1 ;;; GNU Guix --- Functional package management for GNU
2 ;;; Copyright © 2015, 2016, 2017, 2018 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 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 Tobias Geerinckx-Rice <me@tobias.gr>
13 ;;; This file is part of GNU Guix.
15 ;;; GNU Guix is free software; you can redistribute it and/or modify it
16 ;;; under the terms of the GNU General Public License as published by
17 ;;; the Free Software Foundation; either version 3 of the License, or (at
18 ;;; your option) any later version.
20 ;;; GNU Guix is distributed in the hope that it will be useful, but
21 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
22 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
23 ;;; GNU General Public License for more details.
25 ;;; You should have received a copy of the GNU General Public License
26 ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
28 (define-module (gnu packages statistics)
29 #:use-module ((guix licenses) #:prefix license:)
30 #:use-module (guix packages)
31 #:use-module (guix download)
32 #:use-module (guix hg-download)
33 #:use-module (guix git-download)
34 #:use-module (guix utils)
35 #:use-module (guix build-system ant)
36 #:use-module (guix build-system gnu)
37 #:use-module (guix build-system r)
38 #:use-module (guix build-system python)
39 #:use-module (guix build-system trivial)
40 #:use-module (gnu packages)
41 #:use-module (gnu packages algebra)
42 #:use-module (gnu packages bash)
43 #:use-module (gnu packages check)
44 #:use-module (gnu packages compression)
45 #:use-module (gnu packages cran)
46 #:use-module (gnu packages curl)
47 #:use-module (gnu packages gcc)
48 #:use-module (gnu packages gtk)
49 #:use-module (gnu packages gettext)
50 #:use-module (gnu packages glib)
51 #:use-module (gnu packages haskell)
52 #:use-module (gnu packages icu4c)
53 #:use-module (gnu packages image)
54 #:use-module (gnu packages java)
55 #:use-module (gnu packages machine-learning)
56 #:use-module (gnu packages maths)
57 #:use-module (gnu packages multiprecision)
58 #:use-module (gnu packages pcre)
59 #:use-module (gnu packages perl)
60 #:use-module (gnu packages pkg-config)
61 #:use-module (gnu packages python)
62 #:use-module (gnu packages readline)
63 #:use-module (gnu packages ssh)
64 #:use-module (gnu packages tcl)
65 #:use-module (gnu packages texinfo)
66 #:use-module (gnu packages time)
67 #:use-module (gnu packages tls)
68 #:use-module (gnu packages base)
69 #:use-module (gnu packages web)
70 #:use-module (gnu packages xml)
71 #:use-module (gnu packages xorg)
72 #:use-module (srfi srfi-1))
82 (uri (string-append "mirror://gnu/pspp/pspp-"
86 "1r8smr5057993h90nx0mdnff8nxw9x546zzh6qpy4h3xblp1la5s"))))
87 (build-system gnu-build-system)
90 ("gettext" ,gettext-minimal)
94 ("readline" ,readline)
96 ("gtksourceview" ,gtksourceview)
99 `(("glib" ,glib "bin") ;for glib-genmarshal
101 ("pkg-config" ,pkg-config)))
102 (home-page "https://www.gnu.org/software/pspp/")
103 (synopsis "Statistical analysis")
105 "GNU PSPP is a statistical analysis program. It can perform
106 descriptive statistics, T-tests, linear regression and non-parametric tests.
107 It features both a graphical interface as well as command-line input. PSPP
108 is designed to interoperate with Gnumeric, LibreOffice and OpenOffice. Data
109 can be imported from spreadsheets, text files and database sources and it can
110 be output in text, PostScript, PDF or HTML.")
111 (license license:gpl3+)))
113 ;; Update this package together with the set of recommended packages: r-boot,
114 ;; r-class, r-cluster, r-codetools, r-foreign, r-kernsmooth, r-lattice,
115 ;; r-mass, r-matrix, r-mgcv, r-nlme, r-nnet, r-rpart, r-spatial, r-survival.
118 (name "r-with-tests")
122 (uri (string-append "mirror://cran/src/base/R-"
123 (version-major version) "/R-"
127 "0w38865laqg28cdhikxdxhx4rfp0kgcn72gakwypsy91br9ja5zx"))))
128 (build-system gnu-build-system)
130 `(#:disallowed-references (,tzdata-for-tests)
132 (list (string-append "LDFLAGS=-Wl,-rpath="
133 (assoc-ref %outputs "out")
135 ;; This affects the embedded timestamp of only the core packages.
136 "PKG_BUILT_STAMP=1970-01-01")
138 (modify-phases %standard-phases
139 (add-before 'configure 'do-not-compress-serialized-files
140 (lambda* (#:key inputs #:allow-other-keys)
141 ;; This ensures that Guix can detect embedded store references;
142 ;; see bug #28157 for details.
143 (substitute* "src/library/base/makebasedb.R"
144 (("compress = TRUE") "compress = FALSE"))
146 (add-before 'configure 'patch-uname
147 (lambda* (#:key inputs #:allow-other-keys)
148 (let ((uname-bin (string-append (assoc-ref inputs "coreutils")
150 (substitute* "src/scripts/R.sh.in"
151 (("uname") uname-bin)))
153 (add-after 'unpack 'build-reproducibly
155 ;; The documentation contains time stamps to demonstrate
156 ;; documentation generation in different phases.
157 (substitute* "src/library/tools/man/Rd2HTML.Rd"
158 (("\\\\%Y-\\\\%m-\\\\%d at \\\\%H:\\\\%M:\\\\%S")
159 "(removed for reproducibility)"))
161 ;; Remove timestamp from tracing environment. This fixes
162 ;; reproducibility of "methods.rd{b,x}".
163 (substitute* "src/library/methods/R/trace.R"
164 (("dateCreated = Sys.time\\(\\)")
165 "dateCreated = as.POSIXct(\"1970-1-1 00:00:00\", tz = \"UTC\")"))
167 ;; Ensure that gzipped files are reproducible.
168 (substitute* '("src/library/grDevices/Makefile.in"
169 "doc/manual/Makefile.in")
170 (("R_GZIPCMD\\)" line)
171 (string-append line " -n")))
173 ;; The "srcfile" procedure in "src/library/base/R/srcfile.R"
174 ;; queries the mtime of a given file and records it in an object.
175 ;; This is acceptable at runtime to detect stale source files,
176 ;; but it destroys reproducibility at build time.
178 ;; Similarly, the "srcfilecopy" procedure records the current
179 ;; time. We change both of them to respect SOURCE_DATE_EPOCH.
180 (substitute* "src/library/base/R/srcfile.R"
181 (("timestamp <- (timestamp.*|file.mtime.*)" _ time)
182 (string-append "timestamp <- \
183 as.POSIXct(if (\"\" != Sys.getenv(\"SOURCE_DATE_EPOCH\")) {\
184 as.numeric(Sys.getenv(\"SOURCE_DATE_EPOCH\"))\
185 } else { " time "}, origin=\"1970-01-01\")\n")))
187 ;; This library is installed using "install_package_description",
188 ;; so we need to pass the "builtStamp" argument.
189 (substitute* "src/library/tools/Makefile.in"
190 (("(install_package_description\\(.*\"')\\)\"" line prefix)
191 (string-append prefix ", builtStamp='1970-01-01')\"")))
193 ;; R bundles an older version of help2man, which does not respect
194 ;; SOURCE_DATE_EPOCH. We cannot just use the latest help2man,
195 ;; because that breaks a test.
196 (with-fluids ((%default-port-encoding "ISO-8859-1"))
197 (substitute* "tools/help2man.pl"
198 (("my \\$date = strftime \"%B %Y\", localtime" line)
199 (string-append line " 1"))))
201 (add-before 'configure 'set-default-pager
202 ;; Set default pager to "cat", because otherwise it is "false",
203 ;; making "help()" print nothing at all.
204 (lambda _ (setenv "PAGER" "cat") #t))
205 (add-before 'check 'set-timezone
206 ;; Some tests require the timezone to be set. However, the
207 ;; timezone may not just be "UTC", or else a brittle regression
208 ;; test in reg-tests-1d will fail.
209 (lambda* (#:key inputs #:allow-other-keys)
210 (setenv "TZ" "UTC+1")
212 (string-append (assoc-ref inputs "tzdata")
215 (add-after 'build 'make-info
216 (lambda _ (zero? (system* "make" "info"))))
217 (add-after 'build 'install-info
218 (lambda _ (zero? (system* "make" "install-info")))))
220 `(;; We build the recommended packages here, because they are needed in
221 ;; order to run the test suite. We disable them in the r-minimal
224 "--with-blas=-lopenblas"
230 ,(string-append "--with-tcl-config="
231 (assoc-ref %build-inputs "tcl")
233 ,(string-append "--with-tk-config="
234 (assoc-ref %build-inputs "tk")
237 "--enable-BLAS-shlib"
238 "--with-system-tre")))
239 ;; R has some support for Java. When the JDK is available at configure
240 ;; time environment variables pointing to the JDK will be recorded under
241 ;; $R_HOME/etc and ./tools/getsp.java will be compiled which is used by "R
242 ;; CMD javareconf". "R CMD javareconf" appears to only be used to update
243 ;; the recorded environment variables in $R_HOME/etc. Refer to
244 ;; https://cran.r-project.org/doc/manuals/r-release/R-admin.html#Java-support
245 ;; for additional information.
247 ;; As the JDK is a rather large input with only very limited effects on R,
248 ;; we decided to drop it.
252 ("pkg-config" ,pkg-config)
253 ("texinfo" ,texinfo) ; for building HTML manuals
254 ("tzdata" ,tzdata-for-tests)
257 `(;; We need not only cairo here, but pango to ensure that tests for the
258 ;; "cairo" bitmapType plotting backend succeed.
260 ("coreutils" ,coreutils)
262 ("openblas" ,openblas)
263 ("gfortran" ,gfortran)
270 ("readline" ,readline)
271 ;; This avoids a reference to the ungraftable static bash. R uses the
272 ;; detected shell for the "system" procedure.
273 ("bash" ,bash-minimal)
279 (list (search-path-specification
280 (variable "R_LIBS_SITE")
281 (files (list "site-library/")))))
282 (home-page "https://www.r-project.org/")
283 (synopsis "Environment for statistical computing and graphics")
285 "R is a language and environment for statistical computing and graphics.
286 It provides a variety of statistical techniques, such as linear and nonlinear
287 modeling, classical statistical tests, time-series analysis, classification
288 and clustering. It also provides robust support for producing
289 publication-quality data plots. A large amount of 3rd-party packages are
290 available, greatly increasing its breadth and scope.")
291 (license license:gpl3+)))
293 (define-public r-minimal
294 (package (inherit r-with-tests)
298 ,@(substitute-keyword-arguments (package-arguments r-with-tests)
299 ((#:configure-flags flags)
300 ;; Do not build the recommended packages. The build system creates
301 ;; random temporary directories and embeds their names in some
302 ;; package files. We build these packages with the r-build-system
304 `(cons "--without-recommended-packages" ,flags)))))))
306 (define-public rmath-standalone
307 (package (inherit r-minimal)
308 (name "rmath-standalone")
311 (modify-phases %standard-phases
312 (add-after 'configure 'chdir
313 (lambda _ (chdir "src/nmath/standalone/") #t)))))
314 (synopsis "Standalone R math library")
316 "This package provides the R math library as an independent package.")))
318 (define-public r-boot
325 (uri (cran-uri "boot" version))
328 "0ai1qpm0p4z07xr0dvag8sdn9jrxcwanrsk9khzmww094jvr1jxd"))))
329 (build-system r-build-system)
330 (home-page "https://cran.r-project.org/web/packages/boot")
331 (synopsis "Bootstrap functions for R")
333 "This package provides functions and datasets for bootstrapping from the
334 book \"Bootstrap Methods and Their Application\" by A.C. Davison and
335 D.V. Hinkley (1997, CUP), originally written by Angelo Canty for S.")
336 ;; Unlimited distribution
337 (license (license:non-copyleft "file://R/bootfuns.q"))))
339 (define-public r-mass
346 (uri (cran-uri "MASS" version))
349 "16hasv9k4n773jsyzvh8s3gbga49hwdj8n5hxij6zqisy4i0kxq6"))))
350 (properties `((upstream-name . "MASS")))
351 (build-system r-build-system)
352 (home-page "http://www.stats.ox.ac.uk/pub/MASS4/")
353 (synopsis "Support functions and datasets for Venables and Ripley's MASS")
355 "This package provides functions and datasets for the book \"Modern
356 Applied Statistics with S\" (4th edition, 2002) by Venables and Ripley.")
357 ;; Either version may be picked.
358 (license (list license:gpl2 license:gpl3))))
360 (define-public r-class
367 (uri (cran-uri "class" version))
370 "173b8a16lh1i0zjmr784l0xr0azp9v8bgslh12hfdswbq7dpdf0q"))))
371 (build-system r-build-system)
373 `(("r-mass" ,r-mass)))
374 (home-page "http://www.stats.ox.ac.uk/pub/MASS4/")
375 (synopsis "R functions for classification")
377 "This package provides various functions for classification, including
378 k-nearest neighbour, Learning Vector Quantization and Self-Organizing Maps.")
379 ;; Either of the two versions can be picked.
380 (license (list license:gpl2 license:gpl3))))
382 (define-public r-cluster
389 (uri (cran-uri "cluster" version))
392 "1grxbifbc4nwig25dmjgkympnbzb4al0w6k1c0ibdhpk1h4l20di"))))
393 (build-system r-build-system)
395 `(("gfortran" ,gfortran)))
396 (home-page "https://cran.r-project.org/web/packages/cluster")
397 (synopsis "Methods for cluster analysis")
399 "This package provides methods for cluster analysis. It is a much
400 extended version of the original from Peter Rousseeuw, Anja Struyf and Mia
401 Hubert, based on Kaufman and Rousseeuw (1990) \"Finding Groups in Data\".")
402 (license license:gpl2+)))
404 (define-public r-codetools
411 (uri (cran-uri "codetools" version))
414 "0h7sjmvvsi35041jp47cxhsqzgf1y8jrw6fxii7n26i8g7nrh1sf"))))
415 (build-system r-build-system)
416 (home-page "https://cran.r-project.org/web/packages/codetools")
417 (synopsis "Code analysis tools for R")
418 (description "This package provides code analysis tools for R to check R
419 code for possible problems.")
420 ;; Any version of the GPL.
421 (license (list license:gpl2+ license:gpl3+))))
423 (define-public r-foreign
430 (uri (cran-uri "foreign" version))
433 "1mv04w3ycz0ymsszn8aa87k6k5sb8mg8lhf1b8w4zpfrphpkkliv"))))
434 (build-system r-build-system)
435 (home-page "https://cran.r-project.org/web/packages/foreign")
436 (synopsis "Read data stored by other statistics software")
438 "This package provides functions for reading and writing data stored by
439 some versions of Epi Info, Minitab, S, SAS, SPSS, Stata, Systat and Weka and
440 for reading and writing some dBase files.")
441 (license license:gpl2+)))
443 (define-public r-kernsmooth
445 (name "r-kernsmooth")
450 (uri (cran-uri "KernSmooth" version))
453 "1xhha8kw10jv8pv8b61hb5in9qiw3r2a9kdji3qlm991s4zd4wlb"))))
454 (properties `((upstream-name . "KernSmooth")))
455 (build-system r-build-system)
457 `(("gfortran" ,gfortran)))
458 (home-page "https://cran.r-project.org/web/packages/KernSmooth")
459 (synopsis "Functions for kernel smoothing")
461 "This package provides functions for kernel smoothing (and density
462 estimation) corresponding to the book: Wand, M.P. and Jones, M.C. (1995)
463 \"Kernel Smoothing\".")
464 ;; Unlimited use and distribution
465 (license (license:non-copyleft "file://LICENCE.note"))))
467 (define-public r-lattice
473 (uri (cran-uri "lattice" version))
476 "0pcnmaz3lr62ly0dcy5hnnqxshc4yqd43hrvlz3almgc9l7sna88"))))
477 (build-system r-build-system)
478 (home-page "http://lattice.r-forge.r-project.org/")
479 (synopsis "High-level data visualization system")
481 "The lattice package provides a powerful and elegant high-level data
482 visualization system inspired by Trellis graphics, with an emphasis on
483 multivariate data. Lattice is sufficient for typical graphics needs, and is
484 also flexible enough to handle most nonstandard requirements.")
485 (license license:gpl2+)))
487 (define-public r-matrix
494 (uri (cran-uri "Matrix" version))
497 "15hknim84nj3f54vkchca5ac0c3ip15v1by18k5parmn8wsl19j9"))))
498 (properties `((upstream-name . "Matrix")))
499 (build-system r-build-system)
501 `(("r-lattice" ,r-lattice)))
502 (home-page "http://Matrix.R-forge.R-project.org/")
503 (synopsis "Sparse and dense matrix classes and methods")
505 "This package provides classes and methods for dense and sparse matrices
506 and operations on them using LAPACK and SuiteSparse.")
507 (license license:gpl2+)))
509 (define-public r-nlme
516 (uri (cran-uri "nlme" version))
519 "11vyxxc0n36vb8d8g02zr0402ymicvbifwdsqm7gy9iqqnwrn101"))))
520 (build-system r-build-system)
522 `(("r-lattice" ,r-lattice)))
524 `(("gfortran" ,gfortran)))
525 (home-page "https://cran.r-project.org/web/packages/nlme")
526 (synopsis "Linear and nonlinear mixed effects models")
528 "This package provides tools to fit and compare Gaussian linear and
529 nonlinear mixed-effects models.")
530 (license license:gpl2+)))
532 (define-public r-mgcv
539 (uri (cran-uri "mgcv" version))
542 "15b76m1f0hz8dbmj9shqvslihdx5b7c48vck9grj5xs1z2y45r9c"))))
543 (build-system r-build-system)
545 `(("r-matrix" ,r-matrix)
547 (home-page "https://cran.r-project.org/web/packages/mgcv")
548 (synopsis "Mixed generalised additive model computation")
550 "GAMs, GAMMs and other generalized ridge regression with multiple smoothing
551 parameter estimation by GCV, REML or UBRE/AIC. The library includes a
552 @code{gam()} function, a wide variety of smoothers, JAGS support and
553 distributions beyond the exponential family.")
554 (license license:gpl2+)))
556 (define-public r-nnet
563 (uri (cran-uri "nnet" version))
566 "17amqnw9dpap2w8ivx53hxha2xrm0drwfnj32li0xk41hlz548r7"))))
567 (build-system r-build-system)
568 (home-page "http://www.stats.ox.ac.uk/pub/MASS4/")
569 (synopsis "Feed-forward neural networks and multinomial log-linear models")
571 "This package provides functions for feed-forward neural networks with a
572 single hidden layer, and for multinomial log-linear models.")
573 (license (list license:gpl2+ license:gpl3+))))
575 (define-public r-rpart
582 (uri (cran-uri "rpart" version))
585 "0k29qx3k3pj5sgrpg0p47yd8i811rmdakaw57bigpq1449asc4cf"))))
586 (build-system r-build-system)
587 (home-page "https://cran.r-project.org/web/packages/rpart")
588 (synopsis "Recursive partitioning and regression trees")
590 "This package provides recursive partitioning functions for
591 classification, regression and survival trees.")
592 (license (list license:gpl2+ license:gpl3+))))
594 (define-public r-spatial
601 (uri (cran-uri "spatial" version))
604 "04aw8j533sn63ybyrf4hyhrqm4058vfcb7yhjy07kq92mk94hi32"))))
605 (build-system r-build-system)
606 (home-page "http://www.stats.ox.ac.uk/pub/MASS4/")
607 (synopsis "Functions for kriging and point pattern analysis")
609 "This package provides functions for kriging and point pattern
611 ;; Either version may be picked.
612 (license (list license:gpl2 license:gpl3))))
614 (define-public r-survival
621 (uri (cran-uri "survival" version))
624 "1bsxc2fir9pbvdzy9n474fkl7har606h9zhspp0z67wnjpp48g73"))))
625 (build-system r-build-system)
627 `(("r-matrix" ,r-matrix)))
628 (home-page "https://github.com/therneau/survival")
629 (synopsis "Survival analysis")
631 "This package contains the core survival analysis routines, including
632 definition of Surv objects, Kaplan-Meier and Aalen-Johansen (multi-state)
633 curves, Cox models, and parametric accelerated failure time models.")
634 (license license:lgpl2.0+)))
637 (package (inherit r-minimal)
640 (build-system trivial-build-system)
641 (arguments '(#:builder (begin (mkdir %output) #t)))
643 `(("r-minimal" ,r-minimal)
646 ("r-cluster" ,r-cluster)
647 ("r-codetools" ,r-codetools)
648 ("r-foreign" ,r-foreign)
649 ("r-kernsmooth" ,r-kernsmooth)
650 ("r-lattice" ,r-lattice)
652 ("r-matrix" ,r-matrix)
657 ("r-spatial" ,r-spatial)
658 ("r-survival" ,r-survival)))))
667 (uri (cran-uri "bit" version))
670 "0m7jrqzpa1pk8ixcl814x06jf96nlvvr16x6did6cfk4zghsrfjw"))))
671 (build-system r-build-system)
672 (home-page "http://ff.r-forge.r-project.org")
673 (synopsis "Class for vectors of 1-bit booleans")
675 "This package provides bitmapped vectors of booleans (no @code{NA}s),
676 coercion from and to logicals, integers and integer subscripts, fast boolean
677 operators and fast summary statistics. With @code{bit} class vectors of true
678 binary booleans, @code{TRUE} and @code{FALSE} can be stored with 1 bit only.")
679 (license license:gpl2)))
681 (define-public r-bit64
688 (uri (cran-uri "bit64" version))
691 "07znvz9vp1nz1y5ljng4qyskvm943cdbmy996s67560ijxzsm6kv"))))
692 (build-system r-build-system)
695 (home-page "http://ff.r-forge.r-project.org/")
696 (synopsis "S3 class for vectors of 64 bit integers")
698 "The bit64 package provides serializable S3 atomic 64 bit (signed)
699 integers that can be used in vectors, matrices, arrays and @code{data.frames}.
700 Methods are available for coercion from and to logicals, integers, doubles,
701 characters and factors as well as many elementwise and summary functions.
702 Many fast algorithmic operations such as @code{match} and @code{order} support
703 interactive data exploration and manipulation and optionally leverage
705 (license license:gpl2)))
707 (define-public r-dichromat
714 (uri (cran-uri "dichromat" version))
716 (base32 "1l8db1nk29ccqg3mkbafvfiw0775iq4gapysf88xq2zp6spiw59i"))))
717 (build-system r-build-system)
718 (home-page "https://cran.r-project.org/web/packages/dichromat")
719 (synopsis "Color schemes for dichromats")
721 "Dichromat collapses red-green or green-blue distinctions to simulate the
722 effects of different types of color-blindness.")
723 (license license:gpl2+)))
725 (define-public r-digest
732 (uri (cran-uri "digest" version))
734 (base32 "1lhs59pdjhpb63jyy98pi1shk9shw044k6vl0mvw0f40v08326ar"))))
735 (build-system r-build-system)
736 ;; Vignettes require r-knitr, which requires r-digest, so we have to
737 ;; disable them and the tests.
740 #:configure-flags (list "--no-build-vignettes")))
741 (home-page "http://dirk.eddelbuettel.com/code/digest.html")
742 (synopsis "Create cryptographic hash digests of R objects")
744 "This package contains an implementation of a function 'digest()' for the
745 creation of hash digests of arbitrary R objects (using the md5, sha-1,
746 sha-256, crc32, xxhash and murmurhash algorithms) permitting easy comparison
747 of R language objects, as well as a function 'hmac()' to create hash-based
748 message authentication code.
750 Please note that this package is not meant to be deployed for cryptographic
751 purposes for which more comprehensive (and widely tested) libraries such as
752 OpenSSL should be used.")
753 (license license:gpl2+)))
755 (define-public r-estimability
757 (name "r-estimability")
761 (uri (cran-uri "estimability" version))
764 "0cifdaa71spkcxl4db4z884jrya865sg3dhcv4isd8fnzg2pjcd3"))))
765 (build-system r-build-system)
766 (home-page "https://cran.r-project.org/web/packages/estimability")
767 (synopsis "Tools for assessing estimability of linear predictions")
768 (description "Provides tools for determining estimability of linear
769 functions of regression coefficients, and 'epredict' methods that handle
770 non-estimable cases correctly.")
771 (license license:gpl2+)))
773 (define-public r-pheatmap
780 (uri (cran-uri "pheatmap" version))
783 "1jzxs5hwbz3r0z2pp09i7fd14sndxnrbm3zibaac3kny4nzydzf7"))))
784 (build-system r-build-system)
786 `(("r-gtable" ,r-gtable)
787 ("r-rcolorbrewer" ,r-rcolorbrewer)
788 ("r-scales" ,r-scales)))
790 "https://cran.r-project.org/web/packages/pheatmap")
791 (synopsis "Pretty heatmaps")
793 "This package provides an implementation of heatmaps that offers more
794 control over dimensions and appearance.")
795 (license license:gpl2+)))
797 (define-public r-labeling
804 (uri (cran-uri "labeling" version))
806 (base32 "13sk7zrrrzry6ky1bp8mmnzcl9jhvkig8j4id9nny7z993mnk00d"))))
807 (build-system r-build-system)
808 (home-page "https://cran.r-project.org/web/packages/labeling")
809 (synopsis "Axis labeling algorithms")
810 (description "The labeling package provides a range of axis labeling
812 (license license:expat)))
814 (define-public r-magrittr
821 (uri (cran-uri "magrittr" version))
823 (base32 "1s1ar6rag8m277qcqmdp02gn4awn9bdj9ax0r8s32i59mm1mki05"))))
824 (build-system r-build-system)
825 (home-page "https://cran.r-project.org/web/packages/magrittr/index.html")
826 (synopsis "A forward-pipe operator for R")
828 "Magrittr provides a mechanism for chaining commands with a new
829 forward-pipe operator, %>%. This operator will forward a value, or the result
830 of an expression, into the next function call/expression. There is flexible
831 support for the type of right-hand side expressions. For more information,
832 see package vignette. To quote Rene Magritte, \"Ceci n'est pas un pipe.\"")
833 (license license:expat)))
835 (define-public r-munsell
842 (uri (cran-uri "munsell" version))
844 (base32 "16g1fzisbpqb15yh3pqf3iia4csppva5dnv1z88x9dg263xskwyh"))))
845 (build-system r-build-system)
847 `(("r-colorspace" ,r-colorspace)))
848 (home-page "https://cran.r-project.org/web/packages/munsell")
849 (synopsis "Munsell colour system")
851 "The Munsell package contains Functions for exploring and using the
852 Munsell colour system.")
853 (license license:expat)))
855 (define-public r-permute
862 (uri (cran-uri "permute" version))
865 "1w8wzk1fg9q7wvisnfp2js70dg0m9wi12gkdhpyngpbdcgssahd5"))))
866 (build-system r-build-system)
867 ;; Tests do not run correctly, but running them properly would entail a
868 ;; circular dependency with vegan.
869 (home-page "https://github.com/gavinsimpson/permute")
870 (synopsis "Functions for Generating Restricted Permutations of Data")
872 "This package provides a set of restricted permutation designs for freely
873 exchangeable, line transects (time series), spatial grid designs and permutation
874 of blocks (groups of samples). @code{permute} also allows split-plot designs,
875 in which the whole-plots or split-plots or both can be freely exchangeable.")
876 (license license:gpl2+)))
878 (define-public r-plyr
885 (uri (cran-uri "plyr" version))
887 (base32 "1igar5pcjqh0jyxv0z3jah8rz617vfa86vw0r5c7c031b7bj5db0"))))
888 (build-system r-build-system)
889 (native-inputs `(("r-rcpp" ,r-rcpp)))
890 (home-page "http://had.co.nz/plyr")
891 (synopsis "Tools for Splitting, Applying and Combining Data")
893 "Plyr is a set of tools that solves a common set of problems: you need to
894 break a big problem down into manageable pieces, operate on each piece and
895 then put all the pieces back together. For example, you might want to fit a
896 model to each spatial location or time point in your study, summarise data by
897 panels or collapse high-dimensional arrays to simpler summary statistics.")
898 (license license:expat)))
900 (define-public r-proto
907 (uri (cran-uri "proto" version))
909 (base32 "1l843p8vckjckdhgv37ngv47fga5jzy0n00pmipvp05nnaixk54j"))))
910 (build-system r-build-system)
911 (home-page "https://github.com/hadley/proto")
912 (synopsis "Prototype object-based programming")
914 "Proto is an object oriented system using object-based, also called
915 prototype-based, rather than class-based object oriented ideas.")
916 (license license:gpl2+)))
918 (define-public r-rcolorbrewer
920 (name "r-rcolorbrewer")
925 (uri (cran-uri "RColorBrewer" version))
927 (base32 "1pfcl8z1pnsssfaaz9dvdckyfnnc6rcq56dhislbf571hhg7isgk"))))
928 (build-system r-build-system)
929 (home-page "https://cran.r-project.org/web/packages/RColorBrewer")
930 (synopsis "ColorBrewer palettes")
932 "This package provides color schemes for maps (and other graphics)
933 designed by Cynthia Brewer as described at http://colorbrewer2.org")
934 ;; Includes code licensed under bsd-4
935 (license license:asl2.0)))
937 (define-public r-sendmailr
944 (uri (cran-uri "sendmailR" version))
947 "0z7ipywnzgkhfvl4zb2fjwl1xq7b5wib296vn9c9qgbndj6b1zh4"))))
948 (properties `((upstream-name . "sendmailR")))
949 (build-system r-build-system)
951 `(("r-base64enc" ,r-base64enc)))
953 "https://cran.r-project.org/web/packages/sendmailR")
954 (synopsis "Send email using R")
956 "This package contains a simple SMTP client which provides a portable
957 solution for sending email, including attachments, from within R.")
958 (license license:gpl2+)))
960 (define-public r-stringi
967 (uri (cran-uri "stringi" version))
970 "1y46xab7g1lsjmilp4hbl7pjad6pcxp66hdj8wnfdg9518h0lmq1"))))
971 (build-system r-build-system)
972 (inputs `(("icu4c" ,icu4c)))
973 (native-inputs `(("pkg-config" ,pkg-config)))
974 (home-page "http://stringi.rexamine.com/")
975 (synopsis "Character string processing facilities")
977 "This package allows for fast, correct, consistent, portable, as well as
978 convenient character string/text processing in every locale and any native
979 encoding. Owing to the use of the ICU library, the package provides R users
980 with platform-independent functions known to Java, Perl, Python, PHP, and Ruby
981 programmers. Among available features there are: pattern searching
982 (e.g. via regular expressions), random string generation, string collation,
983 transliteration, concatenation, date-time formatting and parsing, etc.")
984 (license license:bsd-3)))
986 (define-public r-stringr
993 (uri (cran-uri "stringr" version))
995 (base32 "0hq3ybz7clnifi5wdm2s6p2i0kzljdkv26blg6yphng472h8x2vs"))))
996 (build-system r-build-system)
999 ("r-magrittr" ,r-magrittr)
1000 ("r-stringi" ,r-stringi)))
1001 (home-page "https://github.com/hadley/stringr")
1002 (synopsis "Simple, consistent wrappers for common string operations")
1004 "Stringr is a consistent, simple and easy to use set of wrappers around
1005 the fantastic 'stringi' package. All function and argument names (and
1006 positions) are consistent, all functions deal with \"NA\"'s and zero length
1007 vectors in the same way, and the output from one function is easy to feed into
1008 the input of another.")
1009 (license license:gpl2+)))
1011 (define-public r-reshape2
1018 (uri (cran-uri "reshape2" version))
1020 (base32 "03ki5ka1dj208fc0dclbm0b4xp9d769pah2j9cs34l776p4r9zwa"))))
1021 (build-system r-build-system)
1023 `(("r-plyr" ,r-plyr)
1025 ("r-stringr" ,r-stringr)))
1026 (home-page "https://github.com/hadley/reshape")
1027 (synopsis "Flexibly reshape data: a reboot of the \"reshape\" package")
1029 "Reshape2 is an R library to flexibly restructure and aggregate data
1030 using just two functions: melt and dcast (or acast).")
1031 (license license:expat)))
1033 (define-public r-scales
1040 (uri (cran-uri "scales" version))
1042 (base32 "0353dkh3d7x78463c6ds80hcml59lrqwr8rlv82a8dnkxla4l7qc"))))
1043 (build-system r-build-system)
1045 `(("r-labeling" ,r-labeling)
1046 ("r-munsell" ,r-munsell)
1047 ("r-rcolorbrewer" ,r-rcolorbrewer)
1050 ("r-viridislite" ,r-viridislite)))
1051 (home-page "https://github.com/hadley/scales")
1052 (synopsis "Scale functions for visualization")
1054 "This package provides graphical scales that map data to aesthetics, and
1055 provides methods for automatically determining breaks and labels for axes and
1057 (license license:expat)))
1059 (define-public r-ggplot2
1066 (uri (cran-uri "ggplot2" version))
1068 (base32 "0kb977hizsvk3b1k3zr717q78bpmbabhl8cj9a3w717nkq1zas67"))))
1069 (build-system r-build-system)
1071 `(("r-digest" ,r-digest)
1072 ("r-gtable" ,r-gtable)
1074 ("r-lazyeval" ,r-lazyeval)
1077 ("r-tibble" ,r-tibble)
1078 ("r-reshape2" ,r-reshape2)
1079 ("r-rlang" ,r-rlang)
1080 ("r-scales" ,r-scales)
1081 ("r-svglite" ,r-svglite) ; Needed for 'ggsave'
1082 ("r-viridislite" ,r-viridislite)
1083 ("r-withr" ,r-withr)))
1084 (home-page "https://ggplot2.tidyverse.org")
1085 (synopsis "An implementation of the grammar of graphics")
1087 "Ggplot2 is an implementation of the grammar of graphics in R. It
1088 combines the advantages of both base and lattice graphics: conditioning and
1089 shared axes are handled automatically, and you can still build up a plot step
1090 by step from multiple data sources. It also implements a sophisticated
1091 multidimensional conditioning system and a consistent interface to map data to
1092 aesthetic attributes.")
1093 (license license:gpl2+)))
1095 (define-public r-ggdendro
1101 (uri (cran-uri "ggdendro" version))
1104 "1zzq1hxd0d1qa5hrzwfkdw6fzscpcafbwbpkrb62dm559y8awp0j"))))
1105 (build-system r-build-system)
1107 `(("r-ggplot2" ,r-ggplot2)
1109 ("r-knitr" ,r-knitr)))
1110 (home-page "https://github.com/andrie/ggdendro")
1111 (synopsis "Create Dendrograms and Tree Diagrams Using ggplot2")
1112 (description "This is a set of tools for dendrograms and tree plots using
1113 ggplot2. The ggplot2 philosophy is to clearly separate data from the
1114 presentation. Unfortunately the plot method for dendrograms plots directly
1115 to a plot device with out exposing the data. The ggdendro package resolves
1116 this by making available functions that extract the dendrogram plot data.
1117 The package provides implementations for tree, rpart, as well as diana and
1118 agnes cluster diagrams.")
1119 (license license:gpl2+)))
1121 (define-public r-gdtools
1128 (uri (cran-uri "gdtools" version))
1131 "122k9spymawfnfyksxyapwq9cigydy5nrjwhrwrhy3qkax3aycf6"))))
1132 (build-system r-build-system)
1134 `(("r-rcpp" ,r-rcpp)
1135 ("pkg-config" ,pkg-config)))
1140 `(("r-withr" ,r-withr)))
1141 (home-page "https://cran.r-project.org/web/packages/gdtools")
1142 (synopsis "Utilities for graphical rendering")
1144 "The @code{gdtools} package provides functionalities to get font metrics
1145 and to generate base64 encoded string from raster matrix.")
1146 (license license:gpl3)))
1148 (define-public r-svglite
1155 (uri (cran-uri "svglite" version))
1158 "1bws3lc4hlhln11zd7lalhiyc43yk6c6vrzy41fkxk1dkjazfx51"))))
1159 (build-system r-build-system)
1160 (native-inputs `(("r-rcpp" ,r-rcpp)))
1163 ("r-gdtools" ,r-gdtools)))
1164 (home-page "https://github.com/hadley/svglite")
1165 (synopsis "SVG graphics device")
1167 "@code{svglite} is a graphics device that produces clean
1168 @dfn{SVG} (Scalable Vector Graphics) output, suitable for use on the web, or
1169 hand editing. Compared to the built-in @code{svg()}, @code{svglite} is
1170 considerably faster, produces smaller files, and leaves text as is.")
1171 (license license:gpl2+)))
1173 (define-public r-assertthat
1175 (name "r-assertthat")
1179 (uri (cran-uri "assertthat" version))
1182 "1wp5znk3xy338x6hknppk702jn596yr735d9i7c3wabm3sdzfgnp"))))
1183 (build-system r-build-system)
1184 (home-page "https://github.com/hadley/assertthat")
1185 (synopsis "Easy pre and post assertions")
1187 "Assertthat is an extension to stopifnot() that makes it easy to declare
1188 the pre and post conditions that your code should satisfy, while also
1189 producing friendly error messages so that your users know what they've done
1191 (license license:gpl3+)))
1193 (define-public r-lazyeval
1199 (uri (cran-uri "lazyeval" version))
1202 "0q9zx78ncy2ffzrf9sh053069kd3w1xn1ss3gsbyf3y4jhza9cw3"))))
1203 (build-system r-build-system)
1204 (home-page "https://github.com/hadley/lazyeval")
1205 (synopsis "Lazy (non-standard) evaluation in R")
1207 "This package provides the tools necessary to do non-standard
1208 evaluation (NSE) in R.")
1209 (license license:gpl3+)))
1211 (define-public r-dbi
1217 (uri (cran-uri "DBI" version))
1220 "1x8wy2vg2gcgd9bww04qmf0dsn3kp0rfjd8q8j1r2x9zxccg25pz"))))
1221 (build-system r-build-system)
1222 (home-page "https://github.com/rstats-db/DBI")
1223 (synopsis "R database interface")
1225 "The DBI package provides a database interface (DBI) definition for
1226 communication between R and relational database management systems. All
1227 classes in this package are virtual and need to be extended by the various
1228 R/DBMS implementations.")
1229 (license license:lgpl2.0+)))
1234 (version "1.66.0-1")
1237 (uri (cran-uri "BH" version))
1240 "14kab6wp0c27d8x4jqyf065p4bj210s9b67c0bfsfjnp29aypn8p"))))
1241 (build-system r-build-system)
1242 (home-page "https://github.com/eddelbuettel/bh")
1243 (synopsis "R package providing subset of Boost headers")
1245 "This package aims to provide the most useful subset of Boost libraries
1246 for template use among CRAN packages.")
1247 (license license:boost1.0)))
1249 (define-public r-evaluate
1255 (uri (cran-uri "evaluate" version))
1258 "1k8vcd4vsgg0hf7kdz8rlqp1dx4ygvg35aj4n3ay50kdnpzhaj5h"))))
1259 (build-system r-build-system)
1261 `(("r-stringr" ,r-stringr)))
1262 (home-page "https://github.com/hadley/evaluate")
1263 (synopsis "Parsing and evaluation tools for R")
1265 "This package provides tools that allow you to recreate the parsing,
1266 evaluation and display of R code, with enough information that you can
1267 accurately recreate what happens at the command line. The tools can easily be
1268 adapted for other output formats, such as HTML or LaTeX.")
1269 (license license:gpl3+)))
1271 (define-public r-formatr
1277 (uri (cran-uri "formatR" version))
1280 "19sd23vgs4ac0fwlw40j3676k6mramb0ajlq8hdw23kjwdx1jk47"))))
1281 (build-system r-build-system)
1282 (home-page "http://yihui.name/formatR")
1283 (synopsis "Format R code automatically")
1285 "This package provides a function to format R source code. Spaces and
1286 indent will be added to the code automatically, and comments will be preserved
1287 under certain conditions, so that R code will be more human-readable and tidy.
1288 There is also a Shiny app as a user interface in this package.")
1289 (license license:gpl3+)))
1291 (define-public r-highr
1297 (uri (cran-uri "highr" version))
1300 "1dzknqk4x7iiiq1jkh9bqm5qcvs7mbqxbkn5955050payavabfya"))))
1301 (build-system r-build-system)
1302 (home-page "https://github.com/yihui/highr")
1303 (synopsis "Syntax highlighting for R source code")
1305 "This package provides syntax highlighting for R source code. Currently
1306 it supports LaTeX and HTML output. Source code of other languages is
1307 supported via Andre Simon's highlight package.")
1308 (license license:gpl3+)))
1310 (define-public r-mime
1316 (uri (cran-uri "mime" version))
1319 "0i91m3ivaja1k33jwcvz16pfjypkci27awm8glil7sxhmwaj3izw"))))
1320 (build-system r-build-system)
1321 (home-page "https://github.com/yihui/mime")
1322 (synopsis "R package to map filenames to MIME types")
1324 "This package guesses the MIME type from a filename extension using the
1325 data derived from /etc/mime.types in UNIX-type systems.")
1326 (license license:gpl2)))
1328 (define-public r-markdown
1334 (uri (cran-uri "markdown" version))
1337 "1vcgsh2m2f5kfgappgg71nbf04ff0j1sbk668krjs3r2n89dk3sk"))))
1338 (build-system r-build-system)
1339 ;; Skip check phase because the tests require the r-knitr package to be
1340 ;; installed. This prevents installation failures. Knitr normally
1341 ;; shouldn't be available since r-markdown is a dependency of the r-knitr
1343 (arguments `(#:tests? #f))
1345 `(("r-mime" ,r-mime)))
1346 (home-page "https://github.com/rstudio/markdown")
1347 (synopsis "Markdown rendering for R")
1349 "This package provides R bindings to the Sundown Markdown rendering
1350 library (https://github.com/vmg/sundown). Markdown is a plain-text formatting
1351 syntax that can be converted to XHTML or other formats.")
1352 (license license:gpl2)))
1354 (define-public r-yaml
1360 (uri (cran-uri "yaml" version))
1363 "0in562nd0i23cg91a8kdbqgim656fgscykwi0icsnq53xj3srg2m"))))
1364 (build-system r-build-system)
1365 (home-page "https://cran.r-project.org/web/packages/yaml/")
1366 (synopsis "Methods to convert R data to YAML and back")
1368 "This package implements the libyaml YAML 1.1 parser and
1369 emitter (http://pyyaml.org/wiki/LibYAML) for R.")
1370 (license license:bsd-3)))
1372 (define-public r-knitr
1378 (uri (cran-uri "knitr" version))
1381 "1408dm25cxahk2clff8hlajaqdj5v1gs40nm3q6rf0ghd82hj93v"))))
1382 (build-system r-build-system)
1384 `(("r-evaluate" ,r-evaluate)
1385 ("r-highr" ,r-highr)
1386 ("r-markdown" ,r-markdown)
1387 ("r-stringr" ,r-stringr)
1388 ("r-yaml" ,r-yaml)))
1389 (home-page "http://yihui.name/knitr/")
1390 (synopsis "General-purpose package for dynamic report generation in R")
1392 "This package provides a general-purpose tool for dynamic report
1393 generation in R using Literate Programming techniques.")
1394 ;; The code is released under any version of the GPL. As it is used by
1395 ;; r-markdown which is available under GPLv2 only, we have chosen GPLv2+
1397 (license license:gpl2+)))
1399 (define-public r-knitrbootstrap
1401 (name "r-knitrbootstrap")
1406 (uri (cran-uri "knitrBootstrap" version))
1409 "1aj60j7f0gcs120fdrnfbnb7vk7lfn1phil0mghg6a5zldz4cqs3"))))
1410 (properties `((upstream-name . "knitrBootstrap")))
1411 (build-system r-build-system)
1413 `(("r-knitr" ,r-knitr)
1414 ("r-rmarkdown" ,r-rmarkdown)
1415 ("r-markdown" ,r-markdown)))
1416 (home-page "https://github.com/jimhester/knitrBootstrap")
1417 (synopsis "Knitr bootstrap framework")
1419 "This package provides a framework to create Bootstrap 3 HTML reports
1420 from knitr Rmarkdown.")
1421 (license license:expat)))
1423 (define-public r-microbenchmark
1425 (name "r-microbenchmark")
1429 (uri (cran-uri "microbenchmark" version))
1432 "0fv2w2vsiz18imf4115nd9chhmf275w2mb49pn7pkxi6z3bamc9c"))))
1433 (build-system r-build-system)
1434 (home-page "https://cran.r-project.org/web/packages/microbenchmark/")
1435 (synopsis "Accurate timing functions for R")
1437 "This package provides infrastructure to accurately measure and compare
1438 the execution time of R expressions.")
1439 (license license:bsd-2)))
1441 (define-public r-pryr
1447 (uri (cran-uri "pryr" version))
1450 "06vj5xl9x37kbd3l5bw7sbgfdnp37spvrjrn976rxi04clqk966k"))))
1451 (build-system r-build-system)
1453 `(("r-stringr" ,r-stringr)
1454 ("r-codetools" ,r-codetools)))
1456 `(("r-rcpp" ,r-rcpp)))
1457 (home-page "https://github.com/hadley/pryr")
1458 (synopsis "Tools for computing on the R language")
1460 "This package provides useful tools to pry back the covers of R and
1461 understand the language at a deeper level.")
1462 (license license:gpl2)))
1464 (define-public r-memoise
1470 (uri (cran-uri "memoise" version))
1473 "034qfc2xlh30x1q2vya239w34a3ir3y2fwnx2agbgbi6592zjxmj"))))
1474 (build-system r-build-system)
1476 `(("r-digest" ,r-digest)))
1477 (home-page "https://github.com/hadley/memoise")
1478 (synopsis "Memoise functions for R")
1480 "This R package allows to cache the results of a function so that when
1481 you call it again with the same arguments it returns the pre-computed value.")
1482 (license license:expat)))
1484 (define-public r-crayon
1490 (uri (cran-uri "crayon" version))
1493 "0s7s6vc3ww8pzanpjisym4jjvwcc5pi2qg8srx7jqlz9j3wrnvpw"))))
1494 (build-system r-build-system)
1496 `(("r-memoise" ,r-memoise)))
1497 (home-page "https://github.com/gaborcsardi/crayon")
1498 (synopsis "Colored terminal output for R")
1500 "Colored terminal output on terminals that support ANSI color and
1501 highlight codes. It also works in Emacs ESS. ANSI color support is
1502 automatically detected. Colors and highlighting can be combined and nested.
1503 New styles can also be created easily. This package was inspired by the
1504 \"chalk\" JavaScript project.")
1505 (license license:expat)))
1507 (define-public r-praise
1514 (uri (cran-uri "praise" version))
1517 "1gfyypnvmih97p2r0php9qa39grzqpsdbq5g0fdsbpq5zms5w0sw"))))
1518 (build-system r-build-system)
1519 (home-page "https://github.com/gaborcsardi/praise")
1520 (synopsis "Functions to praise users")
1522 "This package provides template functions to assist in building friendly
1523 R packages that praise their users.")
1524 (license license:expat)))
1526 (define-public r-testthat
1532 (uri (cran-uri "testthat" version))
1535 "155l53kb69jga5d8c5nvdwqlvlgfmk4vzyyl4d0108j53jnlgh1v"))))
1536 (build-system r-build-system)
1539 ("r-crayon" ,r-crayon)
1540 ("r-digest" ,r-digest)
1541 ("r-magrittr" ,r-magrittr)
1542 ("r-praise" ,r-praise)
1544 ("r-rlang" ,r-rlang)
1545 ("r-withr" ,r-withr)))
1546 (home-page "https://github.com/hadley/testthat")
1547 (synopsis "Unit testing for R")
1549 "This package provides a unit testing system for R designed to be fun,
1550 flexible and easy to set up.")
1551 (license license:expat)))
1559 (uri (cran-uri "R6" version))
1562 "13xfdr19ca7ymisidsanm6w7hsk3qmy5l8c0mlz3nk48f7s5cxq8"))))
1563 (build-system r-build-system)
1564 (home-page "https://github.com/wch/R6/")
1565 (synopsis "Classes with reference semantics in R")
1567 "The R6 package allows the creation of classes with reference semantics,
1568 similar to R's built-in reference classes. Compared to reference classes, R6
1569 classes are simpler and lighter-weight, and they are not built on S4 classes
1570 so they do not require the methods package. These classes allow public and
1571 private members, and they support inheritance, even when the classes are
1572 defined in different packages.")
1573 (license license:expat)))
1575 (define-public r-rlang
1581 (uri (cran-uri "rlang" version))
1584 "0cqd894wzi53rs53prg0j7i75h0yzgi0127fzjqbdbhczwh984f9"))))
1585 (build-system r-build-system)
1586 (home-page "http://rlang.tidyverse.org")
1587 (synopsis "Functions for base types, core R and Tidyverse features")
1588 (description "This package provides a toolbox for working with base types,
1589 core R features like the condition system, and core @code{Tidyverse} features
1590 like tidy evaluation.")
1591 (license license:gpl3)))
1593 (define-public r-tibble
1600 (uri (cran-uri "tibble" version))
1603 "05svbjkm1xqv56ybjgsqqg2pp8nn6hams1yxcr8aanbhzx9h6rqi"))))
1604 (build-system r-build-system)
1606 `(("r-rlang" ,r-rlang)
1608 ("r-crayon" ,r-crayon)
1609 ("r-pillar" ,r-pillar)))
1610 (home-page "https://github.com/hadley/tibble")
1611 (synopsis "Simple data frames")
1613 "This package provides a @code{tbl_df} class that offers better checking
1614 and printing capabilities than traditional data frames.")
1615 (license license:expat)))
1617 (define-public r-dplyr
1623 (uri (cran-uri "dplyr" version))
1626 "0c43h13s5mr0fklikbbm89gs6z5n66rkjzdv6w3w6kl5af5wr2fl"))))
1627 (build-system r-build-system)
1629 `(("r-assertthat" ,r-assertthat)
1631 ("r-magrittr" ,r-magrittr)
1632 ("r-rlang" ,r-rlang)
1633 ("r-plogr" ,r-plogr)
1635 ("r-pkgconfig" ,r-pkgconfig)
1636 ("r-bindrcpp" ,r-bindrcpp)
1637 ("r-tibble" ,r-tibble)
1638 ("r-tidyselect" ,r-tidyselect)))
1640 `(("r-rcpp" ,r-rcpp)
1642 (home-page "https://github.com/hadley/dplyr")
1643 (synopsis "Tools for working with data frames in R")
1645 "dplyr is the next iteration of plyr. It is focussed on tools for
1646 working with data frames. It has three main goals: 1) identify the most
1647 important data manipulation tools needed for data analysis and make them easy
1648 to use in R; 2) provide fast performance for in-memory data by writing key
1649 pieces of code in C++; 3) use the same code interface to work with data no
1650 matter where it is stored, whether in a data frame, a data table or
1652 (license license:expat)))
1654 (define-public r-dbplyr
1661 (uri (cran-uri "dbplyr" version))
1664 "0j5w6a1qim972kv4vmvinp3j50yr4idmm9cd3w7y3zsz0nq0nhcx"))))
1665 (build-system r-build-system)
1667 `(("r-assertthat" ,r-assertthat)
1669 ("r-dplyr" ,r-dplyr)
1671 ("r-purrr" ,r-purrr)
1673 ("r-rlang" ,r-rlang)
1674 ("r-tibble" ,r-tibble)
1675 ("r-tidyselect" ,r-tidyselect)))
1676 (home-page "https://github.com/tidyverse/dbplyr")
1677 (synopsis "Dplyr back end for databases")
1679 "This package provides a dplyr back end for databases that allows you to
1680 work with remote database tables as if they are in-memory data frames. Basic
1681 features works with any database that has a @code{DBI} back end; more advanced
1682 features require SQL translation to be provided by the package author.")
1683 (license license:expat)))
1685 (define-public r-acepack
1692 (uri (cran-uri "acepack" version))
1695 "1f98rpfjmhd92rdc3j004plyfpjailz6j0ycysbac0kgj83haxc2"))))
1696 (build-system r-build-system)
1698 `(("gfortran" ,gfortran)))
1699 (home-page "https://cran.r-project.org/web/packages/acepack")
1700 (synopsis "Functions for regression transformations")
1702 "This package provides ACE and AVAS methods for choosing regression
1704 (license license:expat)))
1706 (define-public r-formula
1713 (uri (cran-uri "Formula" version))
1716 "0wiqh8rr9d5ciy80wj8f5fnmiiw0ywanvvnhkwd622dx42dk848l"))))
1717 (properties `((upstream-name . "Formula")))
1718 (build-system r-build-system)
1719 (home-page "https://cran.r-project.org/web/packages/Formula")
1720 (synopsis "Extended model formulas")
1722 "This package provides a new class @code{Formula}, which extends the base
1723 class @code{formula}. It supports extended formulas with multiple parts of
1724 regressors on the right-hand side and/or multiple responses on the left-hand
1726 (license (list license:gpl2+ license:gpl3+))))
1728 (define-public r-locfit
1735 (uri (cran-uri "locfit" version))
1738 "0lafrmq1q7x026m92h01hc9cjjiximqqi3v1g2hw7ai9vf7i897m"))))
1739 (build-system r-build-system)
1741 `(("r-lattice" ,r-lattice)))
1742 (home-page "https://cran.r-project.org/web/packages/locfit")
1743 (synopsis "Local regression, likelihood and density estimation")
1745 "This package provides functions used for local regression, likelihood
1746 and density estimation.")
1747 (license (list license:gpl2+ license:gpl3+))))
1749 (define-public r-chron
1755 (uri (cran-uri "chron" version))
1758 "185lfp75cv3l4cavg64sccj8lgc5sivch13n6gkannv3pd5cyzy4"))))
1759 (build-system r-build-system)
1760 (home-page "https://cran.r-project.org/web/packages/chron")
1761 (synopsis "Chronological R objects which can handle dates and times")
1763 "This package provides chronological R objects which can handle dates and
1765 (license license:gpl2)))
1767 (define-public r-data-table
1769 (name "r-data-table")
1773 (uri (cran-uri "data.table" version))
1776 "1mc1drqj5i5ar2za3nkh5j70y37s7z7xwqri2r2b72zkqggg3k7x"))))
1777 (build-system r-build-system)
1778 (home-page "https://github.com/Rdatatable/data.table/wiki")
1779 (synopsis "Enhanced version of data.frame R object")
1781 "The R package @code{data.table} is an extension of @code{data.frame}
1782 providing functions for fast aggregation of large data (e.g. 100GB in RAM),
1783 fast ordered joins, fast add/modify/delete of columns by group, column listing
1784 and fast file reading.")
1785 (license license:gpl3+)))
1787 (define-public r-xtable
1794 (uri (cran-uri "xtable" version))
1797 "09f311gq9g7dzf8jdvcx72j11xb7p00jlg066jjbpa6pz3zv1cjk"))))
1798 (build-system r-build-system)
1800 `(("r-knitr" ,r-knitr))) ; for vignettes
1801 (home-page "http://xtable.r-forge.r-project.org/")
1802 (synopsis "Export R tables to LaTeX or HTML")
1804 "This package provides tools to export R data as LaTeX and HTML tables.")
1805 (license license:gpl2+)))
1807 (define-public python-patsy
1809 (name "python-patsy")
1813 (uri (pypi-uri "patsy" version ".zip"))
1816 "1m6knyq8hbqlx242y4da02j0x86j4qggs1j7q186w3jv0j0c476w"))))
1817 (build-system python-build-system)
1820 (modify-phases %standard-phases
1822 (lambda _ (invoke "nosetests" "-v"))))))
1824 `(("python-numpy" ,python-numpy)
1825 ("python-scipy" ,python-scipy)
1826 ("python-six" ,python-six)))
1828 `(("python-nose" ,python-nose)
1830 (home-page "https://github.com/pydata/patsy")
1831 (synopsis "Describe statistical models and build design matrices")
1833 "Patsy is a Python package for describing statistical models and for
1834 building design matrices.")
1835 ;; The majority of the code is distributed under BSD-2. The module
1836 ;; patsy.compat contains code derived from the Python standard library,
1837 ;; and is covered by the PSFL.
1838 (license (list license:bsd-2 license:psfl))))
1840 (define-public python2-patsy
1841 (package-with-python2 python-patsy))
1843 (define-public python-statsmodels
1845 (name "python-statsmodels")
1850 (uri (pypi-uri "statsmodels" version))
1853 "0j30v3932shnj9368c9jr3svkyrvfj90h2l7nxnqkbpv0svilhr6"))))
1854 (build-system python-build-system)
1856 `(;; The test suite is very large and rather brittle. Tests often fail
1857 ;; because of minor changes in dependencies that upstream hasn't fixed
1858 ;; in a new release.
1861 (modify-phases %standard-phases
1862 (add-after 'unpack 'set-matplotlib-backend-to-agg
1864 ;; Set the matplotlib backend to Agg to avoid problems using the
1865 ;; GTK backend without a display.
1866 (substitute* (append (find-files "statsmodels/graphics/tests" "\\.py")
1867 '("statsmodels/tsa/vector_ar/tests/test_var.py"
1868 "statsmodels/duration/tests/test_survfunc.py"))
1869 (("import matplotlib\\.pyplot as plt" line)
1870 (string-append "import matplotlib;matplotlib.use('Agg');"
1873 ;; FIXME: This is a bug in version 0.8 since the upgrade to scipy 1.0.
1874 ;; See https://github.com/statsmodels/statsmodels/issues/3931
1875 ;; This has been fixed in version 0.9.
1876 (add-after 'unpack 'patch-for-scipy
1878 (substitute* "statsmodels/discrete/discrete_model.py"
1879 (("return stats.chisqprob" match)
1881 "stats.chisqprob = lambda chisq, df: stats.chi2.sf(chisq, df);"
1885 `(("python-numpy" ,python-numpy)
1886 ("python-scipy" ,python-scipy)
1887 ("python-pandas" ,python-pandas)
1888 ("python-patsy" ,python-patsy)
1889 ("python-matplotlib" ,python-matplotlib)))
1891 `(("python-cython" ,python-cython)
1892 ("python-nose" ,python-nose)
1893 ("python-sphinx" ,python-sphinx)))
1894 (home-page "http://statsmodels.sourceforge.net/")
1895 (synopsis "Statistical modeling and econometrics in Python")
1897 "Statsmodels is a Python package that provides a complement to scipy for
1898 statistical computations including descriptive statistics and estimation and
1899 inference for statistical models.")
1900 (license license:bsd-3)))
1902 (define-public python2-statsmodels
1903 (let ((stats (package-with-python2 python-statsmodels)))
1904 (package (inherit stats)
1906 `(("python2-pytz" ,python2-pytz)
1907 ("python2-numpy" ,python2-numpy)
1908 ("python2-scipy" ,python2-scipy)
1909 ("python2-pandas" ,python2-pandas)
1910 ("python2-patsy" ,python2-patsy)
1911 ("python2-matplotlib" ,python2-matplotlib))))))
1913 (define-public r-coda
1919 (uri (cran-uri "coda" version))
1922 "14a4a8df4ygj05h37chmdn8kzcqs07fpbflxfrq530563mrza7yl"))))
1923 (build-system r-build-system)
1925 `(("r-lattice" ,r-lattice)))
1926 (home-page "https://cran.r-project.org/web/packages/coda")
1927 (synopsis "This is a package for Output Analysis and Diagnostics for MCMC")
1928 (description "This package provides functions for summarizing and plotting
1929 the output from Markov Chain Monte Carlo (MCMC) simulations, as well as
1930 diagnostic tests of convergence to the equilibrium distribution of the Markov
1932 (license license:gpl2+)))
1934 (define-public r-ade4
1941 (uri (cran-uri "ade4" version))
1944 "16z9jk4qj35ghsk4lwmq241dgc770y8a70dlmp9q4gz6d8ssgl7m"))))
1945 (build-system r-build-system)
1947 `(("r-mass" ,r-mass)))
1948 (home-page "http://pbil.univ-lyon1.fr/ADE-4")
1949 (synopsis "Multivariate data analysis and graphical display")
1951 "The ade4 package contains data analysis functions to analyze ecological
1952 and environmental data in the framework of Euclidean exploratory methods.")
1953 (license license:gpl2+)))
1955 (define-public r-xml2
1962 (uri (cran-uri "xml2" version))
1965 "154lmksfiwkhnlmryas25mjhfg6k4mmnnk7bbb29mnn5x5pr2yha"))))
1966 (build-system r-build-system)
1968 `(("libxml2" ,libxml2)
1971 `(("pkg-config" ,pkg-config)))
1973 `(("r-rcpp" ,r-rcpp)))
1974 (home-page "https://github.com/hadley/xml2")
1975 (synopsis "Parse XML with R")
1977 "This package provides a simple, consistent interface to working with XML
1978 files in R. It is built on top of the libxml2 C library.")
1979 (license license:gpl2+)))
1981 (define-public r-multitaper
1983 (name "r-multitaper")
1988 (uri (cran-uri "multitaper" version))
1991 "04wd9bbhyx7697pfy0fpj02v1csr48hkpqj62h9p8a6w84ji4k68"))))
1992 (build-system r-build-system)
1994 `(("gfortran" ,gfortran)))
1995 (home-page "https://github.com/wesleyburr/multitaper/")
1996 (synopsis "Multitaper spectral analysis tools")
1998 "This package implements multitaper spectral estimation
1999 techniques using prolate spheroidal sequences (Slepians) and sine
2000 tapers for time series analysis. It includes an adaptive weighted
2001 multitaper spectral estimate, a coherence estimate, Thomson's Harmonic
2002 F-test, and complex demodulation. The Slepians sequences are
2003 generated efficiently using a tridiagonal matrix solution, and
2004 jackknifed confidence intervals are available for most estimates.")
2005 (license license:gpl2+)))
2007 (define-public r-rversions
2009 (name "r-rversions")
2013 (uri (cran-uri "rversions" version))
2016 "0i2gi05nrvknr7g89rbppkswyfcwwd4r9gp75fdfhpah8sgq1l11"))))
2017 (build-system r-build-system)
2019 `(("r-curl" ,r-curl)
2020 ("r-xml2" ,r-xml2)))
2021 (home-page "https://github.com/metacran/rversions")
2022 (synopsis "Query R versions, including 'r-release' and 'r-oldrel'")
2024 "This package provides functions to query the main R repository to find
2025 the versions that @code{r-release} and @code{r-oldrel} refer to, and also all
2026 previous R versions and their release dates.")
2027 (license license:expat)))
2029 (define-public r-whisker
2035 (uri (cran-uri "whisker" version))
2038 "0z4cn115gxcl086d6bnqr8afi67b6a7xqg6ivmk3l4ng1x8kcj28"))))
2039 (build-system r-build-system)
2040 (home-page "https://github.com/edwindj/whisker")
2041 (synopsis "Logicless mustache templating for R")
2043 "This package provides logicless templating, with a syntax that is not
2045 (license license:gpl3+)))
2047 (define-public r-backports
2049 (name "r-backports")
2054 (uri (cran-uri "backports" version))
2057 "0mml9h3xagi7144pyb3jj9zbh9qzns7izkhdg7df20v7bikr6nz8"))))
2058 (build-system r-build-system)
2059 (home-page "https://cran.r-project.org/web/packages/backports")
2060 (synopsis "Reimplementations of functions introduced since R 3.0.0")
2062 "Provides implementations of functions which have been introduced in R
2063 since version 3.0.0. The backports are conditionally exported which results
2064 in R resolving the function names to the version shipped with R (if available)
2065 and uses the implemented backports as fallback. This way package developers
2066 can make use of the new functions without worrying about the minimum required
2068 (license license:gpl2+)))
2070 (define-public r-checkmate
2072 (name "r-checkmate")
2077 (uri (cran-uri "checkmate" version))
2080 "1q6igk50lq4fp5d3imgcn1j063h3gsp214ra4nlf534hf4wjlkg9"))))
2081 (build-system r-build-system)
2083 `(("r-backports" ,r-backports)))
2084 (home-page "https://github.com/mllg/checkmate")
2085 (synopsis "Fast and versatile argument checks")
2087 "This package provides tests and assertions to perform frequent argument
2088 checks. A substantial part of the package was written in C to minimize any
2089 worries about execution time overhead.")
2090 (license license:bsd-3)))
2092 (define-public r-bbmisc
2099 (uri (cran-uri "BBmisc" version))
2102 "1lh1n4bvxzivb5rbz69mvd8xdgr3gr2bnqd68a39sd1530l8r90y"))))
2103 (properties `((upstream-name . "BBmisc")))
2104 (build-system r-build-system)
2106 `(("r-checkmate" ,r-checkmate)))
2107 (home-page "https://github.com/berndbischl/BBmisc")
2108 (synopsis "Miscellaneous functions for R package development")
2110 "This package provides miscellaneous helper functions for the development
2112 (license license:bsd-3)))
2114 (define-public r-fail
2121 (uri (cran-uri "fail" version))
2124 "0vfm6kmpmgsamda5p0sl771kbnsscan31l2chzssyw93kwmams7d"))))
2125 (build-system r-build-system)
2127 `(("r-bbmisc" ,r-bbmisc)
2128 ("r-checkmate" ,r-checkmate)))
2129 (home-page "https://github.com/mllg/fail")
2130 (synopsis "File abstraction interface layer (FAIL)")
2132 "This package provides a more comfortable interface to work with R data
2133 or source files in a key-value fashion.")
2134 (license license:bsd-3)))
2136 (define-public r-batchjobs
2138 (name "r-batchjobs")
2143 (uri (cran-uri "BatchJobs" version))
2146 "035658marnw57p4f38g99rwmvmb6hpbq0fhlxp3qbw22zfnnkvs9"))))
2147 (properties `((upstream-name . "BatchJobs")))
2148 (build-system r-build-system)
2150 `(("r-backports" ,r-backports)
2151 ("r-bbmisc" ,r-bbmisc)
2153 ("r-checkmate" ,r-checkmate)
2154 ("r-data-table" ,r-data-table)
2156 ("r-digest" ,r-digest)
2157 ("r-rsqlite" ,r-rsqlite)
2158 ("r-sendmailr" ,r-sendmailr)
2159 ("r-stringi" ,r-stringi)))
2160 (home-page "https://github.com/tudo-r/BatchJobs")
2161 (synopsis "Batch computing with R")
2163 "This package provides @code{Map}, @code{Reduce} and @code{Filter}
2164 variants to generate jobs on batch computing systems like PBS/Torque, LSF,
2165 SLURM and Sun Grid Engine. Multicore and SSH systems are also supported.")
2166 (license license:bsd-2)))
2168 (define-public r-brew
2174 (uri (cran-uri "brew" version))
2177 "1vghazbcha8gvkwwcdagjvzx6yl8zm7kgr0i9wxr4jng06d1l3fp"))))
2178 (build-system r-build-system)
2179 (home-page "https://cran.r-project.org/web/packages/brew")
2180 (synopsis "Templating framework for report generation")
2182 "The brew package implements a templating framework for mixing text and R
2183 code for report generation. The template syntax is similar to PHP, Ruby's erb
2184 module, Java Server Pages, and Python's psp module.")
2185 (license license:gpl2+)))
2187 (define-public r-desc
2194 (uri (cran-uri "desc" version))
2197 "1s6s13fk6sxwcj8wzkwxl9vr33153xx11p5wi9avqx3rzkabavz6"))))
2198 (build-system r-build-system)
2200 `(("r-assertthat" ,r-assertthat)
2201 ("r-crayon" ,r-crayon)
2203 ("r-rprojroot" ,r-rprojroot)))
2204 (home-page "https://github.com/r-pkgs/desc")
2205 (synopsis "Manipulate DESCRIPTION Files")
2207 "This package provides tools to read, write, create, and manipulate
2208 DESCRIPTION files. It is intended for packages that create or manipulate
2210 (license license:expat)))
2212 (define-public r-commonmark
2214 (name "r-commonmark")
2219 (uri (cran-uri "commonmark" version))
2222 "1jwx5rgm0ypd9a3v4jd9za4a644rdzhk1n4dvmgkj9hdpwsida3z"))))
2223 (build-system r-build-system)
2224 (home-page "https://cran.r-project.org/web/packages/commonmark")
2225 (synopsis "CommonMark and Github Markdown Rendering in R")
2227 "The CommonMark specification defines a rationalized version of markdown
2228 syntax. This package uses the 'cmark' reference implementation for converting
2229 markdown text into various formats including HTML, LaTeX and groff man. In
2230 addition, it exposes the markdown parse tree in XML format. The latest
2231 version of this package also adds support for Github extensions including
2232 tables, autolinks and strikethrough text.")
2233 (license license:bsd-2)))
2235 (define-public r-roxygen2
2241 (uri (cran-uri "roxygen2" version))
2244 "0xpzziminf225kjwhyl51kgkzhplyzhk5farhf5s822krl2xqbfj"))))
2245 (build-system r-build-system)
2247 `(("r-brew" ,r-brew)
2248 ("r-commonmark" ,r-commonmark)
2250 ("r-digest" ,r-digest)
2253 ("r-stringi" ,r-stringi)
2254 ("r-stringr" ,r-stringr)
2255 ("r-xml2" ,r-xml2)))
2256 (home-page "https://github.com/klutometis/roxygen")
2257 (synopsis "In-source documentation system for R")
2259 "Roxygen2 is a Doxygen-like in-source documentation system for Rd,
2260 collation, and NAMESPACE files.")
2261 (license license:gpl2+)))
2263 (define-public r-openssl
2270 (uri (cran-uri "openssl" version))
2273 "1djfpnphkcxx8idk5rjfzg8r8dnqsgc0shh2pw8lns5hap2wc5rc"))))
2274 (build-system r-build-system)
2276 `(("libressl" ,libressl)))
2277 (home-page "https://github.com/jeroenooms/openssl")
2278 (synopsis "Toolkit for encryption, signatures and certificates")
2280 "This package provides R bindings to OpenSSL libssl and libcrypto, plus
2281 custom SSH pubkey parsers. It supports RSA, DSA and NIST curves P-256, P-384
2282 and P-521. Cryptographic signatures can either be created and verified
2283 manually or via x509 certificates. AES block cipher is used in CBC mode for
2284 symmetric encryption; RSA for asymmetric (public key) encryption. High-level
2285 envelope functions combine RSA and AES for encrypting arbitrary sized data.
2286 Other utilities include key generators, hash functions (md5, sha1, sha256,
2287 etc), base64 encoder, a secure random number generator, and @code{bignum} math
2288 methods for manually performing crypto calculations on large multibyte
2290 (license license:expat)))
2292 (define-public r-httr
2298 (uri (cran-uri "httr" version))
2301 "0n7jz2digbgv48rbr9vmzv4vmf4rahl9jjy31izs7sxj4rs4s4r2"))))
2302 (build-system r-build-system)
2304 `(("r-curl" ,r-curl)
2305 ("r-jsonlite" ,r-jsonlite)
2306 ("r-openssl" ,r-openssl)
2309 (home-page "https://github.com/hadley/httr")
2310 (synopsis "Tools for working with URLs and HTTP")
2312 "The aim of httr is to provide a wrapper for RCurl customised to the
2313 demands of modern web APIs. It provides useful tools for working with HTTP
2314 organised by HTTP verbs (@code{GET()}, @code{POST()}, etc). Configuration
2315 functions make it easy to control additional request components.")
2316 (license license:expat)))
2318 (define-public r-git2r
2324 (uri (cran-uri "git2r" version))
2327 "11xgddmxzh9cy85k8fb90il43qswpvryz0h9r0j1gbclfg2f9004"))))
2328 (build-system r-build-system)
2329 ;; This R package contains modified sources of libgit2. This modified
2330 ;; version of libgit2 is built as the package is built. Hence libgit2 is
2331 ;; not among the inputs of this package.
2333 `(("libssh2" ,libssh2)
2334 ("openssl" ,openssl)
2336 (home-page "https://github.com/ropensci/git2r")
2337 (synopsis "Access Git repositories with R")
2339 "This package provides an R interface to the libgit2 library, which is a
2340 pure C implementation of the Git core methods.")
2341 ;; GPLv2 only with linking exception.
2342 (license license:gpl2)))
2344 (define-public r-rstudioapi
2346 (name "r-rstudioapi")
2350 (uri (cran-uri "rstudioapi" version))
2353 "133s75q2hr6jg28m1wvs96qrbc9c4vw87migwhkjqb88xxvbqhd5"))))
2354 (build-system r-build-system)
2355 (home-page "https://cran.r-project.org/web/packages/rstudioapi")
2356 (synopsis "Safely access the RStudio API")
2358 "This package provides functions to access the RStudio API and provide
2359 informative error messages when it's not available.")
2360 (license license:expat)))
2362 (define-public r-devtools
2368 (uri (cran-uri "devtools" version))
2371 "1d9n49djydywfyp9w3njgxs5lag4ac7719wmxy1lkgcmn3l9sx5r"))))
2372 (build-system r-build-system)
2374 `(("r-digest" ,r-digest)
2375 ("r-git2r" ,r-git2r)
2377 ("r-jsonlite" ,r-jsonlite)
2378 ("r-memoise" ,r-memoise)
2379 ("r-rstudioapi" ,r-rstudioapi)
2380 ("r-whisker" ,r-whisker)
2381 ("r-withr" ,r-withr)))
2382 (home-page "https://github.com/hadley/devtools")
2383 (synopsis "Tools to make developing R packages easier")
2384 (description "The devtools package is a collection of package development
2385 tools to simplify the devolpment of R packages.")
2386 (license license:gpl2+)))
2388 (define-public r-withr
2394 (uri (cran-uri "withr" version))
2397 "11j6zykklxnvp4xqsr6a2xib665i38m3khdspp887nwagmvnydj1"))))
2398 (build-system r-build-system)
2399 (home-page "https://github.com/jimhester/withr")
2400 (synopsis "Run code with temporarily modified global state")
2402 "This package provides a set of functions to run R code in an environment
2403 in which global state has been temporarily modified. Many of these functions
2404 were originally a part of the r-devtools package.")
2405 (license license:gpl2+)))
2407 (define-public r-hms
2414 (uri (cran-uri "hms" version))
2417 "1g6hslk3z0xga38r71irxq802wskg6nv804mp8y9f7i2wfrj0y55"))))
2418 (build-system r-build-system)
2420 `(("r-rlang" ,r-rlang)
2421 ("r-pkgconfig" ,r-pkgconfig)))
2422 (home-page "https://github.com/rstats-db/hms")
2423 (synopsis "Pretty time of day")
2425 "This package implements an S3 class for storing and formatting
2426 time-of-day values, based on the @code{difftime} class.")
2427 (license license:gpl3+)))
2429 (define-public r-readr
2435 (uri (cran-uri "readr" version))
2438 "1cvw5wdcqk88cp5fyv678mnmp66l3whcd2yh33p2qvx0168bja8s"))))
2439 (build-system r-build-system)
2441 `(("r-rcpp" ,r-rcpp)
2443 ("r-tibble" ,r-tibble)
2446 (home-page "https://github.com/hadley/readr")
2447 (synopsis "Read tabular data")
2449 "This package provides functions to read flat or tabular text files from
2450 disk (or a connection).")
2451 (license license:gpl2+)))
2453 (define-public r-plotrix
2459 (uri (cran-uri "plotrix" version))
2462 "18702y1gbyis56mh219z5ww0nrkh6qx7bgqv3khyn80g2giwk7cf"))))
2463 (build-system r-build-system)
2464 (home-page "https://cran.r-project.org/web/packages/plotrix")
2465 (synopsis "Various plotting functions")
2467 "This package provides lots of plotting, various labeling, axis and color
2468 scaling functions for R.")
2469 (license license:gpl2+)))
2471 (define-public r-gridbase
2477 (uri (cran-uri "gridBase" version))
2480 "09jzw4rzwf2y5lcz7b16mb68pn0fqigv34ff7lr6w3yi9k91i1xy"))))
2481 (build-system r-build-system)
2482 (home-page "https://cran.r-project.org/web/packages/gridBase")
2483 (synopsis "Integration of base and grid graphics")
2485 "This package provides an integration of base and grid graphics for R.")
2486 (license license:gpl2+)))
2488 (define-public r-latticeextra
2490 (name "r-latticeextra")
2495 (uri (cran-uri "latticeExtra" version))
2498 "1hkyqsa7klk5glj9y1hg3rxr5qilqw8h0017zc4c3nps7lr9a1kq"))))
2499 (properties `((upstream-name . "latticeExtra")))
2500 (build-system r-build-system)
2502 `(("r-lattice" ,r-lattice)
2503 ("r-rcolorbrewer" ,r-rcolorbrewer)))
2504 (home-page "http://latticeextra.r-forge.r-project.org/")
2505 (synopsis "Extra graphical utilities based on lattice")
2507 "Building on the infrastructure provided by the lattice package, this
2508 package provides several new high-level graphics functions and methods, as
2509 well as additional utilities such as panel and axis annotation functions.")
2510 (license license:gpl2+)))
2512 (define-public r-rcpparmadillo
2514 (name "r-rcpparmadillo")
2515 (version "0.8.500.0")
2518 (uri (cran-uri "RcppArmadillo" version))
2521 "1sh36dx6inmb56m40nigy94gxlgjva816qnlmjwg7y2bdvqj8vsi"))))
2522 (properties `((upstream-name . "RcppArmadillo")))
2523 (build-system r-build-system)
2525 `(("r-knitr" ,r-knitr))) ; needed for vignettes
2527 `(("r-rcpp" ,r-rcpp)))
2528 (home-page "https://github.com/RcppCore/RcppArmadillo")
2529 (synopsis "Rcpp integration for the Armadillo linear algebra library")
2531 "Armadillo is a templated C++ linear algebra library that aims towards a
2532 good balance between speed and ease of use. Integer, floating point and
2533 complex numbers are supported, as well as a subset of trigonometric and
2534 statistics functions. Various matrix decompositions are provided through
2535 optional integration with LAPACK and ATLAS libraries. This package includes
2536 the header files from the templated Armadillo library.")
2537 ;; Armadillo is licensed under the MPL 2.0, while RcppArmadillo (the Rcpp
2538 ;; bindings to Armadillo) is licensed under the GNU GPL version 2 or
2539 ;; later, as is the rest of 'Rcpp'.
2540 (license license:gpl2+)))
2542 (define-public r-bitops
2548 (uri (cran-uri "bitops" version))
2551 "176nr5wpnkavn5z0yy9f7d47l37ndnn2w3gv854xav8nnybi6wwv"))))
2552 (build-system r-build-system)
2553 (home-page "https://cran.r-project.org/web/packages/bitops")
2554 (synopsis "Bitwise operations")
2556 "This package provides functions for bitwise operations on integer
2558 (license license:gpl2+)))
2560 (define-public r-catools
2563 (version "1.17.1.1")
2566 (uri (cran-uri "caTools" version))
2569 "01hccp05gz25vhz9nnxv1c91lrxlr7drcw9xf124gggifxf2qgnm"))))
2570 (properties `((upstream-name . "caTools")))
2571 (build-system r-build-system)
2573 `(("r-bitops" ,r-bitops)))
2574 (home-page "https://cran.r-project.org/web/packages/caTools")
2575 (synopsis "Various tools including functions for moving window statistics")
2577 "This package contains several basic utility functions including:
2578 moving (rolling, running) window statistic functions, read/write for GIF and
2579 ENVI binary files, fast calculation of AUC, LogitBoost classifier, base64
2580 encoder/decoder, round-off-error-free sum and cumsum, etc.")
2581 (license license:gpl3+)))
2583 (define-public r-rprojroot
2585 (name "r-rprojroot")
2590 (uri (cran-uri "rprojroot" version))
2593 "12r3fdxmi2pmwn6ic3rhg0b20ll5z420m0d8fziv1n21961namnz"))))
2594 (build-system r-build-system)
2596 `(("r-backports" ,r-backports)))
2597 (home-page "https://github.com/krlmlr/rprojroot")
2598 (synopsis "Finding files in project subdirectories")
2600 "This package helps accessing files relative to a project root. It
2601 provides helpers for robust, reliable and flexible paths to files below a
2602 project root. The root of a project is defined as a directory that matches a
2603 certain criterion, e.g., it contains a certain regular file.")
2604 (license license:gpl3)))
2606 (define-public r-rmarkdown
2608 (name "r-rmarkdown")
2613 (uri (cran-uri "rmarkdown" version))
2616 "0mh2f3k98w7pgz0ri34149s4kx5y0kfm27nwq64k0qwxd16hwd9r"))))
2617 (properties `((upstream-name . "rmarkdown")))
2618 (build-system r-build-system)
2620 `(("r-base64enc" ,r-base64enc)
2621 ("r-evaluate" ,r-evaluate)
2622 ("r-htmltools" ,r-htmltools)
2623 ("r-jsonlite" ,r-jsonlite)
2624 ("r-knitr" ,r-knitr)
2626 ("r-rprojroot" ,r-rprojroot)
2627 ("r-stringr" ,r-stringr)
2628 ("r-tinytex" ,r-tinytex)
2630 ;; rmarkdown works with the 2.x release of Pandoc, but with degraded
2631 ;; functionality. For example, tabbed plots do not currently work with
2632 ;; Pandoc 2. The authors of rmarkdown recommend the use of Pandoc 1
2633 ;; for the time being.
2634 ("ghc-pandoc" ,ghc-pandoc-1)))
2635 (home-page "http://rmarkdown.rstudio.com")
2636 (synopsis "Convert R Markdown documents into a variety of formats")
2638 "This package provides tools to convert R Markdown documents into a
2639 variety of formats.")
2640 (license license:gpl3+)))
2642 (define-public r-gtable
2648 (uri (cran-uri "gtable" version))
2651 "0vz7073m0a2q12qzzihrfh5c2kx5jqi5l7z470fxmwqghdllh7l0"))))
2652 (properties `((upstream-name . "gtable")))
2653 (build-system r-build-system)
2654 (home-page "https://cran.r-project.org/web/packages/gtable")
2655 (synopsis "R library to arrange grobs in tables")
2657 "Gtable is a collection of tools to make it easier to work with
2658 \"tables\" of grobs.")
2659 (license license:gpl2+)))
2661 (define-public r-gridextra
2663 (name "r-gridextra")
2667 (uri (cran-uri "gridExtra" version))
2670 "0fwfk3cdwxxim7nd55pn7m31bcaqj48y06j7an2k1v1pybk0rdl1"))))
2671 (properties `((upstream-name . "gridExtra")))
2672 (build-system r-build-system)
2674 `(("r-gtable" ,r-gtable)))
2676 `(("r-knitr" ,r-knitr))) ;for building vignettes
2677 (home-page "https://github.com/baptiste/gridextra")
2678 (synopsis "Miscellaneous functions for \"Grid\" graphics")
2680 "This package provides a number of user-level functions to work with
2681 @code{grid} graphics, notably to arrange multiple grid-based plots on a page,
2683 (license license:gpl2+)))
2685 (define-public r-pkgconfig
2687 (name "r-pkgconfig")
2691 (uri (cran-uri "pkgconfig" version))
2694 "1jk9ip549xphb3anfixqv1yx5kidnndqgy9v3qjpmgmds5a7g695"))))
2695 (build-system r-build-system)
2696 (home-page "https://github.com/gaborcsardi/pkgconfig")
2697 (synopsis "Private configuration for R packages")
2698 (description "This package provides the functionality to set configuration
2699 options on a per-package basis. Options set by a given package only apply to
2700 that package, other packages are unaffected.")
2701 (license license:expat)))
2703 (define-public r-blob
2709 (uri (cran-uri "blob" version))
2712 "0lsg91hk508dd95ivig2lwg62qafwnarjw68110kx63cfk4zkjxc"))))
2713 (build-system r-build-system)
2715 `(("r-prettyunits" ,r-prettyunits)
2716 ("r-tibble" ,r-tibble)))
2717 (home-page "https://github.com/hadley/blob")
2718 (synopsis "Simple S3 Class for representing vectors of binary data")
2719 (description "Raw vectors in R are useful for storing a single binary
2720 object. What if you want to put a vector of them in a data frame? The blob
2721 package provides the blob object, a list of raw vectors, suitable for use as
2722 a column in data frame.")
2723 (license license:gpl3+)))
2725 (define-public r-rsqlite
2731 (uri (cran-uri "RSQLite" version))
2734 "1giwk4335sc6yhj3rs8h070g1mwy38kyqyqv6vcfxvskykj7vp6z"))))
2735 (properties `((upstream-name . "RSQLite")))
2736 (build-system r-build-system)
2740 ("r-memoise" ,r-memoise)
2741 ("r-plogr" ,r-plogr)
2743 ("r-bit64" ,r-bit64)
2745 ("r-pkgconfig" ,r-pkgconfig)))
2746 (home-page "https://github.com/rstats-db/RSQLite")
2747 (synopsis "SQLite interface for R")
2749 "This package embeds the SQLite database engine in R and provides an
2750 interface compliant with the DBI package. The source for the SQLite
2751 engine (version 3.8.8.2) is included.")
2752 (license license:lgpl2.0+)))
2754 (define-public r-rcurl
2757 (version "1.95-0.1.2")
2760 (uri (string-append "https://www.bioconductor.org/packages/"
2761 "release/extra/src/"
2762 "contrib/RCurl_" version ".tar.gz"))
2765 "0l7qi45jxlf898n0jazabnam1yyczvqfdknd00bdirhhiplpd1sc"))))
2766 (properties `((upstream-name . "RCurl")))
2767 (build-system r-build-system)
2770 (modify-phases %standard-phases
2771 (add-after 'unpack 'respect-CURL_CA_BUNDLE
2773 (substitute* "R/options.S"
2774 (("\\.els = rev\\(merge\\(list\\(\\.\\.\\.\\), \\.opts\\)\\)" m)
2776 certs = Sys.getenv(\"CURL_CA_BUNDLE\")
2777 if (certs != \"\") { .opts = merge.list(.opts, list(cainfo=certs)) }
2781 `(("libcurl" ,curl)))
2783 `(("r-bitops" ,r-bitops)))
2784 (home-page "http://www.omegahat.org/RCurl")
2785 (synopsis "General network client interface for R")
2787 "The package allows one to compose general HTTP requests and provides
2788 convenient functions to fetch URIs, GET and POST forms, etc. and process the
2789 results returned by the Web server. This provides a great deal of control
2790 over the HTTP/FTP/... connection and the form of the request while providing a
2791 higher-level interface than is available just using R socket connections.
2792 Additionally, the underlying implementation is robust and extensive,
2793 supporting FTP/FTPS/TFTP (uploads and downloads), SSL/HTTPS, telnet, dict,
2794 ldap, and also supports cookies, redirects, authentication, etc.")
2795 (license license:bsd-3)))
2797 (define-public r-xml
2800 (version "3.98-1.11")
2803 (uri (cran-uri "XML" version))
2806 "18izvlg2x9mzr6yb3yf02ghwbyn00frki3av4lpc44r22m4djnsh"))))
2808 `((upstream-name . "XML")))
2809 (build-system r-build-system)
2811 `(("libxml2" ,libxml2)
2814 `(("pkg-config" ,pkg-config)))
2815 (home-page "http://www.omegahat.org/RSXML")
2816 (synopsis "Tools for parsing and generating XML within R")
2818 "Many approaches for both reading and creating XML (and HTML)
2819 documents (including DTDs), both local and accessible via HTTP or FTP. Also
2820 offers access to an XPath \"interpreter\".")
2821 (license license:bsd-2)))
2823 (define-public r-xnomial
2828 (origin (method url-fetch)
2829 (uri (cran-uri "XNomial" version))
2832 "1mwx302576rmsjllbq2clfxilm3hkyp5bw0wmwqbn0kgv5wpy8z6"))))
2833 (properties (quasiquote ((upstream-name . "XNomial"))))
2834 (build-system r-build-system)
2835 (home-page "https://cran.r-project.org/web/packages/XNomial")
2836 (synopsis "Goodness-of-Fit test for multinomial data")
2838 "This package provides an exact Goodness-of-Fit test for
2839 multinomial data with fixed probabilities. It can be used to
2840 determine whether a set of counts fits a given expected ratio. To see
2841 whether a set of observed counts fits an expectation, one can examine
2842 all possible outcomes with @code{xmulti()} or a random sample of them
2843 with @code{xmonte()} and find the probability of an observation
2844 deviating from the expectation by at least as much as the observed.
2845 As a measure of deviation from the expected, one can use the
2846 log-likelihood ratio, the multinomial probability, or the classic
2847 chi-square statistic. A histogram of the test statistic can also be
2848 plotted and compared with the asymptotic curve.")
2849 (license (list license:gpl2+ license:gpl3+))))
2851 (define-public r-lambda-r
2857 (uri (cran-uri "lambda.r" version))
2860 "0cc6pszs6yccn0hgjpyn9gspv9aiva9d91ba0640i5m0l5xy7n0c"))))
2861 (properties `((upstream-name . "lambda.r")))
2862 (build-system r-build-system)
2864 `(("r-formatr" ,r-formatr)))
2865 (home-page "https://cran.r-project.org/web/packages/lambda.r")
2866 (synopsis "Functional programming extension for R")
2868 "This package provides a language extension to efficiently write
2869 functional programs in R. Syntax extensions include multi-part function
2870 definitions, pattern matching, guard statements, built-in (optional) type
2872 (license license:lgpl3+)))
2874 (define-public r-futile-options
2876 (name "r-futile-options")
2880 (uri (cran-uri "futile.options" version))
2883 "0w15agpi88y3qkv6fl72zy2pzyplzgvnj41a4ixhg64mw1sck73s"))))
2885 `((upstream-name . "futile.options")))
2886 (build-system r-build-system)
2887 (home-page "https://cran.r-project.org/web/packages/futile.options")
2888 (synopsis "Options management framework")
2890 "The futile.options subsystem provides an easy user-defined options
2891 management system that is properly scoped. This means that options created
2892 via @code{futile.options} are fully self-contained and will not collide with
2893 options defined in other packages.")
2894 (license license:lgpl3+)))
2896 (define-public r-futile-logger
2898 (name "r-futile-logger")
2902 (uri (cran-uri "futile.logger" version))
2905 "1r3nayk0z9n1svbf8640vw90dal5q07nkn0gv4bnva3pbzb352sy"))))
2906 (properties `((upstream-name . "futile.logger")))
2907 (build-system r-build-system)
2909 `(("r-futile-options" ,r-futile-options)
2910 ("r-lambda-r" ,r-lambda-r)))
2911 (home-page "https://cran.r-project.org/web/packages/futile.logger")
2912 (synopsis "Logging utility for R")
2914 "This package provides a simple yet powerful logging utility. Based
2915 loosely on log4j, futile.logger takes advantage of R idioms to make logging a
2916 convenient and easy to use replacement for @code{cat} and @code{print}
2918 (license license:lgpl3+)))
2920 (define-public r-segmented
2922 (name "r-segmented")
2927 (uri (cran-uri "segmented" version))
2930 "0nrik5fyq59hwiwjcpbi4p5yfavgfjq6wyrynhkrbm4k6v1g1wlq"))))
2931 (build-system r-build-system)
2932 (home-page "https://cran.r-project.org/web/packages/segmented")
2933 (synopsis "Regression models with breakpoints estimation")
2935 "Given a regression model, segmented updates the model by adding one or
2936 more segmented (i.e., piecewise-linear) relationships. Several variables with
2937 multiple breakpoints are allowed.")
2938 (license (list license:gpl2+ license:gpl3+))))
2940 (define-public r-snow
2946 (uri (cran-uri "snow" version))
2949 "1mxbrkpnmq32x4wd0194d541661yvfrrjlr3lsf7qq53ms3h21zf"))))
2950 (build-system r-build-system)
2951 (home-page "https://cran.r-project.org/web/packages/snow")
2952 (synopsis "Support for simple parallel computing in R")
2954 "The snow package provides support for simple parallel computing on a
2955 network of workstations using R. A master R process calls @code{makeCluster}
2956 to start a cluster of worker processes; the master process then uses functions
2957 such as @code{clusterCall} and @code{clusterApply} to execute R code on the
2958 worker processes and collect and return the results on the master.")
2959 (license (list license:gpl2+ license:gpl3+))))
2961 (define-public r-sparsem
2967 (uri (cran-uri "SparseM" version))
2970 "0p6ljma2h12cq1xmy0cxb48ih8dhxxbnwkqzvx3cckxf2kprycm9"))))
2972 `((upstream-name . "SparseM")))
2974 `(("gfortran" ,gfortran)))
2975 (build-system r-build-system)
2976 (home-page "http://www.econ.uiuc.edu/~roger/research/sparse/sparse.html")
2977 (synopsis "Sparse linear algebra")
2979 "This package provides some basic linear algebra functionality for sparse
2980 matrices. It includes Cholesky decomposition and backsolving as well as
2981 standard R subsetting and Kronecker products.")
2982 (license license:gpl2+)))
2984 (define-public r-iterators
2986 (name "r-iterators")
2991 (uri (cran-uri "iterators" version))
2994 "1s3iykfvccpnzs73z90rx18qvbvgw2dgl4nfcrvm5m1850qb5qd9"))))
2995 (build-system r-build-system)
2996 (home-page "https://cran.r-project.org/web/packages/iterators")
2997 (synopsis "Iterator construct for R")
2999 "This package provides support for iterators, which allow a programmer to
3000 traverse through all the elements of a vector, list, or other collection of
3002 (license license:asl2.0)))
3004 (define-public r-foreach
3011 (uri (cran-uri "foreach" version))
3014 "0j2yj0rn0d5nbzz9nq5rqqgnxhp9pbd92q4klsarl2xpsn8119y0"))))
3015 (build-system r-build-system)
3017 `(("r-codetools" ,r-codetools)
3018 ("r-iterators" ,r-iterators)))
3019 (home-page "https://cran.r-project.org/web/packages/foreach")
3020 (synopsis "Foreach looping construct for R")
3022 "This package provides support for the @code{foreach} looping construct.
3023 @code{foreach} is an idiom that allows for iterating over elements in a
3024 collection, without the use of an explicit loop counter. This package in
3025 particular is intended to be used for its return value, rather than for its
3026 side effects. In that sense, it is similar to the standard @code{lapply}
3027 function, but doesn't require the evaluation of a function. Using
3028 @code{foreach} without side effects also facilitates executing the loop in
3030 (license license:asl2.0)))
3032 (define-public r-doparallel
3034 (name "r-doparallel")
3039 (uri (cran-uri "doParallel" version))
3042 "0sppgxk3d8mfsrb3cjdyn0mv0s4i7pcy8g8c3cjzbr6k8vmx5jsc"))))
3043 (properties `((upstream-name . "doParallel")))
3044 (build-system r-build-system)
3046 `(("r-foreach" ,r-foreach)
3047 ("r-iterators" ,r-iterators)))
3048 (home-page "https://cran.r-project.org/web/packages/doParallel")
3049 (synopsis "Foreach parallel adaptor for the 'parallel' package")
3051 "This package provides a parallel backend for the @code{%dopar%} function
3052 using the parallel package.")
3053 (license license:gpl2+)))
3055 (define-public r-domc
3062 (uri (cran-uri "doMC" version))
3065 "1vfrykvfvsyq12mypd266867ml1dcwc3rj5k9c3wrn5bddcm88kr"))))
3066 (properties `((upstream-name . "doMC")))
3067 (build-system r-build-system)
3069 `(("r-foreach" ,r-foreach)
3070 ("r-iterators" ,r-iterators)))
3071 (home-page "https://cran.r-project.org/web/packages/doMC")
3072 (synopsis "Foreach parallel adaptor for the 'parallel' package")
3074 "This package provides a parallel backend for the @code{%dopar%} function
3075 using the multicore functionality of the parallel package.")
3076 (license license:gpl2+)))
3084 (uri (cran-uri "DT" version))
3087 "06gsqz7p2fv6hc3fm3759gaa50krcfrqrmy7qbxyam6a36w9daix"))))
3089 `((upstream-name . "DT")))
3090 (build-system r-build-system)
3092 `(("r-crosstalk" ,r-crosstalk)
3093 ("r-htmltools" ,r-htmltools)
3094 ("r-htmlwidgets" ,r-htmlwidgets)
3095 ("r-magrittr" ,r-magrittr)))
3096 (home-page "http://rstudio.github.io/DT")
3097 (synopsis "R wrapper of the DataTables JavaScript library")
3099 "This package allows for data objects in R to be rendered as HTML tables
3100 using the JavaScript library 'DataTables' (typically via R Markdown or Shiny).
3101 The 'DataTables' library has been included in this R package.")
3102 ;; The DT package as a whole is distributed under GPLv3. The DT package
3103 ;; inludes other software components under different licenses:
3105 ;; * Expat: jQuery, jquery.highlight.js, DataTables
3106 ;; * ASL2.0: selectize.js
3107 ;; * WTFPL: noUiSlider
3108 (license (list license:gpl3
3111 (license:non-copyleft "http://www.wtfpl.net/txt/copying/")))))
3113 (define-public r-base64enc
3115 (name "r-base64enc")
3119 (uri (cran-uri "base64enc" version))
3122 "13b89fhg1nx7zds82a0biz847ixphg9byf5zl2cw9kab6s56v1bd"))))
3123 (build-system r-build-system)
3124 (home-page "http://www.rforge.net/base64enc")
3125 (synopsis "Tools for Base64 encoding")
3127 "This package provides tools for handling Base64 encoding. It is more
3128 flexible than the orphaned \"base64\" package.")
3129 (license license:gpl2+)))
3131 (define-public r-irlba
3138 (uri (cran-uri "irlba" version))
3141 "0f7wb12wa0zbyllk5adcf4f517wgjpkhsx4j176i9ax6xy7jvprz"))))
3142 (build-system r-build-system)
3144 `(("r-matrix" ,r-matrix)))
3145 (home-page "https://cran.r-project.org/web/packages/irlba")
3146 (synopsis "Methods for eigendecomposition of large matrices")
3148 "This package provides fast and memory efficient methods for truncated
3149 singular and eigenvalue decompositions, as well as for principal component
3150 analysis of large sparse or dense matrices.")
3151 (license (list license:gpl2+ license:gpl3+))))
3153 (define-public r-glmnet
3160 (uri (cran-uri "glmnet" version))
3163 "1brr51z1fzbpyj6myyir4g6dhbp6xwl7nx4xnvrjarnf5y0csk55"))))
3164 (build-system r-build-system)
3166 `(("gfortran" ,gfortran)))
3168 `(("r-foreach" ,r-foreach)
3169 ("r-matrix" ,r-matrix)))
3170 (home-page "http://www.jstatsoft.org/v33/i01")
3171 (synopsis "Lasso and elastic-net regularized generalized linear models")
3173 "The glmnet package provides efficient procedures for fitting the entire
3174 lasso or elastic-net regularization path for linear and Poisson regression, as
3175 well as logistic, multinomial, Cox, multiple-response Gaussian and grouped
3176 multinomial models. The algorithm uses cyclical coordinate descent in a
3177 path-wise fashion.")
3178 (license license:gpl2+)))
3180 (define-public r-pkgmaker
3187 (uri (cran-uri "pkgmaker" version))
3190 "0spcamjncj78kzjps2rw4v1a4494yazv6xvhn0vmdflnypc8k8hp"))))
3191 (build-system r-build-system)
3193 `(("r-bibtex" ,r-bibtex)
3194 ("r-codetools" ,r-codetools)
3195 ("r-digest" ,r-digest)
3196 ("r-magrittr" ,r-magrittr)
3197 ("r-registry" ,r-registry)
3198 ("r-stringi" ,r-stringi)
3199 ("r-stringr" ,r-stringr)
3200 ("r-withr" ,r-withr)
3201 ("r-xtable" ,r-xtable)))
3202 (home-page "https://renozao.github.io/pkgmaker")
3203 (synopsis "Package development utilities")
3205 "This package provides some low-level utilities to use for R package
3206 development. It currently provides managers for multiple package specific
3207 options and registries, vignette, unit test and bibtex related utilities.")
3208 (license license:gpl2+)))
3210 (define-public r-registry
3217 (uri (cran-uri "registry" version))
3220 "1yqfl1g6vsl28zn8brzc39659k8lqsmfms7900j7p64ilydyb2sx"))))
3221 (build-system r-build-system)
3222 (home-page "https://cran.r-project.org/web/packages/registry")
3223 (synopsis "Infrastructure for R package registries")
3225 "This package provides a generic infrastructure for creating and using R
3226 package registries.")
3227 (license license:gpl2+)))
3229 (define-public r-rngtools
3236 (uri (cran-uri "rngtools" version))
3239 "097215qcfw6ybllpzmp1532r59h2srvch3aca4z4s6l2rf9w8gvn"))))
3240 (build-system r-build-system)
3242 `(("r-digest" ,r-digest)
3243 ("r-pkgmaker" ,r-pkgmaker)
3244 ("r-stringr" ,r-stringr)))
3245 (home-page "https://renozao.github.io/rngtools")
3246 (synopsis "Utility functions for working with random number generators")
3248 "This package contains a set of functions for working with Random Number
3249 Generators (RNGs). In particular, it defines a generic S4 framework for
3250 getting/setting the current RNG, or RNG data that are embedded into objects
3251 for reproducibility. Notably, convenient default methods greatly facilitate
3252 the way current RNG settings can be changed.")
3253 (license license:gpl3+)))
3255 (define-public r-rtsne
3262 (uri (cran-uri "Rtsne" version))
3265 "17crbdi80q4g2pwp9v7j3bdaznk96qlrqx01zvj3wwqippizyfqw"))))
3266 (properties `((upstream-name . "Rtsne")))
3267 (build-system r-build-system)
3269 `(("r-rcpp" ,r-rcpp)))
3270 (home-page "https://github.com/jkrijthe/Rtsne")
3271 (synopsis "T-distributed stochastic neighbor embedding")
3273 "This package provides an R wrapper around the fast T-distributed
3274 Stochastic Neighbor Embedding using a Barnes-Hut implementation.")
3275 ;; The declared license for this package is BSD-3, but it also includes
3276 ;; code licensed under BSD-4.
3277 (license (list license:bsd-3 license:bsd-4))))
3279 (define-public r-e1071
3286 (uri (cran-uri "e1071" version))
3289 "08n6i26nfckjpxjkzi8phhanc3ahsrirkv5rz38y2jcv7ds031pn"))))
3290 (build-system r-build-system)
3292 `(("r-class" ,r-class)))
3293 (home-page "https://cran.r-project.org/web/packages/e1071")
3294 (synopsis "Miscellaneous functions for probability theory")
3296 "This package provides functions for latent class analysis, short time
3297 Fourier transform, fuzzy clustering, support vector machines, shortest path
3298 computation, bagged clustering, naive Bayes classifier, and more.")
3299 (license license:gpl2+)))
3301 (define-public r-bigmemory-sri
3303 (name "r-bigmemory-sri")
3308 (uri (cran-uri "bigmemory.sri" version))
3310 (base32 "0mg14ilwdkd64q2ri9jdwnk7mp55dqim7xfifrs65sdsv1934h2m"))))
3312 `((upstream-name . "bigmemory.sri")))
3313 (build-system r-build-system)
3314 (home-page "https://cran.r-project.org/web/packages/bigmemory.sri")
3315 (synopsis "Shared resource interface for the bigmemory package")
3316 (description "This package provides a shared resource interface for the
3317 bigmemory and synchronicity packages.")
3318 ;; Users can choose either LGPLv3 or ASL2.0.
3319 (license (list license:lgpl3 license:asl2.0))))
3321 (define-public r-synchronicity
3323 (name "r-synchronicity")
3328 (uri (cran-uri "synchronicity" version))
3331 "1kgsk64aifjm3mfj102y3va7x1abypq2zi0cqbnjhl8fqyzp69hx"))))
3332 (build-system r-build-system)
3335 ("r-bigmemory-sri" ,r-bigmemory-sri)
3337 ("r-uuid" ,r-uuid)))
3338 (home-page "http://www.bigmemory.org")
3339 (synopsis "Boost mutex functionality in R")
3340 (description "This package provides support for synchronization
3341 via mutexes and may eventually support interprocess communication and
3343 ;; Users can choose either LGPLv3 or ASL2.0.
3344 (license (list license:lgpl3 license:asl2.0))))
3346 (define-public r-bigmemory
3348 (name "r-bigmemory")
3353 (uri (cran-uri "bigmemory" version))
3356 "0ycl9dzm3drpyas625h34rir5bnbjlncxlvawfsfmqwcbmwdjdvj"))))
3357 (build-system r-build-system)
3361 ("r-bigmemory-sri" ,r-bigmemory-sri)))
3362 (home-page "http://www.bigmemory.org")
3363 (synopsis "Manage large matrices with shared memory or memory-mapped files")
3364 (description "This package provides methods to create, store, access, and
3365 manipulate large matrices. Matrices are allocated to shared memory and may use
3366 memory-mapped files.")
3367 ;; Users can choose either LGPLv3 or ASL2.0.
3368 (license (list license:lgpl3 license:asl2.0))))
3370 (define-public r-nmf
3377 (uri (cran-uri "NMF" version))
3380 "1qq25n3k5sgh3srlshb3ic6q92s12c1ilqf5cd5anvq6cqfchc1v"))))
3381 (properties `((upstream-name . "NMF")))
3382 (build-system r-build-system)
3384 `(("r-cluster" ,r-cluster)
3385 ("r-bigmemory" ,r-bigmemory) ; suggested
3386 ("r-synchronicity" ,r-synchronicity) ; suggested
3387 ("r-colorspace" ,r-colorspace)
3388 ("r-digest" ,r-digest)
3389 ("r-doparallel" ,r-doparallel)
3390 ("r-foreach" ,r-foreach)
3391 ("r-ggplot2" ,r-ggplot2)
3392 ("r-gridbase" ,r-gridbase)
3393 ("r-pkgmaker" ,r-pkgmaker)
3394 ("r-rcolorbrewer" ,r-rcolorbrewer)
3395 ("r-registry" ,r-registry)
3396 ("r-reshape2" ,r-reshape2)
3397 ("r-rngtools" ,r-rngtools)
3398 ("r-stringr" ,r-stringr)))
3399 (home-page "http://renozao.github.io/NMF")
3400 (synopsis "Algorithms and framework for nonnegative matrix factorization")
3402 "This package provides a framework to perform Non-negative Matrix
3403 Factorization (NMF). The package implements a set of already published
3404 algorithms and seeding methods, and provides a framework to test, develop and
3405 plug new or custom algorithms. Most of the built-in algorithms have been
3406 optimized in C++, and the main interface function provides an easy way of
3407 performing parallel computations on multicore machines.")
3408 (license license:gpl2+)))
3410 (define-public r-r-methodss3
3412 (name "r-r-methodss3")
3416 (uri (cran-uri "R.methodsS3" version))
3419 "11z6v2i7jl647wxi9p5z66yvfnnqv6s7fxqmz7w2gkb6j8wl1f24"))))
3420 (properties `((upstream-name . "R.methodsS3")))
3421 (build-system r-build-system)
3422 (home-page "https://cran.r-project.org/web/packages/R.methodsS3")
3423 (synopsis "S3 methods simplified")
3425 "This package provides methods that simplify the setup of S3 generic
3426 functions and S3 methods. Major effort has been made in making definition of
3427 methods as simple as possible with a minimum of maintenance for package
3428 developers. For example, generic functions are created automatically, if
3429 missing, and naming conflict are automatically solved, if possible. The
3430 method @code{setMethodS3()} is a good start for those who in the future may
3431 want to migrate to S4.")
3432 (license license:lgpl2.1+)))
3434 (define-public r-r-oo
3440 (uri (cran-uri "R.oo" version))
3443 "0k6xwy93fpb2p7bs76lzk52br9rv5xnd9524xj8qyazv1132x1n0"))))
3444 (properties `((upstream-name . "R.oo")))
3445 (build-system r-build-system)
3447 `(("r-r-methodss3" ,r-r-methodss3)))
3448 (home-page "https://github.com/HenrikBengtsson/R.oo")
3449 (synopsis "R object-oriented programming with or without references")
3451 "This package provides methods and classes for object-oriented
3452 programming in R with or without references. Large effort has been made on
3453 making definition of methods as simple as possible with a minimum of
3454 maintenance for package developers.")
3455 (license license:lgpl2.1+)))
3457 (define-public r-r-utils
3463 (uri (cran-uri "R.utils" version))
3466 "03j7hrs03kyj9qrjxyp5kqv4lpqqpk6xwbkzx6j15d8928yrjr2x"))))
3467 (properties `((upstream-name . "R.utils")))
3468 (build-system r-build-system)
3470 `(("r-r-methodss3" ,r-r-methodss3)
3471 ("r-r-oo" ,r-r-oo)))
3472 (home-page "https://github.com/HenrikBengtsson/R.utils")
3473 (synopsis "Various programming utilities")
3475 "This package provides utility functions useful when programming and
3476 developing R packages.")
3477 (license license:lgpl2.1+)))
3479 (define-public r-r-cache
3485 (uri (cran-uri "R.cache" version))
3488 "1hf5cb7xvnca5zlh9245b5g62sgsaxwdhiv7x59yld37cydakm6k"))))
3489 (properties `((upstream-name . "R.cache")))
3490 (build-system r-build-system)
3492 `(("r-digest" ,r-digest)
3493 ("r-r-methodss3" ,r-r-methodss3)
3495 ("r-r-utils" ,r-r-utils)))
3496 (home-page "https://github.com/HenrikBengtsson/R.cache")
3497 (synopsis "Light-weight caching of objects and results")
3499 "This package provides methods for caching or memoization of objects and
3500 results. With this package, any R object can be cached in a key-value storage
3501 where the key can be an arbitrary set of R objects. The cache memory is
3502 persistent (on the file system).")
3503 (license license:lgpl2.1+)))
3505 (define-public r-r-rsp
3511 (uri (cran-uri "R.rsp" version))
3514 "1zcq0hzi0j7fvj2rs796a1i120wbr0387vck17rrd644awwbsbm0"))))
3515 (properties `((upstream-name . "R.rsp")))
3516 (build-system r-build-system)
3518 `(("r-digest" ,r-digest)
3519 ("r-r-cache" ,r-r-cache)
3520 ("r-r-methodss3" ,r-r-methodss3)
3522 ("r-r-utils" ,r-r-utils)))
3523 (home-page "https://github.com/HenrikBengtsson/R.rsp")
3524 (synopsis "Dynamic generation of scientific reports")
3526 "The RSP markup language provides a powerful markup for controlling the
3527 content and output of LaTeX, HTML, Markdown, AsciiDoc, Sweave and knitr
3528 documents (and more), e.g. @code{Today's date is <%=Sys.Date()%>}. Contrary
3529 to many other literate programming languages, with RSP it is straightforward
3530 to loop over mixtures of code and text sections, e.g. in month-by-month
3531 summaries. RSP has also several preprocessing directives for incorporating
3532 static and dynamic contents of external files (local or online) among other
3533 things. RSP is ideal for self-contained scientific reports and R package
3535 (license license:lgpl2.1+)))
3537 (define-public r-mvtnorm
3543 (uri (cran-uri "mvtnorm" version))
3546 "0la42lylb7cjrcrc285bn69bz9kyg556xw317iz139dp1yswl410"))))
3547 (build-system r-build-system)
3549 `(("gfortran" ,gfortran)))
3550 (home-page "http://mvtnorm.R-forge.R-project.org")
3551 (synopsis "Package for multivariate normal and t-distributions")
3552 (description "This package can compute multivariate normal and
3553 t-probabilities, quantiles, random deviates and densities.")
3554 (license license:gpl2)))
3556 (define-public r-matrixstats
3558 (name "r-matrixstats")
3562 (uri (cran-uri "matrixStats" version))
3565 "0bkiz5fm09d3512mfr2ymj9qsb1b8aic5l5m6fkaf5j7nsgvqw6z"))))
3566 (properties `((upstream-name . "matrixStats")))
3567 (build-system r-build-system)
3569 `(("r-r-rsp" ,r-r-rsp))) ;used to build vignettes
3570 (home-page "https://github.com/HenrikBengtsson/matrixStats")
3571 (synopsis "Methods applying to vectors and matrix rows and columns")
3573 "This package provides methods operating on rows and columns of matrices,
3574 e.g. @code{rowMedians()}, @code{rowRanks()}, and @code{rowSds()}. There are
3575 also some vector-based methods, e.g. @code{binMeans()}, @code{madDiff()} and
3576 @code{weightedMedians()}. All methods have been optimized for speed and
3578 (license license:artistic2.0)))
3580 (define-public r-viridis
3586 (uri (cran-uri "viridis" version))
3589 "060rf1jn29dq53y3nhb0hykvcap6rqsk04rq544ypiiqb18ngwnx"))))
3590 (build-system r-build-system)
3592 `(("r-ggplot2" ,r-ggplot2)
3593 ("r-gridextra" ,r-gridextra)
3594 ("r-viridislite" ,r-viridislite)))
3595 (home-page "https://github.com/sjmgarnier/viridis")
3596 (synopsis "Matplotlib default color map")
3598 "This package is a port of the new @url{matplotlib,
3599 http://matplotlib.org/} color maps (@code{viridis}--the default--,
3600 @code{magma}, @code{plasma}, and @code{inferno}) to R. These color maps are
3601 designed in such a way that they will analytically be perfectly
3602 perceptually-uniform, both in regular form and also when converted to
3603 black-and-white. They are also designed to be perceived by readers with the
3604 most common form of color blindness.")
3605 (license license:x11)))
3607 (define-public r-viridislite
3609 (name "r-viridislite")
3614 (uri (cran-uri "viridisLite" version))
3617 "1by2l05f0yabwvv64lhnv7bbhx0w683s3wr9j2xda920ghpa23kq"))))
3618 (properties `((upstream-name . "viridisLite")))
3619 (build-system r-build-system)
3620 (home-page "https://github.com/sjmgarnier/viridisLite")
3621 (synopsis "Default color maps from matplotlib")
3623 "This package is a port of the new @code{matplotlib} color maps ('viridis',
3624 'magma', 'plasma' and 'inferno') to R. matplotlib is a popular plotting
3625 library for Python. These color maps are designed in such a way that they
3626 will analytically be perfectly perceptually-uniform, both in regular form and
3627 also when converted to black-and-white. They are also designed to be
3628 perceived by readers with the most common form of color blindness. This is
3629 the 'lite' version of the more complete @code{viridis} package.")
3630 (license license:expat)))
3632 (define-public r-tidyselect
3634 (name "r-tidyselect")
3639 (uri (cran-uri "tidyselect" version))
3642 "1592dbzawhd1hpsp9919l4sifyiaaj6xr7lnhsbwa6jwmmb0xcsw"))))
3643 (build-system r-build-system)
3645 `(("r-glue" ,r-glue)
3646 ("r-purrr" ,r-purrr)
3648 ("r-rlang" ,r-rlang)))
3649 (home-page "https://cran.r-project.org/web/packages/tidyselect")
3650 (synopsis "Select from a set of strings")
3652 "This package provides a backend for the selecting functions of the
3653 tidyverse. It makes it easy to implement select-like functions in your own
3654 packages in a way that is consistent with other tidyverse interfaces for
3656 (license license:gpl3)))
3658 (define-public r-tidyr
3665 (uri (cran-uri "tidyr" version))
3668 "0485f19mkkglc4bv57y6bm6l9rfgd878hsz2xdg1nwgbqchjhgix"))))
3669 (build-system r-build-system)
3671 `(("r-dplyr" ,r-dplyr)
3672 ("r-magrittr" ,r-magrittr)
3674 ("r-purrr" ,r-purrr)
3675 ("r-rlang" ,r-rlang)
3676 ("r-tidyselect" ,r-tidyselect)
3678 ("r-stringi" ,r-stringi)
3679 ("r-tibble" ,r-tibble)))
3680 (home-page "https://github.com/hadley/tidyr")
3681 (synopsis "Tidy data with `spread()` and `gather()` functions")
3683 "tidyr is a reframing of the reshape2 package designed to accompany the
3684 tidy data framework, and to work hand-in-hand with magrittr and dplyr to build
3685 a solid pipeline for data analysis. It is designed specifically for tidying
3686 data, not the general reshaping that reshape2 does, or the general aggregation
3687 that reshape did. In particular, built-in methods only work for data frames,
3688 and tidyr provides no margins or aggregation.")
3689 (license license:expat)))
3691 (define-public r-hexbin
3698 (uri (cran-uri "hexbin" version))
3701 "0lpfl0015lg5x7lvv9dr302bca22c7fs91pnd896ypgpzqg7pm26"))))
3702 (build-system r-build-system)
3704 `(("r-lattice" ,r-lattice)))
3706 `(("gfortran" ,gfortran)))
3707 (home-page "https://github.com/edzer/hexbin")
3708 (synopsis "Hexagonal binning routines")
3710 "This package provides binning and plotting functions for hexagonal bins.
3711 It uses and relies on grid graphics and formal (S4) classes and methods.")
3712 (license license:gpl2+)))
3714 (define-public r-purrr
3721 (uri (cran-uri "purrr" version))
3724 "0dc53zzan3km2l9lzxjixcv6yn7dhw2ppmz8qf2awhak7x2qm9m4"))))
3725 (build-system r-build-system)
3727 `(("r-tibble" ,r-tibble)
3728 ("r-magrittr" ,r-magrittr)
3729 ("r-rlang" ,r-rlang)))
3730 (home-page "https://github.com/hadley/purrr")
3731 (synopsis "Functional programming tools")
3733 "This package completes R's functional programming tools with missing
3734 features present in other programming languages.")
3735 (license license:gpl3+)))
3737 (define-public r-plotly
3743 (uri (cran-uri "plotly" version))
3746 "0wj9lw7w28z8w9ip9vadv6sydjhqyg65kfiai9m3bndzz50b1m3w"))))
3747 (build-system r-build-system)
3749 `(("r-base64enc" ,r-base64enc)
3750 ("r-crosstalk" ,r-crosstalk)
3751 ("r-digest" ,r-digest)
3752 ("r-data-table" ,r-data-table)
3753 ("r-dplyr" ,r-dplyr)
3754 ("r-ggplot2" ,r-ggplot2)
3755 ("r-hexbin" ,r-hexbin)
3756 ("r-htmltools" ,r-htmltools)
3757 ("r-htmlwidgets" ,r-htmlwidgets)
3759 ("r-jsonlite" ,r-jsonlite)
3760 ("r-lazyeval" ,r-lazyeval)
3761 ("r-magrittr" ,r-magrittr)
3762 ("r-purrr" ,r-purrr)
3763 ("r-rcolorbrewer" ,r-rcolorbrewer)
3764 ("r-scales" ,r-scales)
3765 ("r-tibble" ,r-tibble)
3766 ("r-tidyr" ,r-tidyr)
3767 ("r-viridislite" ,r-viridislite)))
3768 (home-page "https://plot.ly/r")
3769 (synopsis "Create interactive web graphics")
3771 "This package enables the translation of ggplot2 graphs to an interactive
3772 web-based version and/or the creation of custom web-based visualizations
3773 directly from R. Once uploaded to a plotly account, plotly graphs (and the
3774 data behind them) can be viewed and modified in a web browser.")
3775 (license license:x11)))
3777 (define-public r-biased-urn
3779 (name "r-biased-urn")
3784 (uri (cran-uri "BiasedUrn" version))
3787 "13i2lgfnjhlbbm2yxfc2l5hswqw6x03pwba5csjmirv8kpjw4xr3"))))
3788 (properties `((upstream-name . "BiasedUrn")))
3789 (build-system r-build-system)
3790 (home-page "http://www.agner.org/random/")
3791 (synopsis "Biased urn model distributions")
3793 "This package provides statistical models of biased sampling in the form
3794 of univariate and multivariate noncentral hypergeometric distributions,
3795 including Wallenius' noncentral hypergeometric distribution and Fisher's
3796 noncentral hypergeometric distribution (also called extended hypergeometric
3798 (license license:gpl3+)))
3800 (define-public r-rematch
3807 (uri (cran-uri "rematch" version))
3810 "0y3mshvpvz9csmq8hk8jbabx4nxlv5sckvfzvm6920ndg34xw2d4"))))
3811 (build-system r-build-system)
3812 (home-page "https://github.com/MangoTheCat/rematch")
3813 (synopsis "Match regular expressions with a nicer API")
3815 "This package provides a small wrapper on @code{regexpr} to extract the
3816 matches and captured groups from the match of a regular expression to a
3818 (license license:expat)))
3820 (define-public r-cellranger
3822 (name "r-cellranger")
3827 (uri (cran-uri "cellranger" version))
3830 "16fgi3annn34c3cxi0pxf62mmmmxi21hp0zzlv7bkfsjqy4g4f2x"))))
3831 (build-system r-build-system)
3833 `(("r-rematch" ,r-rematch)
3834 ("r-tibble" ,r-tibble)))
3835 (home-page "https://github.com/rsheets/cellranger")
3836 (synopsis "Translate spreadsheet cell ranges to rows and columns")
3838 "This package provides helper functions to work with spreadsheets and the
3839 @code{A1:D10} style of cell range specification.")
3840 (license license:expat)))
3842 (define-public r-googlesheets
3844 (name "r-googlesheets")
3849 (uri (cran-uri "googlesheets" version))
3852 "18q0xmxn09b52rmky7gr5flp0awndcnsgb7zcvkzvkrkvmwad52b"))))
3853 (build-system r-build-system)
3855 `(("r-cellranger" ,r-cellranger)
3856 ("r-dplyr" ,r-dplyr)
3858 ("r-jsonlite" ,r-jsonlite)
3859 ("r-purrr" ,r-purrr)
3860 ("r-readr" ,r-readr)
3861 ("r-stringr" ,r-stringr)
3862 ("r-tidyr" ,r-tidyr)
3863 ("r-xml2" ,r-xml2)))
3864 (home-page "https://github.com/jennybc/googlesheets")
3865 (synopsis "Manage Google spreadsheets from R")
3866 (description "This package provides tools to interact with Google Sheets
3868 (license license:expat)))
3870 (define-public r-spams
3873 (version "2.6-2017-03-22")
3877 ;; Use the ‘Latest version’ link for a stable URI across releases.
3878 (uri (string-append "https://gforge.inria.fr/frs/download.php/"
3879 "latestfile/4531/spams-R-v" version ".tar.gz"))
3882 "13z2293jixf1r9g8dyy856xrhvpjr2ln2n9smn6644126r9hmhkx"))))
3883 (build-system r-build-system)
3886 (modify-phases %standard-phases
3887 (add-after 'unpack 'chdir
3888 (lambda _ (chdir "spams") #t))
3889 ;; Don't tune for the building machine.
3890 (add-after 'chdir 'no-mtune
3892 (substitute* "src/Makevars"
3893 (("-mtune=native") ""))
3896 `(("r-lattice" ,r-lattice)
3897 ("r-matrix" ,r-matrix)))
3898 (home-page "http://spams-devel.gforge.inria.fr")
3899 (synopsis "Toolbox for solving sparse estimation problems")
3900 (description "SPAMS (SPArse Modeling Software) is an optimization toolbox
3901 for solving various sparse estimation problems. It includes tools for the
3905 @item Dictionary learning and matrix factorization (NMF, sparse @dfn{principle
3906 component analysis} (PCA), ...)
3907 @item Solving sparse decomposition problems with LARS, coordinate descent,
3908 OMP, SOMP, proximal methods
3909 @item Solving structured sparse decomposition problems (l1/l2, l1/linf, sparse
3910 group lasso, tree-structured regularization, structured sparsity with
3911 overlapping groups,...).
3913 (license license:gpl3+)))
3915 (define-public r-base64
3922 (uri (cran-uri "base64" version))
3925 "1labh0ycdm2xcjssj8bhnyjvbk44mcdsi0rb2p8rfqa428mrq9cf"))))
3926 (build-system r-build-system)
3928 `(("r-openssl" ,r-openssl)))
3929 (home-page "https://cran.r-project.org/web/packages/base64")
3930 (synopsis "Base64 encoder and decoder")
3932 "This package is a compatibility wrapper to replace the orphaned package
3933 by Romain Francois. New applications should use the openssl or base64enc
3935 (license license:expat)))
3937 (define-public r-hmisc
3944 (uri (cran-uri "Hmisc" version))
3947 "160l50ppjs69ipcaya1mlcz29zbn5rmqg91r09dvzzvkvwfb47cr"))))
3948 (properties `((upstream-name . "Hmisc")))
3949 (build-system r-build-system)
3951 `(("gfortran" ,gfortran)))
3953 `(("r-acepack" ,r-acepack)
3954 ("r-base64enc" ,r-base64enc)
3955 ("r-cluster" ,r-cluster)
3956 ("r-data-table" ,r-data-table)
3957 ("r-foreign" ,r-foreign)
3958 ("r-formula" ,r-formula)
3959 ("r-ggplot2" ,r-ggplot2)
3960 ("r-gridextra" ,r-gridextra)
3961 ("r-gtable" ,r-gtable)
3962 ("r-lattice" ,r-lattice)
3963 ("r-latticeextra" ,r-latticeextra)
3964 ("r-htmltable" ,r-htmltable)
3965 ("r-htmltools" ,r-htmltools)
3967 ("r-rpart" ,r-rpart)
3968 ("r-survival" ,r-survival)
3969 ("r-viridis" ,r-viridis)))
3970 (home-page "http://biostat.mc.vanderbilt.edu/Hmisc")
3971 (synopsis "Miscellaneous data analysis and graphics functions")
3973 "This package contains many functions useful for data analysis,
3974 high-level graphics, utility operations, functions for computing sample size
3975 and power, importing and annotating datasets, imputing missing values,
3976 advanced table making, variable clustering, character string manipulation,
3977 conversion of R objects to LaTeX code, and recoding variables.")
3978 (license license:gpl2+)))
3980 (define-public r-runit
3987 (uri (cran-uri "RUnit" version))
3990 "1wc1gwb7yw7phf8b0gkig6c23klya3ax11c6i4s0f049k42r78r3"))))
3991 (properties `((upstream-name . "RUnit")))
3992 (build-system r-build-system)
3993 (home-page "https://cran.r-project.org/web/packages/RUnit")
3994 (synopsis "R unit test framework")
3996 "This package provides R functions implementing a standard unit testing
3997 framework, with additional code inspection and report generation tools.")
3998 (license license:gpl2+)))
4000 (define-public r-dynamictreecut
4002 (name "r-dynamictreecut")
4007 (uri (cran-uri "dynamicTreeCut" version))
4010 "1fadbql7g5r2vvlkr89nlrjxwp4yx4xrdqmv077qvmnx9vv0f4w3"))))
4011 (properties `((upstream-name . "dynamicTreeCut")))
4012 (build-system r-build-system)
4014 "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/BranchCutting/")
4015 (synopsis "Detect clusters in hierarchical clustering dendrograms")
4017 "This package contains methods for the detection of clusters in
4018 hierarchical clustering dendrograms.")
4019 (license license:gpl2+)))
4021 (define-public r-preprocesscore
4023 (name "r-preprocesscore")
4028 (uri (bioconductor-uri "preprocessCore" version))
4031 "1afar1z7959v7mbzsqa77vqfh0yc7y3nv5ayx71485a8scwsfwbk"))))
4033 `((upstream-name . "preprocessCore")))
4034 (build-system r-build-system)
4035 (home-page "https://github.com/bmbolstad/preprocessCore")
4036 (synopsis "Collection of pre-processing functions")
4038 "This package provides a library of core pre-processing and normalization
4040 (license license:lgpl2.0+)))
4042 (define-public r-fastcluster
4044 (name "r-fastcluster")
4049 (uri (cran-uri "fastcluster" version))
4052 "01a2xnhhvv1swd4g8p4lzyn7ww7kg49jlnzc7kfz60jqjzpisrpk"))))
4053 (build-system r-build-system)
4054 (home-page "http://danifold.net/fastcluster.html")
4055 (synopsis "Fast hierarchical clustering routines")
4057 "This package implements fast hierarchical, agglomerative clustering
4058 routines. Part of the functionality is designed as drop-in replacement for
4059 existing routines: @code{linkage()} in the SciPy package
4060 @code{scipy.cluster.hierarchy}, @code{hclust()} in R's @code{stats} package,
4061 and the @code{flashClust} package. It provides the same functionality with
4062 the benefit of a much faster implementation. Moreover, there are
4063 memory-saving routines for clustering of vector data, which go beyond what the
4064 existing packages provide.")
4065 (license license:bsd-2)))
4067 (define-public r-sfsmisc
4074 (uri (cran-uri "sfsmisc" version))
4077 "0cgq2h11ngkzd6p34k6mqjnvlvc5vj4lnqrl64k05lb391j391w0"))))
4078 (build-system r-build-system)
4079 (home-page "https://cran.r-project.org/web/packages/sfsmisc")
4080 (synopsis "Utilities from \"Seminar fuer Statistik\" ETH Zurich")
4082 "This package provides useful utilities from Seminar fuer Statistik ETH
4083 Zurich, including many that are related to graphics.")
4084 (license license:gpl2+)))
4086 (define-public r-gtools
4093 (uri (cran-uri "gtools" version))
4096 "1xknwk9xlsj027pg0nwiizigcrsc84hdrig0jn0cgcyxj8dabdl6"))))
4097 (build-system r-build-system)
4100 (modify-phases %standard-phases
4101 (add-after 'unpack 'make-deterministic
4103 (substitute* "R/checkReverseDependencies.R"
4104 (("tempdir\\(\\)") "\"/tmp\""))
4106 (home-page "https://cran.r-project.org/web/packages/gtools")
4107 (synopsis "Various R programming tools")
4109 "This package contains a collection of various functions to assist in R
4110 programming, such as tools to assist in developing, updating, and maintaining
4111 R and R packages, calculating the logit and inverse logit transformations,
4112 tests for whether a value is missing, empty or contains only @code{NA} and
4113 @code{NULL} values, and many more.")
4114 (license license:gpl2)))
4116 (define-public r-gdata
4123 (uri (cran-uri "gdata" version))
4126 "0zwdj7lscgxr8r62ii8hbdh4mb7sa9w4f5nv32zzrxdvymcpya2b"))))
4127 (build-system r-build-system)
4131 `(("r-gtools" ,r-gtools)))
4132 (home-page "https://cran.r-project.org/web/packages/gdata")
4133 (synopsis "Various R programming tools for data manipulation")
4135 "This package provides various R programming tools for data manipulation,
4139 @item medical unit conversions
4140 @item combining objects
4141 @item character vector operations
4142 @item factor manipulation
4143 @item obtaining information about R objects
4144 @item manipulating MS-Excel formatted files
4145 @item generating fixed-width format files
4146 @item extricating components of date and time objects
4147 @item operations on columns of data frames
4148 @item matrix operations
4149 @item operations on vectors and data frames
4150 @item value of last evaluated expression
4151 @item wrapper for @code{sample} that ensures consistent behavior for
4152 both scalar and vector arguments
4154 (license license:gpl2+)))
4156 (define-public r-gplots
4163 (uri (cran-uri "gplots" version))
4166 "02nb8n3s7c1zxq2s7ycaq2ys72y7mzirxrwj954h6gdc4x1zhg9l"))))
4167 (build-system r-build-system)
4169 `(("r-catools" ,r-catools)
4170 ("r-gdata" ,r-gdata)
4171 ("r-gtools" ,r-gtools)
4172 ("r-kernsmooth" ,r-kernsmooth)))
4173 (home-page "https://cran.r-project.org/web/packages/gplots")
4174 (synopsis "Various R programming tools for plotting data")
4176 "This package provides various R programming tools for plotting data,
4180 @item calculating and plotting locally smoothed summary function
4181 @item enhanced versions of standard plots
4182 @item manipulating colors
4183 @item calculating and plotting two-dimensional data summaries
4184 @item enhanced regression diagnostic plots
4185 @item formula-enabled interface to @code{stats::lowess} function
4186 @item displaying textual data in plots
4188 @item plotting \"Venn\" diagrams
4189 @item displaying Open-Office style plots
4190 @item plotting multiple data on same region, with separate axes
4191 @item plotting means and confidence intervals
4192 @item spacing points in an x-y plot so they don't overlap
4194 (license license:gpl2+)))
4196 (define-public r-rocr
4203 (uri (cran-uri "ROCR" version))
4206 "1jay8cm7lgq56i967vm5c2hgaxqkphfpip0gn941li3yhh7p3vz7"))))
4207 (properties `((upstream-name . "ROCR")))
4208 (build-system r-build-system)
4210 `(("r-gplots" ,r-gplots)))
4211 (home-page "http://rocr.bioinf.mpi-sb.mpg.de/")
4212 (synopsis "Visualizing the performance of scoring classifiers")
4214 "ROCR is a flexible tool for creating cutoff-parameterized 2D performance
4215 curves by freely combining two from over 25 performance measures (new
4216 performance measures can be added using a standard interface). Curves from
4217 different cross-validation or bootstrapping runs can be averaged by different
4218 methods, and standard deviations, standard errors or box plots can be used to
4219 visualize the variability across the runs. The parameterization can be
4220 visualized by printing cutoff values at the corresponding curve positions, or
4221 by coloring the curve according to cutoff. All components of a performance
4222 plot can be quickly adjusted using a flexible parameter dispatching
4224 (license license:gpl2+)))
4226 (define-public r-zoo
4232 (uri (cran-uri "zoo" version))
4235 "1lpwigxmi5sc23xrha4gcsccsm4yfsg0sa97y6vac3pg1lliblvx"))))
4236 (build-system r-build-system)
4238 `(("r-lattice" ,r-lattice)))
4239 (home-page "http://zoo.R-Forge.R-project.org/")
4240 (synopsis "S3 infrastructure for regular and irregular time series")
4241 (description "This package contains an S3 class with methods for totally
4242 ordered indexed observations. It is particularly aimed at irregular time
4243 series of numeric vectors/matrices and factors.")
4244 (license license:gpl2+)))
4246 (define-public r-ztable
4252 (uri (cran-uri "ztable" version))
4255 "1hk5k9614n52dpfrhdws06w4gvwhnz8q47x4cwxx88qmrzm8z2m3"))))
4256 (build-system r-build-system)
4257 (home-page "https://cran.r-project.org/web/packages/ztable")
4258 (synopsis "Zebra-striped tables in LaTeX and HTML formats for R")
4260 "This package provides functions to make zebra-striped tables (tables
4261 with alternating row colors) in LaTeX and HTML formats easily from
4262 @code{data.frame}, @code{matrix}, @code{lm}, @code{aov}, @code{anova},
4263 @code{glm}, @code{coxph}, @code{nls}, @code{fitdistr}, @code{mytable} and
4264 @code{cbind.mytable} objects.")
4265 (license license:gpl2+)))
4267 (define-public r-vipor
4273 (uri (cran-uri "vipor" version))
4276 "112gc0d7f8iavgf56pnzfxb7hy75yhd0zlyjzshdcfbnqcd2a6bx"))))
4277 (build-system r-build-system)
4278 (home-page "https://cran.r-project.org/web/packages/vipor")
4279 (synopsis "Plot categorical data using noise and density estimates")
4281 "This package provides tools to generate a violin point plot, a
4282 combination of a violin/histogram plot and a scatter plot by offsetting points
4283 within a category based on their density using quasirandom noise.")
4284 (license license:gpl2+)))
4286 (define-public r-beeswarm
4292 (uri (cran-uri "beeswarm" version))
4295 "0hy89bwv7jixlg91li1fywa77916am2whqp1m1fx1khd45g44581"))))
4296 (build-system r-build-system)
4297 (home-page "http://www.cbs.dtu.dk/~eklund/beeswarm/")
4298 (synopsis "Implementation of bee swarm plots")
4300 "This package provides an implementation of bee swarm plots. The bee
4301 swarm plot is a one-dimensional scatter plot like stripchart, but with
4302 closely-packed, non-overlapping points.")
4303 (license license:artistic2.0)))
4305 (define-public r-sourcetools
4307 (name "r-sourcetools")
4312 (uri (cran-uri "sourcetools" version))
4315 "1jnjir0q2dj724f1mjm6p5h77yzyx6xcqy9r2g7gmcxkxw349627"))))
4316 (build-system r-build-system)
4317 (home-page "https://cran.r-project.org/web/packages/sourcetools")
4318 (synopsis "Tools for reading, tokenizing and parsing R code")
4320 "The sourcetools package provides both an R and C++ interface for the
4321 tokenization of R code, and helpers for interacting with the tokenized
4322 representation of R code.")
4323 (license license:expat)))
4325 (define-public r-ggbeeswarm
4327 (name "r-ggbeeswarm")
4331 (uri (cran-uri "ggbeeswarm" version))
4334 "0crk29p5vi1r3a988kms4y7r0iqwgwzsikgvh18r9wbzyr98bb5v"))))
4335 (build-system r-build-system)
4337 `(("r-beeswarm" ,r-beeswarm)
4338 ("r-ggplot2" ,r-ggplot2)
4339 ("r-vipor" ,r-vipor)))
4340 (home-page "https://github.com/eclarke/ggbeeswarm")
4341 (synopsis "Categorical scatter (violin point) plots")
4343 "This package provides two methods of plotting categorical scatter plots
4344 such that the arrangement of points within a category reflects the density of
4345 data at that region, and avoids over-plotting.")
4346 (license license:gpl2+)))
4348 (define-public r-ggthemes
4354 (uri (cran-uri "ggthemes" version))
4357 "0drbzzb4i5jq1579fx1wmgh87ybnswjn7srak2l8g771ip49xwb8"))))
4358 (build-system r-build-system)
4360 `(("r-assertthat" ,r-assertthat)
4361 ("r-colorspace" ,r-colorspace)
4362 ("r-ggplot2" ,r-ggplot2)
4363 ("r-scales" ,r-scales)))
4364 (home-page "https://cran.rstudio.com/web/packages/ggthemes")
4365 (synopsis "Extra themes, scales and geoms for @code{ggplot2}")
4366 (description "This package provides extra themes and scales for
4367 @code{ggplot2} that replicate the look of plots by Edward Tufte and
4368 Stephen Few in Fivethirtyeight, The Economist, Stata, Excel, and The
4369 Wall Street Journal, among others. This package also provides
4370 @code{geoms} for Tufte's box plot and range frame.")
4371 (license license:gpl2)))
4373 (define-public r-statmod
4379 (uri (cran-uri "statmod" version))
4382 "07v4x8af60alcw6vbiwf5fp25bhra61kvxz9kqx64lszm0i1fb4x"))))
4383 (build-system r-build-system)
4384 (home-page "https://cran.r-project.org/web/packages/statmod")
4386 `(("gfortran" ,gfortran)))
4387 (synopsis "Statistical modeling")
4389 "This package provides a collection of algorithms and functions to aid
4390 statistical modeling. It includes growth curve comparisons, limiting dilution
4391 analysis (aka ELDA), mixed linear models, heteroscedastic regression,
4392 inverse-Gaussian probability calculations, Gauss quadrature and a secure
4393 convergence algorithm for nonlinear models. It also includes advanced
4394 generalized linear model functions that implement secure convergence,
4395 dispersion modeling and Tweedie power-law families.")
4396 ;; Statmod is distributed under either license
4397 (license (list license:gpl2 license:gpl3))))
4399 (define-public r-rann
4405 (uri (cran-uri "RANN" version))
4408 "0il5i99vbcagnxvb15af5n37g04a4q1x96bz73zh3jhki9fpw9vm"))))
4410 `((upstream-name . "RANN")))
4411 (build-system r-build-system)
4412 (home-page "https://github.com/jefferis/RANN")
4413 (synopsis "Fast nearest neighbour search")
4415 "This package finds the k nearest neighbours for every point in a given
4416 dataset in O(N log N) time using Arya and Mount's ANN library. Provides
4417 approximate, exact searches, fixed radius searches, bd and kb trees.")
4418 (license license:gpl3+)))
4420 (define-public r-fivethirtyeight
4422 (name "r-fivethirtyeight")
4427 (uri (string-append "https://mran.microsoft.com/src/contrib/"
4428 "fivethirtyeight_" version ".tar.gz"))
4431 "0fcc8rq745nsghp27dk0lgih90y4zx8hrzcvsn6ih786yv7qxhvl"))))
4432 (build-system r-build-system)
4434 `(("r-knitr" ,r-knitr)
4435 ("r-rmarkdown" ,r-rmarkdown)
4436 ("r-dplyr" ,r-dplyr)
4437 ("r-readr" ,r-readr)
4438 ("r-ggplot2" ,r-ggplot2)
4439 ("r-magrittr" ,r-magrittr)
4440 ("r-stringr" ,r-stringr)))
4441 (home-page "https://mran.microsoft.com/package/fivethirtyeight/")
4442 (synopsis "Data and code behind the stories at FiveThirtyEight")
4443 (description "This R package provides access to the code and data sets
4444 published by the statistics blog FiveThirtyEight.")
4445 (license license:expat)))
4447 (define-public r-compquadform
4449 (name "r-compquadform")
4454 (uri (cran-uri "CompQuadForm" version))
4457 "1i30hrqdk64q17vsn918c3q79brchgx2wzh1gbsgbn0dh1ncabq4"))))
4458 (properties `((upstream-name . "CompQuadForm")))
4459 (build-system r-build-system)
4460 (home-page "https://cran.r-project.org/web/packages/CompQuadForm")
4461 (synopsis "Distribution function of quadratic forms in normal variables")
4463 "This package provides functions to compute the distribution function of
4464 quadratic forms in normal variables using Imhof's method, Davies's algorithm,
4465 Farebrother's algorithm or Liu et al.'s algorithm.")
4466 (license license:gpl2+)))
4468 (define-public r-cowplot
4475 (uri (cran-uri "cowplot" version))
4478 "1jrx1h0blkk577y4cvnjk7xccn7qmjiv2bnpgqlsjvjhsxglf41y"))))
4479 (build-system r-build-system)
4481 `(("r-ggplot2" ,r-ggplot2)
4482 ("r-gtable" ,r-gtable)
4484 ("r-scales" ,r-scales)))
4485 (home-page "https://github.com/wilkelab/cowplot")
4486 (synopsis "Streamlined plot theme and plot annotations for ggplot2")
4488 "This package provides some helpful extensions and modifications to the
4489 ggplot2 package to combine multiple ggplot2 plots into one and label them with
4490 letters, as is often required for scientific publications.")
4491 (license license:gpl2)))
4493 (define-public r-mixtools
4500 (uri (cran-uri "mixtools" version))
4503 "13wdm0xs5bakhpa8ypg6lvhjaqkxyabwz4glxdwn0jwdvkcdhgsl"))))
4504 (build-system r-build-system)
4506 `(("r-mass" ,r-mass)
4507 ("r-segmented" ,r-segmented)
4508 ("r-survival" ,r-survival)))
4509 (home-page "https://cran.r-project.org/web/packages/mixtools")
4510 (synopsis "Tools for analyzing finite mixture models")
4512 "This package provides a collection of R functions for analyzing finite
4514 (license license:gpl2+)))
4516 (define-public r-lars
4523 (uri (cran-uri "lars" version))
4526 "0blj44wqrx6lmym1m9v6wkz8zxzbjax2zl6swgdczci0ixb5nx34"))))
4527 (build-system r-build-system)
4529 `(("gfortran" ,gfortran)))
4530 (home-page "http://www-stat.stanford.edu/~hastie/Papers/#LARS")
4531 (synopsis "Least angle regression software")
4533 "Least Angle Regression (\"LAR\") is a model selection algorithm; a
4534 useful and less greedy version of traditional forward selection methods. A
4535 simple modification of the LAR algorithm implements Tibshirani's Lasso; the
4536 Lasso modification of LARS calculates the entire Lasso path of coefficients
4537 for a given problem at the cost of a single least squares fit. Another LARS
4538 modification efficiently implements epsilon Forward Stagewise linear
4540 (license license:gpl2)))
4542 (define-public r-fastica
4549 (uri (cran-uri "fastICA" version))
4552 "108z2ymby5y4h8l4l2krqwm28rya93gq09yylgilnm3afvfrfabg"))))
4553 (properties `((upstream-name . "fastICA")))
4554 (build-system r-build-system)
4555 (home-page "https://cran.r-project.org/web/packages/fastICA")
4556 (synopsis "FastICA algorithms to perform ICA and projection pursuit")
4558 "This package provides an implementation of the FastICA algorithm to
4559 perform @dfn{independent component analysis} (ICA) and projection pursuit.")
4561 (license license:gpl3+)))
4563 (define-public r-randomforest
4565 (name "r-randomforest")
4570 (uri (cran-uri "randomForest" version))
4573 "0kbmm0l42fc2d1rdq0l7k09d34kd87q4lx651ffsic4y84h8kf7l"))))
4574 (properties `((upstream-name . "randomForest")))
4575 (build-system r-build-system)
4576 (home-page "https://www.stat.berkeley.edu/~breiman/RandomForests/")
4578 `(("gfortran" ,gfortran)))
4579 (synopsis "Breiman and Cutler's random forests for classification and regression")
4581 "This package provides the Breiman and Cutler's random forests algorithm, based on a
4582 forest of trees using random inputs, for classification and regression.")
4583 (license license:gpl2+)))
4585 (define-public r-diptest
4592 (uri (cran-uri "diptest" version))
4595 "06xnc5gv1284ll0addxnxb6ljz6fn8dbyrp5vchyz6551h800aa6"))))
4596 (build-system r-build-system)
4597 (home-page "https://cran.r-project.org/web/packages/diptest")
4598 (synopsis "Hartigan's dip test statistic for unimodality")
4600 "This package computes Hartigan's dip test statistic for unimodality,
4601 multimodality and provides a test with simulation based p-values, where the
4602 original public code has been corrected.")
4603 (license license:gpl2+)))
4605 (define-public r-modeltools
4607 (name "r-modeltools")
4612 (uri (cran-uri "modeltools" version))
4615 "1s9lmkac3rl0nknf4wizfhg7ryq7c8yvvyc4z619238br27hhsi5"))))
4616 (build-system r-build-system)
4617 (home-page "https://cran.r-project.org/web/packages/modeltools")
4618 (synopsis "Tools and classes for statistical models")
4620 "This package provides a collection of tools to deal with statistical
4621 models. The functionality is experimental and the user interface is likely
4622 to change in the future.")
4623 (license license:gpl2)))
4625 (define-public r-flexmix
4632 (uri (cran-uri "flexmix" version))
4635 "0sl4zxh1sb2sr5q7svjw9ihrm219jzn82yrc9d43q6r1b8bpyz43"))))
4636 (build-system r-build-system)
4638 `(("r-lattice" ,r-lattice)
4639 ("r-modeltools" ,r-modeltools)
4640 ("r-nnet" ,r-nnet)))
4641 (home-page "https://cran.r-project.org/web/packages/flexmix")
4642 (synopsis "Flexible mixture modeling")
4644 "This package implements a general framework for finite mixtures of
4645 regression models using the EM algorithm. FlexMix provides the E-step and
4646 all data handling, while the M-step can be supplied by the user to easily
4647 define new models. Existing drivers implement mixtures of standard linear
4648 models, generalized linear models and model-based clustering.")
4649 (license license:gpl2+)))
4651 (define-public r-mclust
4658 (uri (cran-uri "mclust" version))
4661 "1vcl4nl8by2vj2k9k84imy5m850khkgd8q02a8ica1h8vz9ijgn4"))))
4662 (build-system r-build-system)
4664 `(("gfortran" ,gfortran)))
4665 (home-page "http://www.stat.washington.edu/mclust/")
4666 (synopsis "Gaussian mixture modelling for model-based clustering etc.")
4668 "This package provides Gaussian finite mixture models fitted via EM
4669 algorithm for model-based clustering, classification, and density estimation,
4670 including Bayesian regularization, dimension reduction for visualisation,
4671 and resampling-based inference.")
4672 (license license:gpl2+)))
4674 (define-public r-prabclus
4681 (uri (cran-uri "prabclus" version))
4684 "0qjsxrx6yv338bxm4ki0w9h8hind1l98abdrz828588bwj02jya1"))))
4685 (build-system r-build-system)
4687 `(("r-mass" ,r-mass)
4688 ("r-mclust" ,r-mclust)))
4689 (home-page "https://cran.r-project.org/web/packages/prabclus")
4690 (synopsis "Parametric bootstrap tests for spatial neighborhood clustering")
4692 "This package provides distance-based parametric bootstrap tests for
4693 clustering with spatial neighborhood information. It implements some distance
4694 measures, clustering of presence-absence, abundance and multilocus genetical
4695 data for species delimitation, nearest neighbor based noise detection.")
4696 (license license:gpl2+)))
4698 (define-public r-deoptimr
4705 (uri (cran-uri "DEoptimR" version))
4708 "1vz546hyjyhly70z62h5n3mn62b8llhhmim8ffp9y6jnnb0i2sc4"))))
4709 (properties `((upstream-name . "DEoptimR")))
4710 (build-system r-build-system)
4711 (home-page "https://cran.r-project.org/web/packages/DEoptimR")
4712 (synopsis "Differential evolution optimization in pure R")
4714 "This package provides a differential evolution (DE) stochastic
4715 algorithms for global optimization of problems with and without constraints.
4716 The aim is to curate a collection of its state-of-the-art variants that (1) do
4717 not sacrifice simplicity of design, (2) are essentially tuning-free, and (3)
4718 can be efficiently implemented directly in the R language.")
4719 (license license:gpl2+)))
4721 (define-public r-robustbase
4723 (name "r-robustbase")
4728 (uri (cran-uri "robustbase" version))
4731 "130pzibn5cb8mycv8byc6npzcpddghz8m7jqwk15qmx4g3cj8zgy"))))
4732 (build-system r-build-system)
4734 `(("gfortran" ,gfortran)))
4736 `(("r-deoptimr" ,r-deoptimr)))
4737 (home-page "http://robustbase.r-forge.r-project.org/")
4738 (synopsis "Basic robust statistics")
4740 "This packages allows to analyze data with robust methods such as
4741 regression methodology including model selections and multivariate statistics.")
4742 (license license:gpl2+)))
4744 (define-public r-pcapp
4751 (uri (cran-uri "pcaPP" version))
4754 "1z2kdf9gfp965xbcd4rg6vf20d1bl443na0qjkpq7gmzpaq6cifa"))))
4755 (properties `((upstream-name . "pcaPP")))
4756 (build-system r-build-system)
4758 `(("r-mvtnorm" ,r-mvtnorm)))
4759 (home-page "https://cran.r-project.org/web/packages/pcaPP")
4760 (synopsis "Robust PCA by projection pursuit")
4762 "This package provides functions for robust @dfn{principal component
4763 analysis} (PCA) by projection pursuit.")
4764 (license license:gpl3+)))
4766 (define-public r-rrcov
4773 (uri (cran-uri "rrcov" version))
4776 "0wn5h8vi0zyk5ah898m37ysz4kiih6y792nb9zdvhvd8r07f0sc5"))))
4777 (build-system r-build-system)
4779 `(("r-cluster" ,r-cluster)
4780 ("r-lattice" ,r-lattice)
4781 ("r-mvtnorm" ,r-mvtnorm)
4782 ("r-pcapp" ,r-pcapp)
4783 ("r-robustbase" ,r-robustbase)))
4785 `(("gfortran" ,gfortran)))
4786 (home-page "https://cran.r-project.org/web/packages/rrcov")
4787 (synopsis "Scalable robust estimators with high breakdown Point")
4789 "This package provides an implementation of robust location and scatter
4790 estimation and robust multivariate analysis with high breakdown point.")
4791 (license license:gpl2+)))
4793 (define-public r-fit-models
4795 (name "r-fit-models")
4800 (uri (cran-uri "fit.models" version))
4803 "0vjbzmx0ambm6yzidb4vbgmhclwzwv2iz2cwl54ccdkvx4cx3fck"))))
4804 (properties `((upstream-name . "fit.models")))
4805 (build-system r-build-system)
4807 `(("r-lattice" ,r-lattice)))
4808 (home-page "https://cran.r-project.org/web/packages/fit.models")
4809 (synopsis "Compare fitted models")
4811 "The @code{fit.models} function and its associated methods (coefficients, print,
4812 summary, plot, etc.) were originally provided in the @code{robust} package to
4813 compare robustly and classically fitted model objects. The aim of the
4814 @code{fit.models} package is to separate this fitted model object comparison
4815 functionality from the robust package and to extend it to support fitting
4816 methods (e.g., classical, robust, Bayesian, regularized, etc.) more
4818 ;; Any version of the GPL
4819 (license (list license:gpl2+ license:gpl3+))))
4821 (define-public r-robust
4828 (uri (cran-uri "robust" version))
4831 "1b7qh1aff500nd6dh4y2ipmjgdiq8991shflb63pc39vpc0ny6g4"))))
4832 (build-system r-build-system)
4834 `(("r-fit-models" ,r-fit-models)
4835 ("r-lattice" ,r-lattice)
4837 ("r-robustbase" ,r-robustbase)
4838 ("r-rrcov" ,r-rrcov)))
4840 `(("gfortran" ,gfortran)))
4841 (home-page "https://cran.r-project.org/web/packages/robust")
4842 (synopsis "Port of the S+ \"Robust Library\"")
4844 "This package is a port of the S+ \"Robust Library\". It provides
4845 methods for robust statistics, notably for robust regression and robust
4846 multivariate analysis.")
4847 (license license:gpl2)))
4849 (define-public r-trimcluster
4851 (name "r-trimcluster")
4856 (uri (cran-uri "trimcluster" version))
4859 "0013bpyq6mkvjn38qsmwnsxfiwxgwngnqxycxvgpgmiadhm8fjmn"))))
4860 (build-system r-build-system)
4861 (home-page "https://cran.r-project.org/web/packages/trimcluster")
4862 (synopsis "Cluster analysis with trimming")
4864 "The trimmed k-means clustering method by Cuesta-Albertos, Gordaliza and
4865 Matran (1997). This optimizes the k-means criterion under trimming a portion
4868 (license (list license:gpl2+ license:gpl3+))))
4870 (define-public r-fpc
4873 (version "2.1-11.1")
4877 (uri (cran-uri "fpc" version))
4880 "1ari57hkgqsxh6khr6j52cfrzc0096cnn1q7ghxk2z4brdd4rznc"))))
4881 (build-system r-build-system)
4883 `(("r-class" ,r-class)
4884 ("r-cluster" ,r-cluster)
4885 ("r-diptest" ,r-diptest)
4886 ("r-flexmix" ,r-flexmix)
4887 ("r-kernlab" ,r-kernlab)
4889 ("r-mclust" ,r-mclust)
4890 ("r-mvtnorm" ,r-mvtnorm)
4891 ("r-prabclus" ,r-prabclus)
4892 ("r-robustbase" ,r-robustbase)
4893 ("r-trimcluster" ,r-trimcluster)))
4894 (home-page "https://cran.r-project.org/web/packages/fpc")
4895 (synopsis "Flexible procedures for clustering")
4897 "This package provides various methods for clustering and cluster validation.
4898 For example, it provides fixed point clustering, linear regression clustering,
4899 clustering by merging Gaussian mixture components, as well as symmetric and
4900 asymmetric discriminant projections for visualisation of the separation of
4902 (license license:gpl2+)))
4904 (define-public r-vgam
4911 (uri (cran-uri "VGAM" version))
4914 "1fg31xz86jblqraifiy3q36d0hjqnll01jxx85xq87j1cyhj060j"))))
4915 (properties `((upstream-name . "VGAM")))
4916 (build-system r-build-system)
4918 `(("gfortran" ,gfortran)))
4919 (home-page "https://www.stat.auckland.ac.nz/~yee/VGAM")
4920 (synopsis "Vector generalized linear and additive models")
4922 "This package is an implementation of about 6 major classes of statistical
4923 regression models. Currently only fixed-effects models are implemented, i.e.,
4924 no random-effects models. Many (150+) models and distributions are estimated
4925 by maximum likelihood estimation (MLE) or penalized MLE, using Fisher scoring.
4926 VGLMs can be loosely thought of as multivariate generalised linear models.")
4927 (license license:gpl2+)))
4929 (define-public r-pbapply
4936 (uri (cran-uri "pbapply" version))
4939 "0lk5kxac09xzdv6vf7ix6r5bfrm7cnpyr2l5mkd4igpciadszzfd"))))
4940 (build-system r-build-system)
4941 (home-page "https://github.com/psolymos/pbapply")
4942 (synopsis "Adding progress bar to apply functions")
4944 "This lightweight package that adds progress bar to vectorized R
4945 functions apply. The implementation can easily be added to functions where
4946 showing the progress is useful e.g. bootstrap.")
4947 (license license:gpl2)))
4949 (define-public r-minqa
4956 (uri (cran-uri "minqa" version))
4959 "036drja6xz7awja9iwb76x91415p26fb0jmg7y7v0p65m6j978fg"))))
4960 (build-system r-build-system)
4962 `(("r-rcpp" ,r-rcpp)))
4964 `(("gfortran" ,gfortran)))
4965 (home-page "http://optimizer.r-forge.r-project.org")
4966 (synopsis "Derivative-free optimization algorithms by quadratic approximation")
4968 "This package provides a derivative-free optimization by quadratic approximation
4969 based on an interface to Fortran implementations by M. J. D. Powell.")
4970 (license license:gpl2)))
4972 (define-public r-rcppeigen
4974 (name "r-rcppeigen")
4975 (version "0.3.3.4.0")
4979 (uri (cran-uri "RcppEigen" version))
4982 "1m6ssq6lvi36ggf26y4hhq996583pxxdb978jnn1x6r9gdb0q0hi"))))
4983 (properties `((upstream-name . "RcppEigen")))
4984 (build-system r-build-system)
4986 `(("r-rcpp" ,r-rcpp)
4987 ("r-matrix" ,r-matrix)))
4988 (home-page "http://eigen.tuxfamily.org")
4989 (synopsis "Rcpp integration for the Eigen templated linear algebra library")
4991 "This package provides an integration of Eigen in R using a C++ template
4992 library for linear algebra: matrices, vectors, numerical solvers and related algorithms.
4993 It supports dense and sparse matrices on integer, floating point and complex numbers,
4994 decompositions of such matrices, and solutions of linear systems.")
4995 (license license:gpl2+)))
4997 (define-public r-modelmetrics
4999 (name "r-modelmetrics")
5004 (uri (cran-uri "ModelMetrics" version))
5007 "119xxmzb5biq7k1yxqsf0jmmarmfn6lds9x9hfgv593xlpym6za8"))))
5008 (properties `((upstream-name . "ModelMetrics")))
5009 (build-system r-build-system)
5011 `(("r-rcpp" ,r-rcpp)))
5012 (home-page "https://cran.r-project.org/web/packages/ModelMetrics")
5013 (synopsis "Rapid calculation of model metrics")
5015 "Written in C++ using @code{Rcpp}, this package provides a collection of
5016 metrics for evaluating models.")
5017 (license license:gpl2+)))
5019 (define-public r-matrixmodels
5021 (name "r-matrixmodels")
5026 (uri (cran-uri "MatrixModels" version))
5029 "0cyfvhci2p1vr2x52ymkyqqs63x1qchn856dh2j94yb93r08x1zy"))))
5030 (properties `((upstream-name . "MatrixModels")))
5031 (build-system r-build-system)
5033 `(("r-matrix" ,r-matrix)))
5034 (home-page "https://cran.r-project.org/web/packages/MatrixModels")
5035 (synopsis "Modelling with sparse and dense matrices")
5037 "This package models with sparse and dense matrix matrices,
5038 using modular prediction and response module classes.")
5039 (license license:gpl2+)))
5041 (define-public r-quantreg
5048 (uri (cran-uri "quantreg" version))
5051 "023gdzahxp582rpabilpxbl3wyjrgjjnnrhcv9xhrqdfiq5l2yza"))))
5052 (build-system r-build-system)
5054 `(("gfortran" ,gfortran)))
5056 `(("r-matrix" ,r-matrix)
5057 ("r-matrixmodels" ,r-matrixmodels)
5058 ("r-sparsem" ,r-sparsem)))
5059 (home-page "https://www.r-project.org")
5060 (synopsis "Quantile regression")
5062 "This package provides an estimation and inference methods for models
5063 of conditional quantiles: linear and nonlinear parametric and non-parametric
5064 models for conditional quantiles of a univariate response and several methods
5065 for handling censored survival data. Portfolio selection methods based on
5066 expected shortfall risk are also included.")
5067 (license license:gpl2+)))
5069 (define-public r-nloptr
5076 (uri (cran-uri "nloptr" version))
5079 "1sz1xj3785x4vsm4nd6in298bk32hs2jk5nsxma7ivxi7jcmn8l4"))))
5080 (build-system r-build-system)
5082 `(("pkg-config" ,pkg-config)))
5084 `(("nlopt" ,nlopt)))
5085 (home-page "https://cran.r-project.org/web/packages/nloptr")
5086 (synopsis "R interface to NLopt")
5088 "This package is interface to NLopt, a library for nonlinear
5089 optimization. NLopt is a library for nonlinear optimization, providing a
5090 common interface for a number of different free optimization routines
5091 available online as well as original implementations of various other
5093 (license license:lgpl3)))
5095 (define-public r-lme4
5098 (version "1.1-18-1")
5102 (uri (cran-uri "lme4" version))
5105 "01ar4fak8zj7c1vmh9m576wchxj5qzpfqn637s7fh3fl6cpz0alq"))))
5106 (build-system r-build-system)
5108 `(("r-rcpp" ,r-rcpp)
5109 ("r-rcppeigen" ,r-rcppeigen)))
5111 `(("r-lattice" ,r-lattice)
5112 ("r-matrix" ,r-matrix)
5113 ("r-minqa" ,r-minqa)
5114 ("r-nloptr" ,r-nloptr)
5116 ("r-nlme" ,r-nlme)))
5117 (home-page "https://cran.r-project.org/web/packages/lme4")
5118 (synopsis "Linear mixed-effects models using eigen and S4")
5120 "This package provides fit linear and generalized linear mixed-effects
5121 models. The models and their components are represented using S4 classes and
5122 methods. The core computational algorithms are implemented using the Eigen
5123 C++ library for numerical linear algebra and RcppEigen glue.")
5124 (license license:gpl2+)))
5126 (define-public r-pbkrtest
5133 (uri (cran-uri "pbkrtest" version))
5136 "1si3bhi59xc51a0pgjjglccq3h4aljyhw2k1b8574s145fnh7fsw"))))
5137 (build-system r-build-system)
5139 `(("r-lme4" ,r-lme4)
5141 ("r-matrix" ,r-matrix)))
5142 (home-page "http://people.math.aau.dk/~sorenh/software/pbkrtest/")
5143 (synopsis "Methods for linear mixed model comparison")
5145 "This package implements a parametric bootstrap test and a Kenward Roger
5146 modification of F-tests for linear mixed effects models and a parametric
5147 bootstrap test for generalized linear mixed models.")
5148 (license license:gpl2+)))
5150 (define-public r-cardata
5157 (uri (cran-uri "carData" version))
5160 "193pdwgw6gk19v7swk1kwphg3vqdmpsgi555g9nyz93sa39j7r8j"))))
5161 (properties `((upstream-name . "carData")))
5162 (build-system r-build-system)
5163 (home-page "https://r-forge.r-project.org/projects/car/")
5164 (synopsis "Data Sets for the book Companion to Applied Regression")
5166 "This package provides datasets to accompany J. Fox and S. Weisberg, An R
5167 Companion to Applied Regression, Third Edition, Sage.")
5168 (license license:gpl2+)))
5170 (define-public r-car
5177 (uri (cran-uri "car" version))
5180 "0l3wyc9ia0ypcbap2p39slazfpbl84mjzydqvpsywrzdiyxajnfz"))))
5181 (build-system r-build-system)
5183 `(("r-abind" ,r-abind)
5184 ("r-cardata" ,r-cardata)
5186 ("r-maptools" ,r-maptools)
5191 ("r-pbkrtest" ,r-pbkrtest)
5192 ("r-quantreg" ,r-quantreg)
5194 (home-page "https://r-forge.r-project.org/projects/car/")
5195 (synopsis "Companion to applied regression")
5197 "This package provides functions and datasets from book Companion
5198 to Applied regression, Second Edition, Sage, 2011.")
5199 (license license:gpl2+)))
5201 (define-public r-caret
5208 (uri (cran-uri "caret" version))
5211 "0xhdhazzfh0hiqv2hgxglj9ffd2p4ls8acqn2sjn0ndx6158f187"))))
5212 (build-system r-build-system)
5214 `(("r-foreach" ,r-foreach)
5215 ("r-ggplot2" ,r-ggplot2)
5216 ("r-lattice" ,r-lattice)
5217 ("r-modelmetrics" ,r-modelmetrics)
5220 ("r-recipes" ,r-recipes)
5221 ("r-reshape2" ,r-reshape2)
5222 ("r-withr" ,r-withr)))
5223 (home-page "https://github.com/topepo/caret")
5224 (synopsis "Classification and regression training")
5226 "This package provides misc functions for training and plotting
5227 classification and regression models.")
5228 (license license:gpl2+)))
5230 (define-public r-rcppprogress
5232 (name "r-rcppprogress")
5237 (uri (cran-uri "RcppProgress" version))
5240 "0yk01hfv961zyp569682k9igvhnwqyg5j0n5fm63sxigj82l2xhi"))))
5241 (properties `((upstream-name . "RcppProgress")))
5242 (build-system r-build-system)
5244 `(("r-devtools" ,r-devtools)
5245 ("r-rcpp" ,r-rcpp)))
5246 (home-page "https://github.com/kforner/rcpp_progress")
5247 (synopsis "Interruptible progress bar for C++ in R packages")
5249 "This package allows to display a progress bar in the R console for long running
5250 computations taking place in C++ code, and support for interrupting those computations
5251 even in multithreaded code, typically using OpenMP.")
5252 (license license:gpl3+)))
5254 (define-public r-mnormt
5261 (uri (cran-uri "mnormt" version))
5264 "1b34xxrnf35khsx82mhvmk96sgfr2flyasaah7qkb2976pwxay7z"))))
5265 (build-system r-build-system)
5267 `(("gfortran" ,gfortran)))
5268 (home-page "http://azzalini.stat.unipd.it/SW/Pkg-mnormt")
5269 (synopsis "Multivariate normal and \"t\" distributions")
5271 "This package provides functions for computing the density and the
5272 distribution function of multivariate normal and \"t\" random variables, and
5273 for generating random vectors sampled from these distributions. Probabilities
5274 are computed via non-Monte Carlo methods.")
5275 (license license:gpl2+)))
5277 (define-public r-numderiv
5280 (version "2016.8-1")
5284 (uri (cran-uri "numDeriv" version))
5287 "07ni52rwiap4wilfz94w5mrqaxr59axxmgn57857ip4p6qkiss0v"))))
5288 (properties `((upstream-name . "numDeriv")))
5289 (build-system r-build-system)
5290 (home-page "https://cran.r-project.org/web/packages/numDeriv")
5291 (synopsis "Accurate numerical derivatives")
5293 "This package provides methods for calculating accurate numerical
5294 first and second order derivatives.")
5295 (license license:gpl2)))
5304 (uri (cran-uri "sn" version))
5307 "16gwr68zzj5v83bqfmzxnzwig3dnjrkxdhs6clri1caqkvrq6aig"))))
5308 (build-system r-build-system)
5310 `(("r-mnormt" ,r-mnormt)
5311 ("r-numderiv" ,r-numderiv)))
5312 (home-page "http://azzalini.stat.unipd.it/SN")
5313 (synopsis "The skew-normal and skew-t distributions")
5315 "This packages provides functionalities to build and manipulate
5316 probability distributions of the skew-normal family and some related
5317 ones, notably the skew-t family, and provides related statistical
5318 methods for data fitting and diagnostics, in the univariate and the
5319 multivariate case.")
5320 (license license:gpl2+)))
5322 (define-public r-tclust
5329 (uri (cran-uri "tclust" version))
5332 "17md6l9v9dl9b72l84df01b52h2xiynbcjm437mv9mzcr09fc2sb"))))
5333 (build-system r-build-system)
5334 ;; These are all suggested packages, not build dependencies.
5336 `(("r-cluster" ,r-cluster)
5337 ("r-mclust" ,r-mclust)
5338 ("r-mvtnorm" ,r-mvtnorm)
5340 (home-page "https://cran.r-project.org/web/packages/tclust")
5341 (synopsis "Robust trimmed clustering")
5343 "This package implements different robust clustering
5344 algorithms (@code{tclust}) based on trimming and including some graphical
5345 diagnostic tools (@code{ctlcurves} and @code{DiscrFact}).")
5346 (license license:gpl3)))
5348 (define-public r-ranger
5355 (uri (cran-uri "ranger" version))
5358 "12z67xkgdmr5cflpd6cln0mn5xxajanqbfwlckv6cfma0gvf2z1j"))))
5359 (build-system r-build-system)
5361 `(("r-rcpp" ,r-rcpp)
5362 ("r-matrix" ,r-matrix)
5363 ("r-rcppeigen" ,r-rcppeigen)))
5364 (home-page "https://github.com/imbs-hl/ranger")
5365 (synopsis "Fast implementation of random forests")
5367 "This package provides a fast implementation of Random Forests,
5368 particularly suited for high dimensional data. Ensembles of classification,
5369 regression, survival and probability prediction trees are supported. Data from
5370 genome-wide association studies can be analyzed efficiently.")
5371 (license license:gpl3)))
5373 (define-public r-tsne
5380 (uri (cran-uri "tsne" version))
5383 "0s8cv2pndkddq62rzlgzgfdjp1vjv5hz5i5957sllnb97vbzbzb6"))))
5384 (build-system r-build-system)
5385 (home-page "https://github.com/jdonaldson/rtsne/")
5386 (synopsis "t-Distributed Stochastic Neighbor Embedding for R")
5388 "This package provides a pure R implementation of the t-SNE algorithm.")
5389 (license license:gpl2+)))
5391 (define-public r-cairo
5398 (uri (cran-uri "Cairo" version))
5401 "1x1q99r3r978rlkkm5gixkv03p0mcr6k7ydcqdmisrwnmrn7p1ia"))))
5402 (properties `((upstream-name . "Cairo")))
5403 (build-system r-build-system)
5408 `(("pkg-config" ,pkg-config)))
5409 (home-page "http://www.rforge.net/Cairo/")
5410 (synopsis "R graphics device using Cairo graphics library")
5412 "This package provides a Cairo graphics device that can be use to
5413 create high-quality vector (PDF, PostScript and SVG) and bitmap
5414 output (PNG,JPEG,TIFF), and high-quality rendering in displays (X11
5415 and Win32). Since it uses the same back-end for all output, copying
5416 across formats is WYSIWYG. Files are created without the dependence
5417 on X11 or other external programs. This device supports alpha
5418 channel (semi-transparent drawing) and resulting images can contain
5419 transparent and semi-transparent regions. It is ideal for use in
5420 server environments (file output) and as a replacement for other
5421 devices that don't have Cairo's capabilities such as alpha support or
5422 anti-aliasing. Backends are modular such that any subset of backends
5424 (license license:gpl2)))
5426 (define-public r-lubridate
5428 (name "r-lubridate")
5433 (uri (cran-uri "lubridate" version))
5436 "14a823il77w3wmmnzr89vwrqp50y56dh5raycnaw6c8nv5xsh32i"))))
5437 (build-system r-build-system)
5439 `(("r-rcpp" ,r-rcpp)
5440 ("r-stringr" ,r-stringr)))
5442 "https://cran.r-project.org/web/packages/lubridate")
5443 (synopsis "Make dealing with dates a little easier")
5445 "This package provides functions to work with date-times and time-spans:
5446 fast and user friendly parsing of date-time data, extraction and updating of
5447 components of a date-time (years, months, days, hours, minutes, and seconds),
5448 algebraic manipulation on date-time and time-span objects. The 'lubridate'
5449 package has a consistent and memorable syntax that makes working with dates
5451 (license license:gpl2)))
5453 (define-public r-fdrtool
5460 (uri (cran-uri "fdrtool" version))
5463 "1h46frlk7d9f4qx0bg6p55nrm9wwwz2sv6d1nz7061wdfsm69yb5"))))
5464 (build-system r-build-system)
5465 (home-page "http://strimmerlab.org/software/fdrtool/")
5466 (synopsis "Estimation of false discovery rates and higher criticism")
5468 "This package provides tools to estimate tail area-based false discovery
5469 rates as well as local false discovery rates for a variety of null
5470 models (p-values, z-scores, correlation coefficients, t-scores). The
5471 proportion of null values and the parameters of the null distribution are
5472 adaptively estimated from the data. In addition, the package contains
5473 functions for non-parametric density estimation (Grenander estimator), for
5474 monotone regression (isotonic regression and antitonic regression with
5475 weights), for computing the @dfn{greatest convex minorant} (GCM) and the
5476 @dfn{least concave majorant} (LCM), for the half-normal and correlation
5477 distributions, and for computing empirical @dfn{higher criticism} (HC) scores
5478 and the corresponding decision threshold.")
5479 (license license:gpl3+)))
5481 (define-public r-forcats
5488 (uri (cran-uri "forcats" version))
5491 "0mxn1hng43zdjh1v8shd80hrszrqahcpaqxs1s1sif0qxh84d0cm"))))
5492 (build-system r-build-system)
5494 `(("r-magrittr" ,r-magrittr)
5495 ("r-tibble" ,r-tibble)
5496 ("r-rlang" ,r-rlang)))
5497 (home-page "http://forcats.tidyverse.org")
5498 (synopsis "Tools for working with factors")
5499 (description "This package provides helpers for reordering factor
5500 levels (including moving specified levels to front, ordering by first
5501 appearance, reversing, and randomly shuffling), and tools for modifying factor
5502 levels (including collapsing rare levels into other, \"anonymizing\", and
5503 manually \"recoding\").")
5504 (license license:gpl3)))
5506 (define-public r-tgstat
5507 (let ((changeset "4f8e60c03598f49aff6f5beeab40f2b995377e9f")
5511 (version (string-append "1.0.2-" revision "." (string-take changeset 7)))
5516 (url "https://bitbucket.org/tanaylab/tgstat")
5517 (changeset changeset)))
5518 (file-name (string-append name "-" version "-checkout"))
5521 "0ilkkyximy77zbncm91kdfqbxf0qyndg16pd3q3p6a3xc9qcmxvn"))))
5522 (build-system r-build-system)
5525 (modify-phases %standard-phases
5526 (add-after 'unpack 'fix-isnan
5528 (substitute* "src/tgstat.h"
5529 (("#define isnan ::isnan")
5530 "#define isnan std::isnan"))
5533 `(("r-rcpp" ,r-rcpp)))
5534 (home-page "https://bitbucket.org/tanaylab/tgstat/")
5535 (synopsis "Tanay's group statistical utilities")
5537 "The goal of tgstat is to provide fast and efficient statistical
5539 (license license:gpl2))))
5541 (define-public r-tgconfig
5542 (let ((changeset "1e02c7614713bd0866c46f0c679a058f8c6d627e")
5546 (version (string-append "0.0.0.9000-" revision "." (string-take changeset 7)))
5551 (url "https://bitbucket.org/tanaylab/tgconfig")
5552 (changeset changeset)))
5553 (file-name (string-append name "-" version "-checkout"))
5556 "0xy6c7s7mn1yx191154bwbv1bl424bnvc80syqpl1vdl28ba46rj"))))
5557 (build-system r-build-system)
5559 `(("r-yaml" ,r-yaml)))
5560 (home-page "https://bitbucket.org/tanaylab/tgconfig/")
5561 (synopsis "Infrastructure for managing package parameters")
5563 "The goal of tgconfig is to provide infrastructure for managing package
5565 (license license:gpl3))))
5567 (define-public r-directlabels
5569 (name "r-directlabels")
5570 (version "2018.05.22")
5574 (uri (cran-uri "directlabels" version))
5577 "0xcpc56ssb9430b0xcdhayk3qaak2qcakyss2pz14y5w2027hblv"))))
5578 (build-system r-build-system)
5580 `(("r-quadprog" ,r-quadprog)))
5581 (home-page "http://directlabels.r-forge.r-project.org/")
5582 (synopsis "Direct labels for multicolor plots")
5584 "This package provides an extensible framework for automatically placing
5585 direct labels onto multicolor plots. Label positions are described using
5586 positioning methods that can be re-used across several different plots. There
5587 are heuristics for examining @code{trellis} and @code{ggplot} objects and
5588 inferring an appropriate positioning method.")
5589 (license license:gpl3)))
5591 (define-public r-catterplots
5592 (let ((commit "40063ec57f9515d231508f135ca0ec769614efb9")
5595 (name "r-catterplots")
5596 (version (string-append "0-" revision "." (string-take commit 9)))
5600 (url "https://github.com/Gibbsdavidl/CatterPlots.git")
5602 (file-name (string-append name "-" version "-checkout"))
5605 "1wl80pgbz8d9kfpffvkh439hlgz2qldm9m75wqjfrgrg8lcjzrxg"))))
5606 (build-system r-build-system)
5608 `(("r-png" ,r-png)))
5609 (home-page "https://github.com/Gibbsdavidl/CatterPlots")
5610 (synopsis "Scatter plots with cat shaped points")
5611 (description "Did you ever wish you could make scatter plots with cat
5612 shaped points? Now you can!")
5613 (license license:asl2.0))))
5615 (define-public r-colorout
5622 (uri (string-append "https://github.com/jalvesaq/colorout/archive/"
5623 "v" version ".tar.gz"))
5624 (file-name (string-append name "-" version ".tar.gz"))
5627 "07vqx5ihgnq4dzn5jnfjfhdm3957v4prvf8vhnb3cwvlly4l7p9v"))))
5628 (build-system r-build-system)
5629 (home-page "https://github.com/jalvesaq/colorout")
5630 (synopsis "Colorize output in the R REPL")
5631 (description "@code{colorout} is an R package that colorizes R output when
5632 running in terminal emulator.
5634 R STDOUT is parsed and numbers, negative numbers, dates in the standard
5635 format, strings, and R constants are identified and wrapped by special ANSI
5636 scape codes that are interpreted by terminal emulators as commands to colorize
5637 the output. R STDERR is also parsed to identify the expressions warning and
5638 error and their translations to many languages. If these expressions are
5639 found, the output is colorized accordingly; otherwise, it is colorized as
5640 STDERROR (blue, by default).
5642 You can customize the colors according to your taste, guided by the color
5643 table made by the command @code{show256Colors()}. You can also set the colors
5644 to any arbitrary string. In this case, it is up to you to set valid values.")
5645 (license license:gpl3+)))
5647 (define-public r-txtplot
5654 (uri (cran-uri "txtplot" version))
5657 "1949ab1bzvysdb79g8x1gaknj0ih3d6g63pv9512h5m5l3a6c31h"))))
5658 (build-system r-build-system)
5659 (home-page "https://cran.r-project.org/web/packages/txtplot/")
5660 (synopsis "Text-based plotting")
5661 (description "This package provides functions to produce rudimentary ASCII
5662 graphics directly in the terminal window. This package provides a basic
5663 plotting function (and equivalents of curve, density, acf and barplot) as well
5664 as a boxplot function.")
5665 (license license:lgpl3+)))
5667 (define-public java-jdistlib
5669 (name "java-jdistlib")
5673 (uri (string-append "mirror://sourceforge/jdistlib/jdistlib-"
5674 version "-src.jar"))
5677 "1pkj8aahw9ydr1isbaqrkd05nvq98ik5jwwhf3yf3rky3z869v11"))))
5678 (build-system ant-build-system)
5680 `(#:jar-name "jdistlib.jar"
5682 #:tests? #f ; no dedicated test directory
5684 (modify-phases %standard-phases
5685 (add-after 'unpack 'fix-broken-encoding
5687 (with-fluids ((%default-port-encoding "ISO-8859-1"))
5688 (substitute* "src/jdistlib/Beta.java"
5689 (("Scheff.+-Tukey") "Scheffe-Tukey")))
5692 `(("java-jtransforms" ,java-jtransforms)))
5694 `(("java-junit" ,java-junit)))
5695 (home-page "http://jdistlib.sourceforge.net/")
5696 (synopsis "Java library of statistical distributions")
5697 (description "JDistlib is the Java Statistical Distribution Library, a
5698 Java package that provides routines for various statistical distributions.")
5699 ;; The files that were translated from R code are under GPLv2+; some files
5700 ;; are under the GPLv3, which is a mistake. The author confirmed in an
5701 ;; email that this whole project should be under GPLv2+.
5702 (license license:gpl2+)))