1 ;;; GNU Guix --- Functional package management for GNU
2 ;;; Copyright © 2015, 2016, 2017 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 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 utils)
34 #:use-module (guix build-system gnu)
35 #:use-module (guix build-system r)
36 #:use-module (guix build-system python)
37 #:use-module (guix build-system trivial)
38 #:use-module (gnu packages)
39 #:use-module (gnu packages check)
40 #:use-module (gnu packages compression)
41 #:use-module (gnu packages cran)
42 #:use-module (gnu packages curl)
43 #:use-module (gnu packages gcc)
44 #:use-module (gnu packages gtk)
45 #:use-module (gnu packages gettext)
46 #:use-module (gnu packages glib)
47 #:use-module (gnu packages haskell)
48 #:use-module (gnu packages icu4c)
49 #:use-module (gnu packages image)
50 #:use-module (gnu packages java)
51 #:use-module (gnu packages machine-learning)
52 #:use-module (gnu packages maths)
53 #:use-module (gnu packages multiprecision)
54 #:use-module (gnu packages pcre)
55 #:use-module (gnu packages perl)
56 #:use-module (gnu packages pkg-config)
57 #:use-module (gnu packages python)
58 #:use-module (gnu packages readline)
59 #:use-module (gnu packages ssh)
60 #:use-module (gnu packages texinfo)
61 #:use-module (gnu packages time)
62 #:use-module (gnu packages tls)
63 #:use-module (gnu packages base)
64 #:use-module (gnu packages web)
65 #:use-module (gnu packages xml)
66 #:use-module (gnu packages xorg)
67 #:use-module (srfi srfi-1))
77 (uri (string-append "mirror://gnu/pspp/pspp-"
81 "1r8smr5057993h90nx0mdnff8nxw9x546zzh6qpy4h3xblp1la5s"))))
82 (build-system gnu-build-system)
85 ("gettext" ,gettext-minimal)
89 ("readline" ,readline)
91 ("gtksourceview" ,gtksourceview)
94 `(("glib" ,glib "bin") ;for glib-genmarshal
96 ("pkg-config" ,pkg-config)))
97 (home-page "https://www.gnu.org/software/pspp/")
98 (synopsis "Statistical analysis")
100 "GNU PSPP is a statistical analysis program. It can perform
101 descriptive statistics, T-tests, linear regression and non-parametric tests.
102 It features both a graphical interface as well as command-line input. PSPP
103 is designed to interoperate with Gnumeric, LibreOffice and OpenOffice. Data
104 can be imported from spreadsheets, text files and database sources and it can
105 be output in text, PostScript, PDF or HTML.")
106 (license license:gpl3+)))
108 ;; Update this package together with the set of recommended packages: r-boot,
109 ;; r-class, r-cluster, r-codetools, r-foreign, r-kernsmooth, r-lattice,
110 ;; r-mass, r-matrix, r-mgcv, r-nlme, r-nnet, r-rpart, r-spatial, r-survival.
111 (define-public r-minimal
117 (uri (string-append "mirror://cran/src/base/R-"
118 (version-major version) "/R-"
122 "09pl0w01fr09bsrwd7nz2r5psysj0z93w4chz3hm2havvqqvhg3s"))))
123 (build-system gnu-build-system)
125 `(#:disallowed-references (,tzdata-for-tests)
127 (list (string-append "LDFLAGS=-Wl,-rpath="
128 (assoc-ref %outputs "out")
130 ;; This affects the embedded timestamp of only the core packages.
131 "PKG_BUILT_STAMP=1970-01-01")
133 (modify-phases %standard-phases
134 (add-before 'configure 'do-not-compress-serialized-files
135 (lambda* (#:key inputs #:allow-other-keys)
136 ;; This ensures that Guix can detect embedded store references;
137 ;; see bug #28157 for details.
138 (substitute* "src/library/base/makebasedb.R"
139 (("compress = TRUE") "compress = FALSE"))
141 (add-before 'configure 'patch-uname
142 (lambda* (#:key inputs #:allow-other-keys)
143 (let ((uname-bin (string-append (assoc-ref inputs "coreutils")
145 (substitute* "src/scripts/R.sh.in"
146 (("uname") uname-bin)))
148 (add-after 'unpack 'build-reproducibly
150 ;; The documentation contains time stamps to demonstrate
151 ;; documentation generation in different phases.
152 (substitute* "src/library/tools/man/Rd2HTML.Rd"
153 (("\\\\%Y-\\\\%m-\\\\%d at \\\\%H:\\\\%M:\\\\%S")
154 "(removed for reproducibility)"))
156 ;; Remove timestamp from tracing environment. This fixes
157 ;; reproducibility of "methods.rd{b,x}".
158 (substitute* "src/library/methods/R/trace.R"
159 (("dateCreated = Sys.time\\(\\)")
160 "dateCreated = as.POSIXct(\"1970-1-1 00:00:00\", tz = \"UTC\")"))
162 ;; Ensure that gzipped files are reproducible.
163 (substitute* '("src/library/grDevices/Makefile.in"
164 "doc/manual/Makefile.in")
165 (("R_GZIPCMD\\)" line)
166 (string-append line " -n")))
168 ;; The "srcfile" procedure in "src/library/base/R/srcfile.R"
169 ;; queries the mtime of a given file and records it in an object.
170 ;; This is acceptable at runtime to detect stale source files,
171 ;; but it destroys reproducibility at build time.
173 ;; Instead of disabling this feature, which may have unexpected
174 ;; consequences, we reset the mtime of generated files before
175 ;; passing them to the "srcfile" procedure.
176 (substitute* "src/library/Makefile.in"
177 (("@\\(cd base && \\$\\(MAKE\\) mkdesc\\)" line)
178 (string-append line "\n find $(top_builddir)/library/tools | xargs touch -d '1970-01-01'; \n"))
179 (("@\\$\\(MAKE\\) Rdobjects" line)
180 (string-append "@find $(srcdir)/tools | xargs touch -d '1970-01-01'; \n "
182 (substitute* "src/library/tools/Makefile.in"
183 (("@\\$\\(INSTALL_DATA\\) all.R \\$\\(top_builddir\\)/library/\\$\\(pkg\\)/R/\\$\\(pkg\\)" line)
186 "\n find $(srcdir)/$(pkg) $(top_builddir)/library/$(pkg) | xargs touch -d \"1970-01-01\"; \n")))
188 ;; This library is installed using "install_package_description",
189 ;; so we need to pass the "builtStamp" argument.
190 (substitute* "src/library/tools/Makefile.in"
191 (("(install_package_description\\(.*\"')\\)\"" line prefix)
192 (string-append prefix ", builtStamp='1970-01-01')\"")))
194 ;; R bundles an older version of help2man, which does not respect
195 ;; SOURCE_DATE_EPOCH. We cannot just use the latest help2man,
196 ;; because that breaks a test.
197 (with-fluids ((%default-port-encoding "ISO-8859-1"))
198 (substitute* "tools/help2man.pl"
199 (("my \\$date = strftime \"%B %Y\", localtime" line)
200 (string-append line " 1"))))
202 (add-before 'configure 'set-default-pager
203 ;; Set default pager to "cat", because otherwise it is "false",
204 ;; making "help()" print nothing at all.
205 (lambda _ (setenv "PAGER" "cat") #t))
206 (add-before 'check 'set-timezone
207 ;; Some tests require the timezone to be set. However, the
208 ;; timezone may not just be "UTC", or else a brittle regression
209 ;; test in reg-tests-1d will fail.
210 (lambda* (#:key inputs #:allow-other-keys)
211 (setenv "TZ" "UTC+1")
213 (string-append (assoc-ref inputs "tzdata")
216 (add-after 'build 'make-info
217 (lambda _ (zero? (system* "make" "info"))))
218 (add-after 'build 'install-info
219 (lambda _ (zero? (system* "make" "install-info")))))
221 '(;; Do not build the recommended packages. The build system creates
222 ;; random temporary directories and embeds their names in some
223 ;; package files. We build these packages with the r-build-system
225 "--without-recommended-packages"
227 "--with-blas=-lopenblas"
233 "--enable-BLAS-shlib"
234 "--with-system-tre")))
235 ;; R has some support for Java. When the JDK is available at configure
236 ;; time environment variables pointing to the JDK will be recorded under
237 ;; $R_HOME/etc and ./tools/getsp.java will be compiled which is used by "R
238 ;; CMD javareconf". "R CMD javareconf" appears to only be used to update
239 ;; the recorded environment variables in $R_HOME/etc. Refer to
240 ;; https://cran.r-project.org/doc/manuals/r-release/R-admin.html#Java-support
241 ;; for additional information.
243 ;; As the JDK is a rather large input with only very limited effects on R,
244 ;; we decided to drop it.
248 ("pkg-config" ,pkg-config)
249 ("texinfo" ,texinfo) ; for building HTML manuals
250 ("tzdata" ,tzdata-for-tests)
253 `(;; We need not only cairo here, but pango to ensure that tests for the
254 ;; "cairo" bitmapType plotting backend succeed.
256 ("coreutils" ,coreutils)
258 ("openblas" ,openblas)
259 ("gfortran" ,gfortran)
266 ("readline" ,readline)
270 (list (search-path-specification
271 (variable "R_LIBS_SITE")
272 (files (list "site-library/")))))
273 (home-page "http://www.r-project.org/")
274 (synopsis "Environment for statistical computing and graphics")
276 "R is a language and environment for statistical computing and graphics.
277 It provides a variety of statistical techniques, such as linear and nonlinear
278 modeling, classical statistical tests, time-series analysis, classification
279 and clustering. It also provides robust support for producing
280 publication-quality data plots. A large amount of 3rd-party packages are
281 available, greatly increasing its breadth and scope.")
282 (license license:gpl3+)))
284 (define-public rmath-standalone
285 (package (inherit r-minimal)
286 (name "rmath-standalone")
289 (modify-phases %standard-phases
290 (add-after 'configure 'chdir
291 (lambda _ (chdir "src/nmath/standalone/") #t)))))
292 (synopsis "Standalone R math library")
294 "This package provides the R math library as an independent package.")))
296 (define-public r-boot
303 (uri (cran-uri "boot" version))
306 "0ai1qpm0p4z07xr0dvag8sdn9jrxcwanrsk9khzmww094jvr1jxd"))))
307 (build-system r-build-system)
308 (home-page "https://cran.r-project.org/web/packages/boot")
309 (synopsis "Bootstrap functions for R")
311 "This package provides functions and datasets for bootstrapping from the
312 book \"Bootstrap Methods and Their Application\" by A.C. Davison and
313 D.V. Hinkley (1997, CUP), originally written by Angelo Canty for S.")
314 ;; Unlimited distribution
315 (license (license:non-copyleft "file://R/bootfuns.q"))))
317 (define-public r-mass
324 (uri (cran-uri "MASS" version))
327 "1gy6z7ly9wn86rfn9xrmqiqq1ijw3pkasrr2299kbzsgx2mwsi7d"))))
328 (properties `((upstream-name . "MASS")))
329 (build-system r-build-system)
330 (home-page "http://www.stats.ox.ac.uk/pub/MASS4/")
331 (synopsis "Support functions and datasets for Venables and Ripley's MASS")
333 "This package provides functions and datasets for the book \"Modern
334 Applied Statistics with S\" (4th edition, 2002) by Venables and Ripley.")
335 ;; Either version may be picked.
336 (license (list license:gpl2 license:gpl3))))
338 (define-public r-class
345 (uri (cran-uri "class" version))
348 "173b8a16lh1i0zjmr784l0xr0azp9v8bgslh12hfdswbq7dpdf0q"))))
349 (build-system r-build-system)
351 `(("r-mass" ,r-mass)))
352 (home-page "http://www.stats.ox.ac.uk/pub/MASS4/")
353 (synopsis "R functions for classification")
355 "This package provides various functions for classification, including
356 k-nearest neighbour, Learning Vector Quantization and Self-Organizing Maps.")
357 ;; Either of the two versions can be picked.
358 (license (list license:gpl2 license:gpl3))))
360 (define-public r-cluster
367 (uri (cran-uri "cluster" version))
370 "1z4gbz7chxxi4ly6c0yjlikwgf8aa8dlg05cn5cd6pjr21zvh97l"))))
371 (build-system r-build-system)
373 `(("gfortran" ,gfortran)))
374 (home-page "https://cran.r-project.org/web/packages/cluster")
375 (synopsis "Methods for cluster analysis")
377 "This package provides methods for cluster analysis. It is a much
378 extended version of the original from Peter Rousseeuw, Anja Struyf and Mia
379 Hubert, based on Kaufman and Rousseeuw (1990) \"Finding Groups in Data\".")
380 (license license:gpl2+)))
382 (define-public r-codetools
389 (uri (cran-uri "codetools" version))
392 "0h7sjmvvsi35041jp47cxhsqzgf1y8jrw6fxii7n26i8g7nrh1sf"))))
393 (build-system r-build-system)
394 (home-page "https://cran.r-project.org/web/packages/codetools")
395 (synopsis "Code analysis tools for R")
396 (description "This package provides code analysis tools for R to check R
397 code for possible problems.")
398 ;; Any version of the GPL.
399 (license (list license:gpl2+ license:gpl3+))))
401 (define-public r-foreign
408 (uri (cran-uri "foreign" version))
411 "0s1lxmd85dd0kxx8hwk02w9l7pmpk4bpy7787fbyh2dbq5g9ys0k"))))
412 (build-system r-build-system)
413 (home-page "https://cran.r-project.org/web/packages/foreign")
414 (synopsis "Read data stored by other statistics software")
416 "This package provides functions for reading and writing data stored by
417 some versions of Epi Info, Minitab, S, SAS, SPSS, Stata, Systat and Weka and
418 for reading and writing some dBase files.")
419 (license license:gpl2+)))
421 (define-public r-kernsmooth
423 (name "r-kernsmooth")
428 (uri (cran-uri "KernSmooth" version))
431 "1xhha8kw10jv8pv8b61hb5in9qiw3r2a9kdji3qlm991s4zd4wlb"))))
432 (properties `((upstream-name . "KernSmooth")))
433 (build-system r-build-system)
435 `(("gfortran" ,gfortran)))
436 (home-page "https://cran.r-project.org/web/packages/KernSmooth")
437 (synopsis "Functions for kernel smoothing")
439 "This package provides functions for kernel smoothing (and density
440 estimation) corresponding to the book: Wand, M.P. and Jones, M.C. (1995)
441 \"Kernel Smoothing\".")
442 ;; Unlimited use and distribution
443 (license (license:non-copyleft "file://LICENCE.note"))))
445 (define-public r-lattice
451 (uri (cran-uri "lattice" version))
454 "0pcnmaz3lr62ly0dcy5hnnqxshc4yqd43hrvlz3almgc9l7sna88"))))
455 (build-system r-build-system)
456 (home-page "http://lattice.r-forge.r-project.org/")
457 (synopsis "High-level data visualization system")
459 "The lattice package provides a powerful and elegant high-level data
460 visualization system inspired by Trellis graphics, with an emphasis on
461 multivariate data. Lattice is sufficient for typical graphics needs, and is
462 also flexible enough to handle most nonstandard requirements.")
463 (license license:gpl2+)))
465 (define-public r-matrix
472 (uri (cran-uri "Matrix" version))
475 "1wm45hg4x5ay15y03k6rmgkd1n9r01da72mszk24vafwd7pimr8n"))))
476 (properties `((upstream-name . "Matrix")))
477 (build-system r-build-system)
479 `(("r-lattice" ,r-lattice)))
480 (home-page "http://Matrix.R-forge.R-project.org/")
481 (synopsis "Sparse and dense matrix classes and methods")
483 "This package provides classes and methods for dense and sparse matrices
484 and operations on them using LAPACK and SuiteSparse.")
485 (license license:gpl2+)))
487 (define-public r-nlme
494 (uri (cran-uri "nlme" version))
497 "0k2nvdzhic6bzhfsbq6la6q6a1i5nlj4pnh6lpdxiiwvxdks3nkr"))))
498 (build-system r-build-system)
500 `(("r-lattice" ,r-lattice)))
502 `(("gfortran" ,gfortran)))
503 (home-page "https://cran.r-project.org/web/packages/nlme")
504 (synopsis "Linear and nonlinear mixed effects models")
506 "This package provides tools to fit and compare Gaussian linear and
507 nonlinear mixed-effects models.")
508 (license license:gpl2+)))
510 (define-public r-mgcv
517 (uri (cran-uri "mgcv" version))
520 "1546p6aflg3z6xl2mns1n2c3j8q2spr9cjggj9rn33vrrhsv4fss"))))
521 (build-system r-build-system)
523 `(("r-matrix" ,r-matrix)
525 (home-page "https://cran.r-project.org/web/packages/mgcv")
526 (synopsis "Mixed generalised additive model computation")
528 "GAMs, GAMMs and other generalized ridge regression with multiple smoothing
529 parameter estimation by GCV, REML or UBRE/AIC. The library includes a
530 @code{gam()} function, a wide variety of smoothers, JAGS support and
531 distributions beyond the exponential family.")
532 (license license:gpl2+)))
534 (define-public r-nnet
541 (uri (cran-uri "nnet" version))
544 "17amqnw9dpap2w8ivx53hxha2xrm0drwfnj32li0xk41hlz548r7"))))
545 (build-system r-build-system)
546 (home-page "http://www.stats.ox.ac.uk/pub/MASS4/")
547 (synopsis "Feed-forward neural networks and multinomial log-linear models")
549 "This package provides functions for feed-forward neural networks with a
550 single hidden layer, and for multinomial log-linear models.")
551 (license (list license:gpl2+ license:gpl3+))))
553 (define-public r-rpart
560 (uri (cran-uri "rpart" version))
563 "165djqj7lk81jr7z5fwccq3h7ayys26hx1kj9hndvg2rkyaq1arq"))))
564 (build-system r-build-system)
565 (home-page "https://cran.r-project.org/web/packages/rpart")
566 (synopsis "Recursive partitioning and regression trees")
568 "This package provides recursive partitioning functions for
569 classification, regression and survival trees.")
570 (license (list license:gpl2+ license:gpl3+))))
572 (define-public r-spatial
579 (uri (cran-uri "spatial" version))
582 "04aw8j533sn63ybyrf4hyhrqm4058vfcb7yhjy07kq92mk94hi32"))))
583 (build-system r-build-system)
584 (home-page "http://www.stats.ox.ac.uk/pub/MASS4/")
585 (synopsis "Functions for kriging and point pattern analysis")
587 "This package provides functions for kriging and point pattern
589 ;; Either version may be picked.
590 (license (list license:gpl2 license:gpl3))))
592 (define-public r-survival
599 (uri (cran-uri "survival" version))
602 "07cnr0hnki6ybbjll54l4s5lllhk19vni5f8m0mvsfp99ls7qygk"))))
603 (build-system r-build-system)
605 `(("r-matrix" ,r-matrix)))
606 (home-page "https://github.com/therneau/survival")
607 (synopsis "Survival analysis")
609 "This package contains the core survival analysis routines, including
610 definition of Surv objects, Kaplan-Meier and Aalen-Johansen (multi-state)
611 curves, Cox models, and parametric accelerated failure time models.")
612 (license license:lgpl2.0+)))
615 (package (inherit r-minimal)
618 (build-system trivial-build-system)
619 (arguments '(#:builder (mkdir %output)))
621 `(("r-minimal" ,r-minimal)
624 ("r-cluster" ,r-cluster)
625 ("r-codetools" ,r-codetools)
626 ("r-foreign" ,r-foreign)
627 ("r-kernsmooth" ,r-kernsmooth)
628 ("r-lattice" ,r-lattice)
630 ("r-matrix" ,r-matrix)
635 ("r-spatial" ,r-spatial)
636 ("r-survival" ,r-survival)))))
645 (uri (cran-uri "bit" version))
648 "0a6ig6nnjzq80r2ll4hc74za3xwzbzig6wlyb4dby0knzf3iqa6f"))))
649 (build-system r-build-system)
650 (home-page "http://ff.r-forge.r-project.org")
651 (synopsis "Class for vectors of 1-bit booleans")
653 "This package provides bitmapped vectors of booleans (no @code{NA}s),
654 coercion from and to logicals, integers and integer subscripts, fast boolean
655 operators and fast summary statistics. With @code{bit} class vectors of true
656 binary booleans, @code{TRUE} and @code{FALSE} can be stored with 1 bit only.")
657 (license license:gpl2)))
659 (define-public r-bit64
666 (uri (cran-uri "bit64" version))
669 "07znvz9vp1nz1y5ljng4qyskvm943cdbmy996s67560ijxzsm6kv"))))
670 (build-system r-build-system)
673 (home-page "http://ff.r-forge.r-project.org/")
674 (synopsis "S3 class for vectors of 64 bit integers")
676 "The bit64 package provides serializable S3 atomic 64 bit (signed)
677 integers that can be used in vectors, matrices, arrays and @code{data.frames}.
678 Methods are available for coercion from and to logicals, integers, doubles,
679 characters and factors as well as many elementwise and summary functions.
680 Many fast algorithmic operations such as @code{match} and @code{order} support
681 interactive data exploration and manipulation and optionally leverage
683 (license license:gpl2)))
685 (define-public r-dichromat
692 (uri (cran-uri "dichromat" version))
694 (base32 "1l8db1nk29ccqg3mkbafvfiw0775iq4gapysf88xq2zp6spiw59i"))))
695 (build-system r-build-system)
696 (home-page "https://cran.r-project.org/web/packages/dichromat")
697 (synopsis "Color schemes for dichromats")
699 "Dichromat collapses red-green or green-blue distinctions to simulate the
700 effects of different types of color-blindness.")
701 (license license:gpl2+)))
703 (define-public r-digest
710 (uri (cran-uri "digest" version))
712 (base32 "1bsgl07bvf4nk6bn7n3l2ilvk4qvn3nk7yxp22miil7x405xdks6"))))
713 (build-system r-build-system)
714 ;; Vignettes require r-knitr, which requires r-digest, so we have to
715 ;; disable them and the tests.
718 #:configure-flags (list "--no-build-vignettes")))
719 (home-page "http://dirk.eddelbuettel.com/code/digest.html")
720 (synopsis "Create cryptographic hash digests of R objects")
722 "This package contains an implementation of a function 'digest()' for the
723 creation of hash digests of arbitrary R objects (using the md5, sha-1,
724 sha-256, crc32, xxhash and murmurhash algorithms) permitting easy comparison
725 of R language objects, as well as a function 'hmac()' to create hash-based
726 message authentication code.
728 Please note that this package is not meant to be deployed for cryptographic
729 purposes for which more comprehensive (and widely tested) libraries such as
730 OpenSSL should be used.")
731 (license license:gpl2+)))
733 (define-public r-estimability
735 (name "r-estimability")
739 (uri (cran-uri "estimability" version))
742 "13b80bpnbrarazjvnpnk91ljjsqgfm2fm3gy66aj09cmmsmv199h"))))
743 (build-system r-build-system)
744 (home-page "https://cran.r-project.org/web/packages/estimability")
745 (synopsis "Tools for assessing estimability of linear predictions")
746 (description "Provides tools for determining estimability of linear
747 functions of regression coefficients, and 'epredict' methods that handle
748 non-estimable cases correctly.")
749 (license license:gpl2+)))
751 (define-public r-pheatmap
758 (uri (cran-uri "pheatmap" version))
761 "1ik0k69kb4n7xl3bkx4p09kw08ri93855zcsxq1c668171jqfiji"))))
762 (build-system r-build-system)
764 `(("r-gtable" ,r-gtable)
765 ("r-rcolorbrewer" ,r-rcolorbrewer)
766 ("r-scales" ,r-scales)))
768 "https://cran.r-project.org/web/packages/pheatmap")
769 (synopsis "Pretty heatmaps")
771 "This package provides an implementation of heatmaps that offers more
772 control over dimensions and appearance.")
773 (license license:gpl2+)))
775 (define-public r-labeling
782 (uri (cran-uri "labeling" version))
784 (base32 "13sk7zrrrzry6ky1bp8mmnzcl9jhvkig8j4id9nny7z993mnk00d"))))
785 (build-system r-build-system)
786 (home-page "https://cran.r-project.org/web/packages/labeling")
787 (synopsis "Axis labeling algorithms")
788 (description "The labeling package provides a range of axis labeling
790 (license license:expat)))
792 (define-public r-magrittr
799 (uri (cran-uri "magrittr" version))
801 (base32 "1s1ar6rag8m277qcqmdp02gn4awn9bdj9ax0r8s32i59mm1mki05"))))
802 (build-system r-build-system)
803 (home-page "https://cran.r-project.org/web/packages/magrittr/index.html")
804 (synopsis "A forward-pipe operator for R")
806 "Magrittr provides a mechanism for chaining commands with a new
807 forward-pipe operator, %>%. This operator will forward a value, or the result
808 of an expression, into the next function call/expression. There is flexible
809 support for the type of right-hand side expressions. For more information,
810 see package vignette. To quote Rene Magritte, \"Ceci n'est pas un pipe.\"")
811 (license license:expat)))
813 (define-public r-munsell
820 (uri (cran-uri "munsell" version))
822 (base32 "0jdxlbjslkzaqgp058da1cgm85qvqi09wpcgpvp4hvwnmy83qz1r"))))
823 (build-system r-build-system)
825 `(("r-colorspace" ,r-colorspace)))
826 (home-page "https://cran.r-project.org/web/packages/munsell")
827 (synopsis "Munsell colour system")
829 "The Munsell package contains Functions for exploring and using the
830 Munsell colour system.")
831 (license license:expat)))
833 (define-public r-permute
840 (uri (cran-uri "permute" version))
843 "1w8wzk1fg9q7wvisnfp2js70dg0m9wi12gkdhpyngpbdcgssahd5"))))
844 (build-system r-build-system)
845 ;; Tests do not run correctly, but running them properly would entail a
846 ;; circular dependency with vegan.
847 (home-page "https://github.com/gavinsimpson/permute")
848 (synopsis "Functions for Generating Restricted Permutations of Data")
850 "This package provides a set of restricted permutation designs for freely
851 exchangeable, line transects (time series), spatial grid designs and permutation
852 of blocks (groups of samples). @code{permute} also allows split-plot designs,
853 in which the whole-plots or split-plots or both can be freely exchangeable.")
854 (license license:gpl2+)))
856 (define-public r-plyr
863 (uri (cran-uri "plyr" version))
865 (base32 "1igar5pcjqh0jyxv0z3jah8rz617vfa86vw0r5c7c031b7bj5db0"))))
866 (build-system r-build-system)
867 (native-inputs `(("r-rcpp" ,r-rcpp)))
868 (home-page "http://had.co.nz/plyr")
869 (synopsis "Tools for Splitting, Applying and Combining Data")
871 "Plyr is a set of tools that solves a common set of problems: you need to
872 break a big problem down into manageable pieces, operate on each piece and
873 then put all the pieces back together. For example, you might want to fit a
874 model to each spatial location or time point in your study, summarise data by
875 panels or collapse high-dimensional arrays to simpler summary statistics.")
876 (license license:expat)))
878 (define-public r-proto
885 (uri (cran-uri "proto" version))
887 (base32 "1l843p8vckjckdhgv37ngv47fga5jzy0n00pmipvp05nnaixk54j"))))
888 (build-system r-build-system)
889 (home-page "https://github.com/hadley/proto")
890 (synopsis "Prototype object-based programming")
892 "Proto is an object oriented system using object-based, also called
893 prototype-based, rather than class-based object oriented ideas.")
894 (license license:gpl2+)))
896 (define-public r-rcolorbrewer
898 (name "r-rcolorbrewer")
903 (uri (cran-uri "RColorBrewer" version))
905 (base32 "1pfcl8z1pnsssfaaz9dvdckyfnnc6rcq56dhislbf571hhg7isgk"))))
906 (build-system r-build-system)
907 (home-page "https://cran.r-project.org/web/packages/RColorBrewer")
908 (synopsis "ColorBrewer palettes")
910 "This package provides color schemes for maps (and other graphics)
911 designed by Cynthia Brewer as described at http://colorbrewer2.org")
912 ;; Includes code licensed under bsd-4
913 (license license:asl2.0)))
915 (define-public r-sendmailr
922 (uri (cran-uri "sendmailR" version))
925 "0z7ipywnzgkhfvl4zb2fjwl1xq7b5wib296vn9c9qgbndj6b1zh4"))))
926 (properties `((upstream-name . "sendmailR")))
927 (build-system r-build-system)
929 `(("r-base64enc" ,r-base64enc)))
931 "https://cran.r-project.org/web/packages/sendmailR")
932 (synopsis "Send email using R")
934 "This package contains a simple SMTP client which provides a portable
935 solution for sending email, including attachments, from within R.")
936 (license license:gpl2+)))
938 (define-public r-stringi
945 (uri (cran-uri "stringi" version))
948 "122im5m8x9bqpahc0hbxmvdq6hnsmgnxwwyjpvbihyv2jq5kd44m"))))
949 (build-system r-build-system)
950 (inputs `(("icu4c" ,icu4c)))
951 (native-inputs `(("pkg-config" ,pkg-config)))
952 (home-page "http://stringi.rexamine.com/")
953 (synopsis "Character string processing facilities")
955 "This package allows for fast, correct, consistent, portable, as well as
956 convenient character string/text processing in every locale and any native
957 encoding. Owing to the use of the ICU library, the package provides R users
958 with platform-independent functions known to Java, Perl, Python, PHP, and Ruby
959 programmers. Among available features there are: pattern searching
960 (e.g. via regular expressions), random string generation, string collation,
961 transliteration, concatenation, date-time formatting and parsing, etc.")
962 (license license:bsd-3)))
964 (define-public r-stringr
971 (uri (cran-uri "stringr" version))
973 (base32 "16hj2rmv8x03lp6cp2jk0k2plibvbggf444kp05przdvd03v7l31"))))
974 (build-system r-build-system)
976 `(("r-magrittr" ,r-magrittr)
977 ("r-stringi" ,r-stringi)))
978 (home-page "https://github.com/hadley/stringr")
979 (synopsis "Simple, consistent wrappers for common string operations")
981 "Stringr is a consistent, simple and easy to use set of wrappers around
982 the fantastic 'stringi' package. All function and argument names (and
983 positions) are consistent, all functions deal with \"NA\"'s and zero length
984 vectors in the same way, and the output from one function is easy to feed into
985 the input of another.")
986 (license license:gpl2+)))
988 (define-public r-reshape2
995 (uri (cran-uri "reshape2" version))
997 (base32 "03ki5ka1dj208fc0dclbm0b4xp9d769pah2j9cs34l776p4r9zwa"))))
998 (build-system r-build-system)
1000 `(("r-plyr" ,r-plyr)
1002 ("r-stringr" ,r-stringr)))
1003 (home-page "https://github.com/hadley/reshape")
1004 (synopsis "Flexibly reshape data: a reboot of the \"reshape\" package")
1006 "Reshape2 is an R library to flexibly restructure and aggregate data
1007 using just two functions: melt and dcast (or acast).")
1008 (license license:expat)))
1010 (define-public r-scales
1017 (uri (cran-uri "scales" version))
1019 (base32 "0zg9wfzmsdjxpbld0nzv7hcpq5r0wazqxmn7grvvif2agj0w1z6v"))))
1020 (build-system r-build-system)
1022 `(("r-dichromat" ,r-dichromat)
1023 ("r-labeling" ,r-labeling)
1024 ("r-munsell" ,r-munsell)
1026 ("r-rcolorbrewer" ,r-rcolorbrewer)
1029 ("r-viridislite" ,r-viridislite)))
1030 (home-page "https://github.com/hadley/scales")
1031 (synopsis "Scale functions for visualization")
1033 "This package provides graphical scales that map data to aesthetics, and
1034 provides methods for automatically determining breaks and labels for axes and
1036 (license license:expat)))
1038 (define-public r-ggplot2
1045 (uri (cran-uri "ggplot2" version))
1047 (base32 "0543782ddv2hp6s0l702mnxfg8n7a6qlbm8bm55x22hnqgz8kg2z"))))
1048 (build-system r-build-system)
1050 `(("r-digest" ,r-digest)
1051 ("r-gtable" ,r-gtable)
1053 ("r-lazyeval" ,r-lazyeval)
1055 ("r-tibble" ,r-tibble)
1056 ("r-reshape2" ,r-reshape2)
1057 ("r-scales" ,r-scales)
1058 ("r-svglite" ,r-svglite))) ; Needed for 'ggsave'
1059 (home-page "http://ggplot2.org")
1060 (synopsis "An implementation of the grammar of graphics")
1062 "Ggplot2 is an implementation of the grammar of graphics in R. It
1063 combines the advantages of both base and lattice graphics: conditioning and
1064 shared axes are handled automatically, and you can still build up a plot step
1065 by step from multiple data sources. It also implements a sophisticated
1066 multidimensional conditioning system and a consistent interface to map data to
1067 aesthetic attributes.")
1068 (license license:gpl2+)))
1070 (define-public r-ggdendro
1076 (uri (cran-uri "ggdendro" version))
1079 "1zzq1hxd0d1qa5hrzwfkdw6fzscpcafbwbpkrb62dm559y8awp0j"))))
1080 (build-system r-build-system)
1082 `(("r-ggplot2" ,r-ggplot2)
1084 ("r-knitr" ,r-knitr)))
1085 (home-page "https://github.com/andrie/ggdendro")
1086 (synopsis "Create Dendrograms and Tree Diagrams Using ggplot2")
1087 (description "This is a set of tools for dendrograms and tree plots using
1088 ggplot2. The ggplot2 philosophy is to clearly separate data from the
1089 presentation. Unfortunately the plot method for dendrograms plots directly
1090 to a plot device with out exposing the data. The ggdendro package resolves
1091 this by making available functions that extract the dendrogram plot data.
1092 The package provides implementations for tree, rpart, as well as diana and
1093 agnes cluster diagrams.")
1094 (license license:gpl2+)))
1096 (define-public r-gdtools
1103 (uri (cran-uri "gdtools" version))
1106 "103wnc8sq0iwcnj4j14hd420d2dqdyf13s3f25icsznrlyzdkhf5"))))
1107 (build-system r-build-system)
1109 `(("r-rcpp" ,r-rcpp)
1110 ("pkg-config" ,pkg-config)))
1112 `(("cairo" ,cairo)))
1114 `(("r-withr" ,r-withr)))
1115 (home-page "https://cran.r-project.org/web/packages/gdtools")
1116 (synopsis "Utilities for graphical rendering")
1118 "The @code{gdtools} package provides functionalities to get font metrics
1119 and to generate base64 encoded string from raster matrix.")
1120 (license license:gpl3)))
1122 (define-public r-svglite
1129 (uri (cran-uri "svglite" version))
1132 "1bws3lc4hlhln11zd7lalhiyc43yk6c6vrzy41fkxk1dkjazfx51"))))
1133 (build-system r-build-system)
1134 (native-inputs `(("r-rcpp" ,r-rcpp)))
1137 ("r-gdtools" ,r-gdtools)))
1138 (home-page "https://github.com/hadley/svglite")
1139 (synopsis "SVG graphics device")
1141 "@code{svglite} is a graphics device that produces clean
1142 @dfn{SVG} (Scalable Vector Graphics) output, suitable for use on the web, or
1143 hand editing. Compared to the built-in @code{svg()}, @code{svglite} is
1144 considerably faster, produces smaller files, and leaves text as is.")
1145 (license license:gpl2+)))
1147 (define-public r-assertthat
1149 (name "r-assertthat")
1153 (uri (cran-uri "assertthat" version))
1156 "1wp5znk3xy338x6hknppk702jn596yr735d9i7c3wabm3sdzfgnp"))))
1157 (build-system r-build-system)
1158 (home-page "https://github.com/hadley/assertthat")
1159 (synopsis "Easy pre and post assertions")
1161 "Assertthat is an extension to stopifnot() that makes it easy to declare
1162 the pre and post conditions that your code should satisfy, while also
1163 producing friendly error messages so that your users know what they've done
1165 (license license:gpl3+)))
1167 (define-public r-lazyeval
1173 (uri (cran-uri "lazyeval" version))
1176 "0q9zx78ncy2ffzrf9sh053069kd3w1xn1ss3gsbyf3y4jhza9cw3"))))
1177 (build-system r-build-system)
1178 (home-page "https://github.com/hadley/lazyeval")
1179 (synopsis "Lazy (non-standard) evaluation in R")
1181 "This package provides the tools necessary to do non-standard
1182 evaluation (NSE) in R.")
1183 (license license:gpl3+)))
1185 (define-public r-dbi
1191 (uri (cran-uri "DBI" version))
1194 "04fyrxdpqcygg5wviy637y6lgk64xqjjq31lvv4hwqj5kbaxamr5"))))
1195 (build-system r-build-system)
1196 (home-page "https://github.com/rstats-db/DBI")
1197 (synopsis "R database interface")
1199 "The DBI package provides a database interface (DBI) definition for
1200 communication between R and relational database management systems. All
1201 classes in this package are virtual and need to be extended by the various
1202 R/DBMS implementations.")
1203 (license license:lgpl2.0+)))
1208 (version "1.65.0-1")
1211 (uri (cran-uri "BH" version))
1214 "0n6byzrvl1w4hjdxz479q4a7w1118f9ckqc4gqydq7lgzs5agfl2"))))
1215 (build-system r-build-system)
1216 (home-page "https://github.com/eddelbuettel/bh")
1217 (synopsis "R package providing subset of Boost headers")
1219 "This package aims to provide the most useful subset of Boost libraries
1220 for template use among CRAN packages.")
1221 (license license:boost1.0)))
1223 (define-public r-evaluate
1229 (uri (cran-uri "evaluate" version))
1232 "070vvmnbdlp7sz2zhza7fhd2a6mlwiln8fn4hyzhsiizbn4n79y9"))))
1233 (build-system r-build-system)
1235 `(("r-stringr" ,r-stringr)))
1236 (home-page "https://github.com/hadley/evaluate")
1237 (synopsis "Parsing and evaluation tools for R")
1239 "This package provides tools that allow you to recreate the parsing,
1240 evaluation and display of R code, with enough information that you can
1241 accurately recreate what happens at the command line. The tools can easily be
1242 adapted for other output formats, such as HTML or LaTeX.")
1243 (license license:gpl3+)))
1245 (define-public r-formatr
1251 (uri (cran-uri "formatR" version))
1254 "19sd23vgs4ac0fwlw40j3676k6mramb0ajlq8hdw23kjwdx1jk47"))))
1255 (build-system r-build-system)
1256 (home-page "http://yihui.name/formatR")
1257 (synopsis "Format R code automatically")
1259 "This package provides a function to format R source code. Spaces and
1260 indent will be added to the code automatically, and comments will be preserved
1261 under certain conditions, so that R code will be more human-readable and tidy.
1262 There is also a Shiny app as a user interface in this package.")
1263 (license license:gpl3+)))
1265 (define-public r-highr
1271 (uri (cran-uri "highr" version))
1274 "0n9v44dxdy5fhkdmpbpa2p78whyd9z3rhhy42ipdz5m5vsr55qa3"))))
1275 (build-system r-build-system)
1276 (home-page "https://github.com/yihui/highr")
1277 (synopsis "Syntax highlighting for R source code")
1279 "This package provides syntax highlighting for R source code. Currently
1280 it supports LaTeX and HTML output. Source code of other languages is
1281 supported via Andre Simon's highlight package.")
1282 (license license:gpl3+)))
1284 (define-public r-mime
1290 (uri (cran-uri "mime" version))
1293 "0i91m3ivaja1k33jwcvz16pfjypkci27awm8glil7sxhmwaj3izw"))))
1294 (build-system r-build-system)
1295 (home-page "https://github.com/yihui/mime")
1296 (synopsis "R package to map filenames to MIME types")
1298 "This package guesses the MIME type from a filename extension using the
1299 data derived from /etc/mime.types in UNIX-type systems.")
1300 (license license:gpl2)))
1302 (define-public r-markdown
1308 (uri (cran-uri "markdown" version))
1311 "1vcgsh2m2f5kfgappgg71nbf04ff0j1sbk668krjs3r2n89dk3sk"))))
1312 (build-system r-build-system)
1313 ;; Skip check phase because the tests require the r-knitr package to be
1314 ;; installed. This prevents installation failures. Knitr normally
1315 ;; shouldn't be available since r-markdown is a dependency of the r-knitr
1317 (arguments `(#:tests? #f))
1319 `(("r-mime" ,r-mime)))
1320 (home-page "https://github.com/rstudio/markdown")
1321 (synopsis "Markdown rendering for R")
1323 "This package provides R bindings to the Sundown Markdown rendering
1324 library (https://github.com/vmg/sundown). Markdown is a plain-text formatting
1325 syntax that can be converted to XHTML or other formats.")
1326 (license license:gpl2)))
1328 (define-public r-yaml
1334 (uri (cran-uri "yaml" version))
1337 "1xlsmqal607w6c9rx86061y1fwpbyd5lqp9bad5n7cc9a0blpnkm"))))
1338 (build-system r-build-system)
1339 (home-page "https://cran.r-project.org/web/packages/yaml/")
1340 (synopsis "Methods to convert R data to YAML and back")
1342 "This package implements the libyaml YAML 1.1 parser and
1343 emitter (http://pyyaml.org/wiki/LibYAML) for R.")
1344 (license license:bsd-3)))
1346 (define-public r-knitr
1352 (uri (cran-uri "knitr" version))
1355 "00gljbz57n9lkvbd6az4n37gpbs8vg3fxx5p9biamhmhqyra514l"))))
1356 (build-system r-build-system)
1358 `(("r-evaluate" ,r-evaluate)
1359 ("r-digest" ,r-digest)
1360 ("r-highr" ,r-highr)
1361 ("r-markdown" ,r-markdown)
1362 ("r-stringr" ,r-stringr)
1363 ("r-yaml" ,r-yaml)))
1364 (home-page "http://yihui.name/knitr/")
1365 (synopsis "General-purpose package for dynamic report generation in R")
1367 "This package provides a general-purpose tool for dynamic report
1368 generation in R using Literate Programming techniques.")
1369 ;; The code is released under any version of the GPL. As it is used by
1370 ;; r-markdown which is available under GPLv2 only, we have chosen GPLv2+
1372 (license license:gpl2+)))
1374 (define-public r-knitrbootstrap
1376 (name "r-knitrbootstrap")
1381 (uri (cran-uri "knitrBootstrap" version))
1384 "089147g7nqp99rwdxxsfmklsrwc8aia09sr8ndmrc335r33v6r6p"))))
1385 (properties `((upstream-name . "knitrBootstrap")))
1386 (build-system r-build-system)
1388 `(("r-knitr" ,r-knitr)
1389 ("r-rmarkdown" ,r-rmarkdown)))
1390 (home-page "https://github.com/jimhester/knitrBootstrap")
1391 (synopsis "Knitr bootstrap framework")
1393 "This package provides a framework to create Bootstrap 3 HTML reports
1394 from knitr Rmarkdown.")
1395 (license license:expat)))
1397 (define-public r-microbenchmark
1399 (name "r-microbenchmark")
1403 (uri (cran-uri "microbenchmark" version))
1406 "0qn5r1a6qidghcisc2hpbdmj62pnixc3zz6p4ipk8mvakf0hdsvg"))))
1407 (build-system r-build-system)
1409 `(("r-ggplot2" ,r-ggplot2)))
1410 (home-page "https://cran.r-project.org/web/packages/microbenchmark/")
1411 (synopsis "Accurate timing functions for R")
1413 "This package provides infrastructure to accurately measure and compare
1414 the execution time of R expressions.")
1415 (license license:bsd-2)))
1417 (define-public r-pryr
1423 (uri (cran-uri "pryr" version))
1426 "1b1rcywq9sqzgjsnh3ynnx16gp41n94kkzfalm3y4kyy3ls8ikba"))))
1427 (build-system r-build-system)
1429 `(("r-stringr" ,r-stringr)
1430 ("r-codetools" ,r-codetools)))
1432 `(("r-rcpp" ,r-rcpp)))
1433 (home-page "https://github.com/hadley/pryr")
1434 (synopsis "Tools for computing on the R language")
1436 "This package provides useful tools to pry back the covers of R and
1437 understand the language at a deeper level.")
1438 (license license:gpl2)))
1440 (define-public r-memoise
1446 (uri (cran-uri "memoise" version))
1449 "034qfc2xlh30x1q2vya239w34a3ir3y2fwnx2agbgbi6592zjxmj"))))
1450 (build-system r-build-system)
1452 `(("r-digest" ,r-digest)))
1453 (home-page "https://github.com/hadley/memoise")
1454 (synopsis "Memoise functions for R")
1456 "This R package allows to cache the results of a function so that when
1457 you call it again with the same arguments it returns the pre-computed value.")
1458 (license license:expat)))
1460 (define-public r-crayon
1466 (uri (cran-uri "crayon" version))
1469 "0s7s6vc3ww8pzanpjisym4jjvwcc5pi2qg8srx7jqlz9j3wrnvpw"))))
1470 (build-system r-build-system)
1472 `(("r-memoise" ,r-memoise)))
1473 (home-page "https://github.com/gaborcsardi/crayon")
1474 (synopsis "Colored terminal output for R")
1476 "Colored terminal output on terminals that support ANSI color and
1477 highlight codes. It also works in Emacs ESS. ANSI color support is
1478 automatically detected. Colors and highlighting can be combined and nested.
1479 New styles can also be created easily. This package was inspired by the
1480 \"chalk\" JavaScript project.")
1481 (license license:expat)))
1483 (define-public r-praise
1490 (uri (cran-uri "praise" version))
1493 "1gfyypnvmih97p2r0php9qa39grzqpsdbq5g0fdsbpq5zms5w0sw"))))
1494 (build-system r-build-system)
1495 (home-page "https://github.com/gaborcsardi/praise")
1496 (synopsis "Functions to praise users")
1498 "This package provides template functions to assist in building friendly
1499 R packages that praise their users.")
1500 (license license:expat)))
1502 (define-public r-testthat
1508 (uri (cran-uri "testthat" version))
1511 "155l53kb69jga5d8c5nvdwqlvlgfmk4vzyyl4d0108j53jnlgh1v"))))
1512 (build-system r-build-system)
1515 ("r-crayon" ,r-crayon)
1516 ("r-digest" ,r-digest)
1517 ("r-magrittr" ,r-magrittr)
1518 ("r-praise" ,r-praise)
1520 ("r-rlang" ,r-rlang)
1521 ("r-withr" ,r-withr)))
1522 (home-page "https://github.com/hadley/testthat")
1523 (synopsis "Unit testing for R")
1525 "This package provides a unit testing system for R designed to be fun,
1526 flexible and easy to set up.")
1527 (license license:expat)))
1535 (uri (cran-uri "R6" version))
1538 "13xfdr19ca7ymisidsanm6w7hsk3qmy5l8c0mlz3nk48f7s5cxq8"))))
1539 (build-system r-build-system)
1540 (home-page "https://github.com/wch/R6/")
1541 (synopsis "Classes with reference semantics in R")
1543 "The R6 package allows the creation of classes with reference semantics,
1544 similar to R's built-in reference classes. Compared to reference classes, R6
1545 classes are simpler and lighter-weight, and they are not built on S4 classes
1546 so they do not require the methods package. These classes allow public and
1547 private members, and they support inheritance, even when the classes are
1548 defined in different packages.")
1549 (license license:expat)))
1551 (define-public r-rlang
1557 (uri (cran-uri "rlang" version))
1560 "1x5rwwsx7xrlyspy41yl5nhyvfgzl73195nsdb4rc6z85ab6r6wd"))))
1561 (build-system r-build-system)
1562 (home-page "http://rlang.tidyverse.org")
1563 (synopsis "Functions for base types, core R and Tidyverse features")
1564 (description "This package provides a toolbox for working with base types,
1565 core R features like the condition system, and core @code{Tidyverse} features
1566 like tidy evaluation.")
1567 (license license:gpl3)))
1569 (define-public r-tibble
1576 (uri (cran-uri "tibble" version))
1579 "02vn6yqzcvmazy5jaqar3wwbrmh83a1bfgsqgk0hgz38i80zgvm7"))))
1580 (build-system r-build-system)
1582 `(("r-rlang" ,r-rlang)
1583 ("r-rcpp" ,r-rcpp)))
1584 (home-page "https://github.com/hadley/tibble")
1585 (synopsis "Simple data frames")
1587 "This package provides a @code{tbl_df} class that offers better checking
1588 and printing capabilities than traditional data frames.")
1589 (license license:expat)))
1591 (define-public r-dplyr
1597 (uri (cran-uri "dplyr" version))
1600 "1hm8ml7yaraag1ak6kvz2mxx6if568c759ix8a1n9d7va03wj7vv"))))
1601 (build-system r-build-system)
1603 `(("r-assertthat" ,r-assertthat)
1605 ("r-magrittr" ,r-magrittr)
1606 ("r-rlang" ,r-rlang)
1607 ("r-plogr" ,r-plogr)
1609 ("r-pkgconfig" ,r-pkgconfig)
1610 ("r-bindrcpp" ,r-bindrcpp)
1611 ("r-tibble" ,r-tibble)))
1613 `(("r-rcpp" ,r-rcpp)
1615 (home-page "https://github.com/hadley/dplyr")
1616 (synopsis "Tools for working with data frames in R")
1618 "dplyr is the next iteration of plyr. It is focussed on tools for
1619 working with data frames. It has three main goals: 1) identify the most
1620 important data manipulation tools needed for data analysis and make them easy
1621 to use in R; 2) provide fast performance for in-memory data by writing key
1622 pieces of code in C++; 3) use the same code interface to work with data no
1623 matter where it is stored, whether in a data frame, a data table or
1625 (license license:expat)))
1627 (define-public r-dbplyr
1634 (uri (cran-uri "dbplyr" version))
1637 "17gn8vr4a6m9ynarjbm9xsrhcvgn5lnxhb2qhiiglmhh5mm4a7kv"))))
1638 (build-system r-build-system)
1640 `(("r-assertthat" ,r-assertthat)
1642 ("r-dplyr" ,r-dplyr)
1644 ("r-purrr" ,r-purrr)
1646 ("r-rlang" ,r-rlang)
1647 ("r-tibble" ,r-tibble)))
1648 (home-page "https://github.com/tidyverse/dbplyr")
1649 (synopsis "Dplyr back end for databases")
1651 "This package provides a dplyr back end for databases that allows you to
1652 work with remote database tables as if they are in-memory data frames. Basic
1653 features works with any database that has a @code{DBI} back end; more advanced
1654 features require SQL translation to be provided by the package author.")
1655 (license license:expat)))
1657 (define-public r-acepack
1664 (uri (cran-uri "acepack" version))
1667 "1f98rpfjmhd92rdc3j004plyfpjailz6j0ycysbac0kgj83haxc2"))))
1668 (build-system r-build-system)
1670 `(("gfortran" ,gfortran)))
1671 (home-page "https://cran.r-project.org/web/packages/acepack")
1672 (synopsis "Functions for regression transformations")
1674 "This package provides ACE and AVAS methods for choosing regression
1676 (license license:expat)))
1678 (define-public r-formula
1685 (uri (cran-uri "Formula" version))
1688 "0ad49bzip1zqmpj1d8jajwl4bd81fm3k6dq8p26x6mvlzc04dvwd"))))
1689 (properties `((upstream-name . "Formula")))
1690 (build-system r-build-system)
1691 (home-page "https://cran.r-project.org/web/packages/Formula")
1692 (synopsis "Extended model formulas")
1694 "This package provides a new class @code{Formula}, which extends the base
1695 class @code{formula}. It supports extended formulas with multiple parts of
1696 regressors on the right-hand side and/or multiple responses on the left-hand
1698 (license (list license:gpl2+ license:gpl3+))))
1700 (define-public r-locfit
1707 (uri (cran-uri "locfit" version))
1710 "0lafrmq1q7x026m92h01hc9cjjiximqqi3v1g2hw7ai9vf7i897m"))))
1711 (build-system r-build-system)
1713 `(("r-lattice" ,r-lattice)))
1714 (home-page "https://cran.r-project.org/web/packages/locfit")
1715 (synopsis "Local regression, likelihood and density estimation")
1717 "This package provides functions used for local regression, likelihood
1718 and density estimation.")
1719 (license (list license:gpl2+ license:gpl3+))))
1721 (define-public r-chron
1727 (uri (cran-uri "chron" version))
1730 "05aznigw9nwv3hbwjnjbvqhfjqkwsw2csgrjx8500gzr2fvla5w8"))))
1731 (build-system r-build-system)
1732 (home-page "https://cran.r-project.org/web/packages/chron")
1733 (synopsis "Chronological R objects which can handle dates and times")
1735 "This package provides chronological R objects which can handle dates and
1737 (license license:gpl2)))
1739 (define-public r-data-table
1741 (name "r-data-table")
1742 (version "1.10.4-3")
1745 (uri (cran-uri "data.table" version))
1748 "12caklgr19vy9wprdks6zh825vr1iw1cajgwcnbpyvmijqdlz2xs"))))
1749 (build-system r-build-system)
1750 (home-page "https://github.com/Rdatatable/data.table/wiki")
1751 (synopsis "Enhanced version of data.frame R object")
1753 "The R package @code{data.table} is an extension of @code{data.frame}
1754 providing functions for fast aggregation of large data (e.g. 100GB in RAM),
1755 fast ordered joins, fast add/modify/delete of columns by group, column listing
1756 and fast file reading.")
1757 (license license:gpl3+)))
1759 (define-public r-xtable
1766 (uri (cran-uri "xtable" version))
1769 "0398qkpvlw3dv0myz4mjcyqwpwc2m31l127r8vdzwc71wb6s28qn"))))
1770 (build-system r-build-system)
1772 `(("r-knitr" ,r-knitr)))
1773 (home-page "http://xtable.r-forge.r-project.org/")
1774 (synopsis "Export R tables to LaTeX or HTML")
1776 "This package provides tools to export R data as LaTeX and HTML tables.")
1777 (license license:gpl2+)))
1779 (define-public python-patsy
1781 (name "python-patsy")
1785 (uri (pypi-uri "patsy" version ".zip"))
1788 "1m6knyq8hbqlx242y4da02j0x86j4qggs1j7q186w3jv0j0c476w"))))
1789 (build-system python-build-system)
1792 (modify-phases %standard-phases
1793 (replace 'check (lambda _ (zero? (system* "nosetests" "-v")))))))
1795 `(("python-numpy" ,python-numpy)
1796 ("python-scipy" ,python-scipy)
1797 ("python-six" ,python-six)))
1799 `(("python-nose" ,python-nose)
1801 (home-page "https://github.com/pydata/patsy")
1802 (synopsis "Describe statistical models and build design matrices")
1804 "Patsy is a Python package for describing statistical models and for
1805 building design matrices.")
1806 ;; The majority of the code is distributed under BSD-2. The module
1807 ;; patsy.compat contains code derived from the Python standard library,
1808 ;; and is covered by the PSFL.
1809 (license (list license:bsd-2 license:psfl))))
1811 (define-public python2-patsy
1812 (package-with-python2 python-patsy))
1814 (define-public python-statsmodels
1816 (name "python-statsmodels")
1821 (uri (pypi-uri "statsmodels" version))
1824 "0j30v3932shnj9368c9jr3svkyrvfj90h2l7nxnqkbpv0svilhr6"))
1825 (patches (search-patches "python-statsmodels-fix-tests.patch"))))
1826 (build-system python-build-system)
1829 (modify-phases %standard-phases
1830 ;; tests must be run after installation
1832 (add-after 'unpack 'set-matplotlib-backend-to-agg
1834 ;; Set the matplotlib backend to Agg to avoid problems using the
1835 ;; GTK backend without a display.
1836 (substitute* (append (find-files "statsmodels/graphics/tests" "\\.py")
1837 '("statsmodels/tsa/vector_ar/tests/test_var.py"
1838 "statsmodels/duration/tests/test_survfunc.py"))
1839 (("import matplotlib\\.pyplot as plt" line)
1840 (string-append "import matplotlib;matplotlib.use('Agg');"
1843 (add-after 'install 'check
1844 (lambda* (#:key inputs outputs #:allow-other-keys)
1845 ;; Make installed package available for running the tests
1846 (add-installed-pythonpath inputs outputs)
1847 (with-directory-excursion "/tmp"
1848 (zero? (system* "nosetests"
1850 "-v" "statsmodels"))))))))
1852 `(("python-numpy" ,python-numpy)
1853 ("python-scipy" ,python-scipy)
1854 ("python-pandas" ,python-pandas)
1855 ("python-patsy" ,python-patsy)
1856 ("python-matplotlib" ,python-matplotlib)))
1858 `(("python-cython" ,python-cython)
1859 ("python-nose" ,python-nose)
1860 ("python-sphinx" ,python-sphinx)))
1861 (home-page "http://statsmodels.sourceforge.net/")
1862 (synopsis "Statistical modeling and econometrics in Python")
1864 "Statsmodels is a Python package that provides a complement to scipy for
1865 statistical computations including descriptive statistics and estimation and
1866 inference for statistical models.")
1867 (license license:bsd-3)))
1869 (define-public python2-statsmodels
1870 (let ((stats (package-with-python2 python-statsmodels)))
1871 (package (inherit stats)
1873 `(("python2-pytz" ,python2-pytz)
1874 ("python2-numpy" ,python2-numpy)
1875 ("python2-scipy" ,python2-scipy)
1876 ("python2-pandas" ,python2-pandas)
1877 ("python2-patsy" ,python2-patsy)
1878 ("python2-matplotlib" ,python2-matplotlib))))))
1880 (define-public r-coda
1886 (uri (cran-uri "coda" version))
1889 "14a4a8df4ygj05h37chmdn8kzcqs07fpbflxfrq530563mrza7yl"))))
1890 (build-system r-build-system)
1892 `(("r-lattice" ,r-lattice)))
1893 (home-page "https://cran.r-project.org/web/packages/coda")
1894 (synopsis "This is a package for Output Analysis and Diagnostics for MCMC")
1895 (description "This package provides functions for summarizing and plotting
1896 the output from Markov Chain Monte Carlo (MCMC) simulations, as well as
1897 diagnostic tests of convergence to the equilibrium distribution of the Markov
1899 (license license:gpl2+)))
1901 (define-public r-ade4
1908 (uri (cran-uri "ade4" version))
1911 "0zk81x0yn30gbyc0jpzyw1nxd08ccihl6vyk0ijvj3aw3nr5flc6"))))
1912 (build-system r-build-system)
1914 `(("r-mass" ,r-mass)))
1915 (home-page "http://pbil.univ-lyon1.fr/ADE-4")
1916 (synopsis "Multivariate data analysis and graphical display")
1918 "The ade4 package contains data analysis functions to analyze ecological
1919 and environmental data in the framework of Euclidean exploratory methods.")
1920 (license license:gpl2+)))
1922 (define-public r-xml2
1929 (uri (cran-uri "xml2" version))
1932 "05iifrcgzx53w5ciw8bbm4vdwc3giv4xsvazv8chqxkndfvf7wq0"))))
1933 (build-system r-build-system)
1935 `(("libxml2" ,libxml2)))
1937 `(("r-rcpp" ,r-rcpp)
1939 (home-page "https://github.com/hadley/xml2")
1940 (synopsis "Parse XML with R")
1942 "This package provides a simple, consistent interface to working with XML
1943 files in R. It is built on top of the libxml2 C library.")
1944 (license license:gpl2+)))
1946 (define-public r-multitaper
1948 (name "r-multitaper")
1953 (uri (cran-uri "multitaper" version))
1956 "04wd9bbhyx7697pfy0fpj02v1csr48hkpqj62h9p8a6w84ji4k68"))))
1957 (build-system r-build-system)
1959 `(("gfortran" ,gfortran)))
1960 (home-page "https://github.com/wesleyburr/multitaper/")
1961 (synopsis "Multitaper spectral analysis tools")
1963 "This package implements multitaper spectral estimation
1964 techniques using prolate spheroidal sequences (Slepians) and sine
1965 tapers for time series analysis. It includes an adaptive weighted
1966 multitaper spectral estimate, a coherence estimate, Thomson's Harmonic
1967 F-test, and complex demodulation. The Slepians sequences are
1968 generated efficiently using a tridiagonal matrix solution, and
1969 jackknifed confidence intervals are available for most estimates.")
1970 (license license:gpl2+)))
1972 (define-public r-rversions
1974 (name "r-rversions")
1978 (uri (cran-uri "rversions" version))
1981 "0i2gi05nrvknr7g89rbppkswyfcwwd4r9gp75fdfhpah8sgq1l11"))))
1982 (build-system r-build-system)
1984 `(("r-curl" ,r-curl)
1985 ("r-xml2" ,r-xml2)))
1986 (home-page "https://github.com/metacran/rversions")
1987 (synopsis "Query R versions, including 'r-release' and 'r-oldrel'")
1989 "This package provides functions to query the main R repository to find
1990 the versions that @code{r-release} and @code{r-oldrel} refer to, and also all
1991 previous R versions and their release dates.")
1992 (license license:expat)))
1994 (define-public r-whisker
2000 (uri (cran-uri "whisker" version))
2003 "0z4cn115gxcl086d6bnqr8afi67b6a7xqg6ivmk3l4ng1x8kcj28"))))
2004 (build-system r-build-system)
2005 (home-page "https://github.com/edwindj/whisker")
2006 (synopsis "Logicless mustache templating for R")
2008 "This package provides logicless templating, with a syntax that is not
2010 (license license:gpl3+)))
2012 (define-public r-backports
2014 (name "r-backports")
2019 (uri (cran-uri "backports" version))
2022 "0mml9h3xagi7144pyb3jj9zbh9qzns7izkhdg7df20v7bikr6nz8"))))
2023 (build-system r-build-system)
2024 (home-page "https://cran.r-project.org/web/packages/backports")
2025 (synopsis "Reimplementations of functions introduced since R 3.0.0")
2027 "Provides implementations of functions which have been introduced in R
2028 since version 3.0.0. The backports are conditionally exported which results
2029 in R resolving the function names to the version shipped with R (if available)
2030 and uses the implemented backports as fallback. This way package developers
2031 can make use of the new functions without worrying about the minimum required
2033 (license license:gpl2+)))
2035 (define-public r-checkmate
2037 (name "r-checkmate")
2042 (uri (cran-uri "checkmate" version))
2045 "1q6igk50lq4fp5d3imgcn1j063h3gsp214ra4nlf534hf4wjlkg9"))))
2046 (build-system r-build-system)
2048 `(("r-backports" ,r-backports)))
2049 (home-page "https://github.com/mllg/checkmate")
2050 (synopsis "Fast and versatile argument checks")
2052 "This package provides tests and assertions to perform frequent argument
2053 checks. A substantial part of the package was written in C to minimize any
2054 worries about execution time overhead.")
2055 (license license:bsd-3)))
2057 (define-public r-bbmisc
2064 (uri (cran-uri "BBmisc" version))
2067 "1lh1n4bvxzivb5rbz69mvd8xdgr3gr2bnqd68a39sd1530l8r90y"))))
2068 (properties `((upstream-name . "BBmisc")))
2069 (build-system r-build-system)
2071 `(("r-checkmate" ,r-checkmate)))
2072 (home-page "https://github.com/berndbischl/BBmisc")
2073 (synopsis "Miscellaneous functions for R package development")
2075 "This package provides miscellaneous helper functions for the development
2077 (license license:bsd-3)))
2079 (define-public r-fail
2086 (uri (cran-uri "fail" version))
2089 "0vfm6kmpmgsamda5p0sl771kbnsscan31l2chzssyw93kwmams7d"))))
2090 (build-system r-build-system)
2092 `(("r-bbmisc" ,r-bbmisc)
2093 ("r-checkmate" ,r-checkmate)))
2094 (home-page "https://github.com/mllg/fail")
2095 (synopsis "File abstraction interface layer (FAIL)")
2097 "This package provides a more comfortable interface to work with R data
2098 or source files in a key-value fashion.")
2099 (license license:bsd-3)))
2101 (define-public r-batchjobs
2103 (name "r-batchjobs")
2108 (uri (cran-uri "BatchJobs" version))
2111 "035658marnw57p4f38g99rwmvmb6hpbq0fhlxp3qbw22zfnnkvs9"))))
2112 (properties `((upstream-name . "BatchJobs")))
2113 (build-system r-build-system)
2115 `(("r-backports" ,r-backports)
2116 ("r-bbmisc" ,r-bbmisc)
2118 ("r-checkmate" ,r-checkmate)
2119 ("r-data-table" ,r-data-table)
2121 ("r-digest" ,r-digest)
2122 ("r-rsqlite" ,r-rsqlite)
2123 ("r-sendmailr" ,r-sendmailr)
2124 ("r-stringi" ,r-stringi)))
2125 (home-page "https://github.com/tudo-r/BatchJobs")
2126 (synopsis "Batch computing with R")
2128 "This package provides @code{Map}, @code{Reduce} and @code{Filter}
2129 variants to generate jobs on batch computing systems like PBS/Torque, LSF,
2130 SLURM and Sun Grid Engine. Multicore and SSH systems are also supported.")
2131 (license license:bsd-2)))
2133 (define-public r-brew
2139 (uri (cran-uri "brew" version))
2142 "1vghazbcha8gvkwwcdagjvzx6yl8zm7kgr0i9wxr4jng06d1l3fp"))))
2143 (build-system r-build-system)
2144 (home-page "https://cran.r-project.org/web/packages/brew")
2145 (synopsis "Templating framework for report generation")
2147 "The brew package implements a templating framework for mixing text and R
2148 code for report generation. The template syntax is similar to PHP, Ruby's erb
2149 module, Java Server Pages, and Python's psp module.")
2150 (license license:gpl2+)))
2152 (define-public r-desc
2159 (uri (cran-uri "desc" version))
2162 "0k07qighac1xzmm8k988zi7i88a0yfvia3gk5hbz0fyvb2v9kzrj"))))
2163 (build-system r-build-system)
2165 `(("r-assertthat" ,r-assertthat)
2166 ("r-crayon" ,r-crayon)
2168 ("r-rprojroot" ,r-rprojroot)))
2169 (home-page "https://github.com/r-pkgs/desc")
2170 (synopsis "Manipulate DESCRIPTION Files")
2172 "This package provides tools to read, write, create, and manipulate
2173 DESCRIPTION files. It is intended for packages that create or manipulate
2175 (license license:expat)))
2177 (define-public r-commonmark
2179 (name "r-commonmark")
2184 (uri (cran-uri "commonmark" version))
2187 "1vb8r9khpvcf0q7acv8rsplfjjwcll302bg5kp596cvn6aacypl6"))))
2188 (build-system r-build-system)
2189 (home-page "https://cran.r-project.org/web/packages/commonmark")
2190 (synopsis "CommonMark and Github Markdown Rendering in R")
2192 "The CommonMark specification defines a rationalized version of markdown
2193 syntax. This package uses the 'cmark' reference implementation for converting
2194 markdown text into various formats including HTML, LaTeX and groff man. In
2195 addition, it exposes the markdown parse tree in XML format. The latest
2196 version of this package also adds support for Github extensions including
2197 tables, autolinks and strikethrough text.")
2198 (license license:bsd-2)))
2200 (define-public r-roxygen2
2206 (uri (cran-uri "roxygen2" version))
2209 "0xpzziminf225kjwhyl51kgkzhplyzhk5farhf5s822krl2xqbfj"))))
2210 (build-system r-build-system)
2212 `(("r-brew" ,r-brew)
2213 ("r-commonmark" ,r-commonmark)
2215 ("r-digest" ,r-digest)
2218 ("r-stringi" ,r-stringi)
2219 ("r-stringr" ,r-stringr)
2220 ("r-xml2" ,r-xml2)))
2221 (home-page "https://github.com/klutometis/roxygen")
2222 (synopsis "In-source documentation system for R")
2224 "Roxygen2 is a Doxygen-like in-source documentation system for Rd,
2225 collation, and NAMESPACE files.")
2226 (license license:gpl2+)))
2228 (define-public r-openssl
2235 (uri (cran-uri "openssl" version))
2238 "1ir7ggs0rxgn83h40r6jg9dzhb7hbcwhkcj5nsdzj7jz61sfgv77"))))
2239 (build-system r-build-system)
2241 `(("libressl" ,libressl)))
2242 (home-page "https://github.com/jeroenooms/openssl")
2243 (synopsis "Toolkit for encryption, signatures and certificates")
2245 "This package provides R bindings to OpenSSL libssl and libcrypto, plus
2246 custom SSH pubkey parsers. It supports RSA, DSA and NIST curves P-256, P-384
2247 and P-521. Cryptographic signatures can either be created and verified
2248 manually or via x509 certificates. AES block cipher is used in CBC mode for
2249 symmetric encryption; RSA for asymmetric (public key) encryption. High-level
2250 envelope functions combine RSA and AES for encrypting arbitrary sized data.
2251 Other utilities include key generators, hash functions (md5, sha1, sha256,
2252 etc), base64 encoder, a secure random number generator, and @code{bignum} math
2253 methods for manually performing crypto calculations on large multibyte
2255 (license license:expat)))
2257 (define-public r-httr
2263 (uri (cran-uri "httr" version))
2266 "0n7jz2digbgv48rbr9vmzv4vmf4rahl9jjy31izs7sxj4rs4s4r2"))))
2267 (build-system r-build-system)
2269 `(("r-curl" ,r-curl)
2270 ("r-jsonlite" ,r-jsonlite)
2271 ("r-openssl" ,r-openssl)
2274 (home-page "https://github.com/hadley/httr")
2275 (synopsis "Tools for working with URLs and HTTP")
2277 "The aim of httr is to provide a wrapper for RCurl customised to the
2278 demands of modern web APIs. It provides useful tools for working with HTTP
2279 organised by HTTP verbs (@code{GET()}, @code{POST()}, etc). Configuration
2280 functions make it easy to control additional request components.")
2281 (license license:expat)))
2283 (define-public r-git2r
2289 (uri (cran-uri "git2r" version))
2292 "1pqggijvsalb5cc2pr5gwfj3s713s63f4xii1xrd0qagfgbgz846"))))
2293 (build-system r-build-system)
2294 ;; This R package contains modified sources of libgit2. This modified
2295 ;; version of libgit2 is built as the package is built. Hence libgit2 is
2296 ;; not among the inputs of this package.
2298 `(("libssh2" ,libssh2)
2299 ("openssl" ,openssl)
2301 (home-page "https://github.com/ropensci/git2r")
2302 (synopsis "Access Git repositories with R")
2304 "This package provides an R interface to the libgit2 library, which is a
2305 pure C implementation of the Git core methods.")
2306 ;; GPLv2 only with linking exception.
2307 (license license:gpl2)))
2309 (define-public r-rstudioapi
2311 (name "r-rstudioapi")
2315 (uri (cran-uri "rstudioapi" version))
2318 "133s75q2hr6jg28m1wvs96qrbc9c4vw87migwhkjqb88xxvbqhd5"))))
2319 (build-system r-build-system)
2320 (home-page "https://cran.r-project.org/web/packages/rstudioapi")
2321 (synopsis "Safely access the RStudio API")
2323 "This package provides functions to access the RStudio API and provide
2324 informative error messages when it's not available.")
2325 (license license:expat)))
2327 (define-public r-devtools
2333 (uri (cran-uri "devtools" version))
2336 "1az1qf50vyhm4w6k2a6wqw3pqc8jv2iqzdhs36cg079hx9swm0mb"))))
2337 (build-system r-build-system)
2339 `(("r-digest" ,r-digest)
2340 ("r-git2r" ,r-git2r)
2342 ("r-jsonlite" ,r-jsonlite)
2343 ("r-memoise" ,r-memoise)
2344 ("r-rstudioapi" ,r-rstudioapi)
2345 ("r-whisker" ,r-whisker)
2346 ("r-withr" ,r-withr)))
2347 (home-page "https://github.com/hadley/devtools")
2348 (synopsis "Tools to make developing R packages easier")
2349 (description "The devtools package is a collection of package development
2350 tools to simplify the devolpment of R packages.")
2351 (license license:gpl2+)))
2353 (define-public r-withr
2359 (uri (cran-uri "withr" version))
2362 "12v263fj6l3ds9nrsj6q7h6zhbivp3w2jk7w9dpk1610d3nx9gf8"))))
2363 (build-system r-build-system)
2365 `(("r-lattice" ,r-lattice)))
2366 (home-page "https://github.com/jimhester/withr")
2367 (synopsis "Run code with temporarily modified global state")
2369 "This package provides a set of functions to run R code in an environment
2370 in which global state has been temporarily modified. Many of these functions
2371 were originally a part of the r-devtools package.")
2372 (license license:gpl2+)))
2374 (define-public r-hms
2381 (uri (cran-uri "hms" version))
2384 "07sh75flp15lx2b00s3nxh04xr9gk4qhlbh125qx25isf71zw6zl"))))
2385 (build-system r-build-system)
2387 `(("r-rlang" ,r-rlang)
2388 ("r-pkgconfig" ,r-pkgconfig)))
2389 (home-page "https://github.com/rstats-db/hms")
2390 (synopsis "Pretty time of day")
2392 "This package implements an S3 class for storing and formatting
2393 time-of-day values, based on the @code{difftime} class.")
2394 (license license:gpl3+)))
2396 (define-public r-readr
2402 (uri (cran-uri "readr" version))
2405 "1cvw5wdcqk88cp5fyv678mnmp66l3whcd2yh33p2qvx0168bja8s"))))
2406 (build-system r-build-system)
2408 `(("r-rcpp" ,r-rcpp)
2410 ("r-tibble" ,r-tibble)
2413 (home-page "https://github.com/hadley/readr")
2414 (synopsis "Read tabular data")
2416 "This package provides functions to read flat or tabular text files from
2417 disk (or a connection).")
2418 (license license:gpl2+)))
2420 (define-public r-plotrix
2426 (uri (cran-uri "plotrix" version))
2429 "0rw81n9p3d2i03b4pgcfj5blryc94f29bm9a4j9bnp5h8qjj6pry"))))
2430 (build-system r-build-system)
2431 (home-page "https://cran.r-project.org/web/packages/plotrix")
2432 (synopsis "Various plotting functions")
2434 "This package provides lots of plotting, various labeling, axis and color
2435 scaling functions for R.")
2436 (license license:gpl2+)))
2438 (define-public r-gridbase
2444 (uri (cran-uri "gridBase" version))
2447 "09jzw4rzwf2y5lcz7b16mb68pn0fqigv34ff7lr6w3yi9k91i1xy"))))
2448 (build-system r-build-system)
2449 (home-page "https://cran.r-project.org/web/packages/gridBase")
2450 (synopsis "Integration of base and grid graphics")
2452 "This package provides an integration of base and grid graphics for R.")
2453 (license license:gpl2+)))
2455 (define-public r-latticeextra
2457 (name "r-latticeextra")
2462 (uri (cran-uri "latticeExtra" version))
2465 "1hkyqsa7klk5glj9y1hg3rxr5qilqw8h0017zc4c3nps7lr9a1kq"))))
2466 (properties `((upstream-name . "latticeExtra")))
2467 (build-system r-build-system)
2469 `(("r-lattice" ,r-lattice)
2470 ("r-rcolorbrewer" ,r-rcolorbrewer)))
2471 (home-page "http://latticeextra.r-forge.r-project.org/")
2472 (synopsis "Extra graphical utilities based on lattice")
2474 "Building on the infrastructure provided by the lattice package, this
2475 package provides several new high-level graphics functions and methods, as
2476 well as additional utilities such as panel and axis annotation functions.")
2477 (license license:gpl2+)))
2479 (define-public r-rcpparmadillo
2481 (name "r-rcpparmadillo")
2482 (version "0.8.300.1.0")
2485 (uri (cran-uri "RcppArmadillo" version))
2488 "0p6cbnwxgzigf7n5qhqvxdr3nd3pq3c2qq6pskqz7avzf813fy83"))))
2489 (properties `((upstream-name . "RcppArmadillo")))
2490 (build-system r-build-system)
2492 `(("r-knitr" ,r-knitr))) ; needed for vignettes
2494 `(("r-rcpp" ,r-rcpp)))
2495 (home-page "https://github.com/RcppCore/RcppArmadillo")
2496 (synopsis "Rcpp integration for the Armadillo linear algebra library")
2498 "Armadillo is a templated C++ linear algebra library that aims towards a
2499 good balance between speed and ease of use. Integer, floating point and
2500 complex numbers are supported, as well as a subset of trigonometric and
2501 statistics functions. Various matrix decompositions are provided through
2502 optional integration with LAPACK and ATLAS libraries. This package includes
2503 the header files from the templated Armadillo library.")
2504 ;; Armadillo is licensed under the MPL 2.0, while RcppArmadillo (the Rcpp
2505 ;; bindings to Armadillo) is licensed under the GNU GPL version 2 or
2506 ;; later, as is the rest of 'Rcpp'.
2507 (license license:gpl2+)))
2509 (define-public r-bitops
2515 (uri (cran-uri "bitops" version))
2518 "176nr5wpnkavn5z0yy9f7d47l37ndnn2w3gv854xav8nnybi6wwv"))))
2519 (build-system r-build-system)
2520 (home-page "https://cran.r-project.org/web/packages/bitops")
2521 (synopsis "Bitwise operations")
2523 "This package provides functions for bitwise operations on integer
2525 (license license:gpl2+)))
2527 (define-public r-catools
2533 (uri (cran-uri "caTools" version))
2536 "1x4szsn2qmbzpyjfdaiz2q7jwhap2gky9wq0riah74q0pzz76ank"))))
2537 (properties `((upstream-name . "caTools")))
2538 (build-system r-build-system)
2540 `(("r-bitops" ,r-bitops)))
2541 (home-page "https://cran.r-project.org/web/packages/caTools")
2542 (synopsis "Various tools including functions for moving window statistics")
2544 "This package contains several basic utility functions including:
2545 moving (rolling, running) window statistic functions, read/write for GIF and
2546 ENVI binary files, fast calculation of AUC, LogitBoost classifier, base64
2547 encoder/decoder, round-off-error-free sum and cumsum, etc.")
2548 (license license:gpl3+)))
2550 (define-public r-rprojroot
2552 (name "r-rprojroot")
2557 (uri (cran-uri "rprojroot" version))
2560 "1jigr2jh3hzy35h94im52yq81lyikw7nfvmbxij84a1b9c32r332"))))
2561 (build-system r-build-system)
2563 `(("r-backports" ,r-backports)))
2564 (home-page "https://github.com/krlmlr/rprojroot")
2565 (synopsis "Finding files in project subdirectories")
2567 "This package helps accessing files relative to a project root. It
2568 provides helpers for robust, reliable and flexible paths to files below a
2569 project root. The root of a project is defined as a directory that matches a
2570 certain criterion, e.g., it contains a certain regular file.")
2571 (license license:gpl3)))
2573 (define-public r-rmarkdown
2575 (name "r-rmarkdown")
2580 (uri (cran-uri "rmarkdown" version))
2583 "0q1y1qx87xp6vf9h7mfl77rqhmd01xl53l9ap9qj99bfvpabb572"))))
2584 (properties `((upstream-name . "rmarkdown")))
2585 (build-system r-build-system)
2587 `(("r-base64enc" ,r-base64enc)
2588 ("r-evaluate" ,r-evaluate)
2589 ("r-htmltools" ,r-htmltools)
2590 ("r-jsonlite" ,r-jsonlite)
2591 ("r-knitr" ,r-knitr)
2593 ("r-rprojroot" ,r-rprojroot)
2594 ("r-stringr" ,r-stringr)
2596 ("ghc-pandoc" ,ghc-pandoc)))
2597 (home-page "http://rmarkdown.rstudio.com")
2598 (synopsis "Convert R Markdown documents into a variety of formats")
2600 "This package provides tools to convert R Markdown documents into a
2601 variety of formats.")
2602 (license license:gpl3+)))
2604 (define-public r-gtable
2610 (uri (cran-uri "gtable" version))
2613 "0vz7073m0a2q12qzzihrfh5c2kx5jqi5l7z470fxmwqghdllh7l0"))))
2614 (properties `((upstream-name . "gtable")))
2615 (build-system r-build-system)
2616 (home-page "https://cran.r-project.org/web/packages/gtable")
2617 (synopsis "R library to arrange grobs in tables")
2619 "Gtable is a collection of tools to make it easier to work with
2620 \"tables\" of grobs.")
2621 (license license:gpl2+)))
2623 (define-public r-gridextra
2625 (name "r-gridextra")
2629 (uri (cran-uri "gridExtra" version))
2632 "0fwfk3cdwxxim7nd55pn7m31bcaqj48y06j7an2k1v1pybk0rdl1"))))
2633 (properties `((upstream-name . "gridExtra")))
2634 (build-system r-build-system)
2636 `(("r-gtable" ,r-gtable)))
2638 `(("r-knitr" ,r-knitr))) ;for building vignettes
2639 (home-page "https://github.com/baptiste/gridextra")
2640 (synopsis "Miscellaneous functions for \"Grid\" graphics")
2642 "This package provides a number of user-level functions to work with
2643 @code{grid} graphics, notably to arrange multiple grid-based plots on a page,
2645 (license license:gpl2+)))
2647 (define-public r-pkgconfig
2649 (name "r-pkgconfig")
2653 (uri (cran-uri "pkgconfig" version))
2656 "0h2sp93fqqjbfqgq82a3i94ybnndx6ghaal8pbf99firnsjb40mb"))))
2657 (build-system r-build-system)
2658 (home-page "https://github.com/gaborcsardi/pkgconfig")
2659 (synopsis "Private configuration for R packages")
2660 (description "This package provides the functionality to set configuration
2661 options on a per-package basis. Options set by a given package only apply to
2662 that package, other packages are unaffected.")
2663 (license license:expat)))
2665 (define-public r-blob
2671 (uri (cran-uri "blob" version))
2674 "05pazzcyz3c3vd2l70zq9cf172cgjff4dnf419zigfnxycyn1mhn"))))
2675 (build-system r-build-system)
2677 `(("r-tibble" ,r-tibble)))
2678 (home-page "https://github.com/hadley/blob")
2679 (synopsis "Simple S3 Class for representing vectors of binary data")
2680 (description "Raw vectors in R are useful for storing a single binary
2681 object. What if you want to put a vector of them in a data frame? The blob
2682 package provides the blob object, a list of raw vectors, suitable for use as
2683 a column in data frame.")
2684 (license license:gpl3+)))
2686 (define-public r-rsqlite
2692 (uri (cran-uri "RSQLite" version))
2695 "1xpg1i1jkzkzv44k512k90c2vvl960pl2d4a3spwcha6yclyc3vz"))))
2696 (properties `((upstream-name . "RSQLite")))
2697 (build-system r-build-system)
2701 ("r-memoise" ,r-memoise)
2702 ("r-plogr" ,r-plogr)
2704 ("r-bit64" ,r-bit64)
2706 ("r-pkgconfig" ,r-pkgconfig)))
2707 (home-page "https://github.com/rstats-db/RSQLite")
2708 (synopsis "SQLite interface for R")
2710 "This package embeds the SQLite database engine in R and provides an
2711 interface compliant with the DBI package. The source for the SQLite
2712 engine (version 3.8.8.2) is included.")
2713 (license license:lgpl2.0+)))
2715 (define-public r-rcurl
2718 (version "1.95-0.1.2")
2721 (uri (string-append "https://www.bioconductor.org/packages/"
2722 "release/extra/src/"
2723 "contrib/RCurl_" version ".tar.gz"))
2726 "0l7qi45jxlf898n0jazabnam1yyczvqfdknd00bdirhhiplpd1sc"))))
2727 (properties `((upstream-name . "RCurl")))
2728 (build-system r-build-system)
2730 `(("libcurl" ,curl)))
2732 `(("r-bitops" ,r-bitops)))
2733 (home-page "http://www.omegahat.org/RCurl")
2734 (synopsis "General network client interface for R")
2736 "The package allows one to compose general HTTP requests and provides
2737 convenient functions to fetch URIs, GET and POST forms, etc. and process the
2738 results returned by the Web server. This provides a great deal of control
2739 over the HTTP/FTP/... connection and the form of the request while providing a
2740 higher-level interface than is available just using R socket connections.
2741 Additionally, the underlying implementation is robust and extensive,
2742 supporting FTP/FTPS/TFTP (uploads and downloads), SSL/HTTPS, telnet, dict,
2743 ldap, and also supports cookies, redirects, authentication, etc.")
2744 (license license:bsd-3)))
2746 (define-public r-xml
2749 (version "3.98-1.9")
2752 (uri (cran-uri "XML" version))
2755 "1hzkdkgs0nzmfg9wm7kyh1j9i0i2g7925whzlihqvg9grdlh3dx3"))))
2757 `((upstream-name . "XML")))
2758 (build-system r-build-system)
2760 `(("libxml2" ,libxml2)))
2761 (home-page "http://www.omegahat.org/RSXML")
2762 (synopsis "Tools for parsing and generating XML within R")
2764 "Many approaches for both reading and creating XML (and HTML)
2765 documents (including DTDs), both local and accessible via HTTP or FTP. Also
2766 offers access to an XPath \"interpreter\".")
2767 (license license:bsd-2)))
2769 (define-public r-xnomial
2774 (origin (method url-fetch)
2775 (uri (cran-uri "XNomial" version))
2778 "1mwx302576rmsjllbq2clfxilm3hkyp5bw0wmwqbn0kgv5wpy8z6"))))
2779 (properties (quasiquote ((upstream-name . "XNomial"))))
2780 (build-system r-build-system)
2781 (home-page "https://cran.r-project.org/web/packages/XNomial")
2782 (synopsis "Goodness-of-Fit test for multinomial data")
2784 "This package provides an exact Goodness-of-Fit test for
2785 multinomial data with fixed probabilities. It can be used to
2786 determine whether a set of counts fits a given expected ratio. To see
2787 whether a set of observed counts fits an expectation, one can examine
2788 all possible outcomes with @code{xmulti()} or a random sample of them
2789 with @code{xmonte()} and find the probability of an observation
2790 deviating from the expectation by at least as much as the observed.
2791 As a measure of deviation from the expected, one can use the
2792 log-likelihood ratio, the multinomial probability, or the classic
2793 chi-square statistic. A histogram of the test statistic can also be
2794 plotted and compared with the asymptotic curve.")
2795 (license (list license:gpl2+ license:gpl3+))))
2797 (define-public r-lambda-r
2803 (uri (cran-uri "lambda.r" version))
2806 "0vql32np716dpd0kjn7s7wgawd02ysgp2a5il4kb19nlw661ii3x"))))
2807 (properties `((upstream-name . "lambda.r")))
2808 (build-system r-build-system)
2809 (home-page "https://cran.r-project.org/web/packages/lambda.r")
2810 (synopsis "Functional programming extension for R")
2812 "This package provides a language extension to efficiently write
2813 functional programs in R. Syntax extensions include multi-part function
2814 definitions, pattern matching, guard statements, built-in (optional) type
2816 (license license:lgpl3+)))
2818 (define-public r-futile-options
2820 (name "r-futile-options")
2824 (uri (cran-uri "futile.options" version))
2827 "1hp82h6xqq5cck67h7lpf22n3j7mg3v1mla5y5ivnzrrb7iyr17f"))))
2829 `((upstream-name . "futile.options")))
2830 (build-system r-build-system)
2831 (home-page "https://cran.r-project.org/web/packages/futile.options")
2832 (synopsis "Options management framework")
2834 "The futile.options subsystem provides an easy user-defined options
2835 management system that is properly scoped. This means that options created
2836 via @code{futile.options} are fully self-contained and will not collide with
2837 options defined in other packages.")
2838 (license license:lgpl3+)))
2840 (define-public r-futile-logger
2842 (name "r-futile-logger")
2846 (uri (cran-uri "futile.logger" version))
2849 "1r3nayk0z9n1svbf8640vw90dal5q07nkn0gv4bnva3pbzb352sy"))))
2850 (properties `((upstream-name . "futile.logger")))
2851 (build-system r-build-system)
2853 `(("r-futile-options" ,r-futile-options)
2854 ("r-lambda-r" ,r-lambda-r)))
2855 (home-page "https://cran.r-project.org/web/packages/futile.logger")
2856 (synopsis "Logging utility for R")
2858 "This package provides a simple yet powerful logging utility. Based
2859 loosely on log4j, futile.logger takes advantage of R idioms to make logging a
2860 convenient and easy to use replacement for @code{cat} and @code{print}
2862 (license license:lgpl3+)))
2864 (define-public r-segmented
2866 (name "r-segmented")
2871 (uri (cran-uri "segmented" version))
2874 "0nrik5fyq59hwiwjcpbi4p5yfavgfjq6wyrynhkrbm4k6v1g1wlq"))))
2875 (build-system r-build-system)
2876 (home-page "https://cran.r-project.org/web/packages/segmented")
2877 (synopsis "Regression models with breakpoints estimation")
2879 "Given a regression model, segmented updates the model by adding one or
2880 more segmented (i.e., piecewise-linear) relationships. Several variables with
2881 multiple breakpoints are allowed.")
2882 (license (list license:gpl2+ license:gpl3+))))
2884 (define-public r-snow
2890 (uri (cran-uri "snow" version))
2893 "1mxbrkpnmq32x4wd0194d541661yvfrrjlr3lsf7qq53ms3h21zf"))))
2894 (build-system r-build-system)
2895 (home-page "https://cran.r-project.org/web/packages/snow")
2896 (synopsis "Support for simple parallel computing in R")
2898 "The snow package provides support for simple parallel computing on a
2899 network of workstations using R. A master R process calls @code{makeCluster}
2900 to start a cluster of worker processes; the master process then uses functions
2901 such as @code{clusterCall} and @code{clusterApply} to execute R code on the
2902 worker processes and collect and return the results on the master.")
2903 (license (list license:gpl2+ license:gpl3+))))
2905 (define-public r-sparsem
2911 (uri (cran-uri "SparseM" version))
2914 "0p6ljma2h12cq1xmy0cxb48ih8dhxxbnwkqzvx3cckxf2kprycm9"))))
2916 `((upstream-name . "SparseM")))
2918 `(("gfortran" ,gfortran)))
2919 (build-system r-build-system)
2920 (home-page "http://www.econ.uiuc.edu/~roger/research/sparse/sparse.html")
2921 (synopsis "Sparse linear algebra")
2923 "This package provides some basic linear algebra functionality for sparse
2924 matrices. It includes Cholesky decomposition and backsolving as well as
2925 standard R subsetting and Kronecker products.")
2926 (license license:gpl2+)))
2928 (define-public r-iterators
2930 (name "r-iterators")
2935 (uri (cran-uri "iterators" version))
2938 "16sycjq912ix52fjxjhcwiaqr0yj1v5iqmrvjljd3z857031w06y"))))
2939 (build-system r-build-system)
2940 (home-page "https://cran.r-project.org/web/packages/iterators")
2941 (synopsis "Iterator construct for R")
2943 "This package provides support for iterators, which allow a programmer to
2944 traverse through all the elements of a vector, list, or other collection of
2946 (license license:asl2.0)))
2948 (define-public r-foreach
2955 (uri (cran-uri "foreach" version))
2958 "0j2yj0rn0d5nbzz9nq5rqqgnxhp9pbd92q4klsarl2xpsn8119y0"))))
2959 (build-system r-build-system)
2961 `(("r-codetools" ,r-codetools)
2962 ("r-iterators" ,r-iterators)))
2963 (home-page "https://cran.r-project.org/web/packages/foreach")
2964 (synopsis "Foreach looping construct for R")
2966 "This package provides support for the @code{foreach} looping construct.
2967 @code{foreach} is an idiom that allows for iterating over elements in a
2968 collection, without the use of an explicit loop counter. This package in
2969 particular is intended to be used for its return value, rather than for its
2970 side effects. In that sense, it is similar to the standard @code{lapply}
2971 function, but doesn't require the evaluation of a function. Using
2972 @code{foreach} without side effects also facilitates executing the loop in
2974 (license license:asl2.0)))
2976 (define-public r-doparallel
2978 (name "r-doparallel")
2983 (uri (cran-uri "doParallel" version))
2986 "0sppgxk3d8mfsrb3cjdyn0mv0s4i7pcy8g8c3cjzbr6k8vmx5jsc"))))
2987 (properties `((upstream-name . "doParallel")))
2988 (build-system r-build-system)
2990 `(("r-foreach" ,r-foreach)
2991 ("r-iterators" ,r-iterators)))
2992 (home-page "https://cran.r-project.org/web/packages/doParallel")
2993 (synopsis "Foreach parallel adaptor for the 'parallel' package")
2995 "This package provides a parallel backend for the @code{%dopar%} function
2996 using the parallel package.")
2997 (license license:gpl2+)))
2999 (define-public r-domc
3006 (uri (cran-uri "doMC" version))
3009 "1vfrykvfvsyq12mypd266867ml1dcwc3rj5k9c3wrn5bddcm88kr"))))
3010 (properties `((upstream-name . "doMC")))
3011 (build-system r-build-system)
3013 `(("r-foreach" ,r-foreach)
3014 ("r-iterators" ,r-iterators)))
3015 (home-page "https://cran.r-project.org/web/packages/doMC")
3016 (synopsis "Foreach parallel adaptor for the 'parallel' package")
3018 "This package provides a parallel backend for the @code{%dopar%} function
3019 using the multicore functionality of the parallel package.")
3020 (license license:gpl2+)))
3028 (uri (cran-uri "DT" version))
3031 "1g86p0jcjqi2ph5rhm45jkzibsa6yfcj8n5cg3giy90sqgjzkdx1"))))
3033 `((upstream-name . "DT")))
3034 (build-system r-build-system)
3036 `(("r-htmltools" ,r-htmltools)
3037 ("r-htmlwidgets" ,r-htmlwidgets)
3038 ("r-magrittr" ,r-magrittr)))
3039 (home-page "http://rstudio.github.io/DT")
3040 (synopsis "R wrapper of the DataTables JavaScript library")
3042 "This package allows for data objects in R to be rendered as HTML tables
3043 using the JavaScript library 'DataTables' (typically via R Markdown or Shiny).
3044 The 'DataTables' library has been included in this R package.")
3045 ;; The DT package as a whole is distributed under GPLv3. The DT package
3046 ;; inludes other software components under different licenses:
3048 ;; * Expat: jQuery, jquery.highlight.js, DataTables
3049 ;; * ASL2.0: selectize.js
3050 ;; * WTFPL: noUiSlider
3051 (license (list license:gpl3
3054 (license:non-copyleft "http://www.wtfpl.net/txt/copying/")))))
3056 (define-public r-base64enc
3058 (name "r-base64enc")
3062 (uri (cran-uri "base64enc" version))
3065 "13b89fhg1nx7zds82a0biz847ixphg9byf5zl2cw9kab6s56v1bd"))))
3066 (build-system r-build-system)
3067 (home-page "http://www.rforge.net/base64enc")
3068 (synopsis "Tools for Base64 encoding")
3070 "This package provides tools for handling Base64 encoding. It is more
3071 flexible than the orphaned \"base64\" package.")
3072 (license license:gpl2+)))
3074 (define-public r-irlba
3081 (uri (cran-uri "irlba" version))
3084 "1dclzzkm75sbbqda5scj2hlqnw2sksgxbiqagxs4359fwfszi0k0"))))
3085 (build-system r-build-system)
3087 `(("r-matrix" ,r-matrix)))
3088 (home-page "https://cran.r-project.org/web/packages/irlba")
3089 (synopsis "Methods for eigendecomposition of large matrices")
3091 "This package provides fast and memory efficient methods for truncated
3092 singular and eigenvalue decompositions, as well as for principal component
3093 analysis of large sparse or dense matrices.")
3094 (license (list license:gpl2+ license:gpl3+))))
3096 (define-public r-glmnet
3103 (uri (cran-uri "glmnet" version))
3106 "1zdqp6wnqxzp5qn2ky47phbkrxv3cpgbwmdp896h3xxjvp58sa7k"))))
3107 (build-system r-build-system)
3109 `(("gfortran" ,gfortran)))
3111 `(("r-foreach" ,r-foreach)
3112 ("r-matrix" ,r-matrix)))
3113 (home-page "http://www.jstatsoft.org/v33/i01")
3114 (synopsis "Lasso and elastic-net regularized generalized linear models")
3116 "The glmnet package provides efficient procedures for fitting the entire
3117 lasso or elastic-net regularization path for linear and Poisson regression, as
3118 well as logistic, multinomial, Cox, multiple-response Gaussian and grouped
3119 multinomial models. The algorithm uses cyclical coordinate descent in a
3120 path-wise fashion.")
3121 (license license:gpl2+)))
3123 (define-public r-pkgmaker
3130 (uri (cran-uri "pkgmaker" version))
3133 "0vrqnd3kg6liqvpbd969jjsdx0f0rvmmxgdbwwrp6xfmdg0pib8r"))))
3134 (build-system r-build-system)
3136 `(("r-codetools" ,r-codetools)
3137 ("r-digest" ,r-digest)
3138 ("r-registry" ,r-registry)
3139 ("r-stringr" ,r-stringr)
3140 ("r-xtable" ,r-xtable)))
3141 (home-page "https://renozao.github.io/pkgmaker")
3142 (synopsis "Package development utilities")
3144 "This package provides some low-level utilities to use for R package
3145 development. It currently provides managers for multiple package specific
3146 options and registries, vignette, unit test and bibtex related utilities.")
3147 (license license:gpl2+)))
3149 (define-public r-registry
3156 (uri (cran-uri "registry" version))
3159 "1yqfl1g6vsl28zn8brzc39659k8lqsmfms7900j7p64ilydyb2sx"))))
3160 (build-system r-build-system)
3161 (home-page "https://cran.r-project.org/web/packages/registry")
3162 (synopsis "Infrastructure for R package registries")
3164 "This package provides a generic infrastructure for creating and using R
3165 package registries.")
3166 (license license:gpl2+)))
3168 (define-public r-rngtools
3175 (uri (cran-uri "rngtools" version))
3178 "1fcgfqrrb48z37xgy8sffx91p9irp39yqzxv7nqp1x2hnwsrh097"))))
3179 (build-system r-build-system)
3181 `(("r-digest" ,r-digest)
3182 ("r-pkgmaker" ,r-pkgmaker)
3183 ("r-stringr" ,r-stringr)))
3184 (home-page "https://renozao.github.io/rngtools")
3185 (synopsis "Utility functions for working with random number generators")
3187 "This package contains a set of functions for working with Random Number
3188 Generators (RNGs). In particular, it defines a generic S4 framework for
3189 getting/setting the current RNG, or RNG data that are embedded into objects
3190 for reproducibility. Notably, convenient default methods greatly facilitate
3191 the way current RNG settings can be changed.")
3192 (license license:gpl3+)))
3194 (define-public r-rtsne
3201 (uri (cran-uri "Rtsne" version))
3204 "17crbdi80q4g2pwp9v7j3bdaznk96qlrqx01zvj3wwqippizyfqw"))))
3205 (properties `((upstream-name . "Rtsne")))
3206 (build-system r-build-system)
3208 `(("r-rcpp" ,r-rcpp)))
3209 (home-page "https://github.com/jkrijthe/Rtsne")
3210 (synopsis "T-distributed stochastic neighbor embedding")
3212 "This package provides an R wrapper around the fast T-distributed
3213 Stochastic Neighbor Embedding using a Barnes-Hut implementation.")
3214 ;; The declared license for this package is BSD-3, but it also includes
3215 ;; code licensed under BSD-4.
3216 (license (list license:bsd-3 license:bsd-4))))
3218 (define-public r-e1071
3225 (uri (cran-uri "e1071" version))
3228 "08n6i26nfckjpxjkzi8phhanc3ahsrirkv5rz38y2jcv7ds031pn"))))
3229 (build-system r-build-system)
3231 `(("r-class" ,r-class)))
3232 (home-page "https://cran.r-project.org/web/packages/e1071")
3233 (synopsis "Miscellaneous functions for probability theory")
3235 "This package provides functions for latent class analysis, short time
3236 Fourier transform, fuzzy clustering, support vector machines, shortest path
3237 computation, bagged clustering, naive Bayes classifier, and more.")
3238 (license license:gpl2+)))
3240 (define-public r-bigmemory-sri
3242 (name "r-bigmemory-sri")
3247 (uri (cran-uri "bigmemory.sri" version))
3249 (base32 "0mg14ilwdkd64q2ri9jdwnk7mp55dqim7xfifrs65sdsv1934h2m"))))
3251 `((upstream-name . "bigmemory.sri")))
3252 (build-system r-build-system)
3253 (home-page "https://cran.r-project.org/web/packages/bigmemory.sri")
3254 (synopsis "Shared resource interface for the bigmemory package")
3255 (description "This package provides a shared resource interface for the
3256 bigmemory and synchronicity packages.")
3257 ;; Users can choose either LGPLv3 or ASL2.0.
3258 (license (list license:lgpl3 license:asl2.0))))
3260 (define-public r-synchronicity
3262 (name "r-synchronicity")
3267 (uri (cran-uri "synchronicity" version))
3270 "0d9skpwmsnkn4xb3f2kgyyv8bhdi0r9p1kj3cvi0s92fjjnpi00c"))))
3271 (build-system r-build-system)
3274 ("r-bigmemory-sri" ,r-bigmemory-sri)
3275 ("r-rcpp" ,r-rcpp)))
3276 (home-page "http://www.bigmemory.org")
3277 (synopsis "Boost mutex functionality in R")
3278 (description "This package provides support for synchronization
3279 via mutexes and may eventually support interprocess communication and
3281 ;; Users can choose either LGPLv3 or ASL2.0.
3282 (license (list license:lgpl3 license:asl2.0))))
3284 (define-public r-bigmemory
3286 (name "r-bigmemory")
3291 (uri (cran-uri "bigmemory" version))
3294 "0wv0p746zz5a6r1yd0fgpj2kfcyzk2f4rxqz92p6lp9jzakv4lfs"))))
3295 (build-system r-build-system)
3299 ("r-bigmemory-sri" ,r-bigmemory-sri)))
3300 (home-page "http://www.bigmemory.org")
3301 (synopsis "Manage large matrices with shared memory or memory-mapped files")
3302 (description "This package provides methods to create, store, access, and
3303 manipulate large matrices. Matrices are allocated to shared memory and may use
3304 memory-mapped files.")
3305 ;; Users can choose either LGPLv3 or ASL2.0.
3306 (license (list license:lgpl3 license:asl2.0))))
3308 (define-public r-nmf
3315 (uri (cran-uri "NMF" version))
3318 "0mmh9bz0zjwd8h9jplz4rq3g94npaqj8s4px51vcv47csssd9k6z"))))
3319 (properties `((upstream-name . "NMF")))
3320 (build-system r-build-system)
3322 `(("r-cluster" ,r-cluster)
3323 ("r-bigmemory" ,r-bigmemory)
3324 ("r-synchronicity" ,r-synchronicity)
3325 ("r-colorspace" ,r-colorspace)
3326 ("r-digest" ,r-digest)
3327 ("r-doparallel" ,r-doparallel)
3328 ("r-foreach" ,r-foreach)
3329 ("r-ggplot2" ,r-ggplot2)
3330 ("r-gridbase" ,r-gridbase)
3331 ("r-pkgmaker" ,r-pkgmaker)
3332 ("r-rcolorbrewer" ,r-rcolorbrewer)
3333 ("r-registry" ,r-registry)
3334 ("r-reshape2" ,r-reshape2)
3335 ("r-rngtools" ,r-rngtools)
3336 ("r-stringr" ,r-stringr)))
3337 (home-page "http://renozao.github.io/NMF")
3338 (synopsis "Algorithms and framework for nonnegative matrix factorization")
3340 "This package provides a framework to perform Non-negative Matrix
3341 Factorization (NMF). The package implements a set of already published
3342 algorithms and seeding methods, and provides a framework to test, develop and
3343 plug new or custom algorithms. Most of the built-in algorithms have been
3344 optimized in C++, and the main interface function provides an easy way of
3345 performing parallel computations on multicore machines.")
3346 (license license:gpl2+)))
3348 (define-public r-r-methodss3
3350 (name "r-r-methodss3")
3354 (uri (cran-uri "R.methodsS3" version))
3357 "11z6v2i7jl647wxi9p5z66yvfnnqv6s7fxqmz7w2gkb6j8wl1f24"))))
3358 (properties `((upstream-name . "R.methodsS3")))
3359 (build-system r-build-system)
3360 (home-page "https://cran.r-project.org/web/packages/R.methodsS3")
3361 (synopsis "S3 methods simplified")
3363 "This package provides methods that simplify the setup of S3 generic
3364 functions and S3 methods. Major effort has been made in making definition of
3365 methods as simple as possible with a minimum of maintenance for package
3366 developers. For example, generic functions are created automatically, if
3367 missing, and naming conflict are automatically solved, if possible. The
3368 method @code{setMethodS3()} is a good start for those who in the future may
3369 want to migrate to S4.")
3370 (license license:lgpl2.1+)))
3372 (define-public r-r-oo
3378 (uri (cran-uri "R.oo" version))
3381 "0723gxjazgqq7v3lwnl7axw3brzcnizvhbd71ijkkv8mz31fwp34"))))
3382 (properties `((upstream-name . "R.oo")))
3383 (build-system r-build-system)
3385 `(("r-r-methodss3" ,r-r-methodss3)))
3386 (home-page "https://github.com/HenrikBengtsson/R.oo")
3387 (synopsis "R object-oriented programming with or without references")
3389 "This package provides methods and classes for object-oriented
3390 programming in R with or without references. Large effort has been made on
3391 making definition of methods as simple as possible with a minimum of
3392 maintenance for package developers.")
3393 (license license:lgpl2.1+)))
3395 (define-public r-r-utils
3401 (uri (cran-uri "R.utils" version))
3404 "03j7hrs03kyj9qrjxyp5kqv4lpqqpk6xwbkzx6j15d8928yrjr2x"))))
3405 (properties `((upstream-name . "R.utils")))
3406 (build-system r-build-system)
3408 `(("r-r-methodss3" ,r-r-methodss3)
3409 ("r-r-oo" ,r-r-oo)))
3410 (home-page "https://github.com/HenrikBengtsson/R.utils")
3411 (synopsis "Various programming utilities")
3413 "This package provides utility functions useful when programming and
3414 developing R packages.")
3415 (license license:lgpl2.1+)))
3417 (define-public r-r-cache
3423 (uri (cran-uri "R.cache" version))
3426 "006x52w9r8phw5hgqmyp0bz8z42vn8p5yibibnzi1sfa1xlw8iyx"))))
3427 (properties `((upstream-name . "R.cache")))
3428 (build-system r-build-system)
3430 `(("r-digest" ,r-digest)
3431 ("r-r-methodss3" ,r-r-methodss3)
3433 ("r-r-utils" ,r-r-utils)))
3434 (home-page "https://github.com/HenrikBengtsson/R.cache")
3435 (synopsis "Light-weight caching of objects and results")
3437 "This package provides methods for caching or memoization of objects and
3438 results. With this package, any R object can be cached in a key-value storage
3439 where the key can be an arbitrary set of R objects. The cache memory is
3440 persistent (on the file system).")
3441 (license license:lgpl2.1+)))
3443 (define-public r-r-rsp
3449 (uri (cran-uri "R.rsp" version))
3452 "01l430avj5ggmdsla2kiriix72g0dlzx9klniq321bs0za808v3c"))))
3453 (properties `((upstream-name . "R.rsp")))
3454 (build-system r-build-system)
3456 `(("r-r-cache" ,r-r-cache)
3457 ("r-r-methodss3" ,r-r-methodss3)
3459 ("r-r-utils" ,r-r-utils)))
3460 (home-page "https://github.com/HenrikBengtsson/R.rsp")
3461 (synopsis "Dynamic generation of scientific reports")
3463 "The RSP markup language provides a powerful markup for controlling the
3464 content and output of LaTeX, HTML, Markdown, AsciiDoc, Sweave and knitr
3465 documents (and more), e.g. @code{Today's date is <%=Sys.Date()%>}. Contrary
3466 to many other literate programming languages, with RSP it is straightforward
3467 to loop over mixtures of code and text sections, e.g. in month-by-month
3468 summaries. RSP has also several preprocessing directives for incorporating
3469 static and dynamic contents of external files (local or online) among other
3470 things. RSP is ideal for self-contained scientific reports and R package
3472 (license license:lgpl2.1+)))
3474 (define-public r-mvtnorm
3480 (uri (cran-uri "mvtnorm" version))
3483 "0i74s9dl4jf1gln6agra8h38qn9ifd5v0gi13caj1da5nrbmn0aa"))))
3484 (build-system r-build-system)
3486 `(("gfortran" ,gfortran)))
3487 (home-page "http://mvtnorm.R-forge.R-project.org")
3488 (synopsis "Package for multivariate normal and t-distributions")
3489 (description "This package can compute multivariate normal and
3490 t-probabilities, quantiles, random deviates and densities.")
3491 (license license:gpl2)))
3493 (define-public r-matrixstats
3495 (name "r-matrixstats")
3499 (uri (cran-uri "matrixStats" version))
3502 "19fjf19cr0p3j9pj17myz39zpi5bh7ci72db3la9my09n6k6mnir"))))
3503 (properties `((upstream-name . "matrixStats")))
3504 (build-system r-build-system)
3506 `(("r-r-rsp" ,r-r-rsp))) ;used to build vignettes
3507 (home-page "https://github.com/HenrikBengtsson/matrixStats")
3508 (synopsis "Methods applying to vectors and matrix rows and columns")
3510 "This package provides methods operating on rows and columns of matrices,
3511 e.g. @code{rowMedians()}, @code{rowRanks()}, and @code{rowSds()}. There are
3512 also some vector-based methods, e.g. @code{binMeans()}, @code{madDiff()} and
3513 @code{weightedMedians()}. All methods have been optimized for speed and
3515 (license license:artistic2.0)))
3517 (define-public r-viridis
3523 (uri (cran-uri "viridis" version))
3526 "03mha2935k1mw7mjjkq7mrx185hl0m3vq3967iiwbknpivbdxllk"))))
3527 (build-system r-build-system)
3529 `(("r-ggplot2" ,r-ggplot2)
3530 ("r-gridextra" ,r-gridextra)
3531 ("r-viridislite" ,r-viridislite)))
3532 (home-page "https://github.com/sjmgarnier/viridis")
3533 (synopsis "Matplotlib default color map")
3535 "This package is a port of the new @url{matplotlib,
3536 http://matplotlib.org/} color maps (@code{viridis}--the default--,
3537 @code{magma}, @code{plasma}, and @code{inferno}) to R. These color maps are
3538 designed in such a way that they will analytically be perfectly
3539 perceptually-uniform, both in regular form and also when converted to
3540 black-and-white. They are also designed to be perceived by readers with the
3541 most common form of color blindness.")
3542 (license license:x11)))
3544 (define-public r-viridislite
3546 (name "r-viridislite")
3551 (uri (cran-uri "viridisLite" version))
3554 "1546h44ng4dxs130jkh6lkh990hmp90m1w45sq5p47n546gr0k9d"))))
3555 (properties `((upstream-name . "viridisLite")))
3556 (build-system r-build-system)
3557 (home-page "https://github.com/sjmgarnier/viridisLite")
3558 (synopsis "Default color maps from matplotlib")
3560 "This package is a port of the new @code{matplotlib} color maps ('viridis',
3561 'magma', 'plasma' and 'inferno') to R. matplotlib is a popular plotting
3562 library for Python. These color maps are designed in such a way that they
3563 will analytically be perfectly perceptually-uniform, both in regular form and
3564 also when converted to black-and-white. They are also designed to be
3565 perceived by readers with the most common form of color blindness. This is
3566 the 'lite' version of the more complete @code{viridis} package.")
3567 (license license:expat)))
3569 (define-public r-tidyselect
3571 (name "r-tidyselect")
3576 (uri (cran-uri "tidyselect" version))
3579 "0b0w30yq30c7bwpaghp3hp0nncqwcmvrra9j58fhx9jihay3l68c"))))
3580 (build-system r-build-system)
3582 `(("r-glue" ,r-glue)
3583 ("r-purrr" ,r-purrr)
3585 ("r-rlang" ,r-rlang)))
3586 (home-page "https://cran.r-project.org/web/packages/tidyselect")
3587 (synopsis "Select from a set of strings")
3589 "This package provides a backend for the selecting functions of the
3590 tidyverse. It makes it easy to implement select-like functions in your own
3591 packages in a way that is consistent with other tidyverse interfaces for
3593 (license license:gpl3)))
3595 (define-public r-tidyr
3602 (uri (cran-uri "tidyr" version))
3605 "1700fry2b3d3ksj7x2f09xl6agjrdnx1rqsc1r8gvzsp5cpflb06"))))
3606 (build-system r-build-system)
3608 `(("r-dplyr" ,r-dplyr)
3609 ("r-magrittr" ,r-magrittr)
3611 ("r-purrr" ,r-purrr)
3612 ("r-rlang" ,r-rlang)
3613 ("r-tidyselect" ,r-tidyselect)
3615 ("r-stringi" ,r-stringi)
3616 ("r-tibble" ,r-tibble)))
3617 (home-page "https://github.com/hadley/tidyr")
3618 (synopsis "Tidy data with `spread()` and `gather()` functions")
3620 "tidyr is a reframing of the reshape2 package designed to accompany the
3621 tidy data framework, and to work hand-in-hand with magrittr and dplyr to build
3622 a solid pipeline for data analysis. It is designed specifically for tidying
3623 data, not the general reshaping that reshape2 does, or the general aggregation
3624 that reshape did. In particular, built-in methods only work for data frames,
3625 and tidyr provides no margins or aggregation.")
3626 (license license:expat)))
3628 (define-public r-hexbin
3631 ;; The package tarball was updated in place, resulting in a change in the
3632 ;; hash value. We decided to bump the version to 1.27.1-1 instead of
3633 ;; keeping the version at upstream's 1.27.1.
3634 (version "1.27.1-1")
3638 (uri (cran-uri "hexbin" "1.27.1"))
3641 "025d609z1nyy684hwvp34b9mjzkgvild7fvfr95f941dmsikan87"))))
3642 (build-system r-build-system)
3644 `(("r-lattice" ,r-lattice)))
3646 `(("gfortran" ,gfortran)))
3647 (home-page "https://github.com/edzer/hexbin")
3648 (synopsis "Hexagonal binning routines")
3650 "This package provides binning and plotting functions for hexagonal bins.
3651 It uses and relies on grid graphics and formal (S4) classes and methods.")
3652 (license license:gpl2+)))
3654 (define-public r-purrr
3661 (uri (cran-uri "purrr" version))
3664 "0wgbnbrqncjpggg8f9bdpcd1gy351s5f0az5k8lc55cvs9lhz3gd"))))
3665 (build-system r-build-system)
3667 `(("r-tibble" ,r-tibble)
3668 ("r-magrittr" ,r-magrittr)
3669 ("r-rlang" ,r-rlang)))
3670 (home-page "https://github.com/hadley/purrr")
3671 (synopsis "Functional programming tools")
3673 "This package completes R's functional programming tools with missing
3674 features present in other programming languages.")
3675 (license license:gpl3+)))
3677 (define-public r-plotly
3683 (uri (cran-uri "plotly" version))
3686 "0wj9lw7w28z8w9ip9vadv6sydjhqyg65kfiai9m3bndzz50b1m3w"))))
3687 (build-system r-build-system)
3689 `(("r-base64enc" ,r-base64enc)
3690 ("r-crosstalk" ,r-crosstalk)
3691 ("r-digest" ,r-digest)
3692 ("r-data-table" ,r-data-table)
3693 ("r-dplyr" ,r-dplyr)
3694 ("r-ggplot2" ,r-ggplot2)
3695 ("r-hexbin" ,r-hexbin)
3696 ("r-htmltools" ,r-htmltools)
3697 ("r-htmlwidgets" ,r-htmlwidgets)
3699 ("r-jsonlite" ,r-jsonlite)
3700 ("r-lazyeval" ,r-lazyeval)
3701 ("r-magrittr" ,r-magrittr)
3702 ("r-purrr" ,r-purrr)
3703 ("r-rcolorbrewer" ,r-rcolorbrewer)
3704 ("r-scales" ,r-scales)
3705 ("r-tibble" ,r-tibble)
3706 ("r-tidyr" ,r-tidyr)
3707 ("r-viridislite" ,r-viridislite)))
3708 (home-page "https://plot.ly/r")
3709 (synopsis "Create interactive web graphics")
3711 "This package enables the translation of ggplot2 graphs to an interactive
3712 web-based version and/or the creation of custom web-based visualizations
3713 directly from R. Once uploaded to a plotly account, plotly graphs (and the
3714 data behind them) can be viewed and modified in a web browser.")
3715 (license license:x11)))
3717 (define-public r-biased-urn
3719 (name "r-biased-urn")
3724 (uri (cran-uri "BiasedUrn" version))
3727 "13i2lgfnjhlbbm2yxfc2l5hswqw6x03pwba5csjmirv8kpjw4xr3"))))
3728 (properties `((upstream-name . "BiasedUrn")))
3729 (build-system r-build-system)
3730 (home-page "http://www.agner.org/random/")
3731 (synopsis "Biased urn model distributions")
3733 "This package provides statistical models of biased sampling in the form
3734 of univariate and multivariate noncentral hypergeometric distributions,
3735 including Wallenius' noncentral hypergeometric distribution and Fisher's
3736 noncentral hypergeometric distribution (also called extended hypergeometric
3738 (license license:gpl3+)))
3740 (define-public r-rematch
3747 (uri (cran-uri "rematch" version))
3750 "0y3mshvpvz9csmq8hk8jbabx4nxlv5sckvfzvm6920ndg34xw2d4"))))
3751 (build-system r-build-system)
3752 (home-page "https://github.com/MangoTheCat/rematch")
3753 (synopsis "Match regular expressions with a nicer API")
3755 "This package provides a small wrapper on @code{regexpr} to extract the
3756 matches and captured groups from the match of a regular expression to a
3758 (license license:expat)))
3760 (define-public r-cellranger
3762 (name "r-cellranger")
3767 (uri (cran-uri "cellranger" version))
3770 "16fgi3annn34c3cxi0pxf62mmmmxi21hp0zzlv7bkfsjqy4g4f2x"))))
3771 (build-system r-build-system)
3773 `(("r-rematch" ,r-rematch)
3774 ("r-tibble" ,r-tibble)))
3775 (home-page "https://github.com/rsheets/cellranger")
3776 (synopsis "Translate spreadsheet cell ranges to rows and columns")
3778 "This package provides helper functions to work with spreadsheets and the
3779 @code{A1:D10} style of cell range specification.")
3780 (license license:expat)))
3782 (define-public r-googlesheets
3784 (name "r-googlesheets")
3789 (uri (cran-uri "googlesheets" version))
3792 "18q0xmxn09b52rmky7gr5flp0awndcnsgb7zcvkzvkrkvmwad52b"))))
3793 (build-system r-build-system)
3795 `(("r-cellranger" ,r-cellranger)
3796 ("r-dplyr" ,r-dplyr)
3798 ("r-jsonlite" ,r-jsonlite)
3799 ("r-purrr" ,r-purrr)
3800 ("r-readr" ,r-readr)
3801 ("r-stringr" ,r-stringr)
3802 ("r-tidyr" ,r-tidyr)
3803 ("r-xml2" ,r-xml2)))
3804 (home-page "https://github.com/jennybc/googlesheets")
3805 (synopsis "Manage Google spreadsheets from R")
3806 (description "This package provides tools to interact with Google Sheets
3808 (license license:expat)))
3810 (define-public r-spams
3813 (version "2.6-2017-03-22")
3817 (uri (string-append "https://gforge.inria.fr/frs/download.php/36615/"
3818 "spams-R-v" version ".tar.gz"))
3821 "13z2293jixf1r9g8dyy856xrhvpjr2ln2n9smn6644126r9hmhkx"))))
3822 (build-system r-build-system)
3825 (modify-phases %standard-phases
3826 (add-after 'unpack 'chdir
3827 (lambda _ (chdir "spams") #t))
3828 ;; Don't tune for the building machine
3829 (add-after 'chdir 'no-mtune
3831 (substitute* "src/Makevars"
3832 (("-mtune=native") ""))
3835 `(("r-lattice" ,r-lattice)
3836 ("r-matrix" ,r-matrix)))
3837 (home-page "http://spams-devel.gforge.inria.fr")
3838 (synopsis "Toolbox for solving sparse estimation problems")
3839 (description "SPAMS (SPArse Modeling Software) is an optimization toolbox
3840 for solving various sparse estimation problems. It includes tools for the
3844 @item Dictionary learning and matrix factorization (NMF, sparse @dfn{principle
3845 component analysis} (PCA), ...)
3846 @item Solving sparse decomposition problems with LARS, coordinate descent,
3847 OMP, SOMP, proximal methods
3848 @item Solving structured sparse decomposition problems (l1/l2, l1/linf, sparse
3849 group lasso, tree-structured regularization, structured sparsity with
3850 overlapping groups,...).
3852 (license license:gpl3+)))
3854 (define-public r-base64
3861 (uri (cran-uri "base64" version))
3864 "1labh0ycdm2xcjssj8bhnyjvbk44mcdsi0rb2p8rfqa428mrq9cf"))))
3865 (build-system r-build-system)
3867 `(("r-openssl" ,r-openssl)))
3868 (home-page "https://cran.r-project.org/web/packages/base64")
3869 (synopsis "Base64 encoder and decoder")
3871 "This package is a compatibility wrapper to replace the orphaned package
3872 by Romain Francois. New applications should use the openssl or base64enc
3874 (license license:expat)))
3876 (define-public r-hmisc
3883 (uri (cran-uri "Hmisc" version))
3886 "1a7i7azag6pldgala85d8hh7wnx1shamyiriy4jfc65nxrr2lq8w"))))
3887 (properties `((upstream-name . "Hmisc")))
3888 (build-system r-build-system)
3890 `(("gfortran" ,gfortran)))
3892 `(("r-acepack" ,r-acepack)
3893 ("r-base64enc" ,r-base64enc)
3894 ("r-cluster" ,r-cluster)
3895 ("r-data-table" ,r-data-table)
3896 ("r-foreign" ,r-foreign)
3897 ("r-formula" ,r-formula)
3898 ("r-ggplot2" ,r-ggplot2)
3899 ("r-gridextra" ,r-gridextra)
3900 ("r-gtable" ,r-gtable)
3901 ("r-lattice" ,r-lattice)
3902 ("r-latticeextra" ,r-latticeextra)
3903 ("r-htmltable" ,r-htmltable)
3904 ("r-htmltools" ,r-htmltools)
3906 ("r-rpart" ,r-rpart)
3907 ("r-survival" ,r-survival)
3908 ("r-viridis" ,r-viridis)))
3909 (home-page "http://biostat.mc.vanderbilt.edu/Hmisc")
3910 (synopsis "Miscellaneous data analysis and graphics functions")
3912 "This package contains many functions useful for data analysis,
3913 high-level graphics, utility operations, functions for computing sample size
3914 and power, importing and annotating datasets, imputing missing values,
3915 advanced table making, variable clustering, character string manipulation,
3916 conversion of R objects to LaTeX code, and recoding variables.")
3917 (license license:gpl2+)))
3919 (define-public r-runit
3926 (uri (cran-uri "RUnit" version))
3929 "1jqr871jkll2xmk7wk5hv1z3a36hyn2ibgivw7bwk4b346940xlx"))))
3930 (properties `((upstream-name . "RUnit")))
3931 (build-system r-build-system)
3932 (home-page "https://cran.r-project.org/web/packages/RUnit")
3933 (synopsis "R unit test framework")
3935 "This package provides R functions implementing a standard unit testing
3936 framework, with additional code inspection and report generation tools.")
3937 (license license:gpl2+)))
3939 (define-public r-dynamictreecut
3941 (name "r-dynamictreecut")
3946 (uri (cran-uri "dynamicTreeCut" version))
3949 "1fadbql7g5r2vvlkr89nlrjxwp4yx4xrdqmv077qvmnx9vv0f4w3"))))
3950 (properties `((upstream-name . "dynamicTreeCut")))
3951 (build-system r-build-system)
3953 "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/BranchCutting/")
3954 (synopsis "Detect clusters in hierarchical clustering dendrograms")
3956 "This package contains methods for the detection of clusters in
3957 hierarchical clustering dendrograms.")
3958 (license license:gpl2+)))
3960 (define-public r-preprocesscore
3962 (name "r-preprocesscore")
3967 (uri (bioconductor-uri "preprocessCore" version))
3970 "0mrdgbkb9dcfr9gsqyxfpshnxx60mq97pl98b8yl00l2gfwz48ph"))))
3972 `((upstream-name . "preprocessCore")))
3973 (build-system r-build-system)
3974 (home-page "https://github.com/bmbolstad/preprocessCore")
3975 (synopsis "Collection of pre-processing functions")
3977 "This package provides a library of core pre-processing and normalization
3979 (license license:lgpl2.0+)))
3981 (define-public r-fastcluster
3983 (name "r-fastcluster")
3988 (uri (cran-uri "fastcluster" version))
3991 "15drhl22wm8whsy6b3vv754skfddiydb068zn1whrw5sknvkkjc2"))))
3992 (build-system r-build-system)
3993 (home-page "http://danifold.net/fastcluster.html")
3994 (synopsis "Fast hierarchical clustering routines")
3996 "This package implements fast hierarchical, agglomerative clustering
3997 routines. Part of the functionality is designed as drop-in replacement for
3998 existing routines: @code{linkage()} in the SciPy package
3999 @code{scipy.cluster.hierarchy}, @code{hclust()} in R's @code{stats} package,
4000 and the @code{flashClust} package. It provides the same functionality with
4001 the benefit of a much faster implementation. Moreover, there are
4002 memory-saving routines for clustering of vector data, which go beyond what the
4003 existing packages provide.")
4004 (license license:bsd-2)))
4006 (define-public r-sfsmisc
4013 (uri (cran-uri "sfsmisc" version))
4016 "0jzmbywlyzfxs7hlmyd0iynghfc9qp5sa5lnhr73y8r360yv1ahf"))))
4017 (build-system r-build-system)
4018 (home-page "https://cran.r-project.org/web/packages/sfsmisc")
4019 (synopsis "Utilities from \"Seminar fuer Statistik\" ETH Zurich")
4021 "This package provides useful utilities from Seminar fuer Statistik ETH
4022 Zurich, including many that are related to graphics.")
4023 (license license:gpl2+)))
4025 (define-public r-gtools
4032 (uri (cran-uri "gtools" version))
4035 "1xknwk9xlsj027pg0nwiizigcrsc84hdrig0jn0cgcyxj8dabdl6"))))
4036 (build-system r-build-system)
4037 (home-page "https://cran.r-project.org/web/packages/gtools")
4038 (synopsis "Various R programming tools")
4040 "This package contains a collection of various functions to assist in R
4041 programming, such as tools to assist in developing, updating, and maintaining
4042 R and R packages, calculating the logit and inverse logit transformations,
4043 tests for whether a value is missing, empty or contains only @code{NA} and
4044 @code{NULL} values, and many more.")
4045 (license license:gpl2)))
4047 (define-public r-gdata
4054 (uri (cran-uri "gdata" version))
4057 "0zwdj7lscgxr8r62ii8hbdh4mb7sa9w4f5nv32zzrxdvymcpya2b"))))
4058 (build-system r-build-system)
4062 `(("r-gtools" ,r-gtools)))
4063 (home-page "https://cran.r-project.org/web/packages/gdata")
4064 (synopsis "Various R programming tools for data manipulation")
4066 "This package provides various R programming tools for data manipulation,
4070 @item medical unit conversions
4071 @item combining objects
4072 @item character vector operations
4073 @item factor manipulation
4074 @item obtaining information about R objects
4075 @item manipulating MS-Excel formatted files
4076 @item generating fixed-width format files
4077 @item extricating components of date and time objects
4078 @item operations on columns of data frames
4079 @item matrix operations
4080 @item operations on vectors and data frames
4081 @item value of last evaluated expression
4082 @item wrapper for @code{sample} that ensures consistent behavior for
4083 both scalar and vector arguments
4085 (license license:gpl2+)))
4087 (define-public r-gplots
4094 (uri (cran-uri "gplots" version))
4097 "02nb8n3s7c1zxq2s7ycaq2ys72y7mzirxrwj954h6gdc4x1zhg9l"))))
4098 (build-system r-build-system)
4100 `(("r-catools" ,r-catools)
4101 ("r-gdata" ,r-gdata)
4102 ("r-gtools" ,r-gtools)
4103 ("r-kernsmooth" ,r-kernsmooth)))
4104 (home-page "https://cran.r-project.org/web/packages/gplots")
4105 (synopsis "Various R programming tools for plotting data")
4107 "This package provides various R programming tools for plotting data,
4111 @item calculating and plotting locally smoothed summary function
4112 @item enhanced versions of standard plots
4113 @item manipulating colors
4114 @item calculating and plotting two-dimensional data summaries
4115 @item enhanced regression diagnostic plots
4116 @item formula-enabled interface to @code{stats::lowess} function
4117 @item displaying textual data in plots
4119 @item plotting \"Venn\" diagrams
4120 @item displaying Open-Office style plots
4121 @item plotting multiple data on same region, with separate axes
4122 @item plotting means and confidence intervals
4123 @item spacing points in an x-y plot so they don't overlap
4125 (license license:gpl2+)))
4127 (define-public r-rocr
4134 (uri (cran-uri "ROCR" version))
4137 "1jay8cm7lgq56i967vm5c2hgaxqkphfpip0gn941li3yhh7p3vz7"))))
4138 (properties `((upstream-name . "ROCR")))
4139 (build-system r-build-system)
4141 `(("r-gplots" ,r-gplots)))
4142 (home-page "http://rocr.bioinf.mpi-sb.mpg.de/")
4143 (synopsis "Visualizing the performance of scoring classifiers")
4145 "ROCR is a flexible tool for creating cutoff-parameterized 2D performance
4146 curves by freely combining two from over 25 performance measures (new
4147 performance measures can be added using a standard interface). Curves from
4148 different cross-validation or bootstrapping runs can be averaged by different
4149 methods, and standard deviations, standard errors or box plots can be used to
4150 visualize the variability across the runs. The parameterization can be
4151 visualized by printing cutoff values at the corresponding curve positions, or
4152 by coloring the curve according to cutoff. All components of a performance
4153 plot can be quickly adjusted using a flexible parameter dispatching
4155 (license license:gpl2+)))
4157 (define-public r-zoo
4163 (uri (cran-uri "zoo" version))
4166 "0mqklbx92ifwa0awm7gpm4r9dvwa09p55zjxjnypiqsxy532r4h9"))))
4167 (build-system r-build-system)
4169 `(("r-lattice" ,r-lattice)))
4170 (home-page "http://zoo.R-Forge.R-project.org/")
4171 (synopsis "S3 infrastructure for regular and irregular time series")
4172 (description "This package contains an S3 class with methods for totally
4173 ordered indexed observations. It is particularly aimed at irregular time
4174 series of numeric vectors/matrices and factors.")
4175 (license license:gpl2+)))
4177 (define-public r-ztable
4183 (uri (cran-uri "ztable" version))
4186 "1jfqnqy9544gfvz3bsb48v4177nwp4b4n9l2743asq8sbq305b5r"))))
4187 (build-system r-build-system)
4188 (home-page "https://cran.r-project.org/web/packages/ztable")
4189 (synopsis "Zebra-striped tables in LaTeX and HTML formats for R")
4191 "This package provides functions to make zebra-striped tables (tables
4192 with alternating row colors) in LaTeX and HTML formats easily from
4193 @code{data.frame}, @code{matrix}, @code{lm}, @code{aov}, @code{anova},
4194 @code{glm}, @code{coxph}, @code{nls}, @code{fitdistr}, @code{mytable} and
4195 @code{cbind.mytable} objects.")
4196 (license license:gpl2+)))
4198 (define-public r-vipor
4204 (uri (cran-uri "vipor" version))
4207 "112gc0d7f8iavgf56pnzfxb7hy75yhd0zlyjzshdcfbnqcd2a6bx"))))
4208 (build-system r-build-system)
4209 (home-page "https://cran.r-project.org/web/packages/vipor")
4210 (synopsis "Plot categorical data using noise and density estimates")
4212 "This package provides tools to generate a violin point plot, a
4213 combination of a violin/histogram plot and a scatter plot by offsetting points
4214 within a category based on their density using quasirandom noise.")
4215 (license license:gpl2+)))
4217 (define-public r-beeswarm
4223 (uri (cran-uri "beeswarm" version))
4226 "0hy89bwv7jixlg91li1fywa77916am2whqp1m1fx1khd45g44581"))))
4227 (build-system r-build-system)
4228 (home-page "http://www.cbs.dtu.dk/~eklund/beeswarm/")
4229 (synopsis "Implementation of bee swarm plots")
4231 "This package provides an implementation of bee swarm plots. The bee
4232 swarm plot is a one-dimensional scatter plot like stripchart, but with
4233 closely-packed, non-overlapping points.")
4234 (license license:artistic2.0)))
4236 (define-public r-sourcetools
4238 (name "r-sourcetools")
4243 (uri (cran-uri "sourcetools" version))
4246 "0l8c6fql82cb246qh7hfgxb4s35qn0qfgy6dzvkx0zkz1cpqvx69"))))
4247 (build-system r-build-system)
4248 (home-page "https://cran.r-project.org/web/packages/sourcetools")
4249 (synopsis "Tools for reading, tokenizing and parsing R code")
4251 "The sourcetools package provides both an R and C++ interface for the
4252 tokenization of R code, and helpers for interacting with the tokenized
4253 representation of R code.")
4254 (license license:expat)))
4256 (define-public r-ggbeeswarm
4258 (name "r-ggbeeswarm")
4262 (uri (cran-uri "ggbeeswarm" version))
4265 "0crk29p5vi1r3a988kms4y7r0iqwgwzsikgvh18r9wbzyr98bb5v"))))
4266 (build-system r-build-system)
4268 `(("r-beeswarm" ,r-beeswarm)
4269 ("r-ggplot2" ,r-ggplot2)
4270 ("r-vipor" ,r-vipor)))
4271 (home-page "https://github.com/eclarke/ggbeeswarm")
4272 (synopsis "Categorical scatter (violin point) plots")
4274 "This package provides two methods of plotting categorical scatter plots
4275 such that the arrangement of points within a category reflects the density of
4276 data at that region, and avoids over-plotting.")
4277 (license license:gpl2+)))
4279 (define-public r-ggthemes
4285 (uri (cran-uri "ggthemes" version))
4288 "1jj8lp7jbk3489kpgbw4b5phpn01gkfmksc21c6sn3x6wmzyn6hs"))))
4289 (build-system r-build-system)
4291 `(("r-assertthat" ,r-assertthat)
4292 ("r-colorspace" ,r-colorspace)
4293 ("r-ggplot2" ,r-ggplot2)
4294 ("r-scales" ,r-scales)))
4295 (home-page "https://cran.rstudio.com/web/packages/ggthemes")
4296 (synopsis "Extra themes, scales and geoms for @code{ggplot2}")
4297 (description "This package provides extra themes and scales for
4298 @code{ggplot2} that replicate the look of plots by Edward Tufte and
4299 Stephen Few in Fivethirtyeight, The Economist, Stata, Excel, and The
4300 Wall Street Journal, among others. This package also provides
4301 @code{geoms} for Tufte's box plot and range frame.")
4302 (license license:gpl2)))
4304 (define-public r-statmod
4310 (uri (cran-uri "statmod" version))
4313 "07v4x8af60alcw6vbiwf5fp25bhra61kvxz9kqx64lszm0i1fb4x"))))
4314 (build-system r-build-system)
4315 (home-page "https://cran.r-project.org/web/packages/statmod")
4317 `(("gfortran" ,gfortran)))
4318 (synopsis "Statistical modeling")
4320 "This package provides a collection of algorithms and functions to aid
4321 statistical modeling. It includes growth curve comparisons, limiting dilution
4322 analysis (aka ELDA), mixed linear models, heteroscedastic regression,
4323 inverse-Gaussian probability calculations, Gauss quadrature and a secure
4324 convergence algorithm for nonlinear models. It also includes advanced
4325 generalized linear model functions that implement secure convergence,
4326 dispersion modeling and Tweedie power-law families.")
4327 ;; Statmod is distributed under either license
4328 (license (list license:gpl2 license:gpl3))))
4330 (define-public r-rann
4336 (uri (cran-uri "RANN" version))
4339 "0il5i99vbcagnxvb15af5n37g04a4q1x96bz73zh3jhki9fpw9vm"))))
4341 `((upstream-name . "RANN")))
4342 (build-system r-build-system)
4343 (home-page "https://github.com/jefferis/RANN")
4344 (synopsis "Fast nearest neighbour search")
4346 "This package finds the k nearest neighbours for every point in a given
4347 dataset in O(N log N) time using Arya and Mount's ANN library. Provides
4348 approximate, exact searches, fixed radius searches, bd and kb trees.")
4349 (license license:gpl3+)))
4351 (define-public r-fivethirtyeight
4353 (name "r-fivethirtyeight")
4358 (uri (string-append "https://mran.microsoft.com/src/contrib/"
4359 "fivethirtyeight_" version ".tar.gz"))
4362 "0fcc8rq745nsghp27dk0lgih90y4zx8hrzcvsn6ih786yv7qxhvl"))))
4363 (build-system r-build-system)
4365 `(("r-knitr" ,r-knitr)
4366 ("r-rmarkdown" ,r-rmarkdown)
4367 ("r-dplyr" ,r-dplyr)
4368 ("r-readr" ,r-readr)
4369 ("r-ggplot2" ,r-ggplot2)
4370 ("r-magrittr" ,r-magrittr)
4371 ("r-stringr" ,r-stringr)))
4372 (home-page "https://mran.microsoft.com/package/fivethirtyeight/")
4373 (synopsis "Data and code behind the stories at FiveThirtyEight")
4374 (description "This R package provides access to the code and data sets
4375 published by the statistics blog FiveThirtyEight.")
4376 (license license:expat)))
4378 (define-public r-compquadform
4380 (name "r-compquadform")
4385 (uri (cran-uri "CompQuadForm" version))
4388 "1i30hrqdk64q17vsn918c3q79brchgx2wzh1gbsgbn0dh1ncabq4"))))
4389 (properties `((upstream-name . "CompQuadForm")))
4390 (build-system r-build-system)
4391 (home-page "https://cran.r-project.org/web/packages/CompQuadForm")
4392 (synopsis "Distribution function of quadratic forms in normal variables")
4394 "This package provides functions to compute the distribution function of
4395 quadratic forms in normal variables using Imhof's method, Davies's algorithm,
4396 Farebrother's algorithm or Liu et al.'s algorithm.")
4397 (license license:gpl2+)))
4399 (define-public r-cowplot
4406 (uri (cran-uri "cowplot" version))
4409 "13yjw7yv7imyqiawqqp304hkp6x36iv6rf6gn03dwzwkj9zwx4lb"))))
4410 (build-system r-build-system)
4412 `(("r-ggplot2" ,r-ggplot2)
4413 ("r-gtable" ,r-gtable)
4415 ("r-scales" ,r-scales)))
4416 (home-page "https://github.com/wilkelab/cowplot")
4417 (synopsis "Streamlined plot theme and plot annotations for ggplot2")
4419 "This package provides some helpful extensions and modifications to the
4420 ggplot2 package to combine multiple ggplot2 plots into one and label them with
4421 letters, as is often required for scientific publications.")
4422 (license license:gpl2)))
4424 (define-public r-mixtools
4431 (uri (cran-uri "mixtools" version))
4434 "13wdm0xs5bakhpa8ypg6lvhjaqkxyabwz4glxdwn0jwdvkcdhgsl"))))
4435 (build-system r-build-system)
4437 `(("r-mass" ,r-mass)
4438 ("r-segmented" ,r-segmented)
4439 ("r-survival" ,r-survival)))
4440 (home-page "https://cran.r-project.org/web/packages/mixtools")
4441 (synopsis "Tools for analyzing finite mixture models")
4443 "This package provides a collection of R functions for analyzing finite
4445 (license license:gpl2+)))
4447 (define-public r-lars
4454 (uri (cran-uri "lars" version))
4457 "0blj44wqrx6lmym1m9v6wkz8zxzbjax2zl6swgdczci0ixb5nx34"))))
4458 (build-system r-build-system)
4460 `(("gfortran" ,gfortran)))
4461 (home-page "http://www-stat.stanford.edu/~hastie/Papers/#LARS")
4462 (synopsis "Least angle regression software")
4464 "Least Angle Regression (\"LAR\") is a model selection algorithm; a
4465 useful and less greedy version of traditional forward selection methods. A
4466 simple modification of the LAR algorithm implements Tibshirani's Lasso; the
4467 Lasso modification of LARS calculates the entire Lasso path of coefficients
4468 for a given problem at the cost of a single least squares fit. Another LARS
4469 modification efficiently implements epsilon Forward Stagewise linear
4471 (license license:gpl2)))
4473 (define-public r-fastica
4480 (uri (cran-uri "fastICA" version))
4483 "108z2ymby5y4h8l4l2krqwm28rya93gq09yylgilnm3afvfrfabg"))))
4484 (properties `((upstream-name . "fastICA")))
4485 (build-system r-build-system)
4486 (home-page "https://cran.r-project.org/web/packages/fastICA")
4487 (synopsis "FastICA algorithms to perform ICA and projection pursuit")
4489 "This package provides an implementation of the FastICA algorithm to
4490 perform @dfn{independent component analysis} (ICA) and projection pursuit.")
4492 (license license:gpl3+)))
4494 (define-public r-randomforest
4496 (name "r-randomforest")
4501 (uri (cran-uri "randomForest" version))
4504 "1i43idaihhl6nwqw42v9dqpl6f8z3ykcn2in32lh2755i27jylbf"))))
4505 (properties `((upstream-name . "randomForest")))
4506 (build-system r-build-system)
4507 (home-page "https://www.stat.berkeley.edu/~breiman/RandomForests/")
4509 `(("gfortran" ,gfortran)))
4510 (synopsis "Breiman and Cutler's random forests for classification and regression")
4512 "This package provides the Breiman and Cutler's random forests algorithm, based on a
4513 forest of trees using random inputs, for classification and regression.")
4514 (license license:gpl2+)))
4516 (define-public r-diptest
4523 (uri (cran-uri "diptest" version))
4526 "06xnc5gv1284ll0addxnxb6ljz6fn8dbyrp5vchyz6551h800aa6"))))
4527 (build-system r-build-system)
4528 (home-page "https://cran.r-project.org/web/packages/diptest")
4529 (synopsis "Hartigan's dip test statistic for unimodality")
4531 "This package computes Hartigan's dip test statistic for unimodality,
4532 multimodality and provides a test with simulation based p-values, where the
4533 original public code has been corrected.")
4534 (license license:gpl2+)))
4536 (define-public r-modeltools
4538 (name "r-modeltools")
4543 (uri (cran-uri "modeltools" version))
4546 "0ynds453xprxv0jqqzi3blnv5w6vrdww9pvd1sq4lrr5ar3k3cq7"))))
4547 (build-system r-build-system)
4548 (home-page "https://cran.r-project.org/web/packages/modeltools")
4549 (synopsis "Tools and classes for statistical models")
4551 "This package provides a collection of tools to deal with statistical
4552 models. The functionality is experimental and the user interface is likely
4553 to change in the future.")
4554 (license license:gpl2)))
4556 (define-public r-flexmix
4563 (uri (cran-uri "flexmix" version))
4566 "0sl4zxh1sb2sr5q7svjw9ihrm219jzn82yrc9d43q6r1b8bpyz43"))))
4567 (build-system r-build-system)
4569 `(("r-lattice" ,r-lattice)
4570 ("r-modeltools" ,r-modeltools)
4571 ("r-nnet" ,r-nnet)))
4572 (home-page "https://cran.r-project.org/web/packages/flexmix")
4573 (synopsis "Flexible mixture modeling")
4575 "This package implements a general framework for finite mixtures of
4576 regression models using the EM algorithm. FlexMix provides the E-step and
4577 all data handling, while the M-step can be supplied by the user to easily
4578 define new models. Existing drivers implement mixtures of standard linear
4579 models, generalized linear models and model-based clustering.")
4580 (license license:gpl2+)))
4582 (define-public r-mclust
4589 (uri (cran-uri "mclust" version))
4592 "1i3v1q8qq0al3ifvjhcvxfsg68cx9mq8jz67jwmiqai78mw0aqvk"))))
4593 (build-system r-build-system)
4595 `(("gfortran" ,gfortran)))
4596 (home-page "http://www.stat.washington.edu/mclust/")
4597 (synopsis "Gaussian mixture modelling for model-based clustering etc.")
4599 "This package provides Gaussian finite mixture models fitted via EM
4600 algorithm for model-based clustering, classification, and density estimation,
4601 including Bayesian regularization, dimension reduction for visualisation,
4602 and resampling-based inference.")
4603 (license license:gpl2+)))
4605 (define-public r-prabclus
4612 (uri (cran-uri "prabclus" version))
4615 "0qjsxrx6yv338bxm4ki0w9h8hind1l98abdrz828588bwj02jya1"))))
4616 (build-system r-build-system)
4618 `(("r-mass" ,r-mass)
4619 ("r-mclust" ,r-mclust)))
4620 (home-page "https://cran.r-project.org/web/packages/prabclus")
4621 (synopsis "Parametric bootstrap tests for spatial neighborhood clustering")
4623 "This package provides distance-based parametric bootstrap tests for
4624 clustering with spatial neighborhood information. It implements some distance
4625 measures, clustering of presence-absence, abundance and multilocus genetical
4626 data for species delimitation, nearest neighbor based noise detection.")
4627 (license license:gpl2+)))
4629 (define-public r-deoptimr
4636 (uri (cran-uri "DEoptimR" version))
4639 "1vz546hyjyhly70z62h5n3mn62b8llhhmim8ffp9y6jnnb0i2sc4"))))
4640 (properties `((upstream-name . "DEoptimR")))
4641 (build-system r-build-system)
4642 (home-page "https://cran.r-project.org/web/packages/DEoptimR")
4643 (synopsis "Differential evolution optimization in pure R")
4645 "This package provides a differential evolution (DE) stochastic
4646 algorithms for global optimization of problems with and without constraints.
4647 The aim is to curate a collection of its state-of-the-art variants that (1) do
4648 not sacrifice simplicity of design, (2) are essentially tuning-free, and (3)
4649 can be efficiently implemented directly in the R language.")
4650 (license license:gpl2+)))
4652 (define-public r-robustbase
4654 (name "r-robustbase")
4659 (uri (cran-uri "robustbase" version))
4662 "080ynchq8pvhnmbivj4fp74n0x9lyr9923sg0s9gq5irgm68kgxw"))))
4663 (build-system r-build-system)
4665 `(("gfortran" ,gfortran)))
4667 `(("r-deoptimr" ,r-deoptimr)))
4668 (home-page "http://robustbase.r-forge.r-project.org/")
4669 (synopsis "Basic robust statistics")
4671 "This packages allows to analyze data with robust methods such as
4672 regression methodology including model selections and multivariate statistics.")
4673 (license license:gpl2+)))
4675 (define-public r-pcapp
4682 (uri (cran-uri "pcaPP" version))
4685 "0i2822bv86dpqmk3q17x61nsp3gjjnn4nr8191rwvbiib7xhpgaq"))))
4686 (properties `((upstream-name . "pcaPP")))
4687 (build-system r-build-system)
4689 `(("r-mvtnorm" ,r-mvtnorm)))
4690 (home-page "https://cran.r-project.org/web/packages/pcaPP")
4691 (synopsis "Robust PCA by projection pursuit")
4693 "This package provides functions for robust @dfn{principal component
4694 analysis} (PCA) by projection pursuit.")
4695 (license license:gpl3+)))
4697 (define-public r-rrcov
4704 (uri (cran-uri "rrcov" version))
4707 "0kagqggi634mvrhd67ia7mpjrj5v6w2wq0z3kyppg5xkvzh335nq"))))
4708 (build-system r-build-system)
4710 `(("r-cluster" ,r-cluster)
4711 ("r-lattice" ,r-lattice)
4712 ("r-mvtnorm" ,r-mvtnorm)
4713 ("r-pcapp" ,r-pcapp)
4714 ("r-robustbase" ,r-robustbase)))
4716 `(("gfortran" ,gfortran)))
4717 (home-page "https://cran.r-project.org/web/packages/rrcov")
4718 (synopsis "Scalable robust estimators with high breakdown Point")
4720 "This package provides an implementation of robust location and scatter
4721 estimation and robust multivariate analysis with high breakdown point.")
4722 (license license:gpl2+)))
4724 (define-public r-fit-models
4726 (name "r-fit-models")
4731 (uri (cran-uri "fit.models" version))
4734 "0vjbzmx0ambm6yzidb4vbgmhclwzwv2iz2cwl54ccdkvx4cx3fck"))))
4735 (properties `((upstream-name . "fit.models")))
4736 (build-system r-build-system)
4738 `(("r-lattice" ,r-lattice)))
4739 (home-page "https://cran.r-project.org/web/packages/fit.models")
4740 (synopsis "Compare fitted models")
4742 "The @code{fit.models} function and its associated methods (coefficients, print,
4743 summary, plot, etc.) were originally provided in the @code{robust} package to
4744 compare robustly and classically fitted model objects. The aim of the
4745 @code{fit.models} package is to separate this fitted model object comparison
4746 functionality from the robust package and to extend it to support fitting
4747 methods (e.g., classical, robust, Bayesian, regularized, etc.) more
4749 ;; Any version of the GPL
4750 (license (list license:gpl2+ license:gpl3+))))
4752 (define-public r-robust
4759 (uri (cran-uri "robust" version))
4762 "1b7qh1aff500nd6dh4y2ipmjgdiq8991shflb63pc39vpc0ny6g4"))))
4763 (build-system r-build-system)
4765 `(("r-fit-models" ,r-fit-models)
4766 ("r-lattice" ,r-lattice)
4768 ("r-robustbase" ,r-robustbase)
4769 ("r-rrcov" ,r-rrcov)))
4771 `(("gfortran" ,gfortran)))
4772 (home-page "https://cran.r-project.org/web/packages/robust")
4773 (synopsis "Port of the S+ \"Robust Library\"")
4775 "This package is a port of the S+ \"Robust Library\". It provides
4776 methods for robust statistics, notably for robust regression and robust
4777 multivariate analysis.")
4778 (license license:gpl2)))
4780 (define-public r-trimcluster
4782 (name "r-trimcluster")
4787 (uri (cran-uri "trimcluster" version))
4790 "0lsgbg93hm0w1rdb813ry0ks2l0jfpyqzqkf3h3bj6fch0avcbv2"))))
4791 (build-system r-build-system)
4792 (home-page "https://cran.r-project.org/web/packages/trimcluster")
4793 (synopsis "Cluster analysis with trimming")
4795 "The trimmed k-means clustering method by Cuesta-Albertos, Gordaliza and
4796 Matran (1997). This optimizes the k-means criterion under trimming a portion
4799 (license (list license:gpl2+ license:gpl3+))))
4801 (define-public r-fpc
4808 (uri (cran-uri "fpc" version))
4811 "15m0p9l9w2v7sl0cnzyg81i2fmx3hrhvr3371544mwn3fpsca5sx"))))
4812 (build-system r-build-system)
4814 `(("r-class" ,r-class)
4815 ("r-cluster" ,r-cluster)
4816 ("r-diptest" ,r-diptest)
4817 ("r-flexmix" ,r-flexmix)
4818 ("r-kernlab" ,r-kernlab)
4820 ("r-mclust" ,r-mclust)
4821 ("r-mvtnorm" ,r-mvtnorm)
4822 ("r-prabclus" ,r-prabclus)
4823 ("r-robustbase" ,r-robustbase)
4824 ("r-trimcluster" ,r-trimcluster)))
4825 (home-page "https://cran.r-project.org/web/packages/fpc")
4826 (synopsis "Flexible procedures for clustering")
4828 "This package provides various methods for clustering and cluster validation.
4829 For example, it provides fixed point clustering, linear regression clustering,
4830 clustering by merging Gaussian mixture components, as well as symmetric and
4831 asymmetric discriminant projections for visualisation of the separation of
4833 (license license:gpl2+)))
4835 (define-public r-vgam
4842 (uri (cran-uri "VGAM" version))
4845 "0r59hyp3afmvms890b3v2yyckf8v0qkjf2w11rnqd2zgg1gri0g5"))))
4846 (properties `((upstream-name . "VGAM")))
4847 (build-system r-build-system)
4849 `(("gfortran" ,gfortran)))
4850 (home-page "https://www.stat.auckland.ac.nz/~yee/VGAM")
4851 (synopsis "Vector generalized linear and additive models")
4853 "This package is an implementation of about 6 major classes of statistical
4854 regression models. Currently only fixed-effects models are implemented, i.e.,
4855 no random-effects models. Many (150+) models and distributions are estimated
4856 by maximum likelihood estimation (MLE) or penalized MLE, using Fisher scoring.
4857 VGLMs can be loosely thought of as multivariate generalised linear models.")
4858 (license license:gpl2+)))
4860 (define-public r-pbapply
4867 (uri (cran-uri "pbapply" version))
4870 "0iqhymf65jffh00qf056h1p76xf92bfmij6aymlmgnvn24fv4ybk"))))
4871 (build-system r-build-system)
4872 (home-page "https://github.com/psolymos/pbapply")
4873 (synopsis "Adding progress bar to apply functions")
4875 "This lightweight package that adds progress bar to vectorized R
4876 functions apply. The implementation can easily be added to functions where
4877 showing the progress is useful e.g. bootstrap.")
4878 (license license:gpl2)))
4880 (define-public r-fnn
4887 (uri (cran-uri "FNN" version))
4890 "1kncmiaraq1mrykb9fj3fsxswabk3l71fnp1vks0x9aay5xfk8mj"))))
4891 (properties `((upstream-name . "FNN")))
4892 (build-system r-build-system)
4893 (home-page "https://cran.r-project.org/web/packages/FNN")
4894 (synopsis "Fast nearest neighbor search algorithms and applications")
4896 "This package provides cover-tree and kd-tree fast k-nearest neighbor
4897 search algorithms and related applications including KNN classification,
4898 regression and information measures.")
4899 (license license:gpl2+)))
4901 (define-public r-minqa
4908 (uri (cran-uri "minqa" version))
4911 "036drja6xz7awja9iwb76x91415p26fb0jmg7y7v0p65m6j978fg"))))
4912 (build-system r-build-system)
4914 `(("r-rcpp" ,r-rcpp)))
4916 `(("gfortran" ,gfortran)))
4917 (home-page "http://optimizer.r-forge.r-project.org")
4918 (synopsis "Derivative-free optimization algorithms by quadratic approximation")
4920 "This package provides a derivative-free optimization by quadratic approximation
4921 based on an interface to Fortran implementations by M. J. D. Powell.")
4922 (license license:gpl2)))
4924 (define-public r-rcppeigen
4926 (name "r-rcppeigen")
4927 (version "0.3.3.3.1")
4931 (uri (cran-uri "RcppEigen" version))
4934 "093g2wmqyk86693l0lzh2va8119w3k7rvw5q24p842jdfv5x5z8l"))))
4935 (properties `((upstream-name . "RcppEigen")))
4936 (build-system r-build-system)
4938 `(("r-rcpp" ,r-rcpp)
4939 ("r-matrix" ,r-matrix)))
4940 (home-page "http://eigen.tuxfamily.org")
4941 (synopsis "Rcpp integration for the Eigen templated linear algebra library")
4943 "This package provides an integration of Eigen in R using a C++ template
4944 library for linear algebra: matrices, vectors, numerical solvers and related algorithms.
4945 It supports dense and sparse matrices on integer, floating point and complex numbers,
4946 decompositions of such matrices, and solutions of linear systems.")
4947 (license license:gpl2+)))
4949 (define-public r-modelmetrics
4951 (name "r-modelmetrics")
4956 (uri (cran-uri "ModelMetrics" version))
4959 "119xxmzb5biq7k1yxqsf0jmmarmfn6lds9x9hfgv593xlpym6za8"))))
4960 (properties `((upstream-name . "ModelMetrics")))
4961 (build-system r-build-system)
4963 `(("r-rcpp" ,r-rcpp)))
4964 (home-page "https://cran.r-project.org/web/packages/ModelMetrics")
4965 (synopsis "Rapid calculation of model metrics")
4967 "Written in C++ using @code{Rcpp}, this package provides a collection of
4968 metrics for evaluating models.")
4969 (license license:gpl2+)))
4971 (define-public r-matrixmodels
4973 (name "r-matrixmodels")
4978 (uri (cran-uri "MatrixModels" version))
4981 "0cyfvhci2p1vr2x52ymkyqqs63x1qchn856dh2j94yb93r08x1zy"))))
4982 (properties `((upstream-name . "MatrixModels")))
4983 (build-system r-build-system)
4985 `(("r-matrix" ,r-matrix)))
4986 (home-page "https://cran.r-project.org/web/packages/MatrixModels")
4987 (synopsis "Modelling with sparse and dense matrices")
4989 "This package models with sparse and dense matrix matrices,
4990 using modular prediction and response module classes.")
4991 (license license:gpl2+)))
4993 (define-public r-quantreg
5000 (uri (cran-uri "quantreg" version))
5003 "0bmgfgnmzqwmwwaraliry682yb8kcr396q3rlzrd2qzaa9sgxxh4"))))
5004 (build-system r-build-system)
5006 `(("gfortran" ,gfortran)))
5008 `(("r-matrix" ,r-matrix)
5009 ("r-matrixmodels" ,r-matrixmodels)
5010 ("r-sparsem" ,r-sparsem)))
5011 (home-page "http://www.r-project.org")
5012 (synopsis "Quantile regression")
5014 "This package provides an estimation and inference methods for models
5015 of conditional quantiles: linear and nonlinear parametric and non-parametric
5016 models for conditional quantiles of a univariate response and several methods
5017 for handling censored survival data. Portfolio selection methods based on
5018 expected shortfall risk are also included.")
5019 (license license:gpl2+)))
5021 (define-public r-nloptr
5028 (uri (cran-uri "nloptr" version))
5031 "1sz1xj3785x4vsm4nd6in298bk32hs2jk5nsxma7ivxi7jcmn8l4"))))
5032 (build-system r-build-system)
5034 `(("pkg-config" ,pkg-config)))
5036 `(("nlopt" ,nlopt)))
5037 (home-page "https://cran.r-project.org/web/packages/nloptr")
5038 (synopsis "R interface to NLopt")
5040 "This package is interface to NLopt, a library for nonlinear
5041 optimization. NLopt is a library for nonlinear optimization, providing a
5042 common interface for a number of different free optimization routines
5043 available online as well as original implementations of various other
5045 (license license:lgpl3)))
5047 (define-public r-lme4
5054 (uri (cran-uri "lme4" version))
5057 "1vars93604q7kyz6y1f8f886l05jkgj8bs78033l2czypvzki5la"))))
5058 (build-system r-build-system)
5060 `(("r-rcpp" ,r-rcpp)
5061 ("r-rcppeigen" ,r-rcppeigen)))
5063 `(("r-lattice" ,r-lattice)
5064 ("r-matrix" ,r-matrix)
5065 ("r-minqa" ,r-minqa)
5066 ("r-nloptr" ,r-nloptr)
5068 ("r-nlme" ,r-nlme)))
5069 (home-page "https://cran.r-project.org/web/packages/lme4")
5070 (synopsis "Linear mixed-effects models using eigen and S4")
5072 "This package provides fit linear and generalized linear mixed-effects
5073 models. The models and their components are represented using S4 classes and
5074 methods. The core computational algorithms are implemented using the Eigen
5075 C++ library for numerical linear algebra and RcppEigen glue.")
5076 (license license:gpl2+)))
5078 (define-public r-pbkrtest
5085 (uri (cran-uri "pbkrtest" version))
5088 "1si3bhi59xc51a0pgjjglccq3h4aljyhw2k1b8574s145fnh7fsw"))))
5089 (build-system r-build-system)
5091 `(("r-lme4" ,r-lme4)
5093 ("r-matrix" ,r-matrix)))
5094 (home-page "http://people.math.aau.dk/~sorenh/software/pbkrtest/")
5095 (synopsis "Methods for linear mixed model comparison")
5097 "This package implements a parametric bootstrap test and a Kenward Roger
5098 modification of F-tests for linear mixed effects models and a parametric
5099 bootstrap test for generalized linear mixed models.")
5100 (license license:gpl2+)))
5102 (define-public r-car
5109 (uri (cran-uri "car" version))
5112 "14l4d9j87xnb0bz2wgqqbxnlnbcdfb5vx2fw6kdxj91kyrk6lhnj"))))
5113 (build-system r-build-system)
5115 `(("r-mass" ,r-mass)
5118 ("r-pbkrtest" ,r-pbkrtest)
5119 ("r-quantreg" ,r-quantreg)))
5120 (home-page "https://r-forge.r-project.org/projects/car/")
5121 (synopsis "Companion to applied regression")
5123 "This package provides functions and datasets from book Companion
5124 to Applied regression, Second Edition, Sage, 2011.")
5125 (license license:gpl2+)))
5127 (define-public r-caret
5134 (uri (cran-uri "caret" version))
5137 "0h1nxzii2h80aslp1zsjczrlfmaks44sskabk4yq9c5rafc7ka6y"))))
5138 (build-system r-build-system)
5140 `(("r-foreach" ,r-foreach)
5141 ("r-ggplot2" ,r-ggplot2)
5142 ("r-lattice" ,r-lattice)
5143 ("r-modelmetrics" ,r-modelmetrics)
5146 ("r-recipes" ,r-recipes)
5147 ("r-reshape2" ,r-reshape2)
5148 ("r-withr" ,r-withr)))
5149 (home-page "https://github.com/topepo/caret")
5150 (synopsis "Classification and regression training")
5152 "This package provides misc functions for training and plotting
5153 classification and regression models.")
5154 (license license:gpl2+)))
5156 (define-public r-rcppprogress
5158 (name "r-rcppprogress")
5163 (uri (cran-uri "RcppProgress" version))
5166 "09ayw6d69i0lplmaj5md25p5hn1nmiyp6a4sh60v93nrrs1cq7iv"))))
5167 (properties `((upstream-name . "RcppProgress")))
5168 (build-system r-build-system)
5170 `(("r-devtools" ,r-devtools)
5171 ("r-rcpp" ,r-rcpp)))
5172 (home-page "https://github.com/kforner/rcpp_progress")
5173 (synopsis "Interruptible progress bar for C++ in R packages")
5175 "This package allows to display a progress bar in the R console for long running
5176 computations taking place in C++ code, and support for interrupting those computations
5177 even in multithreaded code, typically using OpenMP.")
5178 (license license:gpl3+)))
5180 (define-public r-mnormt
5187 (uri (cran-uri "mnormt" version))
5190 "1b34xxrnf35khsx82mhvmk96sgfr2flyasaah7qkb2976pwxay7z"))))
5191 (build-system r-build-system)
5193 `(("gfortran" ,gfortran)))
5194 (home-page "http://azzalini.stat.unipd.it/SW/Pkg-mnormt")
5195 (synopsis "Multivariate normal and \"t\" distributions")
5197 "This package provides functions for computing the density and the
5198 distribution function of multivariate normal and \"t\" random variables, and
5199 for generating random vectors sampled from these distributions. Probabilities
5200 are computed via non-Monte Carlo methods.")
5201 (license license:gpl2+)))
5203 (define-public r-numderiv
5206 (version "2016.8-1")
5210 (uri (cran-uri "numDeriv" version))
5213 "07ni52rwiap4wilfz94w5mrqaxr59axxmgn57857ip4p6qkiss0v"))))
5214 (properties `((upstream-name . "numDeriv")))
5215 (build-system r-build-system)
5216 (home-page "https://cran.r-project.org/web/packages/numDeriv")
5217 (synopsis "Accurate numerical derivatives")
5219 "This package provides methods for calculating accurate numerical
5220 first and second order derivatives.")
5221 (license license:gpl2)))
5230 (uri (cran-uri "sn" version))
5233 "0l7qlah6dwkp8jswnr2mn3phlm15naba5zkmv0g5pcqy5ix0gz7w"))))
5234 (build-system r-build-system)
5236 `(("r-mnormt" ,r-mnormt)
5237 ("r-numderiv" ,r-numderiv)))
5238 (home-page "http://azzalini.stat.unipd.it/SN")
5239 (synopsis "The skew-normal and skew-t distributions")
5241 "This packages provides functionalities to build and manipulate
5242 probability distributions of the skew-normal family and some related
5243 ones, notably the skew-t family, and provides related statistical
5244 methods for data fitting and diagnostics, in the univariate and the
5245 multivariate case.")
5246 (license license:gpl2+)))
5248 (define-public r-tclust
5255 (uri (cran-uri "tclust" version))
5258 "1li62wynv81kb17fx7nk63a26qlb78l8fdf63in8yzcl7fkpji7y"))))
5259 (build-system r-build-system)
5261 `(("r-cluster" ,r-cluster)
5262 ("r-mclust" ,r-mclust)
5263 ("r-mvtnorm" ,r-mvtnorm)
5265 (home-page "https://cran.r-project.org/web/packages/tclust")
5266 (synopsis "Robust trimmed clustering")
5268 "This package implements different robust clustering
5269 algorithms (@code{tclust}) based on trimming and including some graphical
5270 diagnostic tools (@code{ctlcurves} and @code{DiscrFact}).")
5271 (license license:gpl3)))
5273 (define-public r-ranger
5280 (uri (cran-uri "ranger" version))
5283 "1fdbm879wx3hlng8s4c4f8f2x5yxz57llakcqnpa0lymybidw3vz"))))
5284 (build-system r-build-system)
5286 `(("r-rcpp" ,r-rcpp)
5287 ("r-matrix" ,r-matrix)
5288 ("r-rcppeigen" ,r-rcppeigen)))
5289 (home-page "https://github.com/imbs-hl/ranger")
5290 (synopsis "Fast implementation of random forests")
5292 "This package provides a fast implementation of Random Forests,
5293 particularly suited for high dimensional data. Ensembles of classification,
5294 regression, survival and probability prediction trees are supported. Data from
5295 genome-wide association studies can be analyzed efficiently.")
5296 (license license:gpl3)))
5298 (define-public r-tsne
5305 (uri (cran-uri "tsne" version))
5308 "0s8cv2pndkddq62rzlgzgfdjp1vjv5hz5i5957sllnb97vbzbzb6"))))
5309 (build-system r-build-system)
5310 (home-page "https://github.com/jdonaldson/rtsne/")
5311 (synopsis "t-Distributed Stochastic Neighbor Embedding for R")
5313 "This package provides a pure R implementation of the t-SNE algorithm.")
5314 (license license:gpl2+)))
5316 (define-public r-cairo
5323 (uri (cran-uri "Cairo" version))
5326 "1x1q99r3r978rlkkm5gixkv03p0mcr6k7ydcqdmisrwnmrn7p1ia"))))
5327 (properties `((upstream-name . "Cairo")))
5328 (build-system r-build-system)
5333 `(("pkg-config" ,pkg-config)))
5334 (home-page "http://www.rforge.net/Cairo/")
5335 (synopsis "R graphics device using Cairo graphics library")
5337 "This package provides a Cairo graphics device that can be use to
5338 create high-quality vector (PDF, PostScript and SVG) and bitmap
5339 output (PNG,JPEG,TIFF), and high-quality rendering in displays (X11
5340 and Win32). Since it uses the same back-end for all output, copying
5341 across formats is WYSIWYG. Files are created without the dependence
5342 on X11 or other external programs. This device supports alpha
5343 channel (semi-transparent drawing) and resulting images can contain
5344 transparent and semi-transparent regions. It is ideal for use in
5345 server environments (file output) and as a replacement for other
5346 devices that don't have Cairo's capabilities such as alpha support or
5347 anti-aliasing. Backends are modular such that any subset of backends
5349 (license license:gpl2)))
5351 (define-public r-lubridate
5353 (name "r-lubridate")
5358 (uri (cran-uri "lubridate" version))
5361 "0pzvazzybzvln3y676yims7whsc74g8i7kgf2nsfbxdq5943z349"))))
5362 (build-system r-build-system)
5364 `(("r-rcpp" ,r-rcpp)
5365 ("r-stringr" ,r-stringr)))
5367 "https://cran.r-project.org/web/packages/lubridate")
5368 (synopsis "Make dealing with dates a little easier")
5370 "This package provides functions to work with date-times and time-spans:
5371 fast and user friendly parsing of date-time data, extraction and updating of
5372 components of a date-time (years, months, days, hours, minutes, and seconds),
5373 algebraic manipulation on date-time and time-span objects. The 'lubridate'
5374 package has a consistent and memorable syntax that makes working with dates
5376 (license license:gpl2)))
5378 (define-public r-fdrtool
5385 (uri (cran-uri "fdrtool" version))
5388 "1h46frlk7d9f4qx0bg6p55nrm9wwwz2sv6d1nz7061wdfsm69yb5"))))
5389 (build-system r-build-system)
5390 (home-page "http://strimmerlab.org/software/fdrtool/")
5391 (synopsis "Estimation of false discovery rates and higher criticism")
5393 "This package provides tools to estimate tail area-based false discovery
5394 rates as well as local false discovery rates for a variety of null
5395 models (p-values, z-scores, correlation coefficients, t-scores). The
5396 proportion of null values and the parameters of the null distribution are
5397 adaptively estimated from the data. In addition, the package contains
5398 functions for non-parametric density estimation (Grenander estimator), for
5399 monotone regression (isotonic regression and antitonic regression with
5400 weights), for computing the @dfn{greatest convex minorant} (GCM) and the
5401 @dfn{least concave majorant} (LCM), for the half-normal and correlation
5402 distributions, and for computing empirical @dfn{higher criticism} (HC) scores
5403 and the corresponding decision threshold.")
5404 (license license:gpl3+)))
5406 (define-public r-forcats
5413 (uri (cran-uri "forcats" version))
5416 "1mvwkynvvgz2vi8dyz11x7xrp53kadjawjcja34hwk1d89qf7g5m"))))
5417 (build-system r-build-system)
5419 `(("r-magrittr" ,r-magrittr)
5420 ("r-tibble" ,r-tibble)))
5421 (home-page "http://forcats.tidyverse.org")
5422 (synopsis "Tools for working with factors")
5423 (description "This package provides helpers for reordering factor
5424 levels (including moving specified levels to front, ordering by first
5425 appearance, reversing, and randomly shuffling), and tools for modifying factor
5426 levels (including collapsing rare levels into other, \"anonymizing\", and
5427 manually \"recoding\").")
5428 (license license:gpl3)))
5430 (define-public r-tgstat
5431 (let ((changeset "4f8e60c03598f49aff6f5beeab40f2b995377e9f")
5435 (version (string-append "1.0.2-" revision "." (string-take changeset 7)))
5440 (url "https://bitbucket.org/tanaylab/tgstat")
5441 (changeset changeset)))
5444 "0ilkkyximy77zbncm91kdfqbxf0qyndg16pd3q3p6a3xc9qcmxvn"))))
5445 (build-system r-build-system)
5448 (modify-phases %standard-phases
5449 (add-after 'unpack 'fix-isnan
5451 (substitute* "src/tgstat.h"
5452 (("#define isnan ::isnan")
5453 "#define isnan std::isnan"))
5456 `(("r-rcpp" ,r-rcpp)))
5457 (home-page "https://bitbucket.org/tanaylab/tgstat/")
5458 (synopsis "Tanay's group statistical utilities")
5460 "The goal of tgstat is to provide fast and efficient statistical
5462 (license license:gpl2))))
5464 (define-public r-tgconfig
5465 (let ((changeset "1e02c7614713bd0866c46f0c679a058f8c6d627e")
5469 (version (string-append "0.0.0.9000-" revision "." (string-take changeset 7)))
5474 (url "https://bitbucket.org/tanaylab/tgconfig")
5475 (changeset changeset)))
5478 "0xy6c7s7mn1yx191154bwbv1bl424bnvc80syqpl1vdl28ba46rj"))))
5479 (build-system r-build-system)
5481 `(("r-yaml" ,r-yaml)))
5482 (home-page "https://bitbucket.org/tanaylab/tgconfig/")
5483 (synopsis "Infrastructure for managing package parameters")
5485 "The goal of tgconfig is to provide infrastructure for managing package
5487 (license license:gpl3))))
5489 (define-public r-directlabels
5491 (name "r-directlabels")
5492 (version "2017.03.31")
5496 (uri (cran-uri "directlabels" version))
5499 "01ahw0c56mnzwl611s8hnghicww4c4dgf5v2wv6bl1s1pramw9pr"))))
5500 (build-system r-build-system)
5502 `(("r-quadprog" ,r-quadprog)))
5503 (home-page "http://directlabels.r-forge.r-project.org/")
5504 (synopsis "Direct labels for multicolor plots")
5506 "This package provides an extensible framework for automatically placing
5507 direct labels onto multicolor plots. Label positions are described using
5508 positioning methods that can be re-used across several different plots. There
5509 are heuristics for examining @code{trellis} and @code{ggplot} objects and
5510 inferring an appropriate positioning method.")
5511 (license license:gpl3)))