1 ;;; GNU Guix --- Functional package management for GNU
2 ;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022 Ricardo Wurmus <rekado@elephly.net>
3 ;;; Copyright © 2015 Andreas Enge <andreas@enge.fr>
4 ;;; Copyright © 2015, 2016 Pjotr Prins <pjotr.guix@thebird.nl>
5 ;;; Copyright © 2016, 2017 Ben Woodcroft <donttrustben@gmail.com>
6 ;;; Copyright © 2016, 2017, 2018, 2020, 2021 Roel Janssen <roel@gnu.org>
7 ;;; Copyright © 2017, 2018, 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
8 ;;; Copyright © 2017 Raoul Bonnal <ilpuccio.febo@gmail.com>
9 ;;; Copyright © 2018 Vijayalakshmi Vedantham <vijimay12@gmail.com>
10 ;;; Copyright © 2018 Sahithi Yarlagadda <sahi@swecha.net>
11 ;;; Copyright © 2018 Sandeep Subramanian <sandeepsubramanian94@gmail.com>
12 ;;; Copyright © 2018 Charlie Ritter <chewzeirta@posteo.net>
13 ;;; Copyright © 2018 Konrad Hinsen <konrad.hinsen@fastmail.net>
14 ;;; Copyright © 2018, 2020, 2021, 2022 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
15 ;;; Copyright © 2018 Laura Lazzati <laura.lazzati.15@gmail.com>
16 ;;; Copyright © 2018 Leo Famulari <leo@famulari.name>
17 ;;; Copyright © 2018 Marius Bakke <mbakke@fastmail.com>
18 ;;; Copyright © 2018, 2019 Brett Gilio <brettg@gnu.org>
19 ;;; Copyright © 2019 Nicolò Balzarotti <anothersms@gmail.com>
20 ;;; Copyright © 2019, 2020, 2021 Wiktor Żelazny <wzelazny@vurv.cz>
21 ;;; Copyright © 2019 Arne Babenhauserheide <arne_bab@web.de>
22 ;;; Copyright © 2019, 2020 Efraim Flashner <efraim@flashner.co.il>
23 ;;; Copyright © 2020 Todor Kondić <tk.code@protonmail.com>
24 ;;; Copyright © 2020 Danjela Lura <danielaluraa@gmail.com>
25 ;;; Copyright © 2020 Naga Malleswari <nagamalli@riseup.net>
26 ;;; Copyright © 2020 Eric Brown <ecbrown@ericcbrown.com>
27 ;;; Copyright © 2020 Peter Lo <peterloleungyau@gmail.com>
28 ;;; Copyright © 2020 Rafael Luque Leiva <rafael.luque@osoco.es>
29 ;;; Copyright © 2020, 2021 Lars-Dominik Braun <ldb@leibniz-psychology.org>
30 ;;; Copyright © 2020 Vinicius Monego <monego@posteo.net>
31 ;;; Copyright © 2020 Antoine Côté <antoine.cote@posteo.net>
32 ;;; Copyright © 2020 Arun Isaac <arunisaac@systemreboot.net>
33 ;;; Copyright © 2020 Magali Lemes <magalilemes00@gmail.com>
34 ;;; Copyright © 2020, 2021, 2022 Simon Tournier <zimon.toutoune@gmail.com>
35 ;;; Copyright © 2020 Aniket Patil <aniket112.patil@gmail.com>
36 ;;; Copyright © 2021 Marcel Schilling <marcel.schilling@uni-luebeck.de>
37 ;;; Copyright © 2021 Guillaume Le Vaillant <glv@posteo.net>
38 ;;; Copyright © 2022 Navid Afkhami <navid.afkhami@mdc-berlin.de>
40 ;;; This file is part of GNU Guix.
42 ;;; GNU Guix is free software; you can redistribute it and/or modify it
43 ;;; under the terms of the GNU General Public License as published by
44 ;;; the Free Software Foundation; either version 3 of the License, or (at
45 ;;; your option) any later version.
47 ;;; GNU Guix is distributed in the hope that it will be useful, but
48 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
49 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
50 ;;; GNU General Public License for more details.
52 ;;; You should have received a copy of the GNU General Public License
53 ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
55 (define-module (gnu packages cran)
56 #:use-module ((guix licenses) #:prefix license:)
57 #:use-module (guix packages)
58 #:use-module (guix download)
59 #:use-module (guix gexp)
60 #:use-module (guix git-download)
61 #:use-module (guix utils)
62 #:use-module (guix build-system gnu)
63 #:use-module (guix build-system r)
64 #:use-module (gnu packages)
65 #:use-module (gnu packages algebra)
66 #:use-module (gnu packages autotools)
67 #:use-module (gnu packages base)
68 #:use-module (gnu packages bioinformatics)
69 #:use-module (gnu packages c)
70 #:use-module (gnu packages compression)
71 #:use-module (gnu packages crypto)
72 #:use-module (gnu packages curl)
73 #:use-module (gnu packages databases)
74 #:use-module (gnu packages fontutils)
75 #:use-module (gnu packages fribidi)
76 #:use-module (gnu packages gcc)
77 #:use-module (gnu packages geo)
78 #:use-module (gnu packages ghostscript)
79 #:use-module (gnu packages gl)
80 #:use-module (gnu packages gnome)
81 #:use-module (gnu packages graph)
82 #:use-module (gnu packages gtk)
83 #:use-module (gnu packages haskell-xyz)
84 #:use-module (gnu packages icu4c)
85 #:use-module (gnu packages image)
86 #:use-module (gnu packages imagemagick)
87 #:use-module (gnu packages java)
88 #:use-module (gnu packages javascript)
89 #:use-module (gnu packages libevent)
90 #:use-module (gnu packages machine-learning)
91 #:use-module (gnu packages maths)
92 #:use-module (gnu packages mpi)
93 #:use-module (gnu packages multiprecision)
94 #:use-module (gnu packages networking)
95 #:use-module (gnu packages node)
96 #:use-module (gnu packages pcre)
97 #:use-module (gnu packages pdf)
98 #:use-module (gnu packages perl)
99 #:use-module (gnu packages pkg-config)
100 #:use-module (gnu packages pulseaudio) ;libsndfile
101 #:use-module (gnu packages protobuf)
102 #:use-module (gnu packages python)
103 #:use-module (gnu packages python-xyz)
104 #:use-module (gnu packages sqlite)
105 #:use-module (gnu packages statistics)
106 #:use-module (gnu packages tcl)
107 #:use-module (gnu packages textutils)
108 #:use-module (gnu packages tls)
109 #:use-module (gnu packages uglifyjs)
110 #:use-module (gnu packages version-control)
111 #:use-module (gnu packages video)
112 #:use-module (gnu packages web)
113 #:use-module (gnu packages xml)
114 #:use-module (gnu packages xorg))
116 (define-public r-afpt
122 (uri (cran-uri "afpt" version))
125 "0cg5cdm9nl1hs6f3j0ljpw4bkqvh3ksyj615b9nnbqs5k28lyds9"))))
126 (properties `((upstream-name . "afpt")))
127 (build-system r-build-system)
128 (native-inputs (list r-knitr))
129 (home-page "https://github.com/MarcoKlH/afpt-r/")
130 (synopsis "Tools for modelling of animal flight performance")
132 "This package allows estimation and modelling of flight costs in animal
133 (vertebrate) flight, implementing the aerodynamic power model. Flight
134 performance is estimated based on basic morphological measurements such as
135 body mass, wingspan and wing area. @code{Afpt} can be used to make
136 predictions on how animals should adjust their flight behaviour and wingbeat
137 kinematics to varying flight conditions.")
138 (license license:gpl3+)))
147 (uri (cran-uri "aod" version))
149 (base32 "0p2i536s0aa54rah1l465g77k2ldn6jm6s25y9vc06mk29xvx1cv"))))
150 (properties `((upstream-name . "aod")))
151 (build-system r-build-system)
152 (home-page "https://cran.r-project.org/package=aod")
153 (synopsis "Analysis of overdispersed data")
155 "This package provides a set of functions to analyze overdispersed counts
156 or proportions. Most of the methods are already available elsewhere but are
157 scattered in different packages. The proposed functions should be considered
158 as complements to more sophisticated methods such as @dfn{generalized
159 estimating equations} (GEE) or @dfn{generalized linear mixed effect
161 (license license:gpl2+)))
163 (define-public r-brio
170 (uri (cran-uri "brio" version))
173 "1inwzvlf6zj6gi47gd0byzqv02qajb3l475z8pjvx2b1hm0r1a7a"))))
174 (properties `((upstream-name . "brio")))
175 (build-system r-build-system)
176 (home-page "https://github.com/r-lib/brio")
177 (synopsis "Basic R input output")
179 "This package provides functions to handle basic input output. These
180 functions always read and write UTF-8 (8-bit Unicode Transformation Format)
181 files and provide more explicit control over line endings.")
182 (license license:expat)))
184 (define-public r-cachem
191 (uri (cran-uri "cachem" version))
194 "0r0q5w8lsxak46crnkbi739qzys90hlw7cqqqhv99xzkpkvm554s"))))
195 (properties `((upstream-name . "cachem")))
196 (build-system r-build-system)
198 (list r-fastmap r-rlang))
199 (home-page "https://cachem.r-lib.org/")
200 (synopsis "Cache R objects with automatic pruning")
202 "This package provides key-value stores with automatic pruning. Caches
203 can limit either their total size or the age of the oldest object (or both),
204 automatically pruning objects to maintain the constraints.")
205 (license license:expat)))
207 (define-public r-collections
209 (name "r-collections")
214 (uri (cran-uri "collections" version))
216 (base32 "053ig88pva78wxxwya3v7cz853k563dkpgxrf2xvd0l0d9fanxmz"))))
217 (properties `((upstream-name . "collections")))
218 (build-system r-build-system)
219 (home-page "https://github.com/randy3k/collections")
220 (synopsis "High performance container data types")
222 "This package provides high performance container data types such as
223 queues, stacks, deques, dicts and ordered dicts.")
224 (license license:expat)))
226 (define-public r-curry
233 (uri (cran-uri "curry" version))
236 "1ps9hvbnb02m0b8hlw4admwbziyjvswj08ldi2dk3ymnrpawcc29"))))
237 (properties `((upstream-name . "curry")))
238 (build-system r-build-system)
239 (home-page "https://github.com/thomasp85/curry")
240 (synopsis "Partial function application")
242 "Partial application is the process of reducing the arity of a function
243 by fixing one or more arguments, thus creating a new function lacking the
244 fixed arguments. The @code{curry} package provides three different ways of
245 performing partial function application by fixing arguments from either end of
246 the argument list (currying and tail currying) or by fixing multiple named
247 arguments (partial application). This package provides this functionality
248 through the @code{%<%}, @code{%-<%}, and @code{%><%} operators which allows
249 for a programming style comparable to modern functional languages. Compared
250 to other implementations such a @code{purrr::partial()} the operators in
251 @code{curry} composes functions with named arguments, aiding in autocomplete
253 (license license:gpl2+)))
255 (define-public r-datawizard
257 (name "r-datawizard")
262 (uri (cran-uri "datawizard" version))
265 "09lyh1awm2rplfzgwbdw4iy76mbaqwjd4hwlrsgvxj9pwdnjs4cx"))))
266 (properties `((upstream-name . "datawizard")))
267 (build-system r-build-system)
272 (home-page "https://easystats.github.io/datawizard/")
273 (synopsis "Easy data wrangling")
275 "This package provides a lightweight package to easily manipulate,
276 clean, transform, and prepare your data for analysis. It also forms the data
277 wrangling backend for the packages in the @code{easystats} ecosystem.")
278 (license license:gpl3)))
280 (define-public r-dbscan
287 (uri (cran-uri "dbscan" version))
289 (base32 "1h8x1v9kk5zmw5qd575cyr16yz8l226lsaq71n079l4i8crcrzg1"))))
290 (properties `((upstream-name . "dbscan")))
291 (build-system r-build-system)
292 (propagated-inputs (list r-rcpp))
293 (native-inputs (list r-knitr))
294 (home-page "https://github.com/mhahsler/dbscan")
295 (synopsis "Density-based spatial clustering of applications with noise")
297 "This package provides a fast reimplementation of several density-based
298 algorithms of the DBSCAN family. It includes the clustering algorithms DBSCAN
299 (density-based spatial clustering of applications with noise) and
300 @dfn{hierarchical DBSCAN} (HDBSCAN), the ordering algorithm @dfn{ordering
301 points to identify the clustering structure} (OPTICS), shared nearest neighbor
302 clustering, and the outlier detection algorithms @dfn{local outlier
303 factor} (LOF) and @dfn{global-local outlier score from hierarchies} (GLOSH).
304 The implementations use the kd-tree data structure for faster k-nearest
305 neighbor search. An R interface to fast kNN and fixed-radius NN search is
307 (license license:gpl2+)))
309 (define-public r-diffobj
316 (uri (cran-uri "diffobj" version))
319 "0q6gwd9pqh41f6j5p9jl92aji4p8kx9inffpha93d7jc3ndsfq6q"))))
320 (properties `((upstream-name . "diffobj")))
321 (build-system r-build-system)
322 (propagated-inputs (list r-crayon))
323 (native-inputs (list r-knitr))
324 (home-page "https://github.com/brodieG/diffobj")
325 (synopsis "Diffs for R objects")
327 "Generate a colorized diff of two R objects for an intuitive
328 visualization of their differences.")
329 (license license:gpl2+)))
331 (define-public r-dirichletreg
333 (name "r-dirichletreg")
338 (uri (cran-uri "DirichletReg" version))
340 (base32 "1ql5mwb7zb06y9j6inrlngq7c15as4j17wd8kc71fxs0a2jdj7xi"))))
341 (properties `((upstream-name . "DirichletReg")))
342 (build-system r-build-system)
343 (propagated-inputs (list r-formula r-maxlik))
344 (native-inputs (list r-knitr))
345 (home-page "https://cran.r-project.org/package=DirichletReg")
346 (synopsis "Dirichlet regression")
347 (description "This package implements Dirichlet regression models.")
348 (license license:gpl2+)))
350 (define-public r-emdist
357 (uri (cran-uri "emdist" version))
360 "05mv6xhm15b0mq9kzyiblkb14bdqmjrwl64ghdk66il0w8i7p6nh"))))
361 (properties `((upstream-name . "emdist")))
362 (build-system r-build-system)
363 (home-page "http://www.rforge.net/emd")
364 (synopsis "Earth mover's distance")
366 "This package provides tools to calculate the Earth Mover's
368 (license license:expat)))
370 (define-public r-googledrive
372 (name "r-googledrive")
377 (uri (cran-uri "googledrive" version))
380 "09jsiknzyfgxd0nzdr3wrrjw24allch2x74h96qg8vh8dad4cp30"))))
381 (properties `((upstream-name . "googledrive")))
382 (build-system r-build-system)
400 (home-page "https://googledrive.tidyverse.org")
401 (synopsis "Interface to Google Drive")
402 (description "This package lets you manage Google Drive files from R.")
403 (license license:expat)))
405 (define-public r-guix-install
407 (name "r-guix-install")
412 (uri (cran-uri "guix.install" version))
414 (base32 "0s3wb5781yc43c9zwrn7i87zcbrlx7xr0ms0v9hvgs7qsv02id9j"))))
415 (properties `((upstream-name . "guix.install")))
416 (build-system r-build-system)
417 (propagated-inputs (list r-runit))
418 (home-page "https://github.com/BIMSBbioinfo/guix.install")
419 (synopsis "Install R packages with GNU Guix")
421 "This R package provides a single procedure @code{guix.install()}, which
422 allows users to install R packages via Guix right from within their running R
423 session. If the requested R package does not exist in Guix at this time, the
424 package and all its missing dependencies will be imported recursively and the
425 generated package definitions will be written to @file{~/.Rguix/packages.scm}.
426 This record of imported packages can be used later to reproduce the
427 environment, and to add the packages in question to a proper Guix channel (or
428 Guix itself). @code{guix.install()} not only supports installing packages
429 from CRAN, but also from Bioconductor or even arbitrary git or mercurial
430 repositories, replacing the need for installation via @code{devtools}.")
431 (license license:gpl3+)))
440 (uri (cran-uri "ids" version))
443 "1s6ga94gds5ydr9f8qbjfgfpg2dvbnkcrlybqlb33hk3c0c2l8dn"))))
444 (properties `((upstream-name . "ids")))
445 (build-system r-build-system)
447 (list r-openssl r-uuid))
448 (native-inputs (list r-knitr))
449 (home-page "https://github.com/richfitz/ids")
450 (synopsis "Generate random identifiers")
452 "This package lets you generate random or human readable and
453 pronounceable identifiers.")
454 (license license:expat)))
456 (define-public r-googlesheets4
458 (name "r-googlesheets4")
463 (uri (cran-uri "googlesheets4" version))
466 "0yncqwv9l5knyrv88ys5gwcv44hl1j0mbklpins6v7f9m9v7s40a"))))
467 (properties `((upstream-name . "googlesheets4")))
468 (build-system r-build-system)
484 (home-page "https://github.com/tidyverse/googlesheets4")
485 (synopsis "Access Google Sheets using the Sheets API V4")
487 "This package lets you interact with Google Sheets through the
488 @url{https://developers.google.com/sheets/api,Sheets API v4}. This package
489 can read and write both the metadata and the cell data in a Sheet.")
490 (license license:expat)))
492 (define-public r-waldo
499 (uri (cran-uri "waldo" version))
502 "1aky28rn70l24s0sygl36267cf7hjzhchagsz26abfxwr7p8kvjp"))))
503 (properties `((upstream-name . "waldo")))
504 (build-system r-build-system)
513 (home-page "https://github.com/r-lib/waldo")
514 (synopsis "Find differences between R objects")
516 "Compare complex R objects and reveal the key differences. This package
517 was designed particularly for use in testing packages where being able to
518 quickly isolate key differences makes understanding test failures much
520 (license license:expat)))
522 (define-public r-rticles
529 (uri (cran-uri "rticles" version))
532 "1ipblw3rmkma22jl2hf1pyfm6l8k31zcmm3swmwii6k0x7khiav1"))))
533 (properties `((upstream-name . "rticles")))
534 (build-system r-build-system)
536 (list r-knitr r-rmarkdown r-tinytex r-xfun r-yaml))
537 (home-page "https://github.com/rstudio/rticles")
538 (synopsis "Article formats for R Markdown")
540 "This package provides a suite of custom R Markdown formats and templates
541 for authoring journal articles and conference submissions.")
542 (license license:gpl3)))
544 (define-public r-babelwhale
546 (name "r-babelwhale")
551 (uri (cran-uri "babelwhale" version))
553 (base32 "0ph825dwvr48fhamy1l5564linz7cj7b9sj511as77f1yqycv4a2"))))
554 (properties `((upstream-name . "babelwhale")))
555 (build-system r-build-system)
557 (list r-crayon r-dplyr r-dynutils r-processx r-purrr))
558 (home-page "https://github.com/dynverse/babelwhale")
559 (synopsis "Talking to Docker and Singularity containers")
561 "This package provides a unified interface to interact with Docker and
562 Singularity containers. You can execute a command inside a container, mount a
563 volume or copy a file.")
564 (license license:expat)))
566 (define-public r-benchmarkmedata
568 (name "r-benchmarkmedata")
572 (uri (cran-uri "benchmarkmeData" version))
575 "1n4vjkagqlm6kw2hilf4gjfcdjad0bcg652j9nl2ygbq3kdnh1vf"))))
576 (build-system r-build-system)
578 (list r-dplyr r-tibble))
579 (home-page "https://github.com/csgillespie/benchmarkme-data")
580 (synopsis "Data set for the @code{benchmarkme} package")
581 (description "This package contains the data set for the crowd-sourced
582 benchmarks from running the @code{benchmarkme} package.")
583 (license license:gpl2+)))
585 (define-public r-benchmarkme
587 (name "r-benchmarkme")
591 (uri (cran-uri "benchmarkme" version))
594 "0ymgsxzrvnpyvs0cff09d3lrkl12qyqx5bwammsc4vgl5ng9p69p"))))
595 (build-system r-build-system)
599 (list r-benchmarkmedata
606 (home-page "https://csgillespie.github.io/benchmarkme/")
607 (synopsis "Crowd-sourced system benchmarks")
608 (description "This package provides functionality to benchmark your CPU
609 and compare against other CPUs. Also provides functions for obtaining system
610 specifications, such as RAM, CPU type, and R version.")
611 (license license:gpl2+)))
613 (define-public r-bezier
619 (uri (cran-uri "bezier" version))
622 "1vw5128v8h973xwa1fdm9cw2jvrldj87nd55lddlp3qsz3ag4br6"))))
623 (build-system r-build-system)
624 (home-page "https://cran.r-project.org/web/packages/bezier/")
625 (synopsis "Bezier curve and spline toolkit")
627 "This package is a toolkit for working with Bezier curves and splines.
628 The package provides functions for point generation, arc length estimation,
629 degree elevation and curve fitting.")
630 (license license:gpl2+)))
632 (define-public r-bwstest
639 (uri (cran-uri "BWStest" version))
641 (base32 "02amzlfprmw5pyis0dg0kg0x8xqh50a4vfdcxxmklrzik3b1vzzs"))))
642 (properties `((upstream-name . "BWStest")))
643 (build-system r-build-system)
644 (propagated-inputs (list r-memoise r-rcpp))
645 (home-page "https://github.com/shabbychef/BWStest")
646 (synopsis "Baumgartner Weiss Schindler Test of equal distributions")
648 "This package performs the Baumgartner-Weiss-Schindler two-sample test of
649 equal probability distributions (doi:10.2307/2533862). It also performs
650 similar rank-based tests for equal probability distributions due to Neuhauser
651 (doi:10.1080/10485250108832874) and Murakami
652 (doi:10.1080/00949655.2010.551516).")
653 (license license:lgpl3)))
662 (uri (cran-uri "V8" version))
665 "0hs7ajjw6y3q7mp7z00a9712y4cn6wgcnk5dbjbzlc6cfk4zsqkc"))))
666 (properties `((upstream-name . "V8")))
667 (build-system r-build-system)
670 (modify-phases %standard-phases
671 (add-after 'unpack 'find-v8
672 (lambda* (#:key inputs #:allow-other-keys)
673 (substitute* "configure"
675 (string-append "PKG_LIBS="
676 (assoc-ref inputs "libnode")
677 "/lib/libnode.so.64\n")))
678 (setenv "INCLUDE_DIR"
680 (assoc-ref inputs "libnode")
684 (assoc-ref inputs "libnode") "/lib")))))))
688 (list r-curl r-jsonlite r-rcpp))
691 (home-page "https://jeroen.cran.dev/V8")
692 (synopsis "Embedded JavaScript and WebAssembly engine for R")
694 "This package provides an R interface to V8: Google's JavaScript and
695 WebAssembly engine.")
696 (license license:expat)))
705 (uri (cran-uri "DOT" version))
708 "0qh5n57cp9c2n5yn59q4wggz82943pwfanp3kx869aba2x3sj30i"))))
709 (properties `((upstream-name . "DOT")))
710 (build-system r-build-system)
713 (home-page "http://haghish.com/dot")
714 (synopsis "Render and Export DOT Graphs in R")
716 "This package provides tools to render DOT diagram markup language in R
717 and also provides the possibility to export the graphs in PostScript and
718 SVG (Scalable Vector Graphics) formats. In addition, it supports literate
719 programming packages such as @code{knitr} and @code{rmarkdown}.")
720 (license license:expat)))
722 (define-public r-carrier
729 (uri (cran-uri "carrier" version))
731 (base32 "0bqnwnnjqjk9q0lxq6kkz9s75ss10lfyyywyyi24m8wppxpw1vqc"))))
732 (properties `((upstream-name . "carrier")))
733 (build-system r-build-system)
735 (list r-pryr r-rlang))
736 (home-page "https://github.com/r-lib/carrier")
737 (synopsis "Isolate functions for remote execution")
739 "Sending functions to remote processes can be wasteful of resources
740 because they carry their environments with them. With this package, it is
741 easy to create functions that are isolated from their environment. These
742 isolated functions, also called crates, print to the console with their total
743 size and can be easily tested locally before being sent to a remote.")
744 (license license:gpl3)))
746 (define-public r-clipr
753 (uri (cran-uri "clipr" version))
756 "1s9vvv3cxnz8w11gsi8z9ddv9jzib5qf5qqxnwqrrv7vj8cr7hij"))))
757 (build-system r-build-system)
760 (home-page "https://github.com/mdlincoln/clipr")
761 (synopsis "Read and write from the system clipboard")
763 "This package provides simple utility functions to read from and write to
764 the system clipboards.")
765 (license license:gpl3)))
774 (uri (cran-uri "dlm" version))
776 (base32 "1aksm66sfa7ipl5xgs4j5giac7q2m744wjl40mva56xn6i674h4r"))))
777 (properties `((upstream-name . "dlm")))
778 (build-system r-build-system)
779 (home-page "https://cran.r-project.org/package=dlm")
780 (synopsis "Bayesian and Likelihood Analysis of Dynamic Linear Models")
782 "This package provides routines for Maximum likelihood, Kalman filtering
783 and smoothing, and Bayesian analysis of Normal linear State Space models, also
784 known as Dynamic Linear Models.")
785 (license license:gpl2+)))
793 (uri (cran-uri "zoo" version))
796 "0izd66dywq6qd62hdp64apncainrrb9mgmm19wf6a8jc03c858n9"))))
797 (build-system r-build-system)
800 (home-page "http://zoo.R-Forge.R-project.org/")
801 (synopsis "S3 infrastructure for regular and irregular time series")
802 (description "This package contains an S3 class with methods for totally
803 ordered indexed observations. It is particularly aimed at irregular time
804 series of numeric vectors/matrices and factors.")
805 (license license:gpl2+)))
807 (define-public r-fontawesome
809 (name "r-fontawesome")
814 (uri (cran-uri "fontawesome" version))
816 (base32 "0r6zb5175cr4ybqj6bl0mbhadwv9xjxaf32yjc0y76rw3d6vcbap"))))
817 (properties `((upstream-name . "fontawesome")))
818 (build-system r-build-system)
820 (list r-htmltools r-rlang))
821 (home-page "https://github.com/rstudio/fontawesome")
822 (synopsis "Easily work with Font Awesome icons")
824 "Easily and flexibly insert Font Awesome icons into R Markdown documents
825 and Shiny apps. These icons can be inserted into HTML content through inline
826 SVG tags or @code{i} tags. There is also a utility function for exporting
827 Font Awesome icons as PNG images for those situations where raster graphics
829 (license license:expat)))
831 (define-public r-fingerprint
833 (name "r-fingerprint")
838 (uri (cran-uri "fingerprint" version))
840 (base32 "04jcwkydjrs31pia6kq8z2n9s54im950q08hs2ay15xjxxkmb8ic"))))
841 (properties `((upstream-name . "fingerprint")))
842 (build-system r-build-system)
843 (home-page "https://cran.r-project.org/package=fingerprint")
844 (synopsis "Functions to Operate on Binary Fingerprint Data")
846 "This package provides functions to manipulate binary fingerprints of
847 arbitrary length. A fingerprint is represented by an object of S4 class
848 @code{fingerprint}. The bitwise logical functions in R are overridden so that
849 they can be used directly with @code{fingerprint} objects. A number of
850 distance metrics are also available. Fingerprints can be converted to
851 Euclidean vectors (i.e., points on the unit hypersphere) and can also be
852 folded. Arbitrary fingerprint formats can be handled via line handlers.
853 Currently handlers are provided for CDK, MOE and BCI fingerprint data.")
854 ;; Any version of the GPL
855 (license (list license:gpl2+ license:gpl3+))))
857 (define-public r-fpeek
864 (uri (cran-uri "fpeek" version))
866 (base32 "0kv46g21ndxchg3q8ynq7hjjkh6i2zlc21axn5y1jjzigrw047ii"))))
867 (properties `((upstream-name . "fpeek")))
868 (build-system r-build-system)
869 (propagated-inputs (list r-rcpp))
870 (home-page "https://github.com/davidgohel/fpeek")
871 (synopsis "Check text files content at a glance")
873 "This package provides tools to help working with text files. It can
874 return the number of lines; print the first and last lines; convert encoding.
875 Operations are made without reading the entire file before starting, resulting
876 in good performances with large files.")
877 (license license:expat)))
879 (define-public r-ggalluvial
881 (name "r-ggalluvial")
885 (uri (cran-uri "ggalluvial" version))
888 "0mkan9gxg3yxjism22yxbhvlh2lh7wpbrqpb355za790prcmjbh3"))))
889 (properties `((upstream-name . "ggalluvial")))
890 (build-system r-build-system)
900 (home-page "http://corybrunson.github.io/ggalluvial/")
901 (synopsis "Alluvial plots for ggplot2")
902 (description "This package provides alluvial plots for @code{ggplot2}.
903 Alluvial plots use variable-width ribbons and stacked bar plots to represent
904 multi-dimensional or repeated-measures data with categorical or ordinal
906 (license license:gpl3)))
908 (define-public r-ggpp
915 (uri (cran-uri "ggpp" version))
918 "0wcaczxjav5yg8h2197cf288mqk13p3iq675q0x0di9g8lnblvk1"))))
919 (properties `((upstream-name . "ggpp")))
920 (build-system r-build-system)
938 (home-page "https://docs.r4photobiology.info/ggpp/")
939 (synopsis "Grammar extensions to ggplot2")
941 "This package contains extensions to ggplot2.
944 @item Geomas: @code{geom_table}, @code{geom_plot} and @code{geom_grob} add
945 insets to plots using native data coordinates, while @code{geom_table_npc},
946 @code{geom_plot_npc} and @code{geom_grob_npc} do the same using @code{npc}
947 coordinates through new aesthetics @code{npcx} and @code{npcy}.
948 @item Statistics: select observations based on 2D density.
949 @item Positions: radial nudging away from a center point and nudging away from
953 (license license:gpl2+)))
955 (define-public r-lmds
962 (uri (cran-uri "lmds" version))
964 (base32 "130azb0nc2wwxv0qi8v5s4rd02p9lc92zwn634pv7b8awbw81i65"))))
965 (properties `((upstream-name . "lmds")))
966 (build-system r-build-system)
968 (list r-assertthat r-dynutils r-irlba r-matrix))
969 (home-page "https://github.com/dynverse/lmds")
970 (synopsis "Landmark multi-dimensional scaling")
972 "This package provides a fast dimensionality reduction method scalable
973 to large numbers of samples. @dfn{Landmark Multi-Dimensional Scaling} (LMDS)
974 is an extension of classical Torgerson MDS, but rather than calculating a
975 complete distance matrix between all pairs of samples, only the distances
976 between a set of landmarks and the samples are calculated.")
977 (license license:gpl3)))
979 (define-public r-lmodel2
986 (uri (cran-uri "lmodel2" version))
988 (base32 "1fiin2nkffbihz1s8ixmw9lgf8mn3j9krr8iiflizk10mdv54hnb"))))
989 (properties `((upstream-name . "lmodel2")))
990 (build-system r-build-system)
991 (home-page "https://cran.r-project.org/package=lmodel2")
992 (synopsis "Model II regression")
994 "This package computes model II simple linear regression using
995 @dfn{ordinary least squares} (OLS), @dfn{major axis} (MA), @dfn{standard major
996 axis} (SMA), and @dfn{ranged major axis} (RMA).")
997 (license license:gpl2)))
999 (define-public r-ggpmisc
1005 (uri (cran-uri "ggpmisc" version))
1008 "1iq39rx4nj1lf37hnj4df0c7gbk9374d0mzcnhdr7aqpxaxgs3ys"))))
1009 (build-system r-build-system)
1027 (home-page "https://www.r4photobiology.info/")
1028 (synopsis "Miscellaneous Extensions to @code{ggplot2}")
1029 (description "This package provides extensions to @code{ggplot2},
1030 respecting the grammar of its graphics paradigm.")
1031 (license license:gpl2+)))
1033 (define-public r-ggside
1039 (uri (cran-uri "ggside" version))
1042 "1x505zizv7hf65pxp9j5v92c3bchhxh9dsrkk1m55kwqqnsl5nza"))))
1043 (properties `((upstream-name . "ggside")))
1044 (build-system r-build-system)
1045 (propagated-inputs (list r-ggplot2 r-glue r-gtable r-rlang r-scales))
1046 (native-inputs (list r-knitr))
1047 (home-page "https://cran.r-project.org/package=ggside")
1048 (synopsis "Side grammar graphics that extends @code{ggplot2}")
1050 "The grammar of graphics as shown in @code{ggplot2} has provided an
1051 expressive API for users to build plots. This package @{ggside} extends
1052 @code{ggplot2} by allowing users to add graphical information about one of the
1053 main panel's axis using a familiar @code{ggplot2} style API with tidy data.
1054 This package is particularly useful for visualizing metadata on a discrete
1055 axis, or summary graphics on a continuous axis such as a boxplot or a density
1057 (license license:expat)))
1059 (define-public r-gprofiler
1061 (name "r-gprofiler")
1066 (uri (cran-uri "gProfileR" version))
1069 "1h1v0kgpsn04ald2izznh7fr2riwisj5hcgz4k7h3qc931rf0r4k"))))
1070 (properties `((upstream-name . "gProfileR")))
1071 (build-system r-build-system)
1073 (list r-plyr r-rcurl))
1074 (home-page "https://cran.r-project.org/web/packages/gProfileR/")
1075 (synopsis "Interface to the g:Profiler toolkit")
1077 "This package provides tools for functional enrichment analysis,
1078 gene identifier conversion and mapping homologous genes across related
1079 organisms via the @code{g:Profiler} toolkit.")
1080 (license license:gpl2+)))
1082 (define-public r-gprofiler2
1084 (name "r-gprofiler2")
1089 (uri (cran-uri "gprofiler2" version))
1092 "0r0h34b35xzgd9rh55yndn0anxy0z45zdlqa6qfmpn91b6v1bb1g"))))
1093 (properties `((upstream-name . "gprofiler2")))
1094 (build-system r-build-system)
1105 (native-inputs (list r-knitr))
1106 (home-page "https://cran.r-project.org/web/packages/gprofiler2/")
1107 (synopsis "Interface to the g:Profiler toolset")
1109 "This package provides a toolset for functional enrichment analysis and
1110 visualization, gene/protein/SNP identifier conversion and mapping orthologous
1111 genes across species via @url{https://biit.cs.ut.ee/gprofiler,g:Profiler}.
1115 @item @code{g:GOSt}, functional enrichment analysis and visualization of gene
1117 @item @code{g:Convert}, gene/protein/transcript identifier conversion across
1119 @item @code{g:Orth}, orthology search across species;
1120 @item @code{g:SNPense}, mapping SNP rs identifiers to chromosome positions,
1121 genes and variant effects.
1124 This package is an R interface corresponding to the 2019 update of
1125 @code{g:Profiler} and provides access to versions @code{e94_eg41_p11} and
1127 (license license:gpl2+)))
1129 (define-public r-oenb
1136 (uri (cran-uri "oenb" version))
1139 "1jgxw7ycx2lcdzglg9nix8k08fs4r6i5jdsjzrd6w1dg6smsinl5"))))
1140 (properties `((upstream-name . "oenb")))
1141 (build-system r-build-system)
1143 (list r-dplyr r-xml))
1144 (native-inputs (list r-knitr))
1145 (home-page "https://github.com/franzmohr/oenb")
1146 (synopsis "Tools for the OeNB Data Web Service")
1148 "Tools to access data from the data web service of the
1149 @acronym{OeNB, Oesterreichische Nationalbank},
1150 @url{https://www.oenb.at/en/Statistics/User-Defined-Tables/webservice.html}.")
1151 (license license:gpl2+)))
1153 (define-public r-orgmassspecr
1155 (name "r-orgmassspecr")
1159 (uri (cran-uri "OrgMassSpecR" version))
1162 "1dx9d8rb1dfqyhyc26zhfnxiv3rz2ikvs2mwqnsrq3lsjs9dvyc8"))))
1163 (properties `((upstream-name . "OrgMassSpecR")))
1164 (build-system r-build-system)
1165 (native-inputs (list r-knitr))
1166 (home-page "http://OrgMassSpec.github.io/")
1167 (synopsis "Organic or biological mass spectrometry data analysis")
1169 "This package @code{OrgMassSpecR} is an extension of the @code{R}
1170 statistical computing language. It contains functions to assist with organic
1171 or biological mass spectrometry data analysis. Mass spectral libraries are
1172 available as companion packages.")
1173 (license license:bsd-2)))
1175 (define-public r-scales
1182 (uri (cran-uri "scales" version))
1184 (base32 "1pq2rrix6a5gsi8xw38viiydp1bsxxmcmyy7dv9q8gkb1qj50p8q"))))
1185 (build-system r-build-system)
1195 (home-page "https://github.com/hadley/scales")
1196 (synopsis "Scale functions for visualization")
1198 "This package provides graphical scales that map data to aesthetics, and
1199 provides methods for automatically determining breaks and labels for axes and
1201 (license license:expat)))
1203 (define-public r-pacman
1209 (uri (cran-uri "pacman" version))
1212 "0z7gngd6h83cpjhq1vg75wvzhdjbgjh7gj5d4zvvi9gd2lmagjcy"))))
1213 (build-system r-build-system)
1216 (home-page "https://github.com/trinker/pacman")
1217 (synopsis "Package Management Tool")
1218 (description "This package provides tools to more conveniently perform
1219 tasks associated with add-on packages. @code{pacman} conveniently wraps
1220 library and package related functions and names them in an intuitive and
1221 consistent fashion. It seeks to combine functionality from lower level
1222 functions which can speed up workflow.")
1223 (license license:gpl2)))
1225 (define-public r-paralleldist
1227 (name "r-paralleldist")
1232 (uri (cran-uri "parallelDist" version))
1234 (base32 "01ly4hxwa64a0ya5gla8rvv72s9mcknsfznivjkh937pbjwb7iih"))))
1235 (properties `((upstream-name . "parallelDist")))
1236 (build-system r-build-system)
1237 (propagated-inputs (list r-rcpp r-rcpparmadillo r-rcppparallel))
1238 (home-page "https://github.com/alexeckert/parallelDist")
1239 (synopsis "Parallel Distance Matrix Computation using multiple threads")
1241 "This package provides a fast parallelized alternative to R's native
1242 @code{dist} function to calculate distance matrices for continuous, binary,
1243 and multi-dimensional input matrices, which supports a broad variety of
1244 predefined distance functions from other R packages, as well as user- defined
1245 functions written in C++. For ease of use, the @code{parDist} function
1246 extends the signature of the @code{dist} function and uses the same parameter
1247 naming conventions as distance methods of existing R packages.")
1248 (license license:gpl2+)))
1250 (define-public r-pheatmap
1257 (uri (cran-uri "pheatmap" version))
1260 "1hdh74az3vyzz6dqa311rhxdm74n46lyr03p862kn80p0kp9d7ap"))))
1261 (build-system r-build-system)
1263 (list r-gtable r-rcolorbrewer r-scales))
1264 (home-page "https://cran.r-project.org/web/packages/pheatmap")
1265 (synopsis "Pretty heatmaps")
1267 "This package provides an implementation of heatmaps that offers more
1268 control over dimensions and appearance.")
1269 (license license:gpl2+)))
1271 (define-public r-pnwcolors
1273 (name "r-pnwcolors")
1278 (uri (cran-uri "PNWColors" version))
1281 "1phplnclkficfv8s6wsyrckk4ixzbayiy5iix6dddg40485l9nyj"))))
1282 (properties `((upstream-name . "PNWColors")))
1283 (build-system r-build-system)
1284 (home-page "https://github.com/jakelawlor/PNWColors")
1285 (synopsis "Color palettes for data visualizations")
1287 "This package provides color palettes. They are checked for colorblind
1288 accessibility from hue, saturation, and lightness value scaling using the
1289 Chroma.js Color Palette Helper. See @url{https://gka.github.io/palettes}.")
1290 (license license:cc0)))
1292 (define-public r-plotfunctions
1294 (name "r-plotfunctions")
1299 (uri (cran-uri "plotfunctions" version))
1301 (base32 "0asmxw8283fpvl83h478j5nyg59xqifqaa8f2f6l199gvvswhhg2"))))
1302 (properties `((upstream-name . "plotfunctions")))
1303 (build-system r-build-system)
1304 (native-inputs (list r-knitr))
1305 (home-page "https://jacolienvanrij.com/tutorials.html")
1306 (synopsis "Various functions to facilitate visualization of data and analysis")
1308 "When analyzing data, plots are a helpful tool for visualizing data and
1309 interpreting statistical models. This package provides a set of simple tools
1310 for building plots incrementally, starting with an empty plot region, and
1311 adding bars, data points, regression lines, error bars, gradient legends,
1312 density distributions in the margins, and even pictures. The package builds
1313 further on R graphics by simply combining functions and settings in order to
1314 reduce the amount of code to produce for the user. As a result, the package
1315 does not use formula input or special syntax, but can be used in combination
1316 with default R plot functions.")
1317 (license license:gpl2+)))
1319 (define-public r-polychrome
1321 (name "r-polychrome")
1326 (uri (cran-uri "Polychrome" version))
1328 (base32 "0hyi02m2jpdhk1ky6ihz6dv5pwqwjwk4csjim2qr8ywx8midmrvg"))))
1329 (properties `((upstream-name . "Polychrome")))
1330 (build-system r-build-system)
1332 (list r-colorspace r-scatterplot3d))
1335 (home-page "http://oompa.r-forge.r-project.org/")
1336 (synopsis "Qualitative palettes with many colors")
1338 "This package provides tools for creating, viewing, and assessing
1339 qualitative palettes with many (20-30 or more) colors. See Coombes and
1340 colleagues (2019) @url{https://doi:10.18637/jss.v090.c01}.")
1341 (license license:asl2.0)))
1343 (define-public r-ecp
1349 (uri (cran-uri "ecp" version))
1352 "0n602jssl6rf596nwm6hbl7s9vdlqi20w8mrhxicj373mw5v22m8"))))
1353 (build-system r-build-system)
1356 (home-page "https://cran.r-project.org/web/packages/ecp/")
1357 (synopsis "Multiple change-point analysis of multivariate data")
1359 "This package implements various procedures for finding multiple
1360 change-points. Two methods make use of dynamic programming and pruning, with
1361 no distributional assumptions other than the existence of certain absolute
1362 moments in one method. Hierarchical and exact search methods are included.
1363 All methods return the set of estimated change-points as well as other summary
1365 (license license:gpl2+)))
1367 (define-public r-ellipsis
1374 (uri (cran-uri "ellipsis" version))
1377 "0n0mm9jngklv7j9wa64jdji035z0smmnsp2dfwcz9isrxgjnc0m9"))))
1378 (build-system r-build-system)
1381 (home-page "https://github.com/hadley/ellipsis")
1382 (synopsis "Tools for working with additional arguments")
1384 "In S3 generics, it's useful to take @code{...} so that methods can have
1385 additional arguments. But this flexibility comes at a cost: misspelled
1386 arguments will be silently ignored. The @code{ellipsis} package is an
1387 experiment that allows a generic to warn if any arguments passed in @code{...}
1389 (license license:gpl3)))
1398 (uri (cran-uri "GA" version))
1400 (base32 "135z03lnbj44jihnk6dii5a684jmc666ncpdwyyi910vl4sccib2"))))
1401 (properties `((upstream-name . "GA")))
1402 (build-system r-build-system)
1412 (home-page "https://luca-scr.github.io/GA/")
1413 (synopsis "Genetic algorithms for stochastic optimisation")
1415 "Flexible general-purpose toolbox implementing genetic algorithms (GAs)
1416 for stochastic optimisation. Binary, real-valued, and permutation
1417 representations are available to optimize a fitness function, i.e., a function
1418 provided by users depending on their objective function. Several genetic
1419 operators are available and can be combined to explore the best settings for
1420 the current task. Furthermore, users can define new genetic operators and
1421 easily evaluate their performances. Local search using general-purpose
1422 optimisation algorithms can be applied stochastically to exploit interesting
1423 regions. GAs can be run sequentially or in parallel, using an explicit
1424 master-slave parallelisation or a coarse-grain islands approach.")
1425 (license license:gpl2+)))
1427 (define-public r-grr
1434 (uri (cran-uri "grr" version))
1437 "0arbcgrvhkwb5xk4nry1ffg2qj0v8ivhjghdr505ib4357g0c9i9"))))
1438 (build-system r-build-system)
1439 (home-page "https://cran.r-project.org/web/packages/grr")
1440 (synopsis "Alternative implementations of base R functions")
1442 "This package provides alternative implementations of some base R
1443 functions, including @code{sort}, @code{order}, and @code{match}. The
1444 functions are simplified but can be faster or have other advantages.")
1445 (license license:gpl3)))
1447 (define-public r-matrix-utils
1449 (name "r-matrix-utils")
1454 (uri (cran-uri "Matrix.utils" version))
1457 "0a5fq1scykqk0kc9j051j6fix6j2dqwz5wbgb0amaxsiywz9vigb"))))
1458 (properties `((upstream-name . "Matrix.utils")))
1459 (build-system r-build-system)
1461 (list r-grr r-matrix))
1462 (home-page "https://github.com/cvarrichio/Matrix.utils")
1464 "Data.frame-Like Operations on Sparse and Dense Matrix Objects")
1466 "This package implements data manipulation methods such as @code{cast},
1467 @code{aggregate}, and @code{merge}/@code{join} for Matrix and Matrix-like
1469 (license license:gpl3)))
1471 (define-public r-mboost
1477 (uri (cran-uri "mboost" version))
1480 "01ln0vxbbx1fq77q17sx61si82lhfibbchsnf2yw9032cn8wnhh2"))))
1481 (build-system r-build-system)
1490 (home-page "https://github.com/boost-R/mboost")
1491 (synopsis "Model-based boosting")
1493 "This package provides a functional gradient descent algorithm (boosting)
1494 for optimizing general risk functions utilizing component-wise (penalised)
1495 least squares estimates or regression trees as base-learners for fitting
1496 generalized linear, additive and interaction models to potentially
1497 high-dimensional data.")
1498 (license license:gpl2)))
1500 (define-public r-shadowtext
1502 (name "r-shadowtext")
1506 (uri (cran-uri "shadowtext" version))
1509 "0zdfidrcnmxmfhngv86ppxrjmpmz9kl78l4yfah2lc5vgmrlwg15"))))
1510 (properties `((upstream-name . "shadowtext")))
1511 (build-system r-build-system)
1513 (list r-ggplot2 r-scales))
1516 (home-page "https://github.com/GuangchuangYu/shadowtext/")
1517 (synopsis "Shadow text grob and layer")
1518 (description "This package implements @code{shadowtextGrob()} for
1519 @code{grid} and @code{geom_shadowtext()} layer for @code{ggplot2}.
1520 These functions draw text grob with background shadow.")
1521 (license license:artistic2.0)))
1523 (define-public r-sys
1530 (uri (cran-uri "sys" version))
1533 "11q4zmx62w44p1j34frwmrsp23mc7l4n354i0zyziw92yax8zy0p"))))
1534 (build-system r-build-system)
1535 (home-page "https://github.com/jeroen/sys")
1536 (synopsis "Powerful and reliable tools for running system commands in R")
1538 "This package provides drop-in replacements for the base @code{system2()}
1539 function with fine control and consistent behavior across platforms. It
1540 supports clean interruption, timeout, background tasks, and streaming STDIN /
1541 STDOUT / STDERR over binary or text connections. The package also provides
1542 functions for evaluating expressions inside a temporary fork. Such
1543 evaluations have no side effects on the main R process, and support reliable
1544 interrupts and timeouts. This provides the basis for a sandboxing
1546 (license license:expat)))
1548 (define-public r-ashr
1554 (uri (cran-uri "ashr" version))
1557 "177xs3apnc6yy6737qqv4z8snf0hkpbghab63hrplbyb9wfssfga"))))
1558 (properties `((upstream-name . "ashr")))
1559 (build-system r-build-system)
1570 (home-page "https://github.com/stephens999/ashr")
1571 (synopsis "Methods for adaptive shrinkage, using empirical bayes")
1572 (description "This package implements an empirical Bayes approach for
1573 large-scale hypothesis testing and false discovery rate estimation.")
1574 (license license:gpl3+)))
1576 (define-public r-askpass
1583 (uri (cran-uri "askpass" version))
1586 "07q0ik8jzk44vpwh48rr3fnpd7dzsdhjjsl4l850rffv3dyq4h6v"))))
1587 (build-system r-build-system)
1588 (propagated-inputs (list r-sys))
1589 (home-page "https://github.com/jeroen/askpass")
1590 (synopsis "Safe password entry for R")
1592 "This package provides cross-platform utilities for prompting the user
1593 for credentials or a passphrase, for example to authenticate with a server or
1594 read a protected key.")
1595 (license license:expat)))
1597 (define-public r-astsa
1604 (uri (cran-uri "astsa" version))
1606 (base32 "0mllsq0xdqkviyvs77lq565r1vznsj1qp9cnlj5p48k9v76d7arp"))))
1607 (properties `((upstream-name . "astsa")))
1608 (build-system r-build-system)
1609 (home-page "https://github.com/nickpoison/astsa/")
1610 (synopsis "Applied statistical time series analysis")
1612 "This package provides data sets and scripts to accompany Time Series
1613 Analysis and Its Applications: With R Examples (4th ed), by R.H. Shumway and
1614 D.S. Stoffer. Springer Texts in Statistics, 2017,
1615 @url{https://doi.org/10.1007/978-3-319-52452-8}, and Time Series: A Data
1616 Analysis Approach Using R. Chapman-Hall, 2019,
1617 @url{https://doi.org/10.1201/9780429273285}.")
1618 (license license:gpl3)))
1620 (define-public r-vegan
1627 (uri (cran-uri "vegan" version))
1630 "0nf0ny6jzfy135xiygzzkr0y55y8g27hrbk8c869plarr48d2xxb"))))
1631 (build-system r-build-system)
1633 (list r-knitr ; needed for vignettes
1636 (list r-cluster r-lattice r-mass r-mgcv r-permute))
1637 (home-page "https://cran.r-project.org/web/packages/vegan")
1638 (synopsis "Functions for community ecology")
1640 "The vegan package provides tools for descriptive community ecology. It
1641 has most basic functions of diversity analysis, community ordination and
1642 dissimilarity analysis. Most of its multivariate tools can be used for other
1643 data types as well.")
1644 (license license:gpl2+)))
1646 (define-public r-tidyverse
1648 (name "r-tidyverse")
1653 (uri (cran-uri "tidyverse" version))
1656 "0ck6xmsw5p168jmw2fqv79fzfnw5jckfra7mfii261j6kl89bkw3"))))
1657 (build-system r-build-system)
1690 (home-page "https://tidyverse.tidyverse.org")
1691 (synopsis "Install and load packages from the \"Tidyverse\"")
1693 "The @code{tidyverse} is a set of packages that work in harmony because
1694 they share common data representations and API design. This package is
1695 designed to make it easy to install and load multiple tidyverse packages in a
1697 (license license:gpl3)))
1699 (define-public r-rvest
1706 (uri (cran-uri "rvest" version))
1708 (base32 "1905vxgnj3q09l1wf6rwxpbpydznp06nbkrclnc05j2415z4gfw9"))))
1709 (build-system r-build-system)
1720 (home-page "https://github.com/hadley/rvest")
1721 (synopsis "Simple web scraping for R")
1723 "@code{r-rvest} helps you scrape information from web pages. It is
1724 designed to work with @code{magrittr} to make it easy to express common web
1725 scraping tasks, inspired by libraries like @code{BeautifulSoup}.")
1726 (license license:gpl3)))
1728 (define-public r-selectr
1735 (uri (cran-uri "selectr" version))
1737 (base32 "09y1n3iy297g49xlpl7xrjpwgnm57pskx5991lyfcpizbz8ax22m"))))
1738 (build-system r-build-system)
1740 (list r-stringr r-r6))
1741 (home-page "https://sjp.co.nz/projects/selectr/")
1742 (synopsis "Translate CSS selectors to XPath expressions")
1744 "@code{r-selectr} translates a CSS3 selector into an equivalent XPath
1745 expression. This allows you to use CSS selectors when working with the XML
1746 package as it can only evaluate XPath expressions. Also provided are
1747 convenience functions useful for using CSS selectors on XML nodes. This
1748 package is a port of the Python package @code{cssselect}.")
1749 (license license:bsd-3)))
1751 (define-public r-reprex
1758 (uri (cran-uri "reprex" version))
1761 "09k4rasp7mz6n796dsklcbc5l7prljiznrm7fra16qybr9kqcv8f"))))
1762 (build-system r-build-system)
1776 (home-page "https://github.com/tidyverse/reprex")
1777 (synopsis "Prepare reproducible R code examples for sharing")
1779 "This package provides a convenience wrapper that uses the
1780 @code{rmarkdown} package to render small snippets of code to target formats
1781 that include both code and output. The goal is to encourage the sharing of
1782 small, reproducible, and runnable examples on code-oriented websites or email.
1783 @code{reprex} also extracts clean, runnable R code from various common formats,
1784 such as copy/paste from an R session.")
1785 (license license:expat)))
1787 (define-public r-reordercluster
1789 (name "r-reordercluster")
1793 (uri (cran-uri "ReorderCluster" version))
1796 "0ss750frzvj0bm1w7zblmcsjpszhnbffwlkaw31sm003lbx9hy58"))))
1797 (build-system r-build-system)
1799 (list r-gplots r-rcpp))
1800 (home-page "https://cran.r-project.org/web/packages/ReorderCluster")
1801 (synopsis "Reordering the dendrogram according to the class labels")
1802 (description "This package provides tools for performing the leaf reordering
1803 for the dendrogram that preserves the hierarchical clustering result and at the
1804 same time tries to group instances from the same class together.")
1805 (license license:gpl3+)))
1807 (define-public r-callr
1814 (uri (cran-uri "callr" version))
1817 "02inaf3c7b0hikii7p2zwaphrq5myv4in92d9jxd1ilmhla5awnn"))))
1818 (build-system r-build-system)
1820 (list r-r6 r-processx))
1821 (home-page "https://github.com/r-lib/callr#readme")
1822 (synopsis "Call R from R")
1824 "It is sometimes useful to perform a computation in a separate R process,
1825 without affecting the current R process at all. This package does exactly
1827 (license license:expat)))
1829 (define-public r-depmixs4
1835 (uri (cran-uri "depmixS4" version))
1838 "1pacvhw5m4fsk3ysbal50fdqbvlaz8ywyqp6bn1wh42wipqbb2i8"))))
1840 (list r-nnet r-nlme r-mass r-rsolnp))
1841 (build-system r-build-system)
1842 (home-page "https://cran.r-project.org/web/packages/depmixS4/")
1843 (synopsis "Dependent Mixture Models")
1844 (description "This package fits latent (hidden) Markov models on mixed
1845 categorical and continuous (time series) data, otherwise known as dependent
1847 (license license:gpl2+)))
1849 (define-public r-readxl
1856 (uri (cran-uri "readxl" version))
1859 "1xwi4k5si48hwkgfc59icfmp9dzlvfri59k5fsgn96zp9713k4mb"))))
1860 (build-system r-build-system)
1862 (list r-cellranger r-cpp11 r-progress r-tibble))
1865 (home-page "https://readxl.tidyverse.org")
1866 (synopsis "Read Excel files")
1868 "This package lets you import Excel files into R. It supports
1869 @file{.xls} via the embedded @code{libxls} C library and @file{.xlsx} via
1870 the embedded @code{RapidXML} C++ library.")
1871 ;; XXX: This package bundles a copy of 'libxsl' which is BSD-2 and
1872 ;; 'rapidxml' which is Boost.
1873 (license (list license:gpl3 license:bsd-2 license:boost1.0))))
1875 (define-public r-model4you
1877 (name "r-model4you")
1881 (uri (cran-uri "model4you" version))
1884 "0pni9v3nradvy8sp2m07903vc7z610xrh426lf19dxss12kgrfi8"))))
1885 (build-system r-build-system)
1893 (home-page "https://cran.r-project.org/web/packages/model4you/")
1894 (synopsis "Stratified and personalised models based on trees and forests")
1896 "This package provides procedures for model-based trees for subgroup
1897 analyses in clinical trials and model-based forests for the estimation and
1898 prediction of personalised treatment effects. Currently partitioning of linear
1899 models, @code{lm()}, generalised linear models, @code{glm()}, and
1900 Weibull models, @code{survreg()}, are supported. Advanced plotting functionality is
1901 supported for the trees and a test for parameter heterogeneity is provided for
1902 the personalised models.")
1903 (license license:gpl2+)))
1905 (define-public r-modelr
1912 (uri (cran-uri "modelr" version))
1915 "1i31nff7bqibk6r4hhd4j1vzwbyaf8493v0bjaagn36njmysfnw2"))))
1916 (build-system r-build-system)
1926 (home-page "https://github.com/tidyverse/modelr")
1927 (synopsis "Helper functions for modelling in pipelines")
1929 "Functions for modelling that help you seamlessly integrate modelling
1930 into a pipeline of data manipulation and visualisation.")
1931 (license license:gpl3)))
1933 (define-public r-hmm
1939 (uri (cran-uri "HMM" version))
1942 "03b548bnwqpnd7zypb4gvy9chyi5li2hp99a9vrh4qszxg2ihas7"))))
1943 (properties `((upstream-name . "HMM")))
1944 (build-system r-build-system)
1945 (home-page "https://cran.r-project.org/web/packages/HMM/")
1946 (synopsis "Hidden Markov Models")
1947 (description "This package provides an easy to use library to setup, apply
1948 and make inference with discrete time and discrete space hidden Markov
1950 (license license:gpl2+)))
1952 (define-public r-hiddenmarkov
1954 (name "r-hiddenmarkov")
1958 (uri (cran-uri "HiddenMarkov" version))
1961 "05dm3nl0ffsz2ziw3bz5bivyxk7r5bxs8xhky3hz660qaqzd51ki"))))
1962 (build-system r-build-system)
1965 (home-page "https://cran.r-project.org/web/packages/HiddenMarkov/")
1966 (synopsis "Hidden markov models for R")
1967 (description "This package contains functions for the analysis of Discrete
1968 Time Hidden Markov Models, Markov Modulated GLMs and the Markov Modulated
1969 Poisson Process. It includes functions for simulation, parameter estimation,
1970 and the Viterbi algorithm. The algorithms are based of those of Walter
1972 (license license:gpl2+)))
1974 (define-public r-httpuv
1980 (uri (cran-uri "httpuv" version))
1983 "0mlilxh2mlrsbbrncla2rg02crr8nnajv649d8whx7ayr8lkdxpm"))
1984 ;; Unvendor bundled libraries. As of 1.5.4 the vendored libuv
1985 ;; only contains fixes for building on Solaris.
1986 (patches (search-patches "r-httpuv-1.5.5-unvendor-libuv.patch"))
1987 (modules '((guix build utils)))
1988 ;; Cannot unbundle http-parser, because it contains local
1991 '(delete-file-recursively "src/libuv"))))
1992 (build-system r-build-system)
1995 (modify-phases %standard-phases
1996 (add-after 'unpack 'unbundle-libuv
1997 (lambda* (#:key outputs #:allow-other-keys)
1998 (substitute* (find-files "src" "\\.cpp$|\\.h$")
1999 (("\"libuv/include/uv\\.h\"")
2001 ;; Fix https://github.com/rstudio/httpuv/issues/282
2002 (substitute* "src/http.cpp"
2003 (("uv_pipe_init\\(pLoop, &pSocket->handle\\.pipe, true\\);")
2004 "uv_pipe_init(pLoop, &pSocket->handle.pipe, 0);")))))))
2008 (list r-later r-promises r-r6 r-rcpp))
2009 (home-page "https://github.com/rstudio/httpuv")
2010 (synopsis "HTTP and WebSocket server library for R")
2012 "The httpuv package provides low-level socket and protocol support for
2013 handling HTTP and WebSocket requests directly from within R. It is primarily
2014 intended as a building block for other packages, rather than making it
2015 particularly easy to create complete web applications using httpuv alone.")
2016 ;; This package includes third-party code that was originally released
2017 ;; under various non-copyleft licenses. Full licensing information can be
2018 ;; obtained here: https://github.com/rstudio/httpuv/blob/master/LICENSE
2019 (license license:gpl3+)))
2021 (define-public r-jsonlite
2027 (uri (cran-uri "jsonlite" version))
2030 "0k6dal7gmm19jl5sjsry5gwbnhsbrnn00q3iixig8k6bxgpr463v"))))
2031 (build-system r-build-system)
2034 (home-page "https://arxiv.org/abs/1403.2805")
2035 (synopsis "Robust, high performance JSON parser and generator for R")
2037 "The jsonlite package provides a fast JSON parser and generator optimized
2038 for statistical data and the web. It offers flexible, robust, high
2039 performance tools for working with JSON in R and is particularly powerful for
2040 building pipelines and interacting with a web API. In addition to converting
2041 JSON data from/to R objects, jsonlite contains functions to stream, validate,
2042 and prettify JSON data. The unit tests included with the package verify that
2043 all edge cases are encoded and decoded consistently for use with dynamic data
2044 in systems and applications.")
2045 (license license:expat)))
2047 (define-public r-servr
2053 (uri (cran-uri "servr" version))
2056 "11x0857m3xzdbzr4z0vx4fcdk36arfagyf2qgamvprich0qisknr"))))
2057 (build-system r-build-system)
2059 (list r-httpuv r-jsonlite r-mime r-xfun))
2060 (home-page "https://github.com/yihui/servr")
2061 (synopsis "Simple HTTP server to serve static files or dynamic documents")
2063 "Servr provides an HTTP server in R to serve static files, or dynamic
2064 documents that can be converted to HTML files (e.g., R Markdown) under a given
2066 (license license:expat)))
2068 (define-public r-howmany
2074 (uri (cran-uri "howmany" version))
2077 "045ck8qahfg2swbgyf7dpl32ryq1m4sbalhr7m5qdgpm62vz8h7f"))))
2078 (build-system r-build-system)
2079 (home-page "https://cran.r-project.org/web/packages/howmany/")
2080 (synopsis "Lower bound for the number of correct rejections")
2081 (description "When testing multiple hypotheses simultaneously, this package
2082 provides functionality to calculate a lower bound for the number of correct
2083 rejections (as a function of the number of rejected hypotheses), which holds
2084 simultaneously -with high probability- for all possible number of rejections.
2085 As a special case, a lower bound for the total number of false null hypotheses
2086 can be inferred. Dependent test statistics can be handled for multiple tests
2087 of associations. For independent test statistics, it is sufficient to provide
2088 a list of p-values.")
2089 (license license:gpl2+)))
2091 (define-public r-htmltools
2093 (name "r-htmltools")
2097 (uri (cran-uri "htmltools" version))
2100 "1yv74ydyqm28gfhimmr7825sj1iaawpwsnzq05c2ma756q2dbivx"))))
2101 (build-system r-build-system)
2103 (list r-base64enc r-digest r-fastmap r-rlang))
2104 (home-page "https://cran.r-project.org/web/packages/htmltools")
2105 (synopsis "R tools for HTML")
2107 "This package provides tools for HTML generation and output in R.")
2108 (license license:expat)))
2110 (define-public r-htmlwidgets
2112 (name "r-htmlwidgets")
2116 (uri (cran-uri "htmlwidgets" version))
2119 "1hgz8sx8xrvfcdwa4q15k942w4qsqg8lyxbbf7qyfzbi807wcgqs"))))
2120 (build-system r-build-system)
2122 (list r-htmltools r-jsonlite r-yaml))
2125 (home-page "https://github.com/ramnathv/htmlwidgets")
2126 (synopsis "HTML Widgets for R")
2128 "HTML widgets is a framework for creating HTML widgets that render in
2129 various contexts including the R console, R Markdown documents, and Shiny web
2131 (license license:expat)))
2133 (define-public r-htmltable
2135 (name "r-htmltable")
2140 (uri (cran-uri "htmlTable" version))
2142 (base32 "17csp0ry4iy4m5xy271dn5wd81v4p03l79swmvlfxkvpdmhvb8jc"))))
2143 (properties `((upstream-name . "htmlTable")))
2144 (build-system r-build-system)
2155 (home-page "http://gforge.se/packages/")
2156 (synopsis "Advanced tables for Markdown/HTML")
2158 "This package provides functions to build tables with advanced layout
2159 elements such as row spanners, column spanners, table spanners, zebra
2160 striping, and more. While allowing advanced layout, the underlying
2161 CSS-structure is simple in order to maximize compatibility with word
2162 processors such as LibreOffice. The package also contains a few text
2163 formatting functions that help outputting text compatible with HTML or
2165 (license license:gpl3+)))
2167 (define-public r-curl
2173 (uri (cran-uri "curl" version))
2176 "0s55022hy8shjm1pzax1dqzrg20bv4nvlwnjnddk3dp89g5zmcch"))))
2177 (build-system r-build-system)
2180 (modify-phases %standard-phases
2181 ;; The environment variable CURL_CA_BUNDLE is only respected when
2182 ;; running Windows, so we disable the platform checks.
2183 ;; This can be removed once the libcurl has been patched.
2184 (add-after 'unpack 'allow-CURL_CA_BUNDLE
2186 (substitute* "R/onload.R"
2187 (("if \\(!grepl\\(\"mingw\".*")
2189 (substitute* "src/handle.c"
2190 (("/\\* Only set" m)
2192 const char *_ca_bundle = getenv(\"CURL_CA_BUNDLE\");
2193 if(_ca_bundle != NULL) { curl_easy_setopt(handle, CURLOPT_CAINFO, _ca_bundle); }
2198 (list pkg-config r-knitr))
2199 (home-page "https://github.com/jeroenooms/curl")
2200 (synopsis "HTTP client for R")
2202 "The @code{curl()} and @code{curl_download()} functions provide highly
2203 configurable drop-in replacements for base @code{url()} and
2204 @code{download.file()} with better performance, support for encryption, gzip
2205 compression, authentication, and other @code{libcurl} goodies. The core of
2206 the package implements a framework for performing fully customized requests
2207 where data can be processed either in memory, on disk, or streaming via the
2208 callback or connection interfaces.")
2209 (license license:expat)))
2211 (define-public r-hwriter
2218 (uri (cran-uri "hwriter" version))
2221 "1wxnv8h9cs65m3z01dpnnkgn2cpwfsck70g1jz9nbkr7mdaa4bzd"))))
2222 (build-system r-build-system)
2223 (home-page "https://cran.r-project.org/web/packages/hwriter")
2224 (synopsis "Output R objects in HTML format")
2226 "This package provides easy-to-use and versatile functions to output R
2227 objects in HTML format.")
2228 (license license:lgpl2.1+)))
2230 (define-public r-rjson
2237 (uri (cran-uri "rjson" version))
2240 "1qm27r1w677zg31gsiln60hcciszbymkw78cnaq7s36cbk9mcawq"))))
2241 (build-system r-build-system)
2242 (home-page "https://cran.r-project.org/web/packages/rjson")
2243 (synopsis "JSON library for R")
2245 "This package provides functions to convert R objects into JSON objects
2247 (license license:gpl2+)))
2249 (define-public r-fastmap
2256 (uri (cran-uri "fastmap" version))
2259 "0aw29hnq3ppn7bsnwg9d9sp84k1cvq30lrmfzqn315n0nhkfa4wi"))))
2260 (properties `((upstream-name . "fastmap")))
2261 (build-system r-build-system)
2262 (home-page "https://r-lib.github.io/fastmap/")
2263 (synopsis "Fast implementation of a key-value store")
2265 "This package provides a fast implementation of a key-value store.
2266 Environments are commonly used as key-value stores, but every time a new key
2267 is used, it is added to R's global symbol table, causing a small amount of
2268 memory leakage. This can be problematic in cases where many different keys
2269 are used. Fastmap avoids this memory leak issue by implementing the map using
2270 data structures in C++.")
2271 (license license:expat)))
2273 (define-public r-fastghquad
2275 (name "r-fastghquad")
2280 (uri (cran-uri "fastGHQuad" version))
2283 "1zj7nsbnx4g253m3dpz9vi3zk3jxwrixwjw1ks6n4shpb4dlkp2w"))))
2284 (properties `((upstream-name . "fastGHQuad")))
2285 (build-system r-build-system)
2288 (home-page "https://github.com/awblocker/fastGHQuad")
2289 (synopsis "Fast Rcpp implementation of Gauss-Hermite Quadrature")
2291 "This package implements numerically-stable Gauss-Hermite quadrature
2292 rules and utility functions for adaptive GH quadrature.")
2293 (license license:expat)))
2295 (define-public r-rstpm2
2302 (uri (cran-uri "rstpm2" version))
2305 "17mhzfxh761vl64ar6pynpj3k2jkhjgbacxsjhkrfkbmy3aiv0d1"))))
2306 (properties `((upstream-name . "rstpm2")))
2307 (build-system r-build-system)
2319 (home-page "https://github.com/mclements/rstpm2")
2320 (synopsis "Link-based survival models")
2322 "This package provides R implementations of @dfn{generalized survival
2323 models} (GSMs), smooth @dfn{accelerated failure time} (AFT) models and Markov
2324 multi-state models.")
2325 ;; One of these licenses
2326 (license (list license:gpl2 license:gpl3))))
2328 ;; This package includes minified JavaScript files. When upgrading please
2329 ;; check that there are no new minified JavaScript files.
2330 (define-public r-jquerylib
2332 (name "r-jquerylib")
2337 (uri (cran-uri "jquerylib" version))
2340 "04a40v4znpj98j7y6009d74a6g9dchj5rr3p08cgz9p3rlfw3g7h"))
2342 '(for-each delete-file
2343 '("inst/lib/1.12.4/jquery-1.12.4.min.js"
2344 "inst/lib/2.2.4/jquery-2.2.4.min.js"
2345 "inst/lib/3.6.0/jquery-3.6.0.min.js")))))
2346 (properties `((upstream-name . "jquerylib")))
2347 (build-system r-build-system)
2349 `(#:modules ((guix build utils)
2350 (guix build r-build-system)
2353 (modify-phases %standard-phases
2354 (add-after 'unpack 'process-javascript
2355 (lambda* (#:key inputs #:allow-other-keys)
2356 (with-directory-excursion "inst/lib/"
2360 `(("1.12.4/jquery-1.12.4.js"
2361 "1.12.4/jquery-1.12.4.min.js")
2362 ("2.2.4/jquery-2.2.4.js"
2363 "2.2.4/jquery-2.2.4.min.js")
2364 ("3.6.0/jquery-3.6.0.js"
2365 "3.6.0/jquery-3.6.0.min.js"))))
2366 (lambda (sources targets)
2367 (for-each (lambda (source target)
2368 (format #t "Processing ~a --> ~a~%"
2370 (invoke "esbuild" source "--minify"
2371 (string-append "--outfile=" target)))
2372 sources targets)))))))))
2377 (home-page "https://cran.r-project.org/package=jquerylib")
2378 (synopsis "Obtain jQuery as an HTML dependency object")
2380 "Obtain any major version of jQuery and use it in any webpage generated
2381 by htmltools (e.g. shiny, htmlwidgets, and rmarkdown). Most R users don't
2382 need to use this package directly, but other R packages (e.g. shiny,
2383 rmarkdown, etc.) depend on this package to avoid bundling redundant copies of
2385 (license license:expat)))
2387 (define-public r-sass
2394 (uri (cran-uri "sass" version))
2397 "1fq8wqnxmx10lg0dh4qzmxdkhd22fjh8vhassapxb1chsimwn3w5"))))
2398 (properties `((upstream-name . "sass")))
2399 (build-system r-build-system)
2401 (list r-fs r-htmltools r-r6 r-rappdirs r-rlang))
2402 (native-inputs (list r-knitr))
2403 (home-page "https://github.com/rstudio/sass")
2404 (synopsis "Syntactically Awesome Style Sheets (SASS)")
2406 "This package provides an SCSS compiler, powered by the libsass library.
2407 With this, R developers can use variables, inheritance, and functions to
2408 generate dynamic style sheets. The package uses the Sass CSS extension
2409 language, which is stable, powerful, and CSS compatible.")
2410 (license license:expat)))
2412 (define-public r-saver
2418 (uri (cran-uri "SAVER" version))
2421 "1s1kw8idkaj7j90fw4qn9k0wd4vz0sblsk06ry6lm4afcar0p158"))))
2422 (properties `((upstream-name . "SAVER")))
2423 (build-system r-build-system)
2430 (native-inputs (list r-knitr))
2431 (home-page "https://github.com/mohuangx/SAVER")
2433 "Recovery of gene expression profile in noisy and sparse scRNA-seq data")
2435 "This package is an implementation of a regularized regression prediction
2436 and empirical Bayes method to recover the true gene expression profile in noisy
2437 and sparse single-cell RNA-seq data. In @dfn{single-cell RNA sequencing}
2438 (scRNA-seq) studies, only a small fraction of the transcripts present in each
2439 cell are sequenced. This leads to unreliable quantification of genes with low
2440 or moderate expression, which hinders downstream analysis. This package
2441 @dfn{single-cell analysis via expression recovery} (SAVER) implements an
2442 expression recovery method for unique molecule index (UMI)-based scRNA-seq
2443 data that borrows information across genes and cells to provide accurate
2444 expression estimates for all genes.")
2445 (license license:gpl2)))
2447 ;; This package includes minified JavaScript files. When upgrading please
2448 ;; check that there are no new minified JavaScript files.
2449 (define-public r-bslib
2456 (uri (cran-uri "bslib" version))
2459 "0jcqklry1nkibz0sydsz5xdsnb4wnrrhvmyr9ji3k45bbipbap2z"))
2461 '(for-each delete-file
2462 '("inst/lib/bs-a11y-p/plugins/js/bootstrap-accessibility.min.js"
2463 "inst/lib/bs-colorpicker/js/bootstrap-colorpicker.min.js"
2464 "inst/lib/bs3/assets/javascripts/bootstrap.min.js"
2465 "inst/lib/bs4/dist/js/bootstrap.bundle.min.js"
2466 "inst/lib/bs5/dist/js/bootstrap.bundle.min.js")))))
2467 (properties `((upstream-name . "bslib")))
2468 (build-system r-build-system)
2470 `(#:modules ((guix build utils)
2471 (guix build r-build-system)
2474 (modify-phases %standard-phases
2475 (add-after 'unpack 'process-javascript
2476 (lambda* (#:key inputs #:allow-other-keys)
2477 (with-directory-excursion "inst/lib/"
2481 `(("bs-a11y-p/plugins/js/bootstrap-accessibility.js"
2482 "bs-a11y-p/plugins/js/bootstrap-accessibility.min.js")
2483 ("bs-colorpicker/js/bootstrap-colorpicker.js"
2484 "bs-colorpicker/js/bootstrap-colorpicker.min.js")
2485 ("bs3/assets/javascripts/bootstrap.js"
2486 "bs3/assets/javascripts/bootstrap.min.js")
2487 (,(assoc-ref inputs "js-bootstrap4-bundle")
2488 "bs4/dist/js/bootstrap.bundle.min.js")
2489 (,(assoc-ref inputs "js-bootstrap5-bundle")
2490 "bs5/dist/js/bootstrap.bundle.min.js"))))
2491 (lambda (sources targets)
2492 (for-each (lambda (source target)
2493 (format #t "Processing ~a --> ~a~%"
2495 (invoke "esbuild" source "--minify"
2496 (string-append "--outfile=" target)))
2497 sources targets)))))))))
2499 (list r-htmltools r-jquerylib r-jsonlite r-rlang r-sass))
2501 `(("esbuild" ,esbuild)
2502 ("js-bootstrap4-bundle"
2505 (uri "https://raw.githubusercontent.com/twbs/bootstrap/v4.6.0/dist/js/bootstrap.bundle.js")
2508 "04abvgp923w36qfqkkl2syim3bl119nwxbgials90z1jyb8jgss1"))))
2509 ("js-bootstrap5-bundle"
2512 (uri "https://raw.githubusercontent.com/twbs/bootstrap/v5.0.2/dist/js/bootstrap.bundle.js")
2515 "06vin94nqw1vzs4zrqcms8z9js9fckbj8gwyx07awm8jkjhnqfhl"))))))
2516 (home-page "https://rstudio.github.io/bslib/")
2517 (synopsis "Custom Bootstrap Sass themes for shiny and rmarkdown")
2519 "This package simplifies custom CSS styling of both shiny and rmarkdown
2520 via Bootstrap Sass. It supports both Bootstrap 3 and 4 as well as their
2521 various Bootswatch themes. An interactive widget is also provided for
2522 previewing themes in real time.")
2523 (license license:expat)))
2525 ;; This package includes minified JavaScript files. When upgrading please
2526 ;; check that there are no new minified JavaScript files.
2527 (define-public r-shiny
2535 (url "https://github.com/rstudio/shiny")
2536 (commit (string-append "v" version))))
2537 (file-name (git-file-name name version))
2540 "0wvc6jlgs41p05wbk8gahnl7sfnc4hpliyh9dbi5w52ngsg6wcr7"))
2542 '(for-each delete-file
2543 '("inst/www/shared/bootstrap/js/bootstrap.min.js"
2544 "inst/www/shared/bootstrap/accessibility/js/bootstrap-accessibility.min.js" ; TODO
2545 "inst/www/shared/datatables/js/jquery.dataTables.min.js"
2546 "inst/www/shared/datepicker/js/bootstrap-datepicker.min.js"
2547 "inst/www/shared/highlight/highlight.pack.js"
2548 "inst/www/shared/ionrangeslider/js/ion.rangeSlider.min.js"
2549 "inst/www/shared/jquery.min.js"
2550 "inst/www/shared/jqueryui/jquery-ui.min.js"
2551 "inst/www/shared/legacy/jquery.min.js"
2552 "inst/www/shared/selectize/accessibility/js/selectize-plugin-a11y.min.js"
2553 "inst/www/shared/selectize/js/selectize.min.js"
2554 "inst/www/shared/shiny.min.js"
2555 "inst/www/shared/showdown/compressed/showdown.js"
2556 "inst/www/shared/strftime/strftime-min.js")))))
2557 (build-system r-build-system)
2559 `(#:modules ((guix build r-build-system)
2560 (guix build minify-build-system)
2563 #:imported-modules (,@%r-build-system-modules
2564 (guix build minify-build-system))
2566 (modify-phases (@ (guix build r-build-system) %standard-phases)
2567 (add-after 'unpack 'replace-bundled-minified-JavaScript
2568 (lambda* (#:key inputs #:allow-other-keys)
2569 (let ((replace-file (lambda (old new)
2570 (format #t "replacing ~a with ~a\n" old new)
2571 (symlink new old))))
2572 ;; NOTE: Files in ./inst/www/shared/datepicker/js/locales/
2573 ;; contain just data. They are not minified code, so we don't
2575 (with-directory-excursion "inst/www/shared"
2576 (replace-file "strftime/strftime-min.js"
2577 (search-input-file inputs
2578 "/share/javascript/strftime.min.js"))
2579 (replace-file "highlight/highlight.pack.js"
2580 (search-input-file inputs
2581 "/share/javascript/highlight.min.js"))
2582 (replace-file "datatables/js/jquery.dataTables.min.js"
2583 (search-input-file inputs
2584 "/share/javascript/jquery.dataTables.min.js"))
2585 (replace-file "selectize/js/selectize.min.js"
2586 (search-input-file inputs
2587 "/share/javascript/selectize.min.js"))
2588 (for-each (match-lambda
2590 (minify source #:target target)))
2591 `(("jqueryui/jquery-ui.js" .
2592 "jqueryui/jquery-ui.min.js")
2593 ("datepicker/js/bootstrap-datepicker.js" .
2594 "datepicker/js/bootstrap-datepicker.min.js")
2595 ("ionrangeslider/js/ion.rangeSlider.js" .
2596 "ionrangeslider/js/ion.rangeSlider.min.js")
2597 ("bootstrap/js/bootstrap.js" .
2598 "bootstrap/js/bootstrap.min.js")
2599 (,(assoc-ref inputs "js-bootstrap-accessibility") .
2600 "bootstrap/accessibility/js/bootstrap-accessibility.min.js")
2605 ("legacy/jquery.js" .
2606 "legacy/jquery.min.js")
2607 ("selectize/accessibility/js/selectize-plugin-a11y.js" .
2608 "selectize/accessibility/js/selectize-plugin-a11y.min.js")
2609 ("showdown/src/showdown.js" .
2610 "showdown/compressed/showdown.js"))))))))))
2633 (list js-datatables js-selectize js-strftime js-highlight))
2635 `(("uglifyjs" ,node-uglify-js)
2636 ("gfortran" ,gfortran)
2637 ("js-bootstrap-accessibility"
2640 (uri "https://raw.githubusercontent.com/paypal/bootstrap-accessibility-plugin/\
2641 v1.0.7/_site/plugins/js/bootstrap-accessibility.js")
2644 "1489wyzwrpf86y7vhc13n4v3mszmsfybhd3f75jkpnbvyp5sncm8"))))))
2645 (home-page "https://shiny.rstudio.com")
2646 (synopsis "Easy interactive web applications with R")
2648 "Makes it incredibly easy to build interactive web applications
2649 with R. Automatic \"reactive\" binding between inputs and outputs and
2650 extensive prebuilt widgets make it possible to build beautiful,
2651 responsive, and powerful applications with minimal effort.")
2652 (license license:artistic2.0)))
2654 (define-public r-shinyhelper
2656 (name "r-shinyhelper")
2661 (uri (cran-uri "shinyhelper" version))
2663 (base32 "1c4hvf19j3yyh8r12nx85ldkxs89g98q74csnqs5ml5l79a65vgp"))))
2664 (properties `((upstream-name . "shinyhelper")))
2665 (build-system r-build-system)
2666 (propagated-inputs (list r-markdown r-shiny))
2667 (home-page "https://cran.r-project.org/package=shinyhelper")
2668 (synopsis "Easily add Markdown help files to shiny app elements")
2670 "This package creates a lightweight way to add markdown helpfiles to
2671 Shiny apps, using modal dialog boxes, with no need to observe each help button
2673 (license license:gpl3)))
2675 ;; This package includes minified JavaScript files. When upgrading please
2676 ;; check that there are no new minified JavaScript files.
2677 (define-public r-shinytree
2679 (name "r-shinytree")
2684 (uri (cran-uri "shinyTree" version))
2687 "0jfx2capckv7hf2yx3fn8i4rcmhi222ah91jnmhg497x8wgz31s3"))
2688 (modules '((guix build utils)))
2691 ;; Delete minified JavaScript
2692 (for-each delete-file
2693 '("inst/www/jsTree-3.3.7/libs/require.js"
2694 "inst/www/jsTree-3.3.7/libs/jquery.js"
2695 "inst/www/jsTree-3.3.7/jstree.min.js"))
2697 (properties `((upstream-name . "shinyTree")))
2698 (build-system r-build-system)
2700 `(#:modules ((guix build utils)
2701 (guix build r-build-system)
2705 (modify-phases %standard-phases
2706 (add-after 'unpack 'replace-minified-javascript
2707 (lambda* (#:key inputs #:allow-other-keys)
2708 (with-directory-excursion "inst/www/jsTree-3.3.7/"
2709 (symlink (search-input-file inputs
2710 "/share/javascript/require.min.js")
2715 `((,(assoc-ref inputs "js-jquery")
2719 (lambda (sources targets)
2720 (for-each (lambda (source target)
2721 (format #t "Processing ~a --> ~a~%"
2723 (let ((minified (open-pipe* OPEN_READ "uglifyjs" source)))
2724 (call-with-output-file target
2726 (dump-port minified port)))))
2730 (list r-htmlwidgets r-jsonlite r-promises r-shiny r-stringr))
2732 (list js-requirejs))
2734 `(("uglifyjs" ,node-uglify-js)
2738 (uri "https://code.jquery.com/jquery-3.3.1.js")
2741 "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq"))))))
2742 (home-page "https://cran.r-project.org/web/packages/shinyTree/")
2743 (synopsis "jsTree bindings for Shiny")
2745 "This package exposes R bindings to jsTree, a JavaScript library that
2746 supports interactive trees, to enable rich, editable trees in Shiny.")
2747 (license license:expat)))
2749 (define-public r-shinydashboard
2751 (name "r-shinydashboard")
2755 (uri (cran-uri "shinydashboard" version))
2758 "0hrqkwlpb8rnmp5j74p134g4c4cl16icmwc2ip6k1634fa2y8vm5"))))
2759 (build-system r-build-system)
2760 ;; The directory inst/AdminLTE/ contains a minified JavaScript file.
2761 ;; Regenerate it from the included sources.
2764 (modify-phases %standard-phases
2765 (add-after 'unpack 'generate-minified-javascript
2767 (with-directory-excursion "inst/AdminLTE"
2768 (let ((target "app.min.js")
2770 (format #t "Processing ~a --> ~a~%"
2772 (delete-file target)
2773 (invoke "esbuild" source "--minify"
2774 (string-append "--outfile=" target)))))))))
2776 (list r-htmltools r-promises r-shiny))
2779 (home-page "https://rstudio.github.io/shinydashboard/")
2780 (synopsis "Create dashboards with shiny")
2781 (description "This package provides an extension to the Shiny web
2782 application framework for R, making it easy to create attractive dashboards.")
2783 ;; This package includes software that was released under the Expat
2784 ;; license, but the whole package is released under GPL version 2 or
2786 (license license:gpl2+)))
2788 (define-public r-shinyfiles
2790 (name "r-shinyfiles")
2795 (uri (cran-uri "shinyFiles" version))
2797 (base32 "1l4a4v9ivxkj2vx6xw4z3pk7a8px23icppcgvgpybibq2j74pglg"))))
2798 (properties `((upstream-name . "shinyFiles")))
2799 (build-system r-build-system)
2801 (list r-fs r-htmltools r-jsonlite r-shiny r-tibble))
2802 (home-page "https://github.com/thomasp85/shinyFiles")
2803 (synopsis "Server-side file system viewer for Shiny")
2805 "This package provides functionality for client-side navigation of the
2806 server side file system in shiny apps. In case the app is running locally
2807 this gives the user direct access to the file system without the need to
2808 \"download\" files to a temporary location. Both file and folder selection as
2809 well as file saving is available.")
2810 (license license:gpl2+)))
2812 (define-public r-shinythemes
2814 (name "r-shinythemes")
2819 (uri (cran-uri "shinythemes" version))
2822 "0qr9bfxw8afxns44i2j4msignf6g5qb2nzpay2lpv343rrlqbmip"))))
2823 (properties `((upstream-name . "shinythemes")))
2824 (build-system r-build-system)
2825 (propagated-inputs (list r-shiny))
2826 (home-page "https://rstudio.github.io/shinythemes/")
2827 (synopsis "Themes for Shiny")
2829 "This package provides themes for use with Shiny. It includes several
2830 Bootstrap themes, which are packaged for use with Shiny applications.")
2831 ;; The package is released under version 3 of the GPL, but it includes
2832 ;; source files that are covered by the Expat license. It also includes
2833 ;; fonts under SIL or the ASL.
2834 (license (list license:gpl3 license:expat
2835 license:silofl1.1 license:asl2.0))))
2837 ;; The package sources include minified variants of d3.js and non-minified
2838 ;; source code of d3-jetpack.
2839 (define-public r-d3r
2846 (uri (cran-uri "d3r" version))
2849 "1qijkllfaaw0lb29j8mappm8jz9kg8gkihxq5wqhb4gabsazdwva"))))
2850 (build-system r-build-system)
2852 `(#:modules ((guix build utils)
2853 (guix build r-build-system)
2856 (modify-phases %standard-phases
2857 (add-after 'unpack 'process-javascript
2858 (lambda* (#:key inputs #:allow-other-keys)
2859 (with-directory-excursion "inst/www/d3/"
2863 `((,(assoc-ref inputs "d3.v3.js")
2864 "v3/dist/d3.min.js")
2865 (,(assoc-ref inputs "d3.v4.js")
2866 "v4/dist/d3.min.js")
2867 (,(assoc-ref inputs "d3.v5.js")
2868 "v5/dist/d3.min.js")
2869 (,(assoc-ref inputs "d3.v6.js")
2870 "v6/dist/d3.min.js")
2871 (,(assoc-ref inputs "d3.v7.js")
2872 "v7/dist/d3.min.js"))))
2873 (lambda (sources targets)
2874 (for-each (lambda (source target)
2875 (format #t "Processing ~a --> ~a~%"
2877 (delete-file target)
2878 (invoke "esbuild" source "--minify"
2879 (string-append "--outfile=" target)))
2880 sources targets)))))))))
2882 (list r-dplyr r-htmltools r-rlang r-tidyr))
2884 `(("esbuild" ,esbuild)
2888 (uri "https://d3js.org/d3.v3.js")
2891 "1arr7sr08vy7wh0nvip2mi7dpyjw4576vf3bm45rp4g5lc1k1x41"))))
2895 (uri "https://d3js.org/d3.v4.js")
2898 "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg"))))
2902 (uri "https://d3js.org/d3.v5.js")
2905 "0kxvx5pfagxn6nhavdwsdnzyd26g0z5dsfi1pi5dvcmb0c8ipcdn"))))
2909 (uri "https://d3js.org/d3.v6.js")
2912 "1x6432ca7p1pfxhz3airzw943fincn9izzxkclc1wmphcvv2n2p9"))))
2916 (uri "https://d3js.org/d3.v7.js")
2919 "0sd6vavxs8mx5xyb8xahlqghdiczqd284a7d5wravhqnrj0bw097"))))))
2920 (home-page "https://github.com/timelyportfolio/d3r")
2921 (synopsis "d3.js utilities for R")
2923 "This package provides a suite of functions to help ease the use of the
2924 d3.js visualization library in R. These helpers include
2925 @code{htmltools::htmlDependency} functions, hierarchy builders, and conversion
2926 tools for @code{partykit}, @code{igraph}, @code{table}, and @code{data.frame}
2927 R objects into the JSON format that the d3.js library expects.")
2928 (license license:bsd-3)))
2930 ;; We use the latest commit here because the last release was in 2016 while
2931 ;; the latest commit was in 2018.
2932 (define-public r-sankeyd3
2933 (let ((commit "fd50a74e29056e0d67d75b4d04de47afb2f932bc")
2937 (version (git-version "0.3.2" revision commit))
2942 (url "https://github.com/fbreitwieser/sankeyD3")
2944 (file-name (git-file-name name version))
2947 "0jrcnfax321pszbpjdifnkbrgbjr43bjzvlzv1p5a8wskksqwiyx"))))
2948 (build-system r-build-system)
2950 (list r-d3r r-htmlwidgets r-shiny r-magrittr))
2951 (home-page "https://github.com/fbreitwieser/sankeyD3")
2952 (synopsis "Sankey network graphs from R")
2954 "This package provides an R library to generate Sankey network graphs
2955 in R and Shiny via the D3 visualization library.")
2956 ;; The R code is licensed under GPLv3+. It includes the non-minified
2957 ;; JavaScript source code of d3-sankey, which is released under the
2958 ;; 3-clause BSD license.
2959 (license (list license:gpl3+ license:bsd-3)))))
2961 (define-public r-wesanderson
2963 (name "r-wesanderson")
2968 (uri (cran-uri "wesanderson" version))
2971 "09mr6p2jmqdjq27cz974w5hyxgn929zp9z3inhxqmmh1582fmdi2"))))
2972 (properties `((upstream-name . "wesanderson")))
2973 (build-system r-build-system)
2974 (home-page "https://github.com/karthik/wesanderson")
2975 (synopsis "Wes Anderson color palette generator")
2977 "This package provides color palettes that have been generated mostly
2978 from Wes Anderson movies.")
2979 (license license:expat)))
2981 (define-public r-gg-gap
2988 (uri (cran-uri "gg.gap" version))
2991 "0m66050ryn31xmsmmikjsssllasvjdmp9yjbwfdwfpwdv106zn9h"))))
2992 (properties `((upstream-name . "gg.gap")))
2993 (build-system r-build-system)
2995 (list r-cowplot r-ggplot2))
2996 (home-page "https://github.com/ChrisLou-bioinfo/gg.gap")
2997 (synopsis "Define segments on the y-axis for ggplot2")
2999 "The @code{gg.gap} function enables you to define segments for the y-axis
3000 in a ggplot2 plot.")
3001 (license license:gpl3)))
3003 (define-public r-mbess
3010 (uri (cran-uri "MBESS" version))
3012 (base32 "0qmyvjx2zn5hlzdbz8c94g8l4707swhn7sq9mxkdqiydmflzv0b5"))))
3013 (properties `((upstream-name . "MBESS")))
3014 (build-system r-build-system)
3016 (list r-boot r-lavaan r-mass r-mnormt r-nlme r-openmx r-sem r-semtools))
3017 (home-page "https://www3.nd.edu/~kkelley/site/MBESS.html")
3018 (synopsis "Methods for designing research studies")
3020 "This package implements methods that are useful in designing research
3021 studies and analyzing data, with particular emphasis on methods that are
3022 developed for or used within the behavioral, educational, and social
3023 sciences (broadly defined). That being said, many of the methods implemented
3024 within MBESS are applicable to a wide variety of disciplines. MBESS has a
3025 suite of functions for a variety of related topics, such as effect sizes,
3026 confidence intervals for effect sizes (including standardized effect sizes and
3027 noncentral effect sizes), sample size planning (from the @dfn{accuracy in
3028 parameter estimation} (AIPE), power analytic, equivalence, and minimum-risk
3029 point estimation perspectives), mediation analysis, various properties of
3030 distributions, and a variety of utility functions.")
3031 ;; Either version of the GPL.
3032 (license (list license:gpl2 license:gpl3))))
3034 (define-public r-homologene
3036 (name "r-homologene")
3037 (version "1.4.68.19.3.27")
3041 (uri (cran-uri "homologene" version))
3043 (base32 "0d7wxisk0vqk1n165v1i19bc02zv78h5r5d3jqai5y6nkmwn01sh"))))
3044 (properties `((upstream-name . "homologene")))
3045 (build-system r-build-system)
3047 (list r-dplyr r-magrittr r-purrr r-r-utils r-readr))
3048 (home-page "https://github.com/oganm/homologene")
3049 (synopsis "Quick access to homologene and gene annotation updates")
3051 "This package provides a wrapper for the homologene database by the
3052 National Center for Biotechnology Information (NCBI). It allows searching for
3053 gene homologs across species. The package also includes an updated version of
3054 the homologene database where gene identifiers and symbols are replaced with
3055 their latest (at the time of submission) version and functions to fetch latest
3056 annotation data to keep updated.")
3057 (license license:expat)))
3059 (define-public r-ggtern
3066 (uri (cran-uri "ggtern" version))
3068 (base32 "15hhn8msy0l8zbq8ms0zvg1iajn1c28gd77v3hp6dvwwsla8zzbd"))))
3069 (properties `((upstream-name . "ggtern")))
3070 (build-system r-build-system)
3072 (list r-compositions
3083 (home-page "http://www.ggtern.com")
3084 (synopsis "Extension to ggplot2 for ternary diagrams")
3086 "This package extends the functionality of ggplot2, providing the
3087 capability to plot ternary diagrams for (a subset of) the ggplot2 geometries.
3088 Additionally, ggtern has implemented several new geometries which are
3089 unavailable to the standard ggplot2 release.")
3090 (license license:gpl2)))
3092 (define-public r-tablerdash
3094 (name "r-tablerdash")
3099 (uri (cran-uri "tablerDash" version))
3102 "1mnp6lxa7d669r325aynq1n3f35r9sy4v1fvdh4cymbf33s8mkmm"))
3105 ;; Delete minified JavaScript
3106 (for-each delete-file
3107 '("inst/tablerDash-0.1.0/require.min.js"
3108 "inst/bootstrap-4.0.0/bootstrap.bundle.min.js"))
3110 (properties `((upstream-name . "tablerDash")))
3111 (build-system r-build-system)
3113 `(#:modules ((guix build utils)
3114 (guix build r-build-system)
3117 (modify-phases %standard-phases
3118 (add-after 'unpack 'process-javascript
3119 (lambda* (#:key inputs #:allow-other-keys)
3120 (with-directory-excursion "inst"
3124 `((,(assoc-ref inputs "js-requirejs")
3125 "tablerDash-0.1.0/require.min.js")
3126 (,(assoc-ref inputs "js-bootstrap")
3127 "bootstrap-4.0.0/bootstrap.bundle.min.js"))))
3128 (lambda (sources targets)
3129 (for-each (lambda (source target)
3130 (format #t "Processing ~a --> ~a~%"
3132 (invoke "esbuild" source "--minify"
3133 (string-append "--outfile=" target)))
3137 (list r-htmltools r-knitr r-shiny))
3139 `(("esbuild" ,esbuild)
3143 (uri "https://raw.githubusercontent.com/requirejs/requirejs/2.3.5/require.js")
3146 "06w32mwqii9cx409ivda88z58qbkcdb4p6hf6jawchsgagaziyds"))))
3150 (uri "https://raw.githubusercontent.com/twbs/bootstrap/\
3151 v4.0.0/dist/js/bootstrap.bundle.js")
3154 "0cvfqffn45vfbj3fk6wmrhkyndhk4id89vgydssbbzxjkfwprfrj"))))))
3155 (home-page "https://rinterface.github.io/tablerDash/")
3156 (synopsis "Tabler API for Shiny")
3158 "This package provides an R interface to the
3159 @url{https://tabler.io,Tabler} HTML template. tablerDash is a light Bootstrap
3160 4 dashboard template. There are different layouts available such as a one
3161 page dashboard or a multi-page template, where the navigation menu is
3162 contained in the navigation bar.")
3163 (license license:gpl2+)))
3165 (define-public r-spelling
3172 (uri (cran-uri "spelling" version))
3175 "179nj9w1v27qq9q5240ddvggp0795998sxyqjvbqjvq9dmach3bl"))))
3176 (properties `((upstream-name . "spelling")))
3177 (build-system r-build-system)
3179 (list r-commonmark r-hunspell r-knitr r-xml2))
3180 (home-page "https://docs.ropensci.org/spelling/")
3181 (synopsis "Tools for spell checking in R")
3183 "This is an R package for spell checking common document formats
3184 including LaTeX, markdown, manual pages, and DESCRIPTION files. It includes
3185 utilities to automate checking of documentation and vignettes as a unit test
3186 during @code{R CMD check}. Both British and American English are supported
3187 out of the box and other languages can be added. In addition, packages may
3188 define a wordlist to allow custom terminology without having to abuse
3190 (license license:expat)))
3192 (define-public r-crosstalk
3194 (name "r-crosstalk")
3199 (uri (cran-uri "crosstalk" version))
3202 "180y7mhpj17axpadwhh7s0qvrpdnag7g977vk256l96d6nmvlds2"))))
3203 (build-system r-build-system)
3205 (list r-htmltools r-jsonlite r-lazyeval r-r6))
3206 (home-page "https://rstudio.github.io/crosstalk/")
3207 (synopsis "Inter-widget interactivity for HTML widgets")
3209 "This package provides building blocks for allowing HTML widgets to
3210 communicate with each other, with Shiny or without (i.e. static @code{.html}
3211 files). It currently supports linked brushing and filtering.")
3212 (license license:expat)))
3214 (define-public r-rook
3221 (uri (cran-uri "Rook" version))
3224 "00s9a0kr9rwxvlq433daxjk4ji8m0w60hjdprf502msw9kxfrx00"))))
3225 (properties `((upstream-name . "Rook")))
3226 (build-system r-build-system)
3227 (propagated-inputs (list r-brew))
3228 (home-page "https://cran.r-project.org/web/packages/Rook")
3229 (synopsis "Web server interface for R")
3231 "This package contains the Rook specification and convenience software
3232 for building and running Rook applications. A Rook application is an R
3233 reference class object that implements a @code{call} method or an R closure
3234 that takes exactly one argument, an environment, and returns a list with three
3235 named elements: the @code{status}, the @code{headers}, and the @code{body}.")
3236 (license license:gpl2)))
3238 (define-public r-miniui
3245 (uri (cran-uri "miniUI" version))
3248 "1h5h2sc57h95d6bsgs95l26911g38hvjc1v50bc31xl9689l2as5"))))
3249 (properties `((upstream-name . "miniUI")))
3250 (build-system r-build-system)
3252 (list r-htmltools r-shiny))
3253 (home-page "https://cran.r-project.org/web/packages/miniUI/")
3254 (synopsis "Shiny UI widgets for small screens")
3256 "This package provides UI widget and layout functions for writing Shiny apps that
3257 work well on small screens.")
3258 (license license:gpl3)))
3260 (define-public r-feather
3267 (uri (cran-uri "feather" version))
3270 "1gxd0h2m56sjjlzn4dry6s13nddxc4l5i11gsvavaf2dwbahdzsh"))))
3271 (build-system r-build-system)
3273 (list r-hms r-rcpp r-tibble))
3274 (home-page "https://github.com/wesm/feather")
3275 (synopsis "R Bindings to the Feather API")
3276 (description "Read and write feather files, a lightweight binary columnar
3277 data store designed for maximum speed.")
3278 (license license:asl2.0)))
3280 (define-public r-maps
3287 (uri (cran-uri "maps" version))
3290 "0ispkx1szgwxhr0zzhdzgqqwcgc6psg7vry4sj4rb89w76rcq63r"))))
3291 (build-system r-build-system)
3292 (home-page "https://cran.r-project.org/web/packages/maps")
3293 (synopsis "Draw geographical maps")
3294 (description "This package provides an R module for display of maps.
3295 Projection code and larger maps are in separate packages (@code{mapproj} and
3297 (license license:gpl2)))
3299 (define-public r-mapproj
3306 (uri (cran-uri "mapproj" version))
3309 "10bpib827011fpgvzsmlv4j3i41s0r3cv1hvawwdlk753s7i0pw6"))))
3310 (build-system r-build-system)
3311 (propagated-inputs (list r-maps))
3312 (home-page "https://cran.r-project.org/web/packages/mapproj")
3313 (synopsis "Map projection in R")
3314 (description "This package converts latitude/longitude into projected
3316 (license (list license:gpl2 ; The R interface
3317 (license:non-copyleft ; The C code
3318 "https://www.gnu.org/licenses/license-list.en.html#lucent102"
3319 "Lucent Public License Version 1.02")))))
3321 (define-public r-rgooglemaps
3323 (name "r-rgooglemaps")
3328 (uri (cran-uri "RgoogleMaps" version))
3331 "02v8k0bw70q4qwx4lcdy8p25q7n3ql2ll46lfpqllxa1p26svmfi"))))
3332 (properties `((upstream-name . "RgoogleMaps")))
3333 (build-system r-build-system)
3336 (home-page "https://cran.r-project.org/web/packages/RgoogleMaps")
3337 (synopsis "Use Google Maps in R")
3338 (description "This package serves two purposes:
3340 @item Provide a comfortable R interface to query the Google server for static
3342 @item Use the map as a background image to overlay plots within R. This
3343 requires proper coordinate scaling.
3345 (license license:gpl2+)))
3347 (define-public r-geosphere
3349 (name "r-geosphere")
3354 (uri (cran-uri "geosphere" version))
3357 "0bg4vfmrw140j2ax0p6bflvb77w03ir39wa87l96rj473jpa9hzj"))))
3358 (build-system r-build-system)
3359 (propagated-inputs (list r-sp))
3360 (home-page "https://cran.r-project.org/web/packages/geosphere")
3361 (synopsis "Spherical trigonometry")
3362 (description "This package computes spherical trigonometry for geographic
3363 applications. That is, compute distances and related measures for angular
3364 (longitude/latitude) locations.")
3365 (license license:gpl3+)))
3367 (define-public r-jpeg
3374 (uri (cran-uri "jpeg" version))
3377 "0wihj538wdnr71wdldym83qadb4kh68a6rkallwbh2f25r27b881"))))
3378 (build-system r-build-system)
3379 (inputs (list libjpeg-turbo))
3380 (home-page "https://www.rforge.net/jpeg/")
3381 (synopsis "Read and write JPEG images with R")
3382 (description "This package provides a way to read, write and display
3383 bitmap images stored in the JPEG format with R. It can read and write both
3384 files and in-memory raw vectors.")
3385 (license license:gpl2+)))
3387 (define-public r-ggmap
3394 (uri (cran-uri "ggmap" version))
3397 "13dmzl6z62pzjiffilarkji46vy0sacxa8a7mhrhc3biq3ylzhln"))))
3398 (build-system r-build-system)
3417 (home-page "https://github.com/dkahle/ggmap")
3418 (synopsis "Spatial visualization with ggplot2")
3419 (description "This package provides a collection of functions to visualize
3420 spatial data and models on top of static maps from various online sources (e.g
3421 Google Maps and Stamen Maps). It includes tools common to those tasks,
3422 including functions for geolocation and routing.")
3423 (license license:gpl2)))
3425 (define-public r-haven
3432 (uri (cran-uri "haven" version))
3435 "1x5g6kjrzcyarbjz91f4aaspx7rb50qs6a9y29mzr3mjq4dk305m"))
3436 (modules '((guix build utils)))
3438 ;; unvendor readstat
3439 '(delete-file-recursively "src/readstat"))))
3440 (build-system r-build-system)
3443 (modify-phases %standard-phases
3444 (add-after 'unpack 'unbundle-readstat
3446 ;; Not required, since we’re not building readstat.
3447 (substitute* "src/Makevars"
3448 (("-lz") "-lreadstat")))))))
3464 (home-page "https://haven.tidyverse.org")
3465 (synopsis "Import and export SPSS, Stata and SAS files")
3467 "This package lets you import foreign statistical formats into R via the
3468 @url{https://github.com/WizardMac/ReadStat,ReadStat} C library.")
3469 (license license:expat)))
3471 (define-public r-amap
3477 (uri (cran-uri "amap" version))
3480 "0zpcb73w413na23f6giml9311jh0j0y766w2fh9i40d2h7bbvyvs"))))
3481 (build-system r-build-system)
3484 (home-page "http://mulcyber.toulouse.inra.fr/projects/amap/")
3485 (synopsis "Another multidimensional analysis package")
3486 (description "This package provides tools for clustering and principal
3487 component analysis (with robust methods, and parallelized functions).")
3488 (license license:gpl2+)))
3490 (define-public r-ape
3497 (uri (cran-uri "ape" version))
3500 "0mqjsh7maczd02iwa4fb896q3kgd9jnlilq7y1yz18ch0c54aqlv"))))
3501 (build-system r-build-system)
3503 (list r-lattice r-nlme r-rcpp))
3504 (home-page "http://ape-package.ird.fr/")
3505 (synopsis "Analyses of phylogenetics and evolution")
3507 "This package provides functions for reading, writing, plotting, and
3508 manipulating phylogenetic trees, analyses of comparative data in a
3509 phylogenetic framework, ancestral character analyses, analyses of
3510 diversification and macroevolution, computing distances from DNA sequences,
3511 and several other tools.")
3512 (license license:gpl2+)))
3514 (define-public r-abbyyr
3521 (uri (cran-uri "abbyyR" version))
3524 "1vldnd3dg89aj6a73nhirirqddbfdrnzhb5m3679i60sark8nk6r"))))
3525 (properties `((upstream-name . "abbyyR")))
3526 (build-system r-build-system)
3534 (home-page "https://github.com/soodoku/abbyyR")
3535 (synopsis "Access to Abbyy Optical Character Recognition (OCR) API")
3537 "This package provides tools to get text from images of text using Abbyy
3538 Cloud Optical Character Recognition (OCR) API. With abbyyyR, one can easily
3539 OCR images, barcodes, forms, documents with machine readable zones, e.g.
3540 passports and get the results in a variety of formats including plain text and
3541 XML. To learn more about the Abbyy OCR API, see @url{http://ocrsdk.com/}.")
3542 (license license:expat)))
3544 (define-public r-colorspace
3546 (name "r-colorspace")
3551 (uri (cran-uri "colorspace" version))
3553 (base32 "0zw52s8g2gxp8i1ax96azxmxqrbhb7aad5px0c1vgr6n9p682mp7"))))
3554 (build-system r-build-system)
3557 (home-page "https://cran.r-project.org/web/packages/colorspace")
3558 (synopsis "Color space manipulation")
3560 "This package carries out a mapping between assorted color spaces
3561 including RGB, HSV, HLS, CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB and polar
3562 CIELAB. Qualitative, sequential, and diverging color palettes based on HCL
3563 colors are provided.")
3564 (license license:bsd-3)))
3566 (define-public r-glue
3573 (uri (cran-uri "glue" version))
3576 "1gzxk5jgdh2xq9r7z09xs306ygzf27vhg3pyfl7ck1755gqii9cx"))))
3577 (build-system r-build-system)
3578 ;; knitr depends on glue, so we can't add knitr here to build the
3582 `(("r-knitr" ,r-knitr)))
3583 (home-page "https://github.com/tidyverse/glue")
3584 (synopsis "Interpreted string literals")
3586 "This package provides an implementation of interpreted string literals,
3587 inspired by Python's Literal String Interpolation (PEP-0498) and
3588 Docstrings (PEP-0257) and Julia's Triple-Quoted String Literals.")
3589 (license license:expat)))
3591 (define-public r-palmerpenguins
3593 (name "r-palmerpenguins")
3598 (uri (cran-uri "palmerpenguins" version))
3601 "0q1k3cdkliq7kwrg1n0vs9b6cjwyfarhlgdijhp9c6riy6y5ik7x"))))
3603 `((upstream-name . "palmerpenguins")))
3604 (build-system r-build-system)
3605 (home-page "https://allisonhorst.github.io/palmerpenguins/")
3606 (synopsis "Palmer Archipelago (Antarctica) penguin data")
3608 "This package includes size measurements, clutch observations, and blood
3609 isotope ratios for adult foraging Adélie, Chinstrap, and Gentoo penguins
3610 observed on islands in the Palmer Archipelago near Palmer Station, Antarctica.
3611 Data were collected and made available by Dr. Kristen Gorman and the Palmer
3612 Station Long Term Ecological Research (LTER) Program.")
3613 (license license:cc0)))
3615 (define-public r-pastecs
3621 (uri (cran-uri "pastecs" version))
3624 "0z4dic94ar646w7zc2ggi5hgvf2qnznsani94c5pyql8zspz47lc"))))
3625 (build-system r-build-system)
3628 (home-page "https://github.com/phgrosjean/pastecs")
3629 (synopsis "Analysis of space-time ecological series")
3631 "This package provides functions for regulation, decomposition and analysis
3632 of space-time series. The @code{pastecs} library is a PNEC-Art4 and IFREMER
3633 initiative to bring PASSTEC 2000 functionalities to R.")
3634 (license license:gpl2+)))
3636 (define-public r-partykit
3642 (uri (cran-uri "partykit" version))
3645 "1b73s5l19yicwginqsg5xr7fzb005x372n0wb34kk6jb5x5lbsdj"))))
3646 (build-system r-build-system)
3654 (home-page "http://partykit.R-Forge.R-project.org/partykit")
3655 (synopsis "Toolkit for recursive partytioning")
3657 "This package provides a toolkit with infrastructure for representing,
3658 summarizing, and visualizing tree-structured regression and classification
3660 (license license:gpl2+)))
3662 (define-public r-plogr
3669 (uri (cran-uri "plogr" version))
3672 "0a8dhzlna79ggyhfr0nncgh15a9n6r0dsz664pz0ah323wpblqqf"))))
3673 (build-system r-build-system)
3674 (home-page "https://github.com/krlmlr/plogr")
3675 (synopsis "R bindings for the plog C++ logging library")
3677 "This package provides the header files for a stripped-down version of
3678 the plog header-only C++ logging library, and a method to log to R's standard
3680 (license license:expat)))
3682 (define-public r-pls
3689 (uri (cran-uri "pls" version))
3691 (base32 "1gqq8rcq6p0hs2gfzwfj690rz3pwywmnv8qzcv0wsd6aaqkskwzg"))))
3692 (build-system r-build-system)
3693 (home-page "https://mevik.net/work/software/pls.html")
3694 (synopsis "Partial Least Squares and Principal Component Regression")
3696 "The pls package implements multivariate regression methods: Partial Least
3697 Squares Regression (@dfn{PLSR}), Principal Component Regression (@dfn{PCR}), and
3698 Canonical Powered Partial Least Squares (@dfn{CPPLS}). It supports:
3701 @item several algorithms: the traditional orthogonal scores (@dfn{NIPALS}) PLS
3702 algorithm, kernel PLS, wide kernel PLS, Simpls, and PCR through @code{svd}
3703 @item multi-response models (or @dfn{PLS2})
3704 @item flexible cross-validation
3705 @item Jackknife variance estimates of regression coefficients
3706 @item extensive and flexible plots: scores, loadings, predictions, coefficients,
3707 (R)MSEP, R², and correlation loadings
3708 @item formula interface, modelled after @code{lm()}, with methods for predict,
3709 print, summary, plot, update, etc.
3710 @item extraction functions for coefficients, scores, and loadings
3711 @item MSEP, RMSEP, and R² estimates
3712 @item multiplicative scatter correction (@dfn{MSC})
3714 (license license:gpl2)))
3723 (uri (cran-uri "ps" version))
3725 (base32 "1qaj9gyz7q09aadlnj5al53k2pa4axmzjsbndf5r0b51qqrcy842"))))
3726 (build-system r-build-system)
3727 (home-page "https://ps.r-lib.org")
3728 (synopsis "List, query, and manipulate system processes")
3730 "The ps package implements an API to list, query, and manipulate system
3731 processes. Most of its code is based on the @code{psutil} Python package.")
3732 (license license:bsd-3)))
3734 (define-public r-pkgbuild
3741 (uri (cran-uri "pkgbuild" version))
3743 (base32 "0j6v5nbp8kg1m3j999gd1qsbdmqcqm1mf28ngmm177miwv8q4skw"))))
3744 (build-system r-build-system)
3754 (home-page "https://github.com/r-pkgs/pkgbuild")
3755 (synopsis "Find tools needed to build R packages")
3757 "This package provides functions used to build R packages. It locates
3758 compilers needed to build R packages on various platforms and ensures the PATH
3759 is configured appropriately so R can use them.")
3760 (license license:gpl3)))
3762 (define-public r-pkgload
3769 (uri (cran-uri "pkgload" version))
3772 "03yr9mswx9nij27bp21q6c533zx310xwzhwm52dwr7554k42p4fn"))))
3773 (build-system r-build-system)
3782 (home-page "https://github.com/r-lib/pkgload")
3783 (synopsis "Simulate package installation and attach")
3785 "This package simulates the process of installing a package and then
3786 attaching it. This is a key part of the @code{devtools} package as it allows
3787 you to rapidly iterate while developing a package.")
3788 (license license:gpl3)))
3790 (define-public r-pvclust
3796 (uri (cran-uri "pvclust" version))
3799 "0082icm54k2yq60k06qpr92a626k39j2jr0046lva4ylmhxqb4kq"))))
3800 (build-system r-build-system)
3801 (home-page "https://github.com/shimo-lab/pvclust")
3803 "Hierarchical clustering with P-values via multiscale bootstrap resampling")
3804 (description "This package provides an implementation of multiscale bootstrap
3805 resampling for assessing the uncertainty in hierarchical cluster analysis. It
3806 provides an AU (approximately unbiased) P-value as well as a BP (bootstrap probability)
3807 value for each cluster in a dendrogram.")
3808 (license license:gpl2+)))
3810 (define-public r-rcpp
3817 (uri (cran-uri "Rcpp" version))
3819 (base32 "1gzqfn1xjawzig30ama3rldykqpcn6bd8sg684mrfvpmv96bi9cx"))))
3820 (build-system r-build-system)
3821 (home-page "http://www.rcpp.org")
3822 (synopsis "Seamless R and C++ integration")
3824 "The Rcpp package provides R functions as well as C++ classes which offer
3825 a seamless integration of R and C++. Many R data types and objects can be
3826 mapped back and forth to C++ equivalents which facilitates both writing of new
3827 code as well as easier integration of third-party libraries. Documentation
3828 about Rcpp is provided by several vignettes included in this package, via the
3829 @code{Rcpp Gallery} site at <http://gallery.rcpp.org>, the paper by Eddelbuettel
3830 and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see
3831 @code{citation(\"Rcpp\")} for details on these last two.")
3832 (license license:gpl2+)))
3834 (define-public r-rcppthread
3836 (name "r-rcppthread")
3841 (uri (cran-uri "RcppThread" version))
3844 "0iprpidf7q1wlrgr9dwiikb6apqk80pyjcyni56k64nl7lrkszhj"))))
3845 (properties `((upstream-name . "RcppThread")))
3846 (build-system r-build-system)
3848 "https://github.com/tnagler/RcppThread")
3849 (synopsis "R threading in C++")
3851 "This package provides a C++11-style thread class and thread pool that can
3852 safely be interrupted from R.")
3853 (license license:expat)))
3855 (define-public r-rcppnumerical
3857 (name "r-rcppnumerical")
3861 (uri (cran-uri "RcppNumerical" version))
3864 "1a92fql6mijhnr1kxkcxwivf95pk9lhgmhzkshs51h0ybfv5krik"))))
3865 (build-system r-build-system)
3867 (list r-rcpp r-rcppeigen))
3868 (home-page "https://github.com/yixuan/RcppNumerical")
3869 (synopsis"Numerical computing libraries integration with @code{Rcpp}")
3870 (description "This package provides a collection of libraries for numerical
3871 computing (numerical integration, optimization, etc.) and their integration
3873 (license license:gpl2+)))
3875 (define-public r-rcppxptrutils
3877 (name "r-rcppxptrutils")
3882 (uri (cran-uri "RcppXPtrUtils" version))
3884 (base32 "0hm57nf4dzgsmg4hjj6wikwjx93fgfwkmybw6ly4b58wi6qwml1l"))))
3885 (properties `((upstream-name . "RcppXPtrUtils")))
3886 (build-system r-build-system)
3887 (propagated-inputs (list r-rcpp))
3888 (home-page "https://github.com/Enchufa2/RcppXPtrUtils")
3889 (synopsis "XPtr add-ons for Rcpp")
3891 "This package provides the means to compile user-supplied C++ functions
3892 with Rcpp and retrieve an @code{XPtr} that can be passed to other C++
3894 (license license:expat)))
3896 (define-public r-bindr
3903 (uri (cran-uri "bindr" version))
3906 "1l05fpk2yql3jka321c0bdgx6mqq9pvfrg2844lbjfpbgjkmqy3w"))))
3907 (build-system r-build-system)
3908 (home-page "https://github.com/krlmlr/bindr")
3909 (synopsis "Parametrized active bindings")
3911 "This package provides a simple interface for creating active bindings
3912 where the bound function accepts additional arguments.")
3913 (license license:expat)))
3915 (define-public r-bindrcpp
3922 (uri (cran-uri "bindrcpp" version))
3925 "0rz4ibjdjsxl99ff3ha79z7cnjmilx4rx58fk9kk7ld9xc4hf4s8"))))
3926 (build-system r-build-system)
3928 (list r-bindr r-plogr r-rcpp))
3929 (home-page "https://github.com/krlmlr/bindrcpp")
3930 (synopsis "Rcpp interface to active bindings")
3932 "This package provides an easy way to fill an environment with active
3933 bindings that call a C++ function.")
3934 (license license:expat)))
3936 (define-public r-auc
3943 (uri (cran-uri "AUC" version))
3946 "07xf47kypqbsg2mixmq6mnh4s89aqan9bgl6kfv6lbx8ajv2asw3"))))
3947 (properties `((upstream-name . "AUC")))
3948 (build-system r-build-system)
3949 (home-page "https://cran.r-project.org/web/packages/AUC")
3950 (synopsis "Compute the area under the curve of selected measures")
3952 "This package includes functions to compute the area under the curve of
3953 selected measures: the area under the sensitivity curve (AUSEC), the area
3954 under the specificity curve (AUSPC), the area under the accuracy
3955 curve (AUACC), and the area under the receiver operating characteristic
3956 curve (AUROC). The curves can also be visualized. Support for partial areas
3958 (license license:gpl2+)))
3960 (define-public r-calibrate
3962 (name "r-calibrate")
3967 (uri (cran-uri "calibrate" version))
3969 (base32 "19kgrnsyq67iqv1biyssqi30a6v2836ql20nabpy2m692ns0jfvi"))))
3970 (build-system r-build-system)
3973 (home-page "https://cran.r-project.org/web/packages/calibrate")
3974 (synopsis "Calibration of scatterplot and biplot axes")
3976 "This is a package for drawing calibrated scales with tick marks
3977 on (non-orthogonal) variable vectors in scatterplots and biplots.")
3978 (license license:gpl2)))
3980 (define-public r-shape
3987 (uri (cran-uri "shape" version))
3990 "0yqbrrx2ywmfl99s6d1n6jblc63k1mxbiqyv8y0kq8jws1g3w45r"))))
3991 (build-system r-build-system)
3992 (home-page "https://cran.r-project.org/web/packages/shape")
3993 (synopsis "Functions for plotting graphical shapes")
3995 "This package provides functions for plotting graphical shapes such as
3996 ellipses, circles, cylinders, arrows, ...")
3997 (license license:gpl3+)))
3999 (define-public r-globaloptions
4001 (name "r-globaloptions")
4006 (uri (cran-uri "GlobalOptions" version))
4008 (base32 "0gkm77w6db9ajyncy1xdcivplap06a51zi99m009kylccschd2a7"))))
4009 (properties `((upstream-name . "GlobalOptions")))
4010 (build-system r-build-system)
4013 (home-page "https://github.com/jokergoo/GlobalOptions")
4014 (synopsis "Generate functions to get or set global options")
4016 "This package provides more controls on the option values such as
4017 validation and filtering on the values, making options invisible or private.")
4018 (license license:gpl2+)))
4020 (define-public r-circlize
4027 (uri (cran-uri "circlize" version))
4030 "1iswb7dy08as3pbzxvhx5qlsbnwvp79nwg8m158nfz7y2d9xa0nn"))))
4031 (build-system r-build-system)
4033 (list r-colorspace r-globaloptions r-shape))
4036 (home-page "https://github.com/jokergoo/circlize")
4037 (synopsis "Circular visualization")
4039 "Circular layout is an efficient way to visualise huge amounts of
4040 information. This package provides an implementation of circular layout
4041 generation in R as well as an enhancement of available software. Its
4042 flexibility is based on the usage of low-level graphics functions such that
4043 self-defined high-level graphics can be easily implemented by users for
4044 specific purposes. Together with the seamless connection between the powerful
4045 computational and visual environment in R, it gives users more convenience and
4046 freedom to design figures for better understanding complex patterns behind
4047 multi-dimensional data.")
4048 (license license:gpl2+)))
4050 (define-public r-powerlaw
4057 (uri (cran-uri "poweRlaw" version))
4059 (base32 "14d1myxllvm1grnfiszzzxaiqpb2jpmsi19wq70r8r2wki293h7g"))))
4060 (properties `((upstream-name . "poweRlaw")))
4061 (build-system r-build-system)
4066 (home-page "https://github.com/csgillespie/poweRlaw")
4067 (synopsis "Tools for the analysis of heavy tailed distributions")
4069 "This package provides an implementation of maximum likelihood estimators
4070 for a variety of heavy tailed distributions, including both the discrete and
4071 continuous power law distributions. Additionally, a goodness-of-fit based
4072 approach is used to estimate the lower cut-off for the scaling region.")
4073 ;; Any of these GPL versions.
4074 (license (list license:gpl2 license:gpl3))))
4076 (define-public r-compare
4083 (uri (cran-uri "compare" version))
4086 "0k9zms930b5dz9gy8414li21wy0zg9x9vp7301v5cvyfi0g7xzgw"))))
4087 (build-system r-build-system)
4088 (home-page "https://cran.r-project.org/web/packages/compare")
4089 (synopsis "Comparing objects for differences")
4091 "This package provides functions to compare a model object to a
4092 comparison object. If the objects are not identical, the functions can be
4093 instructed to explore various modifications of the objects (e.g., sorting
4094 rows, dropping names) to see if the modified versions are identical.")
4095 (license license:gpl2+)))
4097 (define-public r-dendextend
4099 (name "r-dendextend")
4104 (uri (cran-uri "dendextend" version))
4107 "06wjs8451hmnimzgngpzbai3yrgy33133vzzapa8jib9crdqi8sb"))))
4108 (build-system r-build-system)
4110 (list r-ggplot2 r-magrittr r-viridis))
4113 (home-page "https://cran.r-project.org/web/packages/dendextend")
4114 (synopsis "Extending 'dendrogram' functionality in R")
4116 "This package offers a set of functions for extending @code{dendrogram}
4117 objects in R, letting you visualize and compare trees of hierarchical
4118 clusterings. You can adjust a tree's graphical parameters (the color, size,
4119 type, etc of its branches, nodes and labels) and visually and statistically
4120 compare different dendrograms to one another.")
4121 ;; Any of these versions
4122 (license (list license:gpl2 license:gpl3))))
4124 (define-public r-getoptlong
4126 (name "r-getoptlong")
4131 (uri (cran-uri "GetoptLong" version))
4134 "00fpm6nd3kqa2ikasxa62jzywi46fvvmx1mdavcp5yrxxn37j8wc"))))
4135 (properties `((upstream-name . "GetoptLong")))
4136 (build-system r-build-system)
4140 (list r-crayon r-globaloptions r-rjson))
4143 (home-page "https://github.com/jokergoo/GetoptLong")
4144 (synopsis "Parsing command-line arguments and variable interpolation")
4146 "This is yet another command-line argument parser which wraps the
4147 powerful Perl module @code{Getopt::Long} and with some adaptation for easier
4148 use in R. It also provides a simple way for variable interpolation in R.")
4149 (license license:gpl2+)))
4151 (define-public r-fastmatch
4153 (name "r-fastmatch")
4158 (uri (cran-uri "fastmatch" version))
4161 "0qcq1gwl9pijgp34giyq5y9rk0ly3d7xza2b7r68xx63ifqa1vqx"))))
4162 (build-system r-build-system)
4163 (home-page "https://www.rforge.net/fastmatch")
4164 (synopsis "Fast match function")
4166 "This package provides a fast @code{match} replacement for cases that
4167 require repeated look-ups. It is slightly faster that R's built-in
4168 @code{match} function on first match against a table, but extremely fast on
4169 any subsequent lookup as it keeps the hash table in memory.")
4170 (license license:gpl2)))
4179 (uri (cran-uri "ff" version))
4182 "1yl3ipzz9bjkfy9bbna7xz5n7iz4lchnw5l7agww7by764yk6iqa"))))
4183 (build-system r-build-system)
4184 (propagated-inputs (list r-bit))
4185 (home-page "http://ff.r-forge.r-project.org/")
4186 (synopsis "Memory-efficient storage of large data on disk and access functions")
4188 "This package provides data structures that are stored on disk but
4189 behave (almost) as if they were in RAM by transparently mapping only a section
4191 ;; error Architecture not supported.
4192 (supported-systems (delete "aarch64-linux" %supported-systems))
4193 (license license:gpl2)))
4195 (define-public r-ffbase
4202 (uri (cran-uri "ffbase" version))
4205 "1dp6lblfq2j7r1b4b8ls47jlx8j27n88d5vp8w116lb8pa01zxmk"))))
4206 (build-system r-build-system)
4208 (list r-bit r-fastmatch r-ff))
4209 (home-page "https://github.com/edwindj/ffbase")
4210 (synopsis "Basic statistical functions for package 'ff'")
4212 "This package extends the out of memory vectors of @code{ff} with
4213 statistical functions and other utilities to ease their usage.")
4214 (license license:gpl3)))
4216 (define-public r-prettyunits
4218 (name "r-prettyunits")
4223 (uri (cran-uri "prettyunits" version))
4226 "1ibmzgknw5896q2i6r59jz2izblxwgb29ivvjzx50pkd1jl9l6cs"))))
4227 (build-system r-build-system)
4228 (home-page "https://github.com/gaborcsardi/prettyunits")
4229 (synopsis "Pretty, human readable formatting of quantities")
4231 "This package provides tools for pretty, human readable formatting of
4233 (license license:expat)))
4235 (define-public r-princurve
4237 (name "r-princurve")
4241 (uri (cran-uri "princurve" version))
4244 "0wzk329bxljkzz57y220lsfckpsn45w348m6dcxh29zbj0ik65h2"))))
4245 (build-system r-build-system)
4248 (home-page "https://github.com/rcannood/princurve")
4249 (synopsis "Fit a principal curve in arbitrary dimension")
4250 (description "This package provides procedures for fitting a principal
4251 curve to a data matrix in arbitrary dimensions.")
4252 (license license:gpl2)))
4254 (define-public r-reshape
4261 (uri (cran-uri "reshape" version))
4264 "0j203qmc076x5lp6q2xi4dq4xdb73jmsa42rpxp1c37knnrph4br"))))
4265 (build-system r-build-system)
4268 (home-page "http://had.co.nz/reshape")
4269 (synopsis "Flexibly reshape data")
4271 "Flexibly restructure and aggregate data using just two functions:
4272 @code{melt} and @code{cast}. This package provides them.")
4273 (license license:expat)))
4275 (define-public r-restrserve
4277 (name "r-restrserve")
4282 (uri (cran-uri "RestRserve" version))
4284 (base32 "1ydsdgy6mxl0zqk7xqf4v6if5nf2qv7k48q340fhaqyjk2gd60p7"))))
4285 (build-system r-build-system)
4297 (home-page "https://restrserve.org")
4298 (synopsis "R web API framework")
4300 "RestRserve is an R web API framework for building high-performance AND
4301 robust microservices and app backends. With Rserve backend on UNIX-like
4302 systems it is parallel by design. It will handle incoming requests in
4303 parallel - each request in a separate fork.")
4304 (license license:gpl2+)))
4306 (define-public r-progress
4313 (uri (cran-uri "progress" version))
4316 "0dgzb362641aqm8xd88iqa8jmpdm43xs0aba0d5kk6fvapnxi95l"))))
4317 (build-system r-build-system)
4319 (list r-crayon r-hms r-prettyunits r-r6))
4320 (home-page "https://github.com/gaborcsardi/progress")
4321 (synopsis "Terminal progress bars")
4323 "This package provides configurable progress bars. They may include
4324 percentage, elapsed time, and/or the estimated completion time. They work in
4325 terminals, in Emacs ESS, RStudio, Windows Rgui, and the macOS R.app. The
4326 package also provides a C++ API, that works with or without Rcpp.")
4327 (license license:expat)))
4329 (define-public r-ggally
4336 (uri (cran-uri "GGally" version))
4339 "1r98zgh2grn8330cf26r1c20gl131zm778szvn5wj6q6pwv2yd9h"))))
4340 (properties `((upstream-name . "GGally")))
4341 (build-system r-build-system)
4357 (home-page "https://ggobi.github.io/ggally")
4358 (synopsis "Extension to ggplot2")
4360 "The R package ggplot2 is a plotting system based on the grammar of
4361 graphics. GGally extends ggplot2 by adding several functions to reduce the
4362 complexity of combining geometric objects with transformed data. Some of
4363 these functions include a pairwise plot matrix, a two group pairwise plot
4364 matrix, a parallel coordinates plot, a survival plot, and several functions to
4366 (license license:gpl2+)))
4368 (define-public r-proxy
4375 (uri (cran-uri "proxy" version))
4378 "0k8sr24mjfvxp12sf1j9228ah3ngy15nqmm0jw14x5s32f1assv7"))))
4379 (build-system r-build-system)
4380 (home-page "https://cran.r-project.org/web/packages/proxy")
4381 (synopsis "Distance and similarity measures")
4383 "This package provides an extensible framework for the efficient
4384 calculation of auto- and cross-proximities, along with implementations of the
4385 most popular ones.")
4386 (license license:gpl2)))
4395 (uri (cran-uri "sp" version))
4397 (base32 "1bdi06n5zkjnnyh0rallf04s0vlcx9rg9p5q7s6vfqvkf19nk501"))))
4398 (build-system r-build-system)
4403 (home-page "https://cran.r-project.org/web/packages/sp")
4404 (synopsis "Classes and methods for spatial data")
4406 "This package provides classes and methods for spatial data; the classes
4407 document where the spatial location information resides, for 2D or 3D data.
4408 Utility functions are provided, e.g. for plotting data as maps, spatial
4409 selection, as well as methods for retrieving coordinates, for subsetting,
4410 print, summary, etc.")
4411 (license license:gpl2+)))
4413 (define-public r-laplacesdemon
4415 (name "r-laplacesdemon")
4420 (uri (cran-uri "LaplacesDemon" version))
4422 (base32 "1dsfp65cg06f25zjzd5ib4qyn1alfhbhpgyvpcw5n6bszn13idap"))))
4423 (properties `((upstream-name . "LaplacesDemon")))
4424 (build-system r-build-system)
4425 (home-page "https://github.com/LaplacesDemonR/LaplacesDemon")
4426 (synopsis "Complete environment for Bayesian inference")
4428 "This package provides a complete environment for Bayesian inference using
4429 a variety of different samplers.")
4430 (license license:expat)))
4432 (define-public r-rmtstat
4439 (uri (cran-uri "RMTstat" version))
4442 "1r1a2sdqv64m9cpm2pz6r8abf7l810126ayd8iq3gx86c7bjfj5v"))))
4443 (properties `((upstream-name . "RMTstat")))
4444 (build-system r-build-system)
4445 (home-page "https://cran.r-project.org/web/packages/RMTstat")
4446 (synopsis "Distributions, statistics and tests derived from random matrix theory")
4448 "This package provides functions for working with the Tracy-Widom laws
4449 and other distributions related to the eigenvalues of large Wishart
4451 (license license:bsd-3)))
4453 (define-public r-rmpi
4459 (uri (cran-uri "Rmpi" version))
4462 "06mxqgrimhfsag5giv810c7ycdbaycqs4qcj41pnfbj0jypw32im"))))
4463 (properties `((upstream-name . "Rmpi")))
4464 (build-system r-build-system)
4466 `(#:configure-flags '("--configure-args=\"--with-Rmpi-type=OPENMPI\"")
4467 #:phases (modify-phases %standard-phases
4468 (add-before 'install 'mpi-setup
4474 (home-page "http://www.stats.uwo.ca/faculty/yu/Rmpi")
4475 (synopsis "R interface to message-passing interface (MPI)")
4477 "This package provides an interface (wrapper) to MPI APIs. It also
4478 provides an interactive R manager and worker environment.")
4479 (license license:gpl2+)))
4481 (define-public r-lmoments
4488 (uri (cran-uri "Lmoments" version))
4491 "0pc63bj9a8hzr5m3yssrc4kin39fffwkl8rggs3sagzr12d4i7bw"))))
4492 (properties `((upstream-name . "Lmoments")))
4493 (build-system r-build-system)
4495 (list r-rcpp r-rcpparmadillo))
4496 (home-page "http://www.tilastotiede.fi/juha_karvanen.html")
4497 (synopsis "L-moments and quantile mixtures")
4499 "This package contains functions to estimate L-moments and trimmed
4500 L-moments from the data. It also contains functions to estimate the
4501 parameters of the normal polynomial quantile mixture and the Cauchy polynomial
4502 quantile mixture from L-moments and trimmed L-moments.")
4503 (license license:gpl2)))
4505 (define-public r-distillery
4507 (name "r-distillery")
4512 (uri (cran-uri "distillery" version))
4515 "1ymmxyamkq0zbz2m4gllln1ihks2hcib6gs0mls92as79srz122b"))))
4516 (build-system r-build-system)
4517 (home-page "https://ral.ucar.edu/staff/ericg/")
4518 (synopsis "Functions for confidence intervals and object information")
4520 "This package provides some very simple method functions for confidence
4521 interval calculation and to distill pertinent information from a potentially
4522 complex object; primarily used in common with the packages extRemes and
4524 (license license:gpl2+)))
4526 (define-public r-etrunct
4532 (uri (cran-uri "etrunct" version))
4535 "0ayazgyqlc8jcqr03cwfmfhm4pck6xri1r6vkgqy4arqkrrnrcqr"))))
4536 (properties `((upstream-name . "etrunct")))
4537 (build-system r-build-system)
4538 (home-page "https://cran.r-project.org/web/packages/etrunct")
4539 (synopsis "Computes moments of univariate truncated T distribution")
4540 (description "This package computes moments of univariate truncated
4541 T distribution. There is only one exported function, @code{e_trunct},
4542 which should be seen for details.")
4543 (license license:expat)))
4545 (define-public r-excelr
4552 (uri (cran-uri "excelR" version))
4554 (base32 "1pb4sy54zjv5vrh7gjjv7qlpab74km6mfsmfyl0yhmr0jx01hrw0"))
4556 '(delete-file "inst/htmlwidgets/lib/jexcel/js/jexcel.min.js"))))
4557 (properties `((upstream-name . "excelR")))
4558 (build-system r-build-system)
4561 (modify-phases %standard-phases
4562 (add-after 'unpack 'process-javascript
4563 (lambda* (#:key inputs #:allow-other-keys)
4564 (with-directory-excursion "inst/htmlwidgets/lib/jexcel/js/"
4565 (let ((source (assoc-ref inputs "js-jexcel"))
4566 (target "jexcel.min.js"))
4567 (format #true "Processing ~a --> ~a~%"
4569 (invoke "esbuild" source "--minify"
4570 (string-append "--outfile=" target)))))))))
4572 `(("esbuild" ,esbuild)
4573 ;; There is no tag for this particular commit, but comparison of the
4574 ;; contents of the JavaScript files point to this commit as the most
4579 (uri (string-append "https://raw.githubusercontent.com/jspreadsheet/ce/"
4580 "8af1960f76e6803bebc5750013d2ebe95354e88a/dist/jexcel.js"))
4583 "0y88hsr9d8cpnvdmbm17m328pc4kc5wbcv02kzmhm0bryzhviw7h"))))))
4584 (propagated-inputs (list r-htmlwidgets r-jsonlite))
4585 (home-page "https://github.com/Swechhya/excelR")
4586 (synopsis "Wrapper of the JavaScript library jExcel")
4588 "This package provides an R interface to the jExcel library to
4589 create web-based interactive tables and spreadsheets compatible with
4590 spreadsheet software.")
4591 (license license:expat)))
4593 (define-public r-extremes
4600 (uri (cran-uri "extRemes" version))
4603 "19q560prq02h3bwk01jb68693qb5bhsv8wiqhia7v5knm34qv8x7"))))
4604 (properties `((upstream-name . "extRemes")))
4605 (build-system r-build-system)
4607 (list r-distillery r-lmoments))
4608 (home-page "https://www.assessment.ucar.edu/toolkit/")
4609 (synopsis "Extreme value analysis")
4611 "ExtRemes is a suite of functions for carrying out analyses on the
4612 extreme values of a process of interest; be they block maxima over long blocks
4613 or excesses over a high threshold.")
4614 (license license:gpl2+)))
4616 (define-public r-lmtest
4623 (uri (cran-uri "lmtest" version))
4626 "15yr2kx08wy085bnziqmj1p6hf9mg3qp2a8465jk2df6di6hsh34"))))
4627 (build-system r-build-system)
4632 (home-page "https://cran.r-project.org/web/packages/lmtest")
4633 (synopsis "Testing linear regression models")
4635 "This package provides a collection of tests, data sets, and examples for
4636 diagnostic checking in linear regression models. Furthermore, some generic
4637 tools for inference in parametric models are provided.")
4638 ;; Either version is okay
4639 (license (list license:gpl2 license:gpl3))))
4641 (define-public r-idr
4647 (uri (cran-uri "idr" version))
4650 "05nvgw1xdg670bsjjrxkgd1mrdkciccpw4krn0zcgdf2r21dzgwb"))))
4651 (build-system r-build-system)
4652 (home-page "https://cran.r-project.org/web/packages/idr/")
4653 (synopsis "Irreproducible discovery rate")
4655 "This is a package for estimating the copula mixture model and plotting
4656 correspondence curves in \"Measuring reproducibility of high-throughput
4657 experiments\" (2011), Annals of Applied Statistics, Vol. 5, No. 3, 1752-1779,
4658 by Li, Brown, Huang, and Bickel")
4659 (license license:gpl2+)))
4661 (define-public r-inline
4667 (uri (cran-uri "inline" version))
4670 "1mcr9hgq6kkq03n7pkcccxa7vg8jma0q7lfxc5vvkc6snydk1s8f"))))
4671 (build-system r-build-system)
4672 (home-page "https://cran.r-project.org/web/packages/inline")
4673 (synopsis "Functions to inline C, C++, Fortran function calls from R")
4675 "This package provides functionality to dynamically define R functions
4676 and S4 methods with inlined C, C++ or Fortran code supporting @code{.C} and
4677 @code{.Call} calling conventions.")
4678 ;; Any version of the LGPL.
4679 (license license:lgpl3+)))
4681 (define-public r-inum
4687 (uri (cran-uri "inum" version))
4690 "1khkzja8lwn9075864vbyajqina9m588ahf1fsrrajrsqilyzssz"))))
4691 (build-system r-build-system)
4694 (home-page "https://cran.r-project.org/web/packages/inum/")
4695 (synopsis "Interval and enum-type representation of vectors")
4697 "This package provides an enum-type representation of vectors and
4698 representation of intervals, including a method of coercing variables
4700 (license license:gpl2)))
4701 (define-public r-invgamma
4707 (uri (cran-uri "invgamma" version))
4710 "12ga2y4wc9bc5zz6vimvxwgjpsx3ys3209nq63gscbw559ydxa5a"))))
4711 (properties `((upstream-name . "invgamma")))
4712 (build-system r-build-system)
4713 (home-page "https://github.com/dkahle/invgamma")
4714 (synopsis "Inverse gamma distribution")
4715 (description "This package provides a light weight implementation of the
4716 standard distribution functions for the inverse gamma distribution, wrapping
4717 those for the gamma distribution in the @code{stats} package.")
4718 (license license:gpl2)))
4720 (define-public r-bdsmatrix
4722 (name "r-bdsmatrix")
4727 (uri (cran-uri "bdsmatrix" version))
4730 "1sh6pg43rgqvips4fx0k4vmp5i9lmniix0bqwj2yq5m06gs227i5"))))
4731 (properties `((upstream-name . "bdsmatrix")))
4732 (build-system r-build-system)
4733 (home-page "https://cran.r-project.org/web/packages/bdsmatrix/")
4734 (synopsis "Routines for block diagonal symmetric matrices")
4736 "This package provides procedures to work with block diagonal symmetric
4737 matrices, a special case of sparse matrices.")
4738 (license license:lgpl2.0)))
4740 (define-public r-bbmle
4747 (uri (cran-uri "bbmle" version))
4750 "0mdj21q7k0fp4cj7la14vmcjmp49zqm57g7r6zrwmxpv0acwda46"))))
4751 (build-system r-build-system)
4761 (home-page "https://cran.r-project.org/web/packages/bbmle")
4762 (synopsis "Tools for General Maximum Likelihood Estimation")
4764 "This package provides methods and functions for fitting maximum
4765 likelihood models in R. This package modifies and extends the @code{mle}
4766 classes in the @code{stats4} package.")
4767 ;; Any version of the GPL
4768 (license license:gpl2+)))
4770 (define-public r-emdbook
4777 (uri (cran-uri "emdbook" version))
4780 "0ls3zxxlwmdv7zn1v9i1y9zc2sn0hbgmyjvsj7zn3ajsw7wwlih6"))))
4781 (build-system r-build-system)
4783 (list r-bbmle r-coda r-lattice r-mass r-plyr))
4784 (home-page "http://www.math.mcmaster.ca/bolker/emdbook")
4785 (synopsis "Support functions and data for \"Ecological Models and Data\"")
4787 "This package provides auxiliary functions and data sets for \"Ecological
4788 Models and Data\", a book presenting maximum likelihood estimation and related
4789 topics for ecologists (ISBN 978-0-691-12522-0).")
4791 (license (list license:gpl2 license:gpl3))))
4793 (define-public r-lpsolve
4800 (uri (cran-uri "lpSolve" version))
4803 "1fpkyjyqykwa1dxnhiky01pm09syxg169lm7hpy39bdbg10vw9s6"))))
4804 (properties `((upstream-name . "lpSolve")))
4805 (build-system r-build-system)
4806 (home-page "https://cran.r-project.org/web/packages/lpSolve")
4807 (synopsis "R interface to Lp_solve to solve linear/integer programs")
4809 "Lp_solve is software for solving linear, integer and mixed integer
4810 programs. This implementation supplies a \"wrapper\" function in C and some R
4811 functions that solve general linear/integer problems, assignment problems, and
4812 transportation problems.")
4813 (license license:lgpl2.0)))
4815 (define-public r-limsolve
4822 (uri (cran-uri "limSolve" version))
4825 "1829rd2cnd8qj80z9a7sgc7gx4sf3kvl5g6d2a0lqqw30f9sjzmr"))))
4826 (properties `((upstream-name . "limSolve")))
4827 (build-system r-build-system)
4829 (list r-lpsolve r-mass r-quadprog))
4830 (native-inputs (list gfortran))
4831 (home-page "https://cran.r-project.org/web/packages/limSolve")
4832 (synopsis "Solving linear inverse models")
4834 "This package provides functions that:
4837 @item find the minimum/maximum of a linear or quadratic function,
4838 @item sample an underdetermined or overdetermined system,
4839 @item solve a linear system Ax=B for the unknown x.
4842 It includes banded and tridiagonal linear systems. The package calls Fortran
4843 functions from LINPACK.")
4845 (license (list license:gpl2+ license:gpl3+))))
4847 (define-public r-fitdistrplus
4849 (name "r-fitdistrplus")
4854 (uri (cran-uri "fitdistrplus" version))
4857 "0nhgjvwya95v6b9khbsgp44lw10xg35w61lmka1v6wq7yh827izk"))))
4858 (build-system r-build-system)
4860 (list r-mass r-survival))
4863 (home-page "http://riskassessment.r-forge.r-project.org")
4864 (synopsis "Fitting a parametric distribution from data")
4866 "This package extends the @code{fitdistr} function of the MASS package
4867 with several functions to help the fit of a parametric distribution to
4868 non-censored or censored data. Censored data may contain left-censored,
4869 right-censored and interval-censored values, with several lower and upper
4870 bounds. In addition to @dfn{maximum likelihood estimation} (MLE), the package
4871 provides moment matching (MME), quantile matching (QME) and maximum
4872 goodness-of-fit estimation (MGE) methods (available only for non-censored
4873 data). Weighted versions of MLE, MME and QME are available.")
4874 (license license:gpl2+)))
4876 (define-public r-energy
4883 (uri (cran-uri "energy" version))
4886 "19xyw5bkyzfk22gly2ca2nsznqnrhaq4a77727kr1k26bj3y8gal"))))
4887 (build-system r-build-system)
4889 (list r-boot r-gsl r-rcpp))
4890 (home-page "https://cran.r-project.org/web/packages/energy")
4891 (synopsis "Multivariate inference via the energy of data")
4893 "This package provides e-statistics (energy) tests and statistics for
4894 multivariate and univariate inference, including distance correlation,
4895 one-sample, two-sample, and multi-sample tests for comparing multivariate
4896 distributions, are implemented. Measuring and testing multivariate
4897 independence based on distance correlation, partial distance correlation,
4898 multivariate goodness-of-fit tests, clustering based on energy distance,
4899 testing for multivariate normality, distance components (disco) for
4900 non-parametric analysis of structured data, and other energy
4901 statistics/methods are implemented.")
4902 (license license:gpl2+)))
4904 (define-public r-suppdists
4906 (name "r-suppdists")
4911 (uri (cran-uri "SuppDists" version))
4914 "025b9nlxz62wk84295csyzbncpn80i3iby3sxdigf3swcgi2fmbb"))))
4915 (properties `((upstream-name . "SuppDists")))
4916 (build-system r-build-system)
4917 (home-page "https://cran.r-project.org/web/packages/SuppDists")
4918 (synopsis "Supplementary distributions")
4920 "This package provides ten distributions supplementing those built into
4921 R. Inverse Gauss, Kruskal-Wallis, Kendall's Tau, Friedman's chi squared,
4922 Spearman's rho, maximum F ratio, the Pearson product moment correlation
4923 coefficient, Johnson distributions, normal scores and generalized
4924 hypergeometric distributions. In addition two random number generators of
4925 George Marsaglia are included.")
4926 (license license:gpl2+)))
4928 (define-public r-ksamples
4935 (uri (cran-uri "kSamples" version))
4938 "1zs22p68d6320kcylisnk0b5wmpapxkyz15py09czxzw7npw8gms"))))
4939 (properties `((upstream-name . "kSamples")))
4940 (build-system r-build-system)
4943 (home-page "https://cran.r-project.org/web/packages/kSamples")
4944 (synopsis "K-Sample rank tests and their combinations")
4946 "This package provides tools to compares k samples using the
4947 Anderson-Darling test, Kruskal-Wallis type tests with different rank score
4948 criteria, Steel's multiple comparison test, and the Jonckheere-Terpstra (JT)
4949 test. It computes asymptotic, simulated or (limited) exact P-values, all
4950 valid under randomization, with or without ties, or conditionally under random
4951 sampling from populations, given the observed tie pattern. Except for Steel's
4952 test and the JT test it also combines these tests across several blocks of
4954 (license license:gpl2+)))
4956 (define-public r-cvst
4963 (uri (cran-uri "CVST" version))
4966 "0bgk0d6w3dyhb5s30idnp6jpb3m8wf3b79wqlg127wwm0cird8pg"))))
4967 (properties `((upstream-name . "CVST")))
4968 (build-system r-build-system)
4970 (list r-kernlab r-matrix))
4971 (home-page "https://cran.r-project.org/web/packages/CVST")
4972 (synopsis "Fast cross-validation via sequential testing")
4974 "This package implements the fast cross-validation via sequential
4975 testing (CVST) procedure. CVST is an improved cross-validation procedure
4976 which uses non-parametric testing coupled with sequential analysis to
4977 determine the best parameter set on linearly increasing subsets of the data.
4978 Additionally to the CVST the package contains an implementation of the
4979 ordinary k-fold cross-validation with a flexible and powerful set of helper
4980 objects and methods to handle the overall model selection process. The
4981 implementations of the Cochran's Q test with permutations and the sequential
4982 testing framework of Wald are generic and can therefore also be used in other
4984 (license license:gpl2+)))
4986 (define-public r-squarem
4993 (uri (cran-uri "SQUAREM" version))
4996 "0n1s32l9p4vdm3h5q6g43s0qbpzry08difsh0yay80wrla6f3rb6"))))
4997 (properties `((upstream-name . "SQUAREM")))
4998 (build-system r-build-system)
4999 (home-page "https://coah.jhu.edu/people/Faculty_personal_Pages/Varadhan.html")
5000 (synopsis "Squared Extrapolation Methods for Accelerating EM-Like Monotone Algorithms")
5002 "This package provides algorithms for accelerating the convergence of
5003 slow, monotone sequences from smooth, contraction mapping such as the EM
5004 algorithm. It can be used to accelerate any smooth, linearly convergent
5005 acceleration scheme. A tutorial style introduction to this package is
5006 available in a vignette.")
5007 (license license:gpl2+)))
5009 (define-public r-progressr
5011 (name "r-progressr")
5016 (uri (cran-uri "progressr" version))
5018 (base32 "1p5s35rzh28n2id2lipgyqmh3wzib66m7x0pz9028y8cql8xr5ac"))))
5019 (properties `((upstream-name . "progressr")))
5020 (build-system r-build-system)
5023 (home-page "https://progressr.futureverse.org")
5024 (synopsis "Inclusive, unifying API for progress updates")
5026 "This package provides a minimal, unifying API for scripts and packages
5027 to report progress updates from anywhere including when using parallel
5028 processing. The package is designed such that the developer can to focus on
5029 what progress should be reported on without having to worry about how to
5030 present it. The end user has full control of how, where, and when to render
5031 these progress updates.")
5032 (license license:gpl3+)))
5034 (define-public r-lava
5041 (uri (cran-uri "lava" version))
5044 "0bi3c1aqwlq7jbz4raz6vga4r264w7lldi0i62xjlbl7hnlgi23s"))))
5045 (build-system r-build-system)
5047 (list r-future-apply r-numderiv r-progressr r-squarem r-survival))
5050 (home-page "https://github.com/kkholst/lava")
5051 (synopsis "Latent variable models")
5053 "This package provides tools for the estimation and simulation of latent
5055 (license license:gpl3)))
5057 (define-public r-drr
5064 (uri (cran-uri "DRR" version))
5067 "1y70si1gig4l7jx5jiqsqliyywfsvimkx53x3zh1lc3yj2j6bqwk"))))
5068 (properties `((upstream-name . "DRR")))
5069 (build-system r-build-system)
5071 (list r-cvst r-kernlab r-matrix))
5072 (home-page "https://cran.r-project.org/web/packages/DRR")
5073 (synopsis "Dimensionality reduction via regression")
5075 "This package provides an implementation of dimensionality reduction via
5076 regression using Kernel Ridge Regression.")
5077 (license license:gpl3)))
5079 (define-public r-prodlim
5082 (version "2019.11.13")
5086 (uri (cran-uri "prodlim" version))
5089 "03wvh3kirp1prac5nky6a5whs97rvaf4hc27x0fnh51sa17r42b8"))))
5090 (build-system r-build-system)
5092 (list r-kernsmooth r-lava r-rcpp r-survival))
5093 (home-page "https://cran.r-project.org/web/packages/prodlim")
5094 (synopsis "Product-limit estimation for censored event history analysis")
5096 "This package provides a fast and user-friendly implementation of
5097 nonparametric estimators for censored event history (survival) analysis with
5098 the Kaplan-Meier and Aalen-Johansen methods.")
5099 (license license:gpl2+)))
5101 (define-public r-dimred
5108 (uri (cran-uri "dimRed" version))
5111 "1z8fqdc8mslvfix8ngxs1y2yrvlanp5581hwp2nzldj6mk5kn15b"))))
5112 (properties `((upstream-name . "dimRed")))
5113 (build-system r-build-system)
5115 (list r-drr r-magrittr))
5118 (home-page "https://github.com/gdkrmr/dimRed")
5119 (synopsis "Framework for dimensionality reduction")
5121 "This package provides a collection of dimensionality reduction
5122 techniques from R packages and provides a common interface for calling the
5124 (license license:gpl3)))
5126 (define-public r-timedate
5129 (version "3043.102")
5133 (uri (cran-uri "timeDate" version))
5136 "0wvl5pq261rvbgly7vilk3x3m9xk3ly6il1i5scwdf6srl1vlz1p"))))
5137 (properties `((upstream-name . "timeDate")))
5138 (build-system r-build-system)
5139 (home-page "https://www.rmetrics.org")
5140 (synopsis "Chronological and calendar objects")
5142 "This package provides an environment for teaching \"Financial
5143 Engineering and Computational Finance\" and for managing chronological and
5145 (license license:gpl2+)))
5147 (define-public r-magic
5154 (uri (cran-uri "magic" version))
5157 "1gybia2aq80ldk1d845y5srncfzbbmpqhgl7vfaz7qqqjs6d85j5"))))
5158 (build-system r-build-system)
5161 (home-page "https://github.com/RobinHankin/magic.git")
5162 (synopsis "Create and investigate magic squares")
5164 "This package provides a collection of efficient, vectorized algorithms
5165 for the creation and investigation of magic squares and hypercubes, including
5166 a variety of functions for the manipulation and analysis of arbitrarily
5167 dimensioned arrays.")
5168 (license license:gpl2)))
5170 (define-public r-rmysql
5177 (uri (cran-uri "RMySQL" version))
5180 "05aavyggyjv46awa7ggbxlfcy9707vak5kh7kj0ljdx8zga7xb7l"))))
5181 (properties `((upstream-name . "RMySQL")))
5182 (build-system r-build-system)
5184 (list `(,mariadb "dev") zlib))
5187 (home-page "https://github.com/r-dbi/RMySQL")
5188 (synopsis "Database interface and MySQL driver for R")
5190 "This package provides a DBI interface to MySQL / MariaDB. The RMySQL
5191 package contains an old implementation based on legacy code from S-PLUS which
5192 is being phased out. A modern MySQL client based on Rcpp is available from
5193 the RMariaDB package.")
5194 (license license:gpl2)))
5196 (define-public r-rpostgresql
5198 (name "r-rpostgresql")
5203 (uri (cran-uri "RPostgreSQL" version))
5206 "1fbixmnjp1kh6yiv8zhg8zi5ryvdf5j2jxv4agq5gcxf541s3g5x"))))
5207 (properties `((upstream-name . "RPostgreSQL")))
5208 (build-system r-build-system)
5213 (home-page "https://github.com/tomoakin/RPostgreSQL")
5214 (synopsis "R interface to the PostgreSQL database system")
5216 "This package provides a Database Interface (DBI) compliant driver for R
5217 to access PostgreSQL database systems.")
5218 ;; The whole package is released under GPL version 2. It includes code
5219 ;; under the PostgreSQL license.
5220 (license license:gpl2)))
5222 (define-public r-linprog
5229 (uri (cran-uri "linprog" version))
5232 "1d34m2nyk7m6j2dci69bhy5mlw479xax1517j7f14pq7vhpsm9l1"))))
5233 (build-system r-build-system)
5234 (propagated-inputs (list r-lpsolve))
5235 (home-page "http://linprog.r-forge.r-project.org/")
5236 (synopsis "Linear programming and optimization")
5238 "This package can be used to solve Linear Programming / Linear
5239 Optimization problems by using the simplex algorithm.")
5240 (license license:gpl2+)))
5242 (define-public r-geometry
5249 (uri (cran-uri "geometry" version))
5252 "1n7m0djqlhrv01l98r76grkki6cv4k4q2z6c7fksqgq4r2l6a14i"))))
5253 (build-system r-build-system)
5255 (list r-magic r-linprog r-lpsolve r-rcpp r-rcppprogress))
5256 (home-page "http://geometry.r-forge.r-project.org/")
5257 (synopsis "Mesh generator and surface tessellator")
5259 "This package makes the qhull library available in R, in a similar manner
5260 as in Octave. Qhull computes convex hulls, Delaunay triangulations, halfspace
5261 intersections about a point, Voronoi diagrams, furthest-site Delaunay
5262 triangulations, and furthest-site Voronoi diagrams. It runs in 2-d, 3-d, 4-d,
5263 and higher dimensions. It implements the Quickhull algorithm for computing
5264 the convex hull. Qhull does not support constrained Delaunay triangulations,
5265 or mesh generation of non-convex objects, but the package does include some R
5266 functions that allow for this. Currently the package only gives access to
5267 Delaunay triangulation and convex hull computation.")
5268 ;; The Qhull sources are included and are distributed under a custom
5269 ;; non-copyleft license. The R sources are released under GPL version 2.
5270 (license (list license:gpl2
5271 (license:non-copyleft "http://www.qhull.org/COPYING.txt")))))
5273 (define-public r-ddalpha
5280 (uri (cran-uri "ddalpha" version))
5283 "1bjfgb3lbzhjb5wx9hzp90jppq7vnj59bmd2n9ymi8sh1570m9p4"))))
5284 (build-system r-build-system)
5295 (home-page "https://cran.r-project.org/web/packages/ddalpha")
5296 (synopsis "Depth-Based classification and calculation of data depth")
5298 "This package contains procedures for depth-based supervised learning,
5299 which are entirely non-parametric, in particular the DDalpha-procedure (Lange,
5300 Mosler and Mozharovskyi, 2014). The training data sample is transformed by a
5301 statistical depth function to a compact low-dimensional space, where the final
5302 classification is done. It also offers an extension to functional data and
5303 routines for calculating certain notions of statistical depth functions. 50
5304 multivariate and 5 functional classification problems are included.")
5305 (license license:gpl2)))
5307 (define-public r-gower
5314 (uri (cran-uri "gower" version))
5317 "0p9qx9aafkdm7wibfwk59jzw6vspsff6zwp84bc40lg0myxbf737"))))
5318 (build-system r-build-system)
5319 (home-page "https://github.com/markvanderloo/gower")
5320 (synopsis "Gower's distance")
5322 "This package provides tools to compute Gower's distance (or similarity)
5323 coefficient between records, and to compute the top-n matches between records.
5324 Core algorithms are executed in parallel on systems supporting OpenMP.")
5325 (license license:gpl3)))
5327 (define-public r-rcpproll
5334 (uri (cran-uri "RcppRoll" version))
5337 "0srzfhzkk42kzrdjnhbb37946jp1p688rgysy6k3i2is8jb21zyb"))))
5338 (properties `((upstream-name . "RcppRoll")))
5339 (build-system r-build-system)
5342 (home-page "https://cran.r-project.org/web/packages/RcppRoll")
5343 (synopsis "Efficient rolling and windowed operations")
5345 "This package provides fast and efficient routines for common rolling /
5346 windowed operations. Routines for the efficient computation of windowed mean,
5347 median, sum, product, minimum, maximum, standard deviation and variance are
5349 (license license:gpl2+)))
5351 (define-public r-ipred
5358 (uri (cran-uri "ipred" version))
5361 "0hsq00382pfd9hzpcgphjxazbxm4zx0k2r6pk6kib56k0ibm7qfn"))))
5362 (build-system r-build-system)
5370 (home-page "https://cran.r-project.org/web/packages/ipred")
5371 (synopsis "Improved predictors")
5373 "This package provides improved predictive models by indirect
5374 classification and bagging for classification, regression and survival
5375 problems as well as resampling based estimators of prediction error.")
5376 (license license:gpl2+)))
5378 (define-public r-psych
5385 (uri (cran-uri "psych" version))
5388 "08f3byqwabgkqcxwpjbsxdcjkdg012iraqinw0fzskfl1srzkhyw"))))
5389 (build-system r-build-system)
5391 (list r-lattice r-mnormt r-nlme))
5394 (home-page "https://cran.r-project.org/web/packages/psych/")
5395 (synopsis "Procedures for psychological, psychometric, and personality research")
5397 "This package provides a general purpose toolbox for personality,
5398 psychometric theory and experimental psychology. Functions are primarily for
5399 multivariate analysis and scale construction using factor analysis, principal
5400 component analysis, cluster analysis and reliability analysis, although others
5401 provide basic descriptive statistics. Item Response Theory is done using
5402 factor analysis of tetrachoric and polychoric correlations. Functions for
5403 analyzing data at multiple levels include within and between group statistics,
5404 including correlations and factor analysis. Functions for simulating and
5405 testing particular item and test structures are included. Several functions
5406 serve as a useful front end for structural equation modeling. Graphical
5407 displays of path diagrams, factor analysis and structural equation models are
5408 created using basic graphics.")
5409 (license license:gpl2+)))
5411 (define-public r-generics
5418 (uri (cran-uri "generics" version))
5421 "162q9hdsnfcwjj255ahbi6v9vnyynvda7gb75p721y28j5xb7sk3"))))
5422 (build-system r-build-system)
5423 (home-page "https://github.com/r-lib/generics")
5424 (synopsis "Common S3 generics not provided by base R methods")
5426 "In order to reduce potential package dependencies and conflicts,
5427 generics provides a number of commonly used S3 generics that are not provided
5428 by base R methods related to model fitting.")
5429 (license license:gpl2)))
5431 (define-public r-broom
5438 (uri (cran-uri "broom" version))
5441 "16grzja9hz5mqpfzbp1r6zif1gp7swfadkm52340si9h8ifhk8b6"))))
5442 (build-system r-build-system)
5457 (home-page "https://github.com/tidyverse/broom")
5458 (synopsis "Convert statistical analysis objects into tidy data frames")
5460 "This package provides tools to convert statistical analysis objects from
5461 R into tidy data frames, so that they can more easily be combined, reshaped
5462 and otherwise processed with tools like @code{dplyr}, @code{tidyr} and
5463 @code{ggplot2}. The package provides three S3 generics: @code{tidy}, which
5464 summarizes a model's statistical findings such as coefficients of a
5465 regression; @code{augment}, which adds columns to the original data such as
5466 predictions, residuals and cluster assignments; and @code{glance}, which
5467 provides a one-row summary of model-level statistics.")
5468 (license license:expat)))
5470 (define-public r-recipes
5477 (uri (cran-uri "recipes" version))
5480 "1950rvva19ms6xy9d3jx94gzy589qprk115zjjd0ib4qxgip601x"))))
5481 (build-system r-build-system)
5504 (home-page "https://github.com/topepo/recipes")
5505 (synopsis "Preprocessing tools to create design matrices")
5507 "Recipes is an extensible framework to create and preprocess design
5508 matrices. Recipes consist of one or more data manipulation and analysis
5509 \"steps\". Statistical parameters for the steps can be estimated from an
5510 initial data set and then applied to other data sets. The resulting design
5511 matrices can then be used as inputs into statistical or machine learning
5513 (license license:gpl2)))
5515 (define-public r-pdist
5522 (uri (cran-uri "pdist" version))
5525 "0bvg8si81hs79v39d7svv4zbv2p0sk2r6m9vamibvkh9qvl4x406"))))
5526 (build-system r-build-system)
5527 (home-page "https://github.com/jeffwong/pdist")
5528 (synopsis "Partitioned distance function")
5530 "Pdist computes the euclidean distance between rows of a matrix X and
5531 rows of another matrix Y. Previously, this could be done by binding the two
5532 matrices together and calling @code{dist}, but this creates unnecessary
5533 computation by computing the distances between a row of X and another row of
5534 X, and likewise for Y. Pdist strictly computes distances across the two
5535 matrices, not within the same matrix, making computations significantly faster
5536 for certain use cases.")
5537 (license license:gpl3+)))
5539 (define-public r-ggrepel
5546 (uri (cran-uri "ggrepel" version))
5549 "1z5xyr5f4aryy0v1gzz9m8m4s5fzzwbrf0fxll1nbflr8xnr3yr9"))))
5550 (build-system r-build-system)
5552 (list r-ggplot2 r-rcpp r-rlang r-scales))
5554 (list r-knitr)) ; for vignettes
5555 (home-page "https://github.com/slowkow/ggrepel")
5556 (synopsis "Repulsive text and label geometries for ggplot2")
5558 "This package provides text and label geometries for ggplot2 that help to
5559 avoid overlapping text labels. Labels repel away from each other and away
5560 from the data points.")
5561 (license license:gpl3)))
5563 (define-public r-coro
5570 (uri (cran-uri "coro" version))
5572 (base32 "14irld29dipgfd34y0k351daqg9vqpnpdx8m3pxmqr1aiyj5f5cv"))))
5573 (properties `((upstream-name . "coro")))
5574 (build-system r-build-system)
5575 (propagated-inputs (list r-rlang))
5576 (native-inputs (list r-knitr))
5577 (home-page "https://github.com/r-lib/coro")
5578 (synopsis "Coroutines for R")
5580 "This package provides coroutines for R, a family of functions that can
5581 be suspended and resumed later on. This includes async functions (which
5582 await) and generators (which yield). Async functions are based on the
5583 concurrency framework of the @code{promises} package. Generators are based on
5584 a dependency free iteration protocol defined in @code{coro} and are compatible
5585 with iterators from the @code{reticulate} package.")
5586 (license license:expat)))
5588 (define-public r-corrplot
5595 (uri (cran-uri "corrplot" version))
5598 "1g98jk6xsl08z4n6sy5vriif99m31zhbz7j3dh1kfj4w7yb9zh78"))))
5599 (build-system r-build-system)
5602 (home-page "https://github.com/taiyun/corrplot")
5603 (synopsis "Visualization of a correlation matrix")
5605 "This package provides a graphical display of a correlation matrix or
5606 general matrix. It also contains some algorithms to do matrix reordering. In
5607 addition, corrplot is good at details, including choosing color, text labels,
5608 color labels, layout, etc.")
5609 ;; Any version of the GPL
5610 (license license:gpl2+)))
5612 (define-public r-stringdist
5614 (name "r-stringdist")
5619 (uri (cran-uri "stringdist" version))
5621 (base32 "1fv1hbdlm8qwx57b2aj50mw0say5k48awzavx65mfk67qp6ddk7g"))))
5622 (build-system r-build-system)
5623 (home-page "https://github.com/markvanderloo/stringdist")
5624 (synopsis "Approximate string matching and string distance functions")
5626 "This package implements an approximate string matching version of R's
5627 native @code{match} function. It can calculate various string distances based
5628 on edits (Damerau-Levenshtein, Hamming, Levenshtein, optimal string alignment),
5629 qgrams (q- gram, cosine, jaccard distance) or heuristic metrics (Jaro,
5630 Jaro-Winkler). An implementation of soundex is provided as well. Distances
5631 can be computed between character vectors while taking proper care of encoding
5632 or between integer vectors representing generic sequences.")
5633 (license license:gpl3+)))
5635 (define-public r-ucminf
5642 (uri (cran-uri "ucminf" version))
5645 "01vggwg1w71k98qs6fhb0x1843vi322mf4g3hbclks94kcpkisx2"))))
5646 (build-system r-build-system)
5647 (native-inputs (list gfortran))
5648 (home-page "https://cran.r-project.org/web/packages/ucminf/")
5649 (synopsis "General-purpose unconstrained non-linear optimization")
5651 "This package provides an implementation of an algorithm for
5652 general-purpose unconstrained non-linear optimization. The algorithm is of
5653 quasi-Newton type with BFGS updating of the inverse Hessian and soft line
5654 search with a trust region type monitoring of the input to the line search
5655 algorithm. The interface of @code{ucminf} is designed for easy interchange
5656 with the package @code{optim}.")
5657 (license license:gpl2+)))
5659 (define-public r-usedist
5666 (uri (cran-uri "usedist" version))
5668 (base32 "0ddf1zcalbrn293qmr9kdzz3x16fzc4k1bwb1pjmwnspisqfi8kj"))))
5669 (properties `((upstream-name . "usedist")))
5670 (build-system r-build-system)
5671 (home-page "https://cran.r-project.org/package=usedist")
5672 (synopsis "Distance matrix utilities")
5674 "This package provides functions to re-arrange, extract, and work with
5676 (license license:gpl3)))
5678 (define-public r-useful
5684 (uri (cran-uri "useful" version))
5687 "0n50v1q75k518sq23id14jphwla35q4sasahrnrnllwrachl67v1"))))
5688 (properties `((upstream-name . "useful")))
5689 (build-system r-build-system)
5699 (home-page "https://github.com/jaredlander/useful")
5700 (synopsis "Collection of handy, useful functions")
5701 (description "This package provides a set of little functions that have been
5702 found useful to do little odds and ends such as plotting the results of K-means
5703 clustering, substituting special text characters, viewing parts of a
5704 @code{data.frame}, constructing formulas from text and building design and
5705 response matrices.")
5706 (license license:bsd-3)))
5708 (define-public r-ordinal
5711 (version "2019.12-10")
5715 (uri (cran-uri "ordinal" version))
5718 "09bpmjmbf4x82kgf6bm4bkncq2apdv9mk20zj4zgma2jx2vyfhbs"))))
5719 (build-system r-build-system)
5721 (list r-mass r-matrix r-numderiv r-ucminf))
5722 (home-page "https://github.com/runehaubo/ordinal")
5723 (synopsis "Regression models for ordinal data")
5725 "This package provides an implementation of cumulative link (mixed)
5726 models also known as ordered regression models, proportional odds models,
5727 proportional hazards models for grouped survival times and ordered models.
5728 Estimation is via maximum likelihood and mixed models are fitted with the
5729 Laplace approximation and adaptive Gauss-Hermite quadrature.")
5730 (license license:gpl2+)))
5732 (define-public r-jomo
5739 (uri (cran-uri "jomo" version))
5742 "0qq03zspmh8x2c8w882ynsw7wshr9b0fyrpwnqx5yc1xlzrqffcx"))))
5743 (build-system r-build-system)
5745 (list r-lme4 r-mass r-ordinal r-survival r-tibble))
5746 (home-page "https://cran.r-project.org/web/packages/jomo/")
5747 (synopsis "Multilevel Joint Modelling Multiple Imputation")
5749 "Similarly to Schafer's package pan, jomo is a package for multilevel
5750 joint modelling multiple imputation @url{Carpenter and Kenward (2013),
5751 http://doi.org/10.1002/9781119942283}. Novel aspects of jomo are the
5752 possibility of handling binary and categorical data through latent normal
5753 variables, the option to use cluster-specific covariance matrices and to
5754 impute compatibly with the substantive model.")
5755 (license license:gpl2)))
5757 (define-public r-pan
5764 (uri (cran-uri "pan" version))
5767 "1dk3jjj826p7xrz10qz04vyc068xnypg7bp0pj4c32z3da0xzh5d"))))
5768 (build-system r-build-system)
5769 (native-inputs (list gfortran))
5770 (home-page "https://cran.r-project.org/web/packages/pan/")
5771 (synopsis "Multiple imputation for multivariate panel or clustered data")
5773 "This package implements multiple imputation for multivariate panel or
5775 (license license:gpl3)))
5777 (define-public r-mitml
5784 (uri (cran-uri "mitml" version))
5787 "00i18nnvrdrg91crgcp2a431xs71cawaip3xkqk2myv0iav3xga9"))))
5788 (build-system r-build-system)
5790 (list r-haven r-jomo r-pan))
5793 (home-page "https://cran.r-project.org/web/packages/mitml/")
5794 (synopsis "Tools for multiple imputation in multilevel modeling")
5796 "This package provides tools for multiple imputation of missing data in
5797 multilevel modeling. It includes a user-friendly interface to the packages
5798 pan and jomo, and several functions for visualization, data management and the
5799 analysis of multiply imputed data sets.")
5800 (license license:gpl2+)))
5802 (define-public r-mice
5809 (uri (cran-uri "mice" version))
5812 "01fnfrr7adp29s5kic95r9q0rdznkz2pjmziyimnrqzyicyvfyzq"))))
5813 (build-system r-build-system)
5824 (home-page "https://cran.r-project.org/web/packages/mice/")
5825 (synopsis "Multivariate imputation by chained equations")
5827 "Multiple imputation using @dfn{Fully Conditional Specification} (FCS)
5828 implemented by the MICE algorithm as described in @url{Van Buuren and
5829 Groothuis-Oudshoorn (2011), http://doi.org/10.18637/jss.v045.i03}. Each
5830 variable has its own imputation model. Built-in imputation models are
5831 provided for continuous data (predictive mean matching, normal), binary
5832 data (logistic regression), unordered categorical data (polytomous logistic
5833 regression) and ordered categorical data (proportional odds). MICE can also
5834 impute continuous two-level data (normal model, pan, second-level variables).
5835 Passive imputation can be used to maintain consistency between variables.
5836 Various diagnostic plots are available to inspect the quality of the
5838 ;; Any of these two versions.
5839 (license (list license:gpl2 license:gpl3))))
5841 (define-public r-truncnorm
5843 (name "r-truncnorm")
5848 (uri (cran-uri "truncnorm" version))
5851 "0zn88wdd58223kibk085rhsikl4yhlrwiyq109hzjg06hy6lwmj9"))))
5852 (build-system r-build-system)
5853 (home-page "https://cran.r-project.org/web/packages/truncnorm/")
5854 (synopsis "Truncated normal distribution")
5855 (description "This package provides functions for the truncated normal
5856 distribution with mean equal to @code{mean} and standard deviation equal to
5857 @code{sd}. It includes density, distribution, quantile, and expected value
5858 functions, as well as a random generation function.")
5859 (license license:gpl2)))
5861 (define-public r-rsolnp
5868 (uri (cran-uri "Rsolnp" version))
5871 "0w7nkj6igr0gi7r7jg950lsx7dj6aipgxi6vbjsf5f5yc9h7fhii"))))
5872 (properties `((upstream-name . "Rsolnp")))
5873 (build-system r-build-system)
5876 (home-page "https://cran.r-project.org/web/packages/Rsolnp/")
5877 (synopsis "General non-linear optimization")
5878 (description "The Rsolnp package implements a general non-linear augmented
5879 Lagrange multiplier method solver, a @dfn{sequential quadratic
5880 programming} (SQP) based solver).")
5881 ;; Any version of the GPL.
5882 (license license:gpl2+)))
5884 (define-public r-hardyweinberg
5886 (name "r-hardyweinberg")
5891 (uri (cran-uri "HardyWeinberg" version))
5894 "0b3szw090dsc3bkas2kvx787ww2i6zzg2qmdyivmqc8amx5arn6g"))))
5895 (properties `((upstream-name . "HardyWeinberg")))
5896 (build-system r-build-system)
5898 (list r-mice r-nnet r-rcpp r-rsolnp))
5899 (home-page "https://cran.r-project.org/package=HardyWeinberg")
5900 (synopsis "Statistical tests and graphics for Hardy-Weinberg equilibrium")
5902 "This package contains tools for exploring Hardy-Weinberg equilibrium for
5903 diallelic genetic marker data. All classical tests (chi-square, exact,
5904 likelihood-ratio and permutation tests) for Hardy-Weinberg equilibrium are
5905 included in the package, as well as functions for power computation and for
5906 the simulation of marker data under equilibrium and disequilibrium. Routines
5907 for dealing with markers on the X-chromosome are included. Functions for
5908 testing equilibrium in the presence of missing data by using multiple
5909 imputation are also provided. Implements several graphics for exploring the
5910 equilibrium status of a large set of diallelic markers: ternary plots with
5911 acceptance regions, log-ratio plots and Q-Q plots.")
5912 (license license:gpl2+)))
5921 (uri (cran-uri "sm" version))
5924 "03z8igsjqr32x407asxvkrbayvm6yhv9xyfs0n8fkmv8zk5a41r6"))))
5925 (build-system r-build-system)
5926 (native-inputs (list gfortran))
5927 (home-page "http://www.stats.gla.ac.uk/~adrian/sm/")
5928 (synopsis "Smoothing methods for nonparametric regression and density estimation")
5930 "This is software accompanying the book 'Applied Smoothing Techniques for
5931 Data Analysis---The Kernel Approach with S-Plus Illustrations', Oxford
5932 University Press. It provides smoothing methods for nonparametric regression
5933 and density estimation")
5934 (license license:gpl2+)))
5936 (define-public r-venndiagram
5938 (name "r-venndiagram")
5942 (uri (cran-uri "VennDiagram" version))
5945 "0ilcxcp8qskmb5cp7fyb7i0qizg42lrx0ny8ws3if90kfrglghp7"))))
5946 (properties `((upstream-name . "VennDiagram")))
5947 (build-system r-build-system)
5949 (list r-futile-logger))
5950 (home-page "https://cran.r-project.org/web/packages/VennDiagram/")
5951 (synopsis "Generate High-Resolution Venn and Euler Plots")
5953 "This package provides a set of functions to generate high-resolution
5954 Venn and Euler plots. It includes handling for several special cases,
5955 including two-case scaling, and extensive customization of plot shape and
5957 (license license:gpl2+)))
5959 (define-public r-vioplot
5966 (uri (cran-uri "vioplot" version))
5969 "1dmdasp3jldc41233z6r08w3j76vyyp9m3jrj7n4ahk48yd5siq6"))))
5970 (build-system r-build-system)
5975 (home-page "http://wsopuppenkiste.wiso.uni-goettingen.de/~dadler")
5976 (synopsis "Violin plot")
5978 "This package provides a violin plot, which is a combination of a box
5979 plot and a kernel density plot.")
5980 (license license:bsd-3)))
5982 (define-public r-rsofia
5988 ;; This package has been removed from CRAN, so we can
5989 ;; only fetch it from the archives.
5990 (uri (string-append "https://cran.r-project.org/src/"
5991 "contrib/Archive/RSofia/RSofia_"
5995 "0q931y9rcf6slb0s2lsxhgqrzy4yqwh8hb1124nxg0bjbxvjbihn"))))
5996 (properties `((upstream-name . "RSofia")))
5997 (build-system r-build-system)
6000 (home-page "https://cran.r-project.org/src/contrib/Archive/RSofia")
6001 (synopsis "Port of sofia-ml to R")
6002 (description "This package is a port of sofia-ml to R. Sofia-ml is a
6003 suite of fast incremental algorithms for machine learning that can be used for
6004 training models for classification or ranking.")
6005 (license license:asl2.0)))
6007 (define-public r-xts
6014 (uri (cran-uri "xts" version))
6017 "0b6a7mpyk9aw6axas7nz01gadczprwwfhii01fz31z26z555i06n"))))
6018 (build-system r-build-system)
6019 (propagated-inputs (list r-zoo))
6020 (home-page "https://github.com/joshuaulrich/xts")
6021 (synopsis "Extensible time series")
6023 "This package provides for uniform handling of R's different time-based
6024 data classes by extending @code{zoo}, maximizing native format information
6025 preservation and allowing for user-level customization and extension, while
6026 simplifying cross-class interoperability.")
6027 (license license:gpl2+)))
6029 (define-public r-performanceanalytics
6031 (name "r-performanceanalytics")
6036 (uri (cran-uri "PerformanceAnalytics" version))
6039 "0ci26hsj4wnw9g0mh4vrn0cg986cpcpx169rvw6v6rbnjxq718bq"))))
6041 `((upstream-name . "PerformanceAnalytics")))
6042 (build-system r-build-system)
6044 (list r-quadprog r-xts r-zoo))
6045 (home-page "https://r-forge.r-project.org/projects/returnanalytics/")
6046 (synopsis "Econometric tools for performance and risk analysis")
6047 (description "This is a collection of econometric functions for
6048 performance and risk analysis. This package aims to aid practitioners and
6049 researchers in utilizing the latest research in analysis of non-normal return
6050 streams. In general, it is most tested on return (rather than price) data on
6051 a regular scale, but most functions will work with irregular return data as
6052 well, and increasing numbers of functions will work with P&L or price data
6054 ;; Either version may be picked.
6055 (license (list license:gpl2 license:gpl3))))
6057 (define-public r-laeken
6064 (uri (cran-uri "laeken" version))
6067 "1p3ccbaydlr52p8qmgmm2l6kryvq6jjjx7mqn2vv0gpjaxqhyy92"))))
6068 (build-system r-build-system)
6070 (list r-boot r-mass))
6071 (home-page "https://cran.r-project.org/web/packages/laeken/")
6072 (synopsis "Estimation of indicators on social exclusion and poverty")
6073 (description "This package provides tools for the estimation of indicators
6074 on social exclusion and poverty, as well as an implementation of Pareto tail
6075 modeling for empirical income distributions.")
6076 (license license:gpl2+)))
6078 (define-public r-vcd
6085 (uri (cran-uri "vcd" version))
6088 "13sn77qdcyll9lz7nab0bxzfvpgj8f5rl2cq5ylpz8pibynj1d55"))))
6089 (build-system r-build-system)
6091 (list r-colorspace r-lmtest r-mass))
6092 (home-page "https://cran.r-project.org/web/packages/vcd/")
6093 (synopsis "Visualizing categorical data")
6094 (description "This package provides visualization techniques, data sets,
6095 summary and inference procedures aimed particularly at categorical data.
6096 Special emphasis is given to highly extensible grid graphics. The package was
6097 originally inspired by the book \"Visualizing Categorical Data\" by Michael
6098 Friendly and is now the main support package for a new book, \"Discrete Data
6099 Analysis with R\" by Michael Friendly and David Meyer (2015).")
6100 (license license:gpl2)))
6102 (define-public r-vcfr
6108 (uri (cran-uri "vcfR" version))
6111 "0lhxb3ac4fafwik9q3cds46svzf0hyca8k54chw3dpk50c0zz1yx"))))
6112 (build-system r-build-system)
6128 (home-page "https://github.com/knausb/vcfR")
6129 (synopsis "Manipulate and visualize VCF data")
6130 (description "This package facilitates easy manipulation of variant call
6131 format (VCF) data. Functions are provided to rapidly read from and write to
6132 VCF files. Once VCF data is read into R, a parser function extracts matrices
6133 of data. This information can then be used for quality control or other
6134 purposes. Additional functions provide visualization of genomic data. Once
6135 processing is complete data may be written to a VCF file. It also may be
6136 converted into other popular R objects. This package provides a link between
6137 VCF data and familiar R software.")
6138 (license license:gpl3)))
6140 (define-public r-ica
6147 (uri (cran-uri "ica" version))
6150 "0ya1nph1zwhad0bfz4yxs27kl45yk1dhnphdlrq34p8pqrpmj8g7"))))
6151 (build-system r-build-system)
6152 (home-page "https://cran.r-project.org/web/packages/ica/")
6153 (synopsis "Independent component analysis")
6154 (description "This package provides tools for @dfn{Independent Component
6155 Analysis} (ICA) using various algorithms: FastICA,
6156 Information-Maximization (Infomax), and @dfn{Joint Approximate Diagonalization
6157 of Eigenmatrices} (JADE).")
6158 (license license:gpl2+)))
6160 (define-public r-dtw
6167 (uri (cran-uri "dtw" version))
6170 "004gm4mzgdzdj807j3bwqsv5lizmnmz5jq514bdjshhkysnzjz6z"))))
6171 (build-system r-build-system)
6172 (propagated-inputs (list r-proxy))
6173 (home-page "http://dtw.r-forge.r-project.org/")
6174 (synopsis "Dynamic Time Warping Algorithms")
6175 (description "This package provides a comprehensive implementation of
6176 @dfn{dynamic time warping} (DTW) algorithms in R. DTW computes the
6177 optimal (least cumulative distance) alignment between points of two time
6178 series. Common DTW variants covered include local (slope) and global (window)
6179 constraints, subsequence matches, arbitrary distance definitions,
6180 normalizations, minimum variance matching, and so on.")
6181 (license license:gpl2+)))
6183 (define-public r-sdmtools
6186 (version "1.1-221.2")
6190 (uri (cran-uri "SDMTools" version))
6193 "1xvcd97ikqsfdpk2fddy3k0z1ajqga7nv9bgac9c1wnjk1gqrpgh"))))
6194 (properties `((upstream-name . "SDMTools")))
6195 (build-system r-build-system)
6196 (propagated-inputs (list r-r-utils))
6197 (home-page "https://www.rforge.net/SDMTools/")
6198 (synopsis "Species distribution modelling tools")
6199 (description "This package provides a set of tools for post processing
6200 the outcomes of species distribution modeling exercises. It includes novel
6201 methods for comparing models and tracking changes in distributions through
6202 time. It further includes methods for visualizing outcomes, selecting
6203 thresholds, calculating measures of accuracy and landscape fragmentation
6205 (license license:gpl3+)))
6207 (define-public r-scatterplot3d
6209 (name "r-scatterplot3d")
6214 (uri (cran-uri "scatterplot3d" version))
6217 "152xqz9c70qab86mpgng049gxsg5f4fpf1m8dh93fb9v1avjd0sc"))))
6218 (build-system r-build-system)
6219 (home-page "https://cran.r-project.org/web/packages/scatterplot3d/")
6220 (synopsis "3D scatter plot")
6221 (description "This package provides an implementation of scatter plots for
6222 plotting. a three dimensional point cloud.")
6223 (license license:gpl2)))
6225 (define-public r-ggridges
6232 (uri (cran-uri "ggridges" version))
6235 "0bmlqy1p6rac90af97ffpdi6php7dblx66l2hcm8ljidgyqzmspm"))))
6236 (build-system r-build-system)
6238 (list r-ggplot2 r-plyr r-scales r-withr))
6241 (home-page "https://github.com/clauswilke/ggridges")
6242 (synopsis "Ridgeline plots in ggplot2")
6244 "Ridgeline plots provide a convenient way of visualizing changes in
6245 distributions over time or space. This package enables the creation of such
6246 plots in @code{ggplot2}.")
6247 (license license:gpl2)))
6249 (define-public r-ggjoy
6256 (uri (cran-uri "ggjoy" version))
6259 "012md2m0jqfcccb933j423m3ck31v3p0pd41gjxpyg9082y7ixyj"))))
6260 (build-system r-build-system)
6262 (list r-ggplot2 r-ggridges))
6263 (home-page "https://github.com/clauswilke/ggjoy")
6264 (synopsis "Joyplots in ggplot2")
6265 (description "Joyplots provide a convenient way of visualizing changes in
6266 distributions over time or space. This package enables the creation of such
6267 plots in @code{ggplot2}.")
6268 (license license:gpl2)))
6270 (define-public r-cli
6277 (uri (cran-uri "cli" version))
6280 "0qqd4mscv8ndjbji7knprdlv2hhyk35gazagvapbjzq1p6yfpaf3"))))
6281 (build-system r-build-system)
6284 (home-page "https://github.com/r-lib/cli#readme")
6285 (synopsis "Helpers for developing command line interfaces")
6286 (description "This package provides a suite of tools designed to build
6287 attractive command line interfaces (CLIs). It includes tools for drawing
6288 rules, boxes, trees, and Unicode symbols with ASCII alternatives.")
6289 (license license:expat)))
6291 (define-public r-argparser
6293 (name "r-argparser")
6298 (uri (cran-uri "argparser" version))
6301 "0xcl0ivsbc4iw8s7027q4cx68j6s5lihbby0xa9pmlv4wjmcvdr6"))))
6302 (build-system r-build-system)
6303 (home-page "https://bitbucket.org/djhshih/argparser")
6304 (synopsis "Command-line argument parser")
6306 "This package provides a cross-platform command-line argument parser
6307 written purely in R with no external dependencies. It is useful with the
6308 Rscript front-end and facilitates turning an R script into an executable
6310 (license license:gpl3+)))
6312 (define-public r-debugme
6319 (uri (cran-uri "debugme" version))
6322 "1c9sg55zvf10h8198jdnpamm6f66lzw3c3jnmdp9ls6na0j0xbjd"))))
6323 (build-system r-build-system)
6324 (propagated-inputs (list r-crayon))
6325 (home-page "https://github.com/r-lib/debugme#readme")
6326 (synopsis "Debug R packages")
6328 "This package allows the user to specify debug messages as special string
6329 constants, and control debugging of packages via environment variables.")
6330 (license license:expat)))
6332 (define-public r-processx
6339 (uri (cran-uri "processx" version))
6341 (base32 "0ail3w8n5g1ibdamgpxcfpla18kqkilmppiasm7ms67cavx2k5k7"))))
6342 (build-system r-build-system)
6345 (home-page "https://github.com/r-lib/processx3")
6346 (synopsis "Execute and control system processes")
6348 "This package provides portable tools to run system processes in the
6349 background. It can check if a background process is running; wait on a
6350 background process to finish; get the exit status of finished processes; kill
6351 background processes and their children; restart processes. It can read the
6352 standard output and error of the processes, using non-blocking connections.
6353 @code{processx} can poll a process for standard output or error, with a
6354 timeout. It can also poll several processes at once.")
6355 (license license:expat)))
6357 (define-public r-tsp
6364 (uri (cran-uri "TSP" version))
6367 "022k0972kcxb0w6qhx09l9cif8fmpkpvwddvgxiy60bx343ywzia"))))
6368 (properties `((upstream-name . "TSP")))
6369 (build-system r-build-system)
6370 (propagated-inputs (list r-foreach))
6371 (home-page "https://cran.r-project.org/web/packages/TSP/")
6372 (synopsis "Traveling salesperson problem (TSP)")
6373 (description "This package provides basic infrastructure and some
6374 algorithms for the @dfn{traveling salesperson problem}(TSP) (also known as the
6375 traveling salesman problem).")
6376 (license license:gpl3)))
6378 (define-public r-qap
6385 (uri (cran-uri "qap" version))
6388 "0d2d1ni1camixyi45lfy00f4pn3p063k7bsi8gj5scp6n15mdgb0"))))
6389 (build-system r-build-system)
6390 (native-inputs (list gfortran))
6391 (home-page "https://cran.r-project.org/web/packages/qap/")
6392 (synopsis "Heuristics for the quadratic assignment problem (QAP)")
6393 (description "This package implements heuristics for the @dfn{quadratic
6394 assignment problem} (QAP). Currently only a simulated annealing heuristic is
6396 (license license:gpl3)))
6398 (define-public r-gclus
6405 (uri (cran-uri "gclus" version))
6408 "1cz0g0i972955hhaji30rx8448x7f3as7z1sww9i5h86ybgirilw"))))
6409 (build-system r-build-system)
6410 (propagated-inputs (list r-cluster))
6411 (home-page "https://cran.r-project.org/web/packages/gclus/")
6412 (synopsis "Clustering graphics")
6413 (description "This package orders panels in scatterplot matrices and
6414 parallel coordinate displays by some merit index. It contains various indices
6415 of merit, ordering functions, and enhanced versions of @code{pairs} and
6416 @code{parcoord} which color panels according to their merit level.")
6417 (license license:gpl2+)))
6419 (define-public r-webshot
6426 (uri (cran-uri "webshot" version))
6429 "1h6v94zwq0ypgi4vf8xlhp5k13j7f9061hx908177i68c6zg5i5p"))))
6430 (build-system r-build-system)
6432 (list r-callr r-jsonlite r-magrittr))
6433 (home-page "https://github.com/wch/webshot/")
6434 (synopsis "Take screenshots of web pages")
6436 "Webshot makes it easy to take screenshots of web pages from within R.
6437 It can also run Shiny applications locally and take screenshots of the
6438 application; and it can render and screenshot static as well as interactive R
6439 Markdown documents.")
6440 (license license:gpl2)))
6442 (define-public r-seriation
6444 (name "r-seriation")
6449 (uri (cran-uri "seriation" version))
6452 "0dlj0mqpg585m6i7yn0h878i8ag6pyqph98xkk42i2nvghpy01gr"))))
6453 (build-system r-build-system)
6462 (native-inputs (list gfortran))
6463 (home-page "https://s2.smu.edu/IDA/seriation/")
6464 (synopsis "Infrastructure for ordering objects using seriation")
6466 "This package provides infrastructure for seriation with an
6467 implementation of several seriation/sequencing techniques to reorder matrices,
6468 dissimilarity matrices, and dendrograms. It also provides (optimally)
6469 reordered heatmaps, color images and clustering visualizations like
6470 dissimilarity plots, and visual assessment of cluster tendency plots (VAT and
6472 (license license:gpl3)))
6474 (define-public r-xfun
6481 (uri (cran-uri "xfun" version))
6483 (base32 "0dgjkrlwl6rxmvdn6s1xrbiaa53hkfx2s7rqrbrc7c6shbkg6sfi"))))
6484 (build-system r-build-system)
6485 ;; knitr itself depends on xfun
6488 `(("r-knitr" ,r-knitr)))
6489 (home-page "https://github.com/yihui/xfun")
6490 (synopsis "Miscellaneous functions")
6492 "This package provides miscellaneous functions commonly used in other
6493 packages maintained by Yihui Xie.")
6494 (license license:expat)))
6496 (define-public r-utf8
6503 (uri (cran-uri "utf8" version))
6506 "1x6qg19z4qih9lk3mvnmx0vailm1khp5lylw4hlwz6rssj3yw6m7"))))
6507 (build-system r-build-system)
6509 (list r-knitr r-rmarkdown)) ; for vignettes
6510 (home-page "https://github.com/patperry/r-utf8")
6511 (synopsis "Unicode text processing")
6513 "This package provides tools to process and print UTF-8 encoded
6514 international text (Unicode). Input, validate, normalize, encode, format, and
6516 (license license:asl2.0)))
6518 (define-public r-zeallot
6525 (uri (cran-uri "zeallot" version))
6528 "1sd1igcfnv27pa3bqxlbyxchi562h7grnjg1l7wxx3bwr49i57s3"))))
6529 (build-system r-build-system)
6530 (home-page "https://github.com/nteetor/zeallot")
6531 (synopsis "Multiple, unpacking, and destructuring assignment")
6533 "This package provides a @code{%<-%} operator to perform multiple,
6534 unpacking, and destructuring assignment in R. The operator unpacks the
6535 right-hand side of an assignment into multiple values and assigns these values
6536 to variables on the left-hand side of the assignment.")
6537 (license license:expat)))
6539 (define-public r-zlog
6545 (uri (cran-uri "zlog" version))
6548 "1d5j31p0h3rrn230087h3ngpvwknlisjv0f1qdbicdj9m177spci"))))
6549 (properties `((upstream-name . "zlog")))
6550 (build-system r-build-system)
6551 (native-inputs (list r-knitr))
6552 (home-page "https://cran.r-project.org/package=zlog")
6553 (synopsis "Transformation for laboratory easurements")
6555 "The @code{zlog} package offers functions to transform laboratory
6556 measurements into standardised z or @math{z(log)-values}. Therefore the lower
6557 and upper reference limits are needed. If these are not known they could be
6558 estimated from a given sample.")
6559 (license license:gpl3+)))
6561 (define-public r-vctrs
6568 (uri (cran-uri "vctrs" version))
6571 "1pb0wjpwix29q8d8p3wi72a9mp9mif7369pk31w238cs00g8hxln"))))
6572 (build-system r-build-system)
6574 (list r-cli r-glue r-rlang))
6577 (home-page "https://github.com/r-lib/vctrs")
6578 (synopsis "Vector helpers")
6580 "There are three main goals to the @code{vctrs} package:
6583 @item To propose @code{vec_size()} and @code{vec_type()} as alternatives to
6584 @code{length()} and @code{class()}. These definitions are paired with a
6585 framework for type-coercion and size-recycling.
6586 @item To define type- and size-stability as desirable function properties, use
6587 them to analyse existing base function, and to propose better alternatives.
6588 This work has been particularly motivated by thinking about the ideal
6589 properties of @code{c()}, @code{ifelse()}, and @code{rbind()}.
6590 @item To provide a new @code{vctr} base class that makes it easy to create new
6591 S3 vectors. @code{vctrs} provides methods for many base generics in terms of
6592 a few new @code{vctrs} generics, making implementation considerably simpler
6595 (license license:gpl3)))
6597 (define-public r-pillar
6604 (uri (cran-uri "pillar" version))
6607 "1fqk18vc9ashf12gdqkdi6n1nj5lh324vwhgiib3b2fcb2bghhbq"))))
6608 (build-system r-build-system)
6621 (home-page "https://github.com/r-lib/pillar")
6622 (synopsis "Coloured formatting for columns")
6624 "This package provides a @code{pillar} generic designed for formatting
6625 columns of data using the full range of colours provided by modern
6627 (license license:gpl3)))
6629 (define-public r-pinfsc50
6635 (uri (cran-uri "pinfsc50" version))
6638 "1547xyxmfb7zi8h9bsm6k67dcw4hpp129xzvmgwfw7r6p4af47zd"))))
6639 (build-system r-build-system)
6640 (home-page "https://cran.r-project.org/web/packages/pinfsc50/")
6641 (synopsis "Genomic data for the plant pathogen Phytophthora infestans")
6642 (description "This package contains genomic data for the plant pathogen
6643 Phytophthora infestans. It includes a variant file, a sequence file and an
6644 annotation file. This package is intended to be used as example data for
6645 packages that work with genomic data.")
6646 (license license:gpl2+)))
6648 (define-public r-uuid
6655 (uri (cran-uri "uuid" version))
6658 "0bzlc2knmr338h4ykx8v8c2a1inizxafj8rh13kwii68gpp50nz7"))))
6659 (build-system r-build-system)
6660 (home-page "https://www.rforge.net/uuid")
6661 (synopsis "Tools for generating and handling of UUIDs")
6663 "This package provides tools for generating and handling of
6664 @dfn{Universally Unique Identifiers} (UUIDs).")
6665 (license license:expat)))
6667 (define-public r-tinytex
6674 (uri (cran-uri "tinytex" version))
6677 "1v95pjxdq0ma90jji5yqh8ihlcf35cmrqx9v0z649zh0q9vrnbpj"))))
6678 (build-system r-build-system)
6681 (home-page "https://github.com/yihui/tinytex")
6682 (synopsis "Helper functions for TeX Live and compiling LaTeX documents")
6684 "This package provides helper functions to install and maintain the LaTeX
6685 distribution named TinyTeX, a lightweight, cross-platform, portable, and
6686 easy-to-maintain version of TeX Live. This package also contains helper
6687 functions to compile LaTeX documents, and install missing LaTeX packages
6689 (license license:expat)))
6691 (define-public r-tinytest
6698 (uri (cran-uri "tinytest" version))
6701 "1mq31f7bzcz5bkgzl9khm1i80axfzra7gcjqxd2yqb4wrw1m3x4s"))))
6702 (properties `((upstream-name . "tinytest")))
6703 (build-system r-build-system)
6704 (home-page "https://github.com/markvanderloo/tinytest")
6705 (synopsis "Lightweight unit testing framework")
6707 "This package provides a lightweight unit testing framework. Main
6711 @item install tests with the package;
6712 @item test results are treated as data that can be stored and manipulated;
6713 @item test files are R scripts interspersed with test commands, that can be
6715 @item fully automated build-install-test sequence for packages;
6716 @item skip tests when not run locally (e.g. on CRAN);
6717 @item flexible and configurable output printing;
6718 @item compare computed output with output stored with the package;
6719 @item run tests in parallel;
6720 @item extensible by other packages;
6721 @item report side effects.
6724 (license license:gpl3)))
6726 (define-public r-network
6733 (uri (cran-uri "network" version))
6736 "1xrhzbci7ls4h05skdlirxl49jsvmylrqivz2kd6i33wh2ca324m"))))
6737 (build-system r-build-system)
6739 (list r-magrittr r-statnet-common r-tibble))
6740 (home-page "https://statnet.org/")
6741 (synopsis "Classes for relational data")
6743 "This package provides tools to create and modify network objects. The
6744 @code{network} class can represent a range of relational data types, and
6745 supports arbitrary vertex/edge/graph attributes.")
6746 (license license:gpl2+)))
6748 (define-public r-stabs
6755 (uri (cran-uri "stabs" version))
6758 "1nf1yg14cgxrs4np1yghpzw1nczaslfv3rvf3918wrlzg0vp6l7q"))))
6759 (build-system r-build-system)
6762 (home-page "https://github.com/hofnerb/stabs")
6763 (synopsis "Stability selection with error control")
6765 "This package provides resampling procedures to assess the stability of
6766 selected variables with additional finite sample error control for
6767 high-dimensional variable selection procedures such as Lasso or boosting.
6768 Both, standard stability selection (Meinshausen & Buhlmann, 2010) and
6769 complementary pairs stability selection with improved error bounds
6770 (Shah & Samworth, 2013) are implemented. The package can be combined with
6771 arbitrary user specified variable selection approaches.")
6772 (license license:gpl2)))
6774 (define-public r-rle
6781 (uri (cran-uri "rle" version))
6784 "0sagl0jggg40lihzy7pfq4593rfvc3b3f7g6ggi85s7n18qvwg40"))))
6785 (properties `((upstream-name . "rle")))
6786 (build-system r-build-system)
6787 (home-page "https://cran.r-project.org/web/packages/rle/")
6788 (synopsis "Common functions for run-length encoded vectors")
6790 "This package provides common @code{base} and @code{stats} methods for
6791 @code{rle} objects, aiming to make it possible to treat them transparently as
6793 (license license:gpl3)))
6795 (define-public r-statnet-common
6797 (name "r-statnet-common")
6802 (uri (cran-uri "statnet.common" version))
6805 "07djgc6qbxahiy5v15lfayxbj4188lxsb8xcs7hnbm2hic953bfx"))))
6807 `((upstream-name . "statnet.common")))
6808 (build-system r-build-system)
6811 (home-page "https://statnet.org")
6812 (synopsis "R scripts and utilities used by the Statnet software")
6813 (description "This package provides non-statistical utilities used by the
6814 software developed by the Statnet Project.")
6815 (license license:gpl3)))
6817 (define-public r-statcheck
6819 (name "r-statcheck")
6824 (uri (cran-uri "statcheck" version))
6827 "0ivybdcrymlsfv6pg6p5bv70qdvgxf2vgp0kf4r0pf2fcvav1mcp"))))
6828 (build-system r-build-system)
6830 (list r-ggplot2 r-plyr r-rmarkdown))
6831 (home-page "https://cran.r-project.org/web/packages/statcheck/")
6832 (synopsis "Extract statistics from articles and recompute p-values")
6833 (description "This package can automatically extract statistical
6834 null-hypothesis significant testing (NHST) results from articles and recompute
6835 the p-values based on the reported test statistic and degrees of freedom to
6836 detect possible inconsistencies.")
6837 (license license:gpl2)))
6839 (define-public r-sna
6846 (uri (cran-uri "sna" version))
6849 "0ai0v4538d30m4wks5s3lch1yfmx1ml0nnrz7ihs097lv586a09s"))))
6850 (build-system r-build-system)
6852 (list r-network r-statnet-common))
6853 (home-page "https://statnet.org")
6854 (synopsis "Tools for social network analysis")
6856 "This package provides a range of tools for social network analysis,
6857 including node and graph-level indices, structural distance and covariance
6858 methods, structural equivalence detection, network regression, random graph
6859 generation, and 2D/3D network visualization.")
6860 (license license:gpl2+)))
6862 (define-public r-tfisher
6869 (uri (cran-uri "TFisher" version))
6872 "0vz74ww1lf1prfwz74hfsi3a8nzq8ss7aqjr85c1d87vss2796xx"))))
6873 (properties `((upstream-name . "TFisher")))
6874 (build-system r-build-system)
6876 (list r-matrix r-mvtnorm r-sn))
6877 (home-page "https://cran.r-project.org/web/packages/TFisher/")
6878 (synopsis "Optimal thresholding Fisher's p-value combination method")
6880 "This package provides the @dfn{cumulative distribution function} (CDF),
6881 quantile, and statistical power calculator for a collection of thresholding
6882 Fisher's p-value combination methods, including Fisher's p-value combination
6883 method, truncated product method and, in particular, soft-thresholding
6884 Fisher's p-value combination method which is proven to be optimal in some
6885 context of signal detection. The p-value calculator for the omnibus version
6886 of these tests are also included.")
6887 (license license:gpl2)))
6889 (define-public r-ttr
6896 (uri (cran-uri "TTR" version))
6899 "11xsmbvmxq2j119j2z58bx1fkkb2xlhmzc35z5fbwr3nchrfz6jd"))))
6900 (properties `((upstream-name . "TTR")))
6901 (build-system r-build-system)
6903 (list r-curl r-xts r-zoo))
6904 (home-page "https://github.com/joshuaulrich/TTR")
6905 (synopsis "Technical trading rules")
6907 "This package provides functions and data to construct technical trading
6909 (license license:gpl2)))
6911 (define-public r-leaflet-providers
6913 (name "r-leaflet-providers")
6918 (uri (cran-uri "leaflet.providers" version))
6920 (base32 "0yynrwv4xd5cdh49cwvfxm4ranarah9iiry2cd3b4fiihdfcg3wy"))))
6921 (properties `((upstream-name . "leaflet.providers")))
6922 (build-system r-build-system)
6923 (home-page "https://github.com/rstudio/leaflet.providers")
6924 (synopsis "Leaflet map tile providers")
6926 "This package contains third-party map tile provider information from
6927 Leaflet.js, to be used with the @code{leaflet} R package. Additionally,
6928 @code{leaflet.providers} enables users to retrieve up-to-date provider
6929 information between package updates.")
6930 (license license:bsd-2)))
6932 ;; This package contains a lot of minified JavaScript with unclear provenance.
6933 ;; When upgrading please make sure that all minified JavaScript files are
6934 ;; removed in a snippet and that the replacement sources correspond to the
6935 ;; original minified scripts.
6936 (define-public r-leaflet
6943 (uri (cran-uri "leaflet" version))
6945 (base32 "0xsng9n08i1w7qj4hbi706m6d8jm9ixrnwq5xac2s3csfm1s1xij"))
6949 (list "inst/htmlwidgets/lib/leaflet/leaflet.js"
6950 "inst/htmlwidgets/lib/leaflet-measure/leaflet-measure.min.js"
6951 "inst/htmlwidgets/lib/leaflet-omnivore/leaflet-omnivore.min.js"
6952 "inst/htmlwidgets/lib/jquery/jquery.min.js"
6953 "inst/htmlwidgets/plugins/Leaflet-MiniMap/Control.MiniMap.min.js"
6954 "inst/htmlwidgets/plugins/Leaflet.awesome-markers/bootstrap.min.js"
6955 "inst/htmlwidgets/plugins/Leaflet.awesome-markers/leaflet.awesome-markers.min.js"
6956 "inst/htmlwidgets/plugins/Leaflet.markercluster/leaflet.markercluster.js"
6957 "inst/htmlwidgets/plugins/Leaflet.markercluster/leaflet.markercluster.freezable.js"
6958 "inst/htmlwidgets/plugins/Leaflet.markercluster/leaflet.markercluster.layersupport.js"
6959 "inst/legacy/www/leaflet.js")))))
6960 (properties `((upstream-name . "leaflet")))
6961 (build-system r-build-system)
6963 `(#:modules ((guix build utils)
6964 (guix build r-build-system)
6967 (modify-phases %standard-phases
6968 (add-after 'unpack 'process-javascript
6969 (lambda* (#:key inputs #:allow-other-keys)
6970 ;; The inst directory contains some minified JavaScript files.
6971 ;; Regenerate them from sources.
6972 (invoke "unzip" "-d" "/tmp" (assoc-ref inputs "js-leaflet"))
6973 (with-directory-excursion "inst/"
6977 `(("/tmp/leaflet-src.js"
6978 "htmlwidgets/lib/leaflet/leaflet.js")
6979 (,(assoc-ref inputs "js-leaflet-measure")
6980 "htmlwidgets/lib/leaflet-measure/leaflet-measure.min.js")
6981 (,(assoc-ref inputs "js-leaflet-omnivore")
6982 "htmlwidgets/lib/leaflet-omnivore/leaflet-omnivore.min.js")
6983 (,(assoc-ref inputs "js-jquery")
6984 "htmlwidgets/lib/jquery/jquery.min.js")
6985 ("htmlwidgets/plugins/Leaflet-MiniMap/Control.MiniMap.js"
6986 "htmlwidgets/plugins/Leaflet-MiniMap/Control.MiniMap.min.js")
6987 (,(assoc-ref inputs "js-bootstrap3")
6988 "htmlwidgets/plugins/Leaflet.awesome-markers/bootstrap.min.js")
6989 ("htmlwidgets/plugins/Leaflet.awesome-markers/leaflet.awesome-markers.js"
6990 "htmlwidgets/plugins/Leaflet.awesome-markers/leaflet.awesome-markers.min.js")
6991 (,(string-append (assoc-ref inputs "js-leaflet-markercluster")
6992 "/dist/leaflet.markercluster-src.js")
6993 "htmlwidgets/plugins/Leaflet.markercluster/leaflet.markercluster.js")
6994 (,(assoc-ref inputs "js-leaflet-markercluster-freezable")
6995 "htmlwidgets/plugins/Leaflet.markercluster/leaflet.markercluster.freezable.js")
6996 (,(assoc-ref inputs "js-leaflet-markercluster-layersupport")
6997 "htmlwidgets/plugins/Leaflet.markercluster/leaflet.markercluster.layersupport.js")
6998 (,(assoc-ref inputs "js-proj4leaflet")
6999 "htmlwidgets/plugins/Proj4Leaflet/proj4.min.js")
7000 ("legacy/www/leaflet-src.js"
7001 "legacy/www/leaflet.js"))))
7002 (lambda (sources targets)
7003 (for-each (lambda (source target)
7004 (format #true "Processing ~a --> ~a~%"
7006 (invoke "esbuild" source "--minify"
7007 (string-append "--outfile=" target)))
7008 sources targets)))))))))
7010 `(("esbuild" ,esbuild)
7015 (uri "https://raw.githubusercontent.com/twbs/bootstrap/v3.3.7/dist/js/bootstrap.js")
7018 "1j1qjagwj0m3q322z9wxxnpkd8zbk6g3kl047dsbmqad6gmqvgha"))))
7022 (uri "https://code.jquery.com/jquery-1.12.4.js")
7025 "0x9mrc1668icvhpwzvgafm8xm11x9lfai9nwr66aw6pjnpwkc3s3"))))
7029 (uri "http://cdn.leafletjs.com/leaflet/v1.3.1/leaflet.zip")
7032 "10phzd2vczy3zm1b64whp2nna69cf9hlj2bndc9yq47vf3ddqx8f"))))
7033 ("js-leaflet-omnivore"
7036 (uri (string-append "https://api.tiles.mapbox.com/mapbox.js/plugins/"
7037 "leaflet-omnivore/v0.3.1/leaflet-omnivore.js"))
7040 "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq"))))
7041 ("js-leaflet-markercluster"
7045 (url "https://github.com/Leaflet/Leaflet.markercluster.git")
7047 (file-name (git-file-name "js-leaflet-markercluster" "1.1.0"))
7050 "0ds8c7picqjmc86bm5n6hm8k71fwsa2cpgib19sbdamzr9hm0rs1"))))
7051 ("js-leaflet-markercluster-freezable"
7055 "https://raw.githubusercontent.com/ghybs/Leaflet.MarkerCluster.Freezable/"
7056 "9db80a3fba7dff4aee940e05d3d4dceaa1fffcf9/src/freezable.js"))
7057 (file-name "leaflet-markercluster-freezable.js")
7060 "1k6sn5n0z2x3an91vwvkzmqq4b8ppswgk5hi5qrr79klas1hbx1k"))))
7061 ("js-leaflet-markercluster-layersupport"
7065 "https://raw.githubusercontent.com/ghybs/Leaflet.MarkerCluster.LayerSupport/"
7066 "87f3848b92e0516d9c98f6d4cd175f7b8a4e3805/src/layersupport.js"))
7067 (file-name "leaflet-markercluster-layersupport.js")
7070 "15qa21xif94y762c65yxxysxykz3mma6y6agw3nxpr3s7wbb75ff"))))
7071 ("js-leaflet-measure"
7074 (uri "https://unpkg.com/leaflet-measure@1.5.2/dist/leaflet-measure.js")
7075 (file-name "js-leaflet-measure-1.5.2.js")
7078 "0ggg3ffmm7pj9ry4gssrh0a17pnad3p6gwi0dg98y819pmpqa7y0"))))
7082 (uri "https://raw.githubusercontent.com/kartena/Proj4Leaflet/1.0.2/lib/proj4.js")
7083 (file-name "js-proj4leaflet-1.0.2.js")
7086 "0vyrbf6gv2lyh4c2bzp5349ivwvvg28gpn87y52a7jdb13rlkpab"))))))
7101 (home-page "https://rstudio.github.io/leaflet/")
7102 (synopsis "Create interactive web maps with the JavaScript Leaflet library")
7104 "Create and customize interactive maps using the Leaflet JavaScript
7105 library and the @code{htmlwidgets} package. These maps can be used directly
7106 from the R console, from RStudio, in Shiny applications and R Markdown
7108 (license license:gpl3)))
7110 (define-public r-leaps
7117 (uri (cran-uri "leaps" version))
7120 "1dn3yl1p03n0iynd1vsdkrr0fhmvgrmfkv37y7n371765h83lz1x"))))
7121 (build-system r-build-system)
7122 (native-inputs (list gfortran))
7123 (home-page "https://cran.r-project.org/web/packages/leaps/")
7124 (synopsis "Regression subset selection")
7126 "This package provides tools for regression subset selection, including
7127 exhaustive search.")
7128 (license license:gpl2+)))
7130 (define-public r-splus2r
7137 (uri (cran-uri "splus2R" version))
7140 "035zd22zcpkh74rik9ws6g8al6vjz7jgrqs5si361bzb5n290p3x"))))
7141 (properties `((upstream-name . "splus2R")))
7142 (build-system r-build-system)
7143 (home-page "https://cran.r-project.org/web/packages/splus2R/")
7144 (synopsis "Supplemental S-PLUS functionality in R")
7146 "Currently there are many functions in S-PLUS that are missing in R. To
7147 facilitate the conversion of S-PLUS packages to R packages, this package
7148 provides some missing S-PLUS functionality in R.")
7149 (license license:gpl2)))
7151 (define-public r-ifultools
7153 (name "r-ifultools")
7158 (uri (cran-uri "ifultools" version))
7161 "16a7rbvlym3bnfm93ikr5kl0l86ppk0s41fva6idvcx765g3fqkk"))))
7162 (build-system r-build-system)
7164 (list r-mass r-splus2r))
7165 (home-page "https://cran.r-project.org/web/packages/ifultools/")
7166 (synopsis "Insightful research tools")
7167 (description "This package provides C code used by the wmtsa, fractal, and
7169 (license license:gpl2)))
7171 (define-public r-sapa
7178 (uri (cran-uri "sapa" version))
7181 "0kj681rd4c2lvqr926lb6f4qwp281x5274dg6vbk8pf5y7s0qlpc"))))
7182 (build-system r-build-system)
7184 (list r-ifultools r-splus2r))
7185 (home-page "https://cran.r-project.org/web/packages/sapa/")
7186 (synopsis "Spectral analysis for physical applications")
7187 (description "This package provides software for the book Spectral
7188 Analysis for Physical Applications, Donald B. Percival and Andrew T. Walden,
7189 Cambridge University Press, 1993.")
7190 (license license:gpl2)))
7192 (define-public r-aggregation
7194 (name "r-aggregation")
7199 (uri (cran-uri "aggregation" version))
7202 "0j9g604m2ccc7hcy02539yja9cf3xcbl25gvp838bp4x8w18my46"))))
7203 (build-system r-build-system)
7204 (home-page "https://cran.r-project.org/web/packages/aggregation/")
7205 (synopsis "Methods for p-value aggregation")
7207 "This package contains functionality for performing the following methods
7208 of p-value aggregation: Fisher's method, the Lancaster method (weighted
7209 Fisher's method), and Sidak correction.")
7210 (license license:gpl3)))
7212 (define-public r-quantmod
7219 (uri (cran-uri "quantmod" version))
7222 "154fqhw46kc7r08zsj5fsg97hg93phsli3z14xwmz22xb50xymzp"))))
7223 (build-system r-build-system)
7225 (list r-curl r-ttr r-xts r-zoo))
7226 (home-page "https://cran.r-project.org/web/packages/quantmod/")
7227 (synopsis "Quantitative financial modelling framework")
7228 (description "This package provides a quantitative financial modelling
7229 framework to allow users to specify, build, trade, and analyse quantitative
7230 financial trading strategies.")
7231 (license license:gpl3)))
7233 (define-public r-tseries
7240 (uri (cran-uri "tseries" version))
7243 "0zr09ikaz96djcvnjbr8ah6waqzjy06f4yd4isshlwc391q20px5"))))
7244 (build-system r-build-system)
7246 (list r-quadprog r-quantmod r-zoo))
7249 (home-page "https://cran.r-project.org/web/packages/tseries/")
7250 (synopsis "Time series analysis and computational finance")
7252 "This package provides functions relating to time series analysis and
7253 computational finance.")
7254 (license license:gpl2)))
7256 (define-public r-wmtsa
7263 (uri (cran-uri "wmtsa" version))
7266 "1q436krz5p1f4a7a7sya6a9rh9x9mi8zzcgq66gbk9w9w4hcqcj6"))))
7267 (build-system r-build-system)
7269 (list r-ifultools r-mass r-splus2r))
7270 (home-page "https://cran.r-project.org/web/packages/wmtsa/")
7271 (synopsis "Wavelet methods for time series analysis")
7273 "This package provides software to accompany the book \"Wavelet Methods
7274 for Time Series Analysis\", Donald B. Percival and Andrew T. Walden, Cambridge
7275 University Press, 2000.")
7276 (license license:gpl2)))
7278 (define-public r-tsa
7285 (uri (cran-uri "TSA" version))
7288 "1bv5q609lhmrcxnjnvcj497fbjlv89zwa8q918hw4iki5nkvwwdb"))))
7289 (properties `((upstream-name . "TSA")))
7290 (build-system r-build-system)
7292 (list r-leaps r-locfit r-mgcv r-tseries))
7293 (home-page "https://homepage.divms.uiowa.edu/~kchan/TSA.htm")
7294 (synopsis "Time series analysis")
7296 "This package contains R functions and datasets detailed in the book
7297 \"Time Series Analysis with Applications in R (second edition)\" by Jonathan
7298 Cryer and Kung-Sik Chan.")
7299 (license license:gpl2+)))
7301 (define-public r-extradistr
7303 (name "r-extradistr")
7308 (uri (cran-uri "extraDistr" version))
7311 "1gypnbvdzczl0mvznvy8r7hzsvc5gvdvi2mmzj21cqdw9n63944r"))))
7312 (properties `((upstream-name . "extraDistr")))
7313 (build-system r-build-system)
7316 (home-page "https://github.com/twolodzko/extraDistr")
7317 (synopsis "Additional univariate and multivariate distributions")
7319 "This package implements density, distribution functions, quantile
7320 functions and random generation functions for a large number of univariate and
7321 multivariate distributions.")
7322 (license license:gpl2)))
7324 (define-public r-fractal
7331 (uri (cran-uri "fractal" version))
7334 "18lr9z0gslvfc3z8vyj3krqj3bfhg60zv1fzinrwwkc4cpk1w7mp"))))
7335 (build-system r-build-system)
7343 (home-page "https://cran.r-project.org/web/packages/fractal/")
7344 (synopsis "Fractal time series modeling and analysis")
7346 "This package provides tools for stochastic fractal and deterministic
7347 chaotic time series analysis.")
7348 (license license:gpl2)))
7350 (define-public r-urca
7357 (uri (cran-uri "urca" version))
7360 "1akaqwf3fvvvx4sgfn641fd4sj51s0701pvfl6s5hnz2k0iwh732"))))
7361 (build-system r-build-system)
7362 (propagated-inputs (list r-nlme))
7363 (native-inputs (list gfortran))
7364 (home-page "https://cran.r-project.org/web/packages/urca/")
7365 (synopsis "Unit root and cointegration tests for time series data")
7367 "This package provides unit root and cointegration tests encountered in
7368 applied econometric analysis.")
7369 (license license:gpl2+)))
7371 (define-public r-cubature
7378 (uri (cran-uri "cubature" version))
7381 "0sfmcy5xpa40w3qn0jbg7b802wksl5k8glz9jpx77n159wn3nyq8"))))
7382 (build-system r-build-system)
7387 (home-page "https://github.com/bnaras/cubature")
7388 (synopsis "Adaptive multivariate integration over hypercubes")
7390 "This package is an R wrapper around the cubature C library for adaptive
7391 multivariate integration over hypercubes. This version provides both
7392 @code{hcubature} and @code{pcubature} routines in addition to a vector
7394 ;; The included cubature C library is released under GPLv2+, but the
7395 ;; wrapper declares the license to be GPLv3+.
7396 (license (list license:gpl2+ license:gpl3+))))
7398 (define-public r-trend
7405 (uri (cran-uri "trend" version))
7408 "1mr5g5gaxiqj6x83ngcbwwh57vhrhcz0x9dh0rmvs9y2ivk29ccs"))))
7409 (build-system r-build-system)
7411 (list r-extradistr))
7414 (home-page "https://cran.r-project.org/web/packages/trend/")
7415 (synopsis "Non-parametric trend tests and change-point detection")
7417 "The analysis of environmental data often requires the detection of
7418 trends and change-points. This package includes tests for trend
7419 detection (Cox-Stuart Trend Test, Mann-Kendall Trend Test, (correlated)
7420 Hirsch-Slack Test, partial Mann-Kendall Trend Test, multivariate (multisite)
7421 Mann-Kendall Trend Test, (Seasonal) Sen's slope, partial Pearson and Spearman
7422 correlation trend test), change-point detection (Lanzante's test procedures,
7423 Pettitt's test, Buishand Range Test, Buishand U Test, Standard Normal
7424 Homogeinity Test), detection of non-randomness (Wallis-Moore Phase Frequency
7425 Test, Bartels rank von Neumann's ratio test, Wald-Wolfowitz Test) and the two
7426 sample Robust Rank-Order Distributional Test.")
7427 (license license:gpl3)))
7429 (define-public r-expm
7436 (uri (cran-uri "expm" version))
7439 "1p5dapwv8ycxaysgi6imnby04i4kh1c5a2czqa4wygz0s8pr2y9c"))))
7440 (build-system r-build-system)
7441 (propagated-inputs (list r-matrix))
7442 (native-inputs (list gfortran))
7443 (home-page "https://r-forge.r-project.org/projects/expm/")
7444 (synopsis "Tools for matrix exponentials and related quantities")
7446 "This package provides tools for the computation of the matrix
7447 exponential, logarithm, square root, and related quantities.")
7448 (license license:gpl2+)))
7450 (define-public r-complexplus
7452 (name "r-complexplus")
7457 (uri (cran-uri "complexplus" version))
7460 "16w9v7d1ckavqmr86l34frr37pkvdn0iqnb17ssb8xaggns5lgqx"))))
7461 (build-system r-build-system)
7463 (list r-expm r-matrix))
7464 (home-page "https://cran.r-project.org/web/packages/complexplus/")
7465 (synopsis "Functions of complex or real variables")
7467 "This package extends several functions to the complex domain, including
7468 the matrix exponential and logarithm, and the determinant.")
7469 (license license:gpl2)))
7471 (define-public r-phontools
7473 (name "r-phontools")
7478 (uri (cran-uri "phonTools" version))
7481 "01i481mhswsys3gpasw9gn6nxkfmi7bz46g5c84m13pg0cv8hxc7"))))
7482 (properties `((upstream-name . "phonTools")))
7483 (build-system r-build-system)
7484 (home-page "http://www.santiagobarreda.com/rscripts.html")
7485 (synopsis "Tools for phonetic and acoustic analyses")
7487 "This package contains tools for the organization, display, and analysis
7488 of the sorts of data frequently encountered in phonetics research and
7489 experimentation, including the easy creation of IPA vowel plots, and the
7490 creation and manipulation of WAVE audio files.")
7491 (license license:bsd-2)))
7500 (uri (cran-uri "np" version))
7503 "1a9kzn37cddwfdki5zjmzanxp75pccdjnsvqfrh84hhcsy51pcx3"))))
7504 (build-system r-build-system)
7506 (list r-boot r-cubature r-quadprog r-quantreg))
7507 (home-page "https://github.com/JeffreyRacine/R-Package-np")
7508 (synopsis "Non-parametric kernel smoothing methods for mixed data types")
7509 (description "This package provides non-parametric (and semi-parametric)
7510 kernel methods that seamlessly handle a mix of continuous, unordered, and
7511 ordered factor data types.")
7512 ;; Any version of the GPL.
7513 (license license:gpl3+)))
7515 (define-public r-powerplus
7517 (name "r-powerplus")
7522 (uri (cran-uri "powerplus" version))
7525 "0ayp6x34hkzgris4j3zbbs0r23n81bhww3wgfyy630ri4sk6brrn"))))
7526 (build-system r-build-system)
7528 (list r-complexplus r-expm r-mass r-matrix r-phontools))
7529 (home-page "https://cran.r-project.org/web/packages/powerplus/")
7530 (synopsis "Exponentiation operations")
7532 "This package provides tools for the computation of matrix and scalar
7534 (license license:gpl2)))
7536 (define-public r-egg
7543 (uri (cran-uri "egg" version))
7546 "1fy7srpiavfn8kyrr1m84an7acgwi6ydzrg71m3b0vk7y9ybmj0m"))))
7547 (properties `((upstream-name . "egg")))
7548 (build-system r-build-system)
7550 (list r-ggplot2 r-gridextra r-gtable))
7551 (home-page "https://cran.r-project.org/web/packages/egg")
7552 (synopsis "Extensions for ggplot2")
7554 "This package provides miscellaneous functions to help customize ggplot2
7555 objects. High-level functions are provided to post-process ggplot2 layouts
7556 and allow alignment between plot panels, as well as setting panel sizes to
7557 fixed values. Other functions include a custom @code{geom}, and helper
7558 functions to enforce symmetric scales or add tags to facetted plots.")
7559 (license license:gpl3)))
7561 (define-public r-heatmap3
7568 (uri (cran-uri "heatmap3" version))
7571 "0sfvizmmwfk1bjhn6zfx5a4qqfgj1ldg8x90b65crqibgfa36k2r"))))
7572 (build-system r-build-system)
7574 (list r-fastcluster))
7577 (home-page "https://cran.r-project.org/web/packages/heatmap3/")
7578 (synopsis "Improved heatmap package")
7580 "This package provides an improved heatmap package. It is completely
7581 compatible with the original R function @code{heatmap}, and provides more
7582 powerful and convenient features.")
7583 (license license:gpl2+)))
7585 (define-public r-heatmaply
7587 (name "r-heatmaply")
7592 (uri (cran-uri "heatmaply" version))
7595 "1w8yyzb68laxd4zxycvgmpqj5wnyidjgv1vbzbxndp9p92f2cp8a"))))
7596 (build-system r-build-system)
7614 (home-page "https://cran.r-project.org/package=heatmaply")
7615 (synopsis "Interactive cluster heat maps using plotly")
7617 "This package enables you to create interactive cluster heatmaps that can
7618 be saved as a stand-alone HTML file, embedded in R Markdown documents or in a
7619 Shiny app, and made available in the RStudio viewer pane. Hover the mouse
7620 pointer over a cell to show details or drag a rectangle to zoom. A heatmap is
7621 a popular graphical method for visualizing high-dimensional data, in which a
7622 table of numbers is encoded as a grid of colored cells. The rows and columns
7623 of the matrix are ordered to highlight patterns and are often accompanied by
7625 ;; Either version of the license.
7626 (license (list license:gpl2 license:gpl3))))
7635 (uri (cran-uri "h5" version))
7638 "14p7i1sj24ky87kd7qr3n9fc9l64s0bp0rwbyl6i2x69xn75gpsx"))))
7639 (build-system r-build-system)
7646 (home-page "https://github.com/mannau/h5")
7647 (synopsis "Interface to the HDF5 Library")
7649 "This package provides an S4 interface to the HDF5 library supporting
7650 fast storage and retrieval of R-objects like vectors, matrices and arrays to
7651 binary files in a language independent format. The HDF5 format can therefore
7652 be used as an alternative to R's save/load mechanism. Since h5 is able to
7653 access only subsets of stored data it can also handle data sets which do not
7655 (license license:bsd-2)))
7657 (define-public r-cgdsr
7664 (uri (cran-uri "cgdsr" version))
7667 "07yc819hkabpzzh0g0cbqza6bcfy67b2marrzz1lj97f9iba78ja"))))
7668 (build-system r-build-system)
7670 (list r-httr r-r-methodss3 r-r-oo))
7671 (home-page "https://github.com/cBioPortal/cgdsr")
7672 (synopsis "R-based API for accessing the MSKCC Cancer Genomics Data Server")
7674 "This package provides a basic set of R functions for querying the Cancer
7675 Genomics Data Server (CGDS), hosted by the Computational Biology Center at
7676 Memorial-Sloan-Kettering Cancer Center (MSKCC).")
7677 (license license:lgpl3)))
7679 (define-public r-import
7686 (uri (cran-uri "import" version))
7689 "19g4jnfg9pkvvsncw62yc15xlb97hfbdqxivpjd9jqi36i6mdjrg"))))
7690 (build-system r-build-system)
7693 (home-page "https://github.com/smbache/import")
7694 (synopsis "Import mechanism for R")
7696 "This is an alternative mechanism for importing objects from packages.
7697 The syntax allows for importing multiple objects from a package with a single
7698 command in an expressive way. The import package bridges some of the gap
7699 between using @code{library} (or @code{require}) and direct (single-object)
7700 imports. Furthermore the imported objects are not placed in the current
7701 environment. It is also possible to import objects from stand-alone @code{.R}
7703 (license license:expat)))
7705 (define-public r-shinyace
7712 (uri (cran-uri "shinyAce" version))
7715 "12mqvdh6rxsr61pc3pzla95r5f4l7xagjs2rcdr7c2lbqyxpx6aa"))))
7716 (properties `((upstream-name . "shinyAce")))
7717 (build-system r-build-system)
7719 (list r-shiny r-jsonlite))
7720 (home-page "https://cran.r-project.org/web/packages/shinyAce/")
7721 (synopsis "Ace editor bindings for Shiny")
7723 "This package provides Ace editor bindings to enable a rich text editing
7724 environment within Shiny.")
7725 (license license:expat)))
7727 (define-public r-rafalib
7734 (uri (cran-uri "rafalib" version))
7736 (base32 "1dmxjl66bfdgrybhwyaa8d4i460liqcdw8b29a6w7shgksh29m0k"))))
7737 (properties `((upstream-name . "rafalib")))
7738 (build-system r-build-system)
7739 (propagated-inputs (list r-rcolorbrewer))
7740 (home-page "https://cran.r-project.org/package=rafalib")
7741 (synopsis "Convenience functions for routine data exploration")
7743 "This package provides a series of shortcuts for routine tasks to
7744 facilitate data exploration.")
7745 (license license:artistic2.0)))
7747 (define-public r-randomizr
7749 (name "r-randomizr")
7754 (uri (cran-uri "randomizr" version))
7757 "1grm0h3xkb0pdbbv0gd531g1kn6njp0gcy5fh153rrmajxgd8hhw"))))
7758 (properties `((upstream-name . "randomizr")))
7759 (build-system r-build-system)
7762 (home-page "https://declaredesign.org/r/randomizr/")
7763 (synopsis "Tools for common forms of random assignment and sampling")
7765 "This package provides tools for generating random assignments for common
7766 experimental designs and random samples for common sampling designs.")
7767 (license license:expat)))
7769 (define-public r-base64url
7771 (name "r-base64url")
7776 (uri (cran-uri "base64url" version))
7779 "0n1c2b68vza1dh7sk38v6biiwm72c4jpl79kpdg1bsb0hq9qy18x"))))
7780 (build-system r-build-system)
7783 (home-page "https://github.com/mllg/base64url")
7784 (synopsis "Fast and URL-safe base64 encoder and decoder")
7786 "This package provides a URL-safe base64 encoder and decoder. In
7787 contrast to RFC3548, the 62nd character (@code{+}) is replaced with @code{-},
7788 the 63rd character (@code{/}) is replaced with @code{_}. Furthermore, the
7789 encoder does not fill the string with trailing @code{=}. The resulting
7790 encoded strings comply to the regular expression pattern @code{[A-Za-z0-9_-]}
7791 and thus are safe to use in URLs or for file names. The package also comes
7792 with a simple base32 encoder/decoder suited for case insensitive file
7794 (license license:gpl3)))
7796 (define-public r-radiant-data
7798 (name "r-radiant-data")
7803 (uri (cran-uri "radiant.data" version))
7806 "0c5c99q13pwv6k0b07x3r2bxmh0h2w15h02xb1pincgs61qwi15k"))
7807 (modules '((guix build utils)))
7810 ;; Delete files that are under CC-NC-SA.
7811 (delete-file-recursively "inst/app/tools/help")
7813 (properties `((upstream-name . "radiant.data")))
7814 (build-system r-build-system)
7848 (home-page "https://github.com/radiant-rstats/radiant.data")
7849 (synopsis "Data menu for Radiant: business analytics using R and Shiny")
7851 "The Radiant Data menu includes interfaces for loading, saving, viewing,
7852 visualizing, summarizing, transforming, and combining data. It also contains
7853 functionality to generate reproducible reports of the analyses conducted in
7855 (license license:agpl3)))
7857 (define-public r-algdesign
7859 (name "r-algdesign")
7864 (uri (cran-uri "AlgDesign" version))
7866 (base32 "01cx63wqr6yvgl5ml1lj6gh9p1sn42b6qcnsppcw7mvba9n652ar"))))
7867 (properties `((upstream-name . "AlgDesign")))
7868 (build-system r-build-system)
7869 (home-page "https://github.com/jvbraun/AlgDesign")
7870 (synopsis "Algorithmic experimental design")
7872 "This package provides tools to calculate exact and approximate theory
7873 experimental designs for D, A, and I criteria. Very large designs may be
7874 created. Experimental designs may be blocked or blocked designs created from
7875 a candidate list, using several criteria. The blocking can be done when whole
7876 and within plot factors interact.")
7877 (license license:gpl2+)))
7879 (define-public r-alluvial
7886 (uri (cran-uri "alluvial" version))
7888 (base32 "039frwrsxq1lb97s7vf2vbyyadimkigs628ymym06fxka53drdkp"))))
7889 (properties `((upstream-name . "alluvial")))
7890 (build-system r-build-system)
7891 (native-inputs (list r-knitr))
7892 (home-page "https://github.com/mbojan/alluvial")
7893 (synopsis "Create parallel sets plots (Alluvial Diagrams)")
7895 "This package creates alluvial diagrams (also known as parallel sets
7896 plots) for multivariate and time series-like data.")
7897 (license license:expat)))
7899 (define-public r-signal
7906 (uri (cran-uri "signal" version))
7909 "0qaf39vfmhn3d0bdjqd805ayfkaj48dkmf5dqd47bpk7dp21b837"))))
7910 (build-system r-build-system)
7911 (propagated-inputs (list r-mass))
7912 (native-inputs (list gfortran))
7913 (home-page "https://cran.r-project.org/web/packages/signal/")
7914 (synopsis "Signal processing")
7916 "This package provides a set of signal processing functions originally
7917 written for Matlab and GNU Octave. It includes filter generation utilities,
7918 filtering functions, resampling routines, and visualization of filter models.
7919 It also includes interpolation functions.")
7920 (license license:gpl2)))
7922 (define-public r-gsubfn
7929 (uri (cran-uri "gsubfn" version))
7932 "00j6b8b6xsx6v370h220x233rpk6asca78165y3d48jpwvwisdc9"))))
7933 (build-system r-build-system)
7934 (propagated-inputs (list r-proto))
7935 (home-page "https://code.google.com/archive/p/gsubfn/")
7936 (synopsis "Utilities for strings and function arguments")
7938 "This package provides @code{gsubfn} which is like @code{gsub} but can
7939 take a replacement function or certain other objects instead of the
7940 replacement string. Matches and back references are input to the replacement
7941 function and replaced by the function output. @code{gsubfn} can be used to
7942 split strings based on content rather than delimiters and for quasi-perl-style
7943 string interpolation. The package also has facilities for translating
7944 formulas to functions and allowing such formulas in function calls instead of
7946 (license license:gpl2+)))
7948 (define-public r-sqldf
7955 (uri (cran-uri "sqldf" version))
7958 "0q12vsb53p2wchgp8wfz5bk08wfnm0jxjrakclj4jyy6x3a7ksff"))))
7959 (build-system r-build-system)
7961 (list r-chron r-dbi r-gsubfn r-proto r-rsqlite))
7962 (home-page "https://github.com/ggrothendieck/sqldf")
7963 (synopsis "Manipulate R data frames using SQL")
7965 "The @code{sqldf} function is typically passed a single argument which is
7966 an SQL select statement where the table names are ordinary R data frame names.
7967 @code{sqldf} transparently sets up a database, imports the data frames into
7968 that database, performs the SQL statement and returns the result using a
7969 heuristic to determine which class to assign to each column of the returned
7970 data frame. The @code{sqldf} or @code{read.csv.sql} functions can also be
7971 used to read filtered files into R even if the original files are larger than
7972 R itself can handle.")
7973 (license license:gpl2)))
7975 (define-public r-abind
7982 (uri (cran-uri "abind" version))
7985 "0b1zd8jbnl6l292cr9rb50m09fy3ylxvzkpgi5lfb1nbzddcwfis"))))
7986 (build-system r-build-system)
7987 (home-page "https://cran.r-project.org/web/packages/abind/")
7988 (synopsis "Combine multidimensional arrays")
7990 "This package provides tools to combine multidimensional arrays into a
7991 single array. This is a generalization of @code{cbind} and @code{rbind}. It
7992 works with vectors, matrices, and higher-dimensional arrays. It also provides
7993 the functions @code{adrop}, @code{asub}, and @code{afill} for manipulating,
7994 extracting and replacing data in arrays.")
7995 (license license:lgpl2.0+)))
7997 (define-public r-prroc
8004 (uri (cran-uri "PRROC" version))
8007 "1m28h8pcd78049lz2qixhkcr9h5b3jik3maqzfbvq9y58z71i4a7"))))
8008 (properties `((upstream-name . "PRROC")))
8009 (build-system r-build-system)
8010 (home-page "https://cran.r-project.org/web/packages/PRROC/")
8011 (synopsis "Precision-Recall and ROC curves for weighted and unweighted data")
8013 "This package computes the areas under the @dfn{precision-recall} (PR)
8014 and ROC curve for weighted (e.g. soft-labeled) and unweighted data. In
8015 contrast to other implementations, the interpolation between points of the PR
8016 curve is done by a non-linear piecewise function. In addition to the areas
8017 under the curves, the curves themselves can also be computed and plotted by a
8018 specific S3-method.")
8019 (license license:gpl3)))
8021 (define-public r-vim
8028 (uri (cran-uri "VIM" version))
8031 "0fbpm6y3hhiw8srnbc38k19b859jcqzsh78ib8yvj86gck5av0bm"))))
8032 (properties `((upstream-name . "VIM")))
8033 (build-system r-build-system)
8050 (home-page "https://github.com/alexkowa/VIM")
8051 (synopsis "Visualization and imputation of missing values")
8053 "This package provides tools for the visualization of missing and/or
8054 imputed values are introduced, which can be used for exploring the data and
8055 the structure of the missing and/or imputed values. Depending on this
8056 structure of the missing values, the corresponding methods may help to
8057 identify the mechanism generating the missing values and explore the
8058 data including missing values. In addition, the quality of imputation can be
8059 visually explored using various univariate, bivariate, multiple and
8060 multivariate plot methods.")
8061 (license license:gpl2+)))
8063 (define-public r-fnn
8070 (uri (cran-uri "FNN" version))
8073 "0nmynpiy3d2dnd5ngjf4m79jy02byhk43gj0xny9a6j8243f5c2j"))))
8074 (properties `((upstream-name . "FNN")))
8075 (build-system r-build-system)
8076 (home-page "https://cran.r-project.org/web/packages/FNN")
8077 (synopsis "Fast nearest neighbor search algorithms and applications")
8079 "This package provides cover-tree and kd-tree fast k-nearest neighbor
8080 search algorithms. Related applications including KNN classification,
8081 regression and information measures are implemented.")
8082 ;; The DESCRIPTION file erroneously states that GPL version 2.1 or
8083 ;; later can be used.
8084 (license license:gpl2+)))
8086 (define-public r-smoother
8093 (uri (cran-uri "smoother" version))
8096 "0nqr1bvlr5bnasqg74zmknjjl4x28kla9h5cxpga3kq5z215pdci"))))
8097 (build-system r-build-system)
8100 (home-page "https://cran.r-project.org/web/packages/smoother")
8101 (synopsis "Functions relating to the smoothing of numerical data")
8103 "This package provides a collection of methods for smoothing numerical
8104 data, commencing with a port of the Matlab gaussian window smoothing function.
8105 In addition, several functions typically used in smoothing of financial data
8107 (license license:gpl2)))
8109 (define-public r-riverplot
8111 (name "r-riverplot")
8116 (uri (cran-uri "riverplot" version))
8119 "04ap1dsa7fx03l73jhv1ql3adaaaz2100qawdplxa9xmrllgcgbj"))))
8120 (build-system r-build-system)
8122 (list r-rcolorbrewer))
8125 (home-page "https://logfc.wordpress.com")
8126 (synopsis "Sankey or ribbon plots")
8128 "Sankey plots are a type of diagram that is convenient to illustrate how
8129 flow of information, resources etc. separates and joins, much like observing
8130 how rivers split and merge. For example, they can be used to compare
8131 different clusterings. This package provides an implementation of Sankey
8133 (license license:gpl2+)))
8135 (define-public r-dyn
8142 (uri (cran-uri "dyn" version))
8145 "16fqv9k7yxdgybwzafjkyqm16qpgqz13lcjpi6a1nc8xbzlzh0gb"))))
8146 (build-system r-build-system)
8149 (home-page "https://cran.r-project.org/web/packages/dyn")
8150 (synopsis "Time series regression")
8152 "This package provides the dyn class interfaces @code{ts}, @code{irts},
8153 @code{zoo} and @code{zooreg} time series classes to @code{lm}, @code{glm},
8154 @code{loess}, @code{quantreg::rq}, @code{MASS::rlm},
8155 @code{MCMCpack::MCMCregress()}, @code{quantreg::rq()},
8156 @code{randomForest::randomForest()} and other regression functions, allowing
8157 those functions to be used with time series including specifications that may
8158 contain lags, diffs and missing values.")
8160 (license license:gpl2+)))
8162 (define-public r-dynutils
8169 (uri (cran-uri "dynutils" version))
8171 (base32 "1pcj4igaw1g898xb42kcpzfmqy80xai5ki5bpnkf8hg738wm00qz"))))
8172 (properties `((upstream-name . "dynutils")))
8173 (build-system r-build-system)
8187 (native-inputs (list r-knitr))
8188 (home-page "https://github.com/dynverse/dynutils")
8189 (synopsis "Common functionality for the dynverse packages")
8191 "This package provides common functionality for the
8192 @url{https://dynverse.org,dynverse} packages. dynverse is created to support
8193 the development, execution, and benchmarking of trajectory inference
8195 (license license:expat)))
8197 (define-public r-catdap
8204 (uri (cran-uri "catdap" version))
8207 "0fyhl69z2lznymvpzxra9qvcg85ggzkfjy68c6mzdmf1ja44d2k5"))))
8208 (build-system r-build-system)
8211 (home-page "https://cran.r-project.org/web/packages/catdap/")
8212 (synopsis "Tools for categorical data analysis")
8214 "This package provides functions for analyzing multivariate data.
8215 Dependencies of the distribution of the specified variable (response
8216 variable) to other variables (explanatory variables) are derived and
8217 evaluated by the @dfn{Akaike Information Criterion} (AIC).")
8218 (license license:gpl2+)))
8220 (define-public r-arules
8227 (uri (cran-uri "arules" version))
8230 "05g6ik4z87g83nlicmb380331f84sqchvv1vch49zb7rq6v8gw6r"))))
8231 (build-system r-build-system)
8233 (list r-generics r-matrix))
8234 (home-page "https://github.com/mhahsler/arules")
8235 (synopsis "Mining association rules and frequent itemsets")
8237 "This package provides an infrastructure for representing, manipulating
8238 and analyzing transaction data and patterns (frequent itemsets and association rules).
8239 It also provides C implementations of the association mining algorithms Apriori
8241 (license license:gpl3)))
8243 (define-public r-parsedate
8245 (name "r-parsedate")
8250 (uri (cran-uri "parsedate" version))
8253 "1c2cpsvma3fkx6zp191bpfvf5rmpsr13g8rzqk6ycyb0n7b9k4qy"))))
8254 (build-system r-build-system)
8255 (home-page "https://github.com/gaborcsardi/parsedate")
8257 "Recognize and parse dates in various formats")
8259 "This package provides three functions for dealing with dates:
8260 @code{parse_iso_8601} recognizes and parses all valid ISO 8601 date and
8261 time formats, @code{parse_date} parses dates in unspecified formats,
8262 and @code{format_iso_8601} formats a date in ISO 8601 format.")
8263 (license license:gpl2)))
8265 (define-public r-abc-data
8272 (uri (cran-uri "abc.data" version))
8275 "1bv1n68ah714ws58cf285n2s2v5vn7382lfjca4jxph57lyg8hmj"))))
8276 (properties `((upstream-name . "abc.data")))
8277 (build-system r-build-system)
8278 (home-page "https://cran.r-project.org/web/packages/abc.data/")
8279 (synopsis "Data for Approximate Bayesian Computation (ABC) package")
8281 "This package contains data which are used by functions of the abc
8282 package which implements several @dfn{Approximate Bayesian Computation} (ABC)
8283 algorithms for performing parameter estimation, model selection, and
8285 (license license:gpl3+)))
8287 (define-public r-abc
8294 (uri (cran-uri "abc" version))
8297 "16753lyzk2dfwgdjfyanwacqw3bvrwby52inq4709804labs6lnv"))))
8298 (build-system r-build-system)
8300 (list r-abc-data r-locfit r-mass r-nnet r-quantreg))
8301 (home-page "https://cran.r-project.org/web/packages/abc/")
8302 (synopsis "Tools for Approximate Bayesian Computation (ABC)")
8304 "This package implements several @dfn{Approximate Bayesian
8305 Computation} (ABC) algorithms for performing parameter estimation, model
8306 selection, and goodness-of-fit. Cross-validation tools are also available for
8307 measuring the accuracy of ABC estimates, and to calculate the
8308 misclassification probabilities of different models.")
8309 (license license:gpl3+)))
8311 (define-public r-zip
8318 (uri (cran-uri "zip" version))
8321 "1n5ryjdj3i16b4mdp29wapgaklz3yzas5k8ffx7q6fa0jry9i5cz"))))
8322 (build-system r-build-system)
8323 (home-page "https://github.com/gaborcsardi/zip")
8324 (synopsis "Cross-platform Zip compression")
8326 "This package provides a cross-platform Zip compression library for R.
8327 It is a replacement for the @code{zip} function, that does not require any
8328 additional external tools on any platform.")
8329 (license license:cc0)))
8331 (define-public r-openxlsx
8338 (uri (cran-uri "openxlsx" version))
8341 "0695b265g7jwiqk5c3vmmfkvagx82bkpwhvqzhqaqmmn34l6vl35"))))
8342 (build-system r-build-system)
8344 (list r-rcpp r-stringi r-zip))
8347 (home-page "https://github.com/awalker89/openxlsx")
8348 (synopsis "Read, write and edit XLSX files")
8350 "This package simplifies the creation of Excel @code{.xlsx} files by
8351 providing a high level interface to writing, styling and editing worksheets.
8352 Through the use of Rcpp, read/write times are comparable to the @code{xlsx}
8353 and @code{XLConnect} packages with the added benefit of removing the
8354 dependency on Java.")
8355 (license license:gpl3)))
8357 (define-public r-rio
8364 (uri (cran-uri "rio" version))
8367 "04jlrhyl0791yxwcpp1s8p1hhkljnijlc5iaxpk56h41w63k39lz"))))
8368 (build-system r-build-system)
8379 (home-page "https://github.com/leeper/rio")
8380 (synopsis "Swiss-army knife for data I/O")
8382 "This package provides streamlined data import and export infrastructure
8383 by making assumptions that the user is probably willing to make: @code{import}
8384 and @code{export} determine the data structure from the file extension,
8385 reasonable defaults are used for data import and export (e.g.,
8386 @code{stringsAsFactors=FALSE}), web-based import is natively
8387 supported (including from SSL/HTTPS), compressed files can be read directly
8388 without explicit decompression, and fast import packages are used where
8389 appropriate. An additional convenience function, @code{convert}, provides a
8390 simple method for converting between file types.")
8391 (license license:gpl2)))
8393 (define-public r-maptools
8400 (uri (cran-uri "maptools" version))
8403 "1jgx8iiirj8qhrmh19mkisa35jcql7352dmc7lvwi5vxg3wjbvpk"))))
8404 (build-system r-build-system)
8406 (list r-foreign r-lattice r-sp))
8407 (home-page "https://r-forge.r-project.org/projects/maptools/")
8408 (synopsis "Tools for reading and handling spatial objects")
8410 "This package provides a set of tools for manipulating and reading
8411 geographic data, in particular ESRI Shapefiles. It includes binary access to
8412 GSHHG shoreline files. The package also provides interface wrappers for
8413 exchanging spatial objects with other R packages.")
8414 ;; The C source files from shapelib are released under the Expat license.
8415 ;; The R code is released under GPL version 2 or later.
8416 (license (list license:gpl2+
8419 (define-public r-later
8426 (uri (cran-uri "later" version))
8429 "0acqg29hcm2iq1418b54np7zb5pnr3xzrwc3ijv2pz9wra10ix88"))))
8430 (build-system r-build-system)
8432 (list r-rcpp r-rlang))
8435 (home-page "https://github.com/r-lib/later")
8436 (synopsis "Utilities for delaying function execution")
8438 "This package provides tools to execute arbitrary R or C functions some
8439 time after the current time, after the R execution stack has emptied.")
8440 (license license:gpl2+)))
8442 (define-public r-promises
8449 (uri (cran-uri "promises" version))
8452 "1dy4cbqw17awh4q8m7cy3anaj0n9iynabfzflb1g94cyj0bq4fld"))))
8453 (build-system r-build-system)
8455 (list r-later r-magrittr r-r6 r-rcpp r-rlang))
8458 (home-page "https://rstudio.github.io/promises")
8459 (synopsis "Abstractions for promise-based asynchronous programming")
8461 "This package provides fundamental abstractions for doing asynchronous
8462 programming in R using promises. Asynchronous programming is useful for
8463 allowing a single R process to orchestrate multiple tasks in the background
8464 while also attending to something else. Semantics are similar to JavaScript
8465 promises, but with a syntax that is idiomatic R.")
8466 (license license:expat)))
8468 (define-public r-dosnow
8475 (uri (cran-uri "doSNOW" version))
8478 "1f5v0k2w0b2478p6iqa3hn2lwd1x3rzc348n57nd38ka2vnsnz4i"))))
8479 (properties `((upstream-name . "doSNOW")))
8480 (build-system r-build-system)
8482 (list r-foreach r-iterators r-snow))
8483 (home-page "https://cran.r-project.org/web/packages/doSNOW")
8484 (synopsis "Foreach parallel adaptor for the snow package")
8486 "This package provides a parallel backend for the @code{%dopar%} function
8487 using the @code{snow} package.")
8488 (license license:gpl2)))
8490 (define-public r-fstcore
8497 (uri (cran-uri "fstcore" version))
8499 (base32 "1a5m68n2dqhi3r8wf5jwg4vjvl550c7wypcf5j0xmkvl836yg1lg"))))
8500 (properties `((upstream-name . "fstcore")))
8501 (build-system r-build-system)
8502 (propagated-inputs (list r-rcpp))
8503 (inputs (list zlib))
8504 (native-inputs (list pkg-config))
8505 (home-page "https://www.fstpackage.org/fstcore/")
8506 (synopsis "R bindings to the fstlib library")
8508 "The fstlib library provides multithreaded serialization of compressed
8509 data frames using the fst format. The fst format allows for random access of
8510 stored data and compression with the LZ4 and ZSTD compressors.")
8511 (license license:mpl2.0)))
8513 (define-public r-fst
8520 (uri (cran-uri "fst" version))
8523 "0r96inwrr960m7wmc80603bw2vvvwab225bh9dq3lalwhy4yiis4"))))
8524 (properties `((upstream-name . "fst")))
8525 (build-system r-build-system)
8526 (propagated-inputs (list r-fstcore r-rcpp))
8527 (home-page "http://www.fstpackage.org")
8528 (synopsis "Fast serialization of data frames")
8530 "The fst package for R provides a fast, easy and flexible way to
8531 serialize data frames. With access speeds of multiple GB/s, fst is
8532 specifically designed to unlock the potential of high speed solid state disks.
8533 Data frames stored in the fst format have full random access, both in column
8534 and rows. The fst format allows for random access of stored data and
8535 compression with the LZ4 and ZSTD compressors.")
8536 (license license:agpl3)))
8538 (define-public r-snowfall
8541 (version "1.84-6.1")
8544 (uri (cran-uri "snowfall" version))
8546 (base32 "13941rlw1jsdjsndp1plzj1cq5aqravizkrqn6l25r9im7rnsi2w"))))
8547 (build-system r-build-system)
8550 (home-page "https://cran.r-project.org/web/packages/snowfall/")
8551 (synopsis "Easier cluster computing")
8552 (description "This package is a usability wrapper around snow for easier
8553 development of parallel R programs. This package offers e.g. extended error
8554 checks, and additional functions. All functions work in sequential mode, too,
8555 if no cluster is present or wished. The package is also designed as connector
8556 to the cluster management tool @code{sfCluster}, but can also used without
8558 (license license:gpl2+)))
8560 (define-public r-rgexf
8567 (uri (cran-uri "rgexf" version))
8570 "00c2zka1n3k7p1l0mlchr063s6x58p9r3fb64d4wgl4rvsq55q3f"))
8571 ;; Delete minified JavaScript files
8573 '(for-each delete-file
8574 '("inst/gexf-js/js/jquery-2.0.2.min.js"
8575 "inst/gexf-js/js/jquery-ui-1.10.3.custom.min.js"
8576 "inst/gexf-js/js/jquery.mousewheel.min.js")))))
8577 (properties `((upstream-name . "rgexf")))
8578 (build-system r-build-system)
8580 `(#:modules ((guix build utils)
8581 (guix build r-build-system)
8585 (modify-phases %standard-phases
8586 (add-after 'unpack 'process-javascript
8587 (lambda* (#:key inputs #:allow-other-keys)
8588 (invoke "unzip" "-d" "/tmp" (assoc-ref inputs "js-jquery-ui"))
8589 (with-directory-excursion "inst/gexf-js/js/"
8593 `((,(assoc-ref inputs "js-jquery")
8594 "jquery-2.0.2.min.js")
8595 ("/tmp/jquery-ui-1.10.3/ui/jquery-ui.js"
8596 "jquery-ui-1.10.3.custom.min.js")
8597 (,(assoc-ref inputs "js-jquery-mousewheel")
8598 "jquery.mousewheel.min.js"))))
8599 (lambda (sources targets)
8600 (for-each (lambda (source target)
8601 (format #true "Processing ~a --> ~a~%"
8603 (invoke "esbuild" source "--minify"
8604 (string-append "--outfile=" target)))
8605 sources targets)))))))))
8607 (list r-igraph r-servr r-xml))
8609 `(("r-knitr" ,r-knitr)
8610 ("esbuild" ,esbuild)
8615 (uri "https://code.jquery.com/jquery-2.0.2.js")
8618 "0v818bxpw48gdk8i95qqqij80r9jcgisi2r4ac6xnxca20h0gvfj"))))
8622 (uri "https://jqueryui.com/resources/download/jquery-ui-1.10.3.zip")
8625 "00xpfy0l69nj2yan4s8k65ldsrlfsjkmyw2dwcg93dc8mv454vxx"))))
8626 ("js-jquery-mousewheel"
8629 (uri "https://raw.githubusercontent.com/jquery/jquery-mousewheel/\
8630 3.0.6/jquery.mousewheel.js")
8633 "19lk5xy2s47bx8hsa7j6bg012f8yw6d770g230bcnm559kf4nc6v"))))))
8634 (home-page "https://gvegayon.github.io/rgexf")
8635 (synopsis "Build, import and export GEXF graph files")
8637 "Create, read and write GEXF (Graph Exchange XML Format) graph
8638 files (used in Gephi and others). It allows the user to easily build/read
8639 graph files including attributes, GEXF visual attributes (such as color, size,
8640 and position), network dynamics (for both edges and nodes) and edge weighting.
8641 Users can build/handle graphs element-by-element or massively through
8642 data-frames, visualize the graph on a web browser through gexf-js (a
8643 JavaScript library) and interact with the igraph package.")
8644 (license license:expat)))
8646 (define-public r-data-tree
8648 (name "r-data-tree")
8653 (uri (cran-uri "data.tree" version))
8656 "0pizmx2312zsym4m42b97q2184bg3hibvbdrblcga05xln84qrs0"))))
8657 (properties `((upstream-name . "data.tree")))
8658 (build-system r-build-system)
8660 (list r-r6 r-stringi))
8663 (home-page "https://github.com/gluc/data.tree")
8664 (synopsis "General purpose hierarchical data structure")
8666 "Create tree structures from hierarchical data, and traverse the tree in
8667 various orders. Aggregate, cumulate, print, plot, convert to and from
8668 data.frame and more. This is useful for decision trees, machine learning,
8669 finance, conversion from and to JSON, and many other applications.")
8670 (license license:gpl2+)))
8672 (define-public r-dtplyr
8679 (uri (cran-uri "dtplyr" version))
8682 "1wyhhn16mvdj55k2xsh7vy489l7xk4mkz7pjrw16z87awk6yjh16"))))
8683 (properties `((upstream-name . "dtplyr")))
8684 (build-system r-build-system)
8698 (home-page "https://github.com/tidyverse/dtplyr")
8699 (synopsis "Data Table back-end for dplyr")
8701 "This package provides a @code{data.table} backend for @code{dplyr}. The
8702 goal of @code{dtplyr} is to allow you to write @code{dplyr} code that is
8703 automatically translated to the equivalent, but usually much faster,
8704 @code{data.table} code.")
8705 (license license:expat)))
8707 (define-public r-collapsibletree
8709 (name "r-collapsibletree")
8714 (uri (cran-uri "collapsibleTree" version))
8717 "0b65pbp1wnpsrayqi630ds4r98jvcvynnlp6wxdqrnnr9nzw5343"))
8720 ;; Delete minified JavaScript file
8721 (delete-file "inst/htmlwidgets/lib/d3-4.10.2/d3.min.js")
8724 `((upstream-name . "collapsibleTree")))
8725 (build-system r-build-system)
8728 (modify-phases %standard-phases
8729 (add-after 'unpack 'process-javascript
8730 (lambda* (#:key inputs #:allow-other-keys)
8731 (with-directory-excursion "inst/htmlwidgets/lib/d3-4.10.2/"
8732 (let ((source (assoc-ref inputs "d3.v4.js"))
8733 (target "d3.min.js"))
8734 (format #t "Processing ~a --> ~a~%"
8736 (invoke "esbuild" source "--minify"
8737 (string-append "--outfile=" target)))))))))
8739 (list r-data-tree r-htmlwidgets))
8741 `(("esbuild" ,esbuild)
8745 (uri "https://d3js.org/d3.v4.js")
8748 "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg"))))))
8749 (home-page "https://github.com/AdeelK93/collapsibleTree")
8750 (synopsis "Interactive collapsible tree diagrams using D3.js")
8752 "This is a package for interactive Reingold-Tilford tree diagrams created
8753 using D3.js, where every node can be expanded and collapsed by clicking on it.
8754 Tooltips and color gradients can be mapped to nodes using a numeric column in
8755 the source data frame.")
8756 (license license:gpl3+)))
8758 (define-public r-rappdirs
8765 (uri (cran-uri "rappdirs" version))
8768 "1161i3jgjvzjv4p8qbz9r976fnggkcrw3mlj4yd1h2svnijrz5a9"))))
8769 (build-system r-build-system)
8770 (home-page "https://cran.r-project.org/web/packages/rappdirs/")
8771 (synopsis "Determine where to save data, caches, and logs")
8773 "This package provides an easy way to determine which directories on the
8774 user's computer should be used to save data, caches and logs. It is a port of
8775 Python's @url{https://github.com/ActiveState/appdirs,Appdirs} to R.")
8776 (license license:expat)))
8778 (define-public r-rastervis
8780 (name "r-rastervis")
8785 (uri (cran-uri "rasterVis" version))
8788 "0kgg6cm7xjqya2d46w0i1i1wjpkb8f99lyqy7rgwa7l9xmwzj5n1"))))
8789 (properties `((upstream-name . "rasterVis")))
8790 (build-system r-build-system)
8801 (home-page "https://oscarperpinan.github.io/rastervis/")
8802 (synopsis "Visualization methods for raster data")
8804 "This package provides methods for enhanced visualization and interaction
8805 with raster data. It implements visualization methods for quantitative data
8806 and categorical data, both for univariate and multivariate rasters. It also
8807 provides methods to display spatiotemporal rasters, and vector fields.")
8808 (license license:gpl3)))
8810 (define-public r-rentrez
8817 (uri (cran-uri "rentrez" version))
8820 "0x1g2f6hvkqqlb39z8m5qxhcvsizddic5i7rpqw0wy77xfbna9gv"))))
8821 (properties `((upstream-name . "rentrez")))
8822 (build-system r-build-system)
8824 (list r-httr r-jsonlite r-xml))
8827 (home-page "https://docs.ropensci.org/rentrez/")
8828 (synopsis "Entrez in R")
8830 "This package provides an R interface to the NCBI's EUtils API,
8831 allowing users to search databases like GenBank PubMed, process the results of
8832 those searches and pull data into their R sessions.")
8833 (license license:expat)))
8835 (define-public r-renv
8842 (uri (cran-uri "renv" version))
8845 "0bjq3ms5dg155clya62m462m93g90sxfxm7b4cqhqbx8vakskwdl"))))
8846 (properties `((upstream-name . "renv")))
8847 (build-system r-build-system)
8850 (home-page "https://rstudio.github.io/renv")
8851 (synopsis "Project environments")
8853 "This package provides a dependency management toolkit for R. Using
8854 renv, you can create and manage project-local R libraries, save the state of
8855 these libraries to a lockfile, and later restore your library as required.
8856 Together, these tools can help make your projects more isolated, portable, and
8858 (license license:expat)))
8860 (define-public r-learnr
8867 (uri (cran-uri "learnr" version))
8870 "08xwmms6x58y3dsfbl9c6d03145hb4ij97nqr1cc9dxxilmr6x31"))))
8871 (build-system r-build-system)
8887 (home-page "https://rstudio.github.io/learnr/")
8888 (synopsis "Interactive tutorials for R")
8890 "This package provides tools to create interactive tutorials using R
8891 Markdown. Use a combination of narrative, figures, videos, exercises, and
8892 quizzes to create self-paced tutorials for learning about R and R packages.")
8893 (license license:asl2.0)))
8895 (define-public r-analytics
8897 (name "r-analytics")
8902 (uri (cran-uri "analytics" version))
8905 "0js3c8lwj3knccb55nq03cbjlf4w390p9aid2mi5x80l3ayd9in1"))))
8906 (build-system r-build-system)
8920 (home-page "https://cran.r-project.org/web/packages/analytics/")
8921 (synopsis "Collection of data analysis tools")
8923 "This package is a collection of data analysis tools. It includes tools
8924 for regression outlier detection in a fitted linear model, stationary
8925 bootstrap using a truncated geometric distribution, a comprehensive test for
8926 weak stationarity, column means by group, weighted biplots, and a heuristic to
8927 obtain a better initial configuration in non-metric MDS.")
8928 (license license:gpl2)))
8930 (define-public r-here
8937 (uri (cran-uri "here" version))
8939 (base32 "0srlr8h8qmr0wrmp7gs4g2ry5dni2hx8n947bik3s3a26f091v88"))))
8940 (properties `((upstream-name . "here")))
8941 (build-system r-build-system)
8942 (propagated-inputs (list r-rprojroot))
8943 (native-inputs (list r-knitr))
8944 (home-page "https://here.r-lib.org/")
8945 (synopsis "Simpler way to find files")
8947 "This package lets you construct paths to your project's files. Use the
8948 @code{here} function as a drop-in replacement for @code{file.path}, it will
8949 always locate the files relative to your project root.")
8950 (license license:expat)))
8952 (define-public r-reticulate
8954 (name "r-reticulate")
8959 (uri (cran-uri "reticulate" version))
8962 "0b1szzsqyc8wcfpkn5517bb1ds064vs2hky71my3p74kfngay991"))))
8963 (build-system r-build-system)
8964 (inputs (list python))
8976 (home-page "https://github.com/rstudio/reticulate")
8977 (synopsis "R interface to Python")
8979 "This package provides an interface from R to Python modules, classes,
8980 and functions. When calling into Python, R data types are automatically
8981 converted to their equivalent Python types. When values are returned from
8982 Python to R they are converted back to R types.")
8983 (license license:asl2.0)))
8985 (define-public r-bibtex
8992 (uri (cran-uri "bibtex" version))
8995 "0vdwx6808r73pk15263f33bkqbfmb08d8jkmr4d7h4ml414ikbbv"))))
8996 (build-system r-build-system)
8997 (propagated-inputs (list r-stringr))
8998 (home-page "https://github.com/romainfrancois/bibtex")
8999 (synopsis "Bibtex parser")
9000 (description "This package provides a utility for R to parse a bibtex
9002 (license license:gpl2+)))
9004 (define-public r-billboarder
9006 (name "r-billboarder")
9011 (uri (cran-uri "billboarder" version))
9013 (base32 "189ngvg84rcwhrivxskmjv3srhadvzr4p1v8pf11axyv2qn01b0x"))
9015 '(delete-file "inst/htmlwidgets/lib/billboard/billboard.pkgd.min.js"))))
9016 (properties `((upstream-name . "billboarder")))
9017 (build-system r-build-system)
9020 (modify-phases %standard-phases
9021 (add-after 'unpack 'process-javascript
9022 (lambda* (#:key inputs #:allow-other-keys)
9023 (with-directory-excursion "inst/htmlwidgets/lib/billboard/"
9024 (let ((source (assoc-ref inputs "js-billboard"))
9025 (target "billboard.pkgd.min.js"))
9026 (format #true "Processing ~a --> ~a~%"
9028 (invoke "esbuild" source "--minify"
9029 (string-append "--outfile=" target)))))))))
9040 `(("r-knitr" ,r-knitr)
9041 ("esbuild" ,esbuild)
9042 ;; It is not ideal to use this concatenated (but not minified)
9043 ;; JavaScript file, as the original source is written in TypeScript.
9044 ;; However, this can still be considered source code as it is readable
9045 ;; and can be modified.
9049 (uri "https://unpkg.com/billboard.js@3.2.0/dist/billboard.js")
9052 "1kx5rqmn87pgal2cwmcij2rrnwa0fgcsw6y99m4i0l2sdm0qffv2"))))))
9053 (home-page "https://github.com/dreamRs/billboarder")
9054 (synopsis "Create interactive charts with the JavaScript Billboard library")
9056 "This package provides an @code{htmlwidgets} interface to billboard.js,
9057 a re-usable easy interface JavaScript chart library, based on D3 v4+. Chart
9058 types include line charts, scatterplots, bar/lollipop charts,
9059 histogram/density plots, pie/donut charts and gauge charts. All charts are
9060 interactive, and a proxy method is implemented to smoothly update a chart
9061 without rendering it again in shiny apps.")
9062 (license license:expat)))
9064 (define-public r-ggseqlogo
9066 (name "r-ggseqlogo")
9071 (uri (cran-uri "ggseqlogo" version))
9074 "13q6kcpxrqxqbji889fx63p0nsi08lk5yymkchig75r5k1d18ky1"))))
9075 (build-system r-build-system)
9076 (propagated-inputs (list r-ggplot2))
9077 (home-page "https://github.com/omarwagih/ggseqlogo")
9078 (synopsis "ggplot2 extension for drawing genetic sequence logos")
9080 "The range of functions provided by this package makes it possible to
9081 draw highly versatile genomic sequence logos. Features include, but are not
9082 limited to, modifying colour schemes and fonts used to draw the logo,
9083 generating multiple logo plots, and aiding the visualisation with annotations.
9084 Sequence logos can easily be combined with other ggplot2 plots.")
9085 ;; Unspecified version of the LGPL.
9086 (license license:lgpl3+)))
9088 (define-public r-ggsci
9095 (uri (cran-uri "ggsci" version))
9098 "0g73x6grbka7ahjh6z23m3wrcifp5rdfdiasbl8lq4sp6rplxwaa"))))
9099 (build-system r-build-system)
9101 (list r-ggplot2 r-scales))
9102 (home-page "https://nanx.me/ggsci/")
9103 (synopsis "Scientific journal and sci-fi themed color palettes for ggplot2")
9105 "This package provides a collection of ggplot2 color palettes inspired by
9106 plots in scientific journals, data visualization libraries, science fiction
9107 movies, and TV shows.")
9108 (license license:gpl3)))
9110 (define-public r-ggsignif
9117 (uri (cran-uri "ggsignif" version))
9120 "1ad774c7s7y4i00xd89lfigr9aybl94q98ch598k3rchanr4b1fa"))))
9121 (build-system r-build-system)
9126 (home-page "https://github.com/const-ae/ggsignif")
9127 (synopsis "Significance brackets for ggplot2")
9129 "Enrich your ggplots with group-wise comparisons. This package provides
9130 an easy way to indicate if two groups are significantly different. Commonly
9131 this is shown by a bracket on top connecting the groups of interest which
9132 itself is annotated with the level of significance. The package provides a
9133 single layer that takes the groups for comparison and the test as arguments
9134 and adds the annotation to the plot.")
9135 (license license:gpl3)))
9137 (define-public r-rstatix
9144 (uri (cran-uri "rstatix" version))
9147 "0330y8iziffqg8j9j5h9zv4qcdyf8ybhmzxrr9fzq9nc6bf1gbm5"))))
9148 (properties `((upstream-name . "rstatix")))
9149 (build-system r-build-system)
9162 (home-page "https://rpkgs.datanovia.com/rstatix/")
9163 (synopsis "Pipe-friendly framework for basic statistical tests")
9165 "This package provides a simple and intuitive pipe-friendly framework,
9166 coherent with the @code{tidyverse} design philosophy, for performing basic
9167 statistical tests, including t-test, Wilcoxon test, ANOVA, Kruskal-Wallis and
9168 correlation analyses. The output of each test is automatically transformed
9169 into a tidy data frame to facilitate visualization. Additional functions are
9170 available for reshaping, reordering, manipulating and visualizing correlation
9172 (license license:gpl2)))
9174 (define-public r-ggpubr
9181 (uri (cran-uri "ggpubr" version))
9184 "0x86lmghr25k8w90yrp360dn42dhp5cjvjpdiv2s2gxfn701xcmb"))))
9185 (build-system r-build-system)
9203 (home-page "http://www.sthda.com/english/rpkgs/ggpubr")
9204 (synopsis "ggplot2-based publication-ready plots")
9206 "The ggplot2 package is an excellent and flexible package for elegant
9207 data visualization in R. However the default generated plots require some
9208 formatting before we can send them for publication. The ggpubr package
9209 provides some easy-to-use functions for creating and customizing ggplot2-based
9210 publication-ready plots.")
9211 (license license:gpl2)))
9213 (define-public r-ellipse
9220 (uri (cran-uri "ellipse" version))
9223 "1wm5v7zdv2drgdba7z96jwsx74mqhlq80qgrvdb4vb5r02dcw68p"))))
9224 (build-system r-build-system)
9225 (home-page "https://cran.r-project.org/web/packages/ellipse/")
9226 (synopsis "Functions for drawing ellipses and ellipse-like confidence regions")
9228 "This package contains various routines for drawing ellipses and
9229 ellipse-like confidence regions, implementing the plots described in Murdoch
9230 and Chow (1996), A graphical display of large correlation matrices, The
9231 American Statistician 50, 178-180. There are also routines implementing the
9232 profile plots described in Bates and Watts (1988), Nonlinear Regression
9233 Analysis and its Applications.")
9234 (license license:gpl2+)))
9236 (define-public r-flashclust
9238 (name "r-flashclust")
9243 (uri (cran-uri "flashClust" version))
9246 "0l4lpz451ll7f7lfxmb7ds24ppzhfg1c3ypvydglcc35p2dq99s8"))))
9247 (properties `((upstream-name . "flashClust")))
9248 (build-system r-build-system)
9249 (native-inputs (list gfortran))
9250 (home-page "https://cran.r-project.org/web/packages/flashClust/")
9251 (synopsis "Implementation of optimal hierarchical clustering")
9253 "This package provides a fast implementation of hierarchical
9255 (license license:gpl2+)))
9257 (define-public r-factominer
9259 (name "r-factominer")
9264 (uri (cran-uri "FactoMineR" version))
9267 "0lg8n9fxxk46nchnj4pbpqqf4swxfsq7r9jzr36dmd36kb7avqxr"))))
9268 (properties `((upstream-name . "FactoMineR")))
9269 (build-system r-build-system)
9284 (home-page "http://factominer.free.fr")
9285 (synopsis "Multivariate exploratory data analysis and data mining")
9287 "This package provides exploratory data analysis methods to summarize,
9288 visualize and describe datasets. The main principal component methods are
9289 available, those with the largest potential in terms of applications:
9290 principal component analysis (PCA) when variables are quantitative,
9291 correspondence analysis (CA) and multiple correspondence analysis (MCA) when
9292 variables are categorical, Multiple Factor Analysis when variables are
9293 structured in groups, etc. and hierarchical cluster analysis.")
9294 (license license:gpl2+)))
9296 (define-public r-factoextra
9298 (name "r-factoextra")
9303 (uri (cran-uri "factoextra" version))
9306 "1allvdjhd3pq8xz30b1cymwcik5iaahghrjrlnn54cwkfhfg0kv2"))))
9307 (build-system r-build-system)
9318 (home-page "http://www.sthda.com/english/rpkgs/factoextra")
9319 (synopsis "Extract and visualize the results of multivariate data analyses")
9321 "This package provides some easy-to-use functions to extract and
9322 visualize the output of multivariate data analyses, including
9323 @code{PCA} (Principal Component Analysis), @code{CA} (Correspondence
9324 Analysis), @code{MCA} (Multiple Correspondence Analysis), @code{FAMD} (Factor
9325 Analysis of Mixed Data), @code{MFA} (Multiple Factor Analysis) and
9326 @code{HMFA} (Hierarchical Multiple Factor Analysis) functions from different R
9327 packages. It contains also functions for simplifying some clustering analysis
9328 steps and provides ggplot2-based elegant data visualization.")
9329 (license license:gpl2)))
9331 (define-public r-fansi
9338 (uri (cran-uri "fansi" version))
9341 "0sn0kflgcn2qrrv646pzqylm02cx8l5ws473ppmvla4xihyvi9w6"))))
9342 (build-system r-build-system)
9344 (list r-knitr)) ; for vignettes
9345 (home-page "https://github.com/brodieG/fansi")
9346 (synopsis "ANSI control sequence aware string functions")
9348 "This package provides counterparts to R string manipulation functions
9349 that account for the effects of ANSI text formatting control sequences.")
9350 (license license:gpl2+)))
9352 (define-public r-nbclust
9359 (uri (cran-uri "NbClust" version))
9362 "0k5hr4zgx4gp1n62xchgz2zvyl35ba2cnczhhvj8rfbg2n4hx6qs"))))
9363 (properties `((upstream-name . "NbClust")))
9364 (build-system r-build-system)
9365 (home-page "https://sites.google.com/site/malikacharrad/research/nbclust-package")
9366 (synopsis "Determine the best number of clusters in a data set")
9368 "NbClust provides 30 indexes for determining the optimal number of
9369 clusters in a data set and offers the best clustering scheme from different
9370 results to the user.")
9371 (license license:gpl2)))
9373 (define-public r-hdf5r
9380 (uri (cran-uri "hdf5r" version))
9383 "0bv2q4ir73sbk5ra2q4mc8wbcmiwkws8k0mjlnx9ysi2mdrm3dw7"))))
9384 (build-system r-build-system)
9388 (list r-bit64 r-r6))
9391 (home-page "https://hhoeflin.github.io/hdf5r")
9392 (synopsis "Interface to the HDF5 binary data format")
9394 "HDF5 is a data model, library and file format for storing and managing
9395 large amounts of data. This package provides a nearly feature complete,
9396 object oriented wrapper for the HDF5 API using R6 classes. Additionally,
9397 functionality is added so that HDF5 objects behave very similar to their
9398 corresponding R counterparts.")
9399 (license license:asl2.0)))
9401 (define-public r-itertools
9403 (name "r-itertools")
9408 (uri (cran-uri "itertools" version))
9411 "1ls5biiva10pb1dj3ph4griykb9vam02hkrdmlr5a5wf660hg6xn"))))
9412 (build-system r-build-system)
9415 (home-page "https://cran.r-project.org/web/packages/itertools/")
9416 (synopsis "Iterator tools")
9418 "This package provides various tools for creating iterators, many
9419 patterned after functions in the Python @code{itertools} module, and others
9420 patterned after functions in the snow package.")
9421 (license license:gpl2)))
9423 (define-public r-itsadug
9430 (uri (cran-uri "itsadug" version))
9432 (base32 "0759l7hhvj05dp92pz59xwrxjm9s1iwkwrdhs68l0fq57550j70l"))))
9433 (properties `((upstream-name . "itsadug")))
9434 (build-system r-build-system)
9435 (propagated-inputs (list r-mgcv r-plotfunctions))
9436 (native-inputs (list r-knitr))
9437 (home-page "https://cran.r-project.org/package=itsadug")
9438 (synopsis "Interpreting time series and autocorrelated data using GAMMs")
9440 "@dfn{Generalized Additive Mixed Modeling} (GAMM; Lin & Zhang, 1999) as
9441 implemented in the R package @code{mgcv} is a nonlinear regression analysis
9442 which is particularly useful for time course data such as EEG, pupil dilation,
9443 gaze data (eye tracking), and articulography recordings, but also for
9444 behavioral data such as reaction times and response data. As time course
9445 measures are sensitive to autocorrelation problems, GAMMs implements methods
9446 to reduce the autocorrelation problems. This package includes functions for
9447 the evaluation of GAMM models (e.g., model comparisons, determining regions of
9448 significance, inspection of autocorrelational structure in residuals) and
9449 interpreting of GAMMs (e.g., visualization of complex interactions, and
9451 (license license:gpl2+)))
9453 (define-public r-polynom
9460 (uri (cran-uri "polynom" version))
9463 "0y4j07syjwpnq5w6a1d90z6h1hjzijmm42pq0f8jk2vcn5xxn7mw"))))
9464 (build-system r-build-system)
9465 (native-inputs (list r-knitr))
9466 (home-page "https://cran.r-project.org/web/packages/polynom/")
9467 (synopsis "Functions for univariate polynomial manipulations")
9469 "This package provides a collection of functions to implement a class for
9470 univariate polynomial manipulations.")
9471 (license license:gpl2)))
9473 (define-public r-pupillometryr
9475 (name "r-pupillometryr")
9480 (uri (cran-uri "PupillometryR" version))
9482 (base32 "0yk30sgl2qqa6pva649swq523vh446ifmydildycfvfmlm1h4qza"))))
9483 (properties `((upstream-name . "PupillometryR")))
9484 (build-system r-build-system)
9497 (native-inputs (list r-knitr))
9498 (home-page "https://cran.r-project.org/package=PupillometryR")
9499 (synopsis "Unified pipeline for pupillometry data")
9501 "This package provides a unified pipeline to clean, prepare, plot, and
9502 run basic analyses on pupillometry experiments.")
9503 (license license:expat)))
9505 (define-public r-gbrd
9512 (uri (cran-uri "gbRd" version))
9515 "06x97rw5i6v6cgjxkfhxnw4dn7lghn5q6ra7ri5ag1x9dkfzcl82"))))
9516 (properties `((upstream-name . "gbRd")))
9517 (build-system r-build-system)
9518 (home-page "https://cran.r-project.org/web/packages/gbRd/")
9519 (synopsis "Utilities for processing Rd objects and files")
9521 "This package provides utilities for processing Rd objects and files.
9522 Extract argument descriptions and other parts of the help pages of
9524 (license license:gpl2+)))
9526 (define-public r-rjags
9533 (uri (cran-uri "rjags" version))
9536 "0cibz6xhmh86fh7ynmdgpmlchizi57pi6dpslgc2if17a56c6p7q"))))
9537 (build-system r-build-system)
9544 (home-page "http://mcmc-jags.sourceforge.net")
9545 (synopsis "Bayesian graphical models using MCMC")
9547 "This package provides an R interface to the JAGS MCMC library. JAGS is
9548 Just Another Gibbs Sampler. It is a program for analysis of Bayesian
9549 hierarchical models using Markov Chain Monte Carlo (MCMC) simulation.")
9550 (license license:gpl2)))
9552 (define-public r-rbibutils
9554 (name "r-rbibutils")
9559 (uri (cran-uri "rbibutils" version))
9562 "0lnia2fk8zlvkkgnl7r7dyi1ip5vqlw448qrvqs2s14rpbpcvbpi"))))
9563 (properties `((upstream-name . "rbibutils")))
9564 (build-system r-build-system)
9565 (home-page "https://geobosh.github.io/rbibutils/")
9566 (synopsis "Convert between bibliography formats")
9568 "This package converts between a number of bibliography formats,
9569 including BibTeX, BibLaTeX and Bibentry. It includes a port of the bibutils
9570 utilities and supports all bibliography formats and character encodings
9571 implemented in bibutils.")
9572 (license license:gpl2)))
9574 (define-public r-rdpack
9581 (uri (cran-uri "Rdpack" version))
9584 "1igpa4hnpiykbdnq57mglby5jsbind6izkkfy81wx4ib6nw1lpn4"))))
9585 (properties `((upstream-name . "Rdpack")))
9586 (build-system r-build-system)
9589 (home-page "https://github.com/GeoBosh/Rdpack")
9590 (synopsis "Update and manipulate Rd documentation objects")
9592 "This package provides functions for manipulation of R documentation
9593 objects, including functions @code{reprompt()} and @code{ereprompt()} for
9594 updating Rd documentation for functions, methods and classes; it also includes
9595 Rd macros for citations and import of references from bibtex files for use in
9596 Rd files and roxygen2 comments, as well as many functions for manipulation of
9597 references and Rd files.")
9598 (license license:gpl2+)))
9600 (define-public r-officer
9607 (uri (cran-uri "officer" version))
9610 "0qmn62srh9zicgizyblanirbdva7f09g967yb86kfrn05ckh5y10"))))
9611 (build-system r-build-system)
9613 (list r-r6 r-uuid r-xml2 r-zip))
9614 (home-page "https://davidgohel.github.io/officer")
9615 (synopsis "Manipulation of Word and PowerPoint documents")
9617 "This package provides tools to access and manipulate Word and PowerPoint
9618 documents from R. The package focuses on tabular and graphical reporting from
9619 R; it also provides two functions that let users get document content into
9620 data objects. A set of functions lets add and remove images, tables and
9621 paragraphs of text in new or existing documents. When working with PowerPoint
9622 presentations, slides can be added or removed; shapes inside slides can also
9623 be added or removed. When working with Word documents, a cursor can be used
9624 to help insert or delete content at a specific location in the document.")
9625 (license license:gpl3)))
9627 (define-public r-profilemodel
9629 (name "r-profilemodel")
9634 (uri (cran-uri "profileModel" version))
9637 "01m5nb8cmq0aq555pxk2a99182si65hhmn68yn9nal2j3zl2bp4i"))))
9638 (properties `((upstream-name . "profileModel")))
9639 (build-system r-build-system)
9640 (home-page "https://github.com/ikosmidis/profileModel")
9641 (synopsis "Profiling inference functions for various model classes")
9643 "This package provides tools that can be used to calculate, evaluate,
9644 plot and use for inference the profiles of *arbitrary* inference functions for
9645 arbitrary @code{glm}-like fitted models with linear predictors. More information
9646 on the methods that are implemented can be found in Kosmidis (2008)
9647 @url{https://www.r-project.org/doc/Rnews/Rnews_2008-2.pdf}.")
9648 (license license:gpl2+)))
9650 (define-public r-brglm
9657 (uri (cran-uri "brglm" version))
9660 "08shcz0j1npdn7xkhsvlzs3z4rdwq3g4rk6a4xx8wirqw8n8s2an"))))
9661 (properties `((upstream-name . "brglm")))
9662 (build-system r-build-system)
9664 (list r-profilemodel))
9665 (home-page "https://github.com/ikosmidis/brglm")
9666 (synopsis "Bias reduction in binomial-response generalized linear models")
9668 "Fit generalized linear models with binomial responses using either an
9669 adjusted-score approach to bias reduction or maximum penalized likelihood
9670 where penalization is by Jeffreys invariant prior. These procedures return
9671 estimates with improved frequentist properties (bias, mean squared error) that
9672 are always finite even in cases where the maximum likelihood estimates are
9673 infinite (data separation). Fitting takes place by fitting generalized linear
9674 models on iteratively updated pseudo-data. The interface is essentially the
9675 same as @code{glm}. More flexibility is provided by the fact that custom
9676 pseudo-data representations can be specified and used for model fitting.
9677 Functions are provided for the construction of confidence intervals for the
9678 reduced-bias estimates.")
9679 (license license:gpl2+)))
9681 (define-public r-entropy
9688 (uri (cran-uri "entropy" version))
9691 "1f0j8jsn6pzf4gi5g0akixx6x5vc69ci5f4m2vnwp40frvsqjnkg"))))
9692 (properties `((upstream-name . "entropy")))
9693 (build-system r-build-system)
9694 (home-page "https://www.strimmerlab.org/software/entropy/")
9695 (synopsis "Estimation of entropy, mutual information and related quantities")
9697 "This package implements various estimators of entropy, such as the
9698 shrinkage estimator by Hausser and Strimmer, the maximum likelihood and the
9699 Millow-Madow estimator, various Bayesian estimators, and the Chao-Shen
9700 estimator. It also offers an R interface to the NSB estimator. Furthermore,
9701 it provides functions for estimating Kullback-Leibler divergence, chi-squared,
9702 mutual information, and chi-squared statistic of independence. In addition
9703 there are functions for discretizing continuous random variables.")
9704 (license license:gpl3+)))
9706 (define-public r-acd
9713 (uri (cran-uri "ACD" version))
9716 "1a67bi3hklq8nlc50r0qnyr4k7m9kpvijy8sqqpm54by5hsysfd6"))))
9717 (properties `((upstream-name . "ACD")))
9718 (build-system r-build-system)
9719 (home-page "https://cran.r-project.org/web/packages/ACD/")
9720 (synopsis "Categorical data analysis with complete or missing responses")
9722 "This package provides tools for categorical data analysis with complete
9723 or missing responses.")
9724 (license license:gpl2+)))
9726 (define-public r-acdm
9733 (uri (cran-uri "ACDm" version))
9736 "0b4f02ga5ra66mbrm79g0bnlzmii82rks9kmxixxqgf18yhlyjil"))))
9737 (properties `((upstream-name . "ACDm")))
9738 (build-system r-build-system)
9740 (list r-dplyr r-ggplot2 r-plyr r-rsolnp r-zoo))
9741 (home-page "https://cran.r-project.org/web/packages/ACDm/")
9742 (synopsis "Tools for Autoregressive Conditional Duration Models")
9744 "ACDm is a package for Autoregressive Conditional Duration (ACD, Engle
9745 and Russell, 1998) models. It creates trade, price or volume durations from
9746 transactions (tic) data, performs diurnal adjustments, fits various ACD models
9748 (license license:gpl2+)))
9750 (define-public r-overlap
9757 (uri (cran-uri "overlap" version))
9760 "1arxprhz035ab78ks88n6scwnlwmnb97mlac5gsx90ipb6gkgcyk"))))
9761 (build-system r-build-system)
9762 (home-page "https://cran.r-project.org/web/packages/overlap/")
9763 (synopsis "Estimates of coefficient of overlapping for animal activity patterns")
9765 "This package provides functions to fit kernel density functions to data
9766 on temporal activity patterns of animals; estimate coefficients of overlapping
9767 of densities for two species; and calculate bootstrap estimates of confidence
9769 (license license:gpl3+)))
9771 (define-public r-snakecase
9773 (name "r-snakecase")
9778 (uri (cran-uri "snakecase" version))
9781 "1ky1x2cp5rd0ffd9m1fji9sq4z4jsrpxzg30brw8bb4ihfjj114r"))))
9782 (build-system r-build-system)
9784 (list r-stringi r-stringr))
9785 (home-page "https://github.com/Tazinho/snakecase")
9786 (synopsis "Convert strings into any case")
9788 "This package provides a consistent, flexible and easy to use tool to
9789 parse and convert strings into cases like snake or camel among others.")
9790 (license license:gpl3)))
9792 (define-public r-prediction
9794 (name "r-prediction")
9799 (uri (cran-uri "prediction" version))
9802 "0awlq5lxfia6m2b91w73rksp93rbwv5gwqb36wbji4rgq41rzbrx"))))
9803 (build-system r-build-system)
9805 (list r-data-table))
9806 (home-page "https://github.com/leeper/prediction")
9807 (synopsis "Tidy, type-safe prediction methods")
9809 "This package provides the @code{prediction()} function, a type-safe
9810 alternative to @code{predict()} that always returns a data frame. The package
9811 currently supports common model types (e.g., @code{\"lm\"}, @code{\"glm\"})
9812 from the @code{stats} package, as well as numerous other model classes from
9813 other add-on packages.")
9814 (license license:expat)))
9816 (define-public r-insight
9823 (uri (cran-uri "insight" version))
9826 "0dffrsimgijdqsgvr9cad4g4w97d5ssjl3l0fm5ssly9l115ag35"))))
9827 (build-system r-build-system)
9830 (home-page "https://easystats.github.io/insight/")
9831 (synopsis "Easy access to model information for various model objects")
9833 "This package provides a tool to provide an easy, intuitive and
9834 consistent access to information contained in various R models, like model
9835 formulas, model terms, information about random effects, data that was used to
9836 fit the model or data from response variables. The package mainly revolves
9837 around two types of functions: Functions that find (the names of) information,
9838 starting with @code{find_}, and functions that get the underlying data,
9839 starting with @code{get_}. The package has a consistent syntax and works with
9840 many different model objects, where otherwise functions to access these
9841 information are missing.")
9842 (license license:gpl3)))
9844 (define-public r-sjlabelled
9846 (name "r-sjlabelled")
9851 (uri (cran-uri "sjlabelled" version))
9854 "1va86q5wddyvqgdpy8d0an2c7v1qbb4hpn0ai6y1v5v1ff87w73k"))))
9855 (build-system r-build-system)
9857 (list r-datawizard r-insight))
9860 (home-page "https://github.com/strengejacke/sjlabelled")
9861 (synopsis "Labelled data utility functions")
9863 "This package provides a collection of functions dealing with labelled
9864 data, like reading and writing data between R and other statistical software
9865 packages. This includes easy ways to get, set or change value and variable
9866 label attributes, to convert labelled vectors into factors or numeric (and
9867 vice versa), or to deal with multiple declared missing values.")
9868 (license license:gpl3)))
9870 (define-public r-sjmisc
9877 (uri (cran-uri "sjmisc" version))
9880 "1gzkq95ckxr0vhrzggflzli9hs7zr8c0yym9zn1wf74yrr0mgc3q"))))
9881 (build-system r-build-system)
9892 (home-page "https://github.com/strengejacke/sjmisc")
9893 (synopsis "Data and variable transformation functions")
9895 "This package is a collection of miscellaneous utility functions,
9896 supporting data transformation tasks like recoding, dichotomizing or grouping
9897 variables, setting and replacing missing values. The data transformation
9898 functions also support labelled data, and all integrate seamlessly into a
9899 tidyverse workflow.")
9900 (license license:gpl3)))
9902 (define-public r-nortest
9909 (uri (cran-uri "nortest" version))
9912 "17r0wpz72z9312c70nwi1i1kp1v9fm1h6jg7q5cx1mc1h420m1d3"))))
9913 (build-system r-build-system)
9914 (home-page "https://cran.r-project.org/web/packages/nortest/")
9915 (synopsis "Tests for normality")
9917 "This package provides five omnibus tests for testing the composite
9918 hypothesis of normality.")
9919 (license license:gpl2+)))
9921 (define-public r-moonbook
9928 (uri (cran-uri "moonBook" version))
9931 "1ml4vvm0mvrprpyi0l50aw38brx18bk2qny4gybmkvlbakalz9bx"))))
9932 (properties `((upstream-name . "moonBook")))
9933 (build-system r-build-system)
9943 (home-page "https://github.com/cardiomoon/moonBook")
9944 (synopsis "Functions and datasets for the book by Keon-Woong Moon")
9946 "This package provides several analysis-related functions for the book
9947 entitled \"R statistics and graph for medical articles\" (written in Korean),
9948 version 1, by Keon-Woong Moon with Korean demographic data with several plot
9950 (license license:gpl2)))
9952 (define-public r-flextable
9954 (name "r-flextable")
9959 (uri (cran-uri "flextable" version))
9962 "15vr5lb87712mymsvv01kz9s1fb54sx5kybsa2x547k5g10dbrbm"))))
9963 (build-system r-build-system)
9977 (home-page "https://davidgohel.github.io/flextable")
9978 (synopsis "Functions for tabular reporting")
9980 "This package provides tools to create pretty tables for HTML documents
9981 and other formats. Functions are provided to let users create tables, modify
9982 and format their content. It extends the @code{officer} package and can be
9983 used within R markdown documents when rendering to HTML and to Word
9985 (license license:gpl3)))
9987 (define-public r-writexl
9994 (uri (cran-uri "writexl" version))
9997 "0mfzyn8n5x5x5gf382bqgq61zpw9dymrp5kzdm2sbszplmxf6xry"))))
9998 (build-system r-build-system)
9999 (inputs (list zlib))
10000 (home-page "https://github.com/ropensci/writexl")
10001 (synopsis "Export data frames to xlsx format")
10003 "This package provides a data frame to xlsx exporter based on
10005 (license license:bsd-2)))
10007 (define-public r-biasedurn
10009 (name "r-biasedurn")
10014 (uri (cran-uri "BiasedUrn" version))
10017 "13i2lgfnjhlbbm2yxfc2l5hswqw6x03pwba5csjmirv8kpjw4xr3"))))
10018 (properties `((upstream-name . "BiasedUrn")))
10019 (build-system r-build-system)
10020 (home-page "https://cran.r-project.org/web/packages/BiasedUrn/")
10021 (synopsis "Biased Urn model distributions")
10023 "This package provides statistical models of biased sampling in the form
10024 of univariate and multivariate noncentral hypergeometric distributions,
10025 including Wallenius' noncentral hypergeometric distribution and Fisher's
10026 noncentral hypergeometric distribution (also called extended hypergeometric
10028 (license license:gpl3)))
10030 (define-public r-goplot
10037 (uri (cran-uri "GOplot" version))
10040 "1y8dv0kbzpr9za91njw0x233vx5d13vqml9hmpddcyi9s6va5nix"))))
10041 (properties `((upstream-name . "GOplot")))
10042 (build-system r-build-system)
10044 (list r-ggdendro r-ggplot2 r-gridextra r-rcolorbrewer))
10045 (home-page "https://github.com/wencke/wencke.github.io")
10046 (synopsis "Visualization of functional analysis data")
10048 "This package provides an implementation of multilayered visualizations
10049 for enhanced graphical representation of functional analysis data. It
10050 combines and integrates omics data derived from expression and functional
10051 annotation enrichment analyses. Its plotting functions have been developed
10052 with an hierarchical structure in mind: starting from a general overview to
10053 identify the most enriched categories (modified bar plot, bubble plot) to a
10054 more detailed one displaying different types of relevant information for the
10055 molecules in a given set of categories (circle plot, chord plot, cluster plot,
10056 Venn diagram, heatmap).")
10057 (license license:gpl2)))
10059 (define-public r-getopt
10066 (uri (cran-uri "getopt" version))
10069 "0zzmzgwl9a4y3s34600vmih22d6y32294f9bvxrnmffnvkgmy7sk"))))
10070 (build-system r-build-system)
10071 (home-page "https://github.com/trevorld/getopt")
10072 (synopsis "Command-line option processor for R")
10074 "This package is designed to be used with Rscript to write shebang
10075 scripts that accept short and long options. Many users will prefer to
10076 use the packages @code{optparse} or @code{argparse} which add extra
10077 features like automatically generated help options and usage texts,
10078 support for default values, positional argument support, etc.")
10079 (license license:gpl2+)))
10081 (define-public r-findpython
10083 (name "r-findpython")
10088 (uri (cran-uri "findpython" version))
10091 "0jf10jpqla90x03kl3k77gnd255zmw9rvr8d724vb17cqawh9yar"))))
10092 (build-system r-build-system)
10093 (home-page "https://github.com/trevorld/findpython")
10094 (synopsis "Functions to find an acceptable Python binary")
10096 "This package was designed to find an acceptable Python binary that
10097 matches version and feature constraints.")
10098 (license license:expat)))
10100 ;; This in not the same as "r-argparser"
10101 (define-public r-argparse
10103 (name "r-argparse")
10108 (uri (cran-uri "argparse" version))
10111 "13b5halfxc7nr57vkz3qmkkcpw1hr4xdk1mjh2cq8cvpnjz15qc3"))))
10112 (build-system r-build-system)
10113 (inputs (list python))
10115 (list r-findpython r-jsonlite r-r6))
10118 (home-page "https://github.com/trevorld/argparse")
10119 (synopsis "Command line optional and positional argument parser")
10121 "This package provides a command line parser to be used with Rscript to
10122 write shebang scripts that gracefully accept positional and optional arguments
10123 and automatically generate usage notices.")
10124 (license license:gpl2+)))
10126 (define-public r-hash
10129 (version "2.2.6.2")
10133 (uri (cran-uri "hash" version))
10136 "17scs675a86c34hjbxmwi8kny4yyv97x3515s449zafj2i0ad8vm"))))
10137 (build-system r-build-system)
10138 (home-page "https://cran.r-project.org/web/packages/hash/")
10139 (synopsis "Implementation of hash/associated arrays/dictionaries")
10141 "This package implements a data structure similar to hashes in Perl and
10142 dictionaries in Python but with a purposefully R flavor. For objects of
10143 appreciable size, access using hashes outperforms native named lists and
10145 (license license:gpl2+)))
10147 (define-public r-orddom
10154 (uri (cran-uri "orddom" version))
10157 "165axs15fvwhrp89xd87l81q3h2qjll1vrwcsap645cwvb85nwsh"))))
10158 (build-system r-build-system)
10159 (propagated-inputs (list r-psych))
10160 (home-page "https://cran.r-project.org/web/packages/orddom/")
10161 (synopsis "Ordinal dominance statistics")
10163 "This package provides tools to compute ordinal, statistics and effect
10164 sizes as an alternative to mean comparison: Cliff's delta or success rate
10165 difference (SRD), Vargha and Delaney's A or the Area Under a Receiver
10166 Operating Characteristic Curve (AUC), the discrete type of McGraw & Wong's
10167 Common Language Effect Size (CLES) or Grissom & Kim's Probability of
10168 Superiority (PS), and the Number needed to treat (NNT) effect size. Moreover,
10169 comparisons to Cohen's d are offered based on Huberty & Lowman's Percentage of
10170 Group (Non-)Overlap considerations.")
10171 (license license:gpl2)))
10173 (define-public r-deriv
10180 (uri (cran-uri "Deriv" version))
10183 "130g3mv0z9sqs6y23a0a94512iiw05yr6fp378vhdxxbignzbnyv"))))
10184 (properties `((upstream-name . "Deriv")))
10185 (build-system r-build-system)
10186 (home-page "https://cran.r-project.org/web/packages/Deriv")
10187 (synopsis "Symbolic differentiation")
10189 "This package provides an R-based solution for symbolic differentiation.
10190 It admits user-defined functions as well as function substitution in arguments
10191 of functions to be differentiated. Some symbolic simplification is part of
10193 (license license:gpl3+)))
10195 (define-public r-doby
10202 (uri (cran-uri "doBy" version))
10205 "0qnfcw4rg5kd1mll3rq6vchz3lgdqfif9469p8x6ixsgrxxpivbz"))))
10206 (properties `((upstream-name . "doBy")))
10207 (build-system r-build-system)
10221 (home-page "https://people.math.aau.dk/~sorenh/software/doBy/")
10222 (synopsis "Groupwise statistics, LSmeans, linear contrasts, and utilities")
10224 "This package contains:
10227 @item facilities for working with grouped data: @code{do}
10228 something to data stratified @code{by} some variables.
10229 @item implementations of least-squares means, general linear contrasts, and
10230 @item miscellaneous other utilities.
10232 (license license:gpl2+)))
10234 (define-public r-refgenome
10236 (name "r-refgenome")
10241 (uri (cran-uri "refGenome" version))
10244 "1za89bn3am1zgvm641qi1ab6kaqpll4rb9p9f1sjwvcgqq6065g5"))))
10245 (properties `((upstream-name . "refGenome")))
10246 (build-system r-build-system)
10248 (list r-dbi r-doby r-rsqlite))
10249 (home-page "https://cran.r-project.org/web/packages/refGenome/")
10251 "Gene and splice site annotation using annotation data from Ensembl and UCSC")
10253 "This package contains functionality for importing and managing of
10254 downloaded genome annotation data from the Ensembl genome browser (European
10255 Bioinformatics Institute) and from the UCSC genome browser (University of
10256 California, Santa Cruz) and annotation routines for genomic positions and
10257 splice site positions.")
10258 (license license:gpl2)))
10260 (define-public r-basix
10267 (uri (cran-uri "BASIX" version))
10270 "18dkvv1iwskfnlpl6xridcgqpalbbpm2616mvc3hfrc0b26v01id"))))
10271 (properties `((upstream-name . "BASIX")))
10272 (build-system r-build-system)
10273 (home-page "https://cran.r-project.org/web/packages/BASIX/")
10274 (synopsis "Efficient C/C++ toolset for R")
10276 "BASIX provides some efficient C/C++ implementations of native R
10277 procedures to speed up calculations in R.")
10278 (license license:gpl2)))
10280 (define-public r-blockfest
10282 (name "r-blockfest")
10287 (uri (cran-uri "BlockFeST" version))
10290 "1fcl3yc1cf09znqbj787d3fd2kl5rp63la7pxawsgmap7nxwkp65"))))
10291 (properties `((upstream-name . "BlockFeST")))
10292 (build-system r-build-system)
10293 (propagated-inputs (list r-basix))
10294 (home-page "https://cran.r-project.org/web/packages/BlockFeST/")
10295 (synopsis "Bayesian calculation of region-specific fixation index")
10297 "This package provides an R implementation of an extension of the
10298 BayeScan software for codominant markers, adding the option to group
10299 individual SNPs into pre-defined blocks. A typical application of this new
10300 approach is the identification of genomic regions, genes, or gene sets
10301 containing one or more SNPs that evolved under directional selection.")
10302 (license license:gpl2)))
10304 (define-public r-proc
10311 (uri (cran-uri "pROC" version))
10314 "1abvbzdss12n64pp9vlgnn0q3abh0nj4n0a8cinwwvhphjrm9vym"))))
10315 (properties `((upstream-name . "pROC")))
10316 (build-system r-build-system)
10318 (list r-plyr r-rcpp))
10319 (home-page "https://web.expasy.org/pROC/")
10320 (synopsis "Display and analyze ROC curves")
10322 "This package provides tools for visualizing, smoothing and comparing
10323 receiver operating characteristic (ROC curves). The area under the
10324 curve (AUC) can be compared with statistical tests based on U-statistics or
10325 bootstrap. Confidence intervals can be computed for (p)AUC or ROC curves.")
10326 (license license:gpl3+)))
10328 (define-public r-rootsolve
10330 (name "r-rootsolve")
10331 (version "1.8.2.3")
10335 (uri (cran-uri "rootSolve" version))
10338 "182bb727sgqi5f3pzmw8jnn328wdjrgj9lfvg49gv8s22rjd3cxm"))))
10339 (properties `((upstream-name . "rootSolve")))
10340 (build-system r-build-system)
10341 (native-inputs (list gfortran))
10342 (home-page "https://cran.r-project.org/web/packages/rootSolve/")
10343 (synopsis "Tools for the analysis of ordinary differential equations")
10345 "This package provides routines to find the root of nonlinear functions,
10346 and to perform steady-state and equilibrium analysis of @dfn{ordinary
10347 differential equations} (ODE). It includes routines that:
10350 @item generate gradient and jacobian matrices (full and banded),
10351 @item find roots of non-linear equations by the Newton-Raphson method,
10352 @item estimate steady-state conditions of a system of (differential) equations
10353 in full, banded or sparse form, using the Newton-Raphson method, or by
10354 dynamically running,
10355 @item solve the steady-state conditions for uni- and multicomponent 1-D, 2-D,
10356 and 3-D partial differential equations, that have been converted to ordinary
10357 differential equations by numerical differencing (using the method-of-lines
10360 (license license:gpl2+)))
10362 (define-public r-abcanalysis
10364 (name "r-abcanalysis")
10369 (uri (cran-uri "ABCanalysis" version))
10371 (base32 "0wac1ksmnxa36v99ca4hv8k0rsh3igwpcllmlv9wf7i9kgqviqwi"))))
10372 (properties `((upstream-name . "ABCanalysis")))
10373 (build-system r-build-system)
10374 (propagated-inputs (list r-plotrix))
10375 (home-page "https://www.uni-marburg.de/fb12/arbeitsgruppen/datenbionik/software-en/")
10376 (synopsis "Computed ABC Analysis")
10378 "Multivariate data sets often differ in several factors or derived statistical
10379 parameters, which have to be selected for a valid interpretation. Basing this
10380 selection on traditional statistical limits leads occasionally to the perception
10381 of losing information from a data set. This package provides tools to calculate
10382 these limits on the basis of the mathematical properties of the distribution of
10383 the analyzed items.")
10384 (license license:gpl3)))
10386 (define-public r-slam
10393 (uri (cran-uri "slam" version))
10395 (base32 "1ggqcf8l1z2hpi7qy4mg0d2ps48bjjb8z1y1xz6fq162cqrbz6bq"))))
10396 (build-system r-build-system)
10397 (home-page "https://cran.r-project.org/web/packages/slam/")
10398 (synopsis "Sparse lightweight arrays and matrices")
10400 "This package contains data structures and algorithms for sparse arrays and matrices,
10401 based on index arrays and simple triplet representations, respectively.")
10402 (license license:gpl2)))
10404 (define-public r-manipulatewidget
10406 (name "r-manipulatewidget")
10411 (uri (cran-uri "manipulateWidget" version))
10413 (base32 "1dpgzmiv08afm57yxr017b014lfn9h3pa4w65prk5k3dgn6p4wsv"))))
10415 `((upstream-name . "manipulateWidget")))
10416 (build-system r-build-system)
10429 (home-page "https://github.com/rte-antares-rpackage/manipulateWidget/")
10430 (synopsis "Add even more interactivity to interactive charts")
10432 "This package lets you create in just a few lines of R code a nice user interface to
10433 modify the data or the graphical parameters of one or multiple interactive
10434 charts. It is useful to quickly explore visually some data or for package
10435 developers to generate user interfaces easy to maintain.")
10436 (license license:gpl2+)))
10438 (define-public r-a3
10445 (uri (cran-uri "A3" version))
10447 (base32 "017hq9pjsv1h9i7cqk5cfx27as54shlhdsdvr6jkhb8jfkpdb6cw"))))
10448 (properties `((upstream-name . "A3")))
10449 (build-system r-build-system)
10451 (list r-pbapply r-xtable))
10452 (home-page "https://cran.r-project.org/web/packages/A3/")
10453 (synopsis "Error metrics for predictive models")
10455 "This package supplies tools for tabulating and analyzing the results of predictive
10456 models. The methods employed are applicable to virtually any predictive model
10457 and make comparisons between different methodologies straightforward.")
10458 (license license:gpl2+)))
10460 (define-public r-infotheo
10462 (name "r-infotheo")
10463 (version "1.2.0.1")
10467 (uri (cran-uri "infotheo" version))
10470 "1m1979vf8rvq3534mp1hihfadikhxrg3p6ac3hirz96kgb4qxyy0"))))
10471 (build-system r-build-system)
10472 (home-page "http://homepage.meyerp.com/software")
10473 (synopsis "Information-theoretic measures")
10475 "This package implements various measures of information theory based on
10476 several entropy estimators.")
10477 (license license:gpl3+)))
10479 (define-public r-nsprcomp
10481 (name "r-nsprcomp")
10482 (version "0.5.1-2")
10486 (uri (cran-uri "nsprcomp" version))
10489 "1zlc1ximx96f235c0l8qfs6vbp1kpnbf943wxsfahnnlnxvwi59f"))))
10490 (properties `((upstream-name . "nsprcomp")))
10491 (build-system r-build-system)
10492 (home-page "https://sigg-iten.ch/research/")
10493 (synopsis "Non-negative and sparse PCA")
10495 "This package implements two methods for performing a constrained
10496 principal component analysis (PCA), where non-negativity and/or sparsity
10497 constraints are enforced on the principal axes (PAs). The function
10498 @code{nsprcomp} computes one principal component (PC) after the other. Each
10499 PA is optimized such that the corresponding PC has maximum additional variance
10500 not explained by the previous components. In contrast, the function
10501 @code{nscumcomp} jointly computes all PCs such that the cumulative variance is
10502 maximal. Both functions have the same interface as the @code{prcomp} function
10503 from the @code{stats} package (plus some extra parameters).")
10504 (license license:gpl2+)))
10506 (define-public r-cmplot
10513 (uri (cran-uri "CMplot" version))
10516 "1h09prpiw7l32mr7jarp8ddrddg1431nfn4kw3bznfnv0sr78zfg"))))
10517 (properties `((upstream-name . "CMplot")))
10518 (build-system r-build-system)
10519 (home-page "https://github.com/YinLiLin/CMplot")
10520 (synopsis "Circle Manhattan plot")
10522 "Circle Manhattan Plot is an R package that can lay out genome-wide
10523 association study P-value results in both traditional rectangular patterns,
10524 QQ-plot and novel circular ones. United in only one bull's eye style plot,
10525 association results from multiple traits can be compared interactively,
10526 thereby to reveal both similarities and differences between signals.
10527 Additional functions include: highlight signals, a group of SNPs, chromosome
10528 visualization and candidate genes around SNPs.")
10529 (license license:gpl2+)))
10531 (define-public r-precrec
10538 (uri (cran-uri "precrec" version))
10541 "1dfz2rqx2ww2l5r40ahg0qdj3rjrwiwh427mw7j5ynhpcj21j2qm"))))
10542 (properties `((upstream-name . "precrec")))
10543 (build-system r-build-system)
10551 (native-inputs (list r-knitr))
10552 (home-page "https://evalclass.github.io/precrec/")
10553 (synopsis "Calculate accurate precision-recall and ROC curves")
10555 "This package provides tools for accurate calculations and visualization
10556 of precision-recall and ROC (Receiver Operator Characteristics) curves.")
10557 (license license:gpl3)))
10559 (define-public r-netrep
10566 (uri (cran-uri "NetRep" version))
10569 "1swlb2k9bc7whvslxbklz864j9ynvna73hvq5rhv61cv5vy05ksd"))))
10570 (properties `((upstream-name . "NetRep")))
10571 (build-system r-build-system)
10581 (native-inputs (list r-knitr))
10582 (home-page "https://cran.r-project.org/package=NetRep")
10583 (synopsis "Permutation testing network module preservation across datasets")
10585 "This package provides functions for assessing the
10586 replication/preservation of a network module's topology across datasets
10587 through permutation testing.")
10588 (license license:gpl2)))
10590 (define-public r-intergraph
10592 (name "r-intergraph")
10597 (uri (cran-uri "intergraph" version))
10600 "18a7xgb2rp0w9jl2rkh8nzyjprrs5w7h2iidvc8c38bzx3qpggkc"))))
10601 (properties `((upstream-name . "intergraph")))
10602 (build-system r-build-system)
10604 (list r-igraph r-network))
10607 (home-page "http://mbojan.github.io/intergraph")
10608 (synopsis "Coercion routines for network data objects")
10610 "Functions implemented in this package allow coercing (i.e. convert)
10611 network data between classes provided by other R packages. Currently
10612 supported classes are those defined in packages @code{network} and
10614 (license license:gpl3)))
10616 (define-public r-abcoptim
10618 (name "r-abcoptim")
10623 (uri (cran-uri "ABCoptim" version))
10625 (base32 "1ih0xk88qhsmpvnxf56041wx5sk8as2f4f2gdnpnwdym9mbr9n4b"))))
10626 (properties `((upstream-name . "ABCoptim")))
10627 (build-system r-build-system)
10628 (propagated-inputs (list r-rcpp))
10629 (home-page "https://github.com/gvegayon/ABCoptim/")
10630 (synopsis "Optimization of Artificial Bee Colony algorithm")
10632 "Artificial Bee Colony (ABC) is one of the most recently defined algorithms by Dervis
10633 Karaboga in 2005, motivated by the intelligent behavior of honey bees. It is as
10634 simple as Particle Swarm Optimization (PSO) and Differential Evolution (DE)
10635 algorithms, and uses only common control parameters such as colony size and
10636 maximum cycle number. The @code{r-abcoptim} implements the Artificial bee
10637 colony optimization algorithm @url{http://mf.erciyes.edu.tr/abc/pub/tr06_2005.pdf}.
10638 This version is a work-in-progress and is written in R code.")
10639 (license license:expat)))
10641 (define-public r-abcp2
10648 (uri (cran-uri "ABCp2" version))
10650 (base32 "1s2skkxpzss7c29i8600psgrp0hl46jcrxqrmy2b4db8hc0kcnbx"))))
10651 (properties `((upstream-name . "ABCp2")))
10652 (build-system r-build-system)
10653 (propagated-inputs (list r-mass))
10654 (home-page "https://cran.r-project.org/web/packages/ABCp2/")
10655 (synopsis "Approximate Bayesian Computational Model for Estimating P2")
10657 "This package tests the goodness of fit of a distribution of offspring to the Normal,
10658 Poisson, and Gamma distribution and estimates the proportional paternity of the
10659 second male (P2) based on the best fit distribution.")
10660 (license license:gpl2)))
10662 (define-public r-abcrf
10669 (uri (cran-uri "abcrf" version))
10671 (base32 "1ghbd24yhqy3xhdxas6ccn84nkavqpgldx5ck8kijknc7qjm8k27"))))
10672 (build-system r-build-system)
10683 (home-page "https://cran.r-project.org/web/packages/abcrf/")
10684 (synopsis "Approximate bayesian computation via random forests")
10686 "This package performs approximate bayesian computation (ABC) model choice and
10687 parameter inference via random forests. This machine learning tool named random
10688 forests (RF) can conduct selection among the highly complex models covered by
10690 (license license:gpl2+)))
10692 (define-public r-abctools
10694 (name "r-abctools")
10699 (uri (cran-uri "abctools" version))
10701 (base32 "07s9dg10i8lsxl73b4n2hynca2fjgb0ykb0dz8c3zv6cgw3cyx97"))))
10702 (build-system r-build-system)
10704 (list r-abc r-abind r-hmisc r-plyr))
10705 (home-page "https://github.com/dennisprangle/abctools/")
10706 (synopsis "Tools for ABC analyses")
10708 "This @code{r-abctools} package provides tools for approximate Bayesian computation
10709 including summary statistic selection and assessing coverage. This includes
10710 recent dimension reduction algorithms to tune the choice of summary statistics,
10711 and coverage methods to tune the choice of threshold.")
10712 (license license:gpl2+)))
10714 (define-public r-ggstance
10716 (name "r-ggstance")
10721 (uri (cran-uri "ggstance" version))
10723 (base32 "0jz9vvnmcc6a38n8nzr458r65sna23bgn5r8mxdhzdlyqibihr7d"))))
10724 (build-system r-build-system)
10726 (list r-ggplot2 r-plyr r-rlang r-withr))
10727 (home-page "https://cran.r-project.org/web/packages/ggstance/")
10728 (synopsis "Horizontal and vertical versions of @code{r-ggplot2}")
10730 "This package is a @code{r-ggplot2} extension that provides flipped components:
10732 @item horizontal versions of @code{r-ggplot2} stats and @code{r-ggplot2} geoms;
10733 @item vertical versions of @code{r-ggplot2} positions.
10735 (license license:gpl3)))
10737 (define-public r-ggnetwork
10739 (name "r-ggnetwork")
10744 (uri (cran-uri "ggnetwork" version))
10747 "0gqdgy5yh700dg0f7xb80hczlnqfisn8l55j7amd1n7fp2x5sr8v"))))
10748 (properties `((upstream-name . "ggnetwork")))
10749 (build-system r-build-system)
10751 (list r-ggplot2 r-ggrepel r-igraph r-network r-sna))
10752 (native-inputs (list r-knitr))
10753 (home-page "https://github.com/briatte/ggnetwork")
10754 (synopsis "Geometries to plot networks with ggplot2")
10756 "This package provides geometries to plot network objects with the
10758 (license license:gpl3)))
10760 (define-public r-cvauc
10767 (uri (cran-uri "cvAUC" version))
10770 "1m2y50a1yapf1c74km9a4r47ds2z2bfp4wwwkqin7swv9v1s7d28"))))
10771 (properties `((upstream-name . "cvAUC")))
10772 (build-system r-build-system)
10774 (list r-data-table r-rocr))
10775 (home-page "https://github.com/ledell/cvAUC")
10776 (synopsis "Cross-validated area under the ROC curve confidence intervals")
10778 "This package contains various tools for working with and evaluating
10779 cross-validated area under the ROC curve (AUC) estimators. The primary
10780 functions of the package are @code{ci.cvAUC} and @code{ci.pooled.cvAUC}, which
10781 report cross-validated AUC and compute confidence intervals for
10782 cross-validated AUC estimates based on influence curves for i.i.d. and pooled
10783 repeated measures data, respectively.")
10784 (license license:asl2.0)))
10786 (define-public r-gam
10793 (uri (cran-uri "gam" version))
10796 "1bbxiqfgi7jc9vw1hspw5q41d69nlw2v6k91zqlvmam5pvxcd1sp"))))
10797 (properties `((upstream-name . "gam")))
10798 (build-system r-build-system)
10803 (home-page "https://cran.r-project.org/package=gam")
10804 (synopsis "Generalized additive models")
10806 "This package provides functions for fitting and working with generalized
10807 additive models, as described in chapter 7 of \"Statistical Models in
10808 S\" (Chambers and Hastie (eds), 1991), and \"Generalized Additive
10809 Models\" (Hastie and Tibshirani, 1990).")
10810 (license license:gpl2)))
10812 (define-public r-superlearner
10814 (name "r-superlearner")
10819 (uri (cran-uri "SuperLearner" version))
10822 "00any24msgflyagy87nznpfjz5g9v15frqda6c679wa8plx26hjz"))))
10823 (properties `((upstream-name . "SuperLearner")))
10824 (build-system r-build-system)
10826 (list r-cvauc r-gam r-nnls))
10829 (home-page "https://github.com/ecpolley/SuperLearner")
10830 (synopsis "Super learner prediction")
10832 "This package implements the super learner prediction method and contains
10833 a library of prediction algorithms to be used in the super learner.")
10834 (license license:gpl3)))
10836 (define-public r-drtmle
10843 (uri (cran-uri "drtmle" version))
10846 "12vplpz9bg5444jy29mbdr70hqby073vb3iw76v2csrwy3ws3f21"))))
10847 (properties `((upstream-name . "drtmle")))
10848 (build-system r-build-system)
10850 (list r-future-apply r-np r-superlearner))
10853 (home-page "https://github.com/benkeser/drtmle")
10854 (synopsis "Doubly-robust nonparametric estimation and inference")
10856 "This package implements targeted minimum loss-based estimators of
10857 counterfactual means and causal effects that are doubly-robust with respect
10858 both to consistency and asymptotic normality.")
10859 (license license:expat)))
10861 (define-public r-dofuture
10863 (name "r-dofuture")
10868 (uri (cran-uri "doFuture" version))
10871 "0w07pmzpsfq4kvfc745s1i9b6dfn1df1wrfi4s9ys4ir3g2s8nk1"))))
10872 (properties `((upstream-name . "doFuture")))
10873 (build-system r-build-system)
10876 (modify-phases %standard-phases
10877 (add-after 'unpack 'set-HOME
10878 (lambda _ (setenv "HOME" "/tmp"))))))
10880 (list r-foreach r-future r-globals r-iterators))
10882 (list r-r-rsp)) ; vignette builder
10883 (home-page "https://github.com/HenrikBengtsson/doFuture")
10884 (synopsis "Foreach parallel adapter using the future API")
10886 "This package provides a @code{%dopar%} adapter such that any type of
10887 futures can be used as backends for the @code{foreach} framework.")
10888 (license license:lgpl2.1+)))
10890 (define-public r-superheat
10892 (name "r-superheat")
10897 (uri (cran-uri "superheat" version))
10900 "01v8s6px1k5fajlm6py3ksr1i853kwwlky1yryzhy3p1cxhwgg83"))))
10901 (properties `((upstream-name . "superheat")))
10902 (build-system r-build-system)
10911 (home-page "https://cran.r-project.org/package=superheat")
10912 (synopsis "Graphical tool for exploring complex datasets using heatmaps")
10914 "This package provides a system for generating extendable and
10915 customizable heatmaps for exploring complex datasets, including big data and
10916 data with multiple data types.")
10917 (license license:cc0)))
10919 (define-public r-qualv
10926 (uri (cran-uri "qualV" version))
10929 "0rkjzva2h158d5c631jmjjh7qjibbyisl0503san80rk9fgxl45b"))))
10930 (properties `((upstream-name . "qualV")))
10931 (build-system r-build-system)
10933 (list r-kernsmooth))
10934 (home-page "http://qualV.R-Forge.R-Project.org/")
10935 (synopsis "Qualitative Validation Methods")
10937 "This package provides qualitative methods for the validation of dynamic
10938 models. It contains
10941 @item an orthogonal set of deviance measures for absolute, relative and
10943 @item approaches accounting for time shifts.
10946 The first approach transforms time to take time delays and speed differences
10947 into account. The second divides the time series into interval units
10948 according to their main features and finds the @dfn{longest common
10949 subsequence} (LCS) using a dynamic programming algorithm.")
10950 (license license:gpl2+)))
10952 (define-public r-mosaiccore
10954 (name "r-mosaiccore")
10959 (uri (cran-uri "mosaicCore" version))
10961 (base32 "1h3ixzna4xy42rdnd89jj0v9q0riy3fnkd33z6l5c0zaidzm58fz"))))
10962 (properties `((upstream-name . "mosaicCore")))
10963 (build-system r-build-system)
10965 (list r-dplyr r-mass r-rlang r-tidyr))
10966 (home-page "https://github.com/ProjectMOSAIC/mosaicCore/")
10967 (synopsis "Common utilities for mosaic family packages")
10969 "Common utilities used in other Mosaic family packages are collected here.")
10970 (license license:gpl2+)))
10972 (define-public r-labelled
10974 (name "r-labelled")
10979 (uri (cran-uri "labelled" version))
10982 "0h7scbyzh7kr51gds222rkhld2b3k36s86hj8rrzpwv4bwj0pccy"))))
10983 (properties `((upstream-name . "labelled")))
10984 (build-system r-build-system)
10995 (home-page "http://larmarange.github.io/labelled/")
10996 (synopsis "Manipulating labelled data")
10998 "This package provides useful functions to deal with the
10999 @code{haven_labelled} and @code{haven_labelled_spss} classes introduced by the
11001 (license license:gpl3)))
11003 (define-public r-ggformula
11005 (name "r-ggformula")
11010 (uri (cran-uri "ggformula" version))
11012 (base32 "1ph5jd8svk8hmshi894vmmpq3zwgdmf4yn3gmdlkad68z8jynhsp"))))
11013 (build-system r-build-system)
11028 (home-page "https://github.com/ProjectMOSAIC/ggformula/")
11029 (synopsis "Formula interface for the @code{r-ggplot2}")
11031 "The @code{r-ggformula} introduces a family of graphics functions, gf_point(),
11032 gf_density(), and so on, bring the formula interface to ggplot(). This captures
11033 and extends the excellent simplicity of the lattice-graphics formula interface,
11034 while providing the intuitive capabilities of @code{r-ggplot2}.")
11035 (license license:expat)))
11037 (define-public r-mosaicdata
11039 (name "r-mosaicdata")
11044 (uri (cran-uri "mosaicData" version))
11046 (base32 "0h3f5fgzkzjfgf3ml0qa5j52921y6wy6jgggxmhs31bs8fd4srg4"))))
11047 (properties `((upstream-name . "mosaicData")))
11048 (build-system r-build-system)
11049 (home-page "https://cran.r-project.org/web/packages/mosaicData/")
11050 (synopsis "Data sets for project Mosaic")
11052 "This package provides data sets from project Mosaic @url{http://mosaic-web.org}
11053 used to teach mathematics, statistics, computation and modeling.")
11054 (license license:gpl2+)))
11056 (define-public r-raster
11063 (uri (cran-uri "raster" version))
11066 "11fnznymwavpph733dayklhcx4phpjgrijfxlaszi122sg2x7ir9"))))
11067 (build-system r-build-system)
11069 (list r-rcpp r-sp r-terra))
11070 (home-page "https://www.rspatial.org/")
11071 (synopsis "Geographic data analysis and modeling")
11073 "The package implements basic and high-level functions for reading,
11074 writing, manipulating, analyzing and modeling of gridded spatial data.
11075 Processing of very large files is supported.")
11076 (license license:gpl3+)))
11078 (define-public r-mosaic
11085 (uri (cran-uri "mosaic" version))
11087 (base32 "1y0isqbva0vi5zlx1xvixbq87n4xp66ljh43qnd0cpzaz0mn21cg"))))
11088 (build-system r-build-system)
11112 (home-page "https://github.com/ProjectMOSAIC/mosaic/")
11113 (synopsis "Mathematics, statistics, and computation teaching utilities")
11115 "This package contain data sets and utilities from
11116 @url{http://mosaic-web.org, Project MOSAIC} used to teach mathematics,
11117 statistics, computation and modeling. Project MOSAIC is a community of
11118 educators working to tie together aspects of quantitative work that students
11119 in science, technology, engineering and mathematics will need in their
11120 professional lives, but which are usually taught in isolation, if at all.")
11121 (license license:gpl2+)))
11123 (define-public r-abd
11130 (uri (cran-uri "abd" version))
11132 (base32 "191gspqzdv573vaw624ri0f5cm6v4j524bjs74d4a1hn3kn6r9b7"))))
11133 (build-system r-build-system)
11135 (list r-lattice r-mosaic r-nlme))
11136 (home-page "https://cran.r-project.org/web/packages/abd/")
11137 (synopsis "Analysis of biological data")
11139 "The @code{r-abd} package contains data sets and sample code for the Analysis of
11140 biological data by Michael Whitlock and Dolph Schluter.")
11141 (license license:gpl2)))
11143 (define-public r-svgui
11150 (uri (cran-uri "svGUI" version))
11152 (base32 "0ch5gdfk834xj9w3vxpm3x4770fz3nnlyn8b0jsw9f3n2as7g979"))))
11153 (properties `((upstream-name . "svGUI")))
11154 (build-system r-build-system)
11157 (home-page "https://github.com/SciViews/svGUI/")
11158 (synopsis "Functions for managing GUI clients in R")
11160 "The SciViews @code{svGUI} package eases the management of Graphical User
11161 Interfaces (GUI) in R. It is independent from any particular GUI widgets. It
11162 centralizes info about GUI elements currently used, and it dispatches GUI
11163 calls to the particular toolkits in use in function of the context.")
11164 (license license:gpl2)))
11166 (define-public r-svdialogs
11168 (name "r-svdialogs")
11173 (uri (cran-uri "svDialogs" version))
11175 (base32 "0z3a5glsi0ab43mdk2yvslxyzg12nbqqqc35jvgzj475mpkbgjif"))))
11176 (properties `((upstream-name . "svDialogs")))
11177 (build-system r-build-system)
11181 (list r-rstudioapi r-svgui))
11184 (home-page "https://github.com/SciViews/svDialogs/")
11185 (synopsis "Portable dialog boxes")
11187 "This package helps to construct standard dialog boxes for your GUI, including
11188 message boxes, input boxes, list, file or directory selection, and others. In
11189 case R cannot display GUI dialog boxes, a simpler command line version of these
11190 interactive elements is also provided as a fallback solution.")
11191 (license license:gpl2)))
11193 (define-public r-abe
11200 (uri (cran-uri "abe" version))
11203 "1f19h3xzzmjhvwc1rrb8z0rai3ip03y4gdi2gg9bfr5sg2nfklk6"))))
11204 (build-system r-build-system)
11205 (home-page "https://cran.r-project.org/web/packages/abe/")
11206 (synopsis "Augmented backward elimination")
11208 "This package performs augmented backward elimination and checks the
11209 stability of the obtained model. Augmented backward elimination combines
11210 significance or information based criteria with the change in estimate to
11211 either select the optimal model for prediction purposes or to serve as a tool
11212 to obtain a practically sound, highly interpretable model.")
11213 (license license:gpl2+)))
11215 (define-public r-abf2
11222 (uri (cran-uri "abf2" version))
11224 (base32 "0d65mc1w4pbiv7xaqzdlw1bfsxf25587rv597hh41vs0j0zlfpxx"))))
11225 (build-system r-build-system)
11226 (home-page "https://cran.r-project.org/web/packages/abf2/")
11227 (synopsis "Load gap-free axon @code{r-abf2} files")
11229 "This package loads electrophysiology data from ABF2 files, as created by
11230 Axon Instruments/Molecular Devices software. Only files recorded in gap-free
11231 mode are currently supported.")
11232 (license license:artistic2.0)))
11234 (define-public r-abhgenotyper
11236 (name "r-abhgenotyper")
11241 (uri (cran-uri "ABHgenotypeR" version))
11243 (base32 "08cpmnaaxsm5c5bjifnfxdlvg5inrf13biqpcl2yq5zpqjmiki0l"))))
11244 (properties `((upstream-name . "ABHgenotypeR")))
11245 (build-system r-build-system)
11247 (list r-ggplot2 r-reshape2))
11248 (home-page "https://github.com/StefanReuscher/ABHgenotypeR/")
11249 (synopsis "Visualize and manipulate ABH genotypes")
11251 "The @code{r-abhgenotyper} package provides simple imputation,
11252 error-correction and plotting capacities for genotype data. The package is
11253 supposed to serve as an intermediate but independent analysis tool between the
11254 TASSEL GBS pipeline and the @code{r-qtl} package. It provides functionalities
11255 not found in either TASSEL or @code{r-qtl} in addition to visualization of
11256 genotypes as \"graphical genotypes\".")
11257 (license license:gpl3)))
11259 (define-public r-furrr
11266 (uri (cran-uri "furrr" version))
11269 "117xj66l14r08macwghgyibzm282ljv1afpa133h952gc70irs9z"))))
11270 (build-system r-build-system)
11278 (home-page "https://github.com/DavisVaughan/furrr")
11279 (synopsis "Apply mapping functions in parallel using futures")
11281 "This package provides implementations of the family of @code{map()}
11282 functions from the @code{purrr} package that can be resolved using any
11283 @code{future}-supported backend, e.g. parallel on the local machine or
11284 distributed on a compute cluster.")
11285 (license license:lgpl2.1+)))
11287 (define-public r-abjutils
11289 (name "r-abjutils")
11294 (uri (cran-uri "abjutils" version))
11296 (base32 "0lmf4va8qnzwg698i2h4fcwvd6dhsgdkqsfh41aa3wg1flimhsr7"))))
11297 (build-system r-build-system)
11307 (home-page "https://github.com/abjur/abjutils/")
11308 (synopsis "Collection of tools for jurimetrical analysis")
11310 "This package implements general purpose tools, such as functions for
11311 sampling and basic manipulation of Brazilian lawsuits identification number.
11312 It also implements functions for text cleaning, such as accentuation
11314 (license license:expat)))
11316 (define-public r-abnormality
11318 (name "r-abnormality")
11323 (uri (cran-uri "abnormality" version))
11325 (base32 "1fzfskl9akl06nliy8hkv2a0pznpj8pwcypg3gj5r2nzvr3kan9v"))))
11326 (build-system r-build-system)
11328 (list r-mass r-matrix))
11329 (home-page "https://cran.r-project.org/web/packages/abnormality/")
11330 (synopsis "Measure a subject's abnormality with respect to a reference population")
11332 "This package contains functions to implement the methodology and
11333 considerations laid out by Marks et al. in the article \"Measuring abnormality
11334 in high dimensional spaces: applications in biomechanical gait analysis\".
11335 Using high-dimensional datasets to measure a subject's overall level of
11336 abnormality as compared to a reference population is often needed in outcomes
11338 (license license:expat)))
11340 (define-public r-abodoutlier
11342 (name "r-abodoutlier")
11347 (uri (cran-uri "abodOutlier" version))
11349 (base32 "1pvhgxmh23br84r0fbmv7g53z2427birdja96a67vqgz18r3fdvj"))))
11350 (properties `((upstream-name . "abodOutlier")))
11351 (build-system r-build-system)
11354 (home-page "https://cran.r-project.org/web/packages/abodOutlier/")
11355 (synopsis "Angle-based outlier detection")
11357 "This package performs angle-based outlier detection on a given data
11358 frame. It offers three methods to process data:
11360 @item full but slow implementation using all the data that has cubic
11362 @item a fully randomized method;
11363 @item a method using k-nearest neighbours.
11365 These algorithms are well suited for high dimensional data outlier
11367 (license license:expat)))
11369 (define-public r-abps
11376 (uri (cran-uri "ABPS" version))
11378 (base32 "0n3f66nmfi5v94il1mxy026mi84w01ph2aljk60vn3mrz8kwf2ll"))))
11379 (properties `((upstream-name . "ABPS")))
11380 (build-system r-build-system)
11381 (propagated-inputs (list r-kernlab))
11382 (home-page "https://cran.r-project.org/web/packages/ABPS/")
11383 (synopsis "Abnormal blood profile score to detect blood doping")
11385 "This package offers an implementation of the @dfn{Abnormal blood profile score} (ABPS).
11386 The ABPS is a part of the Athlete biological passport program of the World
11387 anti-doping agency, which combines several blood parameters into a single
11388 score in order to detect blood doping. The package also contains functions to
11389 calculate other scores used in anti-doping programs, such as the ratio of
11390 hemoglobin to reticulocytes (OFF-score), as well as example data.")
11391 (license license:gpl2+)))
11393 (define-public r-parmigene
11395 (name "r-parmigene")
11400 (uri (cran-uri "parmigene" version))
11403 "067rqxqyzy1fsjj0s1g7af4527whwdhzjzc5b8a8n7683na59ns4"))))
11404 (build-system r-build-system)
11405 (home-page "https://cran.r-project.org/web/packages/parmigene/")
11406 (synopsis "Mutual information estimation for gene network reconstruction")
11408 "This package provides a parallel estimation of the mutual information
11409 based on entropy estimates from k-nearest neighbors distances and algorithms
11410 for the reconstruction of gene regulatory networks.")
11411 (license license:agpl3+)))
11413 (define-public r-pscl
11420 (uri (cran-uri "pscl" version))
11422 (base32 "0vzf5wazs92bhqhqd66v3vwmbfmnh67gb2466g1xxawim649nk05"))))
11423 (build-system r-build-system)
11426 (home-page "https://github.com/atahk/pscl/")
11427 (synopsis "Political science computational laboratory")
11429 "The @code{pscl} is an R package providing classes and methods for:
11431 @item Bayesian analysis of roll call data (item-response models);
11432 @item elementary Bayesian statistics;
11433 @item maximum likelihood estimation of zero-inflated and hurdle models for count
11435 @item utility functions.
11437 (license license:gpl2)))
11439 (define-public r-accelmissing
11441 (name "r-accelmissing")
11446 (uri (cran-uri "accelmissing" version))
11448 (base32 "1nql9inx6azdzi3z4sfm2vdml2mms6krl8wzlf1dn1c97ahn57fy"))))
11449 (build-system r-build-system)
11451 (list r-mice r-pscl))
11452 (home-page "https://cran.r-project.org/web/packages/accelmissing/")
11453 (synopsis "Missing value imputation for accelerometer data")
11455 "This package provides a statistical method to impute the missing values in
11456 accelerometer data. The methodology includes both parametric and
11457 semi-parametric multiple imputations under the zero-inflated Poisson lognormal
11458 model. It also provides multiple functions to preprocess the accelerometer data
11459 previous to the missing data imputation. These include detecting the wearing
11460 and the non-wearing time, selecting valid days and subjects, and creating plots.")
11461 (license license:gpl2+)))
11463 (define-public r-mhsmm
11470 (uri (cran-uri "mhsmm" version))
11472 (base32 "009dj0zkj1zry7jr9hf4cknb686z50a2l967if64xm0dvjmp7dgs"))))
11473 (build-system r-build-system)
11474 (propagated-inputs (list r-mvtnorm))
11475 (home-page "https://github.com/jaredo/mhsmm/")
11476 (synopsis "Inference for hidden Markov and semi-Markov models")
11478 "The @code{r-mhsmm} package implements estimation and prediction methods for
11479 hidden Markov and semi-Markov models for multiple observation sequences. Such
11480 techniques are of interest when observed data is thought to be dependent on some
11481 unobserved (or hidden) state. Also, this package is suitable for equidistant
11482 time series data, with multivariate and/or missing data. Allows user defined
11483 emission distributions.")
11484 (license license:gpl2+)))
11486 (define-public r-nleqslv
11493 (uri (cran-uri "nleqslv" version))
11495 (base32 "1v9znvncyigw9r25wx2ma0b7ib179b488dl0qsrhp5zrcz7mcjgm"))))
11496 (build-system r-build-system)
11497 (native-inputs (list gfortran))
11498 (home-page "https://cran.r-project.org/web/packages/nleqslv/")
11499 (synopsis "Solve systems of nonlinear equations")
11501 "The @code{r-nleqslv} package solves a system of nonlinear equations using a
11502 Broyden or a Newton method with a choice of global strategies such as line
11503 search and trust region. There are options for using a numerical or user
11504 supplied Jacobian, for specifying a banded numerical Jacobian and for allowing a
11505 singular or ill-conditioned Jacobian.")
11506 (license license:gpl2+)))
11508 (define-public r-physicalactivity
11510 (name "r-physicalactivity")
11515 (uri (cran-uri "PhysicalActivity" version))
11517 (base32 "0b27prkv3x6v2afz0y53ccs9scibpc7nj54n0hpd9fgn1wyg4c40"))))
11519 `((upstream-name . "PhysicalActivity")))
11520 (build-system r-build-system)
11521 (home-page "https://cran.r-project.org/web/packages/PhysicalActivity/")
11522 (synopsis "Processing accelerometer data for physical activity measurement")
11524 "This @code{r-physicalactivity} package provides a function @code{wearingMarking}
11525 for classification of monitored wear and nonwear time intervals in accelerometer
11526 data collected to assess physical activity. The package also contains functions
11527 for making plots of accelerometer data and obtaining the summary of various
11528 information including daily monitor wear time and the mean monitor wear time
11529 during valid days. The revised package version 0.2-1 improved the functions
11530 regarding speed, robustness and add better support for time zones and daylight
11531 saving. In addition, several functions were added:
11533 @item the @code{markDelivery} can classify days for ActiGraph delivery by mail;
11534 @item the @code{markPAI} can categorize physical activity intensity level based
11535 on user-defined cut-points of accelerometer counts.
11537 It also supports importing ActiGraph (AGD) files with @code{readActigraph} and
11538 @code{queryActigraph} functions.")
11539 (license license:gpl3+)))
11541 (define-public r-acc
11548 (uri (cran-uri "acc" version))
11550 (base32 "1ii2vm47djxbixa75h690q1s2f9m9x6i8nkygik93j6dayr6kr1m"))))
11551 (build-system r-build-system)
11566 (home-page "https://cran.r-project.org/web/packages/acc/")
11567 (synopsis "Exploring accelerometer data")
11569 "This package processes accelerometer data from uni-axial and tri-axial devices
11570 and generates data summaries. Also, includes functions to plot, analyze, and
11571 simulate accelerometer data.")
11572 (license license:gpl2+)))
11574 (define-public r-rbenchmark
11576 (name "r-rbenchmark")
11581 (uri (cran-uri "rbenchmark" version))
11583 (base32 "010fn3qwnk2k411cbqyvra1d12c3bhhl3spzm8kxffmirj4p2al9"))))
11584 (build-system r-build-system)
11585 (home-page "https://cran.r-project.org/web/packages/rbenchmark/")
11586 (synopsis "Benchmarking routine for R")
11588 "This @code{r-rbenchmark} package is inspired by the Perl module Benchmark,
11589 and is intended to facilitate benchmarking of arbitrary R code. The library
11590 consists of just one function, benchmark, which is a simple wrapper around
11591 system.time. Given a specification of the benchmarking process (counts of
11592 replications, evaluation environment) and an arbitrary number of expressions,
11593 benchmark evaluates each of the expressions in the specified environment,
11594 replicating the evaluation as many times as specified, and returning the results
11595 conveniently wrapped into a data frame.")
11596 (license license:gpl2+)))
11598 (define-public r-mitools
11605 (uri (cran-uri "mitools" version))
11608 "0c2x2n1p53lcw0vx4vmy5j7m2f95i7g2iwbryl89imr99rvz617j"))))
11609 (build-system r-build-system)
11610 (propagated-inputs (list r-dbi))
11611 (home-page "https://cran.r-project.org/web/packages/mitools/")
11612 (synopsis "Tools for multiple imputation of missing data")
11614 "This package provides tools to perform analyses and combine results from
11615 multiple-imputation datasets.")
11616 (license license:gpl2)))
11618 (define-public r-mixsqp
11624 (uri (cran-uri "mixsqp" version))
11627 "1qics04w0swyp216d6g8dmsph8q2kpadpacp66h2qih3521js12q"))))
11628 (properties `((upstream-name . "mixsqp")))
11629 (build-system r-build-system)
11631 (list r-irlba r-rcpp r-rcpparmadillo))
11634 (home-page "https://github.com/stephenslab/mixsqp")
11636 "Sequential quadratic programming for maximum-likelihood estimation")
11638 "This package provides an optimization method based on sequential
11639 quadratic programming for maximum likelihood estimation of the mixture
11640 proportions in a finite mixture model where the component densities are
11641 known. The algorithm is expected to obtain solutions that are at least
11642 as accurate as the state-of-the-art MOSEK interior-point solver, and they
11643 are expected to arrive at solutions more quickly when the number of
11644 samples is large and the number of mixture components is not too large.")
11645 (license license:expat)))
11647 (define-public r-magick
11654 (uri (cran-uri "magick" version))
11657 "0h942bn7wfnzbbgq9hrs75c7igmg5r1c5sad2v0znhza4cp7p1w3"))))
11658 (build-system r-build-system)
11660 (list imagemagick zlib))
11662 (list r-curl r-magrittr r-rcpp))
11664 (list pkg-config r-knitr))
11665 (home-page "https://github.com/ropensci/magick")
11666 (synopsis "Advanced graphics and image-processing in R")
11668 "This package provides bindings to ImageMagick, a comprehensive image
11669 processing library. It supports many common formats (PNG, JPEG, TIFF, PDF,
11670 etc.) and manipulations (rotate, scale, crop, trim, flip, blur, etc). All
11671 operations are vectorized via the Magick++ STL meaning they operate either on
11672 a single frame or a series of frames for working with layers, collages, or
11673 animation. In RStudio, images are automatically previewed when printed to the
11674 console, resulting in an interactive editing environment.")
11675 (license license:expat)))
11677 (define-public r-survey
11684 (uri (cran-uri "survey" version))
11687 "0ljsszybzri531q6xab04r6zq11vchfs7y0snjzk57m3g0b9ms05"))))
11688 (build-system r-build-system)
11696 (home-page "http://r-survey.r-forge.r-project.org/survey/")
11697 (synopsis "Analysis of complex survey samples")
11699 "This package provides tools for the analysis of complex survey samples.
11700 The provided features include: summary statistics, two-sample tests, rank
11701 tests, generalised linear models, cumulative link models, Cox models,
11702 loglinear models, and general maximum pseudolikelihood estimation for
11703 multistage stratified, cluster-sampled, unequally weighted survey samples;
11704 variances by Taylor series linearisation or replicate weights;
11705 post-stratification, calibration, and raking; two-phase subsampling designs;
11706 graphics; PPS sampling without replacement; principal components, and factor
11708 ;; Either version of the GPL.
11709 (license (list license:gpl2 license:gpl3))))
11711 (define-public r-gee
11714 (version "4.13-22")
11718 (uri (cran-uri "gee" version))
11721 "1wbwn7bjqz09l6clh43dy3x5qgv9b9wwn7xnfw9fkkrhn6rvc3rw"))))
11722 (properties `((upstream-name . "gee")))
11723 (build-system r-build-system)
11726 (home-page "https://cran.r-project.org/web/packages/gee/")
11727 (synopsis "Generalized estimation equation solver")
11729 "This package provides a solver for generalized estimation equations.")
11730 (license license:gpl2)))
11732 (define-public r-tab
11739 (uri (cran-uri "tab" version))
11742 "1kg8c1safi9klkx2mdkmsf5dn9piy4jljwd4ma7g4jz2rwl4jzhv"))))
11743 (properties `((upstream-name . "tab")))
11744 (build-system r-build-system)
11746 (list r-dplyr r-kableextra r-knitr r-mass r-survey))
11749 (home-page "https://cran.r-project.org/web/packages/tab/")
11750 (synopsis "Create summary tables for statistical reports")
11752 "This package contains functions for creating various types of summary
11753 tables, e.g. comparing characteristics across levels of a categorical variable
11754 and summarizing fitted generalized linear models, generalized estimating
11755 equations, and Cox proportional hazards models. Functions are available to
11756 handle data from simple random samples as well as complex surveys.")
11757 (license license:gpl3+)))
11759 (define-public r-dvmisc
11766 (uri (cran-uri "dvmisc" version))
11768 (base32 "01v6sixx0f3nrn6ymfifb3pvd2msfrwm21kmdv38laxq29vc4rsi"))))
11769 (build-system r-build-system)
11782 (home-page "https://cran.r-project.org/web/packages/dvmisc/")
11783 (synopsis "Faster computation of common statistics and miscellaneous functions")
11785 "This package implements faster versions of base R functions (e.g. mean, standard
11786 deviation, covariance, weighted mean), mostly written in C++, along with
11787 miscellaneous functions for various purposes (e.g. create the histogram with
11788 fitted probability density function or probability mass function curve, create
11789 the body mass index groups, assess the linearity assumption in logistic
11791 (license license:gpl2)))
11793 (define-public r-accelerometry
11795 (name "r-accelerometry")
11800 (uri (cran-uri "accelerometry" version))
11802 (base32 "13xzrwhr4i1nj9c8vrmfdg2rmrc8n446iihcyxmy99sm99hpzyip"))))
11803 (build-system r-build-system)
11805 (list r-dvmisc r-rcpp))
11806 (home-page "https://cran.r-project.org/web/packages/accelerometry/")
11807 (synopsis "Functions for processing accelerometer data")
11809 "This package provides a collection of functions that perform operations on
11810 time-series accelerometer data, such as identify the non-wear time, flag minutes
11811 that are part of an activity bout, and find the maximum 10-minute average count
11812 value. The functions are generally very flexible, allowing for a variety of
11813 algorithms to be implemented.")
11814 (license license:gpl3)))
11816 (define-public r-absim
11823 (uri (cran-uri "AbSim" version))
11825 (base32 "16ddjk8b6xw80ch4jis1y751i9561wdxh0gifbf15qiz3vjckq8m"))))
11826 (properties `((upstream-name . "AbSim")))
11827 (build-system r-build-system)
11829 (list r-ape r-powerlaw))
11830 (home-page "https://cran.r-project.org/web/packages/AbSim/")
11831 (synopsis "Time resolved simulations of antibody repertoires")
11833 "This package provides simulation methods for the evolution of antibody repertoires.
11834 The heavy and light chain variable region of both human and C57BL/6 mice can
11835 be simulated in a time-dependent fashion. Both single lineages using one set of
11836 V-, D-, and J-genes or full repertoires can be simulated. The algorithm begins
11837 with an initial V-D-J recombination event, starting the first phylogenetic tree.
11838 Upon completion, the main loop of the algorithm begins, with each iteration
11839 representing one simulated time step. Various mutation events are possible at
11840 each time step, contributing to a diverse final repertoire.")
11841 (license license:gpl2)))
11843 (define-public r-quic
11850 (uri (cran-uri "QUIC" version))
11852 (base32 "021bp9xbaih60qmss015ycblbv6d1dvb1z89y93zpqqnc2qhpv3c"))))
11853 (properties `((upstream-name . "QUIC")))
11854 (build-system r-build-system)
11855 (home-page "https://www.cs.utexas.edu/users/sustik/QUIC/")
11856 (synopsis "Regularized sparse inverse covariance matrix estimation")
11858 "This package implements the regularized Gaussian maximum likelihood
11859 estimation of the inverse of a covariance matrix. It uses Newton's method and
11860 coordinate descent to solve the regularized inverse covariance matrix
11861 estimation problem.")
11862 ;; The project home page states that the release is under GPLv3 or later.
11863 ;; The CRAN page only says GPL-3.
11864 (license license:gpl3+)))
11866 (define-public r-abundant
11868 (name "r-abundant")
11873 (uri (cran-uri "abundant" version))
11875 (base32 "15m3ngj5aipjg961yy5kvdg9xlfcpliw30dq6gchzxabhnfzcipd"))))
11876 (build-system r-build-system)
11879 (home-page "https://cran.r-project.org/web/packages/abundant/")
11880 (synopsis "Abundant regression and high-dimensional principal fitted components")
11882 "This package provides tools to fit and predict with the high-dimensional
11883 principal fitted components model. This model is described by Cook, Forzani,
11884 and Rothman (2012) @url{doi:10.1214/11-AOS962}.")
11885 ;; The DESCRIPTION file states GPL-2, but since it directly depends on a
11886 ;; GPLv3+ package (QUIC) this likely means GPLv2+.
11887 (license license:gpl2+)))
11889 (define-public r-ac3net
11896 (uri (cran-uri "Ac3net" version))
11898 (base32 "1ns4n0xxz6p34c11bj0k7nzgmyqr9mis2b0g5nfz37dbikndyqyz"))))
11899 (properties `((upstream-name . "Ac3net")))
11900 (build-system r-build-system)
11902 (list r-data-table))
11903 (home-page "https://cran.r-project.org/web/packages/Ac3net/")
11904 (synopsis "Inferring directional conservative causal core gene networks")
11905 (description "This package infers directional Conservative causal core
11906 (gene) networks (C3NET). This is a version of the algorithm C3NET with
11907 directional network.")
11908 (license license:gpl3+)))
11910 (define-public r-aca
11917 (uri (cran-uri "ACA" version))
11919 (base32 "1i3hm27nvnkvc39xlh0d1blq8q0q02czmvgi3cazmjx3jvxay0vq"))))
11920 (properties `((upstream-name . "ACA")))
11921 (build-system r-build-system)
11922 (home-page "https://cran.r-project.org/web/packages/ACA/")
11923 (synopsis "Abrupt change-point or aberration detection in point series")
11925 "This package offers an interactive function for the detection of breakpoints in
11927 ;; Any version of the GPL
11928 (license (list license:gpl2+ license:gpl3+))))
11930 (define-public r-acceptancesampling
11932 (name "r-acceptancesampling")
11937 (uri (cran-uri "AcceptanceSampling" version))
11939 (base32 "1ja1g0v8qvf7yj81x37wc6i7fkwpc573756jgvazazi8yf1gm12p"))))
11941 `((upstream-name . "AcceptanceSampling")))
11942 (build-system r-build-system)
11943 (home-page "https://cran.r-project.org/web/packages/AcceptanceSampling/")
11944 (synopsis "Creation and evaluation of acceptance sampling plans")
11946 "This @code{r-acceptancesampling} provides functionality for creating and evaluating
11947 acceptance sampling plans. Acceptance sampling is a methodology commonly used
11948 in quality control and improvement. International standards of acceptance
11949 sampling provide sampling plans for specific circumstances. The aim of this
11950 package is to provide an easy-to-use interface to visualize single, double or
11951 multiple sampling plans. In addition, methods have been provided to enable the
11952 user to assess sampling plans against pre-specified levels of performance, as
11953 measured by the probability of acceptance for a given level of quality in the
11955 (license license:gpl3+)))
11957 (define-public r-acclma
11964 (uri (cran-uri "ACCLMA" version))
11966 (base32 "1na27sp18fq12gp6vxgqw1ffsz2yi1d8xvrxbrzx5g1kqxrayy0v"))))
11967 (properties `((upstream-name . "ACCLMA")))
11968 (build-system r-build-system)
11969 (home-page "https://cran.r-project.org/web/packages/ACCLMA/")
11970 (synopsis "ACC & LMA graph plotting")
11972 "This package contains a function that imports data from a @acronym{CSV,
11973 Comma-Separated Values} file, or uses manually entered data from the format (x,
11974 y, weight) and plots the appropriate @acronym{ACC, Absolute Concentration
11975 Curve} vs @acronym{LOI, Line of Independence} graph and
11976 @acronym{LMA, @acronym{LOI} Minus @acronym{ACC}} graph. The main
11977 function is @code{plotLMA} (source file, header) that takes a data set and plots the
11978 appropriate @acronym{LMA} and @acronym{ACC} graphs. If no source file (a
11979 string) was passed, a manual data entry window is opened. The header parameter
11980 indicates by TRUE/FALSE (false by default) if the source @acronym{CSV} file has
11981 a header row or not. The dataset should contain only one independent variable
11982 (x) and one dependent variable (y) and can contain a weight for each
11984 (license license:gpl2)))
11986 (define-public r-aspi
11993 (uri (cran-uri "aspi" version))
11995 (base32 "0rhvxw243vvdv3hxa6pi343gcjc2cbxq1jzqirl9k1l4i3897l87"))))
11996 (build-system r-build-system)
11998 "https://cran.r-project.org/web/packages/aspi/")
12000 "Analysis of symmetry of parasitic infections")
12002 "This package provides tools for the analysis and visualization of bilateral
12003 asymmetry in parasitic infections.")
12004 (license license:gpl3+)))
12006 (define-public r-sandwich
12008 (name "r-sandwich")
12013 (uri (cran-uri "sandwich" version))
12016 "12aa5083k3sfrfq1jy3l94wffss9h0rga8j71jy3n8pkhiq4nn7n"))))
12017 (build-system r-build-system)
12020 (home-page "https://cran.r-project.org/web/packages/sandwich/")
12021 (synopsis "Robust Covariance Matrix Estimators")
12023 "This package provides model-robust standard error estimators for
12024 cross-sectional, time series, clustered, panel, and longitudinal data.")
12025 ;; Either version of the license.
12026 (license (list license:gpl2 license:gpl3))))
12028 (define-public r-th-data
12035 (uri (cran-uri "TH.data" version))
12038 "0ynxacnz002bjsp2ybql7rdqw4zd14af8r7w44nwbx22n4bapwzd"))))
12039 (properties `((upstream-name . "TH.data")))
12040 (build-system r-build-system)
12042 (list r-mass r-survival))
12045 (home-page "https://cran.r-project.org/web/packages/TH.data/")
12046 (synopsis "Shared data sets")
12048 "This package contains supporting data sets that are used in other
12049 packages maintained by Torsten Hothorn.")
12050 (license license:gpl3)))
12052 (define-public r-multcomp
12054 (name "r-multcomp")
12059 (uri (cran-uri "multcomp" version))
12062 "0mz5wdqrqpp2gqijfpp9rgfbq8yvxki4is8fbbc4qwdwryqp6d7h"))))
12063 (build-system r-build-system)
12065 (list r-codetools r-mvtnorm r-sandwich r-survival r-th-data))
12066 (home-page "https://cran.r-project.org/web/packages/multcomp/")
12067 (synopsis "Simultaneous inference in general parametric models")
12069 "Simultaneous tests and confidence intervals for general linear
12070 hypotheses in parametric models, including linear, generalized linear, linear
12071 mixed effects, and survival models. The package includes demos reproducing
12072 analyzes presented in the book \"Multiple Comparisons Using R\" (Bretz,
12073 Hothorn, Westfall, 2010, CRC Press).")
12074 (license license:gpl2)))
12076 (define-public r-multcompview
12078 (name "r-multcompview")
12083 (uri (cran-uri "multcompView" version))
12085 (base32 "1rfq9wvvrghq0542ff40wy8vdmsyd8spzz6ihcywcvxdfa8m6g8j"))))
12086 (properties `((upstream-name . "multcompView")))
12087 (build-system r-build-system)
12088 (home-page "https://cran.r-project.org/package=multcompView")
12089 (synopsis "Visualizations of paired comparisons")
12091 "Convert a logical vector or a vector of p-values or a correlation,
12092 difference, or distance matrix into a display identifying the pairs for which
12093 the differences were not significantly different.")
12094 ;; Any version of the GPL.
12095 (license license:gpl3+)))
12097 (define-public r-emmeans
12100 (version "1.7.4-1")
12104 (uri (cran-uri "emmeans" version))
12107 "08g7ifqhwqa00hc850nwx03dp7isz0281ig6kvixc4xdahmkm8zp"))))
12108 (build-system r-build-system)
12110 (list r-estimability r-mvtnorm r-numderiv r-xtable))
12113 (home-page "https://github.com/rvlenth/emmeans")
12114 (synopsis "Estimated marginal means, aka least-squares means")
12116 "This package provides tools to obtain @dfn{estimated marginal
12117 means} (EMMs) for many linear, generalized linear, and mixed models. It can
12118 be used to compute contrasts or linear functions of EMMs, trends, and
12119 comparisons of slopes.")
12120 ;; Either version of the license.
12121 (license (list license:gpl2 license:gpl3))))
12123 (define-public r-pwr
12130 (uri (cran-uri "pwr" version))
12133 "1kfzy73v3z6ipc3kdfkcjrp4b4p5k54nwk796gqi36srm93hgc2v"))))
12134 (build-system r-build-system)
12137 (home-page "https://github.com/heliosdrm/pwr")
12138 (synopsis "Basic functions for power analysis")
12140 "This package provides power analysis functions along the lines of
12142 (license license:gpl3+)))
12144 (define-public r-libcoin
12151 (uri (cran-uri "libcoin" version))
12153 (base32 "1syrcdj5qg5m3zd3dlxgpfklswbalfg42w058dr09hnzqsvx0z9d"))))
12154 (build-system r-build-system)
12155 (propagated-inputs (list r-mvtnorm))
12156 (home-page "https://cran.r-project.org/web/packages/libcoin")
12157 (synopsis "Linear test statistics for permutation inference")
12159 "This package provides basic infrastructure for linear test statistics
12160 and permutation inference in the framework of Strasser and Weber (1999).")
12161 (license license:gpl2)))
12163 (define-public r-coin
12170 (uri (cran-uri "coin" version))
12173 "1cpv7jx840inzg98bkhrb5yscx0gpag6br237r5qpnc2gbrd2ikm"))))
12174 (build-system r-build-system)
12182 (home-page "http://coin.r-forge.r-project.org")
12183 (synopsis "Conditional inference procedures in a permutation test framework")
12185 "This package provides conditional inference procedures for the general
12186 independence problem including two-sample, K-sample (non-parametric ANOVA),
12187 correlation, censored, ordered and multivariate problems.")
12188 (license license:gpl2)))
12190 (define-public r-bayesplot
12192 (name "r-bayesplot")
12197 (uri (cran-uri "bayesplot" version))
12200 "0hqy597ang53phxnl084hak35ffqz9lw9hygax7370gpkjws908a"))))
12201 (build-system r-build-system)
12216 (home-page "https://mc-stan.org/bayesplot")
12217 (synopsis "Plotting for Bayesian models")
12219 "This package provides plotting functions for posterior analysis, model
12220 checking, and MCMC diagnostics. The package is designed not only to provide
12221 convenient functionality for users, but also a common set of functions that
12222 can be easily used by developers working on a variety of R packages for
12223 Bayesian modeling.")
12224 (license license:gpl3+)))
12226 (define-public r-tmb
12233 (uri (cran-uri "TMB" version))
12236 "1mr5vwamw6ag1fhd83jyy6015296908qwshwq0fcphhiv60x579c"))))
12237 (properties `((upstream-name . "TMB")))
12238 (build-system r-build-system)
12240 (list r-matrix r-rcppeigen))
12241 (home-page "http://tmb-project.org")
12242 (synopsis "Template model builder: a general random effect tool")
12244 "With this tool, a user should be able to quickly implement complex
12245 random effect models through simple C++ templates. The package combines
12246 @code{CppAD} (C++ automatic differentiation), @code{Eigen} (templated
12247 matrix-vector library) and @code{CHOLMOD} (sparse matrix routines available
12248 from R) to obtain an efficient implementation of the applied Laplace
12249 approximation with exact derivatives. Key features are: Automatic sparseness
12250 detection, parallelism through BLAS and parallel user templates.")
12251 (license license:gpl2)))
12253 (define-public r-sjstats
12260 (uri (cran-uri "sjstats" version))
12262 (base32 "1cv80yjnyh6qihxf57zivihhia20gibr5f03x8aspy6382wnwlka"))))
12263 (build-system r-build-system)
12282 (home-page "https://github.com/strengejacke/sjstats")
12283 (synopsis "Functions for common statistical computations")
12285 "This package provides a collection of convenient functions for common
12286 statistical computations, which are not directly provided by R's @code{base}
12287 or @code{stats} packages. This package aims at providing, first, shortcuts
12288 for statistical measures, which otherwise could only be calculated with
12289 additional effort. Second, these shortcut functions are generic, and can be
12290 applied not only to vectors, but also to other objects as well. The focus of
12291 most functions lies on summary statistics or fit measures for regression
12292 models, including generalized linear models, mixed effects models and Bayesian
12294 (license license:gpl3)))
12296 (define-public r-glmmtmb
12303 (uri (cran-uri "glmmTMB" version))
12306 "0xdjc3gx0cj098rrjzlsy9cccxzfvn029xh4ycpya4xjhxsykldr"))))
12307 (properties `((upstream-name . "glmmTMB")))
12308 (build-system r-build-system)
12317 (list r-knitr r-rmarkdown)) ; for vignettes
12318 (home-page "https://github.com/glmmTMB")
12319 (synopsis "Generalized linear mixed models")
12321 "Fit linear and generalized linear mixed models with various extensions,
12322 including zero-inflation. The models are fitted using maximum likelihood
12323 estimation via the Template Model Builder. Random effects are assumed to be
12324 Gaussian on the scale of the linear predictor and are integrated out using the
12325 Laplace approximation. Gradients are calculated using automatic
12327 (license license:agpl3+)))
12329 (define-public r-bayestestr
12331 (name "r-bayestestr")
12336 (uri (cran-uri "bayestestR" version))
12339 "1fbkpagc5zznrafy7h68nhx43a1yg4v7242pbqjkd0h2481c101z"))))
12340 (properties `((upstream-name . "bayestestR")))
12341 (build-system r-build-system)
12343 (list r-datawizard r-insight))
12346 (home-page "https://github.com/easystats/bayestestR")
12347 (synopsis "Describe Bayesian models and posterior distributions")
12349 "This package provides utilities to understand and describe posterior
12350 distributions and Bayesian models. It includes point-estimates such as
12351 @dfn{Maximum A Posteriori} (MAP), measures of dispersion such as @dfn{Highest
12352 Density Interval} (HDI), and indices used for null-hypothesis testing (such as
12353 ROPE percentage and pd).")
12354 (license license:gpl3)))
12356 (define-public r-performance
12358 (name "r-performance")
12363 (uri (cran-uri "performance" version))
12366 "1znr4i1pjv6z3lj6qrma2i3l94rz1z29w92mrxxfy3ch0s71crww"))))
12367 (build-system r-build-system)
12369 (list r-bayestestr r-datawizard r-insight))
12370 (home-page "https://easystats.github.io/performance/")
12371 (synopsis "Assessment of regression models performance")
12373 "This package provides utilities for computing measures to assess model
12374 quality, which are not directly provided by R's @code{base} or @code{stats}
12375 packages. These include e.g. measures like r-squared, intraclass correlation
12376 coefficient, root mean squared error or functions to check models for
12377 overdispersion, singularity or zero-inflation and more. Functions apply to a
12378 large variety of regression models, including generalized linear models, mixed
12379 effects models and Bayesian models.")
12380 (license license:gpl3)))
12382 (define-public r-ggeffects
12384 (name "r-ggeffects")
12389 (uri (cran-uri "ggeffects" version))
12392 "01yyfw7fkbxrp0gpwni5y8m4w9l3xckwc3crnvy1fqs1d6gwx3xx"))))
12393 (build-system r-build-system)
12395 (list r-insight r-mass r-sjlabelled))
12398 (home-page "https://github.com/strengejacke/ggeffects")
12399 (synopsis "Create tidy data frames of marginal effects for ggplot")
12401 "This package provides tools to compute marginal effects from statistical
12402 models and return the result as tidy data frames. These data frames are ready
12403 to use with the @code{ggplot2} package. Marginal effects can be calculated
12404 for many different models. Interaction terms, splines and polynomial terms
12405 are also supported. The two main functions are @code{ggpredict()} and
12406 @code{ggeffect()}. There is a generic @code{plot()} method to plot the
12407 results using @code{ggplot2}.")
12408 (license license:gpl3)))
12410 (define-public r-effectsize
12412 (name "r-effectsize")
12417 (uri (cran-uri "effectsize" version))
12420 "07dbj7n9vwjkb7xrdj224lzc3ppr3jjdgyyilkj7gpkvgjgfrqhz"))))
12421 (properties `((upstream-name . "effectsize")))
12422 (build-system r-build-system)
12424 (list r-bayestestr r-datawizard r-insight r-parameters
12428 (home-page "https://github.com/easystats/effectsize")
12429 (synopsis "Indices of effect size and standardized parameters")
12431 "This package provides utilities to work with indices of effect size and
12432 standardized parameters for a wide variety of models, allowing computation and
12433 conversion of indices such as Cohen's d, r, odds, etc.")
12434 (license license:gpl3)))
12436 (define-public r-sjplot
12443 (uri (cran-uri "sjPlot" version))
12445 (base32 "1rnwhh271xj8xgvvlpqw9ain56mfz37fvl7f6jq9nzx9jxx95bjd"))))
12446 (properties `((upstream-name . "sjPlot")))
12447 (build-system r-build-system)
12469 (home-page "https://strengejacke.github.io/sjPlot/")
12470 (synopsis "Data visualization for statistics in social science")
12472 "This package represents a collection of plotting and table output
12473 functions for data visualization. Results of various statistical
12474 analyses (that are commonly used in social sciences) can be visualized using
12475 this package, including simple and cross tabulated frequencies, histograms,
12476 box plots, (generalized) linear models, mixed effects models, principal
12477 component analysis and correlation matrices, cluster analyses, scatter plots,
12478 stacked scales, effects plots of regression models (including interaction
12479 terms) and much more. This package supports labelled data.")
12480 (license license:gpl3)))
12482 (define-public r-ini
12489 (uri (cran-uri "ini" version))
12492 "04yqij344dwm0xqgara8xia42mlmij3i8711qbb5534w05a1l6bv"))))
12493 (build-system r-build-system)
12494 (home-page "https://github.com/dvdscripter/ini")
12495 (synopsis "Read and write configuration files")
12497 "This package provides tools to parse simple @code{.ini} configuration
12498 files to an structured list. Users can manipulate this resulting list with
12499 @code{lapply()} functions. This same structured list can be used to write
12500 back to file after modifications.")
12501 (license license:gpl3)))
12503 (define-public r-gillespiessa2
12505 (name "r-gillespiessa2")
12510 (uri (cran-uri "GillespieSSA2" version))
12512 (base32 "03ym8qx5yc1a6j9l973lc0rjzs8hiax8fq13j7m1fcb1pvnbvar5"))))
12513 (properties `((upstream-name . "GillespieSSA2")))
12514 (build-system r-build-system)
12527 (native-inputs (list r-knitr))
12528 (home-page "https://github.com/rcannood/GillespieSSA2")
12529 (synopsis "Gillespie's stochastic simulation algorithm")
12531 "This package provides a fast, scalable, and versatile framework for
12532 simulating large systems with Gillespie's @dfn{Stochastic Simulation
12533 Algorithm} (SSA). This package is the spiritual successor to the GillespieSSA
12534 package. Benefits of this package include major speed improvements (>100x),
12535 easier to understand documentation, and many unit tests that try to ensure the
12536 package works as intended.")
12537 (license license:gpl3+)))
12539 (define-public r-gitcreds
12541 (name "r-gitcreds")
12546 (uri (cran-uri "gitcreds" version))
12549 "1snzn7nxy0rwz0bzjsg6k04c0n811dgn8gn9cmn2v78aj57ayjmi"))))
12550 (properties `((upstream-name . "gitcreds")))
12551 (build-system r-build-system)
12552 (inputs (list git-minimal))
12553 (native-inputs (list r-knitr))
12554 (home-page "https://github.com/r-lib/gitcreds")
12555 (synopsis "Query git credentials from R")
12557 "Query, set, and delete credentials from the git credential store.
12558 Manage GitHub tokens and other git credentials. This package is to be used by
12559 other packages that need to authenticate to GitHub and/or other git
12561 (license license:expat)))
12563 (define-public r-gh
12570 (uri (cran-uri "gh" version))
12573 "077drbxz3rx7idv6w24ipj1p6jnzv86a3iyryab699cc9q2kjh54"))))
12574 (build-system r-build-system)
12576 (list r-cli r-gitcreds r-httr r-ini r-jsonlite))
12579 (home-page "https://github.com/r-lib/gh#readme")
12580 (synopsis "Access the GitHub API via R")
12582 "This package provides a minimal R client to access the GitHub API.")
12583 (license license:expat)))
12585 (define-public r-fs
12592 (uri (cran-uri "fs" version))
12595 "11qr3v0xn65vfhgcxl4l6yv48s4w0w3ldp3anpzc25vd3mwd3jim"))))
12596 (build-system r-build-system)
12599 (home-page "https://fs.r-lib.org")
12600 (synopsis "Cross-platform file system operations based on libuv")
12602 "This package provides a cross-platform interface to file system
12603 operations, built on top of the libuv C library.")
12604 (license license:gpl3)))
12606 (define-public r-clisymbols
12608 (name "r-clisymbols")
12613 (uri (cran-uri "clisymbols" version))
12616 "1q7gi2zmykhzas9v8fdnbpdq7pzdcpbhim1yxvd2062l777g4j86"))))
12617 (build-system r-build-system)
12618 (home-page "https://github.com/gaborcsardi/clisymbols")
12619 (synopsis "Unicode symbols at the R prompt")
12621 "This package provides a small subset of Unicode symbols, that are useful
12622 when building command line applications. They fall back to alternatives on
12623 terminals that do not support Unicode.")
12624 (license license:expat)))
12626 (define-public r-credentials
12628 (name "r-credentials")
12633 (uri (cran-uri "credentials" version))
12636 "1f18j3zrq8c9kah57xwahmmljsjg5qphlgamvx507ynvpq8pryig"))))
12637 (properties `((upstream-name . "credentials")))
12638 (build-system r-build-system)
12641 (modify-phases %standard-phases
12642 (add-after 'unpack 'setenv-HOME
12644 ;; This is necessary because git looks for $HOME/.gitconfig
12645 (setenv "HOME" "/tmp"))))))
12647 (list git-minimal))
12649 (list r-askpass r-curl r-jsonlite r-openssl r-sys))
12652 (home-page "https://docs.ropensci.org/credentials/")
12653 (synopsis "Tools for managing SSH and Git credentials")
12655 "This package assists you in setting up and retrieving of HTTPS and SSH
12656 credentials for use with git and other services. For HTTPS remotes the
12657 package interfaces the @command{git-credential} utility which @command{git}
12658 uses to store HTTP usernames and passwords. For SSH remotes this package
12659 provides convenient functions to find or generate appropriate SSH keys. The
12660 package both helps the user to setup a local git installation, and also
12661 provides a back-end for git/ssh client libraries to authenticate with existing
12662 user credentials.")
12663 (license license:expat)))
12665 (define-public r-gert
12672 (uri (cran-uri "gert" version))
12675 "0r19vi77yyjw5gbhgjibdysjlszlw2095v14f6sv675zpbp0li4c"))))
12676 (properties `((upstream-name . "gert")))
12677 (build-system r-build-system)
12679 (list libgit2 zlib))
12688 (list pkg-config r-knitr))
12689 (home-page "https://docs.ropensci.org/gert/")
12690 (synopsis "Simple Git client for R")
12692 "This package provides a simple git client for R based on libgit2 with
12693 support for SSH and HTTPS remotes. All functions in gert use basic R data
12694 types (such as vectors and data-frames) for their arguments and return values.
12695 User credentials are shared with command line git through the
12696 @code{git-credential} store and SSH keys stored on disk or ssh-agent.")
12697 (license license:expat)))
12699 (define-public r-usethis
12706 (uri (cran-uri "usethis" version))
12709 "0638dzl4nm4c36990sf2biy74hjr2fzlqzfb98fsqrbhaw3ngp1i"))))
12710 (build-system r-build-system)
12731 (home-page "https://github.com/r-lib/usethis")
12732 (synopsis "Automate R package and project setup")
12734 "This package helps you to automate R package and project setup tasks
12735 that are otherwise performed manually. This includes setting up unit testing,
12736 test coverage, continuous integration, Git, GitHub integration, licenses,
12737 Rcpp, RStudio projects, and more.")
12738 (license license:gpl3)))
12740 (define-public r-sessioninfo
12742 (name "r-sessioninfo")
12747 (uri (cran-uri "sessioninfo" version))
12750 "1jy7n37qnrb4fgzmn8s8yf7kv29yw27x8zklwf8qdb2kgj2q6qpm"))))
12751 (build-system r-build-system)
12754 (home-page "https://github.com/r-lib/sessioninfo#readme")
12755 (synopsis "R session information")
12757 "This package provides tools to query and print information about the
12758 current R session. It is similar to @code{utils::sessionInfo()}, but includes
12759 more information about packages, and where they were installed from.")
12760 (license license:gpl2)))
12762 (define-public r-remotes
12769 (uri (cran-uri "remotes" version))
12772 "05m5dgv0nba5vhjbdkd8z5lbhpfxgkw31j58am7vz1d44igqgvzj"))))
12773 (build-system r-build-system)
12776 (home-page "https://github.com/r-lib/remotes#readme")
12777 (synopsis "R package installation from remote repositories")
12779 "Download and install R packages stored in GitHub, BitBucket, or plain
12780 subversion or git repositories. This package is a lightweight replacement of
12781 the @code{install_*} functions in the @code{devtools} package. Indeed most of
12782 the code was copied over from @code{devtools}.")
12783 (license license:gpl2+)))
12785 (define-public r-xopen
12792 (uri (cran-uri "xopen" version))
12795 "1vrvgdika1d63dwygynbv2wmd87ll8dji5dy89hj576n8hw601z2"))))
12796 (build-system r-build-system)
12799 (home-page "https://github.com/r-lib/xopen#readme")
12800 (synopsis "Open system files, URLs, anything")
12802 "This package provides a cross-platform solution to open files,
12803 directories or URLs with their associated programs.")
12804 (license license:expat)))
12806 (define-public r-rcmdcheck
12808 (name "r-rcmdcheck")
12813 (uri (cran-uri "rcmdcheck" version))
12816 "1l696byn3kjq2xvz4wxybzaj6ink85h4lz3a35v2132ba5yyzm5v"))))
12817 (build-system r-build-system)
12831 (home-page "https://github.com/r-Lib/rcmdcheck#readme")
12832 (synopsis "Run R CMD check from R and capture results")
12834 "Run @code{R CMD check} from R programmatically, and capture the results
12835 of the individual checks.")
12836 (license license:expat)))
12838 (define-public r-rapportools
12840 (name "r-rapportools")
12845 (uri (cran-uri "rapportools" version))
12848 "0qr86idng12g6hdd764j0wmli700v7rjhw7jdjxj0ka8xm5v7ymm"))))
12849 (build-system r-build-system)
12851 (list r-mass r-pander r-plyr r-reshape2))
12852 (home-page "https://cran.r-project.org/web/packages/rapportools/")
12853 (synopsis "Miscellaneous helper functions with sane defaults for reporting")
12855 "This package provides helper functions that act as wrappers to more
12856 advanced statistical methods with the advantage of having sane defaults for
12858 (license license:agpl3+)))
12860 (define-public r-pander
12867 (uri (cran-uri "pander" version))
12870 "144zkq5w7v6fpzk3x40i0baybbp0y6x2ckh4b9qljryas9mhgp9a"))))
12871 (build-system r-build-system)
12873 (list r-digest r-rcpp))
12876 (home-page "https://rapporter.github.io/pander")
12877 (synopsis "Render R objects into Pandoc's markdown")
12879 "The main aim of the pander R package is to provide a minimal and easy
12880 tool for rendering R objects into Pandoc's markdown. The package is also
12881 capable of exporting/converting complex Pandoc documents (reports) in various
12883 ;; This package is licensed under either the AGPLv3+ or the very rarely
12885 (license license:agpl3+)))
12887 (define-public r-summarytools
12889 (name "r-summarytools")
12894 (uri (cran-uri "summarytools" version))
12897 "0gr95cd1ja8di6s0xghk6w7nj3bh3z4g7j7ixdy7f88q681aixgx"))))
12898 (build-system r-build-system)
12914 (home-page "https://github.com/dcomtois/summarytools")
12915 (synopsis "Tools to quickly and neatly summarize data")
12917 "This package provides tools for data frame summaries, cross-tabulations,
12918 weight-enabled frequency tables and common univariate statistics in concise
12919 tables available in a variety of formats (plain ASCII, Markdown and HTML). A
12920 good point-of-entry for exploring data, both for experienced and new R
12922 (license license:gpl2)))
12924 (define-public r-lsei
12931 (uri (cran-uri "lsei" version))
12934 "1dka0rigfw4vj809qma2dkiwjb3nw5635ynnba5cm299cn7hb2b2"))))
12935 (build-system r-build-system)
12938 (home-page "https://www.stat.auckland.ac.nz/~yongwang")
12939 (synopsis "Solve regression problems under equality/inequality constraints")
12941 "It contains functions that solve least squares linear regression
12942 problems under linear equality/inequality constraints. Functions for solving
12943 quadratic programming problems are also available, which transform such
12944 problems into least squares ones first.")
12945 (license license:gpl2+)))
12947 (define-public r-npsurv
12954 (uri (cran-uri "npsurv" version))
12957 "1ihxhb42cga1hssj2jv4ah0f4hlwsky899ij5261fzh1wxvdp1xw"))))
12958 (build-system r-build-system)
12961 (home-page "https://www.stat.auckland.ac.nz/~yongwang")
12962 (synopsis "Nonparametric survival analysis")
12964 "This package contains functions for non-parametric survival analysis of
12965 exact and interval-censored observations.")
12966 (license license:gpl2+)))
12968 (define-public r-clusteval
12970 (name "r-clusteval")
12975 (uri (cran-uri "clusteval" version))
12978 "1ld0bdl4fy8dsfzm3k7a37cyxc6pfc9qs31x4pxd3z5rslghz7rj"))))
12979 (build-system r-build-system)
12981 (list r-mvtnorm r-rcpp))
12982 (home-page "https://cran.r-project.org/web/packages/clusteval/")
12983 (synopsis "Evaluation of clustering algorithms")
12985 "This R package provides a suite of tools to evaluate clustering
12986 algorithms, clusterings, and individual clusters.")
12987 (license license:expat)))
12989 (define-public r-tweedie
12996 (uri (cran-uri "tweedie" version))
12999 "1nfhaqblvm62j8gfkyrgba5ai0pb2fsnrxp63637mhys2bawlcm0"))))
13000 (build-system r-build-system)
13001 (native-inputs (list gfortran))
13002 (home-page "https://cran.r-project.org/web/packages/tweedie/")
13003 (synopsis "Evaluation of Tweedie exponential family models")
13005 "Maximum likelihood computations for Tweedie families, including the
13006 series expansion (Dunn and Smyth, 2005; <doi10.1007/s11222-005-4070-y>) and
13007 the Fourier inversion (Dunn and Smyth, 2008; <doi:10.1007/s11222-007-9039-6>),
13008 and related methods.")
13009 (license license:gpl2+)))
13011 (define-public r-rcppgsl
13018 (uri (cran-uri "RcppGSL" version))
13020 (base32 "1a5dms0axlzgpv1z2bhfrb77497h0ch1yslq0gidj14vr4kfm57h"))))
13021 (properties `((upstream-name . "RcppGSL")))
13022 (build-system r-build-system)
13025 (home-page "https://cran.r-project.org/web/packages/RcppGSL/")
13026 (synopsis "Rcpp integration for GSL vectors and matrices")
13028 "The GNU Scientific Library (or GSL) is a collection of numerical
13029 routines for scientific computing. It is particularly useful for C and C++
13030 programs as it provides a standard C interface to a wide range of mathematical
13031 routines. There are over 1000 functions in total with an extensive test
13032 suite. The RcppGSL package provides an easy-to-use interface between GSL data
13033 structures and R using concepts from Rcpp which is itself a package that eases
13034 the interfaces between R and C++.")
13035 (license license:gpl2+)))
13037 (define-public r-mvabund
13044 (uri (cran-uri "mvabund" version))
13047 "01kss9dx4an1ir5zs46jypvhj8sdc8wcs00i1223ai09av4lcsgd"))))
13048 (build-system r-build-system)
13050 (list r-mass r-rcpp r-rcppgsl r-statmod r-tweedie))
13051 (home-page "https://cran.r-project.org/web/packages/mvabund/")
13052 (synopsis "Statistical methods for analysing multivariate abundance data")
13054 "This package provides a set of tools for displaying, modeling and
13055 analysing multivariate abundance data in community ecology.")
13056 (license license:lgpl2.1+)))
13058 (define-public r-afex
13065 (uri (cran-uri "afex" version))
13068 "09q426s2zmzxx5ilxy0x5mflpb38pl075ss1s8xvpswkn6cia0b6"))))
13069 (build-system r-build-system)
13070 ;; This is needed for the vignette builder
13073 (modify-phases %standard-phases
13074 (add-after 'unpack 'set-HOME
13075 (lambda _ (setenv "HOME" "/tmp"))))))
13077 (list r-car r-lme4 r-lmertest r-pbkrtest r-reshape2))
13080 r-r-rsp)) ;vignette builder
13081 (home-page "https://afex.singmann.science/")
13082 (synopsis "Analysis of factorial experiments")
13084 "This package provides convenience functions for analyzing factorial
13085 experiments using ANOVA or mixed models.")
13086 (license license:gpl2+)))
13088 (define-public r-lmertest
13090 (name "r-lmertest")
13095 (uri (cran-uri "lmerTest" version))
13098 "1zd8gqjkazhxgpnnr484xwsq30p62fq8592nzyc171zjyplpbaim"))))
13099 (properties `((upstream-name . "lmerTest")))
13100 (build-system r-build-system)
13102 (list r-ggplot2 r-lme4 r-mass r-numderiv))
13103 (home-page "https://github.com/runehaubo/lmerTestR")
13104 (synopsis "Tests in linear mixed effects models")
13106 "This package provides p-values in type I, II or III anova and summary
13107 tables for @code{lmer} model fits via Satterthwaite's degrees of freedom
13108 method. A Kenward-Roger method is also available via the @code{pbkrtest}
13109 package. Model selection methods include step, drop1 and anova-like tables
13110 for random effects (ranova). Methods for Least-Square means (LS-means) and
13111 tests of linear contrasts of fixed effects are also available.")
13112 (license license:gpl2+)))
13114 (define-public r-r2glmm
13121 (uri (cran-uri "r2glmm" version))
13124 "0iim92blpa59vgz97c2pi05yhbjjmaffdbkbmk5kplfb2vmazgiy"))))
13125 (build-system r-build-system)
13137 (home-page "https://github.com/bcjaeger/r2glmm")
13138 (synopsis "Compute R squared for mixed (multilevel) models")
13140 "This package computes model and semi partial R squared with confidence
13141 limits for the linear and generalized linear mixed model (LMM and GLMM). The
13142 R squared measure from L. J. Edwards et al. (2008) is extended to the GLMM
13143 using @dfn{penalized quasi-likelihood} (PQL) estimation (see Jaeger et
13145 (license license:gpl2)))
13147 (define-public r-cmdfun
13154 (uri (cran-uri "cmdfun" version))
13157 "1pbcq7hi2lcmqnghmy3q2fsk0c9fy5m0637acyzmc096fxbx723j"))))
13158 (properties `((upstream-name . "cmdfun")))
13159 (build-system r-build-system)
13169 (home-page "https://snystrom.github.io/cmdfun/")
13170 (synopsis "Framework for building interfaces to shell commands")
13172 "Writing interfaces to command line software is cumbersome. The cmdfun
13173 package provides a framework for building function calls to seamlessly
13174 interface with shell commands by allowing lazy evaluation of command line
13175 arguments. It also provides methods for handling user-specific paths to tool
13176 installs or secrets like API keys. Its focus is to equally serve package
13177 builders who wish to wrap command line software, and to help analysts stay
13178 inside R when they might usually leave to execute non-R software.")
13179 (license license:expat)))
13181 (define-public r-rslurm
13188 (uri (cran-uri "rslurm" version))
13191 "19451icfh7snjbbmpzpr1hrdf52q8ijv0ag1di3y55r2la3jxxcf"))))
13192 (properties `((upstream-name . "rslurm")))
13193 (build-system r-build-system)
13194 (propagated-inputs (list r-whisker))
13195 (native-inputs (list r-knitr))
13196 (home-page "http://cyberhelp.sesync.org/rslurm/")
13197 (synopsis "Submit R calculations to a Slurm cluster")
13199 "This package provides functions that simplify submitting R scripts to a
13200 Slurm workload manager, in part by automating the division of embarrassingly
13201 parallel calculations across cluster nodes.")
13202 (license license:gpl3)))
13204 (define-public r-chk
13211 (uri (cran-uri "chk" version))
13214 "10gcv00mgi88vgxr9jrs0ar67crmdcdi4m9g86cm6pg3ly0v097y"))))
13215 (properties `((upstream-name . "chk")))
13216 (build-system r-build-system)
13218 (list r-lifecycle r-rlang))
13219 (native-inputs (list r-knitr))
13220 (home-page "https://github.com/poissonconsulting/chk")
13221 (synopsis "Check user-supplied function arguments")
13223 "This is a package for developers to check user-supplied function
13224 arguments. It is designed to be simple, fast and customizable. Error
13225 messages follow the tidyverse style guide.")
13226 (license license:expat)))
13228 (define-public r-weights
13235 (uri (cran-uri "weights" version))
13238 "1fnchf7f0hyl514bk8sc3l884kg25kb5xm4mc2l28n6hm7l6bgpg"))))
13239 (build-system r-build-system)
13241 (list r-gdata r-hmisc r-lme4 r-mice))
13242 (home-page "https://cran.r-project.org/web/packages/weights/")
13243 (synopsis "Weighting and weighted statistics")
13244 (description "This package Provides a variety of functions for producing
13245 simple weighted statistics, such as weighted Pearson's correlations, partial
13246 correlations, Chi-Squared statistics, histograms, and t-tests. Also now
13247 includes some software for quickly recoding survey data and plotting point
13248 estimates from interaction terms in regressions (and multiply imputed
13249 regressions). NOTE: Weighted partial correlation calculations pulled to
13251 (license license:gpl2+)))
13253 (define-public r-rcppannoy
13255 (name "r-rcppannoy")
13260 (uri (cran-uri "RcppAnnoy" version))
13263 "12k8ny981dmky5js8yl6bih5r5mq3w43f2f9admhkwqn0n80kcl9"))))
13264 (properties `((upstream-name . "RcppAnnoy")))
13265 (build-system r-build-system)
13268 (home-page "https://cran.r-project.org/web/packages/RcppAnnoy/")
13269 (synopsis "Rcpp bindings for Annoy, a library for Approximate Nearest Neighbors")
13271 "Annoy is a small C++ library for Approximate Nearest Neighbors written
13272 for efficient memory usage as well an ability to load from and save to disk.
13273 This package provides an R interface.")
13274 ;; Annoy is released under ASL 2.0, but this wrapper is released under
13276 (license (list license:gpl2+ license:asl2.0))))
13278 (define-public r-rcpphnsw
13280 (name "r-rcpphnsw")
13285 (uri (cran-uri "RcppHNSW" version))
13288 "01z0plf1i6dyibw4ica8shmijyk1grpqb886hcga72z2cpm4xsx0"))))
13289 (properties `((upstream-name . "RcppHNSW")))
13290 (build-system r-build-system)
13291 (propagated-inputs (list r-rcpp))
13292 (home-page "https://cran.r-project.org/web/packages/RcppHNSW/")
13293 (synopsis "Rcpp bindings for hnswlib, a library for approximate nearest neighbors")
13295 "Hnswlib is a C++ library for approximate nearest neighbors. This
13296 package provides a minimal R interface by relying on the Rcpp package.")
13297 ;; hnswlib is released under Version 2.0 of the Apache License.
13298 (license (list license:gpl3 license:asl2.0))))
13300 (define-public r-rcppparallel
13302 (name "r-rcppparallel")
13307 (uri (cran-uri "RcppParallel" version))
13310 "1sn211ajlb1p12sglxqns175rg078yvww268m8cp0vvd7cmk55k3"))))
13311 (properties `((upstream-name . "RcppParallel")))
13312 (build-system r-build-system)
13313 (home-page "https://rcppcore.github.io/RcppParallel/")
13314 (synopsis "Parallel programming tools for Rcpp")
13316 "This package provides high level functions for parallel programming with
13317 Rcpp. For example, the @code{parallelFor()} function can be used to convert
13318 the work of a standard serial @code{for} loop into a parallel one and the
13319 @code{parallelReduce()} function can be used for accumulating aggregates or
13321 (license license:gpl2)))
13323 (define-public r-ncdf4
13330 (uri (cran-uri "ncdf4" version))
13333 "0qzvin2fjzcb7h2knlnw14s6043pwi1nm7yf6p27ax7w269173fb"))))
13334 (build-system r-build-system)
13336 (list netcdf zlib))
13337 (home-page "https://cran.r-project.org/web/packages/ncdf4/index.html")
13338 (synopsis "R interface to Unidata netCDF format data files")
13340 "This package provides a high-level R interface to data files written
13341 using Unidata's netCDF library (version 4 or earlier), which are binary data
13342 files that are portable across platforms and include metadata information in
13343 addition to the data sets. Using this package, netCDF files can be opened and
13344 data sets read in easily. It is also easy to create new netCDF dimensions,
13345 variables, and files, in either version 3 or 4 format, and manipulate existing
13347 (license license:gpl3+)))
13349 (define-public r-biocmanager
13351 (name "r-biocmanager")
13352 (version "1.30.18")
13356 (uri (cran-uri "BiocManager" version))
13358 (base32 "0dawbd546rznllpw5wq282r0viga4cck398d4s1inkk18mmi4qzp"))))
13359 (properties `((upstream-name . "BiocManager")))
13360 (build-system r-build-system)
13363 (home-page "https://cran.r-project.org/web/packages/BiocManager/")
13364 (synopsis "Access the Bioconductor project package repository")
13366 "This package provides a convenient tool to install and update
13367 Bioconductor packages.")
13368 (license license:artistic2.0)))
13370 (define-public r-rgl
13373 (version "0.108.3.2")
13377 (uri (cran-uri "rgl" version))
13380 "0r9wzhjzl346i37ngs6hqzmizhi53kzqz582lv822v6yxang6fh3"))))
13381 (build-system r-build-system)
13383 (list pkg-config r-knitr))
13398 (home-page "https://r-forge.r-project.org/projects/rgl/")
13399 (synopsis "3D visualization using OpenGL")
13401 "This package provides medium to high level functions for 3D interactive graphics,
13402 including functions modelled on base graphics (@code{plot3d()}, etc.) as well
13403 as functions for constructing representations of geometric
13404 objects (@code{cube3d()}, etc.). Output may be on screen using OpenGL, or to
13405 various standard 3D file formats including WebGL, PLY, OBJ, STL as well as 2D
13406 image formats, including PNG, Postscript, SVG, PGF.")
13407 ;; Any version of the GPL.
13408 (license (list license:gpl2+ license:gpl3+))))
13410 (define-public r-multicool
13412 (name "r-multicool")
13417 (uri (cran-uri "multicool" version))
13420 "0djacq0irfqz4nlnx238kja73yvr1n5qybbfyl6bw1n6qgcjhza8"))))
13421 (build-system r-build-system)
13422 (propagated-inputs (list r-rcpp))
13423 (home-page "https://cran.r-project.org/web/packages/multicool/")
13424 (synopsis "Permutations of multisets in cool-lex order")
13426 "This package provides a set of tools to permute multisets without loops
13427 or hash tables and to generate integer partitions. Cool-lex order is similar
13428 to colexicographical order.")
13429 (license license:gpl2)))
13431 (define-public r-misc3d
13438 (uri (cran-uri "misc3d" version))
13441 "0r9x57s63kx9f6dgam2nhbziq8nrs9wd8pk7g76hds2kw46vnyx0"))))
13442 (build-system r-build-system)
13443 (home-page "https://cran.r-project.org/web/packages/misc3d/")
13444 (synopsis "Miscellaneous 3D Plots")
13446 "This package provides a collection of miscellaneous 3d plots, including
13448 ;; Any version of the GPL.
13449 (license (list license:gpl2+ license:gpl3+))))
13451 (define-public r-ks
13458 (uri (cran-uri "ks" version))
13460 (base32 "05bqrjkbx2kn5aax0hy3xd6pf7nxka9bm1sp8ll1cc2gf1nx1i6i"))))
13461 (build-system r-build-system)
13473 (home-page "https://www.mvstat.net/tduong/")
13474 (synopsis "Kernel smoothing")
13476 "This package provides kernel smoothers for univariate and multivariate
13477 data, including density functions, density derivatives, cumulative
13478 distributions, modal clustering, discriminant analysis, and two-sample
13479 hypothesis testing.")
13480 ;; Either version of the GPL.
13481 (license (list license:gpl2 license:gpl3))))
13483 (define-public r-feature
13490 (uri (cran-uri "feature" version))
13493 "0yzn1w1sasilcp8v0pcjnxjv9l6lspkskqi412i6h040gqmjjf6y"))))
13494 (build-system r-build-system)
13496 (list r-ks r-plot3d))
13499 (home-page "https://www.mvstat.net/tduong/")
13500 (synopsis "Inferential feature significance for kernel density estimation")
13502 "The feature package contains functions to display and compute kernel
13503 density estimates, significant gradient and significant curvature regions.
13504 Significant gradient and/or curvature regions often correspond to significant
13505 features (e.g. local modes).")
13506 ;; Either version of the GPL.
13507 (license (list license:gpl2 license:gpl3))))
13509 (define-public r-arm
13516 (uri (cran-uri "arm" version))
13519 "0pagrc1vkaz460d0lvrgb4xj6gcd920f4mrc8zpzw07c3v1s2sw1"))))
13520 (build-system r-build-system)
13528 (home-page "https://cran.r-project.org/web/packages/arm/")
13529 (synopsis "Data analysis using regression and multilevel/hierarchical models")
13531 "This package provides functions to accompany A. Gelman and J. Hill,
13532 Data Analysis Using Regression and Multilevel/Hierarchical Models, Cambridge
13533 University Press, 2007.")
13534 (license license:gpl3+)))
13536 (define-public r-circular
13538 (name "r-circular")
13543 (uri (cran-uri "circular" version))
13546 "1qmwj1pf37lc2s5r83y7nqckscznqhbsv66bdfgfbby7x4qkwga8"))))
13547 (build-system r-build-system)
13549 (list r-boot r-mvtnorm))
13552 (home-page "https://cran.r-project.org/web/packages/circular/")
13553 (synopsis "Circular statistics")
13555 "This package provides tools for circular statistics, from \"Topics in
13556 circular Statistics\" (2001) S. Rao Jammalamadaka and A. SenGupta, World
13558 (license license:gpl2+)))
13560 (define-public r-activity
13562 (name "r-activity")
13567 (uri (cran-uri "activity" version))
13570 "11n6wmqz7p3428rr615f92m61a5gb908xpn4l8q484h61bwg38c3"))))
13571 (build-system r-build-system)
13573 (list r-insol r-pbapply))
13574 (home-page "https://cran.r-project.org/web/packages/activity/")
13575 (synopsis "Animal activity statistics")
13577 "This package provides functions to fit kernel density functions to
13578 animal activity time data; plot activity distributions; quantify overall
13579 levels of activity; statistically compare activity metrics through
13580 bootstrapping; and evaluate variation in linear variables with time (or other
13581 circular variables).")
13582 (license license:gpl3)))
13584 (define-public r-ouch
13591 (uri (cran-uri "ouch" version))
13594 "119s9llpjy0b4q830xig2xr66fq6izp6mr2k4k79ggmf3gxww8as"))))
13595 (build-system r-build-system)
13596 (propagated-inputs (list r-subplex))
13597 (home-page "https://kingaa.github.io/ouch/")
13598 (synopsis "Ornstein-Uhlenbeck models for phylogenetic comparative hypotheses")
13600 "This package provides tools to fit and compare Ornstein-Uhlenbeck models
13601 for evolution along a phylogenetic tree.")
13602 (license license:gpl2+)))
13604 (define-public r-fmsb
13611 (uri (cran-uri "fmsb" version))
13614 "1gi94xr0b1yk9xzwfprfafxi25yic1lcivd66p73n6iqfzdaimbk"))))
13615 (build-system r-build-system)
13616 (home-page "http://minato.sip21c.org/msb/")
13617 (synopsis "Functions for medical statistics book with demographic data")
13619 "This package provides several utility functions for the book entitled
13620 \"Practices of Medical and Health Data Analysis using R\" (Pearson Education
13621 Japan, 2007) with Japanese demographic data and some demographic analysis
13622 related functions.")
13623 (license license:gpl2+)))
13625 (define-public r-stabledist
13627 (name "r-stabledist")
13632 (uri (cran-uri "stabledist" version))
13635 "0scar396wiq6wkbkvwp4qrxqc1m075y56p37i6iry5rw796p1i86"))))
13636 (build-system r-build-system)
13637 (home-page "https://www.rmetrics.org")
13638 (synopsis "Stable distribution functions")
13640 "This package provides density, probability and quantile functions, and
13641 random number generation for (skew) stable distributions, using the
13642 parametrizations of Nolan.")
13643 (license license:gpl2+)))
13645 (define-public r-gsl
13648 (version "2.1-7.1")
13652 (uri (cran-uri "gsl" version))
13655 "118rj9kjx9rzlynvhrly19qz3yxg8jzws35971ssgzrp5lwd367f"))))
13656 (build-system r-build-system)
13659 (home-page "https://cran.r-project.org/web/packages/gsl")
13660 (synopsis "Wrapper for the GNU Scientific Library")
13662 "This package provides an R wrapper for the special functions and quasi
13663 random number generators of the GNU Scientific Library.")
13664 (license license:gpl2+)))
13666 (define-public r-adgoftest
13668 (name "r-adgoftest")
13673 (uri (cran-uri "ADGofTest" version))
13676 "0ik817qzqp6kfbckjp1z7srlma0w6z2zcwykh0jdiv7nahwk3ncw"))))
13677 (properties `((upstream-name . "ADGofTest")))
13678 (build-system r-build-system)
13679 (home-page "https://cran.r-project.org/web/packages/ADGofTest")
13680 (synopsis "Anderson-Darling GoF test")
13682 "This package provides an implementation of the Anderson-Darling GoF test
13683 with p-value calculation based on Marsaglia's 2004 paper \"Evaluating the
13684 Anderson-Darling Distribution\".")
13685 ;; Any version of the GPL.
13686 (license license:gpl3+)))
13688 (define-public r-admisc
13695 (uri (cran-uri "admisc" version))
13697 (base32 "07hfrhv3pcldsffnyfzpa1q3x32gxr1386r8fik1nhql2w46mm13"))))
13698 (properties `((upstream-name . "admisc")))
13699 (build-system r-build-system)
13700 (home-page "https://github.com/dusadrian/admisc")
13701 (synopsis "Adrian Dusa's miscellaneous")
13703 "This package contains miscellaneous functions used to interpret and
13704 translate, factorize and negate Sum of Products expressions, for both binary
13705 and multi-value crisp sets, and to extract information (set names, set values)
13706 from those expressions. Other functions perform various other checks if
13707 possibly numeric (even if all numbers reside in a character vector) and coerce
13708 to numeric, or check if the numbers are whole. It also offers, among many
13709 others, a highly flexible recoding routine and a more flexible alternative to
13710 the base function @code{with()}.")
13711 (license license:gpl3+)))
13713 (define-public r-sodium
13720 (uri (cran-uri "sodium" version))
13723 "0x4jb3cf1nv1spz1jc9xp8hly2b4a7nj48xr4s33jnfcpdjkmn5q"))))
13724 (properties `((upstream-name . "sodium")))
13725 (build-system r-build-system)
13729 (list pkg-config r-knitr))
13730 (home-page "https://github.com/jeroen/sodium")
13731 (synopsis "R bindings to the libsodium crypto library")
13733 "This package provides bindings to libsodium: a library for encryption,
13734 decryption, signatures, password hashing and more. Sodium uses curve25519, a
13735 Diffie-Hellman function by Daniel Bernstein, which has become very popular
13736 after it was discovered that the NSA had backdoored Dual EC DRBG.")
13737 (license license:expat)))
13739 (define-public r-softimpute
13741 (name "r-softimpute")
13746 (uri (cran-uri "softImpute" version))
13749 "1v2a4d688ij5zcvkzpra9yx40xckdfnllnfnyq2450zf3n1kjk7a"))))
13750 (properties `((upstream-name . "softImpute")))
13751 (build-system r-build-system)
13755 (list gfortran r-knitr))
13756 (home-page "https://cran.r-project.org/web/packages/softImpute")
13757 (synopsis "Matrix completion via iterative soft-thresholded SVD")
13759 "This package provides iterative methods for matrix completion that use
13760 nuclear-norm regularization. The package includes procedures for centering
13761 and scaling rows, columns or both, and for computing low-rank @dfn{single
13762 value decompositions} (SVDs) on large sparse centered matrices (i.e. principal
13764 (license license:gpl2)))
13766 (define-public r-fftwtools
13768 (name "r-fftwtools")
13773 (uri (cran-uri "fftwtools" version))
13776 "0zrchp4l0jdbir2gibjf00x225y9giqk80zvqmr2yyvc12lwkw7i"))))
13777 (build-system r-build-system)
13778 (inputs (list fftw))
13781 (home-page "https://github.com/krahim/fftwtools")
13782 (synopsis "Wrapper for FFTW3")
13784 "This package provides a wrapper for several FFTW functions. It provides
13785 access to the two-dimensional FFT, the multivariate FFT, and the
13786 one-dimensional real to complex FFT using the FFTW3 library. The package
13787 includes the functions @code{fftw()} and @code{mvfftw()} which are designed to
13788 mimic the functionality of the R functions @code{fft()} and @code{mvfft()}.
13789 The FFT functions have a parameter that allows them to not return the
13790 redundant complex conjugate when the input is real data.")
13791 (license license:gpl2+)))
13793 (define-public r-tiff
13800 (uri (cran-uri "tiff" version))
13803 "0xgc7vyndxxahfhc2qqzmwi56bnfyl0pn72l820jz5sd24aymhxq"))))
13804 (build-system r-build-system)
13806 (list libtiff libjpeg-turbo zlib))
13809 (home-page "https://www.rforge.net/tiff/")
13810 (synopsis "Read and write TIFF images")
13812 "This package provides an easy and simple way to read, write and display
13813 bitmap images stored in the TIFF format. It can read and write both files and
13814 in-memory raw vectors.")
13815 ;; Either of these two license versions.
13816 (license (list license:gpl2 license:gpl3))))
13818 (define-public r-nlp
13825 (uri (cran-uri "NLP" version))
13828 "1dpj04fmld2lnhg072ahgjbhmciqqy9h1lrz0wf32mr7mm9s9sh5"))))
13829 (properties `((upstream-name . "NLP")))
13830 (build-system r-build-system)
13831 (home-page "https://cran.r-project.org/web/packages/NLP/")
13832 (synopsis "Natural language processing infrastructure")
13834 "This package provides basic classes and methods for Natural Language
13836 (license license:gpl3)))
13838 (define-public r-tm
13845 (uri (cran-uri "tm" version))
13848 "0mk2lsplynms15nw92vbdgsafg4bw1m0ik31gch1mnsnv61idsxi"))))
13849 (properties `((upstream-name . "tm")))
13850 (build-system r-build-system)
13852 (list r-bh r-nlp r-rcpp r-slam r-xml2))
13853 (home-page "http://tm.r-forge.r-project.org/")
13854 (synopsis "Text mining package")
13856 "This package provides a framework for text mining applications within R.")
13857 (license license:gpl3)))
13859 (define-public r-waveslim
13861 (name "r-waveslim")
13866 (uri (cran-uri "waveslim" version))
13869 "0ibivnhz0l06sss5rrrcvyiwg3qpbyk3qn4vx4pp90kj09x4yg0k"))))
13870 (build-system r-build-system)
13873 (home-page "http://waveslim.blogspot.com")
13874 (synopsis "Basic wavelet routines for signal processing")
13876 "This package provides basic wavelet routines for time series (1D),
13877 image (2D) and array (3D) analysis. The code provided here is based on
13878 wavelet methodology developed in Percival and Walden (2000); Gencay, Selcuk
13879 and Whitcher (2001); the dual-tree complex wavelet transform (DTCWT) from
13880 Kingsbury (1999, 2001) as implemented by Selesnick; and Hilbert wavelet
13881 pairs (Selesnick 2001, 2002).")
13882 (license license:bsd-3)))
13884 (define-public r-wordcloud
13886 (name "r-wordcloud")
13891 (uri (cran-uri "wordcloud" version))
13894 "0j96yyvm6bcrrpbdx4w26piqx44a0vbsr3px9cb4zk8a8da6jwak"))))
13895 (build-system r-build-system)
13897 (list r-rcolorbrewer r-rcpp
13898 ;; The "tm" package is only "suggested" according to CRAN, but the
13899 ;; wordcloud package cannot be loaded without it.
13901 (home-page "https://cran.r-project.org/web/packages/wordcloud")
13902 (synopsis "Word clouds")
13904 "This package provides functionality to create pretty word clouds,
13905 visualize differences and similarity between documents, and avoid
13906 over-plotting in scatter plots with text.")
13907 (license license:lgpl2.1)))
13909 (define-public r-colorramps
13911 (name "r-colorramps")
13916 (uri (cran-uri "colorRamps" version))
13919 "12jnkj50yh2hc5l7j56lrrrmn58akrj9dwj98vzf42iq4h42kwb1"))))
13920 (properties `((upstream-name . "colorRamps")))
13921 (build-system r-build-system)
13922 (home-page "https://cran.r-project.org/web/packages/colorRamps")
13923 (synopsis "Build color tables")
13924 (description "This package provides features to build gradient color
13926 ;; Any version of the GPL
13927 (license license:gpl3+)))
13929 (define-public r-tidytree
13931 (name "r-tidytree")
13936 (uri (cran-uri "tidytree" version))
13938 (base32 "1prfv2jy6z4zp4gyi9krzbysipsbnjrkxcccflm4nwsd9i7mshqj"))))
13939 (build-system r-build-system)
13953 (home-page "https://github.com/GuangchuangYu/tidytree")
13954 (synopsis "Tidy tool for phylogenetic tree data manipulation")
13956 "Phylogenetic trees generally contain multiple components including nodes,
13957 edges, branches and associated data. This package provides an approach to
13958 convert tree objects to tidy data frames. It also provides tidy interfaces to
13959 manipulate tree data.")
13960 (license license:artistic2.0)))
13962 (define-public r-rvcheck
13969 (uri (cran-uri "rvcheck" version))
13971 (base32 "09khjklvzbafd7r55496by01a9g3y291d87hpy43w44dmz9fzn9a"))))
13972 (build-system r-build-system)
13974 (list r-biocmanager r-yulab-utils))
13975 (home-page "https://cran.r-project.org/web/packages/rvcheck")
13976 (synopsis "R package version check")
13978 "This package provides tools to check the latest release version of R and
13979 R packages (on CRAN, Bioconductor or Github).")
13980 (license license:artistic2.0)))
13982 (define-public r-docopt
13989 (uri (cran-uri "docopt" version))
13992 "1zxhwizs916qm5by7nfslqnarl2q5202xc2azlhrnzk0wj3khiwz"))))
13993 (build-system r-build-system)
13994 (home-page "https://github.com/docopt/docopt.R")
13995 (synopsis "Command-line interface specification language")
13997 "This package enables you to define a command-line interface by just
13998 giving it a description in the specific format.")
13999 (license license:expat)))
14001 (define-public r-sparsesvd
14003 (name "r-sparsesvd")
14008 (uri (cran-uri "sparsesvd" version))
14011 "1xm969fjq3fv1p2sqza2apz8picibj4s2agpwf1sx9nwn3b587qs"))))
14012 (build-system r-build-system)
14013 (propagated-inputs (list r-matrix))
14014 (home-page "http://tedlab.mit.edu/~dr/SVDLIBC/")
14015 (synopsis "Sparse truncated singular value decomposition")
14017 "This package provides a Wrapper around the SVDLIBC library
14018 for (truncated) singular value decomposition of a sparse matrix. Currently,
14019 only sparse real matrices in Matrix package format are supported.")
14020 ;; SVDLIBC is released under BSD-2. The R interface is released under
14022 (license (list license:bsd-3 license:bsd-2))))
14024 (define-public r-speedglm
14026 (name "r-speedglm")
14031 (uri (cran-uri "speedglm" version))
14034 "1kj662nfkfhvx37jrbvxd4dyjclz5cm3xh50z7s5rbzapiyxn4hs"))))
14035 (build-system r-build-system)
14037 (list r-mass r-matrix))
14038 (home-page "https://cran.r-project.org/web/packages/speedglm")
14039 (synopsis "Fit linear and generalized linear models to large data sets")
14041 "This package provides tools for fitting linear models and generalized
14042 linear models to large data sets by updating algorithms.")
14043 ;; Any version of the GPL
14044 (license license:gpl2+)))
14046 (define-public r-densityclust
14048 (name "r-densityclust")
14053 (uri (cran-uri "densityClust" version))
14056 "05x2fi1zdnkrg2nimf8k904j3lpyw0f7nmk6ax5p7x7a98wb2iqs"))))
14057 (properties `((upstream-name . "densityClust")))
14058 (build-system r-build-system)
14067 (home-page "https://cran.r-project.org/web/packages/densityClust")
14068 (synopsis "Clustering by fast search and find of density peaks")
14070 "This package provides an improved implementation (based on k-nearest
14071 neighbors) of the density peak clustering algorithm, originally described by
14072 Alex Rodriguez and Alessandro Laio (Science, 2014 vol. 344). It can handle
14073 large datasets (> 100,000 samples) very efficiently.")
14074 (license license:gpl2+)))
14076 (define-public r-combinat
14078 (name "r-combinat")
14083 (uri (cran-uri "combinat" version))
14086 "1h9hr88gigihc4na7lb5i7rn4az1xa7sb34zvnznaj6pdrmwy4qm"))))
14087 (build-system r-build-system)
14088 (home-page "https://cran.r-project.org/web/packages/combinat")
14089 (synopsis "Combinatorics utilities")
14090 (description "This package provides assorted routines for combinatorics.")
14091 (license license:gpl2)))
14093 (define-public r-qlcmatrix
14095 (name "r-qlcmatrix")
14100 (uri (cran-uri "qlcMatrix" version))
14103 "0iqkcvvy8rxlk0s83sjq57dd6fadb18p5z31lzy0gnzv1hsy1x8y"))))
14104 (properties `((upstream-name . "qlcMatrix")))
14105 (build-system r-build-system)
14107 (list r-docopt r-matrix r-slam r-sparsesvd))
14108 (home-page "https://cran.r-project.org/web/packages/qlcMatrix")
14109 (synopsis "Sparse matrix functions for quantitative language comparison")
14111 "This package provides an extension of the functionality of the Matrix
14112 package for using sparse matrices. Some of the functions are very general,
14113 while other are highly specific for the special data format used for
14114 @dfn{quantitative language comparison} (QLC).")
14115 (license license:gpl3)))
14117 (define-public r-ddrtree
14124 (uri (cran-uri "DDRTree" version))
14127 "16s5fjw7kwlxhrkzdny62sx32fvmg3rxjc3wrh6krd31jh1fqlfk"))))
14128 (properties `((upstream-name . "DDRTree")))
14129 (build-system r-build-system)
14131 (list r-bh r-irlba r-rcpp r-rcppeigen))
14132 (home-page "https://cran.r-project.org/web/packages/DDRTree")
14133 (synopsis "Learning principal graphs with DDRTree")
14135 "This package provides an implementation of the framework of
14136 @dfn{reversed graph embedding} (RGE) which projects data into a reduced
14137 dimensional space while constructs a principal tree which passes through the
14138 middle of the data simultaneously. DDRTree shows superiority to
14139 alternatives (Wishbone, DPT) for inferring the ordering as well as the
14140 intrinsic structure of single cell genomics data. In general, it could be
14141 used to reconstruct the temporal progression as well as the bifurcation
14142 structure of any data type.")
14143 (license license:asl2.0)))
14145 (define-public r-corpcor
14152 (uri (cran-uri "corpcor" version))
14155 "028fw61n61i79fhnaqx7gmdifdpbvp3yiaq9vvfrbv4k7i84r83i"))))
14156 (build-system r-build-system)
14157 (home-page "http://strimmerlab.org/software/corpcor/")
14158 (synopsis "Efficient estimation of covariance and (partial) correlation")
14160 "This package implements a James-Stein-type shrinkage estimator for the
14161 covariance matrix, with separate shrinkage for variances and correlations.
14162 Furthermore, functions are available for fast singular value decomposition,
14163 for computing the pseudoinverse, and for checking the rank and positive
14164 definiteness of a matrix.")
14165 (license license:gpl3+)))
14167 (define-public r-rspectra
14169 (name "r-rspectra")
14174 (uri (cran-uri "RSpectra" version))
14177 "16ij84wgpsmqmnxqiii8dgihy3bfxazry9znmckhwzba7m0d79fb"))))
14178 (properties `((upstream-name . "RSpectra")))
14179 (build-system r-build-system)
14181 (list r-matrix r-rcpp r-rcppeigen))
14184 (home-page "https://github.com/yixuan/RSpectra")
14185 (synopsis "Solvers for large-scale Eigenvalue and SVD problems")
14187 "This package provides an R interface to the Spectra library for
14188 large-scale eigenvalue and SVD problems. It is typically used to compute a
14189 few eigenvalues/vectors of an n by n matrix, e.g., the k largest eigenvalues,
14190 which is usually more efficient than @code{eigen()} if k << n.")
14192 (license license:mpl2.0)))
14194 (define-public r-vbsr
14201 (uri (cran-uri "vbsr" version))
14204 "1avskbxxyinjjdga4rnghcfvd4sypv4m39ysfaij5avvmi89bx3b"))))
14205 (build-system r-build-system)
14206 (home-page "https://cran.r-project.org/web/packages/vbsr")
14207 (synopsis "Variational Bayes spike regression regularized linear models")
14209 "This package provides an efficient algorithm for solving ultra-sparse
14210 regularized regression models using a variational Bayes algorithm with a spike
14211 prior. The algorithm is solved on a path, with coordinate updates, and is
14212 capable of generating very sparse models. Very general model
14213 diagnostics for controlling type-1 errors are also provided.")
14214 (license license:gpl2)))
14216 (define-public r-flare
14219 (version "1.7.0.1")
14223 (uri (cran-uri "flare" version))
14226 "1xvrbvq2y7zfp98ijal3z8y1w2xbzfcdykzw4pqc3mnh0qrhq2d5"))))
14227 (build-system r-build-system)
14229 (list r-igraph r-lattice r-mass r-matrix))
14230 (home-page "https://cran.r-project.org/web/packages/flare")
14231 (synopsis "Family of Lasso regression implementations")
14233 "This package provides implementations of a family of Lasso variants
14234 including Dantzig Selector, LAD Lasso, SQRT Lasso, Lq Lasso for estimating
14235 high dimensional sparse linear models.")
14236 (license license:gpl2)))
14238 (define-public r-lassopv
14245 (uri (cran-uri "lassopv" version))
14248 "0yawnjw063jypk3riy9xab9cmliv6c9dnabi18670khd3gzb2r9z"))))
14249 (build-system r-build-system)
14250 (propagated-inputs (list r-lars))
14251 (home-page "https://github.com/lingfeiwang/lassopv")
14252 (synopsis "Non-parametric p-value estimation for predictors in Lasso")
14254 "This package enables you to estimate the p-values for predictors x
14255 against target variable y in Lasso regression, using the regularization
14256 strength when each predictor enters the active set of regularization path for
14257 the first time as the statistic.")
14258 (license license:gpl3)))
14260 (define-public r-splitstackshape
14262 (name "r-splitstackshape")
14267 (uri (cran-uri "splitstackshape" version))
14270 "0mpyf2kkfdl69pdc6brl1r6101vyc6pgr7z17s55ppg3y71k4q35"))))
14271 (build-system r-build-system)
14273 (list r-data-table))
14274 (home-page "https://github.com/mrdwab/splitstackshape")
14275 (synopsis "Stack and reshape datasets after splitting concatenated values")
14277 "Online data collection tools like Google Forms often export
14278 multiple-response questions with data concatenated in cells. The
14279 @code{concat.split} (cSplit) family of functions provided by this package
14280 splits such data into separate cells. This package also includes functions to
14281 stack groups of columns and to reshape wide data, even when the data are
14282 \"unbalanced\"---something which @code{reshape} (from base R) does not handle,
14283 and which @code{melt} and @code{dcast} from @code{reshape2} do not easily
14285 (license license:gpl3)))
14287 (define-public r-tfmpvalue
14289 (name "r-tfmpvalue")
14294 (uri (cran-uri "TFMPvalue" version))
14297 "0h9qkl15k8v17v3g9bdnfwvh2s04ywjgg5y0xn2077dmywlja1bd"))))
14298 (properties `((upstream-name . "TFMPvalue")))
14299 (build-system r-build-system)
14300 (propagated-inputs (list r-rcpp))
14301 (home-page "https://github.com/ge11232002/TFMPvalue")
14302 (synopsis "P-value computation for position weight matrices")
14304 "In putative @dfn{Transcription Factor Binding Sites} (TFBSs)
14305 identification from sequence/alignments, we are interested in the significance
14306 of certain match scores. TFMPvalue provides the accurate calculation of a
14307 p-value with a score threshold for position weight matrices, or the score with
14308 a given p-value. It is an interface to code originally made available by
14309 Helene Touzet and Jean-Stephane Varre, 2007, Algorithms Mol Biol:2, 15.
14310 Touzet and Varre (2007).")
14311 (license license:gpl2)))
14313 (define-public r-rncl
14319 (uri (cran-uri "rncl" version))
14322 "1ywgwqn82z8h6zpcxxq4hgngdpfa6dj0lr7bfq4cwfml9z075jgw"))))
14323 (build-system r-build-system)
14325 (list r-progress r-rcpp))
14326 (home-page "https://github.com/fmichonneau/rncl")
14327 (synopsis "Interface to the Nexus class library")
14328 (description "This package provides an interface to the Nexus class
14329 library which allows parsing of NEXUS, Newick and other phylogenetic tree
14330 file formats. It provides elements of the file that can be used to build
14331 phylogenetic objects such as @code{ape}'s @code{phylo} or @code{phylobase}'s
14332 @code{phylo4(d)}. This functionality is demonstrated with
14333 @code{read_newick_phylo()} and @code{read_nexus_phylo()}.")
14334 (license license:bsd-2)))
14336 (define-public r-phylobase
14338 (name "r-phylobase")
14342 (uri (cran-uri "phylobase" version))
14345 "0jzr1gdvmi4l640hwwzh9bxqmpja69bn3ygnaqx37awvyh7khi2s"))))
14346 (build-system r-build-system)
14348 (list r-ade4 r-ape r-rcpp r-rncl r-rnexml))
14351 (home-page "https://github.com/fmichonneau/phylobase")
14352 (synopsis "Base package for phylogenetic structures and comparative data")
14353 (description "This package provides a base @code{S4} class for comparative
14354 methods, incorporating one or more trees and trait data.")
14355 (license license:gpl2+)))
14357 (define-public r-rnexml
14363 (uri (cran-uri "RNeXML" version))
14366 "1zp6pijsc73jx8cmxb1hng36nvaf5wnhldnzlqhmba9kv9niscfb"))))
14367 (build-system r-build-system)
14384 (home-page "https://docs.ropensci.org/RNeXML/")
14385 (synopsis "Semantically rich I/O for the NeXML Format")
14386 (description "This package provides access to phyloinformatic data in
14387 NeXML format. The package should add new functionality to R such as the
14388 possibility to manipulate NeXML objects in more various and refined way
14389 and compatibility with @code{ape} objects.")
14390 (license license:bsd-3)))
14392 (define-public r-rnifti
14399 (uri (cran-uri "RNifti" version))
14402 "0kkj9dby85iwnlqb7zwrh1xidlvqip7i1mbgckb5qg4b0a3zgibc"))))
14403 (properties `((upstream-name . "RNifti")))
14404 (build-system r-build-system)
14405 (inputs (list zlib))
14406 (propagated-inputs (list r-rcpp))
14407 (home-page "https://github.com/jonclayden/RNifti")
14408 (synopsis "Fast R and C++ access to NIfTI images")
14410 "This package provides very fast read and write access to images stored
14411 in the NIfTI-1 and ANALYZE-7.5 formats, with seamless synchronisation between
14412 compiled C and interpreted R code. It also provides a C/C++ API that can be
14413 used by other packages.")
14414 (license license:gpl2)))
14416 (define-public r-shades
14423 (uri (cran-uri "shades" version))
14426 "1zg95sjhrfvbdlfc387g9p0vnb8nb6agdk1mb3wq3kwkm2da0bqj"))))
14427 (build-system r-build-system)
14428 (home-page "https://github.com/jonclayden/shades")
14429 (synopsis "Simple color manipulation")
14431 "This package provides functions for easily manipulating colors,
14432 creating color scales and calculating color distances.")
14433 (license license:bsd-3)))
14435 (define-public r-ore
14438 (version "1.7.1.1")
14442 (uri (cran-uri "ore" version))
14444 (base32 "0rs5r5h11x4l4nsbl4xqzbl4ahajd5374fq05abcmfjnjr9j64w5"))))
14445 (build-system r-build-system)
14446 (home-page "https://github.com/jonclayden/ore")
14447 (synopsis "R interface to the Onigmo regular expression library")
14449 "This package provides an alternative to R's built-in functionality for
14450 handling regular expressions, based on the Onigmo library. It offers
14451 first-class compiled regex objects, partial matching and function-based
14452 substitutions, amongst other features.")
14453 (license license:bsd-3)))
14455 (define-public r-reportr
14462 (uri (cran-uri "reportr" version))
14465 "0zynplxqvbmf23cm2rsz3wz2jx6mv55z94mn1k44ny3lx625cnpw"))))
14466 (build-system r-build-system)
14467 (propagated-inputs (list r-ore))
14468 (home-page "https://github.com/jonclayden/reportr")
14469 (synopsis "General message and error reporting system")
14471 "This package provides a system for reporting messages, which offers
14472 certain useful features over the standard R system, such as the incorporation
14473 of output consolidation, message filtering, assertions, expression
14474 substitution, automatic generation of stack traces for debugging, and
14475 conditional reporting based on the current \"output level\".")
14476 (license license:gpl2)))
14478 (define-public r-tractor-base
14480 (name "r-tractor-base")
14481 (version "3.3.3.1")
14485 (uri (cran-uri "tractor.base" version))
14488 "0w5jw7pf77npkgig7667yikpbwv4dfk1dcq63qm88l409ga2f95p"))))
14489 (properties `((upstream-name . "tractor.base")))
14490 (build-system r-build-system)
14492 (list r-ore r-reportr r-rnifti r-shades))
14493 (home-page "https://www.tractor-mri.org.uk")
14494 (synopsis "Read, manipulate and visualize magnetic resonance images")
14496 "This package provides functions for working with magnetic resonance
14497 images. It supports reading and writing of popular file formats (DICOM,
14498 Analyze, NIfTI-1, NIfTI-2, MGH); interactive and non-interactive
14499 visualization; flexible image manipulation; metadata and sparse image
14501 (license license:gpl2)))
14503 (define-public r-grimport
14505 (name "r-grimport")
14510 (uri (cran-uri "grImport" version))
14513 "0pbzc45wgp0cpycnw0bzn65ckdszzay0zrp7c7ssxdkifp8bai3a"))))
14514 (properties `((upstream-name . "grImport")))
14515 (build-system r-build-system)
14517 (list ghostscript))
14520 (home-page "https://cran.r-project.org/web/packages/grImport")
14521 (synopsis "Convert, import, and draw PostScript pictures")
14523 "This package provides functions for converting, importing, and drawing
14524 PostScript pictures in R plots.")
14525 (license license:gpl2+)))
14527 (define-public r-grimport2
14529 (name "r-grimport2")
14534 (uri (cran-uri "grImport2" version))
14537 "19q0dd8fpp1g4xf6sg5f8dxybwxjfw553ra6wgjd8b74fzca40m1"))))
14538 (properties `((upstream-name . "grImport2")))
14539 (build-system r-build-system)
14541 (list r-base64enc r-jpeg r-png r-xml))
14542 (home-page "https://cran.r-project.org/web/packages/grImport2/")
14543 (synopsis "Import SVG graphics")
14545 "This package provides functions for importing external vector images and
14546 drawing them as part of R plots. This package is different from the
14547 @code{grImport} package because, where that package imports PostScript format
14548 images, this package imports SVG format images. Furthermore, this package
14549 imports a specific subset of SVG, so external images must be preprocessed
14550 using a package like @code{rsvg} to produce SVG that this package can import.
14551 SVG features that are not supported by R graphics, such as gradient fills, can
14552 be imported and then exported via the @code{gridSVG} package.")
14553 (license license:gpl2+)))
14555 (define-public r-kohonen
14562 (uri (cran-uri "kohonen" version))
14565 "1bk3j0n8w4fhffv89rgyn4n21c0wcx6lr8jv4wbagpxprl585381"))))
14566 (build-system r-build-system)
14569 (home-page "https://cran.r-project.org/web/packages/kohonen")
14570 (synopsis "Supervised and unsupervised self-organising maps")
14572 "This package provides functions to train @dfn{self-organising
14573 maps} (SOMs). Also interrogation of the maps and prediction using trained
14574 maps are supported. The name of the package refers to Teuvo Kohonen, the
14575 inventor of the SOM.")
14576 (license license:gpl2+)))
14578 (define-public r-nnls
14585 (uri (cran-uri "nnls" version))
14588 "07vcrrxvswrvfiha6f3ikn640yg0m2b4yd9lkmim1g0jmsmpfp8f"))))
14589 (build-system r-build-system)
14590 (native-inputs (list gfortran))
14591 (home-page "https://cran.r-project.org/web/packages/nnls")
14592 (synopsis "Lawson-Hanson algorithm for non-negative least squares")
14594 "This package provides an R interface to the Lawson-Hanson implementation
14595 of an algorithm for @dfn{non-negative least squares} (NNLS). It also allows
14596 the combination of non-negative and non-positive constraints.")
14597 (license license:gpl2+)))
14599 (define-public r-iso
14602 (version "0.0-18.1")
14606 (uri (cran-uri "Iso" version))
14609 "0vy6jdyvp751430sf2f690yhasjr70cpk3p3lnaaxjq3fs5gg99g"))))
14610 (properties `((upstream-name . "Iso")))
14611 (build-system r-build-system)
14612 (native-inputs (list gfortran))
14613 (home-page "https://www.stat.auckland.ac.nz/~rolf/")
14614 (synopsis "Functions to perform isotonic regression")
14616 "This package provides support for linear order and unimodal
14617 order (univariate) isotonic regression and bivariate isotonic regression with
14618 linear order on both variables.")
14619 (license license:gpl2+)))
14621 (define-public r-chemometricswithr
14623 (name "r-chemometricswithr")
14628 (uri (cran-uri "ChemometricsWithR" version))
14631 "166va1g3m1wv21qkmw4wpz0bsrclh3jih8smxphdc13l9pqgclpq"))))
14633 `((upstream-name . "ChemometricsWithR")))
14634 (build-system r-build-system)
14636 (list r-devtools r-kohonen r-mass r-pls))
14637 (home-page "https://github.com/rwehrens/CWR")
14638 (synopsis "Chemometrics with R")
14640 "This package provides functions and scripts used in the book
14641 \"Chemometrics with R - Multivariate Data Analysis in the Natural Sciences and
14642 Life Sciences\" by Ron Wehrens, Springer (2011).")
14643 (license license:gpl2+)))
14645 (define-public r-als
14652 (uri (cran-uri "ALS" version))
14655 "1swrn39vy50fazkpf97r7c542gkj6mlvy8gmcxllg7mf2mqx546a"))))
14656 (properties `((upstream-name . "ALS")))
14657 (build-system r-build-system)
14659 (list r-iso r-nnls))
14660 (home-page "https://cran.r-project.org/web/packages/ALS")
14661 (synopsis "Multivariate curve resolution alternating least squares")
14663 "Alternating least squares is often used to resolve components
14664 contributing to data with a bilinear structure; the basic technique may be
14665 extended to alternating constrained least squares. This package provides an
14666 implementation of @dfn{multivariate curve resolution alternating least
14667 squares} (MCR-ALS).
14669 Commonly applied constraints include unimodality, non-negativity, and
14670 normalization of components. Several data matrices may be decomposed
14671 simultaneously by assuming that one of the two matrices in the bilinear
14672 decomposition is shared between datasets.")
14673 (license license:gpl2+)))
14675 (define-public r-strucchange
14677 (name "r-strucchange")
14682 (uri (cran-uri "strucchange" version))
14685 "1y022363a4pp0mnji91sjh1qiyspkh09sybqwj03r9pmwrd7q93x"))))
14686 (build-system r-build-system)
14688 (list r-sandwich r-zoo))
14689 (home-page "https://cran.r-project.org/web/packages/strucchange")
14690 (synopsis "Testing, monitoring, and dating structural changes")
14692 "This package provides tools for testing, monitoring and dating
14693 structural changes in (linear) regression models. It features tests/methods
14694 from the generalized fluctuation test framework as well as from the F
14695 test (Chow test) framework. This includes methods to fit, plot and test
14696 fluctuation processes (e.g., CUSUM, MOSUM, recursive/moving estimates) and F
14697 statistics, respectively. It is possible to monitor incoming data online
14698 using fluctuation processes. Finally, the breakpoints in regression models
14699 with structural changes can be estimated together with confidence intervals.
14700 Emphasis is always given to methods for visualizing the data.")
14701 ;; Either of these two GPL versions
14702 (license (list license:gpl2 license:gpl3))))
14704 (define-public r-pixmap
14711 (uri (cran-uri "pixmap" version))
14714 "1v1a1adsgh5jlvvi98j4nhb1h681s97ip76zdrga12rlsjaahfw9"))))
14715 (build-system r-build-system)
14716 (home-page "https://cran.r-project.org/web/packages/pixmap")
14717 (synopsis "Tools for bitmap images")
14719 "This package provides functions for importing, exporting, plotting and
14720 other manipulations of bitmapped images.")
14721 (license license:gpl2)))
14723 (define-public r-rapidjsonr
14725 (name "r-rapidjsonr")
14730 (uri (cran-uri "rapidjsonr" version))
14733 "07zdirhbzmvq3cp4xn8ngk1lgxbbabzays315zxbs3sxrz6lzjb2"))))
14734 (build-system r-build-system)
14735 (home-page "https://cran.r-project.org/web/packages/rapidjsonr")
14736 (synopsis "JSON parser")
14738 "This package provides JSON parsing capability through the Rapidjson
14740 (license license:expat)))
14742 (define-public r-ontologyindex
14744 (name "r-ontologyindex")
14749 (uri (cran-uri "ontologyIndex" version))
14752 "0j3h1spqwjhh1wbmwivmqcyi042yy7d565c3kxgn70xrmy693x1k"))))
14753 (properties `((upstream-name . "ontologyIndex")))
14754 (build-system r-build-system)
14757 (home-page "https://cran.r-project.org/web/packages/ontologyIndex")
14758 (synopsis "Functions for processing ontologies in R")
14760 "This package provides functions for reading ontologies into R as lists
14761 and manipulating sets of ontological terms.")
14762 (license license:gpl2+)))
14764 (define-public r-gargle
14771 (uri (cran-uri "gargle" version))
14774 "0fypj70c1fjmvs57birik76wfx8a2fs4gzicbb52k57i6clwlijd"))))
14775 (build-system r-build-system)
14788 (home-page "https://gargle.r-lib.org")
14789 (synopsis "Utilities for working with Google APIs")
14791 "This package provides utilities for working with Google APIs. This
14792 includes functions and classes for handling common credential types and for
14793 preparing, executing, and processing HTTP requests.")
14794 (license license:expat)))
14796 (define-public r-bigrquery
14798 (name "r-bigrquery")
14803 (uri (cran-uri "bigrquery" version))
14806 "02msq61l7vamzpvbhvalh3qil1aa7pr68pwpsivbb6pvz6p4zyns"))))
14807 (build-system r-build-system)
14824 (home-page "https://github.com/rstats-db/bigrquery")
14825 (synopsis "R interface to Google's BigQuery API")
14827 "This package provides an R interface to Google's BigQuery database.")
14828 (license license:gpl3)))
14830 (define-public r-gmp
14837 (uri (cran-uri "gmp" version))
14840 "0llyd1wx606vpgvv7d61m0fv2a5yxsmisd38fhzanbjl2wynzrwa"))))
14841 (build-system r-build-system)
14844 (modify-phases %standard-phases
14845 (add-after 'unpack 'set-CC
14846 (lambda _ (setenv "CC" "gcc") #t)))))
14847 (inputs (list gmp))
14848 (home-page "https://cran.r-project.org/web/packages/gmp")
14849 (synopsis "Multiple precision arithmetic")
14851 "This package supports multiple precision arithmetic (big integers and
14852 rationals, prime number tests, matrix computation), \"arithmetic without
14853 limitations\" using the GNU Multiple Precision library.")
14854 ;; Any version of the GPL.
14855 (license license:gpl3+)))
14857 (define-public r-rmpfr
14864 (uri (cran-uri "Rmpfr" version))
14867 "1ljpbxvm4agbxnab5dfffbpw5k964hy3gw57dzydq1gpbxwdphlk"))))
14868 (properties `((upstream-name . "Rmpfr")))
14869 (build-system r-build-system)
14876 (home-page "http://rmpfr.r-forge.r-project.org/")
14877 (synopsis "R bindings to the MPFR library")
14879 "This package supports arithmetic (via S4 classes and methods) for
14880 arbitrary precision floating point numbers, including transcendental
14881 functions. To this end, the package interfaces with the @dfn{Multiple
14882 Precision Floating-Point Reliable} (MPFR) library.")
14883 (license license:gpl2+)))
14885 (define-public r-assertive-base
14887 (name "r-assertive-base")
14892 (uri (cran-uri "assertive.base" version))
14895 "07m0ddz092bgbl2fn1yk932h0iajdcqkri632477wl5a1q5r3w2b"))))
14897 `((upstream-name . "assertive.base")))
14898 (build-system r-build-system)
14899 (home-page "https://bitbucket.org/richierocks/assertive.base")
14900 (synopsis "Core of the assertive package")
14902 "This package provides a minimal set of predicates and assertions used by
14903 the assertive package. This is mainly for use by other package developers who
14904 want to include run-time testing features in their own packages.")
14905 (license license:gpl3+)))
14907 (define-public r-assertive-properties
14909 (name "r-assertive-properties")
14914 (uri (cran-uri "assertive.properties" version))
14917 "1pgljbwwbvbl4kc5c8mcv0qbzq3k6fzi29k88811yml263sm92dn"))))
14919 `((upstream-name . "assertive.properties")))
14920 (build-system r-build-system)
14922 (list r-assertive-base))
14923 (home-page "https://bitbucket.org/richierocks/assertive.properties")
14924 (synopsis "Assertions to check properties of variables")
14926 "This package provides a set of predicates and assertions for checking
14927 the properties of variables, such as length, names and attributes. This is
14928 mainly for use by other package developers who want to include run-time
14929 testing features in their own packages.")
14930 (license license:gpl3+)))
14932 (define-public r-assertive-numbers
14934 (name "r-assertive-numbers")
14939 (uri (cran-uri "assertive.numbers" version))
14942 "0jc3ss64j4m7bjydhagwwmka5n7c72vpw4kfcch0m5jvkq5qrqds"))))
14944 `((upstream-name . "assertive.numbers")))
14945 (build-system r-build-system)
14947 (list r-assertive-base))
14948 (home-page "https://bitbucket.org/richierocks/assertive.numbers")
14949 (synopsis "Assertions to check properties of numbers")
14951 "This package provides a set of predicates and assertions for checking
14952 the properties of numbers. This is mainly for use by other package developers
14953 who want to include run-time testing features in their own packages.")
14954 (license license:gpl3+)))
14956 (define-public r-assertive-sets
14958 (name "r-assertive-sets")
14963 (uri (cran-uri "assertive.sets" version))
14966 "1cqvh2syvh5b6d85h601zjmsdbbf3h8q98ids4dfl4frdshpasc7"))))
14968 `((upstream-name . "assertive.sets")))
14969 (build-system r-build-system)
14971 (list r-assertive-base))
14972 (home-page "https://bitbucket.org/richierocks/assertive.sets")
14973 (synopsis "Assertions to check properties of sets")
14975 "This package provides a set of predicates and assertions for checking
14976 the properties of sets. This is mainly for use by other package developers
14977 who want to include run-time testing features in their own packages.")
14978 (license license:gpl3+)))
14980 (define-public r-assertive-matrices
14982 (name "r-assertive-matrices")
14987 (uri (cran-uri "assertive.matrices" version))
14990 "16sykzcndv6y2d43x6v9n7m95kv76364h39kh10w4z0xw6ksfqil"))))
14992 `((upstream-name . "assertive.matrices")))
14993 (build-system r-build-system)
14995 (list r-assertive-base))
14996 (home-page "https://bitbucket.org/richierocks/assertive.matrices")
14997 (synopsis "Assertions to check properties of matrices")
14999 "This package provides a set of predicates and assertions for checking
15000 the properties of matrices. This is mainly for use by other package
15001 developers who want to include run-time testing features in their own
15003 (license license:gpl3+)))
15005 (define-public r-assertive-models
15007 (name "r-assertive-models")
15012 (uri (cran-uri "assertive.models" version))
15015 "0bn4j4v5qvb2d672cgri61p8d9v258pmz35y3lvm6b9mdxwdi9mr"))))
15017 `((upstream-name . "assertive.models")))
15018 (build-system r-build-system)
15020 (list r-assertive-base))
15021 (home-page "https://bitbucket.org/richierocks/assertive.models")
15022 (synopsis "Assertions to check properties of models")
15024 "This package provides a set of predicates and assertions for checking
15025 the properties of models. This is mainly for use by other package developers
15026 who want to include run-time testing features in their own packages.")
15027 (license license:gpl3+)))
15029 (define-public r-assertive-reflection
15031 (name "r-assertive-reflection")
15036 (uri (cran-uri "assertive.reflection" version))
15039 "1g9lpwzy6r2xmyi2mlbcccnfgyzhzbmx5bsicf3vkffxrlkrpjn2"))))
15041 `((upstream-name . "assertive.reflection")))
15042 (build-system r-build-system)
15044 (list r-assertive-base))
15045 (home-page "https://bitbucket.org/richierocks/assertive.reflection")
15046 (synopsis "Assertions for checking the state of R")
15048 "This package provides a set of predicates and assertions for checking
15049 the state and capabilities of R, the operating system it is running on, and
15050 the IDE being used. This is mainly for use by other package developers who
15051 want to include run-time testing features in their own packages.")
15052 (license license:gpl3+)))
15054 (define-public r-assertive-types
15056 (name "r-assertive-types")
15061 (uri (cran-uri "assertive.types" version))
15064 "0zxq1jfrzgw95ll7alvm0xnk7aihjdksngq4ya2whyvfjbmv4vdb"))))
15066 `((upstream-name . "assertive.types")))
15067 (build-system r-build-system)
15069 (list r-assertive-base r-assertive-properties r-codetools))
15070 (home-page "https://bitbucket.org/richierocks/assertive.types")
15071 (synopsis "Assertions to check types of variables")
15073 "This package provides a set of predicates and assertions for checking
15074 the types of variables. This is mainly for use by other package developers
15075 who want to include run-time testing features in their own packages.")
15076 (license license:gpl3+)))
15078 (define-public r-assertive-files
15080 (name "r-assertive-files")
15085 (uri (cran-uri "assertive.files" version))
15088 "02pfz8j5vwcj5kl6zca46894li7lxwnlrr29j922f14ay6kdssmy"))))
15090 `((upstream-name . "assertive.files")))
15091 (build-system r-build-system)
15093 (list r-assertive-base r-assertive-numbers))
15094 (home-page "https://bitbucket.org/richierocks/assertive.files")
15095 (synopsis "Assertions to check properties of files")
15097 "This package provides a set of predicates and assertions for checking
15098 the properties of files and connections. This is mainly for use by other
15099 package developers who want to include run-time testing features in their own
15101 (license license:gpl3+)))
15103 (define-public r-assertive-code
15105 (name "r-assertive-code")
15110 (uri (cran-uri "assertive.code" version))
15113 "1qhbp668zfvhqs8avkhg9amp4zyazz6dsy4fc6kpdmw3sv8yi07g"))))
15115 `((upstream-name . "assertive.code")))
15116 (build-system r-build-system)
15118 (list r-assertive-base r-assertive-properties r-assertive-types))
15119 (home-page "https://bitbucket.org/richierocks/assertive.code")
15120 (synopsis "Assertions to check properties of code")
15122 "This package provides a set of predicates and assertions for checking
15123 the properties of code. This is mainly for use by other package developers
15124 who want to include run-time testing features in their own packages.")
15125 (license license:gpl3+)))
15127 (define-public r-assertive-datetimes
15129 (name "r-assertive-datetimes")
15134 (uri (cran-uri "assertive.datetimes" version))
15137 "151d05z8n6dpl44pqsa1jfi0ijbigr3zfc43xlw53nd8ymi22kh1"))))
15139 `((upstream-name . "assertive.datetimes")))
15140 (build-system r-build-system)
15142 (list r-assertive-base r-assertive-types))
15143 (home-page "https://bitbucket.org/richierocks/assertive.datetimes")
15144 (synopsis "Assertions to check properties of dates and times")
15146 "This package provides a set of predicates and assertions for checking
15147 the properties of dates and times. This is mainly for use by other package
15148 developers who want to include run-time testing features in their own
15150 (license license:gpl3+)))
15152 (define-public r-assertive-strings
15154 (name "r-assertive-strings")
15159 (uri (cran-uri "assertive.strings" version))
15162 "0n6jrk88670g4ym0r8ii40a08a90z1xadj8wcryk8h0nl04dchfm"))))
15164 `((upstream-name . "assertive.strings")))
15165 (build-system r-build-system)
15167 (list r-assertive-base r-assertive-types r-stringi))
15168 (home-page "https://bitbucket.org/richierocks/assertive.strings")
15169 (synopsis "Assertions to check properties of strings")
15171 "This package provides a set of predicates and assertions for checking
15172 the properties of strings. This is mainly for use by other package developers
15173 who want to include run-time testing features in their own packages.")
15174 (license license:gpl3+)))
15176 (define-public r-assertive-data-us
15178 (name "r-assertive-data-us")
15183 (uri (cran-uri "assertive.data.us" version))
15186 "1bgspn0sccmp9z7s7djvdvprgxlyc5vrxznp4zfjb79kwvgn83hq"))))
15188 `((upstream-name . "assertive.data.us")))
15189 (build-system r-build-system)
15191 (list r-assertive-base r-assertive-strings))
15192 (home-page "https://bitbucket.org/richierocks/assertive.data.us")
15193 (synopsis "Assertions to check properties of strings")
15195 "This package provides a set of predicates and assertions for checking
15196 the properties of US-specific complex data types. This is mainly for use by
15197 other package developers who want to include run-time testing features in
15198 their own packages.")
15199 (license license:gpl3+)))
15201 (define-public r-assertive-data-uk
15203 (name "r-assertive-data-uk")
15208 (uri (cran-uri "assertive.data.uk" version))
15211 "1fzjvhwp7mwkqqix29khvs6zcrc82n6j4czvzzb473vyjyvdlj5b"))))
15213 `((upstream-name . "assertive.data.uk")))
15214 (build-system r-build-system)
15216 (list r-assertive-base r-assertive-strings))
15217 (home-page "https://bitbucket.org/richierocks/assertive.data.uk")
15218 (synopsis "Assertions to check properties of strings")
15220 "This package provides a set of predicates and assertions for checking
15221 the properties of UK-specific complex data types. This is mainly for use by
15222 other package developers who want to include run-time testing features in
15223 their own packages.")
15224 (license license:gpl3+)))
15226 (define-public r-assertive-data
15228 (name "r-assertive-data")
15233 (uri (cran-uri "assertive.data" version))
15236 "00cvg2g36mdl8plrzx40m63qd55742mddqrchwy9n3c7mm4gn02s"))))
15238 `((upstream-name . "assertive.data")))
15239 (build-system r-build-system)
15241 (list r-assertive-base r-assertive-strings))
15242 (home-page "https://bitbucket.org/richierocks/assertive.data")
15243 (synopsis "Assertions to check properties of data")
15245 "This package provides a set of predicates and assertions for checking
15246 the properties of (country independent) complex data types. This is mainly
15247 for use by other package developers who want to include run-time testing
15248 features in their own packages.")
15249 (license license:gpl3+)))
15251 (define-public r-assertive
15253 (name "r-assertive")
15258 (uri (cran-uri "assertive" version))
15261 "02palil82idqhhshcdjsfsja9qkqnd0dczqzj5gbccy4hfg1c0y4"))))
15262 (build-system r-build-system)
15264 (list r-assertive-base
15267 r-assertive-data-uk
15268 r-assertive-data-us
15269 r-assertive-datetimes
15271 r-assertive-matrices
15273 r-assertive-numbers
15274 r-assertive-properties
15275 r-assertive-reflection
15277 r-assertive-strings
15282 (home-page "https://bitbucket.org/richierocks/assertive")
15283 (synopsis "Readable check functions to ensure code integrity")
15285 "This package provides lots of predicates (@code{is_*} functions) to
15286 check the state of your variables, and assertions (@code{assert_*} functions)
15287 to throw errors if they aren't in the right form.")
15288 (license license:gpl3+)))
15290 (define-public r-dotcall64
15292 (name "r-dotcall64")
15297 (uri (cran-uri "dotCall64" version))
15300 "1im5k8jbviwj2i42mq1kmjskh80isa7jr9w8i0fknidrzzy2h2zi"))))
15301 (properties `((upstream-name . "dotCall64")))
15302 (build-system r-build-system)
15303 (native-inputs (list gfortran))
15304 (home-page "https://git.math.uzh.ch/reinhard.furrer/dotCall64")
15305 (synopsis "Enhanced foreign function interface supporting long vectors")
15307 "This package provides @code{.C64()}, an enhanced version of @code{.C()}
15308 and @code{.Fortran()} from the R foreign function interface. @code{.C64()}
15309 supports long vectors, arguments of type 64-bit integer, and provides a
15310 mechanism to avoid unnecessary copies of read-only and write-only arguments.
15311 This makes it a convenient and fast interface to C/C++ and Fortran code.")
15312 (license license:gpl2+)))
15314 (define-public r-spam
15321 (uri (cran-uri "spam" version))
15323 (base32 "1ann2a2ifr3z983fcg1c0pkgmbxz6a0ym5q1dmq1r382bd1pg0fr"))))
15324 (build-system r-build-system)
15326 (list r-dotcall64))
15328 (list gfortran r-knitr))
15329 (home-page "https://www.math.uzh.ch/pages/spam/")
15330 (synopsis "Sparse matrix algebra")
15332 "This package provides a set of functions for sparse matrix algebra.
15333 Differences with other sparse matrix packages are:
15336 @item it only supports (essentially) one sparse matrix format;
15337 @item it is based on transparent and simple structure(s);
15338 @item it is tailored for MCMC calculations within G(M)RF;
15339 @item and it is fast and scalable (with the extension package @code{spam64}).
15341 ;; Either of these licenses
15342 (license (list license:bsd-3 license:lgpl2.0))))
15344 (define-public r-fields
15351 (uri (cran-uri "fields" version))
15353 (base32 "1hs4k5a9hh0r5fsrnpnvs6wvf78xpjzj8a2j6643dsz73a5q6ln6"))))
15354 (build-system r-build-system)
15356 (list r-maps r-spam r-viridis))
15359 (home-page "https://www.image.ucar.edu/fields")
15360 (synopsis "Tools for spatial data")
15362 "This is a package for curve, surface and function fitting with an
15363 emphasis on splines, spatial data and spatial statistics. The major methods
15364 include cubic, and thin plate splines, Kriging, and compactly supported
15365 covariance functions for large data sets.")
15366 (license license:gpl2+)))
15368 (define-public r-spatialextremes
15370 (name "r-spatialextremes")
15375 (uri (cran-uri "SpatialExtremes" version))
15378 "0z1swxp1syz8hdskarjxx4sdd7wx835kcnb783bwqm235yh991j3"))))
15380 `((upstream-name . "SpatialExtremes")))
15381 (build-system r-build-system)
15383 (list r-fields r-maps))
15384 (home-page "http://spatialextremes.r-forge.r-project.org/")
15385 (synopsis "Modelling spatial extremes")
15387 "This package provides tools for the statistical modelling of spatial
15388 extremes using max-stable processes, copula or Bayesian hierarchical models.
15389 More precisely, this package allows (conditional) simulations from various
15390 parametric max-stable models, analysis of the extremal spatial dependence, the
15391 fitting of such processes using composite likelihoods or least square (simple
15392 max-stable processes only), model checking and selection and prediction.")
15393 (license license:gpl2+)))
15395 (define-public r-drc
15402 (uri (cran-uri "drc" version))
15405 "0c8xn8ripzq270hy8d16fcnx02l02alddznd7fqwk3jyi6113h1y"))))
15406 (build-system r-build-system)
15414 (home-page "https://cran.r-project.org/web/packages/drc")
15415 (synopsis "Analysis of dose-response curves")
15417 "This package provides a suite of flexible and versatile model fitting
15418 and after-fitting functions for the analysis of dose-response data.")
15419 (license license:gpl2+)))
15421 (define-public r-rmeta
15428 (uri (cran-uri "rmeta" version))
15431 "0vkbnxp579v8zmcv1isdbzj5swpr6fq17zwparxcvzswjc2x9ydr"))))
15432 (build-system r-build-system)
15433 (home-page "https://cran.r-project.org/web/packages/rmeta")
15434 (synopsis "Tools for meta-analysis")
15436 "This package provides functions for simple fixed and random effects
15437 meta-analysis for two-sample comparisons and cumulative meta-analyses. It
15438 draws standard summary plots, funnel plots, and computes summaries and tests
15439 for association and heterogeneity.")
15440 (license license:gpl2)))
15442 (define-public r-bootstrap
15444 (name "r-bootstrap")
15449 (uri (cran-uri "bootstrap" version))
15452 "1546jqhhw5h177ii8jkdikyd26rv6gwkav816np1zks4p7zgsljj"))))
15453 (build-system r-build-system)
15454 (native-inputs (list gfortran))
15455 (home-page "https://cran.r-project.org/web/packages/bootstrap")
15456 (synopsis "Functions for the book \"An Introduction to the Bootstrap\"")
15458 "This package provides software and data for the book \"An Introduction
15459 to the Bootstrap\" by B. Efron and R. Tibshirani, 1993, Chapman and Hall.
15460 This package is primarily provided for projects already based on it, and for
15461 support of the book. New projects should preferentially use the recommended
15462 package \"boot\".")
15463 (license license:bsd-3)))
15465 (define-public r-survivalroc
15467 (name "r-survivalroc")
15472 (uri (cran-uri "survivalROC" version))
15475 "0wnd65ff5w679hxa1zrpfrx9qg47q21pjxppsga6m3h4iq1yfj8l"))))
15476 (properties `((upstream-name . "survivalROC")))
15477 (build-system r-build-system)
15478 (home-page "https://cran.r-project.org/web/packages/survivalROC")
15479 (synopsis "Time-dependent ROC curve estimation from censored survival data")
15481 "Compute time-dependent ROC curve from censored survival data using
15482 Kaplan-Meier (KM) or Nearest Neighbor Estimation (NNE) method of Heagerty,
15483 Lumley & Pepe (Biometrics, Vol 56 No 2, 2000, PP 337-344)")
15484 (license license:gpl2+)))
15486 (define-public r-locfdr
15492 (uri (cran-uri "locfdr" version))
15495 "1falkbp2xz07am8jlhwlvyqvxnli4nwl188kd0g58vdfjcjy3mj2"))))
15496 (build-system r-build-system)
15497 (home-page "https://cran.r-project.org/web/packages/locfdr/")
15498 (synopsis "Computes local false discovery rates")
15499 (description "This package can be used to compute local false
15501 (license license:gpl2)))
15503 (define-public r-longitudinal
15505 (name "r-longitudinal")
15510 (uri (cran-uri "longitudinal" version))
15513 "046w3xbr535c5jyd68adv42a7limxp1mv57b5w6w673w707lmw2p"))))
15514 (build-system r-build-system)
15515 (propagated-inputs (list r-corpcor))
15516 (home-page "http://strimmerlab.org/software/longitudinal/")
15517 (synopsis "Analysis of multiple time course data")
15519 "This package contains general data structures and functions for
15520 longitudinal data with multiple variables, repeated measurements, and
15521 irregularly spaced time points. It also implements a shrinkage estimator of
15522 dynamical correlation and dynamical covariance.")
15523 (license license:gpl3+)))
15525 (define-public r-genenet
15532 (uri (cran-uri "GeneNet" version))
15535 "1r1khga3nxxjghs4vnbymzp0cwb1q17zw2v3a94qz8fsrirq1sf1"))))
15536 (properties `((upstream-name . "GeneNet")))
15537 (build-system r-build-system)
15539 (list r-corpcor r-fdrtool r-longitudinal))
15540 (home-page "http://strimmerlab.org/software/genenet/")
15541 (synopsis "Modeling and inferring gene networks")
15543 "This package analyzes gene expression (time series) data with focus on
15544 the inference of gene networks. In particular, GeneNet implements the methods
15545 of Schaefer and Strimmer (2005a,b,c) and Opgen-Rhein and Strimmer (2006, 2007)
15546 for learning large-scale gene association networks (including assignment of
15547 putative directions).")
15548 (license license:gpl3+)))
15550 (define-public r-rbamtools
15552 (name "r-rbamtools")
15553 (version "2.16.17")
15557 (uri (cran-uri "rbamtools" version))
15560 "0qj37ljdva3v29s01dkrbg31mcfzy3bl145cp40d54v4h9xhcghc"))))
15561 (build-system r-build-system)
15562 (inputs (list zlib))
15564 (list r-refgenome))
15565 (home-page "https://cran.r-project.org/web/packages/rbamtools")
15566 (synopsis "Read and write BAM (binary alignment) files")
15568 "This package provides an R interface to functions of the SAMtools
15570 (license license:artistic2.0)))
15572 (define-public r-protviz
15579 (uri (cran-uri "protViz" version))
15582 "0f6jwzcqi0w37hvg3i5dlk0c3anpkqh54ibf94vaf17r8sykr4nw"))))
15583 (properties `((upstream-name . "protViz")))
15584 (build-system r-build-system)
15585 (propagated-inputs (list r-rcpp))
15586 (home-page "https://github.com/protViz/protViz/")
15587 (synopsis "Visualizing and analyzing mass spectrometry data in proteomics")
15589 "This package helps with quality checks, visualizations and analysis of
15590 mass spectrometry data, coming from proteomics experiments. The package is
15591 developed, tested and used at the Functional Genomics Center Zurich, where it
15592 is used mainly for prototyping, teaching, and having fun with proteomics data.
15593 But it can also be used to do data analysis for small scale data sets.")
15594 (license license:gpl3)))
15596 (define-public r-cmprsk
15603 (uri (cran-uri "cmprsk" version))
15605 (base32 "050f24l5ab1ds9824c7yjahimf6pg8ih2k83jzpzfb0n5k5jfh44"))))
15606 (build-system r-build-system)
15611 (home-page "https://cran.r-project.org/web/packages/cmprsk")
15612 (synopsis "Subdistribution analysis of competing risks")
15614 "This package provides tool for estimation, testing and regression
15615 modeling of subdistribution functions in competing risks, as described in
15616 Gray (1988), A class of K-sample tests for comparing the cumulative incidence
15617 of a competing risk, Ann. Stat. 16:1141-1154, and Fine JP and Gray RJ (1999),
15618 A proportional hazards model for the subdistribution of a competing risk,
15619 JASA, 94:496-509.")
15620 (license license:gpl2+)))
15622 (define-public r-etm
15629 (uri (cran-uri "etm" version))
15632 "1hvrplmdpjjpjji663rw0vjbbrzj2nvr04d1nkc8bf46p4ixyxgy"))))
15633 (build-system r-build-system)
15635 (list r-data-table r-lattice r-rcpp r-rcpparmadillo r-survival))
15636 (home-page "https://cran.r-project.org/web/packages/etm")
15637 (synopsis "Empirical transition matrix")
15639 "The @dfn{empirical transition matrix} (etm) package estimates
15640 the matrix of transition probabilities for any time-inhomogeneous multistate
15641 model with finite state space using the Aalen-Johansen estimator.")
15642 (license license:expat)))
15644 (define-public r-epi
15651 (uri (cran-uri "Epi" version))
15654 "0s3ij0rya4wd7k97kc4s3pwj1d1ypaxl1s7zqr6sa07hp4a8fzz0"))))
15655 (properties `((upstream-name . "Epi")))
15656 (build-system r-build-system)
15670 (home-page "https://BendixCarstensen.com/Epi/")
15671 (synopsis "Statistical analysis in epidemiology")
15673 "This package provides functions for demographic and epidemiological
15674 analysis in the Lexis diagram, i.e. register and cohort follow-up data, in
15675 particular representation, manipulation and simulation of multistate data -
15676 the Lexis suite of functions, which includes interfaces to the @code{mstate},
15677 @code{etm} and @code{cmprsk} packages. It also contains functions for
15678 Age-Period-Cohort and Lee-Carter modeling and a function for interval censored
15679 data and some useful functions for tabulation and plotting, as well as a
15680 number of epidemiological data sets.")
15681 (license license:gpl2)))
15683 (define-public r-ppls
15686 (version "1.6-1.1")
15690 (uri (cran-uri "ppls" version))
15693 "1zyrisy3c4cz896j1bjh61sf57wdl9p8ywdq268cl819szfq78mx"))))
15694 (build-system r-build-system)
15695 (propagated-inputs (list r-mass))
15696 (home-page "https://cran.r-project.org/web/packages/ppls")
15697 (synopsis "Penalized partial least squares")
15699 "This package contains linear and nonlinear regression methods based on
15700 partial least squares and penalization techniques. Model parameters are
15701 selected via cross-validation, and confidence intervals ans tests for the
15702 regression coefficients can be conducted via jackknifing.")
15703 (license license:gpl2+)))
15705 (define-public r-huge
15712 (uri (cran-uri "huge" version))
15714 (base32 "1sl457a1lndrx98y2j9a2smanawx2iqlhl82iand0g3p5xp8ch4j"))))
15715 (build-system r-build-system)
15717 (list r-igraph r-mass r-matrix r-rcpp r-rcppeigen))
15718 (home-page "https://cran.r-project.org/web/packages/huge")
15719 (synopsis "High-dimensional undirected graph estimation")
15721 "This package provides a general framework for high-dimensional
15722 undirected graph estimation. It integrates data preprocessing, neighborhood
15723 screening, graph estimation, and model selection techniques into a pipeline.")
15724 (license license:gpl2)))
15726 (define-public r-parcor
15733 (uri (cran-uri "parcor" version))
15736 "0vgs6k92vdr0cmb8cwbv2ff6qavw30agskfd8bfh17hsskrisvx0"))))
15737 (build-system r-build-system)
15739 (list r-epi r-genenet r-glmnet r-mass r-ppls))
15740 (home-page "https://cran.r-project.org/web/packages/parcor")
15741 (synopsis "Regularized estimation of partial correlation matrices")
15743 "This package estimates the matrix of partial correlations based on
15744 different regularized regression methods: lasso, adaptive lasso, PLS, and
15745 Ridge Regression. In addition, the package provides model selection for
15746 lasso, adaptive lasso and Ridge regression based on cross-validation.")
15747 (license license:gpl2+)))
15749 (define-public r-mcmc
15756 (uri (cran-uri "mcmc" version))
15759 "0q42m8ab7b6bxhns494ksjdss5f3c5m2jjfdlfj6fk1nz7ax7i5p"))))
15760 (build-system r-build-system)
15761 (home-page "https://www.stat.umn.edu/geyer/mcmc/")
15762 (synopsis "Markov chain Monte Carlo")
15764 "This package simulates continuous distributions of random vectors using
15765 @dfn{Markov chain Monte Carlo} (MCMC). Users specify the distribution by an R
15766 function that evaluates the log unnormalized density. Algorithms are random
15767 walk Metropolis algorithm (function @code{metrop}), simulated
15768 tempering (function @code{temper}), and morphometric random walk
15769 Metropolis (function @code{morph.metrop}), which achieves geometric ergodicity
15770 by change of variable.")
15771 (license license:expat)))
15773 (define-public r-listenv
15780 (uri (cran-uri "listenv" version))
15783 "0ps8bk7zlhbviawrw7vw25skjq81hkk3ijyi6g74dmfqy8zsyapx"))))
15784 (build-system r-build-system)
15787 (modify-phases %standard-phases
15788 (add-after 'unpack 'set-HOME
15789 (lambda _ (setenv "HOME" "/tmp"))))))
15791 (list r-r-rsp)) ; vignette builder
15792 (home-page "https://github.com/HenrikBengtsson/listenv")
15793 (synopsis "Environments behaving (almost) as lists")
15795 "This package implements list environments. List environments are
15796 environments that have list-like properties. For instance, the elements of a
15797 list environment are ordered and can be accessed and iterated over using index
15799 (license license:lgpl2.1+)))
15801 (define-public r-globals
15808 (uri (cran-uri "globals" version))
15811 "15llx4233ihj4w815k7inc17530w9ja0mi29n1i0s2sr42j8jdpq"))))
15812 (build-system r-build-system)
15814 (list r-codetools))
15815 (home-page "https://github.com/HenrikBengtsson/globals")
15816 (synopsis "Identify global objects in R expressions")
15818 "This package provides tools to identify global (\"unknown\" or \"free\")
15819 objects in R expressions by code inspection using various strategies, e.g.
15820 conservative or liberal. The objective of this package is to make it as
15821 simple as possible to identify global objects for the purpose of exporting
15822 them in distributed compute environments.")
15823 (license license:lgpl2.1+)))
15825 (define-public r-parallelly
15827 (name "r-parallelly")
15832 (uri (cran-uri "parallelly" version))
15835 "1nhp66psk3m79is5qm4ppxkj7bdy46jr2h2pir22ia9ghhyzris0"))))
15836 (properties `((upstream-name . "parallelly")))
15837 (build-system r-build-system)
15838 (home-page "https://github.com/HenrikBengtsson/parallelly")
15839 (synopsis "Enhancements of the parallel package")
15841 "This package provides utility functions that enhance the @code{parallel}
15842 package and support the built-in parallel backends of the @code{future}
15843 package. For example, @code{availableCores} gives the number of CPU cores
15844 available to your R process as given by R options and environment variables,
15845 including those set by job schedulers on high-performance compute clusters.
15846 If none is set, it will fall back to @code{parallel::detectCores}. Another
15847 example is @code{makeClusterPSOCK}, which is backward compatible with
15848 @code{parallel::makePSOCKcluster} while doing a better job in setting up
15849 remote cluster workers without the need for configuring the firewall to do
15850 port-forwarding to your local computer.")
15851 (license license:lgpl2.1+)))
15853 (define-public r-future
15860 (uri (cran-uri "future" version))
15863 "1mchjdvvwgs8v0iv8z5m6gav3xzvnq11h8qrc7lfnrb2x3d0np53"))))
15864 (build-system r-build-system)
15867 (modify-phases %standard-phases
15868 (add-after 'unpack 'set-HOME
15869 (lambda _ (setenv "HOME" "/tmp"))))))
15871 (list r-digest r-globals r-listenv r-parallelly))
15873 (list r-r-rsp)) ; vignette builder
15874 (home-page "https://github.com/HenrikBengtsson/future")
15875 (synopsis "Unified parallel and distributed processing in R")
15877 "The purpose of this package is to provide a lightweight and unified
15878 Future API for sequential and parallel processing of R expression via futures.
15879 This package implements sequential, multicore, multisession, and cluster
15880 futures. With these, R expressions can be evaluated on the local machine, in
15881 parallel a set of local machines, or distributed on a mix of local and remote
15882 machines. Extensions to this package implement additional backends for
15883 processing futures via compute cluster schedulers etc. Because of its unified
15884 API, there is no need to modify any code in order to switch from sequential on
15885 the local machine to, say, distributed processing on a remote compute cluster.")
15886 (license license:lgpl2.1+)))
15888 (define-public r-future-apply
15890 (name "r-future-apply")
15895 (uri (cran-uri "future.apply" version))
15898 "1xb7qj8izjwmy4aa92p5f4cdbhgp220hrly3b5879f9hrv2w2rk1"))))
15899 (properties `((upstream-name . "future.apply")))
15900 (build-system r-build-system)
15903 (modify-phases %standard-phases
15904 (add-after 'unpack 'set-HOME
15905 (lambda _ (setenv "HOME" "/tmp"))))))
15907 (list r-future r-globals))
15909 (list r-r-rsp)) ; vignette builder
15910 (home-page "https://github.com/HenrikBengtsson/future.apply")
15911 (synopsis "Apply function to elements in parallel using futures")
15913 "This package provides implementations of @code{apply()},
15914 @code{eapply()}, @code{lapply()}, @code{Map()}, @code{mapply()},
15915 @code{replicate()}, @code{sapply()}, @code{tapply()}, and @code{vapply()} that
15916 can be resolved using any future-supported backend, e.g. parallel on the local
15917 machine or distributed on a compute cluster.")
15918 (license license:gpl2+)))
15920 (define-public r-rsvd
15927 (uri (cran-uri "rsvd" version))
15930 "07p2hjmpcwcsang8z9sjkpy94rydcin7m3hyvcgzgm5cd6w8c1p4"))))
15931 (build-system r-build-system)
15934 (home-page "https://github.com/erichson/rSVD")
15935 (synopsis "Randomized singular value decomposition")
15937 "Low-rank matrix decompositions are fundamental tools and widely used for
15938 data analysis, dimension reduction, and data compression. Classically, highly
15939 accurate deterministic matrix algorithms are used for this task. However, the
15940 emergence of large-scale data has severely challenged our computational
15941 ability to analyze big data. The concept of randomness has been demonstrated
15942 as an effective strategy to quickly produce approximate answers to familiar
15943 problems such as the @dfn{singular value decomposition} (SVD). This package
15944 provides several randomized matrix algorithms such as the randomized singular
15945 value decomposition (@code{rsvd}), randomized principal component
15946 analysis (@code{rpca}), randomized robust principal component
15947 analysis (@code{rrpca}), randomized interpolative decomposition (@code{rid}),
15948 and the randomized CUR decomposition (@code{rcur}). In addition several plot
15949 functions are provided.")
15950 (license license:gpl3+)))
15952 (define-public r-sloop
15959 (uri (cran-uri "sloop" version))
15962 "00fk5fr5zsk2qxc1kfhmshhjxgnamm3401089sx8m2l529zd6r8j"))))
15963 (build-system r-build-system)
15965 (list r-codetools r-crayon r-purrr r-rlang r-tibble))
15966 (home-page "https://github.com/r-lib/sloop")
15967 (synopsis "Helpers for object-oriented programming in R")
15969 "This package provides a collection of helper functions designed to
15970 help you to better understand object oriented programming in R, particularly
15972 (license license:gpl3)))
15974 (define-public r-capushe
15981 (uri (cran-uri "capushe" version))
15984 "1aa76ir1kp67hiz7dr60azyc71yzslshyc640fjh0fpw0sp5kwbc"))))
15985 (build-system r-build-system)
15986 (propagated-inputs (list r-mass))
15987 (home-page "https://cran.r-project.org/web/packages/capushe/index.html")
15988 (synopsis "Calibrating penalties using slope heuristics")
15990 "This package provides tools for the calibration of penalized criteria
15991 for model selection. The calibration methods available are based on the slope
15993 (license license:gpl2+)))
15995 (define-public r-dorng
16002 (uri (cran-uri "doRNG" version))
16005 "1jff27zzrvd1fd61x2m9468h8xn3s1c9f6wibviy5zdhj5dx9s9k"))))
16006 (properties `((upstream-name . "doRNG")))
16007 (build-system r-build-system)
16009 (list r-foreach r-iterators r-rngtools))
16010 (home-page "https://renozao.github.io/doRNG/")
16011 (synopsis "Generic reproducible parallel backend for foreach loops")
16013 "This package provides functions to perform reproducible parallel
16014 @code{foreach} loops, using independent random streams as generated by
16015 L'Ecuyer's combined multiple-recursive generator. It enables to easily
16016 convert standard @code{%dopar%} loops into fully reproducible loops,
16017 independently of the number of workers, the task scheduling strategy, or the
16018 chosen parallel environment and associated foreach backend.")
16019 (license license:gpl2+)))
16021 (define-public r-blockmodeling
16023 (name "r-blockmodeling")
16028 (uri (cran-uri "blockmodeling" version))
16031 "1vc8gy4slsywcwxq532373i0dq73fhs5cac9mr6zz2pjaaxjghhq"))))
16032 (build-system r-build-system)
16035 (native-inputs (list gfortran))
16036 (home-page "https://cran.r-project.org/web/packages/blockmodeling")
16037 (synopsis "Generalized and classical blockmodeling of valued networks")
16039 "This package is primarily meant as an implementation of generalized
16040 blockmodeling for valued networks. In addition, measures of similarity or
16041 dissimilarity based on structural equivalence and regular equivalence (REGE
16042 algorithms) can be computed and partitioned matrices can be plotted.")
16043 (license license:gpl2+)))
16045 (define-public r-upsetr
16052 (uri (cran-uri "UpSetR" version))
16055 "007i0njnjjy7vbrxabwav7a1kk2n0hn2mkvqsdzzfk10ckp5y7im"))))
16056 (properties `((upstream-name . "UpSetR")))
16057 (build-system r-build-system)
16059 (list r-ggplot2 r-gridextra r-plyr r-scales))
16060 (home-page "https://github.com/hms-dbmi/UpSetR")
16061 (synopsis "Visualize intersecting sets")
16063 "This package provides a more scalable alternative to Venn and Euler
16064 diagrams for visualizing intersecting sets. Create visualizations of
16065 intersecting sets using a novel matrix design, along with visualizations of
16066 several common set, element and attribute related tasks.")
16067 (license license:expat)))
16069 ;; This package includes a JavaScript file, which is not minified. When
16070 ;; upgrading please check that there are no new minified JavaScript files.
16071 (define-public r-shinybs
16078 (uri (cran-uri "shinyBS" version))
16081 "0h51685a9qll4agayldjyryi60ih969219ibg071slv0613p5v8a"))))
16082 (properties `((upstream-name . "shinyBS")))
16083 (build-system r-build-system)
16084 ;; The tests spawn Shiny browser apps. They cannot be run
16085 ;; non-interactively.
16086 (arguments '(#:tests? #f))
16088 (list r-htmltools r-shiny))
16089 (home-page "https://ebailey78.github.io/shinyBS/")
16090 (synopsis "Twitter Bootstrap components for Shiny")
16092 "This package adds additional Twitter Bootstrap components to Shiny.")
16093 (license license:gpl3)))
16095 (define-public r-shinyjqui
16097 (name "r-shinyjqui")
16102 (uri (cran-uri "shinyjqui" version))
16105 "135gwz7syyb6pbn0lkvmq0v1c6r1zivavnqhi1rnzbbzlysi27v1"))
16107 '(for-each delete-file
16108 (list "inst/www/shinyjqui.min.js"
16109 "inst/www/jquery.ui.touch-punch.min.js")))))
16110 (properties `((upstream-name . "shinyjqui")))
16111 (build-system r-build-system)
16114 (modify-phases %standard-phases
16115 (add-after 'unpack 'process-javascript
16116 (lambda* (#:key inputs #:allow-other-keys)
16117 (with-directory-excursion "inst/www"
16119 `((,(string-append (assoc-ref inputs "js-jquery.ui.touch-punch")
16120 "/jquery.ui.touch-punch.js")
16121 . "jquery.ui.touch-punch.min.js")
16123 . "shinyjqui.min.js"))))
16124 (for-each (lambda (source target)
16125 (format #true "Processing ~a --> ~a~%"
16127 (invoke "esbuild" source "--minify"
16128 (string-append "--outfile=" target)))
16130 (map cdr mapping)))))))))
16132 (list r-htmltools r-htmlwidgets r-jsonlite r-rlang r-shiny))
16134 `(("r-knitr" ,r-knitr)
16135 ("esbuild" ,esbuild)
16136 ("js-jquery.ui.touch-punch"
16139 (uri (git-reference
16140 (url "https://github.com/furf/jquery-ui-touch-punch")
16141 (commit "8f7559b6e65cdc3ee3648d5fe76d38c653f87ff5")))
16144 "1lzywp2q9hwx6d5fqjla95vp7ra2lahr5dam7lsqjmch9d98r48q"))))))
16145 (home-page "https://github.com/yang-tang/shinyjqui")
16146 (synopsis "jQuery UI interactions and effects for Shiny")
16148 "This is an extension to Shiny that brings interactions and animation
16149 effects from the jQuery UI library.")
16150 (license license:expat)))
16152 (define-public r-shinymanager
16154 (name "r-shinymanager")
16155 (version "1.0.400")
16159 (uri (cran-uri "shinymanager" version))
16161 (base32 "1np2yp5pn8g9i4jhysfgprmdn13cpw4vaaagrd72rnk2r4hpmyx4"))))
16162 (properties `((upstream-name . "shinymanager")))
16163 (build-system r-build-system)
16165 (list r-billboarder
16175 (native-inputs (list r-knitr))
16176 (home-page "https://github.com/datastorm-open/shinymanager")
16177 (synopsis "Authentication management for Shiny applications")
16179 "This package provides simple and secure authentification mechanism for
16180 single Shiny applications. Credentials are stored in an encrypted SQLite
16182 (license license:gpl3)))
16184 (define-public r-outliers
16186 (name "r-outliers")
16191 (uri (cran-uri "outliers" version))
16194 "1yrmwvjjb0a6sbx940k9svf23cykcxz8rrwcgyic7lpgzbrdfcfc"))))
16195 (build-system r-build-system)
16196 (home-page "https://cran.r-project.org/web/packages/outliers/index.html")
16197 (synopsis "Tests for outliers")
16199 "This package provides a collection of some tests commonly used for
16200 identifying outliers.")
16201 (license license:gpl2+)))
16203 (define-public r-bayesm
16210 (uri (cran-uri "bayesm" version))
16212 (base32 "154glks7rsjkza0sfi1kj7wj727py9sl1ba6sswflwmwc9n226q6"))))
16213 (build-system r-build-system)
16215 (list r-rcpp r-rcpparmadillo))
16216 (home-page "http://www.perossi.org/home/bsm-1")
16217 (synopsis "Bayesian inference for marketing/micro-econometrics")
16219 "This package covers many important models used in marketing and
16220 micro-econometrics applications, including Bayes Regression (univariate or
16221 multivariate dep var), Bayes Seemingly Unrelated Regression (SUR), Binary and
16222 Ordinal Probit, Multinomial Logit (MNL) and Multinomial Probit (MNP),
16223 Multivariate Probit, Negative Binomial (Poisson) Regression, Multivariate
16224 Mixtures of Normals (including clustering), Dirichlet Process Prior Density
16225 Estimation with normal base, Hierarchical Linear Models with normal prior and
16226 covariates, Hierarchical Linear Models with a mixture of normals prior and
16227 covariates, Hierarchical Multinomial Logits with a mixture of normals prior
16228 and covariates, Hierarchical Multinomial Logits with a Dirichlet Process prior
16229 and covariates, Hierarchical Negative Binomial Regression Models, Bayesian
16230 analysis of choice-based conjoint data, Bayesian treatment of linear
16231 instrumental variables models, Analysis of Multivariate Ordinal survey data
16232 with scale usage heterogeneity, and Bayesian Analysis of Aggregate Random
16233 Coefficient Logit Models.")
16234 (license license:gpl2+)))
16236 (define-public r-tensora
16243 (uri (cran-uri "tensorA" version))
16246 "19wwh654qlja4z1n7afjpzsrrm53p8ddysa2vra5mdnkddb4g2cf"))))
16247 (properties `((upstream-name . "tensorA")))
16248 (build-system r-build-system)
16249 (home-page "http://www.stat.boogaart.de/tensorA")
16250 (synopsis "Advanced tensor arithmetic with named indices")
16252 "This package provides convenience functions for advanced linear algebra
16253 with tensors and computation with datasets of tensors on a higher level
16254 abstraction. It includes Einstein and Riemann summing conventions, dragging,
16255 co- and contravariate indices, and parallel computations on sequences of
16257 (license license:gpl2+)))
16259 (define-public r-rarpack
16266 (uri (cran-uri "rARPACK" version))
16269 "12h2y46xcfldhjdmm960swgn9b23zvkj5vg2bi42s9qxwgi02d63"))))
16270 (properties `((upstream-name . "rARPACK")))
16271 (build-system r-build-system)
16272 (propagated-inputs (list r-rspectra))
16273 (home-page "https://github.com/yixuan/rARPACK")
16274 (synopsis "Solvers for large scale eigenvalue and SVD problems")
16276 "This package was previously an R wrapper of the ARPACK library, and now
16277 a shell of the R package RSpectra, an R interface to the Spectra library for
16278 solving large scale eigenvalue/vector problems. The current version of
16279 rARPACK simply imports and exports the functions provided by RSpectra. New
16280 users of rARPACK are advised to switch to the RSpectra package.")
16281 (license license:bsd-3)))
16283 (define-public r-compositions
16285 (name "r-compositions")
16290 (uri (cran-uri "compositions" version))
16293 "1bqg0qqzsf92q0jb7hdjycr54bwv8rk7ajhvxgch5yslyqxpm73v"))))
16294 (build-system r-build-system)
16296 (list r-bayesm r-mass r-robustbase r-tensora))
16299 (home-page "http://www.stat.boogaart.de/compositions")
16300 (synopsis "Compositional data analysis")
16302 "This package provides functions for the consistent analysis of
16303 compositional data (e.g. portions of substances) and positive
16304 numbers (e.g. concentrations).")
16305 (license license:gpl2+)))
16307 (define-public r-cobs
16314 (uri (cran-uri "cobs" version))
16317 "0hiw5smk6kgk0gb9840kcqkhkybl7n30s77xhjc395x09izbgix1"))))
16318 (build-system r-build-system)
16320 (list r-quantreg r-sparsem))
16321 (home-page "https://cran.r-project.org/web/packages/cobs")
16322 (synopsis "Constrained B-Splines (sparse matrix based)")
16324 "This package provides qualitatively constrained (regression) smoothing
16325 splines via linear programming and sparse matrices.")
16326 (license license:gpl2+)))
16328 (define-public r-drimpute
16330 (name "r-drimpute")
16335 (uri (cran-uri "DrImpute" version))
16338 "1adzarrwqb282pqgx2yqswp9rpwd1naxsmar54kddr6qyd6b923b"))))
16339 (properties `((upstream-name . "DrImpute")))
16340 (build-system r-build-system)
16342 (list r-rcpp r-rcpparmadillo))
16343 (home-page "https://github.com/ikwak2/DrImpute")
16344 (synopsis "Imputing dropout events in single-cell RNA-Seq data")
16346 "This is an R package for imputing dropout events. Many statistical
16347 methods in cell type identification, visualization and lineage reconstruction
16348 do not account for dropout events. DrImpute can improve the performance of
16349 such software by imputing dropout events.")
16350 (license license:gpl3)))
16352 (define-public r-gamlss-dist
16354 (name "r-gamlss-dist")
16359 (uri (cran-uri "gamlss.dist" version))
16361 (base32 "1gqjr419v8z2ygh0h1xz7bipnsbp820njzwq7z3r9f41rn1ym47c"))))
16362 (properties `((upstream-name . "gamlss.dist")))
16363 (build-system r-build-system)
16364 (propagated-inputs (list r-mass))
16365 (home-page "http://www.gamlss.org/")
16366 (synopsis "Distributions for Generalized Additive Models for location scale and shape")
16368 "This package provides a set of distributions which can be used for
16369 modelling the response variables in Generalized Additive Models for Location
16370 Scale and Shape. The distributions can be continuous, discrete or mixed
16371 distributions. Extra distributions can be created, by transforming, any
16372 continuous distribution defined on the real line, to a distribution defined on
16373 ranges 0 to infinity or 0 to 1, by using a @code{log} or a @code{logit}
16374 transformation, respectively.")
16375 ;; Either version of the GPL.
16376 (license (list license:gpl2 license:gpl3))))
16378 ;; This package includes JavaScript files, which are not minified. When
16379 ;; upgrading please check that there are no new minified JavaScript files.
16380 (define-public r-shinyjs
16387 (uri (cran-uri "shinyjs" version))
16390 "1id9gsrkr28xl80a8794in17rxmmz06zqvd5hlns7mqz3fzhrhky"))))
16391 (build-system r-build-system)
16393 (list r-digest r-jsonlite r-shiny))
16396 (home-page "https://deanattali.com/shinyjs")
16397 (synopsis "Improve the user experience of your Shiny apps")
16399 "Perform common useful JavaScript operations in Shiny apps that will
16400 greatly improve your apps without having to know any JavaScript. Examples
16401 include: hiding an element, disabling an input, resetting an input back to its
16402 original value, delaying code execution by a few seconds, and many more useful
16403 functions for both the end user and the developer. Shinyjs can also be used
16404 to easily call your own custom JavaScript functions from R.")
16405 (license license:agpl3+)))
16407 ;; This package includes minified JavaScript files. When upgrading please
16408 ;; check that there are no new minified JavaScript files.
16409 (define-public r-colourpicker
16411 (name "r-colourpicker")
16416 (uri (cran-uri "colourpicker" version))
16419 "1q1wi3g403fbzp4ys3gsjbwdc86x770cx323qgi47ca8n219kl50"))))
16420 (build-system r-build-system)
16423 (modify-phases %standard-phases
16424 (add-after 'unpack 'process-javascript
16425 (lambda* (#:key inputs #:allow-other-keys)
16426 (with-directory-excursion "inst"
16428 `((,(assoc-ref inputs "js-salvattore")
16429 . "examples/colourInput/www/salvattore.min.js")
16430 (,(assoc-ref inputs "js-jquery")
16431 . "htmlwidgets/lib/jquery/jquery.min.js")
16432 ("www/shared/colourpicker/js/colourpicker.js"
16433 . "www/shared/colourpicker/js/colourpicker.min.js"))))
16434 (for-each (lambda (source target)
16435 (format #true "Processing ~a --> ~a~%"
16437 (delete-file target)
16438 (invoke "esbuild" source "--minify"
16439 (string-append "--outfile=" target)))
16441 (map cdr mapping)))))))))
16451 `(("esbuild" ,esbuild)
16455 (uri "https://code.jquery.com/jquery-1.11.3.js")
16458 "1v956yf5spw0156rni5z77hzqwmby7ajwdcd6mkhb6zvl36awr90"))))
16462 (uri "https://raw.githubusercontent.com/rnmp/salvattore/v1.0.9/dist/salvattore.js")
16465 "0lfrbx7l9w5x89jpc6njmd0pk7h8fpvg537vklai2vf7b1r2nnk5"))))))
16466 (home-page "https://github.com/daattali/colourpicker")
16467 (synopsis "Color picker tool for Shiny and for selecting colors in plots")
16469 "This package provides a color picker that can be used as an input in
16470 Shiny apps or Rmarkdown documents. The color picker supports alpha opacity,
16471 custom color palettes, and many more options. A plot color helper tool is
16472 available as an RStudio Addin, which helps you pick colors to use in your
16473 plots. A more generic color picker RStudio Addin is also provided to let you
16474 select colors to use in your R code.")
16475 (license license:expat)))
16477 (define-public r-ggextra
16484 (uri (cran-uri "ggExtra" version))
16487 "1rd3qv6ah3zphr1jicjhgxms73vi496mjnxnsrcgl7z8nyxmas6w"))))
16488 (properties `((upstream-name . "ggExtra")))
16489 (build-system r-build-system)
16491 (list r-colourpicker
16501 (home-page "https://github.com/daattali/ggExtra")
16502 (synopsis "Marginal histograms for ggplot2 and other enhancements")
16504 "This package is a collection of functions and layers to enhance ggplot2.
16505 The flagship function is @code{ggMarginal()}, which can be used to add
16506 marginal histograms/boxplots/density plots to ggplot2 scatterplots.")
16507 (license license:expat)))
16509 (define-public r-minpack-lm
16511 (name "r-minpack-lm")
16516 (uri (cran-uri "minpack.lm" version))
16519 "11yz6hk2r33571d16kq01cb1x6sgdzi6jmksqlrm8mr84l95c2f7"))))
16520 (properties `((upstream-name . "minpack.lm")))
16521 (build-system r-build-system)
16522 (native-inputs (list gfortran))
16523 (home-page "https://cran.r-project.org/web/packages/minpack.lm")
16524 (synopsis "Levenberg-Marquardt Nonlinear Least-Squares algorithm")
16526 "The @code{nls.lm} function provides an R interface to @code{lmder} and
16527 @code{lmdif} from the MINPACK library, for solving nonlinear least-squares
16528 problems by a modification of the Levenberg-Marquardt algorithm, with support
16529 for lower and upper parameter bounds. The implementation can be used via
16530 @code{nls}-like calls using the @code{nlsLM} function.")
16531 (license license:gpl3)))
16533 (define-public r-moments
16540 (uri (cran-uri "moments" version))
16543 "0r6qf3i1rzh2822bx1p0h8mh91gsbgg6asl2rzh2l4ys094bilif"))))
16544 (build-system r-build-system)
16545 (home-page "https://cran.r-project.org/web/packages/moments")
16546 (synopsis "Moments, cumulants, skewness, kurtosis and related tests")
16548 "This package provides functions to calculate: moments, Pearson's
16549 kurtosis, Geary's kurtosis and skewness; it also includes tests related to
16550 them (Anscombe-Glynn, D'Agostino, Bonett-Seier).")
16551 (license license:gpl2+)))
16553 (define-public r-msir
16560 (uri (cran-uri "msir" version))
16563 "1wm83m3cqd6llxb9p2jwim0wb81v84pgdmgcznygzaaq6kbn3n84"))))
16564 (build-system r-build-system)
16569 (home-page "https://cran.r-project.org/web/packages/msir")
16570 (synopsis "Model-based sliced inverse regression")
16572 "This is an R package for dimension reduction based on finite Gaussian
16573 mixture modeling of inverse regression.")
16574 (license license:gpl2+)))
16576 (define-public r-pbivnorm
16578 (name "r-pbivnorm")
16583 (uri (cran-uri "pbivnorm" version))
16586 "05jzrjqxzbcf6z245hlk7sjxiszv9paadaaimvcx5y5qgi87vhq7"))))
16587 (build-system r-build-system)
16588 (native-inputs (list gfortran))
16589 (home-page "https://github.com/brentonk/pbivnorm")
16590 (synopsis "Vectorized bivariate normal CDF")
16592 "This package provides a vectorized R function for calculating
16593 probabilities from a standard bivariate normal CDF.")
16594 (license license:gpl2+)))
16596 (define-public r-lavaan
16603 (uri (cran-uri "lavaan" version))
16606 "026k32paf51lpy6zxm9m81zg9szx14j37dxdip6nba334jw97h9c"))))
16607 (build-system r-build-system)
16609 (list r-mass r-mnormt r-numderiv r-pbivnorm))
16610 (home-page "https://lavaan.ugent.be")
16611 (synopsis "Latent variable analysis")
16613 "This package provides tools to fit a variety of latent variable models,
16614 including confirmatory factor analysis, structural equation modeling and
16615 latent growth curve models.")
16616 (license license:gpl2+)))
16618 (define-public r-nonnest2
16620 (name "r-nonnest2")
16625 (uri (cran-uri "nonnest2" version))
16628 "1ddaqwx8i3ygwvxf11mc8xhgk4nkvnail99nr5szq8i168752zq2"))))
16629 (build-system r-build-system)
16631 (list r-compquadform r-lavaan r-mvtnorm r-sandwich))
16634 (home-page "https://cran.r-project.org/web/packages/nonnest2/")
16635 (synopsis "Tests of non-nested models")
16637 "This package allows for testing of non-nested models. It includes tests
16638 of model distinguishability and of model fit that can be applied to both
16639 nested and non-nested models. The package also includes functionality to
16640 obtain confidence intervals associated with AIC and BIC.")
16641 ;; Either version of the GPL.
16642 (license (list license:gpl2 license:gpl3))))
16644 (define-public r-penalized
16646 (name "r-penalized")
16651 (uri (cran-uri "penalized" version))
16654 "08badmgygppbqzay20qijyww028yw6s8dyd8ijcp8g4r9rn8xqyq"))))
16655 (build-system r-build-system)
16657 (list r-rcpp r-rcpparmadillo r-survival))
16658 (home-page "https://cran.r-project.org/web/packages/penalized/")
16659 (synopsis "Penalized estimation in GLMs and in the Cox model")
16661 "This package provides tools for fitting possibly high dimensional
16662 penalized regression models. The penalty structure can be any combination of
16663 an L1 penalty (lasso and fused lasso), an L2 penalty (ridge) and a positivity
16664 constraint on the regression coefficients. The supported regression models
16665 are linear, logistic and Poisson regression and the Cox Proportional Hazards
16666 model. Cross-validation routines allow optimization of the tuning
16668 (license license:gpl2+)))
16670 (define-public r-zim
16677 (uri (cran-uri "ZIM" version))
16680 "0scyfjn4ilsvha3x41c3b8bcfi31hlhwm77wn2a8hj5dsvnnmzig"))))
16681 (properties `((upstream-name . "ZIM")))
16682 (build-system r-build-system)
16683 (propagated-inputs (list r-mass))
16684 (home-page "https://github.com/biostatstudio/ZIM")
16685 (synopsis "Zero-inflated models (ZIM) for count time series with excess zeros")
16687 "Analyze count time series with excess zeros. Two types of statistical
16688 models are supported: Markov regression and state-space models. They are also
16689 known as observation-driven and parameter-driven models respectively in the
16690 time series literature. The functions used for Markov regression or
16691 observation-driven models can also be used to fit ordinary regression models
16692 with independent data under the zero-inflated Poisson (ZIP) or zero-inflated
16693 negative binomial (ZINB) assumption. The package also contains miscellaneous
16694 functions to compute density, distribution, quantile, and generate random
16695 numbers from ZIP and ZINB distributions.")
16696 (license license:gpl3)))
16698 (define-public r-nor1mix
16705 (uri (cran-uri "nor1mix" version))
16708 "1817wcvlmxs70vs4db0jkxd7i037744zz8ay3c2a9949z29fxr4w"))))
16709 (build-system r-build-system)
16710 (home-page "https://cran.r-project.org/web/packages/nor1mix/")
16711 (synopsis "Normal (1-d) mixture models")
16713 "This package provides S3 classes and methods for one-dimensional normal
16714 mixture models, for, e.g., density estimation or clustering algorithms
16715 research and teaching; it provides the widely used Marron-Wand densities. It
16716 also provides tools for efficient random number generation and graphics.")
16717 (license license:gpl2+)))
16719 (define-public r-beanplot
16721 (name "r-beanplot")
16726 (uri (cran-uri "beanplot" version))
16729 "1b8mvlcsv5l9g08ag92hndsvk8jmgxvznhzgazc8y4296kp8l5a9"))))
16730 (build-system r-build-system)
16731 (home-page "https://cran.r-project.org/web/packages/beanplot/")
16732 (synopsis "Visualization via beanplots")
16734 "This package provides beanplots, an alternative to
16735 boxplot/stripchart/violin plots. It can be used to plot univariate comparison
16737 (license license:gpl2)))
16739 (define-public r-pbdzmq
16746 (uri (cran-uri "pbdZMQ" version))
16749 "020qy6fq8w8wq0j3bii14ahrlg8wzl0lrnndfr6scmrg9ghjnbfz"))))
16750 (properties `((upstream-name . "pbdZMQ")))
16751 (build-system r-build-system)
16753 (list zeromq zlib))
16756 (home-page "https://pbdr.org/")
16757 (synopsis "R interface to ZeroMQ")
16759 "ZeroMQ is a well-known library for high-performance asynchronous
16760 messaging in scalable, distributed applications. This package provides high
16761 level R wrapper functions to easily utilize ZeroMQ. The main focus is on
16762 interactive client/server programming frameworks. A few wrapper functions
16763 compatible with @code{rzmq} are also provided.")
16764 (license license:gpl3)))
16766 (define-public r-repr
16773 (uri (cran-uri "repr" version))
16776 "0h3h14ybamcbwmm31ib66fx13v75vkzn4bn2v26n2h097sl9qybg"))))
16777 (build-system r-build-system)
16779 (list r-base64enc r-htmltools r-jsonlite r-pillar))
16780 (home-page "https://cran.r-project.org/web/packages/repr/")
16781 (synopsis "Serializable representations")
16783 "This package provides string and binary representations of objects for
16784 several formats and MIME types.")
16785 (license license:gpl3)))
16787 (define-public r-irdisplay
16789 (name "r-irdisplay")
16794 (uri (cran-uri "IRdisplay" version))
16797 "0awdiv4rr93y8jb1d64sm1iy37ywyniqm7w98yv6qm0zz47h7sw3"))))
16798 (properties `((upstream-name . "IRdisplay")))
16799 (build-system r-build-system)
16802 (home-page "https://cran.r-project.org/web/packages/IRdisplay/")
16803 (synopsis "Jupyter display machinery")
16805 "This package provides an interface to the rich display capabilities of
16806 Jupyter front-ends (e.g. Jupyter Notebook). It is designed to be used from a
16807 running IRkernel session.")
16808 (license license:expat)))
16810 (define-public r-irkernel
16812 (name "r-irkernel")
16817 (uri (cran-uri "IRkernel" version))
16820 "00qrmsywpzw2hfp88020zjaijma7q4hqm9h2cz53rywdjzywnzss"))))
16821 (properties `((upstream-name . "IRkernel")))
16822 (build-system r-build-system)
16825 (modify-phases %standard-phases
16826 (add-after 'install 'install-kernelspec
16827 (lambda* (#:key outputs #:allow-other-keys)
16828 (let ((out (assoc-ref outputs "out")))
16829 (setenv "HOME" "/tmp")
16830 (invoke "jupyter" "kernelspec" "install"
16833 (string-append out "/site-library/IRkernel/kernelspec"))
16834 ;; Record the absolute file name of the 'R' executable in
16836 (substitute* (string-append out "/share/jupyter"
16837 "/kernels/ir/kernel.json")
16839 (string-append "[\"" (which "R") "\",")))
16849 ;; sets R_LIBS_SITE, so R can actually find this package (IRkernel)
16854 (home-page "https://cran.r-project.org/web/packages/IRkernel/")
16855 (synopsis "Native R kernel for Jupyter")
16857 "The R kernel for the Jupyter environment executes R code which the
16858 front-end (Jupyter Notebook or other front-ends) submits to the kernel via the
16860 (license license:expat)))
16862 (define-public r-gmodels
16865 (version "2.18.1.1")
16869 (uri (cran-uri "gmodels" version))
16872 "158y7yh4maawn9vki8cq4sil48xib2bbpl6qgj5gvlkw3c14hzfs"))))
16873 (build-system r-build-system)
16875 (list r-gdata r-mass))
16876 (home-page "https://cran.r-project.org/web/packages/gmodels/")
16877 (synopsis "Various R programming tools for model fitting")
16879 "This package provides various R programming tools for model fitting.")
16880 (license license:gpl2)))
16882 (define-public r-apcluster
16884 (name "r-apcluster")
16889 (uri (cran-uri "apcluster" version))
16892 "0wnbb3kj9m7rfq63xr43jjf6n8jxm1r2wvvx6g0qkss0wvipbb1s"))))
16893 (build-system r-build-system)
16895 (list r-matrix r-rcpp))
16896 (native-inputs (list r-knitr))
16897 (home-page "https://cran.r-project.org/web/packages/apcluster/")
16898 (synopsis "Affinity propagation clustering")
16900 "This package implements affinity propagation clustering introduced by
16901 Frey and Dueck (2007). The package further provides leveraged affinity
16902 propagation and an algorithm for exemplar-based agglomerative clustering that
16903 can also be used to join clusters obtained from affinity propagation. Various
16904 plotting functions are available for analyzing clustering results.")
16905 (license license:gpl2+)))
16907 (define-public r-rematch2
16909 (name "r-rematch2")
16914 (uri (cran-uri "rematch2" version))
16917 "1fzpz8vhghw8ygwg6rsvfy3783pqk7ch029i5851lwypkplvz77y"))))
16918 (build-system r-build-system)
16921 (home-page "https://github.com/r-lib/rematch2")
16922 (synopsis "Tidy output from regular expression matching")
16924 "This package provides wrappers on @code{regexpr} and @code{gregexpr} to
16925 return the match results in tidy data frames.")
16926 (license license:expat)))
16928 (define-public r-picante
16935 (uri (cran-uri "picante" version))
16938 "19savjzj44b7ifdxcp02ynj22z4n4ikq2aipc74ljzy3yykmqmjn"))))
16939 (build-system r-build-system)
16941 (list r-ape r-nlme r-vegan))
16942 (home-page "https://cran.r-project.org/web/packages/picante/")
16943 (synopsis "Integrating phylogenies and ecology")
16945 "This package provides functions for phylocom integration, community
16946 analyses, null-models, traits and evolution. It implements numerous
16947 ecophylogenetic approaches including measures of community phylogenetic and
16948 trait diversity, phylogenetic signal, estimation of trait values for
16949 unobserved taxa, null models for community and phylogeny randomizations, and
16950 utility functions for data input/output and phylogeny plotting. A full
16951 description of package functionality and methods are provided by Kembel et
16953 (license license:gpl2)))
16955 (define-public r-reinforcelearn
16957 (name "r-reinforcelearn")
16962 (uri (cran-uri "reinforcelearn" version))
16965 "176z2q69p24i29a8sh19xxn2zl3h1z2ixdssr5i6m4yvkvdrvv3b"))))
16966 (build-system r-build-system)
16968 (list r-checkmate r-nnet r-purrr r-r6))
16969 (home-page "https://markusdumke.github.io/reinforcelearn")
16970 (synopsis "Reinforcement learning")
16972 "This package implements reinforcement learning environments and
16973 algorithms as described in Sutton & Barto (1998). The Q-Learning algorithm
16974 can be used with function approximation, eligibility traces (Singh & Sutton,
16975 1996) and experience replay (Mnih et al., 2013).")
16976 (license license:expat)))
16978 (define-public r-lemon
16985 (uri (cran-uri "lemon" version))
16988 "1y3ljidhqdakxlya2npj2w0az820g8kw6gl1cfm4f0cxvzgd1ly4"))))
16989 (build-system r-build-system)
17001 (home-page "https://github.com/stefanedwards/lemon")
17002 (synopsis "Freshen up your ggplot2 plots")
17004 "This package provides functions for working with legends and axis lines
17005 of ggplot2, facets that repeat axis lines on all panels, and some knitr
17007 (license license:gpl3)))
17009 (define-public r-wgaim
17016 (uri (cran-uri "wgaim" version))
17018 (base32 "1qiyfkpsbzjr9xsq5kqq6rlqpndngkn2irdfh3gyi45h6hn118j4"))))
17019 (build-system r-build-system)
17021 (list r-ggplot2 r-qtl))
17022 (home-page "https://cran.r-project.org/web/packages/wgaim")
17023 (synopsis "Whole genome average interval mapping for QTL detection")
17025 "This package integrates sophisticated mixed modelling methods with a
17026 whole genome approach to detecting significant QTL in linkage maps.")
17027 (license license:gpl2+)))
17029 (define-public r-bedr
17036 (uri (cran-uri "bedr" version))
17039 "0zpqvyjgwyqawxm8qrhcv8zq2b3yxgcqkkc87br29yrl7sjb8h6j"))))
17040 (build-system r-build-system)
17049 htslib)) ; for tabix
17051 (list r-knitr)) ; for vignettes
17052 (home-page "https://cran.r-project.org/web/packages/bedr")
17053 (synopsis "Genomic region processing")
17055 "This package is for genomic regions processing using command line tools
17056 such as BEDTools, BEDOPS and Tabix. These tools offer scalable and efficient
17057 utilities to perform genome arithmetic e.g indexing, formatting and merging.
17058 The bedr package's API enhances access to these tools as well as offers
17059 additional utilities for genomic regions processing.")
17060 (license license:gpl2)))
17062 (define-public r-sets
17069 (uri (cran-uri "sets" version))
17072 "1h1a03b1850kh5hd3gxbspx2nxqxvk2gb0wm0s60b70qb6zg0csp"))))
17073 (properties `((upstream-name . "sets")))
17074 (build-system r-build-system)
17075 (home-page "https://cran.r-project.org/web/packages/sets")
17076 (synopsis "Sets, generalized sets, customizable sets and intervals")
17078 "This package provides data structures and basic operations for ordinary
17079 sets, generalizations such as fuzzy sets, multisets, and fuzzy multisets,
17080 customizable sets, and intervals.")
17081 (license license:gpl2)))
17083 (define-public r-partitions
17085 (name "r-partitions")
17090 (uri (cran-uri "partitions" version))
17093 "1qqy4df28wy4q0g572azrj171jlhvrnzbh7x0wr2g7v6gr20y0ns"))))
17094 (build-system r-build-system)
17096 (list r-gmp r-polynom r-sets))
17097 (home-page "https://cran.r-project.org/web/packages/partitions")
17098 (synopsis "Additive partitions of integers")
17100 "This package provides tools to enumerates the partitions, unequal
17101 partitions, and restricted partitions of an integer; the three corresponding
17102 partition functions are also given.")
17103 ;; Any version of the GPL
17104 (license license:gpl2+)))
17106 (define-public r-brobdingnag
17108 (name "r-brobdingnag")
17113 (uri (cran-uri "Brobdingnag" version))
17116 "0hnp5nrpnscykvgrrbgp7987660hcbv92zc2q8lmpnin4ws399vk"))))
17117 (properties `((upstream-name . "Brobdingnag")))
17118 (build-system r-build-system)
17119 (home-page "https://github.com/RobinHankin/Brobdingnag.git")
17120 (synopsis "Very large numbers in R")
17122 "This package handles very large numbers in R. Real numbers are held
17123 using their natural logarithms, plus a logical flag indicating sign. The
17124 package includes a vignette that gives a step-by-step introduction to using S4
17126 ;; Any version of the GPL
17127 (license license:gpl2+)))
17129 (define-public r-untb
17136 (uri (cran-uri "untb" version))
17139 "1i7m4vfslsix98dwx4jlrsldm7fhhfp25gr7aapcxqxms7ryaby6"))))
17140 (build-system r-build-system)
17142 (list r-brobdingnag r-partitions r-polynom))
17143 (home-page "https://github.com/RobinHankin/untb.git")
17144 (synopsis "Ecological drift under the UNTB")
17146 "This package provides numerical simulations, and visualizations, of
17147 Hubbell's @dfn{Unified Neutral Theory of Biodiversity} (UNTB).")
17148 (license license:gpl2+)))
17150 (define-public r-stepwise
17152 (name "r-stepwise")
17157 (uri (cran-uri "stepwise" version))
17160 "1lbx1bxwkf9dw6q46w40pp7h5nkxgghmx8rkpaymm6iybc7gyir2"))))
17161 (build-system r-build-system)
17162 (home-page "https://stat.sfu.ca/statgen/research/stepwise.html")
17163 (synopsis "Stepwise detection of recombination breakpoints")
17165 "This package provides a stepwise approach to identifying recombination
17166 breakpoints in a genomic sequence alignment.")
17167 (license license:gpl2+)))
17169 (define-public r-snpmaxsel
17171 (name "r-snpmaxsel")
17176 (uri (cran-uri "SNPmaxsel" version))
17179 "0pjvixwqzjd3jwccc8yqq9c76afvbmfq0z1w0cwyj8bblrjpx13z"))))
17180 (properties `((upstream-name . "SNPmaxsel")))
17181 (build-system r-build-system)
17183 (list r-combinat r-mvtnorm))
17184 (home-page "https://cran.r-project.org/web/packages/SNPmaxsel/index.html")
17185 (synopsis "Maximally selected statistics for SNP data")
17187 "This package implements asymptotic methods related to maximally selected
17188 statistics, with applications to @dfn{single-nucleotide polymorphism} (SNP)
17190 (license license:gpl2+)))
17192 (define-public r-acsnminer
17194 (name "r-acsnminer")
17195 (version "0.16.8.25")
17198 (uri (cran-uri "ACSNMineR" version))
17201 "0gh604s8qall6zfjlwcg2ilxjvz08dplf9k5g47idhv43scm748l"))))
17202 (properties `((upstream-name . "ACSNMineR")))
17203 (build-system r-build-system)
17205 (list r-ggplot2 r-gridextra))
17206 (home-page "https://cran.r-project.org/web/packages/ACSNMineR")
17207 (synopsis "Gene enrichment analysis")
17209 "This package provides tools to compute and represent gene set enrichment
17210 or depletion from your data based on pre-saved maps from the @dfn{Atlas of
17211 Cancer Signalling Networks} (ACSN) or user imported maps. The gene set
17212 enrichment can be run with hypergeometric test or Fisher exact test, and can
17213 use multiple corrections. Visualization of data can be done either by
17214 barplots or heatmaps.")
17215 (license license:gpl2+)))
17217 (define-public r-seqinr
17224 (uri (cran-uri "seqinr" version))
17227 "0cj07b7km5mla63qhbkxg1mnqq6vh79lsyyfpnbm29gw68w2bwy4"))))
17228 (build-system r-build-system)
17230 (list r-ade4 r-segmented))
17233 (home-page "http://seqinr.r-forge.r-project.org/")
17234 (synopsis "Biological sequences retrieval and analysis")
17236 "This package provides tools for exploratory data analysis and data
17237 visualization of biological sequence (DNA and protein) data. It also includes
17238 utilities for sequence data management under the ACNUC system.")
17239 (license license:gpl2+)))
17241 (define-public r-units
17248 (uri (cran-uri "units" version))
17251 "06mjprqi06xprj6185k5cmrrdl025x0pd1r6a4x3s74ciq9zwilw"))))
17252 (build-system r-build-system)
17259 (home-page "https://github.com/r-quantities/units/")
17260 (synopsis "Measurement Units for R Vectors")
17262 "This package provides support for measurement units in R vectors,
17263 matrices and arrays: automatic propagation, conversion, derivation and
17264 simplification of units; raising errors in case of unit incompatibility. It
17265 is compatible with the @code{POSIXct}, @code{Date} and @code{difftime}
17267 (license license:gpl2)))
17269 (define-public r-udunits2
17271 (name "r-udunits2")
17272 (version "0.13.2.1")
17276 (uri (cran-uri "udunits2" version))
17279 "00prsy8m41v1camcsz94d7gm8qab2mdnwl3x0dyhz4r49b02jm4z"))))
17280 (properties `((upstream-name . "udunits2")))
17281 (build-system r-build-system)
17284 (home-page "https://cran.r-project.org/package=udunits2")
17285 (synopsis "Udunits-2 bindings for R")
17287 "This package provides simple bindings to Unidata's udunits library.")
17288 (license license:gpl2)))
17290 (define-public r-classint
17292 (name "r-classint")
17297 (uri (cran-uri "classInt" version))
17300 "1b1lqhpzxm6b8pza8l3s0cxy74mm9y45lcd3354i2v3bg8m7mply"))))
17301 (properties `((upstream-name . "classInt")))
17302 (build-system r-build-system)
17304 (list r-class r-e1071 r-kernsmooth))
17306 (list gfortran r-knitr))
17307 (home-page "https://github.com/r-spatial/classInt/")
17308 (synopsis "Choose univariate class intervals")
17310 "This package provides selected commonly used methods for choosing
17311 univariate class intervals for mapping or other graphics purposes.")
17312 (license license:gpl2+)))
17314 (define-public r-spdata
17321 (uri (cran-uri "spData" version))
17324 "1z4hp5ivwzyvl8mkp98j2ng1cl1xksqbjxv85vdlqfqjwpia6df6"))))
17325 (properties `((upstream-name . "spData")))
17326 (build-system r-build-system)
17328 (list r-raster r-sp))
17329 (home-page "https://github.com/Nowosad/spData")
17330 (synopsis "Datasets for spatial analysis")
17332 "This a package containing diverse spatial datasets for demonstrating,
17333 benchmarking and teaching spatial data analysis. It includes R data of class
17334 @code{sf}, @code{Spatial}, and @code{nb}. It also contains data stored in a
17335 range of file formats including GeoJSON, ESRI Shapefile and GeoPackage. Some
17336 of the datasets are designed to illustrate specific analysis techniques.
17337 @code{cycle_hire()} and @code{cycle_hire_osm()}, for example, are designed to
17338 illustrate point pattern analysis techniques.")
17339 (license license:cc0)))
17341 (define-public r-learnbayes
17343 (name "r-learnbayes")
17348 (uri (cran-uri "LearnBayes" version))
17351 "0ch54v2zz2yyyk0lvn5rfikdmyz1qh9j1wk3585wl8v58mc0h4cv"))))
17352 (properties `((upstream-name . "LearnBayes")))
17353 (build-system r-build-system)
17354 (home-page "https://cran.r-project.org/web/packages/LearnBayes")
17355 (synopsis "Functions for learning Bayesian inference")
17357 "This package provides a collection of functions helpful in learning the
17358 basic tenets of Bayesian statistical inference. It contains functions for
17359 summarizing basic one and two parameter posterior distributions and predictive
17360 distributions. It contains MCMC algorithms for summarizing posterior
17361 distributions defined by the user. It also contains functions for regression
17362 models, hierarchical models, Bayesian tests, and illustrations of Gibbs
17364 (license license:gpl2+)))
17366 (define-public r-deldir
17373 (uri (cran-uri "deldir" version))
17376 "1igq0l2knsbhizncgydcsidgkvvlwwlkrifbcdyhnzk0bhrdixkd"))))
17377 (build-system r-build-system)
17378 (native-inputs (list gfortran))
17379 (home-page "https://cran.r-project.org/web/packages/deldir")
17380 (synopsis "Delaunay triangulation and Dirichlet (Voronoi) tessellation")
17382 "This package provides tools for calculating the Delaunay triangulation
17383 and the Dirichlet or Voronoi tessellation (with respect to the entire plane)
17384 of a planar point set. It plots triangulations and tessellations in various
17385 ways, clips tessellations to sub-windows, calculates perimeters of
17386 tessellations, and summarizes information about the tiles of the
17388 (license license:gpl2+)))
17390 (define-public r-wk
17397 (uri (cran-uri "wk" version))
17400 "1xga4rrqsr190g55by39az4nimnn06bf5b6mcjgwqvba0lvjhb5g"))))
17401 (properties `((upstream-name . "wk")))
17402 (build-system r-build-system)
17403 (home-page "https://paleolimbot.github.io/wk/")
17404 (synopsis "Lightweight well-known geometry parsing")
17406 "This package provides a minimal R and C++ API for parsing well-known
17407 binary and well-known text representation of geometries to and from R-native
17408 formats. Well-known binary is compact and fast to parse; well-known text is
17409 human-readable and is useful for writing tests. These formats are only useful
17410 in R if the information they contain can be accessed in R, for which
17411 high-performance functions are provided here.")
17412 (license license:expat)))
17414 (define-public r-s2
17421 (uri (cran-uri "s2" version))
17424 "0gwydn6wdl675ydkcckrci6ylcx30qn8nfhmrp4qx4r9mv3c2410"))))
17425 (properties `((upstream-name . "s2")))
17426 (build-system r-build-system)
17428 (list r-rcpp r-wk))
17433 (home-page "https://r-spatial.github.io/s2/")
17434 (synopsis "Spherical geometry operators using the S2 geometry library")
17436 "This package provides R bindings for Google's s2 library for geometric
17437 calculations on the sphere. High-performance constructors and exporters
17438 provide high compatibility with existing spatial packages, transformers
17439 construct new geometries from existing geometries, predicates provide a means
17440 to select geometries based on spatial relationships, and accessors extract
17441 information about geometries.")
17442 (license license:asl2.0)))
17444 (define-public r-sf
17451 (uri (cran-uri "sf" version))
17454 "0lsl4rh4lbv386hxlsnnwsjb5x1n9d3z0ckjmxakmmrqjjmiywyh"))))
17455 (build-system r-build-system)
17457 (list gdal geos proj sqlite zlib))
17466 (list pkg-config r-knitr))
17467 (home-page "https://github.com/r-spatial/sf/")
17468 (synopsis "Simple features for R")
17470 "This package provides support for simple features, a standardized way to
17471 encode spatial vector data. It binds to GDAL for reading and writing data, to
17472 GEOS for geometrical operations, and to PROJ for projection conversions and
17473 datum transformations.")
17474 ;; Either of these licenses
17475 (license (list license:gpl2 license:expat))))
17477 (define-public r-spdep
17483 (uri (cran-uri "spdep" version))
17486 "0xx6k3rsvsz1hwj0ny8aqfi9ca54x38f8pz8sfya5cggaspxbx59"))
17488 '(for-each delete-file '("inst/doc/CO69.html"
17492 "inst/doc/nb_sf.html"
17494 "inst/doc/nb_sf.Rmd"
17495 "inst/doc/sids.html"
17496 "inst/doc/sids.R")))))
17497 (build-system r-build-system)
17509 (home-page "https://github.com/r-spatial/spdep/")
17510 (synopsis "Spatial dependence: weighting schemes, statistics and models")
17512 "This package provides a collection of functions to create spatial
17513 weights matrix objects from polygon contiguities, from point patterns by
17514 distance and tessellations, for summarizing these objects, and for permitting
17515 their use in spatial data analysis, including regional aggregation by minimum
17517 (license license:gpl2+)))
17519 (define-public r-adegenet
17521 (name "r-adegenet")
17526 (uri (cran-uri "adegenet" version))
17529 "0sx25p7bgz0h9mc3jsdnnjhvmb7sy8nb3r0z923vhk336d4xw8vq"))))
17530 (build-system r-build-system)
17543 (home-page "https://github.com/thibautjombart/adegenet")
17544 (synopsis "Exploratory analysis of genetic and genomic data")
17546 "This package provides a toolset for the exploration of genetic and
17547 genomic data. Adegenet provides formal (S4) classes for storing and handling
17548 various genetic data, including genetic markers with varying ploidy and
17549 hierarchical population structure (@code{genind} class), alleles counts by
17550 populations (@code{genpop}), and genome-wide SNP data (@code{genlight}). It
17551 also implements original multivariate methods (DAPC, sPCA), graphics,
17552 statistical tests, simulation tools, distance and similarity measures, and
17553 several spatial methods. A range of both empirical and simulated datasets is
17554 also provided to illustrate various methods.")
17555 (license license:gpl2+)))
17557 (define-public r-pegas
17564 (uri (cran-uri "pegas" version))
17566 (base32 "0ngd0laqbs139ji9hm9kwsm9rm56agw2yyfcplxgqva936l93fl7"))))
17567 (build-system r-build-system)
17570 (home-page "http://ape-package.ird.fr/pegas.html")
17571 (synopsis "Population and evolutionary genetics analysis system")
17573 "This package provides functions for reading, writing, plotting,
17574 analysing, and manipulating allelic and haplotypic data, including from VCF
17575 files, and for the analysis of population nucleotide sequences and
17576 micro-satellites including coalescent analyses, linkage disequilibrium,
17577 population structure (Fst, Amova) and equilibrium (HWE), haplotype networks,
17578 minimum spanning tree and network, and median-joining networks.")
17579 (license license:gpl2+)))
17581 (define-public r-rmetasim
17583 (name "r-rmetasim")
17588 (uri (cran-uri "rmetasim" version))
17591 "0rdkhfgyr97r2d1kd9g8ipb2pn563qxm1y4m9z678q0kqan2ddl0"))))
17592 (build-system r-build-system)
17594 (list r-ade4 r-adegenet r-gtools r-pegas))
17595 (home-page "https://cran.r-project.org/web/packages/rmetasim")
17596 (synopsis "Individual-based population genetic simulation environment")
17598 "This package provides an interface between R and the metasim simulation
17599 engine. The simulation environment is documented in: Strand, A.(2002),
17600 Metasim 1.0: an individual-based environment for simulating population
17601 genetics of complex population dynamics.")
17603 (license license:gpl2+)))
17605 (define-public r-genetics
17607 (name "r-genetics")
17608 (version "1.3.8.1.3")
17612 (uri (cran-uri "genetics" version))
17615 "0lljxvz7nc6y2z303icphar2niir0i407w5cyhy2pwspd9gwkwpy"))))
17616 (build-system r-build-system)
17618 (list r-combinat r-gdata r-gtools r-mass r-mvtnorm))
17619 (home-page "https://cran.r-project.org/web/packages/genetics/")
17620 (synopsis "Population genetics")
17622 "This package provides classes and methods for handling genetic data.
17623 It includes classes to represent genotypes and haplotypes at single markers up
17624 to multiple markers on multiple chromosomes. Function include allele
17625 frequencies, flagging homo/heterozygotes, flagging carriers of certain
17626 alleles, estimating and testing for Hardy-Weinberg disequilibrium, estimating
17627 and testing for linkage disequilibrium, ...")
17628 ;; Any GPL version.
17629 (license license:gpl2+)))
17631 (define-public r-snp-plotter
17633 (name "r-snp-plotter")
17638 (uri (cran-uri "snp.plotter" version))
17641 "16apsqvkah5l0d5qcwp3lq2jspkb6n62wzr0wskmj84jblx483vv"))))
17642 (properties `((upstream-name . "snp.plotter")))
17643 (build-system r-build-system)
17644 (propagated-inputs (list r-genetics))
17645 (home-page "https://cran.r-project.org/web/packages/snp.plotter/")
17646 (synopsis "Plot p-values using single SNP and/or haplotype data")
17648 "This package helps you create plots of p-values using single SNP and/or
17649 haplotype data. Main features of the package include options to display a
17650 @dfn{linkage disequilibrium} (LD) plot and the ability to plot multiple
17651 datasets simultaneously. Plots can be created using global and/or individual
17652 haplotype p-values along with single SNP p-values. Images are created as
17653 either PDF/EPS files.")
17654 (license license:gpl2+)))
17656 (define-public r-polspline
17658 (name "r-polspline")
17663 (uri (cran-uri "polspline" version))
17665 (base32 "1dd1jwiaglkkhajzvqfkd1x5r3wzjlk5ww0yxzmns0s1kr74i4k9"))))
17666 (build-system r-build-system)
17667 (native-inputs (list gfortran))
17668 (home-page "https://cran.r-project.org/web/packages/polspline/")
17669 (synopsis "Polynomial spline routines")
17671 "This package provides routines for the polynomial spline fitting
17672 routines hazard regression, hazard estimation with flexible tails, logspline,
17673 lspec, polyclass, and polymars.")
17674 (license license:gpl2+)))
17676 (define-public r-rms
17683 (uri (cran-uri "rms" version))
17685 (base32 "1yfk800q4mgmrjkh0hqjkiv907sr1bi1jaigrj8l6pmg1mkynhbc"))))
17686 (build-system r-build-system)
17703 (native-inputs (list gfortran))
17704 (home-page "http://biostat.mc.vanderbilt.edu/rms")
17705 (synopsis "Regression modeling strategies")
17707 "This is a package for regression modeling, testing, estimation,
17708 validation, graphics, prediction, and typesetting by storing enhanced model
17709 design attributes in the fit. The rms package is a collection of functions
17710 that assist with and streamline modeling. It also contains functions for
17711 binary and ordinal logistic regression models, ordinal models for continuous Y
17712 with a variety of distribution families, and the Buckley-James multiple
17713 regression model for right-censored responses, and implements penalized
17714 maximum likelihood estimation for logistic and ordinary linear models. The
17715 package works with almost any regression model, but it was especially written
17716 to work with binary or ordinal regression models, Cox regression, accelerated
17717 failure time models, ordinary linear models, the Buckley-James model,
17718 generalized least squares for serially or spatially correlated observations,
17719 generalized linear models, and quantile regression.")
17720 (license license:gpl2+)))
17722 (define-public r-arsenal
17729 (uri (cran-uri "arsenal" version))
17732 "0qvs3ld28djnjnggdhqjwq8sbv8zz322qahlvf7dnx35yqf6xkms"))))
17733 (properties `((upstream-name . "arsenal")))
17734 (build-system r-build-system)
17735 (propagated-inputs (list r-knitr))
17736 (native-inputs (list r-knitr))
17737 (home-page "https://github.com/mayoverse/arsenal")
17738 (synopsis "Functions for large-scale statistical summaries")
17740 "This package provides an arsenal of R functions for large-scale
17741 statistical summaries, which are streamlined to work within the latest
17742 reporting tools in R and RStudio and which use formulas and versatile
17743 summary statistics for summary tables and models. The primary functions
17747 @item @code{tableby}, a Table-1-like summary of multiple variable types by the
17748 levels of one or more categorical variables;
17749 @item @code{paired}, a Table-1-like summary of multiple variable types paired
17750 across two time points;
17751 @item @code{modelsum}, which performs simple model fits on one or more
17752 endpoints for many variables (univariate or adjusted for covariates);
17753 @item @code{freqlist}, a powerful frequency table across many categorical
17755 @item @code{comparedf}, a function for comparing @code{data.frames}; and
17756 @item @code{write2}, a function to output tables to a document.
17759 (license license:gpl2+)))
17761 (define-public r-haplo-stats
17763 (name "r-haplo-stats")
17768 (uri (cran-uri "haplo.stats" version))
17771 "1q2zn72j92bwhcdswk4qqfgzch56p9pcy2xhkd3safvqp3l9rzpw"))))
17772 (properties `((upstream-name . "haplo.stats")))
17773 (build-system r-build-system)
17775 (list r-arsenal r-rms))
17777 (list r-r-rsp)) ; for vignettes
17778 (home-page "https://www.mayo.edu/research/labs/statistical-genetics-genetic-epidemiology/software")
17779 (synopsis "Analysis of haplotypes when linkage phase is ambiguous")
17781 "This package provides routines for the analysis of indirectly measured
17782 haplotypes. The statistical methods assume that all subjects are unrelated
17783 and that haplotypes are ambiguous (due to unknown linkage phase of the genetic
17784 markers). The main functions are: @code{haplo.em()}, @code{haplo.glm()},
17785 @code{haplo.score()}, and @code{haplo.power()}; all of which have detailed
17786 examples in the vignette.")
17787 (license license:gpl2+)))
17789 (define-public r-bqtl
17796 (uri (cran-uri "bqtl" version))
17799 "1sbzpi9z94f010lw2y1gmifjrvpmiqs4m26za7vr1xz72azrqvs9"))))
17800 (build-system r-build-system)
17801 (native-inputs (list gfortran))
17802 (home-page "http://famprevmed.ucsd.edu/faculty/cberry/bqtl/")
17803 (synopsis "Bayesian QTL mapping toolkit")
17805 "This is a QTL mapping toolkit for inbred crosses and recombinant inbred
17806 lines. It includes maximum likelihood and Bayesian tools.")
17807 (license license:gpl2+)))
17809 (define-public r-ibdreg
17816 (uri (cran-uri "ibdreg" version))
17819 "1x8z0vr2cmdks12hxfm0wwxskb0cr669w5j5rpa2ln8q704yy41g"))))
17820 (build-system r-build-system)
17821 (home-page "https://www.mayo.edu/research/labs/\
17822 statistical-genetics-genetic-epidemiology/software")
17823 (synopsis "Regression methods for IBD linkage with covariates")
17825 "This package provides a method to test genetic linkage with covariates
17826 by regression methods with response IBD sharing for relative pairs. Account
17827 for correlations of IBD statistics and covariates for relative pairs within
17828 the same pedigree.")
17829 (license license:gpl2+)))
17831 (define-public r-dlmap
17838 (uri (cran-uri "dlmap" version))
17841 "0s6wlkggkm3qndwyvw72xv1n0mcjb7ss3ajbq2ll6rv30splq0db"))))
17842 (build-system r-build-system)
17844 (list r-ibdreg r-mgcv r-nlme r-qtl r-wgaim))
17845 (home-page "https://cran.r-project.org/web/packages/dlmap/")
17846 (synopsis "Detection localization mapping for QTL")
17848 "This is package for QTL mapping in a mixed model framework with separate
17849 detection and localization stages. The first stage detects the number of QTL
17850 on each chromosome based on the genetic variation due to grouped markers on
17851 the chromosome; the second stage uses this information to determine the most
17852 likely QTL positions. The mixed model can accommodate general fixed and
17853 random effects, including spatial effects in field trials and pedigree
17854 effects. It is applicable to backcrosses, doubled haploids, recombinant
17855 inbred lines, F2 intercrosses, and association mapping populations.")
17856 (license license:gpl2)))
17858 (define-public r-hwde
17865 (uri (cran-uri "hwde" version))
17868 "0wb2f9i5qi7w77ygh8bvydfpr7j5x8dyvnnhdkajaz0wdcpkyaqy"))))
17869 (build-system r-build-system)
17870 (home-page "https://cran.r-project.org/web/packages/hwde/")
17871 (synopsis "Models and tests for departure from Hardy-Weinberg equilibrium")
17873 "This package fits models for genotypic disequilibria, as described in
17874 Huttley and Wilson (2000), Weir (1996) and Weir and Wilson (1986). Contrast
17875 terms are available that account for first order interactions between loci.
17876 It also implements, for a single locus in a single population, a conditional
17877 exact test for Hardy-Weinberg equilibrium.")
17878 (license license:gpl2+)))
17880 (define-public r-tdthap
17887 (uri (cran-uri "tdthap" version))
17890 "15qlj2bivvz3pizd8dq34wczbkbxhzqh3cqp1ixkdkprlyvcxj5k"))))
17891 (build-system r-build-system)
17892 (home-page "https://cran.r-project.org/web/packages/tdthap/")
17893 (synopsis "TDT tests for extended haplotypes")
17895 "Functions and examples are provided for transmission/disequilibrium
17896 tests for extended marker haplotypes, as in Clayton, D. and Jones, H. (1999)
17897 \"Transmission/disequilibrium tests for extended marker haplotypes\".")
17898 (license license:artistic2.0)))
17900 (define-public r-sparql
17906 (uri (cran-uri "SPARQL" version))
17909 "0gak1q06yyhdmcxb2n3v0h9gr1vqd0viqji52wpw211qp6r6dcrc"))))
17910 (properties `((upstream-name . "SPARQL")))
17911 (build-system r-build-system)
17913 (list r-rcurl r-xml))
17914 (home-page "https://cran.r-project.org/web/packages/SPARQL")
17915 (synopsis "SPARQL client for R")
17916 (description "This package provides an interface to use SPARQL to pose
17917 SELECT or UPDATE queries to an end-point.")
17918 ;; The only license indication is found in the DESCRIPTION file,
17919 ;; which states GPL-3. So we cannot assume GPLv3+.
17920 (license license:gpl3)))
17922 (define-public r-bookdown
17924 (name "r-bookdown")
17928 (uri (cran-uri "bookdown" version))
17931 "11din9h2sgzvg44627xc5is4psbq2b34km5sbiaprskjrf474866"))))
17932 (build-system r-build-system)
17942 ;; We cannot add knitr because this package depends on xfun, which is an
17947 (home-page "https://github.com/rstudio/bookdown")
17948 (synopsis "Authoring books and technical documents with R markdown")
17949 (description "This package provides output formats and utilities for
17950 authoring books and technical documents with R Markdown.")
17951 (license license:gpl3)))
17953 (define-public r-optparse
17955 (name "r-optparse")
17960 (uri (cran-uri "optparse" version))
17963 "1rqz0y4r94y3mwbb9kyz97cjqpnprka96qbncvbnbmgg2d630kij"))))
17964 (build-system r-build-system)
17969 (home-page "https://github.com/trevorld/optparse")
17970 (synopsis "Command line option parser")
17972 "This package provides a command line parser inspired by Python's
17973 @code{optparse} library to be used with Rscript to write shebang scripts
17974 that accept short and long options.")
17975 (license license:gpl2+)))
17977 (define-public r-kernlab
17984 (uri (cran-uri "kernlab" version))
17986 (base32 "10gfb542nbl1d5pfy6r7gcg3j1ikra9l18r6xjv8lzp5ka1kmz28"))))
17987 (build-system r-build-system)
17988 (home-page "https://cran.r-project.org/web/packages/kernlab")
17989 (synopsis "Kernel-based machine learning tools")
17991 "This package provides kernel-based machine learning methods for
17992 classification, regression, clustering, novelty detection, quantile regression
17993 and dimensionality reduction. Among other methods @code{kernlab} includes
17994 Support Vector Machines, Spectral Clustering, Kernel PCA, Gaussian Processes
17996 (license license:gpl2)))
17998 (define-public r-hierfstat
18000 (name "r-hierfstat")
18005 (uri (cran-uri "hierfstat" version))
18008 "0nyb5091lr8ma9vydbssyx9503601rynlrbldv98mmrmh74h6v41"))))
18009 (build-system r-build-system)
18011 (list r-ade4 r-adegenet r-gaston r-gtools))
18014 (home-page "https://cran.r-project.org/web/packages/hierfstat/")
18015 (synopsis "Estimation and tests of hierarchical F-statistics")
18017 "This package allows the estimation of hierarchical F-statistics from
18018 haploid or diploid genetic data with any numbers of levels in the hierarchy,
18019 following the algorithm of Yang (Evolution, 1998, 52(4):950-956). Functions
18020 are also given to test via randomisations the significance of each F and
18021 variance components, using the likelihood-ratio statistics G.")
18022 (license license:gpl2+)))
18024 (define-public r-hapassoc
18026 (name "r-hapassoc")
18031 (uri (cran-uri "hapassoc" version))
18034 "09ijc4sbw743z74fzklmvig11ndkycg6j86k4214wfsj1yj6j9x6"))))
18035 (build-system r-build-system)
18036 (home-page "https://stat.sfu.ca/statgen/research/hapassoc.html")
18037 (synopsis "Inference of trait associations with SNP haplotypes")
18039 "Hapassoc performs likelihood inference of trait associations with
18040 haplotypes and other covariates in @dfn{generalized linear models} (GLMs). The
18041 functions are developed primarily for data collected in cohort or
18042 cross-sectional studies. They can accommodate uncertain haplotype phase and
18043 handle missing genotypes at some SNPs.")
18044 (license license:gpl2)))
18046 (define-public r-sampling
18048 (name "r-sampling")
18053 (uri (cran-uri "sampling" version))
18056 "11xis4vzn2ga8ml9xrgfgqzccvwbnabq35aidzdvpnvciybsanvz"))))
18057 (build-system r-build-system)
18059 (list r-lpsolve r-mass))
18060 (home-page "https://cran.r-project.org/web/packages/sampling/")
18061 (synopsis "Survey sampling")
18063 "This package provides functions for drawing and calibrating samples.")
18064 (license license:gpl2+)))
18066 (define-public r-r2html
18073 (uri (cran-uri "R2HTML" version))
18076 "12qg9rp1j26h2f48dfg5k9jds26ycacv3f3ymk686ks43hd1hzja"))))
18077 (properties `((upstream-name . "R2HTML")))
18078 (build-system r-build-system)
18079 (home-page "https://github.com/nalimilan/R2HTML")
18080 (synopsis "HTML export for R objects")
18082 "This package includes HTML functions and methods to write in an HTML
18083 file. Thus, making HTML reports is easy. It includes a function that allows
18084 redirection on the fly, which appears to be very useful for teaching purposes,
18085 as the student can keep a copy of the produced output to keep all that they
18086 did during the course. The package comes with a vignette describing how to
18087 write HTML reports for statistical analysis. Finally, a driver for Sweave
18088 parses HTML flat files containing R code and to automatically write
18089 the corresponding outputs (tables and graphs).")
18090 (license license:gpl2+)))
18092 (define-public r-rjava
18099 (uri (cran-uri "rJava" version))
18102 "1ijqhvnb8ab38cp9pwdf7zq7xqqlm6x94gkrab2dd98p6d4x1472"))))
18103 (properties `((upstream-name . "rJava")))
18104 (build-system r-build-system)
18106 `(#:modules ((guix build utils)
18107 (guix build r-build-system)
18110 (modify-phases %standard-phases
18111 (add-after 'unpack 'set-JAVA_HOME
18112 (lambda* (#:key inputs #:allow-other-keys)
18113 (let ((jdk (assoc-ref inputs "jdk")))
18114 (setenv "JAVA_HOME" jdk)
18115 (setenv "JAVA" (which "java"))
18116 (setenv "JAR" (which "jar"))
18117 (setenv "JAVAC" (which "javac"))
18118 (setenv "JAVAH" (which "javah"))
18119 (setenv "JAVA_CPPFLAGS"
18120 (string-append "-I" jdk "/include "
18121 "-I" jdk "/include/linux"))
18122 (match (find-files (string-append jdk "/jre/lib/") "libjvm.so")
18123 ((lib) (setenv "JAVA_LIBS" lib))
18124 (_ (error "Could not find libjvm.so"))))
18128 ("jdk" ,icedtea-8 "jdk")
18130 (home-page "https://www.rforge.net/rJava/")
18131 (synopsis "Low-Level R to Java interface")
18133 "This package provides a low-level interface to the Java VM very much
18134 like .C/.Call and friends. It allows the creation of objects, calling methods
18135 and accessing fields.")
18136 (license license:gpl2)))
18138 (define-public r-svmisc
18145 (uri (cran-uri "svMisc" version))
18148 "1r3kih5bnr4plnzdn5f2gg3xl3krgyl7gkdlf58a2l8vk13j3m9d"))))
18149 (properties `((upstream-name . "svMisc")))
18150 (build-system r-build-system)
18153 (home-page "https://github.com/SciViews/svMisc")
18154 (synopsis "Miscellaneous functions for SciViews")
18156 "This package provides miscellaneous functions for SciViews or general
18157 use, including tools to manage a temporary environment attached to the search
18158 path for temporary variables you do not want to @code{save()} or
18159 @code{load()}; test the current platform; showing progress bars, etc.")
18160 (license license:gpl2)))
18162 (define-public r-xyz
18169 (uri (cran-uri "xyz" version))
18172 "13w4sb4pvgciwr8wsz785dafj2k2kpx7znz46r5d32wx88vkycp4"))))
18173 (build-system r-build-system)
18176 (home-page "https://cran.r-project.org/web/packages/xyz/")
18177 (synopsis "Algorithm for fast interaction search in high-dimensional data")
18179 "High dimensional interaction search by brute force requires a quadratic
18180 computational cost in the number of variables. The xyz algorithm provably
18181 finds strong interactions in almost linear time. For details of the algorithm
18182 see: G. Thanei, N. Meinshausen and R. Shah (2016). The xyz algorithm for fast
18183 interaction search in high-dimensional data.")
18184 ;; Any version of the GPL.
18185 (license license:gpl2+)))
18187 (define-public r-rttf2pt1
18189 (name "r-rttf2pt1")
18194 (uri (cran-uri "Rttf2pt1" version))
18197 "1fp1y0kxa5xg8w0dplm12wfm8h78az4k6ql1758wwhb3d17np241"))))
18198 (properties `((upstream-name . "Rttf2pt1")))
18199 (build-system r-build-system)
18200 (home-page "https://github.com/wch/Rttf2pt1")
18201 (synopsis "Font conversion utility")
18203 "This package contains the program @code{ttf2pt1}, for use with the
18204 @code{extrafont} package.")
18205 ;; Most of the files are covered under the Expat license. Some files are
18206 ;; covered under BSD-3. Deviations for individual files are recorded in
18207 ;; the LICENSE file.
18208 (license (list license:bsd-3 license:expat
18209 (license:non-copyleft "file://LICENSE")))))
18211 (define-public r-extrafontdb
18213 (name "r-extrafontdb")
18218 (uri (cran-uri "extrafontdb" version))
18221 "115n42hfvv5h4nn4cfkfmkmn968py4lpy8zd0d6w5yylwpzbm8gs"))))
18222 (build-system r-build-system)
18223 (home-page "https://github.com/wch/extrafontdb")
18224 (synopsis "Database for the extrafont package")
18226 "This package holds the database for the @code{extrafont} package.")
18227 (license license:gpl2)))
18229 (define-public r-extrafont
18231 (name "r-extrafont")
18236 (uri (cran-uri "extrafont" version))
18239 "0mx810mld67vb1w3wkl4fhpjmkq32lgpq5x1c0a9rf8li5wskrj4"))))
18240 (build-system r-build-system)
18242 (list r-extrafontdb r-rttf2pt1))
18243 (home-page "https://github.com/wch/extrafont")
18244 (synopsis "Tools for using fonts in R")
18246 "The extrafont package makes it easier to use fonts other than the basic
18247 PostScript fonts that R uses. Fonts that are imported into extrafont can be
18248 used with PDF or PostScript output files. There are two hurdles for using
18249 fonts in PDF (or Postscript) output files:
18252 @item Making R aware of the font and the dimensions of the characters.
18253 @item Embedding the fonts in the PDF file so that the PDF can be displayed
18254 properly on a device that doesn't have the font. This is usually needed if
18255 you want to print the PDF file or share it with others.
18258 The extrafont package makes both of these things easier.")
18259 (license license:gpl2)))
18261 (define-public r-xkcd
18268 (uri (cran-uri "xkcd" version))
18271 "1z2y0ihn68ppay7xkglhw7djki5654g6z4bbpyy41if57z9q554f"))))
18272 (build-system r-build-system)
18274 (list r-extrafont r-ggplot2 r-hmisc))
18275 (home-page "https://cran.r-project.org/web/packages/xkcd/")
18276 (synopsis "Plot ggplot2 graphics in the XKCD style")
18278 "This package provides the means to plot ggplot2 graphs in the style of
18279 the XKCD web comic.")
18280 (license license:gpl3)))
18282 (define-public r-babelgene
18284 (name "r-babelgene")
18289 (uri (cran-uri "babelgene" version))
18292 "1735h4s2vahv55pmq65zkgxq8d5x71i1is03rf17dric8yynjjhg"))))
18293 (properties `((upstream-name . "babelgene")))
18294 (build-system r-build-system)
18296 (list r-dplyr r-rlang))
18300 "https://igordot.github.io/babelgene/")
18301 (synopsis "Gene orthologs for model organisms in a Tidy data format")
18303 "Genomic analysis of model organisms often requires the use of databases
18304 based on human data or making comparisons to patient-derived resources. This
18305 requires converting genes between human and non-human analogues. The
18306 babelgene R package provides predicted gene orthologs/homologs for frequently
18307 studied model organisms in an R-friendly tidy/long format. The package
18308 integrates orthology assertion predictions sourced from multiple databases as
18309 compiled by the HGNC Comparison of Orthology Predictions (HCOP).")
18310 (license license:expat)))
18312 (define-public r-msigdbr
18319 (uri (cran-uri "msigdbr" version))
18322 "1jna9bkq0a7r6f8nhxziyiw75kfhsyh1rv7sx5d4551mvxxlhc6w"))))
18323 (build-system r-build-system)
18333 (home-page "https://github.com/igordot/msigdbr")
18334 (synopsis "MSigDB gene sets for multiple organisms")
18336 "This package provides the @dfn{Molecular Signatures Database} (MSigDB)
18337 gene sets typically used with the @dfn{Gene Set Enrichment Analysis} (GSEA)
18338 software in a standard R data frame with key-value pairs. Included are the
18339 original human gene symbols and Entrez IDs as well as the equivalents for
18340 various frequently studied model organisms such as mouse, rat, pig, fly, and
18342 ;; The package is covered under the Expat license, but the upstream MSigDB
18343 ;; files are made available under the Creative Commons Attribution 4.0
18344 ;; International license.
18345 (license (list license:expat license:cc-by4.0))))
18347 (define-public r-gridgraphics
18349 (name "r-gridgraphics")
18354 (uri (cran-uri "gridGraphics" version))
18357 "12yswy02j3h5wir7m5jnkhpjmb0sa4snn61vjd68i49qwsa6w219"))))
18358 (properties `((upstream-name . "gridGraphics")))
18359 (build-system r-build-system)
18360 (home-page "https://github.com/pmur002/gridgraphics")
18361 (synopsis "Redraw base graphics using @code{grid} graphics")
18363 "This package provides functions to convert a page of plots drawn with
18364 the @code{graphics} package into identical output drawn with the @code{grid}
18365 package. The result looks like the original @code{graphics}-based plot, but
18366 consists of @code{grid} grobs and viewports that can then be manipulated with
18367 @code{grid} functions (e.g., edit grobs and revisit viewports).")
18368 (license license:gpl2+)))
18370 (define-public r-farver
18377 (uri (cran-uri "farver" version))
18380 "1x6ffwxqbrwlylnk995jz2a6nz2y9z59jaq0ncpni7q40w367j75"))))
18381 (build-system r-build-system)
18382 (home-page "https://github.com/thomasp85/farver")
18383 (synopsis "Vectorized color conversion and comparison")
18385 "The encoding of color can be handled in many different ways, using
18386 different color spaces. As different color spaces have different uses,
18387 efficient conversion between these representations are important. This
18388 package provides a set of functions that gives access to very fast color space
18389 conversion and comparisons implemented in C++, and offers 100-fold speed
18390 improvements over the @code{convertColor} function in the @code{grDevices}
18392 (license license:expat)))
18394 (define-public r-yulab-utils
18396 (name "r-yulab-utils")
18401 (uri (cran-uri "yulab.utils" version))
18404 "1bj93gnj7j4b7dgkbr5v22rsbwfcw5dvipl5irmidaakvrihd19q"))))
18405 (properties `((upstream-name . "yulab.utils")))
18406 (build-system r-build-system)
18407 (home-page "https://cran.r-project.org/package=yulab.utils")
18408 (synopsis "Supporting functions for packages maintained by YuLab-SMU")
18410 "Miscellaneous functions commonly used by YuLab-SMU, such as
18411 @code{install_zip_gh} to install R packages from Github ZIP files.")
18412 (license license:artistic2.0)))
18414 (define-public r-ggplotify
18416 (name "r-ggplotify")
18421 (uri (cran-uri "ggplotify" version))
18424 "12mk3fa8fdjxj7xxz21jkr7h91w5wdgwjqhszcz1qffwsgb773qp"))))
18425 (build-system r-build-system)
18427 (list r-ggplot2 r-gridgraphics r-yulab-utils))
18430 (home-page "https://github.com/GuangchuangYu/ggplotify")
18431 (synopsis "Convert plots to @code{grob} or @code{ggplot} object")
18433 "This package provides tools to convert plot function calls (using
18434 expression or formula) to @code{grob} or @code{ggplot} objects that are
18435 compatible with the @code{grid} and @code{ggplot2} environment. With this
18436 package, we are able to e.g. use @code{cowplot} to align plots produced by
18437 @code{base} graphics, @code{grid}, @code{lattice}, @code{vcd} etc. by
18438 converting them to @code{ggplot} objects.")
18439 (license license:artistic2.0)))
18441 (define-public r-triebeard
18443 (name "r-triebeard")
18448 (uri (cran-uri "triebeard" version))
18451 "1hqyz57gph02c9fdc07lxz113bbklif3g18sw8jan6pakhhdc7dz"))))
18452 (build-system r-build-system)
18453 (propagated-inputs (list r-rcpp))
18454 (home-page "https://github.com/Ironholds/triebeard/")
18455 (synopsis "Radix trees in Rcpp")
18457 "Radix trees, or tries, are key-value data structures optimized for
18458 efficient lookups, similar in purpose to hash tables. This package provides
18459 an implementation of radix trees for use in R programming and in developing
18460 packages with Rcpp.")
18461 (license license:expat)))
18463 (define-public r-tweenr
18470 (uri (cran-uri "tweenr" version))
18473 "17znizh4yabh2zs9mzyr0sl6p0pw49961i61br7cl1b7v9sza18q"))))
18474 (build-system r-build-system)
18476 (list r-farver r-magrittr r-rcpp r-rlang))
18477 (home-page "https://github.com/thomasp85/tweenr")
18478 (synopsis "Interpolate data for smooth animations")
18480 "In order to create smooth animation between states of data, tweening is
18481 necessary. This package provides a range of functions for creating tweened
18482 data that can be used as basis for animation. Furthermore it adds a number of
18483 vectorized interpolaters for common R data types such as numeric, date and
18485 (license license:expat)))
18487 (define-public r-polyclip
18489 (name "r-polyclip")
18494 (uri (cran-uri "polyclip" version))
18497 "0jyk4maqiblvj095jd59dr76kbniyli3v3xvy0a72ljszq6vrnkl"))))
18498 (build-system r-build-system)
18499 (native-inputs (list pkg-config))
18500 (home-page "http://www.angusj.com/delphi/clipper.php")
18501 (synopsis "Polygon clipping")
18503 "This package provides an R port of the library Clipper. It performs
18504 polygon clipping operations (intersection, union, set minus, set difference)
18505 for polygonal regions of arbitrary complexity, including holes. It computes
18506 offset polygons (spatial buffer zones, morphological dilations, Minkowski
18507 dilations) for polygonal regions and polygonal lines. It computes the
18508 Minkowski Sum of general polygons. There is a function for removing
18509 self-intersections from polygon data.")
18510 (license license:boost1.0)))
18512 (define-public r-urltools
18514 (name "r-urltools")
18519 (uri (cran-uri "urltools" version))
18522 "04x3my655dd287cbsszbnf75q0swmjlxxrblcsay7a8n3df3a830"))))
18523 (build-system r-build-system)
18525 (list r-rcpp r-triebeard))
18526 (home-page "https://github.com/Ironholds/urltools/")
18527 (synopsis "Vectorized tools for URL handling and parsing")
18529 "This package provides a toolkit for all URL-handling needs, including
18530 encoding and decoding, parsing, parameter extraction and modification. All
18531 functions are designed to be both fast and entirely vectorized. It is
18532 intended to be useful for people dealing with web-related datasets, such as
18533 server-side logs, although may be useful for other situations involving large
18535 (license license:expat)))
18537 (define-public r-ggforce
18544 (uri (cran-uri "ggforce" version))
18547 "0bwzjbjl678xvc2ihm80dwn9pidwafqjdab3k299csys16s3na1a"))))
18548 (build-system r-build-system)
18561 (home-page "https://ggforce.data-imaginist.com")
18562 (synopsis "Accelerating ggplot2")
18564 "The aim of the ggplot2 package is to aid in visual data investigations.
18565 This focus has led to a lack of facilities for composing specialized plots.
18566 This package aims to be a collection of mainly new statistics and geometries
18567 that fills this gap.")
18568 (license license:expat)))
18570 (define-public r-europepmc
18572 (name "r-europepmc")
18577 (uri (cran-uri "europepmc" version))
18580 "16japbndid34shqg8n0bmjrxn84xmhrylvz832zclcllm6i93fn1"))))
18581 (build-system r-build-system)
18596 (home-page "https://github.com/ropensci/europepmc/")
18597 (synopsis "R Interface to the Europe PubMed Central RESTful Web Service")
18599 "This package provides an R Client for the
18600 @url{https://europepmc.org/RestfulWebService,Europe PubMed Central RESTful Web
18601 Service}. It gives access to both metadata on life science literature and
18602 open access full texts. Europe PMC indexes all PubMed content and other
18603 literature sources including Agricola, a bibliographic database of citations
18604 to the agricultural literature, or Biological Patents. In addition to
18605 bibliographic metadata, the client allows users to fetch citations and
18606 reference lists. Links between life-science literature and other EBI
18607 databases, including ENA, PDB or ChEMBL are also accessible.")
18608 (license license:gpl3)))
18610 (define-public r-ggraph
18617 (uri (cran-uri "ggraph" version))
18620 "0m4n8iw2b9jk8hcy5blg5w59zsqcpsbv27wbw598dvljpafx8sp3"))))
18621 (build-system r-build-system)
18640 (home-page "https://cran.r-project.org/web/packages/ggraph/")
18641 (synopsis "Implementation of grammar of graphics for graphs and networks")
18643 "The grammar of graphics as implemented in ggplot2 is a poor fit for
18644 graph and network visualizations due to its reliance on tabular data input.
18645 The ggraph package is an extension of the ggplot2 API tailored to graph
18646 visualizations and provides the same flexible approach to building up plots
18648 (license license:gpl3)))
18650 (define-public r-gkmsvm
18657 (uri (cran-uri "gkmSVM" version))
18660 "119g5rhc7ffyviz04r04aj5z1g6abnj3ddd01g7db505sdr6lapj"))))
18661 (properties `((upstream-name . "gkmSVM")))
18662 (build-system r-build-system)
18664 (list r-kernlab r-rcpp r-rocr r-seqinr))
18665 (home-page "https://cran.r-project.org/web/packages/gkmSVM")
18666 (synopsis "Gapped-kmer support vector machine")
18668 "This R package provides tools for training gapped-kmer SVM classifiers
18669 for DNA and protein sequences. This package supports several sequence
18670 kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.")
18671 (license license:gpl2+)))
18673 (define-public r-varselrf
18675 (name "r-varselrf")
18680 (uri (cran-uri "varSelRF" version))
18683 "0h49rl1j13yfh97rsfsyh9s2c4wajny4rzms2qw77d0cavxqg53i"))))
18684 (properties `((upstream-name . "varSelRF")))
18685 (build-system r-build-system)
18687 (list r-randomforest))
18688 (home-page "https://www.ligarto.org/rdiaz/software/software")
18689 (synopsis "Variable selection using random forests")
18691 "This package provides tools for the variable selection from random
18692 forests using both backwards variable elimination (for the selection of small
18693 sets of non-redundant variables) and selection based on the importance
18694 spectrum (somewhat similar to scree plots; for the selection of large,
18695 potentially highly-correlated variables). The main applications are in
18696 high-dimensional data (e.g., microarray data, and other genomics and
18697 proteomics applications).")
18698 (license license:gpl2+)))
18700 (define-public r-pamr
18707 (uri (cran-uri "pamr" version))
18710 "0ycpgkk23y3zzkb42n2skcyl35ps1n7jmyzfj7pbxr3f6gr2grfh"))))
18711 (build-system r-build-system)
18713 (list r-cluster r-survival))
18714 (native-inputs (list gfortran))
18715 (home-page "https://cran.r-project.org/web/packages/pamr/")
18716 (synopsis "Prediction Analysis for Microarrays")
18718 "This package provides some functions for sample classification in
18720 (license license:gpl2)))
18722 (define-public r-rda
18725 (version "1.0.2-2.1")
18729 (uri (cran-uri "rda" version))
18732 "1y4fawslr3i6crjaxhsdb47kfsqkyszdx6avq3r5far5a4pvc639"))))
18733 (build-system r-build-system)
18734 (home-page "https://cran.r-project.org/web/packages/rda/")
18735 (synopsis "Shrunken centroids regularized discriminant analysis")
18737 "This package provides tools for shrunken centroids regularized
18738 discriminant analysis for the purpose of classifying high dimensional data.")
18739 (license license:gpl2+)))
18741 (define-public r-ggvis
18748 (uri (cran-uri "ggvis" version))
18751 "1qv512pd4x5vmx15y9nvqmabbbw14h75fmi1sjbcg5yl25z0cswy"))))
18752 (build-system r-build-system)
18761 (home-page "https://ggvis.rstudio.com/")
18762 (synopsis "Interactive grammar of graphics")
18764 "This package is a data visualization package for R providing an
18765 implementation of an interactive grammar of graphics, taking the best parts of
18766 ggplot2, combining them with the reactive framework of Shiny and drawing web
18767 graphics using Vega.")
18768 (license license:gpl2)))
18770 (define-public r-gbm
18777 (uri (cran-uri "gbm" version))
18780 "1h9f4ww9yc3nsvghgr2q7jjrlz29ibabxjbax1sk5wmqh2wy6pbx"))))
18781 (build-system r-build-system)
18783 (list r-lattice r-survival))
18786 (home-page "https://github.com/gbm-developers/gbm")
18787 (synopsis "Generalized boosted regression models")
18789 "This package is an implementation of extensions to Freund and Schapire's
18790 AdaBoost algorithm and Friedman's gradient boosting machine. It includes
18791 regression methods for least squares, absolute loss, t-distribution loss,
18792 quantile regression, logistic, multinomial logistic, Poisson, Cox proportional
18793 hazards partial likelihood, AdaBoost exponential loss, Huberized hinge loss,
18794 and Learning to Rank measures (LambdaMart).")
18795 (license license:gpl2+)))
18797 (define-public r-threejs
18804 (uri (cran-uri "threejs" version))
18807 "1711h351nzxfkbbdwvfzyhciyvi9c6wx3jq1g97lzcqgnb45kivn"))))
18808 (build-system r-build-system)
18810 `(#:modules ((guix build utils)
18811 (guix build r-build-system)
18815 (modify-phases %standard-phases
18816 (add-after 'unpack 'process-javascript
18817 (lambda* (#:key inputs #:allow-other-keys)
18818 (with-directory-excursion "inst"
18822 `((,(assoc-ref inputs "js-jquery")
18823 "htmlwidgets/lib/jquery/jquery.min.js")
18824 (,(assoc-ref inputs "js-threejs-111")
18825 "htmlwidgets/lib/threejs-111/three.min.js"))))
18826 (lambda (sources targets)
18827 (for-each (lambda (source target)
18828 (format #t "Processing ~a --> ~a~%"
18830 (delete-file target)
18831 (let ((minified (open-pipe* OPEN_READ "uglifyjs" source)))
18832 (call-with-output-file target
18834 (dump-port minified port)))))
18835 sources targets))))
18838 (list r-base64enc r-crosstalk r-htmlwidgets r-igraph))
18840 `(("uglifyjs" ,node-uglify-js)
18844 (uri "https://code.jquery.com/jquery-1.12.4.js")
18847 "0x9mrc1668icvhpwzvgafm8xm11x9lfai9nwr66aw6pjnpwkc3s3"))))
18851 (uri "https://raw.githubusercontent.com/mrdoob/three.js/r111/build/three.js")
18854 "1cxdkw3plmlw1xvhbx5dm39gqczgzxip2dm887v6whhsxqxl9cky"))))))
18855 (home-page "https://bwlewis.github.io/rthreejs")
18856 (synopsis "Interactive 3D scatter plots, networks and globes")
18858 "Create interactive 3D scatter plots, network plots, and globes in R
18859 using the three.js visualization library.")
18860 (license license:expat)))
18862 (define-public r-mlbench
18869 (uri (cran-uri "mlbench" version))
18872 "157iqsld0wj8g8cbs7nh6p2x6kasmkhs3078hsmqac946gk2pydi"))))
18873 (build-system r-build-system)
18874 (home-page "https://cran.r-project.org/web/packages/mlbench/")
18875 (synopsis "Machine learning benchmark problems")
18877 "This package provides a collection of artificial and real-world machine
18878 learning benchmark problems, including, e.g., several data sets from the UCI
18880 (license license:gpl2)))
18882 (define-public r-mpm
18889 (uri (cran-uri "mpm" version))
18892 "1jpv2ddmw7aarqbbyfys1yb840arw33319wnny3v2hk84hldmayj"))))
18893 (build-system r-build-system)
18895 (list r-kernsmooth r-mass))
18896 (home-page "http://mpm.r-forge.r-project.org")
18897 (synopsis "Multivariate projection methods")
18899 "This is a package for exploratory graphical analysis of multivariate
18900 data, specifically gene expression data with different projection methods:
18901 principal component analysis, correspondence analysis, spectral map
18903 (license license:gpl2+)))
18905 (define-public r-png
18911 (uri (cran-uri "png" version))
18914 "0g2mcp55lvvpx4kd3mn225mpbxqcq73wy5qx8b4lyf04iybgysg2"))))
18915 (build-system r-build-system)
18917 (list libpng zlib))
18918 (home-page "https://www.rforge.net/png/")
18919 (synopsis "Read and write PNG images")
18921 "This package provides an easy and simple way to read, write and display
18922 bitmap images stored in the PNG format. It can read and write both files and
18923 in-memory raw vectors.")
18924 ;; Any of these GPL versions.
18925 (license (list license:gpl2 license:gpl3))))
18927 (define-public r-ggcorrplot
18929 (name "r-ggcorrplot")
18934 (uri (cran-uri "ggcorrplot" version))
18937 "0hi9lz121ya1l2lbm7rqlxg6fs6bvxck396dngnidrhl5fvqb41b"))))
18938 (build-system r-build-system)
18940 (list r-ggplot2 r-reshape2))
18941 (home-page "http://www.sthda.com/english/wiki/ggcorrplot")
18942 (synopsis "Visualization of a correlation matrix using ggplot2")
18944 "The ggcorrplot package can be used to visualize easily a correlation
18945 matrix using ggplot2. It provides a solution for reordering the correlation
18946 matrix and displays the significance level on the plot. It also includes a
18947 function for computing a matrix of correlation p-values.")
18948 (license license:gpl2)))
18950 (define-public r-ggfun
18957 (uri (cran-uri "ggfun" version))
18960 "06si42b60hp8wprs5nbks93qlb9s269k9kw7akcirizwc399x62r"))))
18961 (properties `((upstream-name . "ggfun")))
18962 (build-system r-build-system)
18964 (list r-ggplot2 r-rlang))
18965 (native-inputs (list r-knitr))
18966 (home-page "https://cran.r-project.org/package=ggfun")
18967 (synopsis "Miscellaneous functions for ggplot2")
18969 "This package provides useful functions to edit ggplot object (e.g.,
18970 setting fonts for theme and layers, adding rounded rectangle as background for
18971 each of the legends).")
18972 (license license:artistic2.0)))
18974 (define-public r-gridtext
18976 (name "r-gridtext")
18981 (uri (cran-uri "gridtext" version))
18984 "131kw7nkfwksviwfifd2kk7lyvhxzzzv1nnj8rahkr3dik3akk61"))))
18985 (properties `((upstream-name . "gridtext")))
18986 (build-system r-build-system)
18996 (home-page "https://wilkelab.org/gridtext/")
18997 (synopsis "Improved text rendering support for Grid graphics")
18999 "This package provides support for rendering of formatted text using Grid
19000 graphics. Text can be formatted via a minimal subset of Markdown, HTML, and
19001 inline CSS directives, and it can be rendered both with and without word
19003 (license license:expat)))
19005 (define-public r-ggtext
19012 (uri (cran-uri "ggtext" version))
19015 "0n19dlcys8v7myfyckr6dnq0kx79k3sbh8nwx1jsx8pgzfbi8a2b"))))
19016 (properties `((upstream-name . "ggtext")))
19017 (build-system r-build-system)
19019 (list r-ggplot2 r-gridtext r-rlang r-scales))
19020 (native-inputs (list r-knitr))
19021 (home-page "https://wilkelab.org/ggtext/")
19022 (synopsis "Improved text rendering support for ggplot2")
19024 "This package provides a ggplot2 extension that enables the rendering of
19025 complex formatted plot labels (titles, subtitles, facet labels, axis labels,
19026 etc.). Text boxes with automatic word wrap are also supported.")
19027 (license license:gpl2)))
19029 ;; This package includes minified JavaScript files. When upgrading please
19030 ;; check that there are no new minified JavaScript files.
19031 (define-public r-flexdashboard
19033 (name "r-flexdashboard")
19038 (uri (cran-uri "flexdashboard" version))
19041 "1bh759llp15fxrx2rwvxd8p3w84vjmkid32ism7zg49a127fjib4"))
19042 (modules '((guix build utils)))
19045 ;; Delete bundled minified JavaScript files
19046 (delete-file "inst/htmlwidgets/lib/raphael/raphael-2.1.4.min.js")
19047 (delete-file "inst/www/sly/sly.min.js")
19048 (delete-file "inst/www/stickytableheaders/jquery.stickytableheaders.min.js")
19049 (delete-file "inst/www/prism/prism.js")
19051 (build-system r-build-system)
19053 `(#:modules ((guix build utils)
19054 (guix build r-build-system)
19058 (ice-9 textual-ports))
19060 (modify-phases %standard-phases
19061 (add-after 'unpack 'process-javascript
19062 (lambda* (#:key inputs #:allow-other-keys)
19063 (with-directory-excursion "inst"
19064 ;; Concatenate all components of prism.js
19065 (let ((contents (string-join
19066 (map (lambda (name)
19067 (call-with-input-file
19068 (assoc-ref inputs name)
19072 "js-prism-line-numbers"))
19074 (call-with-output-file "prism-src.js"
19075 (cut display contents <>)))
19079 `(("www/stickytableheaders/jquery.stickytableheaders.js"
19080 "www/stickytableheaders/jquery.stickytableheaders.min.js")
19082 "www/sly/sly.min.js")
19084 "www/prism/prism.js")
19085 (,(assoc-ref inputs "js-raphael")
19086 "htmlwidgets/lib/raphael/raphael-2.1.4.min.js")
19087 (,(assoc-ref inputs "js-featherlight")
19088 "www/featherlight/featherlight.min.js"))))
19089 (lambda (sources targets)
19090 (for-each (lambda (source target)
19091 (format #t "Processing ~a --> ~a~%"
19093 (let ((minified (open-pipe* OPEN_READ "uglifyjs" source)))
19094 (call-with-output-file target
19096 (dump-port minified port)))))
19097 sources targets))))
19107 `(("uglifyjs" ,node-uglify-js)
19111 (uri "https://raw.githubusercontent.com/DmitryBaranovskiy/raphael/v2.1.4/raphael.js")
19114 "1h4c4akrgcj7wra9j1z1rv2406j0yf68y9c0wg8v7w9ibw2iwf1x"))))
19118 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/prism.js")
19121 "0gqa9irbp9k8p5r3d98cszajzhjnssnl43nrsc5aiy7ki52z500c"))))
19125 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/components/prism-r.js")
19128 "1x31glci7wdgr2305njy0bm2lncb0jyn0j1s2g72rqi29xid9aki"))))
19129 ("js-prism-line-numbers"
19132 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/plugins/line-numbers/prism-line-numbers.js")
19135 "1543wgf3iynrilyb27jq8px3h5gvfz5xmdib5ik2ki400c1sl991"))))
19139 (uri "https://raw.githubusercontent.com/noelboss/featherlight/1.3.4/src/featherlight.js")
19142 "14kkhwzvp8rxq2mrck5i0xcm8v5rqwqhwnmncbng8h4qq42zx3sb"))))))
19143 (home-page "https://rmarkdown.rstudio.com/flexdashboard")
19144 (synopsis "R Markdown format for flexible dashboards")
19146 "This package provides an R Markdown format for converting an R Markdown
19147 document to a grid-oriented dashboard. The dashboard flexibly adapts the size
19148 of its components to the containing web page.")
19149 (license license:expat)))
19151 (define-public r-preseqr
19158 (uri (cran-uri "preseqR" version))
19161 "1g2rnnmi45649vpy6z45v5i3wxm54s138ajqrzwi3a5r7x3xnhq1"))))
19162 (properties `((upstream-name . "preseqR")))
19163 (build-system r-build-system)
19166 (home-page "https://cran.r-project.org/web/packages/preseqR/")
19167 (synopsis "Predicting species accumulation curves")
19169 "This package can be used to predict the r-species accumulation
19170 curve (r-SAC), which is the number of species represented at least r times as
19171 a function of the sampling effort. When r = 1, the curve is known as the
19172 species accumulation curve, or the library complexity curve in high-throughput
19173 genomic sequencing. The package includes both parametric and nonparametric
19174 methods, as described by Deng C, et al. (2018).")
19175 (license license:gpl3)))
19177 (define-public r-mapplots
19179 (name "r-mapplots")
19184 (uri (cran-uri "mapplots" version))
19187 "18s2y66f8vi8g2r8a25zbgp2xm079r8v8qxv0w71h8krycs6vs9p"))))
19188 (build-system r-build-system)
19189 (home-page "https://cran.r-project.org/web/packages/mapplots/")
19190 (synopsis "Data visualization on maps")
19192 "This package helps you create simple maps; add sub-plots like pie plots
19193 to a map or any other plot; format, plot and export gridded data. The package
19194 was developed for displaying fisheries data but most functions can be used for
19195 more generic data visualisation.")
19196 (license license:gpl2+)))
19198 (define-public r-pmcmr
19205 (uri (cran-uri "PMCMR" version))
19208 "05n13pp5yff6pzk4ry07crddfaj3jlglrd1vkcnacyd8jpaxkd77"))))
19209 (properties `((upstream-name . "PMCMR")))
19210 (build-system r-build-system)
19211 (home-page "https://cran.r-project.org/web/packages/PMCMR/")
19212 (synopsis "Calculate pairwise multiple comparisons of mean rank sums")
19214 "This is a deprecated package for calculating pairwise multiple
19215 comparisons of mean rank sums. This package is superseded by the novel
19216 PMCMRplus package. The PMCMR package is no longer maintained, but kept for
19217 compatibility of dependent packages for some time.")
19218 (license license:gpl3+)))
19220 (define-public r-downloader
19222 (name "r-downloader")
19227 (uri (cran-uri "downloader" version))
19230 "1axggnsc27zzgr7snf41j3zd1vp3nfpmq4zj4d01axc709dyg40q"))))
19231 (build-system r-build-system)
19234 (home-page "https://github.com/wch/downloader")
19235 (synopsis "Download files over HTTP and HTTPS")
19237 "This package provides a wrapper for the @code{download.file} function,
19238 making it possible to download files over HTTPS across platforms. The
19239 @code{RCurl} package provides this functionality (and much more) but has
19240 external dependencies. This package has is implemented purely in R.")
19241 (license license:gpl2)))
19243 (define-public r-aplot
19250 (uri (cran-uri "aplot" version))
19253 "1b4jjj05a602dgn6yr1bsmbzlzkj6wf6af3k3w63g3mkqv0xzsfd"))))
19254 (properties `((upstream-name . "aplot")))
19255 (build-system r-build-system)
19262 (home-page "https://github.com/YuLab-SMU/aplot")
19263 (synopsis "Decorate a ggplot with associated information")
19265 "Users may want to align plots with associated information that requires
19266 axes to be exactly matched in subplots, e.g. hierarchical clustering with a
19267 heatmap. This package provides utilities to align associated subplots to a
19268 main plot at different sides (left, right, top and bottom) with axes exactly
19270 (license license:artistic2.0)))
19272 (define-public r-ggnewscale
19274 (name "r-ggnewscale")
19279 (uri (cran-uri "ggnewscale" version))
19282 "108a7y6sqqvzyfk247lbmnacfpwdl405rf1b3fa62cgx8ycsq4kb"))))
19283 (properties `((upstream-name . "ggnewscale")))
19284 (build-system r-build-system)
19287 (home-page "https://cran.r-project.org/package=ggnewscale")
19288 (synopsis "Multiple fill and color scales in ggplot2")
19290 "This package lets you use multiple fill and color scales in ggplot2.")
19291 (license license:gpl3)))
19293 (define-public r-ggpointdensity
19295 (name "r-ggpointdensity")
19300 (uri (cran-uri "ggpointdensity" version))
19303 "0c9a14j3b0hvamqylhzldw2hjdxmfbllwahjkf3gg2rw337ld9iy"))))
19305 `((upstream-name . "ggpointdensity")))
19306 (build-system r-build-system)
19309 (home-page "https://github.com/LKremer/ggpointdensity")
19310 (synopsis "Cross between a 2D density plot and a scatter plot")
19312 "This package provides a cross between a 2D density plot and a scatter
19313 plot, implemented as a ggplot2 @code{geom}. Points in the scatter plot are
19314 colored by the number of neighboring points. This is useful to visualize the
19315 2D-distribution of points in case of overplotting.")
19316 (license license:gpl3)))
19318 (define-public r-arrow
19325 (uri (cran-uri "arrow" version))
19328 "1b85vc5ld7nibqgsdkl5kbzc0rm5jh5lqfdrssvrrcxpd26a16kc"))))
19329 (properties `((upstream-name . "arrow")))
19330 (build-system r-build-system)
19332 (list `(,apache-arrow "lib") zlib))
19343 (list pkg-config r-knitr))
19344 (home-page "https://github.com/apache/arrow/")
19345 (synopsis "R integration to Apache Arrow")
19347 "Apache Arrow is a cross-language development platform for in-memory
19348 data. It specifies a standardized language-independent columnar memory format
19349 for flat and hierarchical data, organized for efficient analytic operations on
19350 modern hardware. This package provides an R interface to the Arrow C++
19352 (license license:asl2.0)))
19354 (define-public r-rex
19361 (uri (cran-uri "rex" version))
19364 "1mmzlc3j7xa0rbjxa369f4sr0iw3gq58g8fmjjxbsjvfq14ychmg"))))
19365 (build-system r-build-system)
19370 (home-page "https://github.com/kevinushey/rex")
19371 (synopsis "Friendly regular expressions")
19373 "This package provides a friendly interface for the construction of
19374 regular expressions. Regular expressions are a very powerful feature, however
19375 they are often difficult to interpret. Rex allows you to build complex
19376 regular expressions from human readable expressions")
19377 (license license:expat)))
19379 (define-public r-mlapi
19386 (uri (cran-uri "mlapi" version))
19389 "1qyiii6x9b89i4pd4yi2zd23aabpmnpj18gqi5va0zy0l8r7kknr"))))
19390 (properties `((upstream-name . "mlapi")))
19391 (build-system r-build-system)
19393 (list r-matrix r-r6))
19396 (home-page "https://cran.r-project.org/package=mlapi")
19397 (synopsis "Abstract classes for building scikit-learn like API")
19399 "This package provides R6 abstract classes for building machine learning
19400 models with a scikit-learn like API. Scikit-learn is a popular module for the
19401 Python programming language whose design became a de facto standard in
19402 industry for machine learning tasks.")
19403 (license license:expat)))
19405 (define-public r-float
19412 (uri (cran-uri "float" version))
19415 "0m7bf3548vlgkk1c78jyrgj72ngwg0gsccap2iqinm3l3qrm4zbs"))))
19416 (properties `((upstream-name . "float")))
19417 (build-system r-build-system)
19420 (home-page "https://github.com/wrathematics/float")
19421 (synopsis "32-bit floats")
19423 "R comes with a suite of utilities for linear algebra with
19424 \"numeric\" (double precision) vectors/matrices. However, sometimes single
19425 precision (or less!) is more than enough for a particular task. This package
19426 extends R's linear algebra facilities to include 32-bit float (single
19427 precision) data. Float vectors/matrices have half the precision of their
19428 \"numeric\"-type counterparts but are generally faster to numerically operate
19429 on, for a performance vs accuracy trade-off.")
19430 (license license:bsd-2)))
19432 (define-public r-rsparse
19439 (uri (cran-uri "rsparse" version))
19442 "0d05h47j29zipyxbkv9cwzv2dzj894z6hh9dqfhwswwjbv6ciwpq"))))
19443 (properties `((upstream-name . "rsparse")))
19444 (build-system r-build-system)
19454 (home-page "https://github.com/rexyai/rsparse")
19455 (synopsis "Statistical learning on sparse matrices")
19457 "This package implements many algorithms for statistical learning on
19458 sparse matrices: matrix factorizations, matrix completion, elastic net
19459 regressions, factorization machines. The rsparse package also enhances the
19460 Matrix package by providing methods for multithreaded <sparse, dense> matrix
19461 products and native slicing of the sparse matrices in @dfn{Compressed Sparse
19462 Row} (CSR) format.")
19463 (license license:gpl2+)))
19465 (define-public r-text2vec
19467 (name "r-text2vec")
19472 (uri (cran-uri "text2vec" version))
19475 "0bisr31051hnshw26rp9r4bm8ksr977dl9k1d3fb1x79pq5aa2pi"))))
19476 (properties `((upstream-name . "text2vec")))
19477 (build-system r-build-system)
19490 (home-page "http://text2vec.org")
19491 (synopsis "Text mining framework for R")
19493 "This package provides fast and memory-friendly tools for text
19494 vectorization, topic modeling (LDA, LSA), word embeddings (GloVe),
19495 similarities. It provides a source-agnostic streaming API, which allows
19496 researchers to perform analysis of collections of documents which are larger
19497 than available RAM. All core functions are parallelized to benefit from
19498 multicore machines.")
19499 (license license:gpl2+)))
19501 (define-public r-mcmcpack
19503 (name "r-mcmcpack")
19508 (uri (cran-uri "MCMCpack" version))
19511 "1cwdjn43b9hxpxf9mnas583myhk6r2258mh57f0zsc8bd4hbl56b"))))
19512 (properties `((upstream-name . "MCMCpack")))
19513 (build-system r-build-system)
19515 (list r-coda r-lattice r-mass r-mcmc r-quantreg))
19516 (home-page "https://cran.r-project.org/package=MCMCpack")
19517 (synopsis "Markov Chain Monte Carlo (MCMC) package")
19519 "This package contains functions to perform Bayesian inference using
19520 posterior simulation for a number of statistical models. Most simulation is
19521 done in compiled C++ written in the Scythe Statistical Library. All models
19522 return @code{coda} @code{mcmc} objects that can then be summarized using the
19523 @code{coda} package. Some useful utility functions such as density functions,
19524 pseudo-random number generators for statistical distributions, a general
19525 purpose Metropolis sampling algorithm, and tools for visualization are
19527 (license license:gpl3)))
19529 (define-public r-xmlparsedata
19531 (name "r-xmlparsedata")
19536 (uri (cran-uri "xmlparsedata" version))
19539 "1c6bnz3ng1qw7sfip8wq3a4dn36a4d6rbja0sadn0a4pbsmk8q3n"))))
19540 (properties `((upstream-name . "xmlparsedata")))
19541 (build-system r-build-system)
19542 (home-page "https://github.com/r-lib/xmlparsedata#readme")
19543 (synopsis "Parse data of @code{R} code as an @code{XML} tree")
19545 "This package provides tools to convert the output of
19546 @code{utils::getParseData()} to an @code{XML} tree, that one can search via
19547 @code{XPath}, and is easier to manipulate in general.")
19548 (license license:expat)))
19550 (define-public r-cyclocomp
19552 (name "r-cyclocomp")
19557 (uri (cran-uri "cyclocomp" version))
19560 "0gky3svk02wiajw7nfjh30684h3qxili4bvsab0m7b6cggw6bgyd"))))
19561 (properties `((upstream-name . "cyclocomp")))
19562 (build-system r-build-system)
19564 (list r-callr r-crayon r-desc r-remotes r-withr))
19565 (home-page "https://github.com/MangoTheCat/cyclocomp")
19566 (synopsis "Cyclomatic complexity of R code")
19568 "Cyclomatic complexity is a software metric, used to indicate the
19569 complexity of a program. It is a quantitative measure of the number of
19570 linearly independent paths through a program's source code. This package
19571 provides tools to compute this metric.")
19572 (license license:expat)))
19574 (define-public r-lintr
19581 (uri (cran-uri "lintr" version))
19584 "14yfh641afg6griaadbdciyr3k94fl55s055qwzghgk5gdsj61zy"))))
19585 (properties `((upstream-name . "lintr")))
19586 (build-system r-build-system)
19600 (home-page "https://github.com/jimhester/lintr")
19601 (synopsis "Linter for R code")
19602 (description "This package checks adherence to a given style, syntax
19603 errors and possible semantic issues. It supports on the fly checking of R
19604 code edited with @code{RStudio IDE}, @code{Emacs} and @code{Vim}.")
19605 (license license:expat)))
19607 (define-public r-sctransform
19609 (name "r-sctransform")
19614 (uri (cran-uri "sctransform" version))
19617 "0aqbcarsvvzkh5h4i65f08y4b8dfcs3zi62hmvfy24gj81f15bw3"))))
19618 (build-system r-build-system)
19633 (home-page "https://github.com/ChristophH/sctransform")
19634 (synopsis "Variance stabilizing transformations for Single Cell UMI Data")
19636 "This package provides a normalization method for single-cell UMI count
19637 data using a variance stabilizing transformation. The transformation is based
19638 on a negative binomial regression model with regularized parameters. As part
19639 of the same regression framework, this package also provides functions for
19640 batch correction, and data correction.")
19641 (license license:gpl3)))
19643 (define-public r-styler
19650 (uri (cran-uri "styler" version))
19653 "1ki260ga0jrmayhdlx2sl788yp5kkmi4wyl32nmvvyb55sng6j9y"))))
19654 (build-system r-build-system)
19655 ;; This is needed by R.cache.
19658 (modify-phases %standard-phases
19659 (add-after 'unpack 'set-HOME
19660 (lambda _ (setenv "HOME" "/tmp"))))))
19673 (home-page "https://github.com/r-lib/styler")
19674 (synopsis "Non-invasive pretty printing of R code")
19676 "This is a package for pretty-printing R code without changing the user's
19677 formatting intent.")
19678 (license license:gpl3)))
19680 (define-public r-scrime
19687 (uri (cran-uri "scrime" version))
19690 "0y2mh9fsffjf3i15bafpasa17z99c1s75r8g6h4hgcwfgpjx75sx"))))
19691 (build-system r-build-system)
19692 (home-page "https://cran.r-project.org/web/packages/scrime/")
19693 (synopsis "Analysis of high-dimensional categorical data such as SNP data")
19695 "This package provides tools for the analysis of high-dimensional data
19696 developed/implemented at the group \"Statistical Complexity Reduction In
19697 Molecular Epidemiology\" (SCRIME). The main focus is on SNP data, but most of
19698 the functions can also be applied to other types of categorical data.")
19699 (license license:gpl2)))
19701 (define-public r-pbmcapply
19703 (name "r-pbmcapply")
19708 (uri (cran-uri "pbmcapply" version))
19711 "1p8jf7c4k45482w72sr0jw4jkz787krrxai3sl6jz5l4lda2iz3z"))))
19712 (build-system r-build-system)
19713 (home-page "https://github.com/kvnkuang/pbmcapply")
19714 (synopsis "Track the progress of apply procedures with a progress bar")
19716 "This light-weight package helps you track and visualize the progress of
19717 parallel versions of vectorized R functions of the @code{mc*apply} family.")
19718 (license license:expat)))
19720 (define-public r-blme
19727 (uri (cran-uri "blme" version))
19730 "0413j7gwr5yj14jamkizj55q7xii1a0kgazzj0ilqn2ascclz6k7"))))
19731 (build-system r-build-system)
19732 (propagated-inputs (list r-lme4))
19733 (home-page "https://github.com/vdorie/blme")
19734 (synopsis "Bayesian linear mixed-effects models")
19736 "This package provides tools for maximum a posteriori estimation for
19737 linear and generalized linear mixed-effects models in a Bayesian setting. It
19738 extends the lme4 package.")
19739 (license license:gpl2+)))
19741 (define-public r-batchtools
19743 (name "r-batchtools")
19748 (uri (cran-uri "batchtools" version))
19751 "0d2xy77hkzhcnyz8zxcv98i80fx6ripjw4rvyx4ww1d0vjjgqf52"))))
19752 (build-system r-build-system)
19768 (home-page "https://github.com/mllg/batchtools")
19769 (synopsis "Tools for computation on batch systems")
19771 "As a successor of the packages BatchJobs and BatchExperiments, this
19772 package provides a parallel implementation of the Map function for high
19773 performance computing systems managed by various schedulers. A multicore and
19774 socket mode allow the parallelization on a local machines, and multiple
19775 machines can be hooked up via SSH to create a makeshift cluster. Moreover,
19776 the package provides an abstraction mechanism to define large-scale computer
19777 experiments in a well-organized and reproducible way.")
19778 (license license:lgpl3)))
19780 (define-public r-clue
19787 (uri (cran-uri "clue" version))
19790 "0apgpdnn74mqg2bnr8yjyxgyvdl411h0r2b1r2xd67k21pyxs8bd"))))
19791 (build-system r-build-system)
19792 (propagated-inputs (list r-cluster))
19793 (home-page "https://cran.r-project.org/web/packages/clue/")
19794 (synopsis "Tools for analyzing cluster ensembles")
19795 (description "Cluster ensembles are collections of individual solutions to
19796 a given clustering problem which are useful or necessary to consider in a wide
19797 range of applications. This R package provides an extensible computational
19798 environment for creating and analyzing cluster ensembles, with basic data
19799 structures for representing partitions and hierarchies, and facilities for
19800 computing on them, including methods for measuring proximity and obtaining
19801 consensus and secondary clusterings.")
19802 (license license:gpl2)))
19804 (define-public r-sitmo
19811 (uri (cran-uri "sitmo" version))
19814 "1hm89zi38ldgbskyx1cn7gm87yqy7zrxli8q05a36y1ndvazi3j4"))))
19815 (build-system r-build-system)
19816 (propagated-inputs (list r-rcpp))
19819 (home-page "https://github.com/coatless/sitmo/")
19820 (synopsis "Parallel pseudo random number generator header files")
19822 "This package provides two high quality and fast PPRNGs that may be used
19823 in an OpenMP parallel environment. In addition, there is a generator for one
19824 dimensional low-discrepancy sequence.")
19825 (license license:expat)))
19827 (define-public r-dqrng
19834 (uri (cran-uri "dqrng" version))
19837 "1fwsldqcri2lccna4icbmmlqic3w4xyjm7rn0xmikrsw4kzapvjb"))))
19838 (build-system r-build-system)
19840 (list r-bh r-rcpp r-sitmo))
19843 (home-page "https://www.daqana.org/dqrng")
19844 (synopsis "Fast pseudo random number generators")
19846 "Several fast random number generators are provided as C++ header-only
19847 libraries: the PCG family as well as Xoroshiro128+ and Xoshiro256+.
19848 Additionally, fast functions for generating random numbers according to a
19849 uniform, normal and exponential distribution are included. The latter two use
19850 the Ziggurat algorithm originally proposed by Marsaglia and Tsang. These
19851 functions are exported to R and as a C++ interface and are enabled for use
19852 with the default 64 bit generator from the PCG family, Xoroshiro128+ and
19853 Xoshiro256+ as well as the 64 bit version of the 20 rounds Threefry
19854 engine (Salmon et al., 2011) as provided by the package @code{sitmo}.")
19855 ;; This package includes code under CC0 and Apache 2.0 or Expat, but as a
19856 ;; whole is distributed under the terms of the AGPL 3.
19857 (license license:agpl3)))
19859 (define-public r-ingredients
19861 (name "r-ingredients")
19866 (uri (cran-uri "ingredients" version))
19869 "11bv4l4fn9kr7y2nfzrwnaya8fi9w3nwcm9vzlqb7dva83rkqbsc"))))
19870 (properties `((upstream-name . "ingredients")))
19871 (build-system r-build-system)
19873 (list r-ggplot2 r-gridextra r-scales))
19874 (native-inputs (list r-knitr))
19875 (home-page "https://ModelOriented.github.io/ingredients/")
19876 (synopsis "Effects and importances of model ingredients")
19878 "This is a collection of tools for assessment of feature importance and
19879 feature effects. Key functions are:
19882 @item @code{feature_importance()} for assessment of global level feature
19884 @item @code{ceteris_paribus()} for calculation of the what-if plots,
19885 @item @code{partial_dependence()} for partial dependence plots,
19886 @item @code{conditional_dependence()} for conditional dependence plots,
19887 @item @code{accumulated_dependence()} for accumulated local effects plots,
19888 @item @code{aggregate_profiles()} and @code{cluster_profiles()} for
19889 aggregation of ceteris paribus profiles,
19890 @item generic @code{print()} and @code{plot()} for better usability of
19891 selected explainers,
19892 @item generic @code{plotD3()} for interactive, D3 based explanations, and
19893 @item generic @code{describe()} for explanations in natural language.
19895 (license license:gpl3)))
19897 (define-public r-ibreakdown
19899 (name "r-ibreakdown")
19904 (uri (cran-uri "iBreakDown" version))
19907 "00jzrndb3ahsv6ihp2pvs732n9cc944m83vdinrl9v1pxd82prkh"))))
19908 (properties `((upstream-name . "iBreakDown")))
19909 (build-system r-build-system)
19910 (propagated-inputs (list r-ggplot2))
19911 (native-inputs (list r-knitr))
19912 (home-page "https://ModelOriented.github.io/iBreakDown/")
19913 (synopsis "Model agnostic instance level variable attributions")
19915 "This package provides a model agnostic tool for decomposition of
19916 predictions from black boxes. It supports additive attributions and
19917 attributions with interactions. The Break Down Table shows contributions of
19918 every variable to a final prediction. The Break Down Plot presents variable
19919 contributions in a concise graphical way. This package works for
19920 classification and regression models.")
19921 (license license:gpl3)))
19923 (define-public r-dae
19930 (uri (cran-uri "dae" version))
19933 "0mq94ah21p1glvsbvdmi2p7nlgz1bvq7w3rz2z3mdqq18kz6nkjw"))))
19934 (build-system r-build-system)
19936 (list r-ggplot2 r-plyr))
19938 (list r-r-rsp)) ; vignette builder
19939 (home-page "http://chris.brien.name")
19940 (synopsis "Functions useful in the design and ANOVA of experiments")
19942 "This package provides functions useful in the design and ANOVA of
19943 experiments. The content falls into the following groupings:
19947 @item factor manipulation functions,
19948 @item design functions,
19949 @item ANOVA functions,
19950 @item matrix functions,
19951 @item projector and canonical efficiency functions, and
19952 @item miscellaneous functions.
19955 There is a vignette called @code{DesignNotes} describing how to use the design
19956 functions for randomizing and assessing designs. The ANOVA functions
19957 facilitate the extraction of information when the @code{Error} function has
19958 been used in the call to @code{aov}.")
19959 (license license:gpl2)))
19961 (define-public r-dalex
19968 (uri (cran-uri "DALEX" version))
19971 "1s7r7k5ihdbj69r27vbcs3ghra9s4yqw7cyh2rkm2ry901zq3114"))))
19972 (properties `((upstream-name . "DALEX")))
19973 (build-system r-build-system)
19975 (list r-ggplot2 r-ibreakdown r-ingredients))
19976 (home-page "https://pbiecek.github.io/DALEX/")
19977 (synopsis "Descriptive machine learning explanations")
19979 "Machine Learning models are widely used and have various applications in
19980 classification or regression. Models created with boosting, bagging, stacking
19981 or similar techniques are often used due to their high performance, but such
19982 black-box models usually lack interpretability. The DALEX package contains
19983 various explainers that help to understand the link between input variables
19984 and model output.")
19985 ;; Any version of the GPL
19986 (license license:gpl3+)))
19988 (define-public r-enrichr
19995 (uri (cran-uri "enrichR" version))
19998 "0i3kfq4fkmx47n61zj5f87iv8ci6gbgy90a7s8dy9zbndzvbgya3"))))
19999 (properties `((upstream-name . "enrichR")))
20000 (build-system r-build-system)
20002 (list r-ggplot2 r-httr r-rjson))
20005 (home-page "https://cran.r-project.org/web/packages/enrichR/")
20006 (synopsis "R Interface to Enrichr database for analyzing gene sets")
20008 "This package provides an R interface to all Enrichr databases, a
20009 web-based tool for analyzing gene sets and returns any enrichment of common
20010 annotated biological functions.")
20011 (license license:gpl2+)))
20013 (define-public r-plot3d
20020 (uri (cran-uri "plot3D" version))
20023 "1h59zlsyzbjylaziwavppl9bjmnba4iiq34772y3dys6fqclajnh"))))
20024 (properties `((upstream-name . "plot3D")))
20025 (build-system r-build-system)
20026 (propagated-inputs (list r-misc3d))
20027 (home-page "https://cran.r-project.org/web/packages/plot3D")
20028 (synopsis "Plot multi-dimensional data")
20030 "This package provides functions for viewing 2D and 3D data, including
20031 perspective plots, slice plots, surface plots, scatter plots, etc. It
20032 includes data sets from oceanography.")
20033 (license license:gpl3+)))
20035 (define-public r-ggfortify
20037 (name "r-ggfortify")
20042 (uri (cran-uri "ggfortify" version))
20045 "038m74azpy43869ax1yi6wxbl1kr59iaxl8raiikjg749vcx6njw"))))
20046 (build-system r-build-system)
20057 (home-page "https://github.com/sinhrks/ggfortify")
20058 (synopsis "Data visualization tools for statistical analysis results")
20060 "This package provides unified plotting tools for statistics commonly
20061 used, such as GLM, time series, PCA families, clustering and survival
20062 analysis. The package offers a single plotting interface for these analysis
20063 results and plots in a unified style using the @code{ggplot2} package.")
20064 (license license:gpl2)))
20066 (define-public r-refmanager
20068 (name "r-refmanager")
20073 (uri (cran-uri "RefManageR" version))
20076 "1spzdp5ni52dybcaxqnhwdphh27wjyrsfy4hsxsplpg9rqwfqfps"))))
20077 (properties `((upstream-name . "RefManageR")))
20078 (build-system r-build-system)
20088 (home-page "https://github.com/ropensci/RefManageR/")
20089 (synopsis "Straightforward BibTeX and BibLaTeX bibliography management")
20091 "This package provides tools for importing and working with bibliographic
20092 references. It greatly enhances the @code{bibentry} class by providing a
20093 class @code{BibEntry} which stores BibTeX and BibLaTeX references, supports
20094 UTF-8 encoding, and can be easily searched by any field, by date ranges, and
20095 by various formats for name lists (author by last names, translator by full
20096 names, etc.). Entries can be updated, combined, sorted, printed in a number
20097 of styles, and exported. BibTeX and BibLaTeX @code{.bib} files can be read
20098 into R and converted to @code{BibEntry} objects.")
20099 ;; Any of these licenses may be picked.
20100 (license (list license:gpl2 license:gpl3 license:bsd-3))))
20102 (define-public r-citr
20109 (uri (cran-uri "citr" version))
20112 "1qbarvafjb8jgkrnrhh6jw7mcglmjwf7dpdiibxf39jkmlhf7las"))))
20113 (build-system r-build-system)
20124 (home-page "https://github.com/crsh/citr")
20125 (synopsis "RStudio add-in to insert Markdown citations")
20127 "This package provides functions and an RStudio add-in that search a
20128 BibTeX or BibLaTeX file to create and insert formatted Markdown citations into
20129 the current document.")
20130 (license license:expat)))
20132 (define-public r-xgboost
20135 (version "1.5.2.1")
20139 (uri (cran-uri "xgboost" version))
20142 "13mi3rmpxhgm4qbm4xcqml9n5d1xyai2k1mi52i8x60jd5m8s319"))))
20143 (build-system r-build-system)
20145 (list r-data-table r-jsonlite r-matrix))
20148 (home-page "https://github.com/dmlc/xgboost")
20149 (synopsis "Extreme gradient boosting")
20151 "This package provides an R interface to Extreme Gradient Boosting, which
20152 is an efficient implementation of the gradient boosting framework from Chen
20153 and Guestrin (2016). The package includes efficient linear model solver and
20154 tree learning algorithms. The package can automatically do parallel
20155 computation on a single machine. It supports various objective functions,
20156 including regression, classification and ranking. The package is made to be
20157 extensible, so that users are also allowed to define their own objectives
20159 (license license:asl2.0)))
20161 (define-public r-umap
20164 (version "0.2.8.0")
20168 (uri (cran-uri "umap" version))
20171 "0aiarnzc8gl932gi8fxd9f9rshaiwh9vj570l135fkiaja3q2wap"))))
20172 (build-system r-build-system)
20174 (list r-matrix r-openssl r-rcpp r-reticulate r-rspectra))
20177 (home-page "https://github.com/tkonopka/umap")
20178 (synopsis "Uniform manifold approximation and projection")
20180 "Uniform manifold approximation and projection is a technique for
20181 dimension reduction. This package provides an interface to the UMAP algorithm
20182 in R, including a translation of the original algorithm into R.")
20183 (license license:expat)))
20185 (define-public r-uwot
20192 (uri (cran-uri "uwot" version))
20195 "06ylzxmdh8jipbrzgqaiivd2lnqmbcva41cyvc0iyals6vqr1ksg"))))
20196 (build-system r-build-system)
20206 (home-page "https://github.com/jlmelville/uwot")
20207 (synopsis "Uniform manifold approximation and projection")
20209 "This package provides an implementation of the Uniform Manifold
20210 Approximation and Projection dimensionality reduction by McInnes et
20211 al. (2018). It also provides means to transform new data and to carry out
20212 supervised dimensionality reduction. An implementation of the related
20213 LargeVis method of Tang et al. (2016) is also provided.")
20214 (license license:gpl3)))
20216 (define-public r-kableextra
20218 (name "r-kableextra")
20223 (uri (cran-uri "kableExtra" version))
20226 "1c5vzy95cbz36jwyssr927qicrayifinv861rvnmg4nghb1gl7q9"))))
20227 (properties `((upstream-name . "kableExtra")))
20228 (build-system r-build-system)
20246 (home-page "https://haozhu233.github.io/kableExtra/")
20247 (synopsis "Construct complex tables with pipe syntax")
20249 "Build complex HTML or LaTeX tables using @code{kable()} from
20250 @code{knitr} and the piping syntax from @code{magrittr}. The function
20251 @code{kable()} is a light weight table generator coming from @code{knitr}.
20252 This package simplifies the way to manipulate the HTML or LaTeX codes
20253 generated by @code{kable()} and allows users to construct complex tables and
20254 customize styles using a readable syntax.")
20255 (license license:expat)))
20257 (define-public r-glasso
20264 (uri (cran-uri "glasso" version))
20266 (base32 "02p3612rpydk195n2qr77lp1j2w8zsw1ckkk98c8angm4r5q8dsc"))))
20267 (build-system r-build-system)
20268 (native-inputs (list gfortran))
20269 (home-page "https://statweb.stanford.edu/~tibs/glasso/")
20270 (synopsis "Graphical Lasso: estimation of Gaussian graphical models")
20272 "This is a package for estimation of a sparse inverse covariance matrix
20273 using a lasso (L1) penalty. Facilities are provided for estimates along a
20274 path of values for the regularization parameter.")
20275 (license license:gpl2)))
20277 (define-public r-rhpcblasctl
20279 (name "r-rhpcblasctl")
20280 (version "0.21-247.1")
20284 (uri (cran-uri "RhpcBLASctl" version))
20287 "0scpr6jq25xx7wmqyc380ann4h536ll0g7wblikk25yqvpamzrav"))))
20288 (properties `((upstream-name . "RhpcBLASctl")))
20289 (build-system r-build-system)
20290 (home-page "https://prs.ism.ac.jp/~nakama/Rhpc/")
20291 (synopsis "Control the number of threads on BLAS")
20293 "This package allows you to control the number of threads the BLAS
20294 library uses. It is also possible to control the number of threads in
20296 (license license:agpl3+)))
20298 (define-public r-lda
20305 (uri (cran-uri "lda" version))
20308 "03r4h5kgr8mfy44p66mfj5bp4k00g8zh4a1mhn46jw14pkhs21jn"))))
20309 (build-system r-build-system)
20310 (home-page "https://cran.r-project.org/web/packages/lda/")
20311 (synopsis "Collapsed Gibbs sampling methods for topic models")
20313 "This package implements @dfn{latent Dirichlet allocation} (LDA) and
20314 related models. This includes (but is not limited to) sLDA, corrLDA, and the
20315 mixed-membership stochastic blockmodel. Inference for all of these models is
20316 implemented via a fast collapsed Gibbs sampler written in C. Utility
20317 functions for reading/writing data typically used in topic models, as well as
20318 tools for examining posterior distributions are also included.")
20319 ;; Any version of the LGPL
20320 (license license:lgpl3+)))
20322 (define-public r-rann-l1
20329 (uri (cran-uri "RANN.L1" version))
20332 "1hanh3my84mdr5wy6b89fawqzfc184vff1y65wy4l5ld9qza1n44"))))
20333 (properties `((upstream-name . "RANN.L1")))
20334 (build-system r-build-system)
20335 (home-page "https://github.com/jefferis/RANN/tree/master-L1")
20336 (synopsis "Fast nearest neighbour search using L1 metric")
20338 "This package provides tools to find the k nearest neighbours for every
20339 point in a given dataset in O(N log N) time using Arya and Mount's ANN
20340 library. There is support for approximate as well as exact searches, fixed
20341 radius searches and @code{bd} as well as @code{kd} trees. The distance is
20342 computed using the L1 (Manhattan, taxicab) metric.")
20343 (license license:gpl3+)))
20345 (define-public r-leiden
20352 (uri (cran-uri "leiden" version))
20355 "03gaxpcab3a1av5lk8r5ll1s858gvyx5ndknci1sia96w1v44xc1"))))
20356 (properties `((upstream-name . "leiden")))
20357 (build-system r-build-system)
20359 (list r-igraph r-matrix r-reticulate))
20362 (home-page "https://github.com/TomKellyGenetics/leiden")
20363 (synopsis "R implementation of Leiden clustering algorithm")
20365 "This package implements the Python @code{leidenalg} module to be called
20366 in R. It enables clustering using the Leiden algorithm for partitioning a
20367 graph into communities. See also Traag et al (2018) \"From Louvain to Leiden:
20368 guaranteeing well-connected communities.\" <arXiv:1810.08473>.")
20369 (license license:gpl3)))
20371 (define-public r-patchwork
20373 (name "r-patchwork")
20378 (uri (cran-uri "patchwork" version))
20381 "10glgkf58lcykcwda1hj6xdps02m3i247qynk6s2jmwljagps3fg"))))
20382 (build-system r-build-system)
20384 (list r-ggplot2 r-gtable))
20387 (home-page "https://github.com/thomasp85/patchwork")
20388 (synopsis "Compose ggplot2 plots")
20390 "The @code{ggplot2} package provides a strong API for sequentially
20391 building up a plot, but does not concern itself with composition of multiple
20392 plots. Patchwork is a package that expands the API to allow for arbitrarily
20393 complex composition of plots by providing mathematical operators for combining
20395 (license license:expat)))
20397 (define-public r-liger
20404 (uri (git-reference
20405 (url "https://github.com/MacoskoLab/liger")
20406 (commit (string-append "v" version))))
20407 (file-name (git-file-name name version))
20410 "16dzwwcpw6n78pxlc5w3kraigki35ix7zhd2cbx5f3y60bbkhlmx"))
20411 (modules '((guix build utils)))
20414 (delete-file "inst/java/ModularityOptimizer.jar")
20416 (build-system r-build-system)
20419 (modify-phases %standard-phases
20420 (add-after 'unpack 'build-java-part
20421 (lambda* (#:key inputs #:allow-other-keys)
20422 (invoke "unzip" (assoc-ref inputs "optimizer-src"))
20423 (for-each (lambda (file) (invoke "javac" file))
20424 (find-files "." "\\.java$"))
20425 (apply invoke "jar" "cf" "inst/java/ModularityOptimizer.jar"
20426 (find-files "." "\\.class$"))
20450 `(("jdk" ,icedtea "jdk")
20451 ;; See https://github.com/MacoskoLab/liger/issues/96
20452 ;; The optimizer is released under the Expat license.
20456 (uri "http://www.ludowaltman.nl/slm/modularity_optimizer_source.zip")
20459 "01hmm6sapcmldvayknqx2w4cav3qv71mwwkdkwj4qgq6dss09g18"))))
20461 ("r-knitr" ,r-knitr))) ; for vignettes
20462 (home-page "https://github.com/MacoskoLab/liger")
20463 (synopsis "Integrate and analyze multiple single-cell datasets")
20465 "LIGER is a package for integrating and analyzing multiple single-cell
20466 datasets, developed and maintained by the Macosko lab. It relies on
20467 integrative non-negative matrix factorization to identify shared and
20468 dataset-specific factors.")
20469 (license license:gpl3)))
20471 (define-public r-harmony
20478 (uri (git-reference
20479 (url "https://github.com/immunogenomics/harmony")
20481 (file-name (git-file-name name version))
20484 "05r401q09rbr6fqhb9mbd95082cjdi3nag1cv6zn96xkr0f6imq9"))
20485 (modules '((guix build utils)))
20488 (for-each delete-file '("config.status" "configure"))
20490 (build-system r-build-system)
20505 (home-page "https://github.com/immunogenomics/harmony")
20506 (synopsis "Integration of single cell sequencing data")
20508 "This package provides an implementation of the Harmony algorithm for
20509 single cell integration, described in Korsunsky et al
20510 @url{doi.org/10.1101/461954}. The package includes a standalone Harmony
20511 function and interfaces to external frameworks.")
20512 (license license:gpl3)))
20514 (define-public r-covr
20521 (uri (cran-uri "covr" version))
20523 (base32 "0v5cv3cw2kpdr6wxmkbd3wclavr17zipypdcb10hhmpa4cvgqk55"))))
20524 (properties `((upstream-name . "covr")))
20525 (build-system r-build-system)
20535 (list r-knitr)) ; for vignettes
20536 (home-page "https://github.com/r-lib/covr")
20537 (synopsis "Test coverage for R packages")
20539 "Thisp package enables you to track and report code coverage for your
20540 package and (optionally) upload the results to a coverage service. Code
20541 coverage is a measure of the amount of code being exercised by a set of tests.
20542 It is an indirect measure of test quality and completeness. This package is
20543 compatible with any testing methodology or framework and tracks coverage of
20544 both R code and compiled C/C++/FORTRAN code.")
20545 (license license:gpl3)))
20547 (define-public r-systemfonts
20549 (name "r-systemfonts")
20554 (uri (cran-uri "systemfonts" version))
20557 "1h44bal845jp7ya8i7ff1kz1n3wklkb00jk6hb9lgwa2p5snqxpg"))))
20558 (properties `((upstream-name . "systemfonts")))
20559 (build-system r-build-system)
20563 (list fontconfig freetype zlib))
20565 (list pkg-config r-knitr))
20566 (home-page "https://github.com/r-lib/systemfonts")
20567 (synopsis "System native font finding")
20569 "This package provides system native access to the font catalogue. As
20570 font handling varies between systems it is difficult to correctly locate
20571 installed fonts across different operating systems. The 'systemfonts' package
20572 provides bindings to the native libraries for finding font files that can then
20573 be used further by e.g. graphic devices.")
20574 (license license:expat)))
20576 (define-public r-graphlayouts
20578 (name "r-graphlayouts")
20583 (uri (cran-uri "graphlayouts" version))
20586 "1l7gkn0r1ijllv3w7cbwcbi0jggs7wlkq9b2lykprng4g1kjc96p"))))
20587 (properties `((upstream-name . "graphlayouts")))
20588 (build-system r-build-system)
20590 (list r-igraph r-rcpp r-rcpparmadillo))
20591 (home-page "https://github.com/schochastics/graphlayouts")
20592 (synopsis "Additional layout algorithms for network visualizations")
20594 "This package provides several layout algorithms to visualize networks
20595 which are not part of the igraph library. Most are based on the concept of
20596 stress majorization by Gansner et al. (2004)
20597 <doi:10.1007/978-3-540-31843-9_25>. Some more specific algorithms
20598 emphasize hidden group structures in networks or focus on specific nodes.")
20599 (license license:expat)))
20601 (define-public r-terra
20608 (uri (cran-uri "terra" version))
20611 "0gzl0ka19jjw0dmaghjk2sgwi78kkz4w3rlfkym62rdarhlfj7h9"))))
20612 (properties `((upstream-name . "terra")))
20613 (build-system r-build-system)
20618 sqlite ; needed for proj
20624 (home-page "https://rspatial.org/terra")
20625 (synopsis "Spatial data analysis")
20627 "This package provides methods for spatial data analysis, especially
20628 raster data. The included methods allow for low-level data manipulation as
20629 well as high-level global, local, zonal, and focal computation. The predict
20630 and interpolate methods facilitate the use of regression type (interpolation,
20631 machine learning) models for spatial prediction. Processing of very large
20632 files is supported.")
20633 (license license:gpl3+)))
20635 (define-public r-tidygraph
20637 (name "r-tidygraph")
20642 (uri (cran-uri "tidygraph" version))
20645 "0dmdff3bkg53xn0c51xd6k2d9c7l250x1lhl5z3libf533dw5g9g"))))
20646 (properties `((upstream-name . "tidygraph")))
20647 (build-system r-build-system)
20659 (home-page "https://github.com/thomasp85/tidygraph")
20660 (synopsis "Tidy API for graph manipulation")
20662 "This package provides a graph implementation that can be thought of as
20663 two tidy data frames describing node and edge data respectively. It provides
20664 an approach to manipulate these two virtual data frames using the API defined
20665 in the @code{dplyr} package, and it also provides tidy interfaces to a lot of
20666 common graph algorithms.")
20667 (license license:expat)))
20669 (define-public r-soupx
20670 (let ((commit "a3354be76fb52fd795be6ddf163cf056c05c6cb8")
20674 (version (git-version "0.3.1" revision commit))
20678 (uri (git-reference
20679 (url "https://github.com/constantAmateur/SoupX")
20681 (file-name (git-file-name name version))
20684 "1zmlyzrl0fz6l79gn2wswid670p88mm3y292is89sa5p3h7frr99"))))
20685 (properties `((upstream-name . "SoupX")))
20686 (build-system r-build-system)
20688 (list r-ggplot2 r-matrix r-seurat))
20689 (home-page "https://github.com/constantAmateur/SoupX")
20690 (synopsis "Single cell mRNA Soup eXterminator")
20692 "This package provides a package for quantifying, profiling and
20693 removing cell free mRNA contamination (the \"soup\") from droplet based single
20694 cell RNA-seq experiments.")
20695 (license license:gpl2))))
20697 (define-public r-assertr
20704 (uri (cran-uri "assertr" version))
20707 "00764vv86r3bn4r85in4w637harffyw605fgq0dj6mrbrwcfb650"))))
20708 (build-system r-build-system)
20710 (list r-dplyr r-mass r-rlang))
20712 (list r-knitr)) ; needed for vignette
20713 (home-page "https://github.com/ropensci/assertr")
20714 (synopsis "Assertive programming for R analysis pipelines")
20716 "This package provides functionality to assert conditions that have to be
20717 met so that errors in data used in analysis pipelines can fail quickly. It is
20718 similar to @code{stopifnot()} but more powerful, friendly, and easier for use
20720 (license license:expat)))
20722 (define-public r-parameters
20724 (name "r-parameters")
20729 (uri (cran-uri "parameters" version))
20732 "0wrhs3rhr62441cghg4nsrlp6r41nf7x5nclzz71v5c0rfn8jh79"))))
20733 (properties `((upstream-name . "parameters")))
20734 (build-system r-build-system)
20736 (list r-bayestestr r-datawizard r-insight))
20739 (home-page "https://cran.r-project.org/web/packages/parameters")
20740 (synopsis "Processing of model parameters")
20742 "This package provides utilities for processing the parameters of various
20743 statistical models. Beyond computing p values, CIs, and other indices for a
20744 wide variety of models, this package implements features like standardization
20745 or bootstrapping of parameters and models, feature reduction (feature
20746 extraction and variable selection) as well as conversion between indices of
20748 (license license:gpl3)))
20750 (define-public r-rgdal
20757 (uri (cran-uri "rgdal" version))
20759 (base32 "1f4zshgkaifbfcgq61vqb7jw5w2cc128d98rq2465r8696q2p0s9"))))
20760 (properties `((upstream-name . "rgdal")))
20761 (build-system r-build-system)
20763 (list gdal proj zlib))
20767 (list pkg-config r-knitr))
20768 (home-page "http://rgdal.r-forge.r-project.org")
20769 (synopsis "Bindings for the Geospatial Data Abstraction Library")
20771 "This package provides bindings to the Geospatial Data Abstraction
20772 Library (GDAL) and access to projection/transformation operations from the
20774 (license license:gpl2+)))
20776 (define-public r-insol
20783 (uri (cran-uri "insol" version))
20786 "166kgxgzbh55y2qqya6c2si22x0v7asi70im054g6xxwc5187kh3"))))
20787 (properties `((upstream-name . "insol")))
20788 (build-system r-build-system)
20793 (home-page "https://meteoexploration.com/R/insol/index.html")
20794 (synopsis "Tools for calculating solar radiation")
20796 "This package provides functions to compute insolation on tilted
20797 surfaces, computes atmospheric transmittance and related parameters such as:
20798 Earth radius vector, declination, sunset and sunrise, daylength, equation of
20799 time, vector in the direction of the sun, vector normal to surface, and some
20800 atmospheric physics.")
20801 (license license:gpl2+)))
20803 (define-public r-lifecycle
20805 (name "r-lifecycle")
20810 (uri (cran-uri "lifecycle" version))
20813 "183v1z1h037pvsgrj6vakpwhnhsr29hsw8p16k59dgpi00f6x9qx"))))
20814 (properties `((upstream-name . "lifecycle")))
20815 (build-system r-build-system)
20817 (list r-glue r-rlang))
20819 (list r-knitr)) ; for vignettes
20820 (home-page "https://github.com/r-lib/lifecycle")
20821 (synopsis "Manage the life cycle of your package functions")
20823 "Manage the life cycle of your exported functions with shared
20824 conventions, documentation badges, and non-invasive deprecation warnings. The
20825 lifecycle package defines four development stages (experimental, maturing,
20826 stable, and questioning) and three deprecation stages (soft-deprecated,
20827 deprecated, and defunct). It makes it easy to insert badges corresponding to
20828 these stages in your documentation. Usage of deprecated functions are
20829 signalled with increasing levels of non-invasive verbosity.")
20830 (license license:gpl3)))
20832 (define-public r-assertable
20834 (name "r-assertable")
20839 (uri (cran-uri "assertable" version))
20842 "1cciil1nzxd8gbj49w99jiv077lbpb59vx7bmb4p218aj2h5hqq4"))))
20843 (build-system r-build-system)
20845 (list r-data-table))
20848 (home-page "https://cran.r-project.org/web/packages/assertable/")
20849 (synopsis "Verbose assertions for tabular data (data.frames and data.tables)")
20850 (description "This package provides simple, flexible assertions on
20851 data.frame or data.table objects with verbose output for vetting. While other
20852 assertion packages apply towards more general use-cases, @code{assertable} is
20853 tailored towards tabular data. It includes functions to check variable names
20854 and values, whether the dataset contains all combinations of a given set of
20855 unique identifiers, and whether it is a certain length. In addition,
20856 @code{assertable} includes utility functions to check the existence of target
20857 files and to efficiently import multiple tabular data files into one
20859 (license license:gpl3)))
20861 (define-public r-quadprog
20863 (name "r-quadprog")
20868 (uri (cran-uri "quadprog" version))
20870 (base32 "1ka9g8zak8sg4y2xbz93dfrldznlk9qpd4pq9z21cdcdn3b8s4i2"))))
20871 (build-system r-build-system)
20874 (home-page "https://cran.r-project.org/web/packages/quadprog")
20875 (synopsis "Functions to solve quadratic programming problems")
20877 "This package contains routines and documentation for solving quadratic
20878 programming problems.")
20879 (license license:gpl3+)))
20881 (define-public r-desolve
20888 (uri (cran-uri "deSolve" version))
20890 (base32 "06gsh514msqdmri78969snhgh22d2bzmnkqfgh0s74aprfd93m8r"))))
20891 (properties `((upstream-name . "deSolve")))
20892 (build-system r-build-system)
20895 (home-page "https://desolve.r-forge.r-project.org/")
20896 (synopsis "Solvers for initial value problems of differential equations")
20897 (description "This package provides functions that solve initial value
20898 problems of a system of first-order @dfn{ordinary differential
20899 equations} (ODE), of @dfn{partial differential equations} (PDE), of
20900 @dfn{differential algebraic equations} (DAE), and of delay differential
20901 equations. The functions provide an interface to the FORTRAN functions
20902 @code{lsoda}, @code{lsodar}, @code{lsode}, @code{lsodes} of the ODEPACK
20903 collection, to the FORTRAN functions @code{dvode} and @code{daspk} and a
20904 C-implementation of solvers of the Runge-Kutta family with fixed or variable
20905 time steps. The package contains routines designed for solving ODEs resulting
20906 from 1-D, 2-D and 3-D partial differential equations that have been converted
20907 to ODEs by numerical differencing.")
20908 (license license:gpl2+)))
20910 (define-public r-pmcmrplus
20912 (name "r-pmcmrplus")
20917 (uri (cran-uri "PMCMRplus" version))
20919 (base32 "16m1pdrzjq9vnx5v7zv56mz9r1205rkw92883cxaqbvdpds6dhqy"))))
20920 (properties `((upstream-name . "PMCMRplus")))
20921 (build-system r-build-system)
20922 (inputs (list gmp))
20932 (native-inputs (list gfortran r-knitr))
20933 (home-page "https://cran.r-project.org/package=PMCMRplus")
20934 (synopsis "Calculate pairwise multiple comparisons of mean rank sums extended")
20936 "This package provides multiple pairwise tests.")
20937 (license license:gpl3+)))
20939 (define-public r-pracma
20945 (uri (cran-uri "pracma" version))
20947 (base32 "0r17siivm37k4gp253v9mlg5m7cwqp85h9kk2hbp2wkf81ad80i3"))))
20948 (build-system r-build-system)
20949 (home-page "https://cran.r-project.org/web/packages/pracma/")
20950 (synopsis "Practical numerical math functions")
20951 (description "This package provides functions for numerical analysis and
20952 linear algebra, numerical optimization, differential equations, plus some
20953 special functions. It uses Matlab function names where appropriate to simplify
20955 (license license:gpl3+)))
20957 (define-public r-subplex
20964 (uri (cran-uri "subplex" version))
20967 "11zqzydbj6ivgvlw1gv1r2yxra7misbc622g575p2vckhjjg9v6m"))))
20968 (build-system r-build-system)
20971 (home-page "https://cran.r-project.org/web/packages/subplex")
20972 (synopsis "Unconstrained optimization using the subplex algorithm")
20974 "This package implements the Subplex optimization algorithm.
20975 It solves unconstrained optimization problems using a simplex method on
20976 subspaces. The method is well suited for optimizing objective functions that
20977 are noisy or are discontinuous at the solution.")
20978 (license license:gpl3+)))
20980 (define-public r-txtplot
20987 (uri (cran-uri "txtplot" version))
20990 "00sriml48y70j18jz235dsfm5x3a81bnzskfp3hnv6cbjwwsmca4"))))
20991 (build-system r-build-system)
20992 (home-page "https://cran.r-project.org/web/packages/txtplot/")
20993 (synopsis "Text-based plotting")
20994 (description "This package provides functions to produce rudimentary ASCII
20995 graphics directly in the terminal window. This package provides a basic
20996 plotting function (and equivalents of curve, density, acf and barplot) as well
20997 as a boxplot function.")
20998 (license license:lgpl3+)))
21000 (define-public r-bio3d
21007 (uri (cran-uri "bio3d" version))
21010 "0x3apqxbk4lvvcnvvdsyjd9f6qh9f9qgml3ih69hl9ikj06iy0y6"))))
21011 (properties `((upstream-name . "bio3d")))
21012 (build-system r-build-system)
21013 (inputs (list zlib))
21014 (propagated-inputs (list r-rcpp))
21017 (home-page "http://thegrantlab.org/bio3d/")
21018 (synopsis "Biological structure analysis")
21020 "This package provides utilities to process, organize and explore protein
21021 structure, sequence and dynamics data. Features include the ability to read
21022 and write structure, sequence and dynamic trajectory data, perform sequence
21023 and structure database searches, data summaries, atom selection, alignment,
21024 superposition, rigid core identification, clustering, torsion analysis,
21025 distance matrix analysis, structure and sequence conservation analysis, normal
21026 mode analysis, principal component analysis of heterogeneous structure data,
21027 and correlation network analysis from normal mode and molecular dynamics data.
21028 In addition, various utility functions are provided to enable the statistical
21029 and graphical power of the R environment to work with biological sequence and
21031 (license license:gpl2+)))
21033 (define-public r-bios2cor
21035 (name "r-bios2cor")
21040 (uri (cran-uri "Bios2cor" version))
21043 "1wkj9vr33m9jilidil9jpw5rzr3pf7gkimxdvch22ks4bgkx7l1w"))))
21044 (properties `((upstream-name . "Bios2cor")))
21045 (build-system r-build-system)
21047 (list r-bigmemory r-bio3d r-circular r-igraph))
21048 (home-page "https://cran.r-project.org/web/packages/Bios2cor/")
21049 (synopsis "From biological sequences and simulations to correlation analysis")
21051 "This package provides utilities for computation and analysis of
21052 correlation/covariation in multiple sequence alignments and in side chain
21053 motions during molecular dynamics simulations. Features include the
21054 computation of correlation/covariation scores using a variety of scoring
21055 functions between either sequence positions in alignments or side chain
21056 dihedral angles in molecular dynamics simulations and utilities to analyze the
21057 correlation/covariation matrix through a variety of tools including network
21058 representation and principal components analysis. In addition, several
21059 utility functions are based on the R graphical environment to provide friendly
21060 tools for help in data interpretation.")
21061 (license license:gpl2+)))
21063 ;; This package includes minified JavaScript files. When upgrading please
21064 ;; check that there are no new minified JavaScript files.
21065 (define-public r-networkd3
21067 (name "r-networkd3")
21072 (uri (cran-uri "networkD3" version))
21075 "02wxki67drppgfka1is1ykg1f2rxf0x0657c0crj7ipfy62jbf1k"))
21078 (delete-file "inst/htmlwidgets/lib/d3-4.5.0/d3.min.js")
21080 (properties `((upstream-name . "networkD3")))
21081 (build-system r-build-system)
21083 `(#:modules ((guix build utils)
21084 (guix build r-build-system)
21088 (modify-phases %standard-phases
21089 (add-after 'unpack 'process-javascript
21090 (lambda* (#:key inputs #:allow-other-keys)
21091 (with-directory-excursion "inst/htmlwidgets/lib/"
21095 `((,(assoc-ref inputs "d3.v4.js")
21096 "d3-4.5.0/d3.min.js"))))
21097 (lambda (sources targets)
21098 (for-each (lambda (source target)
21099 (format #t "Processing ~a --> ~a~%"
21101 (let ((minified (open-pipe* OPEN_READ "uglifyjs" source)))
21102 (call-with-output-file target
21104 (dump-port minified port)))))
21105 sources targets))))
21108 `(("uglifyjs" ,node-uglify-js)
21109 ;; NOTE: Make sure that this version of d3 is still valid when
21110 ;; upgrading the package.
21114 (uri "https://d3js.org/d3.v4.js")
21117 "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg"))))))
21119 (list r-htmlwidgets r-igraph r-magrittr))
21120 (home-page "https://cran.r-project.org/package=networkD3")
21121 (synopsis "D3 JavaScript network graphs from R")
21123 "This package creates D3 JavaScript network, tree, dendrogram, and Sankey
21125 (license license:gpl3+)))
21127 (define-public r-aasea
21134 (uri (cran-uri "aaSEA" version))
21137 "0him4r8qyp0xssgrmdxjs45yn4d28h5anv4jyxxbbs9phb0m6j3h"))))
21138 (properties `((upstream-name . "aaSEA")))
21139 (build-system r-build-system)
21150 (home-page "https://cran.r-project.org/web/packages/aaSEA/")
21151 (synopsis "Amino acid substitution effect analyzer")
21153 "Given a protein multiple sequence alignment, it is a daunting task to
21154 assess the effects of substitutions along sequence length. The aaSEA package
21155 is intended to help researchers to rapidly analyze property changes caused by
21156 single, multiple and correlated amino acid substitutions in proteins.")
21157 (license license:gpl3)))
21159 (define-public r-abacus
21166 (uri (cran-uri "ABACUS" version))
21169 "0m1dnkwjr1522l9ddbzzx7ayxvli17sbmk6s28adpmzzjwh2kd1i"))))
21170 (properties `((upstream-name . "ABACUS")))
21171 (build-system r-build-system)
21173 (list r-ggplot2 r-shiny))
21174 (home-page "https://shiny.abdn.ac.uk/Stats/apps/")
21175 (synopsis "Apps-based activities for communicating and understanding statistics")
21177 "This package provides a set of Shiny apps for effective communication
21178 and understanding in statistics. The current version includes properties of
21179 normal distribution, properties of sampling distribution, one-sample z and t
21180 tests, two samples independent (unpaired) t test and analysis of variance.")
21181 (license license:gpl3)))
21183 (define-public r-abc-rap
21190 (uri (cran-uri "ABC.RAP" version))
21193 "1kdspln17v0krvahcd55vib4dv5azp60b3r1zf489x10qqbp1mxk"))))
21194 (properties `((upstream-name . "ABC.RAP")))
21195 (build-system r-build-system)
21196 (home-page "https://cran.r-project.org/web/packages/ABC.RAP/")
21197 (synopsis "Array-based CpG region analysis pipeline")
21199 "This package aims to identify candidate genes that are differentially
21200 methylated between cases and controls. It applies Student's t-test and delta
21201 beta analysis to identify candidate genes containing multiple CpG sites.")
21202 (license license:gpl3)))
21204 (define-public r-abcadm
21211 (uri (cran-uri "abcADM" version))
21214 "0vcabnnnwc0psv9v3rda5aap9s8cq1pjh02zva3ki64hlavf2a10"))))
21215 (properties `((upstream-name . "abcADM")))
21216 (build-system r-build-system)
21218 (list r-bh r-rcpp))
21219 (home-page "https://cran.r-project.org/web/packages/abcADM/")
21220 (synopsis "Fit accumulated damage models and estimate reliability using ABC")
21222 "This package provides tools to estimate parameters of accumulated
21223 damage (load duration) models based on failure time data under a Bayesian
21224 framework, using @dfn{Approximate Bayesian Computation} (ABC), and to assess
21225 long-term reliability under stochastic load profiles.")
21226 (license license:gpl3)))
21228 (define-public r-rglpk
21235 (uri (cran-uri "Rglpk" version))
21238 "19mzpyimzq9zqnbi05j79b2di3nzaln8swggs9p8sqdr60qvr3d2"))))
21239 (properties `((upstream-name . "Rglpk")))
21240 (build-system r-build-system)
21245 (home-page "https://r-forge.r-project.org/projects/rglp/")
21246 (synopsis "R interface to the GNU Linear Programming Kit")
21248 "This package provides an R interface to the GNU Linear Programming Kit,
21249 software for solving large-scale @dfn{linear programming} (LP), @dfn{mixed
21250 integer linear programming} (MILP) and other related problems.")
21252 (license (list license:gpl2 license:gpl3))))
21254 (define-public r-abcdefba
21256 (name "r-abcdefba")
21261 (uri (cran-uri "abcdeFBA" version))
21264 "1rxjripy8v6bxi25vdfjnbk24zkmf752qbl73cin6nvnqflwxkx4"))))
21265 (properties `((upstream-name . "abcdeFBA")))
21266 (build-system r-build-system)
21268 (list r-corrplot r-lattice r-rgl r-rglpk))
21269 (home-page "https://cran.r-project.org/web/packages/abcdeFBA/")
21270 (synopsis "A-Biologist-Can-Do-Everything of Flux Balance Analysis with this package")
21272 "This package provides functions for Constraint Based Simulation using
21273 Flux Balance Analysis and informative analysis of the data generated during
21275 (license license:gpl2)))
21277 (define-public r-abcrlda
21284 (uri (cran-uri "abcrlda" version))
21287 "04pcdnk2szfpc2ylcw5ds7y895ivy03bycal03kxw7cwylzxasks"))))
21288 (properties `((upstream-name . "abcrlda")))
21289 (build-system r-build-system)
21290 (home-page "https://ieeexplore.ieee.org/document/8720003/")
21291 (synopsis "Asymptotically bias-corrected regularized linear discriminant analysis")
21293 "This package offers methods to perform @dfn{asymptotically
21294 bias-corrected regularized linear discriminant analysis} (ABC_RLDA) for
21295 cost-sensitive binary classification. The bias-correction is an estimate of
21296 the bias term added to regularized discriminant analysis that minimizes the
21298 (license license:gpl3)))
21300 (define-public r-abemus
21307 (uri (cran-uri "abemus" version))
21310 "1dhllb184byp1yl15rg2w02zgw3iajag7cxshirg47mnmm7n70bb"))))
21311 (properties `((upstream-name . "abemus")))
21312 (build-system r-build-system)
21314 (list r-data-table))
21315 (home-page "https://cran.r-project.org/web/packages/abemus/")
21316 (synopsis "Adaptive base error model in ultra-deep sequencing data")
21318 "This package provides an implementation of @dfn{Adaptive Base Error
21319 Model in Ultra-deep Sequencing data} (ABEMUS), which combines
21320 platform-specific genetic knowledge and empirical signal to readily detect and
21321 quantify somatic @dfn{single nucleotide variants} (SNVs) in @dfn{circulating
21322 cell free DNA} (cfDNA).")
21323 (license license:gpl3)))
21325 ;; This package includes minified JavaScript files. When upgrading please
21326 ;; check that there are no new minified JavaScript files.
21327 (define-public r-rintrojs
21329 (name "r-rintrojs")
21334 (uri (cran-uri "rintrojs" version))
21337 "00l5mk80gj3xkbf3m1kip566ic98bhd88lh0bg69ybkpk4gifpyw"))
21339 '(delete-file "inst/javascript/introjs/intro.min.js"))))
21340 (properties `((upstream-name . "rintrojs")))
21341 (build-system r-build-system)
21344 (modify-phases %standard-phases
21345 (add-after 'unpack 'process-javascript
21346 (lambda* (#:key inputs #:allow-other-keys)
21347 (with-directory-excursion "inst/javascript/introjs/"
21348 (let ((source (assoc-ref inputs "intro.js"))
21349 (target "intro.min.js"))
21350 (format #true "Processing ~a --> ~a~%"
21352 (invoke "esbuild" source "--minify"
21353 (string-append "--outfile=" target)))))))))
21355 `(("esbuild" ,esbuild)
21359 (uri "https://cdn.jsdelivr.net/npm/intro.js@3.2.1/intro.js")
21362 "0vh5n7hqqyx2pdvlqq6xadfqibcn78h5961rwhpf817kpxfzv8v7"))))))
21364 (list r-jsonlite r-shiny))
21365 (home-page "https://github.com/carlganz/rintrojs")
21366 (synopsis "Wrapper for the Intro.js library")
21368 "This package provides a wrapper for the @url{http://www.introjs.com,
21369 Intro.js} library. This package makes it easy to include step-by-step
21370 introductions, and clickable hints in a Shiny application. It supports both
21371 static introductions in the UI, and programmatic introductions from the
21373 ;; The intro.js library is licensed under Expat.
21374 (license (list license:agpl3+ license:expat))))
21376 (define-public r-sysfonts
21378 (name "r-sysfonts")
21383 (uri (cran-uri "sysfonts" version))
21386 "1fq5dn4l09sgrbznfz9cakf4vgc3761zwicvqaazh0s8mzbaicpn"))))
21387 (properties `((upstream-name . "sysfonts")))
21388 (build-system r-build-system)
21390 (list freetype libpng zlib))
21393 (home-page "https://github.com/yixuan/sysfonts")
21394 (synopsis "Loading fonts into R")
21396 "This is a package to simplify loading of system fonts and Google Fonts
21397 into R, in order to support other packages.")
21398 (license license:gpl2)))
21400 (define-public r-showtextdb
21402 (name "r-showtextdb")
21407 (uri (cran-uri "showtextdb" version))
21410 "0hlnc3fhgrdkd46n7hb6id0gg1v0bf8s4679nrr7rchyp455szq2"))))
21411 (properties `((upstream-name . "showtextdb")))
21412 (build-system r-build-system)
21415 (home-page "https://cran.r-project.org/web/packages/showtextdb/")
21416 (synopsis "Font files for the 'showtext' package")
21418 "This package provides font files that can be used by the @code{showtext}
21420 (license license:asl2.0)))
21422 (define-public r-showtext
21424 (name "r-showtext")
21429 (uri (cran-uri "showtext" version))
21432 "1larnqxn9nanbqiadm35ah5hh89xrzm4fdj9pfc93zzzhlfrvhb3"))))
21433 (properties `((upstream-name . "showtext")))
21434 (build-system r-build-system)
21436 (list freetype libpng zlib))
21438 (list r-showtextdb r-sysfonts))
21440 (list pkg-config r-knitr))
21441 (home-page "https://github.com/yixuan/showtext")
21442 (synopsis "Using fonts more easily in R graphs")
21444 "This package aims to make it easy to use various types of
21445 fonts (TrueType, OpenType, Type 1, web fonts, etc.) in R graphs, and supports
21446 most output formats of R graphics including PNG, PDF and SVG. Text glyphs
21447 will be converted into polygons or raster images, hence after the plot has
21448 been created, it no longer relies on the font files. No external software
21449 such as Ghostscript is needed to use this package.")
21450 (license license:asl2.0)))
21452 (define-public r-emojifont
21454 (name "r-emojifont")
21459 (uri (cran-uri "emojifont" version))
21462 "1hhrwilv36hd9gs1kcl2zsi6519md0h9aixjrm6lfclxvz8r6k1i"))))
21463 (properties `((upstream-name . "emojifont")))
21464 (build-system r-build-system)
21466 (list r-ggplot2 r-proto r-showtext r-sysfonts))
21469 (home-page "https://guangchuangyu.github.io/emojifont")
21470 (synopsis "Emoji and Font Awesome in R graphics")
21472 "This package enables the use of emoji and the Font Awesome glyphs in
21473 both base and ggplot2 graphics.")
21474 (license license:artistic2.0)))
21476 (define-public r-abstractr
21478 (name "r-abstractr")
21483 (uri (cran-uri "abstractr" version))
21486 "1ymwp7syrynwd4i8aj2x5n8jdi9d96fjzl6jb09n0bnr5fgl7vig"))))
21487 (properties `((upstream-name . "abstractr")))
21488 (build-system r-build-system)
21490 (list r-colourpicker
21497 (home-page "https://matt-kumar.shinyapps.io/portfolio")
21498 (synopsis "R-Shiny application for creating visual abstracts")
21500 "This package provides an R Shiny application to create visual abstracts
21501 for original research. A variety of user defined options and formatting are
21503 (license license:gpl3)))
21505 (define-public r-qgam
21512 (uri (cran-uri "qgam" version))
21515 "1jyamamdffaks89rspyhmg18b4iik0nb1j0vgqzvfnm890514cvn"))))
21516 (properties `((upstream-name . "qgam")))
21517 (build-system r-build-system)
21519 (list r-doparallel r-mgcv r-plyr r-shiny))
21520 (native-inputs (list r-knitr))
21521 (home-page "https://cran.r-project.org/web/packages/qgam/")
21522 (synopsis "Smooth additive quantile regression models")
21524 "This package provides smooth additive quantile regression models, fitted
21525 using the methods of Fasiolo et al. (2017). Differently from @code{quantreg},
21526 the smoothing parameters are estimated automatically by marginal loss
21527 minimization, while the regression coefficients are estimated using either
21528 PIRLS or Newton algorithm. The learning rate is determined so that the
21529 Bayesian credible intervals of the estimated effects have approximately the
21530 correct coverage. The main function is @code{qgam()} which is similar to
21531 @code{gam()} in the @code{mgcv} package, but fits non-parametric quantile
21532 regression models.")
21533 (license license:gpl2+)))
21535 (define-public r-abtest
21542 (uri (cran-uri "abtest" version))
21545 "0jz2ry5364p8h8xlk5a5sycn8xlpxd1iasfg99bcr4jqzd92jfqg"))))
21546 (properties `((upstream-name . "abtest")))
21547 (build-system r-build-system)
21557 (home-page "https://cran.r-project.org/web/packages/abtest/")
21558 (synopsis "Bayesian A/B testing")
21560 "This package provides functions for Bayesian A/B testing including prior
21561 elicitation options based on Kass and Vaidyanathan (1992)
21562 @url{doi:10.1111/j.2517-6161.1992.tb01868.x}.")
21563 (license license:gpl2+)))
21565 (define-public r-reldist
21572 (uri (cran-uri "reldist" version))
21575 "0i04d6w3r6fzm4bykz6lnnh6dngmd61v5wlpli70r3fzdzhi7fji"))))
21576 (properties `((upstream-name . "reldist")))
21577 (build-system r-build-system)
21579 (list r-densestbayes r-hmisc r-mgcv))
21580 (home-page "http://www.stat.ucla.edu/~handcock/RelDist")
21581 (synopsis "Relative distribution methods")
21583 "This package provides tools for the comparison of distributions. This
21584 includes nonparametric estimation of the relative distribution PDF and CDF and
21585 numerical summaries as described in \"Relative Distribution Methods in the
21586 Social Sciences\" by Mark S. Handcock and Martina Morris, Springer-Verlag,
21587 1999, Springer-Verlag, ISBN 0387987789.")
21588 ;; See also https://cran.r-project.org/web/packages/reldist/LICENSE for
21589 ;; attribution requirements.
21590 (license license:gpl3)))
21592 (define-public r-accept
21599 (uri (cran-uri "accept" version))
21602 "13kx8fbnbpasjklgbq2rf4n73j2s8rvy5v77ywqhfzln24937qgh"))))
21603 (properties `((upstream-name . "accept")))
21604 (build-system r-build-system)
21606 (list r-dplyr r-reldist))
21607 (home-page "https://cran.r-project.org/web/packages/accept/")
21608 (synopsis "Acute COPD Exacerbation Prediction Tool (ACCEPT)")
21610 "This package allows clinicians to predict the rate and severity of
21611 future acute exacerbation in @dfn{Chronic Obstructive Pulmonary
21612 Disease} (COPD) patients, based on the clinical prediction model published in
21613 Adibi et al. (2019) @url{doi:10.1101/651901}.")
21614 (license license:gpl3)))
21616 (define-public r-smpracticals
21618 (name "r-smpracticals")
21623 (uri (cran-uri "SMPracticals" version))
21626 "0zxq84f9i3b86xx6msb25b61gyj9k09iab2b7wg4d93yas9qzayf"))))
21627 (properties `((upstream-name . "SMPracticals")))
21628 (build-system r-build-system)
21630 (list r-ellipse r-mass r-nlme r-survival))
21631 (home-page "http://statwww.epfl.ch/davison/SM/")
21632 (synopsis "Practicals for use with Davison (2003) Statistical Models")
21634 "This package contains the datasets and a few functions for use with the
21635 practicals outlined in Appendix A of the book Statistical Models (Davison,
21636 2003, Cambridge University Press). The practicals themselves can be found at
21637 @url{http://statwww.epfl.ch/davison/SM/}.")
21638 (license license:gpl2+)))
21640 (define-public r-fgui
21647 (uri (cran-uri "fgui" version))
21650 "024fzd1c7iwqprn26hwjb9l2qlvvyzl449d7iixy0x69djwsrysv"))))
21651 (properties `((upstream-name . "fgui")))
21652 (build-system r-build-system)
21654 "https://sites.google.com/site/thomashoffmannproject/software/fgui")
21655 (synopsis "Create GUI for R functions")
21657 "Rapidly create a GUI for a function you created by automatically
21658 creating widgets for arguments of the function. This package automatically
21659 parses help routines for context-sensitive help to these arguments. The
21660 interface is essentially a wrapper to some Tcl/Tk routines to both simplify
21661 and facilitate GUI creation. More advanced Tcl/Tk routines/GUI objects can be
21662 incorporated into the interface for greater customization for the more
21664 ;; Any version of the GPL.
21665 (license (list license:gpl2+ license:gpl3+))))
21667 (define-public r-tcltk2
21674 (uri (cran-uri "tcltk2" version))
21677 "1ibxld379600xx7kiqq3fck083s8psry12859980218rnzikl65d"))))
21678 (properties `((upstream-name . "tcltk2")))
21679 (build-system r-build-system)
21682 (home-page "https://www.sciviews.org/SciViews-R")
21683 (synopsis "Tcl/Tk additions")
21685 "This package provides a series of additional Tcl commands and Tk widgets
21686 with style and various functions to supplement the tcltk package")
21687 (license license:lgpl3)))
21689 (define-public r-accrual
21696 (uri (cran-uri "accrual" version))
21699 "11clm9s5c5518nmp6hd6pjnp0s28y92b2i2x0xgj4j5g816p4j3z"))))
21700 (properties `((upstream-name . "accrual")))
21701 (build-system r-build-system)
21703 (list r-fgui r-smpracticals r-tcltk2))
21704 (home-page "https://cran.r-project.org/web/packages/accrual/")
21705 (synopsis "Bayesian accrual prediction")
21707 "Subject recruitment for medical research is challenging. Slow patient
21708 accrual leads to delay in research. Accrual monitoring during the process of
21709 recruitment is critical. Researchers need reliable tools to manage the
21710 accrual rate. This package provides an implementation of a Bayesian method
21711 that integrates researcher's experience on previous trials and data from the
21712 current study, providing reliable prediction on accrual rate for clinical
21713 studies. It provides functions for Bayesian accrual prediction which can be
21714 easily used by statisticians and clinical researchers.")
21715 (license license:gpl2)))
21717 (define-public r-accrued
21724 (uri (cran-uri "accrued" version))
21727 "05g1jb5914z18rcai1ahn7nihn27vr2rnadwv94gc1j7ivvikvs5"))))
21728 (properties `((upstream-name . "accrued")))
21729 (build-system r-build-system)
21730 (home-page "https://cran.r-project.org/web/packages/accrued/")
21731 (synopsis "Data quality visualization tools for partially accruing data")
21733 "This is a package for visualizing data quality of partially accruing
21735 (license license:gpl3)))
21737 (define-public r-mda
21744 (uri (cran-uri "mda" version))
21747 "1hq0zhhz9klmp4zcr1w8hyn7s1h9kfg57d2l2mfm7psx459j0krl"))))
21748 (properties `((upstream-name . "mda")))
21749 (build-system r-build-system)
21750 (propagated-inputs (list r-class))
21751 (native-inputs (list gfortran))
21752 (home-page "https://cran.r-project.org/web/packages/mda/")
21753 (synopsis "Mixture and flexible discriminant analysis")
21755 "This is a package for mixture and flexible discriminant analysis,
21756 @dfn{multivariate adaptive regression splines} (MARS), BRUTO, and so on.")
21757 (license license:gpl2)))
21759 (define-public r-elasticnet
21761 (name "r-elasticnet")
21766 (uri (cran-uri "elasticnet" version))
21769 "0nxcw06d0cp2mbqzg2fm9yys5xm6xx7bfcfvr0avcs8afkvz29j8"))))
21770 (properties `((upstream-name . "elasticnet")))
21771 (build-system r-build-system)
21774 (home-page "http://users.stat.umn.edu/~zouxx019/")
21775 (synopsis "Elastic-Net for sparse estimation and sparse PCA")
21777 "This package provides functions for fitting the entire solution path of
21778 the Elastic-Net and also provides functions for estimating sparse Principal
21779 Components. The Lasso solution paths can be computed by the same function.")
21780 (license license:gpl2+)))
21782 (define-public r-sparselda
21784 (name "r-sparselda")
21789 (uri (cran-uri "sparseLDA" version))
21792 "1k3sw9kc40yxnfss4vrsx34qxmv8ssddyhbfjhxrdldvblhbwchb"))))
21793 (properties `((upstream-name . "sparseLDA")))
21794 (build-system r-build-system)
21796 (list r-elasticnet r-mass r-mda))
21797 (home-page "https://www.imm.dtu.dk/~lkhc/")
21798 (synopsis "Sparse discriminant analysis")
21800 "This package performs sparse linear discriminant analysis for Gaussians
21801 and mixture of Gaussian models.")
21802 (license license:gpl2+)))
21804 (define-public r-accsda
21811 (uri (cran-uri "accSDA" version))
21814 "104xdz63mnibh6827xm0pfr9zbhbi2a7iw4m1x27xjqi7zqvbky6"))))
21815 (properties `((upstream-name . "accSDA")))
21816 (build-system r-build-system)
21822 (home-page "https://github.com/gumeo/accSDA/wiki")
21823 (synopsis "Accelerated sparse discriminant analysis")
21825 "This package provides an implementation of sparse linear discriminant
21826 analysis, which is a supervised classification method for multiple classes.
21827 Various novel optimization approaches to this problem are implemented
21828 including @dfn{alternating direction method of multipliers} (ADMM),
21829 @dfn{proximal gradient} (PG) and @dfn{accelerated proximal gradient} (APG).
21830 Functions for performing cross validation are also supplied along with basic
21831 prediction and plotting functions. @dfn{Sparse zero variance
21832 discriminant} (SZVD) analysis is also included in the package.")
21833 (license license:gpl2+)))
21835 (define-public r-ace2fastq
21837 (name "r-ace2fastq")
21842 (uri (cran-uri "ace2fastq" version))
21845 "09kk3yyqnr2xp820g0p3aai9a21figigjr9lxkr3zjq2d8gzwfic"))))
21846 (properties `((upstream-name . "ace2fastq")))
21847 (build-system r-build-system)
21850 (home-page "https://github.com/c5sire/ace2fastq")
21851 (synopsis "ACE file to FASTQ converter")
21853 "The ACE file format is used in genomics to store contigs from sequencing
21854 machines. This tools converts it into FASTQ format. Both formats contain the
21855 sequence characters and their corresponding quality information. Unlike the
21856 FASTQ file, the ACE file stores the quality values numerically. The
21857 conversion algorithm uses the standard Sanger formula. The package
21858 facilitates insertion into pipelines, and content inspection.")
21859 (license license:gpl3)))
21861 (define-public r-rngwell
21868 (uri (cran-uri "rngWELL" version))
21871 "0f1dxxaimfb0fww8ym9ciqf6q760ai46wxldl37m5mfpd57ca00c"))))
21872 (properties `((upstream-name . "rngWELL")))
21873 (build-system r-build-system)
21874 (home-page "https://cran.r-project.org/web/packages/rngWELL/")
21875 (synopsis "Toolbox for WELL random number generators")
21877 "This is a dedicated package to WELL pseudo random generators, which were
21878 introduced in Panneton et al. (2006), ``Improved Long-Period Generators Based
21879 on Linear Recurrences Modulo 2'', ACM Transactions on Mathematical Software.")
21880 (license license:bsd-3)))
21882 (define-public r-rnmf
21888 (uri (cran-uri "rNMF" version))
21891 "1nz6h0j5ywdh48m0swmhp34hbkycd7n13rclrxaw85qi9wc42597"))))
21892 (build-system r-build-system)
21894 (list r-knitr r-nnls))
21895 (home-page "https://cran.r-project.org/web/packages/rNMF/")
21896 (synopsis "Robust nonnegative matrix factorization")
21898 "This package provides an implementation of robust nonnegative matrix
21899 factorization (rNMF). The rNMF algorithm decomposes a nonnegative high
21900 dimension data matrix into the product of two low rank nonnegative matrices,
21901 while detecting and trimming outliers. The main function is @code{rnmf()}.
21902 The package also includes a visualization tool, @code{see()}, that arranges
21903 and prints vectorized images.")
21904 (license license:gpl2+)))
21906 (define-public r-randtoolbox
21908 (name "r-randtoolbox")
21913 (uri (cran-uri "randtoolbox" version))
21916 "1b9vjzqg014hxp1vfb62m01d7xim5vmpbyxzlbll49bqas0jx69h"))))
21917 (properties `((upstream-name . "randtoolbox")))
21918 (build-system r-build-system)
21923 (home-page "https://cran.r-project.org/web/packages/randtoolbox/")
21924 (synopsis "Toolbox for pseudo and quasi random number generation")
21926 "This package provides
21929 @item pseudo random generators, such as general linear
21930 congruential generators, multiple recursive generators and generalized
21931 feedback shift register (SF-Mersenne Twister algorithm and WELL
21934 @item quasi random generators, such as the Torus algorithm, the Sobol
21935 sequence, the Halton sequence (including the Van der Corput sequence), and
21937 @item some generator tests: the gap test, the serial test, the poker test.
21940 See e.g. Gentle (2003) @url{doi:10.1007/b97336}.")
21941 (license license:bsd-3)))
21943 (define-public r-lhs
21950 (uri (cran-uri "lhs" version))
21953 "0fb3bc3s5pbwg92qkjbg7v8ah36wm6qs05vf098hwjakr7f6yg3s"))))
21954 (properties `((upstream-name . "lhs")))
21955 (build-system r-build-system)
21956 (propagated-inputs (list r-rcpp))
21959 (home-page "https://github.com/bertcarnell/lhs")
21960 (synopsis "Latin Hypercube Samples")
21962 "This package provides a number of methods for creating and augmenting
21963 Latin Hypercube Samples.")
21964 (license license:gpl3)))
21966 (define-public r-acebayes
21968 (name "r-acebayes")
21973 (uri (cran-uri "acebayes" version))
21976 "11bffz430gdfdaxjx3simig66vhynmx6l1ylac4q2shcmj52nx73"))))
21977 (properties `((upstream-name . "acebayes")))
21978 (build-system r-build-system)
21980 (list r-compare r-lhs r-randtoolbox r-rcpp r-rcpparmadillo))
21981 (home-page "https://cran.r-project.org/web/packages/acebayes/")
21982 (synopsis "Optimal Bayesian experimental design using the ACE algorithm")
21984 "Finding an optimal Bayesian experimental design involves maximizing an
21985 objective function given by the expectation of some appropriately chosen
21986 utility function with respect to the joint distribution of unknown
21987 quantities (including responses). This objective function is usually not
21988 available in closed form and the design space can be continuous and of high
21989 dimensionality. This package uses @dfn{Approximate Coordinate Exchange} (ACE)
21990 to maximise an approximation to the expectation of the utility function.")
21991 (license license:gpl2)))
21993 (define-public r-acet
22000 (uri (cran-uri "ACEt" version))
22003 "0b5lfpnppyk0237phr2aybhx29nhm8ngwk2qa1y4lshrvsw97wg4"))))
22004 (properties `((upstream-name . "ACEt")))
22005 (build-system r-build-system)
22007 (list r-bh r-mass r-rcpp r-rcpparmadillo))
22008 (home-page "https://cran.r-project.org/web/packages/ACEt/")
22009 (synopsis "Estimating dynamic heritability and twin model comparison")
22011 "This package supports twin models that are able to estimate the dynamic
22012 behaviour of the variance components in the classical twin models with respect
22013 to age using B-splines and P-splines.")
22014 (license license:gpl2+)))
22016 (define-public r-acfmperiod
22018 (name "r-acfmperiod")
22023 (uri (cran-uri "acfMPeriod" version))
22026 "1yww8isfrbs2v9s94hx7p2imyszcgadwafdgpj438n2ik0q6p9d5"))))
22027 (properties `((upstream-name . "acfMPeriod")))
22028 (build-system r-build-system)
22031 (home-page "https://cran.r-project.org/web/packages/acfMPeriod/")
22032 (synopsis "Estimation of the ACF from the M-periodogram")
22034 "This package support non-robust and robust computations of the sample
22035 autocovariance (ACOVF) and sample autocorrelation functions (ACF) of
22036 univariate and multivariate processes. The methodology consists in reversing
22037 the diagonalization procedure involving the periodogram or the
22038 cross-periodogram and the Fourier transform vectors, and, thus, obtaining the
22039 ACOVF or the ACF as discussed in Fuller (1995)
22040 @url{doi:10.1002/9780470316917}. The robust version is obtained by fitting
22041 robust M-regressors to obtain the M-periodogram or M-cross-periodogram as
22042 discussed in Reisen et al. (2017) @url{doi:10.1016/j.jspi.2017.02.008}.")
22043 (license license:gpl2+)))
22045 (define-public r-gamlss-data
22047 (name "r-gamlss-data")
22052 (uri (cran-uri "gamlss.data" version))
22055 "07mpdl4h9rwmnpl9jmsn6ig8ji11an6pyjfsvg62h2alapwbdcyv"))))
22056 (properties `((upstream-name . "gamlss.data")))
22057 (build-system r-build-system)
22058 (home-page "http://www.gamlss.org/")
22059 (synopsis "GAMLSS data")
22061 "This package provides data used as examples to demonstrate GAMLSS
22063 ;; Either version of the license
22064 (license (list license:gpl2 license:gpl3))))
22066 (define-public r-gamlss
22073 (uri (cran-uri "gamlss" version))
22076 "0fp9bmgykpqd950bk58dk423iy5r1fm3dy2gw0cwwmgivpq2lx0q"))))
22077 (properties `((upstream-name . "gamlss")))
22078 (build-system r-build-system)
22080 (list r-gamlss-data r-gamlss-dist r-mass r-nlme r-survival))
22081 (home-page "http://www.gamlss.org/")
22082 (synopsis "Generalized additive models for location scale and shape")
22084 "This package provides functions for fitting the generalized additive
22085 models for location scale and shape introduced by Rigby and
22086 Stasinopoulos (2005), @url{doi:10.1111/j.1467-9876.2005.00510.x}. The models
22087 use a distributional regression approach where all the parameters of the
22088 conditional distribution of the response variable are modelled using
22089 explanatory variables.")
22090 ;; Either version of the license
22091 (license (list license:gpl2 license:gpl3))))
22093 (define-public r-acid
22100 (uri (cran-uri "acid" version))
22103 "030i0y8s283ivbsmjccpbv9v7mgbcg2jk9df7vgcbbns74swf9hd"))))
22104 (properties `((upstream-name . "acid")))
22105 (build-system r-build-system)
22107 (list r-gamlss r-gamlss-dist r-hmisc))
22108 (home-page "https://cran.r-project.org/web/packages/acid/")
22109 (synopsis "Analysing conditional income distributions")
22111 "This package provides functions for the analysis of income distributions
22112 for subgroups of the population as defined by a set of variables like age,
22113 gender, region, etc. This entails a Kolmogorov-Smirnov test for a mixture
22114 distribution as well as functions for moments, inequality measures, entropy
22115 measures and polarisation measures of income distributions. This package thus
22116 aides the analysis of income inequality by offering tools for the exploratory
22117 analysis of income distributions at the disaggregated level.")
22118 (license license:gpl3)))
22120 (define-public r-acm4r
22127 (uri (cran-uri "acm4r" version))
22130 "1wqzc35i1rshx0zlmas8y4qkkvy6h9r4i4apscjjv1xg2wjflzxa"))))
22131 (properties `((upstream-name . "acm4r")))
22132 (build-system r-build-system)
22133 (propagated-inputs (list r-mass))
22134 (home-page "https://cran.r-project.org/web/packages/acm4r/")
22135 (synopsis "Align-and-count method comparisons of RFLP data")
22137 "This is a package to compare sequence fragment lengths or molecular
22138 weights from pairs of lanes. The number of matching bands in the
22139 @dfn{Restriction Fragment Length Polymorphism} (RFLP) data is calculated using
22140 the align-and-count method.")
22141 ;; Any version of the GPL
22142 (license (list license:gpl2+ license:gpl3+))))
22144 (define-public r-filelock
22146 (name "r-filelock")
22151 (uri (cran-uri "filelock" version))
22154 "00ql5fw1hidpfnm0szaavf43ahmsnvdbi8i5lr1nrcc90yaiaadc"))))
22155 (properties `((upstream-name . "filelock")))
22156 (build-system r-build-system)
22157 (home-page "https://github.com/r-lib/filelock")
22158 (synopsis "Portable file locking")
22160 "This library lets you place an exclusive or shared lock on a file using
22161 the appropriate system call provided by the underlying operating system.")
22162 (license license:expat)))
22164 (define-public r-filematrix
22166 (name "r-filematrix")
22171 (uri (cran-uri "filematrix" version))
22174 "1v3aj1ng742msb0sfdnjsbqb508mqjf8jlq2v33vxldhradw5w0b"))))
22175 (properties `((upstream-name . "filematrix")))
22176 (build-system r-build-system)
22177 ;; These inputs are needed for vignettes
22179 (list r-knitr r-rmarkdown))
22180 (home-page "https://github.com/andreyshabalin/filematrix")
22181 (synopsis "File-backed matrix class with convenient read and write access")
22183 "This package provides an interface for working with large matrices
22184 stored in files, not in computer memory. It supports multiple non-character
22185 data types (double, integer, logical and raw) of various sizes (e.g. 8 and 4
22186 byte real values). Access to parts of the matrix is done by indexing, exactly
22187 as with usual R matrices. It supports very large matrices; the package has
22188 been tested on multi-terabyte matrices. It allows for more than 2^32 rows or
22189 columns, ad allows for quick addition of extra columns to a filematrix.")
22190 (license license:lgpl3)))
22192 (define-public r-acmeeqtl
22194 (name "r-acmeeqtl")
22199 (uri (cran-uri "ACMEeqtl" version))
22202 "049xjv2ym35bbn43zwi68cq27fwdh404vp0r2ca5gxgmmx8kj1cz"))))
22203 (properties `((upstream-name . "ACMEeqtl")))
22204 (build-system r-build-system)
22206 (list r-filematrix))
22207 (home-page "https://github.com/andreyshabalin/ACMEeqtl")
22208 (synopsis "Estimation of interpretable eQTL effect sizes")
22210 "This package provides a non-linear model, termed ACME, that reflects a
22211 parsimonious biological model for allelic contributions of cis-acting eQTLs.
22212 With non-linear least-squares algorithm the maximum likelihood parameters can
22213 be estimated. The ACME model provides interpretable effect size estimates and
22214 p-values with well controlled Type-I error.")
22215 (license license:lgpl3)))
22217 (define-public r-acmer
22224 (uri (cran-uri "acmeR" version))
22227 "000b2hqlhj93958nddw0fqb15ahigs08najv2miivym046x04mf7"))))
22228 (properties `((upstream-name . "acmeR")))
22229 (build-system r-build-system)
22230 (propagated-inputs (list r-foreign))
22231 (home-page "https://cran.r-project.org/web/packages/acmeR/")
22232 (synopsis "ACME estimator of bird and bat mortality by wind turbines")
22234 "This package provides an implementation of the ACME estimator, described
22235 in Wolpert (2015), ACME: A Partially Periodic Estimator of Avian & Chiropteran
22236 Mortality at Wind Turbines. Unlike most other models, this estimator supports
22237 decreasing-hazard Weibull model for persistence; decreasing search proficiency
22238 as carcasses age; variable bleed-through at successive searches; and interval
22239 mortality estimates. The package provides, based on search data, functions
22240 for estimating the mortality inflation factor in Frequentist and Bayesian
22242 (license license:expat)))
22244 (define-public r-r-huge
22251 (uri (cran-uri "R.huge" version))
22254 "13p558qalv60pgr24nsm6mi92ryj65rsbqa6pgdwy0snjqx12bgi"))))
22255 (properties `((upstream-name . "R.huge")))
22256 (build-system r-build-system)
22258 (list r-r-methodss3 r-r-oo r-r-utils))
22259 (home-page "https://github.com/HenrikBengtsson/R.huge")
22260 (synopsis "Methods for accessing huge amounts of data")
22262 "This is a deprecated package for accessing huge amounts of data.
22263 Cross-platform alternatives are the following packages: bigmemory (CRAN),
22264 ff (CRAN), or BufferedMatrix (Bioconductor). The main usage of it was inside
22265 the @code{aroma.affymetrix} package.")
22266 (license license:lgpl2.1+)))
22268 (define-public r-r-filesets
22270 (name "r-r-filesets")
22275 (uri (cran-uri "R.filesets" version))
22278 "08xv8b3c81nf54viyr3w912al18483k5gfnjpg7bxbdfk70dfzbh"))))
22279 (properties `((upstream-name . "R.filesets")))
22280 (build-system r-build-system)
22283 (modify-phases %standard-phases
22284 (add-after 'unpack 'set-HOME
22285 (lambda _ (setenv "HOME" "/tmp"))))))
22287 (list r-digest r-r-cache r-r-methodss3 r-r-oo r-r-utils))
22288 (home-page "https://github.com/HenrikBengtsson/R.filesets")
22289 (synopsis "Easy handling of and access to files")
22291 "This package provides classes and methods to locate, setup, subset,
22292 navigate and iterate file sets, i.e. sets of files located in one or more
22293 directories on the file system. The API is designed such that these classes
22294 can be extended via inheritance to provide a richer API for special file
22295 formats. Moreover, a specific name format is defined such that filenames and
22296 directories can be considered to have full names which consists of a name
22297 followed by comma-separated tags. This adds additional flexibility to
22298 identify file sets and individual files.")
22299 (license license:lgpl2.1+)))
22301 (define-public r-r-devices
22303 (name "r-r-devices")
22308 (uri (cran-uri "R.devices" version))
22311 "1djz6vm1b7sjvx1q319dl47gbnz9kvipaxcz9i0spyp094lv3m62"))))
22312 (properties `((upstream-name . "R.devices")))
22313 (build-system r-build-system)
22315 (list r-base64enc r-r-methodss3 r-r-oo r-r-utils))
22316 (home-page "https://github.com/HenrikBengtsson/R.devices")
22317 (synopsis "Unified handling of graphics devices")
22319 "This package provides functions for creating plots and image files in a
22320 unified way regardless of output format (EPS, PDF, PNG, SVG, TIFF, WMF, etc.).
22321 Default device options as well as scales and aspect ratios are controlled in a
22322 uniform way across all device types. Switching output format requires minimal
22323 changes in code. This package is ideal for large-scale batch processing,
22324 because it will never leave open graphics devices or incomplete image files
22325 behind, even on errors or user interrupts.")
22326 (license license:lgpl2.1+)))
22328 (define-public r-acnr
22335 (uri (cran-uri "acnr" version))
22338 "087hq4i7jp67ba2finzsqjfnqbiprl33na6ryjv9zqzsdawj9cym"))))
22339 (properties `((upstream-name . "acnr")))
22340 (build-system r-build-system)
22341 (home-page "https://github.com/mpierrejean/acnr")
22342 (synopsis "Annotated copy-number regions")
22344 "This package provides SNP array data from different types of copy-number
22345 regions. These regions were identified manually by the authors of the package
22346 and may be used to generate realistic data sets with known truth.")
22347 (license license:lgpl2.1+)))
22349 (define-public r-acopula
22356 (uri (cran-uri "acopula" version))
22359 "0vvbbw8pfs9jwfz5c57lw48pr0qj661r0ys007q6zf9jmlrhx1ln"))))
22360 (properties `((upstream-name . "acopula")))
22361 (build-system r-build-system)
22362 (home-page "https://cran.r-project.org/web/packages/acopula/")
22363 (synopsis "Modelling dependence with multivariate Archimax copulas")
22365 "Archimax copulas are a mixture of Archimedean and EV copulas. This
22366 package provides definitions of several parametric families of generator and
22367 dependence function, computes CDF and PDF, estimates parameters, tests for
22368 goodness of fit, generates random sample and checks copula properties for
22369 custom constructs. In the 2-dimensional case explicit formulas for density
22370 are used, contrary to higher dimensions when all derivatives are linearly
22371 approximated. Several non-archimax families (normal, FGM, Plackett) are
22372 provided as well.")
22373 (license license:gpl2)))
22375 (define-public r-tuner
22382 (uri (cran-uri "tuneR" version))
22385 "1sd0drxzbdy71bh35fccg9ajhpdhdpy0m9nja2lw82p1pzhyl7jn"))))
22386 (properties `((upstream-name . "tuneR")))
22387 (build-system r-build-system)
22388 (propagated-inputs (list r-signal))
22389 (home-page "https://cran.r-project.org/web/packages/tuneR/")
22390 (synopsis "Analysis of music and speech")
22392 "This is a package for the analysis of music and speech. Analyze music
22393 and speech, extract features like MFCCs, handle wave files and their
22394 representation in various ways, read MP3, read MIDI, perform steps of a
22395 transcription, ...")
22396 ;; Either of these versions.
22397 (license (list license:gpl2 license:gpl3))))
22399 (define-public r-seewave
22406 (uri (cran-uri "seewave" version))
22409 "0bi1l47l3846c18k6h2vrv0xp9xh00n544a578jrndahzrj1hfwl"))))
22410 (properties `((upstream-name . "seewave")))
22411 (build-system r-build-system)
22416 (home-page "http://rug.mnhn.fr/seewave")
22417 (synopsis "Sound analysis and synthesis")
22419 "This package provides functions for analysing, manipulating, displaying,
22420 editing and synthesizing time waves (particularly sound). This package
22421 processes time analysis (oscillograms and envelopes), spectral content,
22422 resonance quality factor, entropy, cross correlation and autocorrelation,
22423 zero-crossing, dominant frequency, analytic signal, frequency coherence, 2D
22424 and 3D spectrograms and many other analyses.")
22425 (license license:gpl2+)))
22427 (define-public r-acousticndlcoder
22429 (name "r-acousticndlcoder")
22434 (uri (cran-uri "AcousticNDLCodeR" version))
22437 "1fgzgwanpv2pzy74xdk3hamc44p8qch467wh163dxby8jr9ik0sb"))))
22439 `((upstream-name . "AcousticNDLCodeR")))
22440 (build-system r-build-system)
22442 (list r-seewave r-tuner r-zoo))
22443 (home-page "https://cran.r-project.org/web/packages/AcousticNDLCodeR/")
22444 (synopsis "Coding sound files for use with NDL")
22446 "Make acoustic cues to use with the R package @code{ndl}.
22447 The package implements functions used in the PLoS ONE paper \"Words from
22448 spontaneous conversational speech can be recognized with human-like accuracy
22449 by an error-driven learning algorithm that discriminates between meanings
22450 straight from smart acoustic features, bypassing the phoneme as recognition
22451 unit.\" @url{doi:10.1371/journal.pone.0174623}")
22452 (license license:gpl2+)))
22454 (define-public r-acp
22461 (uri (cran-uri "acp" version))
22464 "0lcwbjcyyr32m6qjmjqh25qjwrbyqj1n092xhgbhxzd8fslppnmn"))))
22465 (properties `((upstream-name . "acp")))
22466 (build-system r-build-system)
22468 (list r-quantmod r-tseries))
22469 (home-page "https://cran.r-project.org/web/packages/acp/")
22470 (synopsis "Autoregressive conditional Poisson")
22472 "This package supports the analysis of count data exhibiting
22473 autoregressive properties, using the @dfn{Autoregressive Conditional Poisson}
22474 model (ACP(p,q)) proposed by Heinen (2003).")
22475 (license license:gpl2)))
22477 (define-public r-ada
22484 (uri (cran-uri "ada" version))
22487 "1h3a07czp0w3hrhjcg1fz721y8vsfclzqi3rq8qfzgpfb4h1f06r"))))
22488 (properties `((upstream-name . "ada")))
22489 (build-system r-build-system)
22490 (propagated-inputs (list r-rpart))
22491 (home-page "https://cran.r-project.org/web/packages/ada/")
22492 (synopsis "Stochastic boosting")
22494 "This package provides a straightforward, well-documented, and broad
22495 boosting routine for classification, ideally suited for small to
22496 moderate-sized data sets. It performs discrete, real, and gentle boost under
22497 both exponential and logistic loss on a given data set.")
22498 ;; Any version of the GPL.
22499 (license (list license:gpl2+ license:gpl3+))))
22501 (define-public r-genalg
22508 (uri (cran-uri "genalg" version))
22511 "1y4qz1s85zpd1r3259gr542arssf2vpd4drhy0wnq5q47ignrvna"))))
22512 (properties `((upstream-name . "genalg")))
22513 (build-system r-build-system)
22514 (home-page "https://github.com/egonw/genalg")
22515 (synopsis "R based genetic algorithm")
22517 "This package provides an R based genetic algorithm for binary and
22518 floating point chromosomes.")
22519 (license license:gpl2)))
22521 (define-public r-kernelfactory
22523 (name "r-kernelfactory")
22528 (uri (cran-uri "kernelFactory" version))
22531 "001kw9k3ivd4drd4mwqapkkk3f4jgljiaprhg2630hmll064s89j"))))
22532 (properties `((upstream-name . "kernelFactory")))
22533 (build-system r-build-system)
22535 (list r-auc r-genalg r-kernlab r-randomforest))
22536 (home-page "https://cran.r-project.org/web/packages/kernelFactory/")
22537 (synopsis "Ensemble of kernel machines")
22539 "Kernel factory is an ensemble method where each base classifier (random
22540 forest) is fit on the kernel matrix of a subset of the training data.")
22541 (license license:gpl2+)))
22543 (define-public r-dummies
22550 (uri (cran-uri "dummies" version))
22553 "01f84crqx17xd6xy55qxlvsj3knm8lhw7jl26p2rh2w3y0nvqlbm"))))
22554 (properties `((upstream-name . "dummies")))
22555 (build-system r-build-system)
22556 (home-page "https://decisionpatterns.com")
22557 (synopsis "Create dummy/indicator variables flexibly and efficiently")
22559 "This package lets you expand factors, characters and other eligible
22560 classes into dummy/indicator variables.")
22561 (license license:gpl2+)))
22563 (define-public r-acrm
22570 (uri (cran-uri "aCRM" version))
22573 "0kzp568hd9c9a9qgniia5s5gv0q5f89xfvvwpzb197gqhs3x092v"))))
22574 (properties `((upstream-name . "aCRM")))
22575 (build-system r-build-system)
22577 (list r-ada r-dummies r-kernelfactory r-randomforest))
22578 (home-page "https://cran.r-project.org/web/packages/aCRM/")
22579 (synopsis "Convenience functions for analytical customer relationship management")
22581 "This package provides convenience functions for data preparation and
22582 modeling often used in @dfn{analytical customer relationship
22583 management} (aCRM).")
22584 (license license:gpl2+)))
22586 (define-public r-tree
22592 (uri (cran-uri "tree" version))
22595 "13jwdxx3na16mly176n01zdkaqn4a8x9fc43rq5xx5vx31drkkr1"))))
22596 (build-system r-build-system)
22597 (home-page "https://cran.r-project.org/web/packages/tree/")
22598 (synopsis "Classification and regression trees")
22599 (description "This package provides procedures to work with classification
22600 and regression trees.")
22601 (license license:gpl2+)))
22603 (define-public r-treeclust
22605 (name "r-treeclust")
22610 (uri (cran-uri "treeClust" version))
22613 "1s7kh6q0bkixsygrip95zf1bi10ihddsa5lq9dfxd68yh8rsby6z"))))
22614 (properties `((upstream-name . "treeClust")))
22615 (build-system r-build-system)
22617 (list r-cluster r-rpart))
22618 (home-page "https://cran.r-project.org/web/packages/treeClust/")
22619 (synopsis "Cluster distances through trees")
22621 "This package provides tools to create a measure of inter-point
22622 dissimilarity useful for clustering mixed data, and, optionally, perform the
22624 (license license:gpl2+)))
22626 (define-public r-acrosstic
22628 (name "r-acrosstic")
22633 (uri (cran-uri "AcrossTic" version))
22636 "03180h79jhjd66ibrnsfp3yyp2jlfysp7cymw46phzj2palghsc0"))))
22637 (properties `((upstream-name . "AcrossTic")))
22638 (build-system r-build-system)
22640 (list r-lpsolve r-treeclust))
22641 (home-page "https://cran.r-project.org/web/packages/AcrossTic/")
22642 (synopsis "Cost-minimal regular spanning subgraph with TreeClust")
22644 "This is a package for constructing minimum-cost regular spanning
22645 subgraph as part of a non-parametric two-sample test for equality of
22647 (license license:gpl2+)))
22649 (define-public r-acrt
22656 (uri (cran-uri "acrt" version))
22659 "0y9ndcq8ffpfrv7w9rikm4zn68jpsj6baqisq9kp2433xrwzdb6s"))))
22660 (properties `((upstream-name . "acrt")))
22661 (build-system r-build-system)
22663 (list r-rcpp r-rcppeigen r-sandwich))
22664 (home-page "https://cran.r-project.org/web/packages/acrt/")
22665 (synopsis "Autocorrelation robust testing")
22667 "This package provides functions for testing affine hypotheses on the
22668 regression coefficient vector in regression models with autocorrelated
22670 (license license:gpl2)))
22672 (define-public r-acs
22679 (uri (cran-uri "acs" version))
22682 "0ajw9rf8l8akcvgqvbxjvryc6wjx74521xyxswz2b0bky3m6kah5"))))
22683 (properties `((upstream-name . "acs")))
22684 (build-system r-build-system)
22686 (list r-httr r-plyr r-rcpp r-stringr r-xml))
22687 (home-page "https://dusp.mit.edu/faculty/ezra-haber-glenn")
22688 (synopsis "Work with data from the US Census")
22690 "This package provides a general toolkit for downloading, managing,
22691 analyzing, and presenting data from the
22692 @url{https://www.census.gov/data/developers/data-sets.html, U.S. Census},
22693 including SF1 (Decennial short-form), SF3 (Decennial long-form), and the
22694 American Community Survey (ACS). Confidence intervals provided with ACS data
22695 are converted to standard errors to be bundled with estimates in complex
22696 @code{acs} objects. The package provides new methods to conduct standard
22697 operations on @code{acs} objects and present/plot data in statistically
22698 appropriate ways.")
22699 (license license:gpl3)))
22701 (define-public r-acss-data
22703 (name "r-acss-data")
22708 (uri (cran-uri "acss.data" version))
22711 "09kl4179ipr8bq19g89xcdi1xxs397zcx5cvgp6viy8gn687ilgv"))))
22712 (properties `((upstream-name . "acss.data")))
22713 (build-system r-build-system)
22714 (home-page "http://complexitycalculator.com/methodology.html")
22715 (synopsis "Data for algorithmic complexity of short strings")
22717 "This is a data only package providing the algorithmic complexity of
22718 short strings, computed using the coding theorem method. For a given set of
22719 symbols in a string, all possible or a large number of random samples of
22720 Turing machines with a given number of states (e.g., 5) and number of symbols
22721 corresponding to the number of symbols in the strings were simulated until
22722 they reached a halting state or failed to end. This package contains data on
22723 4.5 million strings from length 1 to 12 simulated on Turing machines with 2,
22724 4, 5, 6, and 9 symbols. The complexity of the string corresponds to the
22725 distribution of the halting states.")
22726 (license license:gpl2+)))
22728 (define-public r-acss
22735 (uri (cran-uri "acss" version))
22738 "0cqa60544f58l5qd7h6xmsir40b9hqnq6pqgd5hfx2j2l5n7qhmk"))))
22739 (properties `((upstream-name . "acss")))
22740 (build-system r-build-system)
22742 (list r-acss-data r-zoo))
22743 (home-page "http://complexitycalculator.com/methodology.html")
22744 (synopsis "Algorithmic complexity for short strings")
22746 "The main purpose of this package is to provide the algorithmic
22747 complexity for short strings, an approximation of the Kolmogorov Complexity of
22748 a short string using the coding theorem method. While the database containing
22749 the complexity is provided in the data only package @code{acss.data}, this
22750 package provides functions accessing the data such as @code{prob_random}
22751 returning the posterior probability that a given string was produced by a
22752 random process. In addition, two traditional (but problematic) measures of
22753 complexity are also provided: entropy and change complexity.")
22754 (license license:gpl2+)))
22756 (define-public r-acswr
22763 (uri (cran-uri "ACSWR" version))
22766 "195vjrkang5cl7gwsna0aq4p0h4jym9xg9yh94bnf8vq6wf8j83n"))))
22767 (properties `((upstream-name . "ACSWR")))
22768 (build-system r-build-system)
22771 (home-page "https://cran.r-project.org/web/packages/ACSWR/")
22772 (synopsis "Companion package for the book \"A Course in Statistics with R\"")
22774 "This is a companion package for the book \"A Course in Statistics with
22775 R\" (ISBN 978-1-119-15272-9.)")
22776 (license license:gpl2)))
22778 (define-public r-alabama
22781 (version "2015.3-1")
22785 (uri (cran-uri "alabama" version))
22788 "0mlgk929gdismikwx4k2ndqq57nnqj7mlgvd3479b214hksgq036"))))
22789 (properties `((upstream-name . "alabama")))
22790 (build-system r-build-system)
22791 (propagated-inputs (list r-numderiv))
22792 (home-page "https://cran.r-project.org/web/packages/alabama/")
22793 (synopsis "Constrained nonlinear optimization")
22795 "Alabama stands for Augmented Lagrangian Adaptive Barrier Minimization
22796 Algorithm; it is used for optimizing smooth nonlinear objective functions with
22797 constraints. Linear or nonlinear equality and inequality constraints are
22799 (license license:gpl2+)))
22801 (define-public r-gdina
22808 (uri (cran-uri "GDINA" version))
22811 "1slq1npsq8s8aghnrpm6vvc6kxj4svz0kr2x0akblndrcr25wxjr"))))
22812 (properties `((upstream-name . "GDINA")))
22813 (build-system r-build-system)
22826 (home-page "https://github.com/Wenchao-Ma/GDINA")
22827 (synopsis "Generalized DINA model framework")
22829 "This package provides a set of psychometric tools for cognitive
22830 diagnosis modeling based on the generalized deterministic inputs, noisy and
22831 gate (G-DINA) model by de la Torre (2011) @url{doi:10.1007/s11336-011-9207-7}
22832 and its extensions, including the sequential G-DINA model by Ma and de la
22833 Torre (2016) @url{doi:10.1111/bmsp.12070} for polytomous responses, and the
22834 polytomous G-DINA model by Chen and de la Torre
22835 @url{doi:10.1177/0146621613479818} for polytomous attributes. Joint attribute
22836 distribution can be independent, saturated, higher-order, loglinear smoothed
22837 or structured. Q-matrix validation, item and model fit statistics, model
22838 comparison at test and item level and differential item functioning can also
22839 be conducted. A graphical user interface is also provided.")
22840 (license license:gpl3)))
22842 (define-public r-actcd
22849 (uri (cran-uri "ACTCD" version))
22852 "0mzjxxr2zfdidw8ibh6w8mvpkw3q3nvngqi05g9ind26ckvk053p"))))
22853 (properties `((upstream-name . "ACTCD")))
22854 (build-system r-build-system)
22856 (list r-gdina r-r-methodss3))
22859 (home-page "https://cran.r-project.org/web/packages/ACTCD/")
22860 (synopsis "Asymptotic classification theory for cognitive diagnosis")
22862 "This is a package supporting cluster analysis for cognitive diagnosis
22863 based on the Asymptotic Classification Theory (Chiu, Douglas & Li, 2009;
22864 @url{doi:10.1007/s11336-009-9125-0}). Given the sample statistic of
22865 sum-scores, cluster analysis techniques can be used to classify examinees into
22866 latent classes based on their attribute patterns. In addition to the
22867 algorithms used to classify data, three labeling approaches are proposed to
22868 label clusters so that examinees' attribute profiles can be obtained.")
22869 (license license:gpl2+)))
22871 (define-public r-ineq
22878 (uri (cran-uri "ineq" version))
22881 "09fsxyrh0j7mwmb5hkhmrzgcy7kf85jxkh7zlwpgqgcsyl1n91z0"))))
22882 (properties `((upstream-name . "ineq")))
22883 (build-system r-build-system)
22884 (home-page "https://cran.r-project.org/web/packages/ineq/")
22885 (synopsis "Measuring inequality, concentration, and poverty")
22887 "This package provides tools for measuring inequality, concentration, and
22888 poverty measures. It provides both empirical and theoretical Lorenz curves.")
22889 ;; Either of these two versions.
22890 (license (list license:gpl2 license:gpl3))))
22892 (define-public r-actfrag
22899 (uri (cran-uri "ActFrag" version))
22902 "08r3gwjz4fkyy85dxqix0ffm5xyq45032qv3snnzxnlqxslxbqn1"))))
22903 (properties `((upstream-name . "ActFrag")))
22904 (build-system r-build-system)
22906 (list r-accelerometry r-dplyr r-ineq r-survival r-tidyr))
22907 (home-page "https://github.com/junruidi/ActFrag")
22908 (synopsis "Activity fragmentation metrics extraction")
22910 "This package provides functions to extract commonly used fragmentation
22911 metrics to quantify time accumulation strategies based on minute level
22912 actigraphy-measured activity counts data.")
22913 (license license:gpl3)))
22915 (define-public r-ash
22922 (uri (cran-uri "ash" version))
22925 "1ay2a2agdmiz7zzvn26mli0x0iwk09g5pp4yy1r23knhkp1pn2lb"))))
22926 (properties `((upstream-name . "ash")))
22927 (build-system r-build-system)
22928 (native-inputs (list gfortran))
22929 (home-page "https://cran.r-project.org/web/packages/ash/")
22930 (synopsis "David Scott's ASH routines")
22932 "This package provides David Scott's ASH routines ported from S-PLUS to
22934 (license license:gpl2+)))
22936 (define-public r-hdrcde
22943 (uri (cran-uri "hdrcde" version))
22946 "16qlk44cjvn2s0vzaf915df65ksdx20dbxhy7fpdqins46hccha3"))))
22947 (properties `((upstream-name . "hdrcde")))
22948 (build-system r-build-system)
22956 (native-inputs (list gfortran))
22957 (home-page "http://pkg.robjhyndman.com/hdrcde")
22958 (synopsis "Highest density regions and conditional density estimation")
22960 "This is a package for the computation of highest density regions in one
22961 and two dimensions, kernel estimation of univariate density functions
22962 conditional on one covariate, and multimodal regression.")
22963 (license license:gpl3)))
22965 (define-public r-rainbow
22972 (uri (cran-uri "rainbow" version))
22975 "11vfcck17d2xjc049ci5i8l1nqv345anmd110gdz7654i1pj9lb3"))))
22976 (properties `((upstream-name . "rainbow")))
22977 (build-system r-build-system)
22985 (home-page "https://cran.r-project.org/web/packages/rainbow/")
22986 (synopsis "Bagplots, boxplots and rainbow plots for functional data")
22988 "This is a package for visualizing functional data and identifying
22989 functional outliers with bagplots, boxplots and rainbow plots.")
22990 (license license:gpl3)))
22992 (define-public r-fds
22999 (uri (cran-uri "fds" version))
23002 "1284vncixrzrz9x6b52gslrbrbia07sd0xac7nwdqhp5f5v5wfi0"))))
23003 (properties `((upstream-name . "fds")))
23004 (build-system r-build-system)
23006 (list r-rainbow r-rcurl))
23007 (home-page "https://cran.r-project.org/web/packages/fds/")
23008 (synopsis "Functional data sets")
23009 (description "This package contains a list of functional time series,
23010 sliced functional time series, and functional data sets. Functional time
23011 series is a special type of functional data observed over time. Sliced
23012 functional time series is a special type of functional time series with a time
23013 variable observed over time.")
23014 (license license:gpl2+)))
23016 (define-public r-fda
23023 (uri (cran-uri "fda" version))
23026 "0fm2vswc8fdi2p1axby0hjwh8m6lc1zrdikrpiamilr6w9m2zanw"))))
23027 (properties `((upstream-name . "fda")))
23028 (build-system r-build-system)
23030 (list r-desolve r-fds r-matrix))
23031 (home-page "https://www.functionaldata.org")
23032 (synopsis "Functional data analysis")
23034 "These functions were developed to support functional data analysis as
23035 described in Ramsay, J. O. and Silverman, B. W. (2005) Functional Data
23036 Analysis. The package includes data sets and script files working many
23038 (license license:gpl2+)))
23040 (define-public r-actigraphy
23042 (name "r-actigraphy")
23047 (uri (cran-uri "Actigraphy" version))
23050 "0bpmvszzv5fm72nar3wgnmfl5am7znqfajmlbv38ihkbi7jbwk20"))))
23051 (properties `((upstream-name . "Actigraphy")))
23052 (build-system r-build-system)
23055 (home-page "https://cran.r-project.org/web/packages/Actigraphy/")
23056 (synopsis "Actigraphy data analysis")
23058 "This package provides tools for functional linear modeling and analysis
23059 of actigraphy data.")
23060 (license license:asl2.0)))
23062 (define-public r-activedriver
23064 (name "r-activedriver")
23069 (uri (cran-uri "ActiveDriver" version))
23072 "10c7ga48fwvpd5mc4dqiyw4kc2l0iz5qn4hg7xk15r1qmm5rsipa"))))
23073 (properties `((upstream-name . "ActiveDriver")))
23074 (build-system r-build-system)
23077 (home-page "https://cran.r-project.org/web/packages/ActiveDriver/")
23078 (synopsis "Tools for finding cancer driver proteins")
23080 "This package provides a mutation analysis tool that discovers cancer
23081 driver genes with frequent mutations in protein signalling sites such as
23082 post-translational modifications (phosphorylation, ubiquitination, etc). The
23083 Poisson generalized linear regression model identifies genes where cancer
23084 mutations in signalling sites are more frequent than expected from the
23085 sequence of the entire gene. Integration of mutations with signalling
23086 information helps find new driver genes and propose candidate mechanisms to
23088 (license license:gpl2+)))
23090 (define-public r-activitycounts
23092 (name "r-activitycounts")
23097 (uri (cran-uri "activityCounts" version))
23100 "0zgxr2sk3a8kmygfxx1p5hnrfwdkxx7php6jlrhm8wv6052ck8jz"))))
23102 `((upstream-name . "activityCounts")))
23103 (build-system r-build-system)
23105 (list r-lubridate r-magrittr r-seewave r-signal r-tibble))
23106 (home-page "https://github.com/walkabillylab/activityCounts")
23107 (synopsis "Generate ActiLife counts")
23109 "ActiLife generates activity counts from data collected by Actigraph
23110 accelerometers. Actigraph is one of the most common research-grade
23111 accelerometers. There is considerable research validating and developing
23112 algorithms for human activity using ActiLife counts. Unfortunately, ActiLife
23113 counts are proprietary and difficult to implement if researchers use different
23114 accelerometer brands. The code creates ActiLife counts from raw acceleration
23115 data for different accelerometer brands.")
23116 (license license:gpl3)))
23118 (define-public r-activityindex
23120 (name "r-activityindex")
23125 (uri (cran-uri "ActivityIndex" version))
23128 "1zj2b6x31a1kxl80rarmkrlm7ack4154mrkbqs3fpi48zpmjbgd5"))))
23129 (properties `((upstream-name . "ActivityIndex")))
23130 (build-system r-build-system)
23132 (list r-data-table r-matrixstats r-r-utils))
23135 (home-page "https://cran.r-project.org/web/packages/ActivityIndex/")
23136 (synopsis "Activity Index calculation using raw accelerometry data")
23138 "This is a package to read raw accelerometry from GT3X+ accelerometry
23139 data and plain table data to calculate the Activity Index from Bai et
23140 al. (2016) @url{doi:10.1371/journal.pone.0160644}.")
23141 (license license:gpl3)))
23143 (define-public r-activpal
23145 (name "r-activpal")
23150 (uri (cran-uri "activPAL" version))
23153 "1h6hp5z89ji73gdzxy1dgbfwjysiy5lvcqh90xagpb7sa7ahs3na"))))
23154 (properties `((upstream-name . "activPAL")))
23155 (build-system r-build-system)
23163 (home-page "https://cran.r-project.org/web/packages/activPAL")
23164 (synopsis "Processing and chart generation from activPAL events files")
23166 "This package contains functions to generate pre-defined summary
23167 statistics from activPAL events files. The package also contains functions to
23168 produce informative graphics that visualize physical activity behaviour and
23169 trends. This includes generating graphs that align physical activity
23170 behaviour with additional time based observations described by other data
23171 sets, such as sleep diaries and continuous glucose monitoring data.")
23172 (license license:gpl3)))
23174 (define-public r-activpalprocessing
23176 (name "r-activpalprocessing")
23181 (uri (cran-uri "activpalProcessing" version))
23184 "1y0bjx2qx53iy930y9iww4q1yzjj8y16cwgixk1mq3w4g1f116d1"))))
23186 `((upstream-name . "activpalProcessing")))
23187 (build-system r-build-system)
23190 (home-page "https://cran.r-project.org/web/packages/activpalProcessing/")
23191 (synopsis "Process activPAL events files")
23193 "This package performs estimation of physical activity and sedentary
23194 behavior variables from activPAL events files.")
23195 ;; Either version of the GPL.
23196 (license (list license:gpl2 license:gpl3))))
23198 (define-public r-actogrammr
23200 (name "r-actogrammr")
23205 (uri (cran-uri "actogrammr" version))
23208 "1jzvarmd41yqlrkagzlc8m19n5mn0w0b36fy50lyvgrfsafjfbqa"))))
23209 (properties `((upstream-name . "actogrammr")))
23210 (build-system r-build-system)
23212 (list r-dplyr r-ggplot2 r-lubridate r-readr r-tidyr))
23213 (home-page "https://cran.r-project.org/web/packages/actogrammr/")
23214 (synopsis "Read in activity data and plot actograms")
23216 "Read in activity measurements from standard file formats used by
23217 circadian rhythm researchers, currently only ClockLab format, and process and
23218 plot the data. The central type of plot is the actogram, as first described
23219 in \"Activity and distribution of certain wild mice in relation to biotic
23220 communities\" by MS Johnson (1926) @url{doi:10.2307/1373575}.")
23221 (license license:gpl3)))
23223 (define-public r-expint
23230 (uri (cran-uri "expint" version))
23233 "01d0a7pc4qx7044a0cymnv5ld88r90vdvlqjbnzg9qlfbizdgyvw"))))
23234 (properties `((upstream-name . "expint")))
23235 (build-system r-build-system)
23236 (home-page "https://gitlab.com/vigou3/expint")
23237 (synopsis "Exponential integral and incomplete Gamma function")
23239 "This package provides the exponential integrals @code{E_1(x)},
23240 @code{E_2(x)}, @code{E_n(x)} and @code{Ei(x)}, and the incomplete gamma
23241 function @code{G(a, x)} defined for negative values of its first argument.
23242 The package also gives easy access to the underlying C routines through an
23243 API; see the package vignette for details.")
23244 (license license:gpl2+)))
23246 (define-public r-actuar
23253 (uri (cran-uri "actuar" version))
23256 "0dhpaivyga0jwvw1csagbx74biy9jfkw4a8sa871579njxl1x7p1"))))
23257 (properties `((upstream-name . "actuar")))
23258 (build-system r-build-system)
23259 (propagated-inputs (list r-expint))
23260 (home-page "https://gitlab.com/vigou3/actuar")
23261 (synopsis "Actuarial functions and heavy tailed distributions")
23263 "This package provides functions and data sets for actuarial science:
23264 modeling of loss distributions; risk theory and ruin theory; simulation of
23265 compound models, discrete mixtures and compound hierarchical models;
23266 credibility theory. It boasts support for many additional probability
23267 distributions to model insurance loss amounts and loss frequency: 19
23268 continuous heavy tailed distributions; the Poisson-inverse Gaussian discrete
23269 distribution; zero-truncated and zero-modified extensions of the standard
23270 discrete distributions. It also supports phase-type distributions commonly
23271 used to compute ruin probabilities.")
23272 (license license:gpl2+)))
23274 (define-public r-bmp
23281 (uri (cran-uri "bmp" version))
23284 "0jd67r11bn98hjwgyr6gas423787xy7ji2hq7ay80blkkcj91xxx"))))
23285 (properties `((upstream-name . "bmp")))
23286 (build-system r-build-system)
23287 (home-page "https://cran.r-project.org/web/packages/bmp/")
23288 (synopsis "Read Bitmap (BMP) images")
23290 "This package provides pure R tools to read BMP format images. It is
23291 currently limited to 8 bit greyscale images and 24, 32 bit (A)RGB images.")
23292 (license license:gpl2+)))
23294 (define-public r-readbitmap
23296 (name "r-readbitmap")
23301 (uri (cran-uri "readbitmap" version))
23304 "14825906l326w59g6apy00j55jg3h5kx2r6s031f4gdkbrc7szbk"))))
23305 (properties `((upstream-name . "readbitmap")))
23306 (build-system r-build-system)
23308 (list libjpeg-turbo libpng))
23310 (list r-bmp r-jpeg r-png r-tiff))
23311 (home-page "https://github.com/jefferis/readbitmap")
23312 (synopsis "Unified interface to read bitmap images (BMP, JPEG, PNG, TIFF)")
23314 "This package provides tools to identify and read BMP, JPEG, PNG, and
23315 TIFF format bitmap images. Identification defaults to the use of the magic
23316 number embedded in the file rather than the file extension.")
23317 (license license:gpl2+)))
23319 (define-public r-imager
23322 (version "0.42.13")
23326 (uri (cran-uri "imager" version))
23329 "0zygnmxwbbmj5i2l2affzdz90xvsa7b5pbkzkhjbm40is69rh2nr"))))
23330 (properties `((upstream-name . "imager")))
23331 (build-system r-build-system)
23333 (list fftw libtiff libx11 zlib))
23345 (list pkg-config r-knitr))
23346 (home-page "https://dahtah.github.io/imager/")
23347 (synopsis "Image processing library")
23349 "This is a package for fast image processing for images in up to 4
23350 dimensions (two spatial dimensions, one time/depth dimension, one color
23351 dimension). It provides most traditional image processing tools (filtering,
23352 morphology, transformations, etc.) as well as various functions for easily
23353 analyzing image data using R. The package wraps @url{http://cimg.eu, CImg}, a
23354 simple, modern C++ library for image processing.")
23355 (license license:lgpl3)))
23357 (define-public r-acuityview
23359 (name "r-acuityview")
23364 (uri (cran-uri "AcuityView" version))
23367 "0f0iclmnwdc8ixiiai4svk4x1g3pjy7dhm3cm58fv6ckx12d3d2l"))))
23368 (properties `((upstream-name . "AcuityView")))
23369 (build-system r-build-system)
23371 (list r-fftwtools r-imager r-plotrix))
23372 (home-page "https://cran.r-project.org/web/packages/AcuityView/")
23373 (synopsis "Display scenes as seen by an animal with less acute vision")
23375 "This package provides a simple method for representing a visual scene as
23376 it may be seen by an animal with less acute vision.")
23377 (license license:gpl2+)))
23379 (define-public r-caret
23386 (uri (cran-uri "caret" version))
23389 "1kbx51cf71z2x19a0jflwnhx5jd9wk9q9203kzdxlqw5izdjvmdz"))))
23390 (build-system r-build-system)
23405 (home-page "https://github.com/topepo/caret")
23406 (synopsis "Classification and regression training")
23408 "This package provides miscellaneous functions for training and plotting
23409 classification and regression models.")
23410 (license license:gpl2+)))
23412 (define-public r-adabag
23419 (uri (cran-uri "adabag" version))
23422 "109wrl1pwvmyv2l909hrvk7dg4aa9pv449mvdycp50zwrsw9w0a7"))))
23423 (properties `((upstream-name . "adabag")))
23424 (build-system r-build-system)
23426 (list r-caret r-doparallel r-foreach r-rpart))
23427 (home-page "https://cran.r-project.org/web/packages/adabag/")
23428 (synopsis "Multiclass AdaBoost.M1, SAMME and Bagging")
23430 "This package implements Freund and Schapire's Adaboost.M1 algorithm and
23431 Breiman's Bagging algorithm using classification trees as individual
23432 classifiers. Once these classifiers have been trained, they can be used to
23433 predict on new data. Also, cross validation estimation of the error can be
23435 (license license:gpl2+)))
23437 (define-public r-adagio
23444 (uri (cran-uri "adagio" version))
23447 "0ihv05402iq003m0338f85pnqnlnrmx0pf1mg8cz9sgi5h98mbnl"))))
23448 (properties `((upstream-name . "adagio")))
23449 (build-system r-build-system)
23452 (home-page "https://cran.r-project.org/web/packages/adagio/")
23453 (synopsis "Discrete and global optimization routines")
23455 "This package provides methods and algorithms for discrete optimization,
23456 e.g. knapsack and subset sum procedures, derivative-free Nelder-Mead and
23457 Hooke-Jeeves minimization, and some (evolutionary) global optimization
23459 (license license:gpl3+)))
23461 (define-public r-univoutl
23463 (name "r-univoutl")
23468 (uri (cran-uri "univOutl" version))
23471 "1hhpxrpmp2wbrynx9xjndnp2sccirgky2x6ksd6yk6phmk0rbzjp"))))
23472 (properties `((upstream-name . "univOutl")))
23473 (build-system r-build-system)
23475 (list r-hmisc r-robustbase))
23476 (home-page "https://github.com/marcellodo/univOutl")
23477 (synopsis "Detection of univariate outliers")
23479 "This package provides well-known outlier detection techniques in the
23480 univariate case. Methods to deal with skewed distribution are included too.
23481 The Hidiroglou-Berthelot (1986) method to search for outliers in ratios of
23482 historical data is implemented as well. When available, survey weights can be
23483 used in outliers detection.")
23484 (license license:gpl2+)))
23486 (define-public r-tolerance
23488 (name "r-tolerance")
23493 (uri (cran-uri "tolerance" version))
23496 "001snzr2ipag3zprynydlbi9prkjzrllc054qh7m0qwkb3r19jjd"))))
23497 (properties `((upstream-name . "tolerance")))
23498 (build-system r-build-system)
23500 (list r-mass r-rgl))
23501 (home-page "https://cran.r-project.org/web/packages/tolerance/")
23502 (synopsis "Statistical tolerance intervals and regions")
23504 "This package provides functions for estimating tolerance
23505 limits (intervals) for various univariate distributions (binomial, Cauchy,
23506 discrete Pareto, exponential, two-parameter exponential, extreme value,
23507 hypergeometric, Laplace, logistic, negative binomial, negative hypergeometric,
23508 normal, Pareto, Poisson-Lindley, Poisson, uniform, and Zipf-Mandelbrot),
23509 Bayesian normal tolerance limits, multivariate normal tolerance regions,
23510 nonparametric tolerance intervals, tolerance bands for regression
23511 settings (linear regression, nonlinear regression, nonparametric regression,
23512 and multivariate regression), and analysis of variance tolerance intervals.
23513 Visualizations are also available for most of these settings.")
23514 (license license:gpl2+)))
23516 ;; Keep this in sync with the liblantern package.
23517 (define-public r-torch
23524 (uri (cran-uri "torch" version))
23526 (base32 "163pvl3gyz7l2fmqhgg4k6pw4dmvfir71yp9l5ra2k4zc32lz166"))))
23527 (properties `((upstream-name . "torch")))
23528 (build-system r-build-system)
23532 #~(modify-phases %standard-phases
23533 (add-after 'install 'link-libraries
23534 (lambda* (#:key inputs #:allow-other-keys)
23535 (let ((deps (string-append #$output "/site-library/torch/deps")))
23539 inputs "/lib/python3.9/site-packages/torch/lib/libtorch.so")
23540 (string-append deps "/libtorch.so"))
23543 inputs "/lib/liblantern.so")
23544 (string-append deps "/liblantern.so"))))))))
23546 (list python-pytorch-for-r-torch
23559 (native-inputs (list r-knitr))
23560 (home-page "https://torch.mlverse.org/docs")
23561 (synopsis "Tensors and neural networks with GPU acceleration")
23563 "This package provides functionality to define and train neural networks
23564 similar to PyTorch but written entirely in R using the libtorch library. It
23565 also supports low-level tensor operations and GPU acceleration.")
23566 (license license:expat)))
23568 (define-public r-additivitytests
23570 (name "r-additivitytests")
23575 (uri (cran-uri "additivityTests" version))
23578 "048ds90wqjdjy1nyhna3m06asdklbh8sx1n556kss2j1r1pma1sw"))))
23580 `((upstream-name . "additivityTests")))
23581 (build-system r-build-system)
23582 (home-page "https://github.com/simecek/additivityTests")
23583 (synopsis "Additivity tests in the two way Anova with single sub-class numbers")
23585 "This package provides an implementation of the Tukey, Mandel,
23586 Johnson-Graybill, LBI, Tusell and modified Tukey non-additivity tests.")
23587 (license license:gpl3)))
23589 (define-public r-flexclust
23591 (name "r-flexclust")
23596 (uri (cran-uri "flexclust" version))
23599 "13akk3w6a76jpws5v9108c3hdmb8i6gm0sc06lr2hqly0pgpfyfn"))))
23600 (properties `((upstream-name . "flexclust")))
23601 (build-system r-build-system)
23603 (list r-class r-lattice r-modeltools))
23604 (home-page "https://cran.r-project.org/web/packages/flexclust/")
23605 (synopsis "Flexible cluster algorithms")
23607 "The main function @code{kcca} implements a general framework for
23608 k-centroids cluster analysis supporting arbitrary distance measures and
23609 centroid computation. Further cluster methods include hard competitive
23610 learning, neural gas, and QT clustering. There are numerous visualization
23611 methods for cluster results (neighborhood graphs, convex cluster hulls,
23612 barcharts of centroids, ...), and bootstrap methods for the analysis of
23613 cluster stability.")
23614 (license license:gpl2)))
23616 (define-public r-biclust
23623 (uri (cran-uri "biclust" version))
23626 "0lgyc2f04dhr65cwga78pradxsdzgjrpp8vphchqn60ab1z95dlp"))))
23627 (properties `((upstream-name . "biclust")))
23628 (build-system r-build-system)
23630 (list r-additivitytests
23637 (home-page "https://cran.r-project.org/web/packages/biclust/")
23638 (synopsis "BiCluster algorithms")
23640 "The main function @code{biclust()} provides several algorithms to find
23641 biclusters in two-dimensional data, spectral, plaid model, xmotifs, and bimax.
23642 In addition, the package provides methods for data
23643 preprocessing (normalization and discretization), visualization, and
23644 validation of bicluster solutions.")
23645 (license license:gpl3)))
23647 (define-public r-icge
23654 (uri (cran-uri "ICGE" version))
23657 "0w6hbi3h98q6gsxqbb43p95v6xykgrasxcjivwm8hw9fly4avxyi"))))
23658 (properties `((upstream-name . "ICGE")))
23659 (build-system r-build-system)
23661 (list r-cluster r-fastcluster r-mass))
23662 (home-page "https://cran.r-project.org/web/packages/ICGE/")
23663 (synopsis "Cluster estimation and identification of atypical units")
23665 "ICGE is a package that helps to estimate the number of real clusters in
23666 data as well as to identify atypical units. The underlying methods are based
23667 on distances rather than on unit x variables.")
23668 (license license:gpl2+)))
23670 (define-public r-depth
23673 (version "2.1-1.1")
23677 (uri (cran-uri "depth" version))
23680 "0szy0027nh4ps1z919i740i50app5q7cfyg1fj7pdyl45nbl8k6m"))))
23681 (properties `((upstream-name . "depth")))
23682 (build-system r-build-system)
23684 (list r-abind r-circular r-rgl))
23687 (home-page "https://cran.r-project.org/web/packages/depth/")
23688 (synopsis "Nonparametric depth functions for multivariate analysis")
23690 "This package provides tools for depth functions methodology applied to
23691 multivariate analysis. Besides allowing calculation of depth values and
23692 depth-based location estimators, the package includes functions or drawing
23693 contour plots and perspective plots of depth functions. Euclidean and
23694 spherical depths are supported.")
23695 (license license:gpl2)))
23697 (define-public r-archetypes
23699 (name "r-archetypes")
23700 (version "2.2-0.1")
23704 (uri (cran-uri "archetypes" version))
23707 "0ibxsr173ib77gjhid91m85s8gjii4mi2w3d52q5301igv20p7r0"))))
23708 (properties `((upstream-name . "archetypes")))
23709 (build-system r-build-system)
23711 (list r-modeltools r-nnls))
23712 (home-page "https://cran.r-project.org/web/packages/archetypes")
23713 (synopsis "Archetypal analysis")
23715 "The main function @code{archetypes} implements a framework for
23716 archetypal analysis supporting arbitrary problem solving mechanisms for the
23717 different conceptual parts of the algorithm.")
23718 (license license:gpl2+)))
23720 (define-public r-shapes
23727 (uri (cran-uri "shapes" version))
23730 "1p9fr95zk3q2v277c5ksb0nh26mcpzwjzjb2lmag51z6hck8cb66"))))
23731 (properties `((upstream-name . "shapes")))
23732 (build-system r-build-system)
23734 (list r-mass r-minpack-lm r-rgl r-scatterplot3d))
23735 (home-page "http://www.maths.nottingham.ac.uk/~ild/shapes")
23736 (synopsis "Statistical shape analysis")
23738 "This package provides routines for the statistical analysis of landmark
23739 shapes, including Procrustes analysis, graphical displays, principal
23740 components analysis, permutation and bootstrap tests, thin-plate spline
23741 transformation grids and comparing covariance matrices. See Dryden, I.L. and
23742 Mardia, K.V. (2016). Statistical shape analysis, with Applications in R (2nd
23743 Edition), John Wiley and Sons.")
23744 (license license:gpl2)))
23746 (define-public r-anthropometry
23748 (name "r-anthropometry")
23753 (uri (cran-uri "Anthropometry" version))
23756 "0vxjlzxv16bygw8n57f25msq5bd1dydg41my92ximah0nzzvbg41"))))
23757 (properties `((upstream-name . "Anthropometry")))
23758 (build-system r-build-system)
23771 (home-page "https://cran.r-project.org/web/packages/Anthropometry/")
23772 (synopsis "Statistical methods for anthropometric data")
23774 "This package provides statistical methods especially developed to
23775 analyze anthropometric data. These methods are aimed at providing effective
23776 solutions to some commons problems related to Ergonomics and Anthropometry.
23777 They are based on clustering, the statistical concept of data depth,
23778 statistical shape analysis and archetypal analysis.")
23779 (license license:gpl2+)))
23781 (define-public r-anndata
23784 (version "0.7.5.3")
23788 (uri (cran-uri "anndata" version))
23790 (base32 "115v7gdilayd18hd519vzkixp2s6rvvrd1inc1i6amn7d0spy8r1"))))
23791 (properties `((upstream-name . "anndata")))
23792 (build-system r-build-system)
23793 (propagated-inputs (list r-assertthat r-matrix r-r6 r-reticulate))
23794 (native-inputs (list r-knitr))
23795 (home-page "https://anndata.dynverse.org")
23796 (synopsis "Anndata for R")
23798 "This package provides a reticulate wrapper for the Python package
23799 @code{anndata}. It provides a scalable way of keeping track of data and
23800 learned annotations. It is used to read from and write to the h5ad file
23802 (license license:expat)))
23804 (define-public r-adamethods
23806 (name "r-adamethods")
23811 (uri (cran-uri "adamethods" version))
23814 "150awbd3skb1mqca18bqjykhyycqw8crviw66s6qrcnmcsbk77pj"))))
23815 (properties `((upstream-name . "adamethods")))
23816 (build-system r-build-system)
23818 (list r-anthropometry
23825 (home-page "https://cran.r-project.org/web/packages/adamethods/")
23826 (synopsis "Archetypoid algorithms and anomaly detection")
23828 "This package is a collection of several algorithms to obtain
23829 archetypoids with small and large databases and with both classical
23830 multivariate data and functional data (univariate and multivariate). Some of
23831 these algorithms also detect anomalies (outliers).")
23832 (license license:gpl2+)))
23834 (define-public r-idpmisc
23841 (uri (cran-uri "IDPmisc" version))
23844 "0zy6mxqa8arq0vvhsdcifzm3085c23rnwa1n36fhircph1xwvfdw"))))
23845 (properties `((upstream-name . "IDPmisc")))
23846 (build-system r-build-system)
23849 (home-page "https://cran.r-project.org/web/packages/IDPmisc/")
23850 (synopsis "Functions for data analyses and visualization")
23852 "This package provides different high-level graphics functions for
23853 displaying large datasets, displaying circular data in a very flexible way,
23854 finding local maxima, brewing color ramps, drawing nice arrows, zooming
23855 2D-plots, creating figures with differently colored margin and plot region.
23856 In addition, the package contains auxiliary functions for data manipulation
23857 like omitting observations with irregular values or selecting data by logical
23858 vectors, which include NAs. Other functions are especially useful in
23859 spectroscopy and analyses of environmental data: robust baseline fitting,
23860 finding peaks in spectra, converting humidity measures.")
23861 (license license:gpl3+)))
23863 (define-public r-qqman
23870 (uri (cran-uri "qqman" version))
23873 "1a6qp5wv9bvwjchfw8x4jh48hkynlnfr21a8vqgnswldvwbq7njq"))))
23874 (properties `((upstream-name . "qqman")))
23875 (build-system r-build-system)
23877 (list r-calibrate))
23880 (home-page "https://cran.r-project.org/web/packages/qqman/")
23881 (synopsis "Q-Q and Manhattan plots for GWAS data")
23883 "This package allows you to create Q-Q and Manhattan plots for GWAS data
23884 from PLINK results.")
23885 (license license:gpl3)))
23887 (define-public r-gghighlight
23889 (name "r-gghighlight")
23894 (uri (cran-uri "gghighlight" version))
23896 (base32 "0bxgn4srxz1qhawqa8ck57p8hg5ikwfa9ll03zmnn8fb19akwm2v"))))
23897 (properties `((upstream-name . "gghighlight")))
23898 (build-system r-build-system)
23900 (list r-dplyr r-ggplot2 r-ggrepel r-lifecycle r-purrr r-rlang r-tibble))
23901 (native-inputs (list r-knitr))
23902 (home-page "https://github.com/yutannihilation/gghighlight/")
23903 (synopsis "Highlight lines and points in ggplot2")
23904 (description "Suppose we have data that has so many series that it is hard
23905 to identify them by their colors as the differences are so subtle. With
23906 gghighlight we can highlight those lines that match certain criteria. The
23907 result is a usual @code{ggplot} object, so it is fully customizable and can be
23908 used with custom themes and facets.")
23909 (license license:expat)))
23911 (define-public r-ggplot-multistats
23913 (name "r-ggplot-multistats")
23918 (uri (cran-uri "ggplot.multistats" version))
23921 "1afzfa86vc484bcwpg7m1ky03jpax584rigzgai8w06pifkmz0il"))))
23923 `((upstream-name . "ggplot.multistats")))
23924 (build-system r-build-system)
23926 (list r-ggplot2 r-hexbin r-rlang r-scales))
23927 (home-page "https://github.com/flying-sheep/ggplot.multistats")
23928 (synopsis "Multiple summary statistics for binned stats/geometries")
23930 "This package provides the ggplot binning layer @code{stat_summaries_hex()},
23931 which functions similar to its singular form, but allows the use of multiple
23932 statistics per bin. Those statistics can be mapped to multiple bin
23934 (license license:gpl3)))
23936 (define-public r-knn-covertree
23938 (name "r-knn-covertree")
23943 (uri (cran-uri "knn.covertree" version))
23946 "0msfcmwydws7q7m5jdb0dxab0nkbl7mq5llg6v3r4qrnlvrdggvz"))))
23947 (properties `((upstream-name . "knn.covertree")))
23948 (build-system r-build-system)
23950 (list r-matrix r-rcpp r-rcppeigen))
23951 (home-page "https://github.com/flying-sheep/knn.covertree")
23952 (synopsis "Accurate kNN Implementation with multiple distance measures")
23954 "Similarly to the FNN package, this package allows calculation of the k
23955 nearest neighbors (kNN) of a data matrix. The implementation is based on
23956 cover trees introduced by Alina Beygelzimer, Sham Kakade, and John
23957 Langford (2006) @url{doi:10.1145/1143844.1143857}.")
23958 (license license:agpl3+)))
23960 (define-public r-poibin
23967 (uri (cran-uri "poibin" version))
23970 "1sxryvwwz6ldsnkzdy56p8c895s5yvpcai9ndyjv1x5q3l05wf9v"))))
23971 (properties `((upstream-name . "poibin")))
23972 (build-system r-build-system)
23973 (home-page "https://cran.r-project.org/web/packages/poibin/")
23974 (synopsis "Poisson binomial distribution")
23976 "This package provides an implementation of both the exact and
23977 approximation methods for computing the @dfn{cumulative distribution
23978 function} (CDF) of the Poisson binomial distribution. It also provides the
23979 @dfn{probability mass function} (PMF), quantile function, and random number
23980 generation for the Poisson binomial distribution.")
23981 (license license:gpl2)))
23983 (define-public r-diagram
23990 (uri (cran-uri "diagram" version))
23993 "1r3lyl0h7mk9cfg8smr3jydfkjdawaphnxibkxfjqa7029vkxh79"))))
23994 (properties `((upstream-name . "diagram")))
23995 (build-system r-build-system)
23998 (home-page "https://cran.r-project.org/web/packages/diagram/")
23999 (synopsis "Visualize simple graphs (networks) and plot flow diagrams")
24001 "This package provides tools to visualize simple graphs (networks) based
24002 on a transition matrix, utilities to plot flow diagrams, visualizing webs,
24003 electrical networks, etc. It also includes supporting material for the book
24004 \"A practical guide to ecological modelling - using R as a simulation
24005 platform\" by Karline Soetaert and Peter M.J. Herman (2009) and the book
24006 \"Solving Differential Equations in R\" by Karline Soetaert, Jeff Cash and
24007 Francesca Mazzia (2012).")
24008 (license license:gpl2+)))
24010 (define-public r-lim
24017 (uri (cran-uri "LIM" version))
24020 "03x1gnm06bw1wrzc01110bjzd2mvjdzbc2mbrazh22jrmb32w5d8"))))
24021 (properties `((upstream-name . "LIM")))
24022 (build-system r-build-system)
24024 (list r-diagram r-limsolve))
24025 (home-page "https://cran.r-project.org/web/packages/LIM/")
24026 (synopsis "Linear inverse model examples and solution methods")
24028 "This package provides functions that read and solve linear inverse
24029 problems (food web problems, linear programming problems).")
24030 (license license:gpl2+)))
24032 (define-public r-shinycssloaders
24034 (name "r-shinycssloaders")
24039 (uri (cran-uri "shinycssloaders" version))
24042 "0r3xm273lhdhzbs2mkgw1m2kwb7z1dh1pzya8yxy5vacda1l2ikl"))))
24044 `((upstream-name . "shinycssloaders")))
24045 (build-system r-build-system)
24047 (list r-digest r-glue r-shiny))
24048 (home-page "https://github.com/andrewsali/shinycssloaders")
24049 (synopsis "Add CSS loading animations to Shiny outputs")
24051 "This package provides tools to create a lightweight Shiny wrapper for
24052 the css-loaders created by Luke Hass
24053 @url{https://github.com/lukehaas/css-loaders}. Wrapping a Shiny output will
24054 automatically show a loader when the output is (re)calculating.")
24055 (license license:gpl3)))
24057 (define-public r-rsvg
24064 (uri (cran-uri "rsvg" version))
24067 "05mvi1ijnxayyj1f4p8nb56pncmm7x0sbq0d87asv7c7kw765n1a"))))
24068 (properties `((upstream-name . "rsvg")))
24069 (build-system r-build-system)
24071 (list librsvg zlib))
24073 (list pkg-config r-knitr))
24074 (home-page "https://github.com/jeroen/rsvg#readme")
24075 (synopsis "Render SVG images into PDF, PNG, PostScript, or Bitmap arrays")
24077 "This package allows you to render vector-based SVG images into
24078 high-quality custom-size bitmap arrays using the librsvg2 library. The
24079 resulting bitmap can be written to e.g. PNG, JPEG or WEBP format. In
24080 addition, the package can convert images directly to various formats such as
24081 PDF or PostScript.")
24082 (license license:expat)))
24084 (define-public r-influencer
24086 (name "r-influencer")
24087 (version "0.1.0.1")
24091 (uri (cran-uri "influenceR" version))
24094 "0rj7rm236vn3v8302nwl12s0kvpv6xpdbm3q3gxk7vgwfl8nzi33"))))
24095 (properties `((upstream-name . "influenceR")))
24096 (build-system r-build-system)
24098 (list r-igraph r-matrix))
24099 (home-page "https://github.com/rcc-uchicago/influenceR")
24100 (synopsis "Tools to quantify structural importance of nodes in a network")
24102 "This package provides functionality to compute various node centrality
24103 measures on networks. Included are functions to compute betweenness
24104 centrality (by utilizing Madduri and Bader's SNAP library), implementations of
24105 Burt's constraint and @dfn{effective network size} (ENS) metrics, Borgatti's
24106 algorithm to identify key players, and Valente's bridging metric. The
24107 betweenness, Key Players, and bridging implementations are parallelized with
24109 (license license:gpl2)))
24111 (define-public r-emplik
24118 (uri (cran-uri "emplik" version))
24121 "1kw8g8j075bsicdvgkjf4870rfv5c30gvmw6qkkaz3ki22x74w77"))))
24122 (properties `((upstream-name . "emplik")))
24123 (build-system r-build-system)
24126 (home-page "https://www.ms.uky.edu/~mai/EmpLik.html")
24127 (synopsis "Empirical likelihood ratio for censored/truncated data")
24129 "This package provides empirical likelihood ratio tests for
24130 means/quantiles/hazards from possibly censored and/or truncated data. It also
24132 (license license:gpl2+)))
24134 (define-public r-imputeyn
24136 (name "r-imputeyn")
24141 (uri (cran-uri "imputeYn" version))
24144 "1b21w1aa5f7yiq8k0wa86wvbg4ij7f6ldwn6asfqwb0b90rvsgvs"))))
24145 (properties `((upstream-name . "imputeYn")))
24146 (build-system r-build-system)
24148 (list r-boot r-emplik r-mvtnorm r-quadprog r-survival))
24149 (home-page "https://cran.r-project.org/web/packages/imputeYn/")
24150 (synopsis "Impute last largest censored observation under weighted least squares")
24152 "This package allows for the imputation of the last largest censored
24153 observantions. This method brings less bias and more efficient estimates for
24155 (license license:gpl2)))
24157 (define-public r-adapenetclass
24159 (name "r-adapenetclass")
24164 (uri (cran-uri "AdapEnetClass" version))
24167 "01k3mj4g1ckbng7wkzzn9h0k9yf01cpnnkly0sjda574c5jhj0rc"))))
24168 (properties `((upstream-name . "AdapEnetClass")))
24169 (build-system r-build-system)
24171 (list r-glmnet r-imputeyn r-lars r-quadprog))
24172 (home-page "https://cran.r-project.org/web/packages/AdapEnetClass/")
24173 (synopsis "Class of adaptive elastic net methods for censored data")
24175 "This package provides methods for variable selection for AFT models.")
24176 (license license:gpl2)))
24178 (define-public r-flock
24185 (uri (cran-uri "flock" version))
24188 "1zg93p74icj4bhxnmnssj2xp6vw4yaksyavq03497v33xfpdxss7"))))
24189 (properties `((upstream-name . "flock")))
24190 (build-system r-build-system)
24191 (propagated-inputs (list r-rcpp))
24192 (home-page "https://cran.r-project.org/web/packages/flock/")
24193 (synopsis "Process synchronization using file locks")
24195 "This package implements synchronization between R processes (spawned by
24196 using the @code{parallel} package for instance) using file locks. It supports
24197 both exclusive and shared locking.")
24198 (license license:asl2.0)))
24200 (define-public r-archivist
24202 (name "r-archivist")
24207 (uri (cran-uri "archivist" version))
24210 "0q1qysack30xzxdbvvi56rk7r85hsj4ghls9r70ki7bl3rqwr4c9"))))
24211 (properties `((upstream-name . "archivist")))
24212 (build-system r-build-system)
24224 (home-page "https://pbiecek.github.io/archivist/")
24225 (synopsis "Tools for storing, restoring and searching for R objects")
24227 "Data exploration and modelling is a process in which a lot of data
24228 artifacts are produced. Artifacts like: subsets, data aggregates, plots,
24229 statistical models, different versions of data sets and different versions of
24230 results. Archivist helps to store and manage artifacts created in R. It
24231 allows you to store selected artifacts as binary files together with their
24232 metadata and relations. Archivist allows sharing artifacts with others. It
24233 can look for already created artifacts by using its class, name, date of the
24234 creation or other properties. It also makes it easy to restore such
24236 (license license:gpl2)))
24238 (define-public r-versions
24240 (name "r-versions")
24245 (uri (cran-uri "versions" version))
24248 "0zm49j785dgv7fyr1yl9q5f0dsk8hhpim5q5bpkgrkzv7pwjribd"))))
24249 (properties `((upstream-name . "versions")))
24250 (build-system r-build-system)
24251 (home-page "https://cran.r-project.org/web/packages/versions/")
24252 (synopsis "Query and install specific versions of CRAN packages")
24254 "This package allows you to install specified versions of R packages
24255 hosted on CRAN and provides functions to list available versions and the
24256 versions of currently installed packages.")
24257 (license license:bsd-3)))
24259 (define-public r-adapr
24266 (uri (cran-uri "adapr" version))
24269 "1s57jdbi5pik56xjz1d4438ax6cywg2yq2s47h5g6wrwvpgr1qfw"))))
24270 (properties `((upstream-name . "adapr")))
24271 (build-system r-build-system)
24288 (home-page "https://cran.r-project.org/web/packages/adapr/")
24289 (synopsis "Implementation of an accountable data analysis process")
24291 "This package tracks reading and writing within R scripts that are
24292 organized into a directed acyclic graph. It contains an interactive Shiny
24293 application @code{adaprApp()}. It uses Git and file hashes to track version
24294 histories of inputs and outputs.")
24295 (license license:lgpl2.0)))
24297 (define-public r-adapsamp
24299 (name "r-adapsamp")
24304 (uri (cran-uri "AdapSamp" version))
24307 "1jayjrsiib2ij4rxxj59g71r3xhzl5yqh0lhi8k6cfy03i7dkvis"))))
24308 (properties `((upstream-name . "AdapSamp")))
24309 (build-system r-build-system)
24310 (propagated-inputs (list r-pracma))
24311 (home-page "https://cran.r-project.org/web/packages/AdapSamp/")
24312 (synopsis "Adaptive sampling algorithms")
24314 "For distributions whose probability density functions are log-concave,
24315 the adaptive rejection sampling algorithm can be used to build envelope
24316 functions for sampling. For others, the modified adaptive rejection sampling
24317 algorithm, the concave-convex adaptive rejection sampling algorithm, and the
24318 adaptive slice sampling algorithm can be used. This R package mainly includes
24319 these four functions: @code{rARS()}, @code{rMARS()}, @code{rCCARS()}, and
24320 @code{rASS()}. These functions can realize sampling based on the algorithms
24322 (license license:gpl2)))
24324 (define-public r-adaptalint
24326 (name "r-adaptalint")
24331 (uri (cran-uri "adaptalint" version))
24334 "15qdcvnnbgcps8j5k79354wsc9alswijv8lcafg2i3lghaw536yf"))))
24335 (properties `((upstream-name . "adaptalint")))
24336 (build-system r-build-system)
24338 (list r-dplyr r-lintr r-purrr))
24339 (home-page "https://cran.r-project.org/web/packages/adaptalint/")
24340 (synopsis "Check R code style")
24342 "This package provides tools to infer the code style (which style rules
24343 are followed and which ones are not) from one package and use it to check
24344 another. This makes it easier to find and correct the most important problems
24346 (license license:gpl3)))
24348 (define-public r-fracdiff
24350 (name "r-fracdiff")
24355 (uri (cran-uri "fracdiff" version))
24358 "1dhfjlhr9sb38qgpsx0sm73l9lgc13d0fk32l7fmjfnalhr3n45q"))))
24359 (properties `((upstream-name . "fracdiff")))
24360 (build-system r-build-system)
24361 (home-page "https://github.com/mmaechler/fracdiff")
24363 "Fractionally differenced ARIMA aka ARFIMA(P,d,q) models")
24365 "This package provides tools for the maximum likelihood estimation of the
24366 parameters of a fractionally differenced ARIMA(p,d,q) model (Haslett and
24367 Raftery, Appl.Statistics, 1989); it includes inference and basic methods.")
24368 (license license:gpl2+)))
24370 (define-public r-forecast
24372 (name "r-forecast")
24377 (uri (cran-uri "forecast" version))
24380 "0zvn44k7npxai8kj0hgxaaqv1hgd8rxicnvj4cg7wfl8ba4yn0cz"))))
24381 (properties `((upstream-name . "forecast")))
24382 (build-system r-build-system)
24397 (list r-knitr)) ; needed for vignettes
24398 (home-page "https://pkg.robjhyndman.com/forecast/")
24399 (synopsis "Forecasting functions for time series and linear models")
24401 "This package provides methods and tools for displaying and analysing
24402 univariate time series forecasts including exponential smoothing via state
24403 space models and automatic ARIMA modelling.")
24404 (license license:gpl3)))
24406 (define-public r-formattable
24408 (name "r-formattable")
24413 (uri (cran-uri "formattable" version))
24415 (base32 "1vdxi0xmg019qyzjrp8bkjxciz245jcxsrkhfzd44ynqcwi4s3ag"))))
24416 (properties `((upstream-name . "formattable")))
24417 (build-system r-build-system)
24419 (list r-htmltools r-htmlwidgets r-lifecycle r-rmarkdown))
24422 (home-page "https://github.com/renkun-ken/formattable")
24423 (synopsis "Print vectors and data frames with text fromatting")
24425 "This R package provides functions to create formattable vectors and data
24426 frames. @emph{Formattable} vectors are printed with text formatting, and
24427 formattable data frames are printed with multiple types of formatting in HTML
24428 to improve the readability of data presented in tabular form rendered in web
24430 (license license:expat)))
24432 (define-public r-xmisc
24439 (uri (cran-uri "Xmisc" version))
24442 "11gwlcyxhz1p50m68cnqrxmisdk99v8vrsbvyr7k67f0kvsznzs1"))))
24443 (properties `((upstream-name . "Xmisc")))
24444 (build-system r-build-system)
24445 (home-page "https://cran.r-project.org/package=Xmisc")
24447 "Xiaobei's miscellaneous classes and functions")
24449 "This package provides Xiaobei's miscellaneous classes and functions,
24450 which are useful when developing R packages for @dfn{object oriented
24451 programming} (OOP) using R Reference Class.")
24452 (license license:gpl2+)))
24454 (define-public r-proxyc
24461 (uri (cran-uri "proxyC" version))
24464 "1mcimswrx1cjjm7wsgkzfrgh3jpf4sncwfvdvg2f14fzfzy7afd6"))))
24465 (properties `((upstream-name . "proxyC")))
24466 (build-system r-build-system)
24468 (list r-matrix r-rcpp r-rcpparmadillo r-rcppparallel))
24469 (home-page "https://cran.r-project.org/package=proxyC")
24470 (synopsis "Compute proximity in large sparse matrices")
24472 "This package provides efficient tools to compute the proximity between
24473 rows or columns of large matrices. Functions are optimised for large sparse
24474 matrices using the Armadillo and Intel TBB libraries. Among several built-in
24475 similarity/distance measures, computation of correlation, cosine similarity
24476 and Euclidean distance is particularly fast.")
24477 (license license:gpl3)))
24479 (define-public r-isocodes
24481 (name "r-isocodes")
24482 (version "2022.01.10")
24486 (uri (cran-uri "ISOcodes" version))
24489 "0gy7n5bgxnl4rawry0pg078bkks9lzsbsrwjq8q5cvxl4k3dwpdj"))))
24490 (properties `((upstream-name . "ISOcodes")))
24491 (build-system r-build-system)
24492 (home-page "https://cran.r-project.org/package=ISOcodes")
24493 (synopsis "Selected ISO codes")
24495 "This package provides ISO language, territory, currency, script and
24496 character codes. It provides ISO 639 language codes, ISO 3166 territory
24497 codes, ISO 4217 currency codes, ISO 15924 script codes, and the ISO 8859
24498 character codes as well as the UN M.49 area codes.")
24499 (license license:gpl2)))
24501 (define-public r-stopwords
24503 (name "r-stopwords")
24508 (uri (cran-uri "stopwords" version))
24511 "1ci1cgxrcvlhhplximsfv0plvjdbcd5kv0nphxnpildsn5m1rv65"))))
24512 (properties `((upstream-name . "stopwords")))
24513 (build-system r-build-system)
24516 (home-page "https://github.com/quanteda/stopwords")
24517 (synopsis "Multilingual stopword lists")
24519 "This package provides multiple sources of stopwords, for use in text
24520 analysis and natural language processing.")
24521 (license license:expat)))
24523 (define-public r-spacyr
24530 (uri (cran-uri "spacyr" version))
24533 "1b2ccgwsiqkvp7w37x8k7699c676q16vfrybkrfvyczyhki4s6nw"))))
24534 (properties `((upstream-name . "spacyr")))
24535 (build-system r-build-system)
24537 (list r-data-table r-reticulate))
24538 (home-page "https://spacyr.quanteda.io")
24539 (synopsis "R wrapper for the spaCy NLP library")
24541 "This package provides an R wrapper to the Python @dfn{natural language
24542 processing} (NLP) library @code{spaCy}, from @url{http://spacy.io}.")
24543 (license license:gpl3)))
24545 (define-public r-snowballc
24547 (name "r-snowballc")
24552 (uri (cran-uri "SnowballC" version))
24555 "1wwm71mp4b2mjb5985x782p6xj519dfrpd40qli7lmig6afyw3xi"))))
24556 (properties `((upstream-name . "SnowballC")))
24557 (build-system r-build-system)
24558 (home-page "https://r-forge.r-project.org/projects/r-temis/")
24559 (synopsis "Snowball stemmers based on the C libstemmer UTF-8 library")
24561 "This package provides an R interface to the C @code{libstemmer} library
24562 that implements Porter's word stemming algorithm for collapsing words to a
24563 common root to aid comparison of vocabulary. Currently supported languages
24564 are Danish, Dutch, English, Finnish, French, German, Hungarian, Italian,
24565 Norwegian, Portuguese, Romanian, Russian, Spanish, Swedish and Turkish.")
24566 (license license:bsd-3)))
24568 (define-public r-quanteda
24570 (name "r-quanteda")
24575 (uri (cran-uri "quanteda" version))
24578 "102wlx6481fskgdr5wv467n29f666q0qg9kjm0ivqfg9xsbvza12"))))
24579 (properties `((upstream-name . "quanteda")))
24580 (build-system r-build-system)
24595 (home-page "https://quanteda.io")
24596 (synopsis "Quantitative analysis of textual data")
24598 "This package provides a fast, flexible, and comprehensive framework for
24599 quantitative text analysis in R. It provides functionality for corpus
24600 management, creating and manipulating tokens and ngrams, exploring keywords in
24601 context, forming and manipulating sparse matrices of documents by features and
24602 feature co-occurrences, analyzing keywords, computing feature similarities and
24603 distances, applying content dictionaries, applying supervised and unsupervised
24604 machine learning, visually representing text and text analyses, and more.")
24605 (license license:gpl3)))
24607 (define-public r-topicmodels
24609 (name "r-topicmodels")
24614 (uri (cran-uri "topicmodels" version))
24617 "1d6iizmn042b59q2y6qc82z19wq3xm0zvgkf8iqf8fdzh51kmn5g"))))
24618 (properties `((upstream-name . "topicmodels")))
24619 (build-system r-build-system)
24623 (list r-modeltools r-slam r-tm))
24624 (home-page "https://cran.r-project.org/package=topicmodels")
24625 (synopsis "Topic models")
24627 "This package provides an interface to the C code for @dfn{Latent
24628 Dirichlet Allocation} (LDA) models and @dfn{Correlated Topics Models} (CTM) by
24629 David M. Blei and co-authors and the C++ code for fitting LDA models using
24630 Gibbs sampling by Xuan-Hieu Phan and co-authors.")
24631 (license license:gpl2)))
24633 (define-public r-stm
24640 (uri (cran-uri "stm" version))
24643 "0qwq4nin2n9fjd06852r8k7arvcgh46kcfb3lm21swgx6j8bgrhb"))))
24644 (properties `((upstream-name . "stm")))
24645 (build-system r-build-system)
24658 (home-page "http://www.structuraltopicmodel.com/")
24659 (synopsis "Estimation of the Structural Topic Model")
24661 "The @dfn{Structural Topic Model} (STM) allows researchers to estimate
24662 topic models with document-level covariates. The package also includes tools
24663 for model selection, visualization, and estimation of topic-covariate
24665 (license license:expat)))
24667 (define-public r-polycor
24674 (uri (cran-uri "polycor" version))
24677 "0285rvx8238qp8dix0jq0cqq7ks8h6cjwsscbc7dx4n9nph56pzh"))))
24678 (properties `((upstream-name . "polycor")))
24679 (build-system r-build-system)
24681 (list r-admisc r-matrix r-mvtnorm))
24682 (home-page "https://r-forge.r-project.org/projects/polycor/")
24683 (synopsis "Polychoric and polyserial correlations")
24685 "This package provides tools to compute polychoric and polyserial
24686 correlations by quick \"two-step\" methods or ML, optionally with standard
24687 errors; tetrachoric and biserial correlations are special cases.")
24688 (license license:gpl2+)))
24690 (define-public r-msm
24697 (uri (cran-uri "msm" version))
24700 "08vhazswyxr3y1zb9y60mbg3bappzlizxml8s08p65mh82xxkz5f"))))
24701 (properties `((upstream-name . "msm")))
24702 (build-system r-build-system)
24704 (list r-expm r-mvtnorm r-survival))
24705 (home-page "https://github.com/chjackson/msm")
24706 (synopsis "Multi-state Markov and hidden Markov models in continuous time")
24708 "This package provides functions for fitting continuous-time Markov and
24709 hidden Markov multi-state models to longitudinal data. It was designed for
24710 processes observed at arbitrary times in continuous time (panel data) but some
24711 other observation schemes are supported. Both Markov transition rates and the
24712 hidden Markov output process can be modelled in terms of covariates, which may
24713 be constant or piecewise-constant in time.")
24714 (license license:gpl2+)))
24716 (define-public r-ltm
24723 (uri (cran-uri "ltm" version))
24726 "0vhgbk6j0z3limsrbjkjkpfn2whiaij5j4jf1gg66mjs9dlylap1"))))
24727 (properties `((upstream-name . "ltm")))
24728 (build-system r-build-system)
24730 (list r-mass r-msm r-polycor))
24731 (home-page "https://github.com/drizopoulos/ltm")
24732 (synopsis "Latent trait models under IRT")
24734 "This is a package supporting the analysis of multivariate dichotomous
24735 and polytomous data using latent trait models under the Item Response Theory
24736 approach. It includes the Rasch, the Two-Parameter Logistic, the Birnbaum's
24737 Three-Parameter, the Graded Response, and the Generalized Partial Credit
24739 (license license:gpl2+)))
24741 (define-public r-mi
24748 (uri (cran-uri "mi" version))
24751 "1h47k5mpbvhid83277dvvj2di493bgzz9iarpyv3r30y219l7x1l"))))
24752 (properties `((upstream-name . "mi")))
24753 (build-system r-build-system)
24755 (list r-arm r-matrix))
24756 (home-page "http://www.stat.columbia.edu/~gelman/")
24757 (synopsis "Missing data imputation and model checking")
24759 "This package provides functions for data manipulation, imputing missing
24760 values in an approximate Bayesian framework, diagnostics of the models used to
24761 generate the imputations, confidence-building mechanisms to validate some of
24762 the assumptions of the imputation algorithm, and functions to analyze multiply
24763 imputed data sets with the appropriate degree of sampling uncertainty.")
24764 (license license:gpl2+)))
24766 (define-public r-matrixcalc
24768 (name "r-matrixcalc")
24773 (uri (cran-uri "matrixcalc" version))
24776 "1jkgl1v1q7cqpl1rf49qahdr9y0f33f0ldsbgby8xhfv0vpy21jr"))))
24777 (properties `((upstream-name . "matrixcalc")))
24778 (build-system r-build-system)
24779 (home-page "https://cran.r-project.org/web/packages/matrixcalc/")
24780 (synopsis "Collection of functions for matrix calculations")
24782 "This package provides a collection of functions to support matrix
24783 calculations for probability, econometric and numerical analysis. There are
24784 additional functions that are comparable to APL functions which are useful for
24785 actuarial models such as pension mathematics.")
24786 (license license:gpl2+)))
24788 (define-public r-matrixextra
24790 (name "r-matrixextra")
24791 (version "0.1.9-1")
24795 (uri (cran-uri "MatrixExtra" version))
24797 (base32 "098apgqlncgxspa8mi4bx2nk5fbk3880whqiwkvydsfsqrbv1sj0"))))
24798 (properties `((upstream-name . "MatrixExtra")))
24799 (build-system r-build-system)
24801 (list r-float r-matrix r-rcpp r-rhpcblasctl))
24804 (home-page "https://github.com/david-cortes/MatrixExtra")
24805 (synopsis "Extra methods for sparse matrices")
24807 "This package extends sparse matrix and vector classes from the Matrix
24808 package by providing:
24811 @item Methods and operators that work natively on CSR formats (compressed
24812 sparse row, a.k.a. @code{RsparseMatrix}) such as slicing/sub-setting,
24813 assignment, @code{rbind()}, mathematical operators for CSR and COO such as
24814 addition or @code{sqrt()}, and methods such as @code{diag()};
24815 @item Multi-threaded matrix multiplication and cross-product for many
24816 @code{<sparse, dense>} types, including the @code{float32} type from
24818 @item Coercion methods between pairs of classes which are not present in
24819 @code{Matrix}, such as from @code{dgCMatrix} to @code{ngRMatrix}, as well as
24820 convenience conversion functions;
24821 @item Utility functions for sparse matrices such as sorting the indices or
24822 removing zero-valued entries;
24823 @item Fast transposes that work by outputting in the opposite storage format;
24824 @item Faster replacements for many @code{Matrix} methods for all sparse types,
24825 such as slicing and elementwise multiplication.
24826 @item Convenience functions for sparse objects, such as @code{mapSparse} or a
24827 shorter @code{show} method.
24830 (license license:gpl2+)))
24832 (define-public r-sem
24839 (uri (cran-uri "sem" version))
24842 "05hk72zxvyv6kkjhk5y6qw253c64108az7030z8j1sz8wq03n0md"))))
24843 (properties `((upstream-name . "sem")))
24844 (build-system r-build-system)
24846 (list r-boot r-mass r-mi))
24847 (home-page "https://cran.r-project.org/package=sem")
24848 (synopsis "Structural equation models")
24850 "This package provides functions for fitting general linear structural
24851 equation models (with observed and latent variables) using the RAM approach,
24852 and for fitting structural equations in observed-variable models by two-stage
24854 (license license:gpl2+)))
24856 (define-public r-semtools
24858 (name "r-semtools")
24863 (uri (cran-uri "semTools" version))
24866 "1dpsn43ifvfy5v8w2fqdy54yclmy0d3qlzix67lflr2r7isq7y6x"))))
24867 (properties `((upstream-name . "semTools")))
24868 (build-system r-build-system)
24870 (list r-lavaan r-pbivnorm))
24871 (home-page "https://github.com/simsem/semTools/wiki")
24872 (synopsis "Useful tools for structural equation modeling")
24874 "This package provides useful tools for structural equation modeling.")
24875 (license license:gpl2+)))
24877 (define-public r-regsem
24884 (uri (cran-uri "regsem" version))
24887 "1v33wkrsawcvaa06cijp8ybwi82a0x34y59hdknwdbywplnirzr8"))))
24888 (properties `((upstream-name . "regsem")))
24889 (build-system r-build-system)
24891 (list r-lavaan r-rcpp r-rcpparmadillo r-rsolnp))
24894 (home-page "https://cran.r-project.org/package=regsem")
24895 (synopsis "Regularized structural equation modeling")
24897 "This package uses both ridge and lasso penalties (and extensions) to
24898 penalize specific parameters in structural equation models. The package
24899 offers additional cost functions, cross validation, and other extensions
24900 beyond traditional structural equation models. It also contains a function to
24901 perform @dfn{exploratory mediation} (XMed).")
24902 (license license:gpl2+)))
24904 (define-public r-stanheaders
24906 (name "r-stanheaders")
24907 (version "2.21.0-7")
24911 (uri (cran-uri "StanHeaders" version))
24914 "0srkyawyiykn3p5lw1z3zf18s4ax4iasv1ci3l1px40f9w36wm17"))))
24915 (properties `((upstream-name . "StanHeaders")))
24916 (build-system r-build-system)
24917 (inputs (list pandoc))
24919 (list r-rcppeigen r-rcppparallel))
24921 (list gfortran r-knitr)) ; for vignettes
24922 (home-page "https://mc-stan.org/")
24923 (synopsis "C++ header files for Stan")
24925 "The C++ header files of the Stan project are provided by this package.
24926 There is a shared object containing part of the @code{CVODES} library, but it
24927 is not accessible from R. @code{r-stanheaders} is only useful for developers
24928 who want to utilize the @code{LinkingTo} directive of their package's
24929 DESCRIPTION file to build on the Stan library without incurring unnecessary
24932 The Stan project develops a probabilistic programming language that implements
24933 full or approximate Bayesian statistical inference via Markov Chain Monte
24934 Carlo or variational methods and implements (optionally penalized) maximum
24935 likelihood estimation via optimization. The Stan library includes an advanced
24936 automatic differentiation scheme, templated statistical and linear algebra
24937 functions that can handle the automatically differentiable scalar types (and
24938 doubles, ints, etc.), and a parser for the Stan language. The @code{r-rstan}
24939 package provides user-facing R functions to parse, compile, test, estimate,
24940 and analyze Stan models.")
24941 (license license:bsd-3)))
24943 (define-public r-rpf
24950 (uri (cran-uri "rpf" version))
24953 "1yr1i7kswq57mcxv05lh7bvbicz1djqxcl6f13dlgsf3ww56gzg1"))))
24954 (properties `((upstream-name . "rpf")))
24955 (build-system r-build-system)
24957 (list r-lifecycle r-mvtnorm r-rcpp r-rcppeigen))
24960 (home-page "https://github.com/jpritikin/rpf")
24961 (synopsis "Response probability functions")
24963 "The purpose of this package is to factor out logic and math common to
24964 Item Factor Analysis fitting, diagnostics, and analysis. It is envisioned as
24965 core support code suitable for more specialized IRT packages to build upon.
24966 Complete access to optimized C functions is made available with
24967 @code{R_RegisterCCallable()}.")
24968 (license license:gpl3+)))
24970 (define-public r-openmx
24977 (uri (cran-uri "OpenMx" version))
24980 "1v969100hllh0lwlxd2gv0k7krrsp9gc07iinx0nn04wkzh0rib5"))))
24981 (properties `((upstream-name . "OpenMx")))
24982 (build-system r-build-system)
24994 (native-inputs (list r-knitr gfortran))
24995 (home-page "http://openmx.ssri.psu.edu")
24996 (synopsis "Extended structural equation modelling")
24998 "This package allows for the estimation of a wide variety of advanced
24999 multivariate statistical models. It consists of a library of functions and
25000 optimizers that allow you to quickly and flexibly define an SEM model and
25001 estimate parameters given observed data.")
25002 (license license:asl2.0)))
25004 (define-public r-kutils
25011 (uri (cran-uri "kutils" version))
25014 "06jk66wbq3jmdf2jdhqns6r3yk36l2x7c907x977zv80sqxa1l37"))))
25015 (properties `((upstream-name . "kutils")))
25016 (build-system r-build-system)
25018 (list r-foreign r-openxlsx r-plyr r-runit r-xtable))
25019 (home-page "https://cran.r-project.org/package=kutils")
25020 (synopsis "Project management tools")
25022 "This package provides tools for data importation, recoding, and
25023 inspection. There are functions to create new project folders, R code
25024 templates, create uniquely named output directories, and to quickly obtain a
25025 visual summary for each variable in a data frame. The main feature here is
25026 the systematic implementation of the \"variable key\" framework for data
25027 importation and recoding.")
25028 (license license:gpl2)))
25030 (define-public r-rockchalk
25032 (name "r-rockchalk")
25033 (version "1.8.151")
25037 (uri (cran-uri "rockchalk" version))
25040 "17mfaxn3gj0vac5wdmsjj2z2668cszbpvan7hnxp7ic9bvsm1w2y"))))
25041 (properties `((upstream-name . "rockchalk")))
25042 (build-system r-build-system)
25044 (list r-cardata r-kutils r-lme4 r-mass))
25045 (home-page "https://cran.r-project.org/package=rockchalk")
25046 (synopsis "Regression estimation and presentation")
25048 "This package provides a collection of functions for interpretation and
25049 presentation of regression analysis. These functions are used to produce the
25050 statistics lectures in @url{http://pj.freefaculty.org/guides}. The package
25051 includes regression diagnostics, regression tables, and plots of interactions
25052 and \"moderator\" variables. The emphasis is on \"mean-centered\" and
25053 \"residual-centered\" predictors. The vignette @code{rockchalk} offers a
25054 fairly comprehensive overview.")
25055 (license license:gpl3+)))
25057 (define-public r-lisreltor
25059 (name "r-lisreltor")
25064 (uri (cran-uri "lisrelToR" version))
25067 "0zicq0z3hhixan1p1apybnf3v5s6v6ysll4pcz8ivygwr2swv3p5"))))
25068 (properties `((upstream-name . "lisrelToR")))
25069 (build-system r-build-system)
25070 (home-page "https://cran.r-project.org/package=lisrelToR")
25071 (synopsis "Import output from LISREL into R")
25073 "This is an unofficial package aimed at automating the import of LISREL
25075 (license license:gpl2)))
25077 (define-public r-bdgraph
25084 (uri (cran-uri "BDgraph" version))
25087 "0rg3wi9xwsbj90gb60p3vzkfrf76hwh47nc6fwv6c21yzd3s7vm4"))))
25088 (properties `((upstream-name . "BDgraph")))
25089 (build-system r-build-system)
25092 (home-page "https://www.uva.nl/profile/a.mohammadi")
25093 (synopsis "Bayesian structure learning in graphical models")
25095 "This package provides statistical tools for Bayesian structure learning
25096 in undirected graphical models for continuous, discrete, and mixed data. It
25097 uses a trans-dimensional @dfn{Markov Chain Monte Carlo} (MCMC) approach based
25098 on a continuous-time birth-death process.")
25099 (license license:gpl2+)))
25101 (define-public r-d3network
25103 (name "r-d3network")
25104 (version "0.5.2.1")
25108 (uri (cran-uri "d3Network" version))
25111 "1gh979z9wksyxxxdzlfzibn0ysvf6h1ij7vwpd55fvbwr308syaw"))))
25112 (properties `((upstream-name . "d3Network")))
25113 (build-system r-build-system)
25115 (list r-plyr r-rjson r-whisker))
25116 (home-page "http://christophergandrud.github.io/d3Network/")
25117 (synopsis "Create D3 JavaScript network, tree, dendrogram, and Sankey graphs")
25119 "This package is intended to make it easy to create D3 JavaScript
25120 network, tree, dendrogram, and Sankey graphs from R using data frames.")
25121 (license license:gpl3+)))
25123 (define-public r-qgraph
25130 (uri (cran-uri "qgraph" version))
25133 "0r225b7rnsv6wz41ij0msmqr1xy0iqxh9dbsvjixbi1hvgv91wds"))))
25134 (properties `((upstream-name . "qgraph")))
25135 (build-system r-build-system)
25155 (home-page "http://sachaepskamp.com/qgraph/")
25156 (synopsis "Weighted network visualization and analysis")
25158 "This package implements tools for weighted network visualization and
25159 analysis, as well as Gaussian graphical model computation. It contains graph
25160 plotting methods, and tools for psychometric data visualization and graphical
25161 model estimation. See Epskamp et al. (2012)
25162 @url{doi:10.18637/jss.v048.i04}.")
25163 (license license:gpl2)))
25165 (define-public r-semplot
25172 (uri (cran-uri "semPlot" version))
25175 "0d7v9yqc9nhx3hdrp444w1ah66zai3lg5y778m85r7ngh1prxlvc"))))
25176 (properties `((upstream-name . "semPlot")))
25177 (build-system r-build-system)
25190 (home-page "https://github.com/SachaEpskamp/semPlot")
25191 (synopsis "Unified visualizations of structural equation models")
25193 "Structural equation modeling (SEM) has a long history of representing
25194 models graphically as path diagrams. The semPlot package for R fills the gap
25195 between advanced, but time-consuming, graphical software and the limited
25196 graphics produced automatically by SEM software. In addition, semPlot offers
25197 more functionality than drawing path diagrams: it can act as a common ground
25198 for importing SEM results into R. Any result usable as input to semPlot can
25199 also be represented in any of the three popular SEM frame-works, as well as
25200 translated to input syntax for the R packages @code{sem} and @code{lavaan}.")
25201 (license license:gpl2)))
25203 (define-public r-cdm
25210 (uri (cran-uri "CDM" version))
25213 "0k3arkzz7nzswjcsr7fdmpfs94ilg8l265dyn49555fw3673cgqj"))))
25214 (properties `((upstream-name . "CDM")))
25215 (build-system r-build-system)
25217 (list r-mvtnorm r-polycor r-rcpp r-rcpparmadillo))
25219 "https://github.com/alexanderrobitzsch/CDM")
25220 (synopsis "Cognitive diagnosis modeling")
25222 "This package provides functions for cognitive diagnosis modeling and
25223 multidimensional item response modeling for dichotomous and polytomous item
25224 responses. It enables the estimation of the DINA and DINO model, the multiple
25225 group (polytomous) GDINA model, the multiple choice DINA model, the general
25226 diagnostic model (GDM), the structured latent class model (SLCA), and
25227 regularized latent class analysis. See George, Robitzsch, Kiefer, Gross, and
25228 Uenlue (2017) @url{doi:10.18637/jss.v074.i02} for further details on
25229 estimation and the package structure. For tutorials on how to use the CDM
25230 package see George and Robitzsch (2015, @url{doi:10.20982/tqmp.11.3.p189}) as
25231 well as Ravand and Robitzsch (2015).")
25232 (license license:gpl2+)))
25234 (define-public r-tam
25241 (uri (cran-uri "TAM" version))
25244 "1969xm1f7s183h0xnd4g1bxhjp80rl7kad29zwcig0fmw6bs2mpd"))))
25245 (properties `((upstream-name . "TAM")))
25246 (build-system r-build-system)
25248 (list r-cdm r-rcpp r-rcpparmadillo))
25249 (home-page "http://www.edmeasurementsurveys.com/TAM/Tutorials/")
25250 (synopsis "Test analysis modules")
25252 "This package includes tools for marginal maximum likelihood estimation
25253 and joint maximum likelihood estimation for unidimensional and
25254 multidimensional item response models. The package functionality covers the
25255 Rasch model, 2PL model, 3PL model, generalized partial credit model,
25256 multi-faceted Rasch model, nominal item response model, structured latent
25257 class model, mixture distribution IRT models, and located latent class models.
25258 Latent regression models and plausible value imputation are also supported.")
25259 (license license:gpl2+)))
25261 (define-public r-erm
25268 (uri (cran-uri "eRm" version))
25271 "0smym010kswc5vx90qr3x1vl16xj1x1i54rvrj006dc4agc1vmlk"))))
25272 (properties `((upstream-name . "eRm")))
25273 (build-system r-build-system)
25275 (list r-colorspace r-lattice r-mass r-matrix r-psych))
25276 (native-inputs (list gfortran))
25277 (home-page "https://cran.r-project.org/package=eRm")
25278 (synopsis "Extended Rasch modeling")
25280 "This package provides tools to fit @dfn{Rasch models} (RM), @dfn{linear
25281 logistic test models} (LLTM), @dfn{rating scale model} (RSM), @dfn{linear
25282 rating scale models} (LRSM), @dfn{partial credit models} (PCM), and
25283 @dfn{linear partial credit models} (LPCM). Missing values are allowed in the
25284 data matrix. Additional features are the ML estimation of the person
25285 parameters, Andersen's LR-test, item-specific Wald test, Martin-Loef-Test,
25286 nonparametric Monte-Carlo Tests, itemfit and personfit statistics including
25287 infit and outfit measures, ICC and other plots, automated stepwise item
25288 elimination, and a simulation module for various binary data matrices.")
25289 (license license:gpl3)))
25291 (define-public r-irtoys
25298 (uri (cran-uri "irtoys" version))
25301 "0h6iiaxikhbxhbyksbjnb09qdxinlkwr2v9yzs5wslbni14paq5q"))))
25302 (properties `((upstream-name . "irtoys")))
25303 (build-system r-build-system)
25306 (home-page "https://cran.r-project.org/package=irtoys")
25307 (synopsis "Collection of functions related to Item Response Theory (IRT)")
25309 "This package provides a collection of functions useful in learning and
25310 practicing @dfn{Item Response Theory} (IRT), which can be combined into larger
25311 programs. It provides basic CTT analysis, a simple common interface to the
25312 estimation of item parameters in IRT models for binary responses with three
25313 different programs (ICL, BILOG-MG, and ltm), ability estimation (MLE, BME,
25314 EAP, WLE, plausible values), item and person fit statistics, scaling
25315 methods (MM, MS, Stocking-Lord, and the complete Hebaera method), and a rich
25316 array of parametric and non-parametric (kernel) plots. It estimates and plots
25317 Haberman's interaction model when all items are dichotomously scored.")
25318 (license license:gpl2+)))
25320 (define-public r-iheatmapr
25322 (name "r-iheatmapr")
25327 (uri (cran-uri "iheatmapr" version))
25330 "1pwkwh7ljlpr6zyz6j8knpz3iw60xzkw8amc98x4pc2mw148jvzx"))))
25331 (properties `((upstream-name . "iheatmapr")))
25332 (build-system r-build-system)
25334 (list r-fastcluster
25344 (home-page "https://docs.ropensci.org/iheatmapr")
25345 (synopsis "Interactive, Complex Heatmaps")
25347 "iheatmapr is an R package for building complex, interactive heatmaps
25348 using modular building blocks. \"Complex\" heatmaps are heatmaps in which
25349 subplots along the rows or columns of the main heatmap add more information
25350 about each row or column. For example, a one column additional heatmap may
25351 indicate what group a particular row or column belongs to. Complex heatmaps
25352 may also include multiple side by side heatmaps which show different types of
25353 data for the same conditions. Interactivity can improve complex heatmaps by
25354 providing tooltips with information about each cell and enabling zooming into
25355 interesting features. iheatmapr uses the plotly library for interactivity.")
25356 (license license:expat)))
25358 (define-public r-packrat
25365 (uri (cran-uri "packrat" version))
25368 "1hnwhdgqljqs3m7c4rjlyndyc0k85jpa4rbfymxkm3zjg3yy3g78"))))
25369 (properties `((upstream-name . "packrat")))
25370 (build-system r-build-system)
25371 (home-page "https://github.com/rstudio/packrat/")
25372 (synopsis "Dependency management R projects")
25374 "This package provides a dependency manager for R projects that allows
25375 you to manage the R packages your project depends on in an isolated, portable,
25376 and reproducible way.")
25377 (license license:gpl2)))
25379 (define-public r-rsconnect
25381 (name "r-rsconnect")
25386 (uri (cran-uri "rsconnect" version))
25389 "1kyr4v7vds2yw3xmkk2yr56ylz1h95944brylwvwmwj5yxvm419w"))))
25390 (properties `((upstream-name . "rsconnect")))
25391 (build-system r-build-system)
25400 (home-page "https://github.com/rstudio/rsconnect")
25401 (synopsis "Deployment interface for R Markdown documents and Shiny applications")
25403 "This package provides a programmatic deployment interface for RPubs,
25404 shinyapps.io, and RStudio Connect. Supported content types include R Markdown
25405 documents, Shiny applications, Plumber APIs, plots, and static web content.")
25406 (license license:gpl2)))
25408 ;; This package includes minified JavaScript files. When upgrading please
25409 ;; check that there are no new minified JavaScript files.
25410 (define-public r-dygraphs
25412 (name "r-dygraphs")
25413 (version "1.1.1.6")
25417 (uri (cran-uri "dygraphs" version))
25420 "022j007mzfa9k2n31yg4aizcsf571vv3jip092h23rqj03rk3ly3"))))
25421 (properties `((upstream-name . "dygraphs")))
25422 (build-system r-build-system)
25424 `(#:modules ((guix build utils)
25425 (guix build r-build-system)
25429 (modify-phases %standard-phases
25430 (add-after 'unpack 'process-javascript
25431 (lambda* (#:key inputs #:allow-other-keys)
25432 (with-directory-excursion "inst/htmlwidgets/lib/"
25436 `(("dygraphs/dygraph-combined-dev.js"
25437 "dygraph-combined.js")
25438 (,(assoc-ref inputs "js-jquery")
25439 "jquery/jquery.min.js")
25440 (,(assoc-ref inputs "js-fquarter")
25441 "fquarter/moment-fquarter.min.js"))))
25442 (lambda (sources targets)
25443 (for-each (lambda (source target)
25444 (format #t "Processing ~a --> ~a~%"
25446 (let ((minified (open-pipe* OPEN_READ "uglifyjs" source)))
25447 (call-with-output-file target
25449 (dump-port minified port)))))
25450 sources targets))))
25453 `(("uglifyjs" ,node-uglify-js)
25454 ;; They actually use version 1.11.1, but this more recent version
25455 ;; should be just fine.
25459 (uri "https://code.jquery.com/jquery-1.12.4.js")
25462 "0x9mrc1668icvhpwzvgafm8xm11x9lfai9nwr66aw6pjnpwkc3s3"))))
25466 (uri (string-append "https://raw.githubusercontent.com/robgallen/"
25467 "moment-fquarter/1.0.1/moment-fquarter.js"))
25470 "01mdnsaibm9jy2f1qpbn692hpv309lhj5si9nagib4dawmrkffij"))))))
25472 (list r-htmltools r-htmlwidgets r-magrittr r-xts r-zoo))
25473 (home-page "https://github.com/rstudio/dygraphs")
25474 (synopsis "Interface to Dygraphs interactive time series charting library")
25476 "This package provides an R interface to the dygraphs JavaScript charting
25477 library (a copy of which is included in the package). It provides rich
25478 facilities for charting time-series data in R, including highly configurable
25479 series- and axis-display and interactive features like zoom/pan and
25480 series/point highlighting.")
25481 (license license:expat)))
25483 (define-public r-shinystan
25485 (name "r-shinystan")
25490 (uri (cran-uri "shinystan" version))
25493 "0afm703zriyqprz1zvypir80lq2ylfff3qvj5i7p9n365mm8b150"))))
25494 (properties `((upstream-name . "shinystan")))
25495 (build-system r-build-system)
25513 (home-page "https://mc-stan.org/")
25514 (synopsis "Interactive visual and numerical analysis for Bayesian models")
25516 "This package provides a graphical user interface for interactive
25517 @dfn{Markov chain Monte Carlo} (MCMC) diagnostics and plots and tables helpful
25518 for analyzing a posterior sample. The interface is powered by the Shiny web
25519 application framework and works with the output of MCMC programs written in
25520 any programming language (and has extended functionality for Stan models fit
25521 using the @code{rstan} and @code{rstanarm} packages).")
25522 (license license:gpl3+)))
25524 (define-public r-rstantools
25526 (name "r-rstantools")
25531 (uri (cran-uri "rstantools" version))
25534 "1dsfgi02hps878n3vimfdbzpm4gr5n3ccrmnc61ncrqcp6p0p0fb"))))
25535 (properties `((upstream-name . "rstantools")))
25536 (build-system r-build-system)
25537 (inputs (list pandoc))
25539 (list r-desc r-rcpp r-rcppparallel))
25542 (home-page "https://mc-stan.org/rstantools/")
25543 (synopsis "Tools for developing R packages interfacing with Stan")
25545 "This package provides various tools for developers of R packages
25546 interfacing with @url{https://mc-stan.org, Stan}, including functions to set
25547 up the required package structure, S3 generics and default methods to unify
25548 function naming across Stan-based R packages, and vignettes with
25549 recommendations for developers.")
25550 (license license:gpl3+)))
25552 (define-public r-loo
25559 (uri (cran-uri "loo" version))
25561 (base32 "1wa5hxk7lkr88mway6b7xd5arrkkl2ldl9rf0v1nqwp8lia2ysl6"))))
25562 (properties `((upstream-name . "loo")))
25563 (build-system r-build-system)
25567 (list r-checkmate r-matrixstats))
25570 (home-page "https://mc-stan.org/loo/")
25571 (synopsis "Leave-One-Out cross-validation and WAIC for Bayesian models")
25573 "This package provides an implementation of efficient approximate
25574 @dfn{leave-one-out} (LOO) cross-validation for Bayesian models fit using
25575 Markov chain Monte Carlo, as described in @url{doi:10.1007/s11222-016-9696-4}.
25576 The approximation uses @dfn{Pareto smoothed importance sampling} (PSIS), a new
25577 procedure for regularizing importance weights. As a byproduct of the
25578 calculations, we also obtain approximate standard errors for estimated
25579 predictive errors and for the comparison of predictive errors between models.
25580 The package also provides methods for using stacking and other model weighting
25581 techniques to average Bayesian predictive distributions.")
25582 (license license:gpl3+)))
25584 (define-public r-rstan
25591 (uri (cran-uri "rstan" version))
25594 "1smr5cjrqvpdnkmjpjp73p96sy581x15mwrn4fqd1p4d5mbgxr46"))))
25595 (properties `((upstream-name . "rstan")))
25596 (build-system r-build-system)
25599 (modify-phases %standard-phases
25600 (add-before 'install 'set-timezone
25601 ;; This package is picky about timezones.
25602 (lambda* (#:key inputs #:allow-other-keys)
25603 (setenv "TZ" "UTC+1")
25605 (search-input-directory inputs
25606 "share/zoneinfo")))))))
25608 (list tzdata-for-tests pandoc r-knitr))
25620 (home-page "https://discourse.mc-stan.org/")
25621 (synopsis "R interface to Stan")
25623 "User-facing R functions are provided to parse, compile, test, estimate,
25624 and analyze Stan models by accessing the header-only Stan library provided by
25625 the StanHeaders package. The Stan project develops a probabilistic
25626 programming language that implements full Bayesian statistical inference via
25627 Markov Chain Monte Carlo, rough Bayesian inference via 'variational'
25628 approximation, and (optionally penalized) maximum likelihood estimation via
25629 optimization. In all three cases, automatic differentiation is used to
25630 quickly and accurately evaluate gradients without burdening the user with the
25631 need to derive the partial derivatives.")
25632 (license license:gpl3+)))
25634 (define-public r-rstanarm
25636 (name "r-rstanarm")
25641 (uri (cran-uri "rstanarm" version))
25644 "19rj396q84maxnd9d2xcd5rblg3310xn7sqbd6k18kwf3dvd7wp9"))))
25645 (properties `((upstream-name . "rstanarm")))
25646 (build-system r-build-system)
25667 (home-page "https://mc-stan.org/rstanarm/")
25668 (synopsis "Bayesian applied regression modeling via Stan")
25670 "This package estimates previously compiled regression models using the
25671 @code{rstan} package, which provides the R interface to the Stan C++ library
25672 for Bayesian estimation. Users specify models via the customary R syntax with
25673 a formula and @code{data.frame} plus some additional arguments for priors.")
25674 (license license:gpl3+)))
25676 (define-public r-kendall
25683 (uri (cran-uri "Kendall" version))
25686 "1xmk95l4i3kj9jn0xh1chi2rj322k29jq14ra5pa7316gwf9vx2m"))))
25687 (properties `((upstream-name . "Kendall")))
25688 (build-system r-build-system)
25693 (home-page "https://cran.r-project.org/web/packages/Kendall/")
25694 (synopsis "Kendall rank correlation and Mann-Kendall trend test")
25696 "This package computes the Kendall rank correlation and Mann-Kendall
25698 (license license:gpl2+)))
25700 (define-public r-keyring
25707 (uri (cran-uri "keyring" version))
25710 "1j8l6nmh4dr70kwybiais8yh687fdwrj134xynq68igw1b1rm8ga"))))
25711 (properties `((upstream-name . "keyring")))
25712 (build-system r-build-system)
25722 (native-inputs (list pkg-config))
25723 (home-page "https://github.com/r-lib/keyring")
25724 (synopsis "Access the system credential store from R")
25726 "This package provides a platform-independent API to access the operating
25727 system's credential store. It currently supports Keychain on macOS,
25728 Credential Store on Windows, the Secret Service API on GNU/Linux, and a
25729 simple, platform independent store implemented with environment variables.
25730 Additional storage back-ends can be added easily.")
25731 (license license:expat)))
25733 (define-public r-zyp
25736 (version "0.10-1.1")
25740 (uri (cran-uri "zyp" version))
25743 "03cxpkfbhrx1fy8l0dl9a13ghz93cqq6877wa8rig09ksdiivaw9"))))
25744 (properties `((upstream-name . "zyp")))
25745 (build-system r-build-system)
25748 (home-page "https://cran.r-project.org/web/packages/zyp/")
25749 (synopsis "Zhang + Yue-Pilon Trends Package")
25751 "This package contains an efficient implementation of Sen's slope
25752 method (Sen, 1968) plus implementation of Xuebin Zhang's (Zhang, 1999) and
25753 Yue-Pilon's (Yue, 2002) pre-whitening approaches to determining trends in
25755 (license license:lgpl2.1)))
25757 (define-public r-rlinsolve
25759 (name "r-rlinsolve")
25764 (uri (cran-uri "Rlinsolve" version))
25767 "1xv500n1480qyakw0isanw1s5ywykhc207hqja4804s5s2m8zfjw"))))
25768 (properties `((upstream-name . "Rlinsolve")))
25769 (build-system r-build-system)
25771 (list r-matrix r-rcpp r-rcpparmadillo r-rdpack))
25772 (home-page "https://cran.r-project.org/web/packages/Rlinsolve/")
25773 (synopsis "Iterative solvers for (sparse) linear system of equations")
25775 "Solving a system of linear equations is one of the most fundamental
25776 computational problems for many fields of mathematical studies, such as
25777 regression problems from statistics or numerical partial differential
25778 equations. This package provides basic stationary iterative solvers such as
25779 Jacobi, Gauss-Seidel, Successive Over-Relaxation and SSOR methods.
25780 Nonstationary, also known as Krylov subspace methods are also provided.
25781 Sparse matrix computation is also supported in that solving large and sparse
25782 linear systems can be manageable using the @code{Matrix} package along with
25783 @code{RcppArmadillo}.")
25784 (license license:gpl3+)))
25786 (define-public r-zvcv
25793 (uri (cran-uri "ZVCV" version))
25796 "0gc76j9i8fkm2v638nyzzb1qxl4zmapbspkkaffb8gi5qyjja448"))))
25797 (properties `((upstream-name . "ZVCV")))
25798 (build-system r-build-system)
25809 (home-page "https://cran.r-project.org/web/packages/ZVCV/")
25810 (synopsis "Zero-Variance Control Variates")
25812 "@dfn{Zero-variance control variates} (ZV-CV) is a post-processing method
25813 to reduce the variance of Monte Carlo estimators of expectations using the
25814 derivatives of the log target. Once the derivatives are available, the only
25815 additional computational effort is in solving a linear regression problem.
25816 This method has been extended to higher dimensions using regularisation. This
25817 package can be used to easily perform ZV-CV or regularised ZV-CV when a set of
25818 samples, derivatives and function evaluations are available. Additional
25819 functions for applying ZV-CV to two estimators for the normalising constant of
25820 the posterior distribution in Bayesian statistics are also supplied.")
25821 (license license:gpl2+)))
25823 (define-public r-ztype
25830 (uri (cran-uri "ztype" version))
25833 "0brbq2rgkl4mhjbb70kkfv47lzs66k9ppfs2klavcbripirxn5fx"))))
25834 (properties `((upstream-name . "ztype")))
25835 (build-system r-build-system)
25844 (home-page "https://cran.r-project.org/web/packages/ztype/")
25845 (synopsis "Run a Ztype game loaded with R functions")
25847 "How fast can you type R functions on your keyboard? Find out by running
25848 a @code{zty.pe} game: export R functions as instructions to type to destroy
25849 opponents' vessels.")
25850 (license license:gpl3)))
25852 (define-public r-zseq
25859 (uri (cran-uri "Zseq" version))
25862 "06dndi2b1q79bmxax11bv0l5ifcz1mhpvbn90y6a6xymrgcq0ivi"))))
25863 (properties `((upstream-name . "Zseq")))
25864 (build-system r-build-system)
25867 (home-page "https://cran.r-project.org/web/packages/Zseq/")
25868 (synopsis "Integer sequence generator")
25870 "This package generates well-known integer sequences. The @code{gmp}
25871 package is adopted for computing with arbitrarily large numbers. Every
25872 function has a hyperlink to its corresponding item in the @dfn{On-Line
25873 Encyclopedia of Integer Sequences} (OEIS) in the function help page.")
25874 (license license:gpl3+)))
25876 (define-public r-isoband
25883 (uri (cran-uri "isoband" version))
25886 "19bbi0n0kz33xdgmdprcmc6raphd1hcm1w1brc16z5phcsh3zxa6"))))
25887 (properties `((upstream-name . "isoband")))
25888 (build-system r-build-system)
25891 (home-page "https://github.com/wilkelab/isoband")
25892 (synopsis "Generate isolines and isobands from regularly spaced elevation grids")
25894 "This package provides a fast C++ implementation to generate contour
25895 lines (isolines) and contour polygons (isobands) from regularly spaced grids
25896 containing elevation data.")
25897 (license license:expat)))
25899 (define-public r-ppcor
25906 (uri (cran-uri "ppcor" version))
25909 "1x9b2kb8s0bp92b17gby0jwzzr3i4cf3ap9c4nq7m8fav72g0y3a"))))
25910 (properties `((upstream-name . "ppcor")))
25911 (build-system r-build-system)
25914 (home-page "https://cran.r-project.org/web/packages/ppcor/")
25915 (synopsis "Partial and semi-partial correlation")
25917 "This package provides users not only with a function to readily
25918 calculate the higher-order partial and semi-partial correlations but also with
25919 statistics and p-values of the correlation coefficients.")
25920 (license license:gpl2)))
25922 (define-public r-hrbrthemes
25924 (name "r-hrbrthemes")
25929 (uri (cran-uri "hrbrthemes" version))
25931 (base32 "057h60b5p53dcyjyfwlgjc1ry968s9s64dw78p443w8717zk7zpc"))))
25932 (properties `((upstream-name . "hrbrthemes")))
25933 (build-system r-build-system)
25945 (home-page "https://github.com/hrbrmstr/hrbrthemes/")
25946 (synopsis "Additional themes, theme components and utilities for @code{ggplot2}")
25948 "This package provides a compilation of extra @code{ggplot2} themes,
25949 scales and utilities, including a spell check function for plot label fields
25950 and an overall emphasis on typography.")
25951 (license license:expat)))
25953 (define-public r-crochet
25960 (uri (cran-uri "crochet" version))
25963 "0zvjaf6cv0nrjb4l4llkr0mmgha7ig31p4ri2rlnqyjlxi5l8hyq"))))
25964 (build-system r-build-system)
25967 (home-page "https://github.com/agrueneberg/crochet")
25968 (synopsis "Implementation Helper for Matrix-Like Types")
25970 "Functions to help implement the extraction / subsetting / indexing
25971 function @code{[} and replacement function @code{[<-} of custom matrix-like
25972 types (based on S3, S4, etc.), modeled as closely to the base matrix class
25973 as possible (with tests to prove it).")
25974 (license license:expat)))
25976 (define-public r-boa
25979 (version "1.1.8-2")
25983 (uri (cran-uri "boa" version))
25986 "04lhqk5qfvaz1jk90glr2yi5vq7cdy0w8m6g2lnzk359l9y41zhp"))))
25987 (properties `((upstream-name . "boa")))
25988 (build-system r-build-system)
25989 (home-page "https://www.jstatsoft.org/v21/i11")
25990 (synopsis "Library for @dfn{Bayesian Output Analysis Program} (BOA) for MCMC")
25992 "This package provides a menu-driven program and library of functions for
25993 carrying out convergence diagnostics and statistical and graphical analysis of
25994 @dfn{Markov chain Monte Carlo} (MCMC) sampling output.")
25995 (license license:gpl2+)))
25997 (define-public r-httpcode
25999 (name "r-httpcode")
26003 (uri (cran-uri "httpcode" version))
26006 "0xig0rvc81hg7mw0iq9s0an1nw24fg0kfs2p2n6dzhwl9w506fjr"))))
26007 (build-system r-build-system)
26008 (home-page "https://github.com/sckott/httpcode")
26009 (synopsis "HTTP status code helper")
26010 (description "@code{httpcode} provides functionality for finding and
26011 explaining the meaning of @code{HTTP} status codes. Functions are included for
26012 searching for codes by full or partial number, by message, and to get
26013 appropriate dog and cat images for many status codes.")
26014 (license license:expat)))
26016 (define-public r-latex2exp
26018 (name "r-latex2exp")
26022 (uri (cran-uri "latex2exp" version))
26025 "0zbbrbgg524lpm733j8qsqk5ssg75c51s6dgzb18c6fk8byrx945"))))
26026 (build-system r-build-system)
26028 (list r-stringr r-magrittr))
26031 (home-page "https://github.com/stefano-meschiari/latex2exp/")
26032 (synopsis "Use LaTeX expressions in plots")
26033 (description "@code{latex2exp} parses and converts LaTeX math formulas to
26034 R's plotmath expressions, used to enter mathematical formulas and symbols to be
26035 rendered as text, axis labels, etc. throughout R's plotting system.")
26036 (license license:expat)))
26038 (define-public r-oai
26044 (uri (cran-uri "oai" version))
26047 "1zcbcxhw692s0y6izvwazyzhgx0iwsxsbcan2nk0mb7n11p7bypb"))))
26048 (build-system r-build-system)
26050 (list r-xml2 r-httr r-plyr r-stringr r-tibble))
26053 (home-page "https://github.com/ropensci/oai/")
26054 (synopsis "General purpose OAI-PMH services client")
26055 (description "@code{oai} provides a general purpose client to work with
26056 any @dfn{Open Archives Initiative Protocol for 'Metadata' Harvesting} (OAI-PMH)
26057 service. Functions are provided to work with the OAI-PMH verbs:
26058 @code{GetRecord}, @code{Identify}, @code{ListIdentifiers},
26059 @code{ListMetadataFormats}, @code{ListRecords}, and @code{ListSets}.")
26060 (license license:expat)))
26062 (define-public r-argon2
26069 (uri (cran-uri "argon2" version))
26072 "09hzl0wz0lw2v7g64rdv0lij2hq36zl37a6rmxwvinmjdzijcsyw"))))
26073 (properties `((upstream-name . "argon2")))
26074 (build-system r-build-system)
26075 (home-page "https://github.com/wrathematics/argon2")
26076 (synopsis "Secure password hashing based on the argon2 algorithm")
26078 "This package provides utilities for secure password hashing via the
26079 argon2 algorithm.")
26080 (license license:bsd-2)))
26082 (define-public r-getpass
26089 (uri (cran-uri "getPass" version))
26092 "03ydafhh0sk3rcnpr3paajyji64x2ddp6p814p9mvbmyrblcgzcc"))))
26093 (properties `((upstream-name . "getPass")))
26094 (build-system r-build-system)
26096 (list r-rstudioapi))
26097 (home-page "https://github.com/wrathematics/getPass")
26098 (synopsis "Masked user input")
26100 "This package provides a micro-package for reading \"passwords\", i.e.
26101 reading user input with masking, so that the input is not displayed as it is
26102 typed. Currently, RStudio, the command line (every OS), and any platform
26103 where tcltk is present are supported.")
26104 (license license:bsd-2)))
26106 (define-public r-remoter
26113 (uri (cran-uri "remoter" version))
26116 "1a7m63l8phv5jnazvdqdrqkaqjwqzaac5y4jm2jn0ypy4n8jvkfl"))))
26117 (properties `((upstream-name . "remoter")))
26118 (build-system r-build-system)
26120 (list r-argon2 r-getpass r-pbdzmq r-png))
26121 (home-page "https://github.com/RBigData/remoter")
26122 (synopsis "Control a remote R session from a local one")
26124 "This package provides a set of utilities for client/server computing
26125 with R, controlling a remote R session (the server) from a local one (the
26127 (license license:bsd-2)))
26129 (define-public r-asd
26136 (uri (cran-uri "asd" version))
26139 "0p3r4qjam3sl3rpcilb0pgx4xx3ly71xqnvkv31vzjs885lgxz4l"))))
26140 (properties `((upstream-name . "asd")))
26141 (build-system r-build-system)
26144 (home-page "https://cran.r-project.org/web/packages/asd")
26145 (synopsis "Simulations for Adaptive Seamless Designs")
26147 "This package provdes means to run simulations for adaptive seamless
26148 designs with and without early outcomes for treatment selection and
26149 subpopulation type designs.")
26150 (license license:gpl3)))
26152 (define-public r-nbconvertr
26154 (name "r-nbconvertr")
26159 (uri (cran-uri "nbconvertR" version))
26162 "0yhmz177r1miain65vspclahhz8cg7638ldbpsw8ylgf7a60l0sg"))))
26163 (properties `((upstream-name . "nbconvertR")))
26164 (build-system r-build-system)
26166 (list python-nbconvert pandoc))
26167 (home-page "https://cran.r-project.org/web/packages/nbconvertR/")
26168 (synopsis "Vignette engine wrapping Jupyter notebooks")
26170 "This package calls the Jupyter script @code{nbconvert} to create
26171 vignettes from notebooks. Those notebooks (@code{.ipynb} files) are files
26172 containing rich text, code, and its output. Code cells can be edited and
26173 evaluated interactively.")
26174 (license license:gpl3)))
26176 (define-public r-bridgesampling
26178 (name "r-bridgesampling")
26183 (uri (cran-uri "bridgesampling" version))
26186 "0sry1xwiv4y52k44hq6z8y2kysp5kxgl4dix3m94svg3ladd7v2l"))))
26188 `((upstream-name . "bridgesampling")))
26189 (build-system r-build-system)
26191 (list r-brobdingnag
26199 (home-page "https://github.com/quentingronau/bridgesampling")
26200 (synopsis "Bridge sampling for marginal likelihoods and Bayes factors")
26202 "This package provides functions for estimating marginal likelihoods,
26203 Bayes factors, posterior model probabilities, and normalizing constants in
26204 general, via different versions of bridge sampling.")
26205 (license license:gpl2+)))
26207 (define-public r-tea
26214 (uri (cran-uri "tea" version))
26217 "0ql7lrxk0ihm49kqsvz79ig8i54rwiy9nxav4v9hy72j9kj5bgjn"))))
26219 `((upstream-name . "tea")))
26220 (build-system r-build-system)
26223 (home-page "https://cran.r-project.org/web/packages/tea/")
26224 (synopsis "Threshold estimation approaches")
26226 "This package provides different approaches for selecting the threshold
26227 in generalized Pareto distributions. Most of them are based on minimizing the
26228 AMSE-criterion or at least by reducing the bias of the assumed GPD-model.
26229 Others are heuristically motivated by searching for stable sample paths, i.e.
26230 a nearly constant region of the tail index estimator with respect to k, which
26231 is the number of data in the tail. The third class is motivated by graphical
26232 inspection. In addition, a sequential testing procedure for GPD-GoF-tests
26233 is also implemented here.")
26234 (license license:gpl3)))
26236 (define-public r-awsmethods
26238 (name "r-awsmethods")
26243 (uri (cran-uri "awsMethods" version))
26246 "0hbmrcpdyg15zg4rysscsmxpxlpy0dkxx2aa63qibq7l1k14v4sh"))))
26248 `((upstream-name . "awsMethods")))
26249 (build-system r-build-system)
26250 (home-page "http://www.wias-berlin.de/software/imaging/")
26251 (synopsis "Class and methods definitions")
26253 "This package defines the generic method @code{extract} and provides
26254 @code{openMP} support as needed in several packages like
26255 @code{aws}, @code{adimpro}, @code{fmri}, and @code{dwi}.")
26256 (license license:gpl2+)))
26258 (define-public r-aws
26265 (uri (cran-uri "aws" version))
26268 "1fhm87iax6bkvd4vszvjbcqw3b2drs11rjxr7zf2w4sgc72svaz8"))))
26270 `((upstream-name . "aws")))
26271 (build-system r-build-system)
26273 (list r-awsmethods r-gsl))
26276 (home-page "https://cran.r-project.org/web/packages/aws/")
26277 (synopsis "Adaptive weights smoothing")
26279 "This package provides a collection of R-functions implementing adaptive
26280 smoothing procedures in 1D, 2D and 3D. This includes the
26281 Propagation-Separation approach to adaptive smoothing, the @dfn{Intersecting
26282 Confidence Intervals} (ICI), variational approaches, and a non-local means
26284 (license license:gpl2+)))
26286 (define-public r-sgloptim
26288 (name "r-sgloptim")
26293 (uri (cran-uri "sglOptim" version))
26296 "15bkkvgp9v9vsp65wps48g3c2fa0fj1025hbrziywq14j7wayyjr"))))
26298 `((upstream-name . "sglOptim")))
26299 (build-system r-build-system)
26310 (home-page "https://github.com/nielsrhansen/sglOptim")
26311 (synopsis "Generic sparse group Lasso solver")
26313 "This package provides a fast generic solver for sparse group lasso
26314 optimization problems. The loss (objective) function must be defined in a C++
26315 module. The optimization problem is solved using a coordinate gradient
26316 descent algorithm. Convergence of the algorithm is established and the
26317 algorithm is applicable to a broad class of loss functions. Use of parallel
26318 computing for cross validation and subsampling is supported through the
26319 @code{foreach} and @code{doParallel} packages.")
26320 (license license:gpl2+)))
26322 (define-public r-grouped
26329 (uri (cran-uri "grouped" version))
26332 "1glxgacpwk7yjbkwg5ci6bmb2il6hf5zhydwi5bbq6hc032m9976"))))
26334 `((upstream-name . "grouped")))
26335 (build-system r-build-system)
26338 (home-page "https://cran.r-project.org/web/packages/grouped/")
26339 (synopsis "Regression analysis of grouped and coarse data")
26341 "This package provides regression models for grouped and coarse data,
26342 under the coarsened at random assumption.")
26343 (license license:gpl2+)))
26345 (define-public r-stam
26352 (uri (cran-uri "stam" version))
26355 "1x1j45fir64kffny0nssb2hwn4rcp8gd2cjv6fw4yy0l4d0xi5iv"))))
26357 `((upstream-name . "stam")))
26358 (build-system r-build-system)
26361 (home-page "https://cran.r-project.org/web/packages/stam")
26362 (synopsis "Spatio-temporal analysis and modelling")
26364 "This package provides various methods to conduct Spatio-Temporal
26365 Analysis and Modelling, including Exploratory Spatio-Temporal Analysis and
26366 Inferred Spatio-Temporal Modelling.")
26367 (license license:gpl2+)))
26369 (define-public r-dcv
26376 (uri (cran-uri "dcv" version))
26379 "12c716x8dnxnqksibpmyysqp2axggvy9dpd55s9bhnsvqvi6dshj"))))
26381 `((upstream-name . "dcv")))
26382 (build-system r-build-system)
26385 (home-page "https://cran.r-project.org/web/packages/dcv/")
26386 (synopsis "Conventional cross-validation statistics for climate-growth model")
26388 "This package performs several conventional cross-validation statistical
26389 methods for climate-growth model in the climate reconstruction from tree
26390 rings, including Sign Test statistic, Reduction of Error statistic, Product
26391 Mean Test, Durbin-Watson statistic etc.")
26392 (license license:gpl2)))
26394 (define-public r-rcdd
26401 (uri (cran-uri "rcdd" version))
26404 "0zxx0qvv26ba30jkm8mvca4h59rqklay4jwazpcw7h9dzp4189jr"))))
26406 `((upstream-name . "rcdd")))
26407 (build-system r-build-system)
26410 (home-page "https://www.stat.umn.edu/geyer/rcdd/")
26411 (synopsis "Computational geometry")
26413 "This package converts back and forth between two representations of a
26414 convex polytope: as solution of a set of linear equalities and inequalities
26415 and as convex hull of set of points and rays. Also does linear programming
26416 and redundant generator elimination. All functions can use exact
26417 infinite-precision rational arithmetic.")
26418 (license license:gpl2)))
26420 (define-public r-rxnat
26427 (uri (cran-uri "Rxnat" version))
26430 "0siylypjd8cgcmr2c443w8krg8sgr5gz4zapbinanp8vsfzivdv2"))))
26432 `((upstream-name . "Rxnat")))
26433 (build-system r-build-system)
26435 (list r-httr r-rcurl r-tibble))
26438 (home-page "https://cran.r-project.org/web/packages/Rxnat/")
26439 (synopsis "Queries and extracts images from neuroimaging datasets")
26441 "This package allows communication with the Extensible Neuroimaging
26442 Archive Toolkit. Rxnat uses the XNAT REST API to perform data queries and
26444 (license license:gpl2)))
26446 (define-public r-rserve
26453 (uri (string-append "http://www.rforge.net/Rserve/snapshot/Rserve_"
26454 version ".tar.gz"))
26457 "017kkzv9lxlz9qhg3gprrf1wcyflxrif6wjk27x9b4bdzylw6bsx"))))
26458 (build-system r-build-system)
26461 (modify-phases %standard-phases
26462 (add-before 'install 'install-server-binary
26463 ;; Makevars tries to install to R's store directory.
26464 (lambda* (#:key outputs #:allow-other-keys)
26465 (let* ((out (assoc-ref outputs "out"))
26466 (bin (string-append out "/bin")))
26467 (substitute* "src/Makevars.in"
26468 (("\\$\\(R_HOME\\)") out))
26469 (mkdir-p bin)))))))
26479 (list openssl zlib))
26480 (home-page "https://github.com/s-u/Rserve")
26482 "Server providing access to R from many languages and systems")
26484 "Rserve acts as a socket server (TCP/IP or local sockets) which allows
26485 binary requests to be sent to R. Every connection has a separate workspace
26486 and working directory. Client-side implementations are available for popular
26487 languages such as C/C++ and Java, allowing any application to use facilities
26488 of R without the need of linking to R code. Rserve supports remote
26489 connection, user authentication and file transfer. A simple R client is
26490 included in this package as well.")
26491 (license license:gpl2)))
26493 (define-public r-gamm4
26500 (uri (cran-uri "gamm4" version))
26503 "128c725y9s07c1m9cvd9hgi9hldrymcs5divd8pw7bdjh9jvdiap"))))
26504 (properties `((upstream-name . "gamm4")))
26505 (build-system r-build-system)
26507 (list r-lme4 r-matrix r-mgcv))
26508 (home-page "https://cran.r-project.org/web/packages/gamm4/")
26509 (synopsis "Generalized additive mixed models using mgcv and lme4")
26511 "Estimate generalized additive mixed models via a version of function
26512 @code{gamm} from the @code{mgcv} package, using the @code{lme4} packagefor
26514 (license license:gpl2+)))
26516 (define-public r-optimx
26519 (version "2021-10.12")
26523 (uri (cran-uri "optimx" version))
26526 "0hvrpfya767vp3anmb8ih516v4zz1sv4h193rn93kyjydf2lqf1r"))))
26527 (properties `((upstream-name . "optimx")))
26528 (build-system r-build-system)
26529 (propagated-inputs (list r-numderiv))
26530 (native-inputs (list r-knitr))
26531 (home-page "https://cran.r-project.org/web/packages/optimx/")
26532 (synopsis "Expanded replacement and extension of the optim function")
26534 "This package provides a replacement and extension of the @code{optim}
26535 function to call to several function minimization codes in R in a single
26536 statement. These methods handle smooth, possibly box constrained functions of
26537 several or many parameters. Note that the function @code{optimr} was prepared
26538 to simplify the incorporation of minimization codes going forward. This
26539 package also implements some utility codes and some extra solvers, including
26540 safeguarded Newton methods. Many methods previously separate are now included
26542 (license license:gpl2)))
26544 (define-public r-projpred
26546 (name "r-projpred")
26551 (uri (cran-uri "projpred" version))
26554 "170pskvcsyk22xl4q8mklx8nw29miqzb42wajcab7bki8ap1ix46"))))
26555 (properties `((upstream-name . "projpred")))
26556 (build-system r-build-system)
26570 (native-inputs (list r-knitr))
26571 (home-page "https://mc-stan.org/projpred/")
26572 (synopsis "Projection predictive feature selection")
26574 "This package performs projection predictive feature selection for
26575 generalized linear models and generalized linear and additive multilevel
26576 models. The package is compatible with the @code{rstanarm} and @code{brms}
26577 packages, but other reference models can also be used. See the package
26578 vignette for more information and examples.")
26579 (license license:gpl3)))
26581 (define-public r-distributional
26583 (name "r-distributional")
26588 (uri (cran-uri "distributional" version))
26591 "1mji8xlhwrw8msih5wdpbzwv4g59kly0xkdklhn8yzb18rrnrczs"))))
26593 `((upstream-name . "distributional")))
26594 (build-system r-build-system)
26606 (home-page "https://pkg.mitchelloharawild.com/distributional/")
26607 (synopsis "Vectorized probability distributions")
26609 "This package provides vectorized distribution objects with tools for
26610 manipulating, visualizing, and using probability distributions. It was
26611 designed to allow model prediction outputs to return distributions rather than
26612 their parameters, allowing users to directly interact with predictive
26613 distributions in a data-oriented workflow. In addition to providing generic
26614 replacements for p/d/q/r functions, other useful statistics can be computed
26615 including means, variances, intervals, and highest density regions.")
26616 (license license:gpl3)))
26618 (define-public r-posterior
26620 (name "r-posterior")
26625 (uri (cran-uri "posterior" version))
26628 "1qdg22l868daqg2axr36szl1m9z0rfpgx8zmv1x1xwm1hmlf0mxp"))))
26629 (properties `((upstream-name . "posterior")))
26630 (build-system r-build-system)
26643 (home-page "https://mc-stan.org/posterior/")
26644 (synopsis "Tools for working with posterior distributions")
26646 "This package provides useful tools for both users and developers of
26647 packages for fitting Bayesian models or working with output from Bayesian
26648 models. The primary goals of the package are to:
26651 @item Efficiently convert between many different useful formats of
26652 draws (samples) from posterior or prior distributions.
26654 @item Provide consistent methods for operations commonly performed on draws,
26655 for example, subsetting, binding, or mutating draws.
26657 @item Provide various summaries of draws in convenient formats.
26659 @item Provide lightweight implementations of state of the art posterior
26660 inference diagnostics.
26663 (license license:bsd-3)))
26665 (define-public r-brms
26672 (uri (cran-uri "brms" version))
26675 "1q93z4cf3iy4rs6pgvph6z7hc8q05iwif76hcg8p4kr6nl82nc38"))))
26676 (properties `((upstream-name . "brms")))
26677 (build-system r-build-system)
26698 (native-inputs (list r-knitr))
26700 "https://github.com/paul-buerkner/brms")
26702 "Bayesian Regression Models using 'Stan'")
26704 "Fit Bayesian generalized (non-)linear multivariate multilevel models
26705 using 'Stan' for full Bayesian inference. A wide range of distributions and
26706 link functions are supported, allowing users to fit -- among others -- linear,
26707 robust linear, count data, survival, response times, ordinal, zero-inflated,
26708 hurdle, and even self-defined mixture models all in a multilevel context.
26709 Further modeling options include non-linear and smooth terms, auto-correlation
26710 structures, censored data, meta-analytic standard errors, and quite a few
26711 more. In addition, all parameters of the response distribution can be
26712 predicted in order to perform distributional regression. Prior specifications
26713 are flexible and explicitly encourage users to apply prior distributions that
26714 actually reflect their beliefs. Model fit can easily be assessed and compared
26715 with posterior predictive checks and leave-one-out cross-validation.")
26716 (license license:gpl2)))
26718 (define-public r-mstate
26725 (uri (cran-uri "mstate" version))
26728 "054dzrd5b0xjjjl7862q3aq1jwgrxbkqz7zpvbdirqsld3zksirw"))))
26729 (properties `((upstream-name . "mstate")))
26730 (build-system r-build-system)
26741 "https://www.lumc.nl/org/bds/research/medische-statistiek/survival-analysis/")
26743 "Data Preparation, Estimation and Prediction in Multi-State Models")
26745 "Contains functions for data preparation, descriptives, hazard estimation
26746 and prediction with Aalen-Johansen or simulation in competing risks and
26747 multi-state models.")
26748 (license license:gpl2+)))
26750 (define-public r-scatterpie
26752 (name "r-scatterpie")
26757 (uri (cran-uri "scatterpie" version))
26760 "1pmspv8a7k20zyd5xvmav2k9mnjrkfhdij3rr9k504zyki8hfy1z"))))
26761 (properties `((upstream-name . "scatterpie")))
26762 (build-system r-build-system)
26764 (list r-ggforce r-ggfun r-ggplot2 r-rlang r-tidyr))
26767 (home-page "https://cran.r-project.org/web/packages/scatterpie/")
26768 (synopsis "Scatter pie plot")
26770 "This package creates scatterpie plots, especially useful for plotting
26772 (license license:artistic2.0)))
26774 (define-public r-scrypt
26781 (uri (cran-uri "scrypt" version))
26784 "14iblgbp9v2by8fjbrpsd59iknp5babcz7j3yv1yxxzcwyb6wrrm"))))
26785 (properties `((upstream-name . "scrypt")))
26786 (build-system r-build-system)
26789 (home-page "https://github.com/rstudio/rscrypt")
26790 (synopsis "Key derivation functions for R based on Scrypt")
26792 "This package provides functions for working with the scrypt key
26793 derivation functions. Scrypt is a password-based key derivation function
26794 created by Colin Percival. The algorithm was specifically designed to make it
26795 costly to perform large-scale custom hardware attacks by requiring large
26796 amounts of memory.")
26797 (license license:bsd-2)))
26799 (define-public r-boruta
26806 (uri (cran-uri "Boruta" version))
26809 "0y2w4wb45kfnzrxcrdsiwgal9fsnlr3wad1sqdc70qv8gp921xbg"))))
26810 (properties `((upstream-name . "Boruta")))
26811 (build-system r-build-system)
26812 (propagated-inputs (list r-ranger))
26813 (home-page "https://gitlab.com/mbq/Boruta/")
26814 (synopsis "Wrapper algorithm for all relevant feature selection")
26816 "This package provides an all relevant feature selection wrapper
26817 algorithm. It finds relevant features by comparing original attributes'
26818 importance with importance achievable at random, estimated using their
26819 permuted copies (shadows).")
26820 (license license:gpl2+)))
26822 (define-public r-directlabels
26824 (name "r-directlabels")
26825 (version "2021.1.13")
26829 (uri (cran-uri "directlabels" version))
26832 "0415kh9k2qzdwi8zb32fh2icl5wf5335kyj11cyfdmfxji39zv2w"))))
26833 (build-system r-build-system)
26838 (home-page "http://directlabels.r-forge.r-project.org/")
26839 (synopsis "Direct labels for multicolor plots")
26841 "This package provides an extensible framework for automatically placing
26842 direct labels onto multicolor plots. Label positions are described using
26843 positioning methods that can be re-used across several different plots. There
26844 are heuristics for examining @code{trellis} and @code{ggplot} objects and
26845 inferring an appropriate positioning method.")
26846 (license license:gpl3)))
26848 (define-public r-lsd
26855 (uri (cran-uri "LSD" version))
26857 (base32 "17pbdlcbhzf3v7l42mjikln1ga5xjp5r78gjg6a88iahk0lwwlvm"))))
26858 (properties `((upstream-name . "LSD")))
26859 (build-system r-build-system)
26860 (home-page "https://cran.r-project.org/web/packages/LSD/")
26861 (synopsis "Lots of superior depictions tool creates colorful plots")
26863 "This package creates lots of colorful plots in a multitude of variations.
26864 Try a demo of the LSD by running @code{demotour()}.")
26866 (license (list license:gpl2 license:gpl3))))
26868 (define-public r-phylogram
26870 (name "r-phylogram")
26875 (uri (cran-uri "phylogram" version))
26877 (base32 "1p4h5pirc0m5pzc18q0jk3mcmb5n48gdf9abz03vml3a209xxl2v"))))
26878 (properties `((upstream-name . "phylogram")))
26879 (build-system r-build-system)
26880 (propagated-inputs (list r-ape))
26881 (home-page "https://github.com/ropensci/phylogram/")
26882 (synopsis "Dendrograms for evolutionary analysis")
26884 "The @code{r-phylogram} package is a tool for for developing phylogenetic
26885 trees as deeply-nested lists known as \"dendrogram\" objects. It provides
26886 functions for conversion between \"dendrogram\" and \"phylo\" class objects,
26887 as well as several tools for command-line tree manipulation and import/export
26888 via Newick parenthetic text. This improves accessibility to the comprehensive
26889 range of object-specific analytical and tree-visualization functions found
26890 across a wide array of bioinformatic R packages.")
26891 (license license:gpl3)))
26893 (define-public r-kmer
26900 (uri (cran-uri "kmer" version))
26902 (base32 "0jimn9r0abglwxdl1zqz0lxa99cmj6haydkxjzqfbpx9by80wnww"))))
26903 (properties `((upstream-name . "kmer")))
26904 (build-system r-build-system)
26906 (list r-openssl r-phylogram r-rcpp))
26907 (home-page "https://github.com/shaunpwilkinson/kmer/")
26908 (synopsis "Fast K-Mer counting and clustering for biological sequence analysis")
26910 "@code{r-kmer} is an R package for rapidly computing distance matrices
26911 and clustering large sequence datasets using fast alignment-free k-mer
26912 counting and recursive k-means partitioning.")
26913 (license license:gpl3)))
26915 (define-public r-hardhat
26922 (uri (cran-uri "hardhat" version))
26925 "0a4nq93cmps5xy8h0qsv6xyzrbsz9ka4iwkrvb8m8v10wq7wm5wl"))))
26926 (properties `((upstream-name . "hardhat")))
26927 (build-system r-build-system)
26929 (list r-glue r-rlang r-tibble r-vctrs))
26932 (home-page "https://github.com/tidymodels/hardhat")
26933 (synopsis "Construct modeling packages")
26935 "Building modeling packages is hard. A large amount of effort generally
26936 goes into providing an implementation for a new method that is efficient,
26937 fast, and correct, but often less emphasis is put on the user interface. A
26938 good interface requires specialized knowledge about S3 methods and formulas,
26939 which the average package developer might not have. The goal of
26940 @code{hardhat} is to reduce the burden around building new modeling packages
26941 by providing functionality for preprocessing, predicting, and validating
26943 (license license:expat)))
26945 (define-public r-lightgbm
26947 (name "r-lightgbm")
26952 (uri (cran-uri "lightgbm" version))
26955 "12hbvm1va6sb5yny564jvhhzrkcq4j33rcdhqhwxaac2m08cpi8s"))))
26956 (properties `((upstream-name . "lightgbm")))
26957 (build-system r-build-system)
26959 (list r-data-table r-jsonlite r-matrix r-r6))
26960 (home-page "https://github.com/Microsoft/LightGBM")
26961 (synopsis "Light gradient boosting machine")
26963 "Tree based algorithms can be improved by introducing boosting
26964 frameworks. LightGBM is one such framework, based on Ke, Guolin et
26965 al. (2017). This package offers an R interface to work with it. It is
26966 designed to be distributed and efficient with the following goals:
26969 @item Faster training speed and higher efficiency;
26970 @item lower memory usage;
26971 @item better accuracy;
26972 @item parallel learning supported; and
26973 @item capable of handling large-scale data.
26976 (license license:expat)))
26978 (define-public r-shapforxgboost
26980 (name "r-shapforxgboost")
26985 (uri (cran-uri "SHAPforxgboost" version))
26988 "106nsf02b1w3yshb55lwnyw1rl1a60162v2wk8znjz3b4ln3mqj5"))))
26990 `((upstream-name . "SHAPforxgboost")))
26991 (build-system r-build-system)
27003 (home-page "https://github.com/liuyanguu/SHAPforxgboost")
27004 (synopsis "SHAP Plots for XGBoost")
27006 "The aim of @code{SHAPforxgboost} is to aid in visual data investigations
27007 using @dfn{SHAP} (Shapley additive explanation) visualization plots for
27008 @code{XGBoost}. It provides summary plot, dependence plot, interaction plot,
27009 and force plot. It relies on the @code{XGBoost} package to produce SHAP
27011 (license license:expat)))
27013 (define-public r-rismed
27020 (uri (cran-uri "RISmed" version))
27023 "0vpi88gzi9r85v6nhjz9jbw671zkrmyazwna2z881346wfyr3l8b"))))
27024 (properties `((upstream-name . "RISmed")))
27025 (build-system r-build-system)
27027 (list r-httr r-xml2))
27028 (home-page "https://cran.r-project.org/web/packages/RISmed")
27029 (synopsis "Download content from NCBI databases")
27031 "This package provides a set of tools to extract bibliographic
27032 content from the National Center for Biotechnology Information (NCBI)
27033 databases, including PubMed. The name RISmed is a portmanteau of
27034 RIS (for Research Information Systems, a common tag format for
27035 bibliographic data) and PubMed.")
27036 (license license:gpl2+)))
27038 (define-public r-semver
27045 (uri (cran-uri "semver" version))
27048 "10wpkyms2cix3bsin2q0qhkbl445pwwpa5gm2s4jjw1989namkxy"))))
27049 (properties `((upstream-name . "semver")))
27050 (build-system r-build-system)
27052 (list r-assertthat r-rcpp))
27053 (native-inputs (list r-knitr))
27054 (home-page "https://github.com/johndharrison/semver")
27055 (synopsis "Parser for Semantic Versioning 2.0.0")
27057 "This package provides tools and functions for parsing, rendering and
27058 operating on semantic version strings. Semantic versioning is a simple set of
27059 rules and requirements that dictate how version numbers are assigned and
27060 incremented as outlined at @url{http://semver.org}.")
27061 (license license:expat)))
27063 (define-public r-binman
27070 (uri (cran-uri "binman" version))
27073 "00l7m98h41r67gf0qxqis3vx63j7wylnk9vlgcyk41szkrz8ikkc"))))
27074 (properties `((upstream-name . "binman")))
27075 (build-system r-build-system)
27084 (native-inputs (list r-knitr))
27085 (home-page "https://github.com/ropensci/binman")
27086 (synopsis "Binary download manager")
27088 "This package provides tools and functions for managing the download of
27089 binary files. Binary repositories are defined in the YAML format. Defining
27090 new pre-download, download and post-download templates allow additional
27091 repositories to be added.")
27092 (license license:expat)))
27094 (define-public r-wdman
27101 (uri (cran-uri "wdman" version))
27104 "1yf41lsrr9dbf5n4f5hv9mlmzl736fhnp9gxkm2g9apws6gsig02"))))
27105 (properties `((upstream-name . "wdman")))
27106 (build-system r-build-system)
27108 (list r-assertthat r-binman r-processx r-semver r-yaml))
27109 (native-inputs (list r-knitr))
27110 (home-page "https://docs.ropensci.org/wdman/")
27111 (synopsis "Webdriver/Selenium binary manager")
27113 "There are a number of binary files associated with the
27114 Webdriver/Selenium project (see @url{http://www.seleniumhq.org/download/},
27115 @url{https://sites.google.com/a/chromium.org/chromedriver/},
27116 @url{https://github.com/mozilla/geckodriver},
27117 @url{http://phantomjs.org/download.html}, and
27118 @url{https://github.com/SeleniumHQ/selenium/wiki/InternetExplorerDriver} for
27119 more information). This package provides functions to download these binaries
27120 and to manage processes involving them.")
27121 (license license:expat)))
27123 (define-public r-rselenium
27125 (name "r-rselenium")
27130 (uri (cran-uri "RSelenium" version))
27133 "1xn5fdbzmq7b1f5fc9ls23g177bmnd8bn4p4d8aafr6z3jwkmfir"))))
27134 (properties `((upstream-name . "RSelenium")))
27135 (build-system r-build-system)
27143 (native-inputs (list r-knitr))
27144 (home-page "https://docs.ropensci.org/RSelenium/")
27145 (synopsis "R bindings for Selenium WebDriver")
27147 "This package provides a set of R bindings for the Selenium 2.0
27148 WebDriver (see @url{https://selenium.dev/documentation/en/} for more
27149 information) using the @code{JsonWireProtocol} (see
27150 @url{https://github.com/SeleniumHQ/selenium/wiki/JsonWireProtocol} for more
27151 information). Selenium 2.0 WebDriver allows driving a web browser natively as
27152 a user would either locally or on a remote machine using the Selenium server
27153 it marks a leap forward in terms of web browser automation. Selenium
27154 automates web browsers (commonly referred to as browsers). Using RSelenium
27155 you can automate browsers locally or remotely.")
27156 (license license:agpl3+)))
27158 (define-public r-conquer
27165 (uri (cran-uri "conquer" version))
27168 "1ynmaf7lgqjb8grsifx5dzy29cd5kz4x3yh0abnl2vxdr4c4wddc"))))
27169 (properties `((upstream-name . "conquer")))
27170 (build-system r-build-system)
27172 (list r-matrix r-matrixstats r-rcpp r-rcpparmadillo))
27173 (home-page "https://github.com/XiaoouPan/conquer")
27174 (synopsis "Convolution-type smoothed quantile regression")
27176 "This package provides fast and accurate convolution-type smoothed
27177 quantile regression, implemented using Barzilai-Borwein gradient descent with
27178 a Huber regression warm start. Confidence intervals for regression
27179 coefficients are constructed using multiplier bootstrap.")
27180 (license license:gpl3)))
27182 (define-public r-fastshap
27184 (name "r-fastshap")
27189 (uri (cran-uri "fastshap" version))
27192 "0gxch67i3bj6m8nb94m5hswq058w6n1q9war4dy2qnimlv7cmhdv"))))
27193 (properties `((upstream-name . "fastshap")))
27194 (build-system r-build-system)
27204 (home-page "https://github.com/bgreenwell/fastshap")
27205 (synopsis "Fast approximate Shapley values")
27207 "This package computes fast (relative to other implementations)
27208 approximate Shapley values for any supervised learning model. Shapley values
27209 help to explain the predictions from any black box model using ideas from game
27210 theory; see @url{Strumbel and Kononenko (2014),
27211 doi.org/10.1007/s10115-013-0679-x} for details.")
27212 (license license:gpl2+)))
27214 (define-public r-memuse
27220 (uri (cran-uri "memuse" version))
27223 "1wvwnjaaiv2647561z2b55dss35033ildx4kk8hzxfzgsjmdpsgm"))))
27224 (properties `((upstream-name . "memuse")))
27225 (build-system r-build-system)
27226 (home-page "https://github.com/shinra-dev/memuse")
27227 (synopsis "Memory Estimation Utilities")
27229 "This package provides procedures to answer the following questions:
27230 How much ram do you need to store a 100,000 by 100,000 matrix? How much ram is
27231 your current R session using? How much ram do you even have?")
27232 (license license:bsd-2)))
27234 (define-public r-metrics
27241 (uri (cran-uri "Metrics" version))
27244 "0fh8qbjlwzagh272lgwr4bxcqcjb1qpz53mgs8rzlvncax6nk5bk"))))
27245 (properties `((upstream-name . "Metrics")))
27246 (build-system r-build-system)
27247 (home-page "https://github.com/mfrasco/Metrics")
27248 (synopsis "Evaluation metrics for machine learning")
27250 "This package provides an implementation of evaluation metrics in R that
27251 are commonly used in supervised machine learning. It implements metrics for
27252 regression, time series, binary classification, classification, and
27253 information retrieval problems. It has zero dependencies and a consistent,
27254 simple interface for all functions.")
27255 (license license:bsd-3)))
27257 (define-public r-iml
27264 (uri (cran-uri "iml" version))
27267 "1wz6xqhvqkzj723nw7qrlwb1171wvvpxhv3pa8cq7vcbkiflq37r"))))
27268 (properties `((upstream-name . "iml")))
27269 (build-system r-build-system)
27281 (native-inputs (list r-knitr))
27282 (home-page "https://github.com/christophM/iml")
27283 (synopsis "Interpretable machine learning")
27285 "This package provides interpretability methods to analyze the behavior
27286 and predictions of any machine learning model. Implemented methods are:
27289 @item Feature importance described by Fisher et al. (2018),
27290 @item accumulated local effects plots described by Apley (2018),
27291 @item partial dependence plots described by Friedman (2001),
27292 @item individual conditional expectation ('ice') plots described by Goldstein
27293 et al. (2013) @url{https://doi.org/10.1080/10618600.2014.907095},
27294 @item local models (variant of 'lime') described by Ribeiro et. al (2016),
27295 @item the Shapley Value described by Strumbelj et. al (2014)
27296 @url{https://doi.org/10.1007/s10115-013-0679-x},
27297 @item feature interactions described by Friedman et. al
27298 @url{https://doi.org/10.1214/07-AOAS148} and tree surrogate models.
27301 (license license:expat)))
27303 (define-public r-goftest
27310 (uri (cran-uri "goftest" version))
27313 "06bz6k7smr4jbvzmb73qc5fkf4my59w5gbl18wlmpkkymsv78prs"))))
27314 (properties `((upstream-name . "goftest")))
27315 (build-system r-build-system)
27316 (home-page "https://github.com/baddstats/goftest")
27317 (synopsis "Classical Goodness-of-Fit tests for univariate distributions")
27319 "This package provides Cramer-Von Mises and Anderson-Darling tests of
27320 goodness-of-fit for continuous univariate distributions, using efficient
27322 (license license:gpl2+)))
27324 (define-public r-tensor
27331 (uri (cran-uri "tensor" version))
27334 "19mfsgr6vz4lgwidm80i4yw0y1dr3n8i6qz7g4n2xa0k74zc5pp1"))))
27335 (properties `((upstream-name . "tensor")))
27336 (build-system r-build-system)
27337 (home-page "https://cran.r-project.org/web/packages/tensor/")
27338 (synopsis "Tensor product of arrays")
27340 "The tensor product of two arrays is notionally an outer product of the
27341 arrays collapsed in specific extents by summing along the appropriate
27342 diagonals. This package allows you to compute the tensor product of arrays.")
27343 (license license:gpl2+)))
27345 (define-public r-spatstat-utils
27347 (name "r-spatstat-utils")
27352 (uri (cran-uri "spatstat.utils" version))
27355 "06nvn2ffyrskhzaavsy6lmdp0m8askkrp1fnwrhjsj01lbjnq2az"))))
27357 `((upstream-name . "spatstat.utils")))
27358 (build-system r-build-system)
27359 (home-page "http://www.spatstat.org")
27360 (synopsis "Utility functions for spatstat")
27362 "This package contains utility functions for the @code{spatstat} package
27363 which may also be useful for other purposes.")
27364 (license license:gpl2+)))
27366 (define-public r-spatstat-sparse
27368 (name "r-spatstat-sparse")
27373 (uri (cran-uri "spatstat.sparse" version))
27376 "148fxbxss569w73xaqpzwpz9rfjdgznh2ngf06gvm33631222680"))))
27378 `((upstream-name . "spatstat.sparse")))
27379 (build-system r-build-system)
27381 (list r-abind r-matrix r-spatstat-utils r-tensor))
27382 (home-page "http://spatstat.org/")
27383 (synopsis "Sparse three-dimensional arrays and linear algebra utilities")
27385 "This package defines sparse three-dimensional arrays and supports
27386 standard operations on them. The package also includes utility functions for
27387 matrix calculations that are common in statistics, such as quadratic forms.")
27388 (license license:gpl2+)))
27390 (define-public r-spatstat-data
27392 (name "r-spatstat-data")
27397 (uri (cran-uri "spatstat.data" version))
27400 "0bq9randa3lgkh2q932iss5cxazq743q6p8asiqqf0yi32b003jq"))))
27401 (properties `((upstream-name . "spatstat.data")))
27402 (build-system r-build-system)
27404 (list r-matrix r-spatstat-utils))
27405 (home-page "http://www.spatstat.org")
27406 (synopsis "Datasets for spatstat")
27408 "This package contains all the datasets for the @code{spatstat}
27410 (license license:gpl2+)))
27412 (define-public r-spatstat-geom
27414 (name "r-spatstat-geom")
27419 (uri (cran-uri "spatstat.geom" version))
27422 "0rwysq9a0ylbsr53q5kfh7wjk5mcdji211sc3s8gwzz8ki09mf1j"))))
27423 (properties `((upstream-name . "spatstat.geom")))
27424 (build-system r-build-system)
27426 (list r-deldir r-polyclip r-spatstat-data r-spatstat-utils))
27427 (home-page "http://spatstat.org/")
27428 (synopsis "Geometrical functionality of the spatstat package")
27430 "This is a subset of the original spatstat package, containing the
27431 user-level code from spatstat which performs geometrical operations, except
27432 for the geometry of linear networks.")
27433 (license license:gpl2+)))
27435 (define-public r-spatstat-core
27437 (name "r-spatstat-core")
27442 (uri (cran-uri "spatstat.core" version))
27445 "0bhdxyw212yf9y9nsvbz4yy08ka3wr3hkjqpag0ys2s1p22c51b9"))))
27446 (properties `((upstream-name . "spatstat.core")))
27447 (build-system r-build-system)
27461 (home-page "http://spatstat.org/")
27462 (synopsis "Core functionality of the spatstat package")
27464 "This is a subset of the original spatstat package, containing all of the
27465 user-level code from spatstat, except for the code for linear networks.")
27466 (license license:gpl2+)))
27468 (define-public r-spatstat-linnet
27470 (name "r-spatstat-linnet")
27475 (uri (cran-uri "spatstat.linnet" version))
27478 "0y1py6x0xbw4ad3pjwcspi4ysgfh61f5fd79787zzgyyh2va8y4w"))))
27480 `((upstream-name . "spatstat.linnet")))
27481 (build-system r-build-system)
27490 (home-page "http://spatstat.org/")
27491 (synopsis "Linear networks functionality of the spatstat package")
27493 "This is a subset of the spatstat package, containing its functionality
27494 for spatial data on a linear network.")
27495 (license license:gpl2+)))
27497 (define-public r-spatstat-random
27499 (name "r-spatstat-random")
27504 (uri (cran-uri "spatstat.random" version))
27506 (base32 "0kb01s8k67ydcfqcnz3i55vpiksihh4xsg0w2p2bclxxkpdvpw25"))))
27507 (properties `((upstream-name . "spatstat.random")))
27508 (build-system r-build-system)
27509 (propagated-inputs (list r-spatstat-data r-spatstat-geom r-spatstat-utils))
27510 (home-page "http://spatstat.org/")
27511 (synopsis "Random Generation Functionality for the 'spatstat' Family")
27513 "This package provides functionality for random generation of spatial
27514 data in the spatstat family of packages. It generates random spatial patterns
27515 of points according to many simple rules (complete spatial randomness,
27516 Poisson, binomial, random grid, systematic, cell), randomised alteration of
27517 patterns (thinning, random shift, jittering), simulated realisations of random
27518 point processes (simple sequential inhibition, Matern inhibition models,
27519 Matern cluster process, Neyman-Scott cluster processes, log-Gaussian Cox
27520 processes, product shot noise cluster processes) and simulation of Gibbs point
27521 processes (Metropolis-Hastings birth-death-shift algorithm, alternating Gibbs
27523 (license license:gpl2+)))
27525 (define-public r-spatstat
27527 (name "r-spatstat")
27532 (uri (cran-uri "spatstat" version))
27535 "1nlrp7660y68axlm4pczc5rxbdhbbac1ylh69azr4swj1gbzi82f"))))
27536 (properties `((upstream-name . "spatstat")))
27537 (build-system r-build-system)
27539 (list r-spatstat-core r-spatstat-data r-spatstat-geom
27540 r-spatstat-linnet r-spatstat-random r-spatstat-utils))
27541 (home-page "http://www.spatstat.org")
27542 (synopsis "Spatial Point Pattern analysis, model-fitting, simulation, tests")
27544 "This package provides a comprehensive toolbox for analysing Spatial
27545 Point Patterns. It is focused mainly on two-dimensional point patterns,
27546 including multitype/marked points, in any spatial region. It also supports
27547 three-dimensional point patterns, space-time point patterns in any number of
27548 dimensions, point patterns on a linear network, and patterns of other
27549 geometrical objects. It supports spatial covariate data such as pixel images
27550 and contains over 2000 functions for plotting spatial data, exploratory data
27551 analysis, model-fitting, simulation, spatial sampling, model diagnostics, and
27552 formal inference.")
27553 (license license:gpl2+)))
27555 (define-public r-gaston
27562 (uri (cran-uri "gaston" version))
27565 "14z94dpln4dvgrv2w7w9ik7h6rpvbf02qhq1hqzx8c2cndzxr21i"))))
27566 (properties `((upstream-name . "gaston")))
27567 (build-system r-build-system)
27568 (inputs (list zlib))
27570 (list r-rcpp r-rcppeigen r-rcppparallel))
27571 (native-inputs (list r-knitr))
27572 (home-page "https://cran.r-project.org/web/packages/gaston/")
27573 (synopsis "Genetic data handling (QC, GRM, LD, PCA) and linear mixed models")
27575 "This is a package for the manipulation of genetic data (SNPs).
27576 Computation of @dfn{genetic relationship matrix} (GRM) and dominance matrix,
27577 @dfn{linkage disequilibrium} (LD), and heritability with efficient algorithms
27578 for linear mixed models (AIREML).")
27579 (license license:gpl3)))
27581 (define-public r-cpp11
27588 (uri (cran-uri "cpp11" version))
27591 "16cvjfkbc7c0ymdmbcqg9px6pjsqx6qhyfq5frqj739mhazy0g20"))))
27592 (properties `((upstream-name . "cpp11")))
27593 (build-system r-build-system)
27594 (native-inputs (list r-knitr))
27595 (home-page "https://github.com/r-lib/cpp11")
27596 (synopsis "C++11 Interface for R's C Interface")
27598 "This package provides a header only, C++11 interface to R's C interface.
27599 Compared to other approaches @code{cpp11} strives to be safe against long
27600 jumps from the C API as well as C++ exceptions, conform to normal R function
27601 semantics and supports interaction with @code{ALTREP} vectors.")
27602 (license license:expat)))
27604 (define-public r-rcpptoml
27606 (name "r-rcpptoml")
27611 (uri (cran-uri "RcppTOML" version))
27613 (base32 "0h8517ipwqhqkhcfiyqmvsb585g01p0ra0azbpzyxip6pq6g029g"))))
27614 (properties `((upstream-name . "RcppTOML")))
27615 (build-system r-build-system)
27616 (propagated-inputs (list r-rcpp))
27617 (home-page "http://dirk.eddelbuettel.com/code/rcpp.toml.html")
27618 (synopsis "Rcpp bindings to TOML parser")
27620 "The TOML configuration format specifies an excellent format suitable for
27621 both human editing as well as the common uses of a machine-readable format.
27622 This package provides Rcpp bindings to a TOML parser.")
27623 (license license:gpl2+)))
27625 (define-public r-rcppziggurat
27627 (name "r-rcppziggurat")
27632 (uri (cran-uri "RcppZiggurat" version))
27635 "0wgd1v2p7zajnbrjf3hfi56p3pk3ld6iwkanbb04bjbnlif2ay4w"))))
27636 (properties `((upstream-name . "RcppZiggurat")))
27637 (build-system r-build-system)
27639 (list r-rcpp r-rcppgsl))
27640 (native-inputs (list r-knitr))
27641 (home-page "https://cran.r-project.org/web/packages/RcppZiggurat/")
27642 (synopsis "Rcpp integration of different \"Ziggurat\" normal RNG implementations")
27644 "The Ziggurat generator for normally distributed random numbers,
27645 originally proposed by Marsaglia and Tsang (2000,
27646 @url{https://doi.org/10.18637/jss.v005.i08}) has been improved upon a few
27647 times starting with Leong et al (2005,
27648 @url{https://doi.org/10.18637/jss.v012.i07}). This package provides an
27649 aggregation for comparing different implementations in order to provide a
27650 'faster but good enough' alternative for use with R and C++ code.")
27651 (license license:gpl2+)))
27653 (define-public r-rfast
27660 (uri (cran-uri "Rfast" version))
27663 "0zxykq021h57mq0n6giqbx8ncjsdly0arhmaj3fcp3yfcxf4ns9l"))))
27664 (properties `((upstream-name . "Rfast")))
27665 (build-system r-build-system)
27667 (list r-rcpp r-rcpparmadillo r-rcppziggurat))
27668 (home-page "https://github.com/RfastOfficial/Rfast")
27669 (synopsis "Collection of efficient and fast R functions")
27671 "This package provides a collection of fast (utility) functions for data
27672 analysis. Column- and row- wise means, medians, variances, minimums,
27673 maximums, many t, F and G-square tests, many regressions (normal, logistic,
27674 Poisson), are some of the many fast functions.")
27675 (license license:gpl2+)))
27677 (define-public r-rffc
27683 (uri (string-append
27684 "https://download.r-forge.r-project.org/src/contrib/"
27685 "rfFC_" version ".tar.gz"))
27688 "05x9wgzsmx4vb12lmcspymgmpb2xw8bwryb8ysg7vzg2nkh0ma3g"))))
27689 (build-system r-build-system)
27691 (list r-randomforest))
27692 (home-page "https://r-forge.r-project.org/projects/rffc/")
27693 (synopsis "Random Forest Feature Contributions")
27694 (description "This package provides functions for extracting feature
27695 contributions from a random forest model from package @code{randomForest}.
27696 Feature contributions provide detailed information about the relationship
27697 between data variables and the predicted value returned by random forest
27699 (license license:gpl2)))
27701 (define-public r-clusterr
27703 (name "r-clusterr")
27708 (uri (cran-uri "ClusterR" version))
27711 "00mha8madcba83ix4fc04rb7sagfm0lxlh1wvs7dvjdrngps41jr"))))
27712 (properties `((upstream-name . "ClusterR")))
27713 (build-system r-build-system)
27715 (list r-ggplot2 r-gmp r-gtools r-rcpp r-rcpparmadillo))
27716 (native-inputs (list r-knitr))
27717 (home-page "https://github.com/mlampros/ClusterR")
27718 (synopsis "Clustering")
27720 "This package provides Gaussian mixture models, k-means,
27721 mini-batch-kmeans, k-medoids and affinity propagation clustering with the
27722 option to plot, validate, predict (new data) and estimate the optimal number
27723 of clusters. The package takes advantage of @code{RcppArmadillo} to speed up
27724 the computationally intensive parts of the functions. For more information,
27728 @item \"Clustering in an Object-Oriented Environment\" by Anja Struyf, Mia
27729 Hubert, Peter Rousseeuw (1997), Journal of Statistical Software,
27730 @url{https://doi.org/10.18637/jss.v001.i04};
27731 @item \"Web-scale k-means clustering\" by D. Sculley (2010), ACM Digital
27732 Library, @url{https://doi.org/10.1145/1772690.1772862};
27733 @item \"Armadillo: a template-based C++ library
27734 for linear algebra\" by Sanderson et al (2016), The Journal of Open Source
27735 Software, @url{https://doi.org/10.21105/joss.00026};
27736 @item \"Clustering by Passing Messages Between Data Points\" by Brendan
27737 J. Frey and Delbert Dueck, Science 16 Feb 2007: Vol. 315, Issue 5814,
27738 pp. 972-976, @url{https://doi.org/10.1126/science.1136800}.
27741 (license license:gpl3)))
27743 (define-public r-spectrum
27745 (name "r-spectrum")
27750 (uri (cran-uri "Spectrum" version))
27753 "0n38d360azkck6vvhr771zsh0gbvd9qsf9ygg5r18vhz0pb1xcfw"))))
27754 (properties `((upstream-name . "Spectrum")))
27755 (build-system r-build-system)
27757 (list r-clusterr r-diptest r-ggplot2 r-rfast))
27758 (native-inputs (list r-knitr))
27759 (home-page "https://cran.r-project.org/web/packages/Spectrum/")
27760 (synopsis "Fast adaptive spectral clustering for single and multi-view data")
27762 "This package provides a self-tuning spectral clustering method for
27763 single or multi-view data. Spectrum uses a new type of adaptive density aware
27764 kernel that strengthens connections in the graph based on common nearest
27765 neighbours. It uses a tensor product graph data integration and diffusion
27766 procedure to integrate different data sources and reduce noise. Spectrum uses
27767 either the eigengap or multimodality gap heuristics to determine the number of
27768 clusters. The method is sufficiently flexible so that a wide range of
27769 Gaussian and non-Gaussian structures can be clustered with automatic selection
27771 (license license:agpl3+)))
27773 (define-public r-nabor
27780 (uri (cran-uri "nabor" version))
27783 "1nj39cdfwrmhgsi3cq8imxv3n6xzc1v6dzdb2cf2hybjk368v4s7"))))
27784 (properties `((upstream-name . "nabor")))
27785 (build-system r-build-system)
27787 (list r-bh r-rcpp r-rcppeigen))
27788 (home-page "https://cran.r-project.org/web/packages/nabor/")
27789 (synopsis "Wrapper for K nearest neighbour library for low dimensions")
27791 "This package provides an R wrapper for libnabo, an exact or approximate
27792 k nearest neighbour library which is optimised for low dimensional
27793 spaces (e.g. 3D). @code{nabor} includes a @code{knn} function that is
27794 designed as a drop-in replacement for the RANN function @code{nn2}. In
27795 addition, objects which include the k-d tree search structure can be returned
27796 to speed up repeated queries of the same set of target points.")
27797 (license license:bsd-3)))
27799 (define-public r-naturalsort
27801 (name "r-naturalsort")
27805 (uri (cran-uri "naturalsort" version))
27808 "0mz801y9mzld9ypp3xmsjw2d8l9q97sdnv09wrci9xi3yg2sjf6d"))))
27809 (build-system r-build-system)
27810 (home-page "https://cran.r-project.org/web/packages/naturalsort/")
27811 (synopsis "Natural ordering")
27812 (description "This package provides functions related to human natural
27813 ordering. It handles adjacent digits in a character sequence as a number
27814 so that natural sort function arranges a character vector by their numbers,
27815 not digit characters.")
27816 (license license:bsd-3)))
27818 (define-public r-visdat
27824 (uri (cran-uri "visdat" version))
27827 "1ikqp29nncbw1xlwyb9dqqgcdk9q0bs3wxhnhnjpb11vcjv7cz2j"))))
27828 (build-system r-build-system)
27840 (home-page "https://visdat.njtierney.com/")
27841 (synopsis "Preliminary Visualisation of Data")
27842 (description "This package provides procedures to create preliminary exploratory
27843 data visualisations of an entire dataset to identify problems or unexpected features
27844 using @code{ggplot2}.")
27845 (license license:expat)))
27847 (define-public r-muhaz
27850 (version "1.2.6.4")
27854 (uri (cran-uri "muhaz" version))
27857 "1ddy8ayr4rdhzcipdvxdwd7z5g9hfp0ppacl7xf6f2612cn1185g"))))
27858 (properties `((upstream-name . "muhaz")))
27859 (build-system r-build-system)
27864 (home-page "https://cran.r-project.org/web/packages/muhaz/")
27865 (synopsis "Hazard function estimation in survival analysis")
27867 "This package produces a smooth estimate of the hazard function for
27869 ;; Any version of the GPL.
27870 (license license:gpl3+)))
27872 (define-public r-flexsurv
27874 (name "r-flexsurv")
27879 (uri (cran-uri "flexsurv" version))
27882 "0kwij9nkdvnsn1kn12fj3hjkd2qpgw7bdda4qad7basq5p6divlp"))))
27883 (properties `((upstream-name . "flexsurv")))
27884 (build-system r-build-system)
27907 (home-page "https://github.com/chjackson/flexsurv-dev")
27908 (synopsis "Flexible parametric survival and multi-state models")
27910 "This package provides flexible parametric models for time-to-event data,
27911 including the Royston-Parmar spline model, generalized gamma and generalized F
27912 distributions. Any user-defined parametric distribution can be fitted, given
27913 at least an R function defining the probability density or hazard. There are
27914 also tools for fitting and predicting from fully parametric multi-state
27916 (license license:gpl2+)))
27918 (define-public r-transphylo
27920 (name "r-transphylo")
27925 (uri (cran-uri "TransPhylo" version))
27928 "0g92kwi1nlmpc8m4pc9kv9xhczryr2kn9icfr3js7da7vy8g50xy"))))
27929 (properties `((upstream-name . "TransPhylo")))
27930 (build-system r-build-system)
27932 (list r-ape r-rcpp))
27935 (home-page "https://cran.r-project.org/web/packages/TransPhylo/")
27936 (synopsis "Inference of transmission tree from a dated phylogeny")
27938 "This is a package to infer transmission trees from a dated phylogeny.
27939 It includes methods to simulate and analyze outbreaks. The methodology is
27940 described in @url{https://doi.org/10.1093/molbev/msu121,Didelot et al. (2014)}
27941 and @url{https://doi.org/10.1093/molbev/msw275,Didelot et al. (2017)}.")
27942 (license license:gpl2+)))
27944 (define-public r-km-ci
27951 (uri (cran-uri "km.ci" version))
27954 "18sc9vhbdgks8lhk2nfxkkayh8j4j227hl63fm5p04f7z4wm6wc1"))))
27955 (properties `((upstream-name . "km.ci")))
27956 (build-system r-build-system)
27959 (home-page "https://cran.r-project.org/web/packages/km.ci/")
27960 (synopsis "Confidence intervals for the Kaplan-Meier estimator")
27962 "This package computes various @dfn{confidence intervals} (CI) for the
27963 Kaplan-Meier estimator, namely: Petos CI, Rothman CI, CIs based on Greenwoods
27964 variance, Thomas and Grunkemeier CI and the simultaneous confidence bands by
27965 Nair and Hall and Wellner.")
27966 (license license:gpl2+)))
27968 (define-public r-kmsurv
27975 (uri (cran-uri "KMsurv" version))
27978 "0hi5vvk584rl70gbrr75w9hc775xmbxnaig0dd6hlpi4071pnqjm"))))
27979 (properties `((upstream-name . "KMsurv")))
27980 (build-system r-build-system)
27981 (home-page "https://cran.r-project.org/web/packages/KMsurv/")
27982 (synopsis "Data sets from Klein and Moeschberger (1997), Survival Analysis")
27984 "This package provides data sets and functions for Klein and Moeschberger
27985 (1997), \"Survival Analysis, Techniques for Censored and Truncated Data\",
27987 (license license:gpl3+)))
27989 (define-public r-survmisc
27991 (name "r-survmisc")
27996 (uri (cran-uri "survMisc" version))
27999 "014cf7sfndmib9jmj0p3h67sr750k2pvw7m865zwdpvlqddi44fr"))))
28000 (properties `((upstream-name . "survMisc")))
28001 (build-system r-build-system)
28014 (home-page "https://cran.r-project.org/web/packages/survMisc/")
28015 (synopsis "Miscellaneous functions for survival data")
28017 "This package provides a collection of functions to help in the analysis
28018 of right-censored survival data. These extend the methods available in
28019 the @code{survival} package.")
28020 (license license:gpl2)))
28022 (define-public r-exactranktests
28024 (name "r-exactranktests")
28029 (uri (cran-uri "exactRankTests" version))
28032 "1i4mwz61mjlh1ai3dww2pjkicx9ww8c4mljnr8xlawh91479lva9"))))
28034 `((upstream-name . "exactRankTests")))
28035 (build-system r-build-system)
28036 (home-page "https://cran.r-project.org/web/packages/exactRankTests/")
28037 (synopsis "Exact distributions for rank and permutation tests")
28039 "This package computes exact conditional p-values and quantiles using an
28040 implementation of the Shift-Algorithm by Streitberg & Roehmel.")
28041 (license license:gpl2+)))
28043 (define-public r-maxstat
28050 (uri (cran-uri "maxstat" version))
28053 "114z1rwxwvk05ijjhdppzm148n1h192fp0w12ky10zkrhf6kphbg"))))
28054 (properties `((upstream-name . "maxstat")))
28055 (build-system r-build-system)
28057 (list r-exactranktests r-mvtnorm))
28058 (home-page "https://cran.r-project.org/web/packages/maxstat/")
28059 (synopsis "Maximally selected rank statistics")
28061 "This package provides maximally selected rank statistics with several
28062 p-value approximations.")
28063 (license license:gpl2+)))
28065 (define-public r-survminer
28067 (name "r-survminer")
28072 (uri (cran-uri "survminer" version))
28075 "0byh0wxdbjfwdrzsnqv4xlmnik6lj0vkkzfxy7lssk8dv5zmj7nz"))))
28076 (properties `((upstream-name . "survminer")))
28077 (build-system r-build-system)
28096 (home-page "https://rpkgs.datanovia.com/survminer/index.html")
28097 (synopsis "Drawing survival curves using ggplot2")
28099 "This package contains the function @code{ggsurvplot()} for easily
28100 drawing beautiful and 'ready-to-publish' survival curves with the 'number at
28101 risk' table and 'censoring count plot'. Other functions are also available to
28102 plot adjusted curves for Cox model and to visually examine Cox model
28104 (license license:gpl2)))
28106 (define-public r-forge
28113 (uri (cran-uri "forge" version))
28116 "0pjfzsc35agkh0zfw2czwajkbsyn6liys5irl5bhz5r1vim3jmwa"))))
28117 (properties `((upstream-name . "forge")))
28118 (build-system r-build-system)
28120 (list r-magrittr r-rlang))
28121 (home-page "https://cran.r-project.org/web/packages/forge/")
28122 (synopsis "Cast values into shape")
28124 "This package provides helper functions with a consistent interface to
28125 coerce and verify the types and shapes of values for input checking.")
28126 (license license:asl2.0)))
28128 (define-public r-config
28135 (uri (cran-uri "config" version))
28138 "0l2zp7v6qaz72dclcbjrlis633zlwp8rsi5azr7iw127iyz7i26l"))))
28139 (properties `((upstream-name . "config")))
28140 (build-system r-build-system)
28145 (home-page "https://github.com/rstudio/config")
28146 (synopsis "Manage environment specific configuration values")
28148 "This package lets you manage configuration values across multiple
28149 environments (e.g. development, test, production). It reads values using a
28150 function that determines the current environment and returns the appropriate
28152 (license license:gpl3)))
28154 (define-public r-adaptivesparsity
28156 (name "r-adaptivesparsity")
28160 (uri (cran-uri "AdaptiveSparsity" version))
28163 "0imr5m8mll9j6n4icsv6z9rl5kbnwsp9wvzrg7n90nnmcxq2cz91"))))
28165 `((upstream-name . "AdaptiveSparsity")))
28166 (build-system r-build-system)
28169 (modify-phases %standard-phases
28170 (add-after 'unpack 'link-against-armadillo
28172 (substitute* "src/Makevars"
28173 (("PKG_LIBS=" prefix)
28174 (string-append prefix "-larmadillo")))
28177 (list r-mass r-matrix r-rcpp r-rcpparmadillo))
28180 (home-page "https://cran.r-project.org/web/packages/AdaptiveSparsity")
28181 (synopsis "Adaptive sparsity models")
28183 "This package implements the Figueiredo machine learning algorithm for
28184 adaptive sparsity and the Wong algorithm for adaptively sparse Gaussian
28185 geometric models.")
28186 (license license:lgpl3+)))
28188 (define-public r-add2ggplot
28190 (name "r-add2ggplot")
28195 (uri (cran-uri "add2ggplot" version))
28197 (base32 "0c94i1cfp2pvplvxmfvvz2fyj026r1jnax05mrzrc7ppnqzy25y0"))))
28198 (properties `((upstream-name . "add2ggplot")))
28199 (build-system r-build-system)
28201 (list r-ggplot2 r-magick r-magrittr r-rcolorbrewer r-zeallot))
28202 (native-inputs (list r-knitr))
28203 (home-page "https://github.com/JiaxiangBU/add2ggplot")
28204 (synopsis "Extension for ggplot2")
28205 (description "This package provides tools to create themes and color
28206 palettes for the package ggplot2.")
28207 (license license:expat)))
28209 (define-public r-diffusionmap
28211 (name "r-diffusionmap")
28216 (uri (cran-uri "diffusionMap" version))
28219 "1rvk7069brlm1s9kqj4c31mwwr3mw4hmhay95cjjjfmw5xclff2j"))))
28220 (properties `((upstream-name . "diffusionMap")))
28221 (build-system r-build-system)
28223 (list r-igraph r-matrix r-scatterplot3d))
28224 (home-page "https://www.r-project.org")
28225 (synopsis "Diffusion map")
28226 (description "This package implements the diffusion map method of data
28227 parametrization, including creation and visualization of diffusion maps,
28228 clustering with diffusion K-means and regression using the adaptive regression
28230 (license license:gpl2)))
28232 (define-public r-igraph
28239 (uri (cran-uri "igraph" version))
28242 "09dzc8lslljvhj2q46075vxcmlgkvq2qs500zdqyy9g8scq6iqbi"))))
28243 (build-system r-build-system)
28247 (list gmp glpk libxml2 zlib))
28249 (list r-magrittr r-matrix r-pkgconfig))
28250 (home-page "https://igraph.org")
28251 (synopsis "Network analysis and visualization")
28253 "This package provides routines for simple graphs and network analysis.
28254 It can handle large graphs very well and provides functions for generating
28255 random and regular graphs, graph visualization, centrality methods and much
28257 (license license:gpl2+)))
28259 (define-public r-workflows
28261 (name "r-workflows")
28266 (uri (cran-uri "workflows" version))
28269 "0xhc1j25fjipw8hvcpdbvfm640kp0flwvifj5f7g4n6b3wb8cm6a"))))
28270 (properties `((upstream-name . "workflows")))
28271 (build-system r-build-system)
28284 (home-page "https://github.com/tidymodels/workflows")
28285 (synopsis "Modeling workflows")
28287 "A workflow is an object that can bundle together your pre-processing,
28288 modeling, and post-processing requests. For example, if you have a
28289 @code{recipe} and @code{parsnip} model, these can be combined into a
28290 workflow. The advantages are:
28293 @item You don’t have to keep track of separate objects in your workspace.
28294 @item The recipe prepping and model fitting can be executed using a single
28295 call to @code{fit()}.
28296 @item If you have custom tuning parameter settings, these can be defined using
28297 a simpler interface when combined with @code{tune}.
28298 @item In the future, workflows will be able to add post-processing operations,
28299 such as modifying the probability cutoff for two-class models.
28302 (license license:expat)))
28304 (define-public r-lobstr
28311 (uri (cran-uri "lobstr" version))
28314 "0vkif17825x33cz8r89j0qph4wj5l8fzfgl8nh2g7m2v140cxjdq"))))
28315 (properties `((upstream-name . "lobstr")))
28316 (build-system r-build-system)
28318 (list r-crayon r-rcpp r-rlang))
28319 (home-page "https://github.com/r-lib/lobstr")
28320 (synopsis "Visualize R data structures with trees")
28322 "This package provides a set of tools for inspecting and understanding R
28323 data structures inspired by @code{str}. It includes @code{ast} for
28324 visualizing abstract syntax trees, @code{ref} for showing shared references,
28325 @code{cst} for showing call stack trees, and @code{obj_size} for computing
28327 (license license:gpl3)))
28329 (define-public r-gpfit
28336 (uri (cran-uri "GPfit" version))
28339 "05mpiyi2vxv0wqp422n1mnxa8msc4daq40cwpnpngbcwqhlgqkby"))))
28340 (properties `((upstream-name . "GPfit")))
28341 (build-system r-build-system)
28343 (list r-lattice r-lhs))
28344 (home-page "https://cran.r-project.org/web/packages/GPfit/")
28345 (synopsis "Gaussian Processes modeling")
28347 "This package provides a computationally stable approach of fitting a
28348 @dfn{Gaussian Process} (GP) model to a deterministic simulator.")
28349 (license license:gpl2)))
28351 (define-public r-yardstick
28353 (name "r-yardstick")
28358 (uri (cran-uri "yardstick" version))
28361 "00hv4gk1ba4dab8i3dcq7lim4bll7l572rgc8km9x4ja8by95j8h"))))
28362 (properties `((upstream-name . "yardstick")))
28363 (build-system r-build-system)
28373 (home-page "https://github.com/tidymodels/yardstick")
28374 (synopsis "Tidy characterizations of model performance")
28376 "This package provides tidy tools for quantifying how well a model fits
28377 to a data set such as confusion matrices, class probability curve summaries,
28378 and regression metrics (e.g., RMSE).")
28379 (license license:gpl2)))
28381 (define-public r-warp
28388 (uri (cran-uri "warp" version))
28391 "0s0acddc5h14245hi1faycxp0fyvw6nlgaz2df7da4fpyd2f638f"))))
28392 (properties `((upstream-name . "warp")))
28393 (build-system r-build-system)
28394 (native-inputs (list r-knitr))
28395 (home-page "https://github.com/DavisVaughan/warp")
28396 (synopsis "Group dates")
28398 "This package provides tooling to group dates by a variety of periods
28399 including: yearly, monthly, by second, by week of the month, and more. The
28400 groups are defined in such a way that they also represent the distance between
28401 dates in terms of the period. This extracts valuable information that can be
28402 used in further calculations that rely on a specific temporal spacing between
28404 (license license:expat)))
28406 (define-public r-scico
28413 (uri (cran-uri "scico" version))
28415 (base32 "08grfbjd5s0vdw76ni37yjl2242rr8i2jy72sgpwgra282hpnji3"))))
28416 (properties `((upstream-name . "scico")))
28417 (build-system r-build-system)
28418 (propagated-inputs (list r-scales))
28419 (home-page "https://github.com/thomasp85/scico")
28420 (synopsis "Colour Palettes Based on the Scientific Colour-Maps")
28422 "This package provides colour choice in information visualisation. It
28423 important in order to avoid being mislead by inherent bias in the used colour
28424 palette. This package provides access to the perceptually uniform and
28425 colour-blindness friendly palettes developed by Fabio Crameri and released
28426 under the \"Scientific Colour-Maps\" moniker. The package contains 24
28427 different palettes and includes both diverging and sequential types.")
28428 (license license:expat)))
28430 (define-public r-slider
28437 (uri (cran-uri "slider" version))
28440 "1vxk2bc33svwcki2j8zr5jcxswh27i0fqgzjw2a5a1pp9dh3fmd3"))))
28441 (properties `((upstream-name . "slider")))
28442 (build-system r-build-system)
28444 (list r-ellipsis r-glue r-rlang r-vctrs r-warp))
28445 (native-inputs (list r-knitr))
28446 (home-page "https://github.com/DavisVaughan/slider")
28447 (synopsis "Sliding window functions")
28449 "This package provides type-stable rolling window functions over any R
28450 data type. Cumulative and expanding windows are also supported. For more
28451 advanced usage, an index can be used as a secondary vector that defines how
28452 sliding windows are to be created.")
28453 (license license:expat)))
28455 (define-public r-rlist
28458 (version "0.4.6.2")
28462 (uri (cran-uri "rlist" version))
28464 (base32 "15q99rhbbjq8zd976yjmfnny45dd5fg2p2dv1sljg2kwi66nbppb"))))
28465 (properties `((upstream-name . "rlist")))
28466 (build-system r-build-system)
28467 (propagated-inputs (list r-data-table r-jsonlite r-xml r-yaml))
28468 (home-page "https://renkun-ken.github.io/rlist/")
28469 (synopsis "A Toolbox for Non-Tabular Data Manipulation")
28471 "This package provides a set of functions for data manipulation with
28472 list objects, including mapping, filtering, grouping, sorting, updating,
28473 searching, and other useful functions. Most functions are designed to be
28474 pipeline friendly so that data processing with lists can be chained.")
28475 (license license:expat)))
28477 (define-public r-rsample
28484 (uri (cran-uri "rsample" version))
28487 "01xwhj4zfvxbv9cjb6mbz3aphxqc3cnjjx1xy2yx2wd94fbka42z"))))
28488 (properties `((upstream-name . "rsample")))
28489 (build-system r-build-system)
28505 (home-page "https://rsample.tidymodels.org")
28506 (synopsis "General resampling infrastructure")
28508 "This package provides classes and functions to create and summarize
28509 different types of resampling objects (e.g. bootstrap, cross-validation).")
28510 (license license:gpl2)))
28512 (define-public r-dicedesign
28514 (name "r-dicedesign")
28519 (uri (cran-uri "DiceDesign" version))
28522 "1a8ixa65xgyfri03cviic8qi2plbhdyz8m02bwif8w94w0q3ghlk"))))
28523 (properties `((upstream-name . "DiceDesign")))
28524 (build-system r-build-system)
28525 (home-page "http://dice.emse.fr/")
28526 (synopsis "Designs of computer experiments")
28528 "This package provides tools to create some specific @code{Space-Filling
28529 Design} (SFD) and to test their quality.")
28530 (license license:gpl3)))
28532 (define-public r-dials
28539 (uri (cran-uri "dials" version))
28542 "1h695g9vklqn0vd53j9k03s0989xjpjr11h5qhz3a0v6465fwm8a"))))
28543 (properties `((upstream-name . "dials")))
28544 (build-system r-build-system)
28557 (native-inputs (list r-knitr))
28558 (home-page "https://dials.tidymodels.org/")
28559 (synopsis "Tools for creating tuning parameter values")
28561 "Many models contain tuning parameters (i.e. parameters that cannot be
28562 directly estimated from the data). These tools can be used to define objects
28563 for creating, simulating, or validating values for such parameters.")
28564 (license license:gpl2)))
28566 (define-public r-tune
28573 (uri (cran-uri "tune" version))
28576 "05gxlsaqv6sjk11r5g4nkdd6hlb3bnfmc29cx4vln1blha37jx4i"))))
28577 (properties `((upstream-name . "tune")))
28578 (build-system r-build-system)
28601 (home-page "https://github.com/tidymodels/tune")
28602 (synopsis "Tidy tuning tools")
28604 "The ability to tune models is important. @code{tune} contains functions
28605 and classes to be used in conjunction with other @code{tidymodels} packages
28606 for finding reasonable values of hyper-parameters in models, pre-processing
28607 methods, and post-processing steps.")
28608 (license license:expat)))
28610 (define-public r-workflowsets
28612 (name "r-workflowsets")
28617 (uri (cran-uri "workflowsets" version))
28620 "0q42nhnw0mbivadcfb07v71fp39x8fcnjipvn5l5yhjzc56cfxi8"))))
28621 (properties `((upstream-name . "workflowsets")))
28622 (build-system r-build-system)
28642 (home-page "https://github.com/tidymodels/workflowsets")
28643 (synopsis "Create a collection of tidymodels workflows")
28645 "A workflow is a combination of a model and preprocessors (e.g, a
28646 formula, recipe, etc.). In order to try different combinations of these, an
28647 object can be created that contains many workflows. There are functions to
28648 create workflows en masse as well as training them and visualizing the
28650 (license license:expat)))
28652 (define-public r-tidyposterior
28654 (name "r-tidyposterior")
28659 (uri (cran-uri "tidyposterior" version))
28662 "1h1664sjrg6akph6nrk8ynn2kjiswv6gshy35gamam1h4axf6wah"))))
28663 (properties `((upstream-name . "tidyposterior")))
28664 (build-system r-build-system)
28680 (home-page "https://tidyposterior.tidymodels.org")
28681 (synopsis "Bayesian analysis to compare models using resampling statistics")
28683 "This package can be used to conduct post hoc analyses of resampling
28684 results generated by models. For example, if two models are evaluated with
28685 the @dfn{root mean squared error} (RMSE) using 10-fold cross-validation, there
28686 are 10 paired statistics. These can be used to make comparisons between
28687 models without involving a test set.")
28688 (license license:gpl2)))
28690 (define-public r-tidypredict
28692 (name "r-tidypredict")
28697 (uri (cran-uri "tidypredict" version))
28700 "0fff349pkksss8h1k2qza78l81ha6avx63pxziv6dfa8h62qmrdy"))))
28701 (properties `((upstream-name . "tidypredict")))
28702 (build-system r-build-system)
28714 (home-page "https://tidypredict.tidymodels.org")
28715 (synopsis "Run predictions inside the database")
28717 "This package parses a fitted R model object, and returns a formula in
28718 Tidy Eval code that calculates the predictions. It works with several
28719 database backends because it leverages @code{dplyr} and @code{dbplyr} for the
28720 final SQL translation of the algorithm. It currently supports @code{lm()},
28721 @code{glm()}, @code{randomForest()}, @code{ranger()}, @code{earth()},
28722 @code{xgb.Booster.complete()}, @code{cubist()}, and @code{ctree()} models.")
28723 (license license:gpl3)))
28725 (define-public r-janeaustenr
28727 (name "r-janeaustenr")
28732 (uri (cran-uri "janeaustenr" version))
28735 "1wyn4qc28a3sval8shmyi2d7s4nl3jh96s8pzq871brxcmrncbwr"))))
28736 (properties `((upstream-name . "janeaustenr")))
28737 (build-system r-build-system)
28738 (home-page "https://github.com/juliasilge/janeaustenr")
28739 (synopsis "Jane Austen's complete novels")
28741 "This package provides the full texts for Jane Austen's six completed
28742 novels, ready for text analysis. These novels are \"Sense and Sensibility\",
28743 \"Pride and Prejudice\", \"Mansfield Park\", \"Emma\", \"Northanger Abbey\",
28744 and \"Persuasion\".")
28745 (license license:expat)))
28747 (define-public r-tokenizers
28749 (name "r-tokenizers")
28754 (uri (cran-uri "tokenizers" version))
28757 "006xf1vdrmp9skhpss9ldhmk4cwqk512cjp1pxm2gxfybpf7qq98"))))
28758 (properties `((upstream-name . "tokenizers")))
28759 (build-system r-build-system)
28761 (list r-rcpp r-snowballc r-stringi))
28764 (home-page "https://lincolnmullen.com/software/tokenizers/")
28765 (synopsis "Fast, consistent tokenization of natural language text")
28767 "This is a package for converting natural language text into tokens.
28768 It includes tokenizers for shingled n-grams, skip n-grams, words, word stems,
28769 sentences, paragraphs, characters, shingled characters, lines, tweets, Penn
28770 Treebank, regular expressions, as well as functions for counting characters,
28771 words, and sentences, and a function for splitting longer texts into separate
28772 documents, each with the same number of words. The tokenizers have a
28773 consistent interface, and the package is built on the @code{stringi} and
28774 @code{Rcpp} packages for fast yet correct tokenization in UTF-8 encoding.")
28775 (license license:expat)))
28777 (define-public r-hunspell
28779 (name "r-hunspell")
28784 (uri (cran-uri "hunspell" version))
28787 "0ql6y05d4xxpm468rslb0wxdp1x9l3flxzmb5w6pjg617f8vpv8z"))))
28788 (properties `((upstream-name . "hunspell")))
28789 (build-system r-build-system)
28791 (list r-digest r-rcpp))
28794 (home-page "https://github.com/ropensci/hunspell#readme")
28795 (synopsis "High-performance stemmer, tokenizer, and spell checker")
28797 "This package provides a low-level spell checker and morphological
28798 analyzer based on the famous @code{hunspell} library. The package can analyze
28799 or check individual words as well as parse text, LaTeX, HTML or XML documents.
28800 For a more user-friendly interface use the @code{spelling} package which
28801 builds on this package to automate checking of files, documentation and
28802 vignettes in all common formats.")
28803 ;; The hunspell library itself is available under one of GPL2, LGPL2.1, or
28804 ;; MPL; in addition to these licenses the rest of the R wrapper is also
28805 ;; available under the Expat license.
28806 (license (list license:gpl2
28811 (define-public r-tidytext
28813 (name "r-tidytext")
28818 (uri (cran-uri "tidytext" version))
28821 "0as7lscjl6ywk85almmb4f71vxmgkfds46g52ryggkg2isksvq3g"))))
28822 (properties `((upstream-name . "tidytext")))
28823 (build-system r-build-system)
28839 (home-page "https://github.com/juliasilge/tidytext")
28840 (synopsis "Text mining using dplyr, ggplot2, and other Tidy tools")
28842 "This is a package for text mining for word processing and sentiment
28843 analysis using @code{dplyr}, @code{ggplot2}, and other Tidy tools.")
28844 (license license:expat)))
28846 (define-public r-parsnip
28853 (uri (cran-uri "parsnip" version))
28856 "195i4j38mljv9193yx8lmh65h85yhc52y9vc1mk8zvxi52ks1yln"))))
28857 (properties `((upstream-name . "parsnip")))
28858 (build-system r-build-system)
28878 (home-page "https://parsnip.tidymodels.org")
28879 (synopsis "Common API to modeling and analysis functions")
28881 "This package provides a common interface to allow users to specify a
28882 model without having to remember the different argument names across different
28883 functions or computational engines (e.g. R, Spark, Stan, etc).")
28884 (license license:gpl2)))
28886 (define-public r-infer
28893 (uri (cran-uri "infer" version))
28896 "1qbpcn7jqbvgwnpiyylj021j8m33p58a204yd1pfkpzd3x2lbsm6"))))
28897 (properties `((upstream-name . "infer")))
28898 (build-system r-build-system)
28913 (home-page "https://github.com/tidymodels/infer")
28914 (synopsis "Tidy statistical inference")
28916 "The objective of this package is to perform inference using an
28917 expressive statistical grammar that coheres with the Tidy design framework.")
28918 (license license:cc0)))
28920 (define-public r-modeldata
28922 (name "r-modeldata")
28927 (uri (cran-uri "modeldata" version))
28930 "0jgrwf9k8p9j3ywg3yv2wzwsx3snlwm3dd9vfqwhlr7j63jg3cm4"))))
28931 (properties `((upstream-name . "modeldata")))
28932 (build-system r-build-system)
28933 (home-page "https://modeldata.tidymodels.org")
28934 (synopsis "Data sets useful for modeling packages")
28936 "This package provides data sets used for demonstrating or testing
28937 model-related packages.")
28938 (license license:expat)))
28940 (define-public r-conflicted
28942 (name "r-conflicted")
28947 (uri (cran-uri "conflicted" version))
28950 "1qg9ar114r98wm0pnf65mss4v2ksq3924rlpm13mqp4s3p6j9yi4"))))
28951 (properties `((upstream-name . "conflicted")))
28952 (build-system r-build-system)
28954 (list r-memoise r-rlang))
28955 (home-page "https://github.com/r-lib/conflicted")
28956 (synopsis "Alternative conflict resolution strategy")
28958 "R's default conflict management system gives the most recently loaded
28959 package precedence. This can make it hard to detect conflicts, particularly
28960 when they arise because a package update creates ambiguity that did not
28961 previously exist. The @code{conflicted} package takes a different approach,
28962 making every conflict an error and forcing you to choose which function to
28964 (license license:gpl3)))
28966 (define-public r-tidymodels
28968 (name "r-tidymodels")
28973 (uri (cran-uri "tidymodels" version))
28976 "1xkv4s4kn7k9137svb39zrm5302gxpxyp1jv5bb6z0xrvj5wwa4i"))))
28977 (properties `((upstream-name . "tidymodels")))
28978 (build-system r-build-system)
29003 (home-page "https://github.com/tidymodels/tidymodels")
29004 (synopsis "Tidy collection for modeling and statistical analysis")
29006 "The tidy modeling \"verse\" is a collection of packages for modeling and
29007 statistical analysis that share the underlying design philosophy, grammar, and
29008 data structures of the tidyverse.")
29009 (license license:gpl3)))
29011 (define-public r-lsa
29018 (uri (cran-uri "lsa" version))
29021 "1a33irqa6qvbc02z12rgbgv8kxq2gmahy7j5bg8b23lvvaxif06b"))))
29022 (properties `((upstream-name . "lsa")))
29023 (build-system r-build-system)
29025 (list r-snowballc))
29026 (home-page "https://cran.r-project.org/package=lsa")
29027 (synopsis "Latent semantic analysis")
29029 "The basic idea of latent semantic analysis (LSA) is, that text do have a
29030 higher order (=latent semantic) structure which, however, is obscured by word
29031 usage (e.g. through the use of synonyms or polysemy). By using conceptual
29032 indices that are derived statistically via a truncated singular value
29033 decomposition (a two-mode factor analysis) over a given document-term matrix,
29034 this variability problem can be overcome.")
29035 (license license:gpl2+)))
29037 (define-public r-mlecens
29044 (uri (cran-uri "MLEcens" version))
29047 "0cdl0y44clds4sg8hikhk354a5xrfbyfg8lxrbh1bfg410rkj186"))))
29048 (properties `((upstream-name . "MLEcens")))
29049 (build-system r-build-system)
29050 (home-page "http://stat.ethz.ch/~maathuis/")
29051 (synopsis "Computation of the MLE for bivariate (interval) censored data")
29053 "This package contains functions to compute the nonparametric
29054 @dfn{maximum likelihood estimator} (MLE) for the bivariate distribution of
29055 @code{(X,Y)}, when realizations of @code{(X,Y)} cannot be observed directly.
29056 To be more precise, we consider the situation where we observe a set of
29057 rectangles that are known to contain the unobservable realizations of (X,Y).
29058 We compute the MLE based on such a set of rectangles. The methods can also be
29059 used for univariate censored data (see data set @code{cosmesis}), and for
29060 censored data with competing risks (see data set @code{menopause}). The
29061 package also provides functions to visualize the observed data and the MLE.")
29062 (license license:gpl2+)))
29064 (define-public r-metafor
29071 (uri (cran-uri "metafor" version))
29074 "1b599fxk7s0brkchmx698fr5k4g1kzkia2rnlvhg349ffs5nfjmn"))))
29075 (properties `((upstream-name . "metafor")))
29076 (build-system r-build-system)
29078 (list r-matrix r-nlme))
29079 (home-page "https://cran.r-project.org/web/packages/metafor/")
29080 (synopsis "Meta-analysis package for R")
29082 "This package provides a comprehensive collection of functions for
29083 conducting meta-analyses in R. The package includes functions to calculate
29084 various effect sizes or outcome measures, fit fixed-, random-, and
29085 mixed-effects models to such data, carry out moderator and meta-regression
29086 analyses, and create various types of meta-analytical plots (e.g., forest,
29087 funnel, radial, L'Abbe, Baujat, GOSH plots). For meta-analyses of binomial
29088 and person-time data, the package also provides functions that implement
29089 specialized methods, including the Mantel-Haenszel method, Peto's method, and
29090 a variety of suitable generalized linear (mixed-effects) models (i.e.
29091 mixed-effects logistic and Poisson regression models). Finally, the package
29092 provides functionality for fitting meta-analytic multivariate/multilevel
29093 models that account for non-independent sampling errors and/or true
29094 effects (e.g. due to the inclusion of multiple treatment studies, multiple
29095 endpoints, or other forms of clustering). Network meta-analyses and
29096 meta-analyses accounting for known correlation structures (e.g. due to
29097 phylogenetic relatedness) can also be conducted.")
29098 (license license:gpl2+)))
29100 (define-public r-altmeta
29107 (uri (cran-uri "altmeta" version))
29110 "1xq12hnzxh7kgv2i36xprg4lkvqfmxwz3sq4a1jlq2d5g3narvcm"))))
29111 (properties `((upstream-name . "altmeta")))
29112 (build-system r-build-system)
29114 (list r-coda r-lme4 r-matrix r-metafor r-rjags))
29115 (home-page "https://cran.r-project.org/web/packages/altmeta/")
29116 (synopsis "Alternative meta-analysis methods")
29118 "This package provides alternative statistical methods for meta-analysis,
29122 @item bivariate generalized linear mixed models for synthesizing odds ratios,
29123 relative risks, and risk differences
29124 @item heterogeneity tests and measures that are robust to outliers;
29125 @item measures, tests, and visualization tools for publication bias or
29126 small-study effects;
29127 @item meta-analysis of diagnostic tests for synthesizing sensitivities,
29128 specificities, etc.;
29129 @item meta-analysis methods for synthesizing proportions;
29130 @item models for multivariate meta-analysis.
29133 (license license:gpl2+)))
29135 (define-public r-perm
29138 (version "1.0-0.2")
29142 (uri (cran-uri "perm" version))
29145 "182ac1y91yzb34zwdcmx5fdfr5z0cha0gx2bgk36gwxhgfc994kj"))))
29146 (properties `((upstream-name . "perm")))
29147 (build-system r-build-system)
29148 (home-page "https://cran.r-project.org/web/packages/perm/")
29149 (synopsis "Exact or asymptotic permutation tests")
29151 "This package provides several methods for performing permutation tests.
29152 It has three main functions, to perform linear permutation tests. These tests
29153 are tests where the test statistic is the sum of the product of a
29154 covariate (usually group indicator) and the scores.")
29155 ;; Any version of the GPL
29156 (license license:gpl2+)))
29158 (define-public r-qtl
29165 (uri (cran-uri "qtl" version))
29168 "1mcy9wlp5lj5f3z4mf3n5li7x32vj67rmhjnzsp8fhfw0ipnaf1d"))))
29169 (build-system r-build-system)
29170 (home-page "https://rqtl.org/")
29171 (synopsis "R package for analyzing QTL experiments in genetics")
29172 (description "R/qtl is an extension library for the R statistics system.
29173 It is used to analyze experimental crosses for identifying genes contributing
29174 to variation in quantitative traits (so-called quantitative trait loci, QTLs).
29176 Using a hidden Markov model, R/qtl estimates genetic maps, to identify
29177 genotyping errors, and to perform single-QTL and two-QTL, two-dimensional
29179 (license license:gpl3)))
29181 (define-public r-qtl2
29187 (uri (cran-uri "qtl2" version))
29189 (base32 "0ppc6dzlq77mppxc6bczai9gi40jrbxd1466y2cn2s8a4ah1jg9y"))))
29190 (build-system r-build-system)
29198 (home-page "https://kbroman.org/qtl2/")
29199 (synopsis "Quantitative Trait Locus Mapping in Experimental Crosses")
29201 "This package provides a set of tools to perform @dfn{Quantitative Trait
29202 Locus} (QTL) analysis in experimental crosses. It is a reimplementation of the
29203 @code{R/qtl} package to better handle high-dimensional data and complex cross
29204 designs. Broman et al. (2018) <doi:10.1534/genetics.118.301595>.")
29205 (license license:gpl3)))
29207 (define-public r-seqminer
29209 (name "r-seqminer")
29214 (uri (cran-uri "seqminer" version))
29217 "1mbx1hw9dhgry7hhan43g6aiz2lyd5api7wxq3fwajyzjrc6p1g8"))))
29218 (build-system r-build-system)
29221 (home-page "http://seqminer.genomic.codes")
29222 (synopsis "Read nucleotide sequence data (VCF, BCF, and METAL formats)")
29224 "This package provides tools to integrate nucleotide sequencing
29225 data (variant call format, e.g. VCF or BCF) or meta-analysis results in R.")
29226 ;; Any version of the GPL is acceptable
29227 (license (list license:gpl2+ license:gpl3+))))
29229 (define-public r-maldiquant
29231 (name "r-maldiquant")
29236 (uri (cran-uri "MALDIquant" version))
29239 "1y1g3819ss06dry70kfhg2syddw71682qmzkcyppfsma6hhghw87"))))
29240 (properties `((upstream-name . "MALDIquant")))
29241 (build-system r-build-system)
29244 (home-page "https://cran.r-project.org/web/packages/MALDIquant")
29245 (synopsis "Quantitative analysis of mass spectrometry data")
29247 "This package provides a complete analysis pipeline for matrix-assisted
29248 laser desorption/ionization-time-of-flight (MALDI-TOF) and other
29249 two-dimensional mass spectrometry data. In addition to commonly used plotting
29250 and processing methods it includes distinctive features, namely baseline
29251 subtraction methods such as morphological filters (TopHat) or the
29252 statistics-sensitive non-linear iterative peak-clipping algorithm (SNIP), peak
29253 alignment using warping functions, handling of replicated measurements as well
29254 as allowing spectra with different resolutions.")
29255 (license license:gpl3+)))
29257 (define-public r-scattermore
29259 (name "r-scattermore")
29264 (uri (cran-uri "scattermore" version))
29267 "1rgqm7r1k7j3h2y4i6d1a2y8fzivfcbmr7dj9d367c0w4vc77pfv"))))
29268 (properties `((upstream-name . "scattermore")))
29269 (build-system r-build-system)
29271 (list r-ggplot2 r-scales))
29272 (home-page "https://github.com/exaexa/scattermore")
29273 (synopsis "Scatterplots with more points")
29275 "This package provides C-based tools for converting large scatterplot
29276 data to rasters. It speeds up plotting of data with millions of points.")
29277 (license license:gpl3+)))
29279 (define-public r-seuratobject
29281 (name "r-seuratobject")
29286 (uri (cran-uri "SeuratObject" version))
29289 "1308hjbs8br3gp9vwm65awgp6vimwgi2jyl1ryn96l84savn2ljq"))))
29290 (properties `((upstream-name . "SeuratObject")))
29291 (build-system r-build-system)
29293 (list r-matrix r-rcpp r-rcppeigen r-rlang))
29294 (home-page "https://satijalab.org/seurat")
29295 (synopsis "Data structures for single cell data")
29297 "This package defines S4 classes for single-cell genomic data and
29298 associated information, such as dimensionality reduction embeddings,
29299 nearest-neighbor graphs, and spatially-resolved coordinates. It provides data
29300 access methods and R-native hooks to ensure the Seurat object is familiar to
29302 (license license:gpl3)))
29304 (define-public r-seurat
29310 (uri (cran-uri "Seurat" version))
29313 "0p9i3fnkqa3vranr7c7ckzp1kq42d7p0gcfi9ml4kr334yd84195"))))
29314 (properties `((upstream-name . "Seurat")))
29315 (build-system r-build-system)
29360 (home-page "http://www.satijalab.org/seurat")
29361 (synopsis "Seurat is an R toolkit for single cell genomics")
29363 "This package is an R package designed for QC, analysis, and
29364 exploration of single cell RNA-seq data. It easily enables widely-used
29365 analytical techniques, including the identification of highly variable genes,
29366 dimensionality reduction; PCA, ICA, t-SNE, standard unsupervised clustering
29367 algorithms; density clustering, hierarchical clustering, k-means, and the
29368 discovery of differentially expressed genes and markers.")
29369 (license license:gpl3)))
29371 (define-public r-seuratdisk
29372 (let ((commit "163f1aade5bac38ed1e9e9c912283a7e74781610")
29375 (name "r-seuratdisk")
29376 (version (git-version "0.0.0.9019" revision commit))
29380 (uri (git-reference
29381 (url "https://github.com/mojaveazure/seurat-disk")
29383 (file-name (git-file-name name version))
29385 (base32 "1d1v8qi6kknzy5fj6bl8akwy74h5h143i00lyidsnqjbwp9n4qnw"))))
29386 (properties `((upstream-name . "SeuratDisk")))
29387 (build-system r-build-system)
29401 (home-page "https://github.com/mojaveazure/seurat-disk")
29402 (synopsis "Interfaces for HDF5-based single cell file formats")
29404 "The h5Seurat file format is specifically designed for the storage and
29405 analysis of multi-modal single-cell and spatially-resolved expression
29406 experiments, for example, from CITE-seq or 10X Visium technologies. It holds
29407 all molecular information and associated metadata, including (for example)
29408 nearest-neighbor graphs, dimensional reduction information, spatial
29409 coordinates and image data, and cluster labels. This package also supports
29410 rapid and on-disk conversion between h5Seurat and AnnData objects, with the
29411 goal of enhancing interoperability between Seurat and Scanpy.")
29412 (license license:gpl3))))
29414 (define-public r-seuratdata
29415 (let ((commit "b59556b24d7d6728a5744c9c715dd5f7f32ed7a5")
29418 (name "r-seuratdata")
29419 (version (git-version "0.2.1" revision commit))
29423 (uri (git-reference
29424 (url "https://github.com/satijalab/seurat-data")
29426 (file-name (git-file-name name version))
29428 (base32 "1xfdmdmgn4r0z6w4cxa98ic6xk8i6qz054r215dvqbjs1vydsbf9"))))
29429 (properties `((upstream-name . "SeuratData")))
29430 (build-system r-build-system)
29433 (modify-phases %standard-phases
29434 ;; When there is no HOME directory, this package will fail to load
29435 ;; the included list of packages.
29436 (add-after 'unpack 'set-HOME
29437 (lambda _ (setenv "HOME" "/tmp"))))))
29439 (list r-cli r-crayon r-rappdirs))
29440 (home-page "https://github.com/satijalab/seurat-data")
29441 (synopsis "Install and manage Seurat datasets")
29443 "Single cell RNA sequencing datasets can be large, consisting of
29444 matrices that contain expression data for several thousand features across
29445 several thousand cells. This package is designed to easily install, manage,
29446 and learn about various single-cell datasets, provided Seurat objects and
29447 distributed as independent packages.")
29448 (license license:gpl3))))
29450 (define-public r-phangorn
29452 (name "r-phangorn")
29457 (uri (cran-uri "phangorn" version))
29460 "0xfwi7adl1pcfcwk72fj7lkwfm0wiip96ij7m4252xr9mq818ivd"))))
29461 (build-system r-build-system)
29471 (home-page "https://github.com/KlausVigo/phangorn")
29472 (synopsis "Phylogenetic analysis in R")
29474 "Phangorn is a package for phylogenetic analysis in R. It supports
29475 estimation of phylogenetic trees and networks using Maximum Likelihood,
29476 Maximum Parsimony, distance methods and Hadamard conjugation.")
29477 (license license:gpl2+)))
29479 (define-public r-diversitree
29481 (name "r-diversitree")
29486 (uri (cran-uri "diversitree" version))
29489 "0rzrk7xsn4gy271pbcw3azndhx0c06bmsgrg6libjmlfnmq6j8sc"))))
29490 (build-system r-build-system)
29493 (inputs (list fftw gsl))
29495 (list r-ape r-desolve r-rcpp r-subplex))
29496 (home-page "https://www.zoology.ubc.ca/prog/diversitree")
29497 (synopsis "Comparative 'phylogenetic' analyses of diversification")
29498 (description "This package contains a number of comparative \"phylogenetic\"
29499 methods, mostly focusing on analysing diversification and character evolution.
29500 Contains implementations of \"BiSSE\" (Binary State Speciation and Extinction)
29501 and its unresolved tree extensions, \"MuSSE\" (Multiple State Speciation and
29502 Extinction), \"QuaSSE\", \"GeoSSE\", and \"BiSSE-ness\" Other included methods
29503 include Markov models of discrete and continuous trait evolution and constant
29504 rate speciation and extinction.")
29505 (license license:gpl2+)))
29507 (define-public r-calculus
29509 (name "r-calculus")
29514 (uri (cran-uri "calculus" version))
29517 "1fhvr0l2mqik3d95v0vanafxmiab147g5a87q956g2i945wc5f22"))))
29518 (properties `((upstream-name . "calculus")))
29519 (build-system r-build-system)
29524 (home-page "https://github.com/eguidotti/calculus")
29525 (synopsis "High dimensional numerical and symbolic calculus")
29527 "Efficient C++ optimized functions for numerical and symbolic calculus.
29528 It includes basic symbolic arithmetic, tensor calculus, Einstein summing
29529 convention, fast computation of the Levi-Civita symbol and generalized
29530 Kronecker delta, Taylor series expansion, multivariate Hermite polynomials,
29531 accurate high-order derivatives, differential operators (Gradient, Jacobian,
29532 Hessian, Divergence, Curl, Laplacian) and numerical integration in arbitrary
29533 orthogonal coordinate systems: cartesian, polar, spherical, cylindrical,
29534 parabolic or user defined by custom scale factors.")
29535 (license license:gpl3)))
29537 (define-public r-decon
29544 (uri (cran-uri "decon" version))
29547 "036cv56wf42q2p3d5h15hbrp5rc29xxy20qwv4k1qzhkq6hmw0qs"))))
29548 (properties `((upstream-name . "decon")))
29549 (build-system r-build-system)
29553 "https://cran.r-project.org/web/packages/decon/")
29554 (synopsis "Deconvolution Estimation in Measurement Error Models")
29556 "This package contains a collection of functions to deal with
29557 nonparametric measurement error problems using deconvolution
29558 kernel methods. We focus two measurement error models in the
29559 package: (1) an additive measurement error model, where the
29560 goal is to estimate the density or distribution function from
29561 contaminated data; (2) nonparametric regression model with
29562 errors-in-variables. The R functions allow the measurement errors
29563 to be either homoscedastic or heteroscedastic. To make the
29564 deconvolution estimators computationally more efficient in R,
29565 we adapt the \"Fast Fourier Transform\" (FFT) algorithm for
29566 density estimation with error-free data to the deconvolution
29567 kernel estimation. Several methods for the selection of the
29568 data-driven smoothing parameter are also provided in the package.
29569 See details in: Wang, X.F. and Wang, B. (2011). Deconvolution
29570 estimation in measurement error models: The R package decon.
29571 Journal of Statistical Software, 39(10), 1-24.")
29572 (license license:gpl3+)))
29574 (define-public r-densestbayes
29576 (name "r-densestbayes")
29577 (version "1.0-2.1")
29581 (uri (cran-uri "densEstBayes" version))
29583 (base32 "1pzmgn65lv91zg1588qhwczy9f2zgciknlc4l072mvh2i7hncw2b"))))
29584 (properties `((upstream-name . "densEstBayes")))
29585 (build-system r-build-system)
29597 (home-page "https://cran.r-project.org/package=densEstBayes")
29598 (synopsis "Density estimation via Bayesian inference engines")
29600 "Bayesian density estimates for univariate continuous random samples are
29601 provided using the Bayesian inference engine paradigm. The engine options
29602 are: Hamiltonian Monte Carlo, the no U-turn sampler, semiparametric mean field
29603 variational Bayes and slice sampling. The methodology is described in Wand
29604 and Yu (2020), arXiv:2009.06182.")
29605 (license license:gpl2+)))
29607 (define-public r-locpol
29614 (uri (cran-uri "locpol" version))
29617 "1p915n0l09kbwkly627074jslxl01yssp1rf0c7sygvsw6sgy5lm"))))
29618 (properties `((upstream-name . "locpol")))
29619 (build-system r-build-system)
29621 "https://cran.r-project.org/web/packages/locpol/")
29622 (synopsis "Kernel Local Polynomial Regression")
29624 "Computes local polynomial estimators for the regression and
29625 also density. It comprises several different utilities to handle
29626 kernel estimators.")
29627 (license license:gpl2+)))
29629 (define-public r-lpme
29636 (uri (cran-uri "lpme" version))
29639 "1b0w5ji8hjayni1sh5id193cmanf6n11p16fijkxln4sv4lks4aw"))))
29640 (properties `((upstream-name . "lpme")))
29641 (build-system r-build-system)
29643 (list r-decon r-flexmix r-locpol r-rcpp r-rcpparmadillo))
29645 "https://cran.r-project.org/web/packages/lpme/")
29646 (synopsis "Nonparametric Estimation of Measurement Error Models")
29648 "Provide nonparametric methods for mean regression model,
29649 modal regression and conditional density estimation in the
29650 presence/absence of measurement error. Bandwidth selection is
29651 also provided for each method.")
29652 (license license:gpl2+)))
29654 (define-public r-aws-signature
29656 (name "r-aws-signature")
29661 (uri (cran-uri "aws.signature" version))
29664 "15llpcnrdq4y6jsn7079yjmgbr5d1wgy2ymsm3jj3gkrd5l4zzpp"))))
29665 (properties `((upstream-name . "aws.signature")))
29666 (build-system r-build-system)
29668 (list r-base64enc r-digest))
29669 (home-page "https://github.com/cloudyr/aws.signature")
29670 (synopsis "Amazon Web Services Request Signatures")
29672 "This package generates version 2 and 4 request signatures for Amazon Web
29673 Services (AWS) and provides a mechanism for retrieving credentials from
29674 environment variables, AWS credentials files, and EC2 instance metadata. For
29675 use on EC2 instances, the package 'aws.ec2metadata' is suggested.")
29676 (license license:gpl2+)))
29678 (define-public r-aws-s3
29685 (uri (cran-uri "aws.s3" version))
29688 "132cczq0ml7lpp2yl6l4p99dn1zihrncnpa6wyad4m9mnr50a8dx"))))
29689 (properties `((upstream-name . "aws.s3")))
29690 (build-system r-build-system)
29692 (list r-aws-signature
29698 (home-page "https://github.com/cloudyr/aws.s3")
29699 (synopsis "AWS S3 Client Package")
29701 "This package provides a simple client package for the Amazon Web
29702 Services (AWS) Simple Storage Service (S3) REST API.")
29703 (license license:gpl2+)))
29705 (define-public r-lgr
29711 (uri (cran-uri "lgr" version))
29714 "18s92qyakhvp336kk2777ydypwfrfwfz6a1gqkq812zy3kcb4mcc"))))
29715 (build-system r-build-system)
29720 (home-page "https://s-fleck.github.io/lgr/")
29721 (synopsis "Fully featured logging framework")
29722 (description "This package offers a flexible, feature-rich yet
29723 light-weight logging framework based on @code{R6} classes. It supports
29724 hierarchical loggers, custom log levels, arbitrary data fields in log events,
29725 logging to plaintext, JSON, (rotating) files, memory buffers, and databases, as
29726 well as email and push notifications.")
29727 (license license:expat)))
29729 (define-public r-mhg
29736 (uri (cran-uri "mHG" version))
29739 "1rz5ncrvvv9h9grls15apa63v2nh9j87fmp4mwjjil37jx6a5zki"))))
29740 (properties `((upstream-name . "mHG")))
29741 (build-system r-build-system)
29742 (home-page "https://cran.r-project.org/package=mHG")
29743 (synopsis "Minimum-hypergeometric test")
29745 "This package runs a minimum-hypergeometric (mHG) test as described in
29746 \"Discovering Motifs in Ranked Lists of DNA Sequences\" by Eran Eden.")
29747 (license license:gpl2)))
29749 (define-public r-mlr3measures
29751 (name "r-mlr3measures")
29755 (uri (cran-uri "mlr3measures" version))
29758 "1kbw3xd7c9x65v9zzs8i5skmrvl0mf2wsbyssmiif0lvrbzfhcmb"))))
29759 (build-system r-build-system)
29761 (list r-checkmate r-prroc))
29762 (home-page "https://mlr3measures.mlr-org.com/")
29763 (synopsis "Performance measures for mlr3")
29764 (description "This package implements multiple performance measures for
29765 supervised learning. It includes over 40 measures for regression and
29766 classification. Additionally, meta information about the performance measures
29767 can be queried, e.g. what the best and worst possible performances scores
29769 (license license:lgpl3)))
29771 (define-public r-mlr3misc
29773 (name "r-mlr3misc")
29777 (uri (cran-uri "mlr3misc" version))
29780 "1wnzyij1x67smkb3gjb9gpp7iy5andfl0s1c78xx4wylhycc6m11"))))
29781 (build-system r-build-system)
29783 (list r-backports r-checkmate r-data-table r-digest r-r6))
29784 (home-page "https://mlr3misc.mlr-org.com/")
29785 (synopsis "Helper functions for mlr3")
29786 (description "@code{mlr3misc} provides frequently used helper functions
29787 and assertions used in @code{mlr3} and its companion packages. It comes with
29788 helper functions for functional programming, for printing, to work with
29789 @code{data.table}, as well as some generally useful @code{R6} classes. This
29790 package also supersedes the package @code{BBmisc}.")
29791 (license license:lgpl3)))
29793 (define-public r-mlr3pipelines
29795 (name "r-mlr3pipelines")
29799 (uri (cran-uri "mlr3pipelines" version))
29802 "0913f67c1r9bi68gxh1prsp0vch21bl6plahnvjrlbq8rrs1sr6p"))))
29803 (build-system r-build-system)
29815 (home-page "https://mlr3pipelines.mlr-org.com/")
29816 (synopsis "Preprocessing Operators and Pipelines for @code{mlr3}")
29817 (description "@code{mlr3pipelines} enriches @code{mlr3} with a diverse
29818 set of pipelining operators (PipeOps) that can be composed into graphs.
29819 Operations exist for data preprocessing, model fitting, and ensemble learning.
29820 Graphs can themselves be treated as @code{mlr3} Learners and can therefore be
29821 resampled, benchmarked, and tuned.")
29822 (license license:lgpl3)))
29824 (define-public r-mlr3ordinal
29825 (let ((commit "9febac983b11b7b1f477e5cf0212e5999cd2ed44")
29828 (name "r-mlr3ordinal")
29829 (version (git-version "0.1.0-9000" revision commit))
29832 (uri (git-reference
29833 (url "https://github.com/mlr-org/mlr3ordinal")
29835 (file-name (git-file-name name version))
29838 "1icfhz1pjm0mlsn2y60gsrbk31b2p7xmpx3xsg7639rcgdb5f9gl"))))
29839 (build-system r-build-system)
29850 (home-page "https://mlr3ordinal.mlr-org.com/")
29851 (synopsis "Ordinal Regression for mlr3")
29852 (description "This package extends @code{mlr3} with support for
29853 performing ordinal regression.")
29854 (license license:expat))))
29856 (define-public r-paradox
29862 (uri (cran-uri "paradox" version))
29865 "1jfzbpqi1rp3r8hnk37dqwggp48ha5bnilmdz7dwzfdaskssycxa"))))
29866 (build-system r-build-system)
29868 (list r-backports r-checkmate r-data-table r-mlr3misc r-r6))
29869 (home-page "https://paradox.mlr-org.com/")
29870 (synopsis "Define and work with parameter spaces for complex algorithms")
29871 (description "With this package it is possible to define parameter spaces,
29872 constraints and dependencies for arbitrary algorithms, and to program on such
29873 spaces. It also includes statistical designs and random samplers. Objects are
29874 implemented as @code{R6} classes.")
29875 (license license:lgpl3)))
29877 (define-public r-mlr3
29883 (uri (cran-uri "mlr3" version))
29886 "010kl51zsgpc0qv63g1fg9kiw9m0wzqskcr14f1j8b9zi1lwi0bf"))))
29887 (build-system r-build-system)
29904 (home-page "https://mlr3.mlr-org.com/")
29905 (synopsis "Machine Learning in R - Next Generation")
29906 (description "@code{mlr3} enables efficient, object-oriented programming
29907 on the building blocks of machine learning. It provides @code{R6} objects for
29908 tasks, learners, resamplings, and measures. The package is geared towards
29909 scalability and larger datasets by supporting parallelization and out-of-memory
29910 data-backends like databases. While @code{mlr3} focuses on the core
29911 computational operations, add-on packages provide additional functionality.")
29912 (license license:lgpl3)))
29914 (define-public r-mlr3learners
29916 (name "r-mlr3learners")
29920 (uri (cran-uri "mlr3learners" version))
29923 "1d9hcrnj622ynrzg0ii0fkhz2n66ip46yln21jq1pwpwkqwqzv35"))))
29924 (build-system r-build-system)
29932 (home-page "https://mlr3learners.mlr-org.com/")
29933 (synopsis "Recommended Learners for @code{mlr3}")
29934 (description "@code{mlr3learners} extends @code{mlr3} and @code{mlr3proba}
29935 with interfaces to essential machine learning packages on CRAN. This includes,
29936 but is not limited to: (penalized) linear and logistic regression, linear and
29937 quadratic discriminant analysis, k-nearest neighbors, naive Bayes, support
29938 vector machines, and gradient boosting.")
29939 (license license:lgpl3)))
29941 (define-public r-bbotk
29948 (uri (cran-uri "bbotk" version))
29951 "0k1vlh14mfbcgdw2yfhab7shkrqm4d2h6af12mybr9gks26xmw82"))))
29952 (properties `((upstream-name . "bbotk")))
29953 (build-system r-build-system)
29963 (home-page "https://bbotk.mlr-org.com")
29964 (synopsis "Black-Box Optimization Toolkit")
29965 (description "This package provides a common framework for optimization of
29966 black-box functions for other packages, e.g. @code{mlr3}. It offers various
29967 optimization methods e.g. grid search, random search and generalized simulated
29969 (license license:lgpl3)))
29971 (define-public r-mlr3tuning
29973 (name "r-mlr3tuning")
29977 (uri (cran-uri "mlr3tuning" version))
29980 "0czlpi8bshn8cjq7pa1cyy7lpv35g4hv2nbyhc59zrcykzfv8afm"))))
29981 (build-system r-build-system)
29991 (home-page "https://mlr3tuning.mlr-org.com/")
29992 (synopsis "Tuning for @code{mlr3}")
29993 (description "@code{mlr3tuning} implements methods for hyperparameter
29994 tuning, e.g. Grid Search, Random Search, or Simulated Annealing. Various
29995 termination criteria can be set and combined. The class @code{AutoTuner} provides a
29996 convenient way to perform nested resampling in combination with @code{mlr3}.")
29997 (license license:lgpl3)))
29999 (define-public r-fontliberation
30001 (name "r-fontliberation")
30006 (uri (cran-uri "fontLiberation" version))
30009 "1w1rl0g4ayyp8lwppmz9yzj9cizg7i50g07216jkm1q5w0is9pmc"))))
30011 `((upstream-name . "fontLiberation")))
30012 (build-system r-build-system)
30013 (home-page "https://cran.r-project.org/package=fontLiberation")
30014 (synopsis "Liberation fonts")
30016 "This package provides a placeholder for the Liberation fontset intended
30017 for the fontquiver package. This fontset covers the 12 combinations of
30018 families (sans, serif, mono) and faces (plain, bold, italic, bold italic)
30019 supported in R graphics devices.")
30020 (license license:silofl1.1)))
30022 (define-public r-fontbitstreamvera
30024 (name "r-fontbitstreamvera")
30029 (uri (cran-uri "fontBitstreamVera" version))
30032 "0nipdlmhjv1wr3aidcl97nk6mppdkd65krgwqnhdsnv0jpfv761j"))))
30034 `((upstream-name . "fontBitstreamVera")))
30035 (build-system r-build-system)
30036 (home-page "https://cran.r-project.org/package=fontBitstreamVera")
30037 (synopsis "Fonts for fontquiver")
30039 "This package is a placeholder for the Bitstream Vera font. It is
30040 intended for the fontquiver package.")
30042 (license:fsdg-compatible
30043 "https://www.gnome.org/fonts/#Final_Bitstream_Vera_Fonts"
30044 "The Font Software may be sold as part of a larger software package but
30045 no copy of one or more of the Font Software typefaces may be sold by
30048 (define-public r-fontquiver
30050 (name "r-fontquiver")
30055 (uri (cran-uri "fontquiver" version))
30058 "0qv3i9hch7cygl9983s3w68wfh5qvym2jkm52pp06p6mq8a1i1wm"))))
30059 (properties `((upstream-name . "fontquiver")))
30060 (build-system r-build-system)
30062 (list r-fontbitstreamvera r-fontliberation))
30063 (home-page "https://cran.r-project.org/package=fontquiver")
30064 (synopsis "Set of installed fonts")
30066 "This package provides a set of fonts. This is useful when you want to
30067 avoid system fonts to make sure your outputs are reproducible.")
30068 (license license:gpl3)))
30070 (define-public r-freetypeharfbuzz
30072 (name "r-freetypeharfbuzz")
30077 (uri (cran-uri "freetypeharfbuzz" version))
30080 "0r3icgnq3jk4fm6z92cmhzdmflbk5df8zsmjg0dzpc4y48xafnk7"))))
30082 `((upstream-name . "freetypeharfbuzz")))
30083 (build-system r-build-system)
30086 (modify-phases %standard-phases
30087 (add-after 'unpack 'prepare-static-libraries
30088 (lambda* (#:key inputs #:allow-other-keys)
30089 (mkdir-p "src/target/include")
30090 (let ((freetype (assoc-ref inputs "static-freetype"))
30091 (harfbuzz (assoc-ref inputs "static-harfbuzz")))
30092 (substitute* "src/Makevars.in"
30093 (("include @MK_FILE@") "") ; do not build static libs
30094 (("^HB_STATIC_LIB =.*")
30095 (string-append "HB_STATIC_LIB = " harfbuzz "/lib/libharfbuzz.a\n"))
30096 (("^FT_STATIC_LIB =.*")
30097 (string-append "FT_STATIC_LIB = " freetype "/lib/libfreetype.a\n")))
30098 (copy-recursively (string-append freetype "/include")
30099 "src/target/include")
30100 (copy-recursively (string-append harfbuzz "/include")
30101 "src/target/include")))))))
30103 (list r-fontquiver))
30104 ;; This may defeat the purpose of this package as our versions of freetype
30105 ;; and harfbuzz obviously differ from the tarballs offered by this
30106 ;; project. On the other hand, Guix arguably does a better job at
30107 ;; "ensur[ing] deterministic computation".
30109 `(("static-freetype"
30111 (inherit (static-package freetype))
30113 `(#:configure-flags
30114 (list "--enable-static=yes"
30119 "--without-harfbuzz")))))
30122 (inherit (static-package harfbuzz))
30124 `(#:tests? #false ; fail because shared library is disabled
30126 (list "--enable-static=yes"
30127 "--enable-shared=no"
30129 "--with-freetype=yes"
30132 "--without-fontconfig"
30133 "--without-glib")))))))
30136 (home-page "https://cran.r-project.org/package=freetypeharfbuzz")
30137 (synopsis "Deterministic computation of text box metrics")
30139 "Unlike other tools that dynamically link to the Cairo stack,
30140 freetypeharfbuzz is statically linked to specific versions of the FreeType and
30141 harfbuzz libraries. This ensures deterministic computation of text box
30142 extents for situations where reproducible results are crucial (for instance
30143 unit tests of graphics).")
30144 (license license:gpl3)))
30146 (define-public r-vdiffr
30153 (uri (cran-uri "vdiffr" version))
30156 "1z8nn8yh6jfzb9r7ylmigwh1p30lrclqm6khmp323qqphzmzfdwy"))))
30157 (properties `((upstream-name . "vdiffr")))
30158 (build-system r-build-system)
30160 (list libpng zlib))
30170 (home-page "https://github.com/r-lib/vdiffr")
30171 (synopsis "Visual regression testing and graphical diffing")
30173 "This package is an extension to the testthat package that makes it easy
30174 to add graphical unit tests. It provides a Shiny application to manage the
30176 (license license:gpl3)))
30178 (define-public r-highlight
30180 (name "r-highlight")
30185 (uri (cran-uri "highlight" version))
30188 "1shar4y07wyixg0ichdrn2xhgwkl3mv2pxkalqzisc69w605b3hf"))))
30189 (properties `((upstream-name . "highlight")))
30190 (build-system r-build-system)
30191 (home-page "https://github.com/hadley/highlight")
30192 (synopsis "Syntax highlighter for R code")
30194 "This package provides a syntax highlighter for R code based on the
30195 results of the R parser. It supports rendering in HTML and LaTeX markup. It
30196 includes a custom Sweave driver performing syntax highlighting of R code
30198 (license license:gpl3+)))
30200 (define-public r-clustree
30202 (name "r-clustree")
30207 (uri (cran-uri "clustree" version))
30210 "0vwmicajl7c0rmjdmf4f857fii0xrxz25vjkn888svlsikw00qbs"))))
30211 (properties `((upstream-name . "clustree")))
30212 (build-system r-build-system)
30225 (home-page "https://github.com/lazappi/clustree")
30226 (synopsis "Visualize clusterings at different resolutions")
30228 "Deciding what resolution to use can be a difficult question when
30229 approaching a clustering analysis. One way to approach this problem is to
30230 look at how samples move as the number of clusters increases. This package
30231 allows you to produce clustering trees, a visualization for interrogating
30232 clusterings as resolution increases.")
30233 (license license:gpl3)))
30235 (define-public r-textshaping
30237 (name "r-textshaping")
30242 (uri (cran-uri "textshaping" version))
30245 "1niaj1dh09rqrg9hrh98ddnc0f2nkyq9iizv24lcwm9gjs3w1ql0"))))
30246 (properties `((upstream-name . "textshaping")))
30247 (build-system r-build-system)
30249 (list freetype fribidi harfbuzz zlib))
30251 (list r-cpp11 r-systemfonts))
30253 (list pkg-config r-knitr))
30254 (home-page "https://github.com/r-lib/textshaping")
30255 (synopsis "Bindings to the HarfBuzz and Fribidi libraries for text shaping")
30257 "This package provides access to the text shaping functionality in the
30258 HarfBuzz library and the bidirectional algorithm in the Fribidi library. This
30259 is a low-level utility package mainly for graphic devices that expands upon
30260 the font tool-set provided by the @code{systemfonts} package.")
30261 (license license:expat)))
30263 (define-public r-ragg
30270 (uri (cran-uri "ragg" version))
30273 "1q43pwmljsqgrikkh2g1n7bpz9c8py5dnj44cfg3y2br7b4m2q9v"))))
30274 (properties `((upstream-name . "ragg")))
30275 (build-system r-build-system)
30277 (list freetype libjpeg-turbo libpng libtiff zlib))
30279 (list r-systemfonts r-textshaping))
30282 (home-page "https://ragg.r-lib.org")
30283 (synopsis "Graphic devices based on AGG")
30285 "Anti-Grain Geometry (AGG) is a high-quality and high-performance 2D
30286 drawing library. The ragg package provides a set of graphic devices based on
30287 AGG to use as alternative to the raster devices provided through the
30288 @code{grDevices} package.")
30289 (license license:expat)))
30291 (define-public r-downlit
30298 (uri (cran-uri "downlit" version))
30301 "10zvrqdpwavdy97h3q26bqh3k63z61fmc04w9vwsnvmnv8hnh3vl"))))
30302 (properties `((upstream-name . "downlit")))
30303 (build-system r-build-system)
30314 (home-page "https://downlit.r-lib.org/")
30315 (synopsis "Syntax highlighting and automatic linking")
30317 "This package provides syntax highlighting of R code, specifically
30318 designed for the needs of RMarkdown packages like @code{pkgdown},
30319 @code{hugodown}, and @code{bookdown}. It includes linking of function calls
30320 to their documentation on the web, and automatic translation of ANSI escapes
30321 in output to the equivalent HTML.")
30322 (license license:expat)))
30324 (define-public r-pkgdown
30331 (uri (cran-uri "pkgdown" version))
30334 "11grx7a2rz6b4kwspm7c8crjav677c22hysnp4bkwh5g8kr5nm2h"))))
30335 (properties `((upstream-name . "pkgdown")))
30336 (build-system r-build-system)
30337 (inputs (list pandoc))
30361 (home-page "https://pkgdown.r-lib.org")
30362 (synopsis "Make static HTML documentation for an R package")
30364 "The goal of this package is to generate an attractive and useful website
30365 from a source package. @code{pkgdown} converts your documentation, vignettes,
30366 README file, and more to HTML making it easy to share information about your
30368 (license license:expat)))
30370 (define-public r-prereg
30377 (uri (cran-uri "prereg" version))
30380 "039nrl5cirsx1ysh214dr6xnn1h6h3f90im6k9dgmzfksxdqigpw"))))
30381 (properties `((upstream-name . "prereg")))
30382 (build-system r-build-system)
30384 (list r-rmarkdown))
30385 (home-page "https://github.com/crsh/prereg")
30387 "R Markdown Templates to preregister Scientific Studies")
30389 "This package provides a collection of templates to author
30390 preregistration documents for scientific studies in PDF format.")
30391 (license license:gpl3)))
30393 (define-public r-ez
30400 (uri (cran-uri "ez" version))
30403 "0a58s94x576dfz7wcbivrr2hmdh5x1vy16zwkqp9fmdzqx38pagq"))))
30404 (properties `((upstream-name . "ez")))
30405 (build-system r-build-system)
30417 (home-page "https://github.com/mike-lawrence/ez")
30418 (synopsis "Easy Analysis and Visualization of Factorial Experiments")
30420 "Facilitates easy analysis of factorial experiments, including purely
30421 within-Ss designs (a.k.a. \"repeated measures\"), purely between-Ss designs,
30422 and mixed within-and-between-Ss designs. The functions in this package aim to
30423 provide simple, intuitive and consistent specification of data analysis and
30424 visualization. Visualization functions also include design visualization for
30425 pre-analysis data auditing, and correlation matrix visualization. Finally,
30426 this package includes functions for non-parametric analysis, including
30427 permutation tests and bootstrap resampling. The bootstrap function obtains
30428 predictions either by cell means or by more advanced/powerful mixed effects
30429 models, yielding predictions and confidence intervals that may be easily
30430 visualized at any level of the experiment's design.")
30431 (license license:gpl2+)))
30433 (define-public r-qdapregex
30435 (name "r-qdapregex")
30440 (uri (cran-uri "qdapRegex" version))
30443 "1xa8q1way3gjadrjh3mv3xr4c6b4h16nd2c6lgl969difplpfz9p"))))
30444 (properties `((upstream-name . "qdapRegex")))
30445 (build-system r-build-system)
30446 (propagated-inputs (list r-stringi))
30448 "https://trinker.github.com/qdapRegex/")
30450 "Regular Expression Removal, Extraction, and Replacement Tools")
30452 "This package provides a collection of regular expression tools
30453 associated with the @code{qdap} package that may be useful outside of the
30454 context of discourse analysis. Tools include removal/extraction/replacement of
30455 abbreviations, dates, dollar amounts, email addresses, hash tags, numbers,
30456 percentages, citations, person tags, phone numbers, times, and zip codes.")
30457 (license license:gpl2)))
30459 (define-public r-mgsub
30466 (uri (cran-uri "mgsub" version))
30469 "1mci6x65h94qiz9cwikx2inbrwkykv43zbs8abfbx416zrh2bbn9"))))
30470 (properties `((upstream-name . "mgsub")))
30471 (build-system r-build-system)
30472 (native-inputs (list r-knitr))
30474 "https://cran.r-project.org/package=mgsub")
30476 "Safe, Multiple, Simultaneous String Substitution")
30478 "Designed to enable simultaneous substitution in strings in a safe
30479 fashion. Safe means it does not rely on placeholders (which can cause errors
30480 in same length matches).")
30481 (license license:expat)))
30483 (define-public r-textshape
30485 (name "r-textshape")
30490 (uri (cran-uri "textshape" version))
30493 "0k9injxykgj2qprc7dygd7gafvcbh3r9x84qzaa1al21pk0dz7ds"))))
30494 (properties `((upstream-name . "textshape")))
30495 (build-system r-build-system)
30497 (list r-data-table r-slam r-stringi))
30498 (home-page "https://github.com/trinker/textshape")
30499 (synopsis "Tools for Reshaping Text")
30501 "Tools that can be used to reshape and restructure text data.")
30502 (license license:gpl2)))
30504 (define-public r-syuzhet
30511 (uri (cran-uri "syuzhet" version))
30514 "16iccqdbw02iw82nah6kwz3gwfghi864j2y698n4b9dyc386ijzv"))))
30515 (properties `((upstream-name . "syuzhet")))
30516 (build-system r-build-system)
30525 (native-inputs (list r-knitr))
30526 (home-page "https://github.com/mjockers/syuzhet")
30528 "Extracts Sentiment and Sentiment-Derived Plot Arcs from Text")
30530 "Extracts sentiment and sentiment-derived plot arcs from text using a
30531 variety of sentiment dictionaries conveniently packaged for consumption by R
30532 users. Implemented dictionaries include @dfn{syuzhet} (default) developed in the
30533 Nebraska Literary Lab, @dfn{afinn} developed by Finn Arup Nielsen, @dfn{bing}
30534 developed by Minqing Hu and Bing Liu, and @dfn{nrc} developed by Mohammad, Saif
30535 M. and Turney, Peter D. Applicable references are available in
30536 @file{README.md} and in the documentation for the @code{get_sentiment}
30537 function. The package also provides a hack for implementing Stanford's coreNLP
30538 sentiment parser. The package provides several methods for plot arc
30540 (license license:gpl3)))
30542 (define-public r-lexicon
30549 (uri (cran-uri "lexicon" version))
30552 "0x7rscsh6par2lj11sby7bmz41cxn63iiw51lgh29z09cg8j606c"))))
30553 (properties `((upstream-name . "lexicon")))
30554 (build-system r-build-system)
30556 (list r-data-table r-syuzhet))
30557 (home-page "https://github.com/trinker/lexicon")
30558 (synopsis "Lexicons for Text Analysis")
30560 "This package provides a collection of lexical hash tables, dictionaries,
30562 (license license:gpl3)))
30564 (define-public r-english
30571 (uri (cran-uri "english" version))
30574 "1g3nmy5p8wj3ix1vp1qmkmy3dyqisrw0md8cjrx4klqkp0wqlms9"))))
30575 (properties `((upstream-name . "english")))
30576 (build-system r-build-system)
30577 (native-inputs (list r-knitr))
30579 "https://cran.r-project.org/package=english")
30580 (synopsis "Translate Integers into English")
30582 "Allow numbers to be presented in an English language version, one, two,
30583 three, ... Ordinals are also available, first, second, third, ... and
30584 indefinite article choice, \"a\" or \"an\".")
30585 (license license:gpl2)))
30587 (define-public r-textclean
30589 (name "r-textclean")
30594 (uri (cran-uri "textclean" version))
30597 "0kgjh6c4f14qkjc4fds7q7rpf4nkma3p0igm54fplmm3p853nvrz"))))
30598 (properties `((upstream-name . "textclean")))
30599 (build-system r-build-system)
30610 "https://github.com/trinker/textclean")
30611 (synopsis "Text Cleaning Tools")
30613 "Tools to clean and process text. Tools are geared at checking for
30614 substrings that are not optimal for analysis and replacing or removing them
30615 (normalizing) with more analysis friendly substrings (see Sproat, Black, Chen,
30616 Kumar, Ostendorf, & Richards (2001) @url{doi:10.1006/csla.2001.0169}) or
30617 extracting them into new variables. For example, emoticons are often used in
30618 text but not always easily handled by analysis algorithms. The
30619 @code{replace_emoticon()} function replaces emoticons with word equivalents.")
30620 (license license:gpl2)))
30622 (define-public r-striprtf
30624 (name "r-striprtf")
30629 (uri (cran-uri "striprtf" version))
30632 "0dqcsh3fb8j0mmmxvxjl77rryhmrjm7a3scqvk2xkgxk4xq6q316"))))
30633 (properties `((upstream-name . "striprtf")))
30634 (build-system r-build-system)
30636 (list r-magrittr r-rcpp r-stringr))
30637 (home-page "https://github.com/kota7/striprtf")
30638 (synopsis "Extract Text from RTF File")
30640 "Extracts plain text from @dfn{Rich Text Format} (RTF) file.")
30641 (license license:expat)))
30643 (define-public r-ndjson
30650 (uri (cran-uri "ndjson" version))
30653 "0lvzbgfi1sg4kya1mvv67z14qk3vz9q57x22qh57xq8ampdkg812"))
30654 (modules '((guix build utils)))
30657 ;; unvendor gzstream
30658 (for-each delete-file '("src/gzstream.cpp" "src/gzstream.h"))
30660 (properties `((upstream-name . "ndjson")))
30661 (build-system r-build-system)
30664 (modify-phases %standard-phases
30665 (add-after 'unpack 'use-system-gzstream
30666 (lambda* (#:key inputs #:allow-other-keys)
30667 (substitute* "src/Makevars"
30668 (("PKG_LIBS = " all)
30669 (string-append all "-lgzstream ")))
30671 (inputs (list zlib gzstream))
30673 (list r-data-table r-rcpp r-tibble))
30674 (home-page "https://gitlab.com/hrbrmstr/ndjson")
30676 "Wicked-Fast @dfn{Streaming JSON} (ndjson) Reader")
30678 "@dfn{Streaming JSON} (ndjson) has one JSON record per-line and many
30679 modern ndjson files contain large numbers of records. These constructs may not
30680 be columnar in nature, but it is often useful to read in these files and
30681 \"flatten\" the structure out to enable working with the data in an R
30682 @code{data.frame}-like context. Functions are provided that make it possible
30683 to read in plain ndjson files or compressed (@code{gz}) ndjson files and either
30684 validate the format of the records or create \"flat\" @code{data.table}
30685 structures from them.")
30686 (license license:expat)))
30688 (define-public r-streamr
30695 (uri (cran-uri "streamR" version))
30698 "1clx3b0j2515r1nmnl6ki7qw5n54q3x2jvqv3zrc00kq71mlj7ix"))))
30699 (properties `((upstream-name . "streamR")))
30700 (build-system r-build-system)
30702 (list r-ndjson r-rcurl r-rjson))
30704 "https://cran.r-project.org/package=streamR")
30706 "Access to Twitter Streaming API via R")
30708 "This package provides functions to access Twitter's filter, sample, and
30709 user streams, and to parse the output into data frames.")
30710 (license license:gpl2)))
30712 (define-public r-readods
30719 (uri (cran-uri "readODS" version))
30722 "1hi217ab7hp15jsbzi5ak57cqf8jn2rv78bnn74q72gn9mrfra7n"))))
30723 (properties `((upstream-name . "readODS")))
30724 (build-system r-build-system)
30726 (list r-cellranger r-readr r-stringi r-xml2))
30727 (native-inputs (list r-knitr))
30729 "https://cran.r-project.org/package=readODS")
30730 (synopsis "Read and Write ODS Files")
30732 "Import @dfn{OpenDocument Spreadsheet} (ODS) into R as a data frame.
30733 Also support writing data frame into ODS file.")
30734 (license license:gpl3)))
30736 (define-public r-qpdf
30743 (uri (cran-uri "qpdf" version))
30746 "03lnfncw8qd1fwfyqh1mjvnsjr3b63wxbah0wp5g7z7gba90dwbi"))
30747 (modules '((guix build utils)))
30750 ;; unvendor libqpdf
30751 (delete-file-recursively "src/libqpdf")
30752 (delete-file-recursively "src/include/qpdf")
30754 (properties `((upstream-name . "qpdf")))
30755 (build-system r-build-system)
30758 (modify-phases %standard-phases
30759 (add-after 'unpack 'configure
30761 (setenv "EXTERNAL_QPDF" "1")
30766 (list r-askpass r-curl r-rcpp))
30767 (native-inputs (list pkg-config))
30768 (home-page "https://github.com/ropensci/qpdf")
30770 "Split, Combine and Compress PDF Files")
30772 "Content-preserving transformations transformations of PDF files such as
30773 split, combine, and compress. This package interfaces directly to the
30774 @code{qpdf} C++ API and does not require any command line utilities. Note that
30775 @code{qpdf} does not read actual content from PDF files: to extract text and
30776 data you need the @code{pdftools} package.")
30777 (license license:asl2.0)))
30779 (define-public r-pdftools
30781 (name "r-pdftools")
30786 (uri (cran-uri "pdftools" version))
30789 "1lflqf2ypdm4w033vyjykmsy8cl34sp42fzkfgfdhvl2d0xjhl96"))))
30790 (properties `((upstream-name . "pdftools")))
30791 (build-system r-build-system)
30792 (inputs (list zlib poppler))
30793 (propagated-inputs (list r-qpdf r-rcpp))
30794 (native-inputs (list pkg-config))
30795 (home-page "https://docs.ropensci.org/pdftools/")
30796 (synopsis "Text Extraction, Rendering and Converting of PDF Documents")
30798 "This package provides utilities based on @code{libpoppler} for
30799 extracting text, fonts, attachments and metadata from a PDF file. It also
30800 supports high quality rendering of PDF documents into PNG, JPEG, TIFF format,
30801 or into raw bitmap vectors for further processing in R.")
30802 (license license:expat)))
30804 (define-public r-antiword
30806 (name "r-antiword")
30811 (uri (cran-uri "antiword" version))
30814 "123v8zlczwh6fr1v3x7dl3885xlmddq1bqlcxih8zh07w0hlk1k2"))
30815 (modules '((guix build utils)))
30818 ;; unvendor libantiword
30819 (delete-file-recursively "src")
30821 (properties `((upstream-name . "antiword")))
30822 (build-system r-build-system)
30825 (modify-phases %standard-phases
30826 (add-after 'unpack 'use-system-antiword
30827 (lambda* (#:key inputs #:allow-other-keys)
30828 (substitute* "R/antiword.R"
30829 (("system.file\\(\"bin\", package = \"antiword\"\\)")
30830 (string-append "\"" (assoc-ref inputs "antiword") "/bin\"")))
30832 (inputs (list antiword))
30833 (propagated-inputs (list r-sys))
30835 "https://github.com/ropensci/antiword#readme")
30837 "Extract Text from Microsoft Word Documents")
30839 "Wraps the @code{AntiWord} utility to extract text from Microsoft Word
30840 documents. The utility only supports the old @code{doc} format, not the new
30841 xml based @code{docx} format. Use the @code{xml2} package to read the
30843 (license license:gpl2)))
30845 (define-public r-readtext
30847 (name "r-readtext")
30852 (uri (cran-uri "readtext" version))
30855 "0k782h5hns5v5h8a6qyfqck2hc15nq0awg8bsp196q4zviv5jw3c"))))
30856 (properties `((upstream-name . "readtext")))
30857 (build-system r-build-system)
30872 (native-inputs (list r-knitr))
30874 "https://github.com/quanteda/readtext")
30876 "Import and Handling for Plain and Formatted Text Files")
30878 "This package provides functions for importing and handling text files
30879 and formatted text files with additional meta-data, such including @code{.csv},
30880 @code{.tab}, @code{.json}, @code{.xml}, @code{.html}, @code{.pdf}, @code{.doc},
30881 @code{.docx}, @code{.rtf}, @code{.xls}, @code{.xlsx}, and others.")
30882 (license license:gpl3)))
30884 (define-public r-packcircles
30886 (name "r-packcircles")
30891 (uri (cran-uri "packcircles" version))
30894 "05pv5c4k4njkr0xw6i6ksiy34hcyx2lbiqpv5gxw81yrkm0rxfyk"))))
30895 (properties `((upstream-name . "packcircles")))
30896 (build-system r-build-system)
30897 (propagated-inputs (list r-rcpp))
30898 (native-inputs (list r-knitr))
30900 "https://github.com/mbedward/packcircles")
30901 (synopsis "Circle Packing")
30903 "Algorithms to find arrangements of non-overlapping circles.")
30904 (license license:expat)))
30906 ;; Cannot unbundle liblwgeom, because PostGIS does not support building it on
30908 (define-public r-lwgeom
30915 (uri (cran-uri "lwgeom" version))
30918 "0d4b1djwrzla91mmyya2m1250mb44fzmq3d36w5mk81d4bg952pl"))))
30919 (properties `((upstream-name . "lwgeom")))
30920 (build-system r-build-system)
30922 (list geos proj sqlite zlib))
30924 (list r-rcpp r-sf r-units))
30925 (native-inputs (list pkg-config))
30926 (home-page "https://github.com/r-spatial/lwgeom/")
30927 (synopsis "Bindings to Selected 'liblwgeom' Functions for Simple Features")
30929 "Access to selected functions found in
30930 @url{https://github.com/postgis/postgis/tree/master/liblwgeom,liblwgeom}, the
30931 light-weight geometry library used by @url{http://postgis.net/,PostGIS}.")
30932 (license license:gpl2)))
30934 (define-public r-stars
30941 (uri (cran-uri "stars" version))
30944 "0hcbzr8c7wk30qjwrvx6bflzwkjpms79pavaxawnq1h8kry5fngk"))))
30945 (properties `((upstream-name . "stars")))
30946 (build-system r-build-system)
30954 (native-inputs (list r-knitr))
30955 (home-page "https://r-spatial.github.io/stars/")
30957 "Spatiotemporal Arrays, Raster and Vector Data Cubes")
30959 "Reading, manipulating, writing and plotting spatiotemporal arrays
30960 (raster and vector data cubes) in @code{R}, using @code{GDAL} bindings provided
30961 by @code{sf}, and @code{NetCDF} bindings by @code{ncmeta} and @code{RNetCDF}.")
30962 (license license:asl2.0)))
30964 (define-public r-tmaptools
30966 (name "r-tmaptools")
30971 (uri (cran-uri "tmaptools" version))
30974 "0bal3czrdr93qig8s5cf5szld5vjbbks67rismfhlkmlgw6wp2gx"))))
30975 (properties `((upstream-name . "tmaptools")))
30976 (build-system r-build-system)
30988 "https://github.com/mtennekes/tmaptools")
30989 (synopsis "Thematic Map Tools")
30991 "Set of tools for reading and processing spatial data. The aim is to
30992 supply the workflow to create thematic maps. This package also facilitates
30993 @code{tmap}, the package for visualizing thematic maps.")
30994 (license license:gpl3)))
30996 (define-public r-rworldmap
30998 (name "r-rworldmap")
31003 (uri (cran-uri "rworldmap" version))
31006 "1q1h0n9qr0m5pdx10swrh9ddsvdj8kv5nqngrf3lnx9rg9iwivjk"))))
31007 (properties `((upstream-name . "rworldmap")))
31008 (build-system r-build-system)
31010 (list r-fields r-maptools r-sp))
31012 "https://github.com/AndySouth/rworldmap/")
31013 (synopsis "Mapping Global Data")
31015 "Enables mapping of country level and gridded user datasets.")
31016 (license license:gpl2+)))
31018 (define-public r-rtweet
31025 (uri (cran-uri "rtweet" version))
31028 "05pbvxm2vmf6935b9s6663k3aifnkr3m52wh2jvnplmrwyrfpn9n"))))
31029 (properties `((upstream-name . "rtweet")))
31030 (build-system r-build-system)
31039 (native-inputs (list r-knitr))
31041 "https://docs.ropensci.org/rtweet/")
31042 (synopsis "Collecting Twitter Data")
31044 "An implementation of calls designed to collect and organize Twitter data
31045 via @url{https://developer.twitter.com/en/docs,Twitter's REST and stream
31046 Application Program Interfaces (API)}.")
31047 (license license:expat)))
31049 (define-public r-intervals
31051 (name "r-intervals")
31056 (uri (cran-uri "intervals" version))
31059 "0mvwfwc03ifb30a3dzbmkv9adwqb8ajxhcw24d8xip8px063plhb"))))
31060 (properties `((upstream-name . "intervals")))
31061 (build-system r-build-system)
31062 (home-page "https://github.com/edzer/intervals")
31064 "Tools for Working with Points and Intervals")
31066 "Tools for working with and comparing sets of points and intervals.")
31067 (license license:artistic2.0)))
31069 (define-public r-eyelinker
31071 (name "r-eyelinker")
31076 (uri (cran-uri "eyelinker" version))
31079 "0wijd45p6j2qal6wnj7zywks8p9v3m9cmyp7axmk44mrjdjx2i71"))))
31080 (properties `((upstream-name . "eyelinker")))
31081 (build-system r-build-system)
31083 (list r-intervals r-readr r-stringi r-stringr r-tibble))
31084 (native-inputs (list r-knitr))
31086 "https://github.com/a-hurst/eyelinker")
31088 "Import ASC Files from EyeLink Eye Trackers")
31090 "Imports plain-text ASC data files from EyeLink eye trackers into
31091 (relatively) tidy data frames for analysis and visualization.")
31092 (license license:gpl3)))
31094 (define-public r-btm
31101 (uri (cran-uri "BTM" version))
31104 "0ab0wr8nbwn1w1j9hpwfz52lm1sw0qk93713y9k0hpm3pw9dq4jr"))))
31105 (properties `((upstream-name . "BTM")))
31106 (build-system r-build-system)
31107 (propagated-inputs (list r-rcpp))
31108 (home-page "https://github.com/bnosac/BTM")
31109 (synopsis "Biterm Topic Models for Short Text")
31111 "Biterm Topic Models find topics in collections of short texts. It is a
31112 word co-occurrence based topic model that learns topics by modeling word-word
31113 co-occurrences patterns which are called biterms. This in contrast to
31114 traditional topic models like Latent Dirichlet Allocation and Probabilistic
31115 Latent Semantic Analysis which are word-document co-occurrence topic models. A
31116 biterm consists of two words co-occurring in the same short text window. This
31117 context window can for example be a twitter message, a short answer on a
31118 survey, a sentence of a text or a document identifier. The techniques are
31119 explained in detail in the paper 'A Biterm Topic Model For Short Text' by
31120 Xiaohui Yan, Jiafeng Guo, Yanyan Lan, Xueqi Cheng (2013)
31121 @url{https://github.com/xiaohuiyan/xiaohuiyan.github.io/blob/master/paper/\
31123 (license license:asl2.0)))
31125 (define-public r-delaporte
31127 (name "r-delaporte")
31132 (uri (cran-uri "Delaporte" version))
31135 "10xsmms2jfw7x4hmgpd35dv4n4azpjzmfid6585kg6qfh2zg23g5"))))
31136 (properties `((upstream-name . "Delaporte")))
31137 (build-system r-build-system)
31138 (native-inputs (list gfortran))
31139 (home-page "https://github.com/aadler/Delaporte")
31140 (synopsis "Statistical functions for the Delaporte distribution")
31142 "This package provides probability mass, distribution, quantile,
31143 random-variate generation, and method-of-moments parameter-estimation
31144 functions for the Delaporte distribution with parameterization based on
31145 Vose (2008). The Delaporte is a discrete probability distribution which can
31146 be considered the convolution of a negative binomial distribution with a
31147 Poisson distribution. Alternatively, it can be considered a counting
31148 distribution with both Poisson and negative binomial components. It has been
31149 studied in actuarial science as a frequency distribution which has more
31150 variability than the Poisson, but less than the negative binomial.")
31151 (license license:bsd-2)))
31153 (define-public r-rjsonio
31156 (version "1.3-1.6")
31160 (uri (cran-uri "RJSONIO" version))
31163 "17x0ayk7daprbc8w2hvb2jl9mfnw4dic9yc3sr5adcjqfzmcklc2"))))
31164 (properties `((upstream-name . "RJSONIO")))
31165 (build-system r-build-system)
31166 (home-page "https://cran.r-project.org/package=RJSONIO")
31167 (synopsis "Serialize R objects to JSON")
31169 "This is a package that allows conversion to and from data in JavaScript
31170 Object Notation (JSON) format. This allows R objects to be inserted into
31171 Javascript/ECMAScript/ActionScript code and allows R programmers to read and
31172 convert JSON content to R objects. This is an alternative to the @code{rjson}
31174 (license license:bsd-3)))
31176 (define-public r-revgeo
31183 (uri (cran-uri "revgeo" version))
31186 "1ns7d1817475lriss6wwgvdm6lj760p40yxqaifla13c2xb73a55"))))
31187 (properties `((upstream-name . "revgeo")))
31188 (build-system r-build-system)
31190 (list r-rcurl r-rjsonio))
31191 (home-page "https://cran.r-project.org/package=revgeo")
31192 (synopsis "Reverse geocoding")
31194 "The @code{revgeo} procedure allows you to use the Photon geocoder for
31195 OpenStreetMap, Google Maps, and Bing to reverse geocode coordinate pairs with
31197 (license license:gpl3+)))
31199 (define-public r-qpcr
31206 (uri (cran-uri "qpcR" version))
31209 "1r01q7jv3w59yx1gc0qw91rq7rvdhqsi8y57sqqkmwyqfw2x2vsv"))))
31210 (properties `((upstream-name . "qpcR")))
31211 (build-system r-build-system)
31213 (list r-mass r-matrix r-minpack-lm r-rgl r-robustbase))
31214 (home-page "https://cran.r-project.org/package=qpcR")
31215 (synopsis "Modelling and analysis of real-time PCR data")
31217 "This is a package for model fitting, optimal model selection and
31218 calculation of various features that are essential in the analysis of
31219 quantitative real-time polymerase chain reaction (qPCR).")
31220 (license license:gpl2+)))
31222 (define-public r-textplot
31224 (name "r-textplot")
31229 (uri (cran-uri "textplot" version))
31232 "10nxh9axhy6kyp6f3rz7smq08yl35ydx9jx47bs7i0bmcl2kwxvl"))))
31233 (properties `((upstream-name . "textplot")))
31234 (build-system r-build-system)
31236 (list r-data-table r-lattice r-matrix))
31237 (native-inputs (list r-knitr))
31238 (home-page "https://github.com/bnosac/textplot")
31239 (synopsis "Text Plots")
31241 "Visualise complex relations in texts. This is done by providing
31242 functionalities for displaying text co-occurrence networks, text correlation
31243 networks, dependency relationships as well as text clustering. Feel free to
31244 join the effort of providing interesting text visualisations.")
31245 (license license:gpl2)))
31247 (define-public r-gsa
31254 (uri (cran-uri "GSA" version))
31257 "1f1mrxxdbdlnibgav6nsvbpniz2x3km2svc0hf43spb4zicn0z8p"))))
31258 (properties `((upstream-name . "GSA")))
31259 (build-system r-build-system)
31260 (home-page "https://statweb.stanford.edu/~tibs/GSA/")
31261 (synopsis "Gene set analysis")
31262 (description "This package lets you determine the significance of
31263 pre-defined sets of genes with respect to an outcome variable, such as a group
31264 indicator, a quantitative variable or a survival time.")
31265 ;; Any version of the LGPL
31266 (license license:lgpl3+)))
31268 (define-public r-randomforestsrc
31270 (name "r-randomforestsrc")
31275 (uri (cran-uri "randomForestSRC" version))
31278 "05ifvj49jv0n5p6k46milpgj9r10sc5aw23fypyyibdgwpwvwixw"))))
31280 `((upstream-name . "randomForestSRC")))
31281 (build-system r-build-system)
31282 (home-page "https://cran.r-project.org/web/packages/randomForestSRC/")
31283 (synopsis "Random forests for survival, regression, and classification")
31285 "This package implements fast OpenMP parallel computing of Breiman's
31286 random forests for survival, competing risks, regression and classification
31287 based on Ishwaran and Kogalur's popular random survival forests (RSF) package.
31288 It handles missing data and now includes multivariate, unsupervised forests,
31289 quantile regression and solutions for class imbalanced data. It provides a
31290 fast interface using subsampling and confidence regions for variable
31292 (license license:gpl3+)))
31294 (define-public r-contfrac
31296 (name "r-contfrac")
31301 (uri (cran-uri "contfrac" version))
31304 "0sq5c7ny235yrkv2xc4insgxby6rvzc1qsj8h301cd2if3lwbgwm"))))
31305 (properties `((upstream-name . "contfrac")))
31306 (build-system r-build-system)
31308 "https://github.com/RobinHankin/contfrac")
31309 (synopsis "Continued Fractions")
31311 "Various utilities for evaluating continued fractions.")
31312 (license license:gpl2)))
31314 (define-public r-elliptic
31316 (name "r-elliptic")
31321 (uri (cran-uri "elliptic" version))
31324 "1dhba0yfxjd5rlqsxp5a7s2hclfkla9wigsr39dlma67l6qjjmxn"))))
31325 (properties `((upstream-name . "elliptic")))
31326 (build-system r-build-system)
31327 (inputs (list pari-gp))
31328 (propagated-inputs (list r-mass))
31330 "https://github.com/RobinHankin/elliptic")
31332 "Weierstrass and Jacobi Elliptic Functions")
31334 "A suite of elliptic and related functions including Weierstrass and
31335 Jacobi forms. Also includes various tools for manipulating and visualizing
31336 complex functions.")
31337 (license license:gpl2)))
31339 (define-public r-hypergeo
31341 (name "r-hypergeo")
31346 (uri (cran-uri "hypergeo" version))
31349 "13jdiy216znwhr91iqnh03mvkmyscw439syb3h4i67dd78sphnvd"))))
31350 (properties `((upstream-name . "hypergeo")))
31351 (build-system r-build-system)
31353 (list r-contfrac r-desolve r-elliptic))
31355 "https://cran.r-project.org/web/packages/hypergeo/")
31356 (synopsis "The Gauss Hypergeometric Function")
31358 "The Gaussian hypergeometric function for complex numbers.")
31359 (license license:gpl2)))
31361 (define-public r-gganimate
31363 (name "r-gganimate")
31368 (uri (cran-uri "gganimate" version))
31371 "046v6j92xxgaghsnh88dy5h8x040qsfa8csvhp4dmsfmrrf0dz0f"))))
31372 (properties `((upstream-name . "gganimate")))
31373 (build-system r-build-system)
31376 (modify-phases %standard-phases
31377 (add-after 'unpack 'absolute-paths
31378 (lambda* (#:key inputs #:allow-other-keys)
31379 (substitute* "R/renderers.R"
31381 (string-append "'" (assoc-ref inputs "ffmpeg") "/bin/ffmpeg'"))))))))
31383 ;; For video output.
31394 ;; For GIF/SVG output. gifski is faster, but depends on Rust.
31396 ;; For HTML output.
31399 (native-inputs (list r-knitr))
31400 (home-page "https://gganimate.com")
31401 (synopsis "Grammar of Animated Graphics")
31403 "This package extends the grammar of graphics as implemented by
31404 @code{ggplot2} to include the description of animation. It does this by
31405 providing a range of new grammar classes that can be added to the plot object
31406 in order to customise how it should change with time.")
31407 (license license:expat)))
31409 ;; This library bundles ‘date’ from (gnu packages calendar). We cannot unbundle
31410 ;; it, because its C++ libtz.so is built with different compiler flags than
31412 (define-public r-tzdb
31419 (uri (cran-uri "tzdb" version))
31422 "0f3h4zaf9f4l371k6nc1mq6z2f9aj1vaf2inni8jnsds3zng16b0"))))
31423 (properties `((upstream-name . "tzdb")))
31424 (build-system r-build-system)
31425 (propagated-inputs (list r-cpp11))
31426 (home-page "https://github.com/r-lib/tzdb")
31427 (synopsis "Time Zone Database Information")
31429 "This package provides an up-to-date copy of the Internet Assigned
31430 Numbers Authority (IANA) Time Zone Database. It is updated periodically to
31431 reflect changes made by political bodies to time zone boundaries, UTC offsets,
31432 and daylight saving time rules. Additionally, this package provides a C++
31433 interface for working with the @code{date} library. @code{date} provides
31434 comprehensive support for working with dates and date-times, which this package
31435 exposes to make it easier for other R packages to utilize. Headers are
31436 provided for calendar specific calculations, along with a limited interface for
31437 time zone manipulations.")
31438 (license license:expat)))
31440 (define-public r-vroom
31447 (uri (cran-uri "vroom" version))
31450 "1plz20x6s01gkkcac51lhx4r2s024pgh778ri7y25hkiiwacp1yh"))))
31451 (properties `((upstream-name . "vroom")))
31452 (build-system r-build-system)
31468 (native-inputs (list r-knitr))
31469 (home-page "https://vroom.r-lib.org")
31471 "Read and Write Rectangular Text Data")
31473 "This package reads and writes data files like @acronym{CSV},
31474 @acronym{TSV} and @acronym{FWF}. When reading it uses a quick initial indexing
31475 step, then reads the values lazily, so only the data you actually use needs to
31476 be read. The writer formats the data in parallel and writes to disk
31477 asynchronously from formatting.")
31478 (license license:expat)))
31480 (define-public r-rmisc
31486 (uri (cran-uri "Rmisc" version))
31489 "1ijjhfy3v91fspid77rrkc5dkcb2lav37wc3f4k5lwrn24wzy5y8"))))
31490 (build-system r-build-system)
31492 (list r-plyr r-rcpp r-lattice))
31493 (home-page "https://cran.r-project.org/web/packages/Rmisc/")
31494 (synopsis "Ryan Miscellaneous")
31495 (description "The Rmisc library contains functions for data analysis and
31496 utility operations.")
31497 (license license:gpl3)))
31499 (define-public r-webutils
31501 (name "r-webutils")
31506 (uri (cran-uri "webutils" version))
31508 (base32 "16a6ds0fnb6y8i1r9ba1hf1ydb53am57s070b3hi5jmrs84b9qik"))))
31509 (properties `((upstream-name . "webutils")))
31510 (build-system r-build-system)
31512 (list r-curl r-jsonlite))
31513 (home-page "https://github.com/jeroen/webutils")
31514 (synopsis "Utility functions for developing web applications")
31516 "This package parses HTTP request data in @code{application/json},
31517 @code{multipart/form-data}, or @code{application/x-www-form-urlencoded}
31518 format. It includes an example of hosting and parsing HTML form data in R
31519 using either @code{httpuv} or @code{Rhttpd}.")
31520 (license license:expat)))
31522 (define-public r-protolite
31524 (name "r-protolite")
31529 (uri (cran-uri "protolite" version))
31531 (base32 "0g1r3lzmvx1w44qzqzdvxfn21zmz11srlp6cr76kd7pd5wzjv82p"))))
31532 (properties `((upstream-name . "protolite")))
31533 (build-system r-build-system)
31537 (list r-jsonlite r-rcpp))
31539 (list protobuf pkg-config))
31540 (home-page "https://github.com/jeroen/protolite")
31541 (synopsis "Highly optimized protocol buffer serializers")
31543 "This package provides pure C++ implementations for reading and writing
31544 several common data formats based on Google protocol-buffers. It currently
31545 supports @code{rexp.proto} for serialized R objects, @code{geobuf.proto} for
31546 binary geojson, and @code{mvt.proto} for vector tiles. This package uses the
31547 auto-generated C++ code by protobuf-compiler, hence the entire serialization
31548 is optimized at compile time. The @code{RProtoBuf} package on the other hand
31549 uses the protobuf runtime library to provide a general-purpose toolkit for
31550 reading and writing arbitrary protocol-buffer data in R.")
31551 (license license:expat)))
31553 (define-public r-opencpu
31560 (uri (cran-uri "opencpu" version))
31562 (base32 "06jpmk95hm39ib5c75xw0mdrdv9x9zz1qil3m8ysb6pp1xx47jz0"))))
31563 (properties `((upstream-name . "opencpu")))
31564 (build-system r-build-system)
31584 (home-page "https://www.opencpu.org")
31585 (synopsis "API for embedded scientific computing")
31587 "This package provides a system for embedded scientific computing and
31588 reproducible research with R. The OpenCPU server exposes a simple but
31589 powerful HTTP API for RPC and data interchange with R. This provides a
31590 reliable and scalable foundation for statistical services or building R web
31591 applications. The OpenCPU server runs either as a single-user development
31592 server within the interactive R session, or as a multi-user stack based on
31594 (license license:asl2.0)))
31596 (define-public r-exactextractr
31598 (name "r-exactextractr")
31603 (uri (cran-uri "exactextractr" version))
31606 "11s58vc63r9kah815a18ihb0x2nmnjnpngybw3yr2d6715sz89nc"))))
31607 (properties `((upstream-name . "exactextractr")))
31608 (build-system r-build-system)
31609 (inputs (list geos))
31611 (list r-raster r-rcpp r-sf))
31614 (home-page "https://isciences.gitlab.io/exactextractr/")
31615 (synopsis "Fast extraction from raster datasets using polygons")
31617 "This package provides a replacement for the @code{extract} function from
31618 the @code{raster} package that is suitable for extracting raster values using
31619 @code{sf} polygons.")
31620 (license license:asl2.0)))
31622 (define-public r-stringfish
31624 (name "r-stringfish")
31629 (uri (cran-uri "stringfish" version))
31632 "0ac17wl0fcpmipbvhhg5nyccg055671fnlxvnjd5l3kilx313wlx"))))
31633 (properties `((upstream-name . "stringfish")))
31634 (build-system r-build-system)
31636 (list r-rcpp r-rcppparallel))
31638 (list pkg-config r-knitr))
31639 (home-page "https://github.com/traversc/stringfish")
31640 (synopsis "Alternative string implementation")
31642 "This package provides an extendable, performant and multithreaded
31643 @code{alt-string} implementation backed by C++ vectors and strings.")
31644 (license license:gpl3)))
31646 (define-public r-rapiserialize
31648 (name "r-rapiserialize")
31653 (uri (cran-uri "RApiSerialize" version))
31656 "0gm2j8kh40imhncwwx1sx9kmraaxcxycvgwls53lcyy2ap344k9j"))))
31657 (properties `((upstream-name . "RApiSerialize")))
31658 (build-system r-build-system)
31660 "https://cran.r-project.org/package=RApiSerialize")
31661 (synopsis "R API serialization")
31663 "This package provides other packages with access to the internal R
31664 serialization code. Access to this code is provided at the C function level
31665 by using the registration of native function mechanism. Client packages
31666 simply include a single header file RApiSerializeAPI.h provided by this
31668 (license license:gpl2+)))
31670 (define-public r-qs
31677 (uri (cran-uri "qs" version))
31680 "0sxy497v5arjv6lwxng7chkbzrn703waqmgsxv77i7y12ahzdbai"))))
31681 (properties `((upstream-name . "qs")))
31682 (build-system r-build-system)
31683 (inputs (list zlib))
31685 (list r-rapiserialize r-rcpp r-stringfish))
31687 (list pkg-config r-knitr))
31688 (home-page "https://github.com/traversc/qs")
31689 (synopsis "Quick serialization of R objects")
31691 "This package provides functions for quickly writing and reading any R
31692 object to and from disk.")
31693 (license license:gpl3)))
31695 (define-public r-rgeos
31702 (uri (cran-uri "rgeos" version))
31705 "1m73y0nwrdwsjrl48c4fg1kdqnh79835brnmxv9ak01ndbzcp45b"))))
31706 (properties `((upstream-name . "rgeos")))
31707 (build-system r-build-system)
31712 (home-page "https://cran.r-project.org/package=rgeos")
31713 (synopsis "Interface to Geometry Engine (GEOS)")
31715 "This package provides an R interface to Geometry Engine (GEOS) using the
31716 C API for topology operations on geometries.")
31717 (license license:gpl2+)))
31719 (define-public r-tfruns
31726 (uri (cran-uri "tfruns" version))
31729 "04lfckg1if3kfwcl4s4fcc9aw04crwk4m1qr55ag22j2x2jlb2l9"))))
31730 (properties `((upstream-name . "tfruns")))
31731 (build-system r-build-system)
31743 (native-inputs (list r-knitr))
31744 (home-page "https://github.com/rstudio/tfruns")
31745 (synopsis "Training run tools for TensorFlow")
31747 "Create and manage unique directories for each TensorFlow training run.
31748 This package provides a unique, time stamped directory for each run along with
31749 functions to retrieve the directory of the latest run or latest several
31751 (license license:asl2.0)))
31753 (define-public r-tfautograph
31755 (name "r-tfautograph")
31760 (uri (cran-uri "tfautograph" version))
31763 "0fmaq1ggjyxgf2ss7qb8jk74sfwc3s1vc123pd5glclxcy1ib0j2"))))
31764 (properties `((upstream-name . "tfautograph")))
31765 (build-system r-build-system)
31766 (inputs (list tensorflow))
31768 (list r-backports r-reticulate))
31769 (home-page "https://t-kalinowski.github.io/tfautograph/")
31770 (synopsis "Autograph R for Tensorflow")
31772 "This package lets you translate R control flow expressions into
31773 Tensorflow graphs.")
31774 (license license:gpl3)))
31776 (define-public r-tensorflow
31778 (name "r-tensorflow")
31783 (uri (cran-uri "tensorflow" version))
31786 "19ayjvlxmgjais0kx6fj9an1h1i8mh4c9dhah7dj6390p53pgz93"))))
31787 (properties `((upstream-name . "tensorflow")))
31788 (build-system r-build-system)
31789 (inputs (list tensorflow))
31798 (home-page "https://github.com/rstudio/tensorflow")
31799 (synopsis "R interface to TensorFlow")
31801 "R interface to TensorFlow a library for numerical computation using data
31802 flow graphs. Nodes in the graph represent mathematical operations, while the
31803 graph edges represent the multidimensional data arrays (tensors) communicated
31805 (license license:asl2.0)))
31807 (define-public r-keras
31814 (uri (cran-uri "keras" version))
31817 "10zvy4lmhb2sbn0gsm12pf95pxj9bmi8241ap1n6170xsld9phcf"))))
31818 (properties `((upstream-name . "keras")))
31819 (build-system r-build-system)
31831 (native-inputs (list r-knitr))
31832 (home-page "https://keras.rstudio.com")
31833 (synopsis "R Interface to 'Keras'")
31835 "This package provides an interface to Keras, a high-level neural
31836 networks API. Keras was developed with a focus on enabling fast
31837 experimentation, supports both convolution based networks and recurrent
31838 networks (as well as combinations of the two), and runs seamlessly on both CPU
31840 (license license:expat)))
31842 (define-public r-zzlite
31849 (uri (cran-uri "zzlite" version))
31852 "0vi1slx2s4r5zf82lazqv0c3m12xq73wlgsbz6af4y00h0bkr3ps"))))
31853 (properties `((upstream-name . "zzlite")))
31854 (build-system r-build-system)
31856 (list r-httr r-jsonlite))
31859 (home-page "https://cran.r-project.org/package=zzlite")
31860 (synopsis "Wrapper for the Zamzar file conversion API")
31862 "This package provides a minor collection of HTTP wrappers for the Zamzar
31863 file conversion API. The wrappers makes it easy to utilize the API and thus
31864 convert between more than 100 different file formats (ranging from audio
31865 files, images, movie formats, etc., etc.) through an R session.")
31866 (license license:gpl3)))
31868 (define-public r-ztree
31875 (uri (cran-uri "zTree" version))
31878 "005zk6wpchpss6865ki35yawgf668pn70163ah97rnfkhfaswm6y"))))
31879 (properties `((upstream-name . "zTree")))
31880 (build-system r-build-system)
31883 (home-page "https://cran.r-project.org/package=zTree")
31884 (synopsis "Functions to import data from z-Tree into R")
31886 "This package provides tools for reading @code{.xls} and @code{.sbj}
31887 files which are written by the proprietary program z-Tree for developing and
31888 carrying out economic experiments.")
31889 (license license:gpl3)))
31891 (define-public r-distributionutils
31893 (name "r-distributionutils")
31898 (uri (cran-uri "DistributionUtils" version))
31901 "08vq54pyqxlqsj6q6gsg5ikqa0z3x842j52ld5dxaq272p6xchvl"))))
31903 `((upstream-name . "DistributionUtils")))
31904 (build-system r-build-system)
31907 (home-page "https://cran.r-project.org/package=DistributionUtils")
31908 (synopsis "Distribution utilities")
31910 "This package provides utilities for dealing with distributions.
31911 Functionality includes sample skewness and kurtosis, log-histogram, tail
31912 plots, moments by integration, changing the point about which a moment is
31913 calculated, functions for testing distributions using inversion tests and the
31914 Massart inequality. Also included is an implementation of the incomplete
31915 Bessel K function.")
31916 (license license:gpl2+)))
31918 (define-public r-ztpln
31925 (uri (cran-uri "ztpln" version))
31928 "1b22m72a8117yrgq5k1gzsrbx6yrsrj7bpd49lh7x3vbaz56c0wr"))))
31929 (properties `((upstream-name . "ztpln")))
31930 (build-system r-build-system)
31932 (list r-distributionutils r-mixtools r-rcpp r-rcppeigen
31936 (home-page "https://github.com/mattocci27/ztpln")
31937 (synopsis "Zero-truncated Poisson lognormal distribution")
31939 "This package provides functions for obtaining the density, random
31940 variates and maximum likelihood estimates of the Zero-truncated Poisson
31941 lognormal distribution and their mixture distribution.")
31942 (license license:expat)))
31944 (define-public r-zscorer
31951 (uri (cran-uri "zscorer" version))
31954 "0aijhs0fyird5gq68x4dxchb02mxa7ijk10k9zjhngghxbjj7iqn"))))
31955 (properties `((upstream-name . "zscorer")))
31956 (build-system r-build-system)
31961 (home-page "https://github.com/nutriverse/zscorer")
31962 (synopsis "Child Anthropometry z-Score Calculator")
31964 "This package provides a tool for calculating z-scores and centiles for
31965 weight-for-age, length/height-for-age, weight-for-length/height, BMI-for-age,
31966 head circumference-for-age, age circumference-for-age, subscapular
31967 skinfold-for-age, triceps skinfold-for-age based on the WHO Child Growth
31969 (license license:agpl3+)))
31971 (define-public r-zra
31978 (uri (cran-uri "ZRA" version))
31981 "1sx1q5yf68hhlb5j1hicpj594rmgajqr25llg7ax416j0m2rnagi"))))
31982 (properties `((upstream-name . "ZRA")))
31983 (build-system r-build-system)
31985 (list r-dygraphs r-forecast))
31986 (home-page "https://cran.r-project.org/package=ZRA")
31987 (synopsis "Dynamic plots for time series forecasting")
31989 "This package combines a forecast of a time series, using the function @code{forecast},
31990 with the dynamic plots from @code{dygraphs}.")
31991 (license license:gpl2+)))
31993 (define-public r-rfigshare
31995 (name "r-rfigshare")
32000 (uri (cran-uri "rfigshare" version))
32003 "1qgzn0mpjy4czy0pnbi395fxxx84arkg8r7rk8aidmd34584gjiq"))))
32004 (properties `((upstream-name . "rfigshare")))
32005 (build-system r-build-system)
32014 (home-page "https://github.com/ropensci/rfigshare")
32015 (synopsis "R Interface to figshare")
32017 "This package provides an interface to figshare, a scientific repository
32018 to archive and assign DOIs to data, software, figures, and more.")
32019 (license license:cc0)))
32021 (define-public r-dismo
32028 (uri (cran-uri "dismo" version))
32031 "1rqf6h4imbqvs7hjd1k4my6154wg0qnmnp5byan403rcshr1jbl1"))))
32032 (properties `((upstream-name . "dismo")))
32033 (build-system r-build-system)
32035 (list r-raster r-rcpp r-sp r-terra))
32036 (home-page "https://rspatial.org/raster/sdm/")
32037 (synopsis "Species distribution modeling")
32039 "This package provides methods for species distribution modeling, i.e.,
32040 predicting the environmental similarity of any site to that of the locations
32041 of known occurrences of a species.")
32042 (license license:gpl3+)))
32044 (define-public r-zoon
32051 (uri (cran-uri "zoon" version))
32054 "02y29vr2yn8al69km8faiqrwjrc1r3hsvw3dg8lwjr65cxw1krip"))))
32055 (properties `((upstream-name . "zoon")))
32056 (build-system r-build-system)
32071 (home-page "https://github.com/zoonproject/zoon")
32072 (synopsis "Reproducible, accessible and shareable species distribution modelling")
32074 "This package reads user submitted modules from an online repository,
32075 runs full species distribution modelling workflows and returns output that is
32076 fully reproducible.")
32077 (license license:bsd-3)))
32079 (define-public r-paws-common
32081 (name "r-paws-common")
32086 (uri (cran-uri "paws.common" version))
32089 "1dg18hwnrjd6m1vjcxfs2vm1zxciivf4vzhq0z76dmmiqz2yjm28"))))
32090 (properties `((upstream-name . "paws.common")))
32091 (build-system r-build-system)
32093 (list r-base64enc r-digest r-httr r-jsonlite r-xml2))
32094 (home-page "https://cran.r-project.org/package=paws.common")
32095 (synopsis "Paws low-level Amazon Web Services API")
32097 "This package provides functions for making low-level API requests to
32098 Amazon Web Services. The functions handle building, signing, and sending
32099 requests, and receiving responses. They are designed to help build
32100 higher-level interfaces to individual services, such as Simple Storage
32102 (license license:asl2.0)))
32104 (define-public r-paws-customer-engagement
32106 (name "r-paws-customer-engagement")
32111 (uri (cran-uri "paws.customer.engagement" version))
32114 "0ac6hzn4ilfjhzdmc9x80999fl18cz16mky31qd3y09m93w2xkdj"))))
32116 `((upstream-name . "paws.customer.engagement")))
32117 (build-system r-build-system)
32119 (list r-paws-common))
32120 (home-page "https://github.com/paws-r/paws")
32121 (synopsis "Amazon Web Services customer engagement services")
32123 "This package provides an interface to Amazon Web Services customer
32124 engagement services, including Simple Email Service, Connect contact center
32125 service, and more.")
32126 (license license:asl2.0)))
32128 (define-public r-paws-cost-management
32130 (name "r-paws-cost-management")
32135 (uri (cran-uri "paws.cost.management" version))
32138 "0in4f8ygw5g2v6vl3lz2y0v51llglh8b1ymbd04d54xxlgn83knh"))))
32140 `((upstream-name . "paws.cost.management")))
32141 (build-system r-build-system)
32143 (list r-paws-common))
32144 (home-page "https://github.com/paws-r/paws")
32145 (synopsis "Amazon Web Services cost management services")
32147 "This package provides an interface to Amazon Web Services cost
32148 management services, including cost and usage reports, budgets, pricing, and
32150 (license license:asl2.0)))
32152 (define-public r-paws-developer-tools
32154 (name "r-paws-developer-tools")
32159 (uri (cran-uri "paws.developer.tools" version))
32161 (base32 "16gb8g8s67al7qdd95fbigxqkih9a9p7slkyf3cga42wb6miiby2"))))
32162 (properties `((upstream-name . "paws.developer.tools")))
32163 (build-system r-build-system)
32165 (list r-paws-common))
32166 (home-page "https://github.com/paws-r/paws")
32167 (synopsis "Amazon Web Services developer tools services")
32169 "This package provides an interface to Amazon Web Services developer
32170 tools services, including version control, continuous integration and
32171 deployment, and more.")
32172 (license license:asl2.0)))
32174 (define-public r-paws-end-user-computing
32176 (name "r-paws-end-user-computing")
32181 (uri (cran-uri "paws.end.user.computing" version))
32183 (base32 "1xxsz86nx128sizym9np8vldzkbym0p3i6vcy94kq1y0cylaicv3"))))
32184 (properties `((upstream-name . "paws.end.user.computing")))
32185 (build-system r-build-system)
32187 (list r-paws-common))
32188 (home-page "https://github.com/paws-r/paws")
32189 (synopsis "Amazon Web Services end user computing services")
32191 "This package provides an interface to Amazon Web Services end user
32192 computing services, including collaborative document editing, mobile intranet,
32194 (license license:asl2.0)))
32196 (define-public r-paws-application-integration
32198 (name "r-paws-application-integration")
32203 (uri (cran-uri "paws.application.integration" version))
32206 "0llyd9hc679pad1ih0rcc38q5xxpzinhwrl8cvrkgsjgbc3agq42"))))
32208 `((upstream-name . "paws.application.integration")))
32209 (build-system r-build-system)
32211 (list r-paws-common))
32212 (home-page "https://github.com/paws-r/paws")
32213 (synopsis "Amazon Web Services application integration services")
32215 "This package provides an interface to Amazon Web Services application
32216 integration services, including Simple Queue Service (SQS) message queue,
32217 Simple Notification Service (SNS) publish/subscribe messaging, and more.")
32218 (license license:asl2.0)))
32220 (define-public r-paws-security-identity
32222 (name "r-paws-security-identity")
32227 (uri (cran-uri "paws.security.identity" version))
32230 "092lz2ipn5iqr593x7ra8c0bj64yf6315mdc3llgwrjyb4vfxif9"))))
32232 `((upstream-name . "paws.security.identity")))
32233 (build-system r-build-system)
32235 (list r-paws-common))
32236 (home-page "https://github.com/paws-r/paws")
32237 (synopsis "Amazon Web Services security, identity, and compliance services")
32239 "This package provides an interface to Amazon Web Services security,
32240 identity, and compliance services, including the Identity and Access
32241 Management (IAM) service for managing access to services and resources, and
32243 (license license:asl2.0)))
32245 (define-public r-paws-analytics
32247 (name "r-paws-analytics")
32252 (uri (cran-uri "paws.analytics" version))
32255 "04gnaxmj21l312xkrsd9bisi0bz9h6h5fyhwlqylcxi077z1yb2g"))))
32257 `((upstream-name . "paws.analytics")))
32258 (build-system r-build-system)
32260 (list r-paws-common))
32261 (home-page "https://github.com/paws-r/paws")
32262 (synopsis "Amazon Web Services analytics services")
32264 "This package provides an interface to Amazon Web Services analytics
32265 services, including Elastic MapReduce Hadoop and Spark big data service,
32266 Elasticsearch search engine, and more.")
32267 (license license:asl2.0)))
32269 (define-public r-paws-machine-learning
32271 (name "r-paws-machine-learning")
32276 (uri (cran-uri "paws.machine.learning" version))
32279 "01w2y5952pk50xjbzby2pc51xrkrzjpfxbmii1b10cl2xgzfkxsa"))))
32281 `((upstream-name . "paws.machine.learning")))
32282 (build-system r-build-system)
32284 (list r-paws-common))
32285 (home-page "https://github.com/paws-r/paws")
32286 (synopsis "Amazon Web Services machine learning services")
32288 "This package provides an interface to Amazon Web Services machine
32289 learning services, including SageMaker managed machine learning service,
32290 natural language processing, speech recognition, translation, and more.")
32291 (license license:asl2.0)))
32293 (define-public r-paws-management
32295 (name "r-paws-management")
32300 (uri (cran-uri "paws.management" version))
32303 "09k7wg0jlj40zs2yb3vldffpkdcjg7ap98n7c5lxr5plpca08swg"))))
32305 `((upstream-name . "paws.management")))
32306 (build-system r-build-system)
32308 (list r-paws-common))
32309 (home-page "https://github.com/paws-r/paws")
32310 (synopsis "Amazon Web Services management and governance services")
32312 "This package provides an interface to Amazon Web Services management and
32313 governance services, including CloudWatch application and infrastructure
32314 monitoring, Auto Scaling for automatically scaling resources, and more.")
32315 (license license:asl2.0)))
32317 (define-public r-paws-networking
32319 (name "r-paws-networking")
32324 (uri (cran-uri "paws.networking" version))
32327 "02hxaa5nlj70mdggh379ij3fn09xm8h5ldzsyf45c342prpl6zwj"))))
32329 `((upstream-name . "paws.networking")))
32330 (build-system r-build-system)
32332 (list r-paws-common))
32333 (home-page "https://github.com/paws-r/paws")
32334 (synopsis "Amazon Web Services networking and content delivery services")
32336 "This package provides an interface to Amazon Web Services networking and
32337 content delivery services, including Route 53 Domain Name System service,
32338 CloudFront content delivery, load balancing, and more.")
32339 (license license:asl2.0)))
32341 (define-public r-paws-database
32343 (name "r-paws-database")
32348 (uri (cran-uri "paws.database" version))
32351 "08jpwz95fw3f68j0wxh2lg57nn60khflldab0ryhkkbcw1iy0qyz"))))
32352 (properties `((upstream-name . "paws.database")))
32353 (build-system r-build-system)
32355 (list r-paws-common))
32356 (home-page "https://github.com/paws-r/paws")
32358 "Amazon Web Services Database Services")
32360 "This package provides an interface to Amazon Web Services database
32361 services, including Relational Database Service (RDS), DynamoDB NoSQL
32362 database, and more.")
32363 (license license:asl2.0)))
32365 (define-public r-paws-storage
32367 (name "r-paws-storage")
32372 (uri (cran-uri "paws.storage" version))
32375 "06m887vpqp5d6k3zxdlga599dsv8v3rladk7xqaxqnld1f17am04"))))
32376 (properties `((upstream-name . "paws.storage")))
32377 (build-system r-build-system)
32379 (list r-paws-common))
32380 (home-page "https://github.com/paws-r/paws")
32381 (synopsis "Amazon Web Services storage services")
32383 "This package provides an interface to Amazon Web Services storage
32384 services, including Simple Storage Service (S3).")
32385 (license license:asl2.0)))
32387 (define-public r-paws-compute
32389 (name "r-paws-compute")
32394 (uri (cran-uri "paws.compute" version))
32397 "1km6fng6il5fcjlrbbndahsw2dr2ql83hwac9wlpd67zm3wy9lky"))))
32398 (properties `((upstream-name . "paws.compute")))
32399 (build-system r-build-system)
32401 (list r-paws-common))
32402 (home-page "https://github.com/paws-r/paws")
32403 (synopsis "Amazon Web Services compute services")
32405 "This package provides an interface to Amazon Web Services compute
32406 services, including Elastic Compute Cloud (EC2), Lambda
32407 functions-as-a-service, containers, batch processing, and more.")
32408 (license license:asl2.0)))
32410 (define-public r-paws
32417 (uri (cran-uri "paws" version))
32420 "0kn1z045r106fwqcaz52hb02bhrcblh479cajfjiq480s1iljcw6"))))
32421 (properties `((upstream-name . "paws")))
32422 (build-system r-build-system)
32424 (list r-paws-analytics
32425 r-paws-application-integration
32427 r-paws-cost-management
32428 r-paws-customer-engagement
32430 r-paws-developer-tools
32431 r-paws-end-user-computing
32432 r-paws-machine-learning
32435 r-paws-security-identity
32437 (home-page "https://github.com/paws-r/paws")
32438 (synopsis "Amazon Web Services software development kit")
32440 "This package provides an interface to Amazon Web Services, including
32441 storage, database, and compute services, such as Simple Storage Service (S3),
32442 DynamoDB NoSQL database, and Lambda functions-as-a-service.")
32443 (license license:asl2.0)))
32445 (define-public r-zoomgroupstats
32447 (name "r-zoomgroupstats")
32452 (uri (cran-uri "zoomGroupStats" version))
32455 "0gndiq92cy6gi7f833hdjvqii3cn83wz5rjvygcvjl3dw4pwv966"))))
32457 `((upstream-name . "zoomGroupStats")))
32458 (build-system r-build-system)
32469 (native-inputs (list r-knitr))
32470 (home-page "http://zoomgroupstats.org")
32471 (synopsis "Analyze text, audio, and video from Zoom meetings")
32473 "This package provides utilities for processing and analyzing the files
32474 that are exported from a recorded Zoom meeting. This includes analyzing data
32475 captured through video cameras and microphones, the text-based chat, and
32476 meta-data. You can analyze aspects of the conversation among meeting
32477 participants and their emotional expressions throughout the meeting.")
32478 (license license:expat)))
32480 (define-public r-zoom
32487 (uri (cran-uri "zoom" version))
32490 "03f5rxfr6ncf1j6vpn7pip21q7ylj4bx0a5xphqb6x6i33lxf1g5"))))
32491 (properties `((upstream-name . "zoom")))
32492 (build-system r-build-system)
32493 (home-page "https://github.com/cbarbu/R-package-zoom")
32494 (synopsis "Spatial data visualization tool")
32496 "This package provides @code{zm}, a utility that allows you to
32497 zoom/navigate any plot when called with any active plot.")
32498 (license license:gpl3+)))
32500 (define-public r-zoolog
32507 (uri (cran-uri "zoolog" version))
32510 "1wxxxscw4ji4p4599vdw6vcrkqm0g75x1gh13m4758lb51wav9ks"))))
32511 (properties `((upstream-name . "zoolog")))
32512 (build-system r-build-system)
32514 (list r-rdpack r-stringi))
32517 (home-page "https://josempozo.github.io/zoolog/")
32518 (synopsis "Zooarchaeological analysis with log-ratios")
32520 "This package includes functions and reference data to generate and
32521 manipulate log-ratios (also known as @dfn{log size index} (LSI) values) from
32522 measurements obtained on zooarchaeological material. Log ratios are used to
32523 compare the relative (rather than the absolute) dimensions of animals from
32524 archaeological contexts. The zoolog package is also able to seamlessly
32525 integrate data and references with heterogeneous nomenclature, which is
32526 internally managed by a zoolog thesaurus.")
32527 (license license:gpl3)))
32529 (define-public r-filehash
32531 (name "r-filehash")
32536 (uri (cran-uri "filehash" version))
32539 "1ga17smgjd4qsnf5a7qk0giwhpc5969ylqj520favs1k6b4y557k"))))
32540 (properties `((upstream-name . "filehash")))
32541 (build-system r-build-system)
32542 (home-page "http://github.com/rdpeng/filehash")
32543 (synopsis "Simple key-value database")
32545 "This package implements a simple key-value style database where
32546 character string keys are associated with data values that are stored on the
32547 disk. A simple interface is provided for inserting, retrieving, and deleting
32548 data from the database. Utilities are provided that allow filehash databases
32549 to be treated much like environments and lists are already used in R. These
32550 utilities are provided to encourage interactive and exploratory analysis on
32552 (license license:gpl2+)))
32554 (define-public r-mlearning
32556 (name "r-mlearning")
32561 (uri (cran-uri "mlearning" version))
32564 "0r8xfaxw83s2r27b8x5qd0k4r5ayxpkafzn9b1a0jvsr87i6520r"))))
32565 (properties `((upstream-name . "mlearning")))
32566 (build-system r-build-system)
32574 (home-page "http://www.sciviews.org/zooimage")
32575 (synopsis "Machine learning algorithms with unified interface")
32577 "This package provides a unified interface to various machine learning
32578 algorithms. Confusion matrices are provided too.")
32579 (license license:gpl2+)))
32581 (define-public r-zooimage
32583 (name "r-zooimage")
32588 (uri (cran-uri "zooimage" version))
32591 "0ck8w0zb9l1n9xvjwqshq9q9l8pigy3yslq2hnfbgcwk17kk9mp8"))))
32592 (properties `((upstream-name . "zooimage")))
32593 (build-system r-build-system)
32607 (home-page "http://www.sciviews.org/zooimage")
32608 (synopsis "Analysis of numerical plankton images")
32610 "This package provides a solution for analyzing digital images of
32611 plankton. In combination with ImageJ, an image analysis system, it processes
32612 digital images, measures individuals, trains for automatic classification of
32613 taxa, and finally, measures plankton samples (abundances, total and partial
32614 size spectra or biomasses, etc.).")
32615 (license license:gpl2+)))
32617 (define-public r-zooarch
32624 (uri (cran-uri "zooaRch" version))
32627 "0grc378xppv0303sf4flfqz5002vq5a23nzbq4bsff41rww7dihc"))))
32628 (properties `((upstream-name . "zooaRch")))
32629 (build-system r-build-system)
32630 (propagated-inputs (list r-ggplot2))
32631 (native-inputs (list r-knitr))
32633 "https://cran.r-project.org/package=zooaRch")
32635 "Analytical Tools for Zooarchaeological Data")
32637 "The analysis and inference of faunal remains recovered from
32638 archaeological sites concerns the field of zooarchaeology. The zooaRch
32639 package provides analytical tools to make inferences on zooarchaeological
32640 data. Functions in this package allow users to read, manipulate, visualize,
32641 and analyze zooarchaeological data.")
32642 (license license:gpl2+)))
32644 (define-public r-zonebuilder
32646 (name "r-zonebuilder")
32651 (uri (cran-uri "zonebuilder" version))
32654 "0mxf3dz0d6bi5wwjilqivdxhy5ypnq5svky8zygha0clv45l4dmn"))))
32655 (properties `((upstream-name . "zonebuilder")))
32656 (build-system r-build-system)
32658 (list r-rcolorbrewer r-sf))
32661 (home-page "https://github.com/zonebuilders/zonebuilder")
32662 (synopsis "Create and explore geographic zoning systems")
32664 "This package provides functions, documentation and example data to help
32665 divide geographic space into discrete polygons (zones). The functions are
32666 motivated by research into the merits of different zoning systems. A flexible
32667 @code{ClockBoard} zoning system is provided, which breaks-up space by
32668 concentric rings and radial lines emanating from a central point.")
32669 (license license:gpl3)))
32671 (define-public r-zonator
32678 (uri (cran-uri "zonator" version))
32681 "1plxchpd4ypp36phl13pi9yvlrqi3lk83lv5rldrhdqynhcgfw2k"))))
32682 (properties `((upstream-name . "zonator")))
32683 (build-system r-build-system)
32685 (list r-ggplot2 r-raster r-rcolorbrewer r-reshape2 r-rgdal))
32686 (native-inputs (list r-knitr))
32687 (home-page "https://cbig.github.io/zonator/")
32688 (synopsis "Utilities for Zonation spatial conservation prioritization")
32690 "Create new analysis setups and deal with results of Zonation
32691 conservation prioritization software.")
32692 (license license:bsd-2)))
32694 (define-public r-mmwrweek
32696 (name "r-mmwrweek")
32701 (uri (cran-uri "MMWRweek" version))
32704 "1l1ks44v52iggw9nhs56lfj6804yab5b17k8fzrc6h1kvj3vda0s"))))
32705 (properties `((upstream-name . "MMWRweek")))
32706 (build-system r-build-system)
32707 (home-page "http://wwwn.cdc.gov/nndss/document/MMWR_Week_overview.pdf")
32708 (synopsis "Convert dates to MMWR day, week, and year")
32710 "The first day of any MMWR week is Sunday. MMWR week numbering is
32711 sequential beginning with 1 and incrementing with each week to a maximum of 52
32712 or 53. MMWR week #1 of an MMWR year is the first week of the year that has at
32713 least four days in the calendar year. This package provides functionality to
32714 convert dates to MMWR day, week, and year and the reverse.")
32715 (license license:gpl2+)))
32717 (define-public r-cccd
32724 (uri (cran-uri "cccd" version))
32726 (base32 "0cxh19jqappc6zq9nz3m40ybdmsp12mf7yvflsz96wks3ly2ld4y"))))
32727 (properties `((upstream-name . "cccd")))
32728 (build-system r-build-system)
32729 (propagated-inputs (list r-deldir r-fnn r-igraph r-proxy))
32730 (home-page "https://cran.r-project.org/package=cccd")
32731 (synopsis "Class cover catch digraphs")
32733 "This package provides tools to create Class Cover Catch Digraphs,
32734 neighborhood graphs, and relatives.")
32735 (license license:gpl2+)))
32737 (define-public r-crul
32744 (uri (cran-uri "crul" version))
32747 "133g0skz4lifl8hm8pqdryd2m2drbrm6mdfzbbsrw8fg46di86my"))))
32748 (properties `((upstream-name . "crul")))
32749 (build-system r-build-system)
32757 (native-inputs (list r-knitr))
32758 (home-page "https://github.com/ropensci/crul")
32759 (synopsis "HTTP client")
32761 "This package provides a simple HTTP client, with tools for making HTTP
32762 requests, and mocking HTTP requests. The package is built on R6, and takes
32763 inspiration from Ruby's @code{faraday} gem.")
32764 (license license:expat)))
32766 (define-public r-gistr
32773 (uri (cran-uri "gistr" version))
32776 "0ac9ikrdg6i8xvlma0gizvsdva46408lk7hvsgkqirhy2ljy02hp"))))
32777 (properties `((upstream-name . "gistr")))
32778 (build-system r-build-system)
32788 (native-inputs (list r-knitr))
32789 (home-page "https://github.com/ropensci/gistr")
32790 (synopsis "Work with Gists in browser")
32792 "This package allows the user to create new Github gists, update gists
32793 with new files, rename files, delete files, get and delete gists, star and
32794 un-star them, fork them, open a gist in your default browser, get an embed
32795 code for a gist, list gist commits, and get rate limit information when
32797 (license license:expat)))
32799 (define-public r-rbokeh
32806 (uri (cran-uri "rbokeh" version))
32809 "1h2fpzqf17pw9d09r1g1iyxsj5qma4fsk8vnar7f1z4fjyypvi6q"))
32811 '(for-each delete-file '("inst/htmlwidgets/lib/bokehjs/bokeh-widgets.min.js"
32812 "inst/htmlwidgets/lib/bokehjs/bokeh.min.js")))))
32813 (properties `((upstream-name . "rbokeh")))
32814 (build-system r-build-system)
32817 (modify-phases %standard-phases
32818 (add-after 'unpack 'process-javascript
32819 (lambda* (#:key inputs #:allow-other-keys)
32820 (with-directory-excursion "inst/htmlwidgets/lib/bokehjs"
32822 `((,(assoc-ref inputs "js-bokeh-widgets")
32823 . "bokeh-widgets.min.js")
32824 (,(assoc-ref inputs "js-bokeh")
32825 . "bokeh.min.js"))))
32826 (for-each (lambda (source target)
32827 (format #true "Processing ~a --> ~a~%"
32829 (invoke "esbuild" source "--minify"
32830 (string-append "--outfile=" target)))
32832 (map cdr mapping)))))))))
32844 ;; Version 0.12.15 is mentioned in lib/htmlwidgets/rbokeh.yaml.
32846 `(("esbuild" ,esbuild)
32847 ("js-bokeh-widgets"
32850 (uri "https://unpkg.com/bokehjs@0.12.15/build/js/bokeh-widgets.js")
32853 "07v9lrkfcbdznpb10qqwi4m660zp65g85vlnfw7kn83zmkxkhhxy"))))
32857 (uri "https://unpkg.com/bokehjs@0.12.15/build/js/bokeh.js")
32860 "1pq0059aad7d2jv50nv9449p3w0gbkxkl0mhblc76m5d9qjqav2q"))))
32861 ("r-knitr" ,r-knitr)))
32862 (home-page "https://cran.r-project.org/web/packages/rbokeh/")
32863 (synopsis "R interface for the Bokeh visualization library")
32865 "This package provides a native R plotting library that provides a
32866 flexible declarative interface for creating interactive web-based graphics,
32867 backed by the @url{https://bokeh.pydata.org/, Bokeh visualization library}.")
32868 (license license:expat)))
32870 (define-public r-fauxpas
32877 (uri (cran-uri "fauxpas" version))
32880 "129fzqb7wsskbn50s8x0marr4wm8jrns6hiycqcsk166k3dnyyy8"))))
32881 (properties `((upstream-name . "fauxpas")))
32882 (build-system r-build-system)
32884 (list r-httpcode r-r6 r-whisker))
32887 (home-page "https://docs.ropensci.org/fauxpas")
32888 (synopsis "HTTP error helpers")
32890 "This package provides HTTP error helpers. Methods are included for
32891 general purpose HTTP error handling, as well as individual methods for every
32892 HTTP status code, both via status code numbers as well as their descriptive
32893 names. It supports the ability to adjust behavior to stop, message or
32894 warning. It includes the ability to use a custom whisker template to have any
32895 configuration of status code, short description, and verbose message.")
32896 (license license:expat)))
32898 (define-public r-webmockr
32900 (name "r-webmockr")
32905 (uri (cran-uri "webmockr" version))
32908 "0j40srwi0yasmllb9wsww4m6zkiyzqd549cis4dxd7c7p24hak8j"))))
32909 (properties `((upstream-name . "webmockr")))
32910 (build-system r-build-system)
32920 (home-page "https://github.com/ropensci/webmockr")
32921 (synopsis "Stubbing and setting expectations on HTTP Requests")
32923 "This is a package for stubbing and setting expectations on HTTP
32924 requests. It includes tools for stubbing HTTP requests, including expected
32925 request conditions and response conditions. You can match on HTTP method,
32926 query parameters, request body, headers and more. It can be used for unit
32927 tests or outside of a testing context.")
32928 (license license:expat)))
32930 (define-public r-iotools
32937 (uri (cran-uri "iotools" version))
32939 (base32 "07q0z0kszm1xx5hfhisfliyrcsxd8dc5mx0a2bwwnv5l1xzmix17"))))
32940 (properties `((upstream-name . "iotools")))
32941 (build-system r-build-system)
32942 (home-page "https://www.rforge.net/iotools")
32943 (synopsis "I/O tools for streaming")
32944 (description "This package provides basic I/O tools for streaming and data
32947 (license license:gpl3)))
32949 (define-public r-wordspace
32951 (name "r-wordspace")
32956 (uri (cran-uri "wordspace" version))
32958 (base32 "0hrjv5mag7gwl4wj7np248sdyns5i623wl37b11hlgalhbmlypyf"))))
32959 (properties `((upstream-name . "wordspace")))
32960 (build-system r-build-system)
32962 (list r-cluster r-iotools r-mass r-matrix r-rcpp r-sparsesvd))
32963 (native-inputs (list r-knitr))
32964 (home-page "https://wordspace.r-forge.r-project.org/")
32965 (synopsis "Distributional semantic models in R")
32967 "The wordspace package turns R into an interactive laboratory for
32968 empirical research on @dfn{distributional semantic models} (DSM). It consists
32969 of a small set of carefully designed functions, most of which
32972 @item encapsulate non-trivial R operations in a user-friendly manner or
32973 @item provide efficient and memory-lean C implementations of key operations.
32976 (license license:gpl3)))
32978 (define-public r-maxlik
32985 (uri (cran-uri "maxLik" version))
32987 (base32 "0pdigfpyiqacj2ydhpn5w1h89dz1ydk0syzs25lsgdi40sz0bvkw"))))
32988 (properties `((upstream-name . "maxLik")))
32989 (build-system r-build-system)
32990 (propagated-inputs (list r-generics r-misctools r-sandwich))
32991 (home-page "https://cran.r-project.org/package=maxLik")
32992 (synopsis "Maximum Likelihood Estimation and related tools")
32994 "This package provides functions for @dfn{Maximum Likelihood} (ML) estimation,
32995 non-linear optimization, and related tools. It includes a unified way to call
32996 different optimizers, and classes and methods to handle the results from the
32997 Maximum Likelihood viewpoint. It also includes a number of convenience tools
32998 for testing and developing your own models.")
32999 (license license:gpl2+)))
33001 (define-public r-misctools
33003 (name "r-misctools")
33008 (uri (cran-uri "miscTools" version))
33010 (base32 "16pwfxpyl0zv3hjxx2kjchkg7p6kbj0s2rrpskj7rkhjr9imlg5y"))))
33011 (properties `((upstream-name . "miscTools")))
33012 (build-system r-build-system)
33013 (propagated-inputs (list r-digest))
33014 (home-page "http://www.micEcon.org")
33015 (synopsis "Miscellaneous tools and utilities")
33017 "This package provides miscellaneous small tools and utilities. Many of
33018 them facilitate the work with matrices, e.g. inserting rows or columns,
33019 creating symmetric matrices, or checking for semidefiniteness. Other tools
33020 facilitate the work with regression models, e.g. extracting the standard
33021 errors, obtaining the number of (estimated) parameters, or calculating
33022 R-squared values.")
33023 (license license:gpl2+)))
33025 (define-public r-mockery
33032 (uri (cran-uri "mockery" version))
33035 "0sj77m9vgn4bzb8c8nq93xb9lm8ih8rcb7sfccripraibibg3jcz"))))
33036 (properties `((upstream-name . "mockery")))
33037 (build-system r-build-system)
33042 (home-page "https://github.com/jfiksel/mockery")
33043 (synopsis "Mocking library for R")
33045 "The two main functionalities of this package are creating mock
33046 objects (functions) and selectively intercepting calls to a given function
33047 that originate in some other function. It can be used with any testing
33048 framework available for R. Mock objects can be injected with either this
33049 package's own @code{stub} function or a similar @code{with_mock} facility
33050 present in the @code{testthat} package.")
33051 (license license:expat)))
33053 (define-public r-zoltr
33060 (uri (cran-uri "zoltr" version))
33063 "12zh7y3pwidclscgvd0b0iaqq9j5y8mc8xd6pz4vs0jy5qs3ahar"))))
33064 (properties `((upstream-name . "zoltr")))
33065 (build-system r-build-system)
33077 (native-inputs (list r-knitr))
33078 (home-page "https://github.com/reichlab/zoltr")
33079 (synopsis "Interface to the Zoltar forecast repository API")
33081 "Zoltar is a website that provides a repository of model forecast results
33082 in a standardized format and a central location. It supports storing,
33083 retrieving, comparing, and analyzing time series forecasts for prediction
33084 challenges of interest to the modeling community. This package provides
33085 functions for working with the Zoltar API, including connecting and
33086 authenticating, getting information about projects, models, and forecasts,
33087 deleting and uploading forecast data, and downloading scores.")
33088 (license license:gpl3)))
33090 (define-public r-zoib
33097 (uri (cran-uri "zoib" version))
33100 "0inm7f2pc68ksqxvq12xp9jc99vj7ydylvs24ip12nksbj5k1n8f"))))
33101 (properties `((upstream-name . "zoib")))
33102 (build-system r-build-system)
33104 (list r-abind r-coda r-formula r-rjags))
33105 (home-page "https://www.r-project.org")
33106 (synopsis "Bayesian inference for beta regression")
33108 "This package lets you fit beta regression and zero-or-one inflated beta
33109 regression and obtain Bayesian inference of the model via the Markov Chain
33110 Monte Carlo approach implemented in JAGS.")
33111 (license license:gpl3+)))
33113 (define-public r-logger
33120 (uri (cran-uri "logger" version))
33122 (base32 "08kym5i5fvbf5xhh9qdszp4jdgyc7j7zpnwzy68wabqz73aff6sg"))))
33123 (properties `((upstream-name . "logger")))
33124 (build-system r-build-system)
33125 (native-inputs (list r-knitr))
33126 (home-page "https://daroczig.github.io/logger/")
33127 (synopsis "Lightweight and flexible logging utility")
33129 "Inspired by the the @code{futile.logger} R package and @code{logging}
33130 Python module, this utility provides a flexible and extensible way of
33131 formatting and delivering log messages with low overhead.")
33132 (license license:agpl3+)))
33134 (define-public r-fasterize
33136 (name "r-fasterize")
33141 (uri (cran-uri "fasterize" version))
33143 (base32 "10bzl77c1b9jhcn1xp467qzp2n8c7s3wpxn53qjh1nwvbri5kd32"))))
33144 (properties `((upstream-name . "fasterize")))
33145 (build-system r-build-system)
33147 (list r-raster r-rcpp r-rcpparmadillo r-sp))
33148 (native-inputs (list r-knitr))
33149 (home-page "https://github.com/ecohealthalliance/fasterize")
33150 (synopsis "Fast Polygon to Raster Conversion")
33152 "This package provides a drop-in replacement for @code{rasterize} from
33153 the @code{raster} package that takes sf-type objects, and is much faster.
33154 There is support for the main options provided by the @code{rasterize}
33155 function, including setting the field used and background value, and
33156 options for aggregating multi-layer rasters.")
33157 (license license:expat)))
33159 (define-public r-bien
33166 (uri (cran-uri "BIEN" version))
33168 (base32 "0s98n6zbf48vssd3h63k6kashcxv1kawcb026n0ngsfpc5dv6i48"))))
33169 (properties `((upstream-name . "BIEN")))
33170 (build-system r-build-system)
33185 (home-page "https://cran.r-project.org/package=BIEN")
33186 (synopsis "Tools for accessing the BIEN database")
33188 "This package provides tools for accessing the Botanical Information and
33189 Ecology Network (BIEN) database. The BIEN database contains cleaned and
33190 standardized botanical data including occurrence, trait, plot and taxonomic
33191 data. This package provides functions that query the BIEN database by
33192 constructing and executing optimized SQL queries.")
33193 (license license:expat)))
33195 (define-public r-varhandle
33197 (name "r-varhandle")
33202 (uri (cran-uri "varhandle" version))
33204 (base32 "1l42d0s6fbjjc9l28a2m3myxkrx2c0p0b9yj8wjjjgilw19yc3lv"))))
33205 (properties `((upstream-name . "varhandle")))
33206 (build-system r-build-system)
33207 (home-page "https://bitbucket.org/mehrad_mahmoudian/varhandle")
33208 (synopsis "Functions for robust variable handling")
33210 "This package contains some functions to help users (especially data
33211 explorers) to make more sense of their variables and take the most out of
33212 variables and hardware resources. Functions in this package are supposed to
33213 be efficient and easy to use.")
33214 (license license:gpl2+)))
33216 (define-public r-ggh4x
33223 (uri (cran-uri "ggh4x" version))
33226 "1r49yfm5fqv5s7jb92ad6rf8hd9plcry6f500czjhnhhrp16cqfp"))))
33227 (properties `((upstream-name . "ggh4x")))
33228 (build-system r-build-system)
33230 (list r-ggplot2 r-gtable r-rlang r-scales r-vctrs))
33233 (home-page "https://github.com/teunbrand/ggh4x")
33234 (synopsis "Extension for ggplot2")
33235 (description "This package is a @code{ggplot2} extension. It provides some
33236 utility functions that do not entirely fit within the grammar of graphics
33237 concept. The package extends @code{ggpplots} facets through customisation, by
33238 setting individual scales per panel, resizing panels and providing nested
33239 facets. It also allows multiple colour, fill scales per plot and hosts a
33240 smaller collection of stats, geoms and axis guides.")
33241 (license license:expat)))
33243 (define-public r-zoeppritz
33245 (name "r-zoeppritz")
33249 (uri (cran-uri "zoeppritz" version))
33252 "1711szx9zz17q6pfinyzlyrw7m9772c8ywlixqar2l165bkjalgm"))))
33253 (properties `((upstream-name . "zoeppritz")))
33254 (build-system r-build-system)
33255 (home-page "https://cran.r-project.org/package=zoeppritz")
33256 (synopsis "Seismic reflection and scattering coefficients for waves")
33258 "The @code{r-zoeppritz} package calculates and plots scattering matrix
33259 coefficients or scattering amplitudes, for seismological P and S-waves at an
33261 (license license:gpl2+)))