| 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 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 "1.5.1") |
| 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 "0dam8qgbc5ykzaxmrjhpmfm8lnlcdk6cbpzyaya91qwwa80qbj1v")))) |
| 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 "3.6.1") |
| 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 | "128kifbq0w25y8aq77w289ddax5i5w2djcfsqgffrb3i7syrxajv")))) |
| 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 "1.3-23") |
| 403 | (source |
| 404 | (origin |
| 405 | (method url-fetch) |
| 406 | (uri (cran-uri "boot" version)) |
| 407 | (sha256 |
| 408 | (base32 |
| 409 | "0bx07zbb5nfz2xfgnzbspg7r5vxz4bjdz1ry4d1vk434vlcrxj1h")))) |
| 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 "7.3-51.4") |
| 424 | (source |
| 425 | (origin |
| 426 | (method url-fetch) |
| 427 | (uri (cran-uri "MASS" version)) |
| 428 | (sha256 |
| 429 | (base32 |
| 430 | "0x1ckf51y851g0kvbhsgdxb26vfpmbw3xdbcnh3ck7fjm13da4cr")))) |
| 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 "0.8-72") |
| 508 | (source |
| 509 | (origin |
| 510 | (method url-fetch) |
| 511 | (uri (cran-uri "foreign" version)) |
| 512 | (sha256 |
| 513 | (base32 |
| 514 | "124c9229is44p2rv7xyh2q86nsfi7vzyyh5n3c5ihziqrp4ig723")))) |
| 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 "1.1-14") |
| 743 | (source |
| 744 | (origin |
| 745 | (method url-fetch) |
| 746 | (uri (cran-uri "bit" version)) |
| 747 | (sha256 |
| 748 | (base32 |
| 749 | "0m7jrqzpa1pk8ixcl814x06jf96nlvvr16x6did6cfk4zghsrfjw")))) |
| 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 "1.4.3") |
| 1019 | (source |
| 1020 | (origin |
| 1021 | (method url-fetch) |
| 1022 | (uri (cran-uri "stringi" version)) |
| 1023 | (sha256 |
| 1024 | (base32 |
| 1025 | "1vbr6g9p1iyzdj7wfw6afyizvnd1a2srfvkl72pq23vhdcwwpkhk")))) |
| 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 "1.69.0-1") |
| 1264 | (source (origin |
| 1265 | (method url-fetch) |
| 1266 | (uri (cran-uri "BH" version)) |
| 1267 | (sha256 |
| 1268 | (base32 |
| 1269 | "18mckfwxxv8m8rzaz03mg2h6vhaj7y131h6yasfg0s73nxj47zd0")))) |
| 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 "0.7") |
| 1341 | (source (origin |
| 1342 | (method url-fetch) |
| 1343 | (uri (cran-uri "mime" version)) |
| 1344 | (sha256 |
| 1345 | (base32 |
| 1346 | "12vpip67ajb90b8p96w43ir7mavrw2i61bwvpfnrlmlj9kj3w20i")))) |
| 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 "1.26") |
| 1404 | (source (origin |
| 1405 | (method url-fetch) |
| 1406 | (uri (cran-uri "knitr" version)) |
| 1407 | (sha256 |
| 1408 | (base32 |
| 1409 | "08f3bdd5cnnbigybr9vmkhq12n64pbmn4layl3w5rwk8xi5kbnrq")))) |
| 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 "0.4.2") |
| 1611 | (source (origin |
| 1612 | (method url-fetch) |
| 1613 | (uri (cran-uri "rlang" version)) |
| 1614 | (sha256 |
| 1615 | (base32 |
| 1616 | "0fczcp17kaz3s4p0nd4126bppwl20vpxfybhsndpcky9h75wklgv")))) |
| 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 "0.4.1") |
| 1847 | (source (origin |
| 1848 | (method url-fetch) |
| 1849 | (uri (pypi-uri "patsy" version ".zip")) |
| 1850 | (sha256 |
| 1851 | (base32 |
| 1852 | "1m6knyq8hbqlx242y4da02j0x86j4qggs1j7q186w3jv0j0c476w")))) |
| 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 | ("unzip" ,unzip))) |
| 1866 | (home-page "https://github.com/pydata/patsy") |
| 1867 | (synopsis "Describe statistical models and build design matrices") |
| 1868 | (description |
| 1869 | "Patsy is a Python package for describing statistical models and for |
| 1870 | building design matrices.") |
| 1871 | ;; The majority of the code is distributed under BSD-2. The module |
| 1872 | ;; patsy.compat contains code derived from the Python standard library, |
| 1873 | ;; and is covered by the PSFL. |
| 1874 | (license (list license:bsd-2 license:psfl)))) |
| 1875 | |
| 1876 | (define-public python2-patsy |
| 1877 | (package-with-python2 python-patsy)) |
| 1878 | |
| 1879 | (define-public python-statsmodels |
| 1880 | (package |
| 1881 | (name "python-statsmodels") |
| 1882 | (version "0.9.0") |
| 1883 | (source |
| 1884 | (origin |
| 1885 | (method url-fetch) |
| 1886 | (uri (pypi-uri "statsmodels" version)) |
| 1887 | (sha256 |
| 1888 | (base32 |
| 1889 | "0fxs8a7sp4d7jvqlm36yi45i2d28kjfvraf9q8i9jr1chhxgjqb4")))) |
| 1890 | (build-system python-build-system) |
| 1891 | (arguments |
| 1892 | `(;; The test suite is very large and rather brittle. Tests often fail |
| 1893 | ;; because of minor changes in dependencies that upstream hasn't fixed |
| 1894 | ;; in a new release. |
| 1895 | #:tests? #f |
| 1896 | #:phases |
| 1897 | (modify-phases %standard-phases |
| 1898 | (add-after 'unpack 'set-matplotlib-backend-to-agg |
| 1899 | (lambda _ |
| 1900 | ;; Set the matplotlib backend to Agg to avoid problems using the |
| 1901 | ;; GTK backend without a display. |
| 1902 | (substitute* (append (find-files "statsmodels/graphics/tests" "\\.py") |
| 1903 | '("statsmodels/tsa/vector_ar/tests/test_var.py" |
| 1904 | "statsmodels/duration/tests/test_survfunc.py")) |
| 1905 | (("import matplotlib\\.pyplot as plt" line) |
| 1906 | (string-append "import matplotlib;matplotlib.use('Agg');" |
| 1907 | line))) |
| 1908 | #t))))) |
| 1909 | (propagated-inputs |
| 1910 | `(("python-numpy" ,python-numpy) |
| 1911 | ("python-scipy" ,python-scipy) |
| 1912 | ("python-pandas" ,python-pandas) |
| 1913 | ("python-patsy" ,python-patsy) |
| 1914 | ("python-matplotlib" ,python-matplotlib))) |
| 1915 | (native-inputs |
| 1916 | `(("python-cython" ,python-cython) |
| 1917 | ("python-nose" ,python-nose) |
| 1918 | ("python-sphinx" ,python-sphinx))) |
| 1919 | (home-page "http://statsmodels.sourceforge.net/") |
| 1920 | (synopsis "Statistical modeling and econometrics in Python") |
| 1921 | (description |
| 1922 | "Statsmodels is a Python package that provides a complement to scipy for |
| 1923 | statistical computations including descriptive statistics and estimation and |
| 1924 | inference for statistical models.") |
| 1925 | (license license:bsd-3))) |
| 1926 | |
| 1927 | (define-public python2-statsmodels |
| 1928 | (let ((stats (package-with-python2 python-statsmodels))) |
| 1929 | (package (inherit stats) |
| 1930 | (propagated-inputs |
| 1931 | `(("python2-pytz" ,python2-pytz) |
| 1932 | ("python2-numpy" ,python2-numpy) |
| 1933 | ("python2-scipy" ,python2-scipy) |
| 1934 | ("python2-pandas" ,python2-pandas) |
| 1935 | ("python2-patsy" ,python2-patsy) |
| 1936 | ("python2-matplotlib" ,python2-matplotlib)))))) |
| 1937 | |
| 1938 | (define-public r-coda |
| 1939 | (package |
| 1940 | (name "r-coda") |
| 1941 | (version "0.19-3") |
| 1942 | (source (origin |
| 1943 | (method url-fetch) |
| 1944 | (uri (cran-uri "coda" version)) |
| 1945 | (sha256 |
| 1946 | (base32 |
| 1947 | "1mn50bshky968gn4nf6vnkaa768fnvm1xmhkms7szwdw9341zpyk")))) |
| 1948 | (build-system r-build-system) |
| 1949 | (propagated-inputs |
| 1950 | `(("r-lattice" ,r-lattice))) |
| 1951 | (home-page "https://cran.r-project.org/web/packages/coda") |
| 1952 | (synopsis "This is a package for Output Analysis and Diagnostics for MCMC") |
| 1953 | (description "This package provides functions for summarizing and plotting |
| 1954 | the output from Markov Chain Monte Carlo (MCMC) simulations, as well as |
| 1955 | diagnostic tests of convergence to the equilibrium distribution of the Markov |
| 1956 | chain.") |
| 1957 | (license license:gpl2+))) |
| 1958 | |
| 1959 | (define-public r-ade4 |
| 1960 | (package |
| 1961 | (name "r-ade4") |
| 1962 | (version "1.7-13") |
| 1963 | (source |
| 1964 | (origin |
| 1965 | (method url-fetch) |
| 1966 | (uri (cran-uri "ade4" version)) |
| 1967 | (sha256 |
| 1968 | (base32 |
| 1969 | "16z9jk4qj35ghsk4lwmq241dgc770y8a70dlmp9q4gz6d8ssgl7m")))) |
| 1970 | (build-system r-build-system) |
| 1971 | (propagated-inputs |
| 1972 | `(("r-mass" ,r-mass))) |
| 1973 | (home-page "http://pbil.univ-lyon1.fr/ADE-4") |
| 1974 | (synopsis "Multivariate data analysis and graphical display") |
| 1975 | (description |
| 1976 | "The ade4 package contains data analysis functions to analyze ecological |
| 1977 | and environmental data in the framework of Euclidean exploratory methods.") |
| 1978 | (license license:gpl2+))) |
| 1979 | |
| 1980 | (define-public r-xml2 |
| 1981 | (package |
| 1982 | (name "r-xml2") |
| 1983 | (version "1.2.2") |
| 1984 | (source |
| 1985 | (origin |
| 1986 | (method url-fetch) |
| 1987 | (uri (cran-uri "xml2" version)) |
| 1988 | (sha256 |
| 1989 | (base32 |
| 1990 | "1x3q3a0xv8j0nx3hs4d3pfjm5g9nvaxmfrapba9f4nrkqi3z2l1h")))) |
| 1991 | (build-system r-build-system) |
| 1992 | (inputs |
| 1993 | `(("libxml2" ,libxml2) |
| 1994 | ("zlib" ,zlib))) |
| 1995 | (native-inputs |
| 1996 | `(("pkg-config" ,pkg-config))) |
| 1997 | (propagated-inputs |
| 1998 | `(("r-rcpp" ,r-rcpp))) |
| 1999 | (home-page "https://github.com/hadley/xml2") |
| 2000 | (synopsis "Parse XML with R") |
| 2001 | (description |
| 2002 | "This package provides a simple, consistent interface to working with XML |
| 2003 | files in R. It is built on top of the libxml2 C library.") |
| 2004 | (license license:gpl2+))) |
| 2005 | |
| 2006 | (define-public r-multitaper |
| 2007 | (package |
| 2008 | (name "r-multitaper") |
| 2009 | (version "1.0-14") |
| 2010 | (source |
| 2011 | (origin |
| 2012 | (method url-fetch) |
| 2013 | (uri (cran-uri "multitaper" version)) |
| 2014 | (sha256 |
| 2015 | (base32 |
| 2016 | "04wd9bbhyx7697pfy0fpj02v1csr48hkpqj62h9p8a6w84ji4k68")))) |
| 2017 | (build-system r-build-system) |
| 2018 | (native-inputs |
| 2019 | `(("gfortran" ,gfortran))) |
| 2020 | (home-page "https://github.com/wesleyburr/multitaper/") |
| 2021 | (synopsis "Multitaper spectral analysis tools") |
| 2022 | (description |
| 2023 | "This package implements multitaper spectral estimation |
| 2024 | techniques using prolate spheroidal sequences (Slepians) and sine |
| 2025 | tapers for time series analysis. It includes an adaptive weighted |
| 2026 | multitaper spectral estimate, a coherence estimate, Thomson's Harmonic |
| 2027 | F-test, and complex demodulation. The Slepians sequences are |
| 2028 | generated efficiently using a tridiagonal matrix solution, and |
| 2029 | jackknifed confidence intervals are available for most estimates.") |
| 2030 | (license license:gpl2+))) |
| 2031 | |
| 2032 | (define-public r-rversions |
| 2033 | (package |
| 2034 | (name "r-rversions") |
| 2035 | (version "2.0.1") |
| 2036 | (source (origin |
| 2037 | (method url-fetch) |
| 2038 | (uri (cran-uri "rversions" version)) |
| 2039 | (sha256 |
| 2040 | (base32 |
| 2041 | "1ic6sxnyya24d5xsxjg3fba73fhya9fhs0kaf66yha6nwxj1zv2i")))) |
| 2042 | (build-system r-build-system) |
| 2043 | (propagated-inputs |
| 2044 | `(("r-curl" ,r-curl) |
| 2045 | ("r-xml2" ,r-xml2))) |
| 2046 | (home-page "https://github.com/metacran/rversions") |
| 2047 | (synopsis "Query R versions, including 'r-release' and 'r-oldrel'") |
| 2048 | (description |
| 2049 | "This package provides functions to query the main R repository to find |
| 2050 | the versions that @code{r-release} and @code{r-oldrel} refer to, and also all |
| 2051 | previous R versions and their release dates.") |
| 2052 | (license license:expat))) |
| 2053 | |
| 2054 | (define-public r-whisker |
| 2055 | (package |
| 2056 | (name "r-whisker") |
| 2057 | (version "0.4") |
| 2058 | (source (origin |
| 2059 | (method url-fetch) |
| 2060 | (uri (cran-uri "whisker" version)) |
| 2061 | (sha256 |
| 2062 | (base32 |
| 2063 | "1a7vz0dk95xfjvi38wbpw8vmf5qn3g8p490msz2rw0piwidmk1ks")))) |
| 2064 | (build-system r-build-system) |
| 2065 | (home-page "https://github.com/edwindj/whisker") |
| 2066 | (synopsis "Logicless mustache templating for R") |
| 2067 | (description |
| 2068 | "This package provides logicless templating, with a syntax that is not |
| 2069 | limited to R.") |
| 2070 | (license license:gpl3+))) |
| 2071 | |
| 2072 | (define-public r-backports |
| 2073 | (package |
| 2074 | (name "r-backports") |
| 2075 | (version "1.1.5") |
| 2076 | (source |
| 2077 | (origin |
| 2078 | (method url-fetch) |
| 2079 | (uri (cran-uri "backports" version)) |
| 2080 | (sha256 |
| 2081 | (base32 |
| 2082 | "0k19w68b2aihyj5mflw3732gkkzs78sssqdns960pdw3yfnkiv33")))) |
| 2083 | (build-system r-build-system) |
| 2084 | (home-page "https://cran.r-project.org/web/packages/backports") |
| 2085 | (synopsis "Reimplementations of functions introduced since R 3.0.0") |
| 2086 | (description |
| 2087 | "Provides implementations of functions which have been introduced in R |
| 2088 | since version 3.0.0. The backports are conditionally exported which results |
| 2089 | in R resolving the function names to the version shipped with R (if available) |
| 2090 | and uses the implemented backports as fallback. This way package developers |
| 2091 | can make use of the new functions without worrying about the minimum required |
| 2092 | R version.") |
| 2093 | (license license:gpl2+))) |
| 2094 | |
| 2095 | (define-public r-checkmate |
| 2096 | (package |
| 2097 | (name "r-checkmate") |
| 2098 | (version "1.9.4") |
| 2099 | (source |
| 2100 | (origin |
| 2101 | (method url-fetch) |
| 2102 | (uri (cran-uri "checkmate" version)) |
| 2103 | (sha256 |
| 2104 | (base32 |
| 2105 | "08ddpgs4mv5d5y4j054pm8drmxkn7yvhfpbghwxlizjpnxa5g8ps")))) |
| 2106 | (build-system r-build-system) |
| 2107 | (propagated-inputs |
| 2108 | `(("r-backports" ,r-backports))) |
| 2109 | (home-page "https://github.com/mllg/checkmate") |
| 2110 | (synopsis "Fast and versatile argument checks") |
| 2111 | (description |
| 2112 | "This package provides tests and assertions to perform frequent argument |
| 2113 | checks. A substantial part of the package was written in C to minimize any |
| 2114 | worries about execution time overhead.") |
| 2115 | (license license:bsd-3))) |
| 2116 | |
| 2117 | (define-public r-bbmisc |
| 2118 | (package |
| 2119 | (name "r-bbmisc") |
| 2120 | (version "1.11") |
| 2121 | (source |
| 2122 | (origin |
| 2123 | (method url-fetch) |
| 2124 | (uri (cran-uri "BBmisc" version)) |
| 2125 | (sha256 |
| 2126 | (base32 |
| 2127 | "1lh1n4bvxzivb5rbz69mvd8xdgr3gr2bnqd68a39sd1530l8r90y")))) |
| 2128 | (properties `((upstream-name . "BBmisc"))) |
| 2129 | (build-system r-build-system) |
| 2130 | (propagated-inputs |
| 2131 | `(("r-checkmate" ,r-checkmate))) |
| 2132 | (home-page "https://github.com/berndbischl/BBmisc") |
| 2133 | (synopsis "Miscellaneous functions for R package development") |
| 2134 | (description |
| 2135 | "This package provides miscellaneous helper functions for the development |
| 2136 | of R packages.") |
| 2137 | (license license:bsd-3))) |
| 2138 | |
| 2139 | (define-public r-fail |
| 2140 | (package |
| 2141 | (name "r-fail") |
| 2142 | (version "1.3") |
| 2143 | (source |
| 2144 | (origin |
| 2145 | (method url-fetch) |
| 2146 | (uri (cran-uri "fail" version)) |
| 2147 | (sha256 |
| 2148 | (base32 |
| 2149 | "0vfm6kmpmgsamda5p0sl771kbnsscan31l2chzssyw93kwmams7d")))) |
| 2150 | (build-system r-build-system) |
| 2151 | (propagated-inputs |
| 2152 | `(("r-bbmisc" ,r-bbmisc) |
| 2153 | ("r-checkmate" ,r-checkmate))) |
| 2154 | (home-page "https://github.com/mllg/fail") |
| 2155 | (synopsis "File abstraction interface layer (FAIL)") |
| 2156 | (description |
| 2157 | "This package provides a more comfortable interface to work with R data |
| 2158 | or source files in a key-value fashion.") |
| 2159 | (license license:bsd-3))) |
| 2160 | |
| 2161 | (define-public r-batchjobs |
| 2162 | (package |
| 2163 | (name "r-batchjobs") |
| 2164 | (version "1.8") |
| 2165 | (source |
| 2166 | (origin |
| 2167 | (method url-fetch) |
| 2168 | (uri (cran-uri "BatchJobs" version)) |
| 2169 | (sha256 |
| 2170 | (base32 |
| 2171 | "1zz4sspj596pijxlz321g0jy2rg9ki83j6fihbwisjwr66p2vk1m")))) |
| 2172 | (properties `((upstream-name . "BatchJobs"))) |
| 2173 | (build-system r-build-system) |
| 2174 | (propagated-inputs |
| 2175 | `(("r-backports" ,r-backports) |
| 2176 | ("r-bbmisc" ,r-bbmisc) |
| 2177 | ("r-brew" ,r-brew) |
| 2178 | ("r-checkmate" ,r-checkmate) |
| 2179 | ("r-data-table" ,r-data-table) |
| 2180 | ("r-dbi" ,r-dbi) |
| 2181 | ("r-digest" ,r-digest) |
| 2182 | ("r-rsqlite" ,r-rsqlite) |
| 2183 | ("r-sendmailr" ,r-sendmailr) |
| 2184 | ("r-stringi" ,r-stringi))) |
| 2185 | (home-page "https://github.com/tudo-r/BatchJobs") |
| 2186 | (synopsis "Batch computing with R") |
| 2187 | (description |
| 2188 | "This package provides @code{Map}, @code{Reduce} and @code{Filter} |
| 2189 | variants to generate jobs on batch computing systems like PBS/Torque, LSF, |
| 2190 | SLURM and Sun Grid Engine. Multicore and SSH systems are also supported.") |
| 2191 | (license license:bsd-2))) |
| 2192 | |
| 2193 | (define-public r-brew |
| 2194 | (package |
| 2195 | (name "r-brew") |
| 2196 | (version "1.0-6") |
| 2197 | (source (origin |
| 2198 | (method url-fetch) |
| 2199 | (uri (cran-uri "brew" version)) |
| 2200 | (sha256 |
| 2201 | (base32 |
| 2202 | "1vghazbcha8gvkwwcdagjvzx6yl8zm7kgr0i9wxr4jng06d1l3fp")))) |
| 2203 | (build-system r-build-system) |
| 2204 | (home-page "https://cran.r-project.org/web/packages/brew") |
| 2205 | (synopsis "Templating framework for report generation") |
| 2206 | (description |
| 2207 | "The brew package implements a templating framework for mixing text and R |
| 2208 | code for report generation. The template syntax is similar to PHP, Ruby's erb |
| 2209 | module, Java Server Pages, and Python's psp module.") |
| 2210 | (license license:gpl2+))) |
| 2211 | |
| 2212 | (define-public r-desc |
| 2213 | (package |
| 2214 | (name "r-desc") |
| 2215 | (version "1.2.0") |
| 2216 | (source |
| 2217 | (origin |
| 2218 | (method url-fetch) |
| 2219 | (uri (cran-uri "desc" version)) |
| 2220 | (sha256 |
| 2221 | (base32 |
| 2222 | "1s6s13fk6sxwcj8wzkwxl9vr33153xx11p5wi9avqx3rzkabavz6")))) |
| 2223 | (build-system r-build-system) |
| 2224 | (propagated-inputs |
| 2225 | `(("r-assertthat" ,r-assertthat) |
| 2226 | ("r-crayon" ,r-crayon) |
| 2227 | ("r-r6" ,r-r6) |
| 2228 | ("r-rprojroot" ,r-rprojroot))) |
| 2229 | (home-page "https://github.com/r-pkgs/desc") |
| 2230 | (synopsis "Manipulate DESCRIPTION Files") |
| 2231 | (description |
| 2232 | "This package provides tools to read, write, create, and manipulate |
| 2233 | DESCRIPTION files. It is intended for packages that create or manipulate |
| 2234 | other packages.") |
| 2235 | (license license:expat))) |
| 2236 | |
| 2237 | (define-public r-commonmark |
| 2238 | (package |
| 2239 | (name "r-commonmark") |
| 2240 | (version "1.7") |
| 2241 | (source |
| 2242 | (origin |
| 2243 | (method url-fetch) |
| 2244 | (uri (cran-uri "commonmark" version)) |
| 2245 | (sha256 |
| 2246 | (base32 |
| 2247 | "024iz1qp2kv6iz6y69ir0jk3qhjps86rhkzlcmhqsxx97rx7cjni")))) |
| 2248 | (build-system r-build-system) |
| 2249 | (home-page "https://cran.r-project.org/web/packages/commonmark") |
| 2250 | (synopsis "CommonMark and Github Markdown Rendering in R") |
| 2251 | (description |
| 2252 | "The CommonMark specification defines a rationalized version of markdown |
| 2253 | syntax. This package uses the @code{cmark} reference implementation for |
| 2254 | converting markdown text into various formats including HTML, LaTeX and groff |
| 2255 | man. In addition, it exposes the markdown parse tree in XML format. The latest |
| 2256 | version of this package also adds support for Github extensions including |
| 2257 | tables, autolinks and strikethrough text.") |
| 2258 | (license license:bsd-2))) |
| 2259 | |
| 2260 | (define-public r-roxygen2 |
| 2261 | (package |
| 2262 | (name "r-roxygen2") |
| 2263 | (version "7.0.2") |
| 2264 | (source (origin |
| 2265 | (method url-fetch) |
| 2266 | (uri (cran-uri "roxygen2" version)) |
| 2267 | (sha256 |
| 2268 | (base32 |
| 2269 | "162xag27hwwyadfwm5zpyy15nxwhw2vbhwapx3jmi9cfyryr68sq")))) |
| 2270 | (build-system r-build-system) |
| 2271 | (propagated-inputs |
| 2272 | `(("r-brew" ,r-brew) |
| 2273 | ("r-commonmark" ,r-commonmark) |
| 2274 | ("r-desc" ,r-desc) |
| 2275 | ("r-digest" ,r-digest) |
| 2276 | ("r-pkgload" ,r-pkgload) |
| 2277 | ("r-purrr" ,r-purrr) |
| 2278 | ("r-r6" ,r-r6) |
| 2279 | ("r-rcpp" ,r-rcpp) |
| 2280 | ("r-rlang" ,r-rlang) |
| 2281 | ("r-stringi" ,r-stringi) |
| 2282 | ("r-stringr" ,r-stringr) |
| 2283 | ("r-xml2" ,r-xml2))) |
| 2284 | (native-inputs |
| 2285 | `(("r-knitr" ,r-knitr))) ; for vignettes |
| 2286 | (home-page "https://github.com/klutometis/roxygen") |
| 2287 | (synopsis "In-source documentation system for R") |
| 2288 | (description |
| 2289 | "Roxygen2 is a Doxygen-like in-source documentation system for Rd, |
| 2290 | collation, and NAMESPACE files.") |
| 2291 | (license license:gpl2+))) |
| 2292 | |
| 2293 | (define-public r-openssl |
| 2294 | (package |
| 2295 | (name "r-openssl") |
| 2296 | (version "1.4.1") |
| 2297 | (source |
| 2298 | (origin |
| 2299 | (method url-fetch) |
| 2300 | (uri (cran-uri "openssl" version)) |
| 2301 | (sha256 |
| 2302 | (base32 |
| 2303 | "1ihz2qi33lhngl19xdanq0pbmfaacy63794mg8ll7z2lab3yryzp")))) |
| 2304 | (build-system r-build-system) |
| 2305 | (inputs |
| 2306 | `(("libressl" ,libressl))) |
| 2307 | (native-inputs |
| 2308 | `(("pkg-config" ,pkg-config))) |
| 2309 | (propagated-inputs |
| 2310 | `(("r-askpass" ,r-askpass))) |
| 2311 | (home-page "https://github.com/jeroenooms/openssl") |
| 2312 | (synopsis "Toolkit for encryption, signatures and certificates") |
| 2313 | (description |
| 2314 | "This package provides R bindings to OpenSSL libssl and libcrypto, plus |
| 2315 | custom SSH pubkey parsers. It supports RSA, DSA and NIST curves P-256, P-384 |
| 2316 | and P-521. Cryptographic signatures can either be created and verified |
| 2317 | manually or via x509 certificates. AES block cipher is used in CBC mode for |
| 2318 | symmetric encryption; RSA for asymmetric (public key) encryption. High-level |
| 2319 | envelope functions combine RSA and AES for encrypting arbitrary sized data. |
| 2320 | Other utilities include key generators, hash functions (md5, sha1, sha256, |
| 2321 | etc), base64 encoder, a secure random number generator, and @code{bignum} math |
| 2322 | methods for manually performing crypto calculations on large multibyte |
| 2323 | integers.") |
| 2324 | (license license:expat))) |
| 2325 | |
| 2326 | (define-public r-httr |
| 2327 | (package |
| 2328 | (name "r-httr") |
| 2329 | (version "1.4.1") |
| 2330 | (source (origin |
| 2331 | (method url-fetch) |
| 2332 | (uri (cran-uri "httr" version)) |
| 2333 | (sha256 |
| 2334 | (base32 |
| 2335 | "0mp1il13q6n49n2hv1p2p8x6avjan6dr5az19ql4hb78pc3pwp37")))) |
| 2336 | (build-system r-build-system) |
| 2337 | (propagated-inputs |
| 2338 | `(("r-curl" ,r-curl) |
| 2339 | ("r-jsonlite" ,r-jsonlite) |
| 2340 | ("r-openssl" ,r-openssl) |
| 2341 | ("r-mime" ,r-mime) |
| 2342 | ("r-r6" ,r-r6))) |
| 2343 | (home-page "https://github.com/hadley/httr") |
| 2344 | (synopsis "Tools for working with URLs and HTTP") |
| 2345 | (description |
| 2346 | "The aim of httr is to provide a wrapper for RCurl customised to the |
| 2347 | demands of modern web APIs. It provides useful tools for working with HTTP |
| 2348 | organised by HTTP verbs (@code{GET()}, @code{POST()}, etc). Configuration |
| 2349 | functions make it easy to control additional request components.") |
| 2350 | (license license:expat))) |
| 2351 | |
| 2352 | (define-public r-git2r |
| 2353 | (package |
| 2354 | (name "r-git2r") |
| 2355 | (version "0.26.1") |
| 2356 | (source (origin |
| 2357 | (method url-fetch) |
| 2358 | (uri (cran-uri "git2r" version)) |
| 2359 | (sha256 |
| 2360 | (base32 |
| 2361 | "0dbl845sahv2i641ncaf06w06djravwc5wknp9syzx0ad8l0kmhk")))) |
| 2362 | (build-system r-build-system) |
| 2363 | (inputs |
| 2364 | `(("libgit2" ,libgit2) |
| 2365 | ("zlib" ,zlib))) |
| 2366 | (native-inputs |
| 2367 | `(("pkg-config" ,pkg-config))) |
| 2368 | (home-page "https://github.com/ropensci/git2r") |
| 2369 | (synopsis "Access Git repositories with R") |
| 2370 | (description |
| 2371 | "This package provides an R interface to the libgit2 library, which is a |
| 2372 | pure C implementation of the Git core methods.") |
| 2373 | ;; GPLv2 only with linking exception. |
| 2374 | (license license:gpl2))) |
| 2375 | |
| 2376 | (define-public r-rstudioapi |
| 2377 | (package |
| 2378 | (name "r-rstudioapi") |
| 2379 | (version "0.10") |
| 2380 | (source (origin |
| 2381 | (method url-fetch) |
| 2382 | (uri (cran-uri "rstudioapi" version)) |
| 2383 | (sha256 |
| 2384 | (base32 |
| 2385 | "15mbw607ncdf53mgga76n3va5zzdcjqz14nb0jcn9axwccqamic0")))) |
| 2386 | (build-system r-build-system) |
| 2387 | (home-page "https://cran.r-project.org/web/packages/rstudioapi") |
| 2388 | (synopsis "Safely access the RStudio API") |
| 2389 | (description |
| 2390 | "This package provides functions to access the RStudio API and provide |
| 2391 | informative error messages when it's not available.") |
| 2392 | (license license:expat))) |
| 2393 | |
| 2394 | (define-public r-devtools |
| 2395 | (package |
| 2396 | (name "r-devtools") |
| 2397 | (version "2.2.1") |
| 2398 | (source (origin |
| 2399 | (method url-fetch) |
| 2400 | (uri (cran-uri "devtools" version)) |
| 2401 | (sha256 |
| 2402 | (base32 |
| 2403 | "0i2f549hxkn0j1x1avkhwy68c9r48v9284j7x9cak2q6dfsqz61f")))) |
| 2404 | (build-system r-build-system) |
| 2405 | (propagated-inputs |
| 2406 | `(("r-callr" ,r-callr) |
| 2407 | ("r-cli" ,r-cli) |
| 2408 | ("r-covr" ,r-covr) |
| 2409 | ("r-crayon" ,r-crayon) |
| 2410 | ("r-desc" ,r-desc) |
| 2411 | ("r-digest" ,r-digest) |
| 2412 | ("r-dt" ,r-dt) |
| 2413 | ("r-ellipsis" ,r-ellipsis) |
| 2414 | ("r-glue" ,r-glue) |
| 2415 | ("r-git2r" ,r-git2r) |
| 2416 | ("r-httr" ,r-httr) |
| 2417 | ("r-jsonlite" ,r-jsonlite) |
| 2418 | ("r-memoise" ,r-memoise) |
| 2419 | ("r-pkgbuild" ,r-pkgbuild) |
| 2420 | ("r-pkgload" ,r-pkgload) |
| 2421 | ("r-rcmdcheck" ,r-rcmdcheck) |
| 2422 | ("r-remotes" ,r-remotes) |
| 2423 | ("r-rlang" ,r-rlang) |
| 2424 | ("r-roxygen2" ,r-roxygen2) |
| 2425 | ("r-rstudioapi" ,r-rstudioapi) |
| 2426 | ("r-rversions" ,r-rversions) |
| 2427 | ("r-sessioninfo" ,r-sessioninfo) |
| 2428 | ("r-testthat" ,r-testthat) |
| 2429 | ("r-usethis" ,r-usethis) |
| 2430 | ("r-withr" ,r-withr))) |
| 2431 | (home-page "https://github.com/hadley/devtools") |
| 2432 | (synopsis "Tools to make developing R packages easier") |
| 2433 | (description "The devtools package is a collection of package development |
| 2434 | tools to simplify the devolpment of R packages.") |
| 2435 | (license license:gpl2+))) |
| 2436 | |
| 2437 | (define-public r-withr |
| 2438 | (package |
| 2439 | (name "r-withr") |
| 2440 | (version "2.1.2") |
| 2441 | (source (origin |
| 2442 | (method url-fetch) |
| 2443 | (uri (cran-uri "withr" version)) |
| 2444 | (sha256 |
| 2445 | (base32 |
| 2446 | "11j6zykklxnvp4xqsr6a2xib665i38m3khdspp887nwagmvnydj1")))) |
| 2447 | (build-system r-build-system) |
| 2448 | (home-page "https://github.com/jimhester/withr") |
| 2449 | (synopsis "Run code with temporarily modified global state") |
| 2450 | (description |
| 2451 | "This package provides a set of functions to run R code in an environment |
| 2452 | in which global state has been temporarily modified. Many of these functions |
| 2453 | were originally a part of the r-devtools package.") |
| 2454 | (license license:gpl2+))) |
| 2455 | |
| 2456 | (define-public r-hms |
| 2457 | (package |
| 2458 | (name "r-hms") |
| 2459 | (version "0.5.2") |
| 2460 | (source |
| 2461 | (origin |
| 2462 | (method url-fetch) |
| 2463 | (uri (cran-uri "hms" version)) |
| 2464 | (sha256 |
| 2465 | (base32 |
| 2466 | "0h24dsagn4kcr65arn73mpqapcg002kw4kyxfqyff95j6s6cjifl")))) |
| 2467 | (build-system r-build-system) |
| 2468 | (propagated-inputs |
| 2469 | `(("r-rlang" ,r-rlang) |
| 2470 | ("r-pkgconfig" ,r-pkgconfig) |
| 2471 | ("r-vctrs" ,r-vctrs))) |
| 2472 | (home-page "https://github.com/rstats-db/hms") |
| 2473 | (synopsis "Pretty time of day") |
| 2474 | (description |
| 2475 | "This package implements an S3 class for storing and formatting |
| 2476 | time-of-day values, based on the @code{difftime} class.") |
| 2477 | (license license:gpl3+))) |
| 2478 | |
| 2479 | (define-public r-readr |
| 2480 | (package |
| 2481 | (name "r-readr") |
| 2482 | (version "1.3.1") |
| 2483 | (source (origin |
| 2484 | (method url-fetch) |
| 2485 | (uri (cran-uri "readr" version)) |
| 2486 | (sha256 |
| 2487 | (base32 |
| 2488 | "1wz496rw0ah433p755n3xac8gh7yzid4xgdjzd1a7wmpkgilvy9k")))) |
| 2489 | (build-system r-build-system) |
| 2490 | (propagated-inputs |
| 2491 | `(("r-clipr" ,r-clipr) |
| 2492 | ("r-crayon" ,r-crayon) |
| 2493 | ("r-rcpp" ,r-rcpp) |
| 2494 | ("r-hms" ,r-hms) |
| 2495 | ("r-tibble" ,r-tibble) |
| 2496 | ("r-r6" ,r-r6) |
| 2497 | ("r-bh" ,r-bh))) |
| 2498 | (home-page "https://github.com/hadley/readr") |
| 2499 | (synopsis "Read tabular data") |
| 2500 | (description |
| 2501 | "This package provides functions to read flat or tabular text files from |
| 2502 | disk (or a connection).") |
| 2503 | (license license:gpl2+))) |
| 2504 | |
| 2505 | (define-public r-plotrix |
| 2506 | (package |
| 2507 | (name "r-plotrix") |
| 2508 | (version "3.7-7") |
| 2509 | (source (origin |
| 2510 | (method url-fetch) |
| 2511 | (uri (cran-uri "plotrix" version)) |
| 2512 | (sha256 |
| 2513 | (base32 |
| 2514 | "1x92mmyfry127zzr6cmcj6kjsc4zhxrrdlr0jcxn3bb0hpdfps54")))) |
| 2515 | (build-system r-build-system) |
| 2516 | (home-page "https://cran.r-project.org/web/packages/plotrix") |
| 2517 | (synopsis "Various plotting functions") |
| 2518 | (description |
| 2519 | "This package provides lots of plotting, various labeling, axis and color |
| 2520 | scaling functions for R.") |
| 2521 | (license license:gpl2+))) |
| 2522 | |
| 2523 | (define-public r-gridbase |
| 2524 | (package |
| 2525 | (name "r-gridbase") |
| 2526 | (version "0.4-7") |
| 2527 | (source (origin |
| 2528 | (method url-fetch) |
| 2529 | (uri (cran-uri "gridBase" version)) |
| 2530 | (sha256 |
| 2531 | (base32 |
| 2532 | "09jzw4rzwf2y5lcz7b16mb68pn0fqigv34ff7lr6w3yi9k91i1xy")))) |
| 2533 | (build-system r-build-system) |
| 2534 | (home-page "https://cran.r-project.org/web/packages/gridBase") |
| 2535 | (synopsis "Integration of base and grid graphics") |
| 2536 | (description |
| 2537 | "This package provides an integration of base and grid graphics for R.") |
| 2538 | (license license:gpl2+))) |
| 2539 | |
| 2540 | (define-public r-latticeextra |
| 2541 | (package |
| 2542 | (name "r-latticeextra") |
| 2543 | (version "0.6-28") |
| 2544 | (source |
| 2545 | (origin |
| 2546 | (method url-fetch) |
| 2547 | (uri (cran-uri "latticeExtra" version)) |
| 2548 | (sha256 |
| 2549 | (base32 |
| 2550 | "1hkyqsa7klk5glj9y1hg3rxr5qilqw8h0017zc4c3nps7lr9a1kq")))) |
| 2551 | (properties `((upstream-name . "latticeExtra"))) |
| 2552 | (build-system r-build-system) |
| 2553 | (propagated-inputs |
| 2554 | `(("r-lattice" ,r-lattice) |
| 2555 | ("r-rcolorbrewer" ,r-rcolorbrewer))) |
| 2556 | (home-page "http://latticeextra.r-forge.r-project.org/") |
| 2557 | (synopsis "Extra graphical utilities based on lattice") |
| 2558 | (description |
| 2559 | "Building on the infrastructure provided by the lattice package, this |
| 2560 | package provides several new high-level graphics functions and methods, as |
| 2561 | well as additional utilities such as panel and axis annotation functions.") |
| 2562 | (license license:gpl2+))) |
| 2563 | |
| 2564 | (define-public r-rcpparmadillo |
| 2565 | (package |
| 2566 | (name "r-rcpparmadillo") |
| 2567 | (version "0.9.800.3.0") |
| 2568 | (source (origin |
| 2569 | (method url-fetch) |
| 2570 | (uri (cran-uri "RcppArmadillo" version)) |
| 2571 | (sha256 |
| 2572 | (base32 |
| 2573 | "0kpcspg3mafi5kncjfhnbcwimvlf19jvrxilvhbpd20sap473mh3")))) |
| 2574 | (properties `((upstream-name . "RcppArmadillo"))) |
| 2575 | (build-system r-build-system) |
| 2576 | ;; All needed for vignettes |
| 2577 | (native-inputs |
| 2578 | `(("r-knitr" ,r-knitr) |
| 2579 | ("r-rmarkdown" ,r-rmarkdown) |
| 2580 | ("ghc-pandoc" ,ghc-pandoc) |
| 2581 | ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc))) |
| 2582 | (propagated-inputs |
| 2583 | `(("r-rcpp" ,r-rcpp))) |
| 2584 | (home-page "https://github.com/RcppCore/RcppArmadillo") |
| 2585 | (synopsis "Rcpp integration for the Armadillo linear algebra library") |
| 2586 | (description |
| 2587 | "Armadillo is a templated C++ linear algebra library that aims towards a |
| 2588 | good balance between speed and ease of use. Integer, floating point and |
| 2589 | complex numbers are supported, as well as a subset of trigonometric and |
| 2590 | statistics functions. Various matrix decompositions are provided through |
| 2591 | optional integration with LAPACK and ATLAS libraries. This package includes |
| 2592 | the header files from the templated Armadillo library.") |
| 2593 | ;; Armadillo is licensed under the MPL 2.0, while RcppArmadillo (the Rcpp |
| 2594 | ;; bindings to Armadillo) is licensed under the GNU GPL version 2 or |
| 2595 | ;; later, as is the rest of 'Rcpp'. |
| 2596 | (license license:gpl2+))) |
| 2597 | |
| 2598 | (define-public r-bitops |
| 2599 | (package |
| 2600 | (name "r-bitops") |
| 2601 | (version "1.0-6") |
| 2602 | (source (origin |
| 2603 | (method url-fetch) |
| 2604 | (uri (cran-uri "bitops" version)) |
| 2605 | (sha256 |
| 2606 | (base32 |
| 2607 | "176nr5wpnkavn5z0yy9f7d47l37ndnn2w3gv854xav8nnybi6wwv")))) |
| 2608 | (build-system r-build-system) |
| 2609 | (home-page "https://cran.r-project.org/web/packages/bitops") |
| 2610 | (synopsis "Bitwise operations") |
| 2611 | (description |
| 2612 | "This package provides functions for bitwise operations on integer |
| 2613 | vectors.") |
| 2614 | (license license:gpl2+))) |
| 2615 | |
| 2616 | (define-public r-catools |
| 2617 | (package |
| 2618 | (name "r-catools") |
| 2619 | (version "1.17.1.3") |
| 2620 | (source (origin |
| 2621 | (method url-fetch) |
| 2622 | (uri (cran-uri "caTools" version)) |
| 2623 | (sha256 |
| 2624 | (base32 |
| 2625 | "04m7vbydxb1nipday97w29p2miykyzxw572j9lda6jxmmp2kb1yp")))) |
| 2626 | (properties `((upstream-name . "caTools"))) |
| 2627 | (build-system r-build-system) |
| 2628 | (propagated-inputs |
| 2629 | `(("r-bitops" ,r-bitops))) |
| 2630 | (home-page "https://cran.r-project.org/web/packages/caTools") |
| 2631 | (synopsis "Various tools including functions for moving window statistics") |
| 2632 | (description |
| 2633 | "This package contains several basic utility functions including: |
| 2634 | moving (rolling, running) window statistic functions, read/write for GIF and |
| 2635 | ENVI binary files, fast calculation of AUC, LogitBoost classifier, base64 |
| 2636 | encoder/decoder, round-off-error-free sum and cumsum, etc.") |
| 2637 | (license license:gpl3+))) |
| 2638 | |
| 2639 | (define-public r-rprojroot |
| 2640 | (package |
| 2641 | (name "r-rprojroot") |
| 2642 | (version "1.3-2") |
| 2643 | (source |
| 2644 | (origin |
| 2645 | (method url-fetch) |
| 2646 | (uri (cran-uri "rprojroot" version)) |
| 2647 | (sha256 |
| 2648 | (base32 |
| 2649 | "12r3fdxmi2pmwn6ic3rhg0b20ll5z420m0d8fziv1n21961namnz")))) |
| 2650 | (build-system r-build-system) |
| 2651 | (propagated-inputs |
| 2652 | `(("r-backports" ,r-backports))) |
| 2653 | (home-page "https://github.com/krlmlr/rprojroot") |
| 2654 | (synopsis "Finding files in project subdirectories") |
| 2655 | (description |
| 2656 | "This package helps accessing files relative to a project root. It |
| 2657 | provides helpers for robust, reliable and flexible paths to files below a |
| 2658 | project root. The root of a project is defined as a directory that matches a |
| 2659 | certain criterion, e.g., it contains a certain regular file.") |
| 2660 | (license license:gpl3))) |
| 2661 | |
| 2662 | (define-public r-rmarkdown |
| 2663 | (package |
| 2664 | (name "r-rmarkdown") |
| 2665 | (version "1.18") |
| 2666 | (source |
| 2667 | (origin |
| 2668 | (method url-fetch) |
| 2669 | (uri (cran-uri "rmarkdown" version)) |
| 2670 | (sha256 |
| 2671 | (base32 "0fykzbb5kjsqc8v6gjcdma7rmq0gailp30qij6plgna4d8nhjw3w")))) |
| 2672 | (properties `((upstream-name . "rmarkdown"))) |
| 2673 | (build-system r-build-system) |
| 2674 | (propagated-inputs |
| 2675 | `(("r-base64enc" ,r-base64enc) |
| 2676 | ("r-evaluate" ,r-evaluate) |
| 2677 | ("r-htmltools" ,r-htmltools) |
| 2678 | ("r-jsonlite" ,r-jsonlite) |
| 2679 | ("r-knitr" ,r-knitr) |
| 2680 | ("r-mime" ,r-mime) |
| 2681 | ("r-stringr" ,r-stringr) |
| 2682 | ("r-tinytex" ,r-tinytex) |
| 2683 | ("r-xfun" ,r-xfun) |
| 2684 | ("r-yaml" ,r-yaml) |
| 2685 | ("ghc-pandoc" ,ghc-pandoc))) |
| 2686 | (home-page "https://rmarkdown.rstudio.com") |
| 2687 | (synopsis "Convert R Markdown documents into a variety of formats") |
| 2688 | (description |
| 2689 | "This package provides tools to convert R Markdown documents into a |
| 2690 | variety of formats.") |
| 2691 | (license license:gpl3+))) |
| 2692 | |
| 2693 | (define-public r-gtable |
| 2694 | (package |
| 2695 | (name "r-gtable") |
| 2696 | (version "0.3.0") |
| 2697 | (source (origin |
| 2698 | (method url-fetch) |
| 2699 | (uri (cran-uri "gtable" version)) |
| 2700 | (sha256 |
| 2701 | (base32 |
| 2702 | "1lyncxf2dqdjgw1071cn9c8zwzkz6sldnd5cgmicf70bc726qf7x")))) |
| 2703 | (properties `((upstream-name . "gtable"))) |
| 2704 | (build-system r-build-system) |
| 2705 | (home-page "https://cran.r-project.org/web/packages/gtable") |
| 2706 | (synopsis "R library to arrange grobs in tables") |
| 2707 | (description |
| 2708 | "Gtable is a collection of tools to make it easier to work with |
| 2709 | \"tables\" of grobs.") |
| 2710 | (license license:gpl2+))) |
| 2711 | |
| 2712 | (define-public r-gridextra |
| 2713 | (package |
| 2714 | (name "r-gridextra") |
| 2715 | (version "2.3") |
| 2716 | (source (origin |
| 2717 | (method url-fetch) |
| 2718 | (uri (cran-uri "gridExtra" version)) |
| 2719 | (sha256 |
| 2720 | (base32 |
| 2721 | "0fwfk3cdwxxim7nd55pn7m31bcaqj48y06j7an2k1v1pybk0rdl1")))) |
| 2722 | (properties `((upstream-name . "gridExtra"))) |
| 2723 | (build-system r-build-system) |
| 2724 | (propagated-inputs |
| 2725 | `(("r-gtable" ,r-gtable))) |
| 2726 | (native-inputs |
| 2727 | `(("r-knitr" ,r-knitr))) ;for building vignettes |
| 2728 | (home-page "https://github.com/baptiste/gridextra") |
| 2729 | (synopsis "Miscellaneous functions for \"Grid\" graphics") |
| 2730 | (description |
| 2731 | "This package provides a number of user-level functions to work with |
| 2732 | @code{grid} graphics, notably to arrange multiple grid-based plots on a page, |
| 2733 | and draw tables.") |
| 2734 | (license license:gpl2+))) |
| 2735 | |
| 2736 | (define-public r-pkgconfig |
| 2737 | (package |
| 2738 | (name "r-pkgconfig") |
| 2739 | (version "2.0.3") |
| 2740 | (source (origin |
| 2741 | (method url-fetch) |
| 2742 | (uri (cran-uri "pkgconfig" version)) |
| 2743 | (sha256 |
| 2744 | (base32 |
| 2745 | "0l1qph8zyi2sic3k2qcd7vlfl7rzfh1q7z7zvjkl5f7y1x2fy3rk")))) |
| 2746 | (build-system r-build-system) |
| 2747 | (home-page "https://github.com/gaborcsardi/pkgconfig") |
| 2748 | (synopsis "Private configuration for R packages") |
| 2749 | (description "This package provides the functionality to set configuration |
| 2750 | options on a per-package basis. Options set by a given package only apply to |
| 2751 | that package, other packages are unaffected.") |
| 2752 | (license license:expat))) |
| 2753 | |
| 2754 | (define-public r-blob |
| 2755 | (package |
| 2756 | (name "r-blob") |
| 2757 | (version "1.2.0") |
| 2758 | (source (origin |
| 2759 | (method url-fetch) |
| 2760 | (uri (cran-uri "blob" version)) |
| 2761 | (sha256 |
| 2762 | (base32 |
| 2763 | "08z071jzac4gasgfgab0y5g3ilfmlw08ln813wphxg07hsiczw8s")))) |
| 2764 | (build-system r-build-system) |
| 2765 | (propagated-inputs |
| 2766 | `(("r-prettyunits" ,r-prettyunits) |
| 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 "2.1.4") |
| 2781 | (source (origin |
| 2782 | (method url-fetch) |
| 2783 | (uri (cran-uri "RSQLite" version)) |
| 2784 | (sha256 |
| 2785 | (base32 |
| 2786 | "1vhaq6zfqilya669l100adcw51xz0p370zabnk2dnk1xhdih1f34")))) |
| 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 "1.0-0") |
| 2976 | (source |
| 2977 | (origin |
| 2978 | (method url-fetch) |
| 2979 | (uri (cran-uri "segmented" version)) |
| 2980 | (sha256 |
| 2981 | (base32 |
| 2982 | "1igsfkffpa60zn6j45lhw1zgr5pz6rjknv2f3sylnx5l9fdwibgf")))) |
| 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 "1.77") |
| 3017 | (source (origin |
| 3018 | (method url-fetch) |
| 3019 | (uri (cran-uri "SparseM" version)) |
| 3020 | (sha256 |
| 3021 | (base32 |
| 3022 | "0p6ljma2h12cq1xmy0cxb48ih8dhxxbnwkqzvx3cckxf2kprycm9")))) |
| 3023 | (properties |
| 3024 | `((upstream-name . "SparseM"))) |
| 3025 | (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 "0.10") |
| 3134 | (source (origin |
| 3135 | (method url-fetch) |
| 3136 | (uri (cran-uri "DT" version)) |
| 3137 | (sha256 |
| 3138 | (base32 |
| 3139 | "0vwhn1mcwv0hkbxnppf6vip23iiib0szvp1h3prawlkvd74xziiw")))) |
| 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 "3.0-1") |
| 3211 | (source |
| 3212 | (origin |
| 3213 | (method url-fetch) |
| 3214 | (uri (cran-uri "glmnet" version)) |
| 3215 | (sha256 |
| 3216 | (base32 "04wa926mnss53p1fhx0mjgxnmwmmqls12sc0sy7w09kbmyqa3fq7")))) |
| 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 "4.5.33") |
| 3404 | (source |
| 3405 | (origin |
| 3406 | (method url-fetch) |
| 3407 | (uri (cran-uri "bigmemory" version)) |
| 3408 | (sha256 |
| 3409 | (base32 |
| 3410 | "0ycl9dzm3drpyas625h34rir5bnbjlncxlvawfsfmqwcbmwdjdvj")))) |
| 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 "1.0-11") |
| 3595 | (source (origin |
| 3596 | (method url-fetch) |
| 3597 | (uri (cran-uri "mvtnorm" version)) |
| 3598 | (sha256 |
| 3599 | (base32 |
| 3600 | "0lkjph661blc1nwfzg9w48a60wvj6ffh4zjwlisvracsx4nn2883")))) |
| 3601 | (build-system r-build-system) |
| 3602 | (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 "3.0.1.1") |
| 4219 | (source |
| 4220 | (origin |
| 4221 | (method url-fetch) |
| 4222 | (uri (cran-uri "gplots" version)) |
| 4223 | (sha256 |
| 4224 | (base32 |
| 4225 | "033plcfs9w8pmn84n24mdhiixdirc2a7pz6dvm61fpd20gwh7cbx")))) |
| 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 "1.8-6") |
| 4289 | (source (origin |
| 4290 | (method url-fetch) |
| 4291 | (uri (cran-uri "zoo" version)) |
| 4292 | (sha256 |
| 4293 | (base32 |
| 4294 | "1k1pmzr9nfwbxq1xf0jzn3nawv4sgnkxkgzxnm1i887jcbrs85r2")))) |
| 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 "1.4.32") |
| 4445 | (source (origin |
| 4446 | (method url-fetch) |
| 4447 | (uri (cran-uri "statmod" version)) |
| 4448 | (sha256 |
| 4449 | (base32 |
| 4450 | "083yyp84xj85zg4bhz7i90bqzl3p6155ch4abwsfc9k1lv7s2rrg")))) |
| 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 "2.3-1") |
| 4746 | (source |
| 4747 | (origin |
| 4748 | (method url-fetch) |
| 4749 | (uri (cran-uri "prabclus" version)) |
| 4750 | (sha256 |
| 4751 | (base32 |
| 4752 | "1h5k13w8mmmdy74l145zh64f339wy78z1nlg8xr3zg23gmv98cpg")))) |
| 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 "0.4-18.1") |
| 4893 | (source |
| 4894 | (origin |
| 4895 | (method url-fetch) |
| 4896 | (uri (cran-uri "robust" version)) |
| 4897 | (sha256 |
| 4898 | (base32 |
| 4899 | "0xs098pfw5zdcdk3rsxkylfl6d2pyp566s5v92bzhgl7h8c90cfy")))) |
| 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") |
| 5066 | (source |
| 5067 | (origin |
| 5068 | (method url-fetch) |
| 5069 | (uri (cran-uri "ModelMetrics" version)) |
| 5070 | (sha256 |
| 5071 | (base32 |
| 5072 | "158ddbw2snlyzd2q6mdaif5i67kq4qfvadylwjxgv1w2cmszrmk6")))) |
| 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 "5.52") |
| 5111 | (source |
| 5112 | (origin |
| 5113 | (method url-fetch) |
| 5114 | (uri (cran-uri "quantreg" version)) |
| 5115 | (sha256 |
| 5116 | (base32 "0rq9as31wiz41lmi9hmdq3gknpcbpwqzfcn065ysjdxzjdb57dcy")))) |
| 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 "3.0-5") |
| 5240 | (source |
| 5241 | (origin |
| 5242 | (method url-fetch) |
| 5243 | (uri (cran-uri "car" version)) |
| 5244 | (sha256 |
| 5245 | (base32 "0w7fm81pn0wqrwzbjyddnrkpjl8gavg7ijh7rab9f21rkgkzgm3y")))) |
| 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-caret |
| 5267 | (package |
| 5268 | (name "r-caret") |
| 5269 | (version "6.0-84") |
| 5270 | (source |
| 5271 | (origin |
| 5272 | (method url-fetch) |
| 5273 | (uri (cran-uri "caret" version)) |
| 5274 | (sha256 |
| 5275 | (base32 |
| 5276 | "03898irgb70q0p01kq99yb6q6xji0jx4jmj0yxlv8wcwd841r0x1")))) |
| 5277 | (build-system r-build-system) |
| 5278 | (propagated-inputs |
| 5279 | `(("r-foreach" ,r-foreach) |
| 5280 | ("r-ggplot2" ,r-ggplot2) |
| 5281 | ("r-lattice" ,r-lattice) |
| 5282 | ("r-modelmetrics" ,r-modelmetrics) |
| 5283 | ("r-nlme" ,r-nlme) |
| 5284 | ("r-plyr" ,r-plyr) |
| 5285 | ("r-recipes" ,r-recipes) |
| 5286 | ("r-reshape2" ,r-reshape2) |
| 5287 | ("r-withr" ,r-withr))) |
| 5288 | (home-page "https://github.com/topepo/caret") |
| 5289 | (synopsis "Classification and regression training") |
| 5290 | (description |
| 5291 | "This package provides misc functions for training and plotting |
| 5292 | classification and regression models.") |
| 5293 | (license license:gpl2+))) |
| 5294 | |
| 5295 | (define-public r-rcppprogress |
| 5296 | (package |
| 5297 | (name "r-rcppprogress") |
| 5298 | (version "0.4.1") |
| 5299 | (source |
| 5300 | (origin |
| 5301 | (method url-fetch) |
| 5302 | (uri (cran-uri "RcppProgress" version)) |
| 5303 | (sha256 |
| 5304 | (base32 |
| 5305 | "0yk01hfv961zyp569682k9igvhnwqyg5j0n5fm63sxigj82l2xhi")))) |
| 5306 | (properties `((upstream-name . "RcppProgress"))) |
| 5307 | (build-system r-build-system) |
| 5308 | (propagated-inputs |
| 5309 | `(("r-devtools" ,r-devtools) |
| 5310 | ("r-rcpp" ,r-rcpp))) |
| 5311 | (home-page "https://github.com/kforner/rcpp_progress") |
| 5312 | (synopsis "Interruptible progress bar for C++ in R packages") |
| 5313 | (description |
| 5314 | "This package allows to display a progress bar in the R console for long running |
| 5315 | computations taking place in C++ code, and support for interrupting those computations |
| 5316 | even in multithreaded code, typically using OpenMP.") |
| 5317 | (license license:gpl3+))) |
| 5318 | |
| 5319 | (define-public r-mnormt |
| 5320 | (package |
| 5321 | (name "r-mnormt") |
| 5322 | (version "1.5-5") |
| 5323 | (source |
| 5324 | (origin |
| 5325 | (method url-fetch) |
| 5326 | (uri (cran-uri "mnormt" version)) |
| 5327 | (sha256 |
| 5328 | (base32 |
| 5329 | "1b34xxrnf35khsx82mhvmk96sgfr2flyasaah7qkb2976pwxay7z")))) |
| 5330 | (build-system r-build-system) |
| 5331 | (native-inputs |
| 5332 | `(("gfortran" ,gfortran))) |
| 5333 | (home-page "http://azzalini.stat.unipd.it/SW/Pkg-mnormt") |
| 5334 | (synopsis "Multivariate normal and \"t\" distributions") |
| 5335 | (description |
| 5336 | "This package provides functions for computing the density and the |
| 5337 | distribution function of multivariate normal and \"t\" random variables, and |
| 5338 | for generating random vectors sampled from these distributions. Probabilities |
| 5339 | are computed via non-Monte Carlo methods.") |
| 5340 | (license license:gpl2+))) |
| 5341 | |
| 5342 | (define-public r-numderiv |
| 5343 | (package |
| 5344 | (name "r-numderiv") |
| 5345 | (version "2016.8-1.1") |
| 5346 | (source |
| 5347 | (origin |
| 5348 | (method url-fetch) |
| 5349 | (uri (cran-uri "numDeriv" version)) |
| 5350 | (sha256 |
| 5351 | (base32 |
| 5352 | "0idk02pqkziik932bd8k72d1q775g1is3m4bc861pcxfz6gx3i6q")))) |
| 5353 | (properties `((upstream-name . "numDeriv"))) |
| 5354 | (build-system r-build-system) |
| 5355 | (home-page "https://cran.r-project.org/web/packages/numDeriv") |
| 5356 | (synopsis "Accurate numerical derivatives") |
| 5357 | (description |
| 5358 | "This package provides methods for calculating accurate numerical |
| 5359 | first and second order derivatives.") |
| 5360 | (license license:gpl2))) |
| 5361 | |
| 5362 | (define-public r-sn |
| 5363 | (package |
| 5364 | (name "r-sn") |
| 5365 | (version "1.5-4") |
| 5366 | (source |
| 5367 | (origin |
| 5368 | (method url-fetch) |
| 5369 | (uri (cran-uri "sn" version)) |
| 5370 | (sha256 |
| 5371 | (base32 |
| 5372 | "0x46gxkplxbnhaqbpiav1r4xlv4ib7n57kxmca7scqwj22y7wrs6")))) |
| 5373 | (build-system r-build-system) |
| 5374 | (propagated-inputs |
| 5375 | `(("r-mnormt" ,r-mnormt) |
| 5376 | ("r-numderiv" ,r-numderiv))) |
| 5377 | (home-page "http://azzalini.stat.unipd.it/SN") |
| 5378 | (synopsis "The skew-normal and skew-t distributions") |
| 5379 | (description |
| 5380 | "This package provides functionalities to build and manipulate |
| 5381 | probability distributions of the skew-normal family and some related |
| 5382 | ones, notably the skew-t family, and provides related statistical |
| 5383 | methods for data fitting and diagnostics, in the univariate and the |
| 5384 | multivariate case.") |
| 5385 | (license license:gpl2+))) |
| 5386 | |
| 5387 | (define-public r-tclust |
| 5388 | (package |
| 5389 | (name "r-tclust") |
| 5390 | (version "1.4-1") |
| 5391 | (source |
| 5392 | (origin |
| 5393 | (method url-fetch) |
| 5394 | (uri (cran-uri "tclust" version)) |
| 5395 | (sha256 |
| 5396 | (base32 |
| 5397 | "17md6l9v9dl9b72l84df01b52h2xiynbcjm437mv9mzcr09fc2sb")))) |
| 5398 | (build-system r-build-system) |
| 5399 | ;; These are all suggested packages, not build dependencies. |
| 5400 | (propagated-inputs |
| 5401 | `(("r-cluster" ,r-cluster) |
| 5402 | ("r-mclust" ,r-mclust) |
| 5403 | ("r-mvtnorm" ,r-mvtnorm) |
| 5404 | ("r-sn" ,r-sn))) |
| 5405 | (home-page "https://cran.r-project.org/web/packages/tclust") |
| 5406 | (synopsis "Robust trimmed clustering") |
| 5407 | (description |
| 5408 | "This package implements different robust clustering |
| 5409 | algorithms (@code{tclust}) based on trimming and including some graphical |
| 5410 | diagnostic tools (@code{ctlcurves} and @code{DiscrFact}).") |
| 5411 | (license license:gpl3))) |
| 5412 | |
| 5413 | (define-public r-ranger |
| 5414 | (package |
| 5415 | (name "r-ranger") |
| 5416 | (version "0.11.2") |
| 5417 | (source |
| 5418 | (origin |
| 5419 | (method url-fetch) |
| 5420 | (uri (cran-uri "ranger" version)) |
| 5421 | (sha256 |
| 5422 | (base32 |
| 5423 | "1sxyzxmjc6lm8wcmq15j6sscnza7aay4mr3dyri2zngx6fa8mb0k")))) |
| 5424 | (build-system r-build-system) |
| 5425 | (propagated-inputs |
| 5426 | `(("r-rcpp" ,r-rcpp) |
| 5427 | ("r-matrix" ,r-matrix) |
| 5428 | ("r-rcppeigen" ,r-rcppeigen))) |
| 5429 | (home-page "https://github.com/imbs-hl/ranger") |
| 5430 | (synopsis "Fast implementation of random forests") |
| 5431 | (description |
| 5432 | "This package provides a fast implementation of Random Forests, |
| 5433 | particularly suited for high dimensional data. Ensembles of classification, |
| 5434 | regression, survival and probability prediction trees are supported. Data from |
| 5435 | genome-wide association studies can be analyzed efficiently.") |
| 5436 | (license license:gpl3))) |
| 5437 | |
| 5438 | (define-public r-tsne |
| 5439 | (package |
| 5440 | (name "r-tsne") |
| 5441 | (version "0.1-3") |
| 5442 | (source |
| 5443 | (origin |
| 5444 | (method url-fetch) |
| 5445 | (uri (cran-uri "tsne" version)) |
| 5446 | (sha256 |
| 5447 | (base32 |
| 5448 | "0s8cv2pndkddq62rzlgzgfdjp1vjv5hz5i5957sllnb97vbzbzb6")))) |
| 5449 | (build-system r-build-system) |
| 5450 | (home-page "https://github.com/jdonaldson/rtsne/") |
| 5451 | (synopsis "t-Distributed Stochastic Neighbor Embedding for R") |
| 5452 | (description |
| 5453 | "This package provides a pure R implementation of the t-SNE algorithm.") |
| 5454 | (license license:gpl2+))) |
| 5455 | |
| 5456 | (define-public r-cairo |
| 5457 | (package |
| 5458 | (name "r-cairo") |
| 5459 | (version "1.5-10") |
| 5460 | (source |
| 5461 | (origin |
| 5462 | (method url-fetch) |
| 5463 | (uri (cran-uri "Cairo" version)) |
| 5464 | (sha256 |
| 5465 | (base32 |
| 5466 | "1mdmd5zmjkh1b0x928zizgzh42x8swbajffb88rvnjfdhk1z0dvq")))) |
| 5467 | (properties `((upstream-name . "Cairo"))) |
| 5468 | (build-system r-build-system) |
| 5469 | (inputs |
| 5470 | `(("cairo" ,cairo) |
| 5471 | ("libxt" ,libxt) |
| 5472 | ("zlib" ,zlib))) |
| 5473 | (native-inputs |
| 5474 | `(("pkg-config" ,pkg-config))) |
| 5475 | (home-page "http://www.rforge.net/Cairo/") |
| 5476 | (synopsis "R graphics device using Cairo graphics library") |
| 5477 | (description |
| 5478 | "This package provides a Cairo graphics device that can be use to |
| 5479 | create high-quality vector (PDF, PostScript and SVG) and bitmap |
| 5480 | output (PNG,JPEG,TIFF), and high-quality rendering in displays (X11 |
| 5481 | and Win32). Since it uses the same back-end for all output, copying |
| 5482 | across formats is WYSIWYG. Files are created without the dependence |
| 5483 | on X11 or other external programs. This device supports alpha |
| 5484 | channel (semi-transparent drawing) and resulting images can contain |
| 5485 | transparent and semi-transparent regions. It is ideal for use in |
| 5486 | server environments (file output) and as a replacement for other |
| 5487 | devices that don't have Cairo's capabilities such as alpha support or |
| 5488 | anti-aliasing. Backends are modular such that any subset of backends |
| 5489 | is supported.") |
| 5490 | (license license:gpl2))) |
| 5491 | |
| 5492 | (define-public r-lubridate |
| 5493 | (package |
| 5494 | (name "r-lubridate") |
| 5495 | (version "1.7.4") |
| 5496 | (source |
| 5497 | (origin |
| 5498 | (method url-fetch) |
| 5499 | (uri (cran-uri "lubridate" version)) |
| 5500 | (sha256 |
| 5501 | (base32 |
| 5502 | "14a823il77w3wmmnzr89vwrqp50y56dh5raycnaw6c8nv5xsh32i")))) |
| 5503 | (build-system r-build-system) |
| 5504 | (propagated-inputs |
| 5505 | `(("r-rcpp" ,r-rcpp) |
| 5506 | ("r-stringr" ,r-stringr))) |
| 5507 | (home-page |
| 5508 | "https://cran.r-project.org/web/packages/lubridate") |
| 5509 | (synopsis "Make dealing with dates a little easier") |
| 5510 | (description |
| 5511 | "This package provides functions to work with date-times and time-spans: |
| 5512 | fast and user friendly parsing of date-time data, extraction and updating of |
| 5513 | components of a date-time (years, months, days, hours, minutes, and seconds), |
| 5514 | algebraic manipulation on date-time and time-span objects. The @code{lubridate} |
| 5515 | package has a consistent and memorable syntax that makes working with dates |
| 5516 | easy and fun.") |
| 5517 | (license license:gpl2))) |
| 5518 | |
| 5519 | (define-public r-fdrtool |
| 5520 | (package |
| 5521 | (name "r-fdrtool") |
| 5522 | (version "1.2.15") |
| 5523 | (source |
| 5524 | (origin |
| 5525 | (method url-fetch) |
| 5526 | (uri (cran-uri "fdrtool" version)) |
| 5527 | (sha256 |
| 5528 | (base32 |
| 5529 | "1h46frlk7d9f4qx0bg6p55nrm9wwwz2sv6d1nz7061wdfsm69yb5")))) |
| 5530 | (build-system r-build-system) |
| 5531 | (home-page "http://strimmerlab.org/software/fdrtool/") |
| 5532 | (synopsis "Estimation of false discovery rates and higher criticism") |
| 5533 | (description |
| 5534 | "This package provides tools to estimate tail area-based false discovery |
| 5535 | rates as well as local false discovery rates for a variety of null |
| 5536 | models (p-values, z-scores, correlation coefficients, t-scores). The |
| 5537 | proportion of null values and the parameters of the null distribution are |
| 5538 | adaptively estimated from the data. In addition, the package contains |
| 5539 | functions for non-parametric density estimation (Grenander estimator), for |
| 5540 | monotone regression (isotonic regression and antitonic regression with |
| 5541 | weights), for computing the @dfn{greatest convex minorant} (GCM) and the |
| 5542 | @dfn{least concave majorant} (LCM), for the half-normal and correlation |
| 5543 | distributions, and for computing empirical @dfn{higher criticism} (HC) scores |
| 5544 | and the corresponding decision threshold.") |
| 5545 | (license license:gpl3+))) |
| 5546 | |
| 5547 | (define-public r-forcats |
| 5548 | (package |
| 5549 | (name "r-forcats") |
| 5550 | (version "0.4.0") |
| 5551 | (source |
| 5552 | (origin |
| 5553 | (method url-fetch) |
| 5554 | (uri (cran-uri "forcats" version)) |
| 5555 | (sha256 |
| 5556 | (base32 |
| 5557 | "1cnjh23z59fhbjmy7y95425hcq3m5wrwqvahsxwi7zm6d9bwp0vw")))) |
| 5558 | (build-system r-build-system) |
| 5559 | (propagated-inputs |
| 5560 | `(("r-ellipsis" ,r-ellipsis) |
| 5561 | ("r-magrittr" ,r-magrittr) |
| 5562 | ("r-tibble" ,r-tibble) |
| 5563 | ("r-rlang" ,r-rlang))) |
| 5564 | (home-page "http://forcats.tidyverse.org") |
| 5565 | (synopsis "Tools for working with factors") |
| 5566 | (description "This package provides helpers for reordering factor |
| 5567 | levels (including moving specified levels to front, ordering by first |
| 5568 | appearance, reversing, and randomly shuffling), and tools for modifying factor |
| 5569 | levels (including collapsing rare levels into other, \"anonymizing\", and |
| 5570 | manually \"recoding\").") |
| 5571 | (license license:gpl3))) |
| 5572 | |
| 5573 | (define-public r-tgstat |
| 5574 | (let ((changeset "4f8e60c03598f49aff6f5beeab40f2b995377e9f") |
| 5575 | (revision "1")) |
| 5576 | (package |
| 5577 | (name "r-tgstat") |
| 5578 | (version (string-append "1.0.2-" revision "." (string-take changeset 7))) |
| 5579 | (source |
| 5580 | (origin |
| 5581 | (method hg-fetch) |
| 5582 | (uri (hg-reference |
| 5583 | (url "https://bitbucket.org/tanaylab/tgstat") |
| 5584 | (changeset changeset))) |
| 5585 | (file-name (string-append name "-" version "-checkout")) |
| 5586 | (sha256 |
| 5587 | (base32 |
| 5588 | "0ilkkyximy77zbncm91kdfqbxf0qyndg16pd3q3p6a3xc9qcmxvn")))) |
| 5589 | (build-system r-build-system) |
| 5590 | (arguments |
| 5591 | `(#:phases |
| 5592 | (modify-phases %standard-phases |
| 5593 | (add-after 'unpack 'fix-isnan |
| 5594 | (lambda _ |
| 5595 | (substitute* "src/tgstat.h" |
| 5596 | (("#define isnan ::isnan") |
| 5597 | "#define isnan std::isnan")) |
| 5598 | #t))))) |
| 5599 | (propagated-inputs |
| 5600 | `(("r-rcpp" ,r-rcpp))) |
| 5601 | (home-page "https://bitbucket.org/tanaylab/tgstat/") |
| 5602 | (synopsis "Tanay's group statistical utilities") |
| 5603 | (description |
| 5604 | "The goal of tgstat is to provide fast and efficient statistical |
| 5605 | tools.") |
| 5606 | (license license:gpl2)))) |
| 5607 | |
| 5608 | (define-public r-tgconfig |
| 5609 | (let ((changeset "1e02c7614713bd0866c46f0c679a058f8c6d627e") |
| 5610 | (revision "1")) |
| 5611 | (package |
| 5612 | (name "r-tgconfig") |
| 5613 | (version (string-append "0.0.0.9000-" revision "." (string-take changeset 7))) |
| 5614 | (source |
| 5615 | (origin |
| 5616 | (method hg-fetch) |
| 5617 | (uri (hg-reference |
| 5618 | (url "https://bitbucket.org/tanaylab/tgconfig") |
| 5619 | (changeset changeset))) |
| 5620 | (file-name (string-append name "-" version "-checkout")) |
| 5621 | (sha256 |
| 5622 | (base32 |
| 5623 | "0xy6c7s7mn1yx191154bwbv1bl424bnvc80syqpl1vdl28ba46rj")))) |
| 5624 | (build-system r-build-system) |
| 5625 | (propagated-inputs |
| 5626 | `(("r-yaml" ,r-yaml))) |
| 5627 | (home-page "https://bitbucket.org/tanaylab/tgconfig/") |
| 5628 | (synopsis "Infrastructure for managing package parameters") |
| 5629 | (description |
| 5630 | "The goal of tgconfig is to provide infrastructure for managing package |
| 5631 | parameters.") |
| 5632 | (license license:gpl3)))) |
| 5633 | |
| 5634 | (define-public r-directlabels |
| 5635 | (package |
| 5636 | (name "r-directlabels") |
| 5637 | (version "2018.05.22") |
| 5638 | (source |
| 5639 | (origin |
| 5640 | (method url-fetch) |
| 5641 | (uri (cran-uri "directlabels" version)) |
| 5642 | (sha256 |
| 5643 | (base32 |
| 5644 | "0xcpc56ssb9430b0xcdhayk3qaak2qcakyss2pz14y5w2027hblv")))) |
| 5645 | (build-system r-build-system) |
| 5646 | (propagated-inputs |
| 5647 | `(("r-quadprog" ,r-quadprog))) |
| 5648 | (home-page "http://directlabels.r-forge.r-project.org/") |
| 5649 | (synopsis "Direct labels for multicolor plots") |
| 5650 | (description |
| 5651 | "This package provides an extensible framework for automatically placing |
| 5652 | direct labels onto multicolor plots. Label positions are described using |
| 5653 | positioning methods that can be re-used across several different plots. There |
| 5654 | are heuristics for examining @code{trellis} and @code{ggplot} objects and |
| 5655 | inferring an appropriate positioning method.") |
| 5656 | (license license:gpl3))) |
| 5657 | |
| 5658 | (define-public r-catterplots |
| 5659 | (let ((commit "ae17cd5e49ddda4ecfe0eba8a4c21df8c88e72c4") |
| 5660 | (revision "3")) |
| 5661 | (package |
| 5662 | (name "r-catterplots") |
| 5663 | (version (git-version "0" revision commit)) |
| 5664 | (source (origin |
| 5665 | (method git-fetch) |
| 5666 | (uri (git-reference |
| 5667 | (url "https://github.com/Gibbsdavidl/CatterPlots.git") |
| 5668 | (commit commit))) |
| 5669 | (file-name (git-file-name name version)) |
| 5670 | (sha256 |
| 5671 | (base32 |
| 5672 | "0qa8liylffpxgdg8xcgjar5dsvczqhn3akd4w35113hnyg1m4xyg")))) |
| 5673 | (build-system r-build-system) |
| 5674 | (propagated-inputs |
| 5675 | `(("r-png" ,r-png))) |
| 5676 | (home-page "https://github.com/Gibbsdavidl/CatterPlots") |
| 5677 | (synopsis "Scatter plots with cat shaped points") |
| 5678 | (description "Did you ever wish you could make scatter plots with cat |
| 5679 | shaped points? Now you can!") |
| 5680 | (license license:asl2.0)))) |
| 5681 | |
| 5682 | (define-public r-colorout |
| 5683 | (package |
| 5684 | (name "r-colorout") |
| 5685 | (version "1.2-2") |
| 5686 | (source |
| 5687 | (origin |
| 5688 | (method git-fetch) |
| 5689 | (uri (git-reference |
| 5690 | (url "https://github.com/jalvesaq/colorout.git") |
| 5691 | (commit (string-append "v" version)))) |
| 5692 | (file-name (git-file-name name version)) |
| 5693 | (sha256 |
| 5694 | (base32 "1rsx69wjpa73c6x2hacvvvbzdzxn7wg06gizf97kasjdlb7azmp3")))) |
| 5695 | (build-system r-build-system) |
| 5696 | (home-page "https://github.com/jalvesaq/colorout") |
| 5697 | (synopsis "Colorize output in the R REPL") |
| 5698 | (description "@code{colorout} is an R package that colorizes R output when |
| 5699 | running in terminal emulator. |
| 5700 | |
| 5701 | R STDOUT is parsed and numbers, negative numbers, dates in the standard |
| 5702 | format, strings, and R constants are identified and wrapped by special ANSI |
| 5703 | scape codes that are interpreted by terminal emulators as commands to colorize |
| 5704 | the output. R STDERR is also parsed to identify the expressions warning and |
| 5705 | error and their translations to many languages. If these expressions are |
| 5706 | found, the output is colorized accordingly; otherwise, it is colorized as |
| 5707 | STDERROR (blue, by default). |
| 5708 | |
| 5709 | You can customize the colors according to your taste, guided by the color |
| 5710 | table made by the command @code{show256Colors()}. You can also set the colors |
| 5711 | to any arbitrary string. In this case, it is up to you to set valid values.") |
| 5712 | (license license:gpl3+))) |
| 5713 | |
| 5714 | (define-public python-rpy2 |
| 5715 | ;; We need to take this changeset instead of the RELEASE_3_0_4 tag, because |
| 5716 | ;; it fixes a regression when using ggplot 3.2.0. |
| 5717 | (let ((changeset "19868a8") |
| 5718 | (revision "1")) |
| 5719 | (package |
| 5720 | (name "python-rpy2") |
| 5721 | (version (git-version "3.0.4" revision changeset)) |
| 5722 | (source |
| 5723 | (origin |
| 5724 | (method hg-fetch) |
| 5725 | (uri (hg-reference |
| 5726 | (url "https://bitbucket.org/rpy2/rpy2") |
| 5727 | (changeset changeset))) |
| 5728 | (file-name (git-file-name name version)) |
| 5729 | (sha256 |
| 5730 | (base32 |
| 5731 | "1bb0wslcbj3wjvyk3jb9yyzdi6adfqh5vfgcvn22dyzxzbhcs8kk")))) |
| 5732 | (build-system python-build-system) |
| 5733 | (arguments |
| 5734 | '(#:modules ((ice-9 ftw) |
| 5735 | (srfi srfi-1) |
| 5736 | (srfi srfi-26) |
| 5737 | (guix build utils) |
| 5738 | (guix build python-build-system)) |
| 5739 | #:phases |
| 5740 | (modify-phases %standard-phases |
| 5741 | (replace 'check |
| 5742 | (lambda* (#:key outputs inputs #:allow-other-keys) |
| 5743 | (let ((cwd (getcwd))) |
| 5744 | (setenv "TZ" "UTC") |
| 5745 | (setenv "PYTHONPATH" |
| 5746 | (string-append cwd "/build/" |
| 5747 | (find (cut string-prefix? "lib" <>) |
| 5748 | (scandir (string-append cwd "/build"))) |
| 5749 | ":" |
| 5750 | (getenv "PYTHONPATH")))) |
| 5751 | (invoke "pytest" "-v" "rpy/tests/")))))) |
| 5752 | (propagated-inputs |
| 5753 | `(("python-cffi" ,python-cffi) |
| 5754 | ("python-six" ,python-six) |
| 5755 | ("python-jinja2" ,python-jinja2) |
| 5756 | ("python-numpy" ,python-numpy) |
| 5757 | ("python-pandas" ,python-pandas) |
| 5758 | ("python-pytz" ,python-pytz) |
| 5759 | ("python-ipython" ,python-ipython) |
| 5760 | ("python-tzlocal" ,python-tzlocal))) |
| 5761 | (inputs |
| 5762 | `(("readline" ,readline) |
| 5763 | ("icu4c" ,icu4c) |
| 5764 | ("pcre" ,pcre) |
| 5765 | ("r-minimal" ,r-minimal) |
| 5766 | ("r-survival" ,r-survival) |
| 5767 | ("r-ggplot2" ,r-ggplot2) |
| 5768 | ("r-rsqlite" ,r-rsqlite) |
| 5769 | ("r-dplyr" ,r-dplyr) |
| 5770 | ("r-dbplyr" ,r-dbplyr) |
| 5771 | ("python-numpy" ,python-numpy))) |
| 5772 | (native-inputs |
| 5773 | `(("zlib" ,zlib) |
| 5774 | ("python-pytest" ,python-pytest))) |
| 5775 | (home-page "https://rpy2.bitbucket.io/") |
| 5776 | (synopsis "Python interface to the R language") |
| 5777 | (description "rpy2 is a redesign and rewrite of rpy. It is providing a |
| 5778 | low-level interface to R from Python, a proposed high-level interface, |
| 5779 | including wrappers to graphical libraries, as well as R-like structures and |
| 5780 | functions.") |
| 5781 | ;; Any of these licenses can be picked for the R interface. The whole |
| 5782 | ;; project is released under GPLv2+ according to the license declaration |
| 5783 | ;; in "setup.py". |
| 5784 | (license (list license:mpl2.0 license:gpl2+ license:lgpl2.1+))))) |
| 5785 | |
| 5786 | (define-public java-jdistlib |
| 5787 | (package |
| 5788 | (name "java-jdistlib") |
| 5789 | (version "0.4.5") |
| 5790 | (source (origin |
| 5791 | (method url-fetch) |
| 5792 | (uri (string-append "mirror://sourceforge/jdistlib/jdistlib-" |
| 5793 | version "-src.jar")) |
| 5794 | (sha256 |
| 5795 | (base32 |
| 5796 | "1pkj8aahw9ydr1isbaqrkd05nvq98ik5jwwhf3yf3rky3z869v11")))) |
| 5797 | (build-system ant-build-system) |
| 5798 | (arguments |
| 5799 | `(#:jar-name "jdistlib.jar" |
| 5800 | #:jdk ,icedtea-8 |
| 5801 | #:tests? #f ; no dedicated test directory |
| 5802 | #:phases |
| 5803 | (modify-phases %standard-phases |
| 5804 | (add-after 'unpack 'fix-broken-encoding |
| 5805 | (lambda _ |
| 5806 | (with-fluids ((%default-port-encoding "ISO-8859-1")) |
| 5807 | (substitute* "src/jdistlib/Beta.java" |
| 5808 | (("Scheff.+-Tukey") "Scheffe-Tukey"))) |
| 5809 | #t))))) |
| 5810 | (propagated-inputs |
| 5811 | `(("java-jtransforms" ,java-jtransforms))) |
| 5812 | (native-inputs |
| 5813 | `(("java-junit" ,java-junit))) |
| 5814 | (home-page "http://jdistlib.sourceforge.net/") |
| 5815 | (synopsis "Java library of statistical distributions") |
| 5816 | (description "JDistlib is the Java Statistical Distribution Library, a |
| 5817 | Java package that provides routines for various statistical distributions.") |
| 5818 | ;; The files that were translated from R code are under GPLv2+; some files |
| 5819 | ;; are under the GPLv3, which is a mistake. The author confirmed in an |
| 5820 | ;; email that this whole project should be under GPLv2+. |
| 5821 | (license license:gpl2+))) |
| 5822 | |
| 5823 | (define-public emacs-ess |
| 5824 | (package |
| 5825 | (name "emacs-ess") |
| 5826 | (version "17.11") |
| 5827 | (source (origin |
| 5828 | (method url-fetch) |
| 5829 | (uri (string-append "https://github.com/emacs-ess/ESS/archive/v" |
| 5830 | version ".tar.gz")) |
| 5831 | (sha256 |
| 5832 | (base32 |
| 5833 | "0cbilbsiwvcyf6d5y24mymp57m3ana5dkzab3knfs83w4a3a4c5c")) |
| 5834 | (file-name (string-append name "-" version ".tar.gz")) |
| 5835 | (modules '((guix build utils))) |
| 5836 | (snippet |
| 5837 | '(begin |
| 5838 | ;; Stop ESS from trying to bundle an external julia-mode.el. |
| 5839 | (substitute* "lisp/Makefile" |
| 5840 | (("^\tjulia-mode.elc\\\\\n") "") |
| 5841 | (("^dist: all julia-mode.el") |
| 5842 | "dist: all")) |
| 5843 | ;; No need to build docs in so many formats. Also, skipping |
| 5844 | ;; pdf lets us not pull in texlive. |
| 5845 | (substitute* "doc/Makefile" |
| 5846 | (("all : info text html pdf") |
| 5847 | "all : info") |
| 5848 | (("install: install-info install-other-docs") |
| 5849 | "install: install-info")) |
| 5850 | ;; Test fails upstream |
| 5851 | (substitute* "test/ess-r-tests.el" |
| 5852 | (("ert-deftest ess-r-namespaced-eval-no-srcref-in-errors ()") |
| 5853 | "ert-deftest ess-r-namespaced-eval-no-srcref-in-errors () :expected-result :failed")) |
| 5854 | #t)))) |
| 5855 | (build-system gnu-build-system) |
| 5856 | (arguments |
| 5857 | (let ((base-directory "/share/emacs/site-lisp/guix.d/ess")) |
| 5858 | `(#:make-flags (list (string-append "PREFIX=" %output) |
| 5859 | (string-append "ETCDIR=" %output "/" |
| 5860 | ,base-directory "/etc") |
| 5861 | (string-append "LISPDIR=" %output "/" |
| 5862 | ,base-directory)) |
| 5863 | #:phases |
| 5864 | (modify-phases %standard-phases |
| 5865 | (delete 'configure) |
| 5866 | (add-before 'build 'more-shebang-patching |
| 5867 | (lambda* (#:key inputs #:allow-other-keys) |
| 5868 | (substitute* "Makeconf" |
| 5869 | (("SHELL = /bin/sh") |
| 5870 | (string-append "SHELL = " (which "sh")))) |
| 5871 | #t)) |
| 5872 | (replace 'check |
| 5873 | (lambda _ |
| 5874 | (invoke "make" "test"))))))) |
| 5875 | (inputs |
| 5876 | `(("emacs" ,emacs-minimal) |
| 5877 | ("r-minimal" ,r-minimal))) |
| 5878 | (native-inputs |
| 5879 | `(("perl" ,perl) |
| 5880 | ("texinfo" ,texinfo))) |
| 5881 | (propagated-inputs |
| 5882 | `(("emacs-julia-mode" ,emacs-julia-mode))) |
| 5883 | (home-page "https://ess.r-project.org/") |
| 5884 | (synopsis "Emacs mode for statistical analysis programs") |
| 5885 | (description "Emacs Speaks Statistics (ESS) is an add-on package for GNU |
| 5886 | Emacs. It is designed to support editing of scripts and interaction with |
| 5887 | various statistical analysis programs such as R, Julia, and JAGS.") |
| 5888 | (license license:gpl2+))) |