version))
|
|
(sha256
|
|
(base32
|
|
"1zdqp6wnqxzp5qn2ky47phbkrxv3cpgbwmdp896h3xxjvp58sa7k"))))
|
|
(build-system r-build-system)
|
|
(inputs
|
|
`(("gfortran" ,gfortran)))
|
|
(propagated-inputs
|
|
`(("r-foreach" ,r-foreach)
|
|
("r-matrix" ,r-matrix)))
|
|
(home-page "http://www.jstatsoft.org/v33/i01")
|
|
(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 "0.22")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "pkgmaker" version))
|
|
(sha256
|
|
(base32
|
|
"0vrqnd3kg6liqvpbd969jjsdx0f0rvmmxgdbwwrp6xfmdg0pib8r"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-codetools" ,r-codetools)
|
|
("r-digest" ,r-digest)
|
|
("r-registry" ,r-registry)
|
|
("r-stringr" ,r-stringr)
|
|
("r-xtable" ,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 "0.3")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "registry" version))
|
|
(sha256
|
|
(base32
|
|
"0c7lscfxncwwd8zp46h2xfw9gw14dypqv6m2kx85xjhjh0xw99aq"))))
|
|
(build-system r-build-system)
|
|
(home-page "http://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 "1.2.4")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "rngtools" version))
|
|
(sha256
|
|
(base32
|
|
"1fcgfqrrb48z37xgy8sffx91p9irp39yqzxv7nqp1x2hnwsrh097"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-digest" ,r-digest)
|
|
("r-pkgmaker" ,r-pkgmaker)
|
|
("r-stringr" ,r-stringr)))
|
|
(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 "0.13")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "Rtsne" version))
|
|
(sha256
|
|
(base32
|
|
"17crbdi80q4g2pwp9v7j3bdaznk96qlrqx01zvj3wwqippizyfqw"))))
|
|
(properties `((upstream-name . "Rtsne")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-rcpp" ,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 "1.6-8")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "e1071" version))
|
|
(sha256
|
|
(base32
|
|
"08n6i26nfckjpxjkzi8phhanc3ahsrirkv5rz38y2jcv7ds031pn"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-class" ,r-class)))
|
|
(home-page "http://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 "0.1.3")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "bigmemory.sri" version))
|
|
(sha256
|
|
(base32 "0mg14ilwdkd64q2ri9jdwnk7mp55dqim7xfifrs65sdsv1934h2m"))))
|
|
(properties
|
|
`((upstream-name . "bigmemory.sri")))
|
|
(build-system r-build-system)
|
|
(home-page "http://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 "1.1.9.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "synchronicity" version))
|
|
(sha256
|
|
(base32
|
|
"0d9skpwmsnkn4xb3f2kgyyv8bhdi0r9p1kj3cvi0s92fjjnpi00c"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-bh" ,r-bh)
|
|
("r-bigmemory-sri" ,r-bigmemory-sri)
|
|
("r-rcpp" ,r-rcpp)))
|
|
(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 "4.5.31")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "bigmemory" version))
|
|
(sha256
|
|
(base32
|
|
"0wv0p746zz5a6r1yd0fgpj2kfcyzk2f4rxqz92p6lp9jzakv4lfs"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-bh" ,r-bh)
|
|
("r-rcpp" ,r-rcpp)
|
|
("r-bigmemory-sri" ,r-bigmemory-sri)))
|
|
(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-nmf
|
|
(package
|
|
(name "r-nmf")
|
|
(version "0.20.6")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "NMF" version))
|
|
(sha256
|
|
(base32
|
|
"0mmh9bz0zjwd8h9jplz4rq3g94npaqj8s4px51vcv47csssd9k6z"))))
|
|
(properties `((upstream-name . "NMF")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-cluster" ,r-cluster)
|
|
("r-bigmemory" ,r-bigmemory)
|
|
("r-synchronicity" ,r-synchronicity)
|
|
("r-colorspace" ,r-colorspace)
|
|
("r-digest" ,r-digest)
|
|
("r-doparallel" ,r-doparallel)
|
|
("r-foreach" ,r-foreach)
|
|
("r-ggplot2" ,r-ggplot2)
|
|
("r-gridbase" ,r-gridbase)
|
|
("r-pkgmaker" ,r-pkgmaker)
|
|
("r-rcolorbrewer" ,r-rcolorbrewer)
|
|
("r-registry" ,r-registry)
|
|
("r-reshape2" ,r-reshape2)
|
|
("r-rngtools" ,r-rngtools)
|
|
("r-stringr" ,r-stringr)))
|
|
(home-page "http://renozao.github.io/NMF")
|
|
(synopsis "Algorithms and framework for nonnegative matrix factorization")
|
|
(description
|
|
"This package provides a framework to perform Non-negative Matrix
|
|
Factorization (NMF). The package implements a set of already published
|
|
algorithms and seeding methods, and provides a framework to test, develop and
|
|
plug new or custom algorithms. Most of the built-in algorithms have been
|
|
optimized in C++, and the main interface function provides an easy way of
|
|
performing parallel computations on multicore machines.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-r-methodss3
|
|
(package
|
|
(name "r-r-methodss3")
|
|
(version "1.7.1")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "R.methodsS3" version))
|
|
(sha256
|
|
(base32
|
|
"11z6v2i7jl647wxi9p5z66yvfnnqv6s7fxqmz7w2gkb6j8wl1f24"))))
|
|
(properties `((upstream-name . "R.methodsS3")))
|
|
(build-system r-build-system)
|
|
(home-page "http://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 "1.21.0")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "R.oo" version))
|
|
(sha256
|
|
(base32
|
|
"0723gxjazgqq7v3lwnl7axw3brzcnizvhbd71ijkkv8mz31fwp34"))))
|
|
(properties `((upstream-name . "R.oo")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-r-methodss3" ,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 "2.6.0")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "R.utils" version))
|
|
(sha256
|
|
(base32
|
|
"03j7hrs03kyj9qrjxyp5kqv4lpqqpk6xwbkzx6j15d8928yrjr2x"))))
|
|
(properties `((upstream-name . "R.utils")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-r-methodss3" ,r-r-methodss3)
|
|
("r-r-oo" ,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 "0.12.0")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "R.cache" version))
|
|
(sha256
|
|
(base32
|
|
"006x52w9r8phw5hgqmyp0bz8z42vn8p5yibibnzi1sfa1xlw8iyx"))))
|
|
(properties `((upstream-name . "R.cache")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-digest" ,r-digest)
|
|
("r-r-methodss3" ,r-r-methodss3)
|
|
("r-r-oo" ,r-r-oo)
|
|
("r-r-utils" ,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 "0.41.0")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "R.rsp" version))
|
|
(sha256
|
|
(base32
|
|
"01l430avj5ggmdsla2kiriix72g0dlzx9klniq321bs0za808v3c"))))
|
|
(properties `((upstream-name . "R.rsp")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-r-cache" ,r-r-cache)
|
|
("r-r-methodss3" ,r-r-methodss3)
|
|
("r-r-oo" ,r-r-oo)
|
|
("r-r-utils" ,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 "1.0-6")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "mvtnorm" version))
|
|
(sha256
|
|
(base32
|
|
"0i74s9dl4jf1gln6agra8h38qn9ifd5v0gi13caj1da5nrbmn0aa"))))
|
|
(build-system r-build-system)
|
|
(inputs
|
|
`(("gfortran" ,gfortran)))
|
|
(home-page "http://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 "0.52.2")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "matrixStats" version))
|
|
(sha256
|
|
(base32
|
|
"19fjf19cr0p3j9pj17myz39zpi5bh7ci72db3la9my09n6k6mnir"))))
|
|
(properties `((upstream-name . "matrixStats")))
|
|
(build-system r-build-system)
|
|
(native-inputs
|
|
`(("r-r-rsp" ,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 "0.4.0")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "viridis" version))
|
|
(sha256
|
|
(base32
|
|
"03mha2935k1mw7mjjkq7mrx185hl0m3vq3967iiwbknpivbdxllk"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-ggplot2" ,r-ggplot2)
|
|
("r-gridextra" ,r-gridextra)
|
|
("r-viridislite" ,r-viridislite)))
|
|
(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 "0.2.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "viridisLite" version))
|
|
(sha256
|
|
(base32
|
|
"1546h44ng4dxs130jkh6lkh990hmp90m1w45sq5p47n546gr0k9d"))))
|
|
(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 ('viridis',
|
|
'magma', 'plasma' and '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 'lite' version of the more complete @code{viridis} package.")
|
|
(license license:expat)))
|
|
|
|
(define-public r-tidyselect
|
|
(package
|
|
(name "r-tidyselect")
|
|
(version "0.2.3")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "tidyselect" version))
|
|
(sha256
|
|
(base32
|
|
"0b0w30yq30c7bwpaghp3hp0nncqwcmvrra9j58fhx9jihay3l68c"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-glue" ,r-glue)
|
|
("r-purrr" ,r-purrr)
|
|
("r-rcpp" ,r-rcpp)
|
|
("r-rlang" ,r-rlang)))
|
|
(home-page "http://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 "0.7.2")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "tidyr" version))
|
|
(sha256
|
|
(base32
|
|
"1700fry2b3d3ksj7x2f09xl6agjrdnx1rqsc1r8gvzsp5cpflb06"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-dplyr" ,r-dplyr)
|
|
("r-magrittr" ,r-magrittr)
|
|
("r-glue" ,r-glue)
|
|
("r-purrr" ,r-purrr)
|
|
("r-rlang" ,r-rlang)
|
|
("r-tidyselect" ,r-tidyselect)
|
|
("r-rcpp" ,r-rcpp)
|
|
("r-stringi" ,r-stringi)
|
|
("r-tibble" ,r-tibble)))
|
|
(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")
|
|
;; The package tarball was updated in place, resulting in a change in the
|
|
;; hash value. We decided to bump the version to 1.27.1-1 instead of
|
|
;; keeping the version at upstream's 1.27.1.
|
|
(version "1.27.1-1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "hexbin" "1.27.1"))
|
|
(sha256
|
|
(base32
|
|
"025d609z1nyy684hwvp34b9mjzkgvild7fvfr95f941dmsikan87"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-lattice" ,r-lattice)))
|
|
(native-inputs
|
|
`(("gfortran" ,gfortran)))
|
|
(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 "0.2.4")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "purrr" version))
|
|
(sha256
|
|
(base32
|
|
"0wgbnbrqncjpggg8f9bdpcd1gy351s5f0az5k8lc55cvs9lhz3gd"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-tibble" ,r-tibble)
|
|
("r-magrittr" ,r-magrittr)
|
|
("r-rlang" ,r-rlang)))
|
|
(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 "4.7.1")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "plotly" version))
|
|
(sha256
|
|
(base32
|
|
"0wj9lw7w28z8w9ip9vadv6sydjhqyg65kfiai9m3bndzz50b1m3w"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-base64enc" ,r-base64enc)
|
|
("r-crosstalk" ,r-crosstalk)
|
|
("r-digest" ,r-digest)
|
|
("r-data-table" ,r-data-table)
|
|
("r-dplyr" ,r-dplyr)
|
|
("r-ggplot2" ,r-ggplot2)
|
|
("r-hexbin" ,r-hexbin)
|
|
("r-htmltools" ,r-htmltools)
|
|
("r-htmlwidgets" ,r-htmlwidgets)
|
|
("r-httr" ,r-httr)
|
|
("r-jsonlite" ,r-jsonlite)
|
|
("r-lazyeval" ,r-lazyeval)
|
|
("r-magrittr" ,r-magrittr)
|
|
("r-purrr" ,r-purrr)
|
|
("r-rcolorbrewer" ,r-rcolorbrewer)
|
|
("r-scales" ,r-scales)
|
|
("r-tibble" ,r-tibble)
|
|
("r-tidyr" ,r-tidyr)
|
|
("r-viridislite" ,r-viridislite)))
|
|
(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 "1.07")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "BiasedUrn" version))
|
|
(sha256
|
|
(base32
|
|
"13i2lgfnjhlbbm2yxfc2l5hswqw6x03pwba5csjmirv8kpjw4xr3"))))
|
|
(properties `((upstream-name . "BiasedUrn")))
|
|
(build-system r-build-system)
|
|
(home-page "http://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 "1.0.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "rematch" version))
|
|
(sha256
|
|
(base32
|
|
"0y3mshvpvz9csmq8hk8jbabx4nxlv5sckvfzvm6920ndg34xw2d4"))))
|
|
(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
|
|
`(("r-rematch" ,r-rematch)
|
|
("r-tibble" ,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 "0.2.2")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "googlesheets" version))
|
|
(sha256
|
|
(base32
|
|
"18q0xmxn09b52rmky7gr5flp0awndcnsgb7zcvkzvkrkvmwad52b"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-cellranger" ,r-cellranger)
|
|
("r-dplyr" ,r-dplyr)
|
|
("r-httr" ,r-httr)
|
|
("r-jsonlite" ,r-jsonlite)
|
|
("r-purrr" ,r-purrr)
|
|
("r-readr" ,r-readr)
|
|
("r-stringr" ,r-stringr)
|
|
("r-tidyr" ,r-tidyr)
|
|
("r-xml2" ,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 "2.6-2017-03-22")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (string-append "https://gforge.inria.fr/frs/download.php/36615/"
|
|
"spams-R-v" version ".tar.gz"))
|
|
(sha256
|
|
(base32
|
|
"13z2293jixf1r9g8dyy856xrhvpjr2ln2n9smn6644126r9hmhkx"))))
|
|
(build-system r-build-system)
|
|
(arguments
|
|
`(#:phases
|
|
(modify-phases %standard-phases
|
|
(add-after 'unpack 'chdir
|
|
(lambda _ (chdir "spams") #t))
|
|
;; Don't tune for the building machine
|
|
(add-after 'chdir 'no-mtune
|
|
(lambda _
|
|
(substitute* "src/Makevars"
|
|
(("-mtune=native") ""))
|
|
#t)))))
|
|
(propagated-inputs
|
|
`(("r-lattice" ,r-lattice)
|
|
("r-matrix" ,r-matrix)))
|
|
(home-page "http://spams-devel.gforge.inria.fr")
|
|
(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")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "base64" version))
|
|
(sha256
|
|
(base32
|
|
"1labh0ycdm2xcjssj8bhnyjvbk44mcdsi0rb2p8rfqa428mrq9cf"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-openssl" ,r-openssl)))
|
|
(home-page "http://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 "4.0-3")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "Hmisc" version))
|
|
(sha256
|
|
(base32
|
|
"1a7i7azag6pldgala85d8hh7wnx1shamyiriy4jfc65nxrr2lq8w"))))
|
|
(properties `((upstream-name . "Hmisc")))
|
|
(build-system r-build-system)
|
|
(native-inputs
|
|
`(("gfortran" ,gfortran)))
|
|
(propagated-inputs
|
|
`(("r-acepack" ,r-acepack)
|
|
("r-base64enc" ,r-base64enc)
|
|
("r-cluster" ,r-cluster)
|
|
("r-data-table" ,r-data-table)
|
|
("r-foreign" ,r-foreign)
|
|
("r-formula" ,r-formula)
|
|
("r-ggplot2" ,r-ggplot2)
|
|
("r-gridextra" ,r-gridextra)
|
|
("r-gtable" ,r-gtable)
|
|
("r-lattice" ,r-lattice)
|
|
("r-latticeextra" ,r-latticeextra)
|
|
("r-htmltable" ,r-htmltable)
|
|
("r-htmltools" ,r-htmltools)
|
|
("r-nnet" ,r-nnet)
|
|
("r-rpart" ,r-rpart)
|
|
("r-survival" ,r-survival)
|
|
("r-viridis" ,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 "0.4.31")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "RUnit" version))
|
|
(sha256
|
|
(base32
|
|
"1jqr871jkll2xmk7wk5hv1z3a36hyn2ibgivw7bwk4b346940xlx"))))
|
|
(properties `((upstream-name . "RUnit")))
|
|
(build-system r-build-system)
|
|
(home-page "http://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-preprocesscore
|
|
(package
|
|
(name "r-preprocesscore")
|
|
(version "1.40.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (bioconductor-uri "preprocessCore" version))
|
|
(sha256
|
|
(base32
|
|
"0mrdgbkb9dcfr9gsqyxfpshnxx60mq97pl98b8yl00l2gfwz48ph"))))
|
|
(properties
|
|
`((upstream-name . "preprocessCore")))
|
|
(build-system r-build-system)
|
|
(home-page "https://github.com/bmbolstad/preprocessCore")
|
|
(synopsis "Collection of pre-processing functions")
|
|
(description
|
|
"This package provides a library of core pre-processing and normalization
|
|
routines.")
|
|
(license license:lgpl2.0+)))
|
|
|
|
(define-public r-fastcluster
|
|
(package
|
|
(name "r-fastcluster")
|
|
(version "1.1.24")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "fastcluster" version))
|
|
(sha256
|
|
(base32
|
|
"15drhl22wm8whsy6b3vv754skfddiydb068zn1whrw5sknvkkjc2"))))
|
|
(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 "1.1-1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "sfsmisc" version))
|
|
(sha256
|
|
(base32
|
|
"0jzmbywlyzfxs7hlmyd0iynghfc9qp5sa5lnhr73y8r360yv1ahf"))))
|
|
(build-system r-build-system)
|
|
(home-page "http://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 "3.5.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "gtools" version))
|
|
(sha256
|
|
(base32
|
|
"1xknwk9xlsj027pg0nwiizigcrsc84hdrig0jn0cgcyxj8dabdl6"))))
|
|
(build-system r-build-system)
|
|
(home-page "http://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 "2.18.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "gdata" version))
|
|
(sha256
|
|
(base32
|
|
"0zwdj7lscgxr8r62ii8hbdh4mb7sa9w4f5nv32zzrxdvymcpya2b"))))
|
|
(build-system r-build-system)
|
|
(inputs
|
|
`(("perl" ,perl)))
|
|
(propagated-inputs
|
|
`(("r-gtools" ,r-gtools)))
|
|
(home-page "http://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 "3.0.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "gplots" version))
|
|
(sha256
|
|
(base32
|
|
"02nb8n3s7c1zxq2s7ycaq2ys72y7mzirxrwj954h6gdc4x1zhg9l"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-catools" ,r-catools)
|
|
("r-gdata" ,r-gdata)
|
|
("r-gtools" ,r-gtools)
|
|
("r-kernsmooth" ,r-kernsmooth)))
|
|
(home-page "http://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 baloon 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 "1.0-7")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "ROCR" version))
|
|
(sha256
|
|
(base32
|
|
"1jay8cm7lgq56i967vm5c2hgaxqkphfpip0gn941li3yhh7p3vz7"))))
|
|
(properties `((upstream-name . "ROCR")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-gplots" ,r-gplots)))
|
|
(home-page "http://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-zoo
|
|
(package
|
|
(name "r-zoo")
|
|
(version "1.8-0")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "zoo" version))
|
|
(sha256
|
|
(base32
|
|
"0mqklbx92ifwa0awm7gpm4r9dvwa09p55zjxjnypiqsxy532r4h9"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-lattice" ,r-lattice)))
|
|
(home-page "http://zoo.R-Forge.R-project.org/")
|
|
(synopsis "S3 infrastructure for regular and irregular time series")
|
|
(description "This package contains an S3 class with methods for totally
|
|
ordered indexed observations. It is particularly aimed at irregular time
|
|
series of numeric vectors/matrices and factors.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-ztable
|
|
(package
|
|
(name "r-ztable")
|
|
(version "0.1.5")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "ztable" version))
|
|
(sha256
|
|
(base32
|
|
"1jfqnqy9544gfvz3bsb48v4177nwp4b4n9l2743asq8sbq305b5r"))))
|
|
(build-system r-build-system)
|
|
(home-page "http://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 "http://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 "0.2.3")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "beeswarm" version))
|
|
(sha256
|
|
(base32
|
|
"0hy89bwv7jixlg91li1fywa77916am2whqp1m1fx1khd45g44581"))))
|
|
(build-system r-build-system)
|
|
(home-page "http://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 "0.1.6")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "sourcetools" version))
|
|
(sha256
|
|
(base32
|
|
"0l8c6fql82cb246qh7hfgxb4s35qn0qfgy6dzvkx0zkz1cpqvx69"))))
|
|
(build-system r-build-system)
|
|
(home-page "http://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 "0.6.0")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "ggbeeswarm" version))
|
|
(sha256
|
|
(base32
|
|
"0crk29p5vi1r3a988kms4y7r0iqwgwzsikgvh18r9wbzyr98bb5v"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-beeswarm" ,r-beeswarm)
|
|
("r-ggplot2" ,r-ggplot2)
|
|
("r-vipor" ,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 "3.4.0")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "ggthemes" version))
|
|
(sha256
|
|
(base32
|
|
"1jj8lp7jbk3489kpgbw4b5phpn01gkfmksc21c6sn3x6wmzyn6hs"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-assertthat" ,r-assertthat)
|
|
("r-colorspace" ,r-colorspace)
|
|
("r-ggplot2" ,r-ggplot2)
|
|
("r-scales" ,r-scales)))
|
|
(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 "1.4.30")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "statmod" version))
|
|
(sha256
|
|
(base32
|
|
"07v4x8af60alcw6vbiwf5fp25bhra61kvxz9kqx64lszm0i1fb4x"))))
|
|
(build-system r-build-system)
|
|
(home-page "http://cran.r-project.org/web/packages/statmod")
|
|
(native-inputs
|
|
`(("gfortran" ,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 "2.5.1")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "RANN" version))
|
|
(sha256
|
|
(base32
|
|
"0il5i99vbcagnxvb15af5n37g04a4q1x96bz73zh3jhki9fpw9vm"))))
|
|
(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
|
|
`(("r-knitr" ,r-knitr)
|
|
("r-rmarkdown" ,r-rmarkdown)
|
|
("r-dplyr" ,r-dplyr)
|
|
("r-readr" ,r-readr)
|
|
("r-ggplot2" ,r-ggplot2)
|
|
("r-magrittr" ,r-magrittr)
|
|
("r-stringr" ,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 "http://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 "0.9.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "cowplot" version))
|
|
(sha256
|
|
(base32
|
|
"0iq0wsi7467cj8hqml06whk3xsiv89x8dvm9ynwp411pzzbdjgwm"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-ggplot2" ,r-ggplot2)
|
|
("r-gtable" ,r-gtable)
|
|
("r-plyr" ,r-plyr)
|
|
("r-scales" ,r-scales)))
|
|
(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 "1.1.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "mixtools" version))
|
|
(sha256
|
|
(base32
|
|
"13wdm0xs5bakhpa8ypg6lvhjaqkxyabwz4glxdwn0jwdvkcdhgsl"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-mass" ,r-mass)
|
|
("r-segmented" ,r-segmented)
|
|
("r-survival" ,r-survival)))
|
|
(home-page "http://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 "1.2")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "lars" version))
|
|
(sha256
|
|
(base32
|
|
"0blj44wqrx6lmym1m9v6wkz8zxzbjax2zl6swgdczci0ixb5nx34"))))
|
|
(build-system r-build-system)
|
|
(inputs
|
|
`(("gfortran" ,gfortran)))
|
|
(home-page "http://www-stat.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 "1.2-1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "fastICA" version))
|
|
(sha256
|
|
(base32
|
|
"108z2ymby5y4h8l4l2krqwm28rya93gq09yylgilnm3afvfrfabg"))))
|
|
(properties `((upstream-name . "fastICA")))
|
|
(build-system r-build-system)
|
|
(home-page "http://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 "4.6-12")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "randomForest" version))
|
|
(sha256
|
|
(base32
|
|
"1i43idaihhl6nwqw42v9dqpl6f8z3ykcn2in32lh2755i27jylbf"))))
|
|
(properties `((upstream-name . "randomForest")))
|
|
(build-system r-build-system)
|
|
(home-page "https://www.stat.berkeley.edu/~breiman/RandomForests/")
|
|
(native-inputs
|
|
`(("gfortran" ,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 "0.75-7")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "diptest" version))
|
|
(sha256
|
|
(base32
|
|
"06xnc5gv1284ll0addxnxb6ljz6fn8dbyrp5vchyz6551h800aa6"))))
|
|
(build-system r-build-system)
|
|
(home-page "http://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 "0.2-21")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "modeltools" version))
|
|
(sha256
|
|
(base32
|
|
"0ynds453xprxv0jqqzi3blnv5w6vrdww9pvd1sq4lrr5ar3k3cq7"))))
|
|
(build-system r-build-system)
|
|
(home-page "http://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 "2.3-14")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "flexmix" version))
|
|
(sha256
|
|
(base32
|
|
"0sl4zxh1sb2sr5q7svjw9ihrm219jzn82yrc9d43q6r1b8bpyz43"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-lattice" ,r-lattice)
|
|
("r-modeltools" ,r-modeltools)
|
|
("r-nnet" ,r-nnet)))
|
|
(home-page "http://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 "5.4")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "mclust" version))
|
|
(sha256
|
|
(base32
|
|
"1i3v1q8qq0al3ifvjhcvxfsg68cx9mq8jz67jwmiqai78mw0aqvk"))))
|
|
(build-system r-build-system)
|
|
(native-inputs
|
|
`(("gfortran" ,gfortran)))
|
|
(home-page "http://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 "2.2-6")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "prabclus" version))
|
|
(sha256
|
|
(base32
|
|
"0qjsxrx6yv338bxm4ki0w9h8hind1l98abdrz828588bwj02jya1"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-mass" ,r-mass)
|
|
("r-mclust" ,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 "1.0-8")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "DEoptimR" version))
|
|
(sha256
|
|
(base32
|
|
"1vz546hyjyhly70z62h5n3mn62b8llhhmim8ffp9y6jnnb0i2sc4"))))
|
|
(properties `((upstream-name . "DEoptimR")))
|
|
(build-system r-build-system)
|
|
(home-page "http://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 "0.92-8")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "robustbase" version))
|
|
(sha256
|
|
(base32
|
|
"080ynchq8pvhnmbivj4fp74n0x9lyr9923sg0s9gq5irgm68kgxw"))))
|
|
(build-system r-build-system)
|
|
(inputs
|
|
`(("gfortran" ,gfortran)))
|
|
(propagated-inputs
|
|
`(("r-deoptimr" ,r-deoptimr)))
|
|
(home-page "http://robustbase.r-forge.r-project.org/")
|
|
(synopsis "Basic robust statistics")
|
|
(description
|
|
"This packages allows to analyze 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 "1.9-72")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "pcaPP" version))
|
|
(sha256
|
|
(base32
|
|
"0i2822bv86dpqmk3q17x61nsp3gjjnn4nr8191rwvbiib7xhpgaq"))))
|
|
(properties `((upstream-name . "pcaPP")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-mvtnorm" ,r-mvtnorm)))
|
|
(home-page "http://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 "1.4-3")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "rrcov" version))
|
|
(sha256
|
|
(base32
|
|
"0kagqggi634mvrhd67ia7mpjrj5v6w2wq0z3kyppg5xkvzh335nq"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-cluster" ,r-cluster)
|
|
("r-lattice" ,r-lattice)
|
|
("r-mvtnorm" ,r-mvtnorm)
|
|
("r-pcapp" ,r-pcapp)
|
|
("r-robustbase" ,r-robustbase)))
|
|
(native-inputs
|
|
`(("gfortran" ,gfortran)))
|
|
(home-page "http://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 "0.5-14")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "fit.models" version))
|
|
(sha256
|
|
(base32
|
|
"0vjbzmx0ambm6yzidb4vbgmhclwzwv2iz2cwl54ccdkvx4cx3fck"))))
|
|
(properties `((upstream-name . "fit.models")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-lattice" ,r-lattice)))
|
|
(home-page "http://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 "0.4-18")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "robust" version))
|
|
(sha256
|
|
(base32
|
|
"1b7qh1aff500nd6dh4y2ipmjgdiq8991shflb63pc39vpc0ny6g4"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-fit-models" ,r-fit-models)
|
|
("r-lattice" ,r-lattice)
|
|
("r-mass" ,r-mass)
|
|
("r-robustbase" ,r-robustbase)
|
|
("r-rrcov" ,r-rrcov)))
|
|
(native-inputs
|
|
`(("gfortran" ,gfortran)))
|
|
(home-page "http://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 "0.1-2")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "trimcluster" version))
|
|
(sha256
|
|
(base32
|
|
"0lsgbg93hm0w1rdb813ry0ks2l0jfpyqzqkf3h3bj6fch0avcbv2"))))
|
|
(build-system r-build-system)
|
|
(home-page "http://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 "2.1-10")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "fpc" version))
|
|
(sha256
|
|
(base32
|
|
"15m0p9l9w2v7sl0cnzyg81i2fmx3hrhvr3371544mwn3fpsca5sx"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-class" ,r-class)
|
|
("r-cluster" ,r-cluster)
|
|
("r-diptest" ,r-diptest)
|
|
("r-flexmix" ,r-flexmix)
|
|
("r-kernlab" ,r-kernlab)
|
|
("r-mass" ,r-mass)
|
|
("r-mclust" ,r-mclust)
|
|
("r-mvtnorm" ,r-mvtnorm)
|
|
("r-prabclus" ,r-prabclus)
|
|
("r-robustbase" ,r-robustbase)
|
|
("r-trimcluster" ,r-trimcluster)))
|
|
(home-page "http://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 "1.0-4")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "VGAM" version))
|
|
(sha256
|
|
(base32
|
|
"0r59hyp3afmvms890b3v2yyckf8v0qkjf2w11rnqd2zgg1gri0g5"))))
|
|
(properties `((upstream-name . "VGAM")))
|
|
(build-system r-build-system)
|
|
(inputs
|
|
`(("gfortran" ,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 "1.3-3")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "pbapply" version))
|
|
(sha256
|
|
(base32
|
|
"0iqhymf65jffh00qf056h1p76xf92bfmij6aymlmgnvn24fv4ybk"))))
|
|
(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-fnn
|
|
(package
|
|
(name "r-fnn")
|
|
(version "1.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "FNN" version))
|
|
(sha256
|
|
(base32
|
|
"1kncmiaraq1mrykb9fj3fsxswabk3l71fnp1vks0x9aay5xfk8mj"))))
|
|
(properties `((upstream-name . "FNN")))
|
|
(build-system r-build-system)
|
|
(home-page "http://cran.r-project.org/web/packages/FNN")
|
|
(synopsis "Fast nearest neighbor search algorithms and applications")
|
|
(description
|
|
"This package provides cover-tree and kd-tree fast k-nearest neighbor
|
|
search algorithms and related applications including KNN classification,
|
|
regression and information measures.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-minqa
|
|
(package
|
|
(name "r-minqa")
|
|
(version "1.2.4")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "minqa" version))
|
|
(sha256
|
|
(base32
|
|
"036drja6xz7awja9iwb76x91415p26fb0jmg7y7v0p65m6j978fg"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-rcpp" ,r-rcpp)))
|
|
(inputs
|
|
`(("gfortran" ,gfortran)))
|
|
(home-page "http://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 "0.3.3.3.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "RcppEigen" version))
|
|
(sha256
|
|
(base32
|
|
"093g2wmqyk86693l0lzh2va8119w3k7rvw5q24p842jdfv5x5z8l"))))
|
|
(properties `((upstream-name . "RcppEigen")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-rcpp" ,r-rcpp)
|
|
("r-matrix" ,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 "1.1.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "ModelMetrics" version))
|
|
(sha256
|
|
(base32
|
|
"119xxmzb5biq7k1yxqsf0jmmarmfn6lds9x9hfgv593xlpym6za8"))))
|
|
(properties `((upstream-name . "ModelMetrics")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-rcpp" ,r-rcpp)))
|
|
(home-page "http://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 "0.4-1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "MatrixModels" version))
|
|
(sha256
|
|
(base32
|
|
"0cyfvhci2p1vr2x52ymkyqqs63x1qchn856dh2j94yb93r08x1zy"))))
|
|
(properties `((upstream-name . "MatrixModels")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-matrix" ,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 "5.34")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "quantreg" version))
|
|
(sha256
|
|
(base32
|
|
"0bmgfgnmzqwmwwaraliry682yb8kcr396q3rlzrd2qzaa9sgxxh4"))))
|
|
(build-system r-build-system)
|
|
(native-inputs
|
|
`(("gfortran" ,gfortran)))
|
|
(propagated-inputs
|
|
`(("r-matrix" ,r-matrix)
|
|
("r-matrixmodels" ,r-matrixmodels)
|
|
("r-sparsem" ,r-sparsem)))
|
|
(home-page "http://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 "1.0.4")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "nloptr" version))
|
|
(sha256
|
|
(base32
|
|
"1sz1xj3785x4vsm4nd6in298bk32hs2jk5nsxma7ivxi7jcmn8l4"))))
|
|
(build-system r-build-system)
|
|
(native-inputs
|
|
`(("pkg-config" ,pkg-config)))
|
|
(inputs
|
|
`(("nlopt" ,nlopt)))
|
|
(home-page "http://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 "1.1-14")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "lme4" version))
|
|
(sha256
|
|
(base32
|
|
"1vars93604q7kyz6y1f8f886l05jkgj8bs78033l2czypvzki5la"))))
|
|
(build-system r-build-system)
|
|
(native-inputs
|
|
`(("r-rcpp" ,r-rcpp)
|
|
("r-rcppeigen" ,r-rcppeigen)))
|
|
(propagated-inputs
|
|
`(("r-lattice" ,r-lattice)
|
|
("r-matrix" ,r-matrix)
|
|
("r-minqa" ,r-minqa)
|
|
("r-nloptr" ,r-nloptr)
|
|
("r-mass" ,r-mass)
|
|
("r-nlme" ,r-nlme)))
|
|
(home-page "http://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 "0.4-7")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "pbkrtest" version))
|
|
(sha256
|
|
(base32
|
|
"1si3bhi59xc51a0pgjjglccq3h4aljyhw2k1b8574s145fnh7fsw"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-lme4" ,r-lme4)
|
|
("r-mass" ,r-mass)
|
|
("r-matrix" ,r-matrix)))
|
|
(home-page "http://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-car
|
|
(package
|
|
(name "r-car")
|
|
(version "2.1-6")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "car" version))
|
|
(sha256
|
|
(base32
|
|
"14l4d9j87xnb0bz2wgqqbxnlnbcdfb5vx2fw6kdxj91kyrk6lhnj"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-mass" ,r-mass)
|
|
("r-mgcv" ,r-mgcv)
|
|
("r-nnet" ,r-nnet)
|
|
("r-pbkrtest" ,r-pbkrtest)
|
|
("r-quantreg" ,r-quantreg)))
|
|
(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-caret
|
|
(package
|
|
(name "r-caret")
|
|
(version "6.0-77")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "caret" version))
|
|
(sha256
|
|
(base32
|
|
"05c504567s2nppzfgi36mhszbym2pr80nf50dgxcxfx030721v5y"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-foreach" ,r-foreach)
|
|
("r-ggplot2" ,r-ggplot2)
|
|
("r-lattice" ,r-lattice)
|
|
("r-modelmetrics" ,r-modelmetrics)
|
|
("r-nlme" ,r-nlme)
|
|
("r-plyr" ,r-plyr)
|
|
("r-recipes" ,r-recipes)
|
|
("r-reshape2" ,r-reshape2)
|
|
("r-withr" ,r-withr)))
|
|
(home-page "https://github.com/topepo/caret")
|
|
(synopsis "Classification and regression training")
|
|
(description
|
|
"This package provides misc functions for training and plotting
|
|
classification and regression models.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-rcppprogress
|
|
(package
|
|
(name "r-rcppprogress")
|
|
(version "0.4")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "RcppProgress" version))
|
|
(sha256
|
|
(base32
|
|
"09ayw6d69i0lplmaj5md25p5hn1nmiyp6a4sh60v93nrrs1cq7iv"))))
|
|
(properties `((upstream-name . "RcppProgress")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-devtools" ,r-devtools)
|
|
("r-rcpp" ,r-rcpp)))
|
|
(home-page "https://github.com/kforner/rcpp_progress")
|
|
(synopsis "Interruptible progress bar for C++ in R packages")
|
|
(description
|
|
"This package allows to display 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-mnormt
|
|
(package
|
|
(name "r-mnormt")
|
|
(version "1.5-5")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "mnormt" version))
|
|
(sha256
|
|
(base32
|
|
"1b34xxrnf35khsx82mhvmk96sgfr2flyasaah7qkb2976pwxay7z"))))
|
|
(build-system r-build-system)
|
|
(native-inputs
|
|
`(("gfortran" ,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")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "numDeriv" version))
|
|
(sha256
|
|
(base32
|
|
"07ni52rwiap4wilfz94w5mrqaxr59axxmgn57857ip4p6qkiss0v"))))
|
|
(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 "1.5-1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "sn" version))
|
|
(sha256
|
|
(base32
|
|
"0l7qlah6dwkp8jswnr2mn3phlm15naba5zkmv0g5pcqy5ix0gz7w"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-mnormt" ,r-mnormt)
|
|
("r-numderiv" ,r-numderiv)))
|
|
(home-page "http://azzalini.stat.unipd.it/SN")
|
|
(synopsis "The skew-normal and skew-t distributions")
|
|
(description
|
|
"This packages 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 "1.3-1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "tclust" version))
|
|
(sha256
|
|
(base32
|
|
"1li62wynv81kb17fx7nk63a26qlb78l8fdf63in8yzcl7fkpji7y"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-cluster" ,r-cluster)
|
|
("r-mclust" ,r-mclust)
|
|
("r-mvtnorm" ,r-mvtnorm)
|
|
("r-sn" ,r-sn)))
|
|
(home-page "http://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 "0.8.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "ranger" version))
|
|
(sha256
|
|
(base32
|
|
"1fdbm879wx3hlng8s4c4f8f2x5yxz57llakcqnpa0lymybidw3vz"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-rcpp" ,r-rcpp)
|
|
("r-matrix" ,r-matrix)
|
|
("r-rcppeigen" ,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")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "tsne" version))
|
|
(sha256
|
|
(base32
|
|
"0s8cv2pndkddq62rzlgzgfdjp1vjv5hz5i5957sllnb97vbzbzb6"))))
|
|
(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 "1.5-9")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "Cairo" version))
|
|
(sha256
|
|
(base32
|
|
"1x1q99r3r978rlkkm5gixkv03p0mcr6k7ydcqdmisrwnmrn7p1ia"))))
|
|
(properties `((upstream-name . "Cairo")))
|
|
(build-system r-build-system)
|
|
(inputs
|
|
`(("cairo" ,cairo)
|
|
("libxt" ,libxt)))
|
|
(native-inputs
|
|
`(("pkg-config" ,pkg-config)))
|
|
(home-page "http://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 "1.7.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "lubridate" version))
|
|
(sha256
|
|
(base32
|
|
"0pzvazzybzvln3y676yims7whsc74g8i7kgf2nsfbxdq5943z349"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-rcpp" ,r-rcpp)
|
|
("r-stringr" ,r-stringr)))
|
|
(home-page
|
|
"http://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 '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 "1.2.15")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "fdrtool" version))
|
|
(sha256
|
|
(base32
|
|
"1h46frlk7d9f4qx0bg6p55nrm9wwwz2sv6d1nz7061wdfsm69yb5"))))
|
|
(build-system r-build-system)
|
|
(home-page "http://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 "0.2.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "forcats" version))
|
|
(sha256
|
|
(base32
|
|
"1mvwkynvvgz2vi8dyz11x7xrp53kadjawjcja34hwk1d89qf7g5m"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-magrittr" ,r-magrittr)
|
|
("r-tibble" ,r-tibble)))
|
|
(home-page "http://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-tgstat
|
|
(let ((changeset "4f8e60c03598f49aff6f5beeab40f2b995377e9f")
|
|
(revision "1"))
|
|
(package
|
|
(name "r-tgstat")
|
|
(version (string-append "1.0.2-" revision "." (string-take changeset 7)))
|
|
(source
|
|
(origin
|
|
(method hg-fetch)
|
|
(uri (hg-reference
|
|
(url "https://bitbucket.org/tanaylab/tgstat")
|
|
(changeset changeset)))
|
|
(sha256
|
|
(base32
|
|
"0ilkkyximy77zbncm91kdfqbxf0qyndg16pd3q3p6a3xc9qcmxvn"))))
|
|
(build-system r-build-system)
|
|
(arguments
|
|
`(#:phases
|
|
(modify-phases %standard-phases
|
|
(add-after 'unpack 'fix-isnan
|
|
(lambda _
|
|
(substitute* "src/tgstat.h"
|
|
(("#define isnan ::isnan")
|
|
"#define isnan std::isnan"))
|
|
#t)))))
|
|
(propagated-inputs
|
|
`(("r-rcpp" ,r-rcpp)))
|
|
(home-page "https://bitbucket.org/tanaylab/tgstat/")
|
|
(synopsis "Tanay's group statistical utilities")
|
|
(description
|
|
"The goal of tgstat is to provide fast and efficient statistical
|
|
tools.")
|
|
(license license:gpl2))))
|
|
|
|
(define-public r-tgconfig
|
|
(let ((changeset "1e02c7614713bd0866c46f0c679a058f8c6d627e")
|
|
(revision "1"))
|
|
(package
|
|
(name "r-tgconfig")
|
|
(version (string-append "0.0.0.9000-" revision "." (string-take changeset 7)))
|
|
(source
|
|
(origin
|
|
(method hg-fetch)
|
|
(uri (hg-reference
|
|
(url "https://bitbucket.org/tanaylab/tgconfig")
|
|
(changeset changeset)))
|
|
(sha256
|
|
(base32
|
|
"0xy6c7s7mn1yx191154bwbv1bl424bnvc80syqpl1vdl28ba46rj"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-yaml" ,r-yaml)))
|
|
(home-page "https://bitbucket.org/tanaylab/tgconfig/")
|
|
(synopsis "Infrastructure for managing package parameters")
|
|
(description
|
|
"The goal of tgconfig is to provide infrastructure for managing package
|
|
parameters.")
|
|
(license license:gpl3))))
|
|
|
|
(define-public r-directlabels
|
|
(package
|
|
(name "r-directlabels")
|
|
(version "2017.03.31")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "directlabels" version))
|
|
(sha256
|
|
(base32
|
|
"01ahw0c56mnzwl611s8hnghicww4c4dgf5v2wv6bl1s1pramw9pr"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-quadprog" ,r-quadprog)))
|
|
(home-page "http://directlabels.r-forge.r-project.org/")
|
|
(synopsis "Direct labels for multicolor plots")
|
|
(description
|
|
"This package provides an extensible framework for automatically placing
|
|
direct labels onto multicolor plots. Label positions are described using
|
|
positioning methods that can be re-used across several different plots. There
|
|
are heuristics for examining @code{trellis} and @code{ggplot} objects and
|
|
inferring an appropriate positioning method.")
|
|
(license license:gpl3)))
|