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 "02bkywwsxwrxc035hv51dxgdm1fjxdm7dn19ivifln59dfs1862j"))))
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 "0ji9k4s1bvfbl8wimfqj1lqr33h1claaz30vb5pgksxyg77j5xaa"))))
2245 (build-system r-build-system)
2247 `(("r-brew" ,r-brew)
2248 ("r-commonmark" ,r-commonmark)
2250 ("r-digest" ,r-digest)
2251 ("r-pkgload" ,r-pkgload)
2252 ("r-purrr" ,r-purrr)
2255 ("r-stringi" ,r-stringi)
2256 ("r-stringr" ,r-stringr)
2257 ("r-xml2" ,r-xml2)))
2259 `(("r-knitr" ,r-knitr))) ; for vignettes
2260 (home-page "https://github.com/klutometis/roxygen")
2261 (synopsis "In-source documentation system for R")
2263 "Roxygen2 is a Doxygen-like in-source documentation system for Rd,
2264 collation, and NAMESPACE files.")
2265 (license license:gpl2+)))
2267 (define-public r-openssl
2274 (uri (cran-uri "openssl" version))
2277 "1djfpnphkcxx8idk5rjfzg8r8dnqsgc0shh2pw8lns5hap2wc5rc"))))
2278 (build-system r-build-system)
2280 `(("libressl" ,libressl)))
2281 (home-page "https://github.com/jeroenooms/openssl")
2282 (synopsis "Toolkit for encryption, signatures and certificates")
2284 "This package provides R bindings to OpenSSL libssl and libcrypto, plus
2285 custom SSH pubkey parsers. It supports RSA, DSA and NIST curves P-256, P-384
2286 and P-521. Cryptographic signatures can either be created and verified
2287 manually or via x509 certificates. AES block cipher is used in CBC mode for
2288 symmetric encryption; RSA for asymmetric (public key) encryption. High-level
2289 envelope functions combine RSA and AES for encrypting arbitrary sized data.
2290 Other utilities include key generators, hash functions (md5, sha1, sha256,
2291 etc), base64 encoder, a secure random number generator, and @code{bignum} math
2292 methods for manually performing crypto calculations on large multibyte
2294 (license license:expat)))
2296 (define-public r-httr
2302 (uri (cran-uri "httr" version))
2305 "0n7jz2digbgv48rbr9vmzv4vmf4rahl9jjy31izs7sxj4rs4s4r2"))))
2306 (build-system r-build-system)
2308 `(("r-curl" ,r-curl)
2309 ("r-jsonlite" ,r-jsonlite)
2310 ("r-openssl" ,r-openssl)
2313 (home-page "https://github.com/hadley/httr")
2314 (synopsis "Tools for working with URLs and HTTP")
2316 "The aim of httr is to provide a wrapper for RCurl customised to the
2317 demands of modern web APIs. It provides useful tools for working with HTTP
2318 organised by HTTP verbs (@code{GET()}, @code{POST()}, etc). Configuration
2319 functions make it easy to control additional request components.")
2320 (license license:expat)))
2322 (define-public r-git2r
2328 (uri (cran-uri "git2r" version))
2331 "01250jz255fnyy2ap90nskvzhd8nhlmbhwgpvb43mk1fax077lrz"))))
2332 (build-system r-build-system)
2333 ;; This R package contains modified sources of libgit2. This modified
2334 ;; version of libgit2 is built as the package is built. Hence libgit2 is
2335 ;; not among the inputs of this package.
2337 `(("libssh2" ,libssh2)
2338 ("openssl" ,openssl)
2341 `(("pkg-config" ,pkg-config)))
2342 (home-page "https://github.com/ropensci/git2r")
2343 (synopsis "Access Git repositories with R")
2345 "This package provides an R interface to the libgit2 library, which is a
2346 pure C implementation of the Git core methods.")
2347 ;; GPLv2 only with linking exception.
2348 (license license:gpl2)))
2350 (define-public r-rstudioapi
2352 (name "r-rstudioapi")
2356 (uri (cran-uri "rstudioapi" version))
2359 "133s75q2hr6jg28m1wvs96qrbc9c4vw87migwhkjqb88xxvbqhd5"))))
2360 (build-system r-build-system)
2361 (home-page "https://cran.r-project.org/web/packages/rstudioapi")
2362 (synopsis "Safely access the RStudio API")
2364 "This package provides functions to access the RStudio API and provide
2365 informative error messages when it's not available.")
2366 (license license:expat)))
2368 (define-public r-devtools
2374 (uri (cran-uri "devtools" version))
2377 "1d9n49djydywfyp9w3njgxs5lag4ac7719wmxy1lkgcmn3l9sx5r"))))
2378 (build-system r-build-system)
2380 `(("r-digest" ,r-digest)
2381 ("r-git2r" ,r-git2r)
2383 ("r-jsonlite" ,r-jsonlite)
2384 ("r-memoise" ,r-memoise)
2385 ("r-rstudioapi" ,r-rstudioapi)
2386 ("r-whisker" ,r-whisker)
2387 ("r-withr" ,r-withr)))
2388 (home-page "https://github.com/hadley/devtools")
2389 (synopsis "Tools to make developing R packages easier")
2390 (description "The devtools package is a collection of package development
2391 tools to simplify the devolpment of R packages.")
2392 (license license:gpl2+)))
2394 (define-public r-withr
2400 (uri (cran-uri "withr" version))
2403 "11j6zykklxnvp4xqsr6a2xib665i38m3khdspp887nwagmvnydj1"))))
2404 (build-system r-build-system)
2405 (home-page "https://github.com/jimhester/withr")
2406 (synopsis "Run code with temporarily modified global state")
2408 "This package provides a set of functions to run R code in an environment
2409 in which global state has been temporarily modified. Many of these functions
2410 were originally a part of the r-devtools package.")
2411 (license license:gpl2+)))
2413 (define-public r-hms
2420 (uri (cran-uri "hms" version))
2423 "1g6hslk3z0xga38r71irxq802wskg6nv804mp8y9f7i2wfrj0y55"))))
2424 (build-system r-build-system)
2426 `(("r-rlang" ,r-rlang)
2427 ("r-pkgconfig" ,r-pkgconfig)))
2428 (home-page "https://github.com/rstats-db/hms")
2429 (synopsis "Pretty time of day")
2431 "This package implements an S3 class for storing and formatting
2432 time-of-day values, based on the @code{difftime} class.")
2433 (license license:gpl3+)))
2435 (define-public r-readr
2441 (uri (cran-uri "readr" version))
2444 "1cvw5wdcqk88cp5fyv678mnmp66l3whcd2yh33p2qvx0168bja8s"))))
2445 (build-system r-build-system)
2447 `(("r-rcpp" ,r-rcpp)
2449 ("r-tibble" ,r-tibble)
2452 (home-page "https://github.com/hadley/readr")
2453 (synopsis "Read tabular data")
2455 "This package provides functions to read flat or tabular text files from
2456 disk (or a connection).")
2457 (license license:gpl2+)))
2459 (define-public r-plotrix
2465 (uri (cran-uri "plotrix" version))
2468 "18702y1gbyis56mh219z5ww0nrkh6qx7bgqv3khyn80g2giwk7cf"))))
2469 (build-system r-build-system)
2470 (home-page "https://cran.r-project.org/web/packages/plotrix")
2471 (synopsis "Various plotting functions")
2473 "This package provides lots of plotting, various labeling, axis and color
2474 scaling functions for R.")
2475 (license license:gpl2+)))
2477 (define-public r-gridbase
2483 (uri (cran-uri "gridBase" version))
2486 "09jzw4rzwf2y5lcz7b16mb68pn0fqigv34ff7lr6w3yi9k91i1xy"))))
2487 (build-system r-build-system)
2488 (home-page "https://cran.r-project.org/web/packages/gridBase")
2489 (synopsis "Integration of base and grid graphics")
2491 "This package provides an integration of base and grid graphics for R.")
2492 (license license:gpl2+)))
2494 (define-public r-latticeextra
2496 (name "r-latticeextra")
2501 (uri (cran-uri "latticeExtra" version))
2504 "1hkyqsa7klk5glj9y1hg3rxr5qilqw8h0017zc4c3nps7lr9a1kq"))))
2505 (properties `((upstream-name . "latticeExtra")))
2506 (build-system r-build-system)
2508 `(("r-lattice" ,r-lattice)
2509 ("r-rcolorbrewer" ,r-rcolorbrewer)))
2510 (home-page "http://latticeextra.r-forge.r-project.org/")
2511 (synopsis "Extra graphical utilities based on lattice")
2513 "Building on the infrastructure provided by the lattice package, this
2514 package provides several new high-level graphics functions and methods, as
2515 well as additional utilities such as panel and axis annotation functions.")
2516 (license license:gpl2+)))
2518 (define-public r-rcpparmadillo
2520 (name "r-rcpparmadillo")
2521 (version "0.9.100.5.0")
2524 (uri (cran-uri "RcppArmadillo" version))
2527 "1iyjqhfjip1nxrkllzh7r1m01jjnx7cahqkf3s557w34p987f2l1"))))
2528 (properties `((upstream-name . "RcppArmadillo")))
2529 (build-system r-build-system)
2531 `(("r-knitr" ,r-knitr))) ; needed for vignettes
2533 `(("r-rcpp" ,r-rcpp)))
2534 (home-page "https://github.com/RcppCore/RcppArmadillo")
2535 (synopsis "Rcpp integration for the Armadillo linear algebra library")
2537 "Armadillo is a templated C++ linear algebra library that aims towards a
2538 good balance between speed and ease of use. Integer, floating point and
2539 complex numbers are supported, as well as a subset of trigonometric and
2540 statistics functions. Various matrix decompositions are provided through
2541 optional integration with LAPACK and ATLAS libraries. This package includes
2542 the header files from the templated Armadillo library.")
2543 ;; Armadillo is licensed under the MPL 2.0, while RcppArmadillo (the Rcpp
2544 ;; bindings to Armadillo) is licensed under the GNU GPL version 2 or
2545 ;; later, as is the rest of 'Rcpp'.
2546 (license license:gpl2+)))
2548 (define-public r-bitops
2554 (uri (cran-uri "bitops" version))
2557 "176nr5wpnkavn5z0yy9f7d47l37ndnn2w3gv854xav8nnybi6wwv"))))
2558 (build-system r-build-system)
2559 (home-page "https://cran.r-project.org/web/packages/bitops")
2560 (synopsis "Bitwise operations")
2562 "This package provides functions for bitwise operations on integer
2564 (license license:gpl2+)))
2566 (define-public r-catools
2569 (version "1.17.1.1")
2572 (uri (cran-uri "caTools" version))
2575 "01hccp05gz25vhz9nnxv1c91lrxlr7drcw9xf124gggifxf2qgnm"))))
2576 (properties `((upstream-name . "caTools")))
2577 (build-system r-build-system)
2579 `(("r-bitops" ,r-bitops)))
2580 (home-page "https://cran.r-project.org/web/packages/caTools")
2581 (synopsis "Various tools including functions for moving window statistics")
2583 "This package contains several basic utility functions including:
2584 moving (rolling, running) window statistic functions, read/write for GIF and
2585 ENVI binary files, fast calculation of AUC, LogitBoost classifier, base64
2586 encoder/decoder, round-off-error-free sum and cumsum, etc.")
2587 (license license:gpl3+)))
2589 (define-public r-rprojroot
2591 (name "r-rprojroot")
2596 (uri (cran-uri "rprojroot" version))
2599 "12r3fdxmi2pmwn6ic3rhg0b20ll5z420m0d8fziv1n21961namnz"))))
2600 (build-system r-build-system)
2602 `(("r-backports" ,r-backports)))
2603 (home-page "https://github.com/krlmlr/rprojroot")
2604 (synopsis "Finding files in project subdirectories")
2606 "This package helps accessing files relative to a project root. It
2607 provides helpers for robust, reliable and flexible paths to files below a
2608 project root. The root of a project is defined as a directory that matches a
2609 certain criterion, e.g., it contains a certain regular file.")
2610 (license license:gpl3)))
2612 (define-public r-rmarkdown
2614 (name "r-rmarkdown")
2619 (uri (cran-uri "rmarkdown" version))
2622 "0mh2f3k98w7pgz0ri34149s4kx5y0kfm27nwq64k0qwxd16hwd9r"))))
2623 (properties `((upstream-name . "rmarkdown")))
2624 (build-system r-build-system)
2626 `(("r-base64enc" ,r-base64enc)
2627 ("r-evaluate" ,r-evaluate)
2628 ("r-htmltools" ,r-htmltools)
2629 ("r-jsonlite" ,r-jsonlite)
2630 ("r-knitr" ,r-knitr)
2632 ("r-rprojroot" ,r-rprojroot)
2633 ("r-stringr" ,r-stringr)
2634 ("r-tinytex" ,r-tinytex)
2636 ("ghc-pandoc" ,ghc-pandoc)))
2637 (home-page "http://rmarkdown.rstudio.com")
2638 (synopsis "Convert R Markdown documents into a variety of formats")
2640 "This package provides tools to convert R Markdown documents into a
2641 variety of formats.")
2642 (license license:gpl3+)))
2644 (define-public r-gtable
2650 (uri (cran-uri "gtable" version))
2653 "0vz7073m0a2q12qzzihrfh5c2kx5jqi5l7z470fxmwqghdllh7l0"))))
2654 (properties `((upstream-name . "gtable")))
2655 (build-system r-build-system)
2656 (home-page "https://cran.r-project.org/web/packages/gtable")
2657 (synopsis "R library to arrange grobs in tables")
2659 "Gtable is a collection of tools to make it easier to work with
2660 \"tables\" of grobs.")
2661 (license license:gpl2+)))
2663 (define-public r-gridextra
2665 (name "r-gridextra")
2669 (uri (cran-uri "gridExtra" version))
2672 "0fwfk3cdwxxim7nd55pn7m31bcaqj48y06j7an2k1v1pybk0rdl1"))))
2673 (properties `((upstream-name . "gridExtra")))
2674 (build-system r-build-system)
2676 `(("r-gtable" ,r-gtable)))
2678 `(("r-knitr" ,r-knitr))) ;for building vignettes
2679 (home-page "https://github.com/baptiste/gridextra")
2680 (synopsis "Miscellaneous functions for \"Grid\" graphics")
2682 "This package provides a number of user-level functions to work with
2683 @code{grid} graphics, notably to arrange multiple grid-based plots on a page,
2685 (license license:gpl2+)))
2687 (define-public r-pkgconfig
2689 (name "r-pkgconfig")
2693 (uri (cran-uri "pkgconfig" version))
2696 "1jk9ip549xphb3anfixqv1yx5kidnndqgy9v3qjpmgmds5a7g695"))))
2697 (build-system r-build-system)
2698 (home-page "https://github.com/gaborcsardi/pkgconfig")
2699 (synopsis "Private configuration for R packages")
2700 (description "This package provides the functionality to set configuration
2701 options on a per-package basis. Options set by a given package only apply to
2702 that package, other packages are unaffected.")
2703 (license license:expat)))
2705 (define-public r-blob
2711 (uri (cran-uri "blob" version))
2714 "0lsg91hk508dd95ivig2lwg62qafwnarjw68110kx63cfk4zkjxc"))))
2715 (build-system r-build-system)
2717 `(("r-prettyunits" ,r-prettyunits)
2718 ("r-tibble" ,r-tibble)))
2719 (home-page "https://github.com/hadley/blob")
2720 (synopsis "Simple S3 Class for representing vectors of binary data")
2721 (description "Raw vectors in R are useful for storing a single binary
2722 object. What if you want to put a vector of them in a data frame? The blob
2723 package provides the blob object, a list of raw vectors, suitable for use as
2724 a column in data frame.")
2725 (license license:gpl3+)))
2727 (define-public r-rsqlite
2733 (uri (cran-uri "RSQLite" version))
2736 "1giwk4335sc6yhj3rs8h070g1mwy38kyqyqv6vcfxvskykj7vp6z"))))
2737 (properties `((upstream-name . "RSQLite")))
2738 (build-system r-build-system)
2742 ("r-memoise" ,r-memoise)
2743 ("r-plogr" ,r-plogr)
2745 ("r-bit64" ,r-bit64)
2747 ("r-pkgconfig" ,r-pkgconfig)))
2748 (home-page "https://github.com/rstats-db/RSQLite")
2749 (synopsis "SQLite interface for R")
2751 "This package embeds the SQLite database engine in R and provides an
2752 interface compliant with the DBI package. The source for the SQLite
2753 engine (version 3.8.8.2) is included.")
2754 (license license:lgpl2.0+)))
2756 (define-public r-rcurl
2759 (version "1.95-0.1.2")
2762 (uri (string-append "https://www.bioconductor.org/packages/"
2763 "release/extra/src/"
2764 "contrib/RCurl_" version ".tar.gz"))
2767 "0l7qi45jxlf898n0jazabnam1yyczvqfdknd00bdirhhiplpd1sc"))))
2768 (properties `((upstream-name . "RCurl")))
2769 (build-system r-build-system)
2772 (modify-phases %standard-phases
2773 (add-after 'unpack 'respect-CURL_CA_BUNDLE
2775 (substitute* "R/options.S"
2776 (("\\.els = rev\\(merge\\(list\\(\\.\\.\\.\\), \\.opts\\)\\)" m)
2778 certs = Sys.getenv(\"CURL_CA_BUNDLE\")
2779 if (certs != \"\") { .opts = merge.list(.opts, list(cainfo=certs)) }
2783 `(("libcurl" ,curl)))
2785 `(("r-bitops" ,r-bitops)))
2786 (home-page "http://www.omegahat.org/RCurl")
2787 (synopsis "General network client interface for R")
2789 "The package allows one to compose general HTTP requests and provides
2790 convenient functions to fetch URIs, GET and POST forms, etc. and process the
2791 results returned by the Web server. This provides a great deal of control
2792 over the HTTP/FTP/... connection and the form of the request while providing a
2793 higher-level interface than is available just using R socket connections.
2794 Additionally, the underlying implementation is robust and extensive,
2795 supporting FTP/FTPS/TFTP (uploads and downloads), SSL/HTTPS, telnet, dict,
2796 ldap, and also supports cookies, redirects, authentication, etc.")
2797 (license license:bsd-3)))
2799 (define-public r-xml
2802 (version "3.98-1.16")
2805 (uri (cran-uri "XML" version))
2808 "0nl1kk354r8snhj6p9mc74m7awvqc6akmd4y3a46y78yv3g15njp"))))
2810 `((upstream-name . "XML")))
2811 (build-system r-build-system)
2813 `(("libxml2" ,libxml2)
2816 `(("pkg-config" ,pkg-config)))
2817 (home-page "http://www.omegahat.org/RSXML")
2818 (synopsis "Tools for parsing and generating XML within R")
2820 "Many approaches for both reading and creating XML (and HTML)
2821 documents (including DTDs), both local and accessible via HTTP or FTP. Also
2822 offers access to an XPath \"interpreter\".")
2823 (license license:bsd-2)))
2825 (define-public r-xnomial
2830 (origin (method url-fetch)
2831 (uri (cran-uri "XNomial" version))
2834 "1mwx302576rmsjllbq2clfxilm3hkyp5bw0wmwqbn0kgv5wpy8z6"))))
2835 (properties (quasiquote ((upstream-name . "XNomial"))))
2836 (build-system r-build-system)
2837 (home-page "https://cran.r-project.org/web/packages/XNomial")
2838 (synopsis "Goodness-of-Fit test for multinomial data")
2840 "This package provides an exact Goodness-of-Fit test for
2841 multinomial data with fixed probabilities. It can be used to
2842 determine whether a set of counts fits a given expected ratio. To see
2843 whether a set of observed counts fits an expectation, one can examine
2844 all possible outcomes with @code{xmulti()} or a random sample of them
2845 with @code{xmonte()} and find the probability of an observation
2846 deviating from the expectation by at least as much as the observed.
2847 As a measure of deviation from the expected, one can use the
2848 log-likelihood ratio, the multinomial probability, or the classic
2849 chi-square statistic. A histogram of the test statistic can also be
2850 plotted and compared with the asymptotic curve.")
2851 (license (list license:gpl2+ license:gpl3+))))
2853 (define-public r-lambda-r
2859 (uri (cran-uri "lambda.r" version))
2862 "0cc6pszs6yccn0hgjpyn9gspv9aiva9d91ba0640i5m0l5xy7n0c"))))
2863 (properties `((upstream-name . "lambda.r")))
2864 (build-system r-build-system)
2866 `(("r-formatr" ,r-formatr)))
2867 (home-page "https://cran.r-project.org/web/packages/lambda.r")
2868 (synopsis "Functional programming extension for R")
2870 "This package provides a language extension to efficiently write
2871 functional programs in R. Syntax extensions include multi-part function
2872 definitions, pattern matching, guard statements, built-in (optional) type
2874 (license license:lgpl3+)))
2876 (define-public r-futile-options
2878 (name "r-futile-options")
2882 (uri (cran-uri "futile.options" version))
2885 "0w15agpi88y3qkv6fl72zy2pzyplzgvnj41a4ixhg64mw1sck73s"))))
2887 `((upstream-name . "futile.options")))
2888 (build-system r-build-system)
2889 (home-page "https://cran.r-project.org/web/packages/futile.options")
2890 (synopsis "Options management framework")
2892 "The futile.options subsystem provides an easy user-defined options
2893 management system that is properly scoped. This means that options created
2894 via @code{futile.options} are fully self-contained and will not collide with
2895 options defined in other packages.")
2896 (license license:lgpl3+)))
2898 (define-public r-futile-logger
2900 (name "r-futile-logger")
2904 (uri (cran-uri "futile.logger" version))
2907 "1r3nayk0z9n1svbf8640vw90dal5q07nkn0gv4bnva3pbzb352sy"))))
2908 (properties `((upstream-name . "futile.logger")))
2909 (build-system r-build-system)
2911 `(("r-futile-options" ,r-futile-options)
2912 ("r-lambda-r" ,r-lambda-r)))
2913 (home-page "https://cran.r-project.org/web/packages/futile.logger")
2914 (synopsis "Logging utility for R")
2916 "This package provides a simple yet powerful logging utility. Based
2917 loosely on log4j, futile.logger takes advantage of R idioms to make logging a
2918 convenient and easy to use replacement for @code{cat} and @code{print}
2920 (license license:lgpl3+)))
2922 (define-public r-segmented
2924 (name "r-segmented")
2929 (uri (cran-uri "segmented" version))
2932 "0nrik5fyq59hwiwjcpbi4p5yfavgfjq6wyrynhkrbm4k6v1g1wlq"))))
2933 (build-system r-build-system)
2934 (home-page "https://cran.r-project.org/web/packages/segmented")
2935 (synopsis "Regression models with breakpoints estimation")
2937 "Given a regression model, segmented updates the model by adding one or
2938 more segmented (i.e., piecewise-linear) relationships. Several variables with
2939 multiple breakpoints are allowed.")
2940 (license (list license:gpl2+ license:gpl3+))))
2942 (define-public r-snow
2948 (uri (cran-uri "snow" version))
2951 "1mxbrkpnmq32x4wd0194d541661yvfrrjlr3lsf7qq53ms3h21zf"))))
2952 (build-system r-build-system)
2953 (home-page "https://cran.r-project.org/web/packages/snow")
2954 (synopsis "Support for simple parallel computing in R")
2956 "The snow package provides support for simple parallel computing on a
2957 network of workstations using R. A master R process calls @code{makeCluster}
2958 to start a cluster of worker processes; the master process then uses functions
2959 such as @code{clusterCall} and @code{clusterApply} to execute R code on the
2960 worker processes and collect and return the results on the master.")
2961 (license (list license:gpl2+ license:gpl3+))))
2963 (define-public r-sparsem
2969 (uri (cran-uri "SparseM" version))
2972 "0p6ljma2h12cq1xmy0cxb48ih8dhxxbnwkqzvx3cckxf2kprycm9"))))
2974 `((upstream-name . "SparseM")))
2976 `(("gfortran" ,gfortran)))
2977 (build-system r-build-system)
2978 (home-page "http://www.econ.uiuc.edu/~roger/research/sparse/sparse.html")
2979 (synopsis "Sparse linear algebra")
2981 "This package provides some basic linear algebra functionality for sparse
2982 matrices. It includes Cholesky decomposition and backsolving as well as
2983 standard R subsetting and Kronecker products.")
2984 (license license:gpl2+)))
2986 (define-public r-iterators
2988 (name "r-iterators")
2993 (uri (cran-uri "iterators" version))
2996 "1s3iykfvccpnzs73z90rx18qvbvgw2dgl4nfcrvm5m1850qb5qd9"))))
2997 (build-system r-build-system)
2998 (home-page "https://cran.r-project.org/web/packages/iterators")
2999 (synopsis "Iterator construct for R")
3001 "This package provides support for iterators, which allow a programmer to
3002 traverse through all the elements of a vector, list, or other collection of
3004 (license license:asl2.0)))
3006 (define-public r-foreach
3013 (uri (cran-uri "foreach" version))
3016 "0j2yj0rn0d5nbzz9nq5rqqgnxhp9pbd92q4klsarl2xpsn8119y0"))))
3017 (build-system r-build-system)
3019 `(("r-codetools" ,r-codetools)
3020 ("r-iterators" ,r-iterators)))
3021 (home-page "https://cran.r-project.org/web/packages/foreach")
3022 (synopsis "Foreach looping construct for R")
3024 "This package provides support for the @code{foreach} looping construct.
3025 @code{foreach} is an idiom that allows for iterating over elements in a
3026 collection, without the use of an explicit loop counter. This package in
3027 particular is intended to be used for its return value, rather than for its
3028 side effects. In that sense, it is similar to the standard @code{lapply}
3029 function, but doesn't require the evaluation of a function. Using
3030 @code{foreach} without side effects also facilitates executing the loop in
3032 (license license:asl2.0)))
3034 (define-public r-doparallel
3036 (name "r-doparallel")
3041 (uri (cran-uri "doParallel" version))
3044 "0sppgxk3d8mfsrb3cjdyn0mv0s4i7pcy8g8c3cjzbr6k8vmx5jsc"))))
3045 (properties `((upstream-name . "doParallel")))
3046 (build-system r-build-system)
3048 `(("r-foreach" ,r-foreach)
3049 ("r-iterators" ,r-iterators)))
3050 (home-page "https://cran.r-project.org/web/packages/doParallel")
3051 (synopsis "Foreach parallel adaptor for the 'parallel' package")
3053 "This package provides a parallel backend for the @code{%dopar%} function
3054 using the parallel package.")
3055 (license license:gpl2+)))
3057 (define-public r-domc
3064 (uri (cran-uri "doMC" version))
3067 "1vfrykvfvsyq12mypd266867ml1dcwc3rj5k9c3wrn5bddcm88kr"))))
3068 (properties `((upstream-name . "doMC")))
3069 (build-system r-build-system)
3071 `(("r-foreach" ,r-foreach)
3072 ("r-iterators" ,r-iterators)))
3073 (home-page "https://cran.r-project.org/web/packages/doMC")
3074 (synopsis "Foreach parallel adaptor for the 'parallel' package")
3076 "This package provides a parallel backend for the @code{%dopar%} function
3077 using the multicore functionality of the parallel package.")
3078 (license license:gpl2+)))
3086 (uri (cran-uri "DT" version))
3089 "06gsqz7p2fv6hc3fm3759gaa50krcfrqrmy7qbxyam6a36w9daix"))))
3091 `((upstream-name . "DT")))
3092 (build-system r-build-system)
3094 `(("r-crosstalk" ,r-crosstalk)
3095 ("r-htmltools" ,r-htmltools)
3096 ("r-htmlwidgets" ,r-htmlwidgets)
3097 ("r-magrittr" ,r-magrittr)))
3098 (home-page "http://rstudio.github.io/DT")
3099 (synopsis "R wrapper of the DataTables JavaScript library")
3101 "This package allows for data objects in R to be rendered as HTML tables
3102 using the JavaScript library 'DataTables' (typically via R Markdown or Shiny).
3103 The 'DataTables' library has been included in this R package.")
3104 ;; The DT package as a whole is distributed under GPLv3. The DT package
3105 ;; inludes other software components under different licenses:
3107 ;; * Expat: jQuery, jquery.highlight.js, DataTables
3108 ;; * ASL2.0: selectize.js
3109 ;; * WTFPL: noUiSlider
3110 (license (list license:gpl3
3113 (license:non-copyleft "http://www.wtfpl.net/txt/copying/")))))
3115 (define-public r-base64enc
3117 (name "r-base64enc")
3121 (uri (cran-uri "base64enc" version))
3124 "13b89fhg1nx7zds82a0biz847ixphg9byf5zl2cw9kab6s56v1bd"))))
3125 (build-system r-build-system)
3126 (home-page "http://www.rforge.net/base64enc")
3127 (synopsis "Tools for Base64 encoding")
3129 "This package provides tools for handling Base64 encoding. It is more
3130 flexible than the orphaned \"base64\" package.")
3131 (license license:gpl2+)))
3133 (define-public r-irlba
3140 (uri (cran-uri "irlba" version))
3143 "0f7wb12wa0zbyllk5adcf4f517wgjpkhsx4j176i9ax6xy7jvprz"))))
3144 (build-system r-build-system)
3146 `(("r-matrix" ,r-matrix)))
3147 (home-page "https://cran.r-project.org/web/packages/irlba")
3148 (synopsis "Methods for eigendecomposition of large matrices")
3150 "This package provides fast and memory efficient methods for truncated
3151 singular and eigenvalue decompositions, as well as for principal component
3152 analysis of large sparse or dense matrices.")
3153 (license (list license:gpl2+ license:gpl3+))))
3155 (define-public r-glmnet
3162 (uri (cran-uri "glmnet" version))
3165 "1brr51z1fzbpyj6myyir4g6dhbp6xwl7nx4xnvrjarnf5y0csk55"))))
3166 (build-system r-build-system)
3168 `(("gfortran" ,gfortran)))
3170 `(("r-foreach" ,r-foreach)
3171 ("r-matrix" ,r-matrix)))
3172 (home-page "http://www.jstatsoft.org/v33/i01")
3173 (synopsis "Lasso and elastic-net regularized generalized linear models")
3175 "The glmnet package provides efficient procedures for fitting the entire
3176 lasso or elastic-net regularization path for linear and Poisson regression, as
3177 well as logistic, multinomial, Cox, multiple-response Gaussian and grouped
3178 multinomial models. The algorithm uses cyclical coordinate descent in a
3179 path-wise fashion.")
3180 (license license:gpl2+)))
3182 (define-public r-pkgmaker
3189 (uri (cran-uri "pkgmaker" version))
3192 "0spcamjncj78kzjps2rw4v1a4494yazv6xvhn0vmdflnypc8k8hp"))))
3193 (build-system r-build-system)
3195 `(("r-bibtex" ,r-bibtex)
3196 ("r-codetools" ,r-codetools)
3197 ("r-digest" ,r-digest)
3198 ("r-magrittr" ,r-magrittr)
3199 ("r-registry" ,r-registry)
3200 ("r-stringi" ,r-stringi)
3201 ("r-stringr" ,r-stringr)
3202 ("r-withr" ,r-withr)
3203 ("r-xtable" ,r-xtable)))
3204 (home-page "https://renozao.github.io/pkgmaker")
3205 (synopsis "Package development utilities")
3207 "This package provides some low-level utilities to use for R package
3208 development. It currently provides managers for multiple package specific
3209 options and registries, vignette, unit test and bibtex related utilities.")
3210 (license license:gpl2+)))
3212 (define-public r-registry
3219 (uri (cran-uri "registry" version))
3222 "1yqfl1g6vsl28zn8brzc39659k8lqsmfms7900j7p64ilydyb2sx"))))
3223 (build-system r-build-system)
3224 (home-page "https://cran.r-project.org/web/packages/registry")
3225 (synopsis "Infrastructure for R package registries")
3227 "This package provides a generic infrastructure for creating and using R
3228 package registries.")
3229 (license license:gpl2+)))
3231 (define-public r-rngtools
3238 (uri (cran-uri "rngtools" version))
3241 "097215qcfw6ybllpzmp1532r59h2srvch3aca4z4s6l2rf9w8gvn"))))
3242 (build-system r-build-system)
3244 `(("r-digest" ,r-digest)
3245 ("r-pkgmaker" ,r-pkgmaker)
3246 ("r-stringr" ,r-stringr)))
3247 (home-page "https://renozao.github.io/rngtools")
3248 (synopsis "Utility functions for working with random number generators")
3250 "This package contains a set of functions for working with Random Number
3251 Generators (RNGs). In particular, it defines a generic S4 framework for
3252 getting/setting the current RNG, or RNG data that are embedded into objects
3253 for reproducibility. Notably, convenient default methods greatly facilitate
3254 the way current RNG settings can be changed.")
3255 (license license:gpl3+)))
3257 (define-public r-rtsne
3264 (uri (cran-uri "Rtsne" version))
3267 "17crbdi80q4g2pwp9v7j3bdaznk96qlrqx01zvj3wwqippizyfqw"))))
3268 (properties `((upstream-name . "Rtsne")))
3269 (build-system r-build-system)
3271 `(("r-rcpp" ,r-rcpp)))
3272 (home-page "https://github.com/jkrijthe/Rtsne")
3273 (synopsis "T-distributed stochastic neighbor embedding")
3275 "This package provides an R wrapper around the fast T-distributed
3276 Stochastic Neighbor Embedding using a Barnes-Hut implementation.")
3277 ;; The declared license for this package is BSD-3, but it also includes
3278 ;; code licensed under BSD-4.
3279 (license (list license:bsd-3 license:bsd-4))))
3281 (define-public r-e1071
3288 (uri (cran-uri "e1071" version))
3291 "0fk4pw67cw1663d0n9rf1qfdqzz8k5nqkjgp3hi5jr422qp9lsck"))))
3292 (build-system r-build-system)
3294 `(("r-class" ,r-class)))
3295 (home-page "https://cran.r-project.org/web/packages/e1071")
3296 (synopsis "Miscellaneous functions for probability theory")
3298 "This package provides functions for latent class analysis, short time
3299 Fourier transform, fuzzy clustering, support vector machines, shortest path
3300 computation, bagged clustering, naive Bayes classifier, and more.")
3301 (license license:gpl2+)))
3303 (define-public r-bigmemory-sri
3305 (name "r-bigmemory-sri")
3310 (uri (cran-uri "bigmemory.sri" version))
3312 (base32 "0mg14ilwdkd64q2ri9jdwnk7mp55dqim7xfifrs65sdsv1934h2m"))))
3314 `((upstream-name . "bigmemory.sri")))
3315 (build-system r-build-system)
3316 (home-page "https://cran.r-project.org/web/packages/bigmemory.sri")
3317 (synopsis "Shared resource interface for the bigmemory package")
3318 (description "This package provides a shared resource interface for the
3319 bigmemory and synchronicity packages.")
3320 ;; Users can choose either LGPLv3 or ASL2.0.
3321 (license (list license:lgpl3 license:asl2.0))))
3323 (define-public r-synchronicity
3325 (name "r-synchronicity")
3330 (uri (cran-uri "synchronicity" version))
3333 "1kgsk64aifjm3mfj102y3va7x1abypq2zi0cqbnjhl8fqyzp69hx"))))
3334 (build-system r-build-system)
3337 ("r-bigmemory-sri" ,r-bigmemory-sri)
3339 ("r-uuid" ,r-uuid)))
3340 (home-page "http://www.bigmemory.org")
3341 (synopsis "Boost mutex functionality in R")
3342 (description "This package provides support for synchronization
3343 via mutexes and may eventually support interprocess communication and
3345 ;; Users can choose either LGPLv3 or ASL2.0.
3346 (license (list license:lgpl3 license:asl2.0))))
3348 (define-public r-bigmemory
3350 (name "r-bigmemory")
3355 (uri (cran-uri "bigmemory" version))
3358 "0ycl9dzm3drpyas625h34rir5bnbjlncxlvawfsfmqwcbmwdjdvj"))))
3359 (build-system r-build-system)
3363 ("r-bigmemory-sri" ,r-bigmemory-sri)))
3364 (home-page "http://www.bigmemory.org")
3365 (synopsis "Manage large matrices with shared memory or memory-mapped files")
3366 (description "This package provides methods to create, store, access, and
3367 manipulate large matrices. Matrices are allocated to shared memory and may use
3368 memory-mapped files.")
3369 ;; Users can choose either LGPLv3 or ASL2.0.
3370 (license (list license:lgpl3 license:asl2.0))))
3372 (define-public r-nmf
3379 (uri (cran-uri "NMF" version))
3382 "1qq25n3k5sgh3srlshb3ic6q92s12c1ilqf5cd5anvq6cqfchc1v"))))
3383 (properties `((upstream-name . "NMF")))
3384 (build-system r-build-system)
3386 `(("r-cluster" ,r-cluster)
3387 ("r-bigmemory" ,r-bigmemory) ; suggested
3388 ("r-synchronicity" ,r-synchronicity) ; suggested
3389 ("r-colorspace" ,r-colorspace)
3390 ("r-digest" ,r-digest)
3391 ("r-doparallel" ,r-doparallel)
3392 ("r-foreach" ,r-foreach)
3393 ("r-ggplot2" ,r-ggplot2)
3394 ("r-gridbase" ,r-gridbase)
3395 ("r-pkgmaker" ,r-pkgmaker)
3396 ("r-rcolorbrewer" ,r-rcolorbrewer)
3397 ("r-registry" ,r-registry)
3398 ("r-reshape2" ,r-reshape2)
3399 ("r-rngtools" ,r-rngtools)
3400 ("r-stringr" ,r-stringr)))
3401 (home-page "http://renozao.github.io/NMF")
3402 (synopsis "Algorithms and framework for nonnegative matrix factorization")
3404 "This package provides a framework to perform Non-negative Matrix
3405 Factorization (NMF). The package implements a set of already published
3406 algorithms and seeding methods, and provides a framework to test, develop and
3407 plug new or custom algorithms. Most of the built-in algorithms have been
3408 optimized in C++, and the main interface function provides an easy way of
3409 performing parallel computations on multicore machines.")
3410 (license license:gpl2+)))
3412 (define-public r-r-methodss3
3414 (name "r-r-methodss3")
3418 (uri (cran-uri "R.methodsS3" version))
3421 "11z6v2i7jl647wxi9p5z66yvfnnqv6s7fxqmz7w2gkb6j8wl1f24"))))
3422 (properties `((upstream-name . "R.methodsS3")))
3423 (build-system r-build-system)
3424 (home-page "https://cran.r-project.org/web/packages/R.methodsS3")
3425 (synopsis "S3 methods simplified")
3427 "This package provides methods that simplify the setup of S3 generic
3428 functions and S3 methods. Major effort has been made in making definition of
3429 methods as simple as possible with a minimum of maintenance for package
3430 developers. For example, generic functions are created automatically, if
3431 missing, and naming conflict are automatically solved, if possible. The
3432 method @code{setMethodS3()} is a good start for those who in the future may
3433 want to migrate to S4.")
3434 (license license:lgpl2.1+)))
3436 (define-public r-r-oo
3442 (uri (cran-uri "R.oo" version))
3445 "0k6xwy93fpb2p7bs76lzk52br9rv5xnd9524xj8qyazv1132x1n0"))))
3446 (properties `((upstream-name . "R.oo")))
3447 (build-system r-build-system)
3449 `(("r-r-methodss3" ,r-r-methodss3)))
3450 (home-page "https://github.com/HenrikBengtsson/R.oo")
3451 (synopsis "R object-oriented programming with or without references")
3453 "This package provides methods and classes for object-oriented
3454 programming in R with or without references. Large effort has been made on
3455 making definition of methods as simple as possible with a minimum of
3456 maintenance for package developers.")
3457 (license license:lgpl2.1+)))
3459 (define-public r-r-utils
3465 (uri (cran-uri "R.utils" version))
3468 "0cxhn14a57x4gcyrwpfz1d6dw4xh0jcpqkb33hx8imnr340blh7n"))))
3469 (properties `((upstream-name . "R.utils")))
3470 (build-system r-build-system)
3472 `(("r-r-methodss3" ,r-r-methodss3)
3473 ("r-r-oo" ,r-r-oo)))
3474 (home-page "https://github.com/HenrikBengtsson/R.utils")
3475 (synopsis "Various programming utilities")
3477 "This package provides utility functions useful when programming and
3478 developing R packages.")
3479 (license license:lgpl2.1+)))
3481 (define-public r-r-cache
3487 (uri (cran-uri "R.cache" version))
3490 "1hf5cb7xvnca5zlh9245b5g62sgsaxwdhiv7x59yld37cydakm6k"))))
3491 (properties `((upstream-name . "R.cache")))
3492 (build-system r-build-system)
3494 `(("r-digest" ,r-digest)
3495 ("r-r-methodss3" ,r-r-methodss3)
3497 ("r-r-utils" ,r-r-utils)))
3498 (home-page "https://github.com/HenrikBengtsson/R.cache")
3499 (synopsis "Light-weight caching of objects and results")
3501 "This package provides methods for caching or memoization of objects and
3502 results. With this package, any R object can be cached in a key-value storage
3503 where the key can be an arbitrary set of R objects. The cache memory is
3504 persistent (on the file system).")
3505 (license license:lgpl2.1+)))
3507 (define-public r-r-rsp
3513 (uri (cran-uri "R.rsp" version))
3516 "0ax6781kfylx0acz0i3sqnpkxmrq73x29wwfic59ng7vj0ws0gyd"))))
3517 (properties `((upstream-name . "R.rsp")))
3518 (build-system r-build-system)
3520 `(("r-digest" ,r-digest)
3521 ("r-r-cache" ,r-r-cache)
3522 ("r-r-methodss3" ,r-r-methodss3)
3524 ("r-r-utils" ,r-r-utils)))
3525 (home-page "https://github.com/HenrikBengtsson/R.rsp")
3526 (synopsis "Dynamic generation of scientific reports")
3528 "The RSP markup language provides a powerful markup for controlling the
3529 content and output of LaTeX, HTML, Markdown, AsciiDoc, Sweave and knitr
3530 documents (and more), e.g. @code{Today's date is <%=Sys.Date()%>}. Contrary
3531 to many other literate programming languages, with RSP it is straightforward
3532 to loop over mixtures of code and text sections, e.g. in month-by-month
3533 summaries. RSP has also several preprocessing directives for incorporating
3534 static and dynamic contents of external files (local or online) among other
3535 things. RSP is ideal for self-contained scientific reports and R package
3537 (license license:lgpl2.1+)))
3539 (define-public r-mvtnorm
3545 (uri (cran-uri "mvtnorm" version))
3548 "0la42lylb7cjrcrc285bn69bz9kyg556xw317iz139dp1yswl410"))))
3549 (build-system r-build-system)
3551 `(("gfortran" ,gfortran)))
3552 (home-page "http://mvtnorm.R-forge.R-project.org")
3553 (synopsis "Package for multivariate normal and t-distributions")
3554 (description "This package can compute multivariate normal and
3555 t-probabilities, quantiles, random deviates and densities.")
3556 (license license:gpl2)))
3558 (define-public r-matrixstats
3560 (name "r-matrixstats")
3564 (uri (cran-uri "matrixStats" version))
3567 "0vx00ldsg2zvdrjn49jxczk2c9iaabgvzgpdka5j02ihh7hv83cg"))))
3568 (properties `((upstream-name . "matrixStats")))
3569 (build-system r-build-system)
3571 `(("r-r-rsp" ,r-r-rsp))) ;used to build vignettes
3572 (home-page "https://github.com/HenrikBengtsson/matrixStats")
3573 (synopsis "Methods applying to vectors and matrix rows and columns")
3575 "This package provides methods operating on rows and columns of matrices,
3576 e.g. @code{rowMedians()}, @code{rowRanks()}, and @code{rowSds()}. There are
3577 also some vector-based methods, e.g. @code{binMeans()}, @code{madDiff()} and
3578 @code{weightedMedians()}. All methods have been optimized for speed and
3580 (license license:artistic2.0)))
3582 (define-public r-viridis
3588 (uri (cran-uri "viridis" version))
3591 "060rf1jn29dq53y3nhb0hykvcap6rqsk04rq544ypiiqb18ngwnx"))))
3592 (build-system r-build-system)
3594 `(("r-ggplot2" ,r-ggplot2)
3595 ("r-gridextra" ,r-gridextra)
3596 ("r-viridislite" ,r-viridislite)))
3597 (home-page "https://github.com/sjmgarnier/viridis")
3598 (synopsis "Matplotlib default color map")
3600 "This package is a port of the new @url{matplotlib,
3601 http://matplotlib.org/} color maps (@code{viridis}--the default--,
3602 @code{magma}, @code{plasma}, and @code{inferno}) to R. These color maps are
3603 designed in such a way that they will analytically be perfectly
3604 perceptually-uniform, both in regular form and also when converted to
3605 black-and-white. They are also designed to be perceived by readers with the
3606 most common form of color blindness.")
3607 (license license:x11)))
3609 (define-public r-viridislite
3611 (name "r-viridislite")
3616 (uri (cran-uri "viridisLite" version))
3619 "1by2l05f0yabwvv64lhnv7bbhx0w683s3wr9j2xda920ghpa23kq"))))
3620 (properties `((upstream-name . "viridisLite")))
3621 (build-system r-build-system)
3622 (home-page "https://github.com/sjmgarnier/viridisLite")
3623 (synopsis "Default color maps from matplotlib")
3625 "This package is a port of the new @code{matplotlib} color maps ('viridis',
3626 'magma', 'plasma' and 'inferno') to R. matplotlib is a popular plotting
3627 library for Python. These color maps are designed in such a way that they
3628 will analytically be perfectly perceptually-uniform, both in regular form and
3629 also when converted to black-and-white. They are also designed to be
3630 perceived by readers with the most common form of color blindness. This is
3631 the 'lite' version of the more complete @code{viridis} package.")
3632 (license license:expat)))
3634 (define-public r-tidyselect
3636 (name "r-tidyselect")
3641 (uri (cran-uri "tidyselect" version))
3644 "1592dbzawhd1hpsp9919l4sifyiaaj6xr7lnhsbwa6jwmmb0xcsw"))))
3645 (build-system r-build-system)
3647 `(("r-glue" ,r-glue)
3648 ("r-purrr" ,r-purrr)
3650 ("r-rlang" ,r-rlang)))
3651 (home-page "https://cran.r-project.org/web/packages/tidyselect")
3652 (synopsis "Select from a set of strings")
3654 "This package provides a backend for the selecting functions of the
3655 tidyverse. It makes it easy to implement select-like functions in your own
3656 packages in a way that is consistent with other tidyverse interfaces for
3658 (license license:gpl3)))
3660 (define-public r-tidyr
3667 (uri (cran-uri "tidyr" version))
3670 "0485f19mkkglc4bv57y6bm6l9rfgd878hsz2xdg1nwgbqchjhgix"))))
3671 (build-system r-build-system)
3673 `(("r-dplyr" ,r-dplyr)
3674 ("r-magrittr" ,r-magrittr)
3676 ("r-purrr" ,r-purrr)
3677 ("r-rlang" ,r-rlang)
3678 ("r-tidyselect" ,r-tidyselect)
3680 ("r-stringi" ,r-stringi)
3681 ("r-tibble" ,r-tibble)))
3682 (home-page "https://github.com/hadley/tidyr")
3683 (synopsis "Tidy data with `spread()` and `gather()` functions")
3685 "tidyr is a reframing of the reshape2 package designed to accompany the
3686 tidy data framework, and to work hand-in-hand with magrittr and dplyr to build
3687 a solid pipeline for data analysis. It is designed specifically for tidying
3688 data, not the general reshaping that reshape2 does, or the general aggregation
3689 that reshape did. In particular, built-in methods only work for data frames,
3690 and tidyr provides no margins or aggregation.")
3691 (license license:expat)))
3693 (define-public r-hexbin
3700 (uri (cran-uri "hexbin" version))
3703 "0lpfl0015lg5x7lvv9dr302bca22c7fs91pnd896ypgpzqg7pm26"))))
3704 (build-system r-build-system)
3706 `(("r-lattice" ,r-lattice)))
3708 `(("gfortran" ,gfortran)))
3709 (home-page "https://github.com/edzer/hexbin")
3710 (synopsis "Hexagonal binning routines")
3712 "This package provides binning and plotting functions for hexagonal bins.
3713 It uses and relies on grid graphics and formal (S4) classes and methods.")
3714 (license license:gpl2+)))
3716 (define-public r-purrr
3723 (uri (cran-uri "purrr" version))
3726 "0dc53zzan3km2l9lzxjixcv6yn7dhw2ppmz8qf2awhak7x2qm9m4"))))
3727 (build-system r-build-system)
3729 `(("r-tibble" ,r-tibble)
3730 ("r-magrittr" ,r-magrittr)
3731 ("r-rlang" ,r-rlang)))
3732 (home-page "https://github.com/hadley/purrr")
3733 (synopsis "Functional programming tools")
3735 "This package completes R's functional programming tools with missing
3736 features present in other programming languages.")
3737 (license license:gpl3+)))
3739 (define-public r-plotly
3745 (uri (cran-uri "plotly" version))
3748 "19p8pa03q9mw5vaan7r56xgd13d90ssiz0flbrkvpfrir2105ybq"))))
3749 (build-system r-build-system)
3751 `(("r-base64enc" ,r-base64enc)
3752 ("r-crosstalk" ,r-crosstalk)
3753 ("r-digest" ,r-digest)
3754 ("r-data-table" ,r-data-table)
3755 ("r-dplyr" ,r-dplyr)
3756 ("r-ggplot2" ,r-ggplot2)
3757 ("r-hexbin" ,r-hexbin)
3758 ("r-htmltools" ,r-htmltools)
3759 ("r-htmlwidgets" ,r-htmlwidgets)
3761 ("r-jsonlite" ,r-jsonlite)
3762 ("r-lazyeval" ,r-lazyeval)
3763 ("r-magrittr" ,r-magrittr)
3764 ("r-promises" ,r-promises)
3765 ("r-purrr" ,r-purrr)
3766 ("r-rcolorbrewer" ,r-rcolorbrewer)
3767 ("r-rlang" ,r-rlang)
3768 ("r-scales" ,r-scales)
3769 ("r-tibble" ,r-tibble)
3770 ("r-tidyr" ,r-tidyr)
3771 ("r-viridislite" ,r-viridislite)))
3772 (home-page "https://plot.ly/r")
3773 (synopsis "Create interactive web graphics")
3775 "This package enables the translation of ggplot2 graphs to an interactive
3776 web-based version and/or the creation of custom web-based visualizations
3777 directly from R. Once uploaded to a plotly account, plotly graphs (and the
3778 data behind them) can be viewed and modified in a web browser.")
3779 (license license:x11)))
3781 (define-public r-biased-urn
3783 (name "r-biased-urn")
3788 (uri (cran-uri "BiasedUrn" version))
3791 "13i2lgfnjhlbbm2yxfc2l5hswqw6x03pwba5csjmirv8kpjw4xr3"))))
3792 (properties `((upstream-name . "BiasedUrn")))
3793 (build-system r-build-system)
3794 (home-page "http://www.agner.org/random/")
3795 (synopsis "Biased urn model distributions")
3797 "This package provides statistical models of biased sampling in the form
3798 of univariate and multivariate noncentral hypergeometric distributions,
3799 including Wallenius' noncentral hypergeometric distribution and Fisher's
3800 noncentral hypergeometric distribution (also called extended hypergeometric
3802 (license license:gpl3+)))
3804 (define-public r-rematch
3811 (uri (cran-uri "rematch" version))
3814 "0y3mshvpvz9csmq8hk8jbabx4nxlv5sckvfzvm6920ndg34xw2d4"))))
3815 (build-system r-build-system)
3816 (home-page "https://github.com/MangoTheCat/rematch")
3817 (synopsis "Match regular expressions with a nicer API")
3819 "This package provides a small wrapper on @code{regexpr} to extract the
3820 matches and captured groups from the match of a regular expression to a
3822 (license license:expat)))
3824 (define-public r-cellranger
3826 (name "r-cellranger")
3831 (uri (cran-uri "cellranger" version))
3834 "16fgi3annn34c3cxi0pxf62mmmmxi21hp0zzlv7bkfsjqy4g4f2x"))))
3835 (build-system r-build-system)
3837 `(("r-rematch" ,r-rematch)
3838 ("r-tibble" ,r-tibble)))
3839 (home-page "https://github.com/rsheets/cellranger")
3840 (synopsis "Translate spreadsheet cell ranges to rows and columns")
3842 "This package provides helper functions to work with spreadsheets and the
3843 @code{A1:D10} style of cell range specification.")
3844 (license license:expat)))
3846 (define-public r-googlesheets
3848 (name "r-googlesheets")
3853 (uri (cran-uri "googlesheets" version))
3856 "11q07nxys72wkxx9mawmjyf20gvwvrb7h3gpa73h6lgh2vgrwnv8"))))
3857 (build-system r-build-system)
3859 `(("r-cellranger" ,r-cellranger)
3860 ("r-dplyr" ,r-dplyr)
3862 ("r-jsonlite" ,r-jsonlite)
3863 ("r-purrr" ,r-purrr)
3864 ("r-readr" ,r-readr)
3865 ("r-stringr" ,r-stringr)
3866 ("r-tibble" ,r-tibble)
3867 ("r-tidyr" ,r-tidyr)
3868 ("r-xml2" ,r-xml2)))
3869 (home-page "https://github.com/jennybc/googlesheets")
3870 (synopsis "Manage Google spreadsheets from R")
3871 (description "This package provides tools to interact with Google Sheets
3873 (license license:expat)))
3875 (define-public r-spams
3878 (version "2.6-2017-03-22")
3882 ;; Use the ‘Latest version’ link for a stable URI across releases.
3883 (uri (string-append "https://gforge.inria.fr/frs/download.php/"
3884 "latestfile/4531/spams-R-v" version ".tar.gz"))
3887 "13z2293jixf1r9g8dyy856xrhvpjr2ln2n9smn6644126r9hmhkx"))))
3888 (build-system r-build-system)
3891 (modify-phases %standard-phases
3892 (add-after 'unpack 'chdir
3893 (lambda _ (chdir "spams") #t))
3894 ;; Don't tune for the building machine.
3895 (add-after 'chdir 'no-mtune
3897 (substitute* "src/Makevars"
3898 (("-mtune=native") ""))
3901 `(("r-lattice" ,r-lattice)
3902 ("r-matrix" ,r-matrix)))
3903 (home-page "http://spams-devel.gforge.inria.fr")
3904 (synopsis "Toolbox for solving sparse estimation problems")
3905 (description "SPAMS (SPArse Modeling Software) is an optimization toolbox
3906 for solving various sparse estimation problems. It includes tools for the
3910 @item Dictionary learning and matrix factorization (NMF, sparse @dfn{principle
3911 component analysis} (PCA), ...)
3912 @item Solving sparse decomposition problems with LARS, coordinate descent,
3913 OMP, SOMP, proximal methods
3914 @item Solving structured sparse decomposition problems (l1/l2, l1/linf, sparse
3915 group lasso, tree-structured regularization, structured sparsity with
3916 overlapping groups,...).
3918 (license license:gpl3+)))
3920 (define-public r-base64
3927 (uri (cran-uri "base64" version))
3930 "1labh0ycdm2xcjssj8bhnyjvbk44mcdsi0rb2p8rfqa428mrq9cf"))))
3931 (build-system r-build-system)
3933 `(("r-openssl" ,r-openssl)))
3934 (home-page "https://cran.r-project.org/web/packages/base64")
3935 (synopsis "Base64 encoder and decoder")
3937 "This package is a compatibility wrapper to replace the orphaned package
3938 by Romain Francois. New applications should use the openssl or base64enc
3940 (license license:expat)))
3942 (define-public r-hmisc
3949 (uri (cran-uri "Hmisc" version))
3952 "160l50ppjs69ipcaya1mlcz29zbn5rmqg91r09dvzzvkvwfb47cr"))))
3953 (properties `((upstream-name . "Hmisc")))
3954 (build-system r-build-system)
3956 `(("gfortran" ,gfortran)))
3958 `(("r-acepack" ,r-acepack)
3959 ("r-base64enc" ,r-base64enc)
3960 ("r-cluster" ,r-cluster)
3961 ("r-data-table" ,r-data-table)
3962 ("r-foreign" ,r-foreign)
3963 ("r-formula" ,r-formula)
3964 ("r-ggplot2" ,r-ggplot2)
3965 ("r-gridextra" ,r-gridextra)
3966 ("r-gtable" ,r-gtable)
3967 ("r-lattice" ,r-lattice)
3968 ("r-latticeextra" ,r-latticeextra)
3969 ("r-htmltable" ,r-htmltable)
3970 ("r-htmltools" ,r-htmltools)
3972 ("r-rpart" ,r-rpart)
3973 ("r-survival" ,r-survival)
3974 ("r-viridis" ,r-viridis)))
3975 (home-page "http://biostat.mc.vanderbilt.edu/Hmisc")
3976 (synopsis "Miscellaneous data analysis and graphics functions")
3978 "This package contains many functions useful for data analysis,
3979 high-level graphics, utility operations, functions for computing sample size
3980 and power, importing and annotating datasets, imputing missing values,
3981 advanced table making, variable clustering, character string manipulation,
3982 conversion of R objects to LaTeX code, and recoding variables.")
3983 (license license:gpl2+)))
3985 (define-public r-runit
3992 (uri (cran-uri "RUnit" version))
3995 "1wc1gwb7yw7phf8b0gkig6c23klya3ax11c6i4s0f049k42r78r3"))))
3996 (properties `((upstream-name . "RUnit")))
3997 (build-system r-build-system)
3998 (home-page "https://cran.r-project.org/web/packages/RUnit")
3999 (synopsis "R unit test framework")
4001 "This package provides R functions implementing a standard unit testing
4002 framework, with additional code inspection and report generation tools.")
4003 (license license:gpl2+)))
4005 (define-public r-dynamictreecut
4007 (name "r-dynamictreecut")
4012 (uri (cran-uri "dynamicTreeCut" version))
4015 "1fadbql7g5r2vvlkr89nlrjxwp4yx4xrdqmv077qvmnx9vv0f4w3"))))
4016 (properties `((upstream-name . "dynamicTreeCut")))
4017 (build-system r-build-system)
4019 "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/BranchCutting/")
4020 (synopsis "Detect clusters in hierarchical clustering dendrograms")
4022 "This package contains methods for the detection of clusters in
4023 hierarchical clustering dendrograms.")
4024 (license license:gpl2+)))
4026 (define-public r-preprocesscore
4028 (name "r-preprocesscore")
4033 (uri (bioconductor-uri "preprocessCore" version))
4036 "1afar1z7959v7mbzsqa77vqfh0yc7y3nv5ayx71485a8scwsfwbk"))))
4038 `((upstream-name . "preprocessCore")))
4039 (build-system r-build-system)
4040 (home-page "https://github.com/bmbolstad/preprocessCore")
4041 (synopsis "Collection of pre-processing functions")
4043 "This package provides a library of core pre-processing and normalization
4045 (license license:lgpl2.0+)))
4047 (define-public r-fastcluster
4049 (name "r-fastcluster")
4054 (uri (cran-uri "fastcluster" version))
4057 "01a2xnhhvv1swd4g8p4lzyn7ww7kg49jlnzc7kfz60jqjzpisrpk"))))
4058 (build-system r-build-system)
4059 (home-page "http://danifold.net/fastcluster.html")
4060 (synopsis "Fast hierarchical clustering routines")
4062 "This package implements fast hierarchical, agglomerative clustering
4063 routines. Part of the functionality is designed as drop-in replacement for
4064 existing routines: @code{linkage()} in the SciPy package
4065 @code{scipy.cluster.hierarchy}, @code{hclust()} in R's @code{stats} package,
4066 and the @code{flashClust} package. It provides the same functionality with
4067 the benefit of a much faster implementation. Moreover, there are
4068 memory-saving routines for clustering of vector data, which go beyond what the
4069 existing packages provide.")
4070 (license license:bsd-2)))
4072 (define-public r-sfsmisc
4079 (uri (cran-uri "sfsmisc" version))
4082 "0cgq2h11ngkzd6p34k6mqjnvlvc5vj4lnqrl64k05lb391j391w0"))))
4083 (build-system r-build-system)
4084 (home-page "https://cran.r-project.org/web/packages/sfsmisc")
4085 (synopsis "Utilities from \"Seminar fuer Statistik\" ETH Zurich")
4087 "This package provides useful utilities from Seminar fuer Statistik ETH
4088 Zurich, including many that are related to graphics.")
4089 (license license:gpl2+)))
4091 (define-public r-gtools
4098 (uri (cran-uri "gtools" version))
4101 "0f5syk1qq6cjq6hwymvkiyhzwa389z94722v881ipbfqkd2q8505"))))
4102 (build-system r-build-system)
4105 (modify-phases %standard-phases
4106 (add-after 'unpack 'make-deterministic
4108 (substitute* "R/checkReverseDependencies.R"
4109 (("tempdir\\(\\)") "\"/tmp\""))
4111 (home-page "https://cran.r-project.org/web/packages/gtools")
4112 (synopsis "Various R programming tools")
4114 "This package contains a collection of various functions to assist in R
4115 programming, such as tools to assist in developing, updating, and maintaining
4116 R and R packages, calculating the logit and inverse logit transformations,
4117 tests for whether a value is missing, empty or contains only @code{NA} and
4118 @code{NULL} values, and many more.")
4119 (license license:gpl2)))
4121 (define-public r-gdata
4128 (uri (cran-uri "gdata" version))
4131 "0zwdj7lscgxr8r62ii8hbdh4mb7sa9w4f5nv32zzrxdvymcpya2b"))))
4132 (build-system r-build-system)
4136 `(("r-gtools" ,r-gtools)))
4137 (home-page "https://cran.r-project.org/web/packages/gdata")
4138 (synopsis "Various R programming tools for data manipulation")
4140 "This package provides various R programming tools for data manipulation,
4144 @item medical unit conversions
4145 @item combining objects
4146 @item character vector operations
4147 @item factor manipulation
4148 @item obtaining information about R objects
4149 @item manipulating MS-Excel formatted files
4150 @item generating fixed-width format files
4151 @item extricating components of date and time objects
4152 @item operations on columns of data frames
4153 @item matrix operations
4154 @item operations on vectors and data frames
4155 @item value of last evaluated expression
4156 @item wrapper for @code{sample} that ensures consistent behavior for
4157 both scalar and vector arguments
4159 (license license:gpl2+)))
4161 (define-public r-gplots
4168 (uri (cran-uri "gplots" version))
4171 "02nb8n3s7c1zxq2s7ycaq2ys72y7mzirxrwj954h6gdc4x1zhg9l"))))
4172 (build-system r-build-system)
4174 `(("r-catools" ,r-catools)
4175 ("r-gdata" ,r-gdata)
4176 ("r-gtools" ,r-gtools)
4177 ("r-kernsmooth" ,r-kernsmooth)))
4178 (home-page "https://cran.r-project.org/web/packages/gplots")
4179 (synopsis "Various R programming tools for plotting data")
4181 "This package provides various R programming tools for plotting data,
4185 @item calculating and plotting locally smoothed summary function
4186 @item enhanced versions of standard plots
4187 @item manipulating colors
4188 @item calculating and plotting two-dimensional data summaries
4189 @item enhanced regression diagnostic plots
4190 @item formula-enabled interface to @code{stats::lowess} function
4191 @item displaying textual data in plots
4193 @item plotting \"Venn\" diagrams
4194 @item displaying Open-Office style plots
4195 @item plotting multiple data on same region, with separate axes
4196 @item plotting means and confidence intervals
4197 @item spacing points in an x-y plot so they don't overlap
4199 (license license:gpl2+)))
4201 (define-public r-rocr
4208 (uri (cran-uri "ROCR" version))
4211 "1jay8cm7lgq56i967vm5c2hgaxqkphfpip0gn941li3yhh7p3vz7"))))
4212 (properties `((upstream-name . "ROCR")))
4213 (build-system r-build-system)
4215 `(("r-gplots" ,r-gplots)))
4216 (home-page "http://rocr.bioinf.mpi-sb.mpg.de/")
4217 (synopsis "Visualizing the performance of scoring classifiers")
4219 "ROCR is a flexible tool for creating cutoff-parameterized 2D performance
4220 curves by freely combining two from over 25 performance measures (new
4221 performance measures can be added using a standard interface). Curves from
4222 different cross-validation or bootstrapping runs can be averaged by different
4223 methods, and standard deviations, standard errors or box plots can be used to
4224 visualize the variability across the runs. The parameterization can be
4225 visualized by printing cutoff values at the corresponding curve positions, or
4226 by coloring the curve according to cutoff. All components of a performance
4227 plot can be quickly adjusted using a flexible parameter dispatching
4229 (license license:gpl2+)))
4231 (define-public r-zoo
4237 (uri (cran-uri "zoo" version))
4240 "15jmkgwvq2mm9f09vijgx7sff8pszh90fndcwhk2vw9i0p183di0"))))
4241 (build-system r-build-system)
4243 `(("r-lattice" ,r-lattice)))
4244 (home-page "http://zoo.R-Forge.R-project.org/")
4245 (synopsis "S3 infrastructure for regular and irregular time series")
4246 (description "This package contains an S3 class with methods for totally
4247 ordered indexed observations. It is particularly aimed at irregular time
4248 series of numeric vectors/matrices and factors.")
4249 (license license:gpl2+)))
4251 (define-public r-ztable
4257 (uri (cran-uri "ztable" version))
4260 "0g7khk5ifsdh9p31wlwh2l5mn1hzxzpv6qcn1wh34vsfjdmijjwy"))))
4261 (build-system r-build-system)
4263 `(("r-flextable" ,r-flextable)
4264 ("r-magrittr" ,r-magrittr)
4265 ("r-moonbook" ,r-moonbook)
4266 ("r-officer" ,r-officer)
4267 ("r-rcolorbrewer" ,r-rcolorbrewer)
4268 ("r-scales" ,r-scales)
4269 ("r-stringr" ,r-stringr)))
4270 (home-page "https://cran.r-project.org/web/packages/ztable")
4271 (synopsis "Zebra-striped tables in LaTeX and HTML formats for R")
4273 "This package provides functions to make zebra-striped tables (tables
4274 with alternating row colors) in LaTeX and HTML formats easily from
4275 @code{data.frame}, @code{matrix}, @code{lm}, @code{aov}, @code{anova},
4276 @code{glm}, @code{coxph}, @code{nls}, @code{fitdistr}, @code{mytable} and
4277 @code{cbind.mytable} objects.")
4278 (license license:gpl2+)))
4280 (define-public r-vipor
4286 (uri (cran-uri "vipor" version))
4289 "112gc0d7f8iavgf56pnzfxb7hy75yhd0zlyjzshdcfbnqcd2a6bx"))))
4290 (build-system r-build-system)
4291 (home-page "https://cran.r-project.org/web/packages/vipor")
4292 (synopsis "Plot categorical data using noise and density estimates")
4294 "This package provides tools to generate a violin point plot, a
4295 combination of a violin/histogram plot and a scatter plot by offsetting points
4296 within a category based on their density using quasirandom noise.")
4297 (license license:gpl2+)))
4299 (define-public r-beeswarm
4305 (uri (cran-uri "beeswarm" version))
4308 "0hy89bwv7jixlg91li1fywa77916am2whqp1m1fx1khd45g44581"))))
4309 (build-system r-build-system)
4310 (home-page "http://www.cbs.dtu.dk/~eklund/beeswarm/")
4311 (synopsis "Implementation of bee swarm plots")
4313 "This package provides an implementation of bee swarm plots. The bee
4314 swarm plot is a one-dimensional scatter plot like stripchart, but with
4315 closely-packed, non-overlapping points.")
4316 (license license:artistic2.0)))
4318 (define-public r-sourcetools
4320 (name "r-sourcetools")
4325 (uri (cran-uri "sourcetools" version))
4328 "1jnjir0q2dj724f1mjm6p5h77yzyx6xcqy9r2g7gmcxkxw349627"))))
4329 (build-system r-build-system)
4330 (home-page "https://cran.r-project.org/web/packages/sourcetools")
4331 (synopsis "Tools for reading, tokenizing and parsing R code")
4333 "The sourcetools package provides both an R and C++ interface for the
4334 tokenization of R code, and helpers for interacting with the tokenized
4335 representation of R code.")
4336 (license license:expat)))
4338 (define-public r-ggbeeswarm
4340 (name "r-ggbeeswarm")
4344 (uri (cran-uri "ggbeeswarm" version))
4347 "0crk29p5vi1r3a988kms4y7r0iqwgwzsikgvh18r9wbzyr98bb5v"))))
4348 (build-system r-build-system)
4350 `(("r-beeswarm" ,r-beeswarm)
4351 ("r-ggplot2" ,r-ggplot2)
4352 ("r-vipor" ,r-vipor)))
4353 (home-page "https://github.com/eclarke/ggbeeswarm")
4354 (synopsis "Categorical scatter (violin point) plots")
4356 "This package provides two methods of plotting categorical scatter plots
4357 such that the arrangement of points within a category reflects the density of
4358 data at that region, and avoids over-plotting.")
4359 (license license:gpl2+)))
4361 (define-public r-ggthemes
4367 (uri (cran-uri "ggthemes" version))
4370 "0y6570wv135sf7pv57l7bqilzw47rziaqx4vsk45pf1w4lmj0w8b"))))
4371 (build-system r-build-system)
4373 `(("r-ggplot2" ,r-ggplot2)
4374 ("r-purrr" ,r-purrr)
4375 ("r-scales" ,r-scales)
4376 ("r-stringr" ,r-stringr)
4377 ("r-tibble" ,r-tibble)))
4378 (home-page "https://cran.rstudio.com/web/packages/ggthemes")
4379 (synopsis "Extra themes, scales and geoms for @code{ggplot2}")
4380 (description "This package provides extra themes and scales for
4381 @code{ggplot2} that replicate the look of plots by Edward Tufte and
4382 Stephen Few in Fivethirtyeight, The Economist, Stata, Excel, and The
4383 Wall Street Journal, among others. This package also provides
4384 @code{geoms} for Tufte's box plot and range frame.")
4385 (license license:gpl2)))
4387 (define-public r-statmod
4393 (uri (cran-uri "statmod" version))
4396 "07v4x8af60alcw6vbiwf5fp25bhra61kvxz9kqx64lszm0i1fb4x"))))
4397 (build-system r-build-system)
4398 (home-page "https://cran.r-project.org/web/packages/statmod")
4400 `(("gfortran" ,gfortran)))
4401 (synopsis "Statistical modeling")
4403 "This package provides a collection of algorithms and functions to aid
4404 statistical modeling. It includes growth curve comparisons, limiting dilution
4405 analysis (aka ELDA), mixed linear models, heteroscedastic regression,
4406 inverse-Gaussian probability calculations, Gauss quadrature and a secure
4407 convergence algorithm for nonlinear models. It also includes advanced
4408 generalized linear model functions that implement secure convergence,
4409 dispersion modeling and Tweedie power-law families.")
4410 ;; Statmod is distributed under either license
4411 (license (list license:gpl2 license:gpl3))))
4413 (define-public r-rann
4419 (uri (cran-uri "RANN" version))
4422 "1r6rivh9ba4gwnzryip0aiwsbm46zma7nvd9z5y456p2dgzp9lii"))))
4424 `((upstream-name . "RANN")))
4425 (build-system r-build-system)
4426 (home-page "https://github.com/jefferis/RANN")
4427 (synopsis "Fast nearest neighbour search")
4429 "This package finds the k nearest neighbours for every point in a given
4430 dataset in O(N log N) time using Arya and Mount's ANN library. Provides
4431 approximate, exact searches, fixed radius searches, bd and kb trees.")
4432 (license license:gpl3+)))
4434 (define-public r-fivethirtyeight
4436 (name "r-fivethirtyeight")
4441 (uri (string-append "https://mran.microsoft.com/src/contrib/"
4442 "fivethirtyeight_" version ".tar.gz"))
4445 "0fcc8rq745nsghp27dk0lgih90y4zx8hrzcvsn6ih786yv7qxhvl"))))
4446 (build-system r-build-system)
4448 `(("r-knitr" ,r-knitr)
4449 ("r-rmarkdown" ,r-rmarkdown)
4450 ("r-dplyr" ,r-dplyr)
4451 ("r-readr" ,r-readr)
4452 ("r-ggplot2" ,r-ggplot2)
4453 ("r-magrittr" ,r-magrittr)
4454 ("r-stringr" ,r-stringr)))
4455 (home-page "https://mran.microsoft.com/package/fivethirtyeight/")
4456 (synopsis "Data and code behind the stories at FiveThirtyEight")
4457 (description "This R package provides access to the code and data sets
4458 published by the statistics blog FiveThirtyEight.")
4459 (license license:expat)))
4461 (define-public r-compquadform
4463 (name "r-compquadform")
4468 (uri (cran-uri "CompQuadForm" version))
4471 "1i30hrqdk64q17vsn918c3q79brchgx2wzh1gbsgbn0dh1ncabq4"))))
4472 (properties `((upstream-name . "CompQuadForm")))
4473 (build-system r-build-system)
4474 (home-page "https://cran.r-project.org/web/packages/CompQuadForm")
4475 (synopsis "Distribution function of quadratic forms in normal variables")
4477 "This package provides functions to compute the distribution function of
4478 quadratic forms in normal variables using Imhof's method, Davies's algorithm,
4479 Farebrother's algorithm or Liu et al.'s algorithm.")
4480 (license license:gpl2+)))
4482 (define-public r-cowplot
4489 (uri (cran-uri "cowplot" version))
4492 "1jrx1h0blkk577y4cvnjk7xccn7qmjiv2bnpgqlsjvjhsxglf41y"))))
4493 (build-system r-build-system)
4495 `(("r-ggplot2" ,r-ggplot2)
4496 ("r-gtable" ,r-gtable)
4498 ("r-scales" ,r-scales)))
4499 (home-page "https://github.com/wilkelab/cowplot")
4500 (synopsis "Streamlined plot theme and plot annotations for ggplot2")
4502 "This package provides some helpful extensions and modifications to the
4503 ggplot2 package to combine multiple ggplot2 plots into one and label them with
4504 letters, as is often required for scientific publications.")
4505 (license license:gpl2)))
4507 (define-public r-mixtools
4514 (uri (cran-uri "mixtools" version))
4517 "13wdm0xs5bakhpa8ypg6lvhjaqkxyabwz4glxdwn0jwdvkcdhgsl"))))
4518 (build-system r-build-system)
4520 `(("r-mass" ,r-mass)
4521 ("r-segmented" ,r-segmented)
4522 ("r-survival" ,r-survival)))
4523 (home-page "https://cran.r-project.org/web/packages/mixtools")
4524 (synopsis "Tools for analyzing finite mixture models")
4526 "This package provides a collection of R functions for analyzing finite
4528 (license license:gpl2+)))
4530 (define-public r-lars
4537 (uri (cran-uri "lars" version))
4540 "0blj44wqrx6lmym1m9v6wkz8zxzbjax2zl6swgdczci0ixb5nx34"))))
4541 (build-system r-build-system)
4543 `(("gfortran" ,gfortran)))
4544 (home-page "http://www-stat.stanford.edu/~hastie/Papers/#LARS")
4545 (synopsis "Least angle regression software")
4547 "Least Angle Regression (\"LAR\") is a model selection algorithm; a
4548 useful and less greedy version of traditional forward selection methods. A
4549 simple modification of the LAR algorithm implements Tibshirani's Lasso; the
4550 Lasso modification of LARS calculates the entire Lasso path of coefficients
4551 for a given problem at the cost of a single least squares fit. Another LARS
4552 modification efficiently implements epsilon Forward Stagewise linear
4554 (license license:gpl2)))
4556 (define-public r-fastica
4563 (uri (cran-uri "fastICA" version))
4566 "108z2ymby5y4h8l4l2krqwm28rya93gq09yylgilnm3afvfrfabg"))))
4567 (properties `((upstream-name . "fastICA")))
4568 (build-system r-build-system)
4569 (home-page "https://cran.r-project.org/web/packages/fastICA")
4570 (synopsis "FastICA algorithms to perform ICA and projection pursuit")
4572 "This package provides an implementation of the FastICA algorithm to
4573 perform @dfn{independent component analysis} (ICA) and projection pursuit.")
4575 (license license:gpl3+)))
4577 (define-public r-randomforest
4579 (name "r-randomforest")
4584 (uri (cran-uri "randomForest" version))
4587 "0kbmm0l42fc2d1rdq0l7k09d34kd87q4lx651ffsic4y84h8kf7l"))))
4588 (properties `((upstream-name . "randomForest")))
4589 (build-system r-build-system)
4590 (home-page "https://www.stat.berkeley.edu/~breiman/RandomForests/")
4592 `(("gfortran" ,gfortran)))
4593 (synopsis "Breiman and Cutler's random forests for classification and regression")
4595 "This package provides the Breiman and Cutler's random forests algorithm, based on a
4596 forest of trees using random inputs, for classification and regression.")
4597 (license license:gpl2+)))
4599 (define-public r-diptest
4606 (uri (cran-uri "diptest" version))
4609 "06xnc5gv1284ll0addxnxb6ljz6fn8dbyrp5vchyz6551h800aa6"))))
4610 (build-system r-build-system)
4611 (home-page "https://cran.r-project.org/web/packages/diptest")
4612 (synopsis "Hartigan's dip test statistic for unimodality")
4614 "This package computes Hartigan's dip test statistic for unimodality,
4615 multimodality and provides a test with simulation based p-values, where the
4616 original public code has been corrected.")
4617 (license license:gpl2+)))
4619 (define-public r-modeltools
4621 (name "r-modeltools")
4626 (uri (cran-uri "modeltools" version))
4629 "1s9lmkac3rl0nknf4wizfhg7ryq7c8yvvyc4z619238br27hhsi5"))))
4630 (build-system r-build-system)
4631 (home-page "https://cran.r-project.org/web/packages/modeltools")
4632 (synopsis "Tools and classes for statistical models")
4634 "This package provides a collection of tools to deal with statistical
4635 models. The functionality is experimental and the user interface is likely
4636 to change in the future.")
4637 (license license:gpl2)))
4639 (define-public r-flexmix
4646 (uri (cran-uri "flexmix" version))
4649 "0sl4zxh1sb2sr5q7svjw9ihrm219jzn82yrc9d43q6r1b8bpyz43"))))
4650 (build-system r-build-system)
4652 `(("r-lattice" ,r-lattice)
4653 ("r-modeltools" ,r-modeltools)
4654 ("r-nnet" ,r-nnet)))
4655 (home-page "https://cran.r-project.org/web/packages/flexmix")
4656 (synopsis "Flexible mixture modeling")
4658 "This package implements a general framework for finite mixtures of
4659 regression models using the EM algorithm. FlexMix provides the E-step and
4660 all data handling, while the M-step can be supplied by the user to easily
4661 define new models. Existing drivers implement mixtures of standard linear
4662 models, generalized linear models and model-based clustering.")
4663 (license license:gpl2+)))
4665 (define-public r-mclust
4672 (uri (cran-uri "mclust" version))
4675 "1vcl4nl8by2vj2k9k84imy5m850khkgd8q02a8ica1h8vz9ijgn4"))))
4676 (build-system r-build-system)
4678 `(("gfortran" ,gfortran)))
4679 (home-page "http://www.stat.washington.edu/mclust/")
4680 (synopsis "Gaussian mixture modelling for model-based clustering etc.")
4682 "This package provides Gaussian finite mixture models fitted via EM
4683 algorithm for model-based clustering, classification, and density estimation,
4684 including Bayesian regularization, dimension reduction for visualisation,
4685 and resampling-based inference.")
4686 (license license:gpl2+)))
4688 (define-public r-prabclus
4695 (uri (cran-uri "prabclus" version))
4698 "0qjsxrx6yv338bxm4ki0w9h8hind1l98abdrz828588bwj02jya1"))))
4699 (build-system r-build-system)
4701 `(("r-mass" ,r-mass)
4702 ("r-mclust" ,r-mclust)))
4703 (home-page "https://cran.r-project.org/web/packages/prabclus")
4704 (synopsis "Parametric bootstrap tests for spatial neighborhood clustering")
4706 "This package provides distance-based parametric bootstrap tests for
4707 clustering with spatial neighborhood information. It implements some distance
4708 measures, clustering of presence-absence, abundance and multilocus genetical
4709 data for species delimitation, nearest neighbor based noise detection.")
4710 (license license:gpl2+)))
4712 (define-public r-deoptimr
4719 (uri (cran-uri "DEoptimR" version))
4722 "1vz546hyjyhly70z62h5n3mn62b8llhhmim8ffp9y6jnnb0i2sc4"))))
4723 (properties `((upstream-name . "DEoptimR")))
4724 (build-system r-build-system)
4725 (home-page "https://cran.r-project.org/web/packages/DEoptimR")
4726 (synopsis "Differential evolution optimization in pure R")
4728 "This package provides a differential evolution (DE) stochastic
4729 algorithms for global optimization of problems with and without constraints.
4730 The aim is to curate a collection of its state-of-the-art variants that (1) do
4731 not sacrifice simplicity of design, (2) are essentially tuning-free, and (3)
4732 can be efficiently implemented directly in the R language.")
4733 (license license:gpl2+)))
4735 (define-public r-robustbase
4737 (name "r-robustbase")
4742 (uri (cran-uri "robustbase" version))
4745 "1632p73iv9iqqm0v3k9rfv9way0him3fl35si1nly9wi5kpq5ci7"))))
4746 (build-system r-build-system)
4748 `(("gfortran" ,gfortran)))
4750 `(("r-deoptimr" ,r-deoptimr)))
4751 (home-page "http://robustbase.r-forge.r-project.org/")
4752 (synopsis "Basic robust statistics")
4754 "This packages allows to analyze data with robust methods such as
4755 regression methodology including model selections and multivariate statistics.")
4756 (license license:gpl2+)))
4758 (define-public r-pcapp
4765 (uri (cran-uri "pcaPP" version))
4768 "1z2kdf9gfp965xbcd4rg6vf20d1bl443na0qjkpq7gmzpaq6cifa"))))
4769 (properties `((upstream-name . "pcaPP")))
4770 (build-system r-build-system)
4772 `(("r-mvtnorm" ,r-mvtnorm)))
4773 (home-page "https://cran.r-project.org/web/packages/pcaPP")
4774 (synopsis "Robust PCA by projection pursuit")
4776 "This package provides functions for robust @dfn{principal component
4777 analysis} (PCA) by projection pursuit.")
4778 (license license:gpl3+)))
4780 (define-public r-rrcov
4787 (uri (cran-uri "rrcov" version))
4790 "0wn5h8vi0zyk5ah898m37ysz4kiih6y792nb9zdvhvd8r07f0sc5"))))
4791 (build-system r-build-system)
4793 `(("r-cluster" ,r-cluster)
4794 ("r-lattice" ,r-lattice)
4795 ("r-mvtnorm" ,r-mvtnorm)
4796 ("r-pcapp" ,r-pcapp)
4797 ("r-robustbase" ,r-robustbase)))
4799 `(("gfortran" ,gfortran)))
4800 (home-page "https://cran.r-project.org/web/packages/rrcov")
4801 (synopsis "Scalable robust estimators with high breakdown Point")
4803 "This package provides an implementation of robust location and scatter
4804 estimation and robust multivariate analysis with high breakdown point.")
4805 (license license:gpl2+)))
4807 (define-public r-fit-models
4809 (name "r-fit-models")
4814 (uri (cran-uri "fit.models" version))
4817 "0vjbzmx0ambm6yzidb4vbgmhclwzwv2iz2cwl54ccdkvx4cx3fck"))))
4818 (properties `((upstream-name . "fit.models")))
4819 (build-system r-build-system)
4821 `(("r-lattice" ,r-lattice)))
4822 (home-page "https://cran.r-project.org/web/packages/fit.models")
4823 (synopsis "Compare fitted models")
4825 "The @code{fit.models} function and its associated methods (coefficients, print,
4826 summary, plot, etc.) were originally provided in the @code{robust} package to
4827 compare robustly and classically fitted model objects. The aim of the
4828 @code{fit.models} package is to separate this fitted model object comparison
4829 functionality from the robust package and to extend it to support fitting
4830 methods (e.g., classical, robust, Bayesian, regularized, etc.) more
4832 ;; Any version of the GPL
4833 (license (list license:gpl2+ license:gpl3+))))
4835 (define-public r-robust
4842 (uri (cran-uri "robust" version))
4845 "1b7qh1aff500nd6dh4y2ipmjgdiq8991shflb63pc39vpc0ny6g4"))))
4846 (build-system r-build-system)
4848 `(("r-fit-models" ,r-fit-models)
4849 ("r-lattice" ,r-lattice)
4851 ("r-robustbase" ,r-robustbase)
4852 ("r-rrcov" ,r-rrcov)))
4854 `(("gfortran" ,gfortran)))
4855 (home-page "https://cran.r-project.org/web/packages/robust")
4856 (synopsis "Port of the S+ \"Robust Library\"")
4858 "This package is a port of the S+ \"Robust Library\". It provides
4859 methods for robust statistics, notably for robust regression and robust
4860 multivariate analysis.")
4861 (license license:gpl2)))
4863 (define-public r-trimcluster
4865 (name "r-trimcluster")
4870 (uri (cran-uri "trimcluster" version))
4873 "0013bpyq6mkvjn38qsmwnsxfiwxgwngnqxycxvgpgmiadhm8fjmn"))))
4874 (build-system r-build-system)
4875 (home-page "https://cran.r-project.org/web/packages/trimcluster")
4876 (synopsis "Cluster analysis with trimming")
4878 "The trimmed k-means clustering method by Cuesta-Albertos, Gordaliza and
4879 Matran (1997). This optimizes the k-means criterion under trimming a portion
4882 (license (list license:gpl2+ license:gpl3+))))
4884 (define-public r-fpc
4887 (version "2.1-11.1")
4891 (uri (cran-uri "fpc" version))
4894 "1ari57hkgqsxh6khr6j52cfrzc0096cnn1q7ghxk2z4brdd4rznc"))))
4895 (build-system r-build-system)
4897 `(("r-class" ,r-class)
4898 ("r-cluster" ,r-cluster)
4899 ("r-diptest" ,r-diptest)
4900 ("r-flexmix" ,r-flexmix)
4901 ("r-kernlab" ,r-kernlab)
4903 ("r-mclust" ,r-mclust)
4904 ("r-mvtnorm" ,r-mvtnorm)
4905 ("r-prabclus" ,r-prabclus)
4906 ("r-robustbase" ,r-robustbase)
4907 ("r-trimcluster" ,r-trimcluster)))
4908 (home-page "https://cran.r-project.org/web/packages/fpc")
4909 (synopsis "Flexible procedures for clustering")
4911 "This package provides various methods for clustering and cluster validation.
4912 For example, it provides fixed point clustering, linear regression clustering,
4913 clustering by merging Gaussian mixture components, as well as symmetric and
4914 asymmetric discriminant projections for visualisation of the separation of
4916 (license license:gpl2+)))
4918 (define-public r-vgam
4925 (uri (cran-uri "VGAM" version))
4928 "1fg31xz86jblqraifiy3q36d0hjqnll01jxx85xq87j1cyhj060j"))))
4929 (properties `((upstream-name . "VGAM")))
4930 (build-system r-build-system)
4932 `(("gfortran" ,gfortran)))
4933 (home-page "https://www.stat.auckland.ac.nz/~yee/VGAM")
4934 (synopsis "Vector generalized linear and additive models")
4936 "This package is an implementation of about 6 major classes of statistical
4937 regression models. Currently only fixed-effects models are implemented, i.e.,
4938 no random-effects models. Many (150+) models and distributions are estimated
4939 by maximum likelihood estimation (MLE) or penalized MLE, using Fisher scoring.
4940 VGLMs can be loosely thought of as multivariate generalised linear models.")
4941 (license license:gpl2+)))
4943 (define-public r-pbapply
4950 (uri (cran-uri "pbapply" version))
4953 "0lk5kxac09xzdv6vf7ix6r5bfrm7cnpyr2l5mkd4igpciadszzfd"))))
4954 (build-system r-build-system)
4955 (home-page "https://github.com/psolymos/pbapply")
4956 (synopsis "Adding progress bar to apply functions")
4958 "This lightweight package that adds progress bar to vectorized R
4959 functions apply. The implementation can easily be added to functions where
4960 showing the progress is useful e.g. bootstrap.")
4961 (license license:gpl2)))
4963 (define-public r-minqa
4970 (uri (cran-uri "minqa" version))
4973 "036drja6xz7awja9iwb76x91415p26fb0jmg7y7v0p65m6j978fg"))))
4974 (build-system r-build-system)
4976 `(("r-rcpp" ,r-rcpp)))
4978 `(("gfortran" ,gfortran)))
4979 (home-page "http://optimizer.r-forge.r-project.org")
4980 (synopsis "Derivative-free optimization algorithms by quadratic approximation")
4982 "This package provides a derivative-free optimization by quadratic approximation
4983 based on an interface to Fortran implementations by M. J. D. Powell.")
4984 (license license:gpl2)))
4986 (define-public r-rcppeigen
4988 (name "r-rcppeigen")
4989 (version "0.3.3.4.0")
4993 (uri (cran-uri "RcppEigen" version))
4996 "1m6ssq6lvi36ggf26y4hhq996583pxxdb978jnn1x6r9gdb0q0hi"))))
4997 (properties `((upstream-name . "RcppEigen")))
4998 (build-system r-build-system)
5000 `(("r-rcpp" ,r-rcpp)
5001 ("r-matrix" ,r-matrix)))
5002 (home-page "http://eigen.tuxfamily.org")
5003 (synopsis "Rcpp integration for the Eigen templated linear algebra library")
5005 "This package provides an integration of Eigen in R using a C++ template
5006 library for linear algebra: matrices, vectors, numerical solvers and related algorithms.
5007 It supports dense and sparse matrices on integer, floating point and complex numbers,
5008 decompositions of such matrices, and solutions of linear systems.")
5009 (license license:gpl2+)))
5011 (define-public r-modelmetrics
5013 (name "r-modelmetrics")
5018 (uri (cran-uri "ModelMetrics" version))
5021 "1sgdyrf6fbsn18gk8slir4a1yhv133kfhyg2crfs759nff4aw89h"))))
5022 (properties `((upstream-name . "ModelMetrics")))
5023 (build-system r-build-system)
5025 `(("r-rcpp" ,r-rcpp)
5026 ("r-data-table" ,r-data-table)))
5027 (home-page "https://cran.r-project.org/web/packages/ModelMetrics")
5028 (synopsis "Rapid calculation of model metrics")
5030 "Written in C++ using @code{Rcpp}, this package provides a collection of
5031 metrics for evaluating models.")
5032 (license license:gpl2+)))
5034 (define-public r-matrixmodels
5036 (name "r-matrixmodels")
5041 (uri (cran-uri "MatrixModels" version))
5044 "0cyfvhci2p1vr2x52ymkyqqs63x1qchn856dh2j94yb93r08x1zy"))))
5045 (properties `((upstream-name . "MatrixModels")))
5046 (build-system r-build-system)
5048 `(("r-matrix" ,r-matrix)))
5049 (home-page "https://cran.r-project.org/web/packages/MatrixModels")
5050 (synopsis "Modelling with sparse and dense matrices")
5052 "This package models with sparse and dense matrix matrices,
5053 using modular prediction and response module classes.")
5054 (license license:gpl2+)))
5056 (define-public r-quantreg
5063 (uri (cran-uri "quantreg" version))
5066 "023gdzahxp582rpabilpxbl3wyjrgjjnnrhcv9xhrqdfiq5l2yza"))))
5067 (build-system r-build-system)
5069 `(("gfortran" ,gfortran)))
5071 `(("r-matrix" ,r-matrix)
5072 ("r-matrixmodels" ,r-matrixmodels)
5073 ("r-sparsem" ,r-sparsem)))
5074 (home-page "https://www.r-project.org")
5075 (synopsis "Quantile regression")
5077 "This package provides an estimation and inference methods for models
5078 of conditional quantiles: linear and nonlinear parametric and non-parametric
5079 models for conditional quantiles of a univariate response and several methods
5080 for handling censored survival data. Portfolio selection methods based on
5081 expected shortfall risk are also included.")
5082 (license license:gpl2+)))
5084 (define-public r-nloptr
5091 (uri (cran-uri "nloptr" version))
5094 "1sz1xj3785x4vsm4nd6in298bk32hs2jk5nsxma7ivxi7jcmn8l4"))))
5095 (build-system r-build-system)
5097 `(("pkg-config" ,pkg-config)))
5099 `(("nlopt" ,nlopt)))
5100 (home-page "https://cran.r-project.org/web/packages/nloptr")
5101 (synopsis "R interface to NLopt")
5103 "This package is interface to NLopt, a library for nonlinear
5104 optimization. NLopt is a library for nonlinear optimization, providing a
5105 common interface for a number of different free optimization routines
5106 available online as well as original implementations of various other
5108 (license license:lgpl3)))
5110 (define-public r-lme4
5113 (version "1.1-18-1")
5117 (uri (cran-uri "lme4" version))
5120 "01ar4fak8zj7c1vmh9m576wchxj5qzpfqn637s7fh3fl6cpz0alq"))))
5121 (build-system r-build-system)
5123 `(("r-rcpp" ,r-rcpp)
5124 ("r-rcppeigen" ,r-rcppeigen)))
5126 `(("r-lattice" ,r-lattice)
5127 ("r-matrix" ,r-matrix)
5128 ("r-minqa" ,r-minqa)
5129 ("r-nloptr" ,r-nloptr)
5131 ("r-nlme" ,r-nlme)))
5132 (home-page "https://cran.r-project.org/web/packages/lme4")
5133 (synopsis "Linear mixed-effects models using eigen and S4")
5135 "This package provides fit linear and generalized linear mixed-effects
5136 models. The models and their components are represented using S4 classes and
5137 methods. The core computational algorithms are implemented using the Eigen
5138 C++ library for numerical linear algebra and RcppEigen glue.")
5139 (license license:gpl2+)))
5141 (define-public r-pbkrtest
5148 (uri (cran-uri "pbkrtest" version))
5151 "1si3bhi59xc51a0pgjjglccq3h4aljyhw2k1b8574s145fnh7fsw"))))
5152 (build-system r-build-system)
5154 `(("r-lme4" ,r-lme4)
5156 ("r-matrix" ,r-matrix)))
5157 (home-page "http://people.math.aau.dk/~sorenh/software/pbkrtest/")
5158 (synopsis "Methods for linear mixed model comparison")
5160 "This package implements a parametric bootstrap test and a Kenward Roger
5161 modification of F-tests for linear mixed effects models and a parametric
5162 bootstrap test for generalized linear mixed models.")
5163 (license license:gpl2+)))
5165 (define-public r-cardata
5172 (uri (cran-uri "carData" version))
5175 "193pdwgw6gk19v7swk1kwphg3vqdmpsgi555g9nyz93sa39j7r8j"))))
5176 (properties `((upstream-name . "carData")))
5177 (build-system r-build-system)
5178 (home-page "https://r-forge.r-project.org/projects/car/")
5179 (synopsis "Data Sets for the book Companion to Applied Regression")
5181 "This package provides datasets to accompany J. Fox and S. Weisberg, An R
5182 Companion to Applied Regression, Third Edition, Sage.")
5183 (license license:gpl2+)))
5185 (define-public r-car
5192 (uri (cran-uri "car" version))
5195 "0l3wyc9ia0ypcbap2p39slazfpbl84mjzydqvpsywrzdiyxajnfz"))))
5196 (build-system r-build-system)
5198 `(("r-abind" ,r-abind)
5199 ("r-cardata" ,r-cardata)
5201 ("r-maptools" ,r-maptools)
5206 ("r-pbkrtest" ,r-pbkrtest)
5207 ("r-quantreg" ,r-quantreg)
5209 (home-page "https://r-forge.r-project.org/projects/car/")
5210 (synopsis "Companion to applied regression")
5212 "This package provides functions and datasets from book Companion
5213 to Applied regression, Second Edition, Sage, 2011.")
5214 (license license:gpl2+)))
5216 (define-public r-caret
5223 (uri (cran-uri "caret" version))
5226 "0xhdhazzfh0hiqv2hgxglj9ffd2p4ls8acqn2sjn0ndx6158f187"))))
5227 (build-system r-build-system)
5229 `(("r-foreach" ,r-foreach)
5230 ("r-ggplot2" ,r-ggplot2)
5231 ("r-lattice" ,r-lattice)
5232 ("r-modelmetrics" ,r-modelmetrics)
5235 ("r-recipes" ,r-recipes)
5236 ("r-reshape2" ,r-reshape2)
5237 ("r-withr" ,r-withr)))
5238 (home-page "https://github.com/topepo/caret")
5239 (synopsis "Classification and regression training")
5241 "This package provides misc functions for training and plotting
5242 classification and regression models.")
5243 (license license:gpl2+)))
5245 (define-public r-rcppprogress
5247 (name "r-rcppprogress")
5252 (uri (cran-uri "RcppProgress" version))
5255 "0yk01hfv961zyp569682k9igvhnwqyg5j0n5fm63sxigj82l2xhi"))))
5256 (properties `((upstream-name . "RcppProgress")))
5257 (build-system r-build-system)
5259 `(("r-devtools" ,r-devtools)
5260 ("r-rcpp" ,r-rcpp)))
5261 (home-page "https://github.com/kforner/rcpp_progress")
5262 (synopsis "Interruptible progress bar for C++ in R packages")
5264 "This package allows to display a progress bar in the R console for long running
5265 computations taking place in C++ code, and support for interrupting those computations
5266 even in multithreaded code, typically using OpenMP.")
5267 (license license:gpl3+)))
5269 (define-public r-mnormt
5276 (uri (cran-uri "mnormt" version))
5279 "1b34xxrnf35khsx82mhvmk96sgfr2flyasaah7qkb2976pwxay7z"))))
5280 (build-system r-build-system)
5282 `(("gfortran" ,gfortran)))
5283 (home-page "http://azzalini.stat.unipd.it/SW/Pkg-mnormt")
5284 (synopsis "Multivariate normal and \"t\" distributions")
5286 "This package provides functions for computing the density and the
5287 distribution function of multivariate normal and \"t\" random variables, and
5288 for generating random vectors sampled from these distributions. Probabilities
5289 are computed via non-Monte Carlo methods.")
5290 (license license:gpl2+)))
5292 (define-public r-numderiv
5295 (version "2016.8-1")
5299 (uri (cran-uri "numDeriv" version))
5302 "07ni52rwiap4wilfz94w5mrqaxr59axxmgn57857ip4p6qkiss0v"))))
5303 (properties `((upstream-name . "numDeriv")))
5304 (build-system r-build-system)
5305 (home-page "https://cran.r-project.org/web/packages/numDeriv")
5306 (synopsis "Accurate numerical derivatives")
5308 "This package provides methods for calculating accurate numerical
5309 first and second order derivatives.")
5310 (license license:gpl2)))
5319 (uri (cran-uri "sn" version))
5322 "16gwr68zzj5v83bqfmzxnzwig3dnjrkxdhs6clri1caqkvrq6aig"))))
5323 (build-system r-build-system)
5325 `(("r-mnormt" ,r-mnormt)
5326 ("r-numderiv" ,r-numderiv)))
5327 (home-page "http://azzalini.stat.unipd.it/SN")
5328 (synopsis "The skew-normal and skew-t distributions")
5330 "This packages provides functionalities to build and manipulate
5331 probability distributions of the skew-normal family and some related
5332 ones, notably the skew-t family, and provides related statistical
5333 methods for data fitting and diagnostics, in the univariate and the
5334 multivariate case.")
5335 (license license:gpl2+)))
5337 (define-public r-tclust
5344 (uri (cran-uri "tclust" version))
5347 "17md6l9v9dl9b72l84df01b52h2xiynbcjm437mv9mzcr09fc2sb"))))
5348 (build-system r-build-system)
5349 ;; These are all suggested packages, not build dependencies.
5351 `(("r-cluster" ,r-cluster)
5352 ("r-mclust" ,r-mclust)
5353 ("r-mvtnorm" ,r-mvtnorm)
5355 (home-page "https://cran.r-project.org/web/packages/tclust")
5356 (synopsis "Robust trimmed clustering")
5358 "This package implements different robust clustering
5359 algorithms (@code{tclust}) based on trimming and including some graphical
5360 diagnostic tools (@code{ctlcurves} and @code{DiscrFact}).")
5361 (license license:gpl3)))
5363 (define-public r-ranger
5370 (uri (cran-uri "ranger" version))
5373 "12z67xkgdmr5cflpd6cln0mn5xxajanqbfwlckv6cfma0gvf2z1j"))))
5374 (build-system r-build-system)
5376 `(("r-rcpp" ,r-rcpp)
5377 ("r-matrix" ,r-matrix)
5378 ("r-rcppeigen" ,r-rcppeigen)))
5379 (home-page "https://github.com/imbs-hl/ranger")
5380 (synopsis "Fast implementation of random forests")
5382 "This package provides a fast implementation of Random Forests,
5383 particularly suited for high dimensional data. Ensembles of classification,
5384 regression, survival and probability prediction trees are supported. Data from
5385 genome-wide association studies can be analyzed efficiently.")
5386 (license license:gpl3)))
5388 (define-public r-tsne
5395 (uri (cran-uri "tsne" version))
5398 "0s8cv2pndkddq62rzlgzgfdjp1vjv5hz5i5957sllnb97vbzbzb6"))))
5399 (build-system r-build-system)
5400 (home-page "https://github.com/jdonaldson/rtsne/")
5401 (synopsis "t-Distributed Stochastic Neighbor Embedding for R")
5403 "This package provides a pure R implementation of the t-SNE algorithm.")
5404 (license license:gpl2+)))
5406 (define-public r-cairo
5413 (uri (cran-uri "Cairo" version))
5416 "1x1q99r3r978rlkkm5gixkv03p0mcr6k7ydcqdmisrwnmrn7p1ia"))))
5417 (properties `((upstream-name . "Cairo")))
5418 (build-system r-build-system)
5423 `(("pkg-config" ,pkg-config)))
5424 (home-page "http://www.rforge.net/Cairo/")
5425 (synopsis "R graphics device using Cairo graphics library")
5427 "This package provides a Cairo graphics device that can be use to
5428 create high-quality vector (PDF, PostScript and SVG) and bitmap
5429 output (PNG,JPEG,TIFF), and high-quality rendering in displays (X11
5430 and Win32). Since it uses the same back-end for all output, copying
5431 across formats is WYSIWYG. Files are created without the dependence
5432 on X11 or other external programs. This device supports alpha
5433 channel (semi-transparent drawing) and resulting images can contain
5434 transparent and semi-transparent regions. It is ideal for use in
5435 server environments (file output) and as a replacement for other
5436 devices that don't have Cairo's capabilities such as alpha support or
5437 anti-aliasing. Backends are modular such that any subset of backends
5439 (license license:gpl2)))
5441 (define-public r-lubridate
5443 (name "r-lubridate")
5448 (uri (cran-uri "lubridate" version))
5451 "14a823il77w3wmmnzr89vwrqp50y56dh5raycnaw6c8nv5xsh32i"))))
5452 (build-system r-build-system)
5454 `(("r-rcpp" ,r-rcpp)
5455 ("r-stringr" ,r-stringr)))
5457 "https://cran.r-project.org/web/packages/lubridate")
5458 (synopsis "Make dealing with dates a little easier")
5460 "This package provides functions to work with date-times and time-spans:
5461 fast and user friendly parsing of date-time data, extraction and updating of
5462 components of a date-time (years, months, days, hours, minutes, and seconds),
5463 algebraic manipulation on date-time and time-span objects. The 'lubridate'
5464 package has a consistent and memorable syntax that makes working with dates
5466 (license license:gpl2)))
5468 (define-public r-fdrtool
5475 (uri (cran-uri "fdrtool" version))
5478 "1h46frlk7d9f4qx0bg6p55nrm9wwwz2sv6d1nz7061wdfsm69yb5"))))
5479 (build-system r-build-system)
5480 (home-page "http://strimmerlab.org/software/fdrtool/")
5481 (synopsis "Estimation of false discovery rates and higher criticism")
5483 "This package provides tools to estimate tail area-based false discovery
5484 rates as well as local false discovery rates for a variety of null
5485 models (p-values, z-scores, correlation coefficients, t-scores). The
5486 proportion of null values and the parameters of the null distribution are
5487 adaptively estimated from the data. In addition, the package contains
5488 functions for non-parametric density estimation (Grenander estimator), for
5489 monotone regression (isotonic regression and antitonic regression with
5490 weights), for computing the @dfn{greatest convex minorant} (GCM) and the
5491 @dfn{least concave majorant} (LCM), for the half-normal and correlation
5492 distributions, and for computing empirical @dfn{higher criticism} (HC) scores
5493 and the corresponding decision threshold.")
5494 (license license:gpl3+)))
5496 (define-public r-forcats
5503 (uri (cran-uri "forcats" version))
5506 "0mxn1hng43zdjh1v8shd80hrszrqahcpaqxs1s1sif0qxh84d0cm"))))
5507 (build-system r-build-system)
5509 `(("r-magrittr" ,r-magrittr)
5510 ("r-tibble" ,r-tibble)
5511 ("r-rlang" ,r-rlang)))
5512 (home-page "http://forcats.tidyverse.org")
5513 (synopsis "Tools for working with factors")
5514 (description "This package provides helpers for reordering factor
5515 levels (including moving specified levels to front, ordering by first
5516 appearance, reversing, and randomly shuffling), and tools for modifying factor
5517 levels (including collapsing rare levels into other, \"anonymizing\", and
5518 manually \"recoding\").")
5519 (license license:gpl3)))
5521 (define-public r-tgstat
5522 (let ((changeset "4f8e60c03598f49aff6f5beeab40f2b995377e9f")
5526 (version (string-append "1.0.2-" revision "." (string-take changeset 7)))
5531 (url "https://bitbucket.org/tanaylab/tgstat")
5532 (changeset changeset)))
5533 (file-name (string-append name "-" version "-checkout"))
5536 "0ilkkyximy77zbncm91kdfqbxf0qyndg16pd3q3p6a3xc9qcmxvn"))))
5537 (build-system r-build-system)
5540 (modify-phases %standard-phases
5541 (add-after 'unpack 'fix-isnan
5543 (substitute* "src/tgstat.h"
5544 (("#define isnan ::isnan")
5545 "#define isnan std::isnan"))
5548 `(("r-rcpp" ,r-rcpp)))
5549 (home-page "https://bitbucket.org/tanaylab/tgstat/")
5550 (synopsis "Tanay's group statistical utilities")
5552 "The goal of tgstat is to provide fast and efficient statistical
5554 (license license:gpl2))))
5556 (define-public r-tgconfig
5557 (let ((changeset "1e02c7614713bd0866c46f0c679a058f8c6d627e")
5561 (version (string-append "0.0.0.9000-" revision "." (string-take changeset 7)))
5566 (url "https://bitbucket.org/tanaylab/tgconfig")
5567 (changeset changeset)))
5568 (file-name (string-append name "-" version "-checkout"))
5571 "0xy6c7s7mn1yx191154bwbv1bl424bnvc80syqpl1vdl28ba46rj"))))
5572 (build-system r-build-system)
5574 `(("r-yaml" ,r-yaml)))
5575 (home-page "https://bitbucket.org/tanaylab/tgconfig/")
5576 (synopsis "Infrastructure for managing package parameters")
5578 "The goal of tgconfig is to provide infrastructure for managing package
5580 (license license:gpl3))))
5582 (define-public r-directlabels
5584 (name "r-directlabels")
5585 (version "2018.05.22")
5589 (uri (cran-uri "directlabels" version))
5592 "0xcpc56ssb9430b0xcdhayk3qaak2qcakyss2pz14y5w2027hblv"))))
5593 (build-system r-build-system)
5595 `(("r-quadprog" ,r-quadprog)))
5596 (home-page "http://directlabels.r-forge.r-project.org/")
5597 (synopsis "Direct labels for multicolor plots")
5599 "This package provides an extensible framework for automatically placing
5600 direct labels onto multicolor plots. Label positions are described using
5601 positioning methods that can be re-used across several different plots. There
5602 are heuristics for examining @code{trellis} and @code{ggplot} objects and
5603 inferring an appropriate positioning method.")
5604 (license license:gpl3)))
5606 (define-public r-catterplots
5607 (let ((commit "40063ec57f9515d231508f135ca0ec769614efb9")
5610 (name "r-catterplots")
5611 (version (string-append "0-" revision "." (string-take commit 9)))
5615 (url "https://github.com/Gibbsdavidl/CatterPlots.git")
5617 (file-name (string-append name "-" version "-checkout"))
5620 "1wl80pgbz8d9kfpffvkh439hlgz2qldm9m75wqjfrgrg8lcjzrxg"))))
5621 (build-system r-build-system)
5623 `(("r-png" ,r-png)))
5624 (home-page "https://github.com/Gibbsdavidl/CatterPlots")
5625 (synopsis "Scatter plots with cat shaped points")
5626 (description "Did you ever wish you could make scatter plots with cat
5627 shaped points? Now you can!")
5628 (license license:asl2.0))))
5630 (define-public r-colorout
5637 (uri (string-append "https://github.com/jalvesaq/colorout/archive/"
5638 "v" version ".tar.gz"))
5639 (file-name (string-append name "-" version ".tar.gz"))
5642 "07vqx5ihgnq4dzn5jnfjfhdm3957v4prvf8vhnb3cwvlly4l7p9v"))))
5643 (build-system r-build-system)
5644 (home-page "https://github.com/jalvesaq/colorout")
5645 (synopsis "Colorize output in the R REPL")
5646 (description "@code{colorout} is an R package that colorizes R output when
5647 running in terminal emulator.
5649 R STDOUT is parsed and numbers, negative numbers, dates in the standard
5650 format, strings, and R constants are identified and wrapped by special ANSI
5651 scape codes that are interpreted by terminal emulators as commands to colorize
5652 the output. R STDERR is also parsed to identify the expressions warning and
5653 error and their translations to many languages. If these expressions are
5654 found, the output is colorized accordingly; otherwise, it is colorized as
5655 STDERROR (blue, by default).
5657 You can customize the colors according to your taste, guided by the color
5658 table made by the command @code{show256Colors()}. You can also set the colors
5659 to any arbitrary string. In this case, it is up to you to set valid values.")
5660 (license license:gpl3+)))
5662 (define-public r-txtplot
5669 (uri (cran-uri "txtplot" version))
5672 "1949ab1bzvysdb79g8x1gaknj0ih3d6g63pv9512h5m5l3a6c31h"))))
5673 (build-system r-build-system)
5674 (home-page "https://cran.r-project.org/web/packages/txtplot/")
5675 (synopsis "Text-based plotting")
5676 (description "This package provides functions to produce rudimentary ASCII
5677 graphics directly in the terminal window. This package provides a basic
5678 plotting function (and equivalents of curve, density, acf and barplot) as well
5679 as a boxplot function.")
5680 (license license:lgpl3+)))
5682 (define-public java-jdistlib
5684 (name "java-jdistlib")
5688 (uri (string-append "mirror://sourceforge/jdistlib/jdistlib-"
5689 version "-src.jar"))
5692 "1pkj8aahw9ydr1isbaqrkd05nvq98ik5jwwhf3yf3rky3z869v11"))))
5693 (build-system ant-build-system)
5695 `(#:jar-name "jdistlib.jar"
5697 #:tests? #f ; no dedicated test directory
5699 (modify-phases %standard-phases
5700 (add-after 'unpack 'fix-broken-encoding
5702 (with-fluids ((%default-port-encoding "ISO-8859-1"))
5703 (substitute* "src/jdistlib/Beta.java"
5704 (("Scheff.+-Tukey") "Scheffe-Tukey")))
5707 `(("java-jtransforms" ,java-jtransforms)))
5709 `(("java-junit" ,java-junit)))
5710 (home-page "http://jdistlib.sourceforge.net/")
5711 (synopsis "Java library of statistical distributions")
5712 (description "JDistlib is the Java Statistical Distribution Library, a
5713 Java package that provides routines for various statistical distributions.")
5714 ;; The files that were translated from R code are under GPLv2+; some files
5715 ;; are under the GPLv3, which is a mistake. The author confirmed in an
5716 ;; email that this whole project should be under GPLv2+.
5717 (license license:gpl2+)))