gnu/packages/statistics.scm

   1 ;;; GNU Guix --- Functional package management for GNU
   2 ;;; Copyright © 2015, 2016, 2017, 2018, 2019 Ricardo Wurmus <rekado@elephly.net>
   3 ;;; Copyright © 2015 Vicente Vera Parra <vicentemvp@gmail.com>
   4 ;;; Copyright © 2016 Andreas Enge <andreas@enge.fr>
   5 ;;; Copyright © 2016, 2017, 2019 Efraim Flashner <efraim@flashner.co.il>
   6 ;;; Copyright © 2016 Pjotr Prins <pjotr.guix@thebird.nl>
   7 ;;; Copyright © 2016 Roel Janssen <roel@gnu.org>
   8 ;;; Copyright © 2016 Ben Woodcroft <donttrustben@gmail.com>
   9 ;;; Copyright © 2016, 2017 Raoul Bonnal <ilpuccio.febo@gmail.com>
  10 ;;; Copyright © 2017 Kyle Meyer <kyle@kyleam.com>
  11 ;;; Copyright © 2017, 2018, 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
  12 ;;; Copyright © 2017 Alex Kost <alezost@gmail.com>
  13 ;;; Copyright © 2018 Alex Branham <alex.branham@gmail.com>
  14 ;;;
  15 ;;; This file is part of GNU Guix.
  16 ;;;
  17 ;;; GNU Guix is free software; you can redistribute it and/or modify it
  18 ;;; under the terms of the GNU General Public License as published by
  19 ;;; the Free Software Foundation; either version 3 of the License, or (at
  20 ;;; your option) any later version.
  21 ;;;
  22 ;;; GNU Guix is distributed in the hope that it will be useful, but
  23 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
  24 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  25 ;;; GNU General Public License for more details.
  26 ;;;
  27 ;;; You should have received a copy of the GNU General Public License
  28 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
  29
  30 (define-module (gnu packages statistics)
  31   #:use-module ((guix licenses) #:prefix license:)
  32   #:use-module (guix packages)
  33   #:use-module (guix download)
  34   #:use-module (guix hg-download)
  35   #:use-module (guix git-download)
  36   #:use-module (guix utils)
  37   #:use-module (guix build-system ant)
  38   #:use-module (guix build-system gnu)
  39   #:use-module (guix build-system r)
  40   #:use-module (guix build-system python)
  41   #:use-module (guix build-system trivial)
  42   #:use-module (gnu packages)
  43   #:use-module (gnu packages algebra)
  44   #:use-module (gnu packages autotools)
  45   #:use-module (gnu packages bash)
  46   #:use-module (gnu packages check)
  47   #:use-module (gnu packages compression)
  48   #:use-module (gnu packages cran)
  49   #:use-module (gnu packages curl)
  50   #:use-module (gnu packages emacs)
  51   #:use-module (gnu packages emacs-xyz)
  52   #:use-module (gnu packages fontutils)
  53   #:use-module (gnu packages gcc)
  54   #:use-module (gnu packages gtk)
  55   #:use-module (gnu packages gettext)
  56   #:use-module (gnu packages glib)
  57   #:use-module (gnu packages haskell-xyz)
  58   #:use-module (gnu packages icu4c)
  59   #:use-module (gnu packages image)
  60   #:use-module (gnu packages java)
  61   #:use-module (gnu packages libffi)
  62   #:use-module (gnu packages machine-learning)
  63   #:use-module (gnu packages maths)
  64   #:use-module (gnu packages multiprecision)
  65   #:use-module (gnu packages pcre)
  66   #:use-module (gnu packages perl)
  67   #:use-module (gnu packages pkg-config)
  68   #:use-module (gnu packages python)
  69   #:use-module (gnu packages python-science)
  70   #:use-module (gnu packages python-xyz)
  71   #:use-module (gnu packages readline)
  72   #:use-module (gnu packages sphinx)
  73   #:use-module (gnu packages ssh)
  74   #:use-module (gnu packages tcl)
  75   #:use-module (gnu packages tex)
  76   #:use-module (gnu packages texinfo)
  77   #:use-module (gnu packages time)
  78   #:use-module (gnu packages tls)
  79   #:use-module (gnu packages base)
  80   #:use-module (gnu packages version-control)
  81   #:use-module (gnu packages web)
  82   #:use-module (gnu packages xml)
  83   #:use-module (gnu packages xorg)
  84   #:use-module (srfi srfi-1))
  85
  86
  87 (define-public pspp
  88   (package
  89     (name "pspp")
  90     (version "1.2.0")
  91     (source
  92      (origin
  93       (method url-fetch)
  94       (uri (string-append "mirror://gnu/pspp/pspp-"
  95                           version ".tar.gz"))
  96       (sha256
  97        (base32
  98         "07pp27zycrb5x927jwaj9r3q7hy915jh51xs85zxby6gfiwl63m5"))))
  99     (build-system gnu-build-system)
 100     (inputs
 101      `(("cairo" ,cairo)
 102        ("gettext" ,gettext-minimal)
 103        ("gsl" ,gsl)
 104        ("libxml2" ,libxml2)
 105        ("pango" ,pango)
 106        ("readline" ,readline)
 107        ("gtk" ,gtk+)
 108        ("gtksourceview" ,gtksourceview)
 109        ("spread-sheet-widget" ,spread-sheet-widget)
 110        ("zlib" ,zlib)))
 111     (native-inputs
 112      `(("autoconf" ,autoconf)           ;for tests
 113        ("glib" ,glib "bin")             ;for glib-genmarshal
 114        ("perl" ,perl)
 115        ("pkg-config" ,pkg-config)
 116        ("python" ,python-2)             ;for tests
 117        ("texinfo" ,texinfo)))
 118     (home-page "https://www.gnu.org/software/pspp/")
 119     (synopsis "Statistical analysis")
 120     (description
 121      "GNU PSPP is a statistical analysis program.  It can perform
 122 descriptive statistics, T-tests, linear regression and non-parametric tests.
 123 It features both a graphical interface as well as command-line input.  PSPP
 124 is designed to interoperate with Gnumeric, LibreOffice and OpenOffice.  Data
 125 can be imported from spreadsheets, text files and database sources and it can
 126 be output in text, PostScript, PDF or HTML.")
 127     (license license:gpl3+)))
 128
 129 (define-public jags
 130   (package
 131     (name "jags")
 132     (version "4.3.0")
 133     (source (origin
 134               (method url-fetch)
 135               (uri (string-append "mirror://sourceforge/mcmc-jags/JAGS/"
 136                                   (version-major version) ".x/Source/"
 137                                   "JAGS-" version ".tar.gz"))
 138               (sha256
 139                (base32
 140                 "1z3icccg2ic56vmhyrpinlsvpq7kcaflk1731rgpvz9bk1bxvica"))))
 141     (build-system gnu-build-system)
 142     (home-page "http://mcmc-jags.sourceforge.net/")
 143     (native-inputs
 144      `(("gfortran" ,gfortran)
 145        ("lapack" ,lapack)))
 146     (synopsis "Gibbs sampler")
 147     (description "JAGS is Just Another Gibbs Sampler.  It is a program for
 148 analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC)
 149 simulation not wholly unlike BUGS.  JAGS was written with three aims in mind:
 150
 151 @enumerate
 152 @item To have a cross-platform engine for the BUGS language;
 153 @item To be extensible, allowing users to write their own functions,
 154   distributions and samplers;
 155 @item To be a platform for experimentation with ideas in Bayesian modelling.
 156 @end enumerate\n")
 157     (license license:gpl2)))
 158
 159 (define-public libxls
 160   (package
 161     (name "libxls")
 162     (version "1.5.2")
 163     (source
 164      (origin
 165        (method url-fetch)
 166        (uri (string-append "https://github.com/libxls/libxls/releases/download/"
 167                            "v" version "/libxls-" version ".tar.gz"))
 168        (sha256
 169         (base32 "1akadsyl10rp101ccjmrxr7933c3v641k377bn74jv6cdkcm4zld"))))
 170     (build-system gnu-build-system)
 171     (home-page "https://github.com/libxls/libxls")
 172     (synopsis "Read binary (.xls) Excel spreadsheet files")
 173     (description
 174      "libxls is a C library to read .xls spreadsheet files in the binary OLE
 175 BIFF8 format as created by Excel 97 and later versions.  It cannot write them.
 176
 177 This package also provides @command{xls2csv} to export Excel files to CSV.")
 178     (license license:bsd-2)))
 179
 180 ;; Update this package together with the set of recommended packages: r-boot,
 181 ;; r-class, r-cluster, r-codetools, r-foreign, r-kernsmooth, r-lattice,
 182 ;; r-mass, r-matrix, r-mgcv, r-nlme, r-nnet, r-rpart, r-spatial, r-survival.
 183 (define r-with-tests
 184   (package
 185     (name "r-with-tests")
 186     (version "3.6.2")
 187     (source (origin
 188               (method url-fetch)
 189               (uri (string-append "mirror://cran/src/base/R-"
 190                                   (version-major version) "/R-"
 191                                   version ".tar.gz"))
 192               (sha256
 193                (base32
 194                 "0m69pfi0nxyriyb2yz74xfzaxwfkinnf9kpvf1rz727vvmfa8rdx"))))
 195     (build-system gnu-build-system)
 196     (arguments
 197      `(#:disallowed-references (,tzdata-for-tests)
 198        #:make-flags
 199        (list (string-append "LDFLAGS=-Wl,-rpath="
 200                             (assoc-ref %outputs "out")
 201                             "/lib/R/lib")
 202              ;; This affects the embedded timestamp of only the core packages.
 203              "PKG_BUILT_STAMP=1970-01-01")
 204        #:phases
 205        (modify-phases %standard-phases
 206          (add-before 'configure 'do-not-compress-serialized-files
 207            (lambda* (#:key inputs #:allow-other-keys)
 208              ;; This ensures that Guix can detect embedded store references;
 209              ;; see bug #28157 for details.
 210              (substitute* "src/library/base/makebasedb.R"
 211                (("compress = TRUE") "compress = FALSE"))
 212              #t))
 213          (add-before 'configure 'patch-uname
 214            (lambda* (#:key inputs #:allow-other-keys)
 215              (let ((uname-bin (string-append (assoc-ref inputs "coreutils")
 216                                              "/bin/uname")))
 217                (substitute* "src/scripts/R.sh.in"
 218                  (("uname") uname-bin)))
 219              #t))
 220          (add-after 'unpack 'build-reproducibly
 221            (lambda _
 222              ;; The documentation contains time stamps to demonstrate
 223              ;; documentation generation in different phases.
 224              (substitute* "src/library/tools/man/Rd2HTML.Rd"
 225                (("\\\\%Y-\\\\%m-\\\\%d at \\\\%H:\\\\%M:\\\\%S")
 226                 "(removed for reproducibility)"))
 227
 228              ;; Remove timestamp from tracing environment.  This fixes
 229              ;; reproducibility of "methods.rd{b,x}".
 230              (substitute* "src/library/methods/R/trace.R"
 231                (("dateCreated = Sys.time\\(\\)")
 232                 "dateCreated = as.POSIXct(\"1970-1-1 00:00:00\", tz = \"UTC\")"))
 233
 234              ;; Ensure that gzipped files are reproducible.
 235              (substitute* '("src/library/grDevices/Makefile.in"
 236                             "doc/manual/Makefile.in")
 237                (("R_GZIPCMD\\)" line)
 238                 (string-append line " -n")))
 239
 240              ;; The "srcfile" procedure in "src/library/base/R/srcfile.R"
 241              ;; queries the mtime of a given file and records it in an object.
 242              ;; This is acceptable at runtime to detect stale source files,
 243              ;; but it destroys reproducibility at build time.
 244
 245              ;; Similarly, the "srcfilecopy" procedure records the current
 246              ;; time.  We change both of them to respect SOURCE_DATE_EPOCH.
 247              (substitute* "src/library/base/R/srcfile.R"
 248                (("timestamp <- (timestamp.*|file.mtime.*)" _ time)
 249                 (string-append "timestamp <- \
 250 as.POSIXct(if (\"\" != Sys.getenv(\"SOURCE_DATE_EPOCH\")) {\
 251   as.numeric(Sys.getenv(\"SOURCE_DATE_EPOCH\"))\
 252 } else { " time "}, origin=\"1970-01-01\")\n")))
 253
 254              ;; This library is installed using "install_package_description",
 255              ;; so we need to pass the "builtStamp" argument.
 256              (substitute* "src/library/tools/Makefile.in"
 257                (("(install_package_description\\(.*\"')\\)\"" line prefix)
 258                 (string-append prefix ", builtStamp='1970-01-01')\"")))
 259
 260              (substitute* "src/library/Recommended/Makefile.in"
 261                (("INSTALL_OPTS =" m)
 262                 (string-append m " --built-timestamp=1970-01-01" m)))
 263
 264              ;; R bundles an older version of help2man, which does not respect
 265              ;; SOURCE_DATE_EPOCH.  We cannot just use the latest help2man,
 266              ;; because that breaks a test.
 267              (with-fluids ((%default-port-encoding "ISO-8859-1"))
 268                (substitute* "tools/help2man.pl"
 269                  (("my \\$date = strftime \"%B %Y\", localtime" line)
 270                   (string-append line " 1"))))
 271              #t))
 272          (add-before 'configure 'set-default-pager
 273           ;; Set default pager to "cat", because otherwise it is "false",
 274           ;; making "help()" print nothing at all.
 275           (lambda _ (setenv "PAGER" "cat") #t))
 276          (add-before 'check 'set-timezone
 277            ;; Some tests require the timezone to be set.  However, the
 278            ;; timezone may not just be "UTC", or else a brittle regression
 279            ;; test in reg-tests-1d will fail.
 280            (lambda* (#:key inputs #:allow-other-keys)
 281              (setenv "TZ" "UTC+1")
 282              (setenv "TZDIR"
 283                      (string-append (assoc-ref inputs "tzdata")
 284                                     "/share/zoneinfo"))
 285              #t))
 286          (add-after 'build 'make-info
 287           (lambda _ (invoke "make" "info")))
 288          (add-after 'build 'install-info
 289           (lambda _ (invoke "make" "install-info"))))
 290        #:configure-flags
 291        `(;; We build the recommended packages here, because they are needed in
 292          ;; order to run the test suite.  We disable them in the r-minimal
 293          ;; package.
 294          "--with-cairo"
 295          "--with-blas=-lopenblas"
 296          "--with-libpng"
 297          "--with-jpeglib"
 298          "--with-libtiff"
 299          "--with-ICU"
 300          "--with-tcltk"
 301          ,(string-append "--with-tcl-config="
 302                          (assoc-ref %build-inputs "tcl")
 303                          "/lib/tclConfig.sh")
 304          ,(string-append "--with-tk-config="
 305                          (assoc-ref %build-inputs "tk")
 306                          "/lib/tkConfig.sh")
 307          "--enable-R-shlib"
 308          "--enable-BLAS-shlib"
 309          "--with-system-tre")))
 310     ;; R has some support for Java.  When the JDK is available at configure
 311     ;; time environment variables pointing to the JDK will be recorded under
 312     ;; $R_HOME/etc and ./tools/getsp.java will be compiled which is used by "R
 313     ;; CMD javareconf".  "R CMD javareconf" appears to only be used to update
 314     ;; the recorded environment variables in $R_HOME/etc.  Refer to
 315     ;; https://cran.r-project.org/doc/manuals/r-release/R-admin.html#Java-support
 316     ;; for additional information.
 317
 318     ;; As the JDK is a rather large input with only very limited effects on R,
 319     ;; we decided to drop it.
 320     (native-inputs
 321      `(("bzip2" ,bzip2)
 322        ("perl" ,perl)
 323        ("pkg-config" ,pkg-config)
 324        ("texinfo" ,texinfo) ; for building HTML manuals
 325        ("texlive" ,(texlive-union (list texlive-fonts-ec
 326                                         texlive-amsfonts
 327                                         texlive-latex-base
 328                                         texlive-latex-fancyvrb
 329                                         texlive-latex-graphics
 330                                         texlive-latex-hyperref
 331                                         texlive-latex-oberdiek
 332                                         texlive-latex-tools
 333                                         texlive-latex-upquote
 334                                         texlive-latex-url)))
 335        ("tzdata" ,tzdata-for-tests)
 336        ("xz" ,xz)))
 337     (inputs
 338      `(;; We need not only cairo here, but pango to ensure that tests for the
 339        ;; "cairo" bitmapType plotting backend succeed.
 340        ("pango" ,pango)
 341        ("coreutils" ,coreutils)
 342        ("curl" ,curl)
 343        ("openblas" ,openblas)
 344        ("gfortran" ,gfortran)
 345        ("icu4c" ,icu4c)
 346        ("libjpeg" ,libjpeg)
 347        ("libpng" ,libpng)
 348        ("libtiff" ,libtiff)
 349        ("libxt" ,libxt)
 350        ("pcre" ,pcre)
 351        ("readline" ,readline)
 352        ;; This avoids a reference to the ungraftable static bash.  R uses the
 353        ;; detected shell for the "system" procedure.
 354        ("bash" ,bash-minimal)
 355        ("tcl" ,tcl)
 356        ("tk" ,tk)
 357        ("which" ,which)
 358        ("zlib" ,zlib)))
 359     (native-search-paths
 360      (list (search-path-specification
 361             (variable "R_LIBS_SITE")
 362             (files (list "site-library/")))))
 363     (home-page "https://www.r-project.org/")
 364     (synopsis "Environment for statistical computing and graphics")
 365     (description
 366      "R is a language and environment for statistical computing and graphics.
 367 It provides a variety of statistical techniques, such as linear and nonlinear
 368 modeling, classical statistical tests, time-series analysis, classification
 369 and clustering.  It also provides robust support for producing
 370 publication-quality data plots.  A large amount of 3rd-party packages are
 371 available, greatly increasing its breadth and scope.")
 372     (license license:gpl3+)))
 373
 374 (define-public r-minimal
 375   (package (inherit r-with-tests)
 376     (name "r-minimal")
 377     (arguments
 378      `(#:tests? #f
 379        ,@(substitute-keyword-arguments (package-arguments r-with-tests)
 380            ((#:configure-flags flags)
 381             ;; Do not build the recommended packages.  The build system creates
 382             ;; random temporary directories and embeds their names in some
 383             ;; package files.  We build these packages with the r-build-system
 384             ;; instead.
 385             `(cons "--without-recommended-packages" ,flags)))))))
 386
 387 (define-public rmath-standalone
 388   (package (inherit r-minimal)
 389     (name "rmath-standalone")
 390     (arguments
 391      '(#:phases
 392        (modify-phases %standard-phases
 393          (add-after 'configure 'chdir
 394            (lambda _ (chdir "src/nmath/standalone/") #t)))))
 395     (synopsis "Standalone R math library")
 396     (description
 397      "This package provides the R math library as an independent package.")))
 398
 399 (define-public r-boot
 400   (package
 401     (name "r-boot")
 402     (version "1.3-24")
 403     (source
 404      (origin
 405        (method url-fetch)
 406        (uri (cran-uri "boot" version))
 407        (sha256
 408         (base32
 409          "0yv0l55kjmlfdx1xhgyjdi0bskxhfal74wr5jxaib1qj99nmkm49"))))
 410     (build-system r-build-system)
 411     (home-page "https://cran.r-project.org/web/packages/boot")
 412     (synopsis "Bootstrap functions for R")
 413     (description
 414      "This package provides functions and datasets for bootstrapping from the
 415 book \"Bootstrap Methods and Their Application\" by A.C. Davison and
 416 D.V. Hinkley (1997, CUP), originally written by Angelo Canty for S.")
 417     ;; Unlimited distribution
 418     (license (license:non-copyleft "file://R/bootfuns.q"))))
 419
 420 (define-public r-mass
 421   (package
 422     (name "r-mass")
 423     (version "7.3-51.5")
 424     (source
 425      (origin
 426        (method url-fetch)
 427        (uri (cran-uri "MASS" version))
 428        (sha256
 429         (base32
 430          "1k0m7pa4gb5apzrrkb5kx5d7bmkm2pl5g15vwb6j067hrqahck26"))))
 431     (properties `((upstream-name . "MASS")))
 432     (build-system r-build-system)
 433     (home-page "http://www.stats.ox.ac.uk/pub/MASS4/")
 434     (synopsis "Support functions and datasets for Venables and Ripley's MASS")
 435     (description
 436      "This package provides functions and datasets for the book \"Modern
 437 Applied Statistics with S\" (4th edition, 2002) by Venables and Ripley.")
 438     ;; Either version may be picked.
 439     (license (list license:gpl2 license:gpl3))))
 440
 441 (define-public r-class
 442   (package
 443     (name "r-class")
 444     (version "7.3-15")
 445     (source
 446      (origin
 447        (method url-fetch)
 448        (uri (cran-uri "class" version))
 449        (sha256
 450         (base32
 451          "1x1hqz8xyhbpq4krsh02glqnlzcch25agkmn4a3da9n723b37gzn"))))
 452     (build-system r-build-system)
 453     (propagated-inputs
 454      `(("r-mass" ,r-mass)))
 455     (home-page "http://www.stats.ox.ac.uk/pub/MASS4/")
 456     (synopsis "R functions for classification")
 457     (description
 458      "This package provides various functions for classification, including
 459 k-nearest neighbour, Learning Vector Quantization and Self-Organizing Maps.")
 460     ;; Either of the two versions can be picked.
 461     (license (list license:gpl2 license:gpl3))))
 462
 463 (define-public r-cluster
 464   (package
 465     (name "r-cluster")
 466     (version "2.1.0")
 467     (source
 468      (origin
 469        (method url-fetch)
 470        (uri (cran-uri "cluster" version))
 471        (sha256
 472         (base32
 473          "055af3yz2biqbsbwm4arwr1yqnj4gicpzv2i6dbfl5pnz2z5byga"))))
 474     (build-system r-build-system)
 475     (native-inputs
 476      `(("gfortran" ,gfortran)))
 477     (home-page "https://cran.r-project.org/web/packages/cluster")
 478     (synopsis "Methods for cluster analysis")
 479     (description
 480      "This package provides methods for cluster analysis.  It is a much
 481 extended version of the original from Peter Rousseeuw, Anja Struyf and Mia
 482 Hubert, based on Kaufman and Rousseeuw (1990) \"Finding Groups in Data\".")
 483     (license license:gpl2+)))
 484
 485 (define-public r-codetools
 486   (package
 487     (name "r-codetools")
 488     (version "0.2-16")
 489     (source
 490      (origin
 491        (method url-fetch)
 492        (uri (cran-uri "codetools" version))
 493        (sha256
 494         (base32
 495          "00bmhzqprqfn3w6ghx7sakai6s7il8gbksfiawj8in5mbhbncypn"))))
 496     (build-system r-build-system)
 497     (home-page "https://cran.r-project.org/web/packages/codetools")
 498     (synopsis "Code analysis tools for R")
 499     (description "This package provides code analysis tools for R to check R
 500 code for possible problems.")
 501     ;; Any version of the GPL.
 502     (license (list license:gpl2+ license:gpl3+))))
 503
 504 (define-public r-foreign
 505   (package
 506     (name "r-foreign")
 507     (version "0.8-75")
 508     (source
 509      (origin
 510        (method url-fetch)
 511        (uri (cran-uri "foreign" version))
 512        (sha256
 513         (base32
 514          "0g4mi101srjbl17ydb2hl3854m3xj0llj6861lfr30sp08nkqavl"))))
 515     (build-system r-build-system)
 516     (home-page "https://cran.r-project.org/web/packages/foreign")
 517     (synopsis "Read data stored by other statistics software")
 518     (description
 519      "This package provides functions for reading and writing data stored by
 520 some versions of Epi Info, Minitab, S, SAS, SPSS, Stata, Systat and Weka and
 521 for reading and writing some dBase files.")
 522     (license license:gpl2+)))
 523
 524 (define-public r-kernsmooth
 525   (package
 526     (name "r-kernsmooth")
 527     (version "2.23-16")
 528     (source
 529      (origin
 530        (method url-fetch)
 531        (uri (cran-uri "KernSmooth" version))
 532        (sha256
 533         (base32
 534          "1acrkbdn3a74y4dndkcdl1njnpfqz7gk3bsz03g8lfj8l7z53hmq"))))
 535     (properties `((upstream-name . "KernSmooth")))
 536     (build-system r-build-system)
 537     (native-inputs
 538      `(("gfortran" ,gfortran)))
 539     (home-page "https://cran.r-project.org/web/packages/KernSmooth")
 540     (synopsis "Functions for kernel smoothing")
 541     (description
 542      "This package provides functions for kernel smoothing (and density
 543 estimation) corresponding to the book: Wand, M.P. and Jones, M.C. (1995)
 544 \"Kernel Smoothing\".")
 545     ;; Unlimited use and distribution
 546     (license (license:non-copyleft "file://LICENCE.note"))))
 547
 548 (define-public r-lattice
 549   (package
 550     (name "r-lattice")
 551     (version "0.20-38")
 552     (source (origin
 553               (method url-fetch)
 554               (uri (cran-uri "lattice" version))
 555               (sha256
 556                (base32
 557                 "0b8abkz7syscq883mrgv63pkwaqkcpwfx8rgbqy9vgfva0z5xszx"))))
 558     (build-system r-build-system)
 559     (home-page "http://lattice.r-forge.r-project.org/")
 560     (synopsis "High-level data visualization system")
 561     (description
 562      "The lattice package provides a powerful and elegant high-level data
 563 visualization system inspired by Trellis graphics, with an emphasis on
 564 multivariate data.  Lattice is sufficient for typical graphics needs, and is
 565 also flexible enough to handle most nonstandard requirements.")
 566     (license license:gpl2+)))
 567
 568 (define-public r-matrix
 569   (package
 570     (name "r-matrix")
 571     (version "1.2-18")
 572     (source
 573      (origin
 574        (method url-fetch)
 575        (uri (cran-uri "Matrix" version))
 576        (sha256
 577         (base32
 578          "06b1rc1vq65b271f2wpzhqkvhng8hwwnvjflzxkng50i52603zzp"))))
 579     (properties `((upstream-name . "Matrix")))
 580     (build-system r-build-system)
 581     (propagated-inputs
 582      `(("r-lattice" ,r-lattice)))
 583     (home-page "http://Matrix.R-forge.R-project.org/")
 584     (synopsis "Sparse and dense matrix classes and methods")
 585     (description
 586      "This package provides classes and methods for dense and sparse matrices
 587 and operations on them using LAPACK and SuiteSparse.")
 588     (license license:gpl2+)))
 589
 590 (define-public r-nlme
 591   (package
 592     (name "r-nlme")
 593     (version "3.1-143")
 594     (source
 595      (origin
 596        (method url-fetch)
 597        (uri (cran-uri "nlme" version))
 598        (sha256
 599         (base32 "13iixbs2ibldc75rl7rav5n5kx33zwm33xnfw1yvlkpcqf38bd22"))))
 600     (build-system r-build-system)
 601     (propagated-inputs
 602      `(("r-lattice" ,r-lattice)))
 603     (native-inputs
 604      `(("gfortran" ,gfortran)))
 605     (home-page "https://cran.r-project.org/web/packages/nlme")
 606     (synopsis "Linear and nonlinear mixed effects models")
 607     (description
 608      "This package provides tools to fit and compare Gaussian linear and
 609 nonlinear mixed-effects models.")
 610     (license license:gpl2+)))
 611
 612 (define-public r-mgcv
 613   (package
 614    (name "r-mgcv")
 615    (version "1.8-31")
 616    (source
 617     (origin
 618      (method url-fetch)
 619      (uri (cran-uri "mgcv" version))
 620      (sha256
 621       (base32 "1if34mqsn9r7g0l82lxvvx0wjhi9paqdymyd73nschxcl1if8vbk"))))
 622    (build-system r-build-system)
 623    (propagated-inputs
 624     `(("r-matrix" ,r-matrix)
 625       ("r-nlme" ,r-nlme)))
 626    (home-page "https://cran.r-project.org/web/packages/mgcv")
 627    (synopsis "Mixed generalised additive model computation")
 628    (description
 629     "GAMs, GAMMs and other generalized ridge regression with multiple smoothing
 630 parameter estimation by GCV, REML or UBRE/AIC.  The library includes a
 631 @code{gam()} function, a wide variety of smoothers, JAGS support and
 632 distributions beyond the exponential family.")
 633    (license license:gpl2+)))
 634
 635 (define-public r-nnet
 636   (package
 637     (name "r-nnet")
 638     (version "7.3-12")
 639     (source
 640      (origin
 641        (method url-fetch)
 642        (uri (cran-uri "nnet" version))
 643        (sha256
 644         (base32
 645          "17amqnw9dpap2w8ivx53hxha2xrm0drwfnj32li0xk41hlz548r7"))))
 646     (build-system r-build-system)
 647     (home-page "http://www.stats.ox.ac.uk/pub/MASS4/")
 648     (synopsis "Feed-forward neural networks and multinomial log-linear models")
 649     (description
 650      "This package provides functions for feed-forward neural networks with a
 651 single hidden layer, and for multinomial log-linear models.")
 652     (license (list license:gpl2+ license:gpl3+))))
 653
 654 (define-public r-rpart
 655   (package
 656     (name "r-rpart")
 657     (version "4.1-15")
 658     (source
 659      (origin
 660        (method url-fetch)
 661        (uri (cran-uri "rpart" version))
 662        (sha256
 663         (base32
 664          "0p5frya963ppn476p5dxs2mnarsalksr6gw9zzmjsn8ikq7bx3ib"))))
 665     (build-system r-build-system)
 666     (home-page "https://cran.r-project.org/web/packages/rpart")
 667     (synopsis "Recursive partitioning and regression trees")
 668     (description
 669      "This package provides recursive partitioning functions for
 670 classification, regression and survival trees.")
 671     (license (list license:gpl2+ license:gpl3+))))
 672
 673 (define-public r-spatial
 674   (package
 675     (name "r-spatial")
 676     (version "7.3-11")
 677     (source
 678      (origin
 679        (method url-fetch)
 680        (uri (cran-uri "spatial" version))
 681        (sha256
 682         (base32
 683          "04aw8j533sn63ybyrf4hyhrqm4058vfcb7yhjy07kq92mk94hi32"))))
 684     (build-system r-build-system)
 685     (home-page "http://www.stats.ox.ac.uk/pub/MASS4/")
 686     (synopsis "Functions for kriging and point pattern analysis")
 687     (description
 688      "This package provides functions for kriging and point pattern
 689 analysis.")
 690     ;; Either version may be picked.
 691     (license (list license:gpl2 license:gpl3))))
 692
 693 (define-public r-survival
 694   (package
 695     (name "r-survival")
 696     (version "3.1-8")
 697     (source
 698      (origin
 699        (method url-fetch)
 700        (uri (cran-uri "survival" version))
 701        (sha256
 702         (base32
 703          "15fj4y8c107bwq22amx88r5hw7qndlcbr9sapzrpkpr7iqz3kkyf"))))
 704     (build-system r-build-system)
 705     (propagated-inputs
 706      `(("r-matrix" ,r-matrix)))
 707     (home-page "https://github.com/therneau/survival")
 708     (synopsis "Survival analysis")
 709     (description
 710      "This package contains the core survival analysis routines, including
 711 definition of Surv objects, Kaplan-Meier and Aalen-Johansen (multi-state)
 712 curves, Cox models, and parametric accelerated failure time models.")
 713     (license license:lgpl2.0+)))
 714
 715 (define-public r
 716   (package (inherit r-minimal)
 717     (name "r")
 718     (source #f)
 719     (build-system trivial-build-system)
 720     (arguments '(#:builder (begin (mkdir %output) #t)))
 721     (propagated-inputs
 722      `(("r-minimal" ,r-minimal)
 723        ("r-boot" ,r-boot)
 724        ("r-class" ,r-class)
 725        ("r-cluster" ,r-cluster)
 726        ("r-codetools" ,r-codetools)
 727        ("r-foreign" ,r-foreign)
 728        ("r-kernsmooth" ,r-kernsmooth)
 729        ("r-lattice" ,r-lattice)
 730        ("r-mass" ,r-mass)
 731        ("r-matrix" ,r-matrix)
 732        ("r-mgcv" ,r-mgcv)
 733        ("r-nlme" ,r-nlme)
 734        ("r-nnet" ,r-nnet)
 735        ("r-rpart" ,r-rpart)
 736        ("r-spatial" ,r-spatial)
 737        ("r-survival" ,r-survival)))))
 738
 739 (define-public r-bit
 740   (package
 741     (name "r-bit")
 742     (version "1.1-15.1")
 743     (source
 744      (origin
 745        (method url-fetch)
 746        (uri (cran-uri "bit" version))
 747        (sha256
 748         (base32
 749          "0y351ajlrn9ywbiai46mjpwmw5pqc9ik2z24rf0bnbdcvaxdr7r8"))))
 750     (build-system r-build-system)
 751     (home-page "http://ff.r-forge.r-project.org")
 752     (synopsis "Class for vectors of 1-bit booleans")
 753     (description
 754      "This package provides bitmapped vectors of booleans (no @code{NA}s),
 755 coercion from and to logicals, integers and integer subscripts, fast boolean
 756 operators and fast summary statistics.  With @code{bit} class vectors of true
 757 binary booleans, @code{TRUE} and @code{FALSE} can be stored with 1 bit only.")
 758     (license license:gpl2)))
 759
 760 (define-public r-bit64
 761   (package
 762     (name "r-bit64")
 763     (version "0.9-7")
 764     (source
 765      (origin
 766        (method url-fetch)
 767        (uri (cran-uri "bit64" version))
 768        (sha256
 769         (base32
 770          "07znvz9vp1nz1y5ljng4qyskvm943cdbmy996s67560ijxzsm6kv"))))
 771     (build-system r-build-system)
 772     (propagated-inputs
 773      `(("r-bit" ,r-bit)))
 774     (home-page "http://ff.r-forge.r-project.org/")
 775     (synopsis "S3 class for vectors of 64 bit integers")
 776     (description
 777      "The bit64 package provides serializable S3 atomic 64 bit (signed)
 778 integers that can be used in vectors, matrices, arrays and @code{data.frames}.
 779 Methods are available for coercion from and to logicals, integers, doubles,
 780 characters and factors as well as many elementwise and summary functions.
 781 Many fast algorithmic operations such as @code{match} and @code{order} support
 782 interactive data exploration and manipulation and optionally leverage
 783 caching.")
 784     (license license:gpl2)))
 785
 786 (define-public r-dichromat
 787   (package
 788     (name "r-dichromat")
 789     (version "2.0-0")
 790     (source
 791      (origin
 792        (method url-fetch)
 793        (uri (cran-uri "dichromat" version))
 794        (sha256
 795         (base32 "1l8db1nk29ccqg3mkbafvfiw0775iq4gapysf88xq2zp6spiw59i"))))
 796     (build-system r-build-system)
 797     (home-page "https://cran.r-project.org/web/packages/dichromat")
 798     (synopsis "Color schemes for dichromats")
 799     (description
 800      "Dichromat collapses red-green or green-blue distinctions to simulate the
 801 effects of different types of color-blindness.")
 802     (license license:gpl2+)))
 803
 804 (define-public r-digest
 805   (package
 806     (name "r-digest")
 807     (version "0.6.23")
 808     (source
 809      (origin
 810        (method url-fetch)
 811        (uri (cran-uri "digest" version))
 812        (sha256
 813         (base32 "18h5s8vkdcz2vhpsx6g3ig00zalrihr03skn95zw3lr2y56pafmp"))))
 814     (build-system r-build-system)
 815     ;; Vignettes require r-knitr, which requires r-digest, so we have to
 816     ;; disable them and the tests.
 817     (arguments
 818      `(#:tests? #f
 819        #:configure-flags (list "--no-build-vignettes")))
 820     (home-page "http://dirk.eddelbuettel.com/code/digest.html")
 821     (synopsis "Create cryptographic hash digests of R objects")
 822     (description
 823      "This package contains an implementation of a function @code{digest()} for
 824 the creation of hash digests of arbitrary R objects (using the md5, sha-1,
 825 sha-256, crc32, xxhash and murmurhash algorithms) permitting easy comparison
 826 of R language objects, as well as a function @code{hmac()} to create hash-based
 827 message authentication code.
 828
 829 Please note that this package is not meant to be deployed for cryptographic
 830 purposes for which more comprehensive (and widely tested) libraries such as
 831 OpenSSL should be used.")
 832     (license license:gpl2+)))
 833
 834 (define-public r-estimability
 835   (package
 836     (name "r-estimability")
 837     (version "1.3")
 838     (source (origin
 839               (method url-fetch)
 840               (uri (cran-uri "estimability" version))
 841               (sha256
 842                (base32
 843                 "0cifdaa71spkcxl4db4z884jrya865sg3dhcv4isd8fnzg2pjcd3"))))
 844     (build-system r-build-system)
 845     (home-page "https://cran.r-project.org/web/packages/estimability")
 846     (synopsis "Tools for assessing estimability of linear predictions")
 847     (description "Provides tools for determining estimability of linear
 848 functions of regression coefficients, and @code{epredict} methods that handle
 849 non-estimable cases correctly.")
 850     (license license:gpl2+)))
 851
 852 (define-public r-labeling
 853   (package
 854     (name "r-labeling")
 855     (version "0.3")
 856     (source
 857      (origin
 858        (method url-fetch)
 859        (uri (cran-uri "labeling" version))
 860        (sha256
 861         (base32 "13sk7zrrrzry6ky1bp8mmnzcl9jhvkig8j4id9nny7z993mnk00d"))))
 862     (build-system r-build-system)
 863     (home-page "https://cran.r-project.org/web/packages/labeling")
 864     (synopsis "Axis labeling algorithms")
 865     (description "The labeling package provides a range of axis labeling
 866 algorithms.")
 867     (license license:expat)))
 868
 869 (define-public r-magrittr
 870   (package
 871     (name "r-magrittr")
 872     (version "1.5")
 873     (source
 874      (origin
 875        (method url-fetch)
 876        (uri (cran-uri "magrittr" version))
 877        (sha256
 878         (base32 "1s1ar6rag8m277qcqmdp02gn4awn9bdj9ax0r8s32i59mm1mki05"))))
 879     (build-system r-build-system)
 880     (home-page "https://cran.r-project.org/web/packages/magrittr/index.html")
 881     (synopsis "A forward-pipe operator for R")
 882     (description
 883      "Magrittr provides a mechanism for chaining commands with a new
 884 forward-pipe operator, %>%.  This operator will forward a value, or the result
 885 of an expression, into the next function call/expression.  There is flexible
 886 support for the type of right-hand side expressions.  For more information,
 887 see package vignette.  To quote Rene Magritte, \"Ceci n'est pas un pipe.\"")
 888     (license license:expat)))
 889
 890 (define-public r-munsell
 891   (package
 892     (name "r-munsell")
 893     (version "0.5.0")
 894     (source
 895      (origin
 896        (method url-fetch)
 897        (uri (cran-uri "munsell" version))
 898        (sha256
 899         (base32 "16g1fzisbpqb15yh3pqf3iia4csppva5dnv1z88x9dg263xskwyh"))))
 900     (build-system r-build-system)
 901     (propagated-inputs
 902      `(("r-colorspace" ,r-colorspace)))
 903     (home-page "https://cran.r-project.org/web/packages/munsell")
 904     (synopsis "Munsell colour system")
 905     (description
 906      "The Munsell package contains Functions for exploring and using the
 907 Munsell colour system.")
 908     (license license:expat)))
 909
 910 (define-public r-permute
 911   (package
 912    (name "r-permute")
 913    (version "0.9-5")
 914    (source
 915     (origin
 916      (method url-fetch)
 917      (uri (cran-uri "permute" version))
 918      (sha256
 919       (base32
 920        "0ra8p5mf2590azrkas8z2ry7mif77xqxd29n4zgyi5vll225726j"))))
 921    (build-system r-build-system)
 922    ;; Tests do not run correctly, but running them properly would entail a
 923    ;; circular dependency with vegan.
 924    (home-page "https://github.com/gavinsimpson/permute")
 925    (synopsis "Functions for Generating Restricted Permutations of Data")
 926    (description
 927     "This package provides a set of restricted permutation designs for freely
 928 exchangeable, line transects (time series), spatial grid designs and permutation
 929 of blocks (groups of samples).  @code{permute} also allows split-plot designs,
 930 in which the whole-plots or split-plots or both can be freely exchangeable.")
 931    (license license:gpl2+)))
 932
 933 (define-public r-plyr
 934   (package
 935     (name "r-plyr")
 936     (version "1.8.5")
 937     (source
 938      (origin
 939        (method url-fetch)
 940        (uri (cran-uri "plyr" version))
 941        (sha256
 942         (base32 "0x4mbb3rgv1ayxqidw0p9i10khbg51fz5r62vw4il8d7licqq07a"))))
 943     (build-system r-build-system)
 944     (propagated-inputs `(("r-rcpp" ,r-rcpp)))
 945     (home-page "http://had.co.nz/plyr")
 946     (synopsis "Tools for Splitting, Applying and Combining Data")
 947     (description
 948      "Plyr is a set of tools that solves a common set of problems: you need to
 949 break a big problem down into manageable pieces, operate on each piece and
 950 then put all the pieces back together.  For example, you might want to fit a
 951 model to each spatial location or time point in your study, summarise data by
 952 panels or collapse high-dimensional arrays to simpler summary statistics.")
 953     (license license:expat)))
 954
 955 (define-public r-proto
 956   (package
 957     (name "r-proto")
 958     (version "1.0.0")
 959     (source
 960      (origin
 961        (method url-fetch)
 962        (uri (cran-uri "proto" version))
 963        (sha256
 964         (base32 "1l843p8vckjckdhgv37ngv47fga5jzy0n00pmipvp05nnaixk54j"))))
 965     (build-system r-build-system)
 966     (home-page "https://github.com/hadley/proto")
 967     (synopsis "Prototype object-based programming")
 968     (description
 969      "Proto is an object oriented system using object-based, also called
 970 prototype-based, rather than class-based object oriented ideas.")
 971     (license license:gpl2+)))
 972
 973 (define-public r-rcolorbrewer
 974   (package
 975     (name "r-rcolorbrewer")
 976     (version "1.1-2")
 977     (source
 978      (origin
 979        (method url-fetch)
 980        (uri (cran-uri "RColorBrewer" version))
 981        (sha256
 982         (base32 "1pfcl8z1pnsssfaaz9dvdckyfnnc6rcq56dhislbf571hhg7isgk"))))
 983     (build-system r-build-system)
 984     (home-page "https://cran.r-project.org/web/packages/RColorBrewer")
 985     (synopsis "ColorBrewer palettes")
 986     (description
 987      "This package provides color schemes for maps (and other graphics)
 988 designed by Cynthia Brewer as described at http://colorbrewer2.org")
 989     ;; Includes code licensed under bsd-4
 990     (license license:asl2.0)))
 991
 992 (define-public r-sendmailr
 993   (package
 994     (name "r-sendmailr")
 995     (version "1.2-1")
 996     (source
 997      (origin
 998        (method url-fetch)
 999        (uri (cran-uri "sendmailR" version))
1000        (sha256
1001         (base32
1002          "0z7ipywnzgkhfvl4zb2fjwl1xq7b5wib296vn9c9qgbndj6b1zh4"))))
1003     (properties `((upstream-name . "sendmailR")))
1004     (build-system r-build-system)
1005     (propagated-inputs
1006      `(("r-base64enc" ,r-base64enc)))
1007     (home-page
1008      "https://cran.r-project.org/web/packages/sendmailR")
1009     (synopsis "Send email using R")
1010     (description
1011      "This package contains a simple SMTP client which provides a portable
1012 solution for sending email, including attachments, from within R.")
1013     (license license:gpl2+)))
1014
1015 (define-public r-stringi
1016   (package
1017     (name "r-stringi")
1018     (version "1.4.5")
1019     (source
1020      (origin
1021        (method url-fetch)
1022        (uri (cran-uri "stringi" version))
1023        (sha256
1024         (base32
1025          "0gdmdf4i3ik8rcs7af1vlsfnilcmw3z28jx4278rpq2asigps89k"))))
1026     (build-system r-build-system)
1027     (inputs `(("icu4c" ,icu4c)))
1028     (native-inputs `(("pkg-config" ,pkg-config)))
1029     (home-page "http://stringi.rexamine.com/")
1030     (synopsis "Character string processing facilities")
1031     (description
1032      "This package allows for fast, correct, consistent, portable, as well as
1033 convenient character string/text processing in every locale and any native
1034 encoding.  Owing to the use of the ICU library, the package provides R users
1035 with platform-independent functions known to Java, Perl, Python, PHP, and Ruby
1036 programmers.  Among available features there are: pattern searching
1037  (e.g.  via regular expressions), random string generation, string collation,
1038 transliteration, concatenation, date-time formatting and parsing, etc.")
1039     (license license:bsd-3)))
1040
1041 (define-public r-stringr
1042   (package
1043     (name "r-stringr")
1044     (version "1.4.0")
1045     (source
1046      (origin
1047        (method url-fetch)
1048        (uri (cran-uri "stringr" version))
1049        (sha256
1050         (base32 "1p9ip7p87gbbg4s6d3d392svvzz2b5dqdq2c8ilgvn4s78nlsq47"))))
1051     (build-system r-build-system)
1052     (propagated-inputs
1053      `(("r-glue" ,r-glue)
1054        ("r-magrittr" ,r-magrittr)
1055        ("r-stringi" ,r-stringi)))
1056     (home-page "https://github.com/hadley/stringr")
1057     (synopsis "Simple, consistent wrappers for common string operations")
1058     (description
1059      "Stringr is a consistent, simple and easy to use set of wrappers around
1060 the fantastic @code{stringi} package.  All function and argument names (and
1061 positions) are consistent, all functions deal with \"NA\"'s and zero length
1062 vectors in the same way, and the output from one function is easy to feed into
1063 the input of another.")
1064     (license license:gpl2+)))
1065
1066 (define-public r-reshape2
1067   (package
1068     (name "r-reshape2")
1069     (version "1.4.3")
1070     (source
1071      (origin
1072        (method url-fetch)
1073        (uri (cran-uri "reshape2" version))
1074        (sha256
1075         (base32 "03ki5ka1dj208fc0dclbm0b4xp9d769pah2j9cs34l776p4r9zwa"))))
1076     (build-system r-build-system)
1077     (propagated-inputs
1078      `(("r-plyr" ,r-plyr)
1079        ("r-rcpp" ,r-rcpp)
1080        ("r-stringr" ,r-stringr)))
1081     (home-page "https://github.com/hadley/reshape")
1082     (synopsis "Flexibly reshape data: a reboot of the \"reshape\" package")
1083     (description
1084      "Reshape2 is an R library to flexibly restructure and aggregate data
1085 using just two functions: melt and dcast (or acast).")
1086     (license license:expat)))
1087
1088 (define-public r-ggplot2
1089   (package
1090     (name "r-ggplot2")
1091     (version "3.2.1")
1092     (source
1093      (origin
1094        (method url-fetch)
1095        (uri (cran-uri "ggplot2" version))
1096        (sha256
1097         (base32 "0mjswqiqcwm0aqxll16bx2kwa6c9km3aql87bdj4347n1ali94g3"))))
1098     (build-system r-build-system)
1099     (propagated-inputs
1100      `(("r-digest" ,r-digest)
1101        ("r-gtable" ,r-gtable)
1102        ("r-lazyeval" ,r-lazyeval)
1103        ("r-mass" ,r-mass)
1104        ("r-mgcv" ,r-mgcv)
1105        ("r-tibble" ,r-tibble)
1106        ("r-reshape2" ,r-reshape2)
1107        ("r-rlang" ,r-rlang)
1108        ("r-scales" ,r-scales)
1109        ("r-svglite" ,r-svglite) ; Needed for 'ggsave'
1110        ("r-viridislite" ,r-viridislite)
1111        ("r-withr" ,r-withr)))
1112     (home-page "https://ggplot2.tidyverse.org")
1113     (synopsis "An implementation of the grammar of graphics")
1114     (description
1115      "Ggplot2 is an implementation of the grammar of graphics in R.  It
1116 combines the advantages of both base and lattice graphics: conditioning and
1117 shared axes are handled automatically, and you can still build up a plot step
1118 by step from multiple data sources.  It also implements a sophisticated
1119 multidimensional conditioning system and a consistent interface to map data to
1120 aesthetic attributes.")
1121     (license license:gpl2+)))
1122
1123 (define-public r-ggdendro
1124   (package
1125     (name "r-ggdendro")
1126     (version "0.1-20")
1127     (source (origin
1128               (method url-fetch)
1129               (uri (cran-uri "ggdendro" version))
1130               (sha256
1131                (base32
1132                 "1zzq1hxd0d1qa5hrzwfkdw6fzscpcafbwbpkrb62dm559y8awp0j"))))
1133     (build-system r-build-system)
1134     (propagated-inputs
1135      `(("r-ggplot2" ,r-ggplot2)
1136        ("r-mass" ,r-mass)
1137        ("r-knitr" ,r-knitr)))
1138     (home-page "https://github.com/andrie/ggdendro")
1139     (synopsis "Create Dendrograms and Tree Diagrams Using ggplot2")
1140     (description "This is a set of tools for dendrograms and tree plots using
1141 ggplot2.  The ggplot2 philosophy is to clearly separate data from the
1142 presentation.  Unfortunately the plot method for dendrograms plots directly
1143 to a plot device with out exposing the data.  The ggdendro package resolves
1144 this by making available functions that extract the dendrogram plot data.
1145 The package provides implementations for tree, rpart, as well as diana and
1146 agnes cluster diagrams.")
1147     (license license:gpl2+)))
1148
1149 (define-public r-gdtools
1150   (package
1151     (name "r-gdtools")
1152     (version "0.2.1")
1153     (source
1154      (origin
1155        (method url-fetch)
1156        (uri (cran-uri "gdtools" version))
1157        (sha256
1158         (base32
1159          "1aax50wyrs4336zpf247l8wmp4spab2n70msziy1ip4gbjn26wa1"))))
1160     (build-system r-build-system)
1161     (native-inputs
1162      `(("pkg-config" ,pkg-config)))
1163     (inputs
1164      `(("cairo" ,cairo)
1165        ("freetype2" ,freetype)
1166        ("zlib" ,zlib)))
1167     (propagated-inputs
1168      `(("r-rcpp" ,r-rcpp)
1169        ("r-systemfonts" ,r-systemfonts)))
1170     (home-page "https://cran.r-project.org/web/packages/gdtools")
1171     (synopsis "Utilities for graphical rendering")
1172     (description
1173      "The @code{gdtools} package provides functionalities to get font metrics
1174 and to generate base64 encoded string from raster matrix.")
1175     (license license:gpl3)))
1176
1177 (define-public r-svglite
1178   (package
1179     (name "r-svglite")
1180     (version "1.2.2")
1181     (source
1182      (origin
1183        (method url-fetch)
1184        (uri (cran-uri "svglite" version))
1185        (sha256
1186         (base32
1187          "1gwv51wqp6pgm2f9gavsiq65njs77fr49n8y6y9ax60k3a4vvg14"))))
1188     (build-system r-build-system)
1189     (propagated-inputs
1190      `(("r-bh" ,r-bh)
1191        ("r-gdtools" ,r-gdtools)
1192        ("r-rcpp" ,r-rcpp)))
1193     (home-page "https://github.com/hadley/svglite")
1194     (synopsis "SVG graphics device")
1195     (description
1196      "@code{svglite} is a graphics device that produces clean
1197 @dfn{SVG} (Scalable Vector Graphics) output, suitable for use on the web, or
1198 hand editing.  Compared to the built-in @code{svg()}, @code{svglite} is
1199 considerably faster, produces smaller files, and leaves text as is.")
1200     (license license:gpl2+)))
1201
1202 (define-public r-assertthat
1203   (package
1204     (name "r-assertthat")
1205     (version "0.2.1")
1206     (source (origin
1207               (method url-fetch)
1208               (uri (cran-uri "assertthat" version))
1209               (sha256
1210                (base32
1211                 "17wy5bdfzg73sg2clisg1k3zyn1adkj59x56m5nwia2k8z67zkw5"))))
1212     (build-system r-build-system)
1213     (home-page "https://github.com/hadley/assertthat")
1214     (synopsis "Easy pre and post assertions")
1215     (description
1216      "Assertthat is an extension to stopifnot() that makes it easy to declare
1217 the pre and post conditions that your code should satisfy, while also
1218 producing friendly error messages so that your users know what they've done
1219 wrong.")
1220     (license license:gpl3+)))
1221
1222 (define-public r-lazyeval
1223   (package
1224     (name "r-lazyeval")
1225     (version "0.2.2")
1226     (source (origin
1227               (method url-fetch)
1228               (uri (cran-uri "lazyeval" version))
1229               (sha256
1230                (base32
1231                 "1m10i059csrcqkcn59a8wspn784alxsq3symzhn24mhhl894346n"))))
1232     (build-system r-build-system)
1233     (home-page "https://github.com/hadley/lazyeval")
1234     (synopsis "Lazy (non-standard) evaluation in R")
1235     (description
1236      "This package provides the tools necessary to do non-standard
1237 evaluation (NSE) in R.")
1238     (license license:gpl3+)))
1239
1240 (define-public r-dbi
1241   (package
1242     (name "r-dbi")
1243     (version "1.1.0")
1244     (source (origin
1245               (method url-fetch)
1246               (uri (cran-uri "DBI" version))
1247               (sha256
1248                (base32
1249                 "1r03j9rdcxb9bhxk40dkmy10ikz4yzsxhy3f9k9ix3x577xbfvd9"))))
1250     (build-system r-build-system)
1251     (home-page "https://github.com/rstats-db/DBI")
1252     (synopsis "R database interface")
1253     (description
1254      "The DBI package provides a database interface (DBI) definition for
1255 communication between R and relational database management systems.  All
1256 classes in this package are virtual and need to be extended by the various
1257 R/DBMS implementations.")
1258     (license license:lgpl2.0+)))
1259
1260 (define-public r-bh
1261   (package
1262     (name "r-bh")
1263     (version "1.72.0-3")
1264     (source (origin
1265               (method url-fetch)
1266               (uri (cran-uri "BH" version))
1267               (sha256
1268                (base32
1269                 "1ay8vb6i730lipg8b8g3893vqglhw2kqpc29lwdrxdkb66iw33l8"))))
1270     (build-system r-build-system)
1271     (home-page "https://github.com/eddelbuettel/bh")
1272     (synopsis "R package providing subset of Boost headers")
1273     (description
1274      "This package aims to provide the most useful subset of Boost libraries
1275 for template use among CRAN packages.")
1276     (license license:boost1.0)))
1277
1278 (define-public r-evaluate
1279   (package
1280     (name "r-evaluate")
1281     (version "0.14")
1282     (source (origin
1283               (method url-fetch)
1284               (uri (cran-uri "evaluate" version))
1285               (sha256
1286                (base32
1287                 "0a2y7j534gbgixkwj9r1z76l2vssw4g1hznzbpclc076wkdqpj58"))))
1288     (build-system r-build-system)
1289     (home-page "https://github.com/hadley/evaluate")
1290     (synopsis "Parsing and evaluation tools for R")
1291     (description
1292      "This package provides tools that allow you to recreate the parsing,
1293 evaluation and display of R code, with enough information that you can
1294 accurately recreate what happens at the command line.  The tools can easily be
1295 adapted for other output formats, such as HTML or LaTeX.")
1296     (license license:gpl3+)))
1297
1298 (define-public r-formatr
1299   (package
1300     (name "r-formatr")
1301     (version "1.7")
1302     (source (origin
1303               (method url-fetch)
1304               (uri (cran-uri "formatR" version))
1305               (sha256
1306                (base32
1307                 "1nsxbrx31k3y6yql30qkrvdfyznlia2qfvwv95mfiy7m7wdn4rm3"))))
1308     (build-system r-build-system)
1309     (home-page "http://yihui.name/formatR")
1310     (synopsis "Format R code automatically")
1311     (description
1312      "This package provides a function to format R source code.  Spaces and
1313 indent will be added to the code automatically, and comments will be preserved
1314 under certain conditions, so that R code will be more human-readable and tidy.
1315 There is also a Shiny app as a user interface in this package.")
1316     (license license:gpl3+)))
1317
1318 (define-public r-highr
1319   (package
1320     (name "r-highr")
1321     (version "0.8")
1322     (source (origin
1323               (method url-fetch)
1324               (uri (cran-uri "highr" version))
1325               (sha256
1326                (base32
1327                 "0my6idnhmmgs4q1vs40y2lh56yij2p59mpwvm53wjs2zk6x1zl2b"))))
1328     (build-system r-build-system)
1329     (home-page "https://github.com/yihui/highr")
1330     (synopsis "Syntax highlighting for R source code")
1331     (description
1332      "This package provides syntax highlighting for R source code.  Currently
1333 it supports LaTeX and HTML output.  Source code of other languages is
1334 supported via Andre Simon's highlight package.")
1335     (license license:gpl3+)))
1336
1337 (define-public r-mime
1338   (package
1339     (name "r-mime")
1340     (version "0.8")
1341     (source (origin
1342               (method url-fetch)
1343               (uri (cran-uri "mime" version))
1344               (sha256
1345                (base32
1346                 "18w98prfbivvygiyamsf9yg090kzbnvw2fn9b27823gmis4d08ny"))))
1347     (build-system r-build-system)
1348     (home-page "https://github.com/yihui/mime")
1349     (synopsis "R package to map filenames to MIME types")
1350     (description
1351      "This package guesses the MIME type from a filename extension using the
1352 data derived from /etc/mime.types in UNIX-type systems.")
1353     (license license:gpl2)))
1354
1355 (define-public r-markdown
1356   (package
1357     (name "r-markdown")
1358     (version "1.1")
1359     (source (origin
1360               (method url-fetch)
1361               (uri (cran-uri "markdown" version))
1362               (sha256
1363                (base32
1364                 "06zwbrp14bri3470anadd7dvgmw06xf8df6v2pk64wx3f9sd934d"))))
1365     (build-system r-build-system)
1366     ;; Skip check phase because the tests require the r-knitr package to be
1367     ;; installed. This prevents installation failures. Knitr normally
1368     ;; shouldn't be available since r-markdown is a dependency of the r-knitr
1369     ;; package.
1370     (arguments `(#:tests? #f))
1371     (propagated-inputs
1372      `(("r-mime" ,r-mime)
1373        ("r-xfun" ,r-xfun)))
1374     (home-page "https://github.com/rstudio/markdown")
1375     (synopsis "Markdown rendering for R")
1376     (description
1377      "This package provides R bindings to the Sundown Markdown rendering
1378 library (https://github.com/vmg/sundown).  Markdown is a plain-text formatting
1379 syntax that can be converted to XHTML or other formats.")
1380     (license license:gpl2)))
1381
1382 (define-public r-yaml
1383   (package
1384     (name "r-yaml")
1385     (version "2.2.0")
1386     (source (origin
1387               (method url-fetch)
1388               (uri (cran-uri "yaml" version))
1389               (sha256
1390                (base32
1391                 "0in562nd0i23cg91a8kdbqgim656fgscykwi0icsnq53xj3srg2m"))))
1392     (build-system r-build-system)
1393     (home-page "https://cran.r-project.org/web/packages/yaml/")
1394     (synopsis "Methods to convert R data to YAML and back")
1395     (description
1396      "This package implements the libyaml YAML 1.1 parser and
1397 emitter (http://pyyaml.org/wiki/LibYAML) for R.")
1398     (license license:bsd-3)))
1399
1400 (define-public r-knitr
1401   (package
1402     (name "r-knitr")
1403     (version "1.27")
1404     (source (origin
1405               (method url-fetch)
1406               (uri (cran-uri "knitr" version))
1407               (sha256
1408                (base32
1409                 "02nysgnx6xv0kd351s1d59yx4g0drsd9lmcgxs0rsw5f1jiycgdg"))))
1410     (build-system r-build-system)
1411     (propagated-inputs
1412      `(("r-evaluate" ,r-evaluate)
1413        ("r-highr" ,r-highr)
1414        ("r-markdown" ,r-markdown)
1415        ("r-stringr" ,r-stringr)
1416        ("r-xfun" ,r-xfun)
1417        ("r-yaml" ,r-yaml)))
1418     (home-page "http://yihui.name/knitr/")
1419     (synopsis "General-purpose package for dynamic report generation in R")
1420     (description
1421      "This package provides a general-purpose tool for dynamic report
1422 generation in R using Literate Programming techniques.")
1423     ;; The code is released under any version of the GPL.  As it is used by
1424     ;; r-markdown which is available under GPLv2 only, we have chosen GPLv2+
1425     ;; here.
1426     (license license:gpl2+)))
1427
1428 (define-public r-knitrbootstrap
1429   (package
1430     (name "r-knitrbootstrap")
1431     (version "1.0.2")
1432     (source
1433      (origin
1434        (method url-fetch)
1435        (uri (cran-uri "knitrBootstrap" version))
1436        (sha256
1437         (base32
1438          "1aj60j7f0gcs120fdrnfbnb7vk7lfn1phil0mghg6a5zldz4cqs3"))))
1439     (properties `((upstream-name . "knitrBootstrap")))
1440     (build-system r-build-system)
1441     (propagated-inputs
1442      `(("r-knitr" ,r-knitr)
1443        ("r-rmarkdown" ,r-rmarkdown)
1444        ("r-markdown" ,r-markdown)))
1445     (home-page "https://github.com/jimhester/knitrBootstrap")
1446     (synopsis "Knitr bootstrap framework")
1447     (description
1448      "This package provides a framework to create Bootstrap 3 HTML reports
1449 from knitr Rmarkdown.")
1450     (license license:expat)))
1451
1452 (define-public r-microbenchmark
1453   (package
1454     (name "r-microbenchmark")
1455     (version "1.4-7")
1456     (source (origin
1457               (method url-fetch)
1458               (uri (cran-uri "microbenchmark" version))
1459               (sha256
1460                (base32
1461                 "1xl4m4yl4h2zcjiz8wsa7f3sh55qg2xr3sgpvz18rlix6b3173r6"))))
1462     (build-system r-build-system)
1463     (home-page "https://cran.r-project.org/web/packages/microbenchmark/")
1464     (synopsis "Accurate timing functions for R")
1465     (description
1466      "This package provides infrastructure to accurately measure and compare
1467 the execution time of R expressions.")
1468     (license license:bsd-2)))
1469
1470 (define-public r-pryr
1471   (package
1472     (name "r-pryr")
1473     (version "0.1.4")
1474     (source (origin
1475               (method url-fetch)
1476               (uri (cran-uri "pryr" version))
1477               (sha256
1478                (base32
1479                 "06vj5xl9x37kbd3l5bw7sbgfdnp37spvrjrn976rxi04clqk966k"))))
1480     (build-system r-build-system)
1481     (propagated-inputs
1482      `(("r-stringr" ,r-stringr)
1483        ("r-codetools" ,r-codetools)))
1484     (native-inputs
1485      `(("r-rcpp" ,r-rcpp)))
1486     (home-page "https://github.com/hadley/pryr")
1487     (synopsis "Tools for computing on the R language")
1488     (description
1489      "This package provides useful tools to pry back the covers of R and
1490 understand the language at a deeper level.")
1491     (license license:gpl2)))
1492
1493 (define-public r-memoise
1494   (package
1495     (name "r-memoise")
1496     (version "1.1.0")
1497     (source (origin
1498               (method url-fetch)
1499               (uri (cran-uri "memoise" version))
1500               (sha256
1501                (base32
1502                 "034qfc2xlh30x1q2vya239w34a3ir3y2fwnx2agbgbi6592zjxmj"))))
1503     (build-system r-build-system)
1504     (propagated-inputs
1505      `(("r-digest" ,r-digest)))
1506     (home-page "https://github.com/hadley/memoise")
1507     (synopsis "Memoise functions for R")
1508     (description
1509      "This R package allows to cache the results of a function so that when
1510 you call it again with the same arguments it returns the pre-computed value.")
1511     (license license:expat)))
1512
1513 (define-public r-crayon
1514   (package
1515     (name "r-crayon")
1516     (version "1.3.4")
1517     (source (origin
1518               (method url-fetch)
1519               (uri (cran-uri "crayon" version))
1520               (sha256
1521                (base32
1522                 "0s7s6vc3ww8pzanpjisym4jjvwcc5pi2qg8srx7jqlz9j3wrnvpw"))))
1523     (build-system r-build-system)
1524     (propagated-inputs
1525      `(("r-memoise" ,r-memoise)))
1526     (home-page "https://github.com/gaborcsardi/crayon")
1527     (synopsis "Colored terminal output for R")
1528     (description
1529      "Colored terminal output on terminals that support ANSI color and
1530 highlight codes.  It also works in Emacs ESS.  ANSI color support is
1531 automatically detected.  Colors and highlighting can be combined and nested.
1532 New styles can also be created easily.  This package was inspired by the
1533 \"chalk\" JavaScript project.")
1534     (license license:expat)))
1535
1536 (define-public r-praise
1537   (package
1538     (name "r-praise")
1539     (version "1.0.0")
1540     (source
1541      (origin
1542        (method url-fetch)
1543        (uri (cran-uri "praise" version))
1544        (sha256
1545         (base32
1546          "1gfyypnvmih97p2r0php9qa39grzqpsdbq5g0fdsbpq5zms5w0sw"))))
1547     (build-system r-build-system)
1548     (home-page "https://github.com/gaborcsardi/praise")
1549     (synopsis "Functions to praise users")
1550     (description
1551      "This package provides template functions to assist in building friendly
1552 R packages that praise their users.")
1553     (license license:expat)))
1554
1555 (define-public r-testthat
1556   (package
1557     (name "r-testthat")
1558     (version "2.3.1")
1559     (source (origin
1560               (method url-fetch)
1561               (uri (cran-uri "testthat" version))
1562               (sha256
1563                (base32
1564                 "0m8xchdpgn9iwj6gb2qw46zr85v9zf1gkbr9nnahmy5sp1s9bbky"))))
1565     (build-system r-build-system)
1566     (propagated-inputs
1567      `(("r-cli" ,r-cli)
1568        ("r-crayon" ,r-crayon)
1569        ("r-digest" ,r-digest)
1570        ("r-ellipsis" ,r-ellipsis)
1571        ("r-evaluate" ,r-evaluate)
1572        ("r-magrittr" ,r-magrittr)
1573        ("r-pkgload" ,r-pkgload)
1574        ("r-praise" ,r-praise)
1575        ("r-r6" ,r-r6)
1576        ("r-rlang" ,r-rlang)
1577        ("r-withr" ,r-withr)))
1578     (home-page "https://github.com/hadley/testthat")
1579     (synopsis "Unit testing for R")
1580     (description
1581      "This package provides a unit testing system for R designed to be fun,
1582 flexible and easy to set up.")
1583     (license license:expat)))
1584
1585 (define-public r-r6
1586   (package
1587     (name "r-r6")
1588     (version "2.4.1")
1589     (source (origin
1590               (method url-fetch)
1591               (uri (cran-uri "R6" version))
1592               (sha256
1593                (base32
1594                 "0gma5z41mx02ka9h96xdyf3p6i1rx0izczrzj26c4mbnh9jgvc16"))))
1595     (build-system r-build-system)
1596     (home-page "https://github.com/wch/R6/")
1597     (synopsis "Classes with reference semantics in R")
1598     (description
1599      "The R6 package allows the creation of classes with reference semantics,
1600 similar to R's built-in reference classes.  Compared to reference classes, R6
1601 classes are simpler and lighter-weight, and they are not built on S4 classes
1602 so they do not require the methods package.  These classes allow public and
1603 private members, and they support inheritance, even when the classes are
1604 defined in different packages.")
1605     (license license:expat)))
1606
1607 (define-public r-rlang
1608   (package
1609     (name "r-rlang")
1610     (version "0.4.3")
1611     (source (origin
1612               (method url-fetch)
1613               (uri (cran-uri "rlang" version))
1614               (sha256
1615                (base32
1616                 "0qsqfikbsj55x5brghnkzzp7pz0japr4xnzm993f668mlls3f6i4"))))
1617     (build-system r-build-system)
1618     (home-page "http://rlang.tidyverse.org")
1619     (synopsis "Functions for base types, core R and Tidyverse features")
1620     (description "This package provides a toolbox for working with base types,
1621 core R features like the condition system, and core @code{Tidyverse} features
1622 like tidy evaluation.")
1623     (license license:gpl3)))
1624
1625 (define-public r-tibble
1626   (package
1627     (name "r-tibble")
1628     (version "2.1.3")
1629     (source
1630      (origin
1631        (method url-fetch)
1632        (uri (cran-uri "tibble" version))
1633        (sha256
1634         (base32
1635          "06jfayiip8j8ibdhw3fvxn4n8aqbqhwanrszpzlsf92xdfgfm34s"))))
1636     (build-system r-build-system)
1637     (propagated-inputs
1638      `(("r-cli" ,r-cli)
1639        ("r-crayon" ,r-crayon)
1640        ("r-fansi" ,r-fansi)
1641        ("r-pkgconfig" ,r-pkgconfig)
1642        ("r-pillar" ,r-pillar)
1643        ("r-rlang" ,r-rlang)))
1644     (home-page "https://github.com/hadley/tibble")
1645     (synopsis "Simple data frames")
1646     (description
1647      "This package provides a @code{tbl_df} class that offers better checking
1648 and printing capabilities than traditional data frames.")
1649     (license license:expat)))
1650
1651 (define-public r-dplyr
1652   (package
1653     (name "r-dplyr")
1654     (version "0.8.3")
1655     (source (origin
1656               (method url-fetch)
1657               (uri (cran-uri "dplyr" version))
1658               (sha256
1659                (base32
1660                 "032c89wa04g9rih9shyvwl3il0bsrv3xk489x6867sk9bb3amd38"))))
1661     (build-system r-build-system)
1662     (propagated-inputs
1663      `(("r-assertthat" ,r-assertthat)
1664        ("r-bh" ,r-bh)
1665        ("r-glue" ,r-glue)
1666        ("r-magrittr" ,r-magrittr)
1667        ("r-pkgconfig" ,r-pkgconfig)
1668        ("r-plogr" ,r-plogr)
1669        ("r-r6" ,r-r6)
1670        ("r-rcpp" ,r-rcpp)
1671        ("r-rlang" ,r-rlang)
1672        ("r-tibble" ,r-tibble)
1673        ("r-tidyselect" ,r-tidyselect)))
1674     (home-page "https://github.com/hadley/dplyr")
1675     (synopsis "Tools for working with data frames in R")
1676     (description
1677      "dplyr is the next iteration of plyr.  It is focussed on tools for
1678 working with data frames.  It has three main goals: 1) identify the most
1679 important data manipulation tools needed for data analysis and make them easy
1680 to use in R; 2) provide fast performance for in-memory data by writing key
1681 pieces of code in C++; 3) use the same code interface to work with data no
1682 matter where it is stored, whether in a data frame, a data table or
1683 database.")
1684     (license license:expat)))
1685
1686 (define-public r-dbplyr
1687   (package
1688     (name "r-dbplyr")
1689     (version "1.4.2")
1690     (source
1691      (origin
1692        (method url-fetch)
1693        (uri (cran-uri "dbplyr" version))
1694        (sha256
1695         (base32
1696          "1q2dflr88s5a1amzfld3087q422vf70052qn84zyd8895kdg10xp"))))
1697     (build-system r-build-system)
1698     (propagated-inputs
1699      `(("r-assertthat" ,r-assertthat)
1700        ("r-dbi" ,r-dbi)
1701        ("r-dplyr" ,r-dplyr)
1702        ("r-glue" ,r-glue)
1703        ("r-purrr" ,r-purrr)
1704        ("r-r6" ,r-r6)
1705        ("r-rlang" ,r-rlang)
1706        ("r-tibble" ,r-tibble)
1707        ("r-tidyselect" ,r-tidyselect)))
1708     (home-page "https://github.com/tidyverse/dbplyr")
1709     (synopsis "Dplyr back end for databases")
1710     (description
1711      "This package provides a dplyr back end for databases that allows you to
1712 work with remote database tables as if they are in-memory data frames.  Basic
1713 features works with any database that has a @code{DBI} back end; more advanced
1714 features require SQL translation to be provided by the package author.")
1715     (license license:expat)))
1716
1717 (define-public r-acepack
1718   (package
1719     (name "r-acepack")
1720     (version "1.4.1")
1721     (source
1722      (origin
1723        (method url-fetch)
1724        (uri (cran-uri "acepack" version))
1725        (sha256
1726         (base32
1727          "1f98rpfjmhd92rdc3j004plyfpjailz6j0ycysbac0kgj83haxc2"))))
1728     (build-system r-build-system)
1729     (inputs
1730      `(("gfortran" ,gfortran)))
1731     (home-page "https://cran.r-project.org/web/packages/acepack")
1732     (synopsis "Functions for regression transformations")
1733     (description
1734      "This package provides ACE and AVAS methods for choosing regression
1735 transformations.")
1736     (license license:expat)))
1737
1738 (define-public r-formula
1739   (package
1740     (name "r-formula")
1741     (version "1.2-3")
1742     (source
1743      (origin
1744        (method url-fetch)
1745        (uri (cran-uri "Formula" version))
1746        (sha256
1747         (base32
1748          "0wiqh8rr9d5ciy80wj8f5fnmiiw0ywanvvnhkwd622dx42dk848l"))))
1749     (properties `((upstream-name . "Formula")))
1750     (build-system r-build-system)
1751     (home-page "https://cran.r-project.org/web/packages/Formula")
1752     (synopsis "Extended model formulas")
1753     (description
1754      "This package provides a new class @code{Formula}, which extends the base
1755 class @code{formula}.  It supports extended formulas with multiple parts of
1756 regressors on the right-hand side and/or multiple responses on the left-hand
1757 side.")
1758     (license (list license:gpl2+ license:gpl3+))))
1759
1760 (define-public r-locfit
1761   (package
1762     (name "r-locfit")
1763     (version "1.5-9.1")
1764     (source
1765      (origin
1766        (method url-fetch)
1767        (uri (cran-uri "locfit" version))
1768        (sha256
1769         (base32
1770          "0lafrmq1q7x026m92h01hc9cjjiximqqi3v1g2hw7ai9vf7i897m"))))
1771     (build-system r-build-system)
1772     (propagated-inputs
1773      `(("r-lattice" ,r-lattice)))
1774     (home-page "https://cran.r-project.org/web/packages/locfit")
1775     (synopsis "Local regression, likelihood and density estimation")
1776     (description
1777      "This package provides functions used for local regression, likelihood
1778 and density estimation.")
1779     (license (list license:gpl2+ license:gpl3+))))
1780
1781 (define-public r-chron
1782   (package
1783     (name "r-chron")
1784     (version "2.3-54")
1785     (source (origin
1786               (method url-fetch)
1787               (uri (cran-uri "chron" version))
1788               (sha256
1789                (base32
1790                 "0vc7dxqwx0jqzwszax6di3091npsxnhnbvr7sy7rlip0jqzarwqd"))))
1791     (build-system r-build-system)
1792     (home-page "https://cran.r-project.org/web/packages/chron")
1793     (synopsis "Chronological R objects which can handle dates and times")
1794     (description
1795      "This package provides chronological R objects which can handle dates and
1796 times.")
1797     (license license:gpl2)))
1798
1799 (define-public r-data-table
1800   (package
1801     (name "r-data-table")
1802     (version "1.12.8")
1803     (source (origin
1804               (method url-fetch)
1805               (uri (cran-uri "data.table" version))
1806               (sha256
1807                (base32
1808                 "1p7rf4v3ysflpgcmy9krkwmcy7z22wb08xm443649waz6lx5z9yk"))))
1809     (build-system r-build-system)
1810     (inputs
1811      `(("zlib" ,zlib)))
1812     (native-inputs
1813      `(("pkg-config" ,pkg-config)))
1814     (home-page "https://github.com/Rdatatable/data.table/wiki")
1815     (synopsis "Enhanced version of data.frame R object")
1816     (description
1817      "The R package @code{data.table} is an extension of @code{data.frame}
1818 providing functions for fast aggregation of large data (e.g. 100GB in RAM),
1819 fast ordered joins, fast add/modify/delete of columns by group, column listing
1820 and fast file reading.")
1821     (license license:gpl3+)))
1822
1823 (define-public r-xtable
1824   (package
1825     (name "r-xtable")
1826     (version "1.8-4")
1827     (source
1828      (origin
1829        (method url-fetch)
1830        (uri (cran-uri "xtable" version))
1831        (sha256
1832         (base32
1833          "077xfm0gphvhsay75amd9v90zk57kjgrrlgih04fyrbqqblc1gjs"))))
1834     (build-system r-build-system)
1835     (native-inputs
1836      `(("r-knitr" ,r-knitr))) ; for vignettes
1837     (home-page "http://xtable.r-forge.r-project.org/")
1838     (synopsis "Export R tables to LaTeX or HTML")
1839     (description
1840      "This package provides tools to export R data as LaTeX and HTML tables.")
1841     (license license:gpl2+)))
1842
1843 (define-public python-patsy
1844   (package
1845     (name "python-patsy")
1846     (version "0.5.1")
1847     (source (origin
1848               (method url-fetch)
1849               (uri (pypi-uri "patsy" version))
1850               (sha256
1851                (base32
1852                 "149rbrdzwns0ay88caf1zsm1r53v1q5np1mrb36na50y432cw5gi"))))
1853     (build-system python-build-system)
1854     (arguments
1855      `(#:phases
1856        (modify-phases %standard-phases
1857          (replace 'check
1858            (lambda _ (invoke "nosetests" "-v"))))))
1859     (propagated-inputs
1860      `(("python-numpy" ,python-numpy)
1861        ("python-scipy" ,python-scipy)
1862        ("python-six" ,python-six)))
1863     (native-inputs
1864      `(("python-nose" ,python-nose)))
1865     (home-page "https://github.com/pydata/patsy")
1866     (synopsis "Describe statistical models and build design matrices")
1867     (description
1868      "Patsy is a Python package for describing statistical models and for
1869 building design matrices.")
1870     ;; The majority of the code is distributed under BSD-2.  The module
1871     ;; patsy.compat contains code derived from the Python standard library,
1872     ;; and is covered by the PSFL.
1873     (license (list license:bsd-2 license:psfl))))
1874
1875 (define-public python2-patsy
1876   (package-with-python2 python-patsy))
1877
1878 (define-public python-statsmodels
1879   (package
1880     (name "python-statsmodels")
1881     (version "0.9.0")
1882     (source
1883      (origin
1884        (method url-fetch)
1885        (uri (pypi-uri "statsmodels" version))
1886        (sha256
1887         (base32
1888          "0fxs8a7sp4d7jvqlm36yi45i2d28kjfvraf9q8i9jr1chhxgjqb4"))))
1889     (build-system python-build-system)
1890     (arguments
1891      `(;; The test suite is very large and rather brittle.  Tests often fail
1892        ;; because of minor changes in dependencies that upstream hasn't fixed
1893        ;; in a new release.
1894        #:tests? #f
1895        #:phases
1896        (modify-phases %standard-phases
1897          (add-after 'unpack 'set-matplotlib-backend-to-agg
1898           (lambda _
1899             ;; Set the matplotlib backend to Agg to avoid problems using the
1900             ;; GTK backend without a display.
1901             (substitute* (append (find-files "statsmodels/graphics/tests" "\\.py")
1902                                  '("statsmodels/tsa/vector_ar/tests/test_var.py"
1903                                    "statsmodels/duration/tests/test_survfunc.py"))
1904               (("import matplotlib\\.pyplot as plt" line)
1905                (string-append "import matplotlib;matplotlib.use('Agg');"
1906                               line)))
1907             #t)))))
1908     (propagated-inputs
1909      `(("python-numpy" ,python-numpy)
1910        ("python-scipy" ,python-scipy)
1911        ("python-pandas" ,python-pandas)
1912        ("python-patsy" ,python-patsy)
1913        ("python-matplotlib" ,python-matplotlib)))
1914     (native-inputs
1915      `(("python-cython" ,python-cython)
1916        ("python-nose" ,python-nose)
1917        ("python-sphinx" ,python-sphinx)))
1918     (home-page "http://statsmodels.sourceforge.net/")
1919     (synopsis "Statistical modeling and econometrics in Python")
1920     (description
1921      "Statsmodels is a Python package that provides a complement to scipy for
1922 statistical computations including descriptive statistics and estimation and
1923 inference for statistical models.")
1924     (license license:bsd-3)))
1925
1926 (define-public python2-statsmodels
1927   (let ((stats (package-with-python2 python-statsmodels)))
1928     (package (inherit stats)
1929       (propagated-inputs
1930        `(("python2-pytz" ,python2-pytz)
1931          ("python2-numpy" ,python2-numpy)
1932          ("python2-scipy" ,python2-scipy)
1933          ("python2-pandas" ,python2-pandas)
1934          ("python2-patsy" ,python2-patsy)
1935          ("python2-matplotlib" ,python2-matplotlib))))))
1936
1937 (define-public r-coda
1938   (package
1939     (name "r-coda")
1940     (version "0.19-3")
1941     (source (origin
1942               (method url-fetch)
1943               (uri (cran-uri "coda" version))
1944               (sha256
1945                (base32
1946                 "1mn50bshky968gn4nf6vnkaa768fnvm1xmhkms7szwdw9341zpyk"))))
1947     (build-system r-build-system)
1948     (propagated-inputs
1949      `(("r-lattice" ,r-lattice)))
1950     (home-page "https://cran.r-project.org/web/packages/coda")
1951     (synopsis "This is a package for Output Analysis and Diagnostics for MCMC")
1952     (description "This package provides functions for summarizing and plotting
1953 the output from Markov Chain Monte Carlo (MCMC) simulations, as well as
1954 diagnostic tests of convergence to the equilibrium distribution of the Markov
1955 chain.")
1956     (license license:gpl2+)))
1957
1958 (define-public r-ade4
1959   (package
1960     (name "r-ade4")
1961     (version "1.7-13")
1962     (source
1963       (origin
1964         (method url-fetch)
1965         (uri (cran-uri "ade4" version))
1966         (sha256
1967           (base32
1968             "16z9jk4qj35ghsk4lwmq241dgc770y8a70dlmp9q4gz6d8ssgl7m"))))
1969     (build-system r-build-system)
1970     (propagated-inputs
1971      `(("r-mass" ,r-mass)))
1972     (home-page "http://pbil.univ-lyon1.fr/ADE-4")
1973     (synopsis "Multivariate data analysis and graphical display")
1974     (description
1975      "The ade4 package contains data analysis functions to analyze ecological
1976 and environmental data in the framework of Euclidean exploratory methods.")
1977     (license license:gpl2+)))
1978
1979 (define-public r-xml2
1980   (package
1981     (name "r-xml2")
1982     (version "1.2.2")
1983     (source
1984      (origin
1985        (method url-fetch)
1986        (uri (cran-uri "xml2" version))
1987        (sha256
1988         (base32
1989          "1x3q3a0xv8j0nx3hs4d3pfjm5g9nvaxmfrapba9f4nrkqi3z2l1h"))))
1990     (build-system r-build-system)
1991     (inputs
1992      `(("libxml2" ,libxml2)
1993        ("zlib" ,zlib)))
1994     (native-inputs
1995      `(("pkg-config" ,pkg-config)))
1996     (propagated-inputs
1997      `(("r-rcpp" ,r-rcpp)))
1998     (home-page "https://github.com/hadley/xml2")
1999     (synopsis "Parse XML with R")
2000     (description
2001      "This package provides a simple, consistent interface to working with XML
2002 files in R.  It is built on top of the libxml2 C library.")
2003     (license license:gpl2+)))
2004
2005 (define-public r-multitaper
2006   (package
2007     (name "r-multitaper")
2008     (version "1.0-14")
2009     (source
2010      (origin
2011        (method url-fetch)
2012        (uri (cran-uri "multitaper" version))
2013        (sha256
2014         (base32
2015          "04wd9bbhyx7697pfy0fpj02v1csr48hkpqj62h9p8a6w84ji4k68"))))
2016     (build-system r-build-system)
2017     (native-inputs
2018      `(("gfortran" ,gfortran)))
2019     (home-page "https://github.com/wesleyburr/multitaper/")
2020     (synopsis "Multitaper spectral analysis tools")
2021     (description
2022      "This package implements multitaper spectral estimation
2023 techniques using prolate spheroidal sequences (Slepians) and sine
2024 tapers for time series analysis.  It includes an adaptive weighted
2025 multitaper spectral estimate, a coherence estimate, Thomson's Harmonic
2026 F-test, and complex demodulation.  The Slepians sequences are
2027 generated efficiently using a tridiagonal matrix solution, and
2028 jackknifed confidence intervals are available for most estimates.")
2029     (license license:gpl2+)))
2030
2031 (define-public r-rversions
2032   (package
2033     (name "r-rversions")
2034     (version "2.0.1")
2035     (source (origin
2036               (method url-fetch)
2037               (uri (cran-uri "rversions" version))
2038               (sha256
2039                (base32
2040                 "1ic6sxnyya24d5xsxjg3fba73fhya9fhs0kaf66yha6nwxj1zv2i"))))
2041     (build-system r-build-system)
2042     (propagated-inputs
2043      `(("r-curl" ,r-curl)
2044        ("r-xml2" ,r-xml2)))
2045     (home-page "https://github.com/metacran/rversions")
2046     (synopsis "Query R versions, including 'r-release' and 'r-oldrel'")
2047     (description
2048      "This package provides functions to query the main R repository to find
2049 the versions that @code{r-release} and @code{r-oldrel} refer to, and also all
2050 previous R versions and their release dates.")
2051     (license license:expat)))
2052
2053 (define-public r-whisker
2054   (package
2055     (name "r-whisker")
2056     (version "0.4")
2057     (source (origin
2058               (method url-fetch)
2059               (uri (cran-uri "whisker" version))
2060               (sha256
2061                (base32
2062                 "1a7vz0dk95xfjvi38wbpw8vmf5qn3g8p490msz2rw0piwidmk1ks"))))
2063     (build-system r-build-system)
2064     (home-page "https://github.com/edwindj/whisker")
2065     (synopsis "Logicless mustache templating for R")
2066     (description
2067      "This package provides logicless templating, with a syntax that is not
2068 limited to R.")
2069     (license license:gpl3+)))
2070
2071 (define-public r-backports
2072   (package
2073     (name "r-backports")
2074     (version "1.1.5")
2075     (source
2076      (origin
2077        (method url-fetch)
2078        (uri (cran-uri "backports" version))
2079        (sha256
2080         (base32
2081          "0k19w68b2aihyj5mflw3732gkkzs78sssqdns960pdw3yfnkiv33"))))
2082     (build-system r-build-system)
2083     (home-page "https://cran.r-project.org/web/packages/backports")
2084     (synopsis "Reimplementations of functions introduced since R 3.0.0")
2085     (description
2086      "Provides implementations of functions which have been introduced in R
2087 since version 3.0.0.  The backports are conditionally exported which results
2088 in R resolving the function names to the version shipped with R (if available)
2089 and uses the implemented backports as fallback.  This way package developers
2090 can make use of the new functions without worrying about the minimum required
2091 R version.")
2092     (license license:gpl2+)))
2093
2094 (define-public r-checkmate
2095   (package
2096     (name "r-checkmate")
2097     (version "1.9.4")
2098     (source
2099      (origin
2100        (method url-fetch)
2101        (uri (cran-uri "checkmate" version))
2102        (sha256
2103         (base32
2104          "08ddpgs4mv5d5y4j054pm8drmxkn7yvhfpbghwxlizjpnxa5g8ps"))))
2105     (build-system r-build-system)
2106     (propagated-inputs
2107      `(("r-backports" ,r-backports)))
2108     (home-page "https://github.com/mllg/checkmate")
2109     (synopsis "Fast and versatile argument checks")
2110     (description
2111      "This package provides tests and assertions to perform frequent argument
2112 checks.  A substantial part of the package was written in C to minimize any
2113 worries about execution time overhead.")
2114     (license license:bsd-3)))
2115
2116 (define-public r-bbmisc
2117   (package
2118     (name "r-bbmisc")
2119     (version "1.11")
2120     (source
2121      (origin
2122        (method url-fetch)
2123        (uri (cran-uri "BBmisc" version))
2124        (sha256
2125         (base32
2126          "1lh1n4bvxzivb5rbz69mvd8xdgr3gr2bnqd68a39sd1530l8r90y"))))
2127     (properties `((upstream-name . "BBmisc")))
2128     (build-system r-build-system)
2129     (propagated-inputs
2130      `(("r-checkmate" ,r-checkmate)))
2131     (home-page "https://github.com/berndbischl/BBmisc")
2132     (synopsis "Miscellaneous functions for R package development")
2133     (description
2134      "This package provides miscellaneous helper functions for the development
2135 of R packages.")
2136     (license license:bsd-3)))
2137
2138 (define-public r-fail
2139   (package
2140     (name "r-fail")
2141     (version "1.3")
2142     (source
2143      (origin
2144        (method url-fetch)
2145        (uri (cran-uri "fail" version))
2146        (sha256
2147         (base32
2148          "0vfm6kmpmgsamda5p0sl771kbnsscan31l2chzssyw93kwmams7d"))))
2149     (build-system r-build-system)
2150     (propagated-inputs
2151      `(("r-bbmisc" ,r-bbmisc)
2152        ("r-checkmate" ,r-checkmate)))
2153     (home-page "https://github.com/mllg/fail")
2154     (synopsis "File abstraction interface layer (FAIL)")
2155     (description
2156      "This package provides a more comfortable interface to work with R data
2157 or source files in a key-value fashion.")
2158     (license license:bsd-3)))
2159
2160 (define-public r-batchjobs
2161   (package
2162     (name "r-batchjobs")
2163     (version "1.8")
2164     (source
2165      (origin
2166        (method url-fetch)
2167        (uri (cran-uri "BatchJobs" version))
2168        (sha256
2169         (base32
2170          "1zz4sspj596pijxlz321g0jy2rg9ki83j6fihbwisjwr66p2vk1m"))))
2171     (properties `((upstream-name . "BatchJobs")))
2172     (build-system r-build-system)
2173     (propagated-inputs
2174      `(("r-backports" ,r-backports)
2175        ("r-bbmisc" ,r-bbmisc)
2176        ("r-brew" ,r-brew)
2177        ("r-checkmate" ,r-checkmate)
2178        ("r-data-table" ,r-data-table)
2179        ("r-dbi" ,r-dbi)
2180        ("r-digest" ,r-digest)
2181        ("r-rsqlite" ,r-rsqlite)
2182        ("r-sendmailr" ,r-sendmailr)
2183        ("r-stringi" ,r-stringi)))
2184     (home-page "https://github.com/tudo-r/BatchJobs")
2185     (synopsis "Batch computing with R")
2186     (description
2187      "This package provides @code{Map}, @code{Reduce} and @code{Filter}
2188 variants to generate jobs on batch computing systems like PBS/Torque, LSF,
2189 SLURM and Sun Grid Engine.  Multicore and SSH systems are also supported.")
2190     (license license:bsd-2)))
2191
2192 (define-public r-brew
2193   (package
2194     (name "r-brew")
2195     (version "1.0-6")
2196     (source (origin
2197               (method url-fetch)
2198               (uri (cran-uri "brew" version))
2199               (sha256
2200                (base32
2201                 "1vghazbcha8gvkwwcdagjvzx6yl8zm7kgr0i9wxr4jng06d1l3fp"))))
2202     (build-system r-build-system)
2203     (home-page "https://cran.r-project.org/web/packages/brew")
2204     (synopsis "Templating framework for report generation")
2205     (description
2206      "The brew package implements a templating framework for mixing text and R
2207 code for report generation.  The template syntax is similar to PHP, Ruby's erb
2208 module, Java Server Pages, and Python's psp module.")
2209     (license license:gpl2+)))
2210
2211 (define-public r-desc
2212   (package
2213     (name "r-desc")
2214     (version "1.2.0")
2215     (source
2216      (origin
2217        (method url-fetch)
2218        (uri (cran-uri "desc" version))
2219        (sha256
2220         (base32
2221          "1s6s13fk6sxwcj8wzkwxl9vr33153xx11p5wi9avqx3rzkabavz6"))))
2222     (build-system r-build-system)
2223     (propagated-inputs
2224      `(("r-assertthat" ,r-assertthat)
2225        ("r-crayon" ,r-crayon)
2226        ("r-r6" ,r-r6)
2227        ("r-rprojroot" ,r-rprojroot)))
2228     (home-page "https://github.com/r-pkgs/desc")
2229     (synopsis "Manipulate DESCRIPTION Files")
2230     (description
2231      "This package provides tools to read, write, create, and manipulate
2232 DESCRIPTION files.  It is intended for packages that create or manipulate
2233 other packages.")
2234     (license license:expat)))
2235
2236 (define-public r-commonmark
2237   (package
2238     (name "r-commonmark")
2239     (version "1.7")
2240     (source
2241      (origin
2242        (method url-fetch)
2243        (uri (cran-uri "commonmark" version))
2244        (sha256
2245         (base32
2246          "024iz1qp2kv6iz6y69ir0jk3qhjps86rhkzlcmhqsxx97rx7cjni"))))
2247     (build-system r-build-system)
2248     (home-page "https://cran.r-project.org/web/packages/commonmark")
2249     (synopsis "CommonMark and Github Markdown Rendering in R")
2250     (description
2251      "The CommonMark specification defines a rationalized version of markdown
2252 syntax.  This package uses the @code{cmark} reference implementation for
2253 converting markdown text into various formats including HTML, LaTeX and groff
2254 man.  In addition, it exposes the markdown parse tree in XML format.  The latest
2255 version of this package also adds support for Github extensions including
2256 tables, autolinks and strikethrough text.")
2257     (license license:bsd-2)))
2258
2259 (define-public r-roxygen2
2260   (package
2261     (name "r-roxygen2")
2262     (version "7.0.2")
2263     (source (origin
2264               (method url-fetch)
2265               (uri (cran-uri "roxygen2" version))
2266               (sha256
2267                (base32
2268                 "162xag27hwwyadfwm5zpyy15nxwhw2vbhwapx3jmi9cfyryr68sq"))))
2269     (build-system r-build-system)
2270     (propagated-inputs
2271      `(("r-brew" ,r-brew)
2272        ("r-commonmark" ,r-commonmark)
2273        ("r-desc" ,r-desc)
2274        ("r-digest" ,r-digest)
2275        ("r-pkgload" ,r-pkgload)
2276        ("r-purrr" ,r-purrr)
2277        ("r-r6" ,r-r6)
2278        ("r-rcpp" ,r-rcpp)
2279        ("r-rlang" ,r-rlang)
2280        ("r-stringi" ,r-stringi)
2281        ("r-stringr" ,r-stringr)
2282        ("r-xml2" ,r-xml2)))
2283     (native-inputs
2284      `(("r-knitr" ,r-knitr))) ; for vignettes
2285     (home-page "https://github.com/klutometis/roxygen")
2286     (synopsis "In-source documentation system for R")
2287     (description
2288      "Roxygen2 is a Doxygen-like in-source documentation system for Rd,
2289 collation, and NAMESPACE files.")
2290     (license license:gpl2+)))
2291
2292 (define-public r-openssl
2293   (package
2294     (name "r-openssl")
2295     (version "1.4.1")
2296     (source
2297      (origin
2298        (method url-fetch)
2299        (uri (cran-uri "openssl" version))
2300        (sha256
2301         (base32
2302          "1ihz2qi33lhngl19xdanq0pbmfaacy63794mg8ll7z2lab3yryzp"))))
2303     (build-system r-build-system)
2304     (inputs
2305      `(("libressl" ,libressl)))
2306     (native-inputs
2307      `(("pkg-config" ,pkg-config)))
2308     (propagated-inputs
2309      `(("r-askpass" ,r-askpass)))
2310     (home-page "https://github.com/jeroenooms/openssl")
2311     (synopsis "Toolkit for encryption, signatures and certificates")
2312     (description
2313      "This package provides R bindings to OpenSSL libssl and libcrypto, plus
2314 custom SSH pubkey parsers.  It supports RSA, DSA and NIST curves P-256, P-384
2315 and P-521.  Cryptographic signatures can either be created and verified
2316 manually or via x509 certificates.  AES block cipher is used in CBC mode for
2317 symmetric encryption; RSA for asymmetric (public key) encryption.  High-level
2318 envelope functions combine RSA and AES for encrypting arbitrary sized data.
2319 Other utilities include key generators, hash functions (md5, sha1, sha256,
2320 etc), base64 encoder, a secure random number generator, and @code{bignum} math
2321 methods for manually performing crypto calculations on large multibyte
2322 integers.")
2323     (license license:expat)))
2324
2325 (define-public r-httr
2326   (package
2327     (name "r-httr")
2328     (version "1.4.1")
2329     (source (origin
2330               (method url-fetch)
2331               (uri (cran-uri "httr" version))
2332               (sha256
2333                (base32
2334                 "0mp1il13q6n49n2hv1p2p8x6avjan6dr5az19ql4hb78pc3pwp37"))))
2335     (build-system r-build-system)
2336     (propagated-inputs
2337      `(("r-curl" ,r-curl)
2338        ("r-jsonlite" ,r-jsonlite)
2339        ("r-openssl" ,r-openssl)
2340        ("r-mime" ,r-mime)
2341        ("r-r6" ,r-r6)))
2342     (home-page "https://github.com/hadley/httr")
2343     (synopsis "Tools for working with URLs and HTTP")
2344     (description
2345      "The aim of httr is to provide a wrapper for RCurl customised to the
2346 demands of modern web APIs.  It provides useful tools for working with HTTP
2347 organised by HTTP verbs (@code{GET()}, @code{POST()}, etc).  Configuration
2348 functions make it easy to control additional request components.")
2349     (license license:expat)))
2350
2351 (define-public r-git2r
2352   (package
2353     (name "r-git2r")
2354     (version "0.26.1")
2355     (source (origin
2356               (method url-fetch)
2357               (uri (cran-uri "git2r" version))
2358               (sha256
2359                (base32
2360                 "0dbl845sahv2i641ncaf06w06djravwc5wknp9syzx0ad8l0kmhk"))))
2361     (build-system r-build-system)
2362     (inputs
2363      `(("libgit2" ,libgit2)
2364        ("zlib" ,zlib)))
2365     (native-inputs
2366      `(("pkg-config" ,pkg-config)))
2367     (home-page "https://github.com/ropensci/git2r")
2368     (synopsis "Access Git repositories with R")
2369     (description
2370      "This package provides an R interface to the libgit2 library, which is a
2371 pure C implementation of the Git core methods.")
2372     ;; GPLv2 only with linking exception.
2373     (license license:gpl2)))
2374
2375 (define-public r-rstudioapi
2376   (package
2377     (name "r-rstudioapi")
2378     (version "0.10")
2379     (source (origin
2380               (method url-fetch)
2381               (uri (cran-uri "rstudioapi" version))
2382               (sha256
2383                (base32
2384                 "15mbw607ncdf53mgga76n3va5zzdcjqz14nb0jcn9axwccqamic0"))))
2385     (build-system r-build-system)
2386     (home-page "https://cran.r-project.org/web/packages/rstudioapi")
2387     (synopsis "Safely access the RStudio API")
2388     (description
2389      "This package provides functions to access the RStudio API and provide
2390 informative error messages when it's not available.")
2391     (license license:expat)))
2392
2393 (define-public r-devtools
2394   (package
2395     (name "r-devtools")
2396     (version "2.2.1")
2397     (source (origin
2398               (method url-fetch)
2399               (uri (cran-uri "devtools" version))
2400               (sha256
2401                (base32
2402                 "0i2f549hxkn0j1x1avkhwy68c9r48v9284j7x9cak2q6dfsqz61f"))))
2403     (build-system r-build-system)
2404     (propagated-inputs
2405      `(("r-callr" ,r-callr)
2406        ("r-cli" ,r-cli)
2407        ("r-covr" ,r-covr)
2408        ("r-crayon" ,r-crayon)
2409        ("r-desc" ,r-desc)
2410        ("r-digest" ,r-digest)
2411        ("r-dt" ,r-dt)
2412        ("r-ellipsis" ,r-ellipsis)
2413        ("r-glue" ,r-glue)
2414        ("r-git2r" ,r-git2r)
2415        ("r-httr" ,r-httr)
2416        ("r-jsonlite" ,r-jsonlite)
2417        ("r-memoise" ,r-memoise)
2418        ("r-pkgbuild" ,r-pkgbuild)
2419        ("r-pkgload" ,r-pkgload)
2420        ("r-rcmdcheck" ,r-rcmdcheck)
2421        ("r-remotes" ,r-remotes)
2422        ("r-rlang" ,r-rlang)
2423        ("r-roxygen2" ,r-roxygen2)
2424        ("r-rstudioapi" ,r-rstudioapi)
2425        ("r-rversions" ,r-rversions)
2426        ("r-sessioninfo" ,r-sessioninfo)
2427        ("r-testthat" ,r-testthat)
2428        ("r-usethis" ,r-usethis)
2429        ("r-withr" ,r-withr)))
2430     (home-page "https://github.com/hadley/devtools")
2431     (synopsis "Tools to make developing R packages easier")
2432     (description "The devtools package is a collection of package development
2433 tools to simplify the devolpment of R packages.")
2434     (license license:gpl2+)))
2435
2436 (define-public r-withr
2437   (package
2438     (name "r-withr")
2439     (version "2.1.2")
2440     (source (origin
2441               (method url-fetch)
2442               (uri (cran-uri "withr" version))
2443               (sha256
2444                (base32
2445                 "11j6zykklxnvp4xqsr6a2xib665i38m3khdspp887nwagmvnydj1"))))
2446     (build-system r-build-system)
2447     (home-page "https://github.com/jimhester/withr")
2448     (synopsis "Run code with temporarily modified global state")
2449     (description
2450      "This package provides a set of functions to run R code in an environment
2451 in which global state has been temporarily modified.  Many of these functions
2452 were originally a part of the r-devtools package.")
2453     (license license:gpl2+)))
2454
2455 (define-public r-hms
2456   (package
2457     (name "r-hms")
2458     (version "0.5.3")
2459     (source
2460      (origin
2461        (method url-fetch)
2462        (uri (cran-uri "hms" version))
2463        (sha256
2464         (base32
2465          "1baki0qw5ijgiflvsdvqj3apg4yanf12vx14kwbqdzk5rz46fasf"))))
2466     (build-system r-build-system)
2467     (propagated-inputs
2468      `(("r-rlang" ,r-rlang)
2469        ("r-pkgconfig" ,r-pkgconfig)
2470        ("r-vctrs" ,r-vctrs)))
2471     (home-page "https://github.com/rstats-db/hms")
2472     (synopsis "Pretty time of day")
2473     (description
2474      "This package implements an S3 class for storing and formatting
2475 time-of-day values, based on the @code{difftime} class.")
2476     (license license:gpl3+)))
2477
2478 (define-public r-readr
2479   (package
2480     (name "r-readr")
2481     (version "1.3.1")
2482     (source (origin
2483               (method url-fetch)
2484               (uri (cran-uri "readr" version))
2485               (sha256
2486                (base32
2487                 "1wz496rw0ah433p755n3xac8gh7yzid4xgdjzd1a7wmpkgilvy9k"))))
2488     (build-system r-build-system)
2489     (propagated-inputs
2490      `(("r-clipr" ,r-clipr)
2491        ("r-crayon" ,r-crayon)
2492        ("r-rcpp" ,r-rcpp)
2493        ("r-hms" ,r-hms)
2494        ("r-tibble" ,r-tibble)
2495        ("r-r6" ,r-r6)
2496        ("r-bh" ,r-bh)))
2497     (home-page "https://github.com/hadley/readr")
2498     (synopsis "Read tabular data")
2499     (description
2500      "This package provides functions to read flat or tabular text files from
2501 disk (or a connection).")
2502     (license license:gpl2+)))
2503
2504 (define-public r-plotrix
2505   (package
2506     (name "r-plotrix")
2507     (version "3.7-7")
2508     (source (origin
2509               (method url-fetch)
2510               (uri (cran-uri "plotrix" version))
2511               (sha256
2512                (base32
2513                 "1x92mmyfry127zzr6cmcj6kjsc4zhxrrdlr0jcxn3bb0hpdfps54"))))
2514     (build-system r-build-system)
2515     (home-page "https://cran.r-project.org/web/packages/plotrix")
2516     (synopsis "Various plotting functions")
2517     (description
2518      "This package provides lots of plotting, various labeling, axis and color
2519 scaling functions for R.")
2520     (license license:gpl2+)))
2521
2522 (define-public r-gridbase
2523   (package
2524     (name "r-gridbase")
2525     (version "0.4-7")
2526     (source (origin
2527               (method url-fetch)
2528               (uri (cran-uri "gridBase" version))
2529               (sha256
2530                (base32
2531                 "09jzw4rzwf2y5lcz7b16mb68pn0fqigv34ff7lr6w3yi9k91i1xy"))))
2532     (build-system r-build-system)
2533     (home-page "https://cran.r-project.org/web/packages/gridBase")
2534     (synopsis "Integration of base and grid graphics")
2535     (description
2536      "This package provides an integration of base and grid graphics for R.")
2537     (license license:gpl2+)))
2538
2539 (define-public r-latticeextra
2540   (package
2541     (name "r-latticeextra")
2542     (version "0.6-29")
2543     (source
2544      (origin
2545        (method url-fetch)
2546        (uri (cran-uri "latticeExtra" version))
2547        (sha256
2548         (base32
2549          "04fzwcqs594rk5qp98yilh3kdh3sw4xf8wld5rp94ggpaqfw7bbc"))))
2550     (properties `((upstream-name . "latticeExtra")))
2551     (build-system r-build-system)
2552     (propagated-inputs
2553      `(("r-jpeg" ,r-jpeg)
2554        ("r-lattice" ,r-lattice)
2555        ("r-png" ,r-png)
2556        ("r-rcolorbrewer" ,r-rcolorbrewer)))
2557     (home-page "http://latticeextra.r-forge.r-project.org/")
2558     (synopsis "Extra graphical utilities based on lattice")
2559     (description
2560      "Building on the infrastructure provided by the lattice package, this
2561 package provides several new high-level graphics functions and methods, as
2562 well as additional utilities such as panel and axis annotation functions.")
2563     (license license:gpl2+)))
2564
2565 (define-public r-rcpparmadillo
2566   (package
2567     (name "r-rcpparmadillo")
2568     (version "0.9.800.4.0")
2569     (source (origin
2570               (method url-fetch)
2571               (uri (cran-uri "RcppArmadillo" version))
2572               (sha256
2573                (base32
2574                 "1csh54v4d0ccwmk4bqj4rca1d5rqpafvb4459x3q6k9sys0charx"))))
2575     (properties `((upstream-name . "RcppArmadillo")))
2576     (build-system r-build-system)
2577     ;; All needed for vignettes
2578     (native-inputs
2579      `(("r-knitr" ,r-knitr)
2580        ("r-rmarkdown" ,r-rmarkdown)
2581        ("ghc-pandoc" ,ghc-pandoc)
2582        ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc)))
2583     (propagated-inputs
2584      `(("r-rcpp" ,r-rcpp)))
2585     (home-page "https://github.com/RcppCore/RcppArmadillo")
2586     (synopsis "Rcpp integration for the Armadillo linear algebra library")
2587     (description
2588      "Armadillo is a templated C++ linear algebra library that aims towards a
2589 good balance between speed and ease of use.  Integer, floating point and
2590 complex numbers are supported, as well as a subset of trigonometric and
2591 statistics functions.  Various matrix decompositions are provided through
2592 optional integration with LAPACK and ATLAS libraries.  This package includes
2593 the header files from the templated Armadillo library.")
2594     ;; Armadillo is licensed under the MPL 2.0, while RcppArmadillo (the Rcpp
2595     ;; bindings to Armadillo) is licensed under the GNU GPL version 2 or
2596     ;; later, as is the rest of 'Rcpp'.
2597     (license license:gpl2+)))
2598
2599 (define-public r-bitops
2600   (package
2601     (name "r-bitops")
2602     (version "1.0-6")
2603     (source (origin
2604               (method url-fetch)
2605               (uri (cran-uri "bitops" version))
2606               (sha256
2607                (base32
2608                 "176nr5wpnkavn5z0yy9f7d47l37ndnn2w3gv854xav8nnybi6wwv"))))
2609     (build-system r-build-system)
2610     (home-page "https://cran.r-project.org/web/packages/bitops")
2611     (synopsis "Bitwise operations")
2612     (description
2613      "This package provides functions for bitwise operations on integer
2614 vectors.")
2615     (license license:gpl2+)))
2616
2617 (define-public r-catools
2618   (package
2619     (name "r-catools")
2620     (version "1.18.0")
2621     (source (origin
2622               (method url-fetch)
2623               (uri (cran-uri "caTools" version))
2624               (sha256
2625                (base32
2626                 "0y1kgyiy322yhb0phzwvf2zgjz9awp13lhzhk9v1ddg88656jhq3"))))
2627     (properties `((upstream-name . "caTools")))
2628     (build-system r-build-system)
2629     (propagated-inputs
2630      `(("r-bitops" ,r-bitops)))
2631     (home-page "https://cran.r-project.org/web/packages/caTools")
2632     (synopsis "Various tools including functions for moving window statistics")
2633     (description
2634      "This package contains several basic utility functions including:
2635 moving (rolling, running) window statistic functions, read/write for GIF and
2636 ENVI binary files, fast calculation of AUC, LogitBoost classifier, base64
2637 encoder/decoder, round-off-error-free sum and cumsum, etc.")
2638     (license license:gpl3+)))
2639
2640 (define-public r-rprojroot
2641   (package
2642     (name "r-rprojroot")
2643     (version "1.3-2")
2644     (source
2645      (origin
2646        (method url-fetch)
2647        (uri (cran-uri "rprojroot" version))
2648        (sha256
2649         (base32
2650          "12r3fdxmi2pmwn6ic3rhg0b20ll5z420m0d8fziv1n21961namnz"))))
2651     (build-system r-build-system)
2652     (propagated-inputs
2653      `(("r-backports" ,r-backports)))
2654     (home-page "https://github.com/krlmlr/rprojroot")
2655     (synopsis "Finding files in project subdirectories")
2656     (description
2657      "This package helps accessing files relative to a project root.  It
2658 provides helpers for robust, reliable and flexible paths to files below a
2659 project root.  The root of a project is defined as a directory that matches a
2660 certain criterion, e.g., it contains a certain regular file.")
2661     (license license:gpl3)))
2662
2663 (define-public r-rmarkdown
2664   (package
2665     (name "r-rmarkdown")
2666     (version "2.1")
2667     (source
2668       (origin
2669         (method url-fetch)
2670         (uri (cran-uri "rmarkdown" version))
2671         (sha256
2672           (base32 "0pa5xs0vzwn9vsgysjqbks9v5lbqphxh5agciskllibc40hhwigg"))))
2673     (properties `((upstream-name . "rmarkdown")))
2674     (build-system r-build-system)
2675     (propagated-inputs
2676      `(("r-base64enc" ,r-base64enc)
2677        ("r-evaluate" ,r-evaluate)
2678        ("r-htmltools" ,r-htmltools)
2679        ("r-jsonlite" ,r-jsonlite)
2680        ("r-knitr" ,r-knitr)
2681        ("r-mime" ,r-mime)
2682        ("r-stringr" ,r-stringr)
2683        ("r-tinytex" ,r-tinytex)
2684        ("r-xfun" ,r-xfun)
2685        ("r-yaml" ,r-yaml)
2686        ("ghc-pandoc" ,ghc-pandoc)))
2687     (home-page "https://rmarkdown.rstudio.com")
2688     (synopsis "Convert R Markdown documents into a variety of formats")
2689     (description
2690      "This package provides tools to convert R Markdown documents into a
2691 variety of formats.")
2692     (license license:gpl3+)))
2693
2694 (define-public r-gtable
2695   (package
2696     (name "r-gtable")
2697     (version "0.3.0")
2698     (source (origin
2699               (method url-fetch)
2700               (uri (cran-uri "gtable" version))
2701               (sha256
2702                (base32
2703                 "1lyncxf2dqdjgw1071cn9c8zwzkz6sldnd5cgmicf70bc726qf7x"))))
2704     (properties `((upstream-name . "gtable")))
2705     (build-system r-build-system)
2706     (home-page "https://cran.r-project.org/web/packages/gtable")
2707     (synopsis "R library to arrange grobs in tables")
2708     (description
2709      "Gtable is a collection of tools to make it easier to work with
2710 \"tables\" of grobs.")
2711     (license license:gpl2+)))
2712
2713 (define-public r-gridextra
2714   (package
2715     (name "r-gridextra")
2716     (version "2.3")
2717     (source (origin
2718               (method url-fetch)
2719               (uri (cran-uri "gridExtra" version))
2720               (sha256
2721                (base32
2722                 "0fwfk3cdwxxim7nd55pn7m31bcaqj48y06j7an2k1v1pybk0rdl1"))))
2723     (properties `((upstream-name . "gridExtra")))
2724     (build-system r-build-system)
2725     (propagated-inputs
2726      `(("r-gtable" ,r-gtable)))
2727     (native-inputs
2728      `(("r-knitr" ,r-knitr))) ;for building vignettes
2729     (home-page "https://github.com/baptiste/gridextra")
2730     (synopsis "Miscellaneous functions for \"Grid\" graphics")
2731     (description
2732      "This package provides a number of user-level functions to work with
2733 @code{grid} graphics, notably to arrange multiple grid-based plots on a page,
2734 and draw tables.")
2735     (license license:gpl2+)))
2736
2737 (define-public r-pkgconfig
2738   (package
2739     (name "r-pkgconfig")
2740     (version "2.0.3")
2741     (source (origin
2742               (method url-fetch)
2743               (uri (cran-uri "pkgconfig" version))
2744               (sha256
2745                (base32
2746                 "0l1qph8zyi2sic3k2qcd7vlfl7rzfh1q7z7zvjkl5f7y1x2fy3rk"))))
2747     (build-system r-build-system)
2748     (home-page "https://github.com/gaborcsardi/pkgconfig")
2749     (synopsis "Private configuration for R packages")
2750     (description "This package provides the functionality to set configuration
2751 options on a per-package basis.  Options set by a given package only apply to
2752 that package, other packages are unaffected.")
2753     (license license:expat)))
2754
2755 (define-public r-blob
2756   (package
2757     (name "r-blob")
2758     (version "1.2.1")
2759     (source (origin
2760               (method url-fetch)
2761               (uri (cran-uri "blob" version))
2762               (sha256
2763                (base32
2764                 "1slb5mvxfyi92i8ifx2qa31hp57inilwhq1g9lzvgha6jrxbqm7g"))))
2765     (build-system r-build-system)
2766     (propagated-inputs
2767      `(("r-rlang" ,r-rlang)
2768        ("r-vctrs" ,r-vctrs)))
2769     (home-page "https://github.com/hadley/blob")
2770     (synopsis "Simple S3 Class for representing vectors of binary data")
2771     (description "Raw vectors in R are useful for storing a single binary
2772 object.  What if you want to put a vector of them in a data frame?  The blob
2773 package provides the blob object, a list of raw vectors, suitable for use as
2774 a column in data frame.")
2775     (license license:gpl3+)))
2776
2777 (define-public r-rsqlite
2778   (package
2779     (name "r-rsqlite")
2780     (version "2.2.0")
2781     (source (origin
2782               (method url-fetch)
2783               (uri (cran-uri "RSQLite" version))
2784               (sha256
2785                (base32
2786                 "1m38sj8rwbf3p2lhqabcp7c7djk7s9ng37cz39yxk706v9pi4380"))))
2787     (properties `((upstream-name . "RSQLite")))
2788     (build-system r-build-system)
2789     (propagated-inputs
2790      `(("r-dbi" ,r-dbi)
2791        ("r-bh" ,r-bh)
2792        ("r-memoise" ,r-memoise)
2793        ("r-plogr" ,r-plogr)
2794        ("r-rcpp" ,r-rcpp)
2795        ("r-bit64" ,r-bit64)
2796        ("r-blob" ,r-blob)
2797        ("r-pkgconfig" ,r-pkgconfig)))
2798     (home-page "https://github.com/rstats-db/RSQLite")
2799     (synopsis "SQLite interface for R")
2800     (description
2801      "This package embeds the SQLite database engine in R and provides an
2802 interface compliant with the DBI package.  The source for the SQLite
2803 engine (version 3.8.8.2) is included.")
2804     (license license:lgpl2.0+)))
2805
2806 (define-public r-rcurl
2807   (package
2808     (name "r-rcurl")
2809     (version "1.95-0.1.2")
2810     (source (origin
2811               (method url-fetch)
2812               (uri (string-append "https://www.bioconductor.org/packages/"
2813                                   "release/extra/src/"
2814                                   "contrib/RCurl_" version ".tar.gz"))
2815               (sha256
2816                (base32
2817                 "0l7qi45jxlf898n0jazabnam1yyczvqfdknd00bdirhhiplpd1sc"))))
2818     (properties `((upstream-name . "RCurl")))
2819     (build-system r-build-system)
2820     (arguments
2821      `(#:phases
2822        (modify-phases %standard-phases
2823          (add-after 'unpack 'respect-CURL_CA_BUNDLE
2824            (lambda _
2825              (substitute* "R/options.S"
2826                (("\\.els = rev\\(merge\\(list\\(\\.\\.\\.\\), \\.opts\\)\\)" m)
2827                 (string-append "\
2828 certs = Sys.getenv(\"CURL_CA_BUNDLE\")
2829 if (certs != \"\") { .opts = merge.list(.opts, list(cainfo=certs)) }
2830 " m)))
2831              #t)))))
2832     (inputs
2833      `(("libcurl" ,curl)))
2834     (propagated-inputs
2835      `(("r-bitops" ,r-bitops)))
2836     (home-page "http://www.omegahat.org/RCurl")
2837     (synopsis "General network client interface for R")
2838     (description
2839      "The package allows one to compose general HTTP requests and provides
2840 convenient functions to fetch URIs, GET and POST forms, etc. and process the
2841 results returned by the Web server.  This provides a great deal of control
2842 over the HTTP/FTP/... connection and the form of the request while providing a
2843 higher-level interface than is available just using R socket connections.
2844 Additionally, the underlying implementation is robust and extensive,
2845 supporting FTP/FTPS/TFTP (uploads and downloads), SSL/HTTPS, telnet, dict,
2846 ldap, and also supports cookies, redirects, authentication, etc.")
2847     (license license:bsd-3)))
2848
2849 (define-public r-xml
2850   (package
2851     (name "r-xml")
2852     (version "3.98-1.20")
2853     (source (origin
2854               (method url-fetch)
2855               (uri (cran-uri "XML" version))
2856               (sha256
2857                (base32
2858                 "0n28m8iz1wfgixr7fjswl238c5w9kggsrw0c8hdzp859dqvqdbs6"))))
2859     (properties
2860      `((upstream-name . "XML")))
2861     (build-system r-build-system)
2862     (inputs
2863      `(("libxml2" ,libxml2)
2864        ("zlib" ,zlib)))
2865     (native-inputs
2866      `(("pkg-config" ,pkg-config)))
2867     (home-page "http://www.omegahat.org/RSXML")
2868     (synopsis "Tools for parsing and generating XML within R")
2869     (description
2870      "Many approaches for both reading and creating XML (and HTML)
2871 documents (including DTDs), both local and accessible via HTTP or FTP.  Also
2872 offers access to an XPath \"interpreter\".")
2873     (license license:bsd-2)))
2874
2875 (define-public r-xnomial
2876   (package
2877     (name "r-xnomial")
2878     (version "1.0.4")
2879     (source
2880      (origin (method url-fetch)
2881              (uri (cran-uri "XNomial" version))
2882              (sha256
2883               (base32
2884                "1mwx302576rmsjllbq2clfxilm3hkyp5bw0wmwqbn0kgv5wpy8z6"))))
2885     (properties (quasiquote ((upstream-name . "XNomial"))))
2886     (build-system r-build-system)
2887     (home-page "https://cran.r-project.org/web/packages/XNomial")
2888     (synopsis "Goodness-of-Fit test for multinomial data")
2889     (description
2890      "This package provides an exact Goodness-of-Fit test for
2891 multinomial data with fixed probabilities.  It can be used to
2892 determine whether a set of counts fits a given expected ratio.  To see
2893 whether a set of observed counts fits an expectation, one can examine
2894 all possible outcomes with @code{xmulti()} or a random sample of them
2895 with @code{xmonte()} and find the probability of an observation
2896 deviating from the expectation by at least as much as the observed.
2897 As a measure of deviation from the expected, one can use the
2898 log-likelihood ratio, the multinomial probability, or the classic
2899 chi-square statistic.  A histogram of the test statistic can also be
2900 plotted and compared with the asymptotic curve.")
2901     (license (list license:gpl2+ license:gpl3+))))
2902
2903 (define-public r-lambda-r
2904   (package
2905     (name "r-lambda-r")
2906     (version "1.2.4")
2907     (source (origin
2908               (method url-fetch)
2909               (uri (cran-uri "lambda.r" version))
2910               (sha256
2911                (base32
2912                 "1mh1g0gsd58gng0hb29vww2yqb2jfs07kba5kxnnqck5j3izwlnj"))))
2913     (properties `((upstream-name . "lambda.r")))
2914     (build-system r-build-system)
2915     (propagated-inputs
2916      `(("r-formatr" ,r-formatr)))
2917     (home-page "https://cran.r-project.org/web/packages/lambda.r")
2918     (synopsis "Functional programming extension for R")
2919     (description
2920      "This package provides a language extension to efficiently write
2921 functional programs in R.  Syntax extensions include multi-part function
2922 definitions, pattern matching, guard statements, built-in (optional) type
2923 safety.")
2924     (license license:lgpl3+)))
2925
2926 (define-public r-futile-options
2927   (package
2928     (name "r-futile-options")
2929     (version "1.0.1")
2930     (source (origin
2931               (method url-fetch)
2932               (uri (cran-uri "futile.options" version))
2933               (sha256
2934                (base32
2935                 "0w15agpi88y3qkv6fl72zy2pzyplzgvnj41a4ixhg64mw1sck73s"))))
2936     (properties
2937      `((upstream-name . "futile.options")))
2938     (build-system r-build-system)
2939     (home-page "https://cran.r-project.org/web/packages/futile.options")
2940     (synopsis "Options management framework")
2941     (description
2942      "The futile.options subsystem provides an easy user-defined options
2943 management system that is properly scoped.  This means that options created
2944 via @code{futile.options} are fully self-contained and will not collide with
2945 options defined in other packages.")
2946     (license license:lgpl3+)))
2947
2948 (define-public r-futile-logger
2949   (package
2950     (name "r-futile-logger")
2951     (version "1.4.3")
2952     (source (origin
2953               (method url-fetch)
2954               (uri (cran-uri "futile.logger" version))
2955               (sha256
2956                (base32
2957                 "1r3nayk0z9n1svbf8640vw90dal5q07nkn0gv4bnva3pbzb352sy"))))
2958     (properties `((upstream-name . "futile.logger")))
2959     (build-system r-build-system)
2960     (propagated-inputs
2961      `(("r-futile-options" ,r-futile-options)
2962        ("r-lambda-r" ,r-lambda-r)))
2963     (home-page "https://cran.r-project.org/web/packages/futile.logger")
2964     (synopsis "Logging utility for R")
2965     (description
2966      "This package provides a simple yet powerful logging utility.  Based
2967 loosely on log4j, futile.logger takes advantage of R idioms to make logging a
2968 convenient and easy to use replacement for @code{cat} and @code{print}
2969 statements.")
2970     (license license:lgpl3+)))
2971
2972 (define-public r-segmented
2973   (package
2974     (name "r-segmented")
2975     (version "1.1-0")
2976     (source
2977      (origin
2978        (method url-fetch)
2979        (uri (cran-uri "segmented" version))
2980        (sha256
2981         (base32
2982          "06cxdrqgnpk5fvbam5i7qa4n71wry0yvlj0jpwbxf267mvpx10fh"))))
2983     (build-system r-build-system)
2984     (home-page "https://cran.r-project.org/web/packages/segmented")
2985     (synopsis "Regression models with breakpoints estimation")
2986     (description
2987      "Given a regression model, segmented updates the model by adding one or
2988 more segmented (i.e., piecewise-linear) relationships.  Several variables with
2989 multiple breakpoints are allowed.")
2990     (license (list license:gpl2+ license:gpl3+))))
2991
2992 (define-public r-snow
2993   (package
2994     (name "r-snow")
2995     (version "0.4-3")
2996     (source (origin
2997               (method url-fetch)
2998               (uri (cran-uri "snow" version))
2999               (sha256
3000                (base32
3001                 "1n3n8pva9s34fvlw32yng0x416lmbv7q1fsd0ywa4kikmxym64l5"))))
3002     (build-system r-build-system)
3003     (home-page "https://cran.r-project.org/web/packages/snow")
3004     (synopsis "Support for simple parallel computing in R")
3005     (description
3006      "The snow package provides support for simple parallel computing on a
3007 network of workstations using R.  A master R process calls @code{makeCluster}
3008 to start a cluster of worker processes; the master process then uses functions
3009 such as @code{clusterCall} and @code{clusterApply} to execute R code on the
3010 worker processes and collect and return the results on the master.")
3011     (license (list license:gpl2+ license:gpl3+))))
3012
3013 (define-public r-sparsem
3014   (package
3015     (name "r-sparsem")
3016     (version "1.78")
3017     (source (origin
3018               (method url-fetch)
3019               (uri (cran-uri "SparseM" version))
3020               (sha256
3021                (base32
3022                 "0cmlm0lps3daalvp5jzjnjfys388hgkyc8yw0g5r2351h749xdyn"))))
3023     (properties
3024      `((upstream-name . "SparseM")))
3025     (native-inputs
3026      `(("gfortran" ,gfortran)))
3027     (build-system r-build-system)
3028     (home-page "http://www.econ.uiuc.edu/~roger/research/sparse/sparse.html")
3029     (synopsis "Sparse linear algebra")
3030     (description
3031      "This package provides some basic linear algebra functionality for sparse
3032 matrices.  It includes Cholesky decomposition and backsolving as well as
3033 standard R subsetting and Kronecker products.")
3034     (license license:gpl2+)))
3035
3036 (define-public r-iterators
3037   (package
3038     (name "r-iterators")
3039     (version "1.0.12")
3040     (source
3041      (origin
3042        (method url-fetch)
3043        (uri (cran-uri "iterators" version))
3044        (sha256
3045         (base32
3046          "0jwzxaa3jm1xzgfv5pn0xqkk7rhm0xwvgn85w7xaw8xx1vb33gwn"))))
3047     (build-system r-build-system)
3048     (home-page "https://cran.r-project.org/web/packages/iterators")
3049     (synopsis "Iterator construct for R")
3050     (description
3051      "This package provides support for iterators, which allow a programmer to
3052 traverse through all the elements of a vector, list, or other collection of
3053 data.")
3054     (license license:asl2.0)))
3055
3056 (define-public r-foreach
3057   (package
3058     (name "r-foreach")
3059     (version "1.4.7")
3060     (source
3061      (origin
3062        (method url-fetch)
3063        (uri (cran-uri "foreach" version))
3064        (sha256
3065         (base32
3066          "0q7iyniw5iri4hl57bhil3r69s5wnaijzn0q0x4h3z42245jqqwm"))))
3067     (build-system r-build-system)
3068     (propagated-inputs
3069      `(("r-codetools" ,r-codetools)
3070        ("r-iterators" ,r-iterators)))
3071     (home-page "https://cran.r-project.org/web/packages/foreach")
3072     (synopsis "Foreach looping construct for R")
3073     (description
3074      "This package provides support for the @code{foreach} looping construct.
3075 @code{foreach} is an idiom that allows for iterating over elements in a
3076 collection, without the use of an explicit loop counter.  This package in
3077 particular is intended to be used for its return value, rather than for its
3078 side effects.  In that sense, it is similar to the standard @code{lapply}
3079 function, but doesn't require the evaluation of a function.  Using
3080 @code{foreach} without side effects also facilitates executing the loop in
3081 parallel.")
3082     (license license:asl2.0)))
3083
3084 (define-public r-doparallel
3085   (package
3086     (name "r-doparallel")
3087     (version "1.0.15")
3088     (source
3089      (origin
3090        (method url-fetch)
3091        (uri (cran-uri "doParallel" version))
3092        (sha256
3093         (base32
3094          "0vnqbha3gig3awbfvsfx3ni5jir398md1n7xmsb8jihnjsk7xbbi"))))
3095     (properties `((upstream-name . "doParallel")))
3096     (build-system r-build-system)
3097     (propagated-inputs
3098      `(("r-foreach" ,r-foreach)
3099        ("r-iterators" ,r-iterators)))
3100     (home-page "https://cran.r-project.org/web/packages/doParallel")
3101     (synopsis "Foreach parallel adaptor for the 'parallel' package")
3102     (description
3103      "This package provides a parallel backend for the @code{%dopar%} function
3104 using the parallel package.")
3105     (license license:gpl2+)))
3106
3107 (define-public r-domc
3108   (package
3109     (name "r-domc")
3110     (version "1.3.6")
3111     (source
3112      (origin
3113        (method url-fetch)
3114        (uri (cran-uri "doMC" version))
3115        (sha256
3116         (base32
3117          "1cn9gxavhvjswip8pwvkpi7q6wpzdllcsdjabga8akf55nggqxr9"))))
3118     (properties `((upstream-name . "doMC")))
3119     (build-system r-build-system)
3120     (propagated-inputs
3121      `(("r-foreach" ,r-foreach)
3122        ("r-iterators" ,r-iterators)))
3123     (home-page "https://cran.r-project.org/web/packages/doMC")
3124     (synopsis "Foreach parallel adaptor for the 'parallel' package")
3125     (description
3126      "This package provides a parallel backend for the @code{%dopar%} function
3127 using the multicore functionality of the parallel package.")
3128     (license license:gpl2+)))
3129
3130 (define-public r-dt
3131   (package
3132     (name "r-dt")
3133     (version "0.11")
3134     (source (origin
3135               (method url-fetch)
3136               (uri (cran-uri "DT" version))
3137               (sha256
3138                (base32
3139                 "09k9s07aah1apc308sj1abvr27mky6fkpl9j6lxl2x55n4immvkg"))))
3140     (properties
3141      `((upstream-name . "DT")))
3142     (build-system r-build-system)
3143     (propagated-inputs
3144      `(("r-crosstalk" ,r-crosstalk)
3145        ("r-htmltools" ,r-htmltools)
3146        ("r-htmlwidgets" ,r-htmlwidgets)
3147        ("r-jsonlite" ,r-jsonlite)
3148        ("r-magrittr" ,r-magrittr)
3149        ("r-promises" ,r-promises)))
3150     (home-page "http://rstudio.github.io/DT")
3151     (synopsis "R wrapper of the DataTables JavaScript library")
3152     (description
3153      "This package allows for data objects in R to be rendered as HTML tables
3154 using the JavaScript library @code{DataTables} (typically via R Markdown or
3155 Shiny).  The @code{DataTables} library has been included in this R package.")
3156     ;; The DT package as a whole is distributed under GPLv3.  The DT package
3157     ;; inludes other software components under different licenses:
3158     ;;
3159     ;;   * Expat: jQuery, jquery.highlight.js, DataTables
3160     ;;   * ASL2.0: selectize.js
3161     ;;   * WTFPL: noUiSlider
3162     (license (list license:gpl3
3163                    license:expat
3164                    license:asl2.0
3165                    (license:non-copyleft "http://www.wtfpl.net/txt/copying/")))))
3166
3167 (define-public r-base64enc
3168   (package
3169     (name "r-base64enc")
3170     (version "0.1-3")
3171     (source (origin
3172               (method url-fetch)
3173               (uri (cran-uri "base64enc" version))
3174               (sha256
3175                (base32
3176                 "13b89fhg1nx7zds82a0biz847ixphg9byf5zl2cw9kab6s56v1bd"))))
3177     (build-system r-build-system)
3178     (home-page "http://www.rforge.net/base64enc")
3179     (synopsis "Tools for Base64 encoding")
3180     (description
3181      "This package provides tools for handling Base64 encoding.  It is more
3182 flexible than the orphaned \"base64\" package.")
3183     (license license:gpl2+)))
3184
3185 (define-public r-irlba
3186   (package
3187     (name "r-irlba")
3188     (version "2.3.3")
3189     (source
3190      (origin
3191        (method url-fetch)
3192        (uri (cran-uri "irlba" version))
3193        (sha256
3194         (base32
3195          "1h7mzrqdjc41814cf6c93sbyl7nxwvsf3x8apl9rhmydgdlk7qkf"))))
3196     (build-system r-build-system)
3197     (propagated-inputs
3198      `(("r-matrix" ,r-matrix)))
3199     (home-page "https://cran.r-project.org/web/packages/irlba")
3200     (synopsis "Methods for eigendecomposition of large matrices")
3201     (description
3202      "This package provides fast and memory efficient methods for truncated
3203 singular and eigenvalue decompositions, as well as for principal component
3204 analysis of large sparse or dense matrices.")
3205     (license (list license:gpl2+ license:gpl3+))))
3206
3207 (define-public r-glmnet
3208   (package
3209    (name "r-glmnet")
3210    (version "3.0-2")
3211    (source
3212     (origin
3213      (method url-fetch)
3214      (uri (cran-uri "glmnet" version))
3215      (sha256
3216       (base32 "0b3nnfzp8dxcdkvxr0yvy6d58yk3xg4kz1wqa42bxqppbakmd2gl"))))
3217    (build-system r-build-system)
3218    (native-inputs
3219     `(("gfortran" ,gfortran)))
3220    (propagated-inputs
3221     `(("r-foreach" ,r-foreach)
3222       ("r-matrix" ,r-matrix)
3223       ("r-shape" ,r-shape)))
3224    (home-page "http://www.jstatsoft.org/v33/i01")
3225    (synopsis "Lasso and elastic-net regularized generalized linear models")
3226    (description
3227     "The glmnet package provides efficient procedures for fitting the entire
3228 lasso or elastic-net regularization path for linear and Poisson regression, as
3229 well as logistic, multinomial, Cox, multiple-response Gaussian and grouped
3230 multinomial models.  The algorithm uses cyclical coordinate descent in a
3231 path-wise fashion.")
3232    (license license:gpl2+)))
3233
3234 (define-public r-pkgmaker
3235   (package
3236     (name "r-pkgmaker")
3237     (version "0.27")
3238     (source
3239      (origin
3240        (method url-fetch)
3241        (uri (cran-uri "pkgmaker" version))
3242        (sha256
3243         (base32
3244          "0spcamjncj78kzjps2rw4v1a4494yazv6xvhn0vmdflnypc8k8hp"))))
3245     (build-system r-build-system)
3246     (propagated-inputs
3247      `(("r-bibtex" ,r-bibtex)
3248        ("r-codetools" ,r-codetools)
3249        ("r-digest" ,r-digest)
3250        ("r-magrittr" ,r-magrittr)
3251        ("r-registry" ,r-registry)
3252        ("r-stringi" ,r-stringi)
3253        ("r-stringr" ,r-stringr)
3254        ("r-withr" ,r-withr)
3255        ("r-xtable" ,r-xtable)))
3256     (home-page "https://renozao.github.io/pkgmaker")
3257     (synopsis "Package development utilities")
3258     (description
3259      "This package provides some low-level utilities to use for R package
3260 development.  It currently provides managers for multiple package specific
3261 options and registries, vignette, unit test and bibtex related utilities.")
3262     (license license:gpl2+)))
3263
3264  (define-public r-registry
3265    (package
3266      (name "r-registry")
3267      (version "0.5-1")
3268      (source
3269       (origin
3270         (method url-fetch)
3271         (uri (cran-uri "registry" version))
3272         (sha256
3273          (base32
3274           "1k3j6dx350awamr0dwwgkhfs46vsnj4nf08iw5byq0x7n3nkdsnz"))))
3275      (build-system r-build-system)
3276      (home-page "https://cran.r-project.org/web/packages/registry")
3277      (synopsis "Infrastructure for R package registries")
3278      (description
3279       "This package provides a generic infrastructure for creating and using R
3280 package registries.")
3281      (license license:gpl2+)))
3282
3283 (define-public r-rngtools
3284   (package
3285     (name "r-rngtools")
3286     (version "1.4")
3287     (source
3288      (origin
3289        (method url-fetch)
3290        (uri (cran-uri "rngtools" version))
3291        (sha256
3292         (base32
3293          "1kivj594bn774lbn29ws2rmzy2km99sza0j3jqvhal6hwmk27a9s"))))
3294     (build-system r-build-system)
3295     (propagated-inputs
3296      `(("r-digest" ,r-digest)
3297        ("r-pkgmaker" ,r-pkgmaker)
3298        ("r-stringr" ,r-stringr)))
3299     (home-page "https://renozao.github.io/rngtools")
3300     (synopsis "Utility functions for working with random number generators")
3301     (description
3302      "This package contains a set of functions for working with Random Number
3303 Generators (RNGs).  In particular, it defines a generic S4 framework for
3304 getting/setting the current RNG, or RNG data that are embedded into objects
3305 for reproducibility.  Notably, convenient default methods greatly facilitate
3306 the way current RNG settings can be changed.")
3307     (license license:gpl3+)))
3308
3309 (define-public r-rtsne
3310   (package
3311     (name "r-rtsne")
3312     (version "0.15")
3313     (source
3314      (origin
3315        (method url-fetch)
3316        (uri (cran-uri "Rtsne" version))
3317        (sha256
3318         (base32
3319          "0v17vxizrs1msay24xl2bckfajr2c82wpqj07lyssbrq197nwdsn"))))
3320     (properties `((upstream-name . "Rtsne")))
3321     (build-system r-build-system)
3322     (propagated-inputs
3323      `(("r-rcpp" ,r-rcpp)))
3324     (home-page "https://github.com/jkrijthe/Rtsne")
3325     (synopsis "T-distributed stochastic neighbor embedding")
3326     (description
3327      "This package provides an R wrapper around the fast T-distributed
3328 Stochastic Neighbor Embedding using a Barnes-Hut implementation.")
3329     ;; The declared license for this package is BSD-3, but it also includes
3330     ;; code licensed under BSD-4.
3331     (license (list license:bsd-3 license:bsd-4))))
3332
3333 (define-public r-e1071
3334   (package
3335     (name "r-e1071")
3336     (version "1.7-3")
3337     (source
3338      (origin
3339        (method url-fetch)
3340        (uri (cran-uri "e1071" version))
3341        (sha256
3342         (base32
3343          "0pf2pjb590z0jikgv1037xcp7dq06mg3dzmyffjw6gk7dd9blbdv"))))
3344     (build-system r-build-system)
3345     (propagated-inputs
3346      `(("r-class" ,r-class)))
3347     (home-page "https://cran.r-project.org/web/packages/e1071")
3348     (synopsis "Miscellaneous functions for probability theory")
3349     (description
3350      "This package provides functions for latent class analysis, short time
3351 Fourier transform, fuzzy clustering, support vector machines, shortest path
3352 computation, bagged clustering, naive Bayes classifier, and more.")
3353     (license license:gpl2+)))
3354
3355 (define-public r-bigmemory-sri
3356   (package
3357     (name "r-bigmemory-sri")
3358     (version "0.1.3")
3359     (source
3360      (origin
3361        (method url-fetch)
3362        (uri (cran-uri "bigmemory.sri" version))
3363        (sha256
3364         (base32 "0mg14ilwdkd64q2ri9jdwnk7mp55dqim7xfifrs65sdsv1934h2m"))))
3365     (properties
3366      `((upstream-name . "bigmemory.sri")))
3367     (build-system r-build-system)
3368     (home-page "https://cran.r-project.org/web/packages/bigmemory.sri")
3369     (synopsis "Shared resource interface for the bigmemory package")
3370     (description "This package provides a shared resource interface for the
3371 bigmemory and synchronicity packages.")
3372     ;; Users can choose either LGPLv3 or ASL2.0.
3373     (license (list license:lgpl3 license:asl2.0))))
3374
3375 (define-public r-synchronicity
3376   (package
3377     (name "r-synchronicity")
3378     (version "1.3.5")
3379     (source
3380      (origin
3381        (method url-fetch)
3382        (uri (cran-uri "synchronicity" version))
3383        (sha256
3384         (base32
3385          "1kgsk64aifjm3mfj102y3va7x1abypq2zi0cqbnjhl8fqyzp69hx"))))
3386     (build-system r-build-system)
3387     (propagated-inputs
3388      `(("r-bh" ,r-bh)
3389        ("r-bigmemory-sri" ,r-bigmemory-sri)
3390        ("r-rcpp" ,r-rcpp)
3391        ("r-uuid" ,r-uuid)))
3392     (home-page "http://www.bigmemory.org")
3393     (synopsis "Boost mutex functionality in R")
3394     (description "This package provides support for synchronization
3395 via mutexes and may eventually support interprocess communication and
3396 message passing.")
3397     ;; Users can choose either LGPLv3 or ASL2.0.
3398     (license (list license:lgpl3 license:asl2.0))))
3399
3400 (define-public r-bigmemory
3401   (package
3402     (name "r-bigmemory")
3403     (version "4.5.36")
3404     (source
3405      (origin
3406        (method url-fetch)
3407        (uri (cran-uri "bigmemory" version))
3408        (sha256
3409         (base32
3410          "03pg8mxdc7q0249visjmc8bc3xmwxsfg3i2n6higicj4cfz7zihq"))))
3411     (build-system r-build-system)
3412     (propagated-inputs
3413      `(("r-bh" ,r-bh)
3414        ("r-rcpp" ,r-rcpp)
3415        ("r-bigmemory-sri" ,r-bigmemory-sri)))
3416     (home-page "http://www.bigmemory.org")
3417     (synopsis "Manage large matrices with shared memory or memory-mapped files")
3418     (description "This package provides methods to create, store, access, and
3419 manipulate large matrices.  Matrices are allocated to shared memory and may use
3420 memory-mapped files.")
3421     ;; Users can choose either LGPLv3 or ASL2.0.
3422     (license (list license:lgpl3 license:asl2.0))))
3423
3424 (define-public r-nmf
3425   (package
3426     (name "r-nmf")
3427     (version "0.21.0")
3428     (source
3429      (origin
3430        (method url-fetch)
3431        (uri (cran-uri "NMF" version))
3432        (sha256
3433         (base32
3434          "1qq25n3k5sgh3srlshb3ic6q92s12c1ilqf5cd5anvq6cqfchc1v"))))
3435     (properties `((upstream-name . "NMF")))
3436     (build-system r-build-system)
3437     (propagated-inputs
3438      `(("r-cluster" ,r-cluster)
3439        ("r-bigmemory" ,r-bigmemory) ; suggested
3440        ("r-synchronicity" ,r-synchronicity) ; suggested
3441        ("r-colorspace" ,r-colorspace)
3442        ("r-digest" ,r-digest)
3443        ("r-doparallel" ,r-doparallel)
3444        ("r-foreach" ,r-foreach)
3445        ("r-ggplot2" ,r-ggplot2)
3446        ("r-gridbase" ,r-gridbase)
3447        ("r-pkgmaker" ,r-pkgmaker)
3448        ("r-rcolorbrewer" ,r-rcolorbrewer)
3449        ("r-registry" ,r-registry)
3450        ("r-reshape2" ,r-reshape2)
3451        ("r-rngtools" ,r-rngtools)
3452        ("r-stringr" ,r-stringr)))
3453     (home-page "http://renozao.github.io/NMF")
3454     (synopsis "Algorithms and framework for nonnegative matrix factorization")
3455     (description
3456      "This package provides a framework to perform Non-negative Matrix
3457 Factorization (NMF).  The package implements a set of already published
3458 algorithms and seeding methods, and provides a framework to test, develop and
3459 plug new or custom algorithms.  Most of the built-in algorithms have been
3460 optimized in C++, and the main interface function provides an easy way of
3461 performing parallel computations on multicore machines.")
3462     (license license:gpl2+)))
3463
3464 (define-public r-r-methodss3
3465   (package
3466     (name "r-r-methodss3")
3467     (version "1.7.1")
3468     (source (origin
3469               (method url-fetch)
3470               (uri (cran-uri "R.methodsS3" version))
3471               (sha256
3472                (base32
3473                 "11z6v2i7jl647wxi9p5z66yvfnnqv6s7fxqmz7w2gkb6j8wl1f24"))))
3474     (properties `((upstream-name . "R.methodsS3")))
3475     (build-system r-build-system)
3476     (home-page "https://cran.r-project.org/web/packages/R.methodsS3")
3477     (synopsis "S3 methods simplified")
3478     (description
3479      "This package provides methods that simplify the setup of S3 generic
3480 functions and S3 methods.  Major effort has been made in making definition of
3481 methods as simple as possible with a minimum of maintenance for package
3482 developers.  For example, generic functions are created automatically, if
3483 missing, and naming conflict are automatically solved, if possible.  The
3484 method @code{setMethodS3()} is a good start for those who in the future may
3485 want to migrate to S4.")
3486     (license license:lgpl2.1+)))
3487
3488 (define-public r-r-oo
3489   (package
3490     (name "r-r-oo")
3491     (version "1.23.0")
3492     (source (origin
3493               (method url-fetch)
3494               (uri (cran-uri "R.oo" version))
3495               (sha256
3496                (base32
3497                 "189fb7mmyzwg6nn8rza8iip7fbyws7i2vkmzy672x9mhvgilq4pm"))))
3498     (properties `((upstream-name . "R.oo")))
3499     (build-system r-build-system)
3500     (propagated-inputs
3501      `(("r-r-methodss3" ,r-r-methodss3)))
3502     (home-page "https://github.com/HenrikBengtsson/R.oo")
3503     (synopsis "R object-oriented programming with or without references")
3504     (description
3505      "This package provides methods and classes for object-oriented
3506 programming in R with or without references.  Large effort has been made on
3507 making definition of methods as simple as possible with a minimum of
3508 maintenance for package developers.")
3509     (license license:lgpl2.1+)))
3510
3511 (define-public r-r-utils
3512   (package
3513     (name "r-r-utils")
3514     (version "2.9.2")
3515     (source (origin
3516               (method url-fetch)
3517               (uri (cran-uri "R.utils" version))
3518               (sha256
3519                (base32
3520                 "1krj1ny7y43lpm2q8c7swxfdc3ngy2j8knzv71f8bfsgh673nsxc"))))
3521     (properties `((upstream-name . "R.utils")))
3522     (build-system r-build-system)
3523     (propagated-inputs
3524      `(("r-r-methodss3" ,r-r-methodss3)
3525        ("r-r-oo" ,r-r-oo)))
3526     (home-page "https://github.com/HenrikBengtsson/R.utils")
3527     (synopsis "Various programming utilities")
3528     (description
3529      "This package provides utility functions useful when programming and
3530 developing R packages.")
3531     (license license:lgpl2.1+)))
3532
3533 (define-public r-r-cache
3534   (package
3535     (name "r-r-cache")
3536     (version "0.14.0")
3537     (source (origin
3538               (method url-fetch)
3539               (uri (cran-uri "R.cache" version))
3540               (sha256
3541                (base32
3542                 "1n8n5ihkryrbxv630dwhz4r048nyv676qd3i9f5z5fa04hvlxbqq"))))
3543     (properties `((upstream-name . "R.cache")))
3544     (build-system r-build-system)
3545     (propagated-inputs
3546      `(("r-digest" ,r-digest)
3547        ("r-r-methodss3" ,r-r-methodss3)
3548        ("r-r-oo" ,r-r-oo)
3549        ("r-r-utils" ,r-r-utils)))
3550     (home-page "https://github.com/HenrikBengtsson/R.cache")
3551     (synopsis "Light-weight caching of objects and results")
3552     (description
3553      "This package provides methods for caching or memoization of objects and
3554 results.  With this package, any R object can be cached in a key-value storage
3555 where the key can be an arbitrary set of R objects.  The cache memory is
3556 persistent (on the file system).")
3557     (license license:lgpl2.1+)))
3558
3559 (define-public r-r-rsp
3560   (package
3561     (name "r-r-rsp")
3562     (version "0.43.2")
3563     (source (origin
3564               (method url-fetch)
3565               (uri (cran-uri "R.rsp" version))
3566               (sha256
3567                (base32
3568                 "128zqyvbq9hm9gy86jzhj609lkfw57vr24mdxgh46ncmx66ag4gj"))))
3569     (properties `((upstream-name . "R.rsp")))
3570     (build-system r-build-system)
3571     (propagated-inputs
3572      `(("r-digest" ,r-digest)
3573        ("r-r-cache" ,r-r-cache)
3574        ("r-r-methodss3" ,r-r-methodss3)
3575        ("r-r-oo" ,r-r-oo)
3576        ("r-r-utils" ,r-r-utils)))
3577     (home-page "https://github.com/HenrikBengtsson/R.rsp")
3578     (synopsis "Dynamic generation of scientific reports")
3579     (description
3580      "The RSP markup language provides a powerful markup for controlling the
3581 content and output of LaTeX, HTML, Markdown, AsciiDoc, Sweave and knitr
3582 documents (and more), e.g. @code{Today's date is <%=Sys.Date()%>}.  Contrary
3583 to many other literate programming languages, with RSP it is straightforward
3584 to loop over mixtures of code and text sections, e.g.  in month-by-month
3585 summaries.  RSP has also several preprocessing directives for incorporating
3586 static and dynamic contents of external files (local or online) among other
3587 things.  RSP is ideal for self-contained scientific reports and R package
3588 vignettes.")
3589     (license license:lgpl2.1+)))
3590
3591 (define-public r-mvtnorm
3592   (package
3593     (name "r-mvtnorm")
3594     (version "1.0-12")
3595     (source (origin
3596               (method url-fetch)
3597               (uri (cran-uri "mvtnorm" version))
3598               (sha256
3599                (base32
3600                 "03rfmii9j8x8fjv7hp8qd28z0svl4w0x54k2f4jpwv4qa7079i24"))))
3601     (build-system r-build-system)
3602     (native-inputs
3603      `(("gfortran" ,gfortran)))
3604     (home-page "http://mvtnorm.R-forge.R-project.org")
3605     (synopsis "Package for multivariate normal and t-distributions")
3606     (description "This package can compute multivariate normal and
3607 t-probabilities, quantiles, random deviates and densities.")
3608     (license license:gpl2)))
3609
3610 (define-public r-matrixstats
3611   (package
3612     (name "r-matrixstats")
3613     (version "0.55.0")
3614     (source (origin
3615               (method url-fetch)
3616               (uri (cran-uri "matrixStats" version))
3617               (sha256
3618                (base32
3619                 "06fvx0rlaz80k0lkqq2n7v0309xpz7h7ss0m9kgyikp4xs8bvmhn"))))
3620     (properties `((upstream-name . "matrixStats")))
3621     (build-system r-build-system)
3622     (native-inputs
3623      `(("r-r-rsp" ,r-r-rsp))) ;used to build vignettes
3624     (home-page "https://github.com/HenrikBengtsson/matrixStats")
3625     (synopsis "Methods applying to vectors and matrix rows and columns")
3626     (description
3627      "This package provides methods operating on rows and columns of matrices,
3628 e.g.  @code{rowMedians()}, @code{rowRanks()}, and @code{rowSds()}.  There are
3629 also some vector-based methods, e.g. @code{binMeans()}, @code{madDiff()} and
3630 @code{weightedMedians()}.  All methods have been optimized for speed and
3631 memory usage.")
3632     (license license:artistic2.0)))
3633
3634 (define-public r-viridis
3635   (package
3636     (name "r-viridis")
3637     (version "0.5.1")
3638     (source (origin
3639               (method url-fetch)
3640               (uri (cran-uri "viridis" version))
3641               (sha256
3642                (base32
3643                 "060rf1jn29dq53y3nhb0hykvcap6rqsk04rq544ypiiqb18ngwnx"))))
3644     (build-system r-build-system)
3645     (propagated-inputs
3646      `(("r-ggplot2" ,r-ggplot2)
3647        ("r-gridextra" ,r-gridextra)
3648        ("r-viridislite" ,r-viridislite)))
3649     (home-page "https://github.com/sjmgarnier/viridis")
3650     (synopsis "Matplotlib default color map")
3651     (description
3652      "This package is a port of the new @url{matplotlib,
3653 http://matplotlib.org/} color maps (@code{viridis}--the default--,
3654 @code{magma}, @code{plasma}, and @code{inferno}) to R.  These color maps are
3655 designed in such a way that they will analytically be perfectly
3656 perceptually-uniform, both in regular form and also when converted to
3657 black-and-white.  They are also designed to be perceived by readers with the
3658 most common form of color blindness.")
3659     (license license:x11)))
3660
3661 (define-public r-viridislite
3662   (package
3663     (name "r-viridislite")
3664     (version "0.3.0")
3665     (source
3666      (origin
3667        (method url-fetch)
3668        (uri (cran-uri "viridisLite" version))
3669        (sha256
3670         (base32
3671          "1by2l05f0yabwvv64lhnv7bbhx0w683s3wr9j2xda920ghpa23kq"))))
3672     (properties `((upstream-name . "viridisLite")))
3673     (build-system r-build-system)
3674     (home-page "https://github.com/sjmgarnier/viridisLite")
3675     (synopsis "Default color maps from matplotlib")
3676     (description
3677      "This package is a port of the new @code{matplotlib} color maps
3678 (@code{viridis}, @code{magma}, @code{plasma} and @code{inferno}) to R.
3679 matplotlib is a popular plotting library for Python.  These color maps are
3680 designed in such a way that they will analytically be perfectly
3681 perceptually-uniform, both in regular form and also when converted to
3682 black-and-white.  They are also designed to be perceived by readers with the
3683 most common form of color blindness.  This is the @code{lite} version of the
3684 more complete @code{viridis} package.")
3685     (license license:expat)))
3686
3687 (define-public r-tidyselect
3688   (package
3689     (name "r-tidyselect")
3690     (version "0.2.5")
3691     (source
3692      (origin
3693        (method url-fetch)
3694        (uri (cran-uri "tidyselect" version))
3695        (sha256
3696         (base32
3697          "0x3cp36byhfjajikr1lwffjm85ayw3bcs7d7kb0cydgs61ifiqjw"))))
3698     (build-system r-build-system)
3699     (propagated-inputs
3700      `(("r-glue" ,r-glue)
3701        ("r-purrr" ,r-purrr)
3702        ("r-rcpp" ,r-rcpp)
3703        ("r-rlang" ,r-rlang)))
3704     (home-page "https://cran.r-project.org/web/packages/tidyselect")
3705     (synopsis "Select from a set of strings")
3706     (description
3707      "This package provides a backend for the selecting functions of the
3708 tidyverse.  It makes it easy to implement select-like functions in your own
3709 packages in a way that is consistent with other tidyverse interfaces for
3710 selection.")
3711     (license license:gpl3)))
3712
3713 (define-public r-tidyr
3714   (package
3715     (name "r-tidyr")
3716     (version "1.0.0")
3717     (source
3718      (origin
3719        (method url-fetch)
3720        (uri (cran-uri "tidyr" version))
3721        (sha256
3722         (base32
3723          "1403j0xd93l0r7qj738ryd5zc79hbcghrzybib3c3hrnaq5s78cj"))))
3724     (build-system r-build-system)
3725     (propagated-inputs
3726      `(("r-dplyr" ,r-dplyr)
3727        ("r-ellipsis" ,r-ellipsis)
3728        ("r-magrittr" ,r-magrittr)
3729        ("r-glue" ,r-glue)
3730        ("r-lifecycle" ,r-lifecycle)
3731        ("r-purrr" ,r-purrr)
3732        ("r-rlang" ,r-rlang)
3733        ("r-tidyselect" ,r-tidyselect)
3734        ("r-rcpp" ,r-rcpp)
3735        ("r-stringi" ,r-stringi)
3736        ("r-tibble" ,r-tibble)
3737        ("r-vctrs" ,r-vctrs)))
3738     (home-page "https://github.com/hadley/tidyr")
3739     (synopsis "Tidy data with `spread()` and `gather()` functions")
3740     (description
3741      "tidyr is a reframing of the reshape2 package designed to accompany the
3742 tidy data framework, and to work hand-in-hand with magrittr and dplyr to build
3743 a solid pipeline for data analysis.  It is designed specifically for tidying
3744 data, not the general reshaping that reshape2 does, or the general aggregation
3745 that reshape did.  In particular, built-in methods only work for data frames,
3746 and tidyr provides no margins or aggregation.")
3747     (license license:expat)))
3748
3749 (define-public r-hexbin
3750   (package
3751     (name "r-hexbin")
3752     (version "1.28.0")
3753     (source
3754      (origin
3755        (method url-fetch)
3756        (uri (cran-uri "hexbin" version))
3757        (sha256
3758         (base32
3759          "0b58jb1kz39wzrnkv077cfzns889xly7psvhxnm3xmnx6yvd986d"))))
3760     (build-system r-build-system)
3761     (propagated-inputs
3762      `(("r-lattice" ,r-lattice)))
3763     (native-inputs
3764      `(("gfortran" ,gfortran)))
3765     (home-page "https://github.com/edzer/hexbin")
3766     (synopsis "Hexagonal binning routines")
3767     (description
3768      "This package provides binning and plotting functions for hexagonal bins.
3769 It uses and relies on grid graphics and formal (S4) classes and methods.")
3770     (license license:gpl2+)))
3771
3772 (define-public r-purrr
3773   (package
3774     (name "r-purrr")
3775     (version "0.3.3")
3776     (source
3777      (origin
3778        (method url-fetch)
3779        (uri (cran-uri "purrr" version))
3780        (sha256
3781         (base32
3782          "17lyys7dxjrwsfkq7a7hw65iy3qn3pp1sn70srdy64jf8adahc8g"))))
3783     (build-system r-build-system)
3784     (propagated-inputs
3785      `(("r-magrittr" ,r-magrittr)
3786        ("r-rlang" ,r-rlang)))
3787     (home-page "https://github.com/hadley/purrr")
3788     (synopsis "Functional programming tools")
3789     (description
3790      "This package completes R's functional programming tools with missing
3791 features present in other programming languages.")
3792     (license license:gpl3+)))
3793
3794 (define-public r-plotly
3795   (package
3796     (name "r-plotly")
3797     (version "4.9.1")
3798     (source (origin
3799               (method url-fetch)
3800               (uri (cran-uri "plotly" version))
3801               (sha256
3802                (base32
3803                 "0gadam4qw81q9gpjp7sqrpd7ikmcdsc78d8vjn39g0xzs5j8r845"))))
3804     (build-system r-build-system)
3805     (propagated-inputs
3806      `(("r-base64enc" ,r-base64enc)
3807        ("r-crosstalk" ,r-crosstalk)
3808        ("r-digest" ,r-digest)
3809        ("r-data-table" ,r-data-table)
3810        ("r-dplyr" ,r-dplyr)
3811        ("r-ggplot2" ,r-ggplot2)
3812        ("r-hexbin" ,r-hexbin)
3813        ("r-htmltools" ,r-htmltools)
3814        ("r-htmlwidgets" ,r-htmlwidgets)
3815        ("r-httr" ,r-httr)
3816        ("r-jsonlite" ,r-jsonlite)
3817        ("r-lazyeval" ,r-lazyeval)
3818        ("r-magrittr" ,r-magrittr)
3819        ("r-promises" ,r-promises)
3820        ("r-purrr" ,r-purrr)
3821        ("r-rcolorbrewer" ,r-rcolorbrewer)
3822        ("r-rlang" ,r-rlang)
3823        ("r-scales" ,r-scales)
3824        ("r-tibble" ,r-tibble)
3825        ("r-tidyr" ,r-tidyr)
3826        ("r-viridislite" ,r-viridislite)))
3827     (home-page "https://plot.ly/r")
3828     (synopsis "Create interactive web graphics")
3829     (description
3830      "This package enables the translation of ggplot2 graphs to an interactive
3831 web-based version and/or the creation of custom web-based visualizations
3832 directly from R.  Once uploaded to a plotly account, plotly graphs (and the
3833 data behind them) can be viewed and modified in a web browser.")
3834     (license license:x11)))
3835
3836 (define-public r-biased-urn
3837   (package
3838    (name "r-biased-urn")
3839    (version "1.07")
3840    (source
3841     (origin
3842      (method url-fetch)
3843      (uri (cran-uri "BiasedUrn" version))
3844      (sha256
3845       (base32
3846        "13i2lgfnjhlbbm2yxfc2l5hswqw6x03pwba5csjmirv8kpjw4xr3"))))
3847    (properties `((upstream-name . "BiasedUrn")))
3848    (build-system r-build-system)
3849    (home-page "http://www.agner.org/random/")
3850    (synopsis "Biased urn model distributions")
3851    (description
3852     "This package provides statistical models of biased sampling in the form
3853 of univariate and multivariate noncentral hypergeometric distributions,
3854 including Wallenius' noncentral hypergeometric distribution and Fisher's
3855 noncentral hypergeometric distribution (also called extended hypergeometric
3856 distribution).")
3857    (license license:gpl3+)))
3858
3859 (define-public r-rematch
3860   (package
3861     (name "r-rematch")
3862     (version "1.0.1")
3863     (source
3864      (origin
3865        (method url-fetch)
3866        (uri (cran-uri "rematch" version))
3867        (sha256
3868         (base32
3869          "0y3mshvpvz9csmq8hk8jbabx4nxlv5sckvfzvm6920ndg34xw2d4"))))
3870     (build-system r-build-system)
3871     (home-page "https://github.com/MangoTheCat/rematch")
3872     (synopsis "Match regular expressions with a nicer API")
3873     (description
3874      "This package provides a small wrapper on @code{regexpr} to extract the
3875 matches and captured groups from the match of a regular expression to a
3876 character vector.")
3877     (license license:expat)))
3878
3879 (define-public r-cellranger
3880   (package
3881     (name "r-cellranger")
3882     (version "1.1.0")
3883     (source
3884      (origin
3885        (method url-fetch)
3886        (uri (cran-uri "cellranger" version))
3887        (sha256
3888         (base32
3889          "16fgi3annn34c3cxi0pxf62mmmmxi21hp0zzlv7bkfsjqy4g4f2x"))))
3890     (build-system r-build-system)
3891     (propagated-inputs
3892      `(("r-rematch" ,r-rematch)
3893        ("r-tibble" ,r-tibble)))
3894     (home-page "https://github.com/rsheets/cellranger")
3895     (synopsis "Translate spreadsheet cell ranges to rows and columns")
3896     (description
3897      "This package provides helper functions to work with spreadsheets and the
3898 @code{A1:D10} style of cell range specification.")
3899     (license license:expat)))
3900
3901 (define-public r-googlesheets
3902   (package
3903     (name "r-googlesheets")
3904     (version "0.3.0")
3905     (source
3906      (origin
3907        (method url-fetch)
3908        (uri (cran-uri "googlesheets" version))
3909        (sha256
3910         (base32
3911          "11q07nxys72wkxx9mawmjyf20gvwvrb7h3gpa73h6lgh2vgrwnv8"))))
3912     (build-system r-build-system)
3913     (propagated-inputs
3914      `(("r-cellranger" ,r-cellranger)
3915        ("r-dplyr" ,r-dplyr)
3916        ("r-httr" ,r-httr)
3917        ("r-jsonlite" ,r-jsonlite)
3918        ("r-purrr" ,r-purrr)
3919        ("r-readr" ,r-readr)
3920        ("r-stringr" ,r-stringr)
3921        ("r-tibble" ,r-tibble)
3922        ("r-tidyr" ,r-tidyr)
3923        ("r-xml2" ,r-xml2)))
3924     (home-page "https://github.com/jennybc/googlesheets")
3925     (synopsis "Manage Google spreadsheets from R")
3926     (description "This package provides tools to interact with Google Sheets
3927 from within R.")
3928     (license license:expat)))
3929
3930 (define-public r-spams
3931   (package
3932     (name "r-spams")
3933     (version "2.6-2017-03-22")
3934     (source
3935      (origin
3936        (method url-fetch)
3937        ;; Use the ‘Latest version’ link for a stable URI across releases.
3938        (uri (string-append "https://gforge.inria.fr/frs/download.php/"
3939                            "latestfile/4531/spams-R-v" version ".tar.gz"))
3940        (sha256
3941         (base32
3942          "13z2293jixf1r9g8dyy856xrhvpjr2ln2n9smn6644126r9hmhkx"))))
3943     (build-system r-build-system)
3944     (arguments
3945      `(#:phases
3946        (modify-phases %standard-phases
3947          (add-after 'unpack 'chdir
3948            (lambda _ (chdir "spams") #t))
3949          ;; Don't tune for the building machine.
3950          (add-after 'chdir 'no-mtune
3951            (lambda _
3952              (substitute* "src/Makevars"
3953                (("-mtune=native") ""))
3954              #t)))))
3955     (propagated-inputs
3956      `(("r-lattice" ,r-lattice)
3957        ("r-matrix" ,r-matrix)))
3958     (home-page "http://spams-devel.gforge.inria.fr")
3959     (synopsis "Toolbox for solving sparse estimation problems")
3960     (description "SPAMS (SPArse Modeling Software) is an optimization toolbox
3961 for solving various sparse estimation problems.  It includes tools for the
3962 following problems:
3963
3964 @enumerate
3965 @item Dictionary learning and matrix factorization (NMF, sparse @dfn{principle
3966  component analysis} (PCA), ...)
3967 @item Solving sparse decomposition problems with LARS, coordinate descent,
3968  OMP, SOMP, proximal methods
3969 @item Solving structured sparse decomposition problems (l1/l2, l1/linf, sparse
3970  group lasso, tree-structured regularization, structured sparsity with
3971  overlapping groups,...).
3972 @end enumerate\n")
3973     (license license:gpl3+)))
3974
3975 (define-public r-base64
3976   (package
3977     (name "r-base64")
3978     (version "2.0")
3979     (source
3980      (origin
3981        (method url-fetch)
3982        (uri (cran-uri "base64" version))
3983        (sha256
3984         (base32
3985          "1labh0ycdm2xcjssj8bhnyjvbk44mcdsi0rb2p8rfqa428mrq9cf"))))
3986     (build-system r-build-system)
3987     (propagated-inputs
3988      `(("r-openssl" ,r-openssl)))
3989     (home-page "https://cran.r-project.org/web/packages/base64")
3990     (synopsis "Base64 encoder and decoder")
3991     (description
3992      "This package is a compatibility wrapper to replace the orphaned package
3993 by Romain Francois.  New applications should use the openssl or base64enc
3994 package instead.")
3995     (license license:expat)))
3996
3997 (define-public r-hmisc
3998   (package
3999     (name "r-hmisc")
4000     (version "4.3-0")
4001     (source
4002      (origin
4003        (method url-fetch)
4004        (uri (cran-uri "Hmisc" version))
4005        (sha256
4006         (base32 "0rb1m6138lqzb46nss9ggvhghipd10vdnwsy6iq2wzynrynzkwkz"))))
4007     (properties `((upstream-name . "Hmisc")))
4008     (build-system r-build-system)
4009     (native-inputs
4010      `(("gfortran" ,gfortran)))
4011     (propagated-inputs
4012      `(("r-acepack" ,r-acepack)
4013        ("r-base64enc" ,r-base64enc)
4014        ("r-cluster" ,r-cluster)
4015        ("r-data-table" ,r-data-table)
4016        ("r-foreign" ,r-foreign)
4017        ("r-formula" ,r-formula)
4018        ("r-ggplot2" ,r-ggplot2)
4019        ("r-gridextra" ,r-gridextra)
4020        ("r-gtable" ,r-gtable)
4021        ("r-lattice" ,r-lattice)
4022        ("r-latticeextra" ,r-latticeextra)
4023        ("r-htmltable" ,r-htmltable)
4024        ("r-htmltools" ,r-htmltools)
4025        ("r-nnet" ,r-nnet)
4026        ("r-rpart" ,r-rpart)
4027        ("r-survival" ,r-survival)
4028        ("r-viridis" ,r-viridis)))
4029     (home-page "http://biostat.mc.vanderbilt.edu/Hmisc")
4030     (synopsis "Miscellaneous data analysis and graphics functions")
4031     (description
4032      "This package contains many functions useful for data analysis,
4033 high-level graphics, utility operations, functions for computing sample size
4034 and power, importing and annotating datasets, imputing missing values,
4035 advanced table making, variable clustering, character string manipulation,
4036 conversion of R objects to LaTeX code, and recoding variables.")
4037     (license license:gpl2+)))
4038
4039 (define-public r-runit
4040   (package
4041     (name "r-runit")
4042     (version "0.4.32")
4043     (source
4044      (origin
4045        (method url-fetch)
4046        (uri (cran-uri "RUnit" version))
4047        (sha256
4048         (base32
4049          "1wc1gwb7yw7phf8b0gkig6c23klya3ax11c6i4s0f049k42r78r3"))))
4050     (properties `((upstream-name . "RUnit")))
4051     (build-system r-build-system)
4052     (home-page "https://cran.r-project.org/web/packages/RUnit")
4053     (synopsis "R unit test framework")
4054     (description
4055      "This package provides R functions implementing a standard unit testing
4056 framework, with additional code inspection and report generation tools.")
4057     (license license:gpl2+)))
4058
4059 (define-public r-dynamictreecut
4060   (package
4061     (name "r-dynamictreecut")
4062     (version "1.63-1")
4063     (source
4064      (origin
4065        (method url-fetch)
4066        (uri (cran-uri "dynamicTreeCut" version))
4067        (sha256
4068         (base32
4069          "1fadbql7g5r2vvlkr89nlrjxwp4yx4xrdqmv077qvmnx9vv0f4w3"))))
4070     (properties `((upstream-name . "dynamicTreeCut")))
4071     (build-system r-build-system)
4072     (home-page
4073      "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/BranchCutting/")
4074     (synopsis "Detect clusters in hierarchical clustering dendrograms")
4075     (description
4076      "This package contains methods for the detection of clusters in
4077 hierarchical clustering dendrograms.")
4078     (license license:gpl2+)))
4079
4080 (define-public r-preprocesscore
4081   (package
4082     (name "r-preprocesscore")
4083     (version "1.48.0")
4084     (source
4085      (origin
4086        (method url-fetch)
4087        (uri (bioconductor-uri "preprocessCore" version))
4088        (sha256
4089         (base32
4090          "0zrb9hx60vppkg0priczdb301nhq5f0dj8lkc8rcc4xrqqr915qm"))))
4091     (properties
4092      `((upstream-name . "preprocessCore")))
4093     (build-system r-build-system)
4094     (home-page "https://github.com/bmbolstad/preprocessCore")
4095     (synopsis "Collection of pre-processing functions")
4096     (description
4097      "This package provides a library of core pre-processing and normalization
4098 routines.")
4099     (license license:lgpl2.0+)))
4100
4101 (define-public r-fastcluster
4102   (package
4103     (name "r-fastcluster")
4104     (version "1.1.25")
4105     (source
4106      (origin
4107        (method url-fetch)
4108        (uri (cran-uri "fastcluster" version))
4109        (sha256
4110         (base32
4111          "01a2xnhhvv1swd4g8p4lzyn7ww7kg49jlnzc7kfz60jqjzpisrpk"))))
4112     (build-system r-build-system)
4113     (home-page "http://danifold.net/fastcluster.html")
4114     (synopsis "Fast hierarchical clustering routines")
4115     (description
4116      "This package implements fast hierarchical, agglomerative clustering
4117 routines.  Part of the functionality is designed as drop-in replacement for
4118 existing routines: @code{linkage()} in the SciPy package
4119 @code{scipy.cluster.hierarchy}, @code{hclust()} in R's @code{stats} package,
4120 and the @code{flashClust} package.  It provides the same functionality with
4121 the benefit of a much faster implementation.  Moreover, there are
4122 memory-saving routines for clustering of vector data, which go beyond what the
4123 existing packages provide.")
4124     (license license:bsd-2)))
4125
4126 (define-public r-sfsmisc
4127   (package
4128     (name "r-sfsmisc")
4129     (version "1.1-4")
4130     (source
4131      (origin
4132        (method url-fetch)
4133        (uri (cran-uri "sfsmisc" version))
4134        (sha256
4135         (base32
4136          "0zaw617zarmwir8l60riky0z6r1j3mwfnm1f32vqcbljb74akdj4"))))
4137     (build-system r-build-system)
4138     (home-page "https://cran.r-project.org/web/packages/sfsmisc")
4139     (synopsis "Utilities from \"Seminar fuer Statistik\" ETH Zurich")
4140     (description
4141      "This package provides useful utilities from Seminar fuer Statistik ETH
4142 Zurich, including many that are related to graphics.")
4143     (license license:gpl2+)))
4144
4145 (define-public r-gtools
4146   (package
4147     (name "r-gtools")
4148     (version "3.8.1")
4149     (source
4150      (origin
4151        (method url-fetch)
4152        (uri (cran-uri "gtools" version))
4153        (sha256
4154         (base32
4155          "0f5syk1qq6cjq6hwymvkiyhzwa389z94722v881ipbfqkd2q8505"))))
4156     (build-system r-build-system)
4157     (arguments
4158      `(#:phases
4159        (modify-phases %standard-phases
4160          (add-after 'unpack 'make-deterministic
4161            (lambda _
4162              (substitute* "R/checkReverseDependencies.R"
4163                (("tempdir\\(\\)") "\"/tmp\""))
4164              #t)))))
4165     (home-page "https://cran.r-project.org/web/packages/gtools")
4166     (synopsis "Various R programming tools")
4167     (description
4168      "This package contains a collection of various functions to assist in R
4169 programming, such as tools to assist in developing, updating, and maintaining
4170 R and R packages, calculating the logit and inverse logit transformations,
4171 tests for whether a value is missing, empty or contains only @code{NA} and
4172 @code{NULL} values, and many more.")
4173     (license license:gpl2)))
4174
4175 (define-public r-gdata
4176   (package
4177     (name "r-gdata")
4178     (version "2.18.0")
4179     (source
4180      (origin
4181        (method url-fetch)
4182        (uri (cran-uri "gdata" version))
4183        (sha256
4184         (base32
4185          "0zwdj7lscgxr8r62ii8hbdh4mb7sa9w4f5nv32zzrxdvymcpya2b"))))
4186     (build-system r-build-system)
4187     (inputs
4188      `(("perl" ,perl)))
4189     (propagated-inputs
4190      `(("r-gtools" ,r-gtools)))
4191     (home-page "https://cran.r-project.org/web/packages/gdata")
4192     (synopsis "Various R programming tools for data manipulation")
4193     (description
4194      "This package provides various R programming tools for data manipulation,
4195 including:
4196
4197 @itemize
4198 @item medical unit conversions
4199 @item combining objects
4200 @item character vector operations
4201 @item factor manipulation
4202 @item obtaining information about R objects
4203 @item manipulating MS-Excel formatted files
4204 @item generating fixed-width format files
4205 @item extricating components of date and time objects
4206 @item operations on columns of data frames
4207 @item matrix operations
4208 @item operations on vectors and data frames
4209 @item value of last evaluated expression
4210 @item wrapper for @code{sample} that ensures consistent behavior for
4211   both scalar and vector arguments
4212 @end itemize\n")
4213     (license license:gpl2+)))
4214
4215 (define-public r-gplots
4216   (package
4217     (name "r-gplots")
4218     (version "3.0.1.2")
4219     (source
4220      (origin
4221        (method url-fetch)
4222        (uri (cran-uri "gplots" version))
4223        (sha256
4224         (base32
4225          "0vrm7wqrmqsmfrc070r9chpzb0vv60pay2lyar9qxfry6bsrvx86"))))
4226     (build-system r-build-system)
4227     (propagated-inputs
4228      `(("r-catools" ,r-catools)
4229        ("r-gdata" ,r-gdata)
4230        ("r-gtools" ,r-gtools)
4231        ("r-kernsmooth" ,r-kernsmooth)))
4232     (home-page "https://cran.r-project.org/web/packages/gplots")
4233     (synopsis "Various R programming tools for plotting data")
4234     (description
4235      "This package provides various R programming tools for plotting data,
4236 including:
4237
4238 @itemize
4239 @item calculating and plotting locally smoothed summary function
4240 @item enhanced versions of standard plots
4241 @item manipulating colors
4242 @item calculating and plotting two-dimensional data summaries
4243 @item enhanced regression diagnostic plots
4244 @item formula-enabled interface to @code{stats::lowess} function
4245 @item displaying textual data in plots
4246 @item balloon plots
4247 @item plotting \"Venn\" diagrams
4248 @item displaying Open-Office style plots
4249 @item plotting multiple data on same region, with separate axes
4250 @item plotting means and confidence intervals
4251 @item spacing points in an x-y plot so they don't overlap
4252 @end itemize\n")
4253     (license license:gpl2+)))
4254
4255 (define-public r-rocr
4256   (package
4257     (name "r-rocr")
4258     (version "1.0-7")
4259     (source
4260      (origin
4261        (method url-fetch)
4262        (uri (cran-uri "ROCR" version))
4263        (sha256
4264         (base32
4265          "1jay8cm7lgq56i967vm5c2hgaxqkphfpip0gn941li3yhh7p3vz7"))))
4266     (properties `((upstream-name . "ROCR")))
4267     (build-system r-build-system)
4268     (propagated-inputs
4269      `(("r-gplots" ,r-gplots)))
4270     (home-page "http://rocr.bioinf.mpi-sb.mpg.de/")
4271     (synopsis "Visualizing the performance of scoring classifiers")
4272     (description
4273      "ROCR is a flexible tool for creating cutoff-parameterized 2D performance
4274 curves by freely combining two from over 25 performance measures (new
4275 performance measures can be added using a standard interface).  Curves from
4276 different cross-validation or bootstrapping runs can be averaged by different
4277 methods, and standard deviations, standard errors or box plots can be used to
4278 visualize the variability across the runs.  The parameterization can be
4279 visualized by printing cutoff values at the corresponding curve positions, or
4280 by coloring the curve according to cutoff.  All components of a performance
4281 plot can be quickly adjusted using a flexible parameter dispatching
4282 mechanism.")
4283     (license license:gpl2+)))
4284
4285 (define-public r-zoo
4286   (package
4287     (name "r-zoo")
4288     (version "1.8-7")
4289     (source (origin
4290               (method url-fetch)
4291               (uri (cran-uri "zoo" version))
4292               (sha256
4293                (base32
4294                 "1w4542zs53bm261g95086a60576v334g1jrhnbgdqni4izf2s1wy"))))
4295     (build-system r-build-system)
4296     (propagated-inputs
4297      `(("r-lattice" ,r-lattice)))
4298     (home-page "http://zoo.R-Forge.R-project.org/")
4299     (synopsis "S3 infrastructure for regular and irregular time series")
4300     (description "This package contains an S3 class with methods for totally
4301 ordered indexed observations.  It is particularly aimed at irregular time
4302 series of numeric vectors/matrices and factors.")
4303     (license license:gpl2+)))
4304
4305 (define-public r-ztable
4306   (package
4307     (name "r-ztable")
4308     (version "0.2.0")
4309     (source (origin
4310               (method url-fetch)
4311               (uri (cran-uri "ztable" version))
4312               (sha256
4313                (base32
4314                 "0g7khk5ifsdh9p31wlwh2l5mn1hzxzpv6qcn1wh34vsfjdmijjwy"))))
4315     (build-system r-build-system)
4316     (propagated-inputs
4317      `(("r-flextable" ,r-flextable)
4318        ("r-magrittr" ,r-magrittr)
4319        ("r-moonbook" ,r-moonbook)
4320        ("r-officer" ,r-officer)
4321        ("r-rcolorbrewer" ,r-rcolorbrewer)
4322        ("r-scales" ,r-scales)
4323        ("r-stringr" ,r-stringr)))
4324     (home-page "https://cran.r-project.org/web/packages/ztable")
4325     (synopsis "Zebra-striped tables in LaTeX and HTML formats for R")
4326     (description
4327      "This package provides functions to make zebra-striped tables (tables
4328 with alternating row colors) in LaTeX and HTML formats easily from
4329 @code{data.frame}, @code{matrix}, @code{lm}, @code{aov}, @code{anova},
4330 @code{glm}, @code{coxph}, @code{nls}, @code{fitdistr}, @code{mytable} and
4331 @code{cbind.mytable} objects.")
4332     (license license:gpl2+)))
4333
4334 (define-public r-vipor
4335   (package
4336     (name "r-vipor")
4337     (version "0.4.5")
4338     (source (origin
4339               (method url-fetch)
4340               (uri (cran-uri "vipor" version))
4341               (sha256
4342                (base32
4343                 "112gc0d7f8iavgf56pnzfxb7hy75yhd0zlyjzshdcfbnqcd2a6bx"))))
4344     (build-system r-build-system)
4345     (home-page "https://cran.r-project.org/web/packages/vipor")
4346     (synopsis "Plot categorical data using noise and density estimates")
4347     (description
4348      "This package provides tools to generate a violin point plot, a
4349 combination of a violin/histogram plot and a scatter plot by offsetting points
4350 within a category based on their density using quasirandom noise.")
4351     (license license:gpl2+)))
4352
4353 (define-public r-beeswarm
4354   (package
4355     (name "r-beeswarm")
4356     (version "0.2.3")
4357     (source (origin
4358               (method url-fetch)
4359               (uri (cran-uri "beeswarm" version))
4360               (sha256
4361                (base32
4362                 "0hy89bwv7jixlg91li1fywa77916am2whqp1m1fx1khd45g44581"))))
4363     (build-system r-build-system)
4364     (home-page "http://www.cbs.dtu.dk/~eklund/beeswarm/")
4365     (synopsis "Implementation of bee swarm plots")
4366     (description
4367      "This package provides an implementation of bee swarm plots.  The bee
4368 swarm plot is a one-dimensional scatter plot like stripchart, but with
4369 closely-packed, non-overlapping points.")
4370     (license license:artistic2.0)))
4371
4372 (define-public r-sourcetools
4373   (package
4374     (name "r-sourcetools")
4375     (version "0.1.7")
4376     (source
4377      (origin
4378        (method url-fetch)
4379        (uri (cran-uri "sourcetools" version))
4380        (sha256
4381         (base32
4382          "1jnjir0q2dj724f1mjm6p5h77yzyx6xcqy9r2g7gmcxkxw349627"))))
4383     (build-system r-build-system)
4384     (home-page "https://cran.r-project.org/web/packages/sourcetools")
4385     (synopsis "Tools for reading, tokenizing and parsing R code")
4386     (description
4387      "The sourcetools package provides both an R and C++ interface for the
4388 tokenization of R code, and helpers for interacting with the tokenized
4389 representation of R code.")
4390     (license license:expat)))
4391
4392 (define-public r-ggbeeswarm
4393   (package
4394     (name "r-ggbeeswarm")
4395     (version "0.6.0")
4396     (source (origin
4397               (method url-fetch)
4398               (uri (cran-uri "ggbeeswarm" version))
4399               (sha256
4400                (base32
4401                 "0crk29p5vi1r3a988kms4y7r0iqwgwzsikgvh18r9wbzyr98bb5v"))))
4402     (build-system r-build-system)
4403     (propagated-inputs
4404      `(("r-beeswarm" ,r-beeswarm)
4405        ("r-ggplot2" ,r-ggplot2)
4406        ("r-vipor" ,r-vipor)))
4407     (home-page "https://github.com/eclarke/ggbeeswarm")
4408     (synopsis "Categorical scatter (violin point) plots")
4409     (description
4410      "This package provides two methods of plotting categorical scatter plots
4411 such that the arrangement of points within a category reflects the density of
4412 data at that region, and avoids over-plotting.")
4413     (license license:gpl2+)))
4414
4415 (define-public r-ggthemes
4416   (package
4417     (name "r-ggthemes")
4418     (version "4.2.0")
4419     (source (origin
4420               (method url-fetch)
4421               (uri (cran-uri "ggthemes" version))
4422               (sha256
4423                (base32
4424                 "0rrkzfggc1nlda1w1lbqdycx6nawxbkac1szhvkwrqlzh6agxcsv"))))
4425     (build-system r-build-system)
4426     (propagated-inputs
4427      `(("r-ggplot2" ,r-ggplot2)
4428        ("r-purrr" ,r-purrr)
4429        ("r-scales" ,r-scales)
4430        ("r-stringr" ,r-stringr)
4431        ("r-tibble" ,r-tibble)))
4432     (home-page "https://cran.rstudio.com/web/packages/ggthemes")
4433     (synopsis "Extra themes, scales and geoms for @code{ggplot2}")
4434     (description "This package provides extra themes and scales for
4435 @code{ggplot2} that replicate the look of plots by Edward Tufte and
4436 Stephen Few in Fivethirtyeight, The Economist, Stata, Excel, and The
4437 Wall Street Journal, among others.  This package also provides
4438 @code{geoms} for Tufte's box plot and range frame.")
4439     (license license:gpl2)))
4440
4441 (define-public r-statmod
4442   (package
4443     (name "r-statmod")
4444     (version "1.4.33")
4445     (source (origin
4446               (method url-fetch)
4447               (uri (cran-uri "statmod" version))
4448               (sha256
4449                (base32
4450                 "1fbi5m4c0lingm2vvi0g6jf8f2mg1h01xwyz5rnymrq7gs0ibiks"))))
4451     (build-system r-build-system)
4452     (home-page "https://cran.r-project.org/web/packages/statmod")
4453     (native-inputs
4454      `(("gfortran" ,gfortran)))
4455     (synopsis "Statistical modeling")
4456     (description
4457      "This package provides a collection of algorithms and functions to aid
4458 statistical modeling.  It includes growth curve comparisons, limiting dilution
4459 analysis (aka ELDA), mixed linear models, heteroscedastic regression,
4460 inverse-Gaussian probability calculations, Gauss quadrature and a secure
4461 convergence algorithm for nonlinear models.  It also includes advanced
4462 generalized linear model functions that implement secure convergence,
4463 dispersion modeling and Tweedie power-law families.")
4464     ;; Statmod is distributed under either license
4465     (license (list license:gpl2 license:gpl3))))
4466
4467 (define-public r-rann
4468   (package
4469     (name "r-rann")
4470     (version "2.6.1")
4471     (source (origin
4472               (method url-fetch)
4473               (uri (cran-uri "RANN" version))
4474               (sha256
4475                (base32
4476                 "10kid40w9w7vkz2hpcfkdpxr4afxzms5dzvfwr0sl5xynzgw76dj"))))
4477     (properties
4478      `((upstream-name . "RANN")))
4479     (build-system r-build-system)
4480     (home-page "https://github.com/jefferis/RANN")
4481     (synopsis "Fast nearest neighbour search")
4482     (description
4483      "This package finds the k nearest neighbours for every point in a given
4484 dataset in O(N log N) time using Arya and Mount's ANN library.  Provides
4485 approximate, exact searches, fixed radius searches, bd and kb trees.")
4486     (license license:gpl3+)))
4487
4488 (define-public r-fivethirtyeight
4489   (package
4490     (name "r-fivethirtyeight")
4491     (version "0.1.0")
4492     (source
4493      (origin
4494        (method url-fetch)
4495        (uri (string-append "https://mran.microsoft.com/src/contrib/"
4496                            "fivethirtyeight_" version ".tar.gz"))
4497        (sha256
4498         (base32
4499          "0fcc8rq745nsghp27dk0lgih90y4zx8hrzcvsn6ih786yv7qxhvl"))))
4500     (build-system r-build-system)
4501     (propagated-inputs
4502      `(("r-knitr" ,r-knitr)
4503        ("r-rmarkdown" ,r-rmarkdown)
4504        ("r-dplyr" ,r-dplyr)
4505        ("r-readr" ,r-readr)
4506        ("r-ggplot2" ,r-ggplot2)
4507        ("r-magrittr" ,r-magrittr)
4508        ("r-stringr" ,r-stringr)))
4509     (home-page "https://mran.microsoft.com/package/fivethirtyeight/")
4510     (synopsis "Data and code behind the stories at FiveThirtyEight")
4511     (description "This R package provides access to the code and data sets
4512 published by the statistics blog FiveThirtyEight.")
4513     (license license:expat)))
4514
4515 (define-public r-compquadform
4516   (package
4517     (name "r-compquadform")
4518     (version "1.4.3")
4519     (source
4520      (origin
4521        (method url-fetch)
4522        (uri (cran-uri "CompQuadForm" version))
4523        (sha256
4524         (base32
4525          "1i30hrqdk64q17vsn918c3q79brchgx2wzh1gbsgbn0dh1ncabq4"))))
4526     (properties `((upstream-name . "CompQuadForm")))
4527     (build-system r-build-system)
4528     (home-page "https://cran.r-project.org/web/packages/CompQuadForm")
4529     (synopsis "Distribution function of quadratic forms in normal variables")
4530     (description
4531      "This package provides functions to compute the distribution function of
4532 quadratic forms in normal variables using Imhof's method, Davies's algorithm,
4533 Farebrother's algorithm or Liu et al.'s algorithm.")
4534     (license license:gpl2+)))
4535
4536 (define-public r-cowplot
4537   (package
4538     (name "r-cowplot")
4539     (version "1.0.0")
4540     (source
4541      (origin
4542        (method url-fetch)
4543        (uri (cran-uri "cowplot" version))
4544        (sha256
4545         (base32
4546          "19cqdhgfyr1wj0fz0c5ly8f0aiy9sfgzq6lzb78hkx0hdp2agybh"))))
4547     (build-system r-build-system)
4548     (propagated-inputs
4549      `(("r-ggplot2" ,r-ggplot2)
4550        ("r-gtable" ,r-gtable)
4551        ("r-rlang" ,r-rlang)
4552        ("r-scales" ,r-scales)))
4553     (home-page "https://github.com/wilkelab/cowplot")
4554     (synopsis "Streamlined plot theme and plot annotations for ggplot2")
4555     (description
4556      "This package provides some helpful extensions and modifications to the
4557 ggplot2 package to combine multiple ggplot2 plots into one and label them with
4558 letters, as is often required for scientific publications.")
4559     (license license:gpl2)))
4560
4561 (define-public r-mixtools
4562   (package
4563     (name "r-mixtools")
4564     (version "1.1.0")
4565     (source
4566      (origin
4567        (method url-fetch)
4568        (uri (cran-uri "mixtools" version))
4569        (sha256
4570         (base32
4571          "13wdm0xs5bakhpa8ypg6lvhjaqkxyabwz4glxdwn0jwdvkcdhgsl"))))
4572     (build-system r-build-system)
4573     (propagated-inputs
4574      `(("r-mass" ,r-mass)
4575        ("r-segmented" ,r-segmented)
4576        ("r-survival" ,r-survival)))
4577     (home-page "https://cran.r-project.org/web/packages/mixtools")
4578     (synopsis "Tools for analyzing finite mixture models")
4579     (description
4580      "This package provides a collection of R functions for analyzing finite
4581 mixture models.")
4582     (license license:gpl2+)))
4583
4584 (define-public r-lars
4585   (package
4586     (name "r-lars")
4587     (version "1.2")
4588     (source
4589      (origin
4590        (method url-fetch)
4591        (uri (cran-uri "lars" version))
4592        (sha256
4593         (base32
4594          "0blj44wqrx6lmym1m9v6wkz8zxzbjax2zl6swgdczci0ixb5nx34"))))
4595     (build-system r-build-system)
4596     (inputs
4597      `(("gfortran" ,gfortran)))
4598     (home-page "http://www-stat.stanford.edu/~hastie/Papers/#LARS")
4599     (synopsis "Least angle regression software")
4600     (description
4601      "Least Angle Regression (\"LAR\") is a model selection algorithm; a
4602 useful and less greedy version of traditional forward selection methods.  A
4603 simple modification of the LAR algorithm implements Tibshirani's Lasso; the
4604 Lasso modification of LARS calculates the entire Lasso path of coefficients
4605 for a given problem at the cost of a single least squares fit.  Another LARS
4606 modification efficiently implements epsilon Forward Stagewise linear
4607 regression.")
4608     (license license:gpl2)))
4609
4610 (define-public r-fastica
4611   (package
4612     (name "r-fastica")
4613     (version "1.2-2")
4614     (source
4615      (origin
4616        (method url-fetch)
4617        (uri (cran-uri "fastICA" version))
4618        (sha256
4619         (base32
4620          "1zpijqcipm0aa3rxj0mys06lskqy4dbppjpxr1aby0j16y9ka8ij"))))
4621     (properties `((upstream-name . "fastICA")))
4622     (build-system r-build-system)
4623     (home-page "https://cran.r-project.org/web/packages/fastICA")
4624     (synopsis "FastICA algorithms to perform ICA and projection pursuit")
4625     (description
4626      "This package provides an implementation of the FastICA algorithm to
4627 perform @dfn{independent component analysis} (ICA) and projection pursuit.")
4628     ;; Any GPL version.
4629     (license license:gpl3+)))
4630
4631 (define-public r-randomforest
4632   (package
4633     (name "r-randomforest")
4634     (version "4.6-14")
4635     (source
4636      (origin
4637        (method url-fetch)
4638        (uri (cran-uri "randomForest" version))
4639        (sha256
4640         (base32
4641          "0kbmm0l42fc2d1rdq0l7k09d34kd87q4lx651ffsic4y84h8kf7l"))))
4642     (properties `((upstream-name . "randomForest")))
4643     (build-system r-build-system)
4644     (home-page "https://www.stat.berkeley.edu/~breiman/RandomForests/")
4645     (native-inputs
4646      `(("gfortran" ,gfortran)))
4647     (synopsis "Breiman and Cutler's random forests for classification and regression")
4648     (description
4649 "This package provides the Breiman and Cutler's random forests algorithm, based on a
4650 forest of trees using random inputs, for classification and regression.")
4651     (license license:gpl2+)))
4652
4653 (define-public r-diptest
4654   (package
4655     (name "r-diptest")
4656     (version "0.75-7")
4657     (source
4658      (origin
4659        (method url-fetch)
4660        (uri (cran-uri "diptest" version))
4661        (sha256
4662         (base32
4663          "06xnc5gv1284ll0addxnxb6ljz6fn8dbyrp5vchyz6551h800aa6"))))
4664     (build-system r-build-system)
4665     (home-page "https://cran.r-project.org/web/packages/diptest")
4666     (synopsis "Hartigan's dip test statistic for unimodality")
4667     (description
4668      "This package computes Hartigan's dip test statistic for unimodality,
4669 multimodality and provides a test with simulation based p-values, where the
4670 original public code has been corrected.")
4671     (license license:gpl2+)))
4672
4673 (define-public r-modeltools
4674   (package
4675     (name "r-modeltools")
4676     (version "0.2-22")
4677     (source
4678      (origin
4679        (method url-fetch)
4680        (uri (cran-uri "modeltools" version))
4681        (sha256
4682         (base32
4683          "1s9lmkac3rl0nknf4wizfhg7ryq7c8yvvyc4z619238br27hhsi5"))))
4684     (build-system r-build-system)
4685     (home-page "https://cran.r-project.org/web/packages/modeltools")
4686     (synopsis "Tools and classes for statistical models")
4687     (description
4688      "This package provides a collection of tools to deal with statistical
4689 models.  The functionality is experimental and the user interface is likely
4690 to change in the future.")
4691     (license license:gpl2)))
4692
4693 (define-public r-flexmix
4694   (package
4695     (name "r-flexmix")
4696     (version "2.3-15")
4697     (source
4698      (origin
4699        (method url-fetch)
4700        (uri (cran-uri "flexmix" version))
4701        (sha256
4702         (base32
4703          "0hrz2axp2c9548b1r0bmrl57219nn030qndb83a8garkzq5lqi5s"))))
4704     (build-system r-build-system)
4705     (propagated-inputs
4706      `(("r-lattice" ,r-lattice)
4707        ("r-modeltools" ,r-modeltools)
4708        ("r-nnet" ,r-nnet)))
4709     (home-page "https://cran.r-project.org/web/packages/flexmix")
4710     (synopsis "Flexible mixture modeling")
4711     (description
4712      "This package implements a general framework for finite mixtures of
4713 regression models using the EM algorithm.  FlexMix provides the E-step and
4714 all data handling, while the M-step can be supplied by the user to easily
4715 define new models.  Existing drivers implement mixtures of standard linear
4716 models, generalized linear models and model-based clustering.")
4717     (license license:gpl2+)))
4718
4719 (define-public r-mclust
4720   (package
4721     (name "r-mclust")
4722     (version "5.4.5")
4723     (source
4724      (origin
4725        (method url-fetch)
4726        (uri (cran-uri "mclust" version))
4727        (sha256
4728         (base32
4729          "0whandnda1fnjn5k3hgxdbp3b0xr7nlzy1j37saqb536h8q9dwkm"))))
4730     (build-system r-build-system)
4731     (native-inputs
4732      `(("gfortran" ,gfortran)))
4733     (home-page "http://www.stat.washington.edu/mclust/")
4734     (synopsis "Gaussian mixture modelling for model-based clustering etc.")
4735     (description
4736      "This package provides Gaussian finite mixture models fitted via EM
4737 algorithm for model-based clustering, classification, and density estimation,
4738 including Bayesian regularization, dimension reduction for visualisation,
4739 and resampling-based inference.")
4740     (license license:gpl2+)))
4741
4742 (define-public r-prabclus
4743   (package
4744     (name "r-prabclus")
4745     (version "2.3-2")
4746     (source
4747      (origin
4748        (method url-fetch)
4749        (uri (cran-uri "prabclus" version))
4750        (sha256
4751         (base32
4752          "0hg4d7y1w18jpgvw10z8833bbbcnlkwiasx0wh6iwa2pnnybq8gl"))))
4753     (build-system r-build-system)
4754     (propagated-inputs
4755      `(("r-mass" ,r-mass)
4756        ("r-mclust" ,r-mclust)))
4757     (home-page "https://cran.r-project.org/web/packages/prabclus")
4758     (synopsis "Parametric bootstrap tests for spatial neighborhood clustering")
4759     (description
4760      "This package provides distance-based parametric bootstrap tests for
4761 clustering with spatial neighborhood information.  It implements some distance
4762 measures, clustering of presence-absence, abundance and multilocus genetical
4763 data for species delimitation, nearest neighbor based noise detection.")
4764     (license license:gpl2+)))
4765
4766 (define-public r-deoptimr
4767   (package
4768     (name "r-deoptimr")
4769     (version "1.0-8")
4770     (source
4771      (origin
4772        (method url-fetch)
4773        (uri (cran-uri "DEoptimR" version))
4774        (sha256
4775         (base32
4776          "1vz546hyjyhly70z62h5n3mn62b8llhhmim8ffp9y6jnnb0i2sc4"))))
4777     (properties `((upstream-name . "DEoptimR")))
4778     (build-system r-build-system)
4779     (home-page "https://cran.r-project.org/web/packages/DEoptimR")
4780     (synopsis "Differential evolution optimization in pure R")
4781     (description
4782      "This package provides a differential evolution (DE) stochastic
4783 algorithms for global optimization of problems with and without constraints.
4784 The aim is to curate a collection of its state-of-the-art variants that (1) do
4785 not sacrifice simplicity of design, (2) are essentially tuning-free, and (3)
4786 can be efficiently implemented directly in the R language.")
4787     (license license:gpl2+)))
4788
4789 (define-public r-robustbase
4790   (package
4791     (name "r-robustbase")
4792     (version "0.93-5")
4793     (source
4794      (origin
4795        (method url-fetch)
4796        (uri (cran-uri "robustbase" version))
4797        (sha256
4798         (base32
4799          "0mkzbsjl5nihyj7mzks14p6kr3spp44xvygjz4ran11gspdn9rdx"))))
4800     (build-system r-build-system)
4801     (native-inputs
4802      `(("gfortran" ,gfortran)))
4803     (propagated-inputs
4804      `(("r-deoptimr" ,r-deoptimr)))
4805     (home-page "http://robustbase.r-forge.r-project.org/")
4806     (synopsis "Basic robust statistics")
4807     (description
4808      "This package allows to analyze data with robust methods such as
4809 regression methodology including model selections and multivariate statistics.")
4810     (license license:gpl2+)))
4811
4812 (define-public r-pcapp
4813   (package
4814     (name "r-pcapp")
4815     (version "1.9-73")
4816     (source
4817      (origin
4818        (method url-fetch)
4819        (uri (cran-uri "pcaPP" version))
4820        (sha256
4821         (base32
4822          "1z2kdf9gfp965xbcd4rg6vf20d1bl443na0qjkpq7gmzpaq6cifa"))))
4823     (properties `((upstream-name . "pcaPP")))
4824     (build-system r-build-system)
4825     (propagated-inputs
4826      `(("r-mvtnorm" ,r-mvtnorm)))
4827     (home-page "https://cran.r-project.org/web/packages/pcaPP")
4828     (synopsis "Robust PCA by projection pursuit")
4829     (description
4830      "This package provides functions for robust @dfn{principal component
4831 analysis} (PCA) by projection pursuit.")
4832     (license license:gpl3+)))
4833
4834 (define-public r-rrcov
4835   (package
4836     (name "r-rrcov")
4837     (version "1.4-9")
4838     (source
4839      (origin
4840        (method url-fetch)
4841        (uri (cran-uri "rrcov" version))
4842        (sha256
4843         (base32
4844          "11zvxidlb1pr2j5dzvmbjqdgsmmicsq8ppjf5wcfykfyf2fkcmz7"))))
4845     (build-system r-build-system)
4846     (propagated-inputs
4847      `(("r-cluster" ,r-cluster)
4848        ("r-lattice" ,r-lattice)
4849        ("r-mvtnorm" ,r-mvtnorm)
4850        ("r-pcapp" ,r-pcapp)
4851        ("r-robustbase" ,r-robustbase)))
4852     (native-inputs
4853      `(("gfortran" ,gfortran)))
4854     (home-page "https://cran.r-project.org/web/packages/rrcov")
4855     (synopsis "Scalable robust estimators with high breakdown Point")
4856     (description
4857      "This package provides an implementation of robust location and scatter
4858 estimation and robust multivariate analysis with high breakdown point.")
4859     (license license:gpl2+)))
4860
4861 (define-public r-fit-models
4862   (package
4863     (name "r-fit-models")
4864     (version "0.5-14")
4865     (source
4866      (origin
4867        (method url-fetch)
4868        (uri (cran-uri "fit.models" version))
4869        (sha256
4870         (base32
4871          "0vjbzmx0ambm6yzidb4vbgmhclwzwv2iz2cwl54ccdkvx4cx3fck"))))
4872     (properties `((upstream-name . "fit.models")))
4873     (build-system r-build-system)
4874     (propagated-inputs
4875      `(("r-lattice" ,r-lattice)))
4876     (home-page "https://cran.r-project.org/web/packages/fit.models")
4877     (synopsis "Compare fitted models")
4878     (description
4879      "The @code{fit.models} function and its associated methods (coefficients, print,
4880 summary, plot, etc.) were originally provided in the @code{robust} package to
4881 compare robustly and classically fitted model objects.  The aim of the
4882 @code{fit.models} package is to separate this fitted model object comparison
4883 functionality from the robust package and to extend it to support fitting
4884 methods (e.g., classical, robust, Bayesian, regularized, etc.) more
4885 generally.")
4886     ;; Any version of the GPL
4887     (license (list license:gpl2+ license:gpl3+))))
4888
4889 (define-public r-robust
4890   (package
4891     (name "r-robust")
4892     (version "0.4-18.2")
4893     (source
4894      (origin
4895        (method url-fetch)
4896        (uri (cran-uri "robust" version))
4897        (sha256
4898         (base32
4899          "02x7d6dgx3skiadvx5m3c44b4bhz37ycpfhc25dhhv50y1db6l3k"))))
4900     (build-system r-build-system)
4901     (propagated-inputs
4902      `(("r-fit-models" ,r-fit-models)
4903        ("r-lattice" ,r-lattice)
4904        ("r-mass" ,r-mass)
4905        ("r-robustbase" ,r-robustbase)
4906        ("r-rrcov" ,r-rrcov)))
4907     (native-inputs
4908      `(("gfortran" ,gfortran)))
4909     (home-page "https://cran.r-project.org/web/packages/robust")
4910     (synopsis "Port of the S+ \"Robust Library\"")
4911     (description
4912      "This package is a port of the S+ \"Robust Library\".  It provides
4913 methods for robust statistics, notably for robust regression and robust
4914 multivariate analysis.")
4915     (license license:gpl2)))
4916
4917 (define-public r-trimcluster
4918   (package
4919     (name "r-trimcluster")
4920     (version "0.1-2.1")
4921     (source
4922      (origin
4923        (method url-fetch)
4924        (uri (cran-uri "trimcluster" version))
4925        (sha256
4926         (base32
4927          "0013bpyq6mkvjn38qsmwnsxfiwxgwngnqxycxvgpgmiadhm8fjmn"))))
4928     (build-system r-build-system)
4929     (home-page "https://cran.r-project.org/web/packages/trimcluster")
4930     (synopsis "Cluster analysis with trimming")
4931     (description
4932      "The trimmed k-means clustering method by Cuesta-Albertos, Gordaliza and
4933 Matran (1997).  This optimizes the k-means criterion under trimming a portion
4934 of the points.")
4935     ;; Any GPL version
4936     (license (list license:gpl2+ license:gpl3+))))
4937
4938 (define-public r-fpc
4939   (package
4940     (name "r-fpc")
4941     (version "2.2-3")
4942     (source
4943      (origin
4944        (method url-fetch)
4945        (uri (cran-uri "fpc" version))
4946        (sha256
4947         (base32
4948          "1dy3pla4jjgs46izqg2kxajlxr80sbr9896jbzb1qszrdx7af041"))))
4949     (build-system r-build-system)
4950     (propagated-inputs
4951      `(("r-class" ,r-class)
4952        ("r-cluster" ,r-cluster)
4953        ("r-diptest" ,r-diptest)
4954        ("r-flexmix" ,r-flexmix)
4955        ("r-kernlab" ,r-kernlab)
4956        ("r-mass" ,r-mass)
4957        ("r-mclust" ,r-mclust)
4958        ("r-prabclus" ,r-prabclus)
4959        ("r-robustbase" ,r-robustbase)))
4960     (home-page "https://cran.r-project.org/web/packages/fpc")
4961     (synopsis "Flexible procedures for clustering")
4962     (description
4963      "This package provides various methods for clustering and cluster validation.
4964 For example, it provides fixed point clustering, linear regression clustering,
4965 clustering by merging Gaussian mixture components, as well as symmetric and
4966 asymmetric discriminant projections for visualisation of the separation of
4967 groupings.")
4968   (license license:gpl2+)))
4969
4970 (define-public r-vgam
4971   (package
4972     (name "r-vgam")
4973     (version "1.1-2")
4974     (source
4975      (origin
4976        (method url-fetch)
4977        (uri (cran-uri "VGAM" version))
4978        (sha256
4979         (base32 "0kyan3a4ys2xbg9kf167cyf1gk7g963id62cjm2ij4i7y4wi61zq"))))
4980     (properties `((upstream-name . "VGAM")))
4981     (build-system r-build-system)
4982     (inputs
4983      `(("gfortran" ,gfortran)))
4984     (home-page "https://www.stat.auckland.ac.nz/~yee/VGAM")
4985     (synopsis "Vector generalized linear and additive models")
4986     (description
4987     "This package is an implementation of about 6 major classes of statistical
4988 regression models.  Currently only fixed-effects models are implemented, i.e.,
4989 no random-effects models.  Many (150+) models and distributions are estimated
4990 by maximum likelihood estimation (MLE) or penalized MLE, using Fisher scoring.
4991 VGLMs can be loosely thought of as multivariate generalised linear models.")
4992     (license license:gpl2+)))
4993
4994 (define-public r-pbapply
4995   (package
4996     (name "r-pbapply")
4997     (version "1.4-2")
4998     (source
4999      (origin
5000        (method url-fetch)
5001        (uri (cran-uri "pbapply" version))
5002        (sha256
5003         (base32
5004          "1xmk4p006v8gij26rs6kp5prjyf2n32nqjxiyp8a6kvgyc4z46dc"))))
5005     (build-system r-build-system)
5006     (home-page "https://github.com/psolymos/pbapply")
5007     (synopsis "Adding progress bar to apply functions")
5008     (description
5009      "This lightweight package that adds progress bar to vectorized R
5010 functions apply.  The implementation can easily be added to functions where
5011 showing the progress is useful e.g. bootstrap.")
5012     (license license:gpl2)))
5013
5014 (define-public r-minqa
5015   (package
5016     (name "r-minqa")
5017     (version "1.2.4")
5018     (source
5019      (origin
5020        (method url-fetch)
5021        (uri (cran-uri "minqa" version))
5022        (sha256
5023         (base32
5024          "036drja6xz7awja9iwb76x91415p26fb0jmg7y7v0p65m6j978fg"))))
5025     (build-system r-build-system)
5026     (propagated-inputs
5027      `(("r-rcpp" ,r-rcpp)))
5028     (inputs
5029      `(("gfortran" ,gfortran)))
5030     (home-page "http://optimizer.r-forge.r-project.org")
5031     (synopsis "Derivative-free optimization algorithms by quadratic approximation")
5032     (description
5033       "This package provides a derivative-free optimization by quadratic approximation
5034 based on an interface to Fortran implementations by M. J. D. Powell.")
5035     (license license:gpl2)))
5036
5037 (define-public r-rcppeigen
5038   (package
5039     (name "r-rcppeigen")
5040     (version "0.3.3.7.0")
5041     (source
5042      (origin
5043        (method url-fetch)
5044        (uri (cran-uri "RcppEigen" version))
5045        (sha256
5046         (base32
5047          "1b78qcjim0n9klgkr82n794d6bj9r9f33g0kcsszsns2hir65sk2"))))
5048     (properties `((upstream-name . "RcppEigen")))
5049     (build-system r-build-system)
5050     (propagated-inputs
5051      `(("r-rcpp" ,r-rcpp)
5052        ("r-matrix" ,r-matrix)))
5053     (home-page "http://eigen.tuxfamily.org")
5054     (synopsis "Rcpp integration for the Eigen templated linear algebra library")
5055     (description
5056       "This package provides an integration of Eigen in R using a C++ template
5057 library for linear algebra: matrices, vectors, numerical solvers and related algorithms.
5058 It supports dense and sparse matrices on integer, floating point and complex numbers,
5059 decompositions of such matrices, and solutions of linear systems.")
5060     (license license:gpl2+)))
5061
5062 (define-public r-modelmetrics
5063   (package
5064     (name "r-modelmetrics")
5065     (version "1.2.2.1")
5066     (source
5067      (origin
5068        (method url-fetch)
5069         (uri (cran-uri "ModelMetrics" version))
5070         (sha256
5071          (base32
5072           "17yw46yr0n9hddvlhh73jdpmpdlpa581n5xjpwkr6cpr2f7xxpqc"))))
5073     (properties `((upstream-name . "ModelMetrics")))
5074     (build-system r-build-system)
5075     (propagated-inputs
5076      `(("r-rcpp" ,r-rcpp)
5077        ("r-data-table" ,r-data-table)))
5078     (home-page "https://cran.r-project.org/web/packages/ModelMetrics")
5079     (synopsis "Rapid calculation of model metrics")
5080     (description
5081      "Written in C++ using @code{Rcpp}, this package provides a collection of
5082 metrics for evaluating models.")
5083     (license license:gpl2+)))
5084
5085 (define-public r-matrixmodels
5086   (package
5087     (name "r-matrixmodels")
5088     (version "0.4-1")
5089     (source
5090      (origin
5091        (method url-fetch)
5092        (uri (cran-uri "MatrixModels" version))
5093        (sha256
5094         (base32
5095          "0cyfvhci2p1vr2x52ymkyqqs63x1qchn856dh2j94yb93r08x1zy"))))
5096     (properties `((upstream-name . "MatrixModels")))
5097     (build-system r-build-system)
5098     (propagated-inputs
5099      `(("r-matrix" ,r-matrix)))
5100     (home-page "https://cran.r-project.org/web/packages/MatrixModels")
5101     (synopsis "Modelling with sparse and dense matrices")
5102     (description
5103      "This package models with sparse and dense matrix matrices,
5104 using modular prediction and response module classes.")
5105     (license license:gpl2+)))
5106
5107 (define-public r-quantreg
5108   (package
5109     (name "r-quantreg")
5110     (version "5.54")
5111     (source
5112      (origin
5113        (method url-fetch)
5114        (uri (cran-uri "quantreg" version))
5115        (sha256
5116         (base32 "19nh79qrkb75q348nk148l8wqjwnq5jgq29wpzqym5cfv1kjqfvh"))))
5117     (build-system r-build-system)
5118     (native-inputs
5119      `(("gfortran" ,gfortran)))
5120     (propagated-inputs
5121      `(("r-matrix" ,r-matrix)
5122        ("r-matrixmodels" ,r-matrixmodels)
5123        ("r-sparsem" ,r-sparsem)))
5124     (home-page "https://www.r-project.org")
5125     (synopsis "Quantile regression")
5126     (description
5127      "This package provides an estimation and inference methods for models
5128 of conditional quantiles: linear and nonlinear parametric and non-parametric
5129 models for conditional quantiles of a univariate response and several methods
5130 for handling censored survival data.  Portfolio selection methods based on
5131 expected shortfall risk are also included.")
5132     (license license:gpl2+)))
5133
5134 (define-public r-nloptr
5135   (package
5136     (name "r-nloptr")
5137     (version "1.2.1")
5138     (source
5139      (origin
5140        (method url-fetch)
5141        (uri (cran-uri "nloptr" version))
5142        (sha256
5143         (base32
5144          "15yz60kljxwnhm2m3gryjzxl3ynhkhd5jiwc179b1hz6rlzf71hz"))))
5145     (build-system r-build-system)
5146     (native-inputs
5147      `(("r-knitr" ,r-knitr) ; for building vignettes
5148        ("pkg-config" ,pkg-config)
5149        ("gfortran" ,gfortran)))
5150     (inputs
5151      `(("nlopt" ,nlopt)))
5152     (home-page "https://cran.r-project.org/web/packages/nloptr")
5153     (synopsis "R interface to NLopt")
5154     (description
5155      "This package is interface to NLopt, a library for nonlinear
5156 optimization.  NLopt is a library for nonlinear optimization, providing a
5157 common interface for a number of different free optimization routines
5158 available online as well as original implementations of various other
5159 algorithms.")
5160     (license license:lgpl3)))
5161
5162 (define-public r-lme4
5163   (package
5164     (name "r-lme4")
5165     (version "1.1-21")
5166     (source
5167      (origin
5168        (method url-fetch)
5169        (uri (cran-uri "lme4" version))
5170        (sha256
5171         (base32
5172          "035j2hqkwv939xl07pm2vykvf3wlx8qj317846n9pkpqkyv58mbz"))))
5173     (build-system r-build-system)
5174     (propagated-inputs
5175      `(("r-boot" ,r-boot)
5176        ("r-lattice" ,r-lattice)
5177        ("r-mass" ,r-mass)
5178        ("r-matrix" ,r-matrix)
5179        ("r-minqa" ,r-minqa)
5180        ("r-nloptr" ,r-nloptr)
5181        ("r-nlme" ,r-nlme)
5182        ("r-rcpp" ,r-rcpp)
5183        ("r-rcppeigen" ,r-rcppeigen)))
5184     (home-page "https://cran.r-project.org/web/packages/lme4")
5185     (synopsis "Linear mixed-effects models using eigen and S4")
5186     (description
5187       "This package provides fit linear and generalized linear mixed-effects
5188 models.  The models and their components are represented using S4 classes and
5189 methods.  The core computational algorithms are implemented using the Eigen
5190 C++ library for numerical linear algebra and RcppEigen glue.")
5191     (license license:gpl2+)))
5192
5193 (define-public r-pbkrtest
5194   (package
5195     (name "r-pbkrtest")
5196     (version "0.4-7")
5197     (source
5198      (origin
5199        (method url-fetch)
5200        (uri (cran-uri "pbkrtest" version))
5201        (sha256
5202         (base32
5203          "1si3bhi59xc51a0pgjjglccq3h4aljyhw2k1b8574s145fnh7fsw"))))
5204     (build-system r-build-system)
5205     (propagated-inputs
5206      `(("r-lme4" ,r-lme4)
5207        ("r-mass" ,r-mass)
5208        ("r-matrix" ,r-matrix)))
5209     (home-page "http://people.math.aau.dk/~sorenh/software/pbkrtest/")
5210     (synopsis "Methods for linear mixed model comparison")
5211     (description
5212      "This package implements a parametric bootstrap test and a Kenward Roger
5213 modification of F-tests for linear mixed effects models and a parametric
5214 bootstrap test for generalized linear mixed models.")
5215     (license license:gpl2+)))
5216
5217 (define-public r-cardata
5218   (package
5219     (name "r-cardata")
5220     (version "3.0-3")
5221     (source
5222      (origin
5223        (method url-fetch)
5224        (uri (cran-uri "carData" version))
5225        (sha256
5226         (base32 "0cg2yxzn0pdjqykr60my1fzpfkqac21fll5hv3m9w5c9sayq8swq"))))
5227     (properties `((upstream-name . "carData")))
5228     (build-system r-build-system)
5229     (home-page "https://r-forge.r-project.org/projects/car/")
5230     (synopsis "Data Sets for the book Companion to Applied Regression")
5231     (description
5232      "This package provides datasets to accompany J. Fox and S. Weisberg, An R
5233 Companion to Applied Regression, Third Edition, Sage.")
5234     (license license:gpl2+)))
5235
5236 (define-public r-car
5237   (package
5238     (name "r-car")
5239     (version "3.0-6")
5240     (source
5241      (origin
5242        (method url-fetch)
5243        (uri (cran-uri "car" version))
5244        (sha256
5245         (base32 "0yv5mwaa0ymrbis9590mx0zcj3w6j4drhs6ab13zhx4zc3x1b7b6"))))
5246     (build-system r-build-system)
5247     (propagated-inputs
5248      `(("r-abind" ,r-abind)
5249        ("r-cardata" ,r-cardata)
5250        ("r-lme4" ,r-lme4)
5251        ("r-maptools" ,r-maptools)
5252        ("r-mass" ,r-mass)
5253        ("r-mgcv" ,r-mgcv)
5254        ("r-nlme" ,r-nlme)
5255        ("r-nnet" ,r-nnet)
5256        ("r-pbkrtest" ,r-pbkrtest)
5257        ("r-quantreg" ,r-quantreg)
5258        ("r-rio" ,r-rio)))
5259     (home-page "https://r-forge.r-project.org/projects/car/")
5260     (synopsis "Companion to applied regression")
5261     (description
5262       "This package provides functions and datasets from book Companion
5263 to Applied regression, Second Edition, Sage, 2011.")
5264     (license license:gpl2+)))
5265
5266 (define-public r-rcppprogress
5267   (package
5268     (name "r-rcppprogress")
5269     (version "0.4.1")
5270     (source
5271      (origin
5272        (method url-fetch)
5273        (uri (cran-uri "RcppProgress" version))
5274        (sha256
5275         (base32
5276          "0yk01hfv961zyp569682k9igvhnwqyg5j0n5fm63sxigj82l2xhi"))))
5277     (properties `((upstream-name . "RcppProgress")))
5278     (build-system r-build-system)
5279     (propagated-inputs
5280      `(("r-devtools" ,r-devtools)
5281        ("r-rcpp" ,r-rcpp)))
5282     (home-page "https://github.com/kforner/rcpp_progress")
5283     (synopsis "Interruptible progress bar for C++ in R packages")
5284     (description
5285      "This package allows to display a progress bar in the R console for long running
5286 computations taking place in C++ code, and support for interrupting those computations
5287 even in multithreaded code, typically using OpenMP.")
5288     (license license:gpl3+)))
5289
5290 (define-public r-mnormt
5291   (package
5292     (name "r-mnormt")
5293     (version "1.5-5")
5294     (source
5295      (origin
5296        (method url-fetch)
5297         (uri (cran-uri "mnormt" version))
5298         (sha256
5299           (base32
5300            "1b34xxrnf35khsx82mhvmk96sgfr2flyasaah7qkb2976pwxay7z"))))
5301     (build-system r-build-system)
5302     (native-inputs
5303      `(("gfortran" ,gfortran)))
5304     (home-page "http://azzalini.stat.unipd.it/SW/Pkg-mnormt")
5305     (synopsis "Multivariate normal and \"t\" distributions")
5306     (description
5307      "This package provides functions for computing the density and the
5308 distribution function of multivariate normal and \"t\" random variables, and
5309 for generating random vectors sampled from these distributions.  Probabilities
5310 are computed via non-Monte Carlo methods.")
5311     (license license:gpl2+)))
5312
5313 (define-public r-numderiv
5314   (package
5315     (name "r-numderiv")
5316     (version "2016.8-1.1")
5317     (source
5318      (origin
5319        (method url-fetch)
5320        (uri (cran-uri "numDeriv" version))
5321        (sha256
5322         (base32
5323          "0idk02pqkziik932bd8k72d1q775g1is3m4bc861pcxfz6gx3i6q"))))
5324     (properties `((upstream-name . "numDeriv")))
5325     (build-system r-build-system)
5326     (home-page "https://cran.r-project.org/web/packages/numDeriv")
5327     (synopsis "Accurate numerical derivatives")
5328     (description
5329      "This package provides methods for calculating accurate numerical
5330 first and second order derivatives.")
5331     (license license:gpl2)))
5332
5333 (define-public r-sn
5334   (package
5335     (name "r-sn")
5336     (version "1.5-4")
5337     (source
5338      (origin
5339        (method url-fetch)
5340        (uri (cran-uri "sn" version))
5341        (sha256
5342         (base32
5343          "0x46gxkplxbnhaqbpiav1r4xlv4ib7n57kxmca7scqwj22y7wrs6"))))
5344     (build-system r-build-system)
5345     (propagated-inputs
5346      `(("r-mnormt" ,r-mnormt)
5347        ("r-numderiv" ,r-numderiv)))
5348     (home-page "http://azzalini.stat.unipd.it/SN")
5349     (synopsis "The skew-normal and skew-t distributions")
5350     (description
5351      "This package provides functionalities to build and manipulate
5352 probability distributions of the skew-normal family and some related
5353 ones, notably the skew-t family, and provides related statistical
5354 methods for data fitting and diagnostics, in the univariate and the
5355 multivariate case.")
5356     (license license:gpl2+)))
5357
5358 (define-public r-tclust
5359   (package
5360     (name "r-tclust")
5361     (version "1.4-1")
5362     (source
5363      (origin
5364        (method url-fetch)
5365        (uri (cran-uri "tclust" version))
5366        (sha256
5367         (base32
5368          "17md6l9v9dl9b72l84df01b52h2xiynbcjm437mv9mzcr09fc2sb"))))
5369     (build-system r-build-system)
5370     ;; These are all suggested packages, not build dependencies.
5371     (propagated-inputs
5372      `(("r-cluster" ,r-cluster)
5373        ("r-mclust" ,r-mclust)
5374        ("r-mvtnorm" ,r-mvtnorm)
5375        ("r-sn" ,r-sn)))
5376     (home-page "https://cran.r-project.org/web/packages/tclust")
5377     (synopsis "Robust trimmed clustering")
5378     (description
5379      "This package implements different robust clustering
5380 algorithms (@code{tclust}) based on trimming and including some graphical
5381 diagnostic tools (@code{ctlcurves} and @code{DiscrFact}).")
5382     (license license:gpl3)))
5383
5384 (define-public r-ranger
5385   (package
5386     (name "r-ranger")
5387     (version "0.12.1")
5388     (source
5389      (origin
5390        (method url-fetch)
5391        (uri (cran-uri "ranger" version))
5392        (sha256
5393         (base32
5394          "1vr5akgh388iivrxi0g4pl2npq9dc4cim3ljk4kjf637q058wc7w"))))
5395     (build-system r-build-system)
5396     (propagated-inputs
5397      `(("r-rcpp" ,r-rcpp)
5398        ("r-matrix" ,r-matrix)
5399        ("r-rcppeigen" ,r-rcppeigen)))
5400     (home-page "https://github.com/imbs-hl/ranger")
5401     (synopsis "Fast implementation of random forests")
5402     (description
5403      "This package provides a fast implementation of Random Forests,
5404 particularly suited for high dimensional data.  Ensembles of classification,
5405 regression, survival and probability prediction trees are supported.  Data from
5406 genome-wide association studies can be analyzed efficiently.")
5407     (license license:gpl3)))
5408
5409 (define-public r-tsne
5410   (package
5411     (name "r-tsne")
5412     (version "0.1-3")
5413     (source
5414      (origin
5415        (method url-fetch)
5416        (uri (cran-uri "tsne" version))
5417        (sha256
5418         (base32
5419          "0s8cv2pndkddq62rzlgzgfdjp1vjv5hz5i5957sllnb97vbzbzb6"))))
5420     (build-system r-build-system)
5421     (home-page "https://github.com/jdonaldson/rtsne/")
5422     (synopsis "t-Distributed Stochastic Neighbor Embedding for R")
5423     (description
5424      "This package provides a pure R implementation of the t-SNE algorithm.")
5425     (license license:gpl2+)))
5426
5427 (define-public r-cairo
5428   (package
5429     (name "r-cairo")
5430     (version "1.5-10")
5431     (source
5432      (origin
5433        (method url-fetch)
5434        (uri (cran-uri "Cairo" version))
5435        (sha256
5436         (base32
5437          "1mdmd5zmjkh1b0x928zizgzh42x8swbajffb88rvnjfdhk1z0dvq"))))
5438     (properties `((upstream-name . "Cairo")))
5439     (build-system r-build-system)
5440     (inputs
5441      `(("cairo" ,cairo)
5442        ("libxt" ,libxt)
5443        ("zlib" ,zlib)))
5444     (native-inputs
5445      `(("pkg-config" ,pkg-config)))
5446     (home-page "http://www.rforge.net/Cairo/")
5447     (synopsis "R graphics device using Cairo graphics library")
5448     (description
5449      "This package provides a Cairo graphics device that can be use to
5450 create high-quality vector (PDF, PostScript and SVG) and bitmap
5451 output (PNG,JPEG,TIFF), and high-quality rendering in displays (X11
5452 and Win32).  Since it uses the same back-end for all output, copying
5453 across formats is WYSIWYG.  Files are created without the dependence
5454 on X11 or other external programs.  This device supports alpha
5455 channel (semi-transparent drawing) and resulting images can contain
5456 transparent and semi-transparent regions.  It is ideal for use in
5457 server environments (file output) and as a replacement for other
5458 devices that don't have Cairo's capabilities such as alpha support or
5459 anti-aliasing.  Backends are modular such that any subset of backends
5460 is supported.")
5461     (license license:gpl2)))
5462
5463 (define-public r-lubridate
5464   (package
5465     (name "r-lubridate")
5466     (version "1.7.4")
5467     (source
5468      (origin
5469        (method url-fetch)
5470        (uri (cran-uri "lubridate" version))
5471        (sha256
5472         (base32
5473          "14a823il77w3wmmnzr89vwrqp50y56dh5raycnaw6c8nv5xsh32i"))))
5474     (build-system r-build-system)
5475     (propagated-inputs
5476      `(("r-rcpp" ,r-rcpp)
5477        ("r-stringr" ,r-stringr)))
5478     (home-page
5479      "https://cran.r-project.org/web/packages/lubridate")
5480     (synopsis "Make dealing with dates a little easier")
5481     (description
5482      "This package provides functions to work with date-times and time-spans:
5483 fast and user friendly parsing of date-time data, extraction and updating of
5484 components of a date-time (years, months, days, hours, minutes, and seconds),
5485 algebraic manipulation on date-time and time-span objects.  The @code{lubridate}
5486 package has a consistent and memorable syntax that makes working with dates
5487 easy and fun.")
5488     (license license:gpl2)))
5489
5490 (define-public r-fdrtool
5491   (package
5492     (name "r-fdrtool")
5493     (version "1.2.15")
5494     (source
5495      (origin
5496        (method url-fetch)
5497        (uri (cran-uri "fdrtool" version))
5498        (sha256
5499         (base32
5500          "1h46frlk7d9f4qx0bg6p55nrm9wwwz2sv6d1nz7061wdfsm69yb5"))))
5501     (build-system r-build-system)
5502     (home-page "http://strimmerlab.org/software/fdrtool/")
5503     (synopsis "Estimation of false discovery rates and higher criticism")
5504     (description
5505      "This package provides tools to estimate tail area-based false discovery
5506 rates as well as local false discovery rates for a variety of null
5507 models (p-values, z-scores, correlation coefficients, t-scores).  The
5508 proportion of null values and the parameters of the null distribution are
5509 adaptively estimated from the data.  In addition, the package contains
5510 functions for non-parametric density estimation (Grenander estimator), for
5511 monotone regression (isotonic regression and antitonic regression with
5512 weights), for computing the @dfn{greatest convex minorant} (GCM) and the
5513 @dfn{least concave majorant} (LCM), for the half-normal and correlation
5514 distributions, and for computing empirical @dfn{higher criticism} (HC) scores
5515 and the corresponding decision threshold.")
5516     (license license:gpl3+)))
5517
5518 (define-public r-forcats
5519   (package
5520     (name "r-forcats")
5521     (version "0.4.0")
5522     (source
5523      (origin
5524        (method url-fetch)
5525        (uri (cran-uri "forcats" version))
5526        (sha256
5527         (base32
5528          "1cnjh23z59fhbjmy7y95425hcq3m5wrwqvahsxwi7zm6d9bwp0vw"))))
5529     (build-system r-build-system)
5530     (propagated-inputs
5531      `(("r-ellipsis" ,r-ellipsis)
5532        ("r-magrittr" ,r-magrittr)
5533        ("r-tibble" ,r-tibble)
5534        ("r-rlang" ,r-rlang)))
5535     (home-page "http://forcats.tidyverse.org")
5536     (synopsis "Tools for working with factors")
5537     (description "This package provides helpers for reordering factor
5538 levels (including moving specified levels to front, ordering by first
5539 appearance, reversing, and randomly shuffling), and tools for modifying factor
5540 levels (including collapsing rare levels into other, \"anonymizing\", and
5541 manually \"recoding\").")
5542     (license license:gpl3)))
5543
5544 (define-public r-tgstat
5545   (let ((changeset "4f8e60c03598f49aff6f5beeab40f2b995377e9f")
5546         (revision "1"))
5547     (package
5548       (name "r-tgstat")
5549       (version (string-append "1.0.2-" revision "." (string-take changeset 7)))
5550       (source
5551        (origin
5552          (method hg-fetch)
5553          (uri (hg-reference
5554                (url "https://bitbucket.org/tanaylab/tgstat")
5555                (changeset changeset)))
5556          (file-name (string-append name "-" version "-checkout"))
5557          (sha256
5558           (base32
5559            "0ilkkyximy77zbncm91kdfqbxf0qyndg16pd3q3p6a3xc9qcmxvn"))))
5560       (build-system r-build-system)
5561       (arguments
5562        `(#:phases
5563          (modify-phases %standard-phases
5564            (add-after 'unpack 'fix-isnan
5565              (lambda _
5566                (substitute* "src/tgstat.h"
5567                  (("#define isnan ::isnan")
5568                   "#define isnan std::isnan"))
5569                #t)))))
5570       (propagated-inputs
5571        `(("r-rcpp" ,r-rcpp)))
5572       (home-page "https://bitbucket.org/tanaylab/tgstat/")
5573       (synopsis "Tanay's group statistical utilities")
5574       (description
5575        "The goal of tgstat is to provide fast and efficient statistical
5576 tools.")
5577       (license license:gpl2))))
5578
5579 (define-public r-tgconfig
5580   (let ((changeset "1e02c7614713bd0866c46f0c679a058f8c6d627e")
5581         (revision "1"))
5582     (package
5583       (name "r-tgconfig")
5584       (version (string-append "0.0.0.9000-" revision "." (string-take changeset 7)))
5585       (source
5586        (origin
5587          (method hg-fetch)
5588          (uri (hg-reference
5589                (url "https://bitbucket.org/tanaylab/tgconfig")
5590                (changeset changeset)))
5591          (file-name (string-append name "-" version "-checkout"))
5592          (sha256
5593           (base32
5594            "0xy6c7s7mn1yx191154bwbv1bl424bnvc80syqpl1vdl28ba46rj"))))
5595       (build-system r-build-system)
5596       (propagated-inputs
5597        `(("r-yaml" ,r-yaml)))
5598       (home-page "https://bitbucket.org/tanaylab/tgconfig/")
5599       (synopsis "Infrastructure for managing package parameters")
5600       (description
5601        "The goal of tgconfig is to provide infrastructure for managing package
5602 parameters.")
5603       (license license:gpl3))))
5604
5605 (define-public r-directlabels
5606   (package
5607     (name "r-directlabels")
5608     (version "2018.05.22")
5609     (source
5610      (origin
5611        (method url-fetch)
5612        (uri (cran-uri "directlabels" version))
5613        (sha256
5614         (base32
5615          "0xcpc56ssb9430b0xcdhayk3qaak2qcakyss2pz14y5w2027hblv"))))
5616     (build-system r-build-system)
5617     (propagated-inputs
5618      `(("r-quadprog" ,r-quadprog)))
5619     (home-page "http://directlabels.r-forge.r-project.org/")
5620     (synopsis "Direct labels for multicolor plots")
5621     (description
5622      "This package provides an extensible framework for automatically placing
5623 direct labels onto multicolor plots.  Label positions are described using
5624 positioning methods that can be re-used across several different plots.  There
5625 are heuristics for examining @code{trellis} and @code{ggplot} objects and
5626 inferring an appropriate positioning method.")
5627     (license license:gpl3)))
5628
5629 (define-public r-catterplots
5630   (let ((commit "ae17cd5e49ddda4ecfe0eba8a4c21df8c88e72c4")
5631         (revision "3"))
5632     (package
5633       (name "r-catterplots")
5634       (version (git-version "0" revision commit))
5635       (source (origin
5636                 (method git-fetch)
5637                 (uri (git-reference
5638                       (url "https://github.com/Gibbsdavidl/CatterPlots.git")
5639                       (commit commit)))
5640                 (file-name (git-file-name name version))
5641                 (sha256
5642                  (base32
5643                   "0qa8liylffpxgdg8xcgjar5dsvczqhn3akd4w35113hnyg1m4xyg"))))
5644       (build-system r-build-system)
5645       (propagated-inputs
5646        `(("r-png" ,r-png)))
5647       (home-page "https://github.com/Gibbsdavidl/CatterPlots")
5648       (synopsis "Scatter plots with cat shaped points")
5649       (description "Did you ever wish you could make scatter plots with cat
5650 shaped points?  Now you can!")
5651       (license license:asl2.0))))
5652
5653 (define-public r-colorout
5654   (package
5655     (name "r-colorout")
5656     (version "1.2-2")
5657     (source
5658      (origin
5659        (method git-fetch)
5660        (uri (git-reference
5661              (url "https://github.com/jalvesaq/colorout.git")
5662              (commit (string-append "v" version))))
5663        (file-name (git-file-name name version))
5664        (sha256
5665         (base32 "1rsx69wjpa73c6x2hacvvvbzdzxn7wg06gizf97kasjdlb7azmp3"))))
5666     (build-system r-build-system)
5667     (home-page "https://github.com/jalvesaq/colorout")
5668     (synopsis "Colorize output in the R REPL")
5669     (description "@code{colorout} is an R package that colorizes R output when
5670 running in terminal emulator.
5671
5672 R STDOUT is parsed and numbers, negative numbers, dates in the standard
5673 format, strings, and R constants are identified and wrapped by special ANSI
5674 scape codes that are interpreted by terminal emulators as commands to colorize
5675 the output.  R STDERR is also parsed to identify the expressions warning and
5676 error and their translations to many languages.  If these expressions are
5677 found, the output is colorized accordingly; otherwise, it is colorized as
5678 STDERROR (blue, by default).
5679
5680 You can customize the colors according to your taste, guided by the color
5681 table made by the command @code{show256Colors()}.  You can also set the colors
5682 to any arbitrary string.  In this case, it is up to you to set valid values.")
5683     (license license:gpl3+)))
5684
5685 (define-public python-rpy2
5686   ;; We need to take this changeset instead of the RELEASE_3_0_4 tag, because
5687   ;; it fixes a regression when using ggplot 3.2.0.
5688   (let ((changeset "19868a8")
5689         (revision "1"))
5690     (package
5691       (name "python-rpy2")
5692       (version (git-version "3.0.4" revision changeset))
5693       (source
5694        (origin
5695          (method hg-fetch)
5696          (uri (hg-reference
5697                (url "https://bitbucket.org/rpy2/rpy2")
5698                (changeset changeset)))
5699          (file-name (git-file-name name version))
5700          (sha256
5701           (base32
5702            "1bb0wslcbj3wjvyk3jb9yyzdi6adfqh5vfgcvn22dyzxzbhcs8kk"))))
5703       (build-system python-build-system)
5704       (arguments
5705        '(#:modules ((ice-9 ftw)
5706                     (srfi srfi-1)
5707                     (srfi srfi-26)
5708                     (guix build utils)
5709                     (guix build python-build-system))
5710          #:phases
5711          (modify-phases %standard-phases
5712            (replace 'check
5713              (lambda* (#:key outputs inputs #:allow-other-keys)
5714                (let ((cwd (getcwd)))
5715                  (setenv "TZ" "UTC")
5716                  (setenv "PYTHONPATH"
5717                          (string-append cwd "/build/"
5718                                         (find (cut string-prefix? "lib" <>)
5719                                               (scandir (string-append cwd "/build")))
5720                                         ":"
5721                                         (getenv "PYTHONPATH"))))
5722                (invoke "pytest" "-v" "rpy/tests/"))))))
5723       (propagated-inputs
5724        `(("python-cffi" ,python-cffi)
5725          ("python-six" ,python-six)
5726          ("python-jinja2" ,python-jinja2)
5727          ("python-numpy" ,python-numpy)
5728          ("python-pandas" ,python-pandas)
5729          ("python-pytz" ,python-pytz)
5730          ("python-ipython" ,python-ipython)
5731          ("python-tzlocal" ,python-tzlocal)))
5732       (inputs
5733        `(("readline" ,readline)
5734          ("icu4c" ,icu4c)
5735          ("pcre" ,pcre)
5736          ("r-minimal" ,r-minimal)
5737          ("r-survival" ,r-survival)
5738          ("r-ggplot2" ,r-ggplot2)
5739          ("r-rsqlite" ,r-rsqlite)
5740          ("r-dplyr" ,r-dplyr)
5741          ("r-dbplyr" ,r-dbplyr)
5742          ("python-numpy" ,python-numpy)))
5743       (native-inputs
5744        `(("zlib" ,zlib)
5745          ("python-pytest" ,python-pytest)))
5746       (home-page "https://rpy2.bitbucket.io/")
5747       (synopsis "Python interface to the R language")
5748       (description "rpy2 is a redesign and rewrite of rpy.  It is providing a
5749 low-level interface to R from Python, a proposed high-level interface,
5750 including wrappers to graphical libraries, as well as R-like structures and
5751 functions.")
5752       ;; Any of these licenses can be picked for the R interface.  The whole
5753       ;; project is released under GPLv2+ according to the license declaration
5754       ;; in "setup.py".
5755       (license (list license:mpl2.0 license:gpl2+ license:lgpl2.1+)))))
5756
5757 (define-public java-jdistlib
5758   (package
5759     (name "java-jdistlib")
5760     (version "0.4.5")
5761     (source (origin
5762               (method url-fetch)
5763               (uri (string-append "mirror://sourceforge/jdistlib/jdistlib-"
5764                                   version "-src.jar"))
5765               (sha256
5766                (base32
5767                 "1pkj8aahw9ydr1isbaqrkd05nvq98ik5jwwhf3yf3rky3z869v11"))))
5768     (build-system ant-build-system)
5769     (arguments
5770      `(#:jar-name "jdistlib.jar"
5771        #:jdk ,icedtea-8
5772        #:tests? #f ; no dedicated test directory
5773        #:phases
5774        (modify-phases %standard-phases
5775          (add-after 'unpack 'fix-broken-encoding
5776            (lambda _
5777              (with-fluids ((%default-port-encoding "ISO-8859-1"))
5778                (substitute* "src/jdistlib/Beta.java"
5779                  (("Scheff.+-Tukey") "Scheffe-Tukey")))
5780              #t)))))
5781     (propagated-inputs
5782      `(("java-jtransforms" ,java-jtransforms)))
5783     (native-inputs
5784      `(("java-junit" ,java-junit)))
5785     (home-page "http://jdistlib.sourceforge.net/")
5786     (synopsis "Java library of statistical distributions")
5787     (description "JDistlib is the Java Statistical Distribution Library, a
5788 Java package that provides routines for various statistical distributions.")
5789     ;; The files that were translated from R code are under GPLv2+; some files
5790     ;; are under the GPLv3, which is a mistake.  The author confirmed in an
5791     ;; email that this whole project should be under GPLv2+.
5792     (license license:gpl2+)))
5793
5794 (define-public emacs-ess
5795   (package
5796     (name "emacs-ess")
5797     (version "17.11")
5798     (source (origin
5799               (method url-fetch)
5800               (uri (string-append "https://github.com/emacs-ess/ESS/archive/v"
5801                                   version ".tar.gz"))
5802               (sha256
5803                (base32
5804                 "0cbilbsiwvcyf6d5y24mymp57m3ana5dkzab3knfs83w4a3a4c5c"))
5805               (file-name (string-append name "-" version ".tar.gz"))
5806               (modules '((guix build utils)))
5807               (snippet
5808                '(begin
5809                   ;; Stop ESS from trying to bundle an external julia-mode.el.
5810                   (substitute* "lisp/Makefile"
5811                     (("^\tjulia-mode.elc\\\\\n") "")
5812                     (("^dist: all julia-mode.el")
5813                      "dist: all"))
5814                   ;; No need to build docs in so many formats.  Also, skipping
5815                   ;; pdf lets us not pull in texlive.
5816                   (substitute* "doc/Makefile"
5817                     (("all  : info text html pdf")
5818                      "all  : info")
5819                     (("install: install-info install-other-docs")
5820                      "install: install-info"))
5821                   ;; Test fails upstream
5822                   (substitute* "test/ess-r-tests.el"
5823                     (("ert-deftest ess-r-namespaced-eval-no-srcref-in-errors ()")
5824                      "ert-deftest ess-r-namespaced-eval-no-srcref-in-errors () :expected-result :failed"))
5825                   #t))))
5826     (build-system gnu-build-system)
5827     (arguments
5828      (let ((base-directory "/share/emacs/site-lisp/guix.d/ess"))
5829        `(#:make-flags (list (string-append "PREFIX=" %output)
5830                             (string-append "ETCDIR=" %output "/"
5831                                            ,base-directory "/etc")
5832                             (string-append "LISPDIR=" %output "/"
5833                                            ,base-directory))
5834          #:phases
5835          (modify-phases %standard-phases
5836            (delete 'configure)
5837            (add-before 'build 'more-shebang-patching
5838              (lambda* (#:key inputs #:allow-other-keys)
5839                (substitute* "Makeconf"
5840                  (("SHELL = /bin/sh")
5841                   (string-append "SHELL = " (which "sh"))))
5842                #t))
5843            (replace 'check
5844              (lambda _
5845                (invoke "make" "test")))))))
5846     (inputs
5847      `(("emacs" ,emacs-minimal)
5848        ("r-minimal" ,r-minimal)))
5849     (native-inputs
5850      `(("perl" ,perl)
5851        ("texinfo" ,texinfo)))
5852     (propagated-inputs
5853      `(("emacs-julia-mode" ,emacs-julia-mode)))
5854     (home-page "https://ess.r-project.org/")
5855     (synopsis "Emacs mode for statistical analysis programs")
5856     (description "Emacs Speaks Statistics (ESS) is an add-on package for GNU
5857 Emacs.  It is designed to support editing of scripts and interaction with
5858 various statistical analysis programs such as R, Julia, and JAGS.")
5859     (license license:gpl2+)))