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-dixontest
357 (uri (cran-uri "dixonTest" version))
359 (base32 "1a3yc30g5rbb0jhm2b0iir5i1dy4jyl67spkhx4yysg4snz131wv"))))
360 (properties `((upstream-name . "dixonTest")))
361 (build-system r-build-system)
362 (native-inputs (list gfortran))
363 (home-page "https://cran.r-project.org/package=dixonTest")
364 (synopsis "Dixon's ratio test for outlier detection")
366 "For outlier detection in small and normally distributed samples the ratio
367 test of Dixon (Q-test) can be used. Density, distribution function, quantile
368 function and random generation for Dixon's ratio statistics are provided as
369 wrapper functions. The core applies McBane's Fortran functions that use
370 Gaussian quadrature for a numerical solution.")
371 (license license:gpl3)))
373 (define-public r-emdist
380 (uri (cran-uri "emdist" version))
383 "05mv6xhm15b0mq9kzyiblkb14bdqmjrwl64ghdk66il0w8i7p6nh"))))
384 (properties `((upstream-name . "emdist")))
385 (build-system r-build-system)
386 (home-page "http://www.rforge.net/emd")
387 (synopsis "Earth mover's distance")
389 "This package provides tools to calculate the Earth Mover's
391 (license license:expat)))
393 (define-public r-googledrive
395 (name "r-googledrive")
400 (uri (cran-uri "googledrive" version))
403 "09jsiknzyfgxd0nzdr3wrrjw24allch2x74h96qg8vh8dad4cp30"))))
404 (properties `((upstream-name . "googledrive")))
405 (build-system r-build-system)
423 (home-page "https://googledrive.tidyverse.org")
424 (synopsis "Interface to Google Drive")
425 (description "This package lets you manage Google Drive files from R.")
426 (license license:expat)))
428 (define-public r-googlevis
435 (uri (cran-uri "googleVis" version))
437 (base32 "1s82xcs6zrlmnhay764bspzwvabfyi35nq6fwdrrk3v79q13c5jz"))))
438 (properties `((upstream-name . "googleVis")))
439 (build-system r-build-system)
440 (propagated-inputs (list r-jsonlite))
441 (native-inputs (list r-knitr))
442 (home-page "https://mages.github.io/googleVis/")
443 (synopsis "R interface to Google Charts")
445 "The @code{googleVis} package provides an interface between R and the Google
446 Charts API. Google Charts offer interactive charts which can be embedded into
447 web pages. The functions of the @code{googleVis} package allow the user to
448 visualise data stored in R data frames with Google Charts without uploading
449 the data to Google. The output of a @code{googleVis} function is HTML code
450 that contains the data and references to JavaScript functions hosted by
451 Google. @code{googleVis} makes use of the internal R HTTP server to display
452 the output locally.")
453 (license license:gpl2+)))
455 (define-public r-guix-install
457 (name "r-guix-install")
462 (uri (cran-uri "guix.install" version))
464 (base32 "0s3wb5781yc43c9zwrn7i87zcbrlx7xr0ms0v9hvgs7qsv02id9j"))))
465 (properties `((upstream-name . "guix.install")))
466 (build-system r-build-system)
467 (propagated-inputs (list r-runit))
468 (home-page "https://github.com/BIMSBbioinfo/guix.install")
469 (synopsis "Install R packages with GNU Guix")
471 "This R package provides a single procedure @code{guix.install()}, which
472 allows users to install R packages via Guix right from within their running R
473 session. If the requested R package does not exist in Guix at this time, the
474 package and all its missing dependencies will be imported recursively and the
475 generated package definitions will be written to @file{~/.Rguix/packages.scm}.
476 This record of imported packages can be used later to reproduce the
477 environment, and to add the packages in question to a proper Guix channel (or
478 Guix itself). @code{guix.install()} not only supports installing packages
479 from CRAN, but also from Bioconductor or even arbitrary git or mercurial
480 repositories, replacing the need for installation via @code{devtools}.")
481 (license license:gpl3+)))
490 (uri (cran-uri "ids" version))
493 "1s6ga94gds5ydr9f8qbjfgfpg2dvbnkcrlybqlb33hk3c0c2l8dn"))))
494 (properties `((upstream-name . "ids")))
495 (build-system r-build-system)
497 (list r-openssl r-uuid))
498 (native-inputs (list r-knitr))
499 (home-page "https://github.com/richfitz/ids")
500 (synopsis "Generate random identifiers")
502 "This package lets you generate random or human readable and
503 pronounceable identifiers.")
504 (license license:expat)))
506 (define-public r-googlesheets4
508 (name "r-googlesheets4")
513 (uri (cran-uri "googlesheets4" version))
516 "0yncqwv9l5knyrv88ys5gwcv44hl1j0mbklpins6v7f9m9v7s40a"))))
517 (properties `((upstream-name . "googlesheets4")))
518 (build-system r-build-system)
534 (home-page "https://github.com/tidyverse/googlesheets4")
535 (synopsis "Access Google Sheets using the Sheets API V4")
537 "This package lets you interact with Google Sheets through the
538 @url{https://developers.google.com/sheets/api,Sheets API v4}. This package
539 can read and write both the metadata and the cell data in a Sheet.")
540 (license license:expat)))
542 (define-public r-waldo
549 (uri (cran-uri "waldo" version))
552 "1aky28rn70l24s0sygl36267cf7hjzhchagsz26abfxwr7p8kvjp"))))
553 (properties `((upstream-name . "waldo")))
554 (build-system r-build-system)
563 (home-page "https://github.com/r-lib/waldo")
564 (synopsis "Find differences between R objects")
566 "Compare complex R objects and reveal the key differences. This package
567 was designed particularly for use in testing packages where being able to
568 quickly isolate key differences makes understanding test failures much
570 (license license:expat)))
572 (define-public r-rticles
579 (uri (cran-uri "rticles" version))
582 "1ipblw3rmkma22jl2hf1pyfm6l8k31zcmm3swmwii6k0x7khiav1"))))
583 (properties `((upstream-name . "rticles")))
584 (build-system r-build-system)
586 (list r-knitr r-rmarkdown r-tinytex r-xfun r-yaml))
587 (home-page "https://github.com/rstudio/rticles")
588 (synopsis "Article formats for R Markdown")
590 "This package provides a suite of custom R Markdown formats and templates
591 for authoring journal articles and conference submissions.")
592 (license license:gpl3)))
594 (define-public r-babelwhale
596 (name "r-babelwhale")
601 (uri (cran-uri "babelwhale" version))
603 (base32 "0ph825dwvr48fhamy1l5564linz7cj7b9sj511as77f1yqycv4a2"))))
604 (properties `((upstream-name . "babelwhale")))
605 (build-system r-build-system)
607 (list r-crayon r-dplyr r-dynutils r-processx r-purrr))
608 (home-page "https://github.com/dynverse/babelwhale")
609 (synopsis "Talking to Docker and Singularity containers")
611 "This package provides a unified interface to interact with Docker and
612 Singularity containers. You can execute a command inside a container, mount a
613 volume or copy a file.")
614 (license license:expat)))
616 (define-public r-benchmarkmedata
618 (name "r-benchmarkmedata")
622 (uri (cran-uri "benchmarkmeData" version))
625 "1n4vjkagqlm6kw2hilf4gjfcdjad0bcg652j9nl2ygbq3kdnh1vf"))))
626 (build-system r-build-system)
628 (list r-dplyr r-tibble))
629 (home-page "https://github.com/csgillespie/benchmarkme-data")
630 (synopsis "Data set for the @code{benchmarkme} package")
631 (description "This package contains the data set for the crowd-sourced
632 benchmarks from running the @code{benchmarkme} package.")
633 (license license:gpl2+)))
635 (define-public r-benchmarkme
637 (name "r-benchmarkme")
641 (uri (cran-uri "benchmarkme" version))
644 "0ymgsxzrvnpyvs0cff09d3lrkl12qyqx5bwammsc4vgl5ng9p69p"))))
645 (build-system r-build-system)
649 (list r-benchmarkmedata
656 (home-page "https://csgillespie.github.io/benchmarkme/")
657 (synopsis "Crowd-sourced system benchmarks")
658 (description "This package provides functionality to benchmark your CPU
659 and compare against other CPUs. Also provides functions for obtaining system
660 specifications, such as RAM, CPU type, and R version.")
661 (license license:gpl2+)))
663 (define-public r-bezier
669 (uri (cran-uri "bezier" version))
672 "1vw5128v8h973xwa1fdm9cw2jvrldj87nd55lddlp3qsz3ag4br6"))))
673 (build-system r-build-system)
674 (home-page "https://cran.r-project.org/web/packages/bezier/")
675 (synopsis "Bezier curve and spline toolkit")
677 "This package is a toolkit for working with Bezier curves and splines.
678 The package provides functions for point generation, arc length estimation,
679 degree elevation and curve fitting.")
680 (license license:gpl2+)))
682 (define-public r-bwstest
689 (uri (cran-uri "BWStest" version))
691 (base32 "02amzlfprmw5pyis0dg0kg0x8xqh50a4vfdcxxmklrzik3b1vzzs"))))
692 (properties `((upstream-name . "BWStest")))
693 (build-system r-build-system)
694 (propagated-inputs (list r-memoise r-rcpp))
695 (home-page "https://github.com/shabbychef/BWStest")
696 (synopsis "Baumgartner Weiss Schindler Test of equal distributions")
698 "This package performs the Baumgartner-Weiss-Schindler two-sample test of
699 equal probability distributions (doi:10.2307/2533862). It also performs
700 similar rank-based tests for equal probability distributions due to Neuhauser
701 (doi:10.1080/10485250108832874) and Murakami
702 (doi:10.1080/00949655.2010.551516).")
703 (license license:lgpl3)))
712 (uri (cran-uri "V8" version))
715 "0hs7ajjw6y3q7mp7z00a9712y4cn6wgcnk5dbjbzlc6cfk4zsqkc"))))
716 (properties `((upstream-name . "V8")))
717 (build-system r-build-system)
720 (modify-phases %standard-phases
721 (add-after 'unpack 'find-v8
722 (lambda* (#:key inputs #:allow-other-keys)
723 (substitute* "configure"
725 (string-append "PKG_LIBS="
726 (assoc-ref inputs "libnode")
727 "/lib/libnode.so.64\n")))
728 (setenv "INCLUDE_DIR"
730 (assoc-ref inputs "libnode")
734 (assoc-ref inputs "libnode") "/lib")))))))
738 (list r-curl r-jsonlite r-rcpp))
741 (home-page "https://jeroen.cran.dev/V8")
742 (synopsis "Embedded JavaScript and WebAssembly engine for R")
744 "This package provides an R interface to V8: Google's JavaScript and
745 WebAssembly engine.")
746 (license license:expat)))
755 (uri (cran-uri "DOT" version))
758 "0qh5n57cp9c2n5yn59q4wggz82943pwfanp3kx869aba2x3sj30i"))))
759 (properties `((upstream-name . "DOT")))
760 (build-system r-build-system)
763 (home-page "http://haghish.com/dot")
764 (synopsis "Render and Export DOT Graphs in R")
766 "This package provides tools to render DOT diagram markup language in R
767 and also provides the possibility to export the graphs in PostScript and
768 SVG (Scalable Vector Graphics) formats. In addition, it supports literate
769 programming packages such as @code{knitr} and @code{rmarkdown}.")
770 (license license:expat)))
772 (define-public r-carrier
779 (uri (cran-uri "carrier" version))
781 (base32 "0bqnwnnjqjk9q0lxq6kkz9s75ss10lfyyywyyi24m8wppxpw1vqc"))))
782 (properties `((upstream-name . "carrier")))
783 (build-system r-build-system)
785 (list r-pryr r-rlang))
786 (home-page "https://github.com/r-lib/carrier")
787 (synopsis "Isolate functions for remote execution")
789 "Sending functions to remote processes can be wasteful of resources
790 because they carry their environments with them. With this package, it is
791 easy to create functions that are isolated from their environment. These
792 isolated functions, also called crates, print to the console with their total
793 size and can be easily tested locally before being sent to a remote.")
794 (license license:gpl3)))
796 (define-public r-clipr
803 (uri (cran-uri "clipr" version))
806 "1s9vvv3cxnz8w11gsi8z9ddv9jzib5qf5qqxnwqrrv7vj8cr7hij"))))
807 (build-system r-build-system)
810 (home-page "https://github.com/mdlincoln/clipr")
811 (synopsis "Read and write from the system clipboard")
813 "This package provides simple utility functions to read from and write to
814 the system clipboards.")
815 (license license:gpl3)))
824 (uri (cran-uri "dlm" version))
826 (base32 "1aksm66sfa7ipl5xgs4j5giac7q2m744wjl40mva56xn6i674h4r"))))
827 (properties `((upstream-name . "dlm")))
828 (build-system r-build-system)
829 (home-page "https://cran.r-project.org/package=dlm")
830 (synopsis "Bayesian and Likelihood Analysis of Dynamic Linear Models")
832 "This package provides routines for Maximum likelihood, Kalman filtering
833 and smoothing, and Bayesian analysis of Normal linear State Space models, also
834 known as Dynamic Linear Models.")
835 (license license:gpl2+)))
843 (uri (cran-uri "zoo" version))
846 "0izd66dywq6qd62hdp64apncainrrb9mgmm19wf6a8jc03c858n9"))))
847 (build-system r-build-system)
850 (home-page "http://zoo.R-Forge.R-project.org/")
851 (synopsis "S3 infrastructure for regular and irregular time series")
852 (description "This package contains an S3 class with methods for totally
853 ordered indexed observations. It is particularly aimed at irregular time
854 series of numeric vectors/matrices and factors.")
855 (license license:gpl2+)))
857 (define-public r-fontawesome
859 (name "r-fontawesome")
864 (uri (cran-uri "fontawesome" version))
866 (base32 "0r6zb5175cr4ybqj6bl0mbhadwv9xjxaf32yjc0y76rw3d6vcbap"))))
867 (properties `((upstream-name . "fontawesome")))
868 (build-system r-build-system)
870 (list r-htmltools r-rlang))
871 (home-page "https://github.com/rstudio/fontawesome")
872 (synopsis "Easily work with Font Awesome icons")
874 "Easily and flexibly insert Font Awesome icons into R Markdown documents
875 and Shiny apps. These icons can be inserted into HTML content through inline
876 SVG tags or @code{i} tags. There is also a utility function for exporting
877 Font Awesome icons as PNG images for those situations where raster graphics
879 (license license:expat)))
881 (define-public r-fingerprint
883 (name "r-fingerprint")
888 (uri (cran-uri "fingerprint" version))
890 (base32 "04jcwkydjrs31pia6kq8z2n9s54im950q08hs2ay15xjxxkmb8ic"))))
891 (properties `((upstream-name . "fingerprint")))
892 (build-system r-build-system)
893 (home-page "https://cran.r-project.org/package=fingerprint")
894 (synopsis "Functions to Operate on Binary Fingerprint Data")
896 "This package provides functions to manipulate binary fingerprints of
897 arbitrary length. A fingerprint is represented by an object of S4 class
898 @code{fingerprint}. The bitwise logical functions in R are overridden so that
899 they can be used directly with @code{fingerprint} objects. A number of
900 distance metrics are also available. Fingerprints can be converted to
901 Euclidean vectors (i.e., points on the unit hypersphere) and can also be
902 folded. Arbitrary fingerprint formats can be handled via line handlers.
903 Currently handlers are provided for CDK, MOE and BCI fingerprint data.")
904 ;; Any version of the GPL
905 (license (list license:gpl2+ license:gpl3+))))
907 (define-public r-fpeek
914 (uri (cran-uri "fpeek" version))
916 (base32 "0kv46g21ndxchg3q8ynq7hjjkh6i2zlc21axn5y1jjzigrw047ii"))))
917 (properties `((upstream-name . "fpeek")))
918 (build-system r-build-system)
919 (propagated-inputs (list r-rcpp))
920 (home-page "https://github.com/davidgohel/fpeek")
921 (synopsis "Check text files content at a glance")
923 "This package provides tools to help working with text files. It can
924 return the number of lines; print the first and last lines; convert encoding.
925 Operations are made without reading the entire file before starting, resulting
926 in good performances with large files.")
927 (license license:expat)))
929 (define-public r-ggalluvial
931 (name "r-ggalluvial")
935 (uri (cran-uri "ggalluvial" version))
938 "0mkan9gxg3yxjism22yxbhvlh2lh7wpbrqpb355za790prcmjbh3"))))
939 (properties `((upstream-name . "ggalluvial")))
940 (build-system r-build-system)
950 (home-page "http://corybrunson.github.io/ggalluvial/")
951 (synopsis "Alluvial plots for ggplot2")
952 (description "This package provides alluvial plots for @code{ggplot2}.
953 Alluvial plots use variable-width ribbons and stacked bar plots to represent
954 multi-dimensional or repeated-measures data with categorical or ordinal
956 (license license:gpl3)))
958 (define-public r-ggpp
965 (uri (cran-uri "ggpp" version))
968 "0wcaczxjav5yg8h2197cf288mqk13p3iq675q0x0di9g8lnblvk1"))))
969 (properties `((upstream-name . "ggpp")))
970 (build-system r-build-system)
988 (home-page "https://docs.r4photobiology.info/ggpp/")
989 (synopsis "Grammar extensions to ggplot2")
991 "This package contains extensions to ggplot2.
994 @item Geomas: @code{geom_table}, @code{geom_plot} and @code{geom_grob} add
995 insets to plots using native data coordinates, while @code{geom_table_npc},
996 @code{geom_plot_npc} and @code{geom_grob_npc} do the same using @code{npc}
997 coordinates through new aesthetics @code{npcx} and @code{npcy}.
998 @item Statistics: select observations based on 2D density.
999 @item Positions: radial nudging away from a center point and nudging away from
1003 (license license:gpl2+)))
1005 (define-public r-lmds
1012 (uri (cran-uri "lmds" version))
1014 (base32 "130azb0nc2wwxv0qi8v5s4rd02p9lc92zwn634pv7b8awbw81i65"))))
1015 (properties `((upstream-name . "lmds")))
1016 (build-system r-build-system)
1018 (list r-assertthat r-dynutils r-irlba r-matrix))
1019 (home-page "https://github.com/dynverse/lmds")
1020 (synopsis "Landmark multi-dimensional scaling")
1022 "This package provides a fast dimensionality reduction method scalable
1023 to large numbers of samples. @dfn{Landmark Multi-Dimensional Scaling} (LMDS)
1024 is an extension of classical Torgerson MDS, but rather than calculating a
1025 complete distance matrix between all pairs of samples, only the distances
1026 between a set of landmarks and the samples are calculated.")
1027 (license license:gpl3)))
1029 (define-public r-lmodel2
1036 (uri (cran-uri "lmodel2" version))
1038 (base32 "1fiin2nkffbihz1s8ixmw9lgf8mn3j9krr8iiflizk10mdv54hnb"))))
1039 (properties `((upstream-name . "lmodel2")))
1040 (build-system r-build-system)
1041 (home-page "https://cran.r-project.org/package=lmodel2")
1042 (synopsis "Model II regression")
1044 "This package computes model II simple linear regression using
1045 @dfn{ordinary least squares} (OLS), @dfn{major axis} (MA), @dfn{standard major
1046 axis} (SMA), and @dfn{ranged major axis} (RMA).")
1047 (license license:gpl2)))
1049 (define-public r-ggpmisc
1055 (uri (cran-uri "ggpmisc" version))
1058 "1iq39rx4nj1lf37hnj4df0c7gbk9374d0mzcnhdr7aqpxaxgs3ys"))))
1059 (build-system r-build-system)
1077 (home-page "https://www.r4photobiology.info/")
1078 (synopsis "Miscellaneous Extensions to @code{ggplot2}")
1079 (description "This package provides extensions to @code{ggplot2},
1080 respecting the grammar of its graphics paradigm.")
1081 (license license:gpl2+)))
1083 (define-public r-ggside
1089 (uri (cran-uri "ggside" version))
1092 "1x505zizv7hf65pxp9j5v92c3bchhxh9dsrkk1m55kwqqnsl5nza"))))
1093 (properties `((upstream-name . "ggside")))
1094 (build-system r-build-system)
1095 (propagated-inputs (list r-ggplot2 r-glue r-gtable r-rlang r-scales))
1096 (native-inputs (list r-knitr))
1097 (home-page "https://cran.r-project.org/package=ggside")
1098 (synopsis "Side grammar graphics that extends @code{ggplot2}")
1100 "The grammar of graphics as shown in @code{ggplot2} has provided an
1101 expressive API for users to build plots. This package @{ggside} extends
1102 @code{ggplot2} by allowing users to add graphical information about one of the
1103 main panel's axis using a familiar @code{ggplot2} style API with tidy data.
1104 This package is particularly useful for visualizing metadata on a discrete
1105 axis, or summary graphics on a continuous axis such as a boxplot or a density
1107 (license license:expat)))
1109 (define-public r-gprofiler
1111 (name "r-gprofiler")
1116 (uri (cran-uri "gProfileR" version))
1119 "1h1v0kgpsn04ald2izznh7fr2riwisj5hcgz4k7h3qc931rf0r4k"))))
1120 (properties `((upstream-name . "gProfileR")))
1121 (build-system r-build-system)
1123 (list r-plyr r-rcurl))
1124 (home-page "https://cran.r-project.org/web/packages/gProfileR/")
1125 (synopsis "Interface to the g:Profiler toolkit")
1127 "This package provides tools for functional enrichment analysis,
1128 gene identifier conversion and mapping homologous genes across related
1129 organisms via the @code{g:Profiler} toolkit.")
1130 (license license:gpl2+)))
1132 (define-public r-gprofiler2
1134 (name "r-gprofiler2")
1139 (uri (cran-uri "gprofiler2" version))
1142 "0r0h34b35xzgd9rh55yndn0anxy0z45zdlqa6qfmpn91b6v1bb1g"))))
1143 (properties `((upstream-name . "gprofiler2")))
1144 (build-system r-build-system)
1155 (native-inputs (list r-knitr))
1156 (home-page "https://cran.r-project.org/web/packages/gprofiler2/")
1157 (synopsis "Interface to the g:Profiler toolset")
1159 "This package provides a toolset for functional enrichment analysis and
1160 visualization, gene/protein/SNP identifier conversion and mapping orthologous
1161 genes across species via @url{https://biit.cs.ut.ee/gprofiler,g:Profiler}.
1165 @item @code{g:GOSt}, functional enrichment analysis and visualization of gene
1167 @item @code{g:Convert}, gene/protein/transcript identifier conversion across
1169 @item @code{g:Orth}, orthology search across species;
1170 @item @code{g:SNPense}, mapping SNP rs identifiers to chromosome positions,
1171 genes and variant effects.
1174 This package is an R interface corresponding to the 2019 update of
1175 @code{g:Profiler} and provides access to versions @code{e94_eg41_p11} and
1177 (license license:gpl2+)))
1179 (define-public r-oenb
1186 (uri (cran-uri "oenb" version))
1189 "1jgxw7ycx2lcdzglg9nix8k08fs4r6i5jdsjzrd6w1dg6smsinl5"))))
1190 (properties `((upstream-name . "oenb")))
1191 (build-system r-build-system)
1193 (list r-dplyr r-xml))
1194 (native-inputs (list r-knitr))
1195 (home-page "https://github.com/franzmohr/oenb")
1196 (synopsis "Tools for the OeNB Data Web Service")
1198 "Tools to access data from the data web service of the
1199 @acronym{OeNB, Oesterreichische Nationalbank},
1200 @url{https://www.oenb.at/en/Statistics/User-Defined-Tables/webservice.html}.")
1201 (license license:gpl2+)))
1203 (define-public r-orgmassspecr
1205 (name "r-orgmassspecr")
1209 (uri (cran-uri "OrgMassSpecR" version))
1212 "1dx9d8rb1dfqyhyc26zhfnxiv3rz2ikvs2mwqnsrq3lsjs9dvyc8"))))
1213 (properties `((upstream-name . "OrgMassSpecR")))
1214 (build-system r-build-system)
1215 (native-inputs (list r-knitr))
1216 (home-page "http://OrgMassSpec.github.io/")
1217 (synopsis "Organic or biological mass spectrometry data analysis")
1219 "This package @code{OrgMassSpecR} is an extension of the @code{R}
1220 statistical computing language. It contains functions to assist with organic
1221 or biological mass spectrometry data analysis. Mass spectral libraries are
1222 available as companion packages.")
1223 (license license:bsd-2)))
1225 (define-public r-scales
1232 (uri (cran-uri "scales" version))
1234 (base32 "1pq2rrix6a5gsi8xw38viiydp1bsxxmcmyy7dv9q8gkb1qj50p8q"))))
1235 (build-system r-build-system)
1245 (home-page "https://github.com/hadley/scales")
1246 (synopsis "Scale functions for visualization")
1248 "This package provides graphical scales that map data to aesthetics, and
1249 provides methods for automatically determining breaks and labels for axes and
1251 (license license:expat)))
1253 (define-public r-pacman
1259 (uri (cran-uri "pacman" version))
1262 "0z7gngd6h83cpjhq1vg75wvzhdjbgjh7gj5d4zvvi9gd2lmagjcy"))))
1263 (build-system r-build-system)
1266 (home-page "https://github.com/trinker/pacman")
1267 (synopsis "Package Management Tool")
1268 (description "This package provides tools to more conveniently perform
1269 tasks associated with add-on packages. @code{pacman} conveniently wraps
1270 library and package related functions and names them in an intuitive and
1271 consistent fashion. It seeks to combine functionality from lower level
1272 functions which can speed up workflow.")
1273 (license license:gpl2)))
1275 (define-public r-paralleldist
1277 (name "r-paralleldist")
1282 (uri (cran-uri "parallelDist" version))
1284 (base32 "01ly4hxwa64a0ya5gla8rvv72s9mcknsfznivjkh937pbjwb7iih"))))
1285 (properties `((upstream-name . "parallelDist")))
1286 (build-system r-build-system)
1287 (propagated-inputs (list r-rcpp r-rcpparmadillo r-rcppparallel))
1288 (home-page "https://github.com/alexeckert/parallelDist")
1289 (synopsis "Parallel Distance Matrix Computation using multiple threads")
1291 "This package provides a fast parallelized alternative to R's native
1292 @code{dist} function to calculate distance matrices for continuous, binary,
1293 and multi-dimensional input matrices, which supports a broad variety of
1294 predefined distance functions from other R packages, as well as user- defined
1295 functions written in C++. For ease of use, the @code{parDist} function
1296 extends the signature of the @code{dist} function and uses the same parameter
1297 naming conventions as distance methods of existing R packages.")
1298 (license license:gpl2+)))
1300 (define-public r-pheatmap
1307 (uri (cran-uri "pheatmap" version))
1310 "1hdh74az3vyzz6dqa311rhxdm74n46lyr03p862kn80p0kp9d7ap"))))
1311 (build-system r-build-system)
1313 (list r-gtable r-rcolorbrewer r-scales))
1314 (home-page "https://cran.r-project.org/web/packages/pheatmap")
1315 (synopsis "Pretty heatmaps")
1317 "This package provides an implementation of heatmaps that offers more
1318 control over dimensions and appearance.")
1319 (license license:gpl2+)))
1321 (define-public r-pnwcolors
1323 (name "r-pnwcolors")
1328 (uri (cran-uri "PNWColors" version))
1331 "1phplnclkficfv8s6wsyrckk4ixzbayiy5iix6dddg40485l9nyj"))))
1332 (properties `((upstream-name . "PNWColors")))
1333 (build-system r-build-system)
1334 (home-page "https://github.com/jakelawlor/PNWColors")
1335 (synopsis "Color palettes for data visualizations")
1337 "This package provides color palettes. They are checked for colorblind
1338 accessibility from hue, saturation, and lightness value scaling using the
1339 Chroma.js Color Palette Helper. See @url{https://gka.github.io/palettes}.")
1340 (license license:cc0)))
1342 (define-public r-plotfunctions
1344 (name "r-plotfunctions")
1349 (uri (cran-uri "plotfunctions" version))
1351 (base32 "0asmxw8283fpvl83h478j5nyg59xqifqaa8f2f6l199gvvswhhg2"))))
1352 (properties `((upstream-name . "plotfunctions")))
1353 (build-system r-build-system)
1354 (native-inputs (list r-knitr))
1355 (home-page "https://jacolienvanrij.com/tutorials.html")
1356 (synopsis "Various functions to facilitate visualization of data and analysis")
1358 "When analyzing data, plots are a helpful tool for visualizing data and
1359 interpreting statistical models. This package provides a set of simple tools
1360 for building plots incrementally, starting with an empty plot region, and
1361 adding bars, data points, regression lines, error bars, gradient legends,
1362 density distributions in the margins, and even pictures. The package builds
1363 further on R graphics by simply combining functions and settings in order to
1364 reduce the amount of code to produce for the user. As a result, the package
1365 does not use formula input or special syntax, but can be used in combination
1366 with default R plot functions.")
1367 (license license:gpl2+)))
1369 (define-public r-polychrome
1371 (name "r-polychrome")
1376 (uri (cran-uri "Polychrome" version))
1378 (base32 "0hyi02m2jpdhk1ky6ihz6dv5pwqwjwk4csjim2qr8ywx8midmrvg"))))
1379 (properties `((upstream-name . "Polychrome")))
1380 (build-system r-build-system)
1382 (list r-colorspace r-scatterplot3d))
1385 (home-page "http://oompa.r-forge.r-project.org/")
1386 (synopsis "Qualitative palettes with many colors")
1388 "This package provides tools for creating, viewing, and assessing
1389 qualitative palettes with many (20-30 or more) colors. See Coombes and
1390 colleagues (2019) @url{https://doi:10.18637/jss.v090.c01}.")
1391 (license license:asl2.0)))
1393 (define-public r-ecp
1399 (uri (cran-uri "ecp" version))
1402 "0n602jssl6rf596nwm6hbl7s9vdlqi20w8mrhxicj373mw5v22m8"))))
1403 (build-system r-build-system)
1406 (home-page "https://cran.r-project.org/web/packages/ecp/")
1407 (synopsis "Multiple change-point analysis of multivariate data")
1409 "This package implements various procedures for finding multiple
1410 change-points. Two methods make use of dynamic programming and pruning, with
1411 no distributional assumptions other than the existence of certain absolute
1412 moments in one method. Hierarchical and exact search methods are included.
1413 All methods return the set of estimated change-points as well as other summary
1415 (license license:gpl2+)))
1417 (define-public r-ellipsis
1424 (uri (cran-uri "ellipsis" version))
1427 "0n0mm9jngklv7j9wa64jdji035z0smmnsp2dfwcz9isrxgjnc0m9"))))
1428 (build-system r-build-system)
1431 (home-page "https://github.com/hadley/ellipsis")
1432 (synopsis "Tools for working with additional arguments")
1434 "In S3 generics, it's useful to take @code{...} so that methods can have
1435 additional arguments. But this flexibility comes at a cost: misspelled
1436 arguments will be silently ignored. The @code{ellipsis} package is an
1437 experiment that allows a generic to warn if any arguments passed in @code{...}
1439 (license license:gpl3)))
1448 (uri (cran-uri "GA" version))
1450 (base32 "135z03lnbj44jihnk6dii5a684jmc666ncpdwyyi910vl4sccib2"))))
1451 (properties `((upstream-name . "GA")))
1452 (build-system r-build-system)
1462 (home-page "https://luca-scr.github.io/GA/")
1463 (synopsis "Genetic algorithms for stochastic optimisation")
1465 "Flexible general-purpose toolbox implementing genetic algorithms (GAs)
1466 for stochastic optimisation. Binary, real-valued, and permutation
1467 representations are available to optimize a fitness function, i.e., a function
1468 provided by users depending on their objective function. Several genetic
1469 operators are available and can be combined to explore the best settings for
1470 the current task. Furthermore, users can define new genetic operators and
1471 easily evaluate their performances. Local search using general-purpose
1472 optimisation algorithms can be applied stochastically to exploit interesting
1473 regions. GAs can be run sequentially or in parallel, using an explicit
1474 master-slave parallelisation or a coarse-grain islands approach.")
1475 (license license:gpl2+)))
1477 (define-public r-grr
1484 (uri (cran-uri "grr" version))
1487 "0arbcgrvhkwb5xk4nry1ffg2qj0v8ivhjghdr505ib4357g0c9i9"))))
1488 (build-system r-build-system)
1489 (home-page "https://cran.r-project.org/web/packages/grr")
1490 (synopsis "Alternative implementations of base R functions")
1492 "This package provides alternative implementations of some base R
1493 functions, including @code{sort}, @code{order}, and @code{match}. The
1494 functions are simplified but can be faster or have other advantages.")
1495 (license license:gpl3)))
1497 (define-public r-matrix-utils
1499 (name "r-matrix-utils")
1504 (uri (cran-uri "Matrix.utils" version))
1507 "0a5fq1scykqk0kc9j051j6fix6j2dqwz5wbgb0amaxsiywz9vigb"))))
1508 (properties `((upstream-name . "Matrix.utils")))
1509 (build-system r-build-system)
1511 (list r-grr r-matrix))
1512 (home-page "https://github.com/cvarrichio/Matrix.utils")
1514 "Data.frame-Like Operations on Sparse and Dense Matrix Objects")
1516 "This package implements data manipulation methods such as @code{cast},
1517 @code{aggregate}, and @code{merge}/@code{join} for Matrix and Matrix-like
1519 (license license:gpl3)))
1521 (define-public r-mboost
1527 (uri (cran-uri "mboost" version))
1530 "01ln0vxbbx1fq77q17sx61si82lhfibbchsnf2yw9032cn8wnhh2"))))
1531 (build-system r-build-system)
1540 (home-page "https://github.com/boost-R/mboost")
1541 (synopsis "Model-based boosting")
1543 "This package provides a functional gradient descent algorithm (boosting)
1544 for optimizing general risk functions utilizing component-wise (penalised)
1545 least squares estimates or regression trees as base-learners for fitting
1546 generalized linear, additive and interaction models to potentially
1547 high-dimensional data.")
1548 (license license:gpl2)))
1550 (define-public r-shadowtext
1552 (name "r-shadowtext")
1556 (uri (cran-uri "shadowtext" version))
1559 "0zdfidrcnmxmfhngv86ppxrjmpmz9kl78l4yfah2lc5vgmrlwg15"))))
1560 (properties `((upstream-name . "shadowtext")))
1561 (build-system r-build-system)
1563 (list r-ggplot2 r-scales))
1566 (home-page "https://github.com/GuangchuangYu/shadowtext/")
1567 (synopsis "Shadow text grob and layer")
1568 (description "This package implements @code{shadowtextGrob()} for
1569 @code{grid} and @code{geom_shadowtext()} layer for @code{ggplot2}.
1570 These functions draw text grob with background shadow.")
1571 (license license:artistic2.0)))
1573 (define-public r-sys
1580 (uri (cran-uri "sys" version))
1583 "11q4zmx62w44p1j34frwmrsp23mc7l4n354i0zyziw92yax8zy0p"))))
1584 (build-system r-build-system)
1585 (home-page "https://github.com/jeroen/sys")
1586 (synopsis "Powerful and reliable tools for running system commands in R")
1588 "This package provides drop-in replacements for the base @code{system2()}
1589 function with fine control and consistent behavior across platforms. It
1590 supports clean interruption, timeout, background tasks, and streaming STDIN /
1591 STDOUT / STDERR over binary or text connections. The package also provides
1592 functions for evaluating expressions inside a temporary fork. Such
1593 evaluations have no side effects on the main R process, and support reliable
1594 interrupts and timeouts. This provides the basis for a sandboxing
1596 (license license:expat)))
1598 (define-public r-ashr
1604 (uri (cran-uri "ashr" version))
1607 "177xs3apnc6yy6737qqv4z8snf0hkpbghab63hrplbyb9wfssfga"))))
1608 (properties `((upstream-name . "ashr")))
1609 (build-system r-build-system)
1620 (home-page "https://github.com/stephens999/ashr")
1621 (synopsis "Methods for adaptive shrinkage, using empirical bayes")
1622 (description "This package implements an empirical Bayes approach for
1623 large-scale hypothesis testing and false discovery rate estimation.")
1624 (license license:gpl3+)))
1626 (define-public r-askpass
1633 (uri (cran-uri "askpass" version))
1636 "07q0ik8jzk44vpwh48rr3fnpd7dzsdhjjsl4l850rffv3dyq4h6v"))))
1637 (build-system r-build-system)
1638 (propagated-inputs (list r-sys))
1639 (home-page "https://github.com/jeroen/askpass")
1640 (synopsis "Safe password entry for R")
1642 "This package provides cross-platform utilities for prompting the user
1643 for credentials or a passphrase, for example to authenticate with a server or
1644 read a protected key.")
1645 (license license:expat)))
1647 (define-public r-astsa
1654 (uri (cran-uri "astsa" version))
1656 (base32 "0mllsq0xdqkviyvs77lq565r1vznsj1qp9cnlj5p48k9v76d7arp"))))
1657 (properties `((upstream-name . "astsa")))
1658 (build-system r-build-system)
1659 (home-page "https://github.com/nickpoison/astsa/")
1660 (synopsis "Applied statistical time series analysis")
1662 "This package provides data sets and scripts to accompany Time Series
1663 Analysis and Its Applications: With R Examples (4th ed), by R.H. Shumway and
1664 D.S. Stoffer. Springer Texts in Statistics, 2017,
1665 @url{https://doi.org/10.1007/978-3-319-52452-8}, and Time Series: A Data
1666 Analysis Approach Using R. Chapman-Hall, 2019,
1667 @url{https://doi.org/10.1201/9780429273285}.")
1668 (license license:gpl3)))
1670 (define-public r-vegan
1677 (uri (cran-uri "vegan" version))
1680 "0nf0ny6jzfy135xiygzzkr0y55y8g27hrbk8c869plarr48d2xxb"))))
1681 (build-system r-build-system)
1683 (list r-knitr ; needed for vignettes
1686 (list r-cluster r-lattice r-mass r-mgcv r-permute))
1687 (home-page "https://cran.r-project.org/web/packages/vegan")
1688 (synopsis "Functions for community ecology")
1690 "The vegan package provides tools for descriptive community ecology. It
1691 has most basic functions of diversity analysis, community ordination and
1692 dissimilarity analysis. Most of its multivariate tools can be used for other
1693 data types as well.")
1694 (license license:gpl2+)))
1696 (define-public r-tidyverse
1698 (name "r-tidyverse")
1703 (uri (cran-uri "tidyverse" version))
1706 "0ck6xmsw5p168jmw2fqv79fzfnw5jckfra7mfii261j6kl89bkw3"))))
1707 (build-system r-build-system)
1740 (home-page "https://tidyverse.tidyverse.org")
1741 (synopsis "Install and load packages from the \"Tidyverse\"")
1743 "The @code{tidyverse} is a set of packages that work in harmony because
1744 they share common data representations and API design. This package is
1745 designed to make it easy to install and load multiple tidyverse packages in a
1747 (license license:gpl3)))
1749 (define-public r-rvest
1756 (uri (cran-uri "rvest" version))
1758 (base32 "1905vxgnj3q09l1wf6rwxpbpydznp06nbkrclnc05j2415z4gfw9"))))
1759 (build-system r-build-system)
1770 (home-page "https://github.com/hadley/rvest")
1771 (synopsis "Simple web scraping for R")
1773 "@code{r-rvest} helps you scrape information from web pages. It is
1774 designed to work with @code{magrittr} to make it easy to express common web
1775 scraping tasks, inspired by libraries like @code{BeautifulSoup}.")
1776 (license license:gpl3)))
1778 (define-public r-selectr
1785 (uri (cran-uri "selectr" version))
1787 (base32 "09y1n3iy297g49xlpl7xrjpwgnm57pskx5991lyfcpizbz8ax22m"))))
1788 (build-system r-build-system)
1790 (list r-stringr r-r6))
1791 (home-page "https://sjp.co.nz/projects/selectr/")
1792 (synopsis "Translate CSS selectors to XPath expressions")
1794 "@code{r-selectr} translates a CSS3 selector into an equivalent XPath
1795 expression. This allows you to use CSS selectors when working with the XML
1796 package as it can only evaluate XPath expressions. Also provided are
1797 convenience functions useful for using CSS selectors on XML nodes. This
1798 package is a port of the Python package @code{cssselect}.")
1799 (license license:bsd-3)))
1801 (define-public r-reprex
1808 (uri (cran-uri "reprex" version))
1811 "09k4rasp7mz6n796dsklcbc5l7prljiznrm7fra16qybr9kqcv8f"))))
1812 (build-system r-build-system)
1826 (home-page "https://github.com/tidyverse/reprex")
1827 (synopsis "Prepare reproducible R code examples for sharing")
1829 "This package provides a convenience wrapper that uses the
1830 @code{rmarkdown} package to render small snippets of code to target formats
1831 that include both code and output. The goal is to encourage the sharing of
1832 small, reproducible, and runnable examples on code-oriented websites or email.
1833 @code{reprex} also extracts clean, runnable R code from various common formats,
1834 such as copy/paste from an R session.")
1835 (license license:expat)))
1837 (define-public r-reordercluster
1839 (name "r-reordercluster")
1843 (uri (cran-uri "ReorderCluster" version))
1846 "0ss750frzvj0bm1w7zblmcsjpszhnbffwlkaw31sm003lbx9hy58"))))
1847 (build-system r-build-system)
1849 (list r-gplots r-rcpp))
1850 (home-page "https://cran.r-project.org/web/packages/ReorderCluster")
1851 (synopsis "Reordering the dendrogram according to the class labels")
1852 (description "This package provides tools for performing the leaf reordering
1853 for the dendrogram that preserves the hierarchical clustering result and at the
1854 same time tries to group instances from the same class together.")
1855 (license license:gpl3+)))
1857 (define-public r-callr
1864 (uri (cran-uri "callr" version))
1867 "02inaf3c7b0hikii7p2zwaphrq5myv4in92d9jxd1ilmhla5awnn"))))
1868 (build-system r-build-system)
1870 (list r-r6 r-processx))
1871 (home-page "https://github.com/r-lib/callr#readme")
1872 (synopsis "Call R from R")
1874 "It is sometimes useful to perform a computation in a separate R process,
1875 without affecting the current R process at all. This package does exactly
1877 (license license:expat)))
1879 (define-public r-depmixs4
1885 (uri (cran-uri "depmixS4" version))
1888 "1pacvhw5m4fsk3ysbal50fdqbvlaz8ywyqp6bn1wh42wipqbb2i8"))))
1890 (list r-nnet r-nlme r-mass r-rsolnp))
1891 (build-system r-build-system)
1892 (home-page "https://cran.r-project.org/web/packages/depmixS4/")
1893 (synopsis "Dependent Mixture Models")
1894 (description "This package fits latent (hidden) Markov models on mixed
1895 categorical and continuous (time series) data, otherwise known as dependent
1897 (license license:gpl2+)))
1899 (define-public r-readxl
1906 (uri (cran-uri "readxl" version))
1909 "1xwi4k5si48hwkgfc59icfmp9dzlvfri59k5fsgn96zp9713k4mb"))))
1910 (build-system r-build-system)
1912 (list r-cellranger r-cpp11 r-progress r-tibble))
1915 (home-page "https://readxl.tidyverse.org")
1916 (synopsis "Read Excel files")
1918 "This package lets you import Excel files into R. It supports
1919 @file{.xls} via the embedded @code{libxls} C library and @file{.xlsx} via
1920 the embedded @code{RapidXML} C++ library.")
1921 ;; XXX: This package bundles a copy of 'libxsl' which is BSD-2 and
1922 ;; 'rapidxml' which is Boost.
1923 (license (list license:gpl3 license:bsd-2 license:boost1.0))))
1925 (define-public r-model4you
1927 (name "r-model4you")
1931 (uri (cran-uri "model4you" version))
1934 "0pni9v3nradvy8sp2m07903vc7z610xrh426lf19dxss12kgrfi8"))))
1935 (build-system r-build-system)
1943 (home-page "https://cran.r-project.org/web/packages/model4you/")
1944 (synopsis "Stratified and personalised models based on trees and forests")
1946 "This package provides procedures for model-based trees for subgroup
1947 analyses in clinical trials and model-based forests for the estimation and
1948 prediction of personalised treatment effects. Currently partitioning of linear
1949 models, @code{lm()}, generalised linear models, @code{glm()}, and
1950 Weibull models, @code{survreg()}, are supported. Advanced plotting functionality is
1951 supported for the trees and a test for parameter heterogeneity is provided for
1952 the personalised models.")
1953 (license license:gpl2+)))
1955 (define-public r-modelr
1962 (uri (cran-uri "modelr" version))
1965 "1i31nff7bqibk6r4hhd4j1vzwbyaf8493v0bjaagn36njmysfnw2"))))
1966 (build-system r-build-system)
1976 (home-page "https://github.com/tidyverse/modelr")
1977 (synopsis "Helper functions for modelling in pipelines")
1979 "Functions for modelling that help you seamlessly integrate modelling
1980 into a pipeline of data manipulation and visualisation.")
1981 (license license:gpl3)))
1983 (define-public r-hmm
1989 (uri (cran-uri "HMM" version))
1992 "03b548bnwqpnd7zypb4gvy9chyi5li2hp99a9vrh4qszxg2ihas7"))))
1993 (properties `((upstream-name . "HMM")))
1994 (build-system r-build-system)
1995 (home-page "https://cran.r-project.org/web/packages/HMM/")
1996 (synopsis "Hidden Markov Models")
1997 (description "This package provides an easy to use library to setup, apply
1998 and make inference with discrete time and discrete space hidden Markov
2000 (license license:gpl2+)))
2002 (define-public r-hiddenmarkov
2004 (name "r-hiddenmarkov")
2008 (uri (cran-uri "HiddenMarkov" version))
2011 "05dm3nl0ffsz2ziw3bz5bivyxk7r5bxs8xhky3hz660qaqzd51ki"))))
2012 (build-system r-build-system)
2015 (home-page "https://cran.r-project.org/web/packages/HiddenMarkov/")
2016 (synopsis "Hidden markov models for R")
2017 (description "This package contains functions for the analysis of Discrete
2018 Time Hidden Markov Models, Markov Modulated GLMs and the Markov Modulated
2019 Poisson Process. It includes functions for simulation, parameter estimation,
2020 and the Viterbi algorithm. The algorithms are based of those of Walter
2022 (license license:gpl2+)))
2024 (define-public r-httpuv
2030 (uri (cran-uri "httpuv" version))
2033 "0mlilxh2mlrsbbrncla2rg02crr8nnajv649d8whx7ayr8lkdxpm"))
2034 ;; Unvendor bundled libraries. As of 1.5.4 the vendored libuv
2035 ;; only contains fixes for building on Solaris.
2036 (patches (search-patches "r-httpuv-1.5.5-unvendor-libuv.patch"))
2037 (modules '((guix build utils)))
2038 ;; Cannot unbundle http-parser, because it contains local
2041 '(delete-file-recursively "src/libuv"))))
2042 (build-system r-build-system)
2045 (modify-phases %standard-phases
2046 (add-after 'unpack 'unbundle-libuv
2047 (lambda* (#:key outputs #:allow-other-keys)
2048 (substitute* (find-files "src" "\\.cpp$|\\.h$")
2049 (("\"libuv/include/uv\\.h\"")
2051 ;; Fix https://github.com/rstudio/httpuv/issues/282
2052 (substitute* "src/http.cpp"
2053 (("uv_pipe_init\\(pLoop, &pSocket->handle\\.pipe, true\\);")
2054 "uv_pipe_init(pLoop, &pSocket->handle.pipe, 0);")))))))
2058 (list r-later r-promises r-r6 r-rcpp))
2059 (home-page "https://github.com/rstudio/httpuv")
2060 (synopsis "HTTP and WebSocket server library for R")
2062 "The httpuv package provides low-level socket and protocol support for
2063 handling HTTP and WebSocket requests directly from within R. It is primarily
2064 intended as a building block for other packages, rather than making it
2065 particularly easy to create complete web applications using httpuv alone.")
2066 ;; This package includes third-party code that was originally released
2067 ;; under various non-copyleft licenses. Full licensing information can be
2068 ;; obtained here: https://github.com/rstudio/httpuv/blob/master/LICENSE
2069 (license license:gpl3+)))
2071 (define-public r-jsonlite
2077 (uri (cran-uri "jsonlite" version))
2080 "0k6dal7gmm19jl5sjsry5gwbnhsbrnn00q3iixig8k6bxgpr463v"))))
2081 (build-system r-build-system)
2084 (home-page "https://arxiv.org/abs/1403.2805")
2085 (synopsis "Robust, high performance JSON parser and generator for R")
2087 "The jsonlite package provides a fast JSON parser and generator optimized
2088 for statistical data and the web. It offers flexible, robust, high
2089 performance tools for working with JSON in R and is particularly powerful for
2090 building pipelines and interacting with a web API. In addition to converting
2091 JSON data from/to R objects, jsonlite contains functions to stream, validate,
2092 and prettify JSON data. The unit tests included with the package verify that
2093 all edge cases are encoded and decoded consistently for use with dynamic data
2094 in systems and applications.")
2095 (license license:expat)))
2097 (define-public r-servr
2103 (uri (cran-uri "servr" version))
2106 "11x0857m3xzdbzr4z0vx4fcdk36arfagyf2qgamvprich0qisknr"))))
2107 (build-system r-build-system)
2109 (list r-httpuv r-jsonlite r-mime r-xfun))
2110 (home-page "https://github.com/yihui/servr")
2111 (synopsis "Simple HTTP server to serve static files or dynamic documents")
2113 "Servr provides an HTTP server in R to serve static files, or dynamic
2114 documents that can be converted to HTML files (e.g., R Markdown) under a given
2116 (license license:expat)))
2118 (define-public r-howmany
2124 (uri (cran-uri "howmany" version))
2127 "045ck8qahfg2swbgyf7dpl32ryq1m4sbalhr7m5qdgpm62vz8h7f"))))
2128 (build-system r-build-system)
2129 (home-page "https://cran.r-project.org/web/packages/howmany/")
2130 (synopsis "Lower bound for the number of correct rejections")
2131 (description "When testing multiple hypotheses simultaneously, this package
2132 provides functionality to calculate a lower bound for the number of correct
2133 rejections (as a function of the number of rejected hypotheses), which holds
2134 simultaneously -with high probability- for all possible number of rejections.
2135 As a special case, a lower bound for the total number of false null hypotheses
2136 can be inferred. Dependent test statistics can be handled for multiple tests
2137 of associations. For independent test statistics, it is sufficient to provide
2138 a list of p-values.")
2139 (license license:gpl2+)))
2141 (define-public r-htmltools
2143 (name "r-htmltools")
2147 (uri (cran-uri "htmltools" version))
2150 "1yv74ydyqm28gfhimmr7825sj1iaawpwsnzq05c2ma756q2dbivx"))))
2151 (build-system r-build-system)
2153 (list r-base64enc r-digest r-fastmap r-rlang))
2154 (home-page "https://cran.r-project.org/web/packages/htmltools")
2155 (synopsis "R tools for HTML")
2157 "This package provides tools for HTML generation and output in R.")
2158 (license license:expat)))
2160 (define-public r-htmlwidgets
2162 (name "r-htmlwidgets")
2166 (uri (cran-uri "htmlwidgets" version))
2169 "1hgz8sx8xrvfcdwa4q15k942w4qsqg8lyxbbf7qyfzbi807wcgqs"))))
2170 (build-system r-build-system)
2172 (list r-htmltools r-jsonlite r-yaml))
2175 (home-page "https://github.com/ramnathv/htmlwidgets")
2176 (synopsis "HTML Widgets for R")
2178 "HTML widgets is a framework for creating HTML widgets that render in
2179 various contexts including the R console, R Markdown documents, and Shiny web
2181 (license license:expat)))
2183 (define-public r-htmltable
2185 (name "r-htmltable")
2190 (uri (cran-uri "htmlTable" version))
2192 (base32 "17csp0ry4iy4m5xy271dn5wd81v4p03l79swmvlfxkvpdmhvb8jc"))))
2193 (properties `((upstream-name . "htmlTable")))
2194 (build-system r-build-system)
2205 (home-page "http://gforge.se/packages/")
2206 (synopsis "Advanced tables for Markdown/HTML")
2208 "This package provides functions to build tables with advanced layout
2209 elements such as row spanners, column spanners, table spanners, zebra
2210 striping, and more. While allowing advanced layout, the underlying
2211 CSS-structure is simple in order to maximize compatibility with word
2212 processors such as LibreOffice. The package also contains a few text
2213 formatting functions that help outputting text compatible with HTML or
2215 (license license:gpl3+)))
2217 (define-public r-curl
2223 (uri (cran-uri "curl" version))
2226 "0s55022hy8shjm1pzax1dqzrg20bv4nvlwnjnddk3dp89g5zmcch"))))
2227 (build-system r-build-system)
2230 (modify-phases %standard-phases
2231 ;; The environment variable CURL_CA_BUNDLE is only respected when
2232 ;; running Windows, so we disable the platform checks.
2233 ;; This can be removed once the libcurl has been patched.
2234 (add-after 'unpack 'allow-CURL_CA_BUNDLE
2236 (substitute* "R/onload.R"
2237 (("if \\(!grepl\\(\"mingw\".*")
2239 (substitute* "src/handle.c"
2240 (("/\\* Only set" m)
2242 const char *_ca_bundle = getenv(\"CURL_CA_BUNDLE\");
2243 if(_ca_bundle != NULL) { curl_easy_setopt(handle, CURLOPT_CAINFO, _ca_bundle); }
2248 (list pkg-config r-knitr))
2249 (home-page "https://github.com/jeroenooms/curl")
2250 (synopsis "HTTP client for R")
2252 "The @code{curl()} and @code{curl_download()} functions provide highly
2253 configurable drop-in replacements for base @code{url()} and
2254 @code{download.file()} with better performance, support for encryption, gzip
2255 compression, authentication, and other @code{libcurl} goodies. The core of
2256 the package implements a framework for performing fully customized requests
2257 where data can be processed either in memory, on disk, or streaming via the
2258 callback or connection interfaces.")
2259 (license license:expat)))
2261 (define-public r-hwriter
2268 (uri (cran-uri "hwriter" version))
2271 "1wxnv8h9cs65m3z01dpnnkgn2cpwfsck70g1jz9nbkr7mdaa4bzd"))))
2272 (build-system r-build-system)
2273 (home-page "https://cran.r-project.org/web/packages/hwriter")
2274 (synopsis "Output R objects in HTML format")
2276 "This package provides easy-to-use and versatile functions to output R
2277 objects in HTML format.")
2278 (license license:lgpl2.1+)))
2280 (define-public r-rjson
2287 (uri (cran-uri "rjson" version))
2290 "1qm27r1w677zg31gsiln60hcciszbymkw78cnaq7s36cbk9mcawq"))))
2291 (build-system r-build-system)
2292 (home-page "https://cran.r-project.org/web/packages/rjson")
2293 (synopsis "JSON library for R")
2295 "This package provides functions to convert R objects into JSON objects
2297 (license license:gpl2+)))
2299 (define-public r-fastmap
2306 (uri (cran-uri "fastmap" version))
2309 "0aw29hnq3ppn7bsnwg9d9sp84k1cvq30lrmfzqn315n0nhkfa4wi"))))
2310 (properties `((upstream-name . "fastmap")))
2311 (build-system r-build-system)
2312 (home-page "https://r-lib.github.io/fastmap/")
2313 (synopsis "Fast implementation of a key-value store")
2315 "This package provides a fast implementation of a key-value store.
2316 Environments are commonly used as key-value stores, but every time a new key
2317 is used, it is added to R's global symbol table, causing a small amount of
2318 memory leakage. This can be problematic in cases where many different keys
2319 are used. Fastmap avoids this memory leak issue by implementing the map using
2320 data structures in C++.")
2321 (license license:expat)))
2323 (define-public r-fastghquad
2325 (name "r-fastghquad")
2330 (uri (cran-uri "fastGHQuad" version))
2333 "1zj7nsbnx4g253m3dpz9vi3zk3jxwrixwjw1ks6n4shpb4dlkp2w"))))
2334 (properties `((upstream-name . "fastGHQuad")))
2335 (build-system r-build-system)
2338 (home-page "https://github.com/awblocker/fastGHQuad")
2339 (synopsis "Fast Rcpp implementation of Gauss-Hermite Quadrature")
2341 "This package implements numerically-stable Gauss-Hermite quadrature
2342 rules and utility functions for adaptive GH quadrature.")
2343 (license license:expat)))
2345 (define-public r-rstpm2
2352 (uri (cran-uri "rstpm2" version))
2355 "17mhzfxh761vl64ar6pynpj3k2jkhjgbacxsjhkrfkbmy3aiv0d1"))))
2356 (properties `((upstream-name . "rstpm2")))
2357 (build-system r-build-system)
2369 (home-page "https://github.com/mclements/rstpm2")
2370 (synopsis "Link-based survival models")
2372 "This package provides R implementations of @dfn{generalized survival
2373 models} (GSMs), smooth @dfn{accelerated failure time} (AFT) models and Markov
2374 multi-state models.")
2375 ;; One of these licenses
2376 (license (list license:gpl2 license:gpl3))))
2378 ;; This package includes minified JavaScript files. When upgrading please
2379 ;; check that there are no new minified JavaScript files.
2380 (define-public r-jquerylib
2382 (name "r-jquerylib")
2387 (uri (cran-uri "jquerylib" version))
2390 "04a40v4znpj98j7y6009d74a6g9dchj5rr3p08cgz9p3rlfw3g7h"))
2392 '(for-each delete-file
2393 '("inst/lib/1.12.4/jquery-1.12.4.min.js"
2394 "inst/lib/2.2.4/jquery-2.2.4.min.js"
2395 "inst/lib/3.6.0/jquery-3.6.0.min.js")))))
2396 (properties `((upstream-name . "jquerylib")))
2397 (build-system r-build-system)
2399 `(#:modules ((guix build utils)
2400 (guix build r-build-system)
2403 (modify-phases %standard-phases
2404 (add-after 'unpack 'process-javascript
2405 (lambda* (#:key inputs #:allow-other-keys)
2406 (with-directory-excursion "inst/lib/"
2410 `(("1.12.4/jquery-1.12.4.js"
2411 "1.12.4/jquery-1.12.4.min.js")
2412 ("2.2.4/jquery-2.2.4.js"
2413 "2.2.4/jquery-2.2.4.min.js")
2414 ("3.6.0/jquery-3.6.0.js"
2415 "3.6.0/jquery-3.6.0.min.js"))))
2416 (lambda (sources targets)
2417 (for-each (lambda (source target)
2418 (format #t "Processing ~a --> ~a~%"
2420 (invoke "esbuild" source "--minify"
2421 (string-append "--outfile=" target)))
2422 sources targets)))))))))
2427 (home-page "https://cran.r-project.org/package=jquerylib")
2428 (synopsis "Obtain jQuery as an HTML dependency object")
2430 "Obtain any major version of jQuery and use it in any webpage generated
2431 by htmltools (e.g. shiny, htmlwidgets, and rmarkdown). Most R users don't
2432 need to use this package directly, but other R packages (e.g. shiny,
2433 rmarkdown, etc.) depend on this package to avoid bundling redundant copies of
2435 (license license:expat)))
2437 (define-public r-sass
2444 (uri (cran-uri "sass" version))
2447 "1fq8wqnxmx10lg0dh4qzmxdkhd22fjh8vhassapxb1chsimwn3w5"))))
2448 (properties `((upstream-name . "sass")))
2449 (build-system r-build-system)
2451 (list r-fs r-htmltools r-r6 r-rappdirs r-rlang))
2452 (native-inputs (list r-knitr))
2453 (home-page "https://github.com/rstudio/sass")
2454 (synopsis "Syntactically Awesome Style Sheets (SASS)")
2456 "This package provides an SCSS compiler, powered by the libsass library.
2457 With this, R developers can use variables, inheritance, and functions to
2458 generate dynamic style sheets. The package uses the Sass CSS extension
2459 language, which is stable, powerful, and CSS compatible.")
2460 (license license:expat)))
2462 (define-public r-saver
2468 (uri (cran-uri "SAVER" version))
2471 "1s1kw8idkaj7j90fw4qn9k0wd4vz0sblsk06ry6lm4afcar0p158"))))
2472 (properties `((upstream-name . "SAVER")))
2473 (build-system r-build-system)
2480 (native-inputs (list r-knitr))
2481 (home-page "https://github.com/mohuangx/SAVER")
2483 "Recovery of gene expression profile in noisy and sparse scRNA-seq data")
2485 "This package is an implementation of a regularized regression prediction
2486 and empirical Bayes method to recover the true gene expression profile in noisy
2487 and sparse single-cell RNA-seq data. In @dfn{single-cell RNA sequencing}
2488 (scRNA-seq) studies, only a small fraction of the transcripts present in each
2489 cell are sequenced. This leads to unreliable quantification of genes with low
2490 or moderate expression, which hinders downstream analysis. This package
2491 @dfn{single-cell analysis via expression recovery} (SAVER) implements an
2492 expression recovery method for unique molecule index (UMI)-based scRNA-seq
2493 data that borrows information across genes and cells to provide accurate
2494 expression estimates for all genes.")
2495 (license license:gpl2)))
2497 ;; This package includes minified JavaScript files. When upgrading please
2498 ;; check that there are no new minified JavaScript files.
2499 (define-public r-bslib
2506 (uri (cran-uri "bslib" version))
2509 "0jcqklry1nkibz0sydsz5xdsnb4wnrrhvmyr9ji3k45bbipbap2z"))
2511 '(for-each delete-file
2512 '("inst/lib/bs-a11y-p/plugins/js/bootstrap-accessibility.min.js"
2513 "inst/lib/bs-colorpicker/js/bootstrap-colorpicker.min.js"
2514 "inst/lib/bs3/assets/javascripts/bootstrap.min.js"
2515 "inst/lib/bs4/dist/js/bootstrap.bundle.min.js"
2516 "inst/lib/bs5/dist/js/bootstrap.bundle.min.js")))))
2517 (properties `((upstream-name . "bslib")))
2518 (build-system r-build-system)
2520 `(#:modules ((guix build utils)
2521 (guix build r-build-system)
2524 (modify-phases %standard-phases
2525 (add-after 'unpack 'process-javascript
2526 (lambda* (#:key inputs #:allow-other-keys)
2527 (with-directory-excursion "inst/lib/"
2531 `(("bs-a11y-p/plugins/js/bootstrap-accessibility.js"
2532 "bs-a11y-p/plugins/js/bootstrap-accessibility.min.js")
2533 ("bs-colorpicker/js/bootstrap-colorpicker.js"
2534 "bs-colorpicker/js/bootstrap-colorpicker.min.js")
2535 ("bs3/assets/javascripts/bootstrap.js"
2536 "bs3/assets/javascripts/bootstrap.min.js")
2537 (,(assoc-ref inputs "js-bootstrap4-bundle")
2538 "bs4/dist/js/bootstrap.bundle.min.js")
2539 (,(assoc-ref inputs "js-bootstrap5-bundle")
2540 "bs5/dist/js/bootstrap.bundle.min.js"))))
2541 (lambda (sources targets)
2542 (for-each (lambda (source target)
2543 (format #t "Processing ~a --> ~a~%"
2545 (invoke "esbuild" source "--minify"
2546 (string-append "--outfile=" target)))
2547 sources targets)))))))))
2549 (list r-htmltools r-jquerylib r-jsonlite r-rlang r-sass))
2551 `(("esbuild" ,esbuild)
2552 ("js-bootstrap4-bundle"
2555 (uri "https://raw.githubusercontent.com/twbs/bootstrap/v4.6.0/dist/js/bootstrap.bundle.js")
2558 "04abvgp923w36qfqkkl2syim3bl119nwxbgials90z1jyb8jgss1"))))
2559 ("js-bootstrap5-bundle"
2562 (uri "https://raw.githubusercontent.com/twbs/bootstrap/v5.0.2/dist/js/bootstrap.bundle.js")
2565 "06vin94nqw1vzs4zrqcms8z9js9fckbj8gwyx07awm8jkjhnqfhl"))))))
2566 (home-page "https://rstudio.github.io/bslib/")
2567 (synopsis "Custom Bootstrap Sass themes for shiny and rmarkdown")
2569 "This package simplifies custom CSS styling of both shiny and rmarkdown
2570 via Bootstrap Sass. It supports both Bootstrap 3 and 4 as well as their
2571 various Bootswatch themes. An interactive widget is also provided for
2572 previewing themes in real time.")
2573 (license license:expat)))
2575 ;; This package includes minified JavaScript files. When upgrading please
2576 ;; check that there are no new minified JavaScript files.
2577 (define-public r-shiny
2585 (url "https://github.com/rstudio/shiny")
2586 (commit (string-append "v" version))))
2587 (file-name (git-file-name name version))
2590 "0wvc6jlgs41p05wbk8gahnl7sfnc4hpliyh9dbi5w52ngsg6wcr7"))
2592 '(for-each delete-file
2593 '("inst/www/shared/bootstrap/js/bootstrap.min.js"
2594 "inst/www/shared/bootstrap/accessibility/js/bootstrap-accessibility.min.js" ; TODO
2595 "inst/www/shared/datatables/js/jquery.dataTables.min.js"
2596 "inst/www/shared/datepicker/js/bootstrap-datepicker.min.js"
2597 "inst/www/shared/highlight/highlight.pack.js"
2598 "inst/www/shared/ionrangeslider/js/ion.rangeSlider.min.js"
2599 "inst/www/shared/jquery.min.js"
2600 "inst/www/shared/jqueryui/jquery-ui.min.js"
2601 "inst/www/shared/legacy/jquery.min.js"
2602 "inst/www/shared/selectize/accessibility/js/selectize-plugin-a11y.min.js"
2603 "inst/www/shared/selectize/js/selectize.min.js"
2604 "inst/www/shared/shiny.min.js"
2605 "inst/www/shared/showdown/compressed/showdown.js"
2606 "inst/www/shared/strftime/strftime-min.js")))))
2607 (build-system r-build-system)
2609 `(#:modules ((guix build r-build-system)
2610 (guix build minify-build-system)
2613 #:imported-modules (,@%r-build-system-modules
2614 (guix build minify-build-system))
2616 (modify-phases (@ (guix build r-build-system) %standard-phases)
2617 (add-after 'unpack 'replace-bundled-minified-JavaScript
2618 (lambda* (#:key inputs #:allow-other-keys)
2619 (let ((replace-file (lambda (old new)
2620 (format #t "replacing ~a with ~a\n" old new)
2621 (symlink new old))))
2622 ;; NOTE: Files in ./inst/www/shared/datepicker/js/locales/
2623 ;; contain just data. They are not minified code, so we don't
2625 (with-directory-excursion "inst/www/shared"
2626 (replace-file "strftime/strftime-min.js"
2627 (search-input-file inputs
2628 "/share/javascript/strftime.min.js"))
2629 (replace-file "highlight/highlight.pack.js"
2630 (search-input-file inputs
2631 "/share/javascript/highlight.min.js"))
2632 (replace-file "datatables/js/jquery.dataTables.min.js"
2633 (search-input-file inputs
2634 "/share/javascript/jquery.dataTables.min.js"))
2635 (replace-file "selectize/js/selectize.min.js"
2636 (search-input-file inputs
2637 "/share/javascript/selectize.min.js"))
2638 (for-each (match-lambda
2640 (minify source #:target target)))
2641 `(("jqueryui/jquery-ui.js" .
2642 "jqueryui/jquery-ui.min.js")
2643 ("datepicker/js/bootstrap-datepicker.js" .
2644 "datepicker/js/bootstrap-datepicker.min.js")
2645 ("ionrangeslider/js/ion.rangeSlider.js" .
2646 "ionrangeslider/js/ion.rangeSlider.min.js")
2647 ("bootstrap/js/bootstrap.js" .
2648 "bootstrap/js/bootstrap.min.js")
2649 (,(assoc-ref inputs "js-bootstrap-accessibility") .
2650 "bootstrap/accessibility/js/bootstrap-accessibility.min.js")
2655 ("legacy/jquery.js" .
2656 "legacy/jquery.min.js")
2657 ("selectize/accessibility/js/selectize-plugin-a11y.js" .
2658 "selectize/accessibility/js/selectize-plugin-a11y.min.js")
2659 ("showdown/src/showdown.js" .
2660 "showdown/compressed/showdown.js"))))))))))
2683 (list js-datatables js-selectize js-strftime js-highlight))
2685 `(("uglifyjs" ,node-uglify-js)
2686 ("gfortran" ,gfortran)
2687 ("js-bootstrap-accessibility"
2690 (uri "https://raw.githubusercontent.com/paypal/bootstrap-accessibility-plugin/\
2691 v1.0.7/_site/plugins/js/bootstrap-accessibility.js")
2694 "1489wyzwrpf86y7vhc13n4v3mszmsfybhd3f75jkpnbvyp5sncm8"))))))
2695 (home-page "https://shiny.rstudio.com")
2696 (synopsis "Easy interactive web applications with R")
2698 "Makes it incredibly easy to build interactive web applications
2699 with R. Automatic \"reactive\" binding between inputs and outputs and
2700 extensive prebuilt widgets make it possible to build beautiful,
2701 responsive, and powerful applications with minimal effort.")
2702 (license license:artistic2.0)))
2704 (define-public r-shinyhelper
2706 (name "r-shinyhelper")
2711 (uri (cran-uri "shinyhelper" version))
2713 (base32 "1c4hvf19j3yyh8r12nx85ldkxs89g98q74csnqs5ml5l79a65vgp"))))
2714 (properties `((upstream-name . "shinyhelper")))
2715 (build-system r-build-system)
2716 (propagated-inputs (list r-markdown r-shiny))
2717 (home-page "https://cran.r-project.org/package=shinyhelper")
2718 (synopsis "Easily add Markdown help files to shiny app elements")
2720 "This package creates a lightweight way to add markdown helpfiles to
2721 Shiny apps, using modal dialog boxes, with no need to observe each help button
2723 (license license:gpl3)))
2725 ;; This package includes minified JavaScript files. When upgrading please
2726 ;; check that there are no new minified JavaScript files.
2727 (define-public r-shinytree
2729 (name "r-shinytree")
2734 (uri (cran-uri "shinyTree" version))
2737 "0jfx2capckv7hf2yx3fn8i4rcmhi222ah91jnmhg497x8wgz31s3"))
2738 (modules '((guix build utils)))
2741 ;; Delete minified JavaScript
2742 (for-each delete-file
2743 '("inst/www/jsTree-3.3.7/libs/require.js"
2744 "inst/www/jsTree-3.3.7/libs/jquery.js"
2745 "inst/www/jsTree-3.3.7/jstree.min.js"))
2747 (properties `((upstream-name . "shinyTree")))
2748 (build-system r-build-system)
2750 `(#:modules ((guix build utils)
2751 (guix build r-build-system)
2755 (modify-phases %standard-phases
2756 (add-after 'unpack 'replace-minified-javascript
2757 (lambda* (#:key inputs #:allow-other-keys)
2758 (with-directory-excursion "inst/www/jsTree-3.3.7/"
2759 (symlink (search-input-file inputs
2760 "/share/javascript/require.min.js")
2765 `((,(assoc-ref inputs "js-jquery")
2769 (lambda (sources targets)
2770 (for-each (lambda (source target)
2771 (format #t "Processing ~a --> ~a~%"
2773 (let ((minified (open-pipe* OPEN_READ "uglifyjs" source)))
2774 (call-with-output-file target
2776 (dump-port minified port)))))
2780 (list r-htmlwidgets r-jsonlite r-promises r-shiny r-stringr))
2782 (list js-requirejs))
2784 `(("uglifyjs" ,node-uglify-js)
2788 (uri "https://code.jquery.com/jquery-3.3.1.js")
2791 "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq"))))))
2792 (home-page "https://cran.r-project.org/web/packages/shinyTree/")
2793 (synopsis "jsTree bindings for Shiny")
2795 "This package exposes R bindings to jsTree, a JavaScript library that
2796 supports interactive trees, to enable rich, editable trees in Shiny.")
2797 (license license:expat)))
2799 (define-public r-shinydashboard
2801 (name "r-shinydashboard")
2805 (uri (cran-uri "shinydashboard" version))
2808 "0hrqkwlpb8rnmp5j74p134g4c4cl16icmwc2ip6k1634fa2y8vm5"))))
2809 (build-system r-build-system)
2810 ;; The directory inst/AdminLTE/ contains a minified JavaScript file.
2811 ;; Regenerate it from the included sources.
2814 (modify-phases %standard-phases
2815 (add-after 'unpack 'generate-minified-javascript
2817 (with-directory-excursion "inst/AdminLTE"
2818 (let ((target "app.min.js")
2820 (format #t "Processing ~a --> ~a~%"
2822 (delete-file target)
2823 (invoke "esbuild" source "--minify"
2824 (string-append "--outfile=" target)))))))))
2826 (list r-htmltools r-promises r-shiny))
2829 (home-page "https://rstudio.github.io/shinydashboard/")
2830 (synopsis "Create dashboards with shiny")
2831 (description "This package provides an extension to the Shiny web
2832 application framework for R, making it easy to create attractive dashboards.")
2833 ;; This package includes software that was released under the Expat
2834 ;; license, but the whole package is released under GPL version 2 or
2836 (license license:gpl2+)))
2838 (define-public r-shinyfiles
2840 (name "r-shinyfiles")
2845 (uri (cran-uri "shinyFiles" version))
2847 (base32 "1l4a4v9ivxkj2vx6xw4z3pk7a8px23icppcgvgpybibq2j74pglg"))))
2848 (properties `((upstream-name . "shinyFiles")))
2849 (build-system r-build-system)
2851 (list r-fs r-htmltools r-jsonlite r-shiny r-tibble))
2852 (home-page "https://github.com/thomasp85/shinyFiles")
2853 (synopsis "Server-side file system viewer for Shiny")
2855 "This package provides functionality for client-side navigation of the
2856 server side file system in shiny apps. In case the app is running locally
2857 this gives the user direct access to the file system without the need to
2858 \"download\" files to a temporary location. Both file and folder selection as
2859 well as file saving is available.")
2860 (license license:gpl2+)))
2862 (define-public r-shinythemes
2864 (name "r-shinythemes")
2869 (uri (cran-uri "shinythemes" version))
2872 "0qr9bfxw8afxns44i2j4msignf6g5qb2nzpay2lpv343rrlqbmip"))))
2873 (properties `((upstream-name . "shinythemes")))
2874 (build-system r-build-system)
2875 (propagated-inputs (list r-shiny))
2876 (home-page "https://rstudio.github.io/shinythemes/")
2877 (synopsis "Themes for Shiny")
2879 "This package provides themes for use with Shiny. It includes several
2880 Bootstrap themes, which are packaged for use with Shiny applications.")
2881 ;; The package is released under version 3 of the GPL, but it includes
2882 ;; source files that are covered by the Expat license. It also includes
2883 ;; fonts under SIL or the ASL.
2884 (license (list license:gpl3 license:expat
2885 license:silofl1.1 license:asl2.0))))
2887 ;; The package sources include minified variants of d3.js and non-minified
2888 ;; source code of d3-jetpack.
2889 (define-public r-d3r
2896 (uri (cran-uri "d3r" version))
2899 "1qijkllfaaw0lb29j8mappm8jz9kg8gkihxq5wqhb4gabsazdwva"))))
2900 (build-system r-build-system)
2902 `(#:modules ((guix build utils)
2903 (guix build r-build-system)
2906 (modify-phases %standard-phases
2907 (add-after 'unpack 'process-javascript
2908 (lambda* (#:key inputs #:allow-other-keys)
2909 (with-directory-excursion "inst/www/d3/"
2913 `((,(assoc-ref inputs "d3.v3.js")
2914 "v3/dist/d3.min.js")
2915 (,(assoc-ref inputs "d3.v4.js")
2916 "v4/dist/d3.min.js")
2917 (,(assoc-ref inputs "d3.v5.js")
2918 "v5/dist/d3.min.js")
2919 (,(assoc-ref inputs "d3.v6.js")
2920 "v6/dist/d3.min.js")
2921 (,(assoc-ref inputs "d3.v7.js")
2922 "v7/dist/d3.min.js"))))
2923 (lambda (sources targets)
2924 (for-each (lambda (source target)
2925 (format #t "Processing ~a --> ~a~%"
2927 (delete-file target)
2928 (invoke "esbuild" source "--minify"
2929 (string-append "--outfile=" target)))
2930 sources targets)))))))))
2932 (list r-dplyr r-htmltools r-rlang r-tidyr))
2934 `(("esbuild" ,esbuild)
2938 (uri "https://d3js.org/d3.v3.js")
2941 "1arr7sr08vy7wh0nvip2mi7dpyjw4576vf3bm45rp4g5lc1k1x41"))))
2945 (uri "https://d3js.org/d3.v4.js")
2948 "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg"))))
2952 (uri "https://d3js.org/d3.v5.js")
2955 "0kxvx5pfagxn6nhavdwsdnzyd26g0z5dsfi1pi5dvcmb0c8ipcdn"))))
2959 (uri "https://d3js.org/d3.v6.js")
2962 "1x6432ca7p1pfxhz3airzw943fincn9izzxkclc1wmphcvv2n2p9"))))
2966 (uri "https://d3js.org/d3.v7.js")
2969 "0sd6vavxs8mx5xyb8xahlqghdiczqd284a7d5wravhqnrj0bw097"))))))
2970 (home-page "https://github.com/timelyportfolio/d3r")
2971 (synopsis "d3.js utilities for R")
2973 "This package provides a suite of functions to help ease the use of the
2974 d3.js visualization library in R. These helpers include
2975 @code{htmltools::htmlDependency} functions, hierarchy builders, and conversion
2976 tools for @code{partykit}, @code{igraph}, @code{table}, and @code{data.frame}
2977 R objects into the JSON format that the d3.js library expects.")
2978 (license license:bsd-3)))
2980 ;; We use the latest commit here because the last release was in 2016 while
2981 ;; the latest commit was in 2018.
2982 (define-public r-sankeyd3
2983 (let ((commit "fd50a74e29056e0d67d75b4d04de47afb2f932bc")
2987 (version (git-version "0.3.2" revision commit))
2992 (url "https://github.com/fbreitwieser/sankeyD3")
2994 (file-name (git-file-name name version))
2997 "0jrcnfax321pszbpjdifnkbrgbjr43bjzvlzv1p5a8wskksqwiyx"))))
2998 (build-system r-build-system)
3000 (list r-d3r r-htmlwidgets r-shiny r-magrittr))
3001 (home-page "https://github.com/fbreitwieser/sankeyD3")
3002 (synopsis "Sankey network graphs from R")
3004 "This package provides an R library to generate Sankey network graphs
3005 in R and Shiny via the D3 visualization library.")
3006 ;; The R code is licensed under GPLv3+. It includes the non-minified
3007 ;; JavaScript source code of d3-sankey, which is released under the
3008 ;; 3-clause BSD license.
3009 (license (list license:gpl3+ license:bsd-3)))))
3011 (define-public r-wesanderson
3013 (name "r-wesanderson")
3018 (uri (cran-uri "wesanderson" version))
3021 "09mr6p2jmqdjq27cz974w5hyxgn929zp9z3inhxqmmh1582fmdi2"))))
3022 (properties `((upstream-name . "wesanderson")))
3023 (build-system r-build-system)
3024 (home-page "https://github.com/karthik/wesanderson")
3025 (synopsis "Wes Anderson color palette generator")
3027 "This package provides color palettes that have been generated mostly
3028 from Wes Anderson movies.")
3029 (license license:expat)))
3031 (define-public r-gg-gap
3038 (uri (cran-uri "gg.gap" version))
3041 "0m66050ryn31xmsmmikjsssllasvjdmp9yjbwfdwfpwdv106zn9h"))))
3042 (properties `((upstream-name . "gg.gap")))
3043 (build-system r-build-system)
3045 (list r-cowplot r-ggplot2))
3046 (home-page "https://github.com/ChrisLou-bioinfo/gg.gap")
3047 (synopsis "Define segments on the y-axis for ggplot2")
3049 "The @code{gg.gap} function enables you to define segments for the y-axis
3050 in a ggplot2 plot.")
3051 (license license:gpl3)))
3053 (define-public r-mbess
3060 (uri (cran-uri "MBESS" version))
3062 (base32 "0qmyvjx2zn5hlzdbz8c94g8l4707swhn7sq9mxkdqiydmflzv0b5"))))
3063 (properties `((upstream-name . "MBESS")))
3064 (build-system r-build-system)
3066 (list r-boot r-lavaan r-mass r-mnormt r-nlme r-openmx r-sem r-semtools))
3067 (home-page "https://www3.nd.edu/~kkelley/site/MBESS.html")
3068 (synopsis "Methods for designing research studies")
3070 "This package implements methods that are useful in designing research
3071 studies and analyzing data, with particular emphasis on methods that are
3072 developed for or used within the behavioral, educational, and social
3073 sciences (broadly defined). That being said, many of the methods implemented
3074 within MBESS are applicable to a wide variety of disciplines. MBESS has a
3075 suite of functions for a variety of related topics, such as effect sizes,
3076 confidence intervals for effect sizes (including standardized effect sizes and
3077 noncentral effect sizes), sample size planning (from the @dfn{accuracy in
3078 parameter estimation} (AIPE), power analytic, equivalence, and minimum-risk
3079 point estimation perspectives), mediation analysis, various properties of
3080 distributions, and a variety of utility functions.")
3081 ;; Either version of the GPL.
3082 (license (list license:gpl2 license:gpl3))))
3084 (define-public r-homologene
3086 (name "r-homologene")
3087 (version "1.4.68.19.3.27")
3091 (uri (cran-uri "homologene" version))
3093 (base32 "0d7wxisk0vqk1n165v1i19bc02zv78h5r5d3jqai5y6nkmwn01sh"))))
3094 (properties `((upstream-name . "homologene")))
3095 (build-system r-build-system)
3097 (list r-dplyr r-magrittr r-purrr r-r-utils r-readr))
3098 (home-page "https://github.com/oganm/homologene")
3099 (synopsis "Quick access to homologene and gene annotation updates")
3101 "This package provides a wrapper for the homologene database by the
3102 National Center for Biotechnology Information (NCBI). It allows searching for
3103 gene homologs across species. The package also includes an updated version of
3104 the homologene database where gene identifiers and symbols are replaced with
3105 their latest (at the time of submission) version and functions to fetch latest
3106 annotation data to keep updated.")
3107 (license license:expat)))
3109 (define-public r-ggtern
3116 (uri (cran-uri "ggtern" version))
3118 (base32 "15hhn8msy0l8zbq8ms0zvg1iajn1c28gd77v3hp6dvwwsla8zzbd"))))
3119 (properties `((upstream-name . "ggtern")))
3120 (build-system r-build-system)
3122 (list r-compositions
3133 (home-page "http://www.ggtern.com")
3134 (synopsis "Extension to ggplot2 for ternary diagrams")
3136 "This package extends the functionality of ggplot2, providing the
3137 capability to plot ternary diagrams for (a subset of) the ggplot2 geometries.
3138 Additionally, ggtern has implemented several new geometries which are
3139 unavailable to the standard ggplot2 release.")
3140 (license license:gpl2)))
3142 (define-public r-tablerdash
3144 (name "r-tablerdash")
3149 (uri (cran-uri "tablerDash" version))
3152 "1mnp6lxa7d669r325aynq1n3f35r9sy4v1fvdh4cymbf33s8mkmm"))
3155 ;; Delete minified JavaScript
3156 (for-each delete-file
3157 '("inst/tablerDash-0.1.0/require.min.js"
3158 "inst/bootstrap-4.0.0/bootstrap.bundle.min.js"))
3160 (properties `((upstream-name . "tablerDash")))
3161 (build-system r-build-system)
3163 `(#:modules ((guix build utils)
3164 (guix build r-build-system)
3167 (modify-phases %standard-phases
3168 (add-after 'unpack 'process-javascript
3169 (lambda* (#:key inputs #:allow-other-keys)
3170 (with-directory-excursion "inst"
3174 `((,(assoc-ref inputs "js-requirejs")
3175 "tablerDash-0.1.0/require.min.js")
3176 (,(assoc-ref inputs "js-bootstrap")
3177 "bootstrap-4.0.0/bootstrap.bundle.min.js"))))
3178 (lambda (sources targets)
3179 (for-each (lambda (source target)
3180 (format #t "Processing ~a --> ~a~%"
3182 (invoke "esbuild" source "--minify"
3183 (string-append "--outfile=" target)))
3187 (list r-htmltools r-knitr r-shiny))
3189 `(("esbuild" ,esbuild)
3193 (uri "https://raw.githubusercontent.com/requirejs/requirejs/2.3.5/require.js")
3196 "06w32mwqii9cx409ivda88z58qbkcdb4p6hf6jawchsgagaziyds"))))
3200 (uri "https://raw.githubusercontent.com/twbs/bootstrap/\
3201 v4.0.0/dist/js/bootstrap.bundle.js")
3204 "0cvfqffn45vfbj3fk6wmrhkyndhk4id89vgydssbbzxjkfwprfrj"))))))
3205 (home-page "https://rinterface.github.io/tablerDash/")
3206 (synopsis "Tabler API for Shiny")
3208 "This package provides an R interface to the
3209 @url{https://tabler.io,Tabler} HTML template. tablerDash is a light Bootstrap
3210 4 dashboard template. There are different layouts available such as a one
3211 page dashboard or a multi-page template, where the navigation menu is
3212 contained in the navigation bar.")
3213 (license license:gpl2+)))
3215 (define-public r-spelling
3222 (uri (cran-uri "spelling" version))
3225 "179nj9w1v27qq9q5240ddvggp0795998sxyqjvbqjvq9dmach3bl"))))
3226 (properties `((upstream-name . "spelling")))
3227 (build-system r-build-system)
3229 (list r-commonmark r-hunspell r-knitr r-xml2))
3230 (home-page "https://docs.ropensci.org/spelling/")
3231 (synopsis "Tools for spell checking in R")
3233 "This is an R package for spell checking common document formats
3234 including LaTeX, markdown, manual pages, and DESCRIPTION files. It includes
3235 utilities to automate checking of documentation and vignettes as a unit test
3236 during @code{R CMD check}. Both British and American English are supported
3237 out of the box and other languages can be added. In addition, packages may
3238 define a wordlist to allow custom terminology without having to abuse
3240 (license license:expat)))
3242 (define-public r-crosstalk
3244 (name "r-crosstalk")
3249 (uri (cran-uri "crosstalk" version))
3252 "180y7mhpj17axpadwhh7s0qvrpdnag7g977vk256l96d6nmvlds2"))))
3253 (build-system r-build-system)
3255 (list r-htmltools r-jsonlite r-lazyeval r-r6))
3256 (home-page "https://rstudio.github.io/crosstalk/")
3257 (synopsis "Inter-widget interactivity for HTML widgets")
3259 "This package provides building blocks for allowing HTML widgets to
3260 communicate with each other, with Shiny or without (i.e. static @code{.html}
3261 files). It currently supports linked brushing and filtering.")
3262 (license license:expat)))
3264 (define-public r-rook
3271 (uri (cran-uri "Rook" version))
3274 "00s9a0kr9rwxvlq433daxjk4ji8m0w60hjdprf502msw9kxfrx00"))))
3275 (properties `((upstream-name . "Rook")))
3276 (build-system r-build-system)
3277 (propagated-inputs (list r-brew))
3278 (home-page "https://cran.r-project.org/web/packages/Rook")
3279 (synopsis "Web server interface for R")
3281 "This package contains the Rook specification and convenience software
3282 for building and running Rook applications. A Rook application is an R
3283 reference class object that implements a @code{call} method or an R closure
3284 that takes exactly one argument, an environment, and returns a list with three
3285 named elements: the @code{status}, the @code{headers}, and the @code{body}.")
3286 (license license:gpl2)))
3288 (define-public r-miniui
3295 (uri (cran-uri "miniUI" version))
3298 "1h5h2sc57h95d6bsgs95l26911g38hvjc1v50bc31xl9689l2as5"))))
3299 (properties `((upstream-name . "miniUI")))
3300 (build-system r-build-system)
3302 (list r-htmltools r-shiny))
3303 (home-page "https://cran.r-project.org/web/packages/miniUI/")
3304 (synopsis "Shiny UI widgets for small screens")
3306 "This package provides UI widget and layout functions for writing Shiny apps that
3307 work well on small screens.")
3308 (license license:gpl3)))
3310 (define-public r-feather
3317 (uri (cran-uri "feather" version))
3320 "1gxd0h2m56sjjlzn4dry6s13nddxc4l5i11gsvavaf2dwbahdzsh"))))
3321 (build-system r-build-system)
3323 (list r-hms r-rcpp r-tibble))
3324 (home-page "https://github.com/wesm/feather")
3325 (synopsis "R Bindings to the Feather API")
3326 (description "Read and write feather files, a lightweight binary columnar
3327 data store designed for maximum speed.")
3328 (license license:asl2.0)))
3330 (define-public r-maps
3337 (uri (cran-uri "maps" version))
3340 "0ispkx1szgwxhr0zzhdzgqqwcgc6psg7vry4sj4rb89w76rcq63r"))))
3341 (build-system r-build-system)
3342 (home-page "https://cran.r-project.org/web/packages/maps")
3343 (synopsis "Draw geographical maps")
3344 (description "This package provides an R module for display of maps.
3345 Projection code and larger maps are in separate packages (@code{mapproj} and
3347 (license license:gpl2)))
3349 (define-public r-mapproj
3356 (uri (cran-uri "mapproj" version))
3359 "10bpib827011fpgvzsmlv4j3i41s0r3cv1hvawwdlk753s7i0pw6"))))
3360 (build-system r-build-system)
3361 (propagated-inputs (list r-maps))
3362 (home-page "https://cran.r-project.org/web/packages/mapproj")
3363 (synopsis "Map projection in R")
3364 (description "This package converts latitude/longitude into projected
3366 (license (list license:gpl2 ; The R interface
3367 (license:non-copyleft ; The C code
3368 "https://www.gnu.org/licenses/license-list.en.html#lucent102"
3369 "Lucent Public License Version 1.02")))))
3371 (define-public r-rgooglemaps
3373 (name "r-rgooglemaps")
3378 (uri (cran-uri "RgoogleMaps" version))
3381 "02v8k0bw70q4qwx4lcdy8p25q7n3ql2ll46lfpqllxa1p26svmfi"))))
3382 (properties `((upstream-name . "RgoogleMaps")))
3383 (build-system r-build-system)
3386 (home-page "https://cran.r-project.org/web/packages/RgoogleMaps")
3387 (synopsis "Use Google Maps in R")
3388 (description "This package serves two purposes:
3390 @item Provide a comfortable R interface to query the Google server for static
3392 @item Use the map as a background image to overlay plots within R. This
3393 requires proper coordinate scaling.
3395 (license license:gpl2+)))
3397 (define-public r-geosphere
3399 (name "r-geosphere")
3404 (uri (cran-uri "geosphere" version))
3407 "0bg4vfmrw140j2ax0p6bflvb77w03ir39wa87l96rj473jpa9hzj"))))
3408 (build-system r-build-system)
3409 (propagated-inputs (list r-sp))
3410 (home-page "https://cran.r-project.org/web/packages/geosphere")
3411 (synopsis "Spherical trigonometry")
3412 (description "This package computes spherical trigonometry for geographic
3413 applications. That is, compute distances and related measures for angular
3414 (longitude/latitude) locations.")
3415 (license license:gpl3+)))
3417 (define-public r-jpeg
3424 (uri (cran-uri "jpeg" version))
3427 "0wihj538wdnr71wdldym83qadb4kh68a6rkallwbh2f25r27b881"))))
3428 (build-system r-build-system)
3429 (inputs (list libjpeg-turbo))
3430 (home-page "https://www.rforge.net/jpeg/")
3431 (synopsis "Read and write JPEG images with R")
3432 (description "This package provides a way to read, write and display
3433 bitmap images stored in the JPEG format with R. It can read and write both
3434 files and in-memory raw vectors.")
3435 (license license:gpl2+)))
3437 (define-public r-ggmap
3444 (uri (cran-uri "ggmap" version))
3447 "13dmzl6z62pzjiffilarkji46vy0sacxa8a7mhrhc3biq3ylzhln"))))
3448 (build-system r-build-system)
3467 (home-page "https://github.com/dkahle/ggmap")
3468 (synopsis "Spatial visualization with ggplot2")
3469 (description "This package provides a collection of functions to visualize
3470 spatial data and models on top of static maps from various online sources (e.g
3471 Google Maps and Stamen Maps). It includes tools common to those tasks,
3472 including functions for geolocation and routing.")
3473 (license license:gpl2)))
3475 (define-public r-haven
3482 (uri (cran-uri "haven" version))
3485 "1x5g6kjrzcyarbjz91f4aaspx7rb50qs6a9y29mzr3mjq4dk305m"))
3486 (modules '((guix build utils)))
3488 ;; unvendor readstat
3489 '(delete-file-recursively "src/readstat"))))
3490 (build-system r-build-system)
3493 (modify-phases %standard-phases
3494 (add-after 'unpack 'unbundle-readstat
3496 ;; Not required, since we’re not building readstat.
3497 (substitute* "src/Makevars"
3498 (("-lz") "-lreadstat")))))))
3514 (home-page "https://haven.tidyverse.org")
3515 (synopsis "Import and export SPSS, Stata and SAS files")
3517 "This package lets you import foreign statistical formats into R via the
3518 @url{https://github.com/WizardMac/ReadStat,ReadStat} C library.")
3519 (license license:expat)))
3521 (define-public r-amap
3527 (uri (cran-uri "amap" version))
3530 "0zpcb73w413na23f6giml9311jh0j0y766w2fh9i40d2h7bbvyvs"))))
3531 (build-system r-build-system)
3534 (home-page "http://mulcyber.toulouse.inra.fr/projects/amap/")
3535 (synopsis "Another multidimensional analysis package")
3536 (description "This package provides tools for clustering and principal
3537 component analysis (with robust methods, and parallelized functions).")
3538 (license license:gpl2+)))
3540 (define-public r-ape
3547 (uri (cran-uri "ape" version))
3550 "0mqjsh7maczd02iwa4fb896q3kgd9jnlilq7y1yz18ch0c54aqlv"))))
3551 (build-system r-build-system)
3553 (list r-lattice r-nlme r-rcpp))
3554 (home-page "http://ape-package.ird.fr/")
3555 (synopsis "Analyses of phylogenetics and evolution")
3557 "This package provides functions for reading, writing, plotting, and
3558 manipulating phylogenetic trees, analyses of comparative data in a
3559 phylogenetic framework, ancestral character analyses, analyses of
3560 diversification and macroevolution, computing distances from DNA sequences,
3561 and several other tools.")
3562 (license license:gpl2+)))
3564 (define-public r-abbyyr
3571 (uri (cran-uri "abbyyR" version))
3574 "1vldnd3dg89aj6a73nhirirqddbfdrnzhb5m3679i60sark8nk6r"))))
3575 (properties `((upstream-name . "abbyyR")))
3576 (build-system r-build-system)
3584 (home-page "https://github.com/soodoku/abbyyR")
3585 (synopsis "Access to Abbyy Optical Character Recognition (OCR) API")
3587 "This package provides tools to get text from images of text using Abbyy
3588 Cloud Optical Character Recognition (OCR) API. With abbyyyR, one can easily
3589 OCR images, barcodes, forms, documents with machine readable zones, e.g.
3590 passports and get the results in a variety of formats including plain text and
3591 XML. To learn more about the Abbyy OCR API, see @url{http://ocrsdk.com/}.")
3592 (license license:expat)))
3594 (define-public r-colorspace
3596 (name "r-colorspace")
3601 (uri (cran-uri "colorspace" version))
3603 (base32 "0zw52s8g2gxp8i1ax96azxmxqrbhb7aad5px0c1vgr6n9p682mp7"))))
3604 (build-system r-build-system)
3607 (home-page "https://cran.r-project.org/web/packages/colorspace")
3608 (synopsis "Color space manipulation")
3610 "This package carries out a mapping between assorted color spaces
3611 including RGB, HSV, HLS, CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB and polar
3612 CIELAB. Qualitative, sequential, and diverging color palettes based on HCL
3613 colors are provided.")
3614 (license license:bsd-3)))
3616 (define-public r-glue
3623 (uri (cran-uri "glue" version))
3626 "1gzxk5jgdh2xq9r7z09xs306ygzf27vhg3pyfl7ck1755gqii9cx"))))
3627 (build-system r-build-system)
3628 ;; knitr depends on glue, so we can't add knitr here to build the
3632 `(("r-knitr" ,r-knitr)))
3633 (home-page "https://github.com/tidyverse/glue")
3634 (synopsis "Interpreted string literals")
3636 "This package provides an implementation of interpreted string literals,
3637 inspired by Python's Literal String Interpolation (PEP-0498) and
3638 Docstrings (PEP-0257) and Julia's Triple-Quoted String Literals.")
3639 (license license:expat)))
3641 (define-public r-palmerpenguins
3643 (name "r-palmerpenguins")
3648 (uri (cran-uri "palmerpenguins" version))
3651 "0q1k3cdkliq7kwrg1n0vs9b6cjwyfarhlgdijhp9c6riy6y5ik7x"))))
3653 `((upstream-name . "palmerpenguins")))
3654 (build-system r-build-system)
3655 (home-page "https://allisonhorst.github.io/palmerpenguins/")
3656 (synopsis "Palmer Archipelago (Antarctica) penguin data")
3658 "This package includes size measurements, clutch observations, and blood
3659 isotope ratios for adult foraging Adélie, Chinstrap, and Gentoo penguins
3660 observed on islands in the Palmer Archipelago near Palmer Station, Antarctica.
3661 Data were collected and made available by Dr. Kristen Gorman and the Palmer
3662 Station Long Term Ecological Research (LTER) Program.")
3663 (license license:cc0)))
3665 (define-public r-pastecs
3671 (uri (cran-uri "pastecs" version))
3674 "0z4dic94ar646w7zc2ggi5hgvf2qnznsani94c5pyql8zspz47lc"))))
3675 (build-system r-build-system)
3678 (home-page "https://github.com/phgrosjean/pastecs")
3679 (synopsis "Analysis of space-time ecological series")
3681 "This package provides functions for regulation, decomposition and analysis
3682 of space-time series. The @code{pastecs} library is a PNEC-Art4 and IFREMER
3683 initiative to bring PASSTEC 2000 functionalities to R.")
3684 (license license:gpl2+)))
3686 (define-public r-partykit
3692 (uri (cran-uri "partykit" version))
3695 "1b73s5l19yicwginqsg5xr7fzb005x372n0wb34kk6jb5x5lbsdj"))))
3696 (build-system r-build-system)
3704 (home-page "http://partykit.R-Forge.R-project.org/partykit")
3705 (synopsis "Toolkit for recursive partytioning")
3707 "This package provides a toolkit with infrastructure for representing,
3708 summarizing, and visualizing tree-structured regression and classification
3710 (license license:gpl2+)))
3712 (define-public r-plogr
3719 (uri (cran-uri "plogr" version))
3722 "0a8dhzlna79ggyhfr0nncgh15a9n6r0dsz664pz0ah323wpblqqf"))))
3723 (build-system r-build-system)
3724 (home-page "https://github.com/krlmlr/plogr")
3725 (synopsis "R bindings for the plog C++ logging library")
3727 "This package provides the header files for a stripped-down version of
3728 the plog header-only C++ logging library, and a method to log to R's standard
3730 (license license:expat)))
3732 (define-public r-pls
3739 (uri (cran-uri "pls" version))
3741 (base32 "1gqq8rcq6p0hs2gfzwfj690rz3pwywmnv8qzcv0wsd6aaqkskwzg"))))
3742 (build-system r-build-system)
3743 (home-page "https://mevik.net/work/software/pls.html")
3744 (synopsis "Partial Least Squares and Principal Component Regression")
3746 "The pls package implements multivariate regression methods: Partial Least
3747 Squares Regression (@dfn{PLSR}), Principal Component Regression (@dfn{PCR}), and
3748 Canonical Powered Partial Least Squares (@dfn{CPPLS}). It supports:
3751 @item several algorithms: the traditional orthogonal scores (@dfn{NIPALS}) PLS
3752 algorithm, kernel PLS, wide kernel PLS, Simpls, and PCR through @code{svd}
3753 @item multi-response models (or @dfn{PLS2})
3754 @item flexible cross-validation
3755 @item Jackknife variance estimates of regression coefficients
3756 @item extensive and flexible plots: scores, loadings, predictions, coefficients,
3757 (R)MSEP, R², and correlation loadings
3758 @item formula interface, modelled after @code{lm()}, with methods for predict,
3759 print, summary, plot, update, etc.
3760 @item extraction functions for coefficients, scores, and loadings
3761 @item MSEP, RMSEP, and R² estimates
3762 @item multiplicative scatter correction (@dfn{MSC})
3764 (license license:gpl2)))
3773 (uri (cran-uri "ps" version))
3775 (base32 "1qaj9gyz7q09aadlnj5al53k2pa4axmzjsbndf5r0b51qqrcy842"))))
3776 (build-system r-build-system)
3777 (home-page "https://ps.r-lib.org")
3778 (synopsis "List, query, and manipulate system processes")
3780 "The ps package implements an API to list, query, and manipulate system
3781 processes. Most of its code is based on the @code{psutil} Python package.")
3782 (license license:bsd-3)))
3784 (define-public r-pkgbuild
3791 (uri (cran-uri "pkgbuild" version))
3793 (base32 "0j6v5nbp8kg1m3j999gd1qsbdmqcqm1mf28ngmm177miwv8q4skw"))))
3794 (build-system r-build-system)
3804 (home-page "https://github.com/r-pkgs/pkgbuild")
3805 (synopsis "Find tools needed to build R packages")
3807 "This package provides functions used to build R packages. It locates
3808 compilers needed to build R packages on various platforms and ensures the PATH
3809 is configured appropriately so R can use them.")
3810 (license license:gpl3)))
3812 (define-public r-pkgload
3819 (uri (cran-uri "pkgload" version))
3822 "03yr9mswx9nij27bp21q6c533zx310xwzhwm52dwr7554k42p4fn"))))
3823 (build-system r-build-system)
3832 (home-page "https://github.com/r-lib/pkgload")
3833 (synopsis "Simulate package installation and attach")
3835 "This package simulates the process of installing a package and then
3836 attaching it. This is a key part of the @code{devtools} package as it allows
3837 you to rapidly iterate while developing a package.")
3838 (license license:gpl3)))
3840 (define-public r-pvclust
3846 (uri (cran-uri "pvclust" version))
3849 "0082icm54k2yq60k06qpr92a626k39j2jr0046lva4ylmhxqb4kq"))))
3850 (build-system r-build-system)
3851 (home-page "https://github.com/shimo-lab/pvclust")
3853 "Hierarchical clustering with P-values via multiscale bootstrap resampling")
3854 (description "This package provides an implementation of multiscale bootstrap
3855 resampling for assessing the uncertainty in hierarchical cluster analysis. It
3856 provides an AU (approximately unbiased) P-value as well as a BP (bootstrap probability)
3857 value for each cluster in a dendrogram.")
3858 (license license:gpl2+)))
3860 (define-public r-rcpp
3867 (uri (cran-uri "Rcpp" version))
3869 (base32 "1gzqfn1xjawzig30ama3rldykqpcn6bd8sg684mrfvpmv96bi9cx"))))
3870 (build-system r-build-system)
3871 (home-page "http://www.rcpp.org")
3872 (synopsis "Seamless R and C++ integration")
3874 "The Rcpp package provides R functions as well as C++ classes which offer
3875 a seamless integration of R and C++. Many R data types and objects can be
3876 mapped back and forth to C++ equivalents which facilitates both writing of new
3877 code as well as easier integration of third-party libraries. Documentation
3878 about Rcpp is provided by several vignettes included in this package, via the
3879 @code{Rcpp Gallery} site at <http://gallery.rcpp.org>, the paper by Eddelbuettel
3880 and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see
3881 @code{citation(\"Rcpp\")} for details on these last two.")
3882 (license license:gpl2+)))
3884 (define-public r-rcppml
3891 (uri (cran-uri "RcppML" version))
3893 (base32 "1ih8i7i6m221iw227mnl3rvnaw2l53h8fpnc4f8yn9sm10anap1j"))))
3894 (properties `((upstream-name . "RcppML")))
3895 (build-system r-build-system)
3896 (propagated-inputs (list r-matrix r-rcpp r-rcppeigen))
3897 (native-inputs (list r-knitr))
3898 (home-page "https://github.com/zdebruine/RcppML")
3899 (synopsis "Rcpp machine learning library")
3901 "This package provides fast machine learning algorithms including matrix
3902 factorization and divisive clustering for large sparse and dense matrices.")
3903 (license license:gpl2+)))
3905 (define-public r-rcppthread
3907 (name "r-rcppthread")
3912 (uri (cran-uri "RcppThread" version))
3915 "0iprpidf7q1wlrgr9dwiikb6apqk80pyjcyni56k64nl7lrkszhj"))))
3916 (properties `((upstream-name . "RcppThread")))
3917 (build-system r-build-system)
3919 "https://github.com/tnagler/RcppThread")
3920 (synopsis "R threading in C++")
3922 "This package provides a C++11-style thread class and thread pool that can
3923 safely be interrupted from R.")
3924 (license license:expat)))
3926 (define-public r-rcppnumerical
3928 (name "r-rcppnumerical")
3932 (uri (cran-uri "RcppNumerical" version))
3935 "1a92fql6mijhnr1kxkcxwivf95pk9lhgmhzkshs51h0ybfv5krik"))))
3936 (build-system r-build-system)
3938 (list r-rcpp r-rcppeigen))
3939 (home-page "https://github.com/yixuan/RcppNumerical")
3940 (synopsis"Numerical computing libraries integration with @code{Rcpp}")
3941 (description "This package provides a collection of libraries for numerical
3942 computing (numerical integration, optimization, etc.) and their integration
3944 (license license:gpl2+)))
3946 (define-public r-rcppxptrutils
3948 (name "r-rcppxptrutils")
3953 (uri (cran-uri "RcppXPtrUtils" version))
3955 (base32 "0hm57nf4dzgsmg4hjj6wikwjx93fgfwkmybw6ly4b58wi6qwml1l"))))
3956 (properties `((upstream-name . "RcppXPtrUtils")))
3957 (build-system r-build-system)
3958 (propagated-inputs (list r-rcpp))
3959 (home-page "https://github.com/Enchufa2/RcppXPtrUtils")
3960 (synopsis "XPtr add-ons for Rcpp")
3962 "This package provides the means to compile user-supplied C++ functions
3963 with Rcpp and retrieve an @code{XPtr} that can be passed to other C++
3965 (license license:expat)))
3967 (define-public r-bindr
3974 (uri (cran-uri "bindr" version))
3977 "1l05fpk2yql3jka321c0bdgx6mqq9pvfrg2844lbjfpbgjkmqy3w"))))
3978 (build-system r-build-system)
3979 (home-page "https://github.com/krlmlr/bindr")
3980 (synopsis "Parametrized active bindings")
3982 "This package provides a simple interface for creating active bindings
3983 where the bound function accepts additional arguments.")
3984 (license license:expat)))
3986 (define-public r-bindrcpp
3993 (uri (cran-uri "bindrcpp" version))
3996 "0rz4ibjdjsxl99ff3ha79z7cnjmilx4rx58fk9kk7ld9xc4hf4s8"))))
3997 (build-system r-build-system)
3999 (list r-bindr r-plogr r-rcpp))
4000 (home-page "https://github.com/krlmlr/bindrcpp")
4001 (synopsis "Rcpp interface to active bindings")
4003 "This package provides an easy way to fill an environment with active
4004 bindings that call a C++ function.")
4005 (license license:expat)))
4007 (define-public r-auc
4014 (uri (cran-uri "AUC" version))
4017 "07xf47kypqbsg2mixmq6mnh4s89aqan9bgl6kfv6lbx8ajv2asw3"))))
4018 (properties `((upstream-name . "AUC")))
4019 (build-system r-build-system)
4020 (home-page "https://cran.r-project.org/web/packages/AUC")
4021 (synopsis "Compute the area under the curve of selected measures")
4023 "This package includes functions to compute the area under the curve of
4024 selected measures: the area under the sensitivity curve (AUSEC), the area
4025 under the specificity curve (AUSPC), the area under the accuracy
4026 curve (AUACC), and the area under the receiver operating characteristic
4027 curve (AUROC). The curves can also be visualized. Support for partial areas
4029 (license license:gpl2+)))
4031 (define-public r-calibrate
4033 (name "r-calibrate")
4038 (uri (cran-uri "calibrate" version))
4040 (base32 "19kgrnsyq67iqv1biyssqi30a6v2836ql20nabpy2m692ns0jfvi"))))
4041 (build-system r-build-system)
4044 (home-page "https://cran.r-project.org/web/packages/calibrate")
4045 (synopsis "Calibration of scatterplot and biplot axes")
4047 "This is a package for drawing calibrated scales with tick marks
4048 on (non-orthogonal) variable vectors in scatterplots and biplots.")
4049 (license license:gpl2)))
4051 (define-public r-shape
4058 (uri (cran-uri "shape" version))
4061 "0yqbrrx2ywmfl99s6d1n6jblc63k1mxbiqyv8y0kq8jws1g3w45r"))))
4062 (build-system r-build-system)
4063 (home-page "https://cran.r-project.org/web/packages/shape")
4064 (synopsis "Functions for plotting graphical shapes")
4066 "This package provides functions for plotting graphical shapes such as
4067 ellipses, circles, cylinders, arrows, ...")
4068 (license license:gpl3+)))
4070 (define-public r-globaloptions
4072 (name "r-globaloptions")
4077 (uri (cran-uri "GlobalOptions" version))
4079 (base32 "0gkm77w6db9ajyncy1xdcivplap06a51zi99m009kylccschd2a7"))))
4080 (properties `((upstream-name . "GlobalOptions")))
4081 (build-system r-build-system)
4084 (home-page "https://github.com/jokergoo/GlobalOptions")
4085 (synopsis "Generate functions to get or set global options")
4087 "This package provides more controls on the option values such as
4088 validation and filtering on the values, making options invisible or private.")
4089 (license license:gpl2+)))
4091 (define-public r-circlize
4098 (uri (cran-uri "circlize" version))
4101 "1iswb7dy08as3pbzxvhx5qlsbnwvp79nwg8m158nfz7y2d9xa0nn"))))
4102 (build-system r-build-system)
4104 (list r-colorspace r-globaloptions r-shape))
4107 (home-page "https://github.com/jokergoo/circlize")
4108 (synopsis "Circular visualization")
4110 "Circular layout is an efficient way to visualise huge amounts of
4111 information. This package provides an implementation of circular layout
4112 generation in R as well as an enhancement of available software. Its
4113 flexibility is based on the usage of low-level graphics functions such that
4114 self-defined high-level graphics can be easily implemented by users for
4115 specific purposes. Together with the seamless connection between the powerful
4116 computational and visual environment in R, it gives users more convenience and
4117 freedom to design figures for better understanding complex patterns behind
4118 multi-dimensional data.")
4119 (license license:gpl2+)))
4121 (define-public r-powerlaw
4128 (uri (cran-uri "poweRlaw" version))
4130 (base32 "14d1myxllvm1grnfiszzzxaiqpb2jpmsi19wq70r8r2wki293h7g"))))
4131 (properties `((upstream-name . "poweRlaw")))
4132 (build-system r-build-system)
4137 (home-page "https://github.com/csgillespie/poweRlaw")
4138 (synopsis "Tools for the analysis of heavy tailed distributions")
4140 "This package provides an implementation of maximum likelihood estimators
4141 for a variety of heavy tailed distributions, including both the discrete and
4142 continuous power law distributions. Additionally, a goodness-of-fit based
4143 approach is used to estimate the lower cut-off for the scaling region.")
4144 ;; Any of these GPL versions.
4145 (license (list license:gpl2 license:gpl3))))
4147 (define-public r-compare
4154 (uri (cran-uri "compare" version))
4157 "0k9zms930b5dz9gy8414li21wy0zg9x9vp7301v5cvyfi0g7xzgw"))))
4158 (build-system r-build-system)
4159 (home-page "https://cran.r-project.org/web/packages/compare")
4160 (synopsis "Comparing objects for differences")
4162 "This package provides functions to compare a model object to a
4163 comparison object. If the objects are not identical, the functions can be
4164 instructed to explore various modifications of the objects (e.g., sorting
4165 rows, dropping names) to see if the modified versions are identical.")
4166 (license license:gpl2+)))
4168 (define-public r-dendextend
4170 (name "r-dendextend")
4175 (uri (cran-uri "dendextend" version))
4178 "06wjs8451hmnimzgngpzbai3yrgy33133vzzapa8jib9crdqi8sb"))))
4179 (build-system r-build-system)
4181 (list r-ggplot2 r-magrittr r-viridis))
4184 (home-page "https://cran.r-project.org/web/packages/dendextend")
4185 (synopsis "Extending 'dendrogram' functionality in R")
4187 "This package offers a set of functions for extending @code{dendrogram}
4188 objects in R, letting you visualize and compare trees of hierarchical
4189 clusterings. You can adjust a tree's graphical parameters (the color, size,
4190 type, etc of its branches, nodes and labels) and visually and statistically
4191 compare different dendrograms to one another.")
4192 ;; Any of these versions
4193 (license (list license:gpl2 license:gpl3))))
4195 (define-public r-getoptlong
4197 (name "r-getoptlong")
4202 (uri (cran-uri "GetoptLong" version))
4205 "00fpm6nd3kqa2ikasxa62jzywi46fvvmx1mdavcp5yrxxn37j8wc"))))
4206 (properties `((upstream-name . "GetoptLong")))
4207 (build-system r-build-system)
4211 (list r-crayon r-globaloptions r-rjson))
4214 (home-page "https://github.com/jokergoo/GetoptLong")
4215 (synopsis "Parsing command-line arguments and variable interpolation")
4217 "This is yet another command-line argument parser which wraps the
4218 powerful Perl module @code{Getopt::Long} and with some adaptation for easier
4219 use in R. It also provides a simple way for variable interpolation in R.")
4220 (license license:gpl2+)))
4222 (define-public r-fastmatch
4224 (name "r-fastmatch")
4229 (uri (cran-uri "fastmatch" version))
4232 "0qcq1gwl9pijgp34giyq5y9rk0ly3d7xza2b7r68xx63ifqa1vqx"))))
4233 (build-system r-build-system)
4234 (home-page "https://www.rforge.net/fastmatch")
4235 (synopsis "Fast match function")
4237 "This package provides a fast @code{match} replacement for cases that
4238 require repeated look-ups. It is slightly faster that R's built-in
4239 @code{match} function on first match against a table, but extremely fast on
4240 any subsequent lookup as it keeps the hash table in memory.")
4241 (license license:gpl2)))
4250 (uri (cran-uri "ff" version))
4253 "1yl3ipzz9bjkfy9bbna7xz5n7iz4lchnw5l7agww7by764yk6iqa"))))
4254 (build-system r-build-system)
4255 (propagated-inputs (list r-bit))
4256 (home-page "http://ff.r-forge.r-project.org/")
4257 (synopsis "Memory-efficient storage of large data on disk and access functions")
4259 "This package provides data structures that are stored on disk but
4260 behave (almost) as if they were in RAM by transparently mapping only a section
4262 ;; error Architecture not supported.
4263 (supported-systems (delete "aarch64-linux" %supported-systems))
4264 (license license:gpl2)))
4266 (define-public r-ffbase
4273 (uri (cran-uri "ffbase" version))
4276 "1dp6lblfq2j7r1b4b8ls47jlx8j27n88d5vp8w116lb8pa01zxmk"))))
4277 (build-system r-build-system)
4279 (list r-bit r-fastmatch r-ff))
4280 (home-page "https://github.com/edwindj/ffbase")
4281 (synopsis "Basic statistical functions for package 'ff'")
4283 "This package extends the out of memory vectors of @code{ff} with
4284 statistical functions and other utilities to ease their usage.")
4285 (license license:gpl3)))
4287 (define-public r-prettyunits
4289 (name "r-prettyunits")
4294 (uri (cran-uri "prettyunits" version))
4297 "1ibmzgknw5896q2i6r59jz2izblxwgb29ivvjzx50pkd1jl9l6cs"))))
4298 (build-system r-build-system)
4299 (home-page "https://github.com/gaborcsardi/prettyunits")
4300 (synopsis "Pretty, human readable formatting of quantities")
4302 "This package provides tools for pretty, human readable formatting of
4304 (license license:expat)))
4306 (define-public r-princurve
4308 (name "r-princurve")
4312 (uri (cran-uri "princurve" version))
4315 "0wzk329bxljkzz57y220lsfckpsn45w348m6dcxh29zbj0ik65h2"))))
4316 (build-system r-build-system)
4319 (home-page "https://github.com/rcannood/princurve")
4320 (synopsis "Fit a principal curve in arbitrary dimension")
4321 (description "This package provides procedures for fitting a principal
4322 curve to a data matrix in arbitrary dimensions.")
4323 (license license:gpl2)))
4325 (define-public r-reshape
4332 (uri (cran-uri "reshape" version))
4335 "0j203qmc076x5lp6q2xi4dq4xdb73jmsa42rpxp1c37knnrph4br"))))
4336 (build-system r-build-system)
4339 (home-page "http://had.co.nz/reshape")
4340 (synopsis "Flexibly reshape data")
4342 "Flexibly restructure and aggregate data using just two functions:
4343 @code{melt} and @code{cast}. This package provides them.")
4344 (license license:expat)))
4346 (define-public r-restrserve
4348 (name "r-restrserve")
4353 (uri (cran-uri "RestRserve" version))
4355 (base32 "1ydsdgy6mxl0zqk7xqf4v6if5nf2qv7k48q340fhaqyjk2gd60p7"))))
4356 (build-system r-build-system)
4368 (home-page "https://restrserve.org")
4369 (synopsis "R web API framework")
4371 "RestRserve is an R web API framework for building high-performance AND
4372 robust microservices and app backends. With Rserve backend on UNIX-like
4373 systems it is parallel by design. It will handle incoming requests in
4374 parallel - each request in a separate fork.")
4375 (license license:gpl2+)))
4377 (define-public r-progress
4384 (uri (cran-uri "progress" version))
4387 "0dgzb362641aqm8xd88iqa8jmpdm43xs0aba0d5kk6fvapnxi95l"))))
4388 (build-system r-build-system)
4390 (list r-crayon r-hms r-prettyunits r-r6))
4391 (home-page "https://github.com/gaborcsardi/progress")
4392 (synopsis "Terminal progress bars")
4394 "This package provides configurable progress bars. They may include
4395 percentage, elapsed time, and/or the estimated completion time. They work in
4396 terminals, in Emacs ESS, RStudio, Windows Rgui, and the macOS R.app. The
4397 package also provides a C++ API, that works with or without Rcpp.")
4398 (license license:expat)))
4400 (define-public r-ggally
4407 (uri (cran-uri "GGally" version))
4410 "1r98zgh2grn8330cf26r1c20gl131zm778szvn5wj6q6pwv2yd9h"))))
4411 (properties `((upstream-name . "GGally")))
4412 (build-system r-build-system)
4428 (home-page "https://ggobi.github.io/ggally")
4429 (synopsis "Extension to ggplot2")
4431 "The R package ggplot2 is a plotting system based on the grammar of
4432 graphics. GGally extends ggplot2 by adding several functions to reduce the
4433 complexity of combining geometric objects with transformed data. Some of
4434 these functions include a pairwise plot matrix, a two group pairwise plot
4435 matrix, a parallel coordinates plot, a survival plot, and several functions to
4437 (license license:gpl2+)))
4439 (define-public r-proxy
4446 (uri (cran-uri "proxy" version))
4449 "0k8sr24mjfvxp12sf1j9228ah3ngy15nqmm0jw14x5s32f1assv7"))))
4450 (build-system r-build-system)
4451 (home-page "https://cran.r-project.org/web/packages/proxy")
4452 (synopsis "Distance and similarity measures")
4454 "This package provides an extensible framework for the efficient
4455 calculation of auto- and cross-proximities, along with implementations of the
4456 most popular ones.")
4457 (license license:gpl2)))
4466 (uri (cran-uri "sp" version))
4468 (base32 "1bdi06n5zkjnnyh0rallf04s0vlcx9rg9p5q7s6vfqvkf19nk501"))))
4469 (build-system r-build-system)
4474 (home-page "https://cran.r-project.org/web/packages/sp")
4475 (synopsis "Classes and methods for spatial data")
4477 "This package provides classes and methods for spatial data; the classes
4478 document where the spatial location information resides, for 2D or 3D data.
4479 Utility functions are provided, e.g. for plotting data as maps, spatial
4480 selection, as well as methods for retrieving coordinates, for subsetting,
4481 print, summary, etc.")
4482 (license license:gpl2+)))
4484 (define-public r-laplacesdemon
4486 (name "r-laplacesdemon")
4491 (uri (cran-uri "LaplacesDemon" version))
4493 (base32 "1dsfp65cg06f25zjzd5ib4qyn1alfhbhpgyvpcw5n6bszn13idap"))))
4494 (properties `((upstream-name . "LaplacesDemon")))
4495 (build-system r-build-system)
4496 (home-page "https://github.com/LaplacesDemonR/LaplacesDemon")
4497 (synopsis "Complete environment for Bayesian inference")
4499 "This package provides a complete environment for Bayesian inference using
4500 a variety of different samplers.")
4501 (license license:expat)))
4503 (define-public r-rmtstat
4510 (uri (cran-uri "RMTstat" version))
4513 "1r1a2sdqv64m9cpm2pz6r8abf7l810126ayd8iq3gx86c7bjfj5v"))))
4514 (properties `((upstream-name . "RMTstat")))
4515 (build-system r-build-system)
4516 (home-page "https://cran.r-project.org/web/packages/RMTstat")
4517 (synopsis "Distributions, statistics and tests derived from random matrix theory")
4519 "This package provides functions for working with the Tracy-Widom laws
4520 and other distributions related to the eigenvalues of large Wishart
4522 (license license:bsd-3)))
4524 (define-public r-rmpi
4530 (uri (cran-uri "Rmpi" version))
4533 "06mxqgrimhfsag5giv810c7ycdbaycqs4qcj41pnfbj0jypw32im"))))
4534 (properties `((upstream-name . "Rmpi")))
4535 (build-system r-build-system)
4537 `(#:configure-flags '("--configure-args=\"--with-Rmpi-type=OPENMPI\"")
4538 #:phases (modify-phases %standard-phases
4539 (add-before 'install 'mpi-setup
4545 (home-page "http://www.stats.uwo.ca/faculty/yu/Rmpi")
4546 (synopsis "R interface to message-passing interface (MPI)")
4548 "This package provides an interface (wrapper) to MPI APIs. It also
4549 provides an interactive R manager and worker environment.")
4550 (license license:gpl2+)))
4552 (define-public r-lmoments
4559 (uri (cran-uri "Lmoments" version))
4562 "0pc63bj9a8hzr5m3yssrc4kin39fffwkl8rggs3sagzr12d4i7bw"))))
4563 (properties `((upstream-name . "Lmoments")))
4564 (build-system r-build-system)
4566 (list r-rcpp r-rcpparmadillo))
4567 (home-page "http://www.tilastotiede.fi/juha_karvanen.html")
4568 (synopsis "L-moments and quantile mixtures")
4570 "This package contains functions to estimate L-moments and trimmed
4571 L-moments from the data. It also contains functions to estimate the
4572 parameters of the normal polynomial quantile mixture and the Cauchy polynomial
4573 quantile mixture from L-moments and trimmed L-moments.")
4574 (license license:gpl2)))
4576 (define-public r-distillery
4578 (name "r-distillery")
4583 (uri (cran-uri "distillery" version))
4586 "1ymmxyamkq0zbz2m4gllln1ihks2hcib6gs0mls92as79srz122b"))))
4587 (build-system r-build-system)
4588 (home-page "https://ral.ucar.edu/staff/ericg/")
4589 (synopsis "Functions for confidence intervals and object information")
4591 "This package provides some very simple method functions for confidence
4592 interval calculation and to distill pertinent information from a potentially
4593 complex object; primarily used in common with the packages extRemes and
4595 (license license:gpl2+)))
4597 (define-public r-etrunct
4603 (uri (cran-uri "etrunct" version))
4606 "0ayazgyqlc8jcqr03cwfmfhm4pck6xri1r6vkgqy4arqkrrnrcqr"))))
4607 (properties `((upstream-name . "etrunct")))
4608 (build-system r-build-system)
4609 (home-page "https://cran.r-project.org/web/packages/etrunct")
4610 (synopsis "Computes moments of univariate truncated T distribution")
4611 (description "This package computes moments of univariate truncated
4612 T distribution. There is only one exported function, @code{e_trunct},
4613 which should be seen for details.")
4614 (license license:expat)))
4616 (define-public r-excelr
4623 (uri (cran-uri "excelR" version))
4625 (base32 "1pb4sy54zjv5vrh7gjjv7qlpab74km6mfsmfyl0yhmr0jx01hrw0"))
4627 '(delete-file "inst/htmlwidgets/lib/jexcel/js/jexcel.min.js"))))
4628 (properties `((upstream-name . "excelR")))
4629 (build-system r-build-system)
4632 (modify-phases %standard-phases
4633 (add-after 'unpack 'process-javascript
4634 (lambda* (#:key inputs #:allow-other-keys)
4635 (with-directory-excursion "inst/htmlwidgets/lib/jexcel/js/"
4636 (let ((source (assoc-ref inputs "js-jexcel"))
4637 (target "jexcel.min.js"))
4638 (format #true "Processing ~a --> ~a~%"
4640 (invoke "esbuild" source "--minify"
4641 (string-append "--outfile=" target)))))))))
4643 `(("esbuild" ,esbuild)
4644 ;; There is no tag for this particular commit, but comparison of the
4645 ;; contents of the JavaScript files point to this commit as the most
4650 (uri (string-append "https://raw.githubusercontent.com/jspreadsheet/ce/"
4651 "8af1960f76e6803bebc5750013d2ebe95354e88a/dist/jexcel.js"))
4654 "0y88hsr9d8cpnvdmbm17m328pc4kc5wbcv02kzmhm0bryzhviw7h"))))))
4655 (propagated-inputs (list r-htmlwidgets r-jsonlite))
4656 (home-page "https://github.com/Swechhya/excelR")
4657 (synopsis "Wrapper of the JavaScript library jExcel")
4659 "This package provides an R interface to the jExcel library to
4660 create web-based interactive tables and spreadsheets compatible with
4661 spreadsheet software.")
4662 (license license:expat)))
4664 (define-public r-extremes
4671 (uri (cran-uri "extRemes" version))
4674 "19q560prq02h3bwk01jb68693qb5bhsv8wiqhia7v5knm34qv8x7"))))
4675 (properties `((upstream-name . "extRemes")))
4676 (build-system r-build-system)
4678 (list r-distillery r-lmoments))
4679 (home-page "https://www.assessment.ucar.edu/toolkit/")
4680 (synopsis "Extreme value analysis")
4682 "ExtRemes is a suite of functions for carrying out analyses on the
4683 extreme values of a process of interest; be they block maxima over long blocks
4684 or excesses over a high threshold.")
4685 (license license:gpl2+)))
4687 (define-public r-lmtest
4694 (uri (cran-uri "lmtest" version))
4697 "15yr2kx08wy085bnziqmj1p6hf9mg3qp2a8465jk2df6di6hsh34"))))
4698 (build-system r-build-system)
4703 (home-page "https://cran.r-project.org/web/packages/lmtest")
4704 (synopsis "Testing linear regression models")
4706 "This package provides a collection of tests, data sets, and examples for
4707 diagnostic checking in linear regression models. Furthermore, some generic
4708 tools for inference in parametric models are provided.")
4709 ;; Either version is okay
4710 (license (list license:gpl2 license:gpl3))))
4712 (define-public r-idr
4718 (uri (cran-uri "idr" version))
4721 "05nvgw1xdg670bsjjrxkgd1mrdkciccpw4krn0zcgdf2r21dzgwb"))))
4722 (build-system r-build-system)
4723 (home-page "https://cran.r-project.org/web/packages/idr/")
4724 (synopsis "Irreproducible discovery rate")
4726 "This is a package for estimating the copula mixture model and plotting
4727 correspondence curves in \"Measuring reproducibility of high-throughput
4728 experiments\" (2011), Annals of Applied Statistics, Vol. 5, No. 3, 1752-1779,
4729 by Li, Brown, Huang, and Bickel")
4730 (license license:gpl2+)))
4732 (define-public r-inline
4738 (uri (cran-uri "inline" version))
4741 "1mcr9hgq6kkq03n7pkcccxa7vg8jma0q7lfxc5vvkc6snydk1s8f"))))
4742 (build-system r-build-system)
4743 (home-page "https://cran.r-project.org/web/packages/inline")
4744 (synopsis "Functions to inline C, C++, Fortran function calls from R")
4746 "This package provides functionality to dynamically define R functions
4747 and S4 methods with inlined C, C++ or Fortran code supporting @code{.C} and
4748 @code{.Call} calling conventions.")
4749 ;; Any version of the LGPL.
4750 (license license:lgpl3+)))
4752 (define-public r-inum
4758 (uri (cran-uri "inum" version))
4761 "1khkzja8lwn9075864vbyajqina9m588ahf1fsrrajrsqilyzssz"))))
4762 (build-system r-build-system)
4765 (home-page "https://cran.r-project.org/web/packages/inum/")
4766 (synopsis "Interval and enum-type representation of vectors")
4768 "This package provides an enum-type representation of vectors and
4769 representation of intervals, including a method of coercing variables
4771 (license license:gpl2)))
4772 (define-public r-invgamma
4778 (uri (cran-uri "invgamma" version))
4781 "12ga2y4wc9bc5zz6vimvxwgjpsx3ys3209nq63gscbw559ydxa5a"))))
4782 (properties `((upstream-name . "invgamma")))
4783 (build-system r-build-system)
4784 (home-page "https://github.com/dkahle/invgamma")
4785 (synopsis "Inverse gamma distribution")
4786 (description "This package provides a light weight implementation of the
4787 standard distribution functions for the inverse gamma distribution, wrapping
4788 those for the gamma distribution in the @code{stats} package.")
4789 (license license:gpl2)))
4791 (define-public r-bdsmatrix
4793 (name "r-bdsmatrix")
4798 (uri (cran-uri "bdsmatrix" version))
4801 "1sh6pg43rgqvips4fx0k4vmp5i9lmniix0bqwj2yq5m06gs227i5"))))
4802 (properties `((upstream-name . "bdsmatrix")))
4803 (build-system r-build-system)
4804 (home-page "https://cran.r-project.org/web/packages/bdsmatrix/")
4805 (synopsis "Routines for block diagonal symmetric matrices")
4807 "This package provides procedures to work with block diagonal symmetric
4808 matrices, a special case of sparse matrices.")
4809 (license license:lgpl2.0)))
4811 (define-public r-bbmle
4818 (uri (cran-uri "bbmle" version))
4821 "0mdj21q7k0fp4cj7la14vmcjmp49zqm57g7r6zrwmxpv0acwda46"))))
4822 (build-system r-build-system)
4832 (home-page "https://cran.r-project.org/web/packages/bbmle")
4833 (synopsis "Tools for General Maximum Likelihood Estimation")
4835 "This package provides methods and functions for fitting maximum
4836 likelihood models in R. This package modifies and extends the @code{mle}
4837 classes in the @code{stats4} package.")
4838 ;; Any version of the GPL
4839 (license license:gpl2+)))
4841 (define-public r-emdbook
4848 (uri (cran-uri "emdbook" version))
4851 "0ls3zxxlwmdv7zn1v9i1y9zc2sn0hbgmyjvsj7zn3ajsw7wwlih6"))))
4852 (build-system r-build-system)
4854 (list r-bbmle r-coda r-lattice r-mass r-plyr))
4855 (home-page "http://www.math.mcmaster.ca/bolker/emdbook")
4856 (synopsis "Support functions and data for \"Ecological Models and Data\"")
4858 "This package provides auxiliary functions and data sets for \"Ecological
4859 Models and Data\", a book presenting maximum likelihood estimation and related
4860 topics for ecologists (ISBN 978-0-691-12522-0).")
4862 (license (list license:gpl2 license:gpl3))))
4864 (define-public r-lpsolve
4871 (uri (cran-uri "lpSolve" version))
4874 "1fpkyjyqykwa1dxnhiky01pm09syxg169lm7hpy39bdbg10vw9s6"))))
4875 (properties `((upstream-name . "lpSolve")))
4876 (build-system r-build-system)
4877 (home-page "https://cran.r-project.org/web/packages/lpSolve")
4878 (synopsis "R interface to Lp_solve to solve linear/integer programs")
4880 "Lp_solve is software for solving linear, integer and mixed integer
4881 programs. This implementation supplies a \"wrapper\" function in C and some R
4882 functions that solve general linear/integer problems, assignment problems, and
4883 transportation problems.")
4884 (license license:lgpl2.0)))
4886 (define-public r-limsolve
4893 (uri (cran-uri "limSolve" version))
4896 "1829rd2cnd8qj80z9a7sgc7gx4sf3kvl5g6d2a0lqqw30f9sjzmr"))))
4897 (properties `((upstream-name . "limSolve")))
4898 (build-system r-build-system)
4900 (list r-lpsolve r-mass r-quadprog))
4901 (native-inputs (list gfortran))
4902 (home-page "https://cran.r-project.org/web/packages/limSolve")
4903 (synopsis "Solving linear inverse models")
4905 "This package provides functions that:
4908 @item find the minimum/maximum of a linear or quadratic function,
4909 @item sample an underdetermined or overdetermined system,
4910 @item solve a linear system Ax=B for the unknown x.
4913 It includes banded and tridiagonal linear systems. The package calls Fortran
4914 functions from LINPACK.")
4916 (license (list license:gpl2+ license:gpl3+))))
4918 (define-public r-fitdistrplus
4920 (name "r-fitdistrplus")
4925 (uri (cran-uri "fitdistrplus" version))
4928 "0nhgjvwya95v6b9khbsgp44lw10xg35w61lmka1v6wq7yh827izk"))))
4929 (build-system r-build-system)
4931 (list r-mass r-survival))
4934 (home-page "http://riskassessment.r-forge.r-project.org")
4935 (synopsis "Fitting a parametric distribution from data")
4937 "This package extends the @code{fitdistr} function of the MASS package
4938 with several functions to help the fit of a parametric distribution to
4939 non-censored or censored data. Censored data may contain left-censored,
4940 right-censored and interval-censored values, with several lower and upper
4941 bounds. In addition to @dfn{maximum likelihood estimation} (MLE), the package
4942 provides moment matching (MME), quantile matching (QME) and maximum
4943 goodness-of-fit estimation (MGE) methods (available only for non-censored
4944 data). Weighted versions of MLE, MME and QME are available.")
4945 (license license:gpl2+)))
4947 (define-public r-energy
4954 (uri (cran-uri "energy" version))
4957 "19xyw5bkyzfk22gly2ca2nsznqnrhaq4a77727kr1k26bj3y8gal"))))
4958 (build-system r-build-system)
4960 (list r-boot r-gsl r-rcpp))
4961 (home-page "https://cran.r-project.org/web/packages/energy")
4962 (synopsis "Multivariate inference via the energy of data")
4964 "This package provides e-statistics (energy) tests and statistics for
4965 multivariate and univariate inference, including distance correlation,
4966 one-sample, two-sample, and multi-sample tests for comparing multivariate
4967 distributions, are implemented. Measuring and testing multivariate
4968 independence based on distance correlation, partial distance correlation,
4969 multivariate goodness-of-fit tests, clustering based on energy distance,
4970 testing for multivariate normality, distance components (disco) for
4971 non-parametric analysis of structured data, and other energy
4972 statistics/methods are implemented.")
4973 (license license:gpl2+)))
4975 (define-public r-suppdists
4977 (name "r-suppdists")
4982 (uri (cran-uri "SuppDists" version))
4985 "025b9nlxz62wk84295csyzbncpn80i3iby3sxdigf3swcgi2fmbb"))))
4986 (properties `((upstream-name . "SuppDists")))
4987 (build-system r-build-system)
4988 (home-page "https://cran.r-project.org/web/packages/SuppDists")
4989 (synopsis "Supplementary distributions")
4991 "This package provides ten distributions supplementing those built into
4992 R. Inverse Gauss, Kruskal-Wallis, Kendall's Tau, Friedman's chi squared,
4993 Spearman's rho, maximum F ratio, the Pearson product moment correlation
4994 coefficient, Johnson distributions, normal scores and generalized
4995 hypergeometric distributions. In addition two random number generators of
4996 George Marsaglia are included.")
4997 (license license:gpl2+)))
4999 (define-public r-ksamples
5006 (uri (cran-uri "kSamples" version))
5009 "1zs22p68d6320kcylisnk0b5wmpapxkyz15py09czxzw7npw8gms"))))
5010 (properties `((upstream-name . "kSamples")))
5011 (build-system r-build-system)
5014 (home-page "https://cran.r-project.org/web/packages/kSamples")
5015 (synopsis "K-Sample rank tests and their combinations")
5017 "This package provides tools to compares k samples using the
5018 Anderson-Darling test, Kruskal-Wallis type tests with different rank score
5019 criteria, Steel's multiple comparison test, and the Jonckheere-Terpstra (JT)
5020 test. It computes asymptotic, simulated or (limited) exact P-values, all
5021 valid under randomization, with or without ties, or conditionally under random
5022 sampling from populations, given the observed tie pattern. Except for Steel's
5023 test and the JT test it also combines these tests across several blocks of
5025 (license license:gpl2+)))
5027 (define-public r-cvst
5034 (uri (cran-uri "CVST" version))
5037 "0bgk0d6w3dyhb5s30idnp6jpb3m8wf3b79wqlg127wwm0cird8pg"))))
5038 (properties `((upstream-name . "CVST")))
5039 (build-system r-build-system)
5041 (list r-kernlab r-matrix))
5042 (home-page "https://cran.r-project.org/web/packages/CVST")
5043 (synopsis "Fast cross-validation via sequential testing")
5045 "This package implements the fast cross-validation via sequential
5046 testing (CVST) procedure. CVST is an improved cross-validation procedure
5047 which uses non-parametric testing coupled with sequential analysis to
5048 determine the best parameter set on linearly increasing subsets of the data.
5049 Additionally to the CVST the package contains an implementation of the
5050 ordinary k-fold cross-validation with a flexible and powerful set of helper
5051 objects and methods to handle the overall model selection process. The
5052 implementations of the Cochran's Q test with permutations and the sequential
5053 testing framework of Wald are generic and can therefore also be used in other
5055 (license license:gpl2+)))
5057 (define-public r-squarem
5064 (uri (cran-uri "SQUAREM" version))
5067 "0n1s32l9p4vdm3h5q6g43s0qbpzry08difsh0yay80wrla6f3rb6"))))
5068 (properties `((upstream-name . "SQUAREM")))
5069 (build-system r-build-system)
5070 (home-page "https://coah.jhu.edu/people/Faculty_personal_Pages/Varadhan.html")
5071 (synopsis "Squared Extrapolation Methods for Accelerating EM-Like Monotone Algorithms")
5073 "This package provides algorithms for accelerating the convergence of
5074 slow, monotone sequences from smooth, contraction mapping such as the EM
5075 algorithm. It can be used to accelerate any smooth, linearly convergent
5076 acceleration scheme. A tutorial style introduction to this package is
5077 available in a vignette.")
5078 (license license:gpl2+)))
5080 (define-public r-progressr
5082 (name "r-progressr")
5087 (uri (cran-uri "progressr" version))
5089 (base32 "1p5s35rzh28n2id2lipgyqmh3wzib66m7x0pz9028y8cql8xr5ac"))))
5090 (properties `((upstream-name . "progressr")))
5091 (build-system r-build-system)
5094 (home-page "https://progressr.futureverse.org")
5095 (synopsis "Inclusive, unifying API for progress updates")
5097 "This package provides a minimal, unifying API for scripts and packages
5098 to report progress updates from anywhere including when using parallel
5099 processing. The package is designed such that the developer can to focus on
5100 what progress should be reported on without having to worry about how to
5101 present it. The end user has full control of how, where, and when to render
5102 these progress updates.")
5103 (license license:gpl3+)))
5105 (define-public r-lava
5112 (uri (cran-uri "lava" version))
5115 "0bi3c1aqwlq7jbz4raz6vga4r264w7lldi0i62xjlbl7hnlgi23s"))))
5116 (build-system r-build-system)
5118 (list r-future-apply r-numderiv r-progressr r-squarem r-survival))
5121 (home-page "https://github.com/kkholst/lava")
5122 (synopsis "Latent variable models")
5124 "This package provides tools for the estimation and simulation of latent
5126 (license license:gpl3)))
5128 (define-public r-drr
5135 (uri (cran-uri "DRR" version))
5138 "1y70si1gig4l7jx5jiqsqliyywfsvimkx53x3zh1lc3yj2j6bqwk"))))
5139 (properties `((upstream-name . "DRR")))
5140 (build-system r-build-system)
5142 (list r-cvst r-kernlab r-matrix))
5143 (home-page "https://cran.r-project.org/web/packages/DRR")
5144 (synopsis "Dimensionality reduction via regression")
5146 "This package provides an implementation of dimensionality reduction via
5147 regression using Kernel Ridge Regression.")
5148 (license license:gpl3)))
5150 (define-public r-prodlim
5153 (version "2019.11.13")
5157 (uri (cran-uri "prodlim" version))
5160 "03wvh3kirp1prac5nky6a5whs97rvaf4hc27x0fnh51sa17r42b8"))))
5161 (build-system r-build-system)
5163 (list r-kernsmooth r-lava r-rcpp r-survival))
5164 (home-page "https://cran.r-project.org/web/packages/prodlim")
5165 (synopsis "Product-limit estimation for censored event history analysis")
5167 "This package provides a fast and user-friendly implementation of
5168 nonparametric estimators for censored event history (survival) analysis with
5169 the Kaplan-Meier and Aalen-Johansen methods.")
5170 (license license:gpl2+)))
5172 (define-public r-dimred
5179 (uri (cran-uri "dimRed" version))
5182 "1z8fqdc8mslvfix8ngxs1y2yrvlanp5581hwp2nzldj6mk5kn15b"))))
5183 (properties `((upstream-name . "dimRed")))
5184 (build-system r-build-system)
5186 (list r-drr r-magrittr))
5189 (home-page "https://github.com/gdkrmr/dimRed")
5190 (synopsis "Framework for dimensionality reduction")
5192 "This package provides a collection of dimensionality reduction
5193 techniques from R packages and provides a common interface for calling the
5195 (license license:gpl3)))
5197 (define-public r-timedate
5200 (version "3043.102")
5204 (uri (cran-uri "timeDate" version))
5207 "0wvl5pq261rvbgly7vilk3x3m9xk3ly6il1i5scwdf6srl1vlz1p"))))
5208 (properties `((upstream-name . "timeDate")))
5209 (build-system r-build-system)
5210 (home-page "https://www.rmetrics.org")
5211 (synopsis "Chronological and calendar objects")
5213 "This package provides an environment for teaching \"Financial
5214 Engineering and Computational Finance\" and for managing chronological and
5216 (license license:gpl2+)))
5218 (define-public r-magic
5225 (uri (cran-uri "magic" version))
5228 "1gybia2aq80ldk1d845y5srncfzbbmpqhgl7vfaz7qqqjs6d85j5"))))
5229 (build-system r-build-system)
5232 (home-page "https://github.com/RobinHankin/magic.git")
5233 (synopsis "Create and investigate magic squares")
5235 "This package provides a collection of efficient, vectorized algorithms
5236 for the creation and investigation of magic squares and hypercubes, including
5237 a variety of functions for the manipulation and analysis of arbitrarily
5238 dimensioned arrays.")
5239 (license license:gpl2)))
5241 (define-public r-rmysql
5248 (uri (cran-uri "RMySQL" version))
5251 "05aavyggyjv46awa7ggbxlfcy9707vak5kh7kj0ljdx8zga7xb7l"))))
5252 (properties `((upstream-name . "RMySQL")))
5253 (build-system r-build-system)
5255 (list `(,mariadb "dev") zlib))
5258 (home-page "https://github.com/r-dbi/RMySQL")
5259 (synopsis "Database interface and MySQL driver for R")
5261 "This package provides a DBI interface to MySQL / MariaDB. The RMySQL
5262 package contains an old implementation based on legacy code from S-PLUS which
5263 is being phased out. A modern MySQL client based on Rcpp is available from
5264 the RMariaDB package.")
5265 (license license:gpl2)))
5267 (define-public r-rpostgresql
5269 (name "r-rpostgresql")
5274 (uri (cran-uri "RPostgreSQL" version))
5277 "1fbixmnjp1kh6yiv8zhg8zi5ryvdf5j2jxv4agq5gcxf541s3g5x"))))
5278 (properties `((upstream-name . "RPostgreSQL")))
5279 (build-system r-build-system)
5284 (home-page "https://github.com/tomoakin/RPostgreSQL")
5285 (synopsis "R interface to the PostgreSQL database system")
5287 "This package provides a Database Interface (DBI) compliant driver for R
5288 to access PostgreSQL database systems.")
5289 ;; The whole package is released under GPL version 2. It includes code
5290 ;; under the PostgreSQL license.
5291 (license license:gpl2)))
5293 (define-public r-linprog
5300 (uri (cran-uri "linprog" version))
5303 "1d34m2nyk7m6j2dci69bhy5mlw479xax1517j7f14pq7vhpsm9l1"))))
5304 (build-system r-build-system)
5305 (propagated-inputs (list r-lpsolve))
5306 (home-page "http://linprog.r-forge.r-project.org/")
5307 (synopsis "Linear programming and optimization")
5309 "This package can be used to solve Linear Programming / Linear
5310 Optimization problems by using the simplex algorithm.")
5311 (license license:gpl2+)))
5313 (define-public r-geometry
5320 (uri (cran-uri "geometry" version))
5323 "1n7m0djqlhrv01l98r76grkki6cv4k4q2z6c7fksqgq4r2l6a14i"))))
5324 (build-system r-build-system)
5326 (list r-magic r-linprog r-lpsolve r-rcpp r-rcppprogress))
5327 (home-page "http://geometry.r-forge.r-project.org/")
5328 (synopsis "Mesh generator and surface tessellator")
5330 "This package makes the qhull library available in R, in a similar manner
5331 as in Octave. Qhull computes convex hulls, Delaunay triangulations, halfspace
5332 intersections about a point, Voronoi diagrams, furthest-site Delaunay
5333 triangulations, and furthest-site Voronoi diagrams. It runs in 2-d, 3-d, 4-d,
5334 and higher dimensions. It implements the Quickhull algorithm for computing
5335 the convex hull. Qhull does not support constrained Delaunay triangulations,
5336 or mesh generation of non-convex objects, but the package does include some R
5337 functions that allow for this. Currently the package only gives access to
5338 Delaunay triangulation and convex hull computation.")
5339 ;; The Qhull sources are included and are distributed under a custom
5340 ;; non-copyleft license. The R sources are released under GPL version 2.
5341 (license (list license:gpl2
5342 (license:non-copyleft "http://www.qhull.org/COPYING.txt")))))
5344 (define-public r-ddalpha
5351 (uri (cran-uri "ddalpha" version))
5354 "1bjfgb3lbzhjb5wx9hzp90jppq7vnj59bmd2n9ymi8sh1570m9p4"))))
5355 (build-system r-build-system)
5366 (home-page "https://cran.r-project.org/web/packages/ddalpha")
5367 (synopsis "Depth-Based classification and calculation of data depth")
5369 "This package contains procedures for depth-based supervised learning,
5370 which are entirely non-parametric, in particular the DDalpha-procedure (Lange,
5371 Mosler and Mozharovskyi, 2014). The training data sample is transformed by a
5372 statistical depth function to a compact low-dimensional space, where the final
5373 classification is done. It also offers an extension to functional data and
5374 routines for calculating certain notions of statistical depth functions. 50
5375 multivariate and 5 functional classification problems are included.")
5376 (license license:gpl2)))
5378 (define-public r-gower
5385 (uri (cran-uri "gower" version))
5388 "0p9qx9aafkdm7wibfwk59jzw6vspsff6zwp84bc40lg0myxbf737"))))
5389 (build-system r-build-system)
5390 (home-page "https://github.com/markvanderloo/gower")
5391 (synopsis "Gower's distance")
5393 "This package provides tools to compute Gower's distance (or similarity)
5394 coefficient between records, and to compute the top-n matches between records.
5395 Core algorithms are executed in parallel on systems supporting OpenMP.")
5396 (license license:gpl3)))
5398 (define-public r-rcpproll
5405 (uri (cran-uri "RcppRoll" version))
5408 "0srzfhzkk42kzrdjnhbb37946jp1p688rgysy6k3i2is8jb21zyb"))))
5409 (properties `((upstream-name . "RcppRoll")))
5410 (build-system r-build-system)
5413 (home-page "https://cran.r-project.org/web/packages/RcppRoll")
5414 (synopsis "Efficient rolling and windowed operations")
5416 "This package provides fast and efficient routines for common rolling /
5417 windowed operations. Routines for the efficient computation of windowed mean,
5418 median, sum, product, minimum, maximum, standard deviation and variance are
5420 (license license:gpl2+)))
5422 (define-public r-ipred
5429 (uri (cran-uri "ipred" version))
5432 "0hsq00382pfd9hzpcgphjxazbxm4zx0k2r6pk6kib56k0ibm7qfn"))))
5433 (build-system r-build-system)
5441 (home-page "https://cran.r-project.org/web/packages/ipred")
5442 (synopsis "Improved predictors")
5444 "This package provides improved predictive models by indirect
5445 classification and bagging for classification, regression and survival
5446 problems as well as resampling based estimators of prediction error.")
5447 (license license:gpl2+)))
5449 (define-public r-psych
5456 (uri (cran-uri "psych" version))
5459 "08f3byqwabgkqcxwpjbsxdcjkdg012iraqinw0fzskfl1srzkhyw"))))
5460 (build-system r-build-system)
5462 (list r-lattice r-mnormt r-nlme))
5465 (home-page "https://cran.r-project.org/web/packages/psych/")
5466 (synopsis "Procedures for psychological, psychometric, and personality research")
5468 "This package provides a general purpose toolbox for personality,
5469 psychometric theory and experimental psychology. Functions are primarily for
5470 multivariate analysis and scale construction using factor analysis, principal
5471 component analysis, cluster analysis and reliability analysis, although others
5472 provide basic descriptive statistics. Item Response Theory is done using
5473 factor analysis of tetrachoric and polychoric correlations. Functions for
5474 analyzing data at multiple levels include within and between group statistics,
5475 including correlations and factor analysis. Functions for simulating and
5476 testing particular item and test structures are included. Several functions
5477 serve as a useful front end for structural equation modeling. Graphical
5478 displays of path diagrams, factor analysis and structural equation models are
5479 created using basic graphics.")
5480 (license license:gpl2+)))
5482 (define-public r-generics
5489 (uri (cran-uri "generics" version))
5492 "162q9hdsnfcwjj255ahbi6v9vnyynvda7gb75p721y28j5xb7sk3"))))
5493 (build-system r-build-system)
5494 (home-page "https://github.com/r-lib/generics")
5495 (synopsis "Common S3 generics not provided by base R methods")
5497 "In order to reduce potential package dependencies and conflicts,
5498 generics provides a number of commonly used S3 generics that are not provided
5499 by base R methods related to model fitting.")
5500 (license license:gpl2)))
5502 (define-public r-broom
5509 (uri (cran-uri "broom" version))
5512 "16grzja9hz5mqpfzbp1r6zif1gp7swfadkm52340si9h8ifhk8b6"))))
5513 (build-system r-build-system)
5528 (home-page "https://github.com/tidyverse/broom")
5529 (synopsis "Convert statistical analysis objects into tidy data frames")
5531 "This package provides tools to convert statistical analysis objects from
5532 R into tidy data frames, so that they can more easily be combined, reshaped
5533 and otherwise processed with tools like @code{dplyr}, @code{tidyr} and
5534 @code{ggplot2}. The package provides three S3 generics: @code{tidy}, which
5535 summarizes a model's statistical findings such as coefficients of a
5536 regression; @code{augment}, which adds columns to the original data such as
5537 predictions, residuals and cluster assignments; and @code{glance}, which
5538 provides a one-row summary of model-level statistics.")
5539 (license license:expat)))
5541 (define-public r-recipes
5548 (uri (cran-uri "recipes" version))
5551 "1950rvva19ms6xy9d3jx94gzy589qprk115zjjd0ib4qxgip601x"))))
5552 (build-system r-build-system)
5575 (home-page "https://github.com/topepo/recipes")
5576 (synopsis "Preprocessing tools to create design matrices")
5578 "Recipes is an extensible framework to create and preprocess design
5579 matrices. Recipes consist of one or more data manipulation and analysis
5580 \"steps\". Statistical parameters for the steps can be estimated from an
5581 initial data set and then applied to other data sets. The resulting design
5582 matrices can then be used as inputs into statistical or machine learning
5584 (license license:gpl2)))
5586 (define-public r-pdist
5593 (uri (cran-uri "pdist" version))
5596 "0bvg8si81hs79v39d7svv4zbv2p0sk2r6m9vamibvkh9qvl4x406"))))
5597 (build-system r-build-system)
5598 (home-page "https://github.com/jeffwong/pdist")
5599 (synopsis "Partitioned distance function")
5601 "Pdist computes the euclidean distance between rows of a matrix X and
5602 rows of another matrix Y. Previously, this could be done by binding the two
5603 matrices together and calling @code{dist}, but this creates unnecessary
5604 computation by computing the distances between a row of X and another row of
5605 X, and likewise for Y. Pdist strictly computes distances across the two
5606 matrices, not within the same matrix, making computations significantly faster
5607 for certain use cases.")
5608 (license license:gpl3+)))
5610 (define-public r-ggrepel
5617 (uri (cran-uri "ggrepel" version))
5620 "1z5xyr5f4aryy0v1gzz9m8m4s5fzzwbrf0fxll1nbflr8xnr3yr9"))))
5621 (build-system r-build-system)
5623 (list r-ggplot2 r-rcpp r-rlang r-scales))
5625 (list r-knitr)) ; for vignettes
5626 (home-page "https://github.com/slowkow/ggrepel")
5627 (synopsis "Repulsive text and label geometries for ggplot2")
5629 "This package provides text and label geometries for ggplot2 that help to
5630 avoid overlapping text labels. Labels repel away from each other and away
5631 from the data points.")
5632 (license license:gpl3)))
5634 (define-public r-coro
5641 (uri (cran-uri "coro" version))
5643 (base32 "14irld29dipgfd34y0k351daqg9vqpnpdx8m3pxmqr1aiyj5f5cv"))))
5644 (properties `((upstream-name . "coro")))
5645 (build-system r-build-system)
5646 (propagated-inputs (list r-rlang))
5647 (native-inputs (list r-knitr))
5648 (home-page "https://github.com/r-lib/coro")
5649 (synopsis "Coroutines for R")
5651 "This package provides coroutines for R, a family of functions that can
5652 be suspended and resumed later on. This includes async functions (which
5653 await) and generators (which yield). Async functions are based on the
5654 concurrency framework of the @code{promises} package. Generators are based on
5655 a dependency free iteration protocol defined in @code{coro} and are compatible
5656 with iterators from the @code{reticulate} package.")
5657 (license license:expat)))
5659 (define-public r-corrplot
5666 (uri (cran-uri "corrplot" version))
5669 "1g98jk6xsl08z4n6sy5vriif99m31zhbz7j3dh1kfj4w7yb9zh78"))))
5670 (build-system r-build-system)
5673 (home-page "https://github.com/taiyun/corrplot")
5674 (synopsis "Visualization of a correlation matrix")
5676 "This package provides a graphical display of a correlation matrix or
5677 general matrix. It also contains some algorithms to do matrix reordering. In
5678 addition, corrplot is good at details, including choosing color, text labels,
5679 color labels, layout, etc.")
5680 ;; Any version of the GPL
5681 (license license:gpl2+)))
5683 (define-public r-stringdist
5685 (name "r-stringdist")
5690 (uri (cran-uri "stringdist" version))
5692 (base32 "1fv1hbdlm8qwx57b2aj50mw0say5k48awzavx65mfk67qp6ddk7g"))))
5693 (build-system r-build-system)
5694 (home-page "https://github.com/markvanderloo/stringdist")
5695 (synopsis "Approximate string matching and string distance functions")
5697 "This package implements an approximate string matching version of R's
5698 native @code{match} function. It can calculate various string distances based
5699 on edits (Damerau-Levenshtein, Hamming, Levenshtein, optimal string alignment),
5700 qgrams (q- gram, cosine, jaccard distance) or heuristic metrics (Jaro,
5701 Jaro-Winkler). An implementation of soundex is provided as well. Distances
5702 can be computed between character vectors while taking proper care of encoding
5703 or between integer vectors representing generic sequences.")
5704 (license license:gpl3+)))
5706 (define-public r-ucminf
5713 (uri (cran-uri "ucminf" version))
5716 "01vggwg1w71k98qs6fhb0x1843vi322mf4g3hbclks94kcpkisx2"))))
5717 (build-system r-build-system)
5718 (native-inputs (list gfortran))
5719 (home-page "https://cran.r-project.org/web/packages/ucminf/")
5720 (synopsis "General-purpose unconstrained non-linear optimization")
5722 "This package provides an implementation of an algorithm for
5723 general-purpose unconstrained non-linear optimization. The algorithm is of
5724 quasi-Newton type with BFGS updating of the inverse Hessian and soft line
5725 search with a trust region type monitoring of the input to the line search
5726 algorithm. The interface of @code{ucminf} is designed for easy interchange
5727 with the package @code{optim}.")
5728 (license license:gpl2+)))
5730 (define-public r-usedist
5737 (uri (cran-uri "usedist" version))
5739 (base32 "0ddf1zcalbrn293qmr9kdzz3x16fzc4k1bwb1pjmwnspisqfi8kj"))))
5740 (properties `((upstream-name . "usedist")))
5741 (build-system r-build-system)
5742 (home-page "https://cran.r-project.org/package=usedist")
5743 (synopsis "Distance matrix utilities")
5745 "This package provides functions to re-arrange, extract, and work with
5747 (license license:gpl3)))
5749 (define-public r-useful
5755 (uri (cran-uri "useful" version))
5758 "0n50v1q75k518sq23id14jphwla35q4sasahrnrnllwrachl67v1"))))
5759 (properties `((upstream-name . "useful")))
5760 (build-system r-build-system)
5770 (home-page "https://github.com/jaredlander/useful")
5771 (synopsis "Collection of handy, useful functions")
5772 (description "This package provides a set of little functions that have been
5773 found useful to do little odds and ends such as plotting the results of K-means
5774 clustering, substituting special text characters, viewing parts of a
5775 @code{data.frame}, constructing formulas from text and building design and
5776 response matrices.")
5777 (license license:bsd-3)))
5779 (define-public r-ordinal
5782 (version "2019.12-10")
5786 (uri (cran-uri "ordinal" version))
5789 "09bpmjmbf4x82kgf6bm4bkncq2apdv9mk20zj4zgma2jx2vyfhbs"))))
5790 (build-system r-build-system)
5792 (list r-mass r-matrix r-numderiv r-ucminf))
5793 (home-page "https://github.com/runehaubo/ordinal")
5794 (synopsis "Regression models for ordinal data")
5796 "This package provides an implementation of cumulative link (mixed)
5797 models also known as ordered regression models, proportional odds models,
5798 proportional hazards models for grouped survival times and ordered models.
5799 Estimation is via maximum likelihood and mixed models are fitted with the
5800 Laplace approximation and adaptive Gauss-Hermite quadrature.")
5801 (license license:gpl2+)))
5803 (define-public r-jomo
5810 (uri (cran-uri "jomo" version))
5813 "0qq03zspmh8x2c8w882ynsw7wshr9b0fyrpwnqx5yc1xlzrqffcx"))))
5814 (build-system r-build-system)
5816 (list r-lme4 r-mass r-ordinal r-survival r-tibble))
5817 (home-page "https://cran.r-project.org/web/packages/jomo/")
5818 (synopsis "Multilevel Joint Modelling Multiple Imputation")
5820 "Similarly to Schafer's package pan, jomo is a package for multilevel
5821 joint modelling multiple imputation @url{Carpenter and Kenward (2013),
5822 http://doi.org/10.1002/9781119942283}. Novel aspects of jomo are the
5823 possibility of handling binary and categorical data through latent normal
5824 variables, the option to use cluster-specific covariance matrices and to
5825 impute compatibly with the substantive model.")
5826 (license license:gpl2)))
5828 (define-public r-pan
5835 (uri (cran-uri "pan" version))
5838 "1dk3jjj826p7xrz10qz04vyc068xnypg7bp0pj4c32z3da0xzh5d"))))
5839 (build-system r-build-system)
5840 (native-inputs (list gfortran))
5841 (home-page "https://cran.r-project.org/web/packages/pan/")
5842 (synopsis "Multiple imputation for multivariate panel or clustered data")
5844 "This package implements multiple imputation for multivariate panel or
5846 (license license:gpl3)))
5848 (define-public r-mitml
5855 (uri (cran-uri "mitml" version))
5858 "00i18nnvrdrg91crgcp2a431xs71cawaip3xkqk2myv0iav3xga9"))))
5859 (build-system r-build-system)
5861 (list r-haven r-jomo r-pan))
5864 (home-page "https://cran.r-project.org/web/packages/mitml/")
5865 (synopsis "Tools for multiple imputation in multilevel modeling")
5867 "This package provides tools for multiple imputation of missing data in
5868 multilevel modeling. It includes a user-friendly interface to the packages
5869 pan and jomo, and several functions for visualization, data management and the
5870 analysis of multiply imputed data sets.")
5871 (license license:gpl2+)))
5873 (define-public r-mice
5880 (uri (cran-uri "mice" version))
5883 "01fnfrr7adp29s5kic95r9q0rdznkz2pjmziyimnrqzyicyvfyzq"))))
5884 (build-system r-build-system)
5895 (home-page "https://cran.r-project.org/web/packages/mice/")
5896 (synopsis "Multivariate imputation by chained equations")
5898 "Multiple imputation using @dfn{Fully Conditional Specification} (FCS)
5899 implemented by the MICE algorithm as described in @url{Van Buuren and
5900 Groothuis-Oudshoorn (2011), http://doi.org/10.18637/jss.v045.i03}. Each
5901 variable has its own imputation model. Built-in imputation models are
5902 provided for continuous data (predictive mean matching, normal), binary
5903 data (logistic regression), unordered categorical data (polytomous logistic
5904 regression) and ordered categorical data (proportional odds). MICE can also
5905 impute continuous two-level data (normal model, pan, second-level variables).
5906 Passive imputation can be used to maintain consistency between variables.
5907 Various diagnostic plots are available to inspect the quality of the
5909 ;; Any of these two versions.
5910 (license (list license:gpl2 license:gpl3))))
5912 (define-public r-truncnorm
5914 (name "r-truncnorm")
5919 (uri (cran-uri "truncnorm" version))
5922 "0zn88wdd58223kibk085rhsikl4yhlrwiyq109hzjg06hy6lwmj9"))))
5923 (build-system r-build-system)
5924 (home-page "https://cran.r-project.org/web/packages/truncnorm/")
5925 (synopsis "Truncated normal distribution")
5926 (description "This package provides functions for the truncated normal
5927 distribution with mean equal to @code{mean} and standard deviation equal to
5928 @code{sd}. It includes density, distribution, quantile, and expected value
5929 functions, as well as a random generation function.")
5930 (license license:gpl2)))
5932 (define-public r-rsolnp
5939 (uri (cran-uri "Rsolnp" version))
5942 "0w7nkj6igr0gi7r7jg950lsx7dj6aipgxi6vbjsf5f5yc9h7fhii"))))
5943 (properties `((upstream-name . "Rsolnp")))
5944 (build-system r-build-system)
5947 (home-page "https://cran.r-project.org/web/packages/Rsolnp/")
5948 (synopsis "General non-linear optimization")
5949 (description "The Rsolnp package implements a general non-linear augmented
5950 Lagrange multiplier method solver, a @dfn{sequential quadratic
5951 programming} (SQP) based solver).")
5952 ;; Any version of the GPL.
5953 (license license:gpl2+)))
5955 (define-public r-hardyweinberg
5957 (name "r-hardyweinberg")
5962 (uri (cran-uri "HardyWeinberg" version))
5965 "0b3szw090dsc3bkas2kvx787ww2i6zzg2qmdyivmqc8amx5arn6g"))))
5966 (properties `((upstream-name . "HardyWeinberg")))
5967 (build-system r-build-system)
5969 (list r-mice r-nnet r-rcpp r-rsolnp))
5970 (home-page "https://cran.r-project.org/package=HardyWeinberg")
5971 (synopsis "Statistical tests and graphics for Hardy-Weinberg equilibrium")
5973 "This package contains tools for exploring Hardy-Weinberg equilibrium for
5974 diallelic genetic marker data. All classical tests (chi-square, exact,
5975 likelihood-ratio and permutation tests) for Hardy-Weinberg equilibrium are
5976 included in the package, as well as functions for power computation and for
5977 the simulation of marker data under equilibrium and disequilibrium. Routines
5978 for dealing with markers on the X-chromosome are included. Functions for
5979 testing equilibrium in the presence of missing data by using multiple
5980 imputation are also provided. Implements several graphics for exploring the
5981 equilibrium status of a large set of diallelic markers: ternary plots with
5982 acceptance regions, log-ratio plots and Q-Q plots.")
5983 (license license:gpl2+)))
5992 (uri (cran-uri "sm" version))
5995 "03z8igsjqr32x407asxvkrbayvm6yhv9xyfs0n8fkmv8zk5a41r6"))))
5996 (build-system r-build-system)
5997 (native-inputs (list gfortran))
5998 (home-page "http://www.stats.gla.ac.uk/~adrian/sm/")
5999 (synopsis "Smoothing methods for nonparametric regression and density estimation")
6001 "This is software accompanying the book 'Applied Smoothing Techniques for
6002 Data Analysis---The Kernel Approach with S-Plus Illustrations', Oxford
6003 University Press. It provides smoothing methods for nonparametric regression
6004 and density estimation")
6005 (license license:gpl2+)))
6007 (define-public r-venndiagram
6009 (name "r-venndiagram")
6013 (uri (cran-uri "VennDiagram" version))
6016 "0ilcxcp8qskmb5cp7fyb7i0qizg42lrx0ny8ws3if90kfrglghp7"))))
6017 (properties `((upstream-name . "VennDiagram")))
6018 (build-system r-build-system)
6020 (list r-futile-logger))
6021 (home-page "https://cran.r-project.org/web/packages/VennDiagram/")
6022 (synopsis "Generate High-Resolution Venn and Euler Plots")
6024 "This package provides a set of functions to generate high-resolution
6025 Venn and Euler plots. It includes handling for several special cases,
6026 including two-case scaling, and extensive customization of plot shape and
6028 (license license:gpl2+)))
6030 (define-public r-vioplot
6037 (uri (cran-uri "vioplot" version))
6040 "1dmdasp3jldc41233z6r08w3j76vyyp9m3jrj7n4ahk48yd5siq6"))))
6041 (build-system r-build-system)
6046 (home-page "http://wsopuppenkiste.wiso.uni-goettingen.de/~dadler")
6047 (synopsis "Violin plot")
6049 "This package provides a violin plot, which is a combination of a box
6050 plot and a kernel density plot.")
6051 (license license:bsd-3)))
6053 (define-public r-rsofia
6059 ;; This package has been removed from CRAN, so we can
6060 ;; only fetch it from the archives.
6061 (uri (string-append "https://cran.r-project.org/src/"
6062 "contrib/Archive/RSofia/RSofia_"
6066 "0q931y9rcf6slb0s2lsxhgqrzy4yqwh8hb1124nxg0bjbxvjbihn"))))
6067 (properties `((upstream-name . "RSofia")))
6068 (build-system r-build-system)
6071 (home-page "https://cran.r-project.org/src/contrib/Archive/RSofia")
6072 (synopsis "Port of sofia-ml to R")
6073 (description "This package is a port of sofia-ml to R. Sofia-ml is a
6074 suite of fast incremental algorithms for machine learning that can be used for
6075 training models for classification or ranking.")
6076 (license license:asl2.0)))
6078 (define-public r-xts
6085 (uri (cran-uri "xts" version))
6088 "0b6a7mpyk9aw6axas7nz01gadczprwwfhii01fz31z26z555i06n"))))
6089 (build-system r-build-system)
6090 (propagated-inputs (list r-zoo))
6091 (home-page "https://github.com/joshuaulrich/xts")
6092 (synopsis "Extensible time series")
6094 "This package provides for uniform handling of R's different time-based
6095 data classes by extending @code{zoo}, maximizing native format information
6096 preservation and allowing for user-level customization and extension, while
6097 simplifying cross-class interoperability.")
6098 (license license:gpl2+)))
6100 (define-public r-performanceanalytics
6102 (name "r-performanceanalytics")
6107 (uri (cran-uri "PerformanceAnalytics" version))
6110 "0ci26hsj4wnw9g0mh4vrn0cg986cpcpx169rvw6v6rbnjxq718bq"))))
6112 `((upstream-name . "PerformanceAnalytics")))
6113 (build-system r-build-system)
6115 (list r-quadprog r-xts r-zoo))
6116 (home-page "https://r-forge.r-project.org/projects/returnanalytics/")
6117 (synopsis "Econometric tools for performance and risk analysis")
6118 (description "This is a collection of econometric functions for
6119 performance and risk analysis. This package aims to aid practitioners and
6120 researchers in utilizing the latest research in analysis of non-normal return
6121 streams. In general, it is most tested on return (rather than price) data on
6122 a regular scale, but most functions will work with irregular return data as
6123 well, and increasing numbers of functions will work with P&L or price data
6125 ;; Either version may be picked.
6126 (license (list license:gpl2 license:gpl3))))
6128 (define-public r-laeken
6135 (uri (cran-uri "laeken" version))
6138 "1p3ccbaydlr52p8qmgmm2l6kryvq6jjjx7mqn2vv0gpjaxqhyy92"))))
6139 (build-system r-build-system)
6141 (list r-boot r-mass))
6142 (home-page "https://cran.r-project.org/web/packages/laeken/")
6143 (synopsis "Estimation of indicators on social exclusion and poverty")
6144 (description "This package provides tools for the estimation of indicators
6145 on social exclusion and poverty, as well as an implementation of Pareto tail
6146 modeling for empirical income distributions.")
6147 (license license:gpl2+)))
6149 (define-public r-vcd
6156 (uri (cran-uri "vcd" version))
6159 "13sn77qdcyll9lz7nab0bxzfvpgj8f5rl2cq5ylpz8pibynj1d55"))))
6160 (build-system r-build-system)
6162 (list r-colorspace r-lmtest r-mass))
6163 (home-page "https://cran.r-project.org/web/packages/vcd/")
6164 (synopsis "Visualizing categorical data")
6165 (description "This package provides visualization techniques, data sets,
6166 summary and inference procedures aimed particularly at categorical data.
6167 Special emphasis is given to highly extensible grid graphics. The package was
6168 originally inspired by the book \"Visualizing Categorical Data\" by Michael
6169 Friendly and is now the main support package for a new book, \"Discrete Data
6170 Analysis with R\" by Michael Friendly and David Meyer (2015).")
6171 (license license:gpl2)))
6173 (define-public r-vcfr
6179 (uri (cran-uri "vcfR" version))
6182 "0lhxb3ac4fafwik9q3cds46svzf0hyca8k54chw3dpk50c0zz1yx"))))
6183 (build-system r-build-system)
6199 (home-page "https://github.com/knausb/vcfR")
6200 (synopsis "Manipulate and visualize VCF data")
6201 (description "This package facilitates easy manipulation of variant call
6202 format (VCF) data. Functions are provided to rapidly read from and write to
6203 VCF files. Once VCF data is read into R, a parser function extracts matrices
6204 of data. This information can then be used for quality control or other
6205 purposes. Additional functions provide visualization of genomic data. Once
6206 processing is complete data may be written to a VCF file. It also may be
6207 converted into other popular R objects. This package provides a link between
6208 VCF data and familiar R software.")
6209 (license license:gpl3)))
6211 (define-public r-ica
6218 (uri (cran-uri "ica" version))
6221 "0ya1nph1zwhad0bfz4yxs27kl45yk1dhnphdlrq34p8pqrpmj8g7"))))
6222 (build-system r-build-system)
6223 (home-page "https://cran.r-project.org/web/packages/ica/")
6224 (synopsis "Independent component analysis")
6225 (description "This package provides tools for @dfn{Independent Component
6226 Analysis} (ICA) using various algorithms: FastICA,
6227 Information-Maximization (Infomax), and @dfn{Joint Approximate Diagonalization
6228 of Eigenmatrices} (JADE).")
6229 (license license:gpl2+)))
6231 (define-public r-dtw
6238 (uri (cran-uri "dtw" version))
6241 "004gm4mzgdzdj807j3bwqsv5lizmnmz5jq514bdjshhkysnzjz6z"))))
6242 (build-system r-build-system)
6243 (propagated-inputs (list r-proxy))
6244 (home-page "http://dtw.r-forge.r-project.org/")
6245 (synopsis "Dynamic Time Warping Algorithms")
6246 (description "This package provides a comprehensive implementation of
6247 @dfn{dynamic time warping} (DTW) algorithms in R. DTW computes the
6248 optimal (least cumulative distance) alignment between points of two time
6249 series. Common DTW variants covered include local (slope) and global (window)
6250 constraints, subsequence matches, arbitrary distance definitions,
6251 normalizations, minimum variance matching, and so on.")
6252 (license license:gpl2+)))
6254 (define-public r-sdmtools
6257 (version "1.1-221.2")
6261 (uri (cran-uri "SDMTools" version))
6264 "1xvcd97ikqsfdpk2fddy3k0z1ajqga7nv9bgac9c1wnjk1gqrpgh"))))
6265 (properties `((upstream-name . "SDMTools")))
6266 (build-system r-build-system)
6267 (propagated-inputs (list r-r-utils))
6268 (home-page "https://www.rforge.net/SDMTools/")
6269 (synopsis "Species distribution modelling tools")
6270 (description "This package provides a set of tools for post processing
6271 the outcomes of species distribution modeling exercises. It includes novel
6272 methods for comparing models and tracking changes in distributions through
6273 time. It further includes methods for visualizing outcomes, selecting
6274 thresholds, calculating measures of accuracy and landscape fragmentation
6276 (license license:gpl3+)))
6278 (define-public r-scatterplot3d
6280 (name "r-scatterplot3d")
6285 (uri (cran-uri "scatterplot3d" version))
6288 "152xqz9c70qab86mpgng049gxsg5f4fpf1m8dh93fb9v1avjd0sc"))))
6289 (build-system r-build-system)
6290 (home-page "https://cran.r-project.org/web/packages/scatterplot3d/")
6291 (synopsis "3D scatter plot")
6292 (description "This package provides an implementation of scatter plots for
6293 plotting. a three dimensional point cloud.")
6294 (license license:gpl2)))
6296 (define-public r-ggridges
6303 (uri (cran-uri "ggridges" version))
6306 "0bmlqy1p6rac90af97ffpdi6php7dblx66l2hcm8ljidgyqzmspm"))))
6307 (build-system r-build-system)
6309 (list r-ggplot2 r-plyr r-scales r-withr))
6312 (home-page "https://github.com/clauswilke/ggridges")
6313 (synopsis "Ridgeline plots in ggplot2")
6315 "Ridgeline plots provide a convenient way of visualizing changes in
6316 distributions over time or space. This package enables the creation of such
6317 plots in @code{ggplot2}.")
6318 (license license:gpl2)))
6320 (define-public r-ggjoy
6327 (uri (cran-uri "ggjoy" version))
6330 "012md2m0jqfcccb933j423m3ck31v3p0pd41gjxpyg9082y7ixyj"))))
6331 (build-system r-build-system)
6333 (list r-ggplot2 r-ggridges))
6334 (home-page "https://github.com/clauswilke/ggjoy")
6335 (synopsis "Joyplots in ggplot2")
6336 (description "Joyplots provide a convenient way of visualizing changes in
6337 distributions over time or space. This package enables the creation of such
6338 plots in @code{ggplot2}.")
6339 (license license:gpl2)))
6341 (define-public r-cli
6348 (uri (cran-uri "cli" version))
6351 "0qqd4mscv8ndjbji7knprdlv2hhyk35gazagvapbjzq1p6yfpaf3"))))
6352 (build-system r-build-system)
6355 (home-page "https://github.com/r-lib/cli#readme")
6356 (synopsis "Helpers for developing command line interfaces")
6357 (description "This package provides a suite of tools designed to build
6358 attractive command line interfaces (CLIs). It includes tools for drawing
6359 rules, boxes, trees, and Unicode symbols with ASCII alternatives.")
6360 (license license:expat)))
6362 (define-public r-argparser
6364 (name "r-argparser")
6369 (uri (cran-uri "argparser" version))
6372 "0xcl0ivsbc4iw8s7027q4cx68j6s5lihbby0xa9pmlv4wjmcvdr6"))))
6373 (build-system r-build-system)
6374 (home-page "https://bitbucket.org/djhshih/argparser")
6375 (synopsis "Command-line argument parser")
6377 "This package provides a cross-platform command-line argument parser
6378 written purely in R with no external dependencies. It is useful with the
6379 Rscript front-end and facilitates turning an R script into an executable
6381 (license license:gpl3+)))
6383 (define-public r-debugme
6390 (uri (cran-uri "debugme" version))
6393 "1c9sg55zvf10h8198jdnpamm6f66lzw3c3jnmdp9ls6na0j0xbjd"))))
6394 (build-system r-build-system)
6395 (propagated-inputs (list r-crayon))
6396 (home-page "https://github.com/r-lib/debugme#readme")
6397 (synopsis "Debug R packages")
6399 "This package allows the user to specify debug messages as special string
6400 constants, and control debugging of packages via environment variables.")
6401 (license license:expat)))
6403 (define-public r-processx
6410 (uri (cran-uri "processx" version))
6412 (base32 "0ail3w8n5g1ibdamgpxcfpla18kqkilmppiasm7ms67cavx2k5k7"))))
6413 (build-system r-build-system)
6416 (home-page "https://github.com/r-lib/processx3")
6417 (synopsis "Execute and control system processes")
6419 "This package provides portable tools to run system processes in the
6420 background. It can check if a background process is running; wait on a
6421 background process to finish; get the exit status of finished processes; kill
6422 background processes and their children; restart processes. It can read the
6423 standard output and error of the processes, using non-blocking connections.
6424 @code{processx} can poll a process for standard output or error, with a
6425 timeout. It can also poll several processes at once.")
6426 (license license:expat)))
6428 (define-public r-tsp
6435 (uri (cran-uri "TSP" version))
6438 "022k0972kcxb0w6qhx09l9cif8fmpkpvwddvgxiy60bx343ywzia"))))
6439 (properties `((upstream-name . "TSP")))
6440 (build-system r-build-system)
6441 (propagated-inputs (list r-foreach))
6442 (home-page "https://cran.r-project.org/web/packages/TSP/")
6443 (synopsis "Traveling salesperson problem (TSP)")
6444 (description "This package provides basic infrastructure and some
6445 algorithms for the @dfn{traveling salesperson problem}(TSP) (also known as the
6446 traveling salesman problem).")
6447 (license license:gpl3)))
6449 (define-public r-qap
6456 (uri (cran-uri "qap" version))
6459 "0d2d1ni1camixyi45lfy00f4pn3p063k7bsi8gj5scp6n15mdgb0"))))
6460 (build-system r-build-system)
6461 (native-inputs (list gfortran))
6462 (home-page "https://cran.r-project.org/web/packages/qap/")
6463 (synopsis "Heuristics for the quadratic assignment problem (QAP)")
6464 (description "This package implements heuristics for the @dfn{quadratic
6465 assignment problem} (QAP). Currently only a simulated annealing heuristic is
6467 (license license:gpl3)))
6469 (define-public r-gclus
6476 (uri (cran-uri "gclus" version))
6479 "1cz0g0i972955hhaji30rx8448x7f3as7z1sww9i5h86ybgirilw"))))
6480 (build-system r-build-system)
6481 (propagated-inputs (list r-cluster))
6482 (home-page "https://cran.r-project.org/web/packages/gclus/")
6483 (synopsis "Clustering graphics")
6484 (description "This package orders panels in scatterplot matrices and
6485 parallel coordinate displays by some merit index. It contains various indices
6486 of merit, ordering functions, and enhanced versions of @code{pairs} and
6487 @code{parcoord} which color panels according to their merit level.")
6488 (license license:gpl2+)))
6490 (define-public r-webshot
6497 (uri (cran-uri "webshot" version))
6500 "1h6v94zwq0ypgi4vf8xlhp5k13j7f9061hx908177i68c6zg5i5p"))))
6501 (build-system r-build-system)
6503 (list r-callr r-jsonlite r-magrittr))
6504 (home-page "https://github.com/wch/webshot/")
6505 (synopsis "Take screenshots of web pages")
6507 "Webshot makes it easy to take screenshots of web pages from within R.
6508 It can also run Shiny applications locally and take screenshots of the
6509 application; and it can render and screenshot static as well as interactive R
6510 Markdown documents.")
6511 (license license:gpl2)))
6513 (define-public r-seriation
6515 (name "r-seriation")
6520 (uri (cran-uri "seriation" version))
6523 "0dlj0mqpg585m6i7yn0h878i8ag6pyqph98xkk42i2nvghpy01gr"))))
6524 (build-system r-build-system)
6533 (native-inputs (list gfortran))
6534 (home-page "https://s2.smu.edu/IDA/seriation/")
6535 (synopsis "Infrastructure for ordering objects using seriation")
6537 "This package provides infrastructure for seriation with an
6538 implementation of several seriation/sequencing techniques to reorder matrices,
6539 dissimilarity matrices, and dendrograms. It also provides (optimally)
6540 reordered heatmaps, color images and clustering visualizations like
6541 dissimilarity plots, and visual assessment of cluster tendency plots (VAT and
6543 (license license:gpl3)))
6545 (define-public r-xfun
6552 (uri (cran-uri "xfun" version))
6554 (base32 "0dgjkrlwl6rxmvdn6s1xrbiaa53hkfx2s7rqrbrc7c6shbkg6sfi"))))
6555 (build-system r-build-system)
6556 ;; knitr itself depends on xfun
6559 `(("r-knitr" ,r-knitr)))
6560 (home-page "https://github.com/yihui/xfun")
6561 (synopsis "Miscellaneous functions")
6563 "This package provides miscellaneous functions commonly used in other
6564 packages maintained by Yihui Xie.")
6565 (license license:expat)))
6567 (define-public r-utf8
6574 (uri (cran-uri "utf8" version))
6577 "1x6qg19z4qih9lk3mvnmx0vailm1khp5lylw4hlwz6rssj3yw6m7"))))
6578 (build-system r-build-system)
6580 (list r-knitr r-rmarkdown)) ; for vignettes
6581 (home-page "https://github.com/patperry/r-utf8")
6582 (synopsis "Unicode text processing")
6584 "This package provides tools to process and print UTF-8 encoded
6585 international text (Unicode). Input, validate, normalize, encode, format, and
6587 (license license:asl2.0)))
6589 (define-public r-zeallot
6596 (uri (cran-uri "zeallot" version))
6599 "1sd1igcfnv27pa3bqxlbyxchi562h7grnjg1l7wxx3bwr49i57s3"))))
6600 (build-system r-build-system)
6601 (home-page "https://github.com/nteetor/zeallot")
6602 (synopsis "Multiple, unpacking, and destructuring assignment")
6604 "This package provides a @code{%<-%} operator to perform multiple,
6605 unpacking, and destructuring assignment in R. The operator unpacks the
6606 right-hand side of an assignment into multiple values and assigns these values
6607 to variables on the left-hand side of the assignment.")
6608 (license license:expat)))
6610 (define-public r-zlog
6616 (uri (cran-uri "zlog" version))
6619 "1d5j31p0h3rrn230087h3ngpvwknlisjv0f1qdbicdj9m177spci"))))
6620 (properties `((upstream-name . "zlog")))
6621 (build-system r-build-system)
6622 (native-inputs (list r-knitr))
6623 (home-page "https://cran.r-project.org/package=zlog")
6624 (synopsis "Transformation for laboratory easurements")
6626 "The @code{zlog} package offers functions to transform laboratory
6627 measurements into standardised z or @math{z(log)-values}. Therefore the lower
6628 and upper reference limits are needed. If these are not known they could be
6629 estimated from a given sample.")
6630 (license license:gpl3+)))
6632 (define-public r-vctrs
6639 (uri (cran-uri "vctrs" version))
6642 "1pb0wjpwix29q8d8p3wi72a9mp9mif7369pk31w238cs00g8hxln"))))
6643 (build-system r-build-system)
6645 (list r-cli r-glue r-rlang))
6648 (home-page "https://github.com/r-lib/vctrs")
6649 (synopsis "Vector helpers")
6651 "There are three main goals to the @code{vctrs} package:
6654 @item To propose @code{vec_size()} and @code{vec_type()} as alternatives to
6655 @code{length()} and @code{class()}. These definitions are paired with a
6656 framework for type-coercion and size-recycling.
6657 @item To define type- and size-stability as desirable function properties, use
6658 them to analyse existing base function, and to propose better alternatives.
6659 This work has been particularly motivated by thinking about the ideal
6660 properties of @code{c()}, @code{ifelse()}, and @code{rbind()}.
6661 @item To provide a new @code{vctr} base class that makes it easy to create new
6662 S3 vectors. @code{vctrs} provides methods for many base generics in terms of
6663 a few new @code{vctrs} generics, making implementation considerably simpler
6666 (license license:gpl3)))
6668 (define-public r-pillar
6675 (uri (cran-uri "pillar" version))
6678 "1fqk18vc9ashf12gdqkdi6n1nj5lh324vwhgiib3b2fcb2bghhbq"))))
6679 (build-system r-build-system)
6692 (home-page "https://github.com/r-lib/pillar")
6693 (synopsis "Coloured formatting for columns")
6695 "This package provides a @code{pillar} generic designed for formatting
6696 columns of data using the full range of colours provided by modern
6698 (license license:gpl3)))
6700 (define-public r-pinfsc50
6706 (uri (cran-uri "pinfsc50" version))
6709 "1547xyxmfb7zi8h9bsm6k67dcw4hpp129xzvmgwfw7r6p4af47zd"))))
6710 (build-system r-build-system)
6711 (home-page "https://cran.r-project.org/web/packages/pinfsc50/")
6712 (synopsis "Genomic data for the plant pathogen Phytophthora infestans")
6713 (description "This package contains genomic data for the plant pathogen
6714 Phytophthora infestans. It includes a variant file, a sequence file and an
6715 annotation file. This package is intended to be used as example data for
6716 packages that work with genomic data.")
6717 (license license:gpl2+)))
6719 (define-public r-uuid
6726 (uri (cran-uri "uuid" version))
6729 "0bzlc2knmr338h4ykx8v8c2a1inizxafj8rh13kwii68gpp50nz7"))))
6730 (build-system r-build-system)
6731 (home-page "https://www.rforge.net/uuid")
6732 (synopsis "Tools for generating and handling of UUIDs")
6734 "This package provides tools for generating and handling of
6735 @dfn{Universally Unique Identifiers} (UUIDs).")
6736 (license license:expat)))
6738 (define-public r-tinytex
6745 (uri (cran-uri "tinytex" version))
6748 "1v95pjxdq0ma90jji5yqh8ihlcf35cmrqx9v0z649zh0q9vrnbpj"))))
6749 (build-system r-build-system)
6752 (home-page "https://github.com/yihui/tinytex")
6753 (synopsis "Helper functions for TeX Live and compiling LaTeX documents")
6755 "This package provides helper functions to install and maintain the LaTeX
6756 distribution named TinyTeX, a lightweight, cross-platform, portable, and
6757 easy-to-maintain version of TeX Live. This package also contains helper
6758 functions to compile LaTeX documents, and install missing LaTeX packages
6760 (license license:expat)))
6762 (define-public r-tinytest
6769 (uri (cran-uri "tinytest" version))
6772 "1mq31f7bzcz5bkgzl9khm1i80axfzra7gcjqxd2yqb4wrw1m3x4s"))))
6773 (properties `((upstream-name . "tinytest")))
6774 (build-system r-build-system)
6775 (home-page "https://github.com/markvanderloo/tinytest")
6776 (synopsis "Lightweight unit testing framework")
6778 "This package provides a lightweight unit testing framework. Main
6782 @item install tests with the package;
6783 @item test results are treated as data that can be stored and manipulated;
6784 @item test files are R scripts interspersed with test commands, that can be
6786 @item fully automated build-install-test sequence for packages;
6787 @item skip tests when not run locally (e.g. on CRAN);
6788 @item flexible and configurable output printing;
6789 @item compare computed output with output stored with the package;
6790 @item run tests in parallel;
6791 @item extensible by other packages;
6792 @item report side effects.
6795 (license license:gpl3)))
6797 (define-public r-network
6804 (uri (cran-uri "network" version))
6807 "1xrhzbci7ls4h05skdlirxl49jsvmylrqivz2kd6i33wh2ca324m"))))
6808 (build-system r-build-system)
6810 (list r-magrittr r-statnet-common r-tibble))
6811 (home-page "https://statnet.org/")
6812 (synopsis "Classes for relational data")
6814 "This package provides tools to create and modify network objects. The
6815 @code{network} class can represent a range of relational data types, and
6816 supports arbitrary vertex/edge/graph attributes.")
6817 (license license:gpl2+)))
6819 (define-public r-stabs
6826 (uri (cran-uri "stabs" version))
6829 "1nf1yg14cgxrs4np1yghpzw1nczaslfv3rvf3918wrlzg0vp6l7q"))))
6830 (build-system r-build-system)
6833 (home-page "https://github.com/hofnerb/stabs")
6834 (synopsis "Stability selection with error control")
6836 "This package provides resampling procedures to assess the stability of
6837 selected variables with additional finite sample error control for
6838 high-dimensional variable selection procedures such as Lasso or boosting.
6839 Both, standard stability selection (Meinshausen & Buhlmann, 2010) and
6840 complementary pairs stability selection with improved error bounds
6841 (Shah & Samworth, 2013) are implemented. The package can be combined with
6842 arbitrary user specified variable selection approaches.")
6843 (license license:gpl2)))
6845 (define-public r-rle
6852 (uri (cran-uri "rle" version))
6855 "0sagl0jggg40lihzy7pfq4593rfvc3b3f7g6ggi85s7n18qvwg40"))))
6856 (properties `((upstream-name . "rle")))
6857 (build-system r-build-system)
6858 (home-page "https://cran.r-project.org/web/packages/rle/")
6859 (synopsis "Common functions for run-length encoded vectors")
6861 "This package provides common @code{base} and @code{stats} methods for
6862 @code{rle} objects, aiming to make it possible to treat them transparently as
6864 (license license:gpl3)))
6866 (define-public r-statnet-common
6868 (name "r-statnet-common")
6873 (uri (cran-uri "statnet.common" version))
6876 "07djgc6qbxahiy5v15lfayxbj4188lxsb8xcs7hnbm2hic953bfx"))))
6878 `((upstream-name . "statnet.common")))
6879 (build-system r-build-system)
6882 (home-page "https://statnet.org")
6883 (synopsis "R scripts and utilities used by the Statnet software")
6884 (description "This package provides non-statistical utilities used by the
6885 software developed by the Statnet Project.")
6886 (license license:gpl3)))
6888 (define-public r-statcheck
6890 (name "r-statcheck")
6895 (uri (cran-uri "statcheck" version))
6898 "0ivybdcrymlsfv6pg6p5bv70qdvgxf2vgp0kf4r0pf2fcvav1mcp"))))
6899 (build-system r-build-system)
6901 (list r-ggplot2 r-plyr r-rmarkdown))
6902 (home-page "https://cran.r-project.org/web/packages/statcheck/")
6903 (synopsis "Extract statistics from articles and recompute p-values")
6904 (description "This package can automatically extract statistical
6905 null-hypothesis significant testing (NHST) results from articles and recompute
6906 the p-values based on the reported test statistic and degrees of freedom to
6907 detect possible inconsistencies.")
6908 (license license:gpl2)))
6910 (define-public r-sna
6917 (uri (cran-uri "sna" version))
6920 "0ai0v4538d30m4wks5s3lch1yfmx1ml0nnrz7ihs097lv586a09s"))))
6921 (build-system r-build-system)
6923 (list r-network r-statnet-common))
6924 (home-page "https://statnet.org")
6925 (synopsis "Tools for social network analysis")
6927 "This package provides a range of tools for social network analysis,
6928 including node and graph-level indices, structural distance and covariance
6929 methods, structural equivalence detection, network regression, random graph
6930 generation, and 2D/3D network visualization.")
6931 (license license:gpl2+)))
6933 (define-public r-tfisher
6940 (uri (cran-uri "TFisher" version))
6943 "0vz74ww1lf1prfwz74hfsi3a8nzq8ss7aqjr85c1d87vss2796xx"))))
6944 (properties `((upstream-name . "TFisher")))
6945 (build-system r-build-system)
6947 (list r-matrix r-mvtnorm r-sn))
6948 (home-page "https://cran.r-project.org/web/packages/TFisher/")
6949 (synopsis "Optimal thresholding Fisher's p-value combination method")
6951 "This package provides the @dfn{cumulative distribution function} (CDF),
6952 quantile, and statistical power calculator for a collection of thresholding
6953 Fisher's p-value combination methods, including Fisher's p-value combination
6954 method, truncated product method and, in particular, soft-thresholding
6955 Fisher's p-value combination method which is proven to be optimal in some
6956 context of signal detection. The p-value calculator for the omnibus version
6957 of these tests are also included.")
6958 (license license:gpl2)))
6960 (define-public r-ttr
6967 (uri (cran-uri "TTR" version))
6970 "11xsmbvmxq2j119j2z58bx1fkkb2xlhmzc35z5fbwr3nchrfz6jd"))))
6971 (properties `((upstream-name . "TTR")))
6972 (build-system r-build-system)
6974 (list r-curl r-xts r-zoo))
6975 (home-page "https://github.com/joshuaulrich/TTR")
6976 (synopsis "Technical trading rules")
6978 "This package provides functions and data to construct technical trading
6980 (license license:gpl2)))
6982 (define-public r-leaflet-providers
6984 (name "r-leaflet-providers")
6989 (uri (cran-uri "leaflet.providers" version))
6991 (base32 "0yynrwv4xd5cdh49cwvfxm4ranarah9iiry2cd3b4fiihdfcg3wy"))))
6992 (properties `((upstream-name . "leaflet.providers")))
6993 (build-system r-build-system)
6994 (home-page "https://github.com/rstudio/leaflet.providers")
6995 (synopsis "Leaflet map tile providers")
6997 "This package contains third-party map tile provider information from
6998 Leaflet.js, to be used with the @code{leaflet} R package. Additionally,
6999 @code{leaflet.providers} enables users to retrieve up-to-date provider
7000 information between package updates.")
7001 (license license:bsd-2)))
7003 ;; This package contains a lot of minified JavaScript with unclear provenance.
7004 ;; When upgrading please make sure that all minified JavaScript files are
7005 ;; removed in a snippet and that the replacement sources correspond to the
7006 ;; original minified scripts.
7007 (define-public r-leaflet
7014 (uri (cran-uri "leaflet" version))
7016 (base32 "0xsng9n08i1w7qj4hbi706m6d8jm9ixrnwq5xac2s3csfm1s1xij"))
7020 (list "inst/htmlwidgets/lib/leaflet/leaflet.js"
7021 "inst/htmlwidgets/lib/leaflet-measure/leaflet-measure.min.js"
7022 "inst/htmlwidgets/lib/leaflet-omnivore/leaflet-omnivore.min.js"
7023 "inst/htmlwidgets/lib/jquery/jquery.min.js"
7024 "inst/htmlwidgets/plugins/Leaflet-MiniMap/Control.MiniMap.min.js"
7025 "inst/htmlwidgets/plugins/Leaflet.awesome-markers/bootstrap.min.js"
7026 "inst/htmlwidgets/plugins/Leaflet.awesome-markers/leaflet.awesome-markers.min.js"
7027 "inst/htmlwidgets/plugins/Leaflet.markercluster/leaflet.markercluster.js"
7028 "inst/htmlwidgets/plugins/Leaflet.markercluster/leaflet.markercluster.freezable.js"
7029 "inst/htmlwidgets/plugins/Leaflet.markercluster/leaflet.markercluster.layersupport.js"
7030 "inst/legacy/www/leaflet.js")))))
7031 (properties `((upstream-name . "leaflet")))
7032 (build-system r-build-system)
7034 `(#:modules ((guix build utils)
7035 (guix build r-build-system)
7038 (modify-phases %standard-phases
7039 (add-after 'unpack 'process-javascript
7040 (lambda* (#:key inputs #:allow-other-keys)
7041 ;; The inst directory contains some minified JavaScript files.
7042 ;; Regenerate them from sources.
7043 (invoke "unzip" "-d" "/tmp" (assoc-ref inputs "js-leaflet"))
7044 (with-directory-excursion "inst/"
7048 `(("/tmp/leaflet-src.js"
7049 "htmlwidgets/lib/leaflet/leaflet.js")
7050 (,(assoc-ref inputs "js-leaflet-measure")
7051 "htmlwidgets/lib/leaflet-measure/leaflet-measure.min.js")
7052 (,(assoc-ref inputs "js-leaflet-omnivore")
7053 "htmlwidgets/lib/leaflet-omnivore/leaflet-omnivore.min.js")
7054 (,(assoc-ref inputs "js-jquery")
7055 "htmlwidgets/lib/jquery/jquery.min.js")
7056 ("htmlwidgets/plugins/Leaflet-MiniMap/Control.MiniMap.js"
7057 "htmlwidgets/plugins/Leaflet-MiniMap/Control.MiniMap.min.js")
7058 (,(assoc-ref inputs "js-bootstrap3")
7059 "htmlwidgets/plugins/Leaflet.awesome-markers/bootstrap.min.js")
7060 ("htmlwidgets/plugins/Leaflet.awesome-markers/leaflet.awesome-markers.js"
7061 "htmlwidgets/plugins/Leaflet.awesome-markers/leaflet.awesome-markers.min.js")
7062 (,(string-append (assoc-ref inputs "js-leaflet-markercluster")
7063 "/dist/leaflet.markercluster-src.js")
7064 "htmlwidgets/plugins/Leaflet.markercluster/leaflet.markercluster.js")
7065 (,(assoc-ref inputs "js-leaflet-markercluster-freezable")
7066 "htmlwidgets/plugins/Leaflet.markercluster/leaflet.markercluster.freezable.js")
7067 (,(assoc-ref inputs "js-leaflet-markercluster-layersupport")
7068 "htmlwidgets/plugins/Leaflet.markercluster/leaflet.markercluster.layersupport.js")
7069 (,(assoc-ref inputs "js-proj4leaflet")
7070 "htmlwidgets/plugins/Proj4Leaflet/proj4.min.js")
7071 ("legacy/www/leaflet-src.js"
7072 "legacy/www/leaflet.js"))))
7073 (lambda (sources targets)
7074 (for-each (lambda (source target)
7075 (format #true "Processing ~a --> ~a~%"
7077 (invoke "esbuild" source "--minify"
7078 (string-append "--outfile=" target)))
7079 sources targets)))))))))
7081 `(("esbuild" ,esbuild)
7086 (uri "https://raw.githubusercontent.com/twbs/bootstrap/v3.3.7/dist/js/bootstrap.js")
7089 "1j1qjagwj0m3q322z9wxxnpkd8zbk6g3kl047dsbmqad6gmqvgha"))))
7093 (uri "https://code.jquery.com/jquery-1.12.4.js")
7096 "0x9mrc1668icvhpwzvgafm8xm11x9lfai9nwr66aw6pjnpwkc3s3"))))
7100 (uri "http://cdn.leafletjs.com/leaflet/v1.3.1/leaflet.zip")
7103 "10phzd2vczy3zm1b64whp2nna69cf9hlj2bndc9yq47vf3ddqx8f"))))
7104 ("js-leaflet-omnivore"
7107 (uri (string-append "https://api.tiles.mapbox.com/mapbox.js/plugins/"
7108 "leaflet-omnivore/v0.3.1/leaflet-omnivore.js"))
7111 "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq"))))
7112 ("js-leaflet-markercluster"
7116 (url "https://github.com/Leaflet/Leaflet.markercluster.git")
7118 (file-name (git-file-name "js-leaflet-markercluster" "1.1.0"))
7121 "0ds8c7picqjmc86bm5n6hm8k71fwsa2cpgib19sbdamzr9hm0rs1"))))
7122 ("js-leaflet-markercluster-freezable"
7126 "https://raw.githubusercontent.com/ghybs/Leaflet.MarkerCluster.Freezable/"
7127 "9db80a3fba7dff4aee940e05d3d4dceaa1fffcf9/src/freezable.js"))
7128 (file-name "leaflet-markercluster-freezable.js")
7131 "1k6sn5n0z2x3an91vwvkzmqq4b8ppswgk5hi5qrr79klas1hbx1k"))))
7132 ("js-leaflet-markercluster-layersupport"
7136 "https://raw.githubusercontent.com/ghybs/Leaflet.MarkerCluster.LayerSupport/"
7137 "87f3848b92e0516d9c98f6d4cd175f7b8a4e3805/src/layersupport.js"))
7138 (file-name "leaflet-markercluster-layersupport.js")
7141 "15qa21xif94y762c65yxxysxykz3mma6y6agw3nxpr3s7wbb75ff"))))
7142 ("js-leaflet-measure"
7145 (uri "https://unpkg.com/leaflet-measure@1.5.2/dist/leaflet-measure.js")
7146 (file-name "js-leaflet-measure-1.5.2.js")
7149 "0ggg3ffmm7pj9ry4gssrh0a17pnad3p6gwi0dg98y819pmpqa7y0"))))
7153 (uri "https://raw.githubusercontent.com/kartena/Proj4Leaflet/1.0.2/lib/proj4.js")
7154 (file-name "js-proj4leaflet-1.0.2.js")
7157 "0vyrbf6gv2lyh4c2bzp5349ivwvvg28gpn87y52a7jdb13rlkpab"))))))
7172 (home-page "https://rstudio.github.io/leaflet/")
7173 (synopsis "Create interactive web maps with the JavaScript Leaflet library")
7175 "Create and customize interactive maps using the Leaflet JavaScript
7176 library and the @code{htmlwidgets} package. These maps can be used directly
7177 from the R console, from RStudio, in Shiny applications and R Markdown
7179 (license license:gpl3)))
7181 (define-public r-leaps
7188 (uri (cran-uri "leaps" version))
7191 "1dn3yl1p03n0iynd1vsdkrr0fhmvgrmfkv37y7n371765h83lz1x"))))
7192 (build-system r-build-system)
7193 (native-inputs (list gfortran))
7194 (home-page "https://cran.r-project.org/web/packages/leaps/")
7195 (synopsis "Regression subset selection")
7197 "This package provides tools for regression subset selection, including
7198 exhaustive search.")
7199 (license license:gpl2+)))
7201 (define-public r-splus2r
7208 (uri (cran-uri "splus2R" version))
7211 "035zd22zcpkh74rik9ws6g8al6vjz7jgrqs5si361bzb5n290p3x"))))
7212 (properties `((upstream-name . "splus2R")))
7213 (build-system r-build-system)
7214 (home-page "https://cran.r-project.org/web/packages/splus2R/")
7215 (synopsis "Supplemental S-PLUS functionality in R")
7217 "Currently there are many functions in S-PLUS that are missing in R. To
7218 facilitate the conversion of S-PLUS packages to R packages, this package
7219 provides some missing S-PLUS functionality in R.")
7220 (license license:gpl2)))
7222 (define-public r-ifultools
7224 (name "r-ifultools")
7229 (uri (cran-uri "ifultools" version))
7232 "16a7rbvlym3bnfm93ikr5kl0l86ppk0s41fva6idvcx765g3fqkk"))))
7233 (build-system r-build-system)
7235 (list r-mass r-splus2r))
7236 (home-page "https://cran.r-project.org/web/packages/ifultools/")
7237 (synopsis "Insightful research tools")
7238 (description "This package provides C code used by the wmtsa, fractal, and
7240 (license license:gpl2)))
7242 (define-public r-sapa
7249 (uri (cran-uri "sapa" version))
7252 "0kj681rd4c2lvqr926lb6f4qwp281x5274dg6vbk8pf5y7s0qlpc"))))
7253 (build-system r-build-system)
7255 (list r-ifultools r-splus2r))
7256 (home-page "https://cran.r-project.org/web/packages/sapa/")
7257 (synopsis "Spectral analysis for physical applications")
7258 (description "This package provides software for the book Spectral
7259 Analysis for Physical Applications, Donald B. Percival and Andrew T. Walden,
7260 Cambridge University Press, 1993.")
7261 (license license:gpl2)))
7263 (define-public r-aggregation
7265 (name "r-aggregation")
7270 (uri (cran-uri "aggregation" version))
7273 "0j9g604m2ccc7hcy02539yja9cf3xcbl25gvp838bp4x8w18my46"))))
7274 (build-system r-build-system)
7275 (home-page "https://cran.r-project.org/web/packages/aggregation/")
7276 (synopsis "Methods for p-value aggregation")
7278 "This package contains functionality for performing the following methods
7279 of p-value aggregation: Fisher's method, the Lancaster method (weighted
7280 Fisher's method), and Sidak correction.")
7281 (license license:gpl3)))
7283 (define-public r-quantmod
7290 (uri (cran-uri "quantmod" version))
7293 "154fqhw46kc7r08zsj5fsg97hg93phsli3z14xwmz22xb50xymzp"))))
7294 (build-system r-build-system)
7296 (list r-curl r-ttr r-xts r-zoo))
7297 (home-page "https://cran.r-project.org/web/packages/quantmod/")
7298 (synopsis "Quantitative financial modelling framework")
7299 (description "This package provides a quantitative financial modelling
7300 framework to allow users to specify, build, trade, and analyse quantitative
7301 financial trading strategies.")
7302 (license license:gpl3)))
7304 (define-public r-tseries
7311 (uri (cran-uri "tseries" version))
7314 "0zr09ikaz96djcvnjbr8ah6waqzjy06f4yd4isshlwc391q20px5"))))
7315 (build-system r-build-system)
7317 (list r-quadprog r-quantmod r-zoo))
7320 (home-page "https://cran.r-project.org/web/packages/tseries/")
7321 (synopsis "Time series analysis and computational finance")
7323 "This package provides functions relating to time series analysis and
7324 computational finance.")
7325 (license license:gpl2)))
7327 (define-public r-wmtsa
7334 (uri (cran-uri "wmtsa" version))
7337 "1q436krz5p1f4a7a7sya6a9rh9x9mi8zzcgq66gbk9w9w4hcqcj6"))))
7338 (build-system r-build-system)
7340 (list r-ifultools r-mass r-splus2r))
7341 (home-page "https://cran.r-project.org/web/packages/wmtsa/")
7342 (synopsis "Wavelet methods for time series analysis")
7344 "This package provides software to accompany the book \"Wavelet Methods
7345 for Time Series Analysis\", Donald B. Percival and Andrew T. Walden, Cambridge
7346 University Press, 2000.")
7347 (license license:gpl2)))
7349 (define-public r-tsa
7356 (uri (cran-uri "TSA" version))
7359 "1bv5q609lhmrcxnjnvcj497fbjlv89zwa8q918hw4iki5nkvwwdb"))))
7360 (properties `((upstream-name . "TSA")))
7361 (build-system r-build-system)
7363 (list r-leaps r-locfit r-mgcv r-tseries))
7364 (home-page "https://homepage.divms.uiowa.edu/~kchan/TSA.htm")
7365 (synopsis "Time series analysis")
7367 "This package contains R functions and datasets detailed in the book
7368 \"Time Series Analysis with Applications in R (second edition)\" by Jonathan
7369 Cryer and Kung-Sik Chan.")
7370 (license license:gpl2+)))
7372 (define-public r-extradistr
7374 (name "r-extradistr")
7379 (uri (cran-uri "extraDistr" version))
7382 "1gypnbvdzczl0mvznvy8r7hzsvc5gvdvi2mmzj21cqdw9n63944r"))))
7383 (properties `((upstream-name . "extraDistr")))
7384 (build-system r-build-system)
7387 (home-page "https://github.com/twolodzko/extraDistr")
7388 (synopsis "Additional univariate and multivariate distributions")
7390 "This package implements density, distribution functions, quantile
7391 functions and random generation functions for a large number of univariate and
7392 multivariate distributions.")
7393 (license license:gpl2)))
7395 (define-public r-fractal
7402 (uri (cran-uri "fractal" version))
7405 "18lr9z0gslvfc3z8vyj3krqj3bfhg60zv1fzinrwwkc4cpk1w7mp"))))
7406 (build-system r-build-system)
7414 (home-page "https://cran.r-project.org/web/packages/fractal/")
7415 (synopsis "Fractal time series modeling and analysis")
7417 "This package provides tools for stochastic fractal and deterministic
7418 chaotic time series analysis.")
7419 (license license:gpl2)))
7421 (define-public r-urca
7428 (uri (cran-uri "urca" version))
7431 "1akaqwf3fvvvx4sgfn641fd4sj51s0701pvfl6s5hnz2k0iwh732"))))
7432 (build-system r-build-system)
7433 (propagated-inputs (list r-nlme))
7434 (native-inputs (list gfortran))
7435 (home-page "https://cran.r-project.org/web/packages/urca/")
7436 (synopsis "Unit root and cointegration tests for time series data")
7438 "This package provides unit root and cointegration tests encountered in
7439 applied econometric analysis.")
7440 (license license:gpl2+)))
7442 (define-public r-cubature
7449 (uri (cran-uri "cubature" version))
7452 "0sfmcy5xpa40w3qn0jbg7b802wksl5k8glz9jpx77n159wn3nyq8"))))
7453 (build-system r-build-system)
7458 (home-page "https://github.com/bnaras/cubature")
7459 (synopsis "Adaptive multivariate integration over hypercubes")
7461 "This package is an R wrapper around the cubature C library for adaptive
7462 multivariate integration over hypercubes. This version provides both
7463 @code{hcubature} and @code{pcubature} routines in addition to a vector
7465 ;; The included cubature C library is released under GPLv2+, but the
7466 ;; wrapper declares the license to be GPLv3+.
7467 (license (list license:gpl2+ license:gpl3+))))
7469 (define-public r-trend
7476 (uri (cran-uri "trend" version))
7479 "1mr5g5gaxiqj6x83ngcbwwh57vhrhcz0x9dh0rmvs9y2ivk29ccs"))))
7480 (build-system r-build-system)
7482 (list r-extradistr))
7485 (home-page "https://cran.r-project.org/web/packages/trend/")
7486 (synopsis "Non-parametric trend tests and change-point detection")
7488 "The analysis of environmental data often requires the detection of
7489 trends and change-points. This package includes tests for trend
7490 detection (Cox-Stuart Trend Test, Mann-Kendall Trend Test, (correlated)
7491 Hirsch-Slack Test, partial Mann-Kendall Trend Test, multivariate (multisite)
7492 Mann-Kendall Trend Test, (Seasonal) Sen's slope, partial Pearson and Spearman
7493 correlation trend test), change-point detection (Lanzante's test procedures,
7494 Pettitt's test, Buishand Range Test, Buishand U Test, Standard Normal
7495 Homogeinity Test), detection of non-randomness (Wallis-Moore Phase Frequency
7496 Test, Bartels rank von Neumann's ratio test, Wald-Wolfowitz Test) and the two
7497 sample Robust Rank-Order Distributional Test.")
7498 (license license:gpl3)))
7500 (define-public r-expm
7507 (uri (cran-uri "expm" version))
7510 "1p5dapwv8ycxaysgi6imnby04i4kh1c5a2czqa4wygz0s8pr2y9c"))))
7511 (build-system r-build-system)
7512 (propagated-inputs (list r-matrix))
7513 (native-inputs (list gfortran))
7514 (home-page "https://r-forge.r-project.org/projects/expm/")
7515 (synopsis "Tools for matrix exponentials and related quantities")
7517 "This package provides tools for the computation of the matrix
7518 exponential, logarithm, square root, and related quantities.")
7519 (license license:gpl2+)))
7521 (define-public r-complexplus
7523 (name "r-complexplus")
7528 (uri (cran-uri "complexplus" version))
7531 "16w9v7d1ckavqmr86l34frr37pkvdn0iqnb17ssb8xaggns5lgqx"))))
7532 (build-system r-build-system)
7534 (list r-expm r-matrix))
7535 (home-page "https://cran.r-project.org/web/packages/complexplus/")
7536 (synopsis "Functions of complex or real variables")
7538 "This package extends several functions to the complex domain, including
7539 the matrix exponential and logarithm, and the determinant.")
7540 (license license:gpl2)))
7542 (define-public r-phontools
7544 (name "r-phontools")
7549 (uri (cran-uri "phonTools" version))
7552 "01i481mhswsys3gpasw9gn6nxkfmi7bz46g5c84m13pg0cv8hxc7"))))
7553 (properties `((upstream-name . "phonTools")))
7554 (build-system r-build-system)
7555 (home-page "http://www.santiagobarreda.com/rscripts.html")
7556 (synopsis "Tools for phonetic and acoustic analyses")
7558 "This package contains tools for the organization, display, and analysis
7559 of the sorts of data frequently encountered in phonetics research and
7560 experimentation, including the easy creation of IPA vowel plots, and the
7561 creation and manipulation of WAVE audio files.")
7562 (license license:bsd-2)))
7571 (uri (cran-uri "np" version))
7574 "1a9kzn37cddwfdki5zjmzanxp75pccdjnsvqfrh84hhcsy51pcx3"))))
7575 (build-system r-build-system)
7577 (list r-boot r-cubature r-quadprog r-quantreg))
7578 (home-page "https://github.com/JeffreyRacine/R-Package-np")
7579 (synopsis "Non-parametric kernel smoothing methods for mixed data types")
7580 (description "This package provides non-parametric (and semi-parametric)
7581 kernel methods that seamlessly handle a mix of continuous, unordered, and
7582 ordered factor data types.")
7583 ;; Any version of the GPL.
7584 (license license:gpl3+)))
7586 (define-public r-powerplus
7588 (name "r-powerplus")
7593 (uri (cran-uri "powerplus" version))
7596 "0ayp6x34hkzgris4j3zbbs0r23n81bhww3wgfyy630ri4sk6brrn"))))
7597 (build-system r-build-system)
7599 (list r-complexplus r-expm r-mass r-matrix r-phontools))
7600 (home-page "https://cran.r-project.org/web/packages/powerplus/")
7601 (synopsis "Exponentiation operations")
7603 "This package provides tools for the computation of matrix and scalar
7605 (license license:gpl2)))
7607 (define-public r-egg
7614 (uri (cran-uri "egg" version))
7617 "1fy7srpiavfn8kyrr1m84an7acgwi6ydzrg71m3b0vk7y9ybmj0m"))))
7618 (properties `((upstream-name . "egg")))
7619 (build-system r-build-system)
7621 (list r-ggplot2 r-gridextra r-gtable))
7622 (home-page "https://cran.r-project.org/web/packages/egg")
7623 (synopsis "Extensions for ggplot2")
7625 "This package provides miscellaneous functions to help customize ggplot2
7626 objects. High-level functions are provided to post-process ggplot2 layouts
7627 and allow alignment between plot panels, as well as setting panel sizes to
7628 fixed values. Other functions include a custom @code{geom}, and helper
7629 functions to enforce symmetric scales or add tags to facetted plots.")
7630 (license license:gpl3)))
7632 (define-public r-heatmap3
7639 (uri (cran-uri "heatmap3" version))
7642 "0sfvizmmwfk1bjhn6zfx5a4qqfgj1ldg8x90b65crqibgfa36k2r"))))
7643 (build-system r-build-system)
7645 (list r-fastcluster))
7648 (home-page "https://cran.r-project.org/web/packages/heatmap3/")
7649 (synopsis "Improved heatmap package")
7651 "This package provides an improved heatmap package. It is completely
7652 compatible with the original R function @code{heatmap}, and provides more
7653 powerful and convenient features.")
7654 (license license:gpl2+)))
7656 (define-public r-heatmaply
7658 (name "r-heatmaply")
7663 (uri (cran-uri "heatmaply" version))
7666 "1w8yyzb68laxd4zxycvgmpqj5wnyidjgv1vbzbxndp9p92f2cp8a"))))
7667 (build-system r-build-system)
7685 (home-page "https://cran.r-project.org/package=heatmaply")
7686 (synopsis "Interactive cluster heat maps using plotly")
7688 "This package enables you to create interactive cluster heatmaps that can
7689 be saved as a stand-alone HTML file, embedded in R Markdown documents or in a
7690 Shiny app, and made available in the RStudio viewer pane. Hover the mouse
7691 pointer over a cell to show details or drag a rectangle to zoom. A heatmap is
7692 a popular graphical method for visualizing high-dimensional data, in which a
7693 table of numbers is encoded as a grid of colored cells. The rows and columns
7694 of the matrix are ordered to highlight patterns and are often accompanied by
7696 ;; Either version of the license.
7697 (license (list license:gpl2 license:gpl3))))
7706 (uri (cran-uri "h5" version))
7709 "14p7i1sj24ky87kd7qr3n9fc9l64s0bp0rwbyl6i2x69xn75gpsx"))))
7710 (build-system r-build-system)
7717 (home-page "https://github.com/mannau/h5")
7718 (synopsis "Interface to the HDF5 Library")
7720 "This package provides an S4 interface to the HDF5 library supporting
7721 fast storage and retrieval of R-objects like vectors, matrices and arrays to
7722 binary files in a language independent format. The HDF5 format can therefore
7723 be used as an alternative to R's save/load mechanism. Since h5 is able to
7724 access only subsets of stored data it can also handle data sets which do not
7726 (license license:bsd-2)))
7728 (define-public r-cgdsr
7735 (uri (cran-uri "cgdsr" version))
7738 "07yc819hkabpzzh0g0cbqza6bcfy67b2marrzz1lj97f9iba78ja"))))
7739 (build-system r-build-system)
7741 (list r-httr r-r-methodss3 r-r-oo))
7742 (home-page "https://github.com/cBioPortal/cgdsr")
7743 (synopsis "R-based API for accessing the MSKCC Cancer Genomics Data Server")
7745 "This package provides a basic set of R functions for querying the Cancer
7746 Genomics Data Server (CGDS), hosted by the Computational Biology Center at
7747 Memorial-Sloan-Kettering Cancer Center (MSKCC).")
7748 (license license:lgpl3)))
7750 (define-public r-import
7757 (uri (cran-uri "import" version))
7760 "19g4jnfg9pkvvsncw62yc15xlb97hfbdqxivpjd9jqi36i6mdjrg"))))
7761 (build-system r-build-system)
7764 (home-page "https://github.com/smbache/import")
7765 (synopsis "Import mechanism for R")
7767 "This is an alternative mechanism for importing objects from packages.
7768 The syntax allows for importing multiple objects from a package with a single
7769 command in an expressive way. The import package bridges some of the gap
7770 between using @code{library} (or @code{require}) and direct (single-object)
7771 imports. Furthermore the imported objects are not placed in the current
7772 environment. It is also possible to import objects from stand-alone @code{.R}
7774 (license license:expat)))
7776 (define-public r-shinyace
7783 (uri (cran-uri "shinyAce" version))
7786 "12mqvdh6rxsr61pc3pzla95r5f4l7xagjs2rcdr7c2lbqyxpx6aa"))))
7787 (properties `((upstream-name . "shinyAce")))
7788 (build-system r-build-system)
7790 (list r-shiny r-jsonlite))
7791 (home-page "https://cran.r-project.org/web/packages/shinyAce/")
7792 (synopsis "Ace editor bindings for Shiny")
7794 "This package provides Ace editor bindings to enable a rich text editing
7795 environment within Shiny.")
7796 (license license:expat)))
7798 (define-public r-rafalib
7805 (uri (cran-uri "rafalib" version))
7807 (base32 "1dmxjl66bfdgrybhwyaa8d4i460liqcdw8b29a6w7shgksh29m0k"))))
7808 (properties `((upstream-name . "rafalib")))
7809 (build-system r-build-system)
7810 (propagated-inputs (list r-rcolorbrewer))
7811 (home-page "https://cran.r-project.org/package=rafalib")
7812 (synopsis "Convenience functions for routine data exploration")
7814 "This package provides a series of shortcuts for routine tasks to
7815 facilitate data exploration.")
7816 (license license:artistic2.0)))
7818 (define-public r-randomizr
7820 (name "r-randomizr")
7825 (uri (cran-uri "randomizr" version))
7828 "1grm0h3xkb0pdbbv0gd531g1kn6njp0gcy5fh153rrmajxgd8hhw"))))
7829 (properties `((upstream-name . "randomizr")))
7830 (build-system r-build-system)
7833 (home-page "https://declaredesign.org/r/randomizr/")
7834 (synopsis "Tools for common forms of random assignment and sampling")
7836 "This package provides tools for generating random assignments for common
7837 experimental designs and random samples for common sampling designs.")
7838 (license license:expat)))
7840 (define-public r-base64url
7842 (name "r-base64url")
7847 (uri (cran-uri "base64url" version))
7850 "0n1c2b68vza1dh7sk38v6biiwm72c4jpl79kpdg1bsb0hq9qy18x"))))
7851 (build-system r-build-system)
7854 (home-page "https://github.com/mllg/base64url")
7855 (synopsis "Fast and URL-safe base64 encoder and decoder")
7857 "This package provides a URL-safe base64 encoder and decoder. In
7858 contrast to RFC3548, the 62nd character (@code{+}) is replaced with @code{-},
7859 the 63rd character (@code{/}) is replaced with @code{_}. Furthermore, the
7860 encoder does not fill the string with trailing @code{=}. The resulting
7861 encoded strings comply to the regular expression pattern @code{[A-Za-z0-9_-]}
7862 and thus are safe to use in URLs or for file names. The package also comes
7863 with a simple base32 encoder/decoder suited for case insensitive file
7865 (license license:gpl3)))
7867 (define-public r-radiant-data
7869 (name "r-radiant-data")
7874 (uri (cran-uri "radiant.data" version))
7877 "0c5c99q13pwv6k0b07x3r2bxmh0h2w15h02xb1pincgs61qwi15k"))
7878 (modules '((guix build utils)))
7881 ;; Delete files that are under CC-NC-SA.
7882 (delete-file-recursively "inst/app/tools/help")
7884 (properties `((upstream-name . "radiant.data")))
7885 (build-system r-build-system)
7919 (home-page "https://github.com/radiant-rstats/radiant.data")
7920 (synopsis "Data menu for Radiant: business analytics using R and Shiny")
7922 "The Radiant Data menu includes interfaces for loading, saving, viewing,
7923 visualizing, summarizing, transforming, and combining data. It also contains
7924 functionality to generate reproducible reports of the analyses conducted in
7926 (license license:agpl3)))
7928 (define-public r-algdesign
7930 (name "r-algdesign")
7935 (uri (cran-uri "AlgDesign" version))
7937 (base32 "01cx63wqr6yvgl5ml1lj6gh9p1sn42b6qcnsppcw7mvba9n652ar"))))
7938 (properties `((upstream-name . "AlgDesign")))
7939 (build-system r-build-system)
7940 (home-page "https://github.com/jvbraun/AlgDesign")
7941 (synopsis "Algorithmic experimental design")
7943 "This package provides tools to calculate exact and approximate theory
7944 experimental designs for D, A, and I criteria. Very large designs may be
7945 created. Experimental designs may be blocked or blocked designs created from
7946 a candidate list, using several criteria. The blocking can be done when whole
7947 and within plot factors interact.")
7948 (license license:gpl2+)))
7950 (define-public r-alluvial
7957 (uri (cran-uri "alluvial" version))
7959 (base32 "039frwrsxq1lb97s7vf2vbyyadimkigs628ymym06fxka53drdkp"))))
7960 (properties `((upstream-name . "alluvial")))
7961 (build-system r-build-system)
7962 (native-inputs (list r-knitr))
7963 (home-page "https://github.com/mbojan/alluvial")
7964 (synopsis "Create parallel sets plots (Alluvial Diagrams)")
7966 "This package creates alluvial diagrams (also known as parallel sets
7967 plots) for multivariate and time series-like data.")
7968 (license license:expat)))
7970 (define-public r-signal
7977 (uri (cran-uri "signal" version))
7980 "0qaf39vfmhn3d0bdjqd805ayfkaj48dkmf5dqd47bpk7dp21b837"))))
7981 (build-system r-build-system)
7982 (propagated-inputs (list r-mass))
7983 (native-inputs (list gfortran))
7984 (home-page "https://cran.r-project.org/web/packages/signal/")
7985 (synopsis "Signal processing")
7987 "This package provides a set of signal processing functions originally
7988 written for Matlab and GNU Octave. It includes filter generation utilities,
7989 filtering functions, resampling routines, and visualization of filter models.
7990 It also includes interpolation functions.")
7991 (license license:gpl2)))
7993 (define-public r-gsubfn
8000 (uri (cran-uri "gsubfn" version))
8003 "00j6b8b6xsx6v370h220x233rpk6asca78165y3d48jpwvwisdc9"))))
8004 (build-system r-build-system)
8005 (propagated-inputs (list r-proto))
8006 (home-page "https://code.google.com/archive/p/gsubfn/")
8007 (synopsis "Utilities for strings and function arguments")
8009 "This package provides @code{gsubfn} which is like @code{gsub} but can
8010 take a replacement function or certain other objects instead of the
8011 replacement string. Matches and back references are input to the replacement
8012 function and replaced by the function output. @code{gsubfn} can be used to
8013 split strings based on content rather than delimiters and for quasi-perl-style
8014 string interpolation. The package also has facilities for translating
8015 formulas to functions and allowing such formulas in function calls instead of
8017 (license license:gpl2+)))
8019 (define-public r-sqldf
8026 (uri (cran-uri "sqldf" version))
8029 "0q12vsb53p2wchgp8wfz5bk08wfnm0jxjrakclj4jyy6x3a7ksff"))))
8030 (build-system r-build-system)
8032 (list r-chron r-dbi r-gsubfn r-proto r-rsqlite))
8033 (home-page "https://github.com/ggrothendieck/sqldf")
8034 (synopsis "Manipulate R data frames using SQL")
8036 "The @code{sqldf} function is typically passed a single argument which is
8037 an SQL select statement where the table names are ordinary R data frame names.
8038 @code{sqldf} transparently sets up a database, imports the data frames into
8039 that database, performs the SQL statement and returns the result using a
8040 heuristic to determine which class to assign to each column of the returned
8041 data frame. The @code{sqldf} or @code{read.csv.sql} functions can also be
8042 used to read filtered files into R even if the original files are larger than
8043 R itself can handle.")
8044 (license license:gpl2)))
8046 (define-public r-abind
8053 (uri (cran-uri "abind" version))
8056 "0b1zd8jbnl6l292cr9rb50m09fy3ylxvzkpgi5lfb1nbzddcwfis"))))
8057 (build-system r-build-system)
8058 (home-page "https://cran.r-project.org/web/packages/abind/")
8059 (synopsis "Combine multidimensional arrays")
8061 "This package provides tools to combine multidimensional arrays into a
8062 single array. This is a generalization of @code{cbind} and @code{rbind}. It
8063 works with vectors, matrices, and higher-dimensional arrays. It also provides
8064 the functions @code{adrop}, @code{asub}, and @code{afill} for manipulating,
8065 extracting and replacing data in arrays.")
8066 (license license:lgpl2.0+)))
8068 (define-public r-prroc
8075 (uri (cran-uri "PRROC" version))
8078 "1m28h8pcd78049lz2qixhkcr9h5b3jik3maqzfbvq9y58z71i4a7"))))
8079 (properties `((upstream-name . "PRROC")))
8080 (build-system r-build-system)
8081 (home-page "https://cran.r-project.org/web/packages/PRROC/")
8082 (synopsis "Precision-Recall and ROC curves for weighted and unweighted data")
8084 "This package computes the areas under the @dfn{precision-recall} (PR)
8085 and ROC curve for weighted (e.g. soft-labeled) and unweighted data. In
8086 contrast to other implementations, the interpolation between points of the PR
8087 curve is done by a non-linear piecewise function. In addition to the areas
8088 under the curves, the curves themselves can also be computed and plotted by a
8089 specific S3-method.")
8090 (license license:gpl3)))
8092 (define-public r-vim
8099 (uri (cran-uri "VIM" version))
8102 "0fbpm6y3hhiw8srnbc38k19b859jcqzsh78ib8yvj86gck5av0bm"))))
8103 (properties `((upstream-name . "VIM")))
8104 (build-system r-build-system)
8121 (home-page "https://github.com/alexkowa/VIM")
8122 (synopsis "Visualization and imputation of missing values")
8124 "This package provides tools for the visualization of missing and/or
8125 imputed values are introduced, which can be used for exploring the data and
8126 the structure of the missing and/or imputed values. Depending on this
8127 structure of the missing values, the corresponding methods may help to
8128 identify the mechanism generating the missing values and explore the
8129 data including missing values. In addition, the quality of imputation can be
8130 visually explored using various univariate, bivariate, multiple and
8131 multivariate plot methods.")
8132 (license license:gpl2+)))
8134 (define-public r-fnn
8141 (uri (cran-uri "FNN" version))
8144 "0nmynpiy3d2dnd5ngjf4m79jy02byhk43gj0xny9a6j8243f5c2j"))))
8145 (properties `((upstream-name . "FNN")))
8146 (build-system r-build-system)
8147 (home-page "https://cran.r-project.org/web/packages/FNN")
8148 (synopsis "Fast nearest neighbor search algorithms and applications")
8150 "This package provides cover-tree and kd-tree fast k-nearest neighbor
8151 search algorithms. Related applications including KNN classification,
8152 regression and information measures are implemented.")
8153 ;; The DESCRIPTION file erroneously states that GPL version 2.1 or
8154 ;; later can be used.
8155 (license license:gpl2+)))
8157 (define-public r-smoother
8164 (uri (cran-uri "smoother" version))
8167 "0nqr1bvlr5bnasqg74zmknjjl4x28kla9h5cxpga3kq5z215pdci"))))
8168 (build-system r-build-system)
8171 (home-page "https://cran.r-project.org/web/packages/smoother")
8172 (synopsis "Functions relating to the smoothing of numerical data")
8174 "This package provides a collection of methods for smoothing numerical
8175 data, commencing with a port of the Matlab gaussian window smoothing function.
8176 In addition, several functions typically used in smoothing of financial data
8178 (license license:gpl2)))
8180 (define-public r-riverplot
8182 (name "r-riverplot")
8187 (uri (cran-uri "riverplot" version))
8190 "04ap1dsa7fx03l73jhv1ql3adaaaz2100qawdplxa9xmrllgcgbj"))))
8191 (build-system r-build-system)
8193 (list r-rcolorbrewer))
8196 (home-page "https://logfc.wordpress.com")
8197 (synopsis "Sankey or ribbon plots")
8199 "Sankey plots are a type of diagram that is convenient to illustrate how
8200 flow of information, resources etc. separates and joins, much like observing
8201 how rivers split and merge. For example, they can be used to compare
8202 different clusterings. This package provides an implementation of Sankey
8204 (license license:gpl2+)))
8206 (define-public r-dyn
8213 (uri (cran-uri "dyn" version))
8216 "16fqv9k7yxdgybwzafjkyqm16qpgqz13lcjpi6a1nc8xbzlzh0gb"))))
8217 (build-system r-build-system)
8220 (home-page "https://cran.r-project.org/web/packages/dyn")
8221 (synopsis "Time series regression")
8223 "This package provides the dyn class interfaces @code{ts}, @code{irts},
8224 @code{zoo} and @code{zooreg} time series classes to @code{lm}, @code{glm},
8225 @code{loess}, @code{quantreg::rq}, @code{MASS::rlm},
8226 @code{MCMCpack::MCMCregress()}, @code{quantreg::rq()},
8227 @code{randomForest::randomForest()} and other regression functions, allowing
8228 those functions to be used with time series including specifications that may
8229 contain lags, diffs and missing values.")
8231 (license license:gpl2+)))
8233 (define-public r-dynutils
8240 (uri (cran-uri "dynutils" version))
8242 (base32 "1pcj4igaw1g898xb42kcpzfmqy80xai5ki5bpnkf8hg738wm00qz"))))
8243 (properties `((upstream-name . "dynutils")))
8244 (build-system r-build-system)
8258 (native-inputs (list r-knitr))
8259 (home-page "https://github.com/dynverse/dynutils")
8260 (synopsis "Common functionality for the dynverse packages")
8262 "This package provides common functionality for the
8263 @url{https://dynverse.org,dynverse} packages. dynverse is created to support
8264 the development, execution, and benchmarking of trajectory inference
8266 (license license:expat)))
8268 (define-public r-catdap
8275 (uri (cran-uri "catdap" version))
8278 "0fyhl69z2lznymvpzxra9qvcg85ggzkfjy68c6mzdmf1ja44d2k5"))))
8279 (build-system r-build-system)
8282 (home-page "https://cran.r-project.org/web/packages/catdap/")
8283 (synopsis "Tools for categorical data analysis")
8285 "This package provides functions for analyzing multivariate data.
8286 Dependencies of the distribution of the specified variable (response
8287 variable) to other variables (explanatory variables) are derived and
8288 evaluated by the @dfn{Akaike Information Criterion} (AIC).")
8289 (license license:gpl2+)))
8291 (define-public r-arules
8298 (uri (cran-uri "arules" version))
8301 "05g6ik4z87g83nlicmb380331f84sqchvv1vch49zb7rq6v8gw6r"))))
8302 (build-system r-build-system)
8304 (list r-generics r-matrix))
8305 (home-page "https://github.com/mhahsler/arules")
8306 (synopsis "Mining association rules and frequent itemsets")
8308 "This package provides an infrastructure for representing, manipulating
8309 and analyzing transaction data and patterns (frequent itemsets and association rules).
8310 It also provides C implementations of the association mining algorithms Apriori
8312 (license license:gpl3)))
8314 (define-public r-parsedate
8316 (name "r-parsedate")
8321 (uri (cran-uri "parsedate" version))
8324 "1c2cpsvma3fkx6zp191bpfvf5rmpsr13g8rzqk6ycyb0n7b9k4qy"))))
8325 (build-system r-build-system)
8326 (home-page "https://github.com/gaborcsardi/parsedate")
8328 "Recognize and parse dates in various formats")
8330 "This package provides three functions for dealing with dates:
8331 @code{parse_iso_8601} recognizes and parses all valid ISO 8601 date and
8332 time formats, @code{parse_date} parses dates in unspecified formats,
8333 and @code{format_iso_8601} formats a date in ISO 8601 format.")
8334 (license license:gpl2)))
8336 (define-public r-abc-data
8343 (uri (cran-uri "abc.data" version))
8346 "1bv1n68ah714ws58cf285n2s2v5vn7382lfjca4jxph57lyg8hmj"))))
8347 (properties `((upstream-name . "abc.data")))
8348 (build-system r-build-system)
8349 (home-page "https://cran.r-project.org/web/packages/abc.data/")
8350 (synopsis "Data for Approximate Bayesian Computation (ABC) package")
8352 "This package contains data which are used by functions of the abc
8353 package which implements several @dfn{Approximate Bayesian Computation} (ABC)
8354 algorithms for performing parameter estimation, model selection, and
8356 (license license:gpl3+)))
8358 (define-public r-abc
8365 (uri (cran-uri "abc" version))
8368 "16753lyzk2dfwgdjfyanwacqw3bvrwby52inq4709804labs6lnv"))))
8369 (build-system r-build-system)
8371 (list r-abc-data r-locfit r-mass r-nnet r-quantreg))
8372 (home-page "https://cran.r-project.org/web/packages/abc/")
8373 (synopsis "Tools for Approximate Bayesian Computation (ABC)")
8375 "This package implements several @dfn{Approximate Bayesian
8376 Computation} (ABC) algorithms for performing parameter estimation, model
8377 selection, and goodness-of-fit. Cross-validation tools are also available for
8378 measuring the accuracy of ABC estimates, and to calculate the
8379 misclassification probabilities of different models.")
8380 (license license:gpl3+)))
8382 (define-public r-zip
8389 (uri (cran-uri "zip" version))
8392 "1n5ryjdj3i16b4mdp29wapgaklz3yzas5k8ffx7q6fa0jry9i5cz"))))
8393 (build-system r-build-system)
8394 (home-page "https://github.com/gaborcsardi/zip")
8395 (synopsis "Cross-platform Zip compression")
8397 "This package provides a cross-platform Zip compression library for R.
8398 It is a replacement for the @code{zip} function, that does not require any
8399 additional external tools on any platform.")
8400 (license license:cc0)))
8402 (define-public r-openxlsx
8409 (uri (cran-uri "openxlsx" version))
8412 "0695b265g7jwiqk5c3vmmfkvagx82bkpwhvqzhqaqmmn34l6vl35"))))
8413 (build-system r-build-system)
8415 (list r-rcpp r-stringi r-zip))
8418 (home-page "https://github.com/awalker89/openxlsx")
8419 (synopsis "Read, write and edit XLSX files")
8421 "This package simplifies the creation of Excel @code{.xlsx} files by
8422 providing a high level interface to writing, styling and editing worksheets.
8423 Through the use of Rcpp, read/write times are comparable to the @code{xlsx}
8424 and @code{XLConnect} packages with the added benefit of removing the
8425 dependency on Java.")
8426 (license license:gpl3)))
8428 (define-public r-rio
8435 (uri (cran-uri "rio" version))
8438 "04jlrhyl0791yxwcpp1s8p1hhkljnijlc5iaxpk56h41w63k39lz"))))
8439 (build-system r-build-system)
8450 (home-page "https://github.com/leeper/rio")
8451 (synopsis "Swiss-army knife for data I/O")
8453 "This package provides streamlined data import and export infrastructure
8454 by making assumptions that the user is probably willing to make: @code{import}
8455 and @code{export} determine the data structure from the file extension,
8456 reasonable defaults are used for data import and export (e.g.,
8457 @code{stringsAsFactors=FALSE}), web-based import is natively
8458 supported (including from SSL/HTTPS), compressed files can be read directly
8459 without explicit decompression, and fast import packages are used where
8460 appropriate. An additional convenience function, @code{convert}, provides a
8461 simple method for converting between file types.")
8462 (license license:gpl2)))
8464 (define-public r-maptools
8471 (uri (cran-uri "maptools" version))
8474 "1jgx8iiirj8qhrmh19mkisa35jcql7352dmc7lvwi5vxg3wjbvpk"))))
8475 (build-system r-build-system)
8477 (list r-foreign r-lattice r-sp))
8478 (home-page "https://r-forge.r-project.org/projects/maptools/")
8479 (synopsis "Tools for reading and handling spatial objects")
8481 "This package provides a set of tools for manipulating and reading
8482 geographic data, in particular ESRI Shapefiles. It includes binary access to
8483 GSHHG shoreline files. The package also provides interface wrappers for
8484 exchanging spatial objects with other R packages.")
8485 ;; The C source files from shapelib are released under the Expat license.
8486 ;; The R code is released under GPL version 2 or later.
8487 (license (list license:gpl2+
8490 (define-public r-later
8497 (uri (cran-uri "later" version))
8500 "0acqg29hcm2iq1418b54np7zb5pnr3xzrwc3ijv2pz9wra10ix88"))))
8501 (build-system r-build-system)
8503 (list r-rcpp r-rlang))
8506 (home-page "https://github.com/r-lib/later")
8507 (synopsis "Utilities for delaying function execution")
8509 "This package provides tools to execute arbitrary R or C functions some
8510 time after the current time, after the R execution stack has emptied.")
8511 (license license:gpl2+)))
8513 (define-public r-promises
8520 (uri (cran-uri "promises" version))
8523 "1dy4cbqw17awh4q8m7cy3anaj0n9iynabfzflb1g94cyj0bq4fld"))))
8524 (build-system r-build-system)
8526 (list r-later r-magrittr r-r6 r-rcpp r-rlang))
8529 (home-page "https://rstudio.github.io/promises")
8530 (synopsis "Abstractions for promise-based asynchronous programming")
8532 "This package provides fundamental abstractions for doing asynchronous
8533 programming in R using promises. Asynchronous programming is useful for
8534 allowing a single R process to orchestrate multiple tasks in the background
8535 while also attending to something else. Semantics are similar to JavaScript
8536 promises, but with a syntax that is idiomatic R.")
8537 (license license:expat)))
8539 (define-public r-dosnow
8546 (uri (cran-uri "doSNOW" version))
8549 "1f5v0k2w0b2478p6iqa3hn2lwd1x3rzc348n57nd38ka2vnsnz4i"))))
8550 (properties `((upstream-name . "doSNOW")))
8551 (build-system r-build-system)
8553 (list r-foreach r-iterators r-snow))
8554 (home-page "https://cran.r-project.org/web/packages/doSNOW")
8555 (synopsis "Foreach parallel adaptor for the snow package")
8557 "This package provides a parallel backend for the @code{%dopar%} function
8558 using the @code{snow} package.")
8559 (license license:gpl2)))
8561 (define-public r-fstcore
8568 (uri (cran-uri "fstcore" version))
8570 (base32 "1a5m68n2dqhi3r8wf5jwg4vjvl550c7wypcf5j0xmkvl836yg1lg"))))
8571 (properties `((upstream-name . "fstcore")))
8572 (build-system r-build-system)
8573 (propagated-inputs (list r-rcpp))
8574 (inputs (list zlib))
8575 (native-inputs (list pkg-config))
8576 (home-page "https://www.fstpackage.org/fstcore/")
8577 (synopsis "R bindings to the fstlib library")
8579 "The fstlib library provides multithreaded serialization of compressed
8580 data frames using the fst format. The fst format allows for random access of
8581 stored data and compression with the LZ4 and ZSTD compressors.")
8582 (license license:mpl2.0)))
8584 (define-public r-fst
8591 (uri (cran-uri "fst" version))
8594 "0r96inwrr960m7wmc80603bw2vvvwab225bh9dq3lalwhy4yiis4"))))
8595 (properties `((upstream-name . "fst")))
8596 (build-system r-build-system)
8597 (propagated-inputs (list r-fstcore r-rcpp))
8598 (home-page "http://www.fstpackage.org")
8599 (synopsis "Fast serialization of data frames")
8601 "The fst package for R provides a fast, easy and flexible way to
8602 serialize data frames. With access speeds of multiple GB/s, fst is
8603 specifically designed to unlock the potential of high speed solid state disks.
8604 Data frames stored in the fst format have full random access, both in column
8605 and rows. The fst format allows for random access of stored data and
8606 compression with the LZ4 and ZSTD compressors.")
8607 (license license:agpl3)))
8609 (define-public r-snowfall
8612 (version "1.84-6.1")
8615 (uri (cran-uri "snowfall" version))
8617 (base32 "13941rlw1jsdjsndp1plzj1cq5aqravizkrqn6l25r9im7rnsi2w"))))
8618 (build-system r-build-system)
8621 (home-page "https://cran.r-project.org/web/packages/snowfall/")
8622 (synopsis "Easier cluster computing")
8623 (description "This package is a usability wrapper around snow for easier
8624 development of parallel R programs. This package offers e.g. extended error
8625 checks, and additional functions. All functions work in sequential mode, too,
8626 if no cluster is present or wished. The package is also designed as connector
8627 to the cluster management tool @code{sfCluster}, but can also used without
8629 (license license:gpl2+)))
8631 (define-public r-rgexf
8638 (uri (cran-uri "rgexf" version))
8641 "00c2zka1n3k7p1l0mlchr063s6x58p9r3fb64d4wgl4rvsq55q3f"))
8642 ;; Delete minified JavaScript files
8644 '(for-each delete-file
8645 '("inst/gexf-js/js/jquery-2.0.2.min.js"
8646 "inst/gexf-js/js/jquery-ui-1.10.3.custom.min.js"
8647 "inst/gexf-js/js/jquery.mousewheel.min.js")))))
8648 (properties `((upstream-name . "rgexf")))
8649 (build-system r-build-system)
8651 `(#:modules ((guix build utils)
8652 (guix build r-build-system)
8656 (modify-phases %standard-phases
8657 (add-after 'unpack 'process-javascript
8658 (lambda* (#:key inputs #:allow-other-keys)
8659 (invoke "unzip" "-d" "/tmp" (assoc-ref inputs "js-jquery-ui"))
8660 (with-directory-excursion "inst/gexf-js/js/"
8664 `((,(assoc-ref inputs "js-jquery")
8665 "jquery-2.0.2.min.js")
8666 ("/tmp/jquery-ui-1.10.3/ui/jquery-ui.js"
8667 "jquery-ui-1.10.3.custom.min.js")
8668 (,(assoc-ref inputs "js-jquery-mousewheel")
8669 "jquery.mousewheel.min.js"))))
8670 (lambda (sources targets)
8671 (for-each (lambda (source target)
8672 (format #true "Processing ~a --> ~a~%"
8674 (invoke "esbuild" source "--minify"
8675 (string-append "--outfile=" target)))
8676 sources targets)))))))))
8678 (list r-igraph r-servr r-xml))
8680 `(("r-knitr" ,r-knitr)
8681 ("esbuild" ,esbuild)
8686 (uri "https://code.jquery.com/jquery-2.0.2.js")
8689 "0v818bxpw48gdk8i95qqqij80r9jcgisi2r4ac6xnxca20h0gvfj"))))
8693 (uri "https://jqueryui.com/resources/download/jquery-ui-1.10.3.zip")
8696 "00xpfy0l69nj2yan4s8k65ldsrlfsjkmyw2dwcg93dc8mv454vxx"))))
8697 ("js-jquery-mousewheel"
8700 (uri "https://raw.githubusercontent.com/jquery/jquery-mousewheel/\
8701 3.0.6/jquery.mousewheel.js")
8704 "19lk5xy2s47bx8hsa7j6bg012f8yw6d770g230bcnm559kf4nc6v"))))))
8705 (home-page "https://gvegayon.github.io/rgexf")
8706 (synopsis "Build, import and export GEXF graph files")
8708 "Create, read and write GEXF (Graph Exchange XML Format) graph
8709 files (used in Gephi and others). It allows the user to easily build/read
8710 graph files including attributes, GEXF visual attributes (such as color, size,
8711 and position), network dynamics (for both edges and nodes) and edge weighting.
8712 Users can build/handle graphs element-by-element or massively through
8713 data-frames, visualize the graph on a web browser through gexf-js (a
8714 JavaScript library) and interact with the igraph package.")
8715 (license license:expat)))
8717 (define-public r-data-tree
8719 (name "r-data-tree")
8724 (uri (cran-uri "data.tree" version))
8727 "0pizmx2312zsym4m42b97q2184bg3hibvbdrblcga05xln84qrs0"))))
8728 (properties `((upstream-name . "data.tree")))
8729 (build-system r-build-system)
8731 (list r-r6 r-stringi))
8734 (home-page "https://github.com/gluc/data.tree")
8735 (synopsis "General purpose hierarchical data structure")
8737 "Create tree structures from hierarchical data, and traverse the tree in
8738 various orders. Aggregate, cumulate, print, plot, convert to and from
8739 data.frame and more. This is useful for decision trees, machine learning,
8740 finance, conversion from and to JSON, and many other applications.")
8741 (license license:gpl2+)))
8743 (define-public r-dtplyr
8750 (uri (cran-uri "dtplyr" version))
8753 "1wyhhn16mvdj55k2xsh7vy489l7xk4mkz7pjrw16z87awk6yjh16"))))
8754 (properties `((upstream-name . "dtplyr")))
8755 (build-system r-build-system)
8769 (home-page "https://github.com/tidyverse/dtplyr")
8770 (synopsis "Data Table back-end for dplyr")
8772 "This package provides a @code{data.table} backend for @code{dplyr}. The
8773 goal of @code{dtplyr} is to allow you to write @code{dplyr} code that is
8774 automatically translated to the equivalent, but usually much faster,
8775 @code{data.table} code.")
8776 (license license:expat)))
8778 (define-public r-collapsibletree
8780 (name "r-collapsibletree")
8785 (uri (cran-uri "collapsibleTree" version))
8788 "0b65pbp1wnpsrayqi630ds4r98jvcvynnlp6wxdqrnnr9nzw5343"))
8791 ;; Delete minified JavaScript file
8792 (delete-file "inst/htmlwidgets/lib/d3-4.10.2/d3.min.js")
8795 `((upstream-name . "collapsibleTree")))
8796 (build-system r-build-system)
8799 (modify-phases %standard-phases
8800 (add-after 'unpack 'process-javascript
8801 (lambda* (#:key inputs #:allow-other-keys)
8802 (with-directory-excursion "inst/htmlwidgets/lib/d3-4.10.2/"
8803 (let ((source (assoc-ref inputs "d3.v4.js"))
8804 (target "d3.min.js"))
8805 (format #t "Processing ~a --> ~a~%"
8807 (invoke "esbuild" source "--minify"
8808 (string-append "--outfile=" target)))))))))
8810 (list r-data-tree r-htmlwidgets))
8812 `(("esbuild" ,esbuild)
8816 (uri "https://d3js.org/d3.v4.js")
8819 "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg"))))))
8820 (home-page "https://github.com/AdeelK93/collapsibleTree")
8821 (synopsis "Interactive collapsible tree diagrams using D3.js")
8823 "This is a package for interactive Reingold-Tilford tree diagrams created
8824 using D3.js, where every node can be expanded and collapsed by clicking on it.
8825 Tooltips and color gradients can be mapped to nodes using a numeric column in
8826 the source data frame.")
8827 (license license:gpl3+)))
8829 (define-public r-rappdirs
8836 (uri (cran-uri "rappdirs" version))
8839 "1161i3jgjvzjv4p8qbz9r976fnggkcrw3mlj4yd1h2svnijrz5a9"))))
8840 (build-system r-build-system)
8841 (home-page "https://cran.r-project.org/web/packages/rappdirs/")
8842 (synopsis "Determine where to save data, caches, and logs")
8844 "This package provides an easy way to determine which directories on the
8845 user's computer should be used to save data, caches and logs. It is a port of
8846 Python's @url{https://github.com/ActiveState/appdirs,Appdirs} to R.")
8847 (license license:expat)))
8849 (define-public r-rastervis
8851 (name "r-rastervis")
8856 (uri (cran-uri "rasterVis" version))
8859 "0kgg6cm7xjqya2d46w0i1i1wjpkb8f99lyqy7rgwa7l9xmwzj5n1"))))
8860 (properties `((upstream-name . "rasterVis")))
8861 (build-system r-build-system)
8872 (home-page "https://oscarperpinan.github.io/rastervis/")
8873 (synopsis "Visualization methods for raster data")
8875 "This package provides methods for enhanced visualization and interaction
8876 with raster data. It implements visualization methods for quantitative data
8877 and categorical data, both for univariate and multivariate rasters. It also
8878 provides methods to display spatiotemporal rasters, and vector fields.")
8879 (license license:gpl3)))
8881 (define-public r-rentrez
8888 (uri (cran-uri "rentrez" version))
8891 "0x1g2f6hvkqqlb39z8m5qxhcvsizddic5i7rpqw0wy77xfbna9gv"))))
8892 (properties `((upstream-name . "rentrez")))
8893 (build-system r-build-system)
8895 (list r-httr r-jsonlite r-xml))
8898 (home-page "https://docs.ropensci.org/rentrez/")
8899 (synopsis "Entrez in R")
8901 "This package provides an R interface to the NCBI's EUtils API,
8902 allowing users to search databases like GenBank PubMed, process the results of
8903 those searches and pull data into their R sessions.")
8904 (license license:expat)))
8906 (define-public r-renv
8913 (uri (cran-uri "renv" version))
8916 "0bjq3ms5dg155clya62m462m93g90sxfxm7b4cqhqbx8vakskwdl"))))
8917 (properties `((upstream-name . "renv")))
8918 (build-system r-build-system)
8921 (home-page "https://rstudio.github.io/renv")
8922 (synopsis "Project environments")
8924 "This package provides a dependency management toolkit for R. Using
8925 renv, you can create and manage project-local R libraries, save the state of
8926 these libraries to a lockfile, and later restore your library as required.
8927 Together, these tools can help make your projects more isolated, portable, and
8929 (license license:expat)))
8931 (define-public r-learnr
8938 (uri (cran-uri "learnr" version))
8941 "08xwmms6x58y3dsfbl9c6d03145hb4ij97nqr1cc9dxxilmr6x31"))))
8942 (build-system r-build-system)
8958 (home-page "https://rstudio.github.io/learnr/")
8959 (synopsis "Interactive tutorials for R")
8961 "This package provides tools to create interactive tutorials using R
8962 Markdown. Use a combination of narrative, figures, videos, exercises, and
8963 quizzes to create self-paced tutorials for learning about R and R packages.")
8964 (license license:asl2.0)))
8966 (define-public r-analytics
8968 (name "r-analytics")
8973 (uri (cran-uri "analytics" version))
8976 "0js3c8lwj3knccb55nq03cbjlf4w390p9aid2mi5x80l3ayd9in1"))))
8977 (build-system r-build-system)
8991 (home-page "https://cran.r-project.org/web/packages/analytics/")
8992 (synopsis "Collection of data analysis tools")
8994 "This package is a collection of data analysis tools. It includes tools
8995 for regression outlier detection in a fitted linear model, stationary
8996 bootstrap using a truncated geometric distribution, a comprehensive test for
8997 weak stationarity, column means by group, weighted biplots, and a heuristic to
8998 obtain a better initial configuration in non-metric MDS.")
8999 (license license:gpl2)))
9001 (define-public r-here
9008 (uri (cran-uri "here" version))
9010 (base32 "0srlr8h8qmr0wrmp7gs4g2ry5dni2hx8n947bik3s3a26f091v88"))))
9011 (properties `((upstream-name . "here")))
9012 (build-system r-build-system)
9013 (propagated-inputs (list r-rprojroot))
9014 (native-inputs (list r-knitr))
9015 (home-page "https://here.r-lib.org/")
9016 (synopsis "Simpler way to find files")
9018 "This package lets you construct paths to your project's files. Use the
9019 @code{here} function as a drop-in replacement for @code{file.path}, it will
9020 always locate the files relative to your project root.")
9021 (license license:expat)))
9023 (define-public r-reticulate
9025 (name "r-reticulate")
9030 (uri (cran-uri "reticulate" version))
9033 "0b1szzsqyc8wcfpkn5517bb1ds064vs2hky71my3p74kfngay991"))))
9034 (build-system r-build-system)
9035 (inputs (list python))
9047 (home-page "https://github.com/rstudio/reticulate")
9048 (synopsis "R interface to Python")
9050 "This package provides an interface from R to Python modules, classes,
9051 and functions. When calling into Python, R data types are automatically
9052 converted to their equivalent Python types. When values are returned from
9053 Python to R they are converted back to R types.")
9054 (license license:asl2.0)))
9056 (define-public r-bibtex
9063 (uri (cran-uri "bibtex" version))
9066 "0vdwx6808r73pk15263f33bkqbfmb08d8jkmr4d7h4ml414ikbbv"))))
9067 (build-system r-build-system)
9068 (propagated-inputs (list r-stringr))
9069 (home-page "https://github.com/romainfrancois/bibtex")
9070 (synopsis "Bibtex parser")
9071 (description "This package provides a utility for R to parse a bibtex
9073 (license license:gpl2+)))
9075 (define-public r-billboarder
9077 (name "r-billboarder")
9082 (uri (cran-uri "billboarder" version))
9084 (base32 "189ngvg84rcwhrivxskmjv3srhadvzr4p1v8pf11axyv2qn01b0x"))
9086 '(delete-file "inst/htmlwidgets/lib/billboard/billboard.pkgd.min.js"))))
9087 (properties `((upstream-name . "billboarder")))
9088 (build-system r-build-system)
9091 (modify-phases %standard-phases
9092 (add-after 'unpack 'process-javascript
9093 (lambda* (#:key inputs #:allow-other-keys)
9094 (with-directory-excursion "inst/htmlwidgets/lib/billboard/"
9095 (let ((source (assoc-ref inputs "js-billboard"))
9096 (target "billboard.pkgd.min.js"))
9097 (format #true "Processing ~a --> ~a~%"
9099 (invoke "esbuild" source "--minify"
9100 (string-append "--outfile=" target)))))))))
9111 `(("r-knitr" ,r-knitr)
9112 ("esbuild" ,esbuild)
9113 ;; It is not ideal to use this concatenated (but not minified)
9114 ;; JavaScript file, as the original source is written in TypeScript.
9115 ;; However, this can still be considered source code as it is readable
9116 ;; and can be modified.
9120 (uri "https://unpkg.com/billboard.js@3.2.0/dist/billboard.js")
9123 "1kx5rqmn87pgal2cwmcij2rrnwa0fgcsw6y99m4i0l2sdm0qffv2"))))))
9124 (home-page "https://github.com/dreamRs/billboarder")
9125 (synopsis "Create interactive charts with the JavaScript Billboard library")
9127 "This package provides an @code{htmlwidgets} interface to billboard.js,
9128 a re-usable easy interface JavaScript chart library, based on D3 v4+. Chart
9129 types include line charts, scatterplots, bar/lollipop charts,
9130 histogram/density plots, pie/donut charts and gauge charts. All charts are
9131 interactive, and a proxy method is implemented to smoothly update a chart
9132 without rendering it again in shiny apps.")
9133 (license license:expat)))
9135 (define-public r-ggseqlogo
9137 (name "r-ggseqlogo")
9142 (uri (cran-uri "ggseqlogo" version))
9145 "13q6kcpxrqxqbji889fx63p0nsi08lk5yymkchig75r5k1d18ky1"))))
9146 (build-system r-build-system)
9147 (propagated-inputs (list r-ggplot2))
9148 (home-page "https://github.com/omarwagih/ggseqlogo")
9149 (synopsis "ggplot2 extension for drawing genetic sequence logos")
9151 "The range of functions provided by this package makes it possible to
9152 draw highly versatile genomic sequence logos. Features include, but are not
9153 limited to, modifying colour schemes and fonts used to draw the logo,
9154 generating multiple logo plots, and aiding the visualisation with annotations.
9155 Sequence logos can easily be combined with other ggplot2 plots.")
9156 ;; Unspecified version of the LGPL.
9157 (license license:lgpl3+)))
9159 (define-public r-ggsci
9166 (uri (cran-uri "ggsci" version))
9169 "0g73x6grbka7ahjh6z23m3wrcifp5rdfdiasbl8lq4sp6rplxwaa"))))
9170 (build-system r-build-system)
9172 (list r-ggplot2 r-scales))
9173 (home-page "https://nanx.me/ggsci/")
9174 (synopsis "Scientific journal and sci-fi themed color palettes for ggplot2")
9176 "This package provides a collection of ggplot2 color palettes inspired by
9177 plots in scientific journals, data visualization libraries, science fiction
9178 movies, and TV shows.")
9179 (license license:gpl3)))
9181 (define-public r-ggsignif
9188 (uri (cran-uri "ggsignif" version))
9191 "1ad774c7s7y4i00xd89lfigr9aybl94q98ch598k3rchanr4b1fa"))))
9192 (build-system r-build-system)
9197 (home-page "https://github.com/const-ae/ggsignif")
9198 (synopsis "Significance brackets for ggplot2")
9200 "Enrich your ggplots with group-wise comparisons. This package provides
9201 an easy way to indicate if two groups are significantly different. Commonly
9202 this is shown by a bracket on top connecting the groups of interest which
9203 itself is annotated with the level of significance. The package provides a
9204 single layer that takes the groups for comparison and the test as arguments
9205 and adds the annotation to the plot.")
9206 (license license:gpl3)))
9208 (define-public r-rstatix
9215 (uri (cran-uri "rstatix" version))
9218 "0330y8iziffqg8j9j5h9zv4qcdyf8ybhmzxrr9fzq9nc6bf1gbm5"))))
9219 (properties `((upstream-name . "rstatix")))
9220 (build-system r-build-system)
9233 (home-page "https://rpkgs.datanovia.com/rstatix/")
9234 (synopsis "Pipe-friendly framework for basic statistical tests")
9236 "This package provides a simple and intuitive pipe-friendly framework,
9237 coherent with the @code{tidyverse} design philosophy, for performing basic
9238 statistical tests, including t-test, Wilcoxon test, ANOVA, Kruskal-Wallis and
9239 correlation analyses. The output of each test is automatically transformed
9240 into a tidy data frame to facilitate visualization. Additional functions are
9241 available for reshaping, reordering, manipulating and visualizing correlation
9243 (license license:gpl2)))
9245 (define-public r-ggpubr
9252 (uri (cran-uri "ggpubr" version))
9255 "0x86lmghr25k8w90yrp360dn42dhp5cjvjpdiv2s2gxfn701xcmb"))))
9256 (build-system r-build-system)
9274 (home-page "http://www.sthda.com/english/rpkgs/ggpubr")
9275 (synopsis "ggplot2-based publication-ready plots")
9277 "The ggplot2 package is an excellent and flexible package for elegant
9278 data visualization in R. However the default generated plots require some
9279 formatting before we can send them for publication. The ggpubr package
9280 provides some easy-to-use functions for creating and customizing ggplot2-based
9281 publication-ready plots.")
9282 (license license:gpl2)))
9284 (define-public r-ellipse
9291 (uri (cran-uri "ellipse" version))
9294 "1wm5v7zdv2drgdba7z96jwsx74mqhlq80qgrvdb4vb5r02dcw68p"))))
9295 (build-system r-build-system)
9296 (home-page "https://cran.r-project.org/web/packages/ellipse/")
9297 (synopsis "Functions for drawing ellipses and ellipse-like confidence regions")
9299 "This package contains various routines for drawing ellipses and
9300 ellipse-like confidence regions, implementing the plots described in Murdoch
9301 and Chow (1996), A graphical display of large correlation matrices, The
9302 American Statistician 50, 178-180. There are also routines implementing the
9303 profile plots described in Bates and Watts (1988), Nonlinear Regression
9304 Analysis and its Applications.")
9305 (license license:gpl2+)))
9307 (define-public r-flashclust
9309 (name "r-flashclust")
9314 (uri (cran-uri "flashClust" version))
9317 "0l4lpz451ll7f7lfxmb7ds24ppzhfg1c3ypvydglcc35p2dq99s8"))))
9318 (properties `((upstream-name . "flashClust")))
9319 (build-system r-build-system)
9320 (native-inputs (list gfortran))
9321 (home-page "https://cran.r-project.org/web/packages/flashClust/")
9322 (synopsis "Implementation of optimal hierarchical clustering")
9324 "This package provides a fast implementation of hierarchical
9326 (license license:gpl2+)))
9328 (define-public r-factominer
9330 (name "r-factominer")
9335 (uri (cran-uri "FactoMineR" version))
9338 "0lg8n9fxxk46nchnj4pbpqqf4swxfsq7r9jzr36dmd36kb7avqxr"))))
9339 (properties `((upstream-name . "FactoMineR")))
9340 (build-system r-build-system)
9355 (home-page "http://factominer.free.fr")
9356 (synopsis "Multivariate exploratory data analysis and data mining")
9358 "This package provides exploratory data analysis methods to summarize,
9359 visualize and describe datasets. The main principal component methods are
9360 available, those with the largest potential in terms of applications:
9361 principal component analysis (PCA) when variables are quantitative,
9362 correspondence analysis (CA) and multiple correspondence analysis (MCA) when
9363 variables are categorical, Multiple Factor Analysis when variables are
9364 structured in groups, etc. and hierarchical cluster analysis.")
9365 (license license:gpl2+)))
9367 (define-public r-factoextra
9369 (name "r-factoextra")
9374 (uri (cran-uri "factoextra" version))
9377 "1allvdjhd3pq8xz30b1cymwcik5iaahghrjrlnn54cwkfhfg0kv2"))))
9378 (build-system r-build-system)
9389 (home-page "http://www.sthda.com/english/rpkgs/factoextra")
9390 (synopsis "Extract and visualize the results of multivariate data analyses")
9392 "This package provides some easy-to-use functions to extract and
9393 visualize the output of multivariate data analyses, including
9394 @code{PCA} (Principal Component Analysis), @code{CA} (Correspondence
9395 Analysis), @code{MCA} (Multiple Correspondence Analysis), @code{FAMD} (Factor
9396 Analysis of Mixed Data), @code{MFA} (Multiple Factor Analysis) and
9397 @code{HMFA} (Hierarchical Multiple Factor Analysis) functions from different R
9398 packages. It contains also functions for simplifying some clustering analysis
9399 steps and provides ggplot2-based elegant data visualization.")
9400 (license license:gpl2)))
9402 (define-public r-fansi
9409 (uri (cran-uri "fansi" version))
9412 "0sn0kflgcn2qrrv646pzqylm02cx8l5ws473ppmvla4xihyvi9w6"))))
9413 (build-system r-build-system)
9415 (list r-knitr)) ; for vignettes
9416 (home-page "https://github.com/brodieG/fansi")
9417 (synopsis "ANSI control sequence aware string functions")
9419 "This package provides counterparts to R string manipulation functions
9420 that account for the effects of ANSI text formatting control sequences.")
9421 (license license:gpl2+)))
9423 (define-public r-nbclust
9430 (uri (cran-uri "NbClust" version))
9433 "0k5hr4zgx4gp1n62xchgz2zvyl35ba2cnczhhvj8rfbg2n4hx6qs"))))
9434 (properties `((upstream-name . "NbClust")))
9435 (build-system r-build-system)
9436 (home-page "https://sites.google.com/site/malikacharrad/research/nbclust-package")
9437 (synopsis "Determine the best number of clusters in a data set")
9439 "NbClust provides 30 indexes for determining the optimal number of
9440 clusters in a data set and offers the best clustering scheme from different
9441 results to the user.")
9442 (license license:gpl2)))
9444 (define-public r-hdf5r
9451 (uri (cran-uri "hdf5r" version))
9454 "0bv2q4ir73sbk5ra2q4mc8wbcmiwkws8k0mjlnx9ysi2mdrm3dw7"))))
9455 (build-system r-build-system)
9459 (list r-bit64 r-r6))
9462 (home-page "https://hhoeflin.github.io/hdf5r")
9463 (synopsis "Interface to the HDF5 binary data format")
9465 "HDF5 is a data model, library and file format for storing and managing
9466 large amounts of data. This package provides a nearly feature complete,
9467 object oriented wrapper for the HDF5 API using R6 classes. Additionally,
9468 functionality is added so that HDF5 objects behave very similar to their
9469 corresponding R counterparts.")
9470 (license license:asl2.0)))
9472 (define-public r-itertools
9474 (name "r-itertools")
9479 (uri (cran-uri "itertools" version))
9482 "1ls5biiva10pb1dj3ph4griykb9vam02hkrdmlr5a5wf660hg6xn"))))
9483 (build-system r-build-system)
9486 (home-page "https://cran.r-project.org/web/packages/itertools/")
9487 (synopsis "Iterator tools")
9489 "This package provides various tools for creating iterators, many
9490 patterned after functions in the Python @code{itertools} module, and others
9491 patterned after functions in the snow package.")
9492 (license license:gpl2)))
9494 (define-public r-itsadug
9501 (uri (cran-uri "itsadug" version))
9503 (base32 "0759l7hhvj05dp92pz59xwrxjm9s1iwkwrdhs68l0fq57550j70l"))))
9504 (properties `((upstream-name . "itsadug")))
9505 (build-system r-build-system)
9506 (propagated-inputs (list r-mgcv r-plotfunctions))
9507 (native-inputs (list r-knitr))
9508 (home-page "https://cran.r-project.org/package=itsadug")
9509 (synopsis "Interpreting time series and autocorrelated data using GAMMs")
9511 "@dfn{Generalized Additive Mixed Modeling} (GAMM; Lin & Zhang, 1999) as
9512 implemented in the R package @code{mgcv} is a nonlinear regression analysis
9513 which is particularly useful for time course data such as EEG, pupil dilation,
9514 gaze data (eye tracking), and articulography recordings, but also for
9515 behavioral data such as reaction times and response data. As time course
9516 measures are sensitive to autocorrelation problems, GAMMs implements methods
9517 to reduce the autocorrelation problems. This package includes functions for
9518 the evaluation of GAMM models (e.g., model comparisons, determining regions of
9519 significance, inspection of autocorrelational structure in residuals) and
9520 interpreting of GAMMs (e.g., visualization of complex interactions, and
9522 (license license:gpl2+)))
9524 (define-public r-polynom
9531 (uri (cran-uri "polynom" version))
9534 "0y4j07syjwpnq5w6a1d90z6h1hjzijmm42pq0f8jk2vcn5xxn7mw"))))
9535 (build-system r-build-system)
9536 (native-inputs (list r-knitr))
9537 (home-page "https://cran.r-project.org/web/packages/polynom/")
9538 (synopsis "Functions for univariate polynomial manipulations")
9540 "This package provides a collection of functions to implement a class for
9541 univariate polynomial manipulations.")
9542 (license license:gpl2)))
9544 (define-public r-pupillometryr
9546 (name "r-pupillometryr")
9551 (uri (cran-uri "PupillometryR" version))
9553 (base32 "0yk30sgl2qqa6pva649swq523vh446ifmydildycfvfmlm1h4qza"))))
9554 (properties `((upstream-name . "PupillometryR")))
9555 (build-system r-build-system)
9568 (native-inputs (list r-knitr))
9569 (home-page "https://cran.r-project.org/package=PupillometryR")
9570 (synopsis "Unified pipeline for pupillometry data")
9572 "This package provides a unified pipeline to clean, prepare, plot, and
9573 run basic analyses on pupillometry experiments.")
9574 (license license:expat)))
9576 (define-public r-gbrd
9583 (uri (cran-uri "gbRd" version))
9586 "06x97rw5i6v6cgjxkfhxnw4dn7lghn5q6ra7ri5ag1x9dkfzcl82"))))
9587 (properties `((upstream-name . "gbRd")))
9588 (build-system r-build-system)
9589 (home-page "https://cran.r-project.org/web/packages/gbRd/")
9590 (synopsis "Utilities for processing Rd objects and files")
9592 "This package provides utilities for processing Rd objects and files.
9593 Extract argument descriptions and other parts of the help pages of
9595 (license license:gpl2+)))
9597 (define-public r-rjags
9604 (uri (cran-uri "rjags" version))
9607 "0cibz6xhmh86fh7ynmdgpmlchizi57pi6dpslgc2if17a56c6p7q"))))
9608 (build-system r-build-system)
9615 (home-page "http://mcmc-jags.sourceforge.net")
9616 (synopsis "Bayesian graphical models using MCMC")
9618 "This package provides an R interface to the JAGS MCMC library. JAGS is
9619 Just Another Gibbs Sampler. It is a program for analysis of Bayesian
9620 hierarchical models using Markov Chain Monte Carlo (MCMC) simulation.")
9621 (license license:gpl2)))
9623 (define-public r-rbibutils
9625 (name "r-rbibutils")
9630 (uri (cran-uri "rbibutils" version))
9633 "0lnia2fk8zlvkkgnl7r7dyi1ip5vqlw448qrvqs2s14rpbpcvbpi"))))
9634 (properties `((upstream-name . "rbibutils")))
9635 (build-system r-build-system)
9636 (home-page "https://geobosh.github.io/rbibutils/")
9637 (synopsis "Convert between bibliography formats")
9639 "This package converts between a number of bibliography formats,
9640 including BibTeX, BibLaTeX and Bibentry. It includes a port of the bibutils
9641 utilities and supports all bibliography formats and character encodings
9642 implemented in bibutils.")
9643 (license license:gpl2)))
9645 (define-public r-rdpack
9652 (uri (cran-uri "Rdpack" version))
9655 "1igpa4hnpiykbdnq57mglby5jsbind6izkkfy81wx4ib6nw1lpn4"))))
9656 (properties `((upstream-name . "Rdpack")))
9657 (build-system r-build-system)
9660 (home-page "https://github.com/GeoBosh/Rdpack")
9661 (synopsis "Update and manipulate Rd documentation objects")
9663 "This package provides functions for manipulation of R documentation
9664 objects, including functions @code{reprompt()} and @code{ereprompt()} for
9665 updating Rd documentation for functions, methods and classes; it also includes
9666 Rd macros for citations and import of references from bibtex files for use in
9667 Rd files and roxygen2 comments, as well as many functions for manipulation of
9668 references and Rd files.")
9669 (license license:gpl2+)))
9671 (define-public r-officer
9678 (uri (cran-uri "officer" version))
9681 "0qmn62srh9zicgizyblanirbdva7f09g967yb86kfrn05ckh5y10"))))
9682 (build-system r-build-system)
9684 (list r-r6 r-uuid r-xml2 r-zip))
9685 (home-page "https://davidgohel.github.io/officer")
9686 (synopsis "Manipulation of Word and PowerPoint documents")
9688 "This package provides tools to access and manipulate Word and PowerPoint
9689 documents from R. The package focuses on tabular and graphical reporting from
9690 R; it also provides two functions that let users get document content into
9691 data objects. A set of functions lets add and remove images, tables and
9692 paragraphs of text in new or existing documents. When working with PowerPoint
9693 presentations, slides can be added or removed; shapes inside slides can also
9694 be added or removed. When working with Word documents, a cursor can be used
9695 to help insert or delete content at a specific location in the document.")
9696 (license license:gpl3)))
9698 (define-public r-profilemodel
9700 (name "r-profilemodel")
9705 (uri (cran-uri "profileModel" version))
9708 "01m5nb8cmq0aq555pxk2a99182si65hhmn68yn9nal2j3zl2bp4i"))))
9709 (properties `((upstream-name . "profileModel")))
9710 (build-system r-build-system)
9711 (home-page "https://github.com/ikosmidis/profileModel")
9712 (synopsis "Profiling inference functions for various model classes")
9714 "This package provides tools that can be used to calculate, evaluate,
9715 plot and use for inference the profiles of *arbitrary* inference functions for
9716 arbitrary @code{glm}-like fitted models with linear predictors. More information
9717 on the methods that are implemented can be found in Kosmidis (2008)
9718 @url{https://www.r-project.org/doc/Rnews/Rnews_2008-2.pdf}.")
9719 (license license:gpl2+)))
9721 (define-public r-brglm
9728 (uri (cran-uri "brglm" version))
9731 "08shcz0j1npdn7xkhsvlzs3z4rdwq3g4rk6a4xx8wirqw8n8s2an"))))
9732 (properties `((upstream-name . "brglm")))
9733 (build-system r-build-system)
9735 (list r-profilemodel))
9736 (home-page "https://github.com/ikosmidis/brglm")
9737 (synopsis "Bias reduction in binomial-response generalized linear models")
9739 "Fit generalized linear models with binomial responses using either an
9740 adjusted-score approach to bias reduction or maximum penalized likelihood
9741 where penalization is by Jeffreys invariant prior. These procedures return
9742 estimates with improved frequentist properties (bias, mean squared error) that
9743 are always finite even in cases where the maximum likelihood estimates are
9744 infinite (data separation). Fitting takes place by fitting generalized linear
9745 models on iteratively updated pseudo-data. The interface is essentially the
9746 same as @code{glm}. More flexibility is provided by the fact that custom
9747 pseudo-data representations can be specified and used for model fitting.
9748 Functions are provided for the construction of confidence intervals for the
9749 reduced-bias estimates.")
9750 (license license:gpl2+)))
9752 (define-public r-entropy
9759 (uri (cran-uri "entropy" version))
9762 "1f0j8jsn6pzf4gi5g0akixx6x5vc69ci5f4m2vnwp40frvsqjnkg"))))
9763 (properties `((upstream-name . "entropy")))
9764 (build-system r-build-system)
9765 (home-page "https://www.strimmerlab.org/software/entropy/")
9766 (synopsis "Estimation of entropy, mutual information and related quantities")
9768 "This package implements various estimators of entropy, such as the
9769 shrinkage estimator by Hausser and Strimmer, the maximum likelihood and the
9770 Millow-Madow estimator, various Bayesian estimators, and the Chao-Shen
9771 estimator. It also offers an R interface to the NSB estimator. Furthermore,
9772 it provides functions for estimating Kullback-Leibler divergence, chi-squared,
9773 mutual information, and chi-squared statistic of independence. In addition
9774 there are functions for discretizing continuous random variables.")
9775 (license license:gpl3+)))
9777 (define-public r-acd
9784 (uri (cran-uri "ACD" version))
9787 "1a67bi3hklq8nlc50r0qnyr4k7m9kpvijy8sqqpm54by5hsysfd6"))))
9788 (properties `((upstream-name . "ACD")))
9789 (build-system r-build-system)
9790 (home-page "https://cran.r-project.org/web/packages/ACD/")
9791 (synopsis "Categorical data analysis with complete or missing responses")
9793 "This package provides tools for categorical data analysis with complete
9794 or missing responses.")
9795 (license license:gpl2+)))
9797 (define-public r-acdm
9804 (uri (cran-uri "ACDm" version))
9807 "0b4f02ga5ra66mbrm79g0bnlzmii82rks9kmxixxqgf18yhlyjil"))))
9808 (properties `((upstream-name . "ACDm")))
9809 (build-system r-build-system)
9811 (list r-dplyr r-ggplot2 r-plyr r-rsolnp r-zoo))
9812 (home-page "https://cran.r-project.org/web/packages/ACDm/")
9813 (synopsis "Tools for Autoregressive Conditional Duration Models")
9815 "ACDm is a package for Autoregressive Conditional Duration (ACD, Engle
9816 and Russell, 1998) models. It creates trade, price or volume durations from
9817 transactions (tic) data, performs diurnal adjustments, fits various ACD models
9819 (license license:gpl2+)))
9821 (define-public r-overlap
9828 (uri (cran-uri "overlap" version))
9831 "1arxprhz035ab78ks88n6scwnlwmnb97mlac5gsx90ipb6gkgcyk"))))
9832 (build-system r-build-system)
9833 (home-page "https://cran.r-project.org/web/packages/overlap/")
9834 (synopsis "Estimates of coefficient of overlapping for animal activity patterns")
9836 "This package provides functions to fit kernel density functions to data
9837 on temporal activity patterns of animals; estimate coefficients of overlapping
9838 of densities for two species; and calculate bootstrap estimates of confidence
9840 (license license:gpl3+)))
9842 (define-public r-snakecase
9844 (name "r-snakecase")
9849 (uri (cran-uri "snakecase" version))
9852 "1ky1x2cp5rd0ffd9m1fji9sq4z4jsrpxzg30brw8bb4ihfjj114r"))))
9853 (build-system r-build-system)
9855 (list r-stringi r-stringr))
9856 (home-page "https://github.com/Tazinho/snakecase")
9857 (synopsis "Convert strings into any case")
9859 "This package provides a consistent, flexible and easy to use tool to
9860 parse and convert strings into cases like snake or camel among others.")
9861 (license license:gpl3)))
9863 (define-public r-prediction
9865 (name "r-prediction")
9870 (uri (cran-uri "prediction" version))
9873 "0awlq5lxfia6m2b91w73rksp93rbwv5gwqb36wbji4rgq41rzbrx"))))
9874 (build-system r-build-system)
9876 (list r-data-table))
9877 (home-page "https://github.com/leeper/prediction")
9878 (synopsis "Tidy, type-safe prediction methods")
9880 "This package provides the @code{prediction()} function, a type-safe
9881 alternative to @code{predict()} that always returns a data frame. The package
9882 currently supports common model types (e.g., @code{\"lm\"}, @code{\"glm\"})
9883 from the @code{stats} package, as well as numerous other model classes from
9884 other add-on packages.")
9885 (license license:expat)))
9887 (define-public r-insight
9894 (uri (cran-uri "insight" version))
9897 "0dffrsimgijdqsgvr9cad4g4w97d5ssjl3l0fm5ssly9l115ag35"))))
9898 (build-system r-build-system)
9901 (home-page "https://easystats.github.io/insight/")
9902 (synopsis "Easy access to model information for various model objects")
9904 "This package provides a tool to provide an easy, intuitive and
9905 consistent access to information contained in various R models, like model
9906 formulas, model terms, information about random effects, data that was used to
9907 fit the model or data from response variables. The package mainly revolves
9908 around two types of functions: Functions that find (the names of) information,
9909 starting with @code{find_}, and functions that get the underlying data,
9910 starting with @code{get_}. The package has a consistent syntax and works with
9911 many different model objects, where otherwise functions to access these
9912 information are missing.")
9913 (license license:gpl3)))
9915 (define-public r-sjlabelled
9917 (name "r-sjlabelled")
9922 (uri (cran-uri "sjlabelled" version))
9925 "1va86q5wddyvqgdpy8d0an2c7v1qbb4hpn0ai6y1v5v1ff87w73k"))))
9926 (build-system r-build-system)
9928 (list r-datawizard r-insight))
9931 (home-page "https://github.com/strengejacke/sjlabelled")
9932 (synopsis "Labelled data utility functions")
9934 "This package provides a collection of functions dealing with labelled
9935 data, like reading and writing data between R and other statistical software
9936 packages. This includes easy ways to get, set or change value and variable
9937 label attributes, to convert labelled vectors into factors or numeric (and
9938 vice versa), or to deal with multiple declared missing values.")
9939 (license license:gpl3)))
9941 (define-public r-sjmisc
9948 (uri (cran-uri "sjmisc" version))
9951 "1gzkq95ckxr0vhrzggflzli9hs7zr8c0yym9zn1wf74yrr0mgc3q"))))
9952 (build-system r-build-system)
9963 (home-page "https://github.com/strengejacke/sjmisc")
9964 (synopsis "Data and variable transformation functions")
9966 "This package is a collection of miscellaneous utility functions,
9967 supporting data transformation tasks like recoding, dichotomizing or grouping
9968 variables, setting and replacing missing values. The data transformation
9969 functions also support labelled data, and all integrate seamlessly into a
9970 tidyverse workflow.")
9971 (license license:gpl3)))
9973 (define-public r-nortest
9980 (uri (cran-uri "nortest" version))
9983 "17r0wpz72z9312c70nwi1i1kp1v9fm1h6jg7q5cx1mc1h420m1d3"))))
9984 (build-system r-build-system)
9985 (home-page "https://cran.r-project.org/web/packages/nortest/")
9986 (synopsis "Tests for normality")
9988 "This package provides five omnibus tests for testing the composite
9989 hypothesis of normality.")
9990 (license license:gpl2+)))
9992 (define-public r-moonbook
9999 (uri (cran-uri "moonBook" version))
10002 "1ml4vvm0mvrprpyi0l50aw38brx18bk2qny4gybmkvlbakalz9bx"))))
10003 (properties `((upstream-name . "moonBook")))
10004 (build-system r-build-system)
10014 (home-page "https://github.com/cardiomoon/moonBook")
10015 (synopsis "Functions and datasets for the book by Keon-Woong Moon")
10017 "This package provides several analysis-related functions for the book
10018 entitled \"R statistics and graph for medical articles\" (written in Korean),
10019 version 1, by Keon-Woong Moon with Korean demographic data with several plot
10021 (license license:gpl2)))
10023 (define-public r-flextable
10025 (name "r-flextable")
10030 (uri (cran-uri "flextable" version))
10033 "15vr5lb87712mymsvv01kz9s1fb54sx5kybsa2x547k5g10dbrbm"))))
10034 (build-system r-build-system)
10048 (home-page "https://davidgohel.github.io/flextable")
10049 (synopsis "Functions for tabular reporting")
10051 "This package provides tools to create pretty tables for HTML documents
10052 and other formats. Functions are provided to let users create tables, modify
10053 and format their content. It extends the @code{officer} package and can be
10054 used within R markdown documents when rendering to HTML and to Word
10056 (license license:gpl3)))
10058 (define-public r-writexl
10065 (uri (cran-uri "writexl" version))
10068 "0mfzyn8n5x5x5gf382bqgq61zpw9dymrp5kzdm2sbszplmxf6xry"))))
10069 (build-system r-build-system)
10070 (inputs (list zlib))
10071 (home-page "https://github.com/ropensci/writexl")
10072 (synopsis "Export data frames to xlsx format")
10074 "This package provides a data frame to xlsx exporter based on
10076 (license license:bsd-2)))
10078 (define-public r-biasedurn
10080 (name "r-biasedurn")
10085 (uri (cran-uri "BiasedUrn" version))
10088 "13i2lgfnjhlbbm2yxfc2l5hswqw6x03pwba5csjmirv8kpjw4xr3"))))
10089 (properties `((upstream-name . "BiasedUrn")))
10090 (build-system r-build-system)
10091 (home-page "https://cran.r-project.org/web/packages/BiasedUrn/")
10092 (synopsis "Biased Urn model distributions")
10094 "This package provides statistical models of biased sampling in the form
10095 of univariate and multivariate noncentral hypergeometric distributions,
10096 including Wallenius' noncentral hypergeometric distribution and Fisher's
10097 noncentral hypergeometric distribution (also called extended hypergeometric
10099 (license license:gpl3)))
10101 (define-public r-goplot
10108 (uri (cran-uri "GOplot" version))
10111 "1y8dv0kbzpr9za91njw0x233vx5d13vqml9hmpddcyi9s6va5nix"))))
10112 (properties `((upstream-name . "GOplot")))
10113 (build-system r-build-system)
10115 (list r-ggdendro r-ggplot2 r-gridextra r-rcolorbrewer))
10116 (home-page "https://github.com/wencke/wencke.github.io")
10117 (synopsis "Visualization of functional analysis data")
10119 "This package provides an implementation of multilayered visualizations
10120 for enhanced graphical representation of functional analysis data. It
10121 combines and integrates omics data derived from expression and functional
10122 annotation enrichment analyses. Its plotting functions have been developed
10123 with an hierarchical structure in mind: starting from a general overview to
10124 identify the most enriched categories (modified bar plot, bubble plot) to a
10125 more detailed one displaying different types of relevant information for the
10126 molecules in a given set of categories (circle plot, chord plot, cluster plot,
10127 Venn diagram, heatmap).")
10128 (license license:gpl2)))
10130 (define-public r-getopt
10137 (uri (cran-uri "getopt" version))
10140 "0zzmzgwl9a4y3s34600vmih22d6y32294f9bvxrnmffnvkgmy7sk"))))
10141 (build-system r-build-system)
10142 (home-page "https://github.com/trevorld/getopt")
10143 (synopsis "Command-line option processor for R")
10145 "This package is designed to be used with Rscript to write shebang
10146 scripts that accept short and long options. Many users will prefer to
10147 use the packages @code{optparse} or @code{argparse} which add extra
10148 features like automatically generated help options and usage texts,
10149 support for default values, positional argument support, etc.")
10150 (license license:gpl2+)))
10152 (define-public r-findpython
10154 (name "r-findpython")
10159 (uri (cran-uri "findpython" version))
10162 "0jf10jpqla90x03kl3k77gnd255zmw9rvr8d724vb17cqawh9yar"))))
10163 (build-system r-build-system)
10164 (home-page "https://github.com/trevorld/findpython")
10165 (synopsis "Functions to find an acceptable Python binary")
10167 "This package was designed to find an acceptable Python binary that
10168 matches version and feature constraints.")
10169 (license license:expat)))
10171 ;; This in not the same as "r-argparser"
10172 (define-public r-argparse
10174 (name "r-argparse")
10179 (uri (cran-uri "argparse" version))
10182 "13b5halfxc7nr57vkz3qmkkcpw1hr4xdk1mjh2cq8cvpnjz15qc3"))))
10183 (build-system r-build-system)
10184 (inputs (list python))
10186 (list r-findpython r-jsonlite r-r6))
10189 (home-page "https://github.com/trevorld/argparse")
10190 (synopsis "Command line optional and positional argument parser")
10192 "This package provides a command line parser to be used with Rscript to
10193 write shebang scripts that gracefully accept positional and optional arguments
10194 and automatically generate usage notices.")
10195 (license license:gpl2+)))
10197 (define-public r-hash
10200 (version "2.2.6.2")
10204 (uri (cran-uri "hash" version))
10207 "17scs675a86c34hjbxmwi8kny4yyv97x3515s449zafj2i0ad8vm"))))
10208 (build-system r-build-system)
10209 (home-page "https://cran.r-project.org/web/packages/hash/")
10210 (synopsis "Implementation of hash/associated arrays/dictionaries")
10212 "This package implements a data structure similar to hashes in Perl and
10213 dictionaries in Python but with a purposefully R flavor. For objects of
10214 appreciable size, access using hashes outperforms native named lists and
10216 (license license:gpl2+)))
10218 (define-public r-orddom
10225 (uri (cran-uri "orddom" version))
10228 "165axs15fvwhrp89xd87l81q3h2qjll1vrwcsap645cwvb85nwsh"))))
10229 (build-system r-build-system)
10230 (propagated-inputs (list r-psych))
10231 (home-page "https://cran.r-project.org/web/packages/orddom/")
10232 (synopsis "Ordinal dominance statistics")
10234 "This package provides tools to compute ordinal, statistics and effect
10235 sizes as an alternative to mean comparison: Cliff's delta or success rate
10236 difference (SRD), Vargha and Delaney's A or the Area Under a Receiver
10237 Operating Characteristic Curve (AUC), the discrete type of McGraw & Wong's
10238 Common Language Effect Size (CLES) or Grissom & Kim's Probability of
10239 Superiority (PS), and the Number needed to treat (NNT) effect size. Moreover,
10240 comparisons to Cohen's d are offered based on Huberty & Lowman's Percentage of
10241 Group (Non-)Overlap considerations.")
10242 (license license:gpl2)))
10244 (define-public r-deriv
10251 (uri (cran-uri "Deriv" version))
10254 "130g3mv0z9sqs6y23a0a94512iiw05yr6fp378vhdxxbignzbnyv"))))
10255 (properties `((upstream-name . "Deriv")))
10256 (build-system r-build-system)
10257 (home-page "https://cran.r-project.org/web/packages/Deriv")
10258 (synopsis "Symbolic differentiation")
10260 "This package provides an R-based solution for symbolic differentiation.
10261 It admits user-defined functions as well as function substitution in arguments
10262 of functions to be differentiated. Some symbolic simplification is part of
10264 (license license:gpl3+)))
10266 (define-public r-doby
10273 (uri (cran-uri "doBy" version))
10276 "0qnfcw4rg5kd1mll3rq6vchz3lgdqfif9469p8x6ixsgrxxpivbz"))))
10277 (properties `((upstream-name . "doBy")))
10278 (build-system r-build-system)
10292 (home-page "https://people.math.aau.dk/~sorenh/software/doBy/")
10293 (synopsis "Groupwise statistics, LSmeans, linear contrasts, and utilities")
10295 "This package contains:
10298 @item facilities for working with grouped data: @code{do}
10299 something to data stratified @code{by} some variables.
10300 @item implementations of least-squares means, general linear contrasts, and
10301 @item miscellaneous other utilities.
10303 (license license:gpl2+)))
10305 (define-public r-refgenome
10307 (name "r-refgenome")
10312 (uri (cran-uri "refGenome" version))
10315 "1za89bn3am1zgvm641qi1ab6kaqpll4rb9p9f1sjwvcgqq6065g5"))))
10316 (properties `((upstream-name . "refGenome")))
10317 (build-system r-build-system)
10319 (list r-dbi r-doby r-rsqlite))
10320 (home-page "https://cran.r-project.org/web/packages/refGenome/")
10322 "Gene and splice site annotation using annotation data from Ensembl and UCSC")
10324 "This package contains functionality for importing and managing of
10325 downloaded genome annotation data from the Ensembl genome browser (European
10326 Bioinformatics Institute) and from the UCSC genome browser (University of
10327 California, Santa Cruz) and annotation routines for genomic positions and
10328 splice site positions.")
10329 (license license:gpl2)))
10331 (define-public r-basix
10338 (uri (cran-uri "BASIX" version))
10341 "18dkvv1iwskfnlpl6xridcgqpalbbpm2616mvc3hfrc0b26v01id"))))
10342 (properties `((upstream-name . "BASIX")))
10343 (build-system r-build-system)
10344 (home-page "https://cran.r-project.org/web/packages/BASIX/")
10345 (synopsis "Efficient C/C++ toolset for R")
10347 "BASIX provides some efficient C/C++ implementations of native R
10348 procedures to speed up calculations in R.")
10349 (license license:gpl2)))
10351 (define-public r-blockfest
10353 (name "r-blockfest")
10358 (uri (cran-uri "BlockFeST" version))
10361 "1fcl3yc1cf09znqbj787d3fd2kl5rp63la7pxawsgmap7nxwkp65"))))
10362 (properties `((upstream-name . "BlockFeST")))
10363 (build-system r-build-system)
10364 (propagated-inputs (list r-basix))
10365 (home-page "https://cran.r-project.org/web/packages/BlockFeST/")
10366 (synopsis "Bayesian calculation of region-specific fixation index")
10368 "This package provides an R implementation of an extension of the
10369 BayeScan software for codominant markers, adding the option to group
10370 individual SNPs into pre-defined blocks. A typical application of this new
10371 approach is the identification of genomic regions, genes, or gene sets
10372 containing one or more SNPs that evolved under directional selection.")
10373 (license license:gpl2)))
10375 (define-public r-proc
10382 (uri (cran-uri "pROC" version))
10385 "1abvbzdss12n64pp9vlgnn0q3abh0nj4n0a8cinwwvhphjrm9vym"))))
10386 (properties `((upstream-name . "pROC")))
10387 (build-system r-build-system)
10389 (list r-plyr r-rcpp))
10390 (home-page "https://web.expasy.org/pROC/")
10391 (synopsis "Display and analyze ROC curves")
10393 "This package provides tools for visualizing, smoothing and comparing
10394 receiver operating characteristic (ROC curves). The area under the
10395 curve (AUC) can be compared with statistical tests based on U-statistics or
10396 bootstrap. Confidence intervals can be computed for (p)AUC or ROC curves.")
10397 (license license:gpl3+)))
10399 (define-public r-rootsolve
10401 (name "r-rootsolve")
10402 (version "1.8.2.3")
10406 (uri (cran-uri "rootSolve" version))
10409 "182bb727sgqi5f3pzmw8jnn328wdjrgj9lfvg49gv8s22rjd3cxm"))))
10410 (properties `((upstream-name . "rootSolve")))
10411 (build-system r-build-system)
10412 (native-inputs (list gfortran))
10413 (home-page "https://cran.r-project.org/web/packages/rootSolve/")
10414 (synopsis "Tools for the analysis of ordinary differential equations")
10416 "This package provides routines to find the root of nonlinear functions,
10417 and to perform steady-state and equilibrium analysis of @dfn{ordinary
10418 differential equations} (ODE). It includes routines that:
10421 @item generate gradient and jacobian matrices (full and banded),
10422 @item find roots of non-linear equations by the Newton-Raphson method,
10423 @item estimate steady-state conditions of a system of (differential) equations
10424 in full, banded or sparse form, using the Newton-Raphson method, or by
10425 dynamically running,
10426 @item solve the steady-state conditions for uni- and multicomponent 1-D, 2-D,
10427 and 3-D partial differential equations, that have been converted to ordinary
10428 differential equations by numerical differencing (using the method-of-lines
10431 (license license:gpl2+)))
10433 (define-public r-abcanalysis
10435 (name "r-abcanalysis")
10440 (uri (cran-uri "ABCanalysis" version))
10442 (base32 "0wac1ksmnxa36v99ca4hv8k0rsh3igwpcllmlv9wf7i9kgqviqwi"))))
10443 (properties `((upstream-name . "ABCanalysis")))
10444 (build-system r-build-system)
10445 (propagated-inputs (list r-plotrix))
10446 (home-page "https://www.uni-marburg.de/fb12/arbeitsgruppen/datenbionik/software-en/")
10447 (synopsis "Computed ABC Analysis")
10449 "Multivariate data sets often differ in several factors or derived statistical
10450 parameters, which have to be selected for a valid interpretation. Basing this
10451 selection on traditional statistical limits leads occasionally to the perception
10452 of losing information from a data set. This package provides tools to calculate
10453 these limits on the basis of the mathematical properties of the distribution of
10454 the analyzed items.")
10455 (license license:gpl3)))
10457 (define-public r-slam
10464 (uri (cran-uri "slam" version))
10466 (base32 "1ggqcf8l1z2hpi7qy4mg0d2ps48bjjb8z1y1xz6fq162cqrbz6bq"))))
10467 (build-system r-build-system)
10468 (home-page "https://cran.r-project.org/web/packages/slam/")
10469 (synopsis "Sparse lightweight arrays and matrices")
10471 "This package contains data structures and algorithms for sparse arrays and matrices,
10472 based on index arrays and simple triplet representations, respectively.")
10473 (license license:gpl2)))
10475 (define-public r-manipulatewidget
10477 (name "r-manipulatewidget")
10482 (uri (cran-uri "manipulateWidget" version))
10484 (base32 "1dpgzmiv08afm57yxr017b014lfn9h3pa4w65prk5k3dgn6p4wsv"))))
10486 `((upstream-name . "manipulateWidget")))
10487 (build-system r-build-system)
10500 (home-page "https://github.com/rte-antares-rpackage/manipulateWidget/")
10501 (synopsis "Add even more interactivity to interactive charts")
10503 "This package lets you create in just a few lines of R code a nice user interface to
10504 modify the data or the graphical parameters of one or multiple interactive
10505 charts. It is useful to quickly explore visually some data or for package
10506 developers to generate user interfaces easy to maintain.")
10507 (license license:gpl2+)))
10509 (define-public r-a3
10516 (uri (cran-uri "A3" version))
10518 (base32 "017hq9pjsv1h9i7cqk5cfx27as54shlhdsdvr6jkhb8jfkpdb6cw"))))
10519 (properties `((upstream-name . "A3")))
10520 (build-system r-build-system)
10522 (list r-pbapply r-xtable))
10523 (home-page "https://cran.r-project.org/web/packages/A3/")
10524 (synopsis "Error metrics for predictive models")
10526 "This package supplies tools for tabulating and analyzing the results of predictive
10527 models. The methods employed are applicable to virtually any predictive model
10528 and make comparisons between different methodologies straightforward.")
10529 (license license:gpl2+)))
10531 (define-public r-infotheo
10533 (name "r-infotheo")
10534 (version "1.2.0.1")
10538 (uri (cran-uri "infotheo" version))
10541 "1m1979vf8rvq3534mp1hihfadikhxrg3p6ac3hirz96kgb4qxyy0"))))
10542 (build-system r-build-system)
10543 (home-page "http://homepage.meyerp.com/software")
10544 (synopsis "Information-theoretic measures")
10546 "This package implements various measures of information theory based on
10547 several entropy estimators.")
10548 (license license:gpl3+)))
10550 (define-public r-nsprcomp
10552 (name "r-nsprcomp")
10553 (version "0.5.1-2")
10557 (uri (cran-uri "nsprcomp" version))
10560 "1zlc1ximx96f235c0l8qfs6vbp1kpnbf943wxsfahnnlnxvwi59f"))))
10561 (properties `((upstream-name . "nsprcomp")))
10562 (build-system r-build-system)
10563 (home-page "https://sigg-iten.ch/research/")
10564 (synopsis "Non-negative and sparse PCA")
10566 "This package implements two methods for performing a constrained
10567 principal component analysis (PCA), where non-negativity and/or sparsity
10568 constraints are enforced on the principal axes (PAs). The function
10569 @code{nsprcomp} computes one principal component (PC) after the other. Each
10570 PA is optimized such that the corresponding PC has maximum additional variance
10571 not explained by the previous components. In contrast, the function
10572 @code{nscumcomp} jointly computes all PCs such that the cumulative variance is
10573 maximal. Both functions have the same interface as the @code{prcomp} function
10574 from the @code{stats} package (plus some extra parameters).")
10575 (license license:gpl2+)))
10577 (define-public r-cmplot
10584 (uri (cran-uri "CMplot" version))
10587 "1h09prpiw7l32mr7jarp8ddrddg1431nfn4kw3bznfnv0sr78zfg"))))
10588 (properties `((upstream-name . "CMplot")))
10589 (build-system r-build-system)
10590 (home-page "https://github.com/YinLiLin/CMplot")
10591 (synopsis "Circle Manhattan plot")
10593 "Circle Manhattan Plot is an R package that can lay out genome-wide
10594 association study P-value results in both traditional rectangular patterns,
10595 QQ-plot and novel circular ones. United in only one bull's eye style plot,
10596 association results from multiple traits can be compared interactively,
10597 thereby to reveal both similarities and differences between signals.
10598 Additional functions include: highlight signals, a group of SNPs, chromosome
10599 visualization and candidate genes around SNPs.")
10600 (license license:gpl2+)))
10602 (define-public r-precrec
10609 (uri (cran-uri "precrec" version))
10612 "1dfz2rqx2ww2l5r40ahg0qdj3rjrwiwh427mw7j5ynhpcj21j2qm"))))
10613 (properties `((upstream-name . "precrec")))
10614 (build-system r-build-system)
10622 (native-inputs (list r-knitr))
10623 (home-page "https://evalclass.github.io/precrec/")
10624 (synopsis "Calculate accurate precision-recall and ROC curves")
10626 "This package provides tools for accurate calculations and visualization
10627 of precision-recall and ROC (Receiver Operator Characteristics) curves.")
10628 (license license:gpl3)))
10630 (define-public r-netrep
10637 (uri (cran-uri "NetRep" version))
10640 "1swlb2k9bc7whvslxbklz864j9ynvna73hvq5rhv61cv5vy05ksd"))))
10641 (properties `((upstream-name . "NetRep")))
10642 (build-system r-build-system)
10652 (native-inputs (list r-knitr))
10653 (home-page "https://cran.r-project.org/package=NetRep")
10654 (synopsis "Permutation testing network module preservation across datasets")
10656 "This package provides functions for assessing the
10657 replication/preservation of a network module's topology across datasets
10658 through permutation testing.")
10659 (license license:gpl2)))
10661 (define-public r-intergraph
10663 (name "r-intergraph")
10668 (uri (cran-uri "intergraph" version))
10671 "18a7xgb2rp0w9jl2rkh8nzyjprrs5w7h2iidvc8c38bzx3qpggkc"))))
10672 (properties `((upstream-name . "intergraph")))
10673 (build-system r-build-system)
10675 (list r-igraph r-network))
10678 (home-page "http://mbojan.github.io/intergraph")
10679 (synopsis "Coercion routines for network data objects")
10681 "Functions implemented in this package allow coercing (i.e. convert)
10682 network data between classes provided by other R packages. Currently
10683 supported classes are those defined in packages @code{network} and
10685 (license license:gpl3)))
10687 (define-public r-abcoptim
10689 (name "r-abcoptim")
10694 (uri (cran-uri "ABCoptim" version))
10696 (base32 "1ih0xk88qhsmpvnxf56041wx5sk8as2f4f2gdnpnwdym9mbr9n4b"))))
10697 (properties `((upstream-name . "ABCoptim")))
10698 (build-system r-build-system)
10699 (propagated-inputs (list r-rcpp))
10700 (home-page "https://github.com/gvegayon/ABCoptim/")
10701 (synopsis "Optimization of Artificial Bee Colony algorithm")
10703 "Artificial Bee Colony (ABC) is one of the most recently defined algorithms by Dervis
10704 Karaboga in 2005, motivated by the intelligent behavior of honey bees. It is as
10705 simple as Particle Swarm Optimization (PSO) and Differential Evolution (DE)
10706 algorithms, and uses only common control parameters such as colony size and
10707 maximum cycle number. The @code{r-abcoptim} implements the Artificial bee
10708 colony optimization algorithm @url{http://mf.erciyes.edu.tr/abc/pub/tr06_2005.pdf}.
10709 This version is a work-in-progress and is written in R code.")
10710 (license license:expat)))
10712 (define-public r-abcp2
10719 (uri (cran-uri "ABCp2" version))
10721 (base32 "1s2skkxpzss7c29i8600psgrp0hl46jcrxqrmy2b4db8hc0kcnbx"))))
10722 (properties `((upstream-name . "ABCp2")))
10723 (build-system r-build-system)
10724 (propagated-inputs (list r-mass))
10725 (home-page "https://cran.r-project.org/web/packages/ABCp2/")
10726 (synopsis "Approximate Bayesian Computational Model for Estimating P2")
10728 "This package tests the goodness of fit of a distribution of offspring to the Normal,
10729 Poisson, and Gamma distribution and estimates the proportional paternity of the
10730 second male (P2) based on the best fit distribution.")
10731 (license license:gpl2)))
10733 (define-public r-abcrf
10740 (uri (cran-uri "abcrf" version))
10742 (base32 "1ghbd24yhqy3xhdxas6ccn84nkavqpgldx5ck8kijknc7qjm8k27"))))
10743 (build-system r-build-system)
10754 (home-page "https://cran.r-project.org/web/packages/abcrf/")
10755 (synopsis "Approximate bayesian computation via random forests")
10757 "This package performs approximate bayesian computation (ABC) model choice and
10758 parameter inference via random forests. This machine learning tool named random
10759 forests (RF) can conduct selection among the highly complex models covered by
10761 (license license:gpl2+)))
10763 (define-public r-abctools
10765 (name "r-abctools")
10770 (uri (cran-uri "abctools" version))
10772 (base32 "07s9dg10i8lsxl73b4n2hynca2fjgb0ykb0dz8c3zv6cgw3cyx97"))))
10773 (build-system r-build-system)
10775 (list r-abc r-abind r-hmisc r-plyr))
10776 (home-page "https://github.com/dennisprangle/abctools/")
10777 (synopsis "Tools for ABC analyses")
10779 "This @code{r-abctools} package provides tools for approximate Bayesian computation
10780 including summary statistic selection and assessing coverage. This includes
10781 recent dimension reduction algorithms to tune the choice of summary statistics,
10782 and coverage methods to tune the choice of threshold.")
10783 (license license:gpl2+)))
10785 (define-public r-ggstance
10787 (name "r-ggstance")
10792 (uri (cran-uri "ggstance" version))
10794 (base32 "0jz9vvnmcc6a38n8nzr458r65sna23bgn5r8mxdhzdlyqibihr7d"))))
10795 (build-system r-build-system)
10797 (list r-ggplot2 r-plyr r-rlang r-withr))
10798 (home-page "https://cran.r-project.org/web/packages/ggstance/")
10799 (synopsis "Horizontal and vertical versions of @code{r-ggplot2}")
10801 "This package is a @code{r-ggplot2} extension that provides flipped components:
10803 @item horizontal versions of @code{r-ggplot2} stats and @code{r-ggplot2} geoms;
10804 @item vertical versions of @code{r-ggplot2} positions.
10806 (license license:gpl3)))
10808 (define-public r-ggnetwork
10810 (name "r-ggnetwork")
10815 (uri (cran-uri "ggnetwork" version))
10818 "0gqdgy5yh700dg0f7xb80hczlnqfisn8l55j7amd1n7fp2x5sr8v"))))
10819 (properties `((upstream-name . "ggnetwork")))
10820 (build-system r-build-system)
10822 (list r-ggplot2 r-ggrepel r-igraph r-network r-sna))
10823 (native-inputs (list r-knitr))
10824 (home-page "https://github.com/briatte/ggnetwork")
10825 (synopsis "Geometries to plot networks with ggplot2")
10827 "This package provides geometries to plot network objects with the
10829 (license license:gpl3)))
10831 (define-public r-cvauc
10838 (uri (cran-uri "cvAUC" version))
10841 "1m2y50a1yapf1c74km9a4r47ds2z2bfp4wwwkqin7swv9v1s7d28"))))
10842 (properties `((upstream-name . "cvAUC")))
10843 (build-system r-build-system)
10845 (list r-data-table r-rocr))
10846 (home-page "https://github.com/ledell/cvAUC")
10847 (synopsis "Cross-validated area under the ROC curve confidence intervals")
10849 "This package contains various tools for working with and evaluating
10850 cross-validated area under the ROC curve (AUC) estimators. The primary
10851 functions of the package are @code{ci.cvAUC} and @code{ci.pooled.cvAUC}, which
10852 report cross-validated AUC and compute confidence intervals for
10853 cross-validated AUC estimates based on influence curves for i.i.d. and pooled
10854 repeated measures data, respectively.")
10855 (license license:asl2.0)))
10857 (define-public r-gam
10864 (uri (cran-uri "gam" version))
10867 "1bbxiqfgi7jc9vw1hspw5q41d69nlw2v6k91zqlvmam5pvxcd1sp"))))
10868 (properties `((upstream-name . "gam")))
10869 (build-system r-build-system)
10874 (home-page "https://cran.r-project.org/package=gam")
10875 (synopsis "Generalized additive models")
10877 "This package provides functions for fitting and working with generalized
10878 additive models, as described in chapter 7 of \"Statistical Models in
10879 S\" (Chambers and Hastie (eds), 1991), and \"Generalized Additive
10880 Models\" (Hastie and Tibshirani, 1990).")
10881 (license license:gpl2)))
10883 (define-public r-superlearner
10885 (name "r-superlearner")
10890 (uri (cran-uri "SuperLearner" version))
10893 "00any24msgflyagy87nznpfjz5g9v15frqda6c679wa8plx26hjz"))))
10894 (properties `((upstream-name . "SuperLearner")))
10895 (build-system r-build-system)
10897 (list r-cvauc r-gam r-nnls))
10900 (home-page "https://github.com/ecpolley/SuperLearner")
10901 (synopsis "Super learner prediction")
10903 "This package implements the super learner prediction method and contains
10904 a library of prediction algorithms to be used in the super learner.")
10905 (license license:gpl3)))
10907 (define-public r-drtmle
10914 (uri (cran-uri "drtmle" version))
10917 "12vplpz9bg5444jy29mbdr70hqby073vb3iw76v2csrwy3ws3f21"))))
10918 (properties `((upstream-name . "drtmle")))
10919 (build-system r-build-system)
10921 (list r-future-apply r-np r-superlearner))
10924 (home-page "https://github.com/benkeser/drtmle")
10925 (synopsis "Doubly-robust nonparametric estimation and inference")
10927 "This package implements targeted minimum loss-based estimators of
10928 counterfactual means and causal effects that are doubly-robust with respect
10929 both to consistency and asymptotic normality.")
10930 (license license:expat)))
10932 (define-public r-dofuture
10934 (name "r-dofuture")
10939 (uri (cran-uri "doFuture" version))
10942 "0w07pmzpsfq4kvfc745s1i9b6dfn1df1wrfi4s9ys4ir3g2s8nk1"))))
10943 (properties `((upstream-name . "doFuture")))
10944 (build-system r-build-system)
10947 (modify-phases %standard-phases
10948 (add-after 'unpack 'set-HOME
10949 (lambda _ (setenv "HOME" "/tmp"))))))
10951 (list r-foreach r-future r-globals r-iterators))
10953 (list r-r-rsp)) ; vignette builder
10954 (home-page "https://github.com/HenrikBengtsson/doFuture")
10955 (synopsis "Foreach parallel adapter using the future API")
10957 "This package provides a @code{%dopar%} adapter such that any type of
10958 futures can be used as backends for the @code{foreach} framework.")
10959 (license license:lgpl2.1+)))
10961 (define-public r-superheat
10963 (name "r-superheat")
10968 (uri (cran-uri "superheat" version))
10971 "01v8s6px1k5fajlm6py3ksr1i853kwwlky1yryzhy3p1cxhwgg83"))))
10972 (properties `((upstream-name . "superheat")))
10973 (build-system r-build-system)
10982 (home-page "https://cran.r-project.org/package=superheat")
10983 (synopsis "Graphical tool for exploring complex datasets using heatmaps")
10985 "This package provides a system for generating extendable and
10986 customizable heatmaps for exploring complex datasets, including big data and
10987 data with multiple data types.")
10988 (license license:cc0)))
10990 (define-public r-qualv
10997 (uri (cran-uri "qualV" version))
11000 "0rkjzva2h158d5c631jmjjh7qjibbyisl0503san80rk9fgxl45b"))))
11001 (properties `((upstream-name . "qualV")))
11002 (build-system r-build-system)
11004 (list r-kernsmooth))
11005 (home-page "http://qualV.R-Forge.R-Project.org/")
11006 (synopsis "Qualitative Validation Methods")
11008 "This package provides qualitative methods for the validation of dynamic
11009 models. It contains
11012 @item an orthogonal set of deviance measures for absolute, relative and
11014 @item approaches accounting for time shifts.
11017 The first approach transforms time to take time delays and speed differences
11018 into account. The second divides the time series into interval units
11019 according to their main features and finds the @dfn{longest common
11020 subsequence} (LCS) using a dynamic programming algorithm.")
11021 (license license:gpl2+)))
11023 (define-public r-mosaiccore
11025 (name "r-mosaiccore")
11030 (uri (cran-uri "mosaicCore" version))
11032 (base32 "1h3ixzna4xy42rdnd89jj0v9q0riy3fnkd33z6l5c0zaidzm58fz"))))
11033 (properties `((upstream-name . "mosaicCore")))
11034 (build-system r-build-system)
11036 (list r-dplyr r-mass r-rlang r-tidyr))
11037 (home-page "https://github.com/ProjectMOSAIC/mosaicCore/")
11038 (synopsis "Common utilities for mosaic family packages")
11040 "Common utilities used in other Mosaic family packages are collected here.")
11041 (license license:gpl2+)))
11043 (define-public r-labelled
11045 (name "r-labelled")
11050 (uri (cran-uri "labelled" version))
11053 "0h7scbyzh7kr51gds222rkhld2b3k36s86hj8rrzpwv4bwj0pccy"))))
11054 (properties `((upstream-name . "labelled")))
11055 (build-system r-build-system)
11066 (home-page "http://larmarange.github.io/labelled/")
11067 (synopsis "Manipulating labelled data")
11069 "This package provides useful functions to deal with the
11070 @code{haven_labelled} and @code{haven_labelled_spss} classes introduced by the
11072 (license license:gpl3)))
11074 (define-public r-ggformula
11076 (name "r-ggformula")
11081 (uri (cran-uri "ggformula" version))
11083 (base32 "1ph5jd8svk8hmshi894vmmpq3zwgdmf4yn3gmdlkad68z8jynhsp"))))
11084 (build-system r-build-system)
11099 (home-page "https://github.com/ProjectMOSAIC/ggformula/")
11100 (synopsis "Formula interface for the @code{r-ggplot2}")
11102 "The @code{r-ggformula} introduces a family of graphics functions, gf_point(),
11103 gf_density(), and so on, bring the formula interface to ggplot(). This captures
11104 and extends the excellent simplicity of the lattice-graphics formula interface,
11105 while providing the intuitive capabilities of @code{r-ggplot2}.")
11106 (license license:expat)))
11108 (define-public r-mosaicdata
11110 (name "r-mosaicdata")
11115 (uri (cran-uri "mosaicData" version))
11117 (base32 "0h3f5fgzkzjfgf3ml0qa5j52921y6wy6jgggxmhs31bs8fd4srg4"))))
11118 (properties `((upstream-name . "mosaicData")))
11119 (build-system r-build-system)
11120 (home-page "https://cran.r-project.org/web/packages/mosaicData/")
11121 (synopsis "Data sets for project Mosaic")
11123 "This package provides data sets from project Mosaic @url{http://mosaic-web.org}
11124 used to teach mathematics, statistics, computation and modeling.")
11125 (license license:gpl2+)))
11127 (define-public r-raster
11134 (uri (cran-uri "raster" version))
11137 "11fnznymwavpph733dayklhcx4phpjgrijfxlaszi122sg2x7ir9"))))
11138 (build-system r-build-system)
11140 (list r-rcpp r-sp r-terra))
11141 (home-page "https://www.rspatial.org/")
11142 (synopsis "Geographic data analysis and modeling")
11144 "The package implements basic and high-level functions for reading,
11145 writing, manipulating, analyzing and modeling of gridded spatial data.
11146 Processing of very large files is supported.")
11147 (license license:gpl3+)))
11149 (define-public r-mosaic
11156 (uri (cran-uri "mosaic" version))
11158 (base32 "1y0isqbva0vi5zlx1xvixbq87n4xp66ljh43qnd0cpzaz0mn21cg"))))
11159 (build-system r-build-system)
11183 (home-page "https://github.com/ProjectMOSAIC/mosaic/")
11184 (synopsis "Mathematics, statistics, and computation teaching utilities")
11186 "This package contain data sets and utilities from
11187 @url{http://mosaic-web.org, Project MOSAIC} used to teach mathematics,
11188 statistics, computation and modeling. Project MOSAIC is a community of
11189 educators working to tie together aspects of quantitative work that students
11190 in science, technology, engineering and mathematics will need in their
11191 professional lives, but which are usually taught in isolation, if at all.")
11192 (license license:gpl2+)))
11194 (define-public r-abd
11201 (uri (cran-uri "abd" version))
11203 (base32 "191gspqzdv573vaw624ri0f5cm6v4j524bjs74d4a1hn3kn6r9b7"))))
11204 (build-system r-build-system)
11206 (list r-lattice r-mosaic r-nlme))
11207 (home-page "https://cran.r-project.org/web/packages/abd/")
11208 (synopsis "Analysis of biological data")
11210 "The @code{r-abd} package contains data sets and sample code for the Analysis of
11211 biological data by Michael Whitlock and Dolph Schluter.")
11212 (license license:gpl2)))
11214 (define-public r-svgui
11221 (uri (cran-uri "svGUI" version))
11223 (base32 "0ch5gdfk834xj9w3vxpm3x4770fz3nnlyn8b0jsw9f3n2as7g979"))))
11224 (properties `((upstream-name . "svGUI")))
11225 (build-system r-build-system)
11228 (home-page "https://github.com/SciViews/svGUI/")
11229 (synopsis "Functions for managing GUI clients in R")
11231 "The SciViews @code{svGUI} package eases the management of Graphical User
11232 Interfaces (GUI) in R. It is independent from any particular GUI widgets. It
11233 centralizes info about GUI elements currently used, and it dispatches GUI
11234 calls to the particular toolkits in use in function of the context.")
11235 (license license:gpl2)))
11237 (define-public r-svdialogs
11239 (name "r-svdialogs")
11244 (uri (cran-uri "svDialogs" version))
11246 (base32 "0z3a5glsi0ab43mdk2yvslxyzg12nbqqqc35jvgzj475mpkbgjif"))))
11247 (properties `((upstream-name . "svDialogs")))
11248 (build-system r-build-system)
11252 (list r-rstudioapi r-svgui))
11255 (home-page "https://github.com/SciViews/svDialogs/")
11256 (synopsis "Portable dialog boxes")
11258 "This package helps to construct standard dialog boxes for your GUI, including
11259 message boxes, input boxes, list, file or directory selection, and others. In
11260 case R cannot display GUI dialog boxes, a simpler command line version of these
11261 interactive elements is also provided as a fallback solution.")
11262 (license license:gpl2)))
11264 (define-public r-abe
11271 (uri (cran-uri "abe" version))
11274 "1f19h3xzzmjhvwc1rrb8z0rai3ip03y4gdi2gg9bfr5sg2nfklk6"))))
11275 (build-system r-build-system)
11276 (home-page "https://cran.r-project.org/web/packages/abe/")
11277 (synopsis "Augmented backward elimination")
11279 "This package performs augmented backward elimination and checks the
11280 stability of the obtained model. Augmented backward elimination combines
11281 significance or information based criteria with the change in estimate to
11282 either select the optimal model for prediction purposes or to serve as a tool
11283 to obtain a practically sound, highly interpretable model.")
11284 (license license:gpl2+)))
11286 (define-public r-abf2
11293 (uri (cran-uri "abf2" version))
11295 (base32 "0d65mc1w4pbiv7xaqzdlw1bfsxf25587rv597hh41vs0j0zlfpxx"))))
11296 (build-system r-build-system)
11297 (home-page "https://cran.r-project.org/web/packages/abf2/")
11298 (synopsis "Load gap-free axon @code{r-abf2} files")
11300 "This package loads electrophysiology data from ABF2 files, as created by
11301 Axon Instruments/Molecular Devices software. Only files recorded in gap-free
11302 mode are currently supported.")
11303 (license license:artistic2.0)))
11305 (define-public r-abhgenotyper
11307 (name "r-abhgenotyper")
11312 (uri (cran-uri "ABHgenotypeR" version))
11314 (base32 "08cpmnaaxsm5c5bjifnfxdlvg5inrf13biqpcl2yq5zpqjmiki0l"))))
11315 (properties `((upstream-name . "ABHgenotypeR")))
11316 (build-system r-build-system)
11318 (list r-ggplot2 r-reshape2))
11319 (home-page "https://github.com/StefanReuscher/ABHgenotypeR/")
11320 (synopsis "Visualize and manipulate ABH genotypes")
11322 "The @code{r-abhgenotyper} package provides simple imputation,
11323 error-correction and plotting capacities for genotype data. The package is
11324 supposed to serve as an intermediate but independent analysis tool between the
11325 TASSEL GBS pipeline and the @code{r-qtl} package. It provides functionalities
11326 not found in either TASSEL or @code{r-qtl} in addition to visualization of
11327 genotypes as \"graphical genotypes\".")
11328 (license license:gpl3)))
11330 (define-public r-furrr
11337 (uri (cran-uri "furrr" version))
11340 "117xj66l14r08macwghgyibzm282ljv1afpa133h952gc70irs9z"))))
11341 (build-system r-build-system)
11349 (home-page "https://github.com/DavisVaughan/furrr")
11350 (synopsis "Apply mapping functions in parallel using futures")
11352 "This package provides implementations of the family of @code{map()}
11353 functions from the @code{purrr} package that can be resolved using any
11354 @code{future}-supported backend, e.g. parallel on the local machine or
11355 distributed on a compute cluster.")
11356 (license license:lgpl2.1+)))
11358 (define-public r-abjutils
11360 (name "r-abjutils")
11365 (uri (cran-uri "abjutils" version))
11367 (base32 "0lmf4va8qnzwg698i2h4fcwvd6dhsgdkqsfh41aa3wg1flimhsr7"))))
11368 (build-system r-build-system)
11378 (home-page "https://github.com/abjur/abjutils/")
11379 (synopsis "Collection of tools for jurimetrical analysis")
11381 "This package implements general purpose tools, such as functions for
11382 sampling and basic manipulation of Brazilian lawsuits identification number.
11383 It also implements functions for text cleaning, such as accentuation
11385 (license license:expat)))
11387 (define-public r-abnormality
11389 (name "r-abnormality")
11394 (uri (cran-uri "abnormality" version))
11396 (base32 "1fzfskl9akl06nliy8hkv2a0pznpj8pwcypg3gj5r2nzvr3kan9v"))))
11397 (build-system r-build-system)
11399 (list r-mass r-matrix))
11400 (home-page "https://cran.r-project.org/web/packages/abnormality/")
11401 (synopsis "Measure a subject's abnormality with respect to a reference population")
11403 "This package contains functions to implement the methodology and
11404 considerations laid out by Marks et al. in the article \"Measuring abnormality
11405 in high dimensional spaces: applications in biomechanical gait analysis\".
11406 Using high-dimensional datasets to measure a subject's overall level of
11407 abnormality as compared to a reference population is often needed in outcomes
11409 (license license:expat)))
11411 (define-public r-abodoutlier
11413 (name "r-abodoutlier")
11418 (uri (cran-uri "abodOutlier" version))
11420 (base32 "1pvhgxmh23br84r0fbmv7g53z2427birdja96a67vqgz18r3fdvj"))))
11421 (properties `((upstream-name . "abodOutlier")))
11422 (build-system r-build-system)
11425 (home-page "https://cran.r-project.org/web/packages/abodOutlier/")
11426 (synopsis "Angle-based outlier detection")
11428 "This package performs angle-based outlier detection on a given data
11429 frame. It offers three methods to process data:
11431 @item full but slow implementation using all the data that has cubic
11433 @item a fully randomized method;
11434 @item a method using k-nearest neighbours.
11436 These algorithms are well suited for high dimensional data outlier
11438 (license license:expat)))
11440 (define-public r-abps
11447 (uri (cran-uri "ABPS" version))
11449 (base32 "0n3f66nmfi5v94il1mxy026mi84w01ph2aljk60vn3mrz8kwf2ll"))))
11450 (properties `((upstream-name . "ABPS")))
11451 (build-system r-build-system)
11452 (propagated-inputs (list r-kernlab))
11453 (home-page "https://cran.r-project.org/web/packages/ABPS/")
11454 (synopsis "Abnormal blood profile score to detect blood doping")
11456 "This package offers an implementation of the @dfn{Abnormal blood profile score} (ABPS).
11457 The ABPS is a part of the Athlete biological passport program of the World
11458 anti-doping agency, which combines several blood parameters into a single
11459 score in order to detect blood doping. The package also contains functions to
11460 calculate other scores used in anti-doping programs, such as the ratio of
11461 hemoglobin to reticulocytes (OFF-score), as well as example data.")
11462 (license license:gpl2+)))
11464 (define-public r-parmigene
11466 (name "r-parmigene")
11471 (uri (cran-uri "parmigene" version))
11474 "067rqxqyzy1fsjj0s1g7af4527whwdhzjzc5b8a8n7683na59ns4"))))
11475 (build-system r-build-system)
11476 (home-page "https://cran.r-project.org/web/packages/parmigene/")
11477 (synopsis "Mutual information estimation for gene network reconstruction")
11479 "This package provides a parallel estimation of the mutual information
11480 based on entropy estimates from k-nearest neighbors distances and algorithms
11481 for the reconstruction of gene regulatory networks.")
11482 (license license:agpl3+)))
11484 (define-public r-pscl
11491 (uri (cran-uri "pscl" version))
11493 (base32 "0vzf5wazs92bhqhqd66v3vwmbfmnh67gb2466g1xxawim649nk05"))))
11494 (build-system r-build-system)
11497 (home-page "https://github.com/atahk/pscl/")
11498 (synopsis "Political science computational laboratory")
11500 "The @code{pscl} is an R package providing classes and methods for:
11502 @item Bayesian analysis of roll call data (item-response models);
11503 @item elementary Bayesian statistics;
11504 @item maximum likelihood estimation of zero-inflated and hurdle models for count
11506 @item utility functions.
11508 (license license:gpl2)))
11510 (define-public r-accelmissing
11512 (name "r-accelmissing")
11517 (uri (cran-uri "accelmissing" version))
11519 (base32 "1nql9inx6azdzi3z4sfm2vdml2mms6krl8wzlf1dn1c97ahn57fy"))))
11520 (build-system r-build-system)
11522 (list r-mice r-pscl))
11523 (home-page "https://cran.r-project.org/web/packages/accelmissing/")
11524 (synopsis "Missing value imputation for accelerometer data")
11526 "This package provides a statistical method to impute the missing values in
11527 accelerometer data. The methodology includes both parametric and
11528 semi-parametric multiple imputations under the zero-inflated Poisson lognormal
11529 model. It also provides multiple functions to preprocess the accelerometer data
11530 previous to the missing data imputation. These include detecting the wearing
11531 and the non-wearing time, selecting valid days and subjects, and creating plots.")
11532 (license license:gpl2+)))
11534 (define-public r-mhsmm
11541 (uri (cran-uri "mhsmm" version))
11543 (base32 "009dj0zkj1zry7jr9hf4cknb686z50a2l967if64xm0dvjmp7dgs"))))
11544 (build-system r-build-system)
11545 (propagated-inputs (list r-mvtnorm))
11546 (home-page "https://github.com/jaredo/mhsmm/")
11547 (synopsis "Inference for hidden Markov and semi-Markov models")
11549 "The @code{r-mhsmm} package implements estimation and prediction methods for
11550 hidden Markov and semi-Markov models for multiple observation sequences. Such
11551 techniques are of interest when observed data is thought to be dependent on some
11552 unobserved (or hidden) state. Also, this package is suitable for equidistant
11553 time series data, with multivariate and/or missing data. Allows user defined
11554 emission distributions.")
11555 (license license:gpl2+)))
11557 (define-public r-nleqslv
11564 (uri (cran-uri "nleqslv" version))
11566 (base32 "1v9znvncyigw9r25wx2ma0b7ib179b488dl0qsrhp5zrcz7mcjgm"))))
11567 (build-system r-build-system)
11568 (native-inputs (list gfortran))
11569 (home-page "https://cran.r-project.org/web/packages/nleqslv/")
11570 (synopsis "Solve systems of nonlinear equations")
11572 "The @code{r-nleqslv} package solves a system of nonlinear equations using a
11573 Broyden or a Newton method with a choice of global strategies such as line
11574 search and trust region. There are options for using a numerical or user
11575 supplied Jacobian, for specifying a banded numerical Jacobian and for allowing a
11576 singular or ill-conditioned Jacobian.")
11577 (license license:gpl2+)))
11579 (define-public r-physicalactivity
11581 (name "r-physicalactivity")
11586 (uri (cran-uri "PhysicalActivity" version))
11588 (base32 "0b27prkv3x6v2afz0y53ccs9scibpc7nj54n0hpd9fgn1wyg4c40"))))
11590 `((upstream-name . "PhysicalActivity")))
11591 (build-system r-build-system)
11592 (home-page "https://cran.r-project.org/web/packages/PhysicalActivity/")
11593 (synopsis "Processing accelerometer data for physical activity measurement")
11595 "This @code{r-physicalactivity} package provides a function @code{wearingMarking}
11596 for classification of monitored wear and nonwear time intervals in accelerometer
11597 data collected to assess physical activity. The package also contains functions
11598 for making plots of accelerometer data and obtaining the summary of various
11599 information including daily monitor wear time and the mean monitor wear time
11600 during valid days. The revised package version 0.2-1 improved the functions
11601 regarding speed, robustness and add better support for time zones and daylight
11602 saving. In addition, several functions were added:
11604 @item the @code{markDelivery} can classify days for ActiGraph delivery by mail;
11605 @item the @code{markPAI} can categorize physical activity intensity level based
11606 on user-defined cut-points of accelerometer counts.
11608 It also supports importing ActiGraph (AGD) files with @code{readActigraph} and
11609 @code{queryActigraph} functions.")
11610 (license license:gpl3+)))
11612 (define-public r-acc
11619 (uri (cran-uri "acc" version))
11621 (base32 "1ii2vm47djxbixa75h690q1s2f9m9x6i8nkygik93j6dayr6kr1m"))))
11622 (build-system r-build-system)
11637 (home-page "https://cran.r-project.org/web/packages/acc/")
11638 (synopsis "Exploring accelerometer data")
11640 "This package processes accelerometer data from uni-axial and tri-axial devices
11641 and generates data summaries. Also, includes functions to plot, analyze, and
11642 simulate accelerometer data.")
11643 (license license:gpl2+)))
11645 (define-public r-rbenchmark
11647 (name "r-rbenchmark")
11652 (uri (cran-uri "rbenchmark" version))
11654 (base32 "010fn3qwnk2k411cbqyvra1d12c3bhhl3spzm8kxffmirj4p2al9"))))
11655 (build-system r-build-system)
11656 (home-page "https://cran.r-project.org/web/packages/rbenchmark/")
11657 (synopsis "Benchmarking routine for R")
11659 "This @code{r-rbenchmark} package is inspired by the Perl module Benchmark,
11660 and is intended to facilitate benchmarking of arbitrary R code. The library
11661 consists of just one function, benchmark, which is a simple wrapper around
11662 system.time. Given a specification of the benchmarking process (counts of
11663 replications, evaluation environment) and an arbitrary number of expressions,
11664 benchmark evaluates each of the expressions in the specified environment,
11665 replicating the evaluation as many times as specified, and returning the results
11666 conveniently wrapped into a data frame.")
11667 (license license:gpl2+)))
11669 (define-public r-mitools
11676 (uri (cran-uri "mitools" version))
11679 "0c2x2n1p53lcw0vx4vmy5j7m2f95i7g2iwbryl89imr99rvz617j"))))
11680 (build-system r-build-system)
11681 (propagated-inputs (list r-dbi))
11682 (home-page "https://cran.r-project.org/web/packages/mitools/")
11683 (synopsis "Tools for multiple imputation of missing data")
11685 "This package provides tools to perform analyses and combine results from
11686 multiple-imputation datasets.")
11687 (license license:gpl2)))
11689 (define-public r-mixsqp
11695 (uri (cran-uri "mixsqp" version))
11698 "1qics04w0swyp216d6g8dmsph8q2kpadpacp66h2qih3521js12q"))))
11699 (properties `((upstream-name . "mixsqp")))
11700 (build-system r-build-system)
11702 (list r-irlba r-rcpp r-rcpparmadillo))
11705 (home-page "https://github.com/stephenslab/mixsqp")
11707 "Sequential quadratic programming for maximum-likelihood estimation")
11709 "This package provides an optimization method based on sequential
11710 quadratic programming for maximum likelihood estimation of the mixture
11711 proportions in a finite mixture model where the component densities are
11712 known. The algorithm is expected to obtain solutions that are at least
11713 as accurate as the state-of-the-art MOSEK interior-point solver, and they
11714 are expected to arrive at solutions more quickly when the number of
11715 samples is large and the number of mixture components is not too large.")
11716 (license license:expat)))
11718 (define-public r-magick
11725 (uri (cran-uri "magick" version))
11728 "0h942bn7wfnzbbgq9hrs75c7igmg5r1c5sad2v0znhza4cp7p1w3"))))
11729 (build-system r-build-system)
11731 (list imagemagick zlib))
11733 (list r-curl r-magrittr r-rcpp))
11735 (list pkg-config r-knitr))
11736 (home-page "https://github.com/ropensci/magick")
11737 (synopsis "Advanced graphics and image-processing in R")
11739 "This package provides bindings to ImageMagick, a comprehensive image
11740 processing library. It supports many common formats (PNG, JPEG, TIFF, PDF,
11741 etc.) and manipulations (rotate, scale, crop, trim, flip, blur, etc). All
11742 operations are vectorized via the Magick++ STL meaning they operate either on
11743 a single frame or a series of frames for working with layers, collages, or
11744 animation. In RStudio, images are automatically previewed when printed to the
11745 console, resulting in an interactive editing environment.")
11746 (license license:expat)))
11748 (define-public r-survey
11755 (uri (cran-uri "survey" version))
11758 "0ljsszybzri531q6xab04r6zq11vchfs7y0snjzk57m3g0b9ms05"))))
11759 (build-system r-build-system)
11767 (home-page "http://r-survey.r-forge.r-project.org/survey/")
11768 (synopsis "Analysis of complex survey samples")
11770 "This package provides tools for the analysis of complex survey samples.
11771 The provided features include: summary statistics, two-sample tests, rank
11772 tests, generalised linear models, cumulative link models, Cox models,
11773 loglinear models, and general maximum pseudolikelihood estimation for
11774 multistage stratified, cluster-sampled, unequally weighted survey samples;
11775 variances by Taylor series linearisation or replicate weights;
11776 post-stratification, calibration, and raking; two-phase subsampling designs;
11777 graphics; PPS sampling without replacement; principal components, and factor
11779 ;; Either version of the GPL.
11780 (license (list license:gpl2 license:gpl3))))
11782 (define-public r-gee
11785 (version "4.13-22")
11789 (uri (cran-uri "gee" version))
11792 "1wbwn7bjqz09l6clh43dy3x5qgv9b9wwn7xnfw9fkkrhn6rvc3rw"))))
11793 (properties `((upstream-name . "gee")))
11794 (build-system r-build-system)
11797 (home-page "https://cran.r-project.org/web/packages/gee/")
11798 (synopsis "Generalized estimation equation solver")
11800 "This package provides a solver for generalized estimation equations.")
11801 (license license:gpl2)))
11803 (define-public r-tab
11810 (uri (cran-uri "tab" version))
11813 "1kg8c1safi9klkx2mdkmsf5dn9piy4jljwd4ma7g4jz2rwl4jzhv"))))
11814 (properties `((upstream-name . "tab")))
11815 (build-system r-build-system)
11817 (list r-dplyr r-kableextra r-knitr r-mass r-survey))
11820 (home-page "https://cran.r-project.org/web/packages/tab/")
11821 (synopsis "Create summary tables for statistical reports")
11823 "This package contains functions for creating various types of summary
11824 tables, e.g. comparing characteristics across levels of a categorical variable
11825 and summarizing fitted generalized linear models, generalized estimating
11826 equations, and Cox proportional hazards models. Functions are available to
11827 handle data from simple random samples as well as complex surveys.")
11828 (license license:gpl3+)))
11830 (define-public r-dvmisc
11837 (uri (cran-uri "dvmisc" version))
11839 (base32 "01v6sixx0f3nrn6ymfifb3pvd2msfrwm21kmdv38laxq29vc4rsi"))))
11840 (build-system r-build-system)
11853 (home-page "https://cran.r-project.org/web/packages/dvmisc/")
11854 (synopsis "Faster computation of common statistics and miscellaneous functions")
11856 "This package implements faster versions of base R functions (e.g. mean, standard
11857 deviation, covariance, weighted mean), mostly written in C++, along with
11858 miscellaneous functions for various purposes (e.g. create the histogram with
11859 fitted probability density function or probability mass function curve, create
11860 the body mass index groups, assess the linearity assumption in logistic
11862 (license license:gpl2)))
11864 (define-public r-accelerometry
11866 (name "r-accelerometry")
11871 (uri (cran-uri "accelerometry" version))
11873 (base32 "13xzrwhr4i1nj9c8vrmfdg2rmrc8n446iihcyxmy99sm99hpzyip"))))
11874 (build-system r-build-system)
11876 (list r-dvmisc r-rcpp))
11877 (home-page "https://cran.r-project.org/web/packages/accelerometry/")
11878 (synopsis "Functions for processing accelerometer data")
11880 "This package provides a collection of functions that perform operations on
11881 time-series accelerometer data, such as identify the non-wear time, flag minutes
11882 that are part of an activity bout, and find the maximum 10-minute average count
11883 value. The functions are generally very flexible, allowing for a variety of
11884 algorithms to be implemented.")
11885 (license license:gpl3)))
11887 (define-public r-absim
11894 (uri (cran-uri "AbSim" version))
11896 (base32 "16ddjk8b6xw80ch4jis1y751i9561wdxh0gifbf15qiz3vjckq8m"))))
11897 (properties `((upstream-name . "AbSim")))
11898 (build-system r-build-system)
11900 (list r-ape r-powerlaw))
11901 (home-page "https://cran.r-project.org/web/packages/AbSim/")
11902 (synopsis "Time resolved simulations of antibody repertoires")
11904 "This package provides simulation methods for the evolution of antibody repertoires.
11905 The heavy and light chain variable region of both human and C57BL/6 mice can
11906 be simulated in a time-dependent fashion. Both single lineages using one set of
11907 V-, D-, and J-genes or full repertoires can be simulated. The algorithm begins
11908 with an initial V-D-J recombination event, starting the first phylogenetic tree.
11909 Upon completion, the main loop of the algorithm begins, with each iteration
11910 representing one simulated time step. Various mutation events are possible at
11911 each time step, contributing to a diverse final repertoire.")
11912 (license license:gpl2)))
11914 (define-public r-quic
11921 (uri (cran-uri "QUIC" version))
11923 (base32 "021bp9xbaih60qmss015ycblbv6d1dvb1z89y93zpqqnc2qhpv3c"))))
11924 (properties `((upstream-name . "QUIC")))
11925 (build-system r-build-system)
11926 (home-page "https://www.cs.utexas.edu/users/sustik/QUIC/")
11927 (synopsis "Regularized sparse inverse covariance matrix estimation")
11929 "This package implements the regularized Gaussian maximum likelihood
11930 estimation of the inverse of a covariance matrix. It uses Newton's method and
11931 coordinate descent to solve the regularized inverse covariance matrix
11932 estimation problem.")
11933 ;; The project home page states that the release is under GPLv3 or later.
11934 ;; The CRAN page only says GPL-3.
11935 (license license:gpl3+)))
11937 (define-public r-abundant
11939 (name "r-abundant")
11944 (uri (cran-uri "abundant" version))
11946 (base32 "15m3ngj5aipjg961yy5kvdg9xlfcpliw30dq6gchzxabhnfzcipd"))))
11947 (build-system r-build-system)
11950 (home-page "https://cran.r-project.org/web/packages/abundant/")
11951 (synopsis "Abundant regression and high-dimensional principal fitted components")
11953 "This package provides tools to fit and predict with the high-dimensional
11954 principal fitted components model. This model is described by Cook, Forzani,
11955 and Rothman (2012) @url{doi:10.1214/11-AOS962}.")
11956 ;; The DESCRIPTION file states GPL-2, but since it directly depends on a
11957 ;; GPLv3+ package (QUIC) this likely means GPLv2+.
11958 (license license:gpl2+)))
11960 (define-public r-ac3net
11967 (uri (cran-uri "Ac3net" version))
11969 (base32 "1ns4n0xxz6p34c11bj0k7nzgmyqr9mis2b0g5nfz37dbikndyqyz"))))
11970 (properties `((upstream-name . "Ac3net")))
11971 (build-system r-build-system)
11973 (list r-data-table))
11974 (home-page "https://cran.r-project.org/web/packages/Ac3net/")
11975 (synopsis "Inferring directional conservative causal core gene networks")
11976 (description "This package infers directional Conservative causal core
11977 (gene) networks (C3NET). This is a version of the algorithm C3NET with
11978 directional network.")
11979 (license license:gpl3+)))
11981 (define-public r-aca
11988 (uri (cran-uri "ACA" version))
11990 (base32 "1i3hm27nvnkvc39xlh0d1blq8q0q02czmvgi3cazmjx3jvxay0vq"))))
11991 (properties `((upstream-name . "ACA")))
11992 (build-system r-build-system)
11993 (home-page "https://cran.r-project.org/web/packages/ACA/")
11994 (synopsis "Abrupt change-point or aberration detection in point series")
11996 "This package offers an interactive function for the detection of breakpoints in
11998 ;; Any version of the GPL
11999 (license (list license:gpl2+ license:gpl3+))))
12001 (define-public r-acceptancesampling
12003 (name "r-acceptancesampling")
12008 (uri (cran-uri "AcceptanceSampling" version))
12010 (base32 "1ja1g0v8qvf7yj81x37wc6i7fkwpc573756jgvazazi8yf1gm12p"))))
12012 `((upstream-name . "AcceptanceSampling")))
12013 (build-system r-build-system)
12014 (home-page "https://cran.r-project.org/web/packages/AcceptanceSampling/")
12015 (synopsis "Creation and evaluation of acceptance sampling plans")
12017 "This @code{r-acceptancesampling} provides functionality for creating and evaluating
12018 acceptance sampling plans. Acceptance sampling is a methodology commonly used
12019 in quality control and improvement. International standards of acceptance
12020 sampling provide sampling plans for specific circumstances. The aim of this
12021 package is to provide an easy-to-use interface to visualize single, double or
12022 multiple sampling plans. In addition, methods have been provided to enable the
12023 user to assess sampling plans against pre-specified levels of performance, as
12024 measured by the probability of acceptance for a given level of quality in the
12026 (license license:gpl3+)))
12028 (define-public r-acclma
12035 (uri (cran-uri "ACCLMA" version))
12037 (base32 "1na27sp18fq12gp6vxgqw1ffsz2yi1d8xvrxbrzx5g1kqxrayy0v"))))
12038 (properties `((upstream-name . "ACCLMA")))
12039 (build-system r-build-system)
12040 (home-page "https://cran.r-project.org/web/packages/ACCLMA/")
12041 (synopsis "ACC & LMA graph plotting")
12043 "This package contains a function that imports data from a @acronym{CSV,
12044 Comma-Separated Values} file, or uses manually entered data from the format (x,
12045 y, weight) and plots the appropriate @acronym{ACC, Absolute Concentration
12046 Curve} vs @acronym{LOI, Line of Independence} graph and
12047 @acronym{LMA, @acronym{LOI} Minus @acronym{ACC}} graph. The main
12048 function is @code{plotLMA} (source file, header) that takes a data set and plots the
12049 appropriate @acronym{LMA} and @acronym{ACC} graphs. If no source file (a
12050 string) was passed, a manual data entry window is opened. The header parameter
12051 indicates by TRUE/FALSE (false by default) if the source @acronym{CSV} file has
12052 a header row or not. The dataset should contain only one independent variable
12053 (x) and one dependent variable (y) and can contain a weight for each
12055 (license license:gpl2)))
12057 (define-public r-aspi
12064 (uri (cran-uri "aspi" version))
12066 (base32 "0rhvxw243vvdv3hxa6pi343gcjc2cbxq1jzqirl9k1l4i3897l87"))))
12067 (build-system r-build-system)
12069 "https://cran.r-project.org/web/packages/aspi/")
12071 "Analysis of symmetry of parasitic infections")
12073 "This package provides tools for the analysis and visualization of bilateral
12074 asymmetry in parasitic infections.")
12075 (license license:gpl3+)))
12077 (define-public r-sandwich
12079 (name "r-sandwich")
12084 (uri (cran-uri "sandwich" version))
12087 "12aa5083k3sfrfq1jy3l94wffss9h0rga8j71jy3n8pkhiq4nn7n"))))
12088 (build-system r-build-system)
12091 (home-page "https://cran.r-project.org/web/packages/sandwich/")
12092 (synopsis "Robust Covariance Matrix Estimators")
12094 "This package provides model-robust standard error estimators for
12095 cross-sectional, time series, clustered, panel, and longitudinal data.")
12096 ;; Either version of the license.
12097 (license (list license:gpl2 license:gpl3))))
12099 (define-public r-th-data
12106 (uri (cran-uri "TH.data" version))
12109 "0ynxacnz002bjsp2ybql7rdqw4zd14af8r7w44nwbx22n4bapwzd"))))
12110 (properties `((upstream-name . "TH.data")))
12111 (build-system r-build-system)
12113 (list r-mass r-survival))
12116 (home-page "https://cran.r-project.org/web/packages/TH.data/")
12117 (synopsis "Shared data sets")
12119 "This package contains supporting data sets that are used in other
12120 packages maintained by Torsten Hothorn.")
12121 (license license:gpl3)))
12123 (define-public r-multcomp
12125 (name "r-multcomp")
12130 (uri (cran-uri "multcomp" version))
12133 "0mz5wdqrqpp2gqijfpp9rgfbq8yvxki4is8fbbc4qwdwryqp6d7h"))))
12134 (build-system r-build-system)
12136 (list r-codetools r-mvtnorm r-sandwich r-survival r-th-data))
12137 (home-page "https://cran.r-project.org/web/packages/multcomp/")
12138 (synopsis "Simultaneous inference in general parametric models")
12140 "Simultaneous tests and confidence intervals for general linear
12141 hypotheses in parametric models, including linear, generalized linear, linear
12142 mixed effects, and survival models. The package includes demos reproducing
12143 analyzes presented in the book \"Multiple Comparisons Using R\" (Bretz,
12144 Hothorn, Westfall, 2010, CRC Press).")
12145 (license license:gpl2)))
12147 (define-public r-multcompview
12149 (name "r-multcompview")
12154 (uri (cran-uri "multcompView" version))
12156 (base32 "1rfq9wvvrghq0542ff40wy8vdmsyd8spzz6ihcywcvxdfa8m6g8j"))))
12157 (properties `((upstream-name . "multcompView")))
12158 (build-system r-build-system)
12159 (home-page "https://cran.r-project.org/package=multcompView")
12160 (synopsis "Visualizations of paired comparisons")
12162 "Convert a logical vector or a vector of p-values or a correlation,
12163 difference, or distance matrix into a display identifying the pairs for which
12164 the differences were not significantly different.")
12165 ;; Any version of the GPL.
12166 (license license:gpl3+)))
12168 (define-public r-emmeans
12171 (version "1.7.4-1")
12175 (uri (cran-uri "emmeans" version))
12178 "08g7ifqhwqa00hc850nwx03dp7isz0281ig6kvixc4xdahmkm8zp"))))
12179 (build-system r-build-system)
12181 (list r-estimability r-mvtnorm r-numderiv r-xtable))
12184 (home-page "https://github.com/rvlenth/emmeans")
12185 (synopsis "Estimated marginal means, aka least-squares means")
12187 "This package provides tools to obtain @dfn{estimated marginal
12188 means} (EMMs) for many linear, generalized linear, and mixed models. It can
12189 be used to compute contrasts or linear functions of EMMs, trends, and
12190 comparisons of slopes.")
12191 ;; Either version of the license.
12192 (license (list license:gpl2 license:gpl3))))
12194 (define-public r-pwr
12201 (uri (cran-uri "pwr" version))
12204 "1kfzy73v3z6ipc3kdfkcjrp4b4p5k54nwk796gqi36srm93hgc2v"))))
12205 (build-system r-build-system)
12208 (home-page "https://github.com/heliosdrm/pwr")
12209 (synopsis "Basic functions for power analysis")
12211 "This package provides power analysis functions along the lines of
12213 (license license:gpl3+)))
12215 (define-public r-libcoin
12222 (uri (cran-uri "libcoin" version))
12224 (base32 "1syrcdj5qg5m3zd3dlxgpfklswbalfg42w058dr09hnzqsvx0z9d"))))
12225 (build-system r-build-system)
12226 (propagated-inputs (list r-mvtnorm))
12227 (home-page "https://cran.r-project.org/web/packages/libcoin")
12228 (synopsis "Linear test statistics for permutation inference")
12230 "This package provides basic infrastructure for linear test statistics
12231 and permutation inference in the framework of Strasser and Weber (1999).")
12232 (license license:gpl2)))
12234 (define-public r-coin
12241 (uri (cran-uri "coin" version))
12244 "1cpv7jx840inzg98bkhrb5yscx0gpag6br237r5qpnc2gbrd2ikm"))))
12245 (build-system r-build-system)
12253 (home-page "http://coin.r-forge.r-project.org")
12254 (synopsis "Conditional inference procedures in a permutation test framework")
12256 "This package provides conditional inference procedures for the general
12257 independence problem including two-sample, K-sample (non-parametric ANOVA),
12258 correlation, censored, ordered and multivariate problems.")
12259 (license license:gpl2)))
12261 (define-public r-bayesplot
12263 (name "r-bayesplot")
12268 (uri (cran-uri "bayesplot" version))
12271 "0hqy597ang53phxnl084hak35ffqz9lw9hygax7370gpkjws908a"))))
12272 (build-system r-build-system)
12287 (home-page "https://mc-stan.org/bayesplot")
12288 (synopsis "Plotting for Bayesian models")
12290 "This package provides plotting functions for posterior analysis, model
12291 checking, and MCMC diagnostics. The package is designed not only to provide
12292 convenient functionality for users, but also a common set of functions that
12293 can be easily used by developers working on a variety of R packages for
12294 Bayesian modeling.")
12295 (license license:gpl3+)))
12297 (define-public r-tmb
12304 (uri (cran-uri "TMB" version))
12307 "1mr5vwamw6ag1fhd83jyy6015296908qwshwq0fcphhiv60x579c"))))
12308 (properties `((upstream-name . "TMB")))
12309 (build-system r-build-system)
12311 (list r-matrix r-rcppeigen))
12312 (home-page "http://tmb-project.org")
12313 (synopsis "Template model builder: a general random effect tool")
12315 "With this tool, a user should be able to quickly implement complex
12316 random effect models through simple C++ templates. The package combines
12317 @code{CppAD} (C++ automatic differentiation), @code{Eigen} (templated
12318 matrix-vector library) and @code{CHOLMOD} (sparse matrix routines available
12319 from R) to obtain an efficient implementation of the applied Laplace
12320 approximation with exact derivatives. Key features are: Automatic sparseness
12321 detection, parallelism through BLAS and parallel user templates.")
12322 (license license:gpl2)))
12324 (define-public r-sjstats
12331 (uri (cran-uri "sjstats" version))
12333 (base32 "1cv80yjnyh6qihxf57zivihhia20gibr5f03x8aspy6382wnwlka"))))
12334 (build-system r-build-system)
12353 (home-page "https://github.com/strengejacke/sjstats")
12354 (synopsis "Functions for common statistical computations")
12356 "This package provides a collection of convenient functions for common
12357 statistical computations, which are not directly provided by R's @code{base}
12358 or @code{stats} packages. This package aims at providing, first, shortcuts
12359 for statistical measures, which otherwise could only be calculated with
12360 additional effort. Second, these shortcut functions are generic, and can be
12361 applied not only to vectors, but also to other objects as well. The focus of
12362 most functions lies on summary statistics or fit measures for regression
12363 models, including generalized linear models, mixed effects models and Bayesian
12365 (license license:gpl3)))
12367 (define-public r-glmmtmb
12374 (uri (cran-uri "glmmTMB" version))
12377 "0xdjc3gx0cj098rrjzlsy9cccxzfvn029xh4ycpya4xjhxsykldr"))))
12378 (properties `((upstream-name . "glmmTMB")))
12379 (build-system r-build-system)
12388 (list r-knitr r-rmarkdown)) ; for vignettes
12389 (home-page "https://github.com/glmmTMB")
12390 (synopsis "Generalized linear mixed models")
12392 "Fit linear and generalized linear mixed models with various extensions,
12393 including zero-inflation. The models are fitted using maximum likelihood
12394 estimation via the Template Model Builder. Random effects are assumed to be
12395 Gaussian on the scale of the linear predictor and are integrated out using the
12396 Laplace approximation. Gradients are calculated using automatic
12398 (license license:agpl3+)))
12400 (define-public r-bayestestr
12402 (name "r-bayestestr")
12407 (uri (cran-uri "bayestestR" version))
12410 "1fbkpagc5zznrafy7h68nhx43a1yg4v7242pbqjkd0h2481c101z"))))
12411 (properties `((upstream-name . "bayestestR")))
12412 (build-system r-build-system)
12414 (list r-datawizard r-insight))
12417 (home-page "https://github.com/easystats/bayestestR")
12418 (synopsis "Describe Bayesian models and posterior distributions")
12420 "This package provides utilities to understand and describe posterior
12421 distributions and Bayesian models. It includes point-estimates such as
12422 @dfn{Maximum A Posteriori} (MAP), measures of dispersion such as @dfn{Highest
12423 Density Interval} (HDI), and indices used for null-hypothesis testing (such as
12424 ROPE percentage and pd).")
12425 (license license:gpl3)))
12427 (define-public r-performance
12429 (name "r-performance")
12434 (uri (cran-uri "performance" version))
12437 "1znr4i1pjv6z3lj6qrma2i3l94rz1z29w92mrxxfy3ch0s71crww"))))
12438 (build-system r-build-system)
12440 (list r-bayestestr r-datawizard r-insight))
12441 (home-page "https://easystats.github.io/performance/")
12442 (synopsis "Assessment of regression models performance")
12444 "This package provides utilities for computing measures to assess model
12445 quality, which are not directly provided by R's @code{base} or @code{stats}
12446 packages. These include e.g. measures like r-squared, intraclass correlation
12447 coefficient, root mean squared error or functions to check models for
12448 overdispersion, singularity or zero-inflation and more. Functions apply to a
12449 large variety of regression models, including generalized linear models, mixed
12450 effects models and Bayesian models.")
12451 (license license:gpl3)))
12453 (define-public r-ggeffects
12455 (name "r-ggeffects")
12460 (uri (cran-uri "ggeffects" version))
12463 "01yyfw7fkbxrp0gpwni5y8m4w9l3xckwc3crnvy1fqs1d6gwx3xx"))))
12464 (build-system r-build-system)
12466 (list r-insight r-mass r-sjlabelled))
12469 (home-page "https://github.com/strengejacke/ggeffects")
12470 (synopsis "Create tidy data frames of marginal effects for ggplot")
12472 "This package provides tools to compute marginal effects from statistical
12473 models and return the result as tidy data frames. These data frames are ready
12474 to use with the @code{ggplot2} package. Marginal effects can be calculated
12475 for many different models. Interaction terms, splines and polynomial terms
12476 are also supported. The two main functions are @code{ggpredict()} and
12477 @code{ggeffect()}. There is a generic @code{plot()} method to plot the
12478 results using @code{ggplot2}.")
12479 (license license:gpl3)))
12481 (define-public r-effectsize
12483 (name "r-effectsize")
12488 (uri (cran-uri "effectsize" version))
12491 "07dbj7n9vwjkb7xrdj224lzc3ppr3jjdgyyilkj7gpkvgjgfrqhz"))))
12492 (properties `((upstream-name . "effectsize")))
12493 (build-system r-build-system)
12495 (list r-bayestestr r-datawizard r-insight r-parameters
12499 (home-page "https://github.com/easystats/effectsize")
12500 (synopsis "Indices of effect size and standardized parameters")
12502 "This package provides utilities to work with indices of effect size and
12503 standardized parameters for a wide variety of models, allowing computation and
12504 conversion of indices such as Cohen's d, r, odds, etc.")
12505 (license license:gpl3)))
12507 (define-public r-sjplot
12514 (uri (cran-uri "sjPlot" version))
12516 (base32 "1rnwhh271xj8xgvvlpqw9ain56mfz37fvl7f6jq9nzx9jxx95bjd"))))
12517 (properties `((upstream-name . "sjPlot")))
12518 (build-system r-build-system)
12540 (home-page "https://strengejacke.github.io/sjPlot/")
12541 (synopsis "Data visualization for statistics in social science")
12543 "This package represents a collection of plotting and table output
12544 functions for data visualization. Results of various statistical
12545 analyses (that are commonly used in social sciences) can be visualized using
12546 this package, including simple and cross tabulated frequencies, histograms,
12547 box plots, (generalized) linear models, mixed effects models, principal
12548 component analysis and correlation matrices, cluster analyses, scatter plots,
12549 stacked scales, effects plots of regression models (including interaction
12550 terms) and much more. This package supports labelled data.")
12551 (license license:gpl3)))
12553 (define-public r-ini
12560 (uri (cran-uri "ini" version))
12563 "04yqij344dwm0xqgara8xia42mlmij3i8711qbb5534w05a1l6bv"))))
12564 (build-system r-build-system)
12565 (home-page "https://github.com/dvdscripter/ini")
12566 (synopsis "Read and write configuration files")
12568 "This package provides tools to parse simple @code{.ini} configuration
12569 files to an structured list. Users can manipulate this resulting list with
12570 @code{lapply()} functions. This same structured list can be used to write
12571 back to file after modifications.")
12572 (license license:gpl3)))
12574 (define-public r-gillespiessa2
12576 (name "r-gillespiessa2")
12581 (uri (cran-uri "GillespieSSA2" version))
12583 (base32 "03ym8qx5yc1a6j9l973lc0rjzs8hiax8fq13j7m1fcb1pvnbvar5"))))
12584 (properties `((upstream-name . "GillespieSSA2")))
12585 (build-system r-build-system)
12598 (native-inputs (list r-knitr))
12599 (home-page "https://github.com/rcannood/GillespieSSA2")
12600 (synopsis "Gillespie's stochastic simulation algorithm")
12602 "This package provides a fast, scalable, and versatile framework for
12603 simulating large systems with Gillespie's @dfn{Stochastic Simulation
12604 Algorithm} (SSA). This package is the spiritual successor to the GillespieSSA
12605 package. Benefits of this package include major speed improvements (>100x),
12606 easier to understand documentation, and many unit tests that try to ensure the
12607 package works as intended.")
12608 (license license:gpl3+)))
12610 (define-public r-gitcreds
12612 (name "r-gitcreds")
12617 (uri (cran-uri "gitcreds" version))
12620 "1snzn7nxy0rwz0bzjsg6k04c0n811dgn8gn9cmn2v78aj57ayjmi"))))
12621 (properties `((upstream-name . "gitcreds")))
12622 (build-system r-build-system)
12623 (inputs (list git-minimal))
12624 (native-inputs (list r-knitr))
12625 (home-page "https://github.com/r-lib/gitcreds")
12626 (synopsis "Query git credentials from R")
12628 "Query, set, and delete credentials from the git credential store.
12629 Manage GitHub tokens and other git credentials. This package is to be used by
12630 other packages that need to authenticate to GitHub and/or other git
12632 (license license:expat)))
12634 (define-public r-gh
12641 (uri (cran-uri "gh" version))
12644 "077drbxz3rx7idv6w24ipj1p6jnzv86a3iyryab699cc9q2kjh54"))))
12645 (build-system r-build-system)
12647 (list r-cli r-gitcreds r-httr r-ini r-jsonlite))
12650 (home-page "https://github.com/r-lib/gh#readme")
12651 (synopsis "Access the GitHub API via R")
12653 "This package provides a minimal R client to access the GitHub API.")
12654 (license license:expat)))
12656 (define-public r-fs
12663 (uri (cran-uri "fs" version))
12666 "11qr3v0xn65vfhgcxl4l6yv48s4w0w3ldp3anpzc25vd3mwd3jim"))))
12667 (build-system r-build-system)
12670 (home-page "https://fs.r-lib.org")
12671 (synopsis "Cross-platform file system operations based on libuv")
12673 "This package provides a cross-platform interface to file system
12674 operations, built on top of the libuv C library.")
12675 (license license:gpl3)))
12677 (define-public r-clisymbols
12679 (name "r-clisymbols")
12684 (uri (cran-uri "clisymbols" version))
12687 "1q7gi2zmykhzas9v8fdnbpdq7pzdcpbhim1yxvd2062l777g4j86"))))
12688 (build-system r-build-system)
12689 (home-page "https://github.com/gaborcsardi/clisymbols")
12690 (synopsis "Unicode symbols at the R prompt")
12692 "This package provides a small subset of Unicode symbols, that are useful
12693 when building command line applications. They fall back to alternatives on
12694 terminals that do not support Unicode.")
12695 (license license:expat)))
12697 (define-public r-credentials
12699 (name "r-credentials")
12704 (uri (cran-uri "credentials" version))
12707 "1f18j3zrq8c9kah57xwahmmljsjg5qphlgamvx507ynvpq8pryig"))))
12708 (properties `((upstream-name . "credentials")))
12709 (build-system r-build-system)
12712 (modify-phases %standard-phases
12713 (add-after 'unpack 'setenv-HOME
12715 ;; This is necessary because git looks for $HOME/.gitconfig
12716 (setenv "HOME" "/tmp"))))))
12718 (list git-minimal))
12720 (list r-askpass r-curl r-jsonlite r-openssl r-sys))
12723 (home-page "https://docs.ropensci.org/credentials/")
12724 (synopsis "Tools for managing SSH and Git credentials")
12726 "This package assists you in setting up and retrieving of HTTPS and SSH
12727 credentials for use with git and other services. For HTTPS remotes the
12728 package interfaces the @command{git-credential} utility which @command{git}
12729 uses to store HTTP usernames and passwords. For SSH remotes this package
12730 provides convenient functions to find or generate appropriate SSH keys. The
12731 package both helps the user to setup a local git installation, and also
12732 provides a back-end for git/ssh client libraries to authenticate with existing
12733 user credentials.")
12734 (license license:expat)))
12736 (define-public r-gert
12743 (uri (cran-uri "gert" version))
12746 "0r19vi77yyjw5gbhgjibdysjlszlw2095v14f6sv675zpbp0li4c"))))
12747 (properties `((upstream-name . "gert")))
12748 (build-system r-build-system)
12750 (list libgit2 zlib))
12759 (list pkg-config r-knitr))
12760 (home-page "https://docs.ropensci.org/gert/")
12761 (synopsis "Simple Git client for R")
12763 "This package provides a simple git client for R based on libgit2 with
12764 support for SSH and HTTPS remotes. All functions in gert use basic R data
12765 types (such as vectors and data-frames) for their arguments and return values.
12766 User credentials are shared with command line git through the
12767 @code{git-credential} store and SSH keys stored on disk or ssh-agent.")
12768 (license license:expat)))
12770 (define-public r-usethis
12777 (uri (cran-uri "usethis" version))
12780 "0638dzl4nm4c36990sf2biy74hjr2fzlqzfb98fsqrbhaw3ngp1i"))))
12781 (build-system r-build-system)
12802 (home-page "https://github.com/r-lib/usethis")
12803 (synopsis "Automate R package and project setup")
12805 "This package helps you to automate R package and project setup tasks
12806 that are otherwise performed manually. This includes setting up unit testing,
12807 test coverage, continuous integration, Git, GitHub integration, licenses,
12808 Rcpp, RStudio projects, and more.")
12809 (license license:gpl3)))
12811 (define-public r-sessioninfo
12813 (name "r-sessioninfo")
12818 (uri (cran-uri "sessioninfo" version))
12821 "1jy7n37qnrb4fgzmn8s8yf7kv29yw27x8zklwf8qdb2kgj2q6qpm"))))
12822 (build-system r-build-system)
12825 (home-page "https://github.com/r-lib/sessioninfo#readme")
12826 (synopsis "R session information")
12828 "This package provides tools to query and print information about the
12829 current R session. It is similar to @code{utils::sessionInfo()}, but includes
12830 more information about packages, and where they were installed from.")
12831 (license license:gpl2)))
12833 (define-public r-remotes
12840 (uri (cran-uri "remotes" version))
12843 "05m5dgv0nba5vhjbdkd8z5lbhpfxgkw31j58am7vz1d44igqgvzj"))))
12844 (build-system r-build-system)
12847 (home-page "https://github.com/r-lib/remotes#readme")
12848 (synopsis "R package installation from remote repositories")
12850 "Download and install R packages stored in GitHub, BitBucket, or plain
12851 subversion or git repositories. This package is a lightweight replacement of
12852 the @code{install_*} functions in the @code{devtools} package. Indeed most of
12853 the code was copied over from @code{devtools}.")
12854 (license license:gpl2+)))
12856 (define-public r-xopen
12863 (uri (cran-uri "xopen" version))
12866 "1vrvgdika1d63dwygynbv2wmd87ll8dji5dy89hj576n8hw601z2"))))
12867 (build-system r-build-system)
12870 (home-page "https://github.com/r-lib/xopen#readme")
12871 (synopsis "Open system files, URLs, anything")
12873 "This package provides a cross-platform solution to open files,
12874 directories or URLs with their associated programs.")
12875 (license license:expat)))
12877 (define-public r-rcmdcheck
12879 (name "r-rcmdcheck")
12884 (uri (cran-uri "rcmdcheck" version))
12887 "1l696byn3kjq2xvz4wxybzaj6ink85h4lz3a35v2132ba5yyzm5v"))))
12888 (build-system r-build-system)
12902 (home-page "https://github.com/r-Lib/rcmdcheck#readme")
12903 (synopsis "Run R CMD check from R and capture results")
12905 "Run @code{R CMD check} from R programmatically, and capture the results
12906 of the individual checks.")
12907 (license license:expat)))
12909 (define-public r-rapportools
12911 (name "r-rapportools")
12916 (uri (cran-uri "rapportools" version))
12919 "0qr86idng12g6hdd764j0wmli700v7rjhw7jdjxj0ka8xm5v7ymm"))))
12920 (build-system r-build-system)
12922 (list r-mass r-pander r-plyr r-reshape2))
12923 (home-page "https://cran.r-project.org/web/packages/rapportools/")
12924 (synopsis "Miscellaneous helper functions with sane defaults for reporting")
12926 "This package provides helper functions that act as wrappers to more
12927 advanced statistical methods with the advantage of having sane defaults for
12929 (license license:agpl3+)))
12931 (define-public r-pander
12938 (uri (cran-uri "pander" version))
12941 "144zkq5w7v6fpzk3x40i0baybbp0y6x2ckh4b9qljryas9mhgp9a"))))
12942 (build-system r-build-system)
12944 (list r-digest r-rcpp))
12947 (home-page "https://rapporter.github.io/pander")
12948 (synopsis "Render R objects into Pandoc's markdown")
12950 "The main aim of the pander R package is to provide a minimal and easy
12951 tool for rendering R objects into Pandoc's markdown. The package is also
12952 capable of exporting/converting complex Pandoc documents (reports) in various
12954 ;; This package is licensed under either the AGPLv3+ or the very rarely
12956 (license license:agpl3+)))
12958 (define-public r-summarytools
12960 (name "r-summarytools")
12965 (uri (cran-uri "summarytools" version))
12968 "0gr95cd1ja8di6s0xghk6w7nj3bh3z4g7j7ixdy7f88q681aixgx"))))
12969 (build-system r-build-system)
12985 (home-page "https://github.com/dcomtois/summarytools")
12986 (synopsis "Tools to quickly and neatly summarize data")
12988 "This package provides tools for data frame summaries, cross-tabulations,
12989 weight-enabled frequency tables and common univariate statistics in concise
12990 tables available in a variety of formats (plain ASCII, Markdown and HTML). A
12991 good point-of-entry for exploring data, both for experienced and new R
12993 (license license:gpl2)))
12995 (define-public r-lsei
13002 (uri (cran-uri "lsei" version))
13005 "1dka0rigfw4vj809qma2dkiwjb3nw5635ynnba5cm299cn7hb2b2"))))
13006 (build-system r-build-system)
13009 (home-page "https://www.stat.auckland.ac.nz/~yongwang")
13010 (synopsis "Solve regression problems under equality/inequality constraints")
13012 "It contains functions that solve least squares linear regression
13013 problems under linear equality/inequality constraints. Functions for solving
13014 quadratic programming problems are also available, which transform such
13015 problems into least squares ones first.")
13016 (license license:gpl2+)))
13018 (define-public r-npsurv
13025 (uri (cran-uri "npsurv" version))
13028 "1ihxhb42cga1hssj2jv4ah0f4hlwsky899ij5261fzh1wxvdp1xw"))))
13029 (build-system r-build-system)
13032 (home-page "https://www.stat.auckland.ac.nz/~yongwang")
13033 (synopsis "Nonparametric survival analysis")
13035 "This package contains functions for non-parametric survival analysis of
13036 exact and interval-censored observations.")
13037 (license license:gpl2+)))
13039 (define-public r-clusteval
13041 (name "r-clusteval")
13046 (uri (cran-uri "clusteval" version))
13049 "1ld0bdl4fy8dsfzm3k7a37cyxc6pfc9qs31x4pxd3z5rslghz7rj"))))
13050 (build-system r-build-system)
13052 (list r-mvtnorm r-rcpp))
13053 (home-page "https://cran.r-project.org/web/packages/clusteval/")
13054 (synopsis "Evaluation of clustering algorithms")
13056 "This R package provides a suite of tools to evaluate clustering
13057 algorithms, clusterings, and individual clusters.")
13058 (license license:expat)))
13060 (define-public r-tweedie
13067 (uri (cran-uri "tweedie" version))
13070 "1nfhaqblvm62j8gfkyrgba5ai0pb2fsnrxp63637mhys2bawlcm0"))))
13071 (build-system r-build-system)
13072 (native-inputs (list gfortran))
13073 (home-page "https://cran.r-project.org/web/packages/tweedie/")
13074 (synopsis "Evaluation of Tweedie exponential family models")
13076 "Maximum likelihood computations for Tweedie families, including the
13077 series expansion (Dunn and Smyth, 2005; <doi10.1007/s11222-005-4070-y>) and
13078 the Fourier inversion (Dunn and Smyth, 2008; <doi:10.1007/s11222-007-9039-6>),
13079 and related methods.")
13080 (license license:gpl2+)))
13082 (define-public r-rcppgsl
13089 (uri (cran-uri "RcppGSL" version))
13091 (base32 "1a5dms0axlzgpv1z2bhfrb77497h0ch1yslq0gidj14vr4kfm57h"))))
13092 (properties `((upstream-name . "RcppGSL")))
13093 (build-system r-build-system)
13096 (home-page "https://cran.r-project.org/web/packages/RcppGSL/")
13097 (synopsis "Rcpp integration for GSL vectors and matrices")
13099 "The GNU Scientific Library (or GSL) is a collection of numerical
13100 routines for scientific computing. It is particularly useful for C and C++
13101 programs as it provides a standard C interface to a wide range of mathematical
13102 routines. There are over 1000 functions in total with an extensive test
13103 suite. The RcppGSL package provides an easy-to-use interface between GSL data
13104 structures and R using concepts from Rcpp which is itself a package that eases
13105 the interfaces between R and C++.")
13106 (license license:gpl2+)))
13108 (define-public r-mvabund
13115 (uri (cran-uri "mvabund" version))
13118 "01kss9dx4an1ir5zs46jypvhj8sdc8wcs00i1223ai09av4lcsgd"))))
13119 (build-system r-build-system)
13121 (list r-mass r-rcpp r-rcppgsl r-statmod r-tweedie))
13122 (home-page "https://cran.r-project.org/web/packages/mvabund/")
13123 (synopsis "Statistical methods for analysing multivariate abundance data")
13125 "This package provides a set of tools for displaying, modeling and
13126 analysing multivariate abundance data in community ecology.")
13127 (license license:lgpl2.1+)))
13129 (define-public r-afex
13136 (uri (cran-uri "afex" version))
13139 "09q426s2zmzxx5ilxy0x5mflpb38pl075ss1s8xvpswkn6cia0b6"))))
13140 (build-system r-build-system)
13141 ;; This is needed for the vignette builder
13144 (modify-phases %standard-phases
13145 (add-after 'unpack 'set-HOME
13146 (lambda _ (setenv "HOME" "/tmp"))))))
13148 (list r-car r-lme4 r-lmertest r-pbkrtest r-reshape2))
13151 r-r-rsp)) ;vignette builder
13152 (home-page "https://afex.singmann.science/")
13153 (synopsis "Analysis of factorial experiments")
13155 "This package provides convenience functions for analyzing factorial
13156 experiments using ANOVA or mixed models.")
13157 (license license:gpl2+)))
13159 (define-public r-lmertest
13161 (name "r-lmertest")
13166 (uri (cran-uri "lmerTest" version))
13169 "1zd8gqjkazhxgpnnr484xwsq30p62fq8592nzyc171zjyplpbaim"))))
13170 (properties `((upstream-name . "lmerTest")))
13171 (build-system r-build-system)
13173 (list r-ggplot2 r-lme4 r-mass r-numderiv))
13174 (home-page "https://github.com/runehaubo/lmerTestR")
13175 (synopsis "Tests in linear mixed effects models")
13177 "This package provides p-values in type I, II or III anova and summary
13178 tables for @code{lmer} model fits via Satterthwaite's degrees of freedom
13179 method. A Kenward-Roger method is also available via the @code{pbkrtest}
13180 package. Model selection methods include step, drop1 and anova-like tables
13181 for random effects (ranova). Methods for Least-Square means (LS-means) and
13182 tests of linear contrasts of fixed effects are also available.")
13183 (license license:gpl2+)))
13185 (define-public r-r2glmm
13192 (uri (cran-uri "r2glmm" version))
13195 "0iim92blpa59vgz97c2pi05yhbjjmaffdbkbmk5kplfb2vmazgiy"))))
13196 (build-system r-build-system)
13208 (home-page "https://github.com/bcjaeger/r2glmm")
13209 (synopsis "Compute R squared for mixed (multilevel) models")
13211 "This package computes model and semi partial R squared with confidence
13212 limits for the linear and generalized linear mixed model (LMM and GLMM). The
13213 R squared measure from L. J. Edwards et al. (2008) is extended to the GLMM
13214 using @dfn{penalized quasi-likelihood} (PQL) estimation (see Jaeger et
13216 (license license:gpl2)))
13218 (define-public r-cmdfun
13225 (uri (cran-uri "cmdfun" version))
13228 "1pbcq7hi2lcmqnghmy3q2fsk0c9fy5m0637acyzmc096fxbx723j"))))
13229 (properties `((upstream-name . "cmdfun")))
13230 (build-system r-build-system)
13240 (home-page "https://snystrom.github.io/cmdfun/")
13241 (synopsis "Framework for building interfaces to shell commands")
13243 "Writing interfaces to command line software is cumbersome. The cmdfun
13244 package provides a framework for building function calls to seamlessly
13245 interface with shell commands by allowing lazy evaluation of command line
13246 arguments. It also provides methods for handling user-specific paths to tool
13247 installs or secrets like API keys. Its focus is to equally serve package
13248 builders who wish to wrap command line software, and to help analysts stay
13249 inside R when they might usually leave to execute non-R software.")
13250 (license license:expat)))
13252 (define-public r-rslurm
13259 (uri (cran-uri "rslurm" version))
13262 "19451icfh7snjbbmpzpr1hrdf52q8ijv0ag1di3y55r2la3jxxcf"))))
13263 (properties `((upstream-name . "rslurm")))
13264 (build-system r-build-system)
13265 (propagated-inputs (list r-whisker))
13266 (native-inputs (list r-knitr))
13267 (home-page "http://cyberhelp.sesync.org/rslurm/")
13268 (synopsis "Submit R calculations to a Slurm cluster")
13270 "This package provides functions that simplify submitting R scripts to a
13271 Slurm workload manager, in part by automating the division of embarrassingly
13272 parallel calculations across cluster nodes.")
13273 (license license:gpl3)))
13275 (define-public r-chk
13282 (uri (cran-uri "chk" version))
13285 "10gcv00mgi88vgxr9jrs0ar67crmdcdi4m9g86cm6pg3ly0v097y"))))
13286 (properties `((upstream-name . "chk")))
13287 (build-system r-build-system)
13289 (list r-lifecycle r-rlang))
13290 (native-inputs (list r-knitr))
13291 (home-page "https://github.com/poissonconsulting/chk")
13292 (synopsis "Check user-supplied function arguments")
13294 "This is a package for developers to check user-supplied function
13295 arguments. It is designed to be simple, fast and customizable. Error
13296 messages follow the tidyverse style guide.")
13297 (license license:expat)))
13299 (define-public r-weights
13306 (uri (cran-uri "weights" version))
13309 "1fnchf7f0hyl514bk8sc3l884kg25kb5xm4mc2l28n6hm7l6bgpg"))))
13310 (build-system r-build-system)
13312 (list r-gdata r-hmisc r-lme4 r-mice))
13313 (home-page "https://cran.r-project.org/web/packages/weights/")
13314 (synopsis "Weighting and weighted statistics")
13315 (description "This package Provides a variety of functions for producing
13316 simple weighted statistics, such as weighted Pearson's correlations, partial
13317 correlations, Chi-Squared statistics, histograms, and t-tests. Also now
13318 includes some software for quickly recoding survey data and plotting point
13319 estimates from interaction terms in regressions (and multiply imputed
13320 regressions). NOTE: Weighted partial correlation calculations pulled to
13322 (license license:gpl2+)))
13324 (define-public r-rcppannoy
13326 (name "r-rcppannoy")
13331 (uri (cran-uri "RcppAnnoy" version))
13334 "12k8ny981dmky5js8yl6bih5r5mq3w43f2f9admhkwqn0n80kcl9"))))
13335 (properties `((upstream-name . "RcppAnnoy")))
13336 (build-system r-build-system)
13339 (home-page "https://cran.r-project.org/web/packages/RcppAnnoy/")
13340 (synopsis "Rcpp bindings for Annoy, a library for Approximate Nearest Neighbors")
13342 "Annoy is a small C++ library for Approximate Nearest Neighbors written
13343 for efficient memory usage as well an ability to load from and save to disk.
13344 This package provides an R interface.")
13345 ;; Annoy is released under ASL 2.0, but this wrapper is released under
13347 (license (list license:gpl2+ license:asl2.0))))
13349 (define-public r-rcpphnsw
13351 (name "r-rcpphnsw")
13356 (uri (cran-uri "RcppHNSW" version))
13359 "01z0plf1i6dyibw4ica8shmijyk1grpqb886hcga72z2cpm4xsx0"))))
13360 (properties `((upstream-name . "RcppHNSW")))
13361 (build-system r-build-system)
13362 (propagated-inputs (list r-rcpp))
13363 (home-page "https://cran.r-project.org/web/packages/RcppHNSW/")
13364 (synopsis "Rcpp bindings for hnswlib, a library for approximate nearest neighbors")
13366 "Hnswlib is a C++ library for approximate nearest neighbors. This
13367 package provides a minimal R interface by relying on the Rcpp package.")
13368 ;; hnswlib is released under Version 2.0 of the Apache License.
13369 (license (list license:gpl3 license:asl2.0))))
13371 (define-public r-rcppparallel
13373 (name "r-rcppparallel")
13378 (uri (cran-uri "RcppParallel" version))
13381 "1sn211ajlb1p12sglxqns175rg078yvww268m8cp0vvd7cmk55k3"))))
13382 (properties `((upstream-name . "RcppParallel")))
13383 (build-system r-build-system)
13384 (home-page "https://rcppcore.github.io/RcppParallel/")
13385 (synopsis "Parallel programming tools for Rcpp")
13387 "This package provides high level functions for parallel programming with
13388 Rcpp. For example, the @code{parallelFor()} function can be used to convert
13389 the work of a standard serial @code{for} loop into a parallel one and the
13390 @code{parallelReduce()} function can be used for accumulating aggregates or
13392 (license license:gpl2)))
13394 (define-public r-ncdf4
13401 (uri (cran-uri "ncdf4" version))
13404 "0qzvin2fjzcb7h2knlnw14s6043pwi1nm7yf6p27ax7w269173fb"))))
13405 (build-system r-build-system)
13407 (list netcdf zlib))
13408 (home-page "https://cran.r-project.org/web/packages/ncdf4/index.html")
13409 (synopsis "R interface to Unidata netCDF format data files")
13411 "This package provides a high-level R interface to data files written
13412 using Unidata's netCDF library (version 4 or earlier), which are binary data
13413 files that are portable across platforms and include metadata information in
13414 addition to the data sets. Using this package, netCDF files can be opened and
13415 data sets read in easily. It is also easy to create new netCDF dimensions,
13416 variables, and files, in either version 3 or 4 format, and manipulate existing
13418 (license license:gpl3+)))
13420 (define-public r-biocmanager
13422 (name "r-biocmanager")
13423 (version "1.30.18")
13427 (uri (cran-uri "BiocManager" version))
13429 (base32 "0dawbd546rznllpw5wq282r0viga4cck398d4s1inkk18mmi4qzp"))))
13430 (properties `((upstream-name . "BiocManager")))
13431 (build-system r-build-system)
13434 (home-page "https://cran.r-project.org/web/packages/BiocManager/")
13435 (synopsis "Access the Bioconductor project package repository")
13437 "This package provides a convenient tool to install and update
13438 Bioconductor packages.")
13439 (license license:artistic2.0)))
13441 (define-public r-rgl
13444 (version "0.108.3.2")
13448 (uri (cran-uri "rgl" version))
13451 "0r9wzhjzl346i37ngs6hqzmizhi53kzqz582lv822v6yxang6fh3"))))
13452 (build-system r-build-system)
13454 (list pkg-config r-knitr))
13469 (home-page "https://r-forge.r-project.org/projects/rgl/")
13470 (synopsis "3D visualization using OpenGL")
13472 "This package provides medium to high level functions for 3D interactive graphics,
13473 including functions modelled on base graphics (@code{plot3d()}, etc.) as well
13474 as functions for constructing representations of geometric
13475 objects (@code{cube3d()}, etc.). Output may be on screen using OpenGL, or to
13476 various standard 3D file formats including WebGL, PLY, OBJ, STL as well as 2D
13477 image formats, including PNG, Postscript, SVG, PGF.")
13478 ;; Any version of the GPL.
13479 (license (list license:gpl2+ license:gpl3+))))
13481 (define-public r-multicool
13483 (name "r-multicool")
13488 (uri (cran-uri "multicool" version))
13491 "0djacq0irfqz4nlnx238kja73yvr1n5qybbfyl6bw1n6qgcjhza8"))))
13492 (build-system r-build-system)
13493 (propagated-inputs (list r-rcpp))
13494 (home-page "https://cran.r-project.org/web/packages/multicool/")
13495 (synopsis "Permutations of multisets in cool-lex order")
13497 "This package provides a set of tools to permute multisets without loops
13498 or hash tables and to generate integer partitions. Cool-lex order is similar
13499 to colexicographical order.")
13500 (license license:gpl2)))
13502 (define-public r-misc3d
13509 (uri (cran-uri "misc3d" version))
13512 "0r9x57s63kx9f6dgam2nhbziq8nrs9wd8pk7g76hds2kw46vnyx0"))))
13513 (build-system r-build-system)
13514 (home-page "https://cran.r-project.org/web/packages/misc3d/")
13515 (synopsis "Miscellaneous 3D Plots")
13517 "This package provides a collection of miscellaneous 3d plots, including
13519 ;; Any version of the GPL.
13520 (license (list license:gpl2+ license:gpl3+))))
13522 (define-public r-ks
13529 (uri (cran-uri "ks" version))
13531 (base32 "05bqrjkbx2kn5aax0hy3xd6pf7nxka9bm1sp8ll1cc2gf1nx1i6i"))))
13532 (build-system r-build-system)
13544 (home-page "https://www.mvstat.net/tduong/")
13545 (synopsis "Kernel smoothing")
13547 "This package provides kernel smoothers for univariate and multivariate
13548 data, including density functions, density derivatives, cumulative
13549 distributions, modal clustering, discriminant analysis, and two-sample
13550 hypothesis testing.")
13551 ;; Either version of the GPL.
13552 (license (list license:gpl2 license:gpl3))))
13554 (define-public r-feature
13561 (uri (cran-uri "feature" version))
13564 "0yzn1w1sasilcp8v0pcjnxjv9l6lspkskqi412i6h040gqmjjf6y"))))
13565 (build-system r-build-system)
13567 (list r-ks r-plot3d))
13570 (home-page "https://www.mvstat.net/tduong/")
13571 (synopsis "Inferential feature significance for kernel density estimation")
13573 "The feature package contains functions to display and compute kernel
13574 density estimates, significant gradient and significant curvature regions.
13575 Significant gradient and/or curvature regions often correspond to significant
13576 features (e.g. local modes).")
13577 ;; Either version of the GPL.
13578 (license (list license:gpl2 license:gpl3))))
13580 (define-public r-arm
13587 (uri (cran-uri "arm" version))
13590 "0pagrc1vkaz460d0lvrgb4xj6gcd920f4mrc8zpzw07c3v1s2sw1"))))
13591 (build-system r-build-system)
13599 (home-page "https://cran.r-project.org/web/packages/arm/")
13600 (synopsis "Data analysis using regression and multilevel/hierarchical models")
13602 "This package provides functions to accompany A. Gelman and J. Hill,
13603 Data Analysis Using Regression and Multilevel/Hierarchical Models, Cambridge
13604 University Press, 2007.")
13605 (license license:gpl3+)))
13607 (define-public r-circular
13609 (name "r-circular")
13614 (uri (cran-uri "circular" version))
13617 "1qmwj1pf37lc2s5r83y7nqckscznqhbsv66bdfgfbby7x4qkwga8"))))
13618 (build-system r-build-system)
13620 (list r-boot r-mvtnorm))
13623 (home-page "https://cran.r-project.org/web/packages/circular/")
13624 (synopsis "Circular statistics")
13626 "This package provides tools for circular statistics, from \"Topics in
13627 circular Statistics\" (2001) S. Rao Jammalamadaka and A. SenGupta, World
13629 (license license:gpl2+)))
13631 (define-public r-activity
13633 (name "r-activity")
13638 (uri (cran-uri "activity" version))
13641 "11n6wmqz7p3428rr615f92m61a5gb908xpn4l8q484h61bwg38c3"))))
13642 (build-system r-build-system)
13644 (list r-insol r-pbapply))
13645 (home-page "https://cran.r-project.org/web/packages/activity/")
13646 (synopsis "Animal activity statistics")
13648 "This package provides functions to fit kernel density functions to
13649 animal activity time data; plot activity distributions; quantify overall
13650 levels of activity; statistically compare activity metrics through
13651 bootstrapping; and evaluate variation in linear variables with time (or other
13652 circular variables).")
13653 (license license:gpl3)))
13655 (define-public r-ouch
13662 (uri (cran-uri "ouch" version))
13665 "119s9llpjy0b4q830xig2xr66fq6izp6mr2k4k79ggmf3gxww8as"))))
13666 (build-system r-build-system)
13667 (propagated-inputs (list r-subplex))
13668 (home-page "https://kingaa.github.io/ouch/")
13669 (synopsis "Ornstein-Uhlenbeck models for phylogenetic comparative hypotheses")
13671 "This package provides tools to fit and compare Ornstein-Uhlenbeck models
13672 for evolution along a phylogenetic tree.")
13673 (license license:gpl2+)))
13675 (define-public r-fmsb
13682 (uri (cran-uri "fmsb" version))
13685 "1gi94xr0b1yk9xzwfprfafxi25yic1lcivd66p73n6iqfzdaimbk"))))
13686 (build-system r-build-system)
13687 (home-page "http://minato.sip21c.org/msb/")
13688 (synopsis "Functions for medical statistics book with demographic data")
13690 "This package provides several utility functions for the book entitled
13691 \"Practices of Medical and Health Data Analysis using R\" (Pearson Education
13692 Japan, 2007) with Japanese demographic data and some demographic analysis
13693 related functions.")
13694 (license license:gpl2+)))
13696 (define-public r-stabledist
13698 (name "r-stabledist")
13703 (uri (cran-uri "stabledist" version))
13706 "0scar396wiq6wkbkvwp4qrxqc1m075y56p37i6iry5rw796p1i86"))))
13707 (build-system r-build-system)
13708 (home-page "https://www.rmetrics.org")
13709 (synopsis "Stable distribution functions")
13711 "This package provides density, probability and quantile functions, and
13712 random number generation for (skew) stable distributions, using the
13713 parametrizations of Nolan.")
13714 (license license:gpl2+)))
13716 (define-public r-gsl
13719 (version "2.1-7.1")
13723 (uri (cran-uri "gsl" version))
13726 "118rj9kjx9rzlynvhrly19qz3yxg8jzws35971ssgzrp5lwd367f"))))
13727 (build-system r-build-system)
13730 (home-page "https://cran.r-project.org/web/packages/gsl")
13731 (synopsis "Wrapper for the GNU Scientific Library")
13733 "This package provides an R wrapper for the special functions and quasi
13734 random number generators of the GNU Scientific Library.")
13735 (license license:gpl2+)))
13737 (define-public r-adgoftest
13739 (name "r-adgoftest")
13744 (uri (cran-uri "ADGofTest" version))
13747 "0ik817qzqp6kfbckjp1z7srlma0w6z2zcwykh0jdiv7nahwk3ncw"))))
13748 (properties `((upstream-name . "ADGofTest")))
13749 (build-system r-build-system)
13750 (home-page "https://cran.r-project.org/web/packages/ADGofTest")
13751 (synopsis "Anderson-Darling GoF test")
13753 "This package provides an implementation of the Anderson-Darling GoF test
13754 with p-value calculation based on Marsaglia's 2004 paper \"Evaluating the
13755 Anderson-Darling Distribution\".")
13756 ;; Any version of the GPL.
13757 (license license:gpl3+)))
13759 (define-public r-admisc
13766 (uri (cran-uri "admisc" version))
13768 (base32 "07hfrhv3pcldsffnyfzpa1q3x32gxr1386r8fik1nhql2w46mm13"))))
13769 (properties `((upstream-name . "admisc")))
13770 (build-system r-build-system)
13771 (home-page "https://github.com/dusadrian/admisc")
13772 (synopsis "Adrian Dusa's miscellaneous")
13774 "This package contains miscellaneous functions used to interpret and
13775 translate, factorize and negate Sum of Products expressions, for both binary
13776 and multi-value crisp sets, and to extract information (set names, set values)
13777 from those expressions. Other functions perform various other checks if
13778 possibly numeric (even if all numbers reside in a character vector) and coerce
13779 to numeric, or check if the numbers are whole. It also offers, among many
13780 others, a highly flexible recoding routine and a more flexible alternative to
13781 the base function @code{with()}.")
13782 (license license:gpl3+)))
13784 (define-public r-sodium
13791 (uri (cran-uri "sodium" version))
13794 "0x4jb3cf1nv1spz1jc9xp8hly2b4a7nj48xr4s33jnfcpdjkmn5q"))))
13795 (properties `((upstream-name . "sodium")))
13796 (build-system r-build-system)
13800 (list pkg-config r-knitr))
13801 (home-page "https://github.com/jeroen/sodium")
13802 (synopsis "R bindings to the libsodium crypto library")
13804 "This package provides bindings to libsodium: a library for encryption,
13805 decryption, signatures, password hashing and more. Sodium uses curve25519, a
13806 Diffie-Hellman function by Daniel Bernstein, which has become very popular
13807 after it was discovered that the NSA had backdoored Dual EC DRBG.")
13808 (license license:expat)))
13810 (define-public r-softimpute
13812 (name "r-softimpute")
13817 (uri (cran-uri "softImpute" version))
13820 "1v2a4d688ij5zcvkzpra9yx40xckdfnllnfnyq2450zf3n1kjk7a"))))
13821 (properties `((upstream-name . "softImpute")))
13822 (build-system r-build-system)
13826 (list gfortran r-knitr))
13827 (home-page "https://cran.r-project.org/web/packages/softImpute")
13828 (synopsis "Matrix completion via iterative soft-thresholded SVD")
13830 "This package provides iterative methods for matrix completion that use
13831 nuclear-norm regularization. The package includes procedures for centering
13832 and scaling rows, columns or both, and for computing low-rank @dfn{single
13833 value decompositions} (SVDs) on large sparse centered matrices (i.e. principal
13835 (license license:gpl2)))
13837 (define-public r-fftwtools
13839 (name "r-fftwtools")
13844 (uri (cran-uri "fftwtools" version))
13847 "0zrchp4l0jdbir2gibjf00x225y9giqk80zvqmr2yyvc12lwkw7i"))))
13848 (build-system r-build-system)
13849 (inputs (list fftw))
13852 (home-page "https://github.com/krahim/fftwtools")
13853 (synopsis "Wrapper for FFTW3")
13855 "This package provides a wrapper for several FFTW functions. It provides
13856 access to the two-dimensional FFT, the multivariate FFT, and the
13857 one-dimensional real to complex FFT using the FFTW3 library. The package
13858 includes the functions @code{fftw()} and @code{mvfftw()} which are designed to
13859 mimic the functionality of the R functions @code{fft()} and @code{mvfft()}.
13860 The FFT functions have a parameter that allows them to not return the
13861 redundant complex conjugate when the input is real data.")
13862 (license license:gpl2+)))
13864 (define-public r-tiff
13871 (uri (cran-uri "tiff" version))
13874 "0xgc7vyndxxahfhc2qqzmwi56bnfyl0pn72l820jz5sd24aymhxq"))))
13875 (build-system r-build-system)
13877 (list libtiff libjpeg-turbo zlib))
13880 (home-page "https://www.rforge.net/tiff/")
13881 (synopsis "Read and write TIFF images")
13883 "This package provides an easy and simple way to read, write and display
13884 bitmap images stored in the TIFF format. It can read and write both files and
13885 in-memory raw vectors.")
13886 ;; Either of these two license versions.
13887 (license (list license:gpl2 license:gpl3))))
13889 (define-public r-nlp
13896 (uri (cran-uri "NLP" version))
13899 "1dpj04fmld2lnhg072ahgjbhmciqqy9h1lrz0wf32mr7mm9s9sh5"))))
13900 (properties `((upstream-name . "NLP")))
13901 (build-system r-build-system)
13902 (home-page "https://cran.r-project.org/web/packages/NLP/")
13903 (synopsis "Natural language processing infrastructure")
13905 "This package provides basic classes and methods for Natural Language
13907 (license license:gpl3)))
13909 (define-public r-tm
13916 (uri (cran-uri "tm" version))
13919 "0mk2lsplynms15nw92vbdgsafg4bw1m0ik31gch1mnsnv61idsxi"))))
13920 (properties `((upstream-name . "tm")))
13921 (build-system r-build-system)
13923 (list r-bh r-nlp r-rcpp r-slam r-xml2))
13924 (home-page "http://tm.r-forge.r-project.org/")
13925 (synopsis "Text mining package")
13927 "This package provides a framework for text mining applications within R.")
13928 (license license:gpl3)))
13930 (define-public r-waveslim
13932 (name "r-waveslim")
13937 (uri (cran-uri "waveslim" version))
13940 "0ibivnhz0l06sss5rrrcvyiwg3qpbyk3qn4vx4pp90kj09x4yg0k"))))
13941 (build-system r-build-system)
13944 (home-page "http://waveslim.blogspot.com")
13945 (synopsis "Basic wavelet routines for signal processing")
13947 "This package provides basic wavelet routines for time series (1D),
13948 image (2D) and array (3D) analysis. The code provided here is based on
13949 wavelet methodology developed in Percival and Walden (2000); Gencay, Selcuk
13950 and Whitcher (2001); the dual-tree complex wavelet transform (DTCWT) from
13951 Kingsbury (1999, 2001) as implemented by Selesnick; and Hilbert wavelet
13952 pairs (Selesnick 2001, 2002).")
13953 (license license:bsd-3)))
13955 (define-public r-wordcloud
13957 (name "r-wordcloud")
13962 (uri (cran-uri "wordcloud" version))
13965 "0j96yyvm6bcrrpbdx4w26piqx44a0vbsr3px9cb4zk8a8da6jwak"))))
13966 (build-system r-build-system)
13968 (list r-rcolorbrewer r-rcpp
13969 ;; The "tm" package is only "suggested" according to CRAN, but the
13970 ;; wordcloud package cannot be loaded without it.
13972 (home-page "https://cran.r-project.org/web/packages/wordcloud")
13973 (synopsis "Word clouds")
13975 "This package provides functionality to create pretty word clouds,
13976 visualize differences and similarity between documents, and avoid
13977 over-plotting in scatter plots with text.")
13978 (license license:lgpl2.1)))
13980 (define-public r-colorramps
13982 (name "r-colorramps")
13987 (uri (cran-uri "colorRamps" version))
13990 "12jnkj50yh2hc5l7j56lrrrmn58akrj9dwj98vzf42iq4h42kwb1"))))
13991 (properties `((upstream-name . "colorRamps")))
13992 (build-system r-build-system)
13993 (home-page "https://cran.r-project.org/web/packages/colorRamps")
13994 (synopsis "Build color tables")
13995 (description "This package provides features to build gradient color
13997 ;; Any version of the GPL
13998 (license license:gpl3+)))
14000 (define-public r-tidytree
14002 (name "r-tidytree")
14007 (uri (cran-uri "tidytree" version))
14009 (base32 "1prfv2jy6z4zp4gyi9krzbysipsbnjrkxcccflm4nwsd9i7mshqj"))))
14010 (build-system r-build-system)
14024 (home-page "https://github.com/GuangchuangYu/tidytree")
14025 (synopsis "Tidy tool for phylogenetic tree data manipulation")
14027 "Phylogenetic trees generally contain multiple components including nodes,
14028 edges, branches and associated data. This package provides an approach to
14029 convert tree objects to tidy data frames. It also provides tidy interfaces to
14030 manipulate tree data.")
14031 (license license:artistic2.0)))
14033 (define-public r-rvcheck
14040 (uri (cran-uri "rvcheck" version))
14042 (base32 "09khjklvzbafd7r55496by01a9g3y291d87hpy43w44dmz9fzn9a"))))
14043 (build-system r-build-system)
14045 (list r-biocmanager r-yulab-utils))
14046 (home-page "https://cran.r-project.org/web/packages/rvcheck")
14047 (synopsis "R package version check")
14049 "This package provides tools to check the latest release version of R and
14050 R packages (on CRAN, Bioconductor or Github).")
14051 (license license:artistic2.0)))
14053 (define-public r-docopt
14060 (uri (cran-uri "docopt" version))
14063 "1zxhwizs916qm5by7nfslqnarl2q5202xc2azlhrnzk0wj3khiwz"))))
14064 (build-system r-build-system)
14065 (home-page "https://github.com/docopt/docopt.R")
14066 (synopsis "Command-line interface specification language")
14068 "This package enables you to define a command-line interface by just
14069 giving it a description in the specific format.")
14070 (license license:expat)))
14072 (define-public r-sparsesvd
14074 (name "r-sparsesvd")
14079 (uri (cran-uri "sparsesvd" version))
14082 "1xm969fjq3fv1p2sqza2apz8picibj4s2agpwf1sx9nwn3b587qs"))))
14083 (build-system r-build-system)
14084 (propagated-inputs (list r-matrix))
14085 (home-page "http://tedlab.mit.edu/~dr/SVDLIBC/")
14086 (synopsis "Sparse truncated singular value decomposition")
14088 "This package provides a Wrapper around the SVDLIBC library
14089 for (truncated) singular value decomposition of a sparse matrix. Currently,
14090 only sparse real matrices in Matrix package format are supported.")
14091 ;; SVDLIBC is released under BSD-2. The R interface is released under
14093 (license (list license:bsd-3 license:bsd-2))))
14095 (define-public r-speedglm
14097 (name "r-speedglm")
14102 (uri (cran-uri "speedglm" version))
14105 "1kj662nfkfhvx37jrbvxd4dyjclz5cm3xh50z7s5rbzapiyxn4hs"))))
14106 (build-system r-build-system)
14108 (list r-mass r-matrix))
14109 (home-page "https://cran.r-project.org/web/packages/speedglm")
14110 (synopsis "Fit linear and generalized linear models to large data sets")
14112 "This package provides tools for fitting linear models and generalized
14113 linear models to large data sets by updating algorithms.")
14114 ;; Any version of the GPL
14115 (license license:gpl2+)))
14117 (define-public r-densityclust
14119 (name "r-densityclust")
14124 (uri (cran-uri "densityClust" version))
14127 "05x2fi1zdnkrg2nimf8k904j3lpyw0f7nmk6ax5p7x7a98wb2iqs"))))
14128 (properties `((upstream-name . "densityClust")))
14129 (build-system r-build-system)
14138 (home-page "https://cran.r-project.org/web/packages/densityClust")
14139 (synopsis "Clustering by fast search and find of density peaks")
14141 "This package provides an improved implementation (based on k-nearest
14142 neighbors) of the density peak clustering algorithm, originally described by
14143 Alex Rodriguez and Alessandro Laio (Science, 2014 vol. 344). It can handle
14144 large datasets (> 100,000 samples) very efficiently.")
14145 (license license:gpl2+)))
14147 (define-public r-combinat
14149 (name "r-combinat")
14154 (uri (cran-uri "combinat" version))
14157 "1h9hr88gigihc4na7lb5i7rn4az1xa7sb34zvnznaj6pdrmwy4qm"))))
14158 (build-system r-build-system)
14159 (home-page "https://cran.r-project.org/web/packages/combinat")
14160 (synopsis "Combinatorics utilities")
14161 (description "This package provides assorted routines for combinatorics.")
14162 (license license:gpl2)))
14164 (define-public r-qlcmatrix
14166 (name "r-qlcmatrix")
14171 (uri (cran-uri "qlcMatrix" version))
14174 "0iqkcvvy8rxlk0s83sjq57dd6fadb18p5z31lzy0gnzv1hsy1x8y"))))
14175 (properties `((upstream-name . "qlcMatrix")))
14176 (build-system r-build-system)
14178 (list r-docopt r-matrix r-slam r-sparsesvd))
14179 (home-page "https://cran.r-project.org/web/packages/qlcMatrix")
14180 (synopsis "Sparse matrix functions for quantitative language comparison")
14182 "This package provides an extension of the functionality of the Matrix
14183 package for using sparse matrices. Some of the functions are very general,
14184 while other are highly specific for the special data format used for
14185 @dfn{quantitative language comparison} (QLC).")
14186 (license license:gpl3)))
14188 (define-public r-ddrtree
14195 (uri (cran-uri "DDRTree" version))
14198 "16s5fjw7kwlxhrkzdny62sx32fvmg3rxjc3wrh6krd31jh1fqlfk"))))
14199 (properties `((upstream-name . "DDRTree")))
14200 (build-system r-build-system)
14202 (list r-bh r-irlba r-rcpp r-rcppeigen))
14203 (home-page "https://cran.r-project.org/web/packages/DDRTree")
14204 (synopsis "Learning principal graphs with DDRTree")
14206 "This package provides an implementation of the framework of
14207 @dfn{reversed graph embedding} (RGE) which projects data into a reduced
14208 dimensional space while constructs a principal tree which passes through the
14209 middle of the data simultaneously. DDRTree shows superiority to
14210 alternatives (Wishbone, DPT) for inferring the ordering as well as the
14211 intrinsic structure of single cell genomics data. In general, it could be
14212 used to reconstruct the temporal progression as well as the bifurcation
14213 structure of any data type.")
14214 (license license:asl2.0)))
14216 (define-public r-corpcor
14223 (uri (cran-uri "corpcor" version))
14226 "028fw61n61i79fhnaqx7gmdifdpbvp3yiaq9vvfrbv4k7i84r83i"))))
14227 (build-system r-build-system)
14228 (home-page "http://strimmerlab.org/software/corpcor/")
14229 (synopsis "Efficient estimation of covariance and (partial) correlation")
14231 "This package implements a James-Stein-type shrinkage estimator for the
14232 covariance matrix, with separate shrinkage for variances and correlations.
14233 Furthermore, functions are available for fast singular value decomposition,
14234 for computing the pseudoinverse, and for checking the rank and positive
14235 definiteness of a matrix.")
14236 (license license:gpl3+)))
14238 (define-public r-rspectra
14240 (name "r-rspectra")
14245 (uri (cran-uri "RSpectra" version))
14248 "16ij84wgpsmqmnxqiii8dgihy3bfxazry9znmckhwzba7m0d79fb"))))
14249 (properties `((upstream-name . "RSpectra")))
14250 (build-system r-build-system)
14252 (list r-matrix r-rcpp r-rcppeigen))
14255 (home-page "https://github.com/yixuan/RSpectra")
14256 (synopsis "Solvers for large-scale Eigenvalue and SVD problems")
14258 "This package provides an R interface to the Spectra library for
14259 large-scale eigenvalue and SVD problems. It is typically used to compute a
14260 few eigenvalues/vectors of an n by n matrix, e.g., the k largest eigenvalues,
14261 which is usually more efficient than @code{eigen()} if k << n.")
14263 (license license:mpl2.0)))
14265 (define-public r-vbsr
14272 (uri (cran-uri "vbsr" version))
14275 "1avskbxxyinjjdga4rnghcfvd4sypv4m39ysfaij5avvmi89bx3b"))))
14276 (build-system r-build-system)
14277 (home-page "https://cran.r-project.org/web/packages/vbsr")
14278 (synopsis "Variational Bayes spike regression regularized linear models")
14280 "This package provides an efficient algorithm for solving ultra-sparse
14281 regularized regression models using a variational Bayes algorithm with a spike
14282 prior. The algorithm is solved on a path, with coordinate updates, and is
14283 capable of generating very sparse models. Very general model
14284 diagnostics for controlling type-1 errors are also provided.")
14285 (license license:gpl2)))
14287 (define-public r-flare
14290 (version "1.7.0.1")
14294 (uri (cran-uri "flare" version))
14297 "1xvrbvq2y7zfp98ijal3z8y1w2xbzfcdykzw4pqc3mnh0qrhq2d5"))))
14298 (build-system r-build-system)
14300 (list r-igraph r-lattice r-mass r-matrix))
14301 (home-page "https://cran.r-project.org/web/packages/flare")
14302 (synopsis "Family of Lasso regression implementations")
14304 "This package provides implementations of a family of Lasso variants
14305 including Dantzig Selector, LAD Lasso, SQRT Lasso, Lq Lasso for estimating
14306 high dimensional sparse linear models.")
14307 (license license:gpl2)))
14309 (define-public r-lassopv
14316 (uri (cran-uri "lassopv" version))
14319 "0yawnjw063jypk3riy9xab9cmliv6c9dnabi18670khd3gzb2r9z"))))
14320 (build-system r-build-system)
14321 (propagated-inputs (list r-lars))
14322 (home-page "https://github.com/lingfeiwang/lassopv")
14323 (synopsis "Non-parametric p-value estimation for predictors in Lasso")
14325 "This package enables you to estimate the p-values for predictors x
14326 against target variable y in Lasso regression, using the regularization
14327 strength when each predictor enters the active set of regularization path for
14328 the first time as the statistic.")
14329 (license license:gpl3)))
14331 (define-public r-splitstackshape
14333 (name "r-splitstackshape")
14338 (uri (cran-uri "splitstackshape" version))
14341 "0mpyf2kkfdl69pdc6brl1r6101vyc6pgr7z17s55ppg3y71k4q35"))))
14342 (build-system r-build-system)
14344 (list r-data-table))
14345 (home-page "https://github.com/mrdwab/splitstackshape")
14346 (synopsis "Stack and reshape datasets after splitting concatenated values")
14348 "Online data collection tools like Google Forms often export
14349 multiple-response questions with data concatenated in cells. The
14350 @code{concat.split} (cSplit) family of functions provided by this package
14351 splits such data into separate cells. This package also includes functions to
14352 stack groups of columns and to reshape wide data, even when the data are
14353 \"unbalanced\"---something which @code{reshape} (from base R) does not handle,
14354 and which @code{melt} and @code{dcast} from @code{reshape2} do not easily
14356 (license license:gpl3)))
14358 (define-public r-tfmpvalue
14360 (name "r-tfmpvalue")
14365 (uri (cran-uri "TFMPvalue" version))
14368 "0h9qkl15k8v17v3g9bdnfwvh2s04ywjgg5y0xn2077dmywlja1bd"))))
14369 (properties `((upstream-name . "TFMPvalue")))
14370 (build-system r-build-system)
14371 (propagated-inputs (list r-rcpp))
14372 (home-page "https://github.com/ge11232002/TFMPvalue")
14373 (synopsis "P-value computation for position weight matrices")
14375 "In putative @dfn{Transcription Factor Binding Sites} (TFBSs)
14376 identification from sequence/alignments, we are interested in the significance
14377 of certain match scores. TFMPvalue provides the accurate calculation of a
14378 p-value with a score threshold for position weight matrices, or the score with
14379 a given p-value. It is an interface to code originally made available by
14380 Helene Touzet and Jean-Stephane Varre, 2007, Algorithms Mol Biol:2, 15.
14381 Touzet and Varre (2007).")
14382 (license license:gpl2)))
14384 (define-public r-rncl
14390 (uri (cran-uri "rncl" version))
14393 "1ywgwqn82z8h6zpcxxq4hgngdpfa6dj0lr7bfq4cwfml9z075jgw"))))
14394 (build-system r-build-system)
14396 (list r-progress r-rcpp))
14397 (home-page "https://github.com/fmichonneau/rncl")
14398 (synopsis "Interface to the Nexus class library")
14399 (description "This package provides an interface to the Nexus class
14400 library which allows parsing of NEXUS, Newick and other phylogenetic tree
14401 file formats. It provides elements of the file that can be used to build
14402 phylogenetic objects such as @code{ape}'s @code{phylo} or @code{phylobase}'s
14403 @code{phylo4(d)}. This functionality is demonstrated with
14404 @code{read_newick_phylo()} and @code{read_nexus_phylo()}.")
14405 (license license:bsd-2)))
14407 (define-public r-phylobase
14409 (name "r-phylobase")
14413 (uri (cran-uri "phylobase" version))
14416 "0jzr1gdvmi4l640hwwzh9bxqmpja69bn3ygnaqx37awvyh7khi2s"))))
14417 (build-system r-build-system)
14419 (list r-ade4 r-ape r-rcpp r-rncl r-rnexml))
14422 (home-page "https://github.com/fmichonneau/phylobase")
14423 (synopsis "Base package for phylogenetic structures and comparative data")
14424 (description "This package provides a base @code{S4} class for comparative
14425 methods, incorporating one or more trees and trait data.")
14426 (license license:gpl2+)))
14428 (define-public r-rnexml
14434 (uri (cran-uri "RNeXML" version))
14437 "1zp6pijsc73jx8cmxb1hng36nvaf5wnhldnzlqhmba9kv9niscfb"))))
14438 (build-system r-build-system)
14455 (home-page "https://docs.ropensci.org/RNeXML/")
14456 (synopsis "Semantically rich I/O for the NeXML Format")
14457 (description "This package provides access to phyloinformatic data in
14458 NeXML format. The package should add new functionality to R such as the
14459 possibility to manipulate NeXML objects in more various and refined way
14460 and compatibility with @code{ape} objects.")
14461 (license license:bsd-3)))
14463 (define-public r-rnifti
14470 (uri (cran-uri "RNifti" version))
14473 "0kkj9dby85iwnlqb7zwrh1xidlvqip7i1mbgckb5qg4b0a3zgibc"))))
14474 (properties `((upstream-name . "RNifti")))
14475 (build-system r-build-system)
14476 (inputs (list zlib))
14477 (propagated-inputs (list r-rcpp))
14478 (home-page "https://github.com/jonclayden/RNifti")
14479 (synopsis "Fast R and C++ access to NIfTI images")
14481 "This package provides very fast read and write access to images stored
14482 in the NIfTI-1 and ANALYZE-7.5 formats, with seamless synchronisation between
14483 compiled C and interpreted R code. It also provides a C/C++ API that can be
14484 used by other packages.")
14485 (license license:gpl2)))
14487 (define-public r-shades
14494 (uri (cran-uri "shades" version))
14497 "1zg95sjhrfvbdlfc387g9p0vnb8nb6agdk1mb3wq3kwkm2da0bqj"))))
14498 (build-system r-build-system)
14499 (home-page "https://github.com/jonclayden/shades")
14500 (synopsis "Simple color manipulation")
14502 "This package provides functions for easily manipulating colors,
14503 creating color scales and calculating color distances.")
14504 (license license:bsd-3)))
14506 (define-public r-ore
14509 (version "1.7.1.1")
14513 (uri (cran-uri "ore" version))
14515 (base32 "0rs5r5h11x4l4nsbl4xqzbl4ahajd5374fq05abcmfjnjr9j64w5"))))
14516 (build-system r-build-system)
14517 (home-page "https://github.com/jonclayden/ore")
14518 (synopsis "R interface to the Onigmo regular expression library")
14520 "This package provides an alternative to R's built-in functionality for
14521 handling regular expressions, based on the Onigmo library. It offers
14522 first-class compiled regex objects, partial matching and function-based
14523 substitutions, amongst other features.")
14524 (license license:bsd-3)))
14526 (define-public r-reportr
14533 (uri (cran-uri "reportr" version))
14536 "0zynplxqvbmf23cm2rsz3wz2jx6mv55z94mn1k44ny3lx625cnpw"))))
14537 (build-system r-build-system)
14538 (propagated-inputs (list r-ore))
14539 (home-page "https://github.com/jonclayden/reportr")
14540 (synopsis "General message and error reporting system")
14542 "This package provides a system for reporting messages, which offers
14543 certain useful features over the standard R system, such as the incorporation
14544 of output consolidation, message filtering, assertions, expression
14545 substitution, automatic generation of stack traces for debugging, and
14546 conditional reporting based on the current \"output level\".")
14547 (license license:gpl2)))
14549 (define-public r-tractor-base
14551 (name "r-tractor-base")
14552 (version "3.3.3.1")
14556 (uri (cran-uri "tractor.base" version))
14559 "0w5jw7pf77npkgig7667yikpbwv4dfk1dcq63qm88l409ga2f95p"))))
14560 (properties `((upstream-name . "tractor.base")))
14561 (build-system r-build-system)
14563 (list r-ore r-reportr r-rnifti r-shades))
14564 (home-page "https://www.tractor-mri.org.uk")
14565 (synopsis "Read, manipulate and visualize magnetic resonance images")
14567 "This package provides functions for working with magnetic resonance
14568 images. It supports reading and writing of popular file formats (DICOM,
14569 Analyze, NIfTI-1, NIfTI-2, MGH); interactive and non-interactive
14570 visualization; flexible image manipulation; metadata and sparse image
14572 (license license:gpl2)))
14574 (define-public r-grimport
14576 (name "r-grimport")
14581 (uri (cran-uri "grImport" version))
14584 "0pbzc45wgp0cpycnw0bzn65ckdszzay0zrp7c7ssxdkifp8bai3a"))))
14585 (properties `((upstream-name . "grImport")))
14586 (build-system r-build-system)
14588 (list ghostscript))
14591 (home-page "https://cran.r-project.org/web/packages/grImport")
14592 (synopsis "Convert, import, and draw PostScript pictures")
14594 "This package provides functions for converting, importing, and drawing
14595 PostScript pictures in R plots.")
14596 (license license:gpl2+)))
14598 (define-public r-grimport2
14600 (name "r-grimport2")
14605 (uri (cran-uri "grImport2" version))
14608 "19q0dd8fpp1g4xf6sg5f8dxybwxjfw553ra6wgjd8b74fzca40m1"))))
14609 (properties `((upstream-name . "grImport2")))
14610 (build-system r-build-system)
14612 (list r-base64enc r-jpeg r-png r-xml))
14613 (home-page "https://cran.r-project.org/web/packages/grImport2/")
14614 (synopsis "Import SVG graphics")
14616 "This package provides functions for importing external vector images and
14617 drawing them as part of R plots. This package is different from the
14618 @code{grImport} package because, where that package imports PostScript format
14619 images, this package imports SVG format images. Furthermore, this package
14620 imports a specific subset of SVG, so external images must be preprocessed
14621 using a package like @code{rsvg} to produce SVG that this package can import.
14622 SVG features that are not supported by R graphics, such as gradient fills, can
14623 be imported and then exported via the @code{gridSVG} package.")
14624 (license license:gpl2+)))
14626 (define-public r-kohonen
14633 (uri (cran-uri "kohonen" version))
14636 "1bk3j0n8w4fhffv89rgyn4n21c0wcx6lr8jv4wbagpxprl585381"))))
14637 (build-system r-build-system)
14640 (home-page "https://cran.r-project.org/web/packages/kohonen")
14641 (synopsis "Supervised and unsupervised self-organising maps")
14643 "This package provides functions to train @dfn{self-organising
14644 maps} (SOMs). Also interrogation of the maps and prediction using trained
14645 maps are supported. The name of the package refers to Teuvo Kohonen, the
14646 inventor of the SOM.")
14647 (license license:gpl2+)))
14649 (define-public r-nnls
14656 (uri (cran-uri "nnls" version))
14659 "07vcrrxvswrvfiha6f3ikn640yg0m2b4yd9lkmim1g0jmsmpfp8f"))))
14660 (build-system r-build-system)
14661 (native-inputs (list gfortran))
14662 (home-page "https://cran.r-project.org/web/packages/nnls")
14663 (synopsis "Lawson-Hanson algorithm for non-negative least squares")
14665 "This package provides an R interface to the Lawson-Hanson implementation
14666 of an algorithm for @dfn{non-negative least squares} (NNLS). It also allows
14667 the combination of non-negative and non-positive constraints.")
14668 (license license:gpl2+)))
14670 (define-public r-iso
14673 (version "0.0-18.1")
14677 (uri (cran-uri "Iso" version))
14680 "0vy6jdyvp751430sf2f690yhasjr70cpk3p3lnaaxjq3fs5gg99g"))))
14681 (properties `((upstream-name . "Iso")))
14682 (build-system r-build-system)
14683 (native-inputs (list gfortran))
14684 (home-page "https://www.stat.auckland.ac.nz/~rolf/")
14685 (synopsis "Functions to perform isotonic regression")
14687 "This package provides support for linear order and unimodal
14688 order (univariate) isotonic regression and bivariate isotonic regression with
14689 linear order on both variables.")
14690 (license license:gpl2+)))
14692 (define-public r-chemometricswithr
14694 (name "r-chemometricswithr")
14699 (uri (cran-uri "ChemometricsWithR" version))
14702 "166va1g3m1wv21qkmw4wpz0bsrclh3jih8smxphdc13l9pqgclpq"))))
14704 `((upstream-name . "ChemometricsWithR")))
14705 (build-system r-build-system)
14707 (list r-devtools r-kohonen r-mass r-pls))
14708 (home-page "https://github.com/rwehrens/CWR")
14709 (synopsis "Chemometrics with R")
14711 "This package provides functions and scripts used in the book
14712 \"Chemometrics with R - Multivariate Data Analysis in the Natural Sciences and
14713 Life Sciences\" by Ron Wehrens, Springer (2011).")
14714 (license license:gpl2+)))
14716 (define-public r-als
14723 (uri (cran-uri "ALS" version))
14726 "1swrn39vy50fazkpf97r7c542gkj6mlvy8gmcxllg7mf2mqx546a"))))
14727 (properties `((upstream-name . "ALS")))
14728 (build-system r-build-system)
14730 (list r-iso r-nnls))
14731 (home-page "https://cran.r-project.org/web/packages/ALS")
14732 (synopsis "Multivariate curve resolution alternating least squares")
14734 "Alternating least squares is often used to resolve components
14735 contributing to data with a bilinear structure; the basic technique may be
14736 extended to alternating constrained least squares. This package provides an
14737 implementation of @dfn{multivariate curve resolution alternating least
14738 squares} (MCR-ALS).
14740 Commonly applied constraints include unimodality, non-negativity, and
14741 normalization of components. Several data matrices may be decomposed
14742 simultaneously by assuming that one of the two matrices in the bilinear
14743 decomposition is shared between datasets.")
14744 (license license:gpl2+)))
14746 (define-public r-strucchange
14748 (name "r-strucchange")
14753 (uri (cran-uri "strucchange" version))
14756 "1y022363a4pp0mnji91sjh1qiyspkh09sybqwj03r9pmwrd7q93x"))))
14757 (build-system r-build-system)
14759 (list r-sandwich r-zoo))
14760 (home-page "https://cran.r-project.org/web/packages/strucchange")
14761 (synopsis "Testing, monitoring, and dating structural changes")
14763 "This package provides tools for testing, monitoring and dating
14764 structural changes in (linear) regression models. It features tests/methods
14765 from the generalized fluctuation test framework as well as from the F
14766 test (Chow test) framework. This includes methods to fit, plot and test
14767 fluctuation processes (e.g., CUSUM, MOSUM, recursive/moving estimates) and F
14768 statistics, respectively. It is possible to monitor incoming data online
14769 using fluctuation processes. Finally, the breakpoints in regression models
14770 with structural changes can be estimated together with confidence intervals.
14771 Emphasis is always given to methods for visualizing the data.")
14772 ;; Either of these two GPL versions
14773 (license (list license:gpl2 license:gpl3))))
14775 (define-public r-pixmap
14782 (uri (cran-uri "pixmap" version))
14785 "1v1a1adsgh5jlvvi98j4nhb1h681s97ip76zdrga12rlsjaahfw9"))))
14786 (build-system r-build-system)
14787 (home-page "https://cran.r-project.org/web/packages/pixmap")
14788 (synopsis "Tools for bitmap images")
14790 "This package provides functions for importing, exporting, plotting and
14791 other manipulations of bitmapped images.")
14792 (license license:gpl2)))
14794 (define-public r-rapidjsonr
14796 (name "r-rapidjsonr")
14801 (uri (cran-uri "rapidjsonr" version))
14804 "07zdirhbzmvq3cp4xn8ngk1lgxbbabzays315zxbs3sxrz6lzjb2"))))
14805 (build-system r-build-system)
14806 (home-page "https://cran.r-project.org/web/packages/rapidjsonr")
14807 (synopsis "JSON parser")
14809 "This package provides JSON parsing capability through the Rapidjson
14811 (license license:expat)))
14813 (define-public r-ontologyindex
14815 (name "r-ontologyindex")
14820 (uri (cran-uri "ontologyIndex" version))
14823 "0j3h1spqwjhh1wbmwivmqcyi042yy7d565c3kxgn70xrmy693x1k"))))
14824 (properties `((upstream-name . "ontologyIndex")))
14825 (build-system r-build-system)
14828 (home-page "https://cran.r-project.org/web/packages/ontologyIndex")
14829 (synopsis "Functions for processing ontologies in R")
14831 "This package provides functions for reading ontologies into R as lists
14832 and manipulating sets of ontological terms.")
14833 (license license:gpl2+)))
14835 (define-public r-gargle
14842 (uri (cran-uri "gargle" version))
14845 "0fypj70c1fjmvs57birik76wfx8a2fs4gzicbb52k57i6clwlijd"))))
14846 (build-system r-build-system)
14859 (home-page "https://gargle.r-lib.org")
14860 (synopsis "Utilities for working with Google APIs")
14862 "This package provides utilities for working with Google APIs. This
14863 includes functions and classes for handling common credential types and for
14864 preparing, executing, and processing HTTP requests.")
14865 (license license:expat)))
14867 (define-public r-bigrquery
14869 (name "r-bigrquery")
14874 (uri (cran-uri "bigrquery" version))
14877 "02msq61l7vamzpvbhvalh3qil1aa7pr68pwpsivbb6pvz6p4zyns"))))
14878 (build-system r-build-system)
14895 (home-page "https://github.com/rstats-db/bigrquery")
14896 (synopsis "R interface to Google's BigQuery API")
14898 "This package provides an R interface to Google's BigQuery database.")
14899 (license license:gpl3)))
14901 (define-public r-gmp
14908 (uri (cran-uri "gmp" version))
14911 "0llyd1wx606vpgvv7d61m0fv2a5yxsmisd38fhzanbjl2wynzrwa"))))
14912 (build-system r-build-system)
14915 (modify-phases %standard-phases
14916 (add-after 'unpack 'set-CC
14917 (lambda _ (setenv "CC" "gcc") #t)))))
14918 (inputs (list gmp))
14919 (home-page "https://cran.r-project.org/web/packages/gmp")
14920 (synopsis "Multiple precision arithmetic")
14922 "This package supports multiple precision arithmetic (big integers and
14923 rationals, prime number tests, matrix computation), \"arithmetic without
14924 limitations\" using the GNU Multiple Precision library.")
14925 ;; Any version of the GPL.
14926 (license license:gpl3+)))
14928 (define-public r-rmpfr
14935 (uri (cran-uri "Rmpfr" version))
14938 "1ljpbxvm4agbxnab5dfffbpw5k964hy3gw57dzydq1gpbxwdphlk"))))
14939 (properties `((upstream-name . "Rmpfr")))
14940 (build-system r-build-system)
14947 (home-page "http://rmpfr.r-forge.r-project.org/")
14948 (synopsis "R bindings to the MPFR library")
14950 "This package supports arithmetic (via S4 classes and methods) for
14951 arbitrary precision floating point numbers, including transcendental
14952 functions. To this end, the package interfaces with the @dfn{Multiple
14953 Precision Floating-Point Reliable} (MPFR) library.")
14954 (license license:gpl2+)))
14956 (define-public r-assertive-base
14958 (name "r-assertive-base")
14963 (uri (cran-uri "assertive.base" version))
14966 "07m0ddz092bgbl2fn1yk932h0iajdcqkri632477wl5a1q5r3w2b"))))
14968 `((upstream-name . "assertive.base")))
14969 (build-system r-build-system)
14970 (home-page "https://bitbucket.org/richierocks/assertive.base")
14971 (synopsis "Core of the assertive package")
14973 "This package provides a minimal set of predicates and assertions used by
14974 the assertive package. This is mainly for use by other package developers who
14975 want to include run-time testing features in their own packages.")
14976 (license license:gpl3+)))
14978 (define-public r-assertive-properties
14980 (name "r-assertive-properties")
14985 (uri (cran-uri "assertive.properties" version))
14988 "1pgljbwwbvbl4kc5c8mcv0qbzq3k6fzi29k88811yml263sm92dn"))))
14990 `((upstream-name . "assertive.properties")))
14991 (build-system r-build-system)
14993 (list r-assertive-base))
14994 (home-page "https://bitbucket.org/richierocks/assertive.properties")
14995 (synopsis "Assertions to check properties of variables")
14997 "This package provides a set of predicates and assertions for checking
14998 the properties of variables, such as length, names and attributes. This is
14999 mainly for use by other package developers who want to include run-time
15000 testing features in their own packages.")
15001 (license license:gpl3+)))
15003 (define-public r-assertive-numbers
15005 (name "r-assertive-numbers")
15010 (uri (cran-uri "assertive.numbers" version))
15013 "0jc3ss64j4m7bjydhagwwmka5n7c72vpw4kfcch0m5jvkq5qrqds"))))
15015 `((upstream-name . "assertive.numbers")))
15016 (build-system r-build-system)
15018 (list r-assertive-base))
15019 (home-page "https://bitbucket.org/richierocks/assertive.numbers")
15020 (synopsis "Assertions to check properties of numbers")
15022 "This package provides a set of predicates and assertions for checking
15023 the properties of numbers. This is mainly for use by other package developers
15024 who want to include run-time testing features in their own packages.")
15025 (license license:gpl3+)))
15027 (define-public r-assertive-sets
15029 (name "r-assertive-sets")
15034 (uri (cran-uri "assertive.sets" version))
15037 "1cqvh2syvh5b6d85h601zjmsdbbf3h8q98ids4dfl4frdshpasc7"))))
15039 `((upstream-name . "assertive.sets")))
15040 (build-system r-build-system)
15042 (list r-assertive-base))
15043 (home-page "https://bitbucket.org/richierocks/assertive.sets")
15044 (synopsis "Assertions to check properties of sets")
15046 "This package provides a set of predicates and assertions for checking
15047 the properties of sets. This is mainly for use by other package developers
15048 who want to include run-time testing features in their own packages.")
15049 (license license:gpl3+)))
15051 (define-public r-assertive-matrices
15053 (name "r-assertive-matrices")
15058 (uri (cran-uri "assertive.matrices" version))
15061 "16sykzcndv6y2d43x6v9n7m95kv76364h39kh10w4z0xw6ksfqil"))))
15063 `((upstream-name . "assertive.matrices")))
15064 (build-system r-build-system)
15066 (list r-assertive-base))
15067 (home-page "https://bitbucket.org/richierocks/assertive.matrices")
15068 (synopsis "Assertions to check properties of matrices")
15070 "This package provides a set of predicates and assertions for checking
15071 the properties of matrices. This is mainly for use by other package
15072 developers who want to include run-time testing features in their own
15074 (license license:gpl3+)))
15076 (define-public r-assertive-models
15078 (name "r-assertive-models")
15083 (uri (cran-uri "assertive.models" version))
15086 "0bn4j4v5qvb2d672cgri61p8d9v258pmz35y3lvm6b9mdxwdi9mr"))))
15088 `((upstream-name . "assertive.models")))
15089 (build-system r-build-system)
15091 (list r-assertive-base))
15092 (home-page "https://bitbucket.org/richierocks/assertive.models")
15093 (synopsis "Assertions to check properties of models")
15095 "This package provides a set of predicates and assertions for checking
15096 the properties of models. This is mainly for use by other package developers
15097 who want to include run-time testing features in their own packages.")
15098 (license license:gpl3+)))
15100 (define-public r-assertive-reflection
15102 (name "r-assertive-reflection")
15107 (uri (cran-uri "assertive.reflection" version))
15110 "1g9lpwzy6r2xmyi2mlbcccnfgyzhzbmx5bsicf3vkffxrlkrpjn2"))))
15112 `((upstream-name . "assertive.reflection")))
15113 (build-system r-build-system)
15115 (list r-assertive-base))
15116 (home-page "https://bitbucket.org/richierocks/assertive.reflection")
15117 (synopsis "Assertions for checking the state of R")
15119 "This package provides a set of predicates and assertions for checking
15120 the state and capabilities of R, the operating system it is running on, and
15121 the IDE being used. This is mainly for use by other package developers who
15122 want to include run-time testing features in their own packages.")
15123 (license license:gpl3+)))
15125 (define-public r-assertive-types
15127 (name "r-assertive-types")
15132 (uri (cran-uri "assertive.types" version))
15135 "0zxq1jfrzgw95ll7alvm0xnk7aihjdksngq4ya2whyvfjbmv4vdb"))))
15137 `((upstream-name . "assertive.types")))
15138 (build-system r-build-system)
15140 (list r-assertive-base r-assertive-properties r-codetools))
15141 (home-page "https://bitbucket.org/richierocks/assertive.types")
15142 (synopsis "Assertions to check types of variables")
15144 "This package provides a set of predicates and assertions for checking
15145 the types of variables. This is mainly for use by other package developers
15146 who want to include run-time testing features in their own packages.")
15147 (license license:gpl3+)))
15149 (define-public r-assertive-files
15151 (name "r-assertive-files")
15156 (uri (cran-uri "assertive.files" version))
15159 "02pfz8j5vwcj5kl6zca46894li7lxwnlrr29j922f14ay6kdssmy"))))
15161 `((upstream-name . "assertive.files")))
15162 (build-system r-build-system)
15164 (list r-assertive-base r-assertive-numbers))
15165 (home-page "https://bitbucket.org/richierocks/assertive.files")
15166 (synopsis "Assertions to check properties of files")
15168 "This package provides a set of predicates and assertions for checking
15169 the properties of files and connections. This is mainly for use by other
15170 package developers who want to include run-time testing features in their own
15172 (license license:gpl3+)))
15174 (define-public r-assertive-code
15176 (name "r-assertive-code")
15181 (uri (cran-uri "assertive.code" version))
15184 "1qhbp668zfvhqs8avkhg9amp4zyazz6dsy4fc6kpdmw3sv8yi07g"))))
15186 `((upstream-name . "assertive.code")))
15187 (build-system r-build-system)
15189 (list r-assertive-base r-assertive-properties r-assertive-types))
15190 (home-page "https://bitbucket.org/richierocks/assertive.code")
15191 (synopsis "Assertions to check properties of code")
15193 "This package provides a set of predicates and assertions for checking
15194 the properties of code. This is mainly for use by other package developers
15195 who want to include run-time testing features in their own packages.")
15196 (license license:gpl3+)))
15198 (define-public r-assertive-datetimes
15200 (name "r-assertive-datetimes")
15205 (uri (cran-uri "assertive.datetimes" version))
15208 "151d05z8n6dpl44pqsa1jfi0ijbigr3zfc43xlw53nd8ymi22kh1"))))
15210 `((upstream-name . "assertive.datetimes")))
15211 (build-system r-build-system)
15213 (list r-assertive-base r-assertive-types))
15214 (home-page "https://bitbucket.org/richierocks/assertive.datetimes")
15215 (synopsis "Assertions to check properties of dates and times")
15217 "This package provides a set of predicates and assertions for checking
15218 the properties of dates and times. This is mainly for use by other package
15219 developers who want to include run-time testing features in their own
15221 (license license:gpl3+)))
15223 (define-public r-assertive-strings
15225 (name "r-assertive-strings")
15230 (uri (cran-uri "assertive.strings" version))
15233 "0n6jrk88670g4ym0r8ii40a08a90z1xadj8wcryk8h0nl04dchfm"))))
15235 `((upstream-name . "assertive.strings")))
15236 (build-system r-build-system)
15238 (list r-assertive-base r-assertive-types r-stringi))
15239 (home-page "https://bitbucket.org/richierocks/assertive.strings")
15240 (synopsis "Assertions to check properties of strings")
15242 "This package provides a set of predicates and assertions for checking
15243 the properties of strings. This is mainly for use by other package developers
15244 who want to include run-time testing features in their own packages.")
15245 (license license:gpl3+)))
15247 (define-public r-assertive-data-us
15249 (name "r-assertive-data-us")
15254 (uri (cran-uri "assertive.data.us" version))
15257 "1bgspn0sccmp9z7s7djvdvprgxlyc5vrxznp4zfjb79kwvgn83hq"))))
15259 `((upstream-name . "assertive.data.us")))
15260 (build-system r-build-system)
15262 (list r-assertive-base r-assertive-strings))
15263 (home-page "https://bitbucket.org/richierocks/assertive.data.us")
15264 (synopsis "Assertions to check properties of strings")
15266 "This package provides a set of predicates and assertions for checking
15267 the properties of US-specific complex data types. This is mainly for use by
15268 other package developers who want to include run-time testing features in
15269 their own packages.")
15270 (license license:gpl3+)))
15272 (define-public r-assertive-data-uk
15274 (name "r-assertive-data-uk")
15279 (uri (cran-uri "assertive.data.uk" version))
15282 "1fzjvhwp7mwkqqix29khvs6zcrc82n6j4czvzzb473vyjyvdlj5b"))))
15284 `((upstream-name . "assertive.data.uk")))
15285 (build-system r-build-system)
15287 (list r-assertive-base r-assertive-strings))
15288 (home-page "https://bitbucket.org/richierocks/assertive.data.uk")
15289 (synopsis "Assertions to check properties of strings")
15291 "This package provides a set of predicates and assertions for checking
15292 the properties of UK-specific complex data types. This is mainly for use by
15293 other package developers who want to include run-time testing features in
15294 their own packages.")
15295 (license license:gpl3+)))
15297 (define-public r-assertive-data
15299 (name "r-assertive-data")
15304 (uri (cran-uri "assertive.data" version))
15307 "00cvg2g36mdl8plrzx40m63qd55742mddqrchwy9n3c7mm4gn02s"))))
15309 `((upstream-name . "assertive.data")))
15310 (build-system r-build-system)
15312 (list r-assertive-base r-assertive-strings))
15313 (home-page "https://bitbucket.org/richierocks/assertive.data")
15314 (synopsis "Assertions to check properties of data")
15316 "This package provides a set of predicates and assertions for checking
15317 the properties of (country independent) complex data types. This is mainly
15318 for use by other package developers who want to include run-time testing
15319 features in their own packages.")
15320 (license license:gpl3+)))
15322 (define-public r-assertive
15324 (name "r-assertive")
15329 (uri (cran-uri "assertive" version))
15332 "02palil82idqhhshcdjsfsja9qkqnd0dczqzj5gbccy4hfg1c0y4"))))
15333 (build-system r-build-system)
15335 (list r-assertive-base
15338 r-assertive-data-uk
15339 r-assertive-data-us
15340 r-assertive-datetimes
15342 r-assertive-matrices
15344 r-assertive-numbers
15345 r-assertive-properties
15346 r-assertive-reflection
15348 r-assertive-strings
15353 (home-page "https://bitbucket.org/richierocks/assertive")
15354 (synopsis "Readable check functions to ensure code integrity")
15356 "This package provides lots of predicates (@code{is_*} functions) to
15357 check the state of your variables, and assertions (@code{assert_*} functions)
15358 to throw errors if they aren't in the right form.")
15359 (license license:gpl3+)))
15361 (define-public r-dotcall64
15363 (name "r-dotcall64")
15368 (uri (cran-uri "dotCall64" version))
15371 "1im5k8jbviwj2i42mq1kmjskh80isa7jr9w8i0fknidrzzy2h2zi"))))
15372 (properties `((upstream-name . "dotCall64")))
15373 (build-system r-build-system)
15374 (native-inputs (list gfortran))
15375 (home-page "https://git.math.uzh.ch/reinhard.furrer/dotCall64")
15376 (synopsis "Enhanced foreign function interface supporting long vectors")
15378 "This package provides @code{.C64()}, an enhanced version of @code{.C()}
15379 and @code{.Fortran()} from the R foreign function interface. @code{.C64()}
15380 supports long vectors, arguments of type 64-bit integer, and provides a
15381 mechanism to avoid unnecessary copies of read-only and write-only arguments.
15382 This makes it a convenient and fast interface to C/C++ and Fortran code.")
15383 (license license:gpl2+)))
15385 (define-public r-spam
15392 (uri (cran-uri "spam" version))
15394 (base32 "1ann2a2ifr3z983fcg1c0pkgmbxz6a0ym5q1dmq1r382bd1pg0fr"))))
15395 (build-system r-build-system)
15397 (list r-dotcall64))
15399 (list gfortran r-knitr))
15400 (home-page "https://www.math.uzh.ch/pages/spam/")
15401 (synopsis "Sparse matrix algebra")
15403 "This package provides a set of functions for sparse matrix algebra.
15404 Differences with other sparse matrix packages are:
15407 @item it only supports (essentially) one sparse matrix format;
15408 @item it is based on transparent and simple structure(s);
15409 @item it is tailored for MCMC calculations within G(M)RF;
15410 @item and it is fast and scalable (with the extension package @code{spam64}).
15412 ;; Either of these licenses
15413 (license (list license:bsd-3 license:lgpl2.0))))
15415 (define-public r-fields
15422 (uri (cran-uri "fields" version))
15424 (base32 "1hs4k5a9hh0r5fsrnpnvs6wvf78xpjzj8a2j6643dsz73a5q6ln6"))))
15425 (build-system r-build-system)
15427 (list r-maps r-spam r-viridis))
15430 (home-page "https://www.image.ucar.edu/fields")
15431 (synopsis "Tools for spatial data")
15433 "This is a package for curve, surface and function fitting with an
15434 emphasis on splines, spatial data and spatial statistics. The major methods
15435 include cubic, and thin plate splines, Kriging, and compactly supported
15436 covariance functions for large data sets.")
15437 (license license:gpl2+)))
15439 (define-public r-spatialextremes
15441 (name "r-spatialextremes")
15446 (uri (cran-uri "SpatialExtremes" version))
15449 "0z1swxp1syz8hdskarjxx4sdd7wx835kcnb783bwqm235yh991j3"))))
15451 `((upstream-name . "SpatialExtremes")))
15452 (build-system r-build-system)
15454 (list r-fields r-maps))
15455 (home-page "http://spatialextremes.r-forge.r-project.org/")
15456 (synopsis "Modelling spatial extremes")
15458 "This package provides tools for the statistical modelling of spatial
15459 extremes using max-stable processes, copula or Bayesian hierarchical models.
15460 More precisely, this package allows (conditional) simulations from various
15461 parametric max-stable models, analysis of the extremal spatial dependence, the
15462 fitting of such processes using composite likelihoods or least square (simple
15463 max-stable processes only), model checking and selection and prediction.")
15464 (license license:gpl2+)))
15466 (define-public r-drc
15473 (uri (cran-uri "drc" version))
15476 "0c8xn8ripzq270hy8d16fcnx02l02alddznd7fqwk3jyi6113h1y"))))
15477 (build-system r-build-system)
15485 (home-page "https://cran.r-project.org/web/packages/drc")
15486 (synopsis "Analysis of dose-response curves")
15488 "This package provides a suite of flexible and versatile model fitting
15489 and after-fitting functions for the analysis of dose-response data.")
15490 (license license:gpl2+)))
15492 (define-public r-rmeta
15499 (uri (cran-uri "rmeta" version))
15502 "0vkbnxp579v8zmcv1isdbzj5swpr6fq17zwparxcvzswjc2x9ydr"))))
15503 (build-system r-build-system)
15504 (home-page "https://cran.r-project.org/web/packages/rmeta")
15505 (synopsis "Tools for meta-analysis")
15507 "This package provides functions for simple fixed and random effects
15508 meta-analysis for two-sample comparisons and cumulative meta-analyses. It
15509 draws standard summary plots, funnel plots, and computes summaries and tests
15510 for association and heterogeneity.")
15511 (license license:gpl2)))
15513 (define-public r-bootstrap
15515 (name "r-bootstrap")
15520 (uri (cran-uri "bootstrap" version))
15523 "1546jqhhw5h177ii8jkdikyd26rv6gwkav816np1zks4p7zgsljj"))))
15524 (build-system r-build-system)
15525 (native-inputs (list gfortran))
15526 (home-page "https://cran.r-project.org/web/packages/bootstrap")
15527 (synopsis "Functions for the book \"An Introduction to the Bootstrap\"")
15529 "This package provides software and data for the book \"An Introduction
15530 to the Bootstrap\" by B. Efron and R. Tibshirani, 1993, Chapman and Hall.
15531 This package is primarily provided for projects already based on it, and for
15532 support of the book. New projects should preferentially use the recommended
15533 package \"boot\".")
15534 (license license:bsd-3)))
15536 (define-public r-survivalroc
15538 (name "r-survivalroc")
15543 (uri (cran-uri "survivalROC" version))
15546 "0wnd65ff5w679hxa1zrpfrx9qg47q21pjxppsga6m3h4iq1yfj8l"))))
15547 (properties `((upstream-name . "survivalROC")))
15548 (build-system r-build-system)
15549 (home-page "https://cran.r-project.org/web/packages/survivalROC")
15550 (synopsis "Time-dependent ROC curve estimation from censored survival data")
15552 "Compute time-dependent ROC curve from censored survival data using
15553 Kaplan-Meier (KM) or Nearest Neighbor Estimation (NNE) method of Heagerty,
15554 Lumley & Pepe (Biometrics, Vol 56 No 2, 2000, PP 337-344)")
15555 (license license:gpl2+)))
15557 (define-public r-locfdr
15563 (uri (cran-uri "locfdr" version))
15566 "1falkbp2xz07am8jlhwlvyqvxnli4nwl188kd0g58vdfjcjy3mj2"))))
15567 (build-system r-build-system)
15568 (home-page "https://cran.r-project.org/web/packages/locfdr/")
15569 (synopsis "Computes local false discovery rates")
15570 (description "This package can be used to compute local false
15572 (license license:gpl2)))
15574 (define-public r-longitudinal
15576 (name "r-longitudinal")
15581 (uri (cran-uri "longitudinal" version))
15584 "046w3xbr535c5jyd68adv42a7limxp1mv57b5w6w673w707lmw2p"))))
15585 (build-system r-build-system)
15586 (propagated-inputs (list r-corpcor))
15587 (home-page "http://strimmerlab.org/software/longitudinal/")
15588 (synopsis "Analysis of multiple time course data")
15590 "This package contains general data structures and functions for
15591 longitudinal data with multiple variables, repeated measurements, and
15592 irregularly spaced time points. It also implements a shrinkage estimator of
15593 dynamical correlation and dynamical covariance.")
15594 (license license:gpl3+)))
15596 (define-public r-genenet
15603 (uri (cran-uri "GeneNet" version))
15606 "1r1khga3nxxjghs4vnbymzp0cwb1q17zw2v3a94qz8fsrirq1sf1"))))
15607 (properties `((upstream-name . "GeneNet")))
15608 (build-system r-build-system)
15610 (list r-corpcor r-fdrtool r-longitudinal))
15611 (home-page "http://strimmerlab.org/software/genenet/")
15612 (synopsis "Modeling and inferring gene networks")
15614 "This package analyzes gene expression (time series) data with focus on
15615 the inference of gene networks. In particular, GeneNet implements the methods
15616 of Schaefer and Strimmer (2005a,b,c) and Opgen-Rhein and Strimmer (2006, 2007)
15617 for learning large-scale gene association networks (including assignment of
15618 putative directions).")
15619 (license license:gpl3+)))
15621 (define-public r-rbamtools
15623 (name "r-rbamtools")
15624 (version "2.16.17")
15628 (uri (cran-uri "rbamtools" version))
15631 "0qj37ljdva3v29s01dkrbg31mcfzy3bl145cp40d54v4h9xhcghc"))))
15632 (build-system r-build-system)
15633 (inputs (list zlib))
15635 (list r-refgenome))
15636 (home-page "https://cran.r-project.org/web/packages/rbamtools")
15637 (synopsis "Read and write BAM (binary alignment) files")
15639 "This package provides an R interface to functions of the SAMtools
15641 (license license:artistic2.0)))
15643 (define-public r-protviz
15650 (uri (cran-uri "protViz" version))
15653 "0f6jwzcqi0w37hvg3i5dlk0c3anpkqh54ibf94vaf17r8sykr4nw"))))
15654 (properties `((upstream-name . "protViz")))
15655 (build-system r-build-system)
15656 (propagated-inputs (list r-rcpp))
15657 (home-page "https://github.com/protViz/protViz/")
15658 (synopsis "Visualizing and analyzing mass spectrometry data in proteomics")
15660 "This package helps with quality checks, visualizations and analysis of
15661 mass spectrometry data, coming from proteomics experiments. The package is
15662 developed, tested and used at the Functional Genomics Center Zurich, where it
15663 is used mainly for prototyping, teaching, and having fun with proteomics data.
15664 But it can also be used to do data analysis for small scale data sets.")
15665 (license license:gpl3)))
15667 (define-public r-cmprsk
15674 (uri (cran-uri "cmprsk" version))
15676 (base32 "050f24l5ab1ds9824c7yjahimf6pg8ih2k83jzpzfb0n5k5jfh44"))))
15677 (build-system r-build-system)
15682 (home-page "https://cran.r-project.org/web/packages/cmprsk")
15683 (synopsis "Subdistribution analysis of competing risks")
15685 "This package provides tool for estimation, testing and regression
15686 modeling of subdistribution functions in competing risks, as described in
15687 Gray (1988), A class of K-sample tests for comparing the cumulative incidence
15688 of a competing risk, Ann. Stat. 16:1141-1154, and Fine JP and Gray RJ (1999),
15689 A proportional hazards model for the subdistribution of a competing risk,
15690 JASA, 94:496-509.")
15691 (license license:gpl2+)))
15693 (define-public r-etm
15700 (uri (cran-uri "etm" version))
15703 "1hvrplmdpjjpjji663rw0vjbbrzj2nvr04d1nkc8bf46p4ixyxgy"))))
15704 (build-system r-build-system)
15706 (list r-data-table r-lattice r-rcpp r-rcpparmadillo r-survival))
15707 (home-page "https://cran.r-project.org/web/packages/etm")
15708 (synopsis "Empirical transition matrix")
15710 "The @dfn{empirical transition matrix} (etm) package estimates
15711 the matrix of transition probabilities for any time-inhomogeneous multistate
15712 model with finite state space using the Aalen-Johansen estimator.")
15713 (license license:expat)))
15715 (define-public r-epi
15722 (uri (cran-uri "Epi" version))
15725 "0s3ij0rya4wd7k97kc4s3pwj1d1ypaxl1s7zqr6sa07hp4a8fzz0"))))
15726 (properties `((upstream-name . "Epi")))
15727 (build-system r-build-system)
15741 (home-page "https://BendixCarstensen.com/Epi/")
15742 (synopsis "Statistical analysis in epidemiology")
15744 "This package provides functions for demographic and epidemiological
15745 analysis in the Lexis diagram, i.e. register and cohort follow-up data, in
15746 particular representation, manipulation and simulation of multistate data -
15747 the Lexis suite of functions, which includes interfaces to the @code{mstate},
15748 @code{etm} and @code{cmprsk} packages. It also contains functions for
15749 Age-Period-Cohort and Lee-Carter modeling and a function for interval censored
15750 data and some useful functions for tabulation and plotting, as well as a
15751 number of epidemiological data sets.")
15752 (license license:gpl2)))
15754 (define-public r-ppls
15757 (version "1.6-1.1")
15761 (uri (cran-uri "ppls" version))
15764 "1zyrisy3c4cz896j1bjh61sf57wdl9p8ywdq268cl819szfq78mx"))))
15765 (build-system r-build-system)
15766 (propagated-inputs (list r-mass))
15767 (home-page "https://cran.r-project.org/web/packages/ppls")
15768 (synopsis "Penalized partial least squares")
15770 "This package contains linear and nonlinear regression methods based on
15771 partial least squares and penalization techniques. Model parameters are
15772 selected via cross-validation, and confidence intervals ans tests for the
15773 regression coefficients can be conducted via jackknifing.")
15774 (license license:gpl2+)))
15776 (define-public r-huge
15783 (uri (cran-uri "huge" version))
15785 (base32 "1sl457a1lndrx98y2j9a2smanawx2iqlhl82iand0g3p5xp8ch4j"))))
15786 (build-system r-build-system)
15788 (list r-igraph r-mass r-matrix r-rcpp r-rcppeigen))
15789 (home-page "https://cran.r-project.org/web/packages/huge")
15790 (synopsis "High-dimensional undirected graph estimation")
15792 "This package provides a general framework for high-dimensional
15793 undirected graph estimation. It integrates data preprocessing, neighborhood
15794 screening, graph estimation, and model selection techniques into a pipeline.")
15795 (license license:gpl2)))
15797 (define-public r-parcor
15804 (uri (cran-uri "parcor" version))
15807 "0vgs6k92vdr0cmb8cwbv2ff6qavw30agskfd8bfh17hsskrisvx0"))))
15808 (build-system r-build-system)
15810 (list r-epi r-genenet r-glmnet r-mass r-ppls))
15811 (home-page "https://cran.r-project.org/web/packages/parcor")
15812 (synopsis "Regularized estimation of partial correlation matrices")
15814 "This package estimates the matrix of partial correlations based on
15815 different regularized regression methods: lasso, adaptive lasso, PLS, and
15816 Ridge Regression. In addition, the package provides model selection for
15817 lasso, adaptive lasso and Ridge regression based on cross-validation.")
15818 (license license:gpl2+)))
15820 (define-public r-mcmc
15827 (uri (cran-uri "mcmc" version))
15830 "0q42m8ab7b6bxhns494ksjdss5f3c5m2jjfdlfj6fk1nz7ax7i5p"))))
15831 (build-system r-build-system)
15832 (home-page "https://www.stat.umn.edu/geyer/mcmc/")
15833 (synopsis "Markov chain Monte Carlo")
15835 "This package simulates continuous distributions of random vectors using
15836 @dfn{Markov chain Monte Carlo} (MCMC). Users specify the distribution by an R
15837 function that evaluates the log unnormalized density. Algorithms are random
15838 walk Metropolis algorithm (function @code{metrop}), simulated
15839 tempering (function @code{temper}), and morphometric random walk
15840 Metropolis (function @code{morph.metrop}), which achieves geometric ergodicity
15841 by change of variable.")
15842 (license license:expat)))
15844 (define-public r-listenv
15851 (uri (cran-uri "listenv" version))
15854 "0ps8bk7zlhbviawrw7vw25skjq81hkk3ijyi6g74dmfqy8zsyapx"))))
15855 (build-system r-build-system)
15858 (modify-phases %standard-phases
15859 (add-after 'unpack 'set-HOME
15860 (lambda _ (setenv "HOME" "/tmp"))))))
15862 (list r-r-rsp)) ; vignette builder
15863 (home-page "https://github.com/HenrikBengtsson/listenv")
15864 (synopsis "Environments behaving (almost) as lists")
15866 "This package implements list environments. List environments are
15867 environments that have list-like properties. For instance, the elements of a
15868 list environment are ordered and can be accessed and iterated over using index
15870 (license license:lgpl2.1+)))
15872 (define-public r-globals
15879 (uri (cran-uri "globals" version))
15882 "15llx4233ihj4w815k7inc17530w9ja0mi29n1i0s2sr42j8jdpq"))))
15883 (build-system r-build-system)
15885 (list r-codetools))
15886 (home-page "https://github.com/HenrikBengtsson/globals")
15887 (synopsis "Identify global objects in R expressions")
15889 "This package provides tools to identify global (\"unknown\" or \"free\")
15890 objects in R expressions by code inspection using various strategies, e.g.
15891 conservative or liberal. The objective of this package is to make it as
15892 simple as possible to identify global objects for the purpose of exporting
15893 them in distributed compute environments.")
15894 (license license:lgpl2.1+)))
15896 (define-public r-parallelly
15898 (name "r-parallelly")
15903 (uri (cran-uri "parallelly" version))
15906 "1nhp66psk3m79is5qm4ppxkj7bdy46jr2h2pir22ia9ghhyzris0"))))
15907 (properties `((upstream-name . "parallelly")))
15908 (build-system r-build-system)
15909 (home-page "https://github.com/HenrikBengtsson/parallelly")
15910 (synopsis "Enhancements of the parallel package")
15912 "This package provides utility functions that enhance the @code{parallel}
15913 package and support the built-in parallel backends of the @code{future}
15914 package. For example, @code{availableCores} gives the number of CPU cores
15915 available to your R process as given by R options and environment variables,
15916 including those set by job schedulers on high-performance compute clusters.
15917 If none is set, it will fall back to @code{parallel::detectCores}. Another
15918 example is @code{makeClusterPSOCK}, which is backward compatible with
15919 @code{parallel::makePSOCKcluster} while doing a better job in setting up
15920 remote cluster workers without the need for configuring the firewall to do
15921 port-forwarding to your local computer.")
15922 (license license:lgpl2.1+)))
15924 (define-public r-future
15931 (uri (cran-uri "future" version))
15934 "1mchjdvvwgs8v0iv8z5m6gav3xzvnq11h8qrc7lfnrb2x3d0np53"))))
15935 (build-system r-build-system)
15938 (modify-phases %standard-phases
15939 (add-after 'unpack 'set-HOME
15940 (lambda _ (setenv "HOME" "/tmp"))))))
15942 (list r-digest r-globals r-listenv r-parallelly))
15944 (list r-r-rsp)) ; vignette builder
15945 (home-page "https://github.com/HenrikBengtsson/future")
15946 (synopsis "Unified parallel and distributed processing in R")
15948 "The purpose of this package is to provide a lightweight and unified
15949 Future API for sequential and parallel processing of R expression via futures.
15950 This package implements sequential, multicore, multisession, and cluster
15951 futures. With these, R expressions can be evaluated on the local machine, in
15952 parallel a set of local machines, or distributed on a mix of local and remote
15953 machines. Extensions to this package implement additional backends for
15954 processing futures via compute cluster schedulers etc. Because of its unified
15955 API, there is no need to modify any code in order to switch from sequential on
15956 the local machine to, say, distributed processing on a remote compute cluster.")
15957 (license license:lgpl2.1+)))
15959 (define-public r-future-apply
15961 (name "r-future-apply")
15966 (uri (cran-uri "future.apply" version))
15969 "1xb7qj8izjwmy4aa92p5f4cdbhgp220hrly3b5879f9hrv2w2rk1"))))
15970 (properties `((upstream-name . "future.apply")))
15971 (build-system r-build-system)
15974 (modify-phases %standard-phases
15975 (add-after 'unpack 'set-HOME
15976 (lambda _ (setenv "HOME" "/tmp"))))))
15978 (list r-future r-globals))
15980 (list r-r-rsp)) ; vignette builder
15981 (home-page "https://github.com/HenrikBengtsson/future.apply")
15982 (synopsis "Apply function to elements in parallel using futures")
15984 "This package provides implementations of @code{apply()},
15985 @code{eapply()}, @code{lapply()}, @code{Map()}, @code{mapply()},
15986 @code{replicate()}, @code{sapply()}, @code{tapply()}, and @code{vapply()} that
15987 can be resolved using any future-supported backend, e.g. parallel on the local
15988 machine or distributed on a compute cluster.")
15989 (license license:gpl2+)))
15991 (define-public r-rsvd
15998 (uri (cran-uri "rsvd" version))
16001 "07p2hjmpcwcsang8z9sjkpy94rydcin7m3hyvcgzgm5cd6w8c1p4"))))
16002 (build-system r-build-system)
16005 (home-page "https://github.com/erichson/rSVD")
16006 (synopsis "Randomized singular value decomposition")
16008 "Low-rank matrix decompositions are fundamental tools and widely used for
16009 data analysis, dimension reduction, and data compression. Classically, highly
16010 accurate deterministic matrix algorithms are used for this task. However, the
16011 emergence of large-scale data has severely challenged our computational
16012 ability to analyze big data. The concept of randomness has been demonstrated
16013 as an effective strategy to quickly produce approximate answers to familiar
16014 problems such as the @dfn{singular value decomposition} (SVD). This package
16015 provides several randomized matrix algorithms such as the randomized singular
16016 value decomposition (@code{rsvd}), randomized principal component
16017 analysis (@code{rpca}), randomized robust principal component
16018 analysis (@code{rrpca}), randomized interpolative decomposition (@code{rid}),
16019 and the randomized CUR decomposition (@code{rcur}). In addition several plot
16020 functions are provided.")
16021 (license license:gpl3+)))
16023 (define-public r-sloop
16030 (uri (cran-uri "sloop" version))
16033 "00fk5fr5zsk2qxc1kfhmshhjxgnamm3401089sx8m2l529zd6r8j"))))
16034 (build-system r-build-system)
16036 (list r-codetools r-crayon r-purrr r-rlang r-tibble))
16037 (home-page "https://github.com/r-lib/sloop")
16038 (synopsis "Helpers for object-oriented programming in R")
16040 "This package provides a collection of helper functions designed to
16041 help you to better understand object oriented programming in R, particularly
16043 (license license:gpl3)))
16045 (define-public r-capushe
16052 (uri (cran-uri "capushe" version))
16055 "1aa76ir1kp67hiz7dr60azyc71yzslshyc640fjh0fpw0sp5kwbc"))))
16056 (build-system r-build-system)
16057 (propagated-inputs (list r-mass))
16058 (home-page "https://cran.r-project.org/web/packages/capushe/index.html")
16059 (synopsis "Calibrating penalties using slope heuristics")
16061 "This package provides tools for the calibration of penalized criteria
16062 for model selection. The calibration methods available are based on the slope
16064 (license license:gpl2+)))
16066 (define-public r-dorng
16073 (uri (cran-uri "doRNG" version))
16076 "1jff27zzrvd1fd61x2m9468h8xn3s1c9f6wibviy5zdhj5dx9s9k"))))
16077 (properties `((upstream-name . "doRNG")))
16078 (build-system r-build-system)
16080 (list r-foreach r-iterators r-rngtools))
16081 (home-page "https://renozao.github.io/doRNG/")
16082 (synopsis "Generic reproducible parallel backend for foreach loops")
16084 "This package provides functions to perform reproducible parallel
16085 @code{foreach} loops, using independent random streams as generated by
16086 L'Ecuyer's combined multiple-recursive generator. It enables to easily
16087 convert standard @code{%dopar%} loops into fully reproducible loops,
16088 independently of the number of workers, the task scheduling strategy, or the
16089 chosen parallel environment and associated foreach backend.")
16090 (license license:gpl2+)))
16092 (define-public r-blockmodeling
16094 (name "r-blockmodeling")
16099 (uri (cran-uri "blockmodeling" version))
16102 "1vc8gy4slsywcwxq532373i0dq73fhs5cac9mr6zz2pjaaxjghhq"))))
16103 (build-system r-build-system)
16106 (native-inputs (list gfortran))
16107 (home-page "https://cran.r-project.org/web/packages/blockmodeling")
16108 (synopsis "Generalized and classical blockmodeling of valued networks")
16110 "This package is primarily meant as an implementation of generalized
16111 blockmodeling for valued networks. In addition, measures of similarity or
16112 dissimilarity based on structural equivalence and regular equivalence (REGE
16113 algorithms) can be computed and partitioned matrices can be plotted.")
16114 (license license:gpl2+)))
16116 (define-public r-upsetr
16123 (uri (cran-uri "UpSetR" version))
16126 "007i0njnjjy7vbrxabwav7a1kk2n0hn2mkvqsdzzfk10ckp5y7im"))))
16127 (properties `((upstream-name . "UpSetR")))
16128 (build-system r-build-system)
16130 (list r-ggplot2 r-gridextra r-plyr r-scales))
16131 (home-page "https://github.com/hms-dbmi/UpSetR")
16132 (synopsis "Visualize intersecting sets")
16134 "This package provides a more scalable alternative to Venn and Euler
16135 diagrams for visualizing intersecting sets. Create visualizations of
16136 intersecting sets using a novel matrix design, along with visualizations of
16137 several common set, element and attribute related tasks.")
16138 (license license:expat)))
16140 ;; This package includes a JavaScript file, which is not minified. When
16141 ;; upgrading please check that there are no new minified JavaScript files.
16142 (define-public r-shinybs
16149 (uri (cran-uri "shinyBS" version))
16152 "0h51685a9qll4agayldjyryi60ih969219ibg071slv0613p5v8a"))))
16153 (properties `((upstream-name . "shinyBS")))
16154 (build-system r-build-system)
16155 ;; The tests spawn Shiny browser apps. They cannot be run
16156 ;; non-interactively.
16157 (arguments '(#:tests? #f))
16159 (list r-htmltools r-shiny))
16160 (home-page "https://ebailey78.github.io/shinyBS/")
16161 (synopsis "Twitter Bootstrap components for Shiny")
16163 "This package adds additional Twitter Bootstrap components to Shiny.")
16164 (license license:gpl3)))
16166 (define-public r-shinyjqui
16168 (name "r-shinyjqui")
16173 (uri (cran-uri "shinyjqui" version))
16176 "135gwz7syyb6pbn0lkvmq0v1c6r1zivavnqhi1rnzbbzlysi27v1"))
16178 '(for-each delete-file
16179 (list "inst/www/shinyjqui.min.js"
16180 "inst/www/jquery.ui.touch-punch.min.js")))))
16181 (properties `((upstream-name . "shinyjqui")))
16182 (build-system r-build-system)
16185 (modify-phases %standard-phases
16186 (add-after 'unpack 'process-javascript
16187 (lambda* (#:key inputs #:allow-other-keys)
16188 (with-directory-excursion "inst/www"
16190 `((,(string-append (assoc-ref inputs "js-jquery.ui.touch-punch")
16191 "/jquery.ui.touch-punch.js")
16192 . "jquery.ui.touch-punch.min.js")
16194 . "shinyjqui.min.js"))))
16195 (for-each (lambda (source target)
16196 (format #true "Processing ~a --> ~a~%"
16198 (invoke "esbuild" source "--minify"
16199 (string-append "--outfile=" target)))
16201 (map cdr mapping)))))))))
16203 (list r-htmltools r-htmlwidgets r-jsonlite r-rlang r-shiny))
16205 `(("r-knitr" ,r-knitr)
16206 ("esbuild" ,esbuild)
16207 ("js-jquery.ui.touch-punch"
16210 (uri (git-reference
16211 (url "https://github.com/furf/jquery-ui-touch-punch")
16212 (commit "8f7559b6e65cdc3ee3648d5fe76d38c653f87ff5")))
16215 "1lzywp2q9hwx6d5fqjla95vp7ra2lahr5dam7lsqjmch9d98r48q"))))))
16216 (home-page "https://github.com/yang-tang/shinyjqui")
16217 (synopsis "jQuery UI interactions and effects for Shiny")
16219 "This is an extension to Shiny that brings interactions and animation
16220 effects from the jQuery UI library.")
16221 (license license:expat)))
16223 (define-public r-shinymanager
16225 (name "r-shinymanager")
16226 (version "1.0.400")
16230 (uri (cran-uri "shinymanager" version))
16232 (base32 "1np2yp5pn8g9i4jhysfgprmdn13cpw4vaaagrd72rnk2r4hpmyx4"))))
16233 (properties `((upstream-name . "shinymanager")))
16234 (build-system r-build-system)
16236 (list r-billboarder
16246 (native-inputs (list r-knitr))
16247 (home-page "https://github.com/datastorm-open/shinymanager")
16248 (synopsis "Authentication management for Shiny applications")
16250 "This package provides simple and secure authentification mechanism for
16251 single Shiny applications. Credentials are stored in an encrypted SQLite
16253 (license license:gpl3)))
16255 (define-public r-outliers
16257 (name "r-outliers")
16262 (uri (cran-uri "outliers" version))
16265 "1yrmwvjjb0a6sbx940k9svf23cykcxz8rrwcgyic7lpgzbrdfcfc"))))
16266 (build-system r-build-system)
16267 (home-page "https://cran.r-project.org/web/packages/outliers/index.html")
16268 (synopsis "Tests for outliers")
16270 "This package provides a collection of some tests commonly used for
16271 identifying outliers.")
16272 (license license:gpl2+)))
16274 (define-public r-bayesm
16281 (uri (cran-uri "bayesm" version))
16283 (base32 "154glks7rsjkza0sfi1kj7wj727py9sl1ba6sswflwmwc9n226q6"))))
16284 (build-system r-build-system)
16286 (list r-rcpp r-rcpparmadillo))
16287 (home-page "http://www.perossi.org/home/bsm-1")
16288 (synopsis "Bayesian inference for marketing/micro-econometrics")
16290 "This package covers many important models used in marketing and
16291 micro-econometrics applications, including Bayes Regression (univariate or
16292 multivariate dep var), Bayes Seemingly Unrelated Regression (SUR), Binary and
16293 Ordinal Probit, Multinomial Logit (MNL) and Multinomial Probit (MNP),
16294 Multivariate Probit, Negative Binomial (Poisson) Regression, Multivariate
16295 Mixtures of Normals (including clustering), Dirichlet Process Prior Density
16296 Estimation with normal base, Hierarchical Linear Models with normal prior and
16297 covariates, Hierarchical Linear Models with a mixture of normals prior and
16298 covariates, Hierarchical Multinomial Logits with a mixture of normals prior
16299 and covariates, Hierarchical Multinomial Logits with a Dirichlet Process prior
16300 and covariates, Hierarchical Negative Binomial Regression Models, Bayesian
16301 analysis of choice-based conjoint data, Bayesian treatment of linear
16302 instrumental variables models, Analysis of Multivariate Ordinal survey data
16303 with scale usage heterogeneity, and Bayesian Analysis of Aggregate Random
16304 Coefficient Logit Models.")
16305 (license license:gpl2+)))
16307 (define-public r-tensora
16314 (uri (cran-uri "tensorA" version))
16317 "19wwh654qlja4z1n7afjpzsrrm53p8ddysa2vra5mdnkddb4g2cf"))))
16318 (properties `((upstream-name . "tensorA")))
16319 (build-system r-build-system)
16320 (home-page "http://www.stat.boogaart.de/tensorA")
16321 (synopsis "Advanced tensor arithmetic with named indices")
16323 "This package provides convenience functions for advanced linear algebra
16324 with tensors and computation with datasets of tensors on a higher level
16325 abstraction. It includes Einstein and Riemann summing conventions, dragging,
16326 co- and contravariate indices, and parallel computations on sequences of
16328 (license license:gpl2+)))
16330 (define-public r-rarpack
16337 (uri (cran-uri "rARPACK" version))
16340 "12h2y46xcfldhjdmm960swgn9b23zvkj5vg2bi42s9qxwgi02d63"))))
16341 (properties `((upstream-name . "rARPACK")))
16342 (build-system r-build-system)
16343 (propagated-inputs (list r-rspectra))
16344 (home-page "https://github.com/yixuan/rARPACK")
16345 (synopsis "Solvers for large scale eigenvalue and SVD problems")
16347 "This package was previously an R wrapper of the ARPACK library, and now
16348 a shell of the R package RSpectra, an R interface to the Spectra library for
16349 solving large scale eigenvalue/vector problems. The current version of
16350 rARPACK simply imports and exports the functions provided by RSpectra. New
16351 users of rARPACK are advised to switch to the RSpectra package.")
16352 (license license:bsd-3)))
16354 (define-public r-compositions
16356 (name "r-compositions")
16361 (uri (cran-uri "compositions" version))
16364 "1bqg0qqzsf92q0jb7hdjycr54bwv8rk7ajhvxgch5yslyqxpm73v"))))
16365 (build-system r-build-system)
16367 (list r-bayesm r-mass r-robustbase r-tensora))
16370 (home-page "http://www.stat.boogaart.de/compositions")
16371 (synopsis "Compositional data analysis")
16373 "This package provides functions for the consistent analysis of
16374 compositional data (e.g. portions of substances) and positive
16375 numbers (e.g. concentrations).")
16376 (license license:gpl2+)))
16378 (define-public r-cobs
16385 (uri (cran-uri "cobs" version))
16388 "0hiw5smk6kgk0gb9840kcqkhkybl7n30s77xhjc395x09izbgix1"))))
16389 (build-system r-build-system)
16391 (list r-quantreg r-sparsem))
16392 (home-page "https://cran.r-project.org/web/packages/cobs")
16393 (synopsis "Constrained B-Splines (sparse matrix based)")
16395 "This package provides qualitatively constrained (regression) smoothing
16396 splines via linear programming and sparse matrices.")
16397 (license license:gpl2+)))
16399 (define-public r-drimpute
16401 (name "r-drimpute")
16406 (uri (cran-uri "DrImpute" version))
16409 "1adzarrwqb282pqgx2yqswp9rpwd1naxsmar54kddr6qyd6b923b"))))
16410 (properties `((upstream-name . "DrImpute")))
16411 (build-system r-build-system)
16413 (list r-rcpp r-rcpparmadillo))
16414 (home-page "https://github.com/ikwak2/DrImpute")
16415 (synopsis "Imputing dropout events in single-cell RNA-Seq data")
16417 "This is an R package for imputing dropout events. Many statistical
16418 methods in cell type identification, visualization and lineage reconstruction
16419 do not account for dropout events. DrImpute can improve the performance of
16420 such software by imputing dropout events.")
16421 (license license:gpl3)))
16423 (define-public r-gamlss-dist
16425 (name "r-gamlss-dist")
16430 (uri (cran-uri "gamlss.dist" version))
16432 (base32 "1gqjr419v8z2ygh0h1xz7bipnsbp820njzwq7z3r9f41rn1ym47c"))))
16433 (properties `((upstream-name . "gamlss.dist")))
16434 (build-system r-build-system)
16435 (propagated-inputs (list r-mass))
16436 (home-page "http://www.gamlss.org/")
16437 (synopsis "Distributions for Generalized Additive Models for location scale and shape")
16439 "This package provides a set of distributions which can be used for
16440 modelling the response variables in Generalized Additive Models for Location
16441 Scale and Shape. The distributions can be continuous, discrete or mixed
16442 distributions. Extra distributions can be created, by transforming, any
16443 continuous distribution defined on the real line, to a distribution defined on
16444 ranges 0 to infinity or 0 to 1, by using a @code{log} or a @code{logit}
16445 transformation, respectively.")
16446 ;; Either version of the GPL.
16447 (license (list license:gpl2 license:gpl3))))
16449 ;; This package includes JavaScript files, which are not minified. When
16450 ;; upgrading please check that there are no new minified JavaScript files.
16451 (define-public r-shinyjs
16458 (uri (cran-uri "shinyjs" version))
16461 "1id9gsrkr28xl80a8794in17rxmmz06zqvd5hlns7mqz3fzhrhky"))))
16462 (build-system r-build-system)
16464 (list r-digest r-jsonlite r-shiny))
16467 (home-page "https://deanattali.com/shinyjs")
16468 (synopsis "Improve the user experience of your Shiny apps")
16470 "Perform common useful JavaScript operations in Shiny apps that will
16471 greatly improve your apps without having to know any JavaScript. Examples
16472 include: hiding an element, disabling an input, resetting an input back to its
16473 original value, delaying code execution by a few seconds, and many more useful
16474 functions for both the end user and the developer. Shinyjs can also be used
16475 to easily call your own custom JavaScript functions from R.")
16476 (license license:agpl3+)))
16478 ;; This package includes minified JavaScript files. When upgrading please
16479 ;; check that there are no new minified JavaScript files.
16480 (define-public r-colourpicker
16482 (name "r-colourpicker")
16487 (uri (cran-uri "colourpicker" version))
16490 "1q1wi3g403fbzp4ys3gsjbwdc86x770cx323qgi47ca8n219kl50"))))
16491 (build-system r-build-system)
16494 (modify-phases %standard-phases
16495 (add-after 'unpack 'process-javascript
16496 (lambda* (#:key inputs #:allow-other-keys)
16497 (with-directory-excursion "inst"
16499 `((,(assoc-ref inputs "js-salvattore")
16500 . "examples/colourInput/www/salvattore.min.js")
16501 (,(assoc-ref inputs "js-jquery")
16502 . "htmlwidgets/lib/jquery/jquery.min.js")
16503 ("www/shared/colourpicker/js/colourpicker.js"
16504 . "www/shared/colourpicker/js/colourpicker.min.js"))))
16505 (for-each (lambda (source target)
16506 (format #true "Processing ~a --> ~a~%"
16508 (delete-file target)
16509 (invoke "esbuild" source "--minify"
16510 (string-append "--outfile=" target)))
16512 (map cdr mapping)))))))))
16522 `(("esbuild" ,esbuild)
16526 (uri "https://code.jquery.com/jquery-1.11.3.js")
16529 "1v956yf5spw0156rni5z77hzqwmby7ajwdcd6mkhb6zvl36awr90"))))
16533 (uri "https://raw.githubusercontent.com/rnmp/salvattore/v1.0.9/dist/salvattore.js")
16536 "0lfrbx7l9w5x89jpc6njmd0pk7h8fpvg537vklai2vf7b1r2nnk5"))))))
16537 (home-page "https://github.com/daattali/colourpicker")
16538 (synopsis "Color picker tool for Shiny and for selecting colors in plots")
16540 "This package provides a color picker that can be used as an input in
16541 Shiny apps or Rmarkdown documents. The color picker supports alpha opacity,
16542 custom color palettes, and many more options. A plot color helper tool is
16543 available as an RStudio Addin, which helps you pick colors to use in your
16544 plots. A more generic color picker RStudio Addin is also provided to let you
16545 select colors to use in your R code.")
16546 (license license:expat)))
16548 (define-public r-ggextra
16555 (uri (cran-uri "ggExtra" version))
16558 "1rd3qv6ah3zphr1jicjhgxms73vi496mjnxnsrcgl7z8nyxmas6w"))))
16559 (properties `((upstream-name . "ggExtra")))
16560 (build-system r-build-system)
16562 (list r-colourpicker
16572 (home-page "https://github.com/daattali/ggExtra")
16573 (synopsis "Marginal histograms for ggplot2 and other enhancements")
16575 "This package is a collection of functions and layers to enhance ggplot2.
16576 The flagship function is @code{ggMarginal()}, which can be used to add
16577 marginal histograms/boxplots/density plots to ggplot2 scatterplots.")
16578 (license license:expat)))
16580 (define-public r-minpack-lm
16582 (name "r-minpack-lm")
16587 (uri (cran-uri "minpack.lm" version))
16590 "11yz6hk2r33571d16kq01cb1x6sgdzi6jmksqlrm8mr84l95c2f7"))))
16591 (properties `((upstream-name . "minpack.lm")))
16592 (build-system r-build-system)
16593 (native-inputs (list gfortran))
16594 (home-page "https://cran.r-project.org/web/packages/minpack.lm")
16595 (synopsis "Levenberg-Marquardt Nonlinear Least-Squares algorithm")
16597 "The @code{nls.lm} function provides an R interface to @code{lmder} and
16598 @code{lmdif} from the MINPACK library, for solving nonlinear least-squares
16599 problems by a modification of the Levenberg-Marquardt algorithm, with support
16600 for lower and upper parameter bounds. The implementation can be used via
16601 @code{nls}-like calls using the @code{nlsLM} function.")
16602 (license license:gpl3)))
16604 (define-public r-moments
16611 (uri (cran-uri "moments" version))
16614 "0r6qf3i1rzh2822bx1p0h8mh91gsbgg6asl2rzh2l4ys094bilif"))))
16615 (build-system r-build-system)
16616 (home-page "https://cran.r-project.org/web/packages/moments")
16617 (synopsis "Moments, cumulants, skewness, kurtosis and related tests")
16619 "This package provides functions to calculate: moments, Pearson's
16620 kurtosis, Geary's kurtosis and skewness; it also includes tests related to
16621 them (Anscombe-Glynn, D'Agostino, Bonett-Seier).")
16622 (license license:gpl2+)))
16624 (define-public r-msir
16631 (uri (cran-uri "msir" version))
16634 "1wm83m3cqd6llxb9p2jwim0wb81v84pgdmgcznygzaaq6kbn3n84"))))
16635 (build-system r-build-system)
16640 (home-page "https://cran.r-project.org/web/packages/msir")
16641 (synopsis "Model-based sliced inverse regression")
16643 "This is an R package for dimension reduction based on finite Gaussian
16644 mixture modeling of inverse regression.")
16645 (license license:gpl2+)))
16647 (define-public r-pbivnorm
16649 (name "r-pbivnorm")
16654 (uri (cran-uri "pbivnorm" version))
16657 "05jzrjqxzbcf6z245hlk7sjxiszv9paadaaimvcx5y5qgi87vhq7"))))
16658 (build-system r-build-system)
16659 (native-inputs (list gfortran))
16660 (home-page "https://github.com/brentonk/pbivnorm")
16661 (synopsis "Vectorized bivariate normal CDF")
16663 "This package provides a vectorized R function for calculating
16664 probabilities from a standard bivariate normal CDF.")
16665 (license license:gpl2+)))
16667 (define-public r-lavaan
16674 (uri (cran-uri "lavaan" version))
16677 "026k32paf51lpy6zxm9m81zg9szx14j37dxdip6nba334jw97h9c"))))
16678 (build-system r-build-system)
16680 (list r-mass r-mnormt r-numderiv r-pbivnorm))
16681 (home-page "https://lavaan.ugent.be")
16682 (synopsis "Latent variable analysis")
16684 "This package provides tools to fit a variety of latent variable models,
16685 including confirmatory factor analysis, structural equation modeling and
16686 latent growth curve models.")
16687 (license license:gpl2+)))
16689 (define-public r-nonnest2
16691 (name "r-nonnest2")
16696 (uri (cran-uri "nonnest2" version))
16699 "1ddaqwx8i3ygwvxf11mc8xhgk4nkvnail99nr5szq8i168752zq2"))))
16700 (build-system r-build-system)
16702 (list r-compquadform r-lavaan r-mvtnorm r-sandwich))
16705 (home-page "https://cran.r-project.org/web/packages/nonnest2/")
16706 (synopsis "Tests of non-nested models")
16708 "This package allows for testing of non-nested models. It includes tests
16709 of model distinguishability and of model fit that can be applied to both
16710 nested and non-nested models. The package also includes functionality to
16711 obtain confidence intervals associated with AIC and BIC.")
16712 ;; Either version of the GPL.
16713 (license (list license:gpl2 license:gpl3))))
16715 (define-public r-penalized
16717 (name "r-penalized")
16722 (uri (cran-uri "penalized" version))
16725 "08badmgygppbqzay20qijyww028yw6s8dyd8ijcp8g4r9rn8xqyq"))))
16726 (build-system r-build-system)
16728 (list r-rcpp r-rcpparmadillo r-survival))
16729 (home-page "https://cran.r-project.org/web/packages/penalized/")
16730 (synopsis "Penalized estimation in GLMs and in the Cox model")
16732 "This package provides tools for fitting possibly high dimensional
16733 penalized regression models. The penalty structure can be any combination of
16734 an L1 penalty (lasso and fused lasso), an L2 penalty (ridge) and a positivity
16735 constraint on the regression coefficients. The supported regression models
16736 are linear, logistic and Poisson regression and the Cox Proportional Hazards
16737 model. Cross-validation routines allow optimization of the tuning
16739 (license license:gpl2+)))
16741 (define-public r-zim
16748 (uri (cran-uri "ZIM" version))
16751 "0scyfjn4ilsvha3x41c3b8bcfi31hlhwm77wn2a8hj5dsvnnmzig"))))
16752 (properties `((upstream-name . "ZIM")))
16753 (build-system r-build-system)
16754 (propagated-inputs (list r-mass))
16755 (home-page "https://github.com/biostatstudio/ZIM")
16756 (synopsis "Zero-inflated models (ZIM) for count time series with excess zeros")
16758 "Analyze count time series with excess zeros. Two types of statistical
16759 models are supported: Markov regression and state-space models. They are also
16760 known as observation-driven and parameter-driven models respectively in the
16761 time series literature. The functions used for Markov regression or
16762 observation-driven models can also be used to fit ordinary regression models
16763 with independent data under the zero-inflated Poisson (ZIP) or zero-inflated
16764 negative binomial (ZINB) assumption. The package also contains miscellaneous
16765 functions to compute density, distribution, quantile, and generate random
16766 numbers from ZIP and ZINB distributions.")
16767 (license license:gpl3)))
16769 (define-public r-nor1mix
16776 (uri (cran-uri "nor1mix" version))
16779 "1817wcvlmxs70vs4db0jkxd7i037744zz8ay3c2a9949z29fxr4w"))))
16780 (build-system r-build-system)
16781 (home-page "https://cran.r-project.org/web/packages/nor1mix/")
16782 (synopsis "Normal (1-d) mixture models")
16784 "This package provides S3 classes and methods for one-dimensional normal
16785 mixture models, for, e.g., density estimation or clustering algorithms
16786 research and teaching; it provides the widely used Marron-Wand densities. It
16787 also provides tools for efficient random number generation and graphics.")
16788 (license license:gpl2+)))
16790 (define-public r-beanplot
16792 (name "r-beanplot")
16797 (uri (cran-uri "beanplot" version))
16800 "1b8mvlcsv5l9g08ag92hndsvk8jmgxvznhzgazc8y4296kp8l5a9"))))
16801 (build-system r-build-system)
16802 (home-page "https://cran.r-project.org/web/packages/beanplot/")
16803 (synopsis "Visualization via beanplots")
16805 "This package provides beanplots, an alternative to
16806 boxplot/stripchart/violin plots. It can be used to plot univariate comparison
16808 (license license:gpl2)))
16810 (define-public r-pbdzmq
16817 (uri (cran-uri "pbdZMQ" version))
16820 "020qy6fq8w8wq0j3bii14ahrlg8wzl0lrnndfr6scmrg9ghjnbfz"))))
16821 (properties `((upstream-name . "pbdZMQ")))
16822 (build-system r-build-system)
16824 (list zeromq zlib))
16827 (home-page "https://pbdr.org/")
16828 (synopsis "R interface to ZeroMQ")
16830 "ZeroMQ is a well-known library for high-performance asynchronous
16831 messaging in scalable, distributed applications. This package provides high
16832 level R wrapper functions to easily utilize ZeroMQ. The main focus is on
16833 interactive client/server programming frameworks. A few wrapper functions
16834 compatible with @code{rzmq} are also provided.")
16835 (license license:gpl3)))
16837 (define-public r-repr
16844 (uri (cran-uri "repr" version))
16847 "0h3h14ybamcbwmm31ib66fx13v75vkzn4bn2v26n2h097sl9qybg"))))
16848 (build-system r-build-system)
16850 (list r-base64enc r-htmltools r-jsonlite r-pillar))
16851 (home-page "https://cran.r-project.org/web/packages/repr/")
16852 (synopsis "Serializable representations")
16854 "This package provides string and binary representations of objects for
16855 several formats and MIME types.")
16856 (license license:gpl3)))
16858 (define-public r-irdisplay
16860 (name "r-irdisplay")
16865 (uri (cran-uri "IRdisplay" version))
16868 "0awdiv4rr93y8jb1d64sm1iy37ywyniqm7w98yv6qm0zz47h7sw3"))))
16869 (properties `((upstream-name . "IRdisplay")))
16870 (build-system r-build-system)
16873 (home-page "https://cran.r-project.org/web/packages/IRdisplay/")
16874 (synopsis "Jupyter display machinery")
16876 "This package provides an interface to the rich display capabilities of
16877 Jupyter front-ends (e.g. Jupyter Notebook). It is designed to be used from a
16878 running IRkernel session.")
16879 (license license:expat)))
16881 (define-public r-irkernel
16883 (name "r-irkernel")
16888 (uri (cran-uri "IRkernel" version))
16891 "00qrmsywpzw2hfp88020zjaijma7q4hqm9h2cz53rywdjzywnzss"))))
16892 (properties `((upstream-name . "IRkernel")))
16893 (build-system r-build-system)
16896 (modify-phases %standard-phases
16897 (add-after 'install 'install-kernelspec
16898 (lambda* (#:key outputs #:allow-other-keys)
16899 (let ((out (assoc-ref outputs "out")))
16900 (setenv "HOME" "/tmp")
16901 (invoke "jupyter" "kernelspec" "install"
16904 (string-append out "/site-library/IRkernel/kernelspec"))
16905 ;; Record the absolute file name of the 'R' executable in
16907 (substitute* (string-append out "/share/jupyter"
16908 "/kernels/ir/kernel.json")
16910 (string-append "[\"" (which "R") "\",")))
16920 ;; sets R_LIBS_SITE, so R can actually find this package (IRkernel)
16925 (home-page "https://cran.r-project.org/web/packages/IRkernel/")
16926 (synopsis "Native R kernel for Jupyter")
16928 "The R kernel for the Jupyter environment executes R code which the
16929 front-end (Jupyter Notebook or other front-ends) submits to the kernel via the
16931 (license license:expat)))
16933 (define-public r-gmodels
16936 (version "2.18.1.1")
16940 (uri (cran-uri "gmodels" version))
16943 "158y7yh4maawn9vki8cq4sil48xib2bbpl6qgj5gvlkw3c14hzfs"))))
16944 (build-system r-build-system)
16946 (list r-gdata r-mass))
16947 (home-page "https://cran.r-project.org/web/packages/gmodels/")
16948 (synopsis "Various R programming tools for model fitting")
16950 "This package provides various R programming tools for model fitting.")
16951 (license license:gpl2)))
16953 (define-public r-apcluster
16955 (name "r-apcluster")
16960 (uri (cran-uri "apcluster" version))
16963 "0wnbb3kj9m7rfq63xr43jjf6n8jxm1r2wvvx6g0qkss0wvipbb1s"))))
16964 (build-system r-build-system)
16966 (list r-matrix r-rcpp))
16967 (native-inputs (list r-knitr))
16968 (home-page "https://cran.r-project.org/web/packages/apcluster/")
16969 (synopsis "Affinity propagation clustering")
16971 "This package implements affinity propagation clustering introduced by
16972 Frey and Dueck (2007). The package further provides leveraged affinity
16973 propagation and an algorithm for exemplar-based agglomerative clustering that
16974 can also be used to join clusters obtained from affinity propagation. Various
16975 plotting functions are available for analyzing clustering results.")
16976 (license license:gpl2+)))
16978 (define-public r-rematch2
16980 (name "r-rematch2")
16985 (uri (cran-uri "rematch2" version))
16988 "1fzpz8vhghw8ygwg6rsvfy3783pqk7ch029i5851lwypkplvz77y"))))
16989 (build-system r-build-system)
16992 (home-page "https://github.com/r-lib/rematch2")
16993 (synopsis "Tidy output from regular expression matching")
16995 "This package provides wrappers on @code{regexpr} and @code{gregexpr} to
16996 return the match results in tidy data frames.")
16997 (license license:expat)))
16999 (define-public r-picante
17006 (uri (cran-uri "picante" version))
17009 "19savjzj44b7ifdxcp02ynj22z4n4ikq2aipc74ljzy3yykmqmjn"))))
17010 (build-system r-build-system)
17012 (list r-ape r-nlme r-vegan))
17013 (home-page "https://cran.r-project.org/web/packages/picante/")
17014 (synopsis "Integrating phylogenies and ecology")
17016 "This package provides functions for phylocom integration, community
17017 analyses, null-models, traits and evolution. It implements numerous
17018 ecophylogenetic approaches including measures of community phylogenetic and
17019 trait diversity, phylogenetic signal, estimation of trait values for
17020 unobserved taxa, null models for community and phylogeny randomizations, and
17021 utility functions for data input/output and phylogeny plotting. A full
17022 description of package functionality and methods are provided by Kembel et
17024 (license license:gpl2)))
17026 (define-public r-reinforcelearn
17028 (name "r-reinforcelearn")
17033 (uri (cran-uri "reinforcelearn" version))
17036 "176z2q69p24i29a8sh19xxn2zl3h1z2ixdssr5i6m4yvkvdrvv3b"))))
17037 (build-system r-build-system)
17039 (list r-checkmate r-nnet r-purrr r-r6))
17040 (home-page "https://markusdumke.github.io/reinforcelearn")
17041 (synopsis "Reinforcement learning")
17043 "This package implements reinforcement learning environments and
17044 algorithms as described in Sutton & Barto (1998). The Q-Learning algorithm
17045 can be used with function approximation, eligibility traces (Singh & Sutton,
17046 1996) and experience replay (Mnih et al., 2013).")
17047 (license license:expat)))
17049 (define-public r-lemon
17056 (uri (cran-uri "lemon" version))
17059 "1y3ljidhqdakxlya2npj2w0az820g8kw6gl1cfm4f0cxvzgd1ly4"))))
17060 (build-system r-build-system)
17072 (home-page "https://github.com/stefanedwards/lemon")
17073 (synopsis "Freshen up your ggplot2 plots")
17075 "This package provides functions for working with legends and axis lines
17076 of ggplot2, facets that repeat axis lines on all panels, and some knitr
17078 (license license:gpl3)))
17080 (define-public r-wgaim
17087 (uri (cran-uri "wgaim" version))
17089 (base32 "1qiyfkpsbzjr9xsq5kqq6rlqpndngkn2irdfh3gyi45h6hn118j4"))))
17090 (build-system r-build-system)
17092 (list r-ggplot2 r-qtl))
17093 (home-page "https://cran.r-project.org/web/packages/wgaim")
17094 (synopsis "Whole genome average interval mapping for QTL detection")
17096 "This package integrates sophisticated mixed modelling methods with a
17097 whole genome approach to detecting significant QTL in linkage maps.")
17098 (license license:gpl2+)))
17100 (define-public r-bedr
17107 (uri (cran-uri "bedr" version))
17110 "0zpqvyjgwyqawxm8qrhcv8zq2b3yxgcqkkc87br29yrl7sjb8h6j"))))
17111 (build-system r-build-system)
17120 htslib)) ; for tabix
17122 (list r-knitr)) ; for vignettes
17123 (home-page "https://cran.r-project.org/web/packages/bedr")
17124 (synopsis "Genomic region processing")
17126 "This package is for genomic regions processing using command line tools
17127 such as BEDTools, BEDOPS and Tabix. These tools offer scalable and efficient
17128 utilities to perform genome arithmetic e.g indexing, formatting and merging.
17129 The bedr package's API enhances access to these tools as well as offers
17130 additional utilities for genomic regions processing.")
17131 (license license:gpl2)))
17133 (define-public r-sets
17140 (uri (cran-uri "sets" version))
17143 "1h1a03b1850kh5hd3gxbspx2nxqxvk2gb0wm0s60b70qb6zg0csp"))))
17144 (properties `((upstream-name . "sets")))
17145 (build-system r-build-system)
17146 (home-page "https://cran.r-project.org/web/packages/sets")
17147 (synopsis "Sets, generalized sets, customizable sets and intervals")
17149 "This package provides data structures and basic operations for ordinary
17150 sets, generalizations such as fuzzy sets, multisets, and fuzzy multisets,
17151 customizable sets, and intervals.")
17152 (license license:gpl2)))
17154 (define-public r-partitions
17156 (name "r-partitions")
17161 (uri (cran-uri "partitions" version))
17164 "1qqy4df28wy4q0g572azrj171jlhvrnzbh7x0wr2g7v6gr20y0ns"))))
17165 (build-system r-build-system)
17167 (list r-gmp r-polynom r-sets))
17168 (home-page "https://cran.r-project.org/web/packages/partitions")
17169 (synopsis "Additive partitions of integers")
17171 "This package provides tools to enumerates the partitions, unequal
17172 partitions, and restricted partitions of an integer; the three corresponding
17173 partition functions are also given.")
17174 ;; Any version of the GPL
17175 (license license:gpl2+)))
17177 (define-public r-brobdingnag
17179 (name "r-brobdingnag")
17184 (uri (cran-uri "Brobdingnag" version))
17187 "0hnp5nrpnscykvgrrbgp7987660hcbv92zc2q8lmpnin4ws399vk"))))
17188 (properties `((upstream-name . "Brobdingnag")))
17189 (build-system r-build-system)
17190 (home-page "https://github.com/RobinHankin/Brobdingnag.git")
17191 (synopsis "Very large numbers in R")
17193 "This package handles very large numbers in R. Real numbers are held
17194 using their natural logarithms, plus a logical flag indicating sign. The
17195 package includes a vignette that gives a step-by-step introduction to using S4
17197 ;; Any version of the GPL
17198 (license license:gpl2+)))
17200 (define-public r-untb
17207 (uri (cran-uri "untb" version))
17210 "1i7m4vfslsix98dwx4jlrsldm7fhhfp25gr7aapcxqxms7ryaby6"))))
17211 (build-system r-build-system)
17213 (list r-brobdingnag r-partitions r-polynom))
17214 (home-page "https://github.com/RobinHankin/untb.git")
17215 (synopsis "Ecological drift under the UNTB")
17217 "This package provides numerical simulations, and visualizations, of
17218 Hubbell's @dfn{Unified Neutral Theory of Biodiversity} (UNTB).")
17219 (license license:gpl2+)))
17221 (define-public r-stepwise
17223 (name "r-stepwise")
17228 (uri (cran-uri "stepwise" version))
17231 "1lbx1bxwkf9dw6q46w40pp7h5nkxgghmx8rkpaymm6iybc7gyir2"))))
17232 (build-system r-build-system)
17233 (home-page "https://stat.sfu.ca/statgen/research/stepwise.html")
17234 (synopsis "Stepwise detection of recombination breakpoints")
17236 "This package provides a stepwise approach to identifying recombination
17237 breakpoints in a genomic sequence alignment.")
17238 (license license:gpl2+)))
17240 (define-public r-snpmaxsel
17242 (name "r-snpmaxsel")
17247 (uri (cran-uri "SNPmaxsel" version))
17250 "0pjvixwqzjd3jwccc8yqq9c76afvbmfq0z1w0cwyj8bblrjpx13z"))))
17251 (properties `((upstream-name . "SNPmaxsel")))
17252 (build-system r-build-system)
17254 (list r-combinat r-mvtnorm))
17255 (home-page "https://cran.r-project.org/web/packages/SNPmaxsel/index.html")
17256 (synopsis "Maximally selected statistics for SNP data")
17258 "This package implements asymptotic methods related to maximally selected
17259 statistics, with applications to @dfn{single-nucleotide polymorphism} (SNP)
17261 (license license:gpl2+)))
17263 (define-public r-acsnminer
17265 (name "r-acsnminer")
17266 (version "0.16.8.25")
17269 (uri (cran-uri "ACSNMineR" version))
17272 "0gh604s8qall6zfjlwcg2ilxjvz08dplf9k5g47idhv43scm748l"))))
17273 (properties `((upstream-name . "ACSNMineR")))
17274 (build-system r-build-system)
17276 (list r-ggplot2 r-gridextra))
17277 (home-page "https://cran.r-project.org/web/packages/ACSNMineR")
17278 (synopsis "Gene enrichment analysis")
17280 "This package provides tools to compute and represent gene set enrichment
17281 or depletion from your data based on pre-saved maps from the @dfn{Atlas of
17282 Cancer Signalling Networks} (ACSN) or user imported maps. The gene set
17283 enrichment can be run with hypergeometric test or Fisher exact test, and can
17284 use multiple corrections. Visualization of data can be done either by
17285 barplots or heatmaps.")
17286 (license license:gpl2+)))
17288 (define-public r-seqinr
17295 (uri (cran-uri "seqinr" version))
17298 "0cj07b7km5mla63qhbkxg1mnqq6vh79lsyyfpnbm29gw68w2bwy4"))))
17299 (build-system r-build-system)
17301 (list r-ade4 r-segmented))
17304 (home-page "http://seqinr.r-forge.r-project.org/")
17305 (synopsis "Biological sequences retrieval and analysis")
17307 "This package provides tools for exploratory data analysis and data
17308 visualization of biological sequence (DNA and protein) data. It also includes
17309 utilities for sequence data management under the ACNUC system.")
17310 (license license:gpl2+)))
17312 (define-public r-units
17319 (uri (cran-uri "units" version))
17322 "06mjprqi06xprj6185k5cmrrdl025x0pd1r6a4x3s74ciq9zwilw"))))
17323 (build-system r-build-system)
17330 (home-page "https://github.com/r-quantities/units/")
17331 (synopsis "Measurement Units for R Vectors")
17333 "This package provides support for measurement units in R vectors,
17334 matrices and arrays: automatic propagation, conversion, derivation and
17335 simplification of units; raising errors in case of unit incompatibility. It
17336 is compatible with the @code{POSIXct}, @code{Date} and @code{difftime}
17338 (license license:gpl2)))
17340 (define-public r-udunits2
17342 (name "r-udunits2")
17343 (version "0.13.2.1")
17347 (uri (cran-uri "udunits2" version))
17350 "00prsy8m41v1camcsz94d7gm8qab2mdnwl3x0dyhz4r49b02jm4z"))))
17351 (properties `((upstream-name . "udunits2")))
17352 (build-system r-build-system)
17355 (home-page "https://cran.r-project.org/package=udunits2")
17356 (synopsis "Udunits-2 bindings for R")
17358 "This package provides simple bindings to Unidata's udunits library.")
17359 (license license:gpl2)))
17361 (define-public r-classint
17363 (name "r-classint")
17368 (uri (cran-uri "classInt" version))
17371 "1b1lqhpzxm6b8pza8l3s0cxy74mm9y45lcd3354i2v3bg8m7mply"))))
17372 (properties `((upstream-name . "classInt")))
17373 (build-system r-build-system)
17375 (list r-class r-e1071 r-kernsmooth))
17377 (list gfortran r-knitr))
17378 (home-page "https://github.com/r-spatial/classInt/")
17379 (synopsis "Choose univariate class intervals")
17381 "This package provides selected commonly used methods for choosing
17382 univariate class intervals for mapping or other graphics purposes.")
17383 (license license:gpl2+)))
17385 (define-public r-spdata
17392 (uri (cran-uri "spData" version))
17395 "1z4hp5ivwzyvl8mkp98j2ng1cl1xksqbjxv85vdlqfqjwpia6df6"))))
17396 (properties `((upstream-name . "spData")))
17397 (build-system r-build-system)
17399 (list r-raster r-sp))
17400 (home-page "https://github.com/Nowosad/spData")
17401 (synopsis "Datasets for spatial analysis")
17403 "This a package containing diverse spatial datasets for demonstrating,
17404 benchmarking and teaching spatial data analysis. It includes R data of class
17405 @code{sf}, @code{Spatial}, and @code{nb}. It also contains data stored in a
17406 range of file formats including GeoJSON, ESRI Shapefile and GeoPackage. Some
17407 of the datasets are designed to illustrate specific analysis techniques.
17408 @code{cycle_hire()} and @code{cycle_hire_osm()}, for example, are designed to
17409 illustrate point pattern analysis techniques.")
17410 (license license:cc0)))
17412 (define-public r-learnbayes
17414 (name "r-learnbayes")
17419 (uri (cran-uri "LearnBayes" version))
17422 "0ch54v2zz2yyyk0lvn5rfikdmyz1qh9j1wk3585wl8v58mc0h4cv"))))
17423 (properties `((upstream-name . "LearnBayes")))
17424 (build-system r-build-system)
17425 (home-page "https://cran.r-project.org/web/packages/LearnBayes")
17426 (synopsis "Functions for learning Bayesian inference")
17428 "This package provides a collection of functions helpful in learning the
17429 basic tenets of Bayesian statistical inference. It contains functions for
17430 summarizing basic one and two parameter posterior distributions and predictive
17431 distributions. It contains MCMC algorithms for summarizing posterior
17432 distributions defined by the user. It also contains functions for regression
17433 models, hierarchical models, Bayesian tests, and illustrations of Gibbs
17435 (license license:gpl2+)))
17437 (define-public r-deldir
17444 (uri (cran-uri "deldir" version))
17447 "1igq0l2knsbhizncgydcsidgkvvlwwlkrifbcdyhnzk0bhrdixkd"))))
17448 (build-system r-build-system)
17449 (native-inputs (list gfortran))
17450 (home-page "https://cran.r-project.org/web/packages/deldir")
17451 (synopsis "Delaunay triangulation and Dirichlet (Voronoi) tessellation")
17453 "This package provides tools for calculating the Delaunay triangulation
17454 and the Dirichlet or Voronoi tessellation (with respect to the entire plane)
17455 of a planar point set. It plots triangulations and tessellations in various
17456 ways, clips tessellations to sub-windows, calculates perimeters of
17457 tessellations, and summarizes information about the tiles of the
17459 (license license:gpl2+)))
17461 (define-public r-wk
17468 (uri (cran-uri "wk" version))
17471 "1xga4rrqsr190g55by39az4nimnn06bf5b6mcjgwqvba0lvjhb5g"))))
17472 (properties `((upstream-name . "wk")))
17473 (build-system r-build-system)
17474 (home-page "https://paleolimbot.github.io/wk/")
17475 (synopsis "Lightweight well-known geometry parsing")
17477 "This package provides a minimal R and C++ API for parsing well-known
17478 binary and well-known text representation of geometries to and from R-native
17479 formats. Well-known binary is compact and fast to parse; well-known text is
17480 human-readable and is useful for writing tests. These formats are only useful
17481 in R if the information they contain can be accessed in R, for which
17482 high-performance functions are provided here.")
17483 (license license:expat)))
17485 (define-public r-s2
17492 (uri (cran-uri "s2" version))
17495 "0gwydn6wdl675ydkcckrci6ylcx30qn8nfhmrp4qx4r9mv3c2410"))))
17496 (properties `((upstream-name . "s2")))
17497 (build-system r-build-system)
17499 (list r-rcpp r-wk))
17504 (home-page "https://r-spatial.github.io/s2/")
17505 (synopsis "Spherical geometry operators using the S2 geometry library")
17507 "This package provides R bindings for Google's s2 library for geometric
17508 calculations on the sphere. High-performance constructors and exporters
17509 provide high compatibility with existing spatial packages, transformers
17510 construct new geometries from existing geometries, predicates provide a means
17511 to select geometries based on spatial relationships, and accessors extract
17512 information about geometries.")
17513 (license license:asl2.0)))
17515 (define-public r-sf
17522 (uri (cran-uri "sf" version))
17525 "0lsl4rh4lbv386hxlsnnwsjb5x1n9d3z0ckjmxakmmrqjjmiywyh"))))
17526 (build-system r-build-system)
17528 (list gdal geos proj sqlite zlib))
17537 (list pkg-config r-knitr))
17538 (home-page "https://github.com/r-spatial/sf/")
17539 (synopsis "Simple features for R")
17541 "This package provides support for simple features, a standardized way to
17542 encode spatial vector data. It binds to GDAL for reading and writing data, to
17543 GEOS for geometrical operations, and to PROJ for projection conversions and
17544 datum transformations.")
17545 ;; Either of these licenses
17546 (license (list license:gpl2 license:expat))))
17548 (define-public r-spdep
17554 (uri (cran-uri "spdep" version))
17557 "0xx6k3rsvsz1hwj0ny8aqfi9ca54x38f8pz8sfya5cggaspxbx59"))
17559 '(for-each delete-file '("inst/doc/CO69.html"
17563 "inst/doc/nb_sf.html"
17565 "inst/doc/nb_sf.Rmd"
17566 "inst/doc/sids.html"
17567 "inst/doc/sids.R")))))
17568 (build-system r-build-system)
17580 (home-page "https://github.com/r-spatial/spdep/")
17581 (synopsis "Spatial dependence: weighting schemes, statistics and models")
17583 "This package provides a collection of functions to create spatial
17584 weights matrix objects from polygon contiguities, from point patterns by
17585 distance and tessellations, for summarizing these objects, and for permitting
17586 their use in spatial data analysis, including regional aggregation by minimum
17588 (license license:gpl2+)))
17590 (define-public r-adegenet
17592 (name "r-adegenet")
17597 (uri (cran-uri "adegenet" version))
17600 "0sx25p7bgz0h9mc3jsdnnjhvmb7sy8nb3r0z923vhk336d4xw8vq"))))
17601 (build-system r-build-system)
17614 (home-page "https://github.com/thibautjombart/adegenet")
17615 (synopsis "Exploratory analysis of genetic and genomic data")
17617 "This package provides a toolset for the exploration of genetic and
17618 genomic data. Adegenet provides formal (S4) classes for storing and handling
17619 various genetic data, including genetic markers with varying ploidy and
17620 hierarchical population structure (@code{genind} class), alleles counts by
17621 populations (@code{genpop}), and genome-wide SNP data (@code{genlight}). It
17622 also implements original multivariate methods (DAPC, sPCA), graphics,
17623 statistical tests, simulation tools, distance and similarity measures, and
17624 several spatial methods. A range of both empirical and simulated datasets is
17625 also provided to illustrate various methods.")
17626 (license license:gpl2+)))
17628 (define-public r-pegas
17635 (uri (cran-uri "pegas" version))
17637 (base32 "0ngd0laqbs139ji9hm9kwsm9rm56agw2yyfcplxgqva936l93fl7"))))
17638 (build-system r-build-system)
17641 (home-page "http://ape-package.ird.fr/pegas.html")
17642 (synopsis "Population and evolutionary genetics analysis system")
17644 "This package provides functions for reading, writing, plotting,
17645 analysing, and manipulating allelic and haplotypic data, including from VCF
17646 files, and for the analysis of population nucleotide sequences and
17647 micro-satellites including coalescent analyses, linkage disequilibrium,
17648 population structure (Fst, Amova) and equilibrium (HWE), haplotype networks,
17649 minimum spanning tree and network, and median-joining networks.")
17650 (license license:gpl2+)))
17652 (define-public r-rmetasim
17654 (name "r-rmetasim")
17659 (uri (cran-uri "rmetasim" version))
17662 "0rdkhfgyr97r2d1kd9g8ipb2pn563qxm1y4m9z678q0kqan2ddl0"))))
17663 (build-system r-build-system)
17665 (list r-ade4 r-adegenet r-gtools r-pegas))
17666 (home-page "https://cran.r-project.org/web/packages/rmetasim")
17667 (synopsis "Individual-based population genetic simulation environment")
17669 "This package provides an interface between R and the metasim simulation
17670 engine. The simulation environment is documented in: Strand, A.(2002),
17671 Metasim 1.0: an individual-based environment for simulating population
17672 genetics of complex population dynamics.")
17674 (license license:gpl2+)))
17676 (define-public r-genetics
17678 (name "r-genetics")
17679 (version "1.3.8.1.3")
17683 (uri (cran-uri "genetics" version))
17686 "0lljxvz7nc6y2z303icphar2niir0i407w5cyhy2pwspd9gwkwpy"))))
17687 (build-system r-build-system)
17689 (list r-combinat r-gdata r-gtools r-mass r-mvtnorm))
17690 (home-page "https://cran.r-project.org/web/packages/genetics/")
17691 (synopsis "Population genetics")
17693 "This package provides classes and methods for handling genetic data.
17694 It includes classes to represent genotypes and haplotypes at single markers up
17695 to multiple markers on multiple chromosomes. Function include allele
17696 frequencies, flagging homo/heterozygotes, flagging carriers of certain
17697 alleles, estimating and testing for Hardy-Weinberg disequilibrium, estimating
17698 and testing for linkage disequilibrium, ...")
17699 ;; Any GPL version.
17700 (license license:gpl2+)))
17702 (define-public r-snp-plotter
17704 (name "r-snp-plotter")
17709 (uri (cran-uri "snp.plotter" version))
17712 "16apsqvkah5l0d5qcwp3lq2jspkb6n62wzr0wskmj84jblx483vv"))))
17713 (properties `((upstream-name . "snp.plotter")))
17714 (build-system r-build-system)
17715 (propagated-inputs (list r-genetics))
17716 (home-page "https://cran.r-project.org/web/packages/snp.plotter/")
17717 (synopsis "Plot p-values using single SNP and/or haplotype data")
17719 "This package helps you create plots of p-values using single SNP and/or
17720 haplotype data. Main features of the package include options to display a
17721 @dfn{linkage disequilibrium} (LD) plot and the ability to plot multiple
17722 datasets simultaneously. Plots can be created using global and/or individual
17723 haplotype p-values along with single SNP p-values. Images are created as
17724 either PDF/EPS files.")
17725 (license license:gpl2+)))
17727 (define-public r-polspline
17729 (name "r-polspline")
17734 (uri (cran-uri "polspline" version))
17736 (base32 "1dd1jwiaglkkhajzvqfkd1x5r3wzjlk5ww0yxzmns0s1kr74i4k9"))))
17737 (build-system r-build-system)
17738 (native-inputs (list gfortran))
17739 (home-page "https://cran.r-project.org/web/packages/polspline/")
17740 (synopsis "Polynomial spline routines")
17742 "This package provides routines for the polynomial spline fitting
17743 routines hazard regression, hazard estimation with flexible tails, logspline,
17744 lspec, polyclass, and polymars.")
17745 (license license:gpl2+)))
17747 (define-public r-rms
17754 (uri (cran-uri "rms" version))
17756 (base32 "1yfk800q4mgmrjkh0hqjkiv907sr1bi1jaigrj8l6pmg1mkynhbc"))))
17757 (build-system r-build-system)
17774 (native-inputs (list gfortran))
17775 (home-page "http://biostat.mc.vanderbilt.edu/rms")
17776 (synopsis "Regression modeling strategies")
17778 "This is a package for regression modeling, testing, estimation,
17779 validation, graphics, prediction, and typesetting by storing enhanced model
17780 design attributes in the fit. The rms package is a collection of functions
17781 that assist with and streamline modeling. It also contains functions for
17782 binary and ordinal logistic regression models, ordinal models for continuous Y
17783 with a variety of distribution families, and the Buckley-James multiple
17784 regression model for right-censored responses, and implements penalized
17785 maximum likelihood estimation for logistic and ordinary linear models. The
17786 package works with almost any regression model, but it was especially written
17787 to work with binary or ordinal regression models, Cox regression, accelerated
17788 failure time models, ordinary linear models, the Buckley-James model,
17789 generalized least squares for serially or spatially correlated observations,
17790 generalized linear models, and quantile regression.")
17791 (license license:gpl2+)))
17793 (define-public r-arsenal
17800 (uri (cran-uri "arsenal" version))
17803 "0qvs3ld28djnjnggdhqjwq8sbv8zz322qahlvf7dnx35yqf6xkms"))))
17804 (properties `((upstream-name . "arsenal")))
17805 (build-system r-build-system)
17806 (propagated-inputs (list r-knitr))
17807 (native-inputs (list r-knitr))
17808 (home-page "https://github.com/mayoverse/arsenal")
17809 (synopsis "Functions for large-scale statistical summaries")
17811 "This package provides an arsenal of R functions for large-scale
17812 statistical summaries, which are streamlined to work within the latest
17813 reporting tools in R and RStudio and which use formulas and versatile
17814 summary statistics for summary tables and models. The primary functions
17818 @item @code{tableby}, a Table-1-like summary of multiple variable types by the
17819 levels of one or more categorical variables;
17820 @item @code{paired}, a Table-1-like summary of multiple variable types paired
17821 across two time points;
17822 @item @code{modelsum}, which performs simple model fits on one or more
17823 endpoints for many variables (univariate or adjusted for covariates);
17824 @item @code{freqlist}, a powerful frequency table across many categorical
17826 @item @code{comparedf}, a function for comparing @code{data.frames}; and
17827 @item @code{write2}, a function to output tables to a document.
17830 (license license:gpl2+)))
17832 (define-public r-haplo-stats
17834 (name "r-haplo-stats")
17839 (uri (cran-uri "haplo.stats" version))
17842 "1q2zn72j92bwhcdswk4qqfgzch56p9pcy2xhkd3safvqp3l9rzpw"))))
17843 (properties `((upstream-name . "haplo.stats")))
17844 (build-system r-build-system)
17846 (list r-arsenal r-rms))
17848 (list r-r-rsp)) ; for vignettes
17849 (home-page "https://www.mayo.edu/research/labs/statistical-genetics-genetic-epidemiology/software")
17850 (synopsis "Analysis of haplotypes when linkage phase is ambiguous")
17852 "This package provides routines for the analysis of indirectly measured
17853 haplotypes. The statistical methods assume that all subjects are unrelated
17854 and that haplotypes are ambiguous (due to unknown linkage phase of the genetic
17855 markers). The main functions are: @code{haplo.em()}, @code{haplo.glm()},
17856 @code{haplo.score()}, and @code{haplo.power()}; all of which have detailed
17857 examples in the vignette.")
17858 (license license:gpl2+)))
17860 (define-public r-bqtl
17867 (uri (cran-uri "bqtl" version))
17870 "1sbzpi9z94f010lw2y1gmifjrvpmiqs4m26za7vr1xz72azrqvs9"))))
17871 (build-system r-build-system)
17872 (native-inputs (list gfortran))
17873 (home-page "http://famprevmed.ucsd.edu/faculty/cberry/bqtl/")
17874 (synopsis "Bayesian QTL mapping toolkit")
17876 "This is a QTL mapping toolkit for inbred crosses and recombinant inbred
17877 lines. It includes maximum likelihood and Bayesian tools.")
17878 (license license:gpl2+)))
17880 (define-public r-ibdreg
17887 (uri (cran-uri "ibdreg" version))
17890 "1x8z0vr2cmdks12hxfm0wwxskb0cr669w5j5rpa2ln8q704yy41g"))))
17891 (build-system r-build-system)
17892 (home-page "https://www.mayo.edu/research/labs/\
17893 statistical-genetics-genetic-epidemiology/software")
17894 (synopsis "Regression methods for IBD linkage with covariates")
17896 "This package provides a method to test genetic linkage with covariates
17897 by regression methods with response IBD sharing for relative pairs. Account
17898 for correlations of IBD statistics and covariates for relative pairs within
17899 the same pedigree.")
17900 (license license:gpl2+)))
17902 (define-public r-dlmap
17909 (uri (cran-uri "dlmap" version))
17912 "0s6wlkggkm3qndwyvw72xv1n0mcjb7ss3ajbq2ll6rv30splq0db"))))
17913 (build-system r-build-system)
17915 (list r-ibdreg r-mgcv r-nlme r-qtl r-wgaim))
17916 (home-page "https://cran.r-project.org/web/packages/dlmap/")
17917 (synopsis "Detection localization mapping for QTL")
17919 "This is package for QTL mapping in a mixed model framework with separate
17920 detection and localization stages. The first stage detects the number of QTL
17921 on each chromosome based on the genetic variation due to grouped markers on
17922 the chromosome; the second stage uses this information to determine the most
17923 likely QTL positions. The mixed model can accommodate general fixed and
17924 random effects, including spatial effects in field trials and pedigree
17925 effects. It is applicable to backcrosses, doubled haploids, recombinant
17926 inbred lines, F2 intercrosses, and association mapping populations.")
17927 (license license:gpl2)))
17929 (define-public r-hwde
17936 (uri (cran-uri "hwde" version))
17939 "0wb2f9i5qi7w77ygh8bvydfpr7j5x8dyvnnhdkajaz0wdcpkyaqy"))))
17940 (build-system r-build-system)
17941 (home-page "https://cran.r-project.org/web/packages/hwde/")
17942 (synopsis "Models and tests for departure from Hardy-Weinberg equilibrium")
17944 "This package fits models for genotypic disequilibria, as described in
17945 Huttley and Wilson (2000), Weir (1996) and Weir and Wilson (1986). Contrast
17946 terms are available that account for first order interactions between loci.
17947 It also implements, for a single locus in a single population, a conditional
17948 exact test for Hardy-Weinberg equilibrium.")
17949 (license license:gpl2+)))
17951 (define-public r-tdthap
17958 (uri (cran-uri "tdthap" version))
17961 "15qlj2bivvz3pizd8dq34wczbkbxhzqh3cqp1ixkdkprlyvcxj5k"))))
17962 (build-system r-build-system)
17963 (home-page "https://cran.r-project.org/web/packages/tdthap/")
17964 (synopsis "TDT tests for extended haplotypes")
17966 "Functions and examples are provided for transmission/disequilibrium
17967 tests for extended marker haplotypes, as in Clayton, D. and Jones, H. (1999)
17968 \"Transmission/disequilibrium tests for extended marker haplotypes\".")
17969 (license license:artistic2.0)))
17971 (define-public r-sparql
17977 (uri (cran-uri "SPARQL" version))
17980 "0gak1q06yyhdmcxb2n3v0h9gr1vqd0viqji52wpw211qp6r6dcrc"))))
17981 (properties `((upstream-name . "SPARQL")))
17982 (build-system r-build-system)
17984 (list r-rcurl r-xml))
17985 (home-page "https://cran.r-project.org/web/packages/SPARQL")
17986 (synopsis "SPARQL client for R")
17987 (description "This package provides an interface to use SPARQL to pose
17988 SELECT or UPDATE queries to an end-point.")
17989 ;; The only license indication is found in the DESCRIPTION file,
17990 ;; which states GPL-3. So we cannot assume GPLv3+.
17991 (license license:gpl3)))
17993 (define-public r-bookdown
17995 (name "r-bookdown")
17999 (uri (cran-uri "bookdown" version))
18002 "11din9h2sgzvg44627xc5is4psbq2b34km5sbiaprskjrf474866"))))
18003 (build-system r-build-system)
18013 ;; We cannot add knitr because this package depends on xfun, which is an
18018 (home-page "https://github.com/rstudio/bookdown")
18019 (synopsis "Authoring books and technical documents with R markdown")
18020 (description "This package provides output formats and utilities for
18021 authoring books and technical documents with R Markdown.")
18022 (license license:gpl3)))
18024 (define-public r-optparse
18026 (name "r-optparse")
18031 (uri (cran-uri "optparse" version))
18034 "1rqz0y4r94y3mwbb9kyz97cjqpnprka96qbncvbnbmgg2d630kij"))))
18035 (build-system r-build-system)
18040 (home-page "https://github.com/trevorld/optparse")
18041 (synopsis "Command line option parser")
18043 "This package provides a command line parser inspired by Python's
18044 @code{optparse} library to be used with Rscript to write shebang scripts
18045 that accept short and long options.")
18046 (license license:gpl2+)))
18048 (define-public r-kernlab
18055 (uri (cran-uri "kernlab" version))
18057 (base32 "10gfb542nbl1d5pfy6r7gcg3j1ikra9l18r6xjv8lzp5ka1kmz28"))))
18058 (build-system r-build-system)
18059 (home-page "https://cran.r-project.org/web/packages/kernlab")
18060 (synopsis "Kernel-based machine learning tools")
18062 "This package provides kernel-based machine learning methods for
18063 classification, regression, clustering, novelty detection, quantile regression
18064 and dimensionality reduction. Among other methods @code{kernlab} includes
18065 Support Vector Machines, Spectral Clustering, Kernel PCA, Gaussian Processes
18067 (license license:gpl2)))
18069 (define-public r-hierfstat
18071 (name "r-hierfstat")
18076 (uri (cran-uri "hierfstat" version))
18079 "0nyb5091lr8ma9vydbssyx9503601rynlrbldv98mmrmh74h6v41"))))
18080 (build-system r-build-system)
18082 (list r-ade4 r-adegenet r-gaston r-gtools))
18085 (home-page "https://cran.r-project.org/web/packages/hierfstat/")
18086 (synopsis "Estimation and tests of hierarchical F-statistics")
18088 "This package allows the estimation of hierarchical F-statistics from
18089 haploid or diploid genetic data with any numbers of levels in the hierarchy,
18090 following the algorithm of Yang (Evolution, 1998, 52(4):950-956). Functions
18091 are also given to test via randomisations the significance of each F and
18092 variance components, using the likelihood-ratio statistics G.")
18093 (license license:gpl2+)))
18095 (define-public r-hapassoc
18097 (name "r-hapassoc")
18102 (uri (cran-uri "hapassoc" version))
18105 "09ijc4sbw743z74fzklmvig11ndkycg6j86k4214wfsj1yj6j9x6"))))
18106 (build-system r-build-system)
18107 (home-page "https://stat.sfu.ca/statgen/research/hapassoc.html")
18108 (synopsis "Inference of trait associations with SNP haplotypes")
18110 "Hapassoc performs likelihood inference of trait associations with
18111 haplotypes and other covariates in @dfn{generalized linear models} (GLMs). The
18112 functions are developed primarily for data collected in cohort or
18113 cross-sectional studies. They can accommodate uncertain haplotype phase and
18114 handle missing genotypes at some SNPs.")
18115 (license license:gpl2)))
18117 (define-public r-sampling
18119 (name "r-sampling")
18124 (uri (cran-uri "sampling" version))
18127 "11xis4vzn2ga8ml9xrgfgqzccvwbnabq35aidzdvpnvciybsanvz"))))
18128 (build-system r-build-system)
18130 (list r-lpsolve r-mass))
18131 (home-page "https://cran.r-project.org/web/packages/sampling/")
18132 (synopsis "Survey sampling")
18134 "This package provides functions for drawing and calibrating samples.")
18135 (license license:gpl2+)))
18137 (define-public r-r2html
18144 (uri (cran-uri "R2HTML" version))
18147 "12qg9rp1j26h2f48dfg5k9jds26ycacv3f3ymk686ks43hd1hzja"))))
18148 (properties `((upstream-name . "R2HTML")))
18149 (build-system r-build-system)
18150 (home-page "https://github.com/nalimilan/R2HTML")
18151 (synopsis "HTML export for R objects")
18153 "This package includes HTML functions and methods to write in an HTML
18154 file. Thus, making HTML reports is easy. It includes a function that allows
18155 redirection on the fly, which appears to be very useful for teaching purposes,
18156 as the student can keep a copy of the produced output to keep all that they
18157 did during the course. The package comes with a vignette describing how to
18158 write HTML reports for statistical analysis. Finally, a driver for Sweave
18159 parses HTML flat files containing R code and to automatically write
18160 the corresponding outputs (tables and graphs).")
18161 (license license:gpl2+)))
18163 (define-public r-rjava
18170 (uri (cran-uri "rJava" version))
18173 "1ijqhvnb8ab38cp9pwdf7zq7xqqlm6x94gkrab2dd98p6d4x1472"))))
18174 (properties `((upstream-name . "rJava")))
18175 (build-system r-build-system)
18177 `(#:modules ((guix build utils)
18178 (guix build r-build-system)
18181 (modify-phases %standard-phases
18182 (add-after 'unpack 'set-JAVA_HOME
18183 (lambda* (#:key inputs #:allow-other-keys)
18184 (let ((jdk (assoc-ref inputs "jdk")))
18185 (setenv "JAVA_HOME" jdk)
18186 (setenv "JAVA" (which "java"))
18187 (setenv "JAR" (which "jar"))
18188 (setenv "JAVAC" (which "javac"))
18189 (setenv "JAVAH" (which "javah"))
18190 (setenv "JAVA_CPPFLAGS"
18191 (string-append "-I" jdk "/include "
18192 "-I" jdk "/include/linux"))
18193 (match (find-files (string-append jdk "/jre/lib/") "libjvm.so")
18194 ((lib) (setenv "JAVA_LIBS" lib))
18195 (_ (error "Could not find libjvm.so"))))
18199 ("jdk" ,icedtea-8 "jdk")
18201 (home-page "https://www.rforge.net/rJava/")
18202 (synopsis "Low-Level R to Java interface")
18204 "This package provides a low-level interface to the Java VM very much
18205 like .C/.Call and friends. It allows the creation of objects, calling methods
18206 and accessing fields.")
18207 (license license:gpl2)))
18209 (define-public r-svmisc
18216 (uri (cran-uri "svMisc" version))
18219 "1r3kih5bnr4plnzdn5f2gg3xl3krgyl7gkdlf58a2l8vk13j3m9d"))))
18220 (properties `((upstream-name . "svMisc")))
18221 (build-system r-build-system)
18224 (home-page "https://github.com/SciViews/svMisc")
18225 (synopsis "Miscellaneous functions for SciViews")
18227 "This package provides miscellaneous functions for SciViews or general
18228 use, including tools to manage a temporary environment attached to the search
18229 path for temporary variables you do not want to @code{save()} or
18230 @code{load()}; test the current platform; showing progress bars, etc.")
18231 (license license:gpl2)))
18233 (define-public r-xyz
18240 (uri (cran-uri "xyz" version))
18243 "13w4sb4pvgciwr8wsz785dafj2k2kpx7znz46r5d32wx88vkycp4"))))
18244 (build-system r-build-system)
18247 (home-page "https://cran.r-project.org/web/packages/xyz/")
18248 (synopsis "Algorithm for fast interaction search in high-dimensional data")
18250 "High dimensional interaction search by brute force requires a quadratic
18251 computational cost in the number of variables. The xyz algorithm provably
18252 finds strong interactions in almost linear time. For details of the algorithm
18253 see: G. Thanei, N. Meinshausen and R. Shah (2016). The xyz algorithm for fast
18254 interaction search in high-dimensional data.")
18255 ;; Any version of the GPL.
18256 (license license:gpl2+)))
18258 (define-public r-rttf2pt1
18260 (name "r-rttf2pt1")
18265 (uri (cran-uri "Rttf2pt1" version))
18268 "1fp1y0kxa5xg8w0dplm12wfm8h78az4k6ql1758wwhb3d17np241"))))
18269 (properties `((upstream-name . "Rttf2pt1")))
18270 (build-system r-build-system)
18271 (home-page "https://github.com/wch/Rttf2pt1")
18272 (synopsis "Font conversion utility")
18274 "This package contains the program @code{ttf2pt1}, for use with the
18275 @code{extrafont} package.")
18276 ;; Most of the files are covered under the Expat license. Some files are
18277 ;; covered under BSD-3. Deviations for individual files are recorded in
18278 ;; the LICENSE file.
18279 (license (list license:bsd-3 license:expat
18280 (license:non-copyleft "file://LICENSE")))))
18282 (define-public r-extrafontdb
18284 (name "r-extrafontdb")
18289 (uri (cran-uri "extrafontdb" version))
18292 "115n42hfvv5h4nn4cfkfmkmn968py4lpy8zd0d6w5yylwpzbm8gs"))))
18293 (build-system r-build-system)
18294 (home-page "https://github.com/wch/extrafontdb")
18295 (synopsis "Database for the extrafont package")
18297 "This package holds the database for the @code{extrafont} package.")
18298 (license license:gpl2)))
18300 (define-public r-extrafont
18302 (name "r-extrafont")
18307 (uri (cran-uri "extrafont" version))
18310 "0mx810mld67vb1w3wkl4fhpjmkq32lgpq5x1c0a9rf8li5wskrj4"))))
18311 (build-system r-build-system)
18313 (list r-extrafontdb r-rttf2pt1))
18314 (home-page "https://github.com/wch/extrafont")
18315 (synopsis "Tools for using fonts in R")
18317 "The extrafont package makes it easier to use fonts other than the basic
18318 PostScript fonts that R uses. Fonts that are imported into extrafont can be
18319 used with PDF or PostScript output files. There are two hurdles for using
18320 fonts in PDF (or Postscript) output files:
18323 @item Making R aware of the font and the dimensions of the characters.
18324 @item Embedding the fonts in the PDF file so that the PDF can be displayed
18325 properly on a device that doesn't have the font. This is usually needed if
18326 you want to print the PDF file or share it with others.
18329 The extrafont package makes both of these things easier.")
18330 (license license:gpl2)))
18332 (define-public r-xkcd
18339 (uri (cran-uri "xkcd" version))
18342 "1z2y0ihn68ppay7xkglhw7djki5654g6z4bbpyy41if57z9q554f"))))
18343 (build-system r-build-system)
18345 (list r-extrafont r-ggplot2 r-hmisc))
18346 (home-page "https://cran.r-project.org/web/packages/xkcd/")
18347 (synopsis "Plot ggplot2 graphics in the XKCD style")
18349 "This package provides the means to plot ggplot2 graphs in the style of
18350 the XKCD web comic.")
18351 (license license:gpl3)))
18353 (define-public r-babelgene
18355 (name "r-babelgene")
18360 (uri (cran-uri "babelgene" version))
18363 "1735h4s2vahv55pmq65zkgxq8d5x71i1is03rf17dric8yynjjhg"))))
18364 (properties `((upstream-name . "babelgene")))
18365 (build-system r-build-system)
18367 (list r-dplyr r-rlang))
18371 "https://igordot.github.io/babelgene/")
18372 (synopsis "Gene orthologs for model organisms in a Tidy data format")
18374 "Genomic analysis of model organisms often requires the use of databases
18375 based on human data or making comparisons to patient-derived resources. This
18376 requires converting genes between human and non-human analogues. The
18377 babelgene R package provides predicted gene orthologs/homologs for frequently
18378 studied model organisms in an R-friendly tidy/long format. The package
18379 integrates orthology assertion predictions sourced from multiple databases as
18380 compiled by the HGNC Comparison of Orthology Predictions (HCOP).")
18381 (license license:expat)))
18383 (define-public r-msigdbr
18390 (uri (cran-uri "msigdbr" version))
18393 "1jna9bkq0a7r6f8nhxziyiw75kfhsyh1rv7sx5d4551mvxxlhc6w"))))
18394 (build-system r-build-system)
18404 (home-page "https://github.com/igordot/msigdbr")
18405 (synopsis "MSigDB gene sets for multiple organisms")
18407 "This package provides the @dfn{Molecular Signatures Database} (MSigDB)
18408 gene sets typically used with the @dfn{Gene Set Enrichment Analysis} (GSEA)
18409 software in a standard R data frame with key-value pairs. Included are the
18410 original human gene symbols and Entrez IDs as well as the equivalents for
18411 various frequently studied model organisms such as mouse, rat, pig, fly, and
18413 ;; The package is covered under the Expat license, but the upstream MSigDB
18414 ;; files are made available under the Creative Commons Attribution 4.0
18415 ;; International license.
18416 (license (list license:expat license:cc-by4.0))))
18418 (define-public r-gridgraphics
18420 (name "r-gridgraphics")
18425 (uri (cran-uri "gridGraphics" version))
18428 "12yswy02j3h5wir7m5jnkhpjmb0sa4snn61vjd68i49qwsa6w219"))))
18429 (properties `((upstream-name . "gridGraphics")))
18430 (build-system r-build-system)
18431 (home-page "https://github.com/pmur002/gridgraphics")
18432 (synopsis "Redraw base graphics using @code{grid} graphics")
18434 "This package provides functions to convert a page of plots drawn with
18435 the @code{graphics} package into identical output drawn with the @code{grid}
18436 package. The result looks like the original @code{graphics}-based plot, but
18437 consists of @code{grid} grobs and viewports that can then be manipulated with
18438 @code{grid} functions (e.g., edit grobs and revisit viewports).")
18439 (license license:gpl2+)))
18441 (define-public r-farver
18448 (uri (cran-uri "farver" version))
18451 "1x6ffwxqbrwlylnk995jz2a6nz2y9z59jaq0ncpni7q40w367j75"))))
18452 (build-system r-build-system)
18453 (home-page "https://github.com/thomasp85/farver")
18454 (synopsis "Vectorized color conversion and comparison")
18456 "The encoding of color can be handled in many different ways, using
18457 different color spaces. As different color spaces have different uses,
18458 efficient conversion between these representations are important. This
18459 package provides a set of functions that gives access to very fast color space
18460 conversion and comparisons implemented in C++, and offers 100-fold speed
18461 improvements over the @code{convertColor} function in the @code{grDevices}
18463 (license license:expat)))
18465 (define-public r-yulab-utils
18467 (name "r-yulab-utils")
18472 (uri (cran-uri "yulab.utils" version))
18475 "1bj93gnj7j4b7dgkbr5v22rsbwfcw5dvipl5irmidaakvrihd19q"))))
18476 (properties `((upstream-name . "yulab.utils")))
18477 (build-system r-build-system)
18478 (home-page "https://cran.r-project.org/package=yulab.utils")
18479 (synopsis "Supporting functions for packages maintained by YuLab-SMU")
18481 "Miscellaneous functions commonly used by YuLab-SMU, such as
18482 @code{install_zip_gh} to install R packages from Github ZIP files.")
18483 (license license:artistic2.0)))
18485 (define-public r-ggplotify
18487 (name "r-ggplotify")
18492 (uri (cran-uri "ggplotify" version))
18495 "12mk3fa8fdjxj7xxz21jkr7h91w5wdgwjqhszcz1qffwsgb773qp"))))
18496 (build-system r-build-system)
18498 (list r-ggplot2 r-gridgraphics r-yulab-utils))
18501 (home-page "https://github.com/GuangchuangYu/ggplotify")
18502 (synopsis "Convert plots to @code{grob} or @code{ggplot} object")
18504 "This package provides tools to convert plot function calls (using
18505 expression or formula) to @code{grob} or @code{ggplot} objects that are
18506 compatible with the @code{grid} and @code{ggplot2} environment. With this
18507 package, we are able to e.g. use @code{cowplot} to align plots produced by
18508 @code{base} graphics, @code{grid}, @code{lattice}, @code{vcd} etc. by
18509 converting them to @code{ggplot} objects.")
18510 (license license:artistic2.0)))
18512 (define-public r-triebeard
18514 (name "r-triebeard")
18519 (uri (cran-uri "triebeard" version))
18522 "1hqyz57gph02c9fdc07lxz113bbklif3g18sw8jan6pakhhdc7dz"))))
18523 (build-system r-build-system)
18524 (propagated-inputs (list r-rcpp))
18525 (home-page "https://github.com/Ironholds/triebeard/")
18526 (synopsis "Radix trees in Rcpp")
18528 "Radix trees, or tries, are key-value data structures optimized for
18529 efficient lookups, similar in purpose to hash tables. This package provides
18530 an implementation of radix trees for use in R programming and in developing
18531 packages with Rcpp.")
18532 (license license:expat)))
18534 (define-public r-tweenr
18541 (uri (cran-uri "tweenr" version))
18544 "17znizh4yabh2zs9mzyr0sl6p0pw49961i61br7cl1b7v9sza18q"))))
18545 (build-system r-build-system)
18547 (list r-farver r-magrittr r-rcpp r-rlang))
18548 (home-page "https://github.com/thomasp85/tweenr")
18549 (synopsis "Interpolate data for smooth animations")
18551 "In order to create smooth animation between states of data, tweening is
18552 necessary. This package provides a range of functions for creating tweened
18553 data that can be used as basis for animation. Furthermore it adds a number of
18554 vectorized interpolaters for common R data types such as numeric, date and
18556 (license license:expat)))
18558 (define-public r-polyclip
18560 (name "r-polyclip")
18565 (uri (cran-uri "polyclip" version))
18568 "0jyk4maqiblvj095jd59dr76kbniyli3v3xvy0a72ljszq6vrnkl"))))
18569 (build-system r-build-system)
18570 (native-inputs (list pkg-config))
18571 (home-page "http://www.angusj.com/delphi/clipper.php")
18572 (synopsis "Polygon clipping")
18574 "This package provides an R port of the library Clipper. It performs
18575 polygon clipping operations (intersection, union, set minus, set difference)
18576 for polygonal regions of arbitrary complexity, including holes. It computes
18577 offset polygons (spatial buffer zones, morphological dilations, Minkowski
18578 dilations) for polygonal regions and polygonal lines. It computes the
18579 Minkowski Sum of general polygons. There is a function for removing
18580 self-intersections from polygon data.")
18581 (license license:boost1.0)))
18583 (define-public r-urltools
18585 (name "r-urltools")
18590 (uri (cran-uri "urltools" version))
18593 "04x3my655dd287cbsszbnf75q0swmjlxxrblcsay7a8n3df3a830"))))
18594 (build-system r-build-system)
18596 (list r-rcpp r-triebeard))
18597 (home-page "https://github.com/Ironholds/urltools/")
18598 (synopsis "Vectorized tools for URL handling and parsing")
18600 "This package provides a toolkit for all URL-handling needs, including
18601 encoding and decoding, parsing, parameter extraction and modification. All
18602 functions are designed to be both fast and entirely vectorized. It is
18603 intended to be useful for people dealing with web-related datasets, such as
18604 server-side logs, although may be useful for other situations involving large
18606 (license license:expat)))
18608 (define-public r-ggforce
18615 (uri (cran-uri "ggforce" version))
18618 "0bwzjbjl678xvc2ihm80dwn9pidwafqjdab3k299csys16s3na1a"))))
18619 (build-system r-build-system)
18632 (home-page "https://ggforce.data-imaginist.com")
18633 (synopsis "Accelerating ggplot2")
18635 "The aim of the ggplot2 package is to aid in visual data investigations.
18636 This focus has led to a lack of facilities for composing specialized plots.
18637 This package aims to be a collection of mainly new statistics and geometries
18638 that fills this gap.")
18639 (license license:expat)))
18641 (define-public r-europepmc
18643 (name "r-europepmc")
18648 (uri (cran-uri "europepmc" version))
18651 "16japbndid34shqg8n0bmjrxn84xmhrylvz832zclcllm6i93fn1"))))
18652 (build-system r-build-system)
18667 (home-page "https://github.com/ropensci/europepmc/")
18668 (synopsis "R Interface to the Europe PubMed Central RESTful Web Service")
18670 "This package provides an R Client for the
18671 @url{https://europepmc.org/RestfulWebService,Europe PubMed Central RESTful Web
18672 Service}. It gives access to both metadata on life science literature and
18673 open access full texts. Europe PMC indexes all PubMed content and other
18674 literature sources including Agricola, a bibliographic database of citations
18675 to the agricultural literature, or Biological Patents. In addition to
18676 bibliographic metadata, the client allows users to fetch citations and
18677 reference lists. Links between life-science literature and other EBI
18678 databases, including ENA, PDB or ChEMBL are also accessible.")
18679 (license license:gpl3)))
18681 (define-public r-ggraph
18688 (uri (cran-uri "ggraph" version))
18691 "0m4n8iw2b9jk8hcy5blg5w59zsqcpsbv27wbw598dvljpafx8sp3"))))
18692 (build-system r-build-system)
18711 (home-page "https://cran.r-project.org/web/packages/ggraph/")
18712 (synopsis "Implementation of grammar of graphics for graphs and networks")
18714 "The grammar of graphics as implemented in ggplot2 is a poor fit for
18715 graph and network visualizations due to its reliance on tabular data input.
18716 The ggraph package is an extension of the ggplot2 API tailored to graph
18717 visualizations and provides the same flexible approach to building up plots
18719 (license license:gpl3)))
18721 (define-public r-gkmsvm
18728 (uri (cran-uri "gkmSVM" version))
18731 "119g5rhc7ffyviz04r04aj5z1g6abnj3ddd01g7db505sdr6lapj"))))
18732 (properties `((upstream-name . "gkmSVM")))
18733 (build-system r-build-system)
18735 (list r-kernlab r-rcpp r-rocr r-seqinr))
18736 (home-page "https://cran.r-project.org/web/packages/gkmSVM")
18737 (synopsis "Gapped-kmer support vector machine")
18739 "This R package provides tools for training gapped-kmer SVM classifiers
18740 for DNA and protein sequences. This package supports several sequence
18741 kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.")
18742 (license license:gpl2+)))
18744 (define-public r-varselrf
18746 (name "r-varselrf")
18751 (uri (cran-uri "varSelRF" version))
18754 "0h49rl1j13yfh97rsfsyh9s2c4wajny4rzms2qw77d0cavxqg53i"))))
18755 (properties `((upstream-name . "varSelRF")))
18756 (build-system r-build-system)
18758 (list r-randomforest))
18759 (home-page "https://www.ligarto.org/rdiaz/software/software")
18760 (synopsis "Variable selection using random forests")
18762 "This package provides tools for the variable selection from random
18763 forests using both backwards variable elimination (for the selection of small
18764 sets of non-redundant variables) and selection based on the importance
18765 spectrum (somewhat similar to scree plots; for the selection of large,
18766 potentially highly-correlated variables). The main applications are in
18767 high-dimensional data (e.g., microarray data, and other genomics and
18768 proteomics applications).")
18769 (license license:gpl2+)))
18771 (define-public r-pamr
18778 (uri (cran-uri "pamr" version))
18781 "0ycpgkk23y3zzkb42n2skcyl35ps1n7jmyzfj7pbxr3f6gr2grfh"))))
18782 (build-system r-build-system)
18784 (list r-cluster r-survival))
18785 (native-inputs (list gfortran))
18786 (home-page "https://cran.r-project.org/web/packages/pamr/")
18787 (synopsis "Prediction Analysis for Microarrays")
18789 "This package provides some functions for sample classification in
18791 (license license:gpl2)))
18793 (define-public r-rda
18796 (version "1.0.2-2.1")
18800 (uri (cran-uri "rda" version))
18803 "1y4fawslr3i6crjaxhsdb47kfsqkyszdx6avq3r5far5a4pvc639"))))
18804 (build-system r-build-system)
18805 (home-page "https://cran.r-project.org/web/packages/rda/")
18806 (synopsis "Shrunken centroids regularized discriminant analysis")
18808 "This package provides tools for shrunken centroids regularized
18809 discriminant analysis for the purpose of classifying high dimensional data.")
18810 (license license:gpl2+)))
18812 (define-public r-ggvis
18819 (uri (cran-uri "ggvis" version))
18822 "1qv512pd4x5vmx15y9nvqmabbbw14h75fmi1sjbcg5yl25z0cswy"))))
18823 (build-system r-build-system)
18832 (home-page "https://ggvis.rstudio.com/")
18833 (synopsis "Interactive grammar of graphics")
18835 "This package is a data visualization package for R providing an
18836 implementation of an interactive grammar of graphics, taking the best parts of
18837 ggplot2, combining them with the reactive framework of Shiny and drawing web
18838 graphics using Vega.")
18839 (license license:gpl2)))
18841 (define-public r-gbm
18848 (uri (cran-uri "gbm" version))
18851 "1h9f4ww9yc3nsvghgr2q7jjrlz29ibabxjbax1sk5wmqh2wy6pbx"))))
18852 (build-system r-build-system)
18854 (list r-lattice r-survival))
18857 (home-page "https://github.com/gbm-developers/gbm")
18858 (synopsis "Generalized boosted regression models")
18860 "This package is an implementation of extensions to Freund and Schapire's
18861 AdaBoost algorithm and Friedman's gradient boosting machine. It includes
18862 regression methods for least squares, absolute loss, t-distribution loss,
18863 quantile regression, logistic, multinomial logistic, Poisson, Cox proportional
18864 hazards partial likelihood, AdaBoost exponential loss, Huberized hinge loss,
18865 and Learning to Rank measures (LambdaMart).")
18866 (license license:gpl2+)))
18868 (define-public r-threejs
18875 (uri (cran-uri "threejs" version))
18878 "1711h351nzxfkbbdwvfzyhciyvi9c6wx3jq1g97lzcqgnb45kivn"))))
18879 (build-system r-build-system)
18881 `(#:modules ((guix build utils)
18882 (guix build r-build-system)
18886 (modify-phases %standard-phases
18887 (add-after 'unpack 'process-javascript
18888 (lambda* (#:key inputs #:allow-other-keys)
18889 (with-directory-excursion "inst"
18893 `((,(assoc-ref inputs "js-jquery")
18894 "htmlwidgets/lib/jquery/jquery.min.js")
18895 (,(assoc-ref inputs "js-threejs-111")
18896 "htmlwidgets/lib/threejs-111/three.min.js"))))
18897 (lambda (sources targets)
18898 (for-each (lambda (source target)
18899 (format #t "Processing ~a --> ~a~%"
18901 (delete-file target)
18902 (let ((minified (open-pipe* OPEN_READ "uglifyjs" source)))
18903 (call-with-output-file target
18905 (dump-port minified port)))))
18906 sources targets))))
18909 (list r-base64enc r-crosstalk r-htmlwidgets r-igraph))
18911 `(("uglifyjs" ,node-uglify-js)
18915 (uri "https://code.jquery.com/jquery-1.12.4.js")
18918 "0x9mrc1668icvhpwzvgafm8xm11x9lfai9nwr66aw6pjnpwkc3s3"))))
18922 (uri "https://raw.githubusercontent.com/mrdoob/three.js/r111/build/three.js")
18925 "1cxdkw3plmlw1xvhbx5dm39gqczgzxip2dm887v6whhsxqxl9cky"))))))
18926 (home-page "https://bwlewis.github.io/rthreejs")
18927 (synopsis "Interactive 3D scatter plots, networks and globes")
18929 "Create interactive 3D scatter plots, network plots, and globes in R
18930 using the three.js visualization library.")
18931 (license license:expat)))
18933 (define-public r-mlbench
18940 (uri (cran-uri "mlbench" version))
18943 "157iqsld0wj8g8cbs7nh6p2x6kasmkhs3078hsmqac946gk2pydi"))))
18944 (build-system r-build-system)
18945 (home-page "https://cran.r-project.org/web/packages/mlbench/")
18946 (synopsis "Machine learning benchmark problems")
18948 "This package provides a collection of artificial and real-world machine
18949 learning benchmark problems, including, e.g., several data sets from the UCI
18951 (license license:gpl2)))
18953 (define-public r-mpm
18960 (uri (cran-uri "mpm" version))
18963 "1jpv2ddmw7aarqbbyfys1yb840arw33319wnny3v2hk84hldmayj"))))
18964 (build-system r-build-system)
18966 (list r-kernsmooth r-mass))
18967 (home-page "http://mpm.r-forge.r-project.org")
18968 (synopsis "Multivariate projection methods")
18970 "This is a package for exploratory graphical analysis of multivariate
18971 data, specifically gene expression data with different projection methods:
18972 principal component analysis, correspondence analysis, spectral map
18974 (license license:gpl2+)))
18976 (define-public r-png
18982 (uri (cran-uri "png" version))
18985 "0g2mcp55lvvpx4kd3mn225mpbxqcq73wy5qx8b4lyf04iybgysg2"))))
18986 (build-system r-build-system)
18988 (list libpng zlib))
18989 (home-page "https://www.rforge.net/png/")
18990 (synopsis "Read and write PNG images")
18992 "This package provides an easy and simple way to read, write and display
18993 bitmap images stored in the PNG format. It can read and write both files and
18994 in-memory raw vectors.")
18995 ;; Any of these GPL versions.
18996 (license (list license:gpl2 license:gpl3))))
18998 (define-public r-ggcorrplot
19000 (name "r-ggcorrplot")
19005 (uri (cran-uri "ggcorrplot" version))
19008 "0hi9lz121ya1l2lbm7rqlxg6fs6bvxck396dngnidrhl5fvqb41b"))))
19009 (build-system r-build-system)
19011 (list r-ggplot2 r-reshape2))
19012 (home-page "http://www.sthda.com/english/wiki/ggcorrplot")
19013 (synopsis "Visualization of a correlation matrix using ggplot2")
19015 "The ggcorrplot package can be used to visualize easily a correlation
19016 matrix using ggplot2. It provides a solution for reordering the correlation
19017 matrix and displays the significance level on the plot. It also includes a
19018 function for computing a matrix of correlation p-values.")
19019 (license license:gpl2)))
19021 (define-public r-ggfun
19028 (uri (cran-uri "ggfun" version))
19031 "06si42b60hp8wprs5nbks93qlb9s269k9kw7akcirizwc399x62r"))))
19032 (properties `((upstream-name . "ggfun")))
19033 (build-system r-build-system)
19035 (list r-ggplot2 r-rlang))
19036 (native-inputs (list r-knitr))
19037 (home-page "https://cran.r-project.org/package=ggfun")
19038 (synopsis "Miscellaneous functions for ggplot2")
19040 "This package provides useful functions to edit ggplot object (e.g.,
19041 setting fonts for theme and layers, adding rounded rectangle as background for
19042 each of the legends).")
19043 (license license:artistic2.0)))
19045 (define-public r-gridtext
19047 (name "r-gridtext")
19052 (uri (cran-uri "gridtext" version))
19055 "131kw7nkfwksviwfifd2kk7lyvhxzzzv1nnj8rahkr3dik3akk61"))))
19056 (properties `((upstream-name . "gridtext")))
19057 (build-system r-build-system)
19067 (home-page "https://wilkelab.org/gridtext/")
19068 (synopsis "Improved text rendering support for Grid graphics")
19070 "This package provides support for rendering of formatted text using Grid
19071 graphics. Text can be formatted via a minimal subset of Markdown, HTML, and
19072 inline CSS directives, and it can be rendered both with and without word
19074 (license license:expat)))
19076 (define-public r-ggtext
19083 (uri (cran-uri "ggtext" version))
19086 "0n19dlcys8v7myfyckr6dnq0kx79k3sbh8nwx1jsx8pgzfbi8a2b"))))
19087 (properties `((upstream-name . "ggtext")))
19088 (build-system r-build-system)
19090 (list r-ggplot2 r-gridtext r-rlang r-scales))
19091 (native-inputs (list r-knitr))
19092 (home-page "https://wilkelab.org/ggtext/")
19093 (synopsis "Improved text rendering support for ggplot2")
19095 "This package provides a ggplot2 extension that enables the rendering of
19096 complex formatted plot labels (titles, subtitles, facet labels, axis labels,
19097 etc.). Text boxes with automatic word wrap are also supported.")
19098 (license license:gpl2)))
19100 ;; This package includes minified JavaScript files. When upgrading please
19101 ;; check that there are no new minified JavaScript files.
19102 (define-public r-flexdashboard
19104 (name "r-flexdashboard")
19109 (uri (cran-uri "flexdashboard" version))
19112 "1bh759llp15fxrx2rwvxd8p3w84vjmkid32ism7zg49a127fjib4"))
19113 (modules '((guix build utils)))
19116 ;; Delete bundled minified JavaScript files
19117 (delete-file "inst/htmlwidgets/lib/raphael/raphael-2.1.4.min.js")
19118 (delete-file "inst/www/sly/sly.min.js")
19119 (delete-file "inst/www/stickytableheaders/jquery.stickytableheaders.min.js")
19120 (delete-file "inst/www/prism/prism.js")
19122 (build-system r-build-system)
19124 `(#:modules ((guix build utils)
19125 (guix build r-build-system)
19129 (ice-9 textual-ports))
19131 (modify-phases %standard-phases
19132 (add-after 'unpack 'process-javascript
19133 (lambda* (#:key inputs #:allow-other-keys)
19134 (with-directory-excursion "inst"
19135 ;; Concatenate all components of prism.js
19136 (let ((contents (string-join
19137 (map (lambda (name)
19138 (call-with-input-file
19139 (assoc-ref inputs name)
19143 "js-prism-line-numbers"))
19145 (call-with-output-file "prism-src.js"
19146 (cut display contents <>)))
19150 `(("www/stickytableheaders/jquery.stickytableheaders.js"
19151 "www/stickytableheaders/jquery.stickytableheaders.min.js")
19153 "www/sly/sly.min.js")
19155 "www/prism/prism.js")
19156 (,(assoc-ref inputs "js-raphael")
19157 "htmlwidgets/lib/raphael/raphael-2.1.4.min.js")
19158 (,(assoc-ref inputs "js-featherlight")
19159 "www/featherlight/featherlight.min.js"))))
19160 (lambda (sources targets)
19161 (for-each (lambda (source target)
19162 (format #t "Processing ~a --> ~a~%"
19164 (let ((minified (open-pipe* OPEN_READ "uglifyjs" source)))
19165 (call-with-output-file target
19167 (dump-port minified port)))))
19168 sources targets))))
19178 `(("uglifyjs" ,node-uglify-js)
19182 (uri "https://raw.githubusercontent.com/DmitryBaranovskiy/raphael/v2.1.4/raphael.js")
19185 "1h4c4akrgcj7wra9j1z1rv2406j0yf68y9c0wg8v7w9ibw2iwf1x"))))
19189 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/prism.js")
19192 "0gqa9irbp9k8p5r3d98cszajzhjnssnl43nrsc5aiy7ki52z500c"))))
19196 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/components/prism-r.js")
19199 "1x31glci7wdgr2305njy0bm2lncb0jyn0j1s2g72rqi29xid9aki"))))
19200 ("js-prism-line-numbers"
19203 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/plugins/line-numbers/prism-line-numbers.js")
19206 "1543wgf3iynrilyb27jq8px3h5gvfz5xmdib5ik2ki400c1sl991"))))
19210 (uri "https://raw.githubusercontent.com/noelboss/featherlight/1.3.4/src/featherlight.js")
19213 "14kkhwzvp8rxq2mrck5i0xcm8v5rqwqhwnmncbng8h4qq42zx3sb"))))))
19214 (home-page "https://rmarkdown.rstudio.com/flexdashboard")
19215 (synopsis "R Markdown format for flexible dashboards")
19217 "This package provides an R Markdown format for converting an R Markdown
19218 document to a grid-oriented dashboard. The dashboard flexibly adapts the size
19219 of its components to the containing web page.")
19220 (license license:expat)))
19222 (define-public r-preseqr
19229 (uri (cran-uri "preseqR" version))
19232 "1g2rnnmi45649vpy6z45v5i3wxm54s138ajqrzwi3a5r7x3xnhq1"))))
19233 (properties `((upstream-name . "preseqR")))
19234 (build-system r-build-system)
19237 (home-page "https://cran.r-project.org/web/packages/preseqR/")
19238 (synopsis "Predicting species accumulation curves")
19240 "This package can be used to predict the r-species accumulation
19241 curve (r-SAC), which is the number of species represented at least r times as
19242 a function of the sampling effort. When r = 1, the curve is known as the
19243 species accumulation curve, or the library complexity curve in high-throughput
19244 genomic sequencing. The package includes both parametric and nonparametric
19245 methods, as described by Deng C, et al. (2018).")
19246 (license license:gpl3)))
19248 (define-public r-mapplots
19250 (name "r-mapplots")
19255 (uri (cran-uri "mapplots" version))
19258 "18s2y66f8vi8g2r8a25zbgp2xm079r8v8qxv0w71h8krycs6vs9p"))))
19259 (build-system r-build-system)
19260 (home-page "https://cran.r-project.org/web/packages/mapplots/")
19261 (synopsis "Data visualization on maps")
19263 "This package helps you create simple maps; add sub-plots like pie plots
19264 to a map or any other plot; format, plot and export gridded data. The package
19265 was developed for displaying fisheries data but most functions can be used for
19266 more generic data visualisation.")
19267 (license license:gpl2+)))
19269 (define-public r-pmcmr
19276 (uri (cran-uri "PMCMR" version))
19279 "05n13pp5yff6pzk4ry07crddfaj3jlglrd1vkcnacyd8jpaxkd77"))))
19280 (properties `((upstream-name . "PMCMR")))
19281 (build-system r-build-system)
19282 (home-page "https://cran.r-project.org/web/packages/PMCMR/")
19283 (synopsis "Calculate pairwise multiple comparisons of mean rank sums")
19285 "This is a deprecated package for calculating pairwise multiple
19286 comparisons of mean rank sums. This package is superseded by the novel
19287 PMCMRplus package. The PMCMR package is no longer maintained, but kept for
19288 compatibility of dependent packages for some time.")
19289 (license license:gpl3+)))
19291 (define-public r-downloader
19293 (name "r-downloader")
19298 (uri (cran-uri "downloader" version))
19301 "1axggnsc27zzgr7snf41j3zd1vp3nfpmq4zj4d01axc709dyg40q"))))
19302 (build-system r-build-system)
19305 (home-page "https://github.com/wch/downloader")
19306 (synopsis "Download files over HTTP and HTTPS")
19308 "This package provides a wrapper for the @code{download.file} function,
19309 making it possible to download files over HTTPS across platforms. The
19310 @code{RCurl} package provides this functionality (and much more) but has
19311 external dependencies. This package has is implemented purely in R.")
19312 (license license:gpl2)))
19314 (define-public r-aplot
19321 (uri (cran-uri "aplot" version))
19324 "1b4jjj05a602dgn6yr1bsmbzlzkj6wf6af3k3w63g3mkqv0xzsfd"))))
19325 (properties `((upstream-name . "aplot")))
19326 (build-system r-build-system)
19333 (home-page "https://github.com/YuLab-SMU/aplot")
19334 (synopsis "Decorate a ggplot with associated information")
19336 "Users may want to align plots with associated information that requires
19337 axes to be exactly matched in subplots, e.g. hierarchical clustering with a
19338 heatmap. This package provides utilities to align associated subplots to a
19339 main plot at different sides (left, right, top and bottom) with axes exactly
19341 (license license:artistic2.0)))
19343 (define-public r-ggnewscale
19345 (name "r-ggnewscale")
19350 (uri (cran-uri "ggnewscale" version))
19353 "108a7y6sqqvzyfk247lbmnacfpwdl405rf1b3fa62cgx8ycsq4kb"))))
19354 (properties `((upstream-name . "ggnewscale")))
19355 (build-system r-build-system)
19358 (home-page "https://cran.r-project.org/package=ggnewscale")
19359 (synopsis "Multiple fill and color scales in ggplot2")
19361 "This package lets you use multiple fill and color scales in ggplot2.")
19362 (license license:gpl3)))
19364 (define-public r-ggpointdensity
19366 (name "r-ggpointdensity")
19371 (uri (cran-uri "ggpointdensity" version))
19374 "0c9a14j3b0hvamqylhzldw2hjdxmfbllwahjkf3gg2rw337ld9iy"))))
19376 `((upstream-name . "ggpointdensity")))
19377 (build-system r-build-system)
19380 (home-page "https://github.com/LKremer/ggpointdensity")
19381 (synopsis "Cross between a 2D density plot and a scatter plot")
19383 "This package provides a cross between a 2D density plot and a scatter
19384 plot, implemented as a ggplot2 @code{geom}. Points in the scatter plot are
19385 colored by the number of neighboring points. This is useful to visualize the
19386 2D-distribution of points in case of overplotting.")
19387 (license license:gpl3)))
19389 (define-public r-arrow
19396 (uri (cran-uri "arrow" version))
19399 "1b85vc5ld7nibqgsdkl5kbzc0rm5jh5lqfdrssvrrcxpd26a16kc"))))
19400 (properties `((upstream-name . "arrow")))
19401 (build-system r-build-system)
19403 (list `(,apache-arrow "lib") zlib))
19414 (list pkg-config r-knitr))
19415 (home-page "https://github.com/apache/arrow/")
19416 (synopsis "R integration to Apache Arrow")
19418 "Apache Arrow is a cross-language development platform for in-memory
19419 data. It specifies a standardized language-independent columnar memory format
19420 for flat and hierarchical data, organized for efficient analytic operations on
19421 modern hardware. This package provides an R interface to the Arrow C++
19423 (license license:asl2.0)))
19425 (define-public r-rex
19432 (uri (cran-uri "rex" version))
19435 "1mmzlc3j7xa0rbjxa369f4sr0iw3gq58g8fmjjxbsjvfq14ychmg"))))
19436 (build-system r-build-system)
19441 (home-page "https://github.com/kevinushey/rex")
19442 (synopsis "Friendly regular expressions")
19444 "This package provides a friendly interface for the construction of
19445 regular expressions. Regular expressions are a very powerful feature, however
19446 they are often difficult to interpret. Rex allows you to build complex
19447 regular expressions from human readable expressions")
19448 (license license:expat)))
19450 (define-public r-mlapi
19457 (uri (cran-uri "mlapi" version))
19460 "1qyiii6x9b89i4pd4yi2zd23aabpmnpj18gqi5va0zy0l8r7kknr"))))
19461 (properties `((upstream-name . "mlapi")))
19462 (build-system r-build-system)
19464 (list r-matrix r-r6))
19467 (home-page "https://cran.r-project.org/package=mlapi")
19468 (synopsis "Abstract classes for building scikit-learn like API")
19470 "This package provides R6 abstract classes for building machine learning
19471 models with a scikit-learn like API. Scikit-learn is a popular module for the
19472 Python programming language whose design became a de facto standard in
19473 industry for machine learning tasks.")
19474 (license license:expat)))
19476 (define-public r-float
19483 (uri (cran-uri "float" version))
19486 "0m7bf3548vlgkk1c78jyrgj72ngwg0gsccap2iqinm3l3qrm4zbs"))))
19487 (properties `((upstream-name . "float")))
19488 (build-system r-build-system)
19491 (home-page "https://github.com/wrathematics/float")
19492 (synopsis "32-bit floats")
19494 "R comes with a suite of utilities for linear algebra with
19495 \"numeric\" (double precision) vectors/matrices. However, sometimes single
19496 precision (or less!) is more than enough for a particular task. This package
19497 extends R's linear algebra facilities to include 32-bit float (single
19498 precision) data. Float vectors/matrices have half the precision of their
19499 \"numeric\"-type counterparts but are generally faster to numerically operate
19500 on, for a performance vs accuracy trade-off.")
19501 (license license:bsd-2)))
19503 (define-public r-rsparse
19510 (uri (cran-uri "rsparse" version))
19513 "0d05h47j29zipyxbkv9cwzv2dzj894z6hh9dqfhwswwjbv6ciwpq"))))
19514 (properties `((upstream-name . "rsparse")))
19515 (build-system r-build-system)
19525 (home-page "https://github.com/rexyai/rsparse")
19526 (synopsis "Statistical learning on sparse matrices")
19528 "This package implements many algorithms for statistical learning on
19529 sparse matrices: matrix factorizations, matrix completion, elastic net
19530 regressions, factorization machines. The rsparse package also enhances the
19531 Matrix package by providing methods for multithreaded <sparse, dense> matrix
19532 products and native slicing of the sparse matrices in @dfn{Compressed Sparse
19533 Row} (CSR) format.")
19534 (license license:gpl2+)))
19536 (define-public r-text2vec
19538 (name "r-text2vec")
19543 (uri (cran-uri "text2vec" version))
19546 "0bisr31051hnshw26rp9r4bm8ksr977dl9k1d3fb1x79pq5aa2pi"))))
19547 (properties `((upstream-name . "text2vec")))
19548 (build-system r-build-system)
19561 (home-page "http://text2vec.org")
19562 (synopsis "Text mining framework for R")
19564 "This package provides fast and memory-friendly tools for text
19565 vectorization, topic modeling (LDA, LSA), word embeddings (GloVe),
19566 similarities. It provides a source-agnostic streaming API, which allows
19567 researchers to perform analysis of collections of documents which are larger
19568 than available RAM. All core functions are parallelized to benefit from
19569 multicore machines.")
19570 (license license:gpl2+)))
19572 (define-public r-mcmcpack
19574 (name "r-mcmcpack")
19579 (uri (cran-uri "MCMCpack" version))
19582 "1cwdjn43b9hxpxf9mnas583myhk6r2258mh57f0zsc8bd4hbl56b"))))
19583 (properties `((upstream-name . "MCMCpack")))
19584 (build-system r-build-system)
19586 (list r-coda r-lattice r-mass r-mcmc r-quantreg))
19587 (home-page "https://cran.r-project.org/package=MCMCpack")
19588 (synopsis "Markov Chain Monte Carlo (MCMC) package")
19590 "This package contains functions to perform Bayesian inference using
19591 posterior simulation for a number of statistical models. Most simulation is
19592 done in compiled C++ written in the Scythe Statistical Library. All models
19593 return @code{coda} @code{mcmc} objects that can then be summarized using the
19594 @code{coda} package. Some useful utility functions such as density functions,
19595 pseudo-random number generators for statistical distributions, a general
19596 purpose Metropolis sampling algorithm, and tools for visualization are
19598 (license license:gpl3)))
19600 (define-public r-xmlparsedata
19602 (name "r-xmlparsedata")
19607 (uri (cran-uri "xmlparsedata" version))
19610 "1c6bnz3ng1qw7sfip8wq3a4dn36a4d6rbja0sadn0a4pbsmk8q3n"))))
19611 (properties `((upstream-name . "xmlparsedata")))
19612 (build-system r-build-system)
19613 (home-page "https://github.com/r-lib/xmlparsedata#readme")
19614 (synopsis "Parse data of @code{R} code as an @code{XML} tree")
19616 "This package provides tools to convert the output of
19617 @code{utils::getParseData()} to an @code{XML} tree, that one can search via
19618 @code{XPath}, and is easier to manipulate in general.")
19619 (license license:expat)))
19621 (define-public r-cyclocomp
19623 (name "r-cyclocomp")
19628 (uri (cran-uri "cyclocomp" version))
19631 "0gky3svk02wiajw7nfjh30684h3qxili4bvsab0m7b6cggw6bgyd"))))
19632 (properties `((upstream-name . "cyclocomp")))
19633 (build-system r-build-system)
19635 (list r-callr r-crayon r-desc r-remotes r-withr))
19636 (home-page "https://github.com/MangoTheCat/cyclocomp")
19637 (synopsis "Cyclomatic complexity of R code")
19639 "Cyclomatic complexity is a software metric, used to indicate the
19640 complexity of a program. It is a quantitative measure of the number of
19641 linearly independent paths through a program's source code. This package
19642 provides tools to compute this metric.")
19643 (license license:expat)))
19645 (define-public r-lintr
19652 (uri (cran-uri "lintr" version))
19655 "14yfh641afg6griaadbdciyr3k94fl55s055qwzghgk5gdsj61zy"))))
19656 (properties `((upstream-name . "lintr")))
19657 (build-system r-build-system)
19671 (home-page "https://github.com/jimhester/lintr")
19672 (synopsis "Linter for R code")
19673 (description "This package checks adherence to a given style, syntax
19674 errors and possible semantic issues. It supports on the fly checking of R
19675 code edited with @code{RStudio IDE}, @code{Emacs} and @code{Vim}.")
19676 (license license:expat)))
19678 (define-public r-sctransform
19680 (name "r-sctransform")
19685 (uri (cran-uri "sctransform" version))
19688 "0aqbcarsvvzkh5h4i65f08y4b8dfcs3zi62hmvfy24gj81f15bw3"))))
19689 (build-system r-build-system)
19704 (home-page "https://github.com/ChristophH/sctransform")
19705 (synopsis "Variance stabilizing transformations for Single Cell UMI Data")
19707 "This package provides a normalization method for single-cell UMI count
19708 data using a variance stabilizing transformation. The transformation is based
19709 on a negative binomial regression model with regularized parameters. As part
19710 of the same regression framework, this package also provides functions for
19711 batch correction, and data correction.")
19712 (license license:gpl3)))
19714 (define-public r-styler
19721 (uri (cran-uri "styler" version))
19724 "1ki260ga0jrmayhdlx2sl788yp5kkmi4wyl32nmvvyb55sng6j9y"))))
19725 (build-system r-build-system)
19726 ;; This is needed by R.cache.
19729 (modify-phases %standard-phases
19730 (add-after 'unpack 'set-HOME
19731 (lambda _ (setenv "HOME" "/tmp"))))))
19744 (home-page "https://github.com/r-lib/styler")
19745 (synopsis "Non-invasive pretty printing of R code")
19747 "This is a package for pretty-printing R code without changing the user's
19748 formatting intent.")
19749 (license license:gpl3)))
19751 (define-public r-scrime
19758 (uri (cran-uri "scrime" version))
19761 "0y2mh9fsffjf3i15bafpasa17z99c1s75r8g6h4hgcwfgpjx75sx"))))
19762 (build-system r-build-system)
19763 (home-page "https://cran.r-project.org/web/packages/scrime/")
19764 (synopsis "Analysis of high-dimensional categorical data such as SNP data")
19766 "This package provides tools for the analysis of high-dimensional data
19767 developed/implemented at the group \"Statistical Complexity Reduction In
19768 Molecular Epidemiology\" (SCRIME). The main focus is on SNP data, but most of
19769 the functions can also be applied to other types of categorical data.")
19770 (license license:gpl2)))
19772 (define-public r-pbmcapply
19774 (name "r-pbmcapply")
19779 (uri (cran-uri "pbmcapply" version))
19782 "1p8jf7c4k45482w72sr0jw4jkz787krrxai3sl6jz5l4lda2iz3z"))))
19783 (build-system r-build-system)
19784 (home-page "https://github.com/kvnkuang/pbmcapply")
19785 (synopsis "Track the progress of apply procedures with a progress bar")
19787 "This light-weight package helps you track and visualize the progress of
19788 parallel versions of vectorized R functions of the @code{mc*apply} family.")
19789 (license license:expat)))
19791 (define-public r-blme
19798 (uri (cran-uri "blme" version))
19801 "0413j7gwr5yj14jamkizj55q7xii1a0kgazzj0ilqn2ascclz6k7"))))
19802 (build-system r-build-system)
19803 (propagated-inputs (list r-lme4))
19804 (home-page "https://github.com/vdorie/blme")
19805 (synopsis "Bayesian linear mixed-effects models")
19807 "This package provides tools for maximum a posteriori estimation for
19808 linear and generalized linear mixed-effects models in a Bayesian setting. It
19809 extends the lme4 package.")
19810 (license license:gpl2+)))
19812 (define-public r-batchtools
19814 (name "r-batchtools")
19819 (uri (cran-uri "batchtools" version))
19822 "0d2xy77hkzhcnyz8zxcv98i80fx6ripjw4rvyx4ww1d0vjjgqf52"))))
19823 (build-system r-build-system)
19839 (home-page "https://github.com/mllg/batchtools")
19840 (synopsis "Tools for computation on batch systems")
19842 "As a successor of the packages BatchJobs and BatchExperiments, this
19843 package provides a parallel implementation of the Map function for high
19844 performance computing systems managed by various schedulers. A multicore and
19845 socket mode allow the parallelization on a local machines, and multiple
19846 machines can be hooked up via SSH to create a makeshift cluster. Moreover,
19847 the package provides an abstraction mechanism to define large-scale computer
19848 experiments in a well-organized and reproducible way.")
19849 (license license:lgpl3)))
19851 (define-public r-clue
19858 (uri (cran-uri "clue" version))
19861 "0apgpdnn74mqg2bnr8yjyxgyvdl411h0r2b1r2xd67k21pyxs8bd"))))
19862 (build-system r-build-system)
19863 (propagated-inputs (list r-cluster))
19864 (home-page "https://cran.r-project.org/web/packages/clue/")
19865 (synopsis "Tools for analyzing cluster ensembles")
19866 (description "Cluster ensembles are collections of individual solutions to
19867 a given clustering problem which are useful or necessary to consider in a wide
19868 range of applications. This R package provides an extensible computational
19869 environment for creating and analyzing cluster ensembles, with basic data
19870 structures for representing partitions and hierarchies, and facilities for
19871 computing on them, including methods for measuring proximity and obtaining
19872 consensus and secondary clusterings.")
19873 (license license:gpl2)))
19875 (define-public r-sitmo
19882 (uri (cran-uri "sitmo" version))
19885 "1hm89zi38ldgbskyx1cn7gm87yqy7zrxli8q05a36y1ndvazi3j4"))))
19886 (build-system r-build-system)
19887 (propagated-inputs (list r-rcpp))
19890 (home-page "https://github.com/coatless/sitmo/")
19891 (synopsis "Parallel pseudo random number generator header files")
19893 "This package provides two high quality and fast PPRNGs that may be used
19894 in an OpenMP parallel environment. In addition, there is a generator for one
19895 dimensional low-discrepancy sequence.")
19896 (license license:expat)))
19898 (define-public r-dqrng
19905 (uri (cran-uri "dqrng" version))
19908 "1fwsldqcri2lccna4icbmmlqic3w4xyjm7rn0xmikrsw4kzapvjb"))))
19909 (build-system r-build-system)
19911 (list r-bh r-rcpp r-sitmo))
19914 (home-page "https://www.daqana.org/dqrng")
19915 (synopsis "Fast pseudo random number generators")
19917 "Several fast random number generators are provided as C++ header-only
19918 libraries: the PCG family as well as Xoroshiro128+ and Xoshiro256+.
19919 Additionally, fast functions for generating random numbers according to a
19920 uniform, normal and exponential distribution are included. The latter two use
19921 the Ziggurat algorithm originally proposed by Marsaglia and Tsang. These
19922 functions are exported to R and as a C++ interface and are enabled for use
19923 with the default 64 bit generator from the PCG family, Xoroshiro128+ and
19924 Xoshiro256+ as well as the 64 bit version of the 20 rounds Threefry
19925 engine (Salmon et al., 2011) as provided by the package @code{sitmo}.")
19926 ;; This package includes code under CC0 and Apache 2.0 or Expat, but as a
19927 ;; whole is distributed under the terms of the AGPL 3.
19928 (license license:agpl3)))
19930 (define-public r-ingredients
19932 (name "r-ingredients")
19937 (uri (cran-uri "ingredients" version))
19940 "11bv4l4fn9kr7y2nfzrwnaya8fi9w3nwcm9vzlqb7dva83rkqbsc"))))
19941 (properties `((upstream-name . "ingredients")))
19942 (build-system r-build-system)
19944 (list r-ggplot2 r-gridextra r-scales))
19945 (native-inputs (list r-knitr))
19946 (home-page "https://ModelOriented.github.io/ingredients/")
19947 (synopsis "Effects and importances of model ingredients")
19949 "This is a collection of tools for assessment of feature importance and
19950 feature effects. Key functions are:
19953 @item @code{feature_importance()} for assessment of global level feature
19955 @item @code{ceteris_paribus()} for calculation of the what-if plots,
19956 @item @code{partial_dependence()} for partial dependence plots,
19957 @item @code{conditional_dependence()} for conditional dependence plots,
19958 @item @code{accumulated_dependence()} for accumulated local effects plots,
19959 @item @code{aggregate_profiles()} and @code{cluster_profiles()} for
19960 aggregation of ceteris paribus profiles,
19961 @item generic @code{print()} and @code{plot()} for better usability of
19962 selected explainers,
19963 @item generic @code{plotD3()} for interactive, D3 based explanations, and
19964 @item generic @code{describe()} for explanations in natural language.
19966 (license license:gpl3)))
19968 (define-public r-ibreakdown
19970 (name "r-ibreakdown")
19975 (uri (cran-uri "iBreakDown" version))
19978 "00jzrndb3ahsv6ihp2pvs732n9cc944m83vdinrl9v1pxd82prkh"))))
19979 (properties `((upstream-name . "iBreakDown")))
19980 (build-system r-build-system)
19981 (propagated-inputs (list r-ggplot2))
19982 (native-inputs (list r-knitr))
19983 (home-page "https://ModelOriented.github.io/iBreakDown/")
19984 (synopsis "Model agnostic instance level variable attributions")
19986 "This package provides a model agnostic tool for decomposition of
19987 predictions from black boxes. It supports additive attributions and
19988 attributions with interactions. The Break Down Table shows contributions of
19989 every variable to a final prediction. The Break Down Plot presents variable
19990 contributions in a concise graphical way. This package works for
19991 classification and regression models.")
19992 (license license:gpl3)))
19994 (define-public r-dae
20001 (uri (cran-uri "dae" version))
20004 "0mq94ah21p1glvsbvdmi2p7nlgz1bvq7w3rz2z3mdqq18kz6nkjw"))))
20005 (build-system r-build-system)
20007 (list r-ggplot2 r-plyr))
20009 (list r-r-rsp)) ; vignette builder
20010 (home-page "http://chris.brien.name")
20011 (synopsis "Functions useful in the design and ANOVA of experiments")
20013 "This package provides functions useful in the design and ANOVA of
20014 experiments. The content falls into the following groupings:
20018 @item factor manipulation functions,
20019 @item design functions,
20020 @item ANOVA functions,
20021 @item matrix functions,
20022 @item projector and canonical efficiency functions, and
20023 @item miscellaneous functions.
20026 There is a vignette called @code{DesignNotes} describing how to use the design
20027 functions for randomizing and assessing designs. The ANOVA functions
20028 facilitate the extraction of information when the @code{Error} function has
20029 been used in the call to @code{aov}.")
20030 (license license:gpl2)))
20032 (define-public r-dalex
20039 (uri (cran-uri "DALEX" version))
20042 "0mcdd2bd8zlsz7x174g87dp8vy4wc06w58dyr27f6lgv9shzya8j"))))
20043 (properties `((upstream-name . "DALEX")))
20044 (build-system r-build-system)
20046 (list r-ggplot2 r-ibreakdown r-ingredients))
20047 (home-page "https://pbiecek.github.io/DALEX/")
20048 (synopsis "Descriptive machine learning explanations")
20050 "Machine Learning models are widely used and have various applications in
20051 classification or regression. Models created with boosting, bagging, stacking
20052 or similar techniques are often used due to their high performance, but such
20053 black-box models usually lack interpretability. The DALEX package contains
20054 various explainers that help to understand the link between input variables
20055 and model output.")
20056 ;; Any version of the GPL
20057 (license license:gpl3+)))
20059 (define-public r-enrichr
20066 (uri (cran-uri "enrichR" version))
20069 "0i3kfq4fkmx47n61zj5f87iv8ci6gbgy90a7s8dy9zbndzvbgya3"))))
20070 (properties `((upstream-name . "enrichR")))
20071 (build-system r-build-system)
20073 (list r-ggplot2 r-httr r-rjson))
20076 (home-page "https://cran.r-project.org/web/packages/enrichR/")
20077 (synopsis "R Interface to Enrichr database for analyzing gene sets")
20079 "This package provides an R interface to all Enrichr databases, a
20080 web-based tool for analyzing gene sets and returns any enrichment of common
20081 annotated biological functions.")
20082 (license license:gpl2+)))
20084 (define-public r-plot3d
20091 (uri (cran-uri "plot3D" version))
20094 "1h59zlsyzbjylaziwavppl9bjmnba4iiq34772y3dys6fqclajnh"))))
20095 (properties `((upstream-name . "plot3D")))
20096 (build-system r-build-system)
20097 (propagated-inputs (list r-misc3d))
20098 (home-page "https://cran.r-project.org/web/packages/plot3D")
20099 (synopsis "Plot multi-dimensional data")
20101 "This package provides functions for viewing 2D and 3D data, including
20102 perspective plots, slice plots, surface plots, scatter plots, etc. It
20103 includes data sets from oceanography.")
20104 (license license:gpl3+)))
20106 (define-public r-ggfortify
20108 (name "r-ggfortify")
20113 (uri (cran-uri "ggfortify" version))
20116 "038m74azpy43869ax1yi6wxbl1kr59iaxl8raiikjg749vcx6njw"))))
20117 (build-system r-build-system)
20128 (home-page "https://github.com/sinhrks/ggfortify")
20129 (synopsis "Data visualization tools for statistical analysis results")
20131 "This package provides unified plotting tools for statistics commonly
20132 used, such as GLM, time series, PCA families, clustering and survival
20133 analysis. The package offers a single plotting interface for these analysis
20134 results and plots in a unified style using the @code{ggplot2} package.")
20135 (license license:gpl2)))
20137 (define-public r-refmanager
20139 (name "r-refmanager")
20144 (uri (cran-uri "RefManageR" version))
20147 "1spzdp5ni52dybcaxqnhwdphh27wjyrsfy4hsxsplpg9rqwfqfps"))))
20148 (properties `((upstream-name . "RefManageR")))
20149 (build-system r-build-system)
20159 (home-page "https://github.com/ropensci/RefManageR/")
20160 (synopsis "Straightforward BibTeX and BibLaTeX bibliography management")
20162 "This package provides tools for importing and working with bibliographic
20163 references. It greatly enhances the @code{bibentry} class by providing a
20164 class @code{BibEntry} which stores BibTeX and BibLaTeX references, supports
20165 UTF-8 encoding, and can be easily searched by any field, by date ranges, and
20166 by various formats for name lists (author by last names, translator by full
20167 names, etc.). Entries can be updated, combined, sorted, printed in a number
20168 of styles, and exported. BibTeX and BibLaTeX @code{.bib} files can be read
20169 into R and converted to @code{BibEntry} objects.")
20170 ;; Any of these licenses may be picked.
20171 (license (list license:gpl2 license:gpl3 license:bsd-3))))
20173 (define-public r-citr
20180 (uri (cran-uri "citr" version))
20183 "1qbarvafjb8jgkrnrhh6jw7mcglmjwf7dpdiibxf39jkmlhf7las"))))
20184 (build-system r-build-system)
20195 (home-page "https://github.com/crsh/citr")
20196 (synopsis "RStudio add-in to insert Markdown citations")
20198 "This package provides functions and an RStudio add-in that search a
20199 BibTeX or BibLaTeX file to create and insert formatted Markdown citations into
20200 the current document.")
20201 (license license:expat)))
20203 (define-public r-xgboost
20206 (version "1.6.0.1")
20210 (uri (cran-uri "xgboost" version))
20213 "1gafjv6vcpny03lqw8s68xszalsylniavaqwsbzh46vyk4h9mscs"))))
20214 (build-system r-build-system)
20216 (list r-data-table r-jsonlite r-matrix))
20219 (home-page "https://github.com/dmlc/xgboost")
20220 (synopsis "Extreme gradient boosting")
20222 "This package provides an R interface to Extreme Gradient Boosting, which
20223 is an efficient implementation of the gradient boosting framework from Chen
20224 and Guestrin (2016). The package includes efficient linear model solver and
20225 tree learning algorithms. The package can automatically do parallel
20226 computation on a single machine. It supports various objective functions,
20227 including regression, classification and ranking. The package is made to be
20228 extensible, so that users are also allowed to define their own objectives
20230 (license license:asl2.0)))
20232 (define-public r-umap
20235 (version "0.2.8.0")
20239 (uri (cran-uri "umap" version))
20242 "0aiarnzc8gl932gi8fxd9f9rshaiwh9vj570l135fkiaja3q2wap"))))
20243 (build-system r-build-system)
20245 (list r-matrix r-openssl r-rcpp r-reticulate r-rspectra))
20248 (home-page "https://github.com/tkonopka/umap")
20249 (synopsis "Uniform manifold approximation and projection")
20251 "Uniform manifold approximation and projection is a technique for
20252 dimension reduction. This package provides an interface to the UMAP algorithm
20253 in R, including a translation of the original algorithm into R.")
20254 (license license:expat)))
20256 (define-public r-uwot
20263 (uri (cran-uri "uwot" version))
20266 "06ylzxmdh8jipbrzgqaiivd2lnqmbcva41cyvc0iyals6vqr1ksg"))))
20267 (build-system r-build-system)
20277 (home-page "https://github.com/jlmelville/uwot")
20278 (synopsis "Uniform manifold approximation and projection")
20280 "This package provides an implementation of the Uniform Manifold
20281 Approximation and Projection dimensionality reduction by McInnes et
20282 al. (2018). It also provides means to transform new data and to carry out
20283 supervised dimensionality reduction. An implementation of the related
20284 LargeVis method of Tang et al. (2016) is also provided.")
20285 (license license:gpl3)))
20287 (define-public r-kableextra
20289 (name "r-kableextra")
20294 (uri (cran-uri "kableExtra" version))
20297 "1c5vzy95cbz36jwyssr927qicrayifinv861rvnmg4nghb1gl7q9"))))
20298 (properties `((upstream-name . "kableExtra")))
20299 (build-system r-build-system)
20317 (home-page "https://haozhu233.github.io/kableExtra/")
20318 (synopsis "Construct complex tables with pipe syntax")
20320 "Build complex HTML or LaTeX tables using @code{kable()} from
20321 @code{knitr} and the piping syntax from @code{magrittr}. The function
20322 @code{kable()} is a light weight table generator coming from @code{knitr}.
20323 This package simplifies the way to manipulate the HTML or LaTeX codes
20324 generated by @code{kable()} and allows users to construct complex tables and
20325 customize styles using a readable syntax.")
20326 (license license:expat)))
20328 (define-public r-glasso
20335 (uri (cran-uri "glasso" version))
20337 (base32 "02p3612rpydk195n2qr77lp1j2w8zsw1ckkk98c8angm4r5q8dsc"))))
20338 (build-system r-build-system)
20339 (native-inputs (list gfortran))
20340 (home-page "https://statweb.stanford.edu/~tibs/glasso/")
20341 (synopsis "Graphical Lasso: estimation of Gaussian graphical models")
20343 "This is a package for estimation of a sparse inverse covariance matrix
20344 using a lasso (L1) penalty. Facilities are provided for estimates along a
20345 path of values for the regularization parameter.")
20346 (license license:gpl2)))
20348 (define-public r-rhpcblasctl
20350 (name "r-rhpcblasctl")
20351 (version "0.21-247.1")
20355 (uri (cran-uri "RhpcBLASctl" version))
20358 "0scpr6jq25xx7wmqyc380ann4h536ll0g7wblikk25yqvpamzrav"))))
20359 (properties `((upstream-name . "RhpcBLASctl")))
20360 (build-system r-build-system)
20361 (home-page "https://prs.ism.ac.jp/~nakama/Rhpc/")
20362 (synopsis "Control the number of threads on BLAS")
20364 "This package allows you to control the number of threads the BLAS
20365 library uses. It is also possible to control the number of threads in
20367 (license license:agpl3+)))
20369 (define-public r-lda
20376 (uri (cran-uri "lda" version))
20379 "03r4h5kgr8mfy44p66mfj5bp4k00g8zh4a1mhn46jw14pkhs21jn"))))
20380 (build-system r-build-system)
20381 (home-page "https://cran.r-project.org/web/packages/lda/")
20382 (synopsis "Collapsed Gibbs sampling methods for topic models")
20384 "This package implements @dfn{latent Dirichlet allocation} (LDA) and
20385 related models. This includes (but is not limited to) sLDA, corrLDA, and the
20386 mixed-membership stochastic blockmodel. Inference for all of these models is
20387 implemented via a fast collapsed Gibbs sampler written in C. Utility
20388 functions for reading/writing data typically used in topic models, as well as
20389 tools for examining posterior distributions are also included.")
20390 ;; Any version of the LGPL
20391 (license license:lgpl3+)))
20393 (define-public r-rann-l1
20400 (uri (cran-uri "RANN.L1" version))
20403 "1hanh3my84mdr5wy6b89fawqzfc184vff1y65wy4l5ld9qza1n44"))))
20404 (properties `((upstream-name . "RANN.L1")))
20405 (build-system r-build-system)
20406 (home-page "https://github.com/jefferis/RANN/tree/master-L1")
20407 (synopsis "Fast nearest neighbour search using L1 metric")
20409 "This package provides tools to find the k nearest neighbours for every
20410 point in a given dataset in O(N log N) time using Arya and Mount's ANN
20411 library. There is support for approximate as well as exact searches, fixed
20412 radius searches and @code{bd} as well as @code{kd} trees. The distance is
20413 computed using the L1 (Manhattan, taxicab) metric.")
20414 (license license:gpl3+)))
20416 (define-public r-leiden
20423 (uri (cran-uri "leiden" version))
20426 "1gg24afwbz818041bhmswmdqgxv35zp5h1i1102p58aaiis8dkna"))))
20427 (properties `((upstream-name . "leiden")))
20428 (build-system r-build-system)
20430 (list r-igraph r-matrix r-reticulate))
20433 (home-page "https://github.com/TomKellyGenetics/leiden")
20434 (synopsis "R implementation of Leiden clustering algorithm")
20436 "This package implements the Python @code{leidenalg} module to be called
20437 in R. It enables clustering using the Leiden algorithm for partitioning a
20438 graph into communities. See also Traag et al (2018) \"From Louvain to Leiden:
20439 guaranteeing well-connected communities.\" <arXiv:1810.08473>.")
20440 (license license:gpl3)))
20442 (define-public r-patchwork
20444 (name "r-patchwork")
20449 (uri (cran-uri "patchwork" version))
20452 "10glgkf58lcykcwda1hj6xdps02m3i247qynk6s2jmwljagps3fg"))))
20453 (build-system r-build-system)
20455 (list r-ggplot2 r-gtable))
20458 (home-page "https://github.com/thomasp85/patchwork")
20459 (synopsis "Compose ggplot2 plots")
20461 "The @code{ggplot2} package provides a strong API for sequentially
20462 building up a plot, but does not concern itself with composition of multiple
20463 plots. Patchwork is a package that expands the API to allow for arbitrarily
20464 complex composition of plots by providing mathematical operators for combining
20466 (license license:expat)))
20468 (define-public r-liger
20475 (uri (git-reference
20476 (url "https://github.com/MacoskoLab/liger")
20477 (commit (string-append "v" version))))
20478 (file-name (git-file-name name version))
20481 "16dzwwcpw6n78pxlc5w3kraigki35ix7zhd2cbx5f3y60bbkhlmx"))
20482 (modules '((guix build utils)))
20485 (delete-file "inst/java/ModularityOptimizer.jar")
20487 (build-system r-build-system)
20490 (modify-phases %standard-phases
20491 (add-after 'unpack 'build-java-part
20492 (lambda* (#:key inputs #:allow-other-keys)
20493 (invoke "unzip" (assoc-ref inputs "optimizer-src"))
20494 (for-each (lambda (file) (invoke "javac" file))
20495 (find-files "." "\\.java$"))
20496 (apply invoke "jar" "cf" "inst/java/ModularityOptimizer.jar"
20497 (find-files "." "\\.class$"))
20521 `(("jdk" ,icedtea "jdk")
20522 ;; See https://github.com/MacoskoLab/liger/issues/96
20523 ;; The optimizer is released under the Expat license.
20527 (uri "http://www.ludowaltman.nl/slm/modularity_optimizer_source.zip")
20530 "01hmm6sapcmldvayknqx2w4cav3qv71mwwkdkwj4qgq6dss09g18"))))
20532 ("r-knitr" ,r-knitr))) ; for vignettes
20533 (home-page "https://github.com/MacoskoLab/liger")
20534 (synopsis "Integrate and analyze multiple single-cell datasets")
20536 "LIGER is a package for integrating and analyzing multiple single-cell
20537 datasets, developed and maintained by the Macosko lab. It relies on
20538 integrative non-negative matrix factorization to identify shared and
20539 dataset-specific factors.")
20540 (license license:gpl3)))
20542 (define-public r-harmony
20549 (uri (git-reference
20550 (url "https://github.com/immunogenomics/harmony")
20552 (file-name (git-file-name name version))
20555 "05r401q09rbr6fqhb9mbd95082cjdi3nag1cv6zn96xkr0f6imq9"))
20556 (modules '((guix build utils)))
20559 (for-each delete-file '("config.status" "configure"))
20561 (build-system r-build-system)
20576 (home-page "https://github.com/immunogenomics/harmony")
20577 (synopsis "Integration of single cell sequencing data")
20579 "This package provides an implementation of the Harmony algorithm for
20580 single cell integration, described in Korsunsky et al
20581 @url{doi.org/10.1101/461954}. The package includes a standalone Harmony
20582 function and interfaces to external frameworks.")
20583 (license license:gpl3)))
20585 (define-public r-covr
20592 (uri (cran-uri "covr" version))
20594 (base32 "0v5cv3cw2kpdr6wxmkbd3wclavr17zipypdcb10hhmpa4cvgqk55"))))
20595 (properties `((upstream-name . "covr")))
20596 (build-system r-build-system)
20606 (list r-knitr)) ; for vignettes
20607 (home-page "https://github.com/r-lib/covr")
20608 (synopsis "Test coverage for R packages")
20610 "Thisp package enables you to track and report code coverage for your
20611 package and (optionally) upload the results to a coverage service. Code
20612 coverage is a measure of the amount of code being exercised by a set of tests.
20613 It is an indirect measure of test quality and completeness. This package is
20614 compatible with any testing methodology or framework and tracks coverage of
20615 both R code and compiled C/C++/FORTRAN code.")
20616 (license license:gpl3)))
20618 (define-public r-systemfonts
20620 (name "r-systemfonts")
20625 (uri (cran-uri "systemfonts" version))
20628 "1h44bal845jp7ya8i7ff1kz1n3wklkb00jk6hb9lgwa2p5snqxpg"))))
20629 (properties `((upstream-name . "systemfonts")))
20630 (build-system r-build-system)
20634 (list fontconfig freetype zlib))
20636 (list pkg-config r-knitr))
20637 (home-page "https://github.com/r-lib/systemfonts")
20638 (synopsis "System native font finding")
20640 "This package provides system native access to the font catalogue. As
20641 font handling varies between systems it is difficult to correctly locate
20642 installed fonts across different operating systems. The 'systemfonts' package
20643 provides bindings to the native libraries for finding font files that can then
20644 be used further by e.g. graphic devices.")
20645 (license license:expat)))
20647 (define-public r-graphlayouts
20649 (name "r-graphlayouts")
20654 (uri (cran-uri "graphlayouts" version))
20657 "1l7gkn0r1ijllv3w7cbwcbi0jggs7wlkq9b2lykprng4g1kjc96p"))))
20658 (properties `((upstream-name . "graphlayouts")))
20659 (build-system r-build-system)
20661 (list r-igraph r-rcpp r-rcpparmadillo))
20662 (home-page "https://github.com/schochastics/graphlayouts")
20663 (synopsis "Additional layout algorithms for network visualizations")
20665 "This package provides several layout algorithms to visualize networks
20666 which are not part of the igraph library. Most are based on the concept of
20667 stress majorization by Gansner et al. (2004)
20668 <doi:10.1007/978-3-540-31843-9_25>. Some more specific algorithms
20669 emphasize hidden group structures in networks or focus on specific nodes.")
20670 (license license:expat)))
20672 (define-public r-terra
20679 (uri (cran-uri "terra" version))
20682 "0gzl0ka19jjw0dmaghjk2sgwi78kkz4w3rlfkym62rdarhlfj7h9"))))
20683 (properties `((upstream-name . "terra")))
20684 (build-system r-build-system)
20689 sqlite ; needed for proj
20695 (home-page "https://rspatial.org/terra")
20696 (synopsis "Spatial data analysis")
20698 "This package provides methods for spatial data analysis, especially
20699 raster data. The included methods allow for low-level data manipulation as
20700 well as high-level global, local, zonal, and focal computation. The predict
20701 and interpolate methods facilitate the use of regression type (interpolation,
20702 machine learning) models for spatial prediction. Processing of very large
20703 files is supported.")
20704 (license license:gpl3+)))
20706 (define-public r-tidygraph
20708 (name "r-tidygraph")
20713 (uri (cran-uri "tidygraph" version))
20716 "0dmdff3bkg53xn0c51xd6k2d9c7l250x1lhl5z3libf533dw5g9g"))))
20717 (properties `((upstream-name . "tidygraph")))
20718 (build-system r-build-system)
20730 (home-page "https://github.com/thomasp85/tidygraph")
20731 (synopsis "Tidy API for graph manipulation")
20733 "This package provides a graph implementation that can be thought of as
20734 two tidy data frames describing node and edge data respectively. It provides
20735 an approach to manipulate these two virtual data frames using the API defined
20736 in the @code{dplyr} package, and it also provides tidy interfaces to a lot of
20737 common graph algorithms.")
20738 (license license:expat)))
20740 (define-public r-soupx
20741 (let ((commit "a3354be76fb52fd795be6ddf163cf056c05c6cb8")
20745 (version (git-version "0.3.1" revision commit))
20749 (uri (git-reference
20750 (url "https://github.com/constantAmateur/SoupX")
20752 (file-name (git-file-name name version))
20755 "1zmlyzrl0fz6l79gn2wswid670p88mm3y292is89sa5p3h7frr99"))))
20756 (properties `((upstream-name . "SoupX")))
20757 (build-system r-build-system)
20759 (list r-ggplot2 r-matrix r-seurat))
20760 (home-page "https://github.com/constantAmateur/SoupX")
20761 (synopsis "Single cell mRNA Soup eXterminator")
20763 "This package provides a package for quantifying, profiling and
20764 removing cell free mRNA contamination (the \"soup\") from droplet based single
20765 cell RNA-seq experiments.")
20766 (license license:gpl2))))
20768 (define-public r-assertr
20775 (uri (cran-uri "assertr" version))
20778 "00764vv86r3bn4r85in4w637harffyw605fgq0dj6mrbrwcfb650"))))
20779 (build-system r-build-system)
20781 (list r-dplyr r-mass r-rlang))
20783 (list r-knitr)) ; needed for vignette
20784 (home-page "https://github.com/ropensci/assertr")
20785 (synopsis "Assertive programming for R analysis pipelines")
20787 "This package provides functionality to assert conditions that have to be
20788 met so that errors in data used in analysis pipelines can fail quickly. It is
20789 similar to @code{stopifnot()} but more powerful, friendly, and easier for use
20791 (license license:expat)))
20793 (define-public r-parameters
20795 (name "r-parameters")
20800 (uri (cran-uri "parameters" version))
20803 "0r6bj29frhqyv75cviw0p8kns6h8z10n7g7khyk0hzq2fqjsjrwh"))))
20804 (properties `((upstream-name . "parameters")))
20805 (build-system r-build-system)
20807 (list r-bayestestr r-datawizard r-insight))
20810 (home-page "https://cran.r-project.org/web/packages/parameters")
20811 (synopsis "Processing of model parameters")
20813 "This package provides utilities for processing the parameters of various
20814 statistical models. Beyond computing p values, CIs, and other indices for a
20815 wide variety of models, this package implements features like standardization
20816 or bootstrapping of parameters and models, feature reduction (feature
20817 extraction and variable selection) as well as conversion between indices of
20819 (license license:gpl3)))
20821 (define-public r-rgdal
20828 (uri (cran-uri "rgdal" version))
20830 (base32 "1vbkyhw8nd7dw1r53qisphav31x6zvpbzilvnlvbjbj9hzhs90s5"))))
20831 (properties `((upstream-name . "rgdal")))
20832 (build-system r-build-system)
20834 (list gdal proj zlib))
20838 (list pkg-config r-knitr))
20839 (home-page "http://rgdal.r-forge.r-project.org")
20840 (synopsis "Bindings for the Geospatial Data Abstraction Library")
20842 "This package provides bindings to the Geospatial Data Abstraction
20843 Library (GDAL) and access to projection/transformation operations from the
20845 (license license:gpl2+)))
20847 (define-public r-insol
20854 (uri (cran-uri "insol" version))
20857 "166kgxgzbh55y2qqya6c2si22x0v7asi70im054g6xxwc5187kh3"))))
20858 (properties `((upstream-name . "insol")))
20859 (build-system r-build-system)
20864 (home-page "https://meteoexploration.com/R/insol/index.html")
20865 (synopsis "Tools for calculating solar radiation")
20867 "This package provides functions to compute insolation on tilted
20868 surfaces, computes atmospheric transmittance and related parameters such as:
20869 Earth radius vector, declination, sunset and sunrise, daylength, equation of
20870 time, vector in the direction of the sun, vector normal to surface, and some
20871 atmospheric physics.")
20872 (license license:gpl2+)))
20874 (define-public r-lifecycle
20876 (name "r-lifecycle")
20881 (uri (cran-uri "lifecycle" version))
20884 "183v1z1h037pvsgrj6vakpwhnhsr29hsw8p16k59dgpi00f6x9qx"))))
20885 (properties `((upstream-name . "lifecycle")))
20886 (build-system r-build-system)
20888 (list r-glue r-rlang))
20890 (list r-knitr)) ; for vignettes
20891 (home-page "https://github.com/r-lib/lifecycle")
20892 (synopsis "Manage the life cycle of your package functions")
20894 "Manage the life cycle of your exported functions with shared
20895 conventions, documentation badges, and non-invasive deprecation warnings. The
20896 lifecycle package defines four development stages (experimental, maturing,
20897 stable, and questioning) and three deprecation stages (soft-deprecated,
20898 deprecated, and defunct). It makes it easy to insert badges corresponding to
20899 these stages in your documentation. Usage of deprecated functions are
20900 signalled with increasing levels of non-invasive verbosity.")
20901 (license license:gpl3)))
20903 (define-public r-assertable
20905 (name "r-assertable")
20910 (uri (cran-uri "assertable" version))
20913 "1cciil1nzxd8gbj49w99jiv077lbpb59vx7bmb4p218aj2h5hqq4"))))
20914 (build-system r-build-system)
20916 (list r-data-table))
20919 (home-page "https://cran.r-project.org/web/packages/assertable/")
20920 (synopsis "Verbose assertions for tabular data (data.frames and data.tables)")
20921 (description "This package provides simple, flexible assertions on
20922 data.frame or data.table objects with verbose output for vetting. While other
20923 assertion packages apply towards more general use-cases, @code{assertable} is
20924 tailored towards tabular data. It includes functions to check variable names
20925 and values, whether the dataset contains all combinations of a given set of
20926 unique identifiers, and whether it is a certain length. In addition,
20927 @code{assertable} includes utility functions to check the existence of target
20928 files and to efficiently import multiple tabular data files into one
20930 (license license:gpl3)))
20932 (define-public r-quadprog
20934 (name "r-quadprog")
20939 (uri (cran-uri "quadprog" version))
20941 (base32 "1ka9g8zak8sg4y2xbz93dfrldznlk9qpd4pq9z21cdcdn3b8s4i2"))))
20942 (build-system r-build-system)
20945 (home-page "https://cran.r-project.org/web/packages/quadprog")
20946 (synopsis "Functions to solve quadratic programming problems")
20948 "This package contains routines and documentation for solving quadratic
20949 programming problems.")
20950 (license license:gpl3+)))
20952 (define-public r-desolve
20959 (uri (cran-uri "deSolve" version))
20961 (base32 "1bfr4w760nr7mjhpmf32z39swr6isnn1665cld2d1pdgx8b0yrvl"))))
20962 (properties `((upstream-name . "deSolve")))
20963 (build-system r-build-system)
20966 (home-page "https://desolve.r-forge.r-project.org/")
20967 (synopsis "Solvers for initial value problems of differential equations")
20968 (description "This package provides functions that solve initial value
20969 problems of a system of first-order @dfn{ordinary differential
20970 equations} (ODE), of @dfn{partial differential equations} (PDE), of
20971 @dfn{differential algebraic equations} (DAE), and of delay differential
20972 equations. The functions provide an interface to the FORTRAN functions
20973 @code{lsoda}, @code{lsodar}, @code{lsode}, @code{lsodes} of the ODEPACK
20974 collection, to the FORTRAN functions @code{dvode} and @code{daspk} and a
20975 C-implementation of solvers of the Runge-Kutta family with fixed or variable
20976 time steps. The package contains routines designed for solving ODEs resulting
20977 from 1-D, 2-D and 3-D partial differential equations that have been converted
20978 to ODEs by numerical differencing.")
20979 (license license:gpl2+)))
20981 (define-public r-pmcmrplus
20983 (name "r-pmcmrplus")
20988 (uri (cran-uri "PMCMRplus" version))
20990 (base32 "16m1pdrzjq9vnx5v7zv56mz9r1205rkw92883cxaqbvdpds6dhqy"))))
20991 (properties `((upstream-name . "PMCMRplus")))
20992 (build-system r-build-system)
20993 (inputs (list gmp))
21003 (native-inputs (list gfortran r-knitr))
21004 (home-page "https://cran.r-project.org/package=PMCMRplus")
21005 (synopsis "Calculate pairwise multiple comparisons of mean rank sums extended")
21007 "This package provides multiple pairwise tests.")
21008 (license license:gpl3+)))
21010 (define-public r-pracma
21016 (uri (cran-uri "pracma" version))
21018 (base32 "0r17siivm37k4gp253v9mlg5m7cwqp85h9kk2hbp2wkf81ad80i3"))))
21019 (build-system r-build-system)
21020 (home-page "https://cran.r-project.org/web/packages/pracma/")
21021 (synopsis "Practical numerical math functions")
21022 (description "This package provides functions for numerical analysis and
21023 linear algebra, numerical optimization, differential equations, plus some
21024 special functions. It uses Matlab function names where appropriate to simplify
21026 (license license:gpl3+)))
21028 (define-public r-subplex
21035 (uri (cran-uri "subplex" version))
21038 "19g5bd39gmcn27xdsklkzxg99x1r5v5q8zcw1iwry31qj24ivhrv"))))
21039 (build-system r-build-system)
21042 (home-page "https://cran.r-project.org/web/packages/subplex")
21043 (synopsis "Unconstrained optimization using the subplex algorithm")
21045 "This package implements the Subplex optimization algorithm.
21046 It solves unconstrained optimization problems using a simplex method on
21047 subspaces. The method is well suited for optimizing objective functions that
21048 are noisy or are discontinuous at the solution.")
21049 (license license:gpl3+)))
21051 (define-public r-txtplot
21058 (uri (cran-uri "txtplot" version))
21061 "00sriml48y70j18jz235dsfm5x3a81bnzskfp3hnv6cbjwwsmca4"))))
21062 (build-system r-build-system)
21063 (home-page "https://cran.r-project.org/web/packages/txtplot/")
21064 (synopsis "Text-based plotting")
21065 (description "This package provides functions to produce rudimentary ASCII
21066 graphics directly in the terminal window. This package provides a basic
21067 plotting function (and equivalents of curve, density, acf and barplot) as well
21068 as a boxplot function.")
21069 (license license:lgpl3+)))
21071 (define-public r-bio3d
21078 (uri (cran-uri "bio3d" version))
21081 "0x3apqxbk4lvvcnvvdsyjd9f6qh9f9qgml3ih69hl9ikj06iy0y6"))))
21082 (properties `((upstream-name . "bio3d")))
21083 (build-system r-build-system)
21084 (inputs (list zlib))
21085 (propagated-inputs (list r-rcpp))
21088 (home-page "http://thegrantlab.org/bio3d/")
21089 (synopsis "Biological structure analysis")
21091 "This package provides utilities to process, organize and explore protein
21092 structure, sequence and dynamics data. Features include the ability to read
21093 and write structure, sequence and dynamic trajectory data, perform sequence
21094 and structure database searches, data summaries, atom selection, alignment,
21095 superposition, rigid core identification, clustering, torsion analysis,
21096 distance matrix analysis, structure and sequence conservation analysis, normal
21097 mode analysis, principal component analysis of heterogeneous structure data,
21098 and correlation network analysis from normal mode and molecular dynamics data.
21099 In addition, various utility functions are provided to enable the statistical
21100 and graphical power of the R environment to work with biological sequence and
21102 (license license:gpl2+)))
21104 (define-public r-bios2cor
21106 (name "r-bios2cor")
21111 (uri (cran-uri "Bios2cor" version))
21114 "1wkj9vr33m9jilidil9jpw5rzr3pf7gkimxdvch22ks4bgkx7l1w"))))
21115 (properties `((upstream-name . "Bios2cor")))
21116 (build-system r-build-system)
21118 (list r-bigmemory r-bio3d r-circular r-igraph))
21119 (home-page "https://cran.r-project.org/web/packages/Bios2cor/")
21120 (synopsis "From biological sequences and simulations to correlation analysis")
21122 "This package provides utilities for computation and analysis of
21123 correlation/covariation in multiple sequence alignments and in side chain
21124 motions during molecular dynamics simulations. Features include the
21125 computation of correlation/covariation scores using a variety of scoring
21126 functions between either sequence positions in alignments or side chain
21127 dihedral angles in molecular dynamics simulations and utilities to analyze the
21128 correlation/covariation matrix through a variety of tools including network
21129 representation and principal components analysis. In addition, several
21130 utility functions are based on the R graphical environment to provide friendly
21131 tools for help in data interpretation.")
21132 (license license:gpl2+)))
21134 ;; This package includes minified JavaScript files. When upgrading please
21135 ;; check that there are no new minified JavaScript files.
21136 (define-public r-networkd3
21138 (name "r-networkd3")
21143 (uri (cran-uri "networkD3" version))
21146 "02wxki67drppgfka1is1ykg1f2rxf0x0657c0crj7ipfy62jbf1k"))
21149 (delete-file "inst/htmlwidgets/lib/d3-4.5.0/d3.min.js")
21151 (properties `((upstream-name . "networkD3")))
21152 (build-system r-build-system)
21154 `(#:modules ((guix build utils)
21155 (guix build r-build-system)
21159 (modify-phases %standard-phases
21160 (add-after 'unpack 'process-javascript
21161 (lambda* (#:key inputs #:allow-other-keys)
21162 (with-directory-excursion "inst/htmlwidgets/lib/"
21166 `((,(assoc-ref inputs "d3.v4.js")
21167 "d3-4.5.0/d3.min.js"))))
21168 (lambda (sources targets)
21169 (for-each (lambda (source target)
21170 (format #t "Processing ~a --> ~a~%"
21172 (let ((minified (open-pipe* OPEN_READ "uglifyjs" source)))
21173 (call-with-output-file target
21175 (dump-port minified port)))))
21176 sources targets))))
21179 `(("uglifyjs" ,node-uglify-js)
21180 ;; NOTE: Make sure that this version of d3 is still valid when
21181 ;; upgrading the package.
21185 (uri "https://d3js.org/d3.v4.js")
21188 "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg"))))))
21190 (list r-htmlwidgets r-igraph r-magrittr))
21191 (home-page "https://cran.r-project.org/package=networkD3")
21192 (synopsis "D3 JavaScript network graphs from R")
21194 "This package creates D3 JavaScript network, tree, dendrogram, and Sankey
21196 (license license:gpl3+)))
21198 (define-public r-aasea
21205 (uri (cran-uri "aaSEA" version))
21208 "0him4r8qyp0xssgrmdxjs45yn4d28h5anv4jyxxbbs9phb0m6j3h"))))
21209 (properties `((upstream-name . "aaSEA")))
21210 (build-system r-build-system)
21221 (home-page "https://cran.r-project.org/web/packages/aaSEA/")
21222 (synopsis "Amino acid substitution effect analyzer")
21224 "Given a protein multiple sequence alignment, it is a daunting task to
21225 assess the effects of substitutions along sequence length. The aaSEA package
21226 is intended to help researchers to rapidly analyze property changes caused by
21227 single, multiple and correlated amino acid substitutions in proteins.")
21228 (license license:gpl3)))
21230 (define-public r-abacus
21237 (uri (cran-uri "ABACUS" version))
21240 "0m1dnkwjr1522l9ddbzzx7ayxvli17sbmk6s28adpmzzjwh2kd1i"))))
21241 (properties `((upstream-name . "ABACUS")))
21242 (build-system r-build-system)
21244 (list r-ggplot2 r-shiny))
21245 (home-page "https://shiny.abdn.ac.uk/Stats/apps/")
21246 (synopsis "Apps-based activities for communicating and understanding statistics")
21248 "This package provides a set of Shiny apps for effective communication
21249 and understanding in statistics. The current version includes properties of
21250 normal distribution, properties of sampling distribution, one-sample z and t
21251 tests, two samples independent (unpaired) t test and analysis of variance.")
21252 (license license:gpl3)))
21254 (define-public r-abc-rap
21261 (uri (cran-uri "ABC.RAP" version))
21264 "1kdspln17v0krvahcd55vib4dv5azp60b3r1zf489x10qqbp1mxk"))))
21265 (properties `((upstream-name . "ABC.RAP")))
21266 (build-system r-build-system)
21267 (home-page "https://cran.r-project.org/web/packages/ABC.RAP/")
21268 (synopsis "Array-based CpG region analysis pipeline")
21270 "This package aims to identify candidate genes that are differentially
21271 methylated between cases and controls. It applies Student's t-test and delta
21272 beta analysis to identify candidate genes containing multiple CpG sites.")
21273 (license license:gpl3)))
21275 (define-public r-abcadm
21282 (uri (cran-uri "abcADM" version))
21285 "0vcabnnnwc0psv9v3rda5aap9s8cq1pjh02zva3ki64hlavf2a10"))))
21286 (properties `((upstream-name . "abcADM")))
21287 (build-system r-build-system)
21289 (list r-bh r-rcpp))
21290 (home-page "https://cran.r-project.org/web/packages/abcADM/")
21291 (synopsis "Fit accumulated damage models and estimate reliability using ABC")
21293 "This package provides tools to estimate parameters of accumulated
21294 damage (load duration) models based on failure time data under a Bayesian
21295 framework, using @dfn{Approximate Bayesian Computation} (ABC), and to assess
21296 long-term reliability under stochastic load profiles.")
21297 (license license:gpl3)))
21299 (define-public r-rglpk
21306 (uri (cran-uri "Rglpk" version))
21309 "19mzpyimzq9zqnbi05j79b2di3nzaln8swggs9p8sqdr60qvr3d2"))))
21310 (properties `((upstream-name . "Rglpk")))
21311 (build-system r-build-system)
21316 (home-page "https://r-forge.r-project.org/projects/rglp/")
21317 (synopsis "R interface to the GNU Linear Programming Kit")
21319 "This package provides an R interface to the GNU Linear Programming Kit,
21320 software for solving large-scale @dfn{linear programming} (LP), @dfn{mixed
21321 integer linear programming} (MILP) and other related problems.")
21323 (license (list license:gpl2 license:gpl3))))
21325 (define-public r-abcdefba
21327 (name "r-abcdefba")
21332 (uri (cran-uri "abcdeFBA" version))
21335 "1rxjripy8v6bxi25vdfjnbk24zkmf752qbl73cin6nvnqflwxkx4"))))
21336 (properties `((upstream-name . "abcdeFBA")))
21337 (build-system r-build-system)
21339 (list r-corrplot r-lattice r-rgl r-rglpk))
21340 (home-page "https://cran.r-project.org/web/packages/abcdeFBA/")
21341 (synopsis "A-Biologist-Can-Do-Everything of Flux Balance Analysis with this package")
21343 "This package provides functions for Constraint Based Simulation using
21344 Flux Balance Analysis and informative analysis of the data generated during
21346 (license license:gpl2)))
21348 (define-public r-abcrlda
21355 (uri (cran-uri "abcrlda" version))
21358 "04pcdnk2szfpc2ylcw5ds7y895ivy03bycal03kxw7cwylzxasks"))))
21359 (properties `((upstream-name . "abcrlda")))
21360 (build-system r-build-system)
21361 (home-page "https://ieeexplore.ieee.org/document/8720003/")
21362 (synopsis "Asymptotically bias-corrected regularized linear discriminant analysis")
21364 "This package offers methods to perform @dfn{asymptotically
21365 bias-corrected regularized linear discriminant analysis} (ABC_RLDA) for
21366 cost-sensitive binary classification. The bias-correction is an estimate of
21367 the bias term added to regularized discriminant analysis that minimizes the
21369 (license license:gpl3)))
21371 (define-public r-abemus
21378 (uri (cran-uri "abemus" version))
21381 "1dhllb184byp1yl15rg2w02zgw3iajag7cxshirg47mnmm7n70bb"))))
21382 (properties `((upstream-name . "abemus")))
21383 (build-system r-build-system)
21385 (list r-data-table))
21386 (home-page "https://cran.r-project.org/web/packages/abemus/")
21387 (synopsis "Adaptive base error model in ultra-deep sequencing data")
21389 "This package provides an implementation of @dfn{Adaptive Base Error
21390 Model in Ultra-deep Sequencing data} (ABEMUS), which combines
21391 platform-specific genetic knowledge and empirical signal to readily detect and
21392 quantify somatic @dfn{single nucleotide variants} (SNVs) in @dfn{circulating
21393 cell free DNA} (cfDNA).")
21394 (license license:gpl3)))
21396 ;; This package includes minified JavaScript files. When upgrading please
21397 ;; check that there are no new minified JavaScript files.
21398 (define-public r-rintrojs
21400 (name "r-rintrojs")
21405 (uri (cran-uri "rintrojs" version))
21408 "00l5mk80gj3xkbf3m1kip566ic98bhd88lh0bg69ybkpk4gifpyw"))
21410 '(delete-file "inst/javascript/introjs/intro.min.js"))))
21411 (properties `((upstream-name . "rintrojs")))
21412 (build-system r-build-system)
21415 (modify-phases %standard-phases
21416 (add-after 'unpack 'process-javascript
21417 (lambda* (#:key inputs #:allow-other-keys)
21418 (with-directory-excursion "inst/javascript/introjs/"
21419 (let ((source (assoc-ref inputs "intro.js"))
21420 (target "intro.min.js"))
21421 (format #true "Processing ~a --> ~a~%"
21423 (invoke "esbuild" source "--minify"
21424 (string-append "--outfile=" target)))))))))
21426 `(("esbuild" ,esbuild)
21430 (uri "https://cdn.jsdelivr.net/npm/intro.js@3.2.1/intro.js")
21433 "0vh5n7hqqyx2pdvlqq6xadfqibcn78h5961rwhpf817kpxfzv8v7"))))))
21435 (list r-jsonlite r-shiny))
21436 (home-page "https://github.com/carlganz/rintrojs")
21437 (synopsis "Wrapper for the Intro.js library")
21439 "This package provides a wrapper for the @url{http://www.introjs.com,
21440 Intro.js} library. This package makes it easy to include step-by-step
21441 introductions, and clickable hints in a Shiny application. It supports both
21442 static introductions in the UI, and programmatic introductions from the
21444 ;; The intro.js library is licensed under Expat.
21445 (license (list license:agpl3+ license:expat))))
21447 (define-public r-sysfonts
21449 (name "r-sysfonts")
21454 (uri (cran-uri "sysfonts" version))
21457 "1fq5dn4l09sgrbznfz9cakf4vgc3761zwicvqaazh0s8mzbaicpn"))))
21458 (properties `((upstream-name . "sysfonts")))
21459 (build-system r-build-system)
21461 (list freetype libpng zlib))
21464 (home-page "https://github.com/yixuan/sysfonts")
21465 (synopsis "Loading fonts into R")
21467 "This is a package to simplify loading of system fonts and Google Fonts
21468 into R, in order to support other packages.")
21469 (license license:gpl2)))
21471 (define-public r-showtextdb
21473 (name "r-showtextdb")
21478 (uri (cran-uri "showtextdb" version))
21481 "0hlnc3fhgrdkd46n7hb6id0gg1v0bf8s4679nrr7rchyp455szq2"))))
21482 (properties `((upstream-name . "showtextdb")))
21483 (build-system r-build-system)
21486 (home-page "https://cran.r-project.org/web/packages/showtextdb/")
21487 (synopsis "Font files for the 'showtext' package")
21489 "This package provides font files that can be used by the @code{showtext}
21491 (license license:asl2.0)))
21493 (define-public r-showtext
21495 (name "r-showtext")
21500 (uri (cran-uri "showtext" version))
21503 "1larnqxn9nanbqiadm35ah5hh89xrzm4fdj9pfc93zzzhlfrvhb3"))))
21504 (properties `((upstream-name . "showtext")))
21505 (build-system r-build-system)
21507 (list freetype libpng zlib))
21509 (list r-showtextdb r-sysfonts))
21511 (list pkg-config r-knitr))
21512 (home-page "https://github.com/yixuan/showtext")
21513 (synopsis "Using fonts more easily in R graphs")
21515 "This package aims to make it easy to use various types of
21516 fonts (TrueType, OpenType, Type 1, web fonts, etc.) in R graphs, and supports
21517 most output formats of R graphics including PNG, PDF and SVG. Text glyphs
21518 will be converted into polygons or raster images, hence after the plot has
21519 been created, it no longer relies on the font files. No external software
21520 such as Ghostscript is needed to use this package.")
21521 (license license:asl2.0)))
21523 (define-public r-emojifont
21525 (name "r-emojifont")
21530 (uri (cran-uri "emojifont" version))
21533 "1hhrwilv36hd9gs1kcl2zsi6519md0h9aixjrm6lfclxvz8r6k1i"))))
21534 (properties `((upstream-name . "emojifont")))
21535 (build-system r-build-system)
21537 (list r-ggplot2 r-proto r-showtext r-sysfonts))
21540 (home-page "https://guangchuangyu.github.io/emojifont")
21541 (synopsis "Emoji and Font Awesome in R graphics")
21543 "This package enables the use of emoji and the Font Awesome glyphs in
21544 both base and ggplot2 graphics.")
21545 (license license:artistic2.0)))
21547 (define-public r-abstractr
21549 (name "r-abstractr")
21554 (uri (cran-uri "abstractr" version))
21557 "1ymwp7syrynwd4i8aj2x5n8jdi9d96fjzl6jb09n0bnr5fgl7vig"))))
21558 (properties `((upstream-name . "abstractr")))
21559 (build-system r-build-system)
21561 (list r-colourpicker
21568 (home-page "https://matt-kumar.shinyapps.io/portfolio")
21569 (synopsis "R-Shiny application for creating visual abstracts")
21571 "This package provides an R Shiny application to create visual abstracts
21572 for original research. A variety of user defined options and formatting are
21574 (license license:gpl3)))
21576 (define-public r-qgam
21583 (uri (cran-uri "qgam" version))
21586 "1jyamamdffaks89rspyhmg18b4iik0nb1j0vgqzvfnm890514cvn"))))
21587 (properties `((upstream-name . "qgam")))
21588 (build-system r-build-system)
21590 (list r-doparallel r-mgcv r-plyr r-shiny))
21591 (native-inputs (list r-knitr))
21592 (home-page "https://cran.r-project.org/web/packages/qgam/")
21593 (synopsis "Smooth additive quantile regression models")
21595 "This package provides smooth additive quantile regression models, fitted
21596 using the methods of Fasiolo et al. (2017). Differently from @code{quantreg},
21597 the smoothing parameters are estimated automatically by marginal loss
21598 minimization, while the regression coefficients are estimated using either
21599 PIRLS or Newton algorithm. The learning rate is determined so that the
21600 Bayesian credible intervals of the estimated effects have approximately the
21601 correct coverage. The main function is @code{qgam()} which is similar to
21602 @code{gam()} in the @code{mgcv} package, but fits non-parametric quantile
21603 regression models.")
21604 (license license:gpl2+)))
21606 (define-public r-abtest
21613 (uri (cran-uri "abtest" version))
21616 "0jz2ry5364p8h8xlk5a5sycn8xlpxd1iasfg99bcr4jqzd92jfqg"))))
21617 (properties `((upstream-name . "abtest")))
21618 (build-system r-build-system)
21628 (home-page "https://cran.r-project.org/web/packages/abtest/")
21629 (synopsis "Bayesian A/B testing")
21631 "This package provides functions for Bayesian A/B testing including prior
21632 elicitation options based on Kass and Vaidyanathan (1992)
21633 @url{doi:10.1111/j.2517-6161.1992.tb01868.x}.")
21634 (license license:gpl2+)))
21636 (define-public r-reldist
21643 (uri (cran-uri "reldist" version))
21646 "17kbqqapqmckghv7jizibmicv3bzbycfr3mz4xg3yjp3c2bap4r6"))))
21647 (properties `((upstream-name . "reldist")))
21648 (build-system r-build-system)
21650 (list r-densestbayes r-mgcv))
21651 (home-page "http://www.stat.ucla.edu/~handcock/RelDist")
21652 (synopsis "Relative distribution methods")
21654 "This package provides tools for the comparison of distributions. This
21655 includes nonparametric estimation of the relative distribution PDF and CDF and
21656 numerical summaries as described in \"Relative Distribution Methods in the
21657 Social Sciences\" by Mark S. Handcock and Martina Morris, Springer-Verlag,
21658 1999, Springer-Verlag, ISBN 0387987789.")
21659 ;; See also https://cran.r-project.org/web/packages/reldist/LICENSE for
21660 ;; attribution requirements.
21661 (license license:gpl3)))
21663 (define-public r-accept
21670 (uri (cran-uri "accept" version))
21673 "13kx8fbnbpasjklgbq2rf4n73j2s8rvy5v77ywqhfzln24937qgh"))))
21674 (properties `((upstream-name . "accept")))
21675 (build-system r-build-system)
21677 (list r-dplyr r-reldist))
21678 (home-page "https://cran.r-project.org/web/packages/accept/")
21679 (synopsis "Acute COPD Exacerbation Prediction Tool (ACCEPT)")
21681 "This package allows clinicians to predict the rate and severity of
21682 future acute exacerbation in @dfn{Chronic Obstructive Pulmonary
21683 Disease} (COPD) patients, based on the clinical prediction model published in
21684 Adibi et al. (2019) @url{doi:10.1101/651901}.")
21685 (license license:gpl3)))
21687 (define-public r-smpracticals
21689 (name "r-smpracticals")
21694 (uri (cran-uri "SMPracticals" version))
21697 "0zxq84f9i3b86xx6msb25b61gyj9k09iab2b7wg4d93yas9qzayf"))))
21698 (properties `((upstream-name . "SMPracticals")))
21699 (build-system r-build-system)
21701 (list r-ellipse r-mass r-nlme r-survival))
21702 (home-page "http://statwww.epfl.ch/davison/SM/")
21703 (synopsis "Practicals for use with Davison (2003) Statistical Models")
21705 "This package contains the datasets and a few functions for use with the
21706 practicals outlined in Appendix A of the book Statistical Models (Davison,
21707 2003, Cambridge University Press). The practicals themselves can be found at
21708 @url{http://statwww.epfl.ch/davison/SM/}.")
21709 (license license:gpl2+)))
21711 (define-public r-fgui
21718 (uri (cran-uri "fgui" version))
21721 "024fzd1c7iwqprn26hwjb9l2qlvvyzl449d7iixy0x69djwsrysv"))))
21722 (properties `((upstream-name . "fgui")))
21723 (build-system r-build-system)
21725 "https://sites.google.com/site/thomashoffmannproject/software/fgui")
21726 (synopsis "Create GUI for R functions")
21728 "Rapidly create a GUI for a function you created by automatically
21729 creating widgets for arguments of the function. This package automatically
21730 parses help routines for context-sensitive help to these arguments. The
21731 interface is essentially a wrapper to some Tcl/Tk routines to both simplify
21732 and facilitate GUI creation. More advanced Tcl/Tk routines/GUI objects can be
21733 incorporated into the interface for greater customization for the more
21735 ;; Any version of the GPL.
21736 (license (list license:gpl2+ license:gpl3+))))
21738 (define-public r-tcltk2
21745 (uri (cran-uri "tcltk2" version))
21748 "1ibxld379600xx7kiqq3fck083s8psry12859980218rnzikl65d"))))
21749 (properties `((upstream-name . "tcltk2")))
21750 (build-system r-build-system)
21753 (home-page "https://www.sciviews.org/SciViews-R")
21754 (synopsis "Tcl/Tk additions")
21756 "This package provides a series of additional Tcl commands and Tk widgets
21757 with style and various functions to supplement the tcltk package")
21758 (license license:lgpl3)))
21760 (define-public r-accrual
21767 (uri (cran-uri "accrual" version))
21770 "11clm9s5c5518nmp6hd6pjnp0s28y92b2i2x0xgj4j5g816p4j3z"))))
21771 (properties `((upstream-name . "accrual")))
21772 (build-system r-build-system)
21774 (list r-fgui r-smpracticals r-tcltk2))
21775 (home-page "https://cran.r-project.org/web/packages/accrual/")
21776 (synopsis "Bayesian accrual prediction")
21778 "Subject recruitment for medical research is challenging. Slow patient
21779 accrual leads to delay in research. Accrual monitoring during the process of
21780 recruitment is critical. Researchers need reliable tools to manage the
21781 accrual rate. This package provides an implementation of a Bayesian method
21782 that integrates researcher's experience on previous trials and data from the
21783 current study, providing reliable prediction on accrual rate for clinical
21784 studies. It provides functions for Bayesian accrual prediction which can be
21785 easily used by statisticians and clinical researchers.")
21786 (license license:gpl2)))
21788 (define-public r-accrued
21795 (uri (cran-uri "accrued" version))
21798 "05g1jb5914z18rcai1ahn7nihn27vr2rnadwv94gc1j7ivvikvs5"))))
21799 (properties `((upstream-name . "accrued")))
21800 (build-system r-build-system)
21801 (home-page "https://cran.r-project.org/web/packages/accrued/")
21802 (synopsis "Data quality visualization tools for partially accruing data")
21804 "This is a package for visualizing data quality of partially accruing
21806 (license license:gpl3)))
21808 (define-public r-mda
21815 (uri (cran-uri "mda" version))
21818 "0qw4scc2w7jmnxssj5w2mdxb9rrl4dscqn54gplzm1gk2yf419mx"))))
21819 (properties `((upstream-name . "mda")))
21820 (build-system r-build-system)
21821 (propagated-inputs (list r-class))
21822 (native-inputs (list gfortran))
21823 (home-page "https://cran.r-project.org/web/packages/mda/")
21824 (synopsis "Mixture and flexible discriminant analysis")
21826 "This is a package for mixture and flexible discriminant analysis,
21827 @dfn{multivariate adaptive regression splines} (MARS), BRUTO, and so on.")
21828 (license license:gpl2)))
21830 (define-public r-elasticnet
21832 (name "r-elasticnet")
21837 (uri (cran-uri "elasticnet" version))
21840 "0nxcw06d0cp2mbqzg2fm9yys5xm6xx7bfcfvr0avcs8afkvz29j8"))))
21841 (properties `((upstream-name . "elasticnet")))
21842 (build-system r-build-system)
21845 (home-page "http://users.stat.umn.edu/~zouxx019/")
21846 (synopsis "Elastic-Net for sparse estimation and sparse PCA")
21848 "This package provides functions for fitting the entire solution path of
21849 the Elastic-Net and also provides functions for estimating sparse Principal
21850 Components. The Lasso solution paths can be computed by the same function.")
21851 (license license:gpl2+)))
21853 (define-public r-sparselda
21855 (name "r-sparselda")
21860 (uri (cran-uri "sparseLDA" version))
21863 "1k3sw9kc40yxnfss4vrsx34qxmv8ssddyhbfjhxrdldvblhbwchb"))))
21864 (properties `((upstream-name . "sparseLDA")))
21865 (build-system r-build-system)
21867 (list r-elasticnet r-mass r-mda))
21868 (home-page "https://www.imm.dtu.dk/~lkhc/")
21869 (synopsis "Sparse discriminant analysis")
21871 "This package performs sparse linear discriminant analysis for Gaussians
21872 and mixture of Gaussian models.")
21873 (license license:gpl2+)))
21875 (define-public r-accsda
21882 (uri (cran-uri "accSDA" version))
21885 "104xdz63mnibh6827xm0pfr9zbhbi2a7iw4m1x27xjqi7zqvbky6"))))
21886 (properties `((upstream-name . "accSDA")))
21887 (build-system r-build-system)
21893 (home-page "https://github.com/gumeo/accSDA/wiki")
21894 (synopsis "Accelerated sparse discriminant analysis")
21896 "This package provides an implementation of sparse linear discriminant
21897 analysis, which is a supervised classification method for multiple classes.
21898 Various novel optimization approaches to this problem are implemented
21899 including @dfn{alternating direction method of multipliers} (ADMM),
21900 @dfn{proximal gradient} (PG) and @dfn{accelerated proximal gradient} (APG).
21901 Functions for performing cross validation are also supplied along with basic
21902 prediction and plotting functions. @dfn{Sparse zero variance
21903 discriminant} (SZVD) analysis is also included in the package.")
21904 (license license:gpl2+)))
21906 (define-public r-ace2fastq
21908 (name "r-ace2fastq")
21913 (uri (cran-uri "ace2fastq" version))
21916 "09kk3yyqnr2xp820g0p3aai9a21figigjr9lxkr3zjq2d8gzwfic"))))
21917 (properties `((upstream-name . "ace2fastq")))
21918 (build-system r-build-system)
21921 (home-page "https://github.com/c5sire/ace2fastq")
21922 (synopsis "ACE file to FASTQ converter")
21924 "The ACE file format is used in genomics to store contigs from sequencing
21925 machines. This tools converts it into FASTQ format. Both formats contain the
21926 sequence characters and their corresponding quality information. Unlike the
21927 FASTQ file, the ACE file stores the quality values numerically. The
21928 conversion algorithm uses the standard Sanger formula. The package
21929 facilitates insertion into pipelines, and content inspection.")
21930 (license license:gpl3)))
21932 (define-public r-rngwell
21939 (uri (cran-uri "rngWELL" version))
21942 "0f1dxxaimfb0fww8ym9ciqf6q760ai46wxldl37m5mfpd57ca00c"))))
21943 (properties `((upstream-name . "rngWELL")))
21944 (build-system r-build-system)
21945 (home-page "https://cran.r-project.org/web/packages/rngWELL/")
21946 (synopsis "Toolbox for WELL random number generators")
21948 "This is a dedicated package to WELL pseudo random generators, which were
21949 introduced in Panneton et al. (2006), ``Improved Long-Period Generators Based
21950 on Linear Recurrences Modulo 2'', ACM Transactions on Mathematical Software.")
21951 (license license:bsd-3)))
21953 (define-public r-rnmf
21959 (uri (cran-uri "rNMF" version))
21962 "1nz6h0j5ywdh48m0swmhp34hbkycd7n13rclrxaw85qi9wc42597"))))
21963 (build-system r-build-system)
21965 (list r-knitr r-nnls))
21966 (home-page "https://cran.r-project.org/web/packages/rNMF/")
21967 (synopsis "Robust nonnegative matrix factorization")
21969 "This package provides an implementation of robust nonnegative matrix
21970 factorization (rNMF). The rNMF algorithm decomposes a nonnegative high
21971 dimension data matrix into the product of two low rank nonnegative matrices,
21972 while detecting and trimming outliers. The main function is @code{rnmf()}.
21973 The package also includes a visualization tool, @code{see()}, that arranges
21974 and prints vectorized images.")
21975 (license license:gpl2+)))
21977 (define-public r-randtoolbox
21979 (name "r-randtoolbox")
21984 (uri (cran-uri "randtoolbox" version))
21987 "005x2igljc6vm0nsmkld9aqjqz1ccwapc8z3aw5c3ivh4n2bghf9"))))
21988 (properties `((upstream-name . "randtoolbox")))
21989 (build-system r-build-system)
21992 (home-page "https://cran.r-project.org/web/packages/randtoolbox/")
21993 (synopsis "Toolbox for pseudo and quasi random number generation")
21995 "This package provides
21998 @item pseudo random generators, such as general linear
21999 congruential generators, multiple recursive generators and generalized
22000 feedback shift register (SF-Mersenne Twister algorithm and WELL
22003 @item quasi random generators, such as the Torus algorithm, the Sobol
22004 sequence, the Halton sequence (including the Van der Corput sequence), and
22006 @item some generator tests: the gap test, the serial test, the poker test.
22009 See e.g. Gentle (2003) @url{doi:10.1007/b97336}.")
22010 (license license:bsd-3)))
22012 (define-public r-lhs
22019 (uri (cran-uri "lhs" version))
22022 "0fb3bc3s5pbwg92qkjbg7v8ah36wm6qs05vf098hwjakr7f6yg3s"))))
22023 (properties `((upstream-name . "lhs")))
22024 (build-system r-build-system)
22025 (propagated-inputs (list r-rcpp))
22028 (home-page "https://github.com/bertcarnell/lhs")
22029 (synopsis "Latin Hypercube Samples")
22031 "This package provides a number of methods for creating and augmenting
22032 Latin Hypercube Samples.")
22033 (license license:gpl3)))
22035 (define-public r-acebayes
22037 (name "r-acebayes")
22042 (uri (cran-uri "acebayes" version))
22045 "11bffz430gdfdaxjx3simig66vhynmx6l1ylac4q2shcmj52nx73"))))
22046 (properties `((upstream-name . "acebayes")))
22047 (build-system r-build-system)
22049 (list r-compare r-lhs r-randtoolbox r-rcpp r-rcpparmadillo))
22050 (home-page "https://cran.r-project.org/web/packages/acebayes/")
22051 (synopsis "Optimal Bayesian experimental design using the ACE algorithm")
22053 "Finding an optimal Bayesian experimental design involves maximizing an
22054 objective function given by the expectation of some appropriately chosen
22055 utility function with respect to the joint distribution of unknown
22056 quantities (including responses). This objective function is usually not
22057 available in closed form and the design space can be continuous and of high
22058 dimensionality. This package uses @dfn{Approximate Coordinate Exchange} (ACE)
22059 to maximise an approximation to the expectation of the utility function.")
22060 (license license:gpl2)))
22062 (define-public r-acet
22069 (uri (cran-uri "ACEt" version))
22072 "0b5lfpnppyk0237phr2aybhx29nhm8ngwk2qa1y4lshrvsw97wg4"))))
22073 (properties `((upstream-name . "ACEt")))
22074 (build-system r-build-system)
22076 (list r-bh r-mass r-rcpp r-rcpparmadillo))
22077 (home-page "https://cran.r-project.org/web/packages/ACEt/")
22078 (synopsis "Estimating dynamic heritability and twin model comparison")
22080 "This package supports twin models that are able to estimate the dynamic
22081 behaviour of the variance components in the classical twin models with respect
22082 to age using B-splines and P-splines.")
22083 (license license:gpl2+)))
22085 (define-public r-acfmperiod
22087 (name "r-acfmperiod")
22092 (uri (cran-uri "acfMPeriod" version))
22095 "1yww8isfrbs2v9s94hx7p2imyszcgadwafdgpj438n2ik0q6p9d5"))))
22096 (properties `((upstream-name . "acfMPeriod")))
22097 (build-system r-build-system)
22100 (home-page "https://cran.r-project.org/web/packages/acfMPeriod/")
22101 (synopsis "Estimation of the ACF from the M-periodogram")
22103 "This package support non-robust and robust computations of the sample
22104 autocovariance (ACOVF) and sample autocorrelation functions (ACF) of
22105 univariate and multivariate processes. The methodology consists in reversing
22106 the diagonalization procedure involving the periodogram or the
22107 cross-periodogram and the Fourier transform vectors, and, thus, obtaining the
22108 ACOVF or the ACF as discussed in Fuller (1995)
22109 @url{doi:10.1002/9780470316917}. The robust version is obtained by fitting
22110 robust M-regressors to obtain the M-periodogram or M-cross-periodogram as
22111 discussed in Reisen et al. (2017) @url{doi:10.1016/j.jspi.2017.02.008}.")
22112 (license license:gpl2+)))
22114 (define-public r-gamlss-data
22116 (name "r-gamlss-data")
22121 (uri (cran-uri "gamlss.data" version))
22124 "07mpdl4h9rwmnpl9jmsn6ig8ji11an6pyjfsvg62h2alapwbdcyv"))))
22125 (properties `((upstream-name . "gamlss.data")))
22126 (build-system r-build-system)
22127 (home-page "http://www.gamlss.org/")
22128 (synopsis "GAMLSS data")
22130 "This package provides data used as examples to demonstrate GAMLSS
22132 ;; Either version of the license
22133 (license (list license:gpl2 license:gpl3))))
22135 (define-public r-gamlss
22142 (uri (cran-uri "gamlss" version))
22145 "0xih19zqgpjl5qv5j38ana6x29y84shn2jfl2lk4kaw3q7yx86b6"))))
22146 (properties `((upstream-name . "gamlss")))
22147 (build-system r-build-system)
22149 (list r-gamlss-data r-gamlss-dist r-mass r-nlme r-survival))
22150 (home-page "http://www.gamlss.org/")
22151 (synopsis "Generalized additive models for location scale and shape")
22153 "This package provides functions for fitting the generalized additive
22154 models for location scale and shape introduced by Rigby and
22155 Stasinopoulos (2005), @url{doi:10.1111/j.1467-9876.2005.00510.x}. The models
22156 use a distributional regression approach where all the parameters of the
22157 conditional distribution of the response variable are modelled using
22158 explanatory variables.")
22159 ;; Either version of the license
22160 (license (list license:gpl2 license:gpl3))))
22162 (define-public r-acid
22169 (uri (cran-uri "acid" version))
22172 "030i0y8s283ivbsmjccpbv9v7mgbcg2jk9df7vgcbbns74swf9hd"))))
22173 (properties `((upstream-name . "acid")))
22174 (build-system r-build-system)
22176 (list r-gamlss r-gamlss-dist r-hmisc))
22177 (home-page "https://cran.r-project.org/web/packages/acid/")
22178 (synopsis "Analysing conditional income distributions")
22180 "This package provides functions for the analysis of income distributions
22181 for subgroups of the population as defined by a set of variables like age,
22182 gender, region, etc. This entails a Kolmogorov-Smirnov test for a mixture
22183 distribution as well as functions for moments, inequality measures, entropy
22184 measures and polarisation measures of income distributions. This package thus
22185 aides the analysis of income inequality by offering tools for the exploratory
22186 analysis of income distributions at the disaggregated level.")
22187 (license license:gpl3)))
22189 (define-public r-acm4r
22196 (uri (cran-uri "acm4r" version))
22199 "1wqzc35i1rshx0zlmas8y4qkkvy6h9r4i4apscjjv1xg2wjflzxa"))))
22200 (properties `((upstream-name . "acm4r")))
22201 (build-system r-build-system)
22202 (propagated-inputs (list r-mass))
22203 (home-page "https://cran.r-project.org/web/packages/acm4r/")
22204 (synopsis "Align-and-count method comparisons of RFLP data")
22206 "This is a package to compare sequence fragment lengths or molecular
22207 weights from pairs of lanes. The number of matching bands in the
22208 @dfn{Restriction Fragment Length Polymorphism} (RFLP) data is calculated using
22209 the align-and-count method.")
22210 ;; Any version of the GPL
22211 (license (list license:gpl2+ license:gpl3+))))
22213 (define-public r-filelock
22215 (name "r-filelock")
22220 (uri (cran-uri "filelock" version))
22223 "00ql5fw1hidpfnm0szaavf43ahmsnvdbi8i5lr1nrcc90yaiaadc"))))
22224 (properties `((upstream-name . "filelock")))
22225 (build-system r-build-system)
22226 (home-page "https://github.com/r-lib/filelock")
22227 (synopsis "Portable file locking")
22229 "This library lets you place an exclusive or shared lock on a file using
22230 the appropriate system call provided by the underlying operating system.")
22231 (license license:expat)))
22233 (define-public r-filematrix
22235 (name "r-filematrix")
22240 (uri (cran-uri "filematrix" version))
22243 "1v3aj1ng742msb0sfdnjsbqb508mqjf8jlq2v33vxldhradw5w0b"))))
22244 (properties `((upstream-name . "filematrix")))
22245 (build-system r-build-system)
22246 ;; These inputs are needed for vignettes
22248 (list r-knitr r-rmarkdown))
22249 (home-page "https://github.com/andreyshabalin/filematrix")
22250 (synopsis "File-backed matrix class with convenient read and write access")
22252 "This package provides an interface for working with large matrices
22253 stored in files, not in computer memory. It supports multiple non-character
22254 data types (double, integer, logical and raw) of various sizes (e.g. 8 and 4
22255 byte real values). Access to parts of the matrix is done by indexing, exactly
22256 as with usual R matrices. It supports very large matrices; the package has
22257 been tested on multi-terabyte matrices. It allows for more than 2^32 rows or
22258 columns, ad allows for quick addition of extra columns to a filematrix.")
22259 (license license:lgpl3)))
22261 (define-public r-acmeeqtl
22263 (name "r-acmeeqtl")
22268 (uri (cran-uri "ACMEeqtl" version))
22271 "049xjv2ym35bbn43zwi68cq27fwdh404vp0r2ca5gxgmmx8kj1cz"))))
22272 (properties `((upstream-name . "ACMEeqtl")))
22273 (build-system r-build-system)
22275 (list r-filematrix))
22276 (home-page "https://github.com/andreyshabalin/ACMEeqtl")
22277 (synopsis "Estimation of interpretable eQTL effect sizes")
22279 "This package provides a non-linear model, termed ACME, that reflects a
22280 parsimonious biological model for allelic contributions of cis-acting eQTLs.
22281 With non-linear least-squares algorithm the maximum likelihood parameters can
22282 be estimated. The ACME model provides interpretable effect size estimates and
22283 p-values with well controlled Type-I error.")
22284 (license license:lgpl3)))
22286 (define-public r-acmer
22293 (uri (cran-uri "acmeR" version))
22296 "000b2hqlhj93958nddw0fqb15ahigs08najv2miivym046x04mf7"))))
22297 (properties `((upstream-name . "acmeR")))
22298 (build-system r-build-system)
22299 (propagated-inputs (list r-foreign))
22300 (home-page "https://cran.r-project.org/web/packages/acmeR/")
22301 (synopsis "ACME estimator of bird and bat mortality by wind turbines")
22303 "This package provides an implementation of the ACME estimator, described
22304 in Wolpert (2015), ACME: A Partially Periodic Estimator of Avian & Chiropteran
22305 Mortality at Wind Turbines. Unlike most other models, this estimator supports
22306 decreasing-hazard Weibull model for persistence; decreasing search proficiency
22307 as carcasses age; variable bleed-through at successive searches; and interval
22308 mortality estimates. The package provides, based on search data, functions
22309 for estimating the mortality inflation factor in Frequentist and Bayesian
22311 (license license:expat)))
22313 (define-public r-r-huge
22320 (uri (cran-uri "R.huge" version))
22323 "13p558qalv60pgr24nsm6mi92ryj65rsbqa6pgdwy0snjqx12bgi"))))
22324 (properties `((upstream-name . "R.huge")))
22325 (build-system r-build-system)
22327 (list r-r-methodss3 r-r-oo r-r-utils))
22328 (home-page "https://github.com/HenrikBengtsson/R.huge")
22329 (synopsis "Methods for accessing huge amounts of data")
22331 "This is a deprecated package for accessing huge amounts of data.
22332 Cross-platform alternatives are the following packages: bigmemory (CRAN),
22333 ff (CRAN), or BufferedMatrix (Bioconductor). The main usage of it was inside
22334 the @code{aroma.affymetrix} package.")
22335 (license license:lgpl2.1+)))
22337 (define-public r-r-filesets
22339 (name "r-r-filesets")
22344 (uri (cran-uri "R.filesets" version))
22347 "08xv8b3c81nf54viyr3w912al18483k5gfnjpg7bxbdfk70dfzbh"))))
22348 (properties `((upstream-name . "R.filesets")))
22349 (build-system r-build-system)
22352 (modify-phases %standard-phases
22353 (add-after 'unpack 'set-HOME
22354 (lambda _ (setenv "HOME" "/tmp"))))))
22356 (list r-digest r-r-cache r-r-methodss3 r-r-oo r-r-utils))
22357 (home-page "https://github.com/HenrikBengtsson/R.filesets")
22358 (synopsis "Easy handling of and access to files")
22360 "This package provides classes and methods to locate, setup, subset,
22361 navigate and iterate file sets, i.e. sets of files located in one or more
22362 directories on the file system. The API is designed such that these classes
22363 can be extended via inheritance to provide a richer API for special file
22364 formats. Moreover, a specific name format is defined such that filenames and
22365 directories can be considered to have full names which consists of a name
22366 followed by comma-separated tags. This adds additional flexibility to
22367 identify file sets and individual files.")
22368 (license license:lgpl2.1+)))
22370 (define-public r-r-devices
22372 (name "r-r-devices")
22377 (uri (cran-uri "R.devices" version))
22380 "1djz6vm1b7sjvx1q319dl47gbnz9kvipaxcz9i0spyp094lv3m62"))))
22381 (properties `((upstream-name . "R.devices")))
22382 (build-system r-build-system)
22384 (list r-base64enc r-r-methodss3 r-r-oo r-r-utils))
22385 (home-page "https://github.com/HenrikBengtsson/R.devices")
22386 (synopsis "Unified handling of graphics devices")
22388 "This package provides functions for creating plots and image files in a
22389 unified way regardless of output format (EPS, PDF, PNG, SVG, TIFF, WMF, etc.).
22390 Default device options as well as scales and aspect ratios are controlled in a
22391 uniform way across all device types. Switching output format requires minimal
22392 changes in code. This package is ideal for large-scale batch processing,
22393 because it will never leave open graphics devices or incomplete image files
22394 behind, even on errors or user interrupts.")
22395 (license license:lgpl2.1+)))
22397 (define-public r-acnr
22404 (uri (cran-uri "acnr" version))
22407 "087hq4i7jp67ba2finzsqjfnqbiprl33na6ryjv9zqzsdawj9cym"))))
22408 (properties `((upstream-name . "acnr")))
22409 (build-system r-build-system)
22410 (home-page "https://github.com/mpierrejean/acnr")
22411 (synopsis "Annotated copy-number regions")
22413 "This package provides SNP array data from different types of copy-number
22414 regions. These regions were identified manually by the authors of the package
22415 and may be used to generate realistic data sets with known truth.")
22416 (license license:lgpl2.1+)))
22418 (define-public r-acopula
22425 (uri (cran-uri "acopula" version))
22428 "0vvbbw8pfs9jwfz5c57lw48pr0qj661r0ys007q6zf9jmlrhx1ln"))))
22429 (properties `((upstream-name . "acopula")))
22430 (build-system r-build-system)
22431 (home-page "https://cran.r-project.org/web/packages/acopula/")
22432 (synopsis "Modelling dependence with multivariate Archimax copulas")
22434 "Archimax copulas are a mixture of Archimedean and EV copulas. This
22435 package provides definitions of several parametric families of generator and
22436 dependence function, computes CDF and PDF, estimates parameters, tests for
22437 goodness of fit, generates random sample and checks copula properties for
22438 custom constructs. In the 2-dimensional case explicit formulas for density
22439 are used, contrary to higher dimensions when all derivatives are linearly
22440 approximated. Several non-archimax families (normal, FGM, Plackett) are
22441 provided as well.")
22442 (license license:gpl2)))
22444 (define-public r-tuner
22451 (uri (cran-uri "tuneR" version))
22454 "1sd0drxzbdy71bh35fccg9ajhpdhdpy0m9nja2lw82p1pzhyl7jn"))))
22455 (properties `((upstream-name . "tuneR")))
22456 (build-system r-build-system)
22457 (propagated-inputs (list r-signal))
22458 (home-page "https://cran.r-project.org/web/packages/tuneR/")
22459 (synopsis "Analysis of music and speech")
22461 "This is a package for the analysis of music and speech. Analyze music
22462 and speech, extract features like MFCCs, handle wave files and their
22463 representation in various ways, read MP3, read MIDI, perform steps of a
22464 transcription, ...")
22465 ;; Either of these versions.
22466 (license (list license:gpl2 license:gpl3))))
22468 (define-public r-seewave
22475 (uri (cran-uri "seewave" version))
22478 "0bi1l47l3846c18k6h2vrv0xp9xh00n544a578jrndahzrj1hfwl"))))
22479 (properties `((upstream-name . "seewave")))
22480 (build-system r-build-system)
22485 (home-page "http://rug.mnhn.fr/seewave")
22486 (synopsis "Sound analysis and synthesis")
22488 "This package provides functions for analysing, manipulating, displaying,
22489 editing and synthesizing time waves (particularly sound). This package
22490 processes time analysis (oscillograms and envelopes), spectral content,
22491 resonance quality factor, entropy, cross correlation and autocorrelation,
22492 zero-crossing, dominant frequency, analytic signal, frequency coherence, 2D
22493 and 3D spectrograms and many other analyses.")
22494 (license license:gpl2+)))
22496 (define-public r-acousticndlcoder
22498 (name "r-acousticndlcoder")
22503 (uri (cran-uri "AcousticNDLCodeR" version))
22506 "1fgzgwanpv2pzy74xdk3hamc44p8qch467wh163dxby8jr9ik0sb"))))
22508 `((upstream-name . "AcousticNDLCodeR")))
22509 (build-system r-build-system)
22511 (list r-seewave r-tuner r-zoo))
22512 (home-page "https://cran.r-project.org/web/packages/AcousticNDLCodeR/")
22513 (synopsis "Coding sound files for use with NDL")
22515 "Make acoustic cues to use with the R package @code{ndl}.
22516 The package implements functions used in the PLoS ONE paper \"Words from
22517 spontaneous conversational speech can be recognized with human-like accuracy
22518 by an error-driven learning algorithm that discriminates between meanings
22519 straight from smart acoustic features, bypassing the phoneme as recognition
22520 unit.\" @url{doi:10.1371/journal.pone.0174623}")
22521 (license license:gpl2+)))
22523 (define-public r-acp
22530 (uri (cran-uri "acp" version))
22533 "0lcwbjcyyr32m6qjmjqh25qjwrbyqj1n092xhgbhxzd8fslppnmn"))))
22534 (properties `((upstream-name . "acp")))
22535 (build-system r-build-system)
22537 (list r-quantmod r-tseries))
22538 (home-page "https://cran.r-project.org/web/packages/acp/")
22539 (synopsis "Autoregressive conditional Poisson")
22541 "This package supports the analysis of count data exhibiting
22542 autoregressive properties, using the @dfn{Autoregressive Conditional Poisson}
22543 model (ACP(p,q)) proposed by Heinen (2003).")
22544 (license license:gpl2)))
22546 (define-public r-ada
22553 (uri (cran-uri "ada" version))
22556 "1h3a07czp0w3hrhjcg1fz721y8vsfclzqi3rq8qfzgpfb4h1f06r"))))
22557 (properties `((upstream-name . "ada")))
22558 (build-system r-build-system)
22559 (propagated-inputs (list r-rpart))
22560 (home-page "https://cran.r-project.org/web/packages/ada/")
22561 (synopsis "Stochastic boosting")
22563 "This package provides a straightforward, well-documented, and broad
22564 boosting routine for classification, ideally suited for small to
22565 moderate-sized data sets. It performs discrete, real, and gentle boost under
22566 both exponential and logistic loss on a given data set.")
22567 ;; Any version of the GPL.
22568 (license (list license:gpl2+ license:gpl3+))))
22570 (define-public r-genalg
22577 (uri (cran-uri "genalg" version))
22580 "1y4qz1s85zpd1r3259gr542arssf2vpd4drhy0wnq5q47ignrvna"))))
22581 (properties `((upstream-name . "genalg")))
22582 (build-system r-build-system)
22583 (home-page "https://github.com/egonw/genalg")
22584 (synopsis "R based genetic algorithm")
22586 "This package provides an R based genetic algorithm for binary and
22587 floating point chromosomes.")
22588 (license license:gpl2)))
22590 (define-public r-kernelfactory
22592 (name "r-kernelfactory")
22597 (uri (cran-uri "kernelFactory" version))
22600 "001kw9k3ivd4drd4mwqapkkk3f4jgljiaprhg2630hmll064s89j"))))
22601 (properties `((upstream-name . "kernelFactory")))
22602 (build-system r-build-system)
22604 (list r-auc r-genalg r-kernlab r-randomforest))
22605 (home-page "https://cran.r-project.org/web/packages/kernelFactory/")
22606 (synopsis "Ensemble of kernel machines")
22608 "Kernel factory is an ensemble method where each base classifier (random
22609 forest) is fit on the kernel matrix of a subset of the training data.")
22610 (license license:gpl2+)))
22612 (define-public r-dummies
22619 (uri (cran-uri "dummies" version))
22622 "01f84crqx17xd6xy55qxlvsj3knm8lhw7jl26p2rh2w3y0nvqlbm"))))
22623 (properties `((upstream-name . "dummies")))
22624 (build-system r-build-system)
22625 (home-page "https://decisionpatterns.com")
22626 (synopsis "Create dummy/indicator variables flexibly and efficiently")
22628 "This package lets you expand factors, characters and other eligible
22629 classes into dummy/indicator variables.")
22630 (license license:gpl2+)))
22632 (define-public r-acrm
22639 (uri (cran-uri "aCRM" version))
22642 "0kzp568hd9c9a9qgniia5s5gv0q5f89xfvvwpzb197gqhs3x092v"))))
22643 (properties `((upstream-name . "aCRM")))
22644 (build-system r-build-system)
22646 (list r-ada r-dummies r-kernelfactory r-randomforest))
22647 (home-page "https://cran.r-project.org/web/packages/aCRM/")
22648 (synopsis "Convenience functions for analytical customer relationship management")
22650 "This package provides convenience functions for data preparation and
22651 modeling often used in @dfn{analytical customer relationship
22652 management} (aCRM).")
22653 (license license:gpl2+)))
22655 (define-public r-tree
22661 (uri (cran-uri "tree" version))
22664 "13jwdxx3na16mly176n01zdkaqn4a8x9fc43rq5xx5vx31drkkr1"))))
22665 (build-system r-build-system)
22666 (home-page "https://cran.r-project.org/web/packages/tree/")
22667 (synopsis "Classification and regression trees")
22668 (description "This package provides procedures to work with classification
22669 and regression trees.")
22670 (license license:gpl2+)))
22672 (define-public r-treeclust
22674 (name "r-treeclust")
22679 (uri (cran-uri "treeClust" version))
22682 "1s7kh6q0bkixsygrip95zf1bi10ihddsa5lq9dfxd68yh8rsby6z"))))
22683 (properties `((upstream-name . "treeClust")))
22684 (build-system r-build-system)
22686 (list r-cluster r-rpart))
22687 (home-page "https://cran.r-project.org/web/packages/treeClust/")
22688 (synopsis "Cluster distances through trees")
22690 "This package provides tools to create a measure of inter-point
22691 dissimilarity useful for clustering mixed data, and, optionally, perform the
22693 (license license:gpl2+)))
22695 (define-public r-acrosstic
22697 (name "r-acrosstic")
22702 (uri (cran-uri "AcrossTic" version))
22705 "03180h79jhjd66ibrnsfp3yyp2jlfysp7cymw46phzj2palghsc0"))))
22706 (properties `((upstream-name . "AcrossTic")))
22707 (build-system r-build-system)
22709 (list r-lpsolve r-treeclust))
22710 (home-page "https://cran.r-project.org/web/packages/AcrossTic/")
22711 (synopsis "Cost-minimal regular spanning subgraph with TreeClust")
22713 "This is a package for constructing minimum-cost regular spanning
22714 subgraph as part of a non-parametric two-sample test for equality of
22716 (license license:gpl2+)))
22718 (define-public r-acrt
22725 (uri (cran-uri "acrt" version))
22728 "0y9ndcq8ffpfrv7w9rikm4zn68jpsj6baqisq9kp2433xrwzdb6s"))))
22729 (properties `((upstream-name . "acrt")))
22730 (build-system r-build-system)
22732 (list r-rcpp r-rcppeigen r-sandwich))
22733 (home-page "https://cran.r-project.org/web/packages/acrt/")
22734 (synopsis "Autocorrelation robust testing")
22736 "This package provides functions for testing affine hypotheses on the
22737 regression coefficient vector in regression models with autocorrelated
22739 (license license:gpl2)))
22741 (define-public r-acs
22748 (uri (cran-uri "acs" version))
22751 "0ajw9rf8l8akcvgqvbxjvryc6wjx74521xyxswz2b0bky3m6kah5"))))
22752 (properties `((upstream-name . "acs")))
22753 (build-system r-build-system)
22755 (list r-httr r-plyr r-rcpp r-stringr r-xml))
22756 (home-page "https://dusp.mit.edu/faculty/ezra-haber-glenn")
22757 (synopsis "Work with data from the US Census")
22759 "This package provides a general toolkit for downloading, managing,
22760 analyzing, and presenting data from the
22761 @url{https://www.census.gov/data/developers/data-sets.html, U.S. Census},
22762 including SF1 (Decennial short-form), SF3 (Decennial long-form), and the
22763 American Community Survey (ACS). Confidence intervals provided with ACS data
22764 are converted to standard errors to be bundled with estimates in complex
22765 @code{acs} objects. The package provides new methods to conduct standard
22766 operations on @code{acs} objects and present/plot data in statistically
22767 appropriate ways.")
22768 (license license:gpl3)))
22770 (define-public r-acss-data
22772 (name "r-acss-data")
22777 (uri (cran-uri "acss.data" version))
22780 "09kl4179ipr8bq19g89xcdi1xxs397zcx5cvgp6viy8gn687ilgv"))))
22781 (properties `((upstream-name . "acss.data")))
22782 (build-system r-build-system)
22783 (home-page "http://complexitycalculator.com/methodology.html")
22784 (synopsis "Data for algorithmic complexity of short strings")
22786 "This is a data only package providing the algorithmic complexity of
22787 short strings, computed using the coding theorem method. For a given set of
22788 symbols in a string, all possible or a large number of random samples of
22789 Turing machines with a given number of states (e.g., 5) and number of symbols
22790 corresponding to the number of symbols in the strings were simulated until
22791 they reached a halting state or failed to end. This package contains data on
22792 4.5 million strings from length 1 to 12 simulated on Turing machines with 2,
22793 4, 5, 6, and 9 symbols. The complexity of the string corresponds to the
22794 distribution of the halting states.")
22795 (license license:gpl2+)))
22797 (define-public r-acss
22804 (uri (cran-uri "acss" version))
22807 "0cqa60544f58l5qd7h6xmsir40b9hqnq6pqgd5hfx2j2l5n7qhmk"))))
22808 (properties `((upstream-name . "acss")))
22809 (build-system r-build-system)
22811 (list r-acss-data r-zoo))
22812 (home-page "http://complexitycalculator.com/methodology.html")
22813 (synopsis "Algorithmic complexity for short strings")
22815 "The main purpose of this package is to provide the algorithmic
22816 complexity for short strings, an approximation of the Kolmogorov Complexity of
22817 a short string using the coding theorem method. While the database containing
22818 the complexity is provided in the data only package @code{acss.data}, this
22819 package provides functions accessing the data such as @code{prob_random}
22820 returning the posterior probability that a given string was produced by a
22821 random process. In addition, two traditional (but problematic) measures of
22822 complexity are also provided: entropy and change complexity.")
22823 (license license:gpl2+)))
22825 (define-public r-acswr
22832 (uri (cran-uri "ACSWR" version))
22835 "195vjrkang5cl7gwsna0aq4p0h4jym9xg9yh94bnf8vq6wf8j83n"))))
22836 (properties `((upstream-name . "ACSWR")))
22837 (build-system r-build-system)
22840 (home-page "https://cran.r-project.org/web/packages/ACSWR/")
22841 (synopsis "Companion package for the book \"A Course in Statistics with R\"")
22843 "This is a companion package for the book \"A Course in Statistics with
22844 R\" (ISBN 978-1-119-15272-9.)")
22845 (license license:gpl2)))
22847 (define-public r-alabama
22850 (version "2022.4-1")
22854 (uri (cran-uri "alabama" version))
22857 "0v6kl6ndm8wvp9xzya3x4gj5kh03qgx13x5vyzn410wsndcjiim8"))))
22858 (properties `((upstream-name . "alabama")))
22859 (build-system r-build-system)
22860 (propagated-inputs (list r-numderiv))
22861 (home-page "https://cran.r-project.org/web/packages/alabama/")
22862 (synopsis "Constrained nonlinear optimization")
22864 "Alabama stands for Augmented Lagrangian Adaptive Barrier Minimization
22865 Algorithm; it is used for optimizing smooth nonlinear objective functions with
22866 constraints. Linear or nonlinear equality and inequality constraints are
22868 (license license:gpl2+)))
22870 (define-public r-gdina
22877 (uri (cran-uri "GDINA" version))
22880 "1slq1npsq8s8aghnrpm6vvc6kxj4svz0kr2x0akblndrcr25wxjr"))))
22881 (properties `((upstream-name . "GDINA")))
22882 (build-system r-build-system)
22895 (home-page "https://github.com/Wenchao-Ma/GDINA")
22896 (synopsis "Generalized DINA model framework")
22898 "This package provides a set of psychometric tools for cognitive
22899 diagnosis modeling based on the generalized deterministic inputs, noisy and
22900 gate (G-DINA) model by de la Torre (2011) @url{doi:10.1007/s11336-011-9207-7}
22901 and its extensions, including the sequential G-DINA model by Ma and de la
22902 Torre (2016) @url{doi:10.1111/bmsp.12070} for polytomous responses, and the
22903 polytomous G-DINA model by Chen and de la Torre
22904 @url{doi:10.1177/0146621613479818} for polytomous attributes. Joint attribute
22905 distribution can be independent, saturated, higher-order, loglinear smoothed
22906 or structured. Q-matrix validation, item and model fit statistics, model
22907 comparison at test and item level and differential item functioning can also
22908 be conducted. A graphical user interface is also provided.")
22909 (license license:gpl3)))
22911 (define-public r-actcd
22918 (uri (cran-uri "ACTCD" version))
22921 "0mzjxxr2zfdidw8ibh6w8mvpkw3q3nvngqi05g9ind26ckvk053p"))))
22922 (properties `((upstream-name . "ACTCD")))
22923 (build-system r-build-system)
22925 (list r-gdina r-r-methodss3))
22928 (home-page "https://cran.r-project.org/web/packages/ACTCD/")
22929 (synopsis "Asymptotic classification theory for cognitive diagnosis")
22931 "This is a package supporting cluster analysis for cognitive diagnosis
22932 based on the Asymptotic Classification Theory (Chiu, Douglas & Li, 2009;
22933 @url{doi:10.1007/s11336-009-9125-0}). Given the sample statistic of
22934 sum-scores, cluster analysis techniques can be used to classify examinees into
22935 latent classes based on their attribute patterns. In addition to the
22936 algorithms used to classify data, three labeling approaches are proposed to
22937 label clusters so that examinees' attribute profiles can be obtained.")
22938 (license license:gpl2+)))
22940 (define-public r-ineq
22947 (uri (cran-uri "ineq" version))
22950 "09fsxyrh0j7mwmb5hkhmrzgcy7kf85jxkh7zlwpgqgcsyl1n91z0"))))
22951 (properties `((upstream-name . "ineq")))
22952 (build-system r-build-system)
22953 (home-page "https://cran.r-project.org/web/packages/ineq/")
22954 (synopsis "Measuring inequality, concentration, and poverty")
22956 "This package provides tools for measuring inequality, concentration, and
22957 poverty measures. It provides both empirical and theoretical Lorenz curves.")
22958 ;; Either of these two versions.
22959 (license (list license:gpl2 license:gpl3))))
22961 (define-public r-actfrag
22968 (uri (cran-uri "ActFrag" version))
22971 "08r3gwjz4fkyy85dxqix0ffm5xyq45032qv3snnzxnlqxslxbqn1"))))
22972 (properties `((upstream-name . "ActFrag")))
22973 (build-system r-build-system)
22975 (list r-accelerometry r-dplyr r-ineq r-survival r-tidyr))
22976 (home-page "https://github.com/junruidi/ActFrag")
22977 (synopsis "Activity fragmentation metrics extraction")
22979 "This package provides functions to extract commonly used fragmentation
22980 metrics to quantify time accumulation strategies based on minute level
22981 actigraphy-measured activity counts data.")
22982 (license license:gpl3)))
22984 (define-public r-ash
22991 (uri (cran-uri "ash" version))
22994 "1ay2a2agdmiz7zzvn26mli0x0iwk09g5pp4yy1r23knhkp1pn2lb"))))
22995 (properties `((upstream-name . "ash")))
22996 (build-system r-build-system)
22997 (native-inputs (list gfortran))
22998 (home-page "https://cran.r-project.org/web/packages/ash/")
22999 (synopsis "David Scott's ASH routines")
23001 "This package provides David Scott's ASH routines ported from S-PLUS to
23003 (license license:gpl2+)))
23005 (define-public r-hdrcde
23012 (uri (cran-uri "hdrcde" version))
23015 "16qlk44cjvn2s0vzaf915df65ksdx20dbxhy7fpdqins46hccha3"))))
23016 (properties `((upstream-name . "hdrcde")))
23017 (build-system r-build-system)
23025 (native-inputs (list gfortran))
23026 (home-page "http://pkg.robjhyndman.com/hdrcde")
23027 (synopsis "Highest density regions and conditional density estimation")
23029 "This is a package for the computation of highest density regions in one
23030 and two dimensions, kernel estimation of univariate density functions
23031 conditional on one covariate, and multimodal regression.")
23032 (license license:gpl3)))
23034 (define-public r-rainbow
23041 (uri (cran-uri "rainbow" version))
23044 "11vfcck17d2xjc049ci5i8l1nqv345anmd110gdz7654i1pj9lb3"))))
23045 (properties `((upstream-name . "rainbow")))
23046 (build-system r-build-system)
23054 (home-page "https://cran.r-project.org/web/packages/rainbow/")
23055 (synopsis "Bagplots, boxplots and rainbow plots for functional data")
23057 "This is a package for visualizing functional data and identifying
23058 functional outliers with bagplots, boxplots and rainbow plots.")
23059 (license license:gpl3)))
23061 (define-public r-fds
23068 (uri (cran-uri "fds" version))
23071 "1284vncixrzrz9x6b52gslrbrbia07sd0xac7nwdqhp5f5v5wfi0"))))
23072 (properties `((upstream-name . "fds")))
23073 (build-system r-build-system)
23075 (list r-rainbow r-rcurl))
23076 (home-page "https://cran.r-project.org/web/packages/fds/")
23077 (synopsis "Functional data sets")
23078 (description "This package contains a list of functional time series,
23079 sliced functional time series, and functional data sets. Functional time
23080 series is a special type of functional data observed over time. Sliced
23081 functional time series is a special type of functional time series with a time
23082 variable observed over time.")
23083 (license license:gpl2+)))
23085 (define-public r-fda
23092 (uri (cran-uri "fda" version))
23095 "1lvp4i4hqz650k27sa5flbdlkalihc79xy9128hfhr16h6wi8n10"))))
23096 (properties `((upstream-name . "fda")))
23097 (build-system r-build-system)
23099 (list r-desolve r-fds))
23102 (home-page "https://www.functionaldata.org")
23103 (synopsis "Functional data analysis")
23105 "These functions were developed to support functional data analysis as
23106 described in Ramsay, J. O. and Silverman, B. W. (2005) Functional Data
23107 Analysis. The package includes data sets and script files working many
23109 (license license:gpl2+)))
23111 (define-public r-actigraphy
23113 (name "r-actigraphy")
23118 (uri (cran-uri "Actigraphy" version))
23121 "0bpmvszzv5fm72nar3wgnmfl5am7znqfajmlbv38ihkbi7jbwk20"))))
23122 (properties `((upstream-name . "Actigraphy")))
23123 (build-system r-build-system)
23126 (home-page "https://cran.r-project.org/web/packages/Actigraphy/")
23127 (synopsis "Actigraphy data analysis")
23129 "This package provides tools for functional linear modeling and analysis
23130 of actigraphy data.")
23131 (license license:asl2.0)))
23133 (define-public r-activedriver
23135 (name "r-activedriver")
23140 (uri (cran-uri "ActiveDriver" version))
23143 "10c7ga48fwvpd5mc4dqiyw4kc2l0iz5qn4hg7xk15r1qmm5rsipa"))))
23144 (properties `((upstream-name . "ActiveDriver")))
23145 (build-system r-build-system)
23148 (home-page "https://cran.r-project.org/web/packages/ActiveDriver/")
23149 (synopsis "Tools for finding cancer driver proteins")
23151 "This package provides a mutation analysis tool that discovers cancer
23152 driver genes with frequent mutations in protein signalling sites such as
23153 post-translational modifications (phosphorylation, ubiquitination, etc). The
23154 Poisson generalized linear regression model identifies genes where cancer
23155 mutations in signalling sites are more frequent than expected from the
23156 sequence of the entire gene. Integration of mutations with signalling
23157 information helps find new driver genes and propose candidate mechanisms to
23159 (license license:gpl2+)))
23161 (define-public r-activitycounts
23163 (name "r-activitycounts")
23168 (uri (cran-uri "activityCounts" version))
23171 "0zgxr2sk3a8kmygfxx1p5hnrfwdkxx7php6jlrhm8wv6052ck8jz"))))
23173 `((upstream-name . "activityCounts")))
23174 (build-system r-build-system)
23176 (list r-lubridate r-magrittr r-seewave r-signal r-tibble))
23177 (home-page "https://github.com/walkabillylab/activityCounts")
23178 (synopsis "Generate ActiLife counts")
23180 "ActiLife generates activity counts from data collected by Actigraph
23181 accelerometers. Actigraph is one of the most common research-grade
23182 accelerometers. There is considerable research validating and developing
23183 algorithms for human activity using ActiLife counts. Unfortunately, ActiLife
23184 counts are proprietary and difficult to implement if researchers use different
23185 accelerometer brands. The code creates ActiLife counts from raw acceleration
23186 data for different accelerometer brands.")
23187 (license license:gpl3)))
23189 (define-public r-activityindex
23191 (name "r-activityindex")
23196 (uri (cran-uri "ActivityIndex" version))
23199 "1zj2b6x31a1kxl80rarmkrlm7ack4154mrkbqs3fpi48zpmjbgd5"))))
23200 (properties `((upstream-name . "ActivityIndex")))
23201 (build-system r-build-system)
23203 (list r-data-table r-matrixstats r-r-utils))
23206 (home-page "https://cran.r-project.org/web/packages/ActivityIndex/")
23207 (synopsis "Activity Index calculation using raw accelerometry data")
23209 "This is a package to read raw accelerometry from GT3X+ accelerometry
23210 data and plain table data to calculate the Activity Index from Bai et
23211 al. (2016) @url{doi:10.1371/journal.pone.0160644}.")
23212 (license license:gpl3)))
23214 (define-public r-activpal
23216 (name "r-activpal")
23221 (uri (cran-uri "activPAL" version))
23224 "1h6hp5z89ji73gdzxy1dgbfwjysiy5lvcqh90xagpb7sa7ahs3na"))))
23225 (properties `((upstream-name . "activPAL")))
23226 (build-system r-build-system)
23234 (home-page "https://cran.r-project.org/web/packages/activPAL")
23235 (synopsis "Processing and chart generation from activPAL events files")
23237 "This package contains functions to generate pre-defined summary
23238 statistics from activPAL events files. The package also contains functions to
23239 produce informative graphics that visualize physical activity behaviour and
23240 trends. This includes generating graphs that align physical activity
23241 behaviour with additional time based observations described by other data
23242 sets, such as sleep diaries and continuous glucose monitoring data.")
23243 (license license:gpl3)))
23245 (define-public r-activpalprocessing
23247 (name "r-activpalprocessing")
23252 (uri (cran-uri "activpalProcessing" version))
23255 "1y0bjx2qx53iy930y9iww4q1yzjj8y16cwgixk1mq3w4g1f116d1"))))
23257 `((upstream-name . "activpalProcessing")))
23258 (build-system r-build-system)
23261 (home-page "https://cran.r-project.org/web/packages/activpalProcessing/")
23262 (synopsis "Process activPAL events files")
23264 "This package performs estimation of physical activity and sedentary
23265 behavior variables from activPAL events files.")
23266 ;; Either version of the GPL.
23267 (license (list license:gpl2 license:gpl3))))
23269 (define-public r-actogrammr
23271 (name "r-actogrammr")
23276 (uri (cran-uri "actogrammr" version))
23279 "1jzvarmd41yqlrkagzlc8m19n5mn0w0b36fy50lyvgrfsafjfbqa"))))
23280 (properties `((upstream-name . "actogrammr")))
23281 (build-system r-build-system)
23283 (list r-dplyr r-ggplot2 r-lubridate r-readr r-tidyr))
23284 (home-page "https://cran.r-project.org/web/packages/actogrammr/")
23285 (synopsis "Read in activity data and plot actograms")
23287 "Read in activity measurements from standard file formats used by
23288 circadian rhythm researchers, currently only ClockLab format, and process and
23289 plot the data. The central type of plot is the actogram, as first described
23290 in \"Activity and distribution of certain wild mice in relation to biotic
23291 communities\" by MS Johnson (1926) @url{doi:10.2307/1373575}.")
23292 (license license:gpl3)))
23294 (define-public r-expint
23301 (uri (cran-uri "expint" version))
23304 "01d0a7pc4qx7044a0cymnv5ld88r90vdvlqjbnzg9qlfbizdgyvw"))))
23305 (properties `((upstream-name . "expint")))
23306 (build-system r-build-system)
23307 (home-page "https://gitlab.com/vigou3/expint")
23308 (synopsis "Exponential integral and incomplete Gamma function")
23310 "This package provides the exponential integrals @code{E_1(x)},
23311 @code{E_2(x)}, @code{E_n(x)} and @code{Ei(x)}, and the incomplete gamma
23312 function @code{G(a, x)} defined for negative values of its first argument.
23313 The package also gives easy access to the underlying C routines through an
23314 API; see the package vignette for details.")
23315 (license license:gpl2+)))
23317 (define-public r-actuar
23324 (uri (cran-uri "actuar" version))
23327 "0dhpaivyga0jwvw1csagbx74biy9jfkw4a8sa871579njxl1x7p1"))))
23328 (properties `((upstream-name . "actuar")))
23329 (build-system r-build-system)
23330 (propagated-inputs (list r-expint))
23331 (home-page "https://gitlab.com/vigou3/actuar")
23332 (synopsis "Actuarial functions and heavy tailed distributions")
23334 "This package provides functions and data sets for actuarial science:
23335 modeling of loss distributions; risk theory and ruin theory; simulation of
23336 compound models, discrete mixtures and compound hierarchical models;
23337 credibility theory. It boasts support for many additional probability
23338 distributions to model insurance loss amounts and loss frequency: 19
23339 continuous heavy tailed distributions; the Poisson-inverse Gaussian discrete
23340 distribution; zero-truncated and zero-modified extensions of the standard
23341 discrete distributions. It also supports phase-type distributions commonly
23342 used to compute ruin probabilities.")
23343 (license license:gpl2+)))
23345 (define-public r-bmp
23352 (uri (cran-uri "bmp" version))
23355 "0jd67r11bn98hjwgyr6gas423787xy7ji2hq7ay80blkkcj91xxx"))))
23356 (properties `((upstream-name . "bmp")))
23357 (build-system r-build-system)
23358 (home-page "https://cran.r-project.org/web/packages/bmp/")
23359 (synopsis "Read Bitmap (BMP) images")
23361 "This package provides pure R tools to read BMP format images. It is
23362 currently limited to 8 bit greyscale images and 24, 32 bit (A)RGB images.")
23363 (license license:gpl2+)))
23365 (define-public r-readbitmap
23367 (name "r-readbitmap")
23372 (uri (cran-uri "readbitmap" version))
23375 "14825906l326w59g6apy00j55jg3h5kx2r6s031f4gdkbrc7szbk"))))
23376 (properties `((upstream-name . "readbitmap")))
23377 (build-system r-build-system)
23379 (list libjpeg-turbo libpng))
23381 (list r-bmp r-jpeg r-png r-tiff))
23382 (home-page "https://github.com/jefferis/readbitmap")
23383 (synopsis "Unified interface to read bitmap images (BMP, JPEG, PNG, TIFF)")
23385 "This package provides tools to identify and read BMP, JPEG, PNG, and
23386 TIFF format bitmap images. Identification defaults to the use of the magic
23387 number embedded in the file rather than the file extension.")
23388 (license license:gpl2+)))
23390 (define-public r-imager
23393 (version "0.42.13")
23397 (uri (cran-uri "imager" version))
23400 "0zygnmxwbbmj5i2l2affzdz90xvsa7b5pbkzkhjbm40is69rh2nr"))))
23401 (properties `((upstream-name . "imager")))
23402 (build-system r-build-system)
23404 (list fftw libtiff libx11 zlib))
23416 (list pkg-config r-knitr))
23417 (home-page "https://dahtah.github.io/imager/")
23418 (synopsis "Image processing library")
23420 "This is a package for fast image processing for images in up to 4
23421 dimensions (two spatial dimensions, one time/depth dimension, one color
23422 dimension). It provides most traditional image processing tools (filtering,
23423 morphology, transformations, etc.) as well as various functions for easily
23424 analyzing image data using R. The package wraps @url{http://cimg.eu, CImg}, a
23425 simple, modern C++ library for image processing.")
23426 (license license:lgpl3)))
23428 (define-public r-acuityview
23430 (name "r-acuityview")
23435 (uri (cran-uri "AcuityView" version))
23438 "0f0iclmnwdc8ixiiai4svk4x1g3pjy7dhm3cm58fv6ckx12d3d2l"))))
23439 (properties `((upstream-name . "AcuityView")))
23440 (build-system r-build-system)
23442 (list r-fftwtools r-imager r-plotrix))
23443 (home-page "https://cran.r-project.org/web/packages/AcuityView/")
23444 (synopsis "Display scenes as seen by an animal with less acute vision")
23446 "This package provides a simple method for representing a visual scene as
23447 it may be seen by an animal with less acute vision.")
23448 (license license:gpl2+)))
23450 (define-public r-caret
23457 (uri (cran-uri "caret" version))
23460 "048mp325ndfl83a8p4dkd1b6zh5bws4gg9kxka5ss8qsj8m4m08x"))))
23461 (build-system r-build-system)
23476 (home-page "https://github.com/topepo/caret")
23477 (synopsis "Classification and regression training")
23479 "This package provides miscellaneous functions for training and plotting
23480 classification and regression models.")
23481 (license license:gpl2+)))
23483 (define-public r-adabag
23490 (uri (cran-uri "adabag" version))
23493 "109wrl1pwvmyv2l909hrvk7dg4aa9pv449mvdycp50zwrsw9w0a7"))))
23494 (properties `((upstream-name . "adabag")))
23495 (build-system r-build-system)
23497 (list r-caret r-doparallel r-foreach r-rpart))
23498 (home-page "https://cran.r-project.org/web/packages/adabag/")
23499 (synopsis "Multiclass AdaBoost.M1, SAMME and Bagging")
23501 "This package implements Freund and Schapire's Adaboost.M1 algorithm and
23502 Breiman's Bagging algorithm using classification trees as individual
23503 classifiers. Once these classifiers have been trained, they can be used to
23504 predict on new data. Also, cross validation estimation of the error can be
23506 (license license:gpl2+)))
23508 (define-public r-adagio
23515 (uri (cran-uri "adagio" version))
23518 "0ihv05402iq003m0338f85pnqnlnrmx0pf1mg8cz9sgi5h98mbnl"))))
23519 (properties `((upstream-name . "adagio")))
23520 (build-system r-build-system)
23523 (home-page "https://cran.r-project.org/web/packages/adagio/")
23524 (synopsis "Discrete and global optimization routines")
23526 "This package provides methods and algorithms for discrete optimization,
23527 e.g. knapsack and subset sum procedures, derivative-free Nelder-Mead and
23528 Hooke-Jeeves minimization, and some (evolutionary) global optimization
23530 (license license:gpl3+)))
23532 (define-public r-univoutl
23534 (name "r-univoutl")
23539 (uri (cran-uri "univOutl" version))
23542 "1hhpxrpmp2wbrynx9xjndnp2sccirgky2x6ksd6yk6phmk0rbzjp"))))
23543 (properties `((upstream-name . "univOutl")))
23544 (build-system r-build-system)
23546 (list r-hmisc r-robustbase))
23547 (home-page "https://github.com/marcellodo/univOutl")
23548 (synopsis "Detection of univariate outliers")
23550 "This package provides well-known outlier detection techniques in the
23551 univariate case. Methods to deal with skewed distribution are included too.
23552 The Hidiroglou-Berthelot (1986) method to search for outliers in ratios of
23553 historical data is implemented as well. When available, survey weights can be
23554 used in outliers detection.")
23555 (license license:gpl2+)))
23557 (define-public r-tolerance
23559 (name "r-tolerance")
23564 (uri (cran-uri "tolerance" version))
23567 "001snzr2ipag3zprynydlbi9prkjzrllc054qh7m0qwkb3r19jjd"))))
23568 (properties `((upstream-name . "tolerance")))
23569 (build-system r-build-system)
23571 (list r-mass r-rgl))
23572 (home-page "https://cran.r-project.org/web/packages/tolerance/")
23573 (synopsis "Statistical tolerance intervals and regions")
23575 "This package provides functions for estimating tolerance
23576 limits (intervals) for various univariate distributions (binomial, Cauchy,
23577 discrete Pareto, exponential, two-parameter exponential, extreme value,
23578 hypergeometric, Laplace, logistic, negative binomial, negative hypergeometric,
23579 normal, Pareto, Poisson-Lindley, Poisson, uniform, and Zipf-Mandelbrot),
23580 Bayesian normal tolerance limits, multivariate normal tolerance regions,
23581 nonparametric tolerance intervals, tolerance bands for regression
23582 settings (linear regression, nonlinear regression, nonparametric regression,
23583 and multivariate regression), and analysis of variance tolerance intervals.
23584 Visualizations are also available for most of these settings.")
23585 (license license:gpl2+)))
23587 ;; Keep this in sync with the liblantern package.
23588 (define-public r-torch
23595 (uri (cran-uri "torch" version))
23597 (base32 "163pvl3gyz7l2fmqhgg4k6pw4dmvfir71yp9l5ra2k4zc32lz166"))))
23598 (properties `((upstream-name . "torch")))
23599 (build-system r-build-system)
23603 #~(modify-phases %standard-phases
23604 (add-after 'install 'link-libraries
23605 (lambda* (#:key inputs #:allow-other-keys)
23606 (let ((deps (string-append #$output "/site-library/torch/deps")))
23610 inputs "/lib/python3.9/site-packages/torch/lib/libtorch.so")
23611 (string-append deps "/libtorch.so"))
23614 inputs "/lib/liblantern.so")
23615 (string-append deps "/liblantern.so"))))))))
23617 (list python-pytorch-for-r-torch
23630 (native-inputs (list r-knitr))
23631 (home-page "https://torch.mlverse.org/docs")
23632 (synopsis "Tensors and neural networks with GPU acceleration")
23634 "This package provides functionality to define and train neural networks
23635 similar to PyTorch but written entirely in R using the libtorch library. It
23636 also supports low-level tensor operations and GPU acceleration.")
23637 (license license:expat)))
23639 (define-public r-additivitytests
23641 (name "r-additivitytests")
23646 (uri (cran-uri "additivityTests" version))
23649 "048ds90wqjdjy1nyhna3m06asdklbh8sx1n556kss2j1r1pma1sw"))))
23651 `((upstream-name . "additivityTests")))
23652 (build-system r-build-system)
23653 (home-page "https://github.com/simecek/additivityTests")
23654 (synopsis "Additivity tests in the two way Anova with single sub-class numbers")
23656 "This package provides an implementation of the Tukey, Mandel,
23657 Johnson-Graybill, LBI, Tusell and modified Tukey non-additivity tests.")
23658 (license license:gpl3)))
23660 (define-public r-flexclust
23662 (name "r-flexclust")
23667 (uri (cran-uri "flexclust" version))
23670 "13akk3w6a76jpws5v9108c3hdmb8i6gm0sc06lr2hqly0pgpfyfn"))))
23671 (properties `((upstream-name . "flexclust")))
23672 (build-system r-build-system)
23674 (list r-class r-lattice r-modeltools))
23675 (home-page "https://cran.r-project.org/web/packages/flexclust/")
23676 (synopsis "Flexible cluster algorithms")
23678 "The main function @code{kcca} implements a general framework for
23679 k-centroids cluster analysis supporting arbitrary distance measures and
23680 centroid computation. Further cluster methods include hard competitive
23681 learning, neural gas, and QT clustering. There are numerous visualization
23682 methods for cluster results (neighborhood graphs, convex cluster hulls,
23683 barcharts of centroids, ...), and bootstrap methods for the analysis of
23684 cluster stability.")
23685 (license license:gpl2)))
23687 (define-public r-biclust
23694 (uri (cran-uri "biclust" version))
23697 "0lgyc2f04dhr65cwga78pradxsdzgjrpp8vphchqn60ab1z95dlp"))))
23698 (properties `((upstream-name . "biclust")))
23699 (build-system r-build-system)
23701 (list r-additivitytests
23708 (home-page "https://cran.r-project.org/web/packages/biclust/")
23709 (synopsis "BiCluster algorithms")
23711 "The main function @code{biclust()} provides several algorithms to find
23712 biclusters in two-dimensional data, spectral, plaid model, xmotifs, and bimax.
23713 In addition, the package provides methods for data
23714 preprocessing (normalization and discretization), visualization, and
23715 validation of bicluster solutions.")
23716 (license license:gpl3)))
23718 (define-public r-icge
23725 (uri (cran-uri "ICGE" version))
23728 "0w6hbi3h98q6gsxqbb43p95v6xykgrasxcjivwm8hw9fly4avxyi"))))
23729 (properties `((upstream-name . "ICGE")))
23730 (build-system r-build-system)
23732 (list r-cluster r-fastcluster r-mass))
23733 (home-page "https://cran.r-project.org/web/packages/ICGE/")
23734 (synopsis "Cluster estimation and identification of atypical units")
23736 "ICGE is a package that helps to estimate the number of real clusters in
23737 data as well as to identify atypical units. The underlying methods are based
23738 on distances rather than on unit x variables.")
23739 (license license:gpl2+)))
23741 (define-public r-depth
23744 (version "2.1-1.1")
23748 (uri (cran-uri "depth" version))
23751 "0szy0027nh4ps1z919i740i50app5q7cfyg1fj7pdyl45nbl8k6m"))))
23752 (properties `((upstream-name . "depth")))
23753 (build-system r-build-system)
23755 (list r-abind r-circular r-rgl))
23758 (home-page "https://cran.r-project.org/web/packages/depth/")
23759 (synopsis "Nonparametric depth functions for multivariate analysis")
23761 "This package provides tools for depth functions methodology applied to
23762 multivariate analysis. Besides allowing calculation of depth values and
23763 depth-based location estimators, the package includes functions or drawing
23764 contour plots and perspective plots of depth functions. Euclidean and
23765 spherical depths are supported.")
23766 (license license:gpl2)))
23768 (define-public r-archetypes
23770 (name "r-archetypes")
23771 (version "2.2-0.1")
23775 (uri (cran-uri "archetypes" version))
23778 "0ibxsr173ib77gjhid91m85s8gjii4mi2w3d52q5301igv20p7r0"))))
23779 (properties `((upstream-name . "archetypes")))
23780 (build-system r-build-system)
23782 (list r-modeltools r-nnls))
23783 (home-page "https://cran.r-project.org/web/packages/archetypes")
23784 (synopsis "Archetypal analysis")
23786 "The main function @code{archetypes} implements a framework for
23787 archetypal analysis supporting arbitrary problem solving mechanisms for the
23788 different conceptual parts of the algorithm.")
23789 (license license:gpl2+)))
23791 (define-public r-shapes
23798 (uri (cran-uri "shapes" version))
23801 "1p9fr95zk3q2v277c5ksb0nh26mcpzwjzjb2lmag51z6hck8cb66"))))
23802 (properties `((upstream-name . "shapes")))
23803 (build-system r-build-system)
23805 (list r-mass r-minpack-lm r-rgl r-scatterplot3d))
23806 (home-page "http://www.maths.nottingham.ac.uk/~ild/shapes")
23807 (synopsis "Statistical shape analysis")
23809 "This package provides routines for the statistical analysis of landmark
23810 shapes, including Procrustes analysis, graphical displays, principal
23811 components analysis, permutation and bootstrap tests, thin-plate spline
23812 transformation grids and comparing covariance matrices. See Dryden, I.L. and
23813 Mardia, K.V. (2016). Statistical shape analysis, with Applications in R (2nd
23814 Edition), John Wiley and Sons.")
23815 (license license:gpl2)))
23817 (define-public r-anthropometry
23819 (name "r-anthropometry")
23824 (uri (cran-uri "Anthropometry" version))
23827 "0vxjlzxv16bygw8n57f25msq5bd1dydg41my92ximah0nzzvbg41"))))
23828 (properties `((upstream-name . "Anthropometry")))
23829 (build-system r-build-system)
23842 (home-page "https://cran.r-project.org/web/packages/Anthropometry/")
23843 (synopsis "Statistical methods for anthropometric data")
23845 "This package provides statistical methods especially developed to
23846 analyze anthropometric data. These methods are aimed at providing effective
23847 solutions to some commons problems related to Ergonomics and Anthropometry.
23848 They are based on clustering, the statistical concept of data depth,
23849 statistical shape analysis and archetypal analysis.")
23850 (license license:gpl2+)))
23852 (define-public r-anndata
23855 (version "0.7.5.3")
23859 (uri (cran-uri "anndata" version))
23861 (base32 "115v7gdilayd18hd519vzkixp2s6rvvrd1inc1i6amn7d0spy8r1"))))
23862 (properties `((upstream-name . "anndata")))
23863 (build-system r-build-system)
23864 (propagated-inputs (list r-assertthat r-matrix r-r6 r-reticulate))
23865 (native-inputs (list r-knitr))
23866 (home-page "https://anndata.dynverse.org")
23867 (synopsis "Anndata for R")
23869 "This package provides a reticulate wrapper for the Python package
23870 @code{anndata}. It provides a scalable way of keeping track of data and
23871 learned annotations. It is used to read from and write to the h5ad file
23873 (license license:expat)))
23875 (define-public r-adamethods
23877 (name "r-adamethods")
23882 (uri (cran-uri "adamethods" version))
23885 "150awbd3skb1mqca18bqjykhyycqw8crviw66s6qrcnmcsbk77pj"))))
23886 (properties `((upstream-name . "adamethods")))
23887 (build-system r-build-system)
23889 (list r-anthropometry
23896 (home-page "https://cran.r-project.org/web/packages/adamethods/")
23897 (synopsis "Archetypoid algorithms and anomaly detection")
23899 "This package is a collection of several algorithms to obtain
23900 archetypoids with small and large databases and with both classical
23901 multivariate data and functional data (univariate and multivariate). Some of
23902 these algorithms also detect anomalies (outliers).")
23903 (license license:gpl2+)))
23905 (define-public r-idpmisc
23912 (uri (cran-uri "IDPmisc" version))
23915 "0zy6mxqa8arq0vvhsdcifzm3085c23rnwa1n36fhircph1xwvfdw"))))
23916 (properties `((upstream-name . "IDPmisc")))
23917 (build-system r-build-system)
23920 (home-page "https://cran.r-project.org/web/packages/IDPmisc/")
23921 (synopsis "Functions for data analyses and visualization")
23923 "This package provides different high-level graphics functions for
23924 displaying large datasets, displaying circular data in a very flexible way,
23925 finding local maxima, brewing color ramps, drawing nice arrows, zooming
23926 2D-plots, creating figures with differently colored margin and plot region.
23927 In addition, the package contains auxiliary functions for data manipulation
23928 like omitting observations with irregular values or selecting data by logical
23929 vectors, which include NAs. Other functions are especially useful in
23930 spectroscopy and analyses of environmental data: robust baseline fitting,
23931 finding peaks in spectra, converting humidity measures.")
23932 (license license:gpl3+)))
23934 (define-public r-qqman
23941 (uri (cran-uri "qqman" version))
23944 "1a6qp5wv9bvwjchfw8x4jh48hkynlnfr21a8vqgnswldvwbq7njq"))))
23945 (properties `((upstream-name . "qqman")))
23946 (build-system r-build-system)
23948 (list r-calibrate))
23951 (home-page "https://cran.r-project.org/web/packages/qqman/")
23952 (synopsis "Q-Q and Manhattan plots for GWAS data")
23954 "This package allows you to create Q-Q and Manhattan plots for GWAS data
23955 from PLINK results.")
23956 (license license:gpl3)))
23958 (define-public r-gghighlight
23960 (name "r-gghighlight")
23965 (uri (cran-uri "gghighlight" version))
23967 (base32 "0bxgn4srxz1qhawqa8ck57p8hg5ikwfa9ll03zmnn8fb19akwm2v"))))
23968 (properties `((upstream-name . "gghighlight")))
23969 (build-system r-build-system)
23971 (list r-dplyr r-ggplot2 r-ggrepel r-lifecycle r-purrr r-rlang r-tibble))
23972 (native-inputs (list r-knitr))
23973 (home-page "https://github.com/yutannihilation/gghighlight/")
23974 (synopsis "Highlight lines and points in ggplot2")
23975 (description "Suppose we have data that has so many series that it is hard
23976 to identify them by their colors as the differences are so subtle. With
23977 gghighlight we can highlight those lines that match certain criteria. The
23978 result is a usual @code{ggplot} object, so it is fully customizable and can be
23979 used with custom themes and facets.")
23980 (license license:expat)))
23982 (define-public r-ggplot-multistats
23984 (name "r-ggplot-multistats")
23989 (uri (cran-uri "ggplot.multistats" version))
23992 "1afzfa86vc484bcwpg7m1ky03jpax584rigzgai8w06pifkmz0il"))))
23994 `((upstream-name . "ggplot.multistats")))
23995 (build-system r-build-system)
23997 (list r-ggplot2 r-hexbin r-rlang r-scales))
23998 (home-page "https://github.com/flying-sheep/ggplot.multistats")
23999 (synopsis "Multiple summary statistics for binned stats/geometries")
24001 "This package provides the ggplot binning layer @code{stat_summaries_hex()},
24002 which functions similar to its singular form, but allows the use of multiple
24003 statistics per bin. Those statistics can be mapped to multiple bin
24005 (license license:gpl3)))
24007 (define-public r-knn-covertree
24009 (name "r-knn-covertree")
24014 (uri (cran-uri "knn.covertree" version))
24017 "0msfcmwydws7q7m5jdb0dxab0nkbl7mq5llg6v3r4qrnlvrdggvz"))))
24018 (properties `((upstream-name . "knn.covertree")))
24019 (build-system r-build-system)
24021 (list r-matrix r-rcpp r-rcppeigen))
24022 (home-page "https://github.com/flying-sheep/knn.covertree")
24023 (synopsis "Accurate kNN Implementation with multiple distance measures")
24025 "Similarly to the FNN package, this package allows calculation of the k
24026 nearest neighbors (kNN) of a data matrix. The implementation is based on
24027 cover trees introduced by Alina Beygelzimer, Sham Kakade, and John
24028 Langford (2006) @url{doi:10.1145/1143844.1143857}.")
24029 (license license:agpl3+)))
24031 (define-public r-poibin
24038 (uri (cran-uri "poibin" version))
24041 "1sxryvwwz6ldsnkzdy56p8c895s5yvpcai9ndyjv1x5q3l05wf9v"))))
24042 (properties `((upstream-name . "poibin")))
24043 (build-system r-build-system)
24044 (home-page "https://cran.r-project.org/web/packages/poibin/")
24045 (synopsis "Poisson binomial distribution")
24047 "This package provides an implementation of both the exact and
24048 approximation methods for computing the @dfn{cumulative distribution
24049 function} (CDF) of the Poisson binomial distribution. It also provides the
24050 @dfn{probability mass function} (PMF), quantile function, and random number
24051 generation for the Poisson binomial distribution.")
24052 (license license:gpl2)))
24054 (define-public r-diagram
24061 (uri (cran-uri "diagram" version))
24064 "1r3lyl0h7mk9cfg8smr3jydfkjdawaphnxibkxfjqa7029vkxh79"))))
24065 (properties `((upstream-name . "diagram")))
24066 (build-system r-build-system)
24069 (home-page "https://cran.r-project.org/web/packages/diagram/")
24070 (synopsis "Visualize simple graphs (networks) and plot flow diagrams")
24072 "This package provides tools to visualize simple graphs (networks) based
24073 on a transition matrix, utilities to plot flow diagrams, visualizing webs,
24074 electrical networks, etc. It also includes supporting material for the book
24075 \"A practical guide to ecological modelling - using R as a simulation
24076 platform\" by Karline Soetaert and Peter M.J. Herman (2009) and the book
24077 \"Solving Differential Equations in R\" by Karline Soetaert, Jeff Cash and
24078 Francesca Mazzia (2012).")
24079 (license license:gpl2+)))
24081 (define-public r-lim
24088 (uri (cran-uri "LIM" version))
24091 "0d9bgyd0mnag8wds993dsvlbpkhyakydlzwc3nghxzv2n8504hjj"))))
24092 (properties `((upstream-name . "LIM")))
24093 (build-system r-build-system)
24095 (list r-diagram r-limsolve))
24096 (home-page "https://cran.r-project.org/web/packages/LIM/")
24097 (synopsis "Linear inverse model examples and solution methods")
24099 "This package provides functions that read and solve linear inverse
24100 problems (food web problems, linear programming problems).")
24101 (license license:gpl2+)))
24103 (define-public r-shinycssloaders
24105 (name "r-shinycssloaders")
24110 (uri (cran-uri "shinycssloaders" version))
24113 "0r3xm273lhdhzbs2mkgw1m2kwb7z1dh1pzya8yxy5vacda1l2ikl"))))
24115 `((upstream-name . "shinycssloaders")))
24116 (build-system r-build-system)
24118 (list r-digest r-glue r-shiny))
24119 (home-page "https://github.com/andrewsali/shinycssloaders")
24120 (synopsis "Add CSS loading animations to Shiny outputs")
24122 "This package provides tools to create a lightweight Shiny wrapper for
24123 the css-loaders created by Luke Hass
24124 @url{https://github.com/lukehaas/css-loaders}. Wrapping a Shiny output will
24125 automatically show a loader when the output is (re)calculating.")
24126 (license license:gpl3)))
24128 (define-public r-rsvg
24135 (uri (cran-uri "rsvg" version))
24138 "096w4d1gvfc65d4jg7ykp23k9f7cf7f8zvzfhvhd7qkfsbjpxqkj"))))
24139 (properties `((upstream-name . "rsvg")))
24140 (build-system r-build-system)
24142 (list librsvg zlib))
24144 (list pkg-config r-knitr))
24145 (home-page "https://github.com/jeroen/rsvg#readme")
24146 (synopsis "Render SVG images into PDF, PNG, PostScript, or Bitmap arrays")
24148 "This package allows you to render vector-based SVG images into
24149 high-quality custom-size bitmap arrays using the librsvg2 library. The
24150 resulting bitmap can be written to e.g. PNG, JPEG or WEBP format. In
24151 addition, the package can convert images directly to various formats such as
24152 PDF or PostScript.")
24153 (license license:expat)))
24155 (define-public r-influencer
24157 (name "r-influencer")
24158 (version "0.1.0.1")
24162 (uri (cran-uri "influenceR" version))
24165 "0rj7rm236vn3v8302nwl12s0kvpv6xpdbm3q3gxk7vgwfl8nzi33"))))
24166 (properties `((upstream-name . "influenceR")))
24167 (build-system r-build-system)
24169 (list r-igraph r-matrix))
24170 (home-page "https://github.com/rcc-uchicago/influenceR")
24171 (synopsis "Tools to quantify structural importance of nodes in a network")
24173 "This package provides functionality to compute various node centrality
24174 measures on networks. Included are functions to compute betweenness
24175 centrality (by utilizing Madduri and Bader's SNAP library), implementations of
24176 Burt's constraint and @dfn{effective network size} (ENS) metrics, Borgatti's
24177 algorithm to identify key players, and Valente's bridging metric. The
24178 betweenness, Key Players, and bridging implementations are parallelized with
24180 (license license:gpl2)))
24182 (define-public r-emplik
24189 (uri (cran-uri "emplik" version))
24192 "1kw8g8j075bsicdvgkjf4870rfv5c30gvmw6qkkaz3ki22x74w77"))))
24193 (properties `((upstream-name . "emplik")))
24194 (build-system r-build-system)
24197 (home-page "https://www.ms.uky.edu/~mai/EmpLik.html")
24198 (synopsis "Empirical likelihood ratio for censored/truncated data")
24200 "This package provides empirical likelihood ratio tests for
24201 means/quantiles/hazards from possibly censored and/or truncated data. It also
24203 (license license:gpl2+)))
24205 (define-public r-imputeyn
24207 (name "r-imputeyn")
24212 (uri (cran-uri "imputeYn" version))
24215 "1b21w1aa5f7yiq8k0wa86wvbg4ij7f6ldwn6asfqwb0b90rvsgvs"))))
24216 (properties `((upstream-name . "imputeYn")))
24217 (build-system r-build-system)
24219 (list r-boot r-emplik r-mvtnorm r-quadprog r-survival))
24220 (home-page "https://cran.r-project.org/web/packages/imputeYn/")
24221 (synopsis "Impute last largest censored observation under weighted least squares")
24223 "This package allows for the imputation of the last largest censored
24224 observantions. This method brings less bias and more efficient estimates for
24226 (license license:gpl2)))
24228 (define-public r-adapenetclass
24230 (name "r-adapenetclass")
24235 (uri (cran-uri "AdapEnetClass" version))
24238 "01k3mj4g1ckbng7wkzzn9h0k9yf01cpnnkly0sjda574c5jhj0rc"))))
24239 (properties `((upstream-name . "AdapEnetClass")))
24240 (build-system r-build-system)
24242 (list r-glmnet r-imputeyn r-lars r-quadprog))
24243 (home-page "https://cran.r-project.org/web/packages/AdapEnetClass/")
24244 (synopsis "Class of adaptive elastic net methods for censored data")
24246 "This package provides methods for variable selection for AFT models.")
24247 (license license:gpl2)))
24249 (define-public r-flock
24256 (uri (cran-uri "flock" version))
24259 "1zg93p74icj4bhxnmnssj2xp6vw4yaksyavq03497v33xfpdxss7"))))
24260 (properties `((upstream-name . "flock")))
24261 (build-system r-build-system)
24262 (propagated-inputs (list r-rcpp))
24263 (home-page "https://cran.r-project.org/web/packages/flock/")
24264 (synopsis "Process synchronization using file locks")
24266 "This package implements synchronization between R processes (spawned by
24267 using the @code{parallel} package for instance) using file locks. It supports
24268 both exclusive and shared locking.")
24269 (license license:asl2.0)))
24271 (define-public r-archivist
24273 (name "r-archivist")
24278 (uri (cran-uri "archivist" version))
24281 "0q1qysack30xzxdbvvi56rk7r85hsj4ghls9r70ki7bl3rqwr4c9"))))
24282 (properties `((upstream-name . "archivist")))
24283 (build-system r-build-system)
24295 (home-page "https://pbiecek.github.io/archivist/")
24296 (synopsis "Tools for storing, restoring and searching for R objects")
24298 "Data exploration and modelling is a process in which a lot of data
24299 artifacts are produced. Artifacts like: subsets, data aggregates, plots,
24300 statistical models, different versions of data sets and different versions of
24301 results. Archivist helps to store and manage artifacts created in R. It
24302 allows you to store selected artifacts as binary files together with their
24303 metadata and relations. Archivist allows sharing artifacts with others. It
24304 can look for already created artifacts by using its class, name, date of the
24305 creation or other properties. It also makes it easy to restore such
24307 (license license:gpl2)))
24309 (define-public r-versions
24311 (name "r-versions")
24316 (uri (cran-uri "versions" version))
24319 "0zm49j785dgv7fyr1yl9q5f0dsk8hhpim5q5bpkgrkzv7pwjribd"))))
24320 (properties `((upstream-name . "versions")))
24321 (build-system r-build-system)
24322 (home-page "https://cran.r-project.org/web/packages/versions/")
24323 (synopsis "Query and install specific versions of CRAN packages")
24325 "This package allows you to install specified versions of R packages
24326 hosted on CRAN and provides functions to list available versions and the
24327 versions of currently installed packages.")
24328 (license license:bsd-3)))
24330 (define-public r-adapr
24337 (uri (cran-uri "adapr" version))
24340 "1s57jdbi5pik56xjz1d4438ax6cywg2yq2s47h5g6wrwvpgr1qfw"))))
24341 (properties `((upstream-name . "adapr")))
24342 (build-system r-build-system)
24359 (home-page "https://cran.r-project.org/web/packages/adapr/")
24360 (synopsis "Implementation of an accountable data analysis process")
24362 "This package tracks reading and writing within R scripts that are
24363 organized into a directed acyclic graph. It contains an interactive Shiny
24364 application @code{adaprApp()}. It uses Git and file hashes to track version
24365 histories of inputs and outputs.")
24366 (license license:lgpl2.0)))
24368 (define-public r-adapsamp
24370 (name "r-adapsamp")
24375 (uri (cran-uri "AdapSamp" version))
24378 "1jayjrsiib2ij4rxxj59g71r3xhzl5yqh0lhi8k6cfy03i7dkvis"))))
24379 (properties `((upstream-name . "AdapSamp")))
24380 (build-system r-build-system)
24381 (propagated-inputs (list r-pracma))
24382 (home-page "https://cran.r-project.org/web/packages/AdapSamp/")
24383 (synopsis "Adaptive sampling algorithms")
24385 "For distributions whose probability density functions are log-concave,
24386 the adaptive rejection sampling algorithm can be used to build envelope
24387 functions for sampling. For others, the modified adaptive rejection sampling
24388 algorithm, the concave-convex adaptive rejection sampling algorithm, and the
24389 adaptive slice sampling algorithm can be used. This R package mainly includes
24390 these four functions: @code{rARS()}, @code{rMARS()}, @code{rCCARS()}, and
24391 @code{rASS()}. These functions can realize sampling based on the algorithms
24393 (license license:gpl2)))
24395 (define-public r-adaptalint
24397 (name "r-adaptalint")
24402 (uri (cran-uri "adaptalint" version))
24405 "15qdcvnnbgcps8j5k79354wsc9alswijv8lcafg2i3lghaw536yf"))))
24406 (properties `((upstream-name . "adaptalint")))
24407 (build-system r-build-system)
24409 (list r-dplyr r-lintr r-purrr))
24410 (home-page "https://cran.r-project.org/web/packages/adaptalint/")
24411 (synopsis "Check R code style")
24413 "This package provides tools to infer the code style (which style rules
24414 are followed and which ones are not) from one package and use it to check
24415 another. This makes it easier to find and correct the most important problems
24417 (license license:gpl3)))
24419 (define-public r-fracdiff
24421 (name "r-fracdiff")
24426 (uri (cran-uri "fracdiff" version))
24429 "1dhfjlhr9sb38qgpsx0sm73l9lgc13d0fk32l7fmjfnalhr3n45q"))))
24430 (properties `((upstream-name . "fracdiff")))
24431 (build-system r-build-system)
24432 (home-page "https://github.com/mmaechler/fracdiff")
24434 "Fractionally differenced ARIMA aka ARFIMA(P,d,q) models")
24436 "This package provides tools for the maximum likelihood estimation of the
24437 parameters of a fractionally differenced ARIMA(p,d,q) model (Haslett and
24438 Raftery, Appl.Statistics, 1989); it includes inference and basic methods.")
24439 (license license:gpl2+)))
24441 (define-public r-forecast
24443 (name "r-forecast")
24448 (uri (cran-uri "forecast" version))
24451 "0zvn44k7npxai8kj0hgxaaqv1hgd8rxicnvj4cg7wfl8ba4yn0cz"))))
24452 (properties `((upstream-name . "forecast")))
24453 (build-system r-build-system)
24468 (list r-knitr)) ; needed for vignettes
24469 (home-page "https://pkg.robjhyndman.com/forecast/")
24470 (synopsis "Forecasting functions for time series and linear models")
24472 "This package provides methods and tools for displaying and analysing
24473 univariate time series forecasts including exponential smoothing via state
24474 space models and automatic ARIMA modelling.")
24475 (license license:gpl3)))
24477 (define-public r-formattable
24479 (name "r-formattable")
24484 (uri (cran-uri "formattable" version))
24486 (base32 "1vdxi0xmg019qyzjrp8bkjxciz245jcxsrkhfzd44ynqcwi4s3ag"))))
24487 (properties `((upstream-name . "formattable")))
24488 (build-system r-build-system)
24490 (list r-htmltools r-htmlwidgets r-lifecycle r-rmarkdown))
24493 (home-page "https://github.com/renkun-ken/formattable")
24494 (synopsis "Print vectors and data frames with text fromatting")
24496 "This R package provides functions to create formattable vectors and data
24497 frames. @emph{Formattable} vectors are printed with text formatting, and
24498 formattable data frames are printed with multiple types of formatting in HTML
24499 to improve the readability of data presented in tabular form rendered in web
24501 (license license:expat)))
24503 (define-public r-xmisc
24510 (uri (cran-uri "Xmisc" version))
24513 "11gwlcyxhz1p50m68cnqrxmisdk99v8vrsbvyr7k67f0kvsznzs1"))))
24514 (properties `((upstream-name . "Xmisc")))
24515 (build-system r-build-system)
24516 (home-page "https://cran.r-project.org/package=Xmisc")
24518 "Xiaobei's miscellaneous classes and functions")
24520 "This package provides Xiaobei's miscellaneous classes and functions,
24521 which are useful when developing R packages for @dfn{object oriented
24522 programming} (OOP) using R Reference Class.")
24523 (license license:gpl2+)))
24525 (define-public r-proxyc
24532 (uri (cran-uri "proxyC" version))
24535 "1mcimswrx1cjjm7wsgkzfrgh3jpf4sncwfvdvg2f14fzfzy7afd6"))))
24536 (properties `((upstream-name . "proxyC")))
24537 (build-system r-build-system)
24539 (list r-matrix r-rcpp r-rcpparmadillo r-rcppparallel))
24540 (home-page "https://cran.r-project.org/package=proxyC")
24541 (synopsis "Compute proximity in large sparse matrices")
24543 "This package provides efficient tools to compute the proximity between
24544 rows or columns of large matrices. Functions are optimised for large sparse
24545 matrices using the Armadillo and Intel TBB libraries. Among several built-in
24546 similarity/distance measures, computation of correlation, cosine similarity
24547 and Euclidean distance is particularly fast.")
24548 (license license:gpl3)))
24550 (define-public r-isocodes
24552 (name "r-isocodes")
24553 (version "2022.01.10")
24557 (uri (cran-uri "ISOcodes" version))
24560 "0gy7n5bgxnl4rawry0pg078bkks9lzsbsrwjq8q5cvxl4k3dwpdj"))))
24561 (properties `((upstream-name . "ISOcodes")))
24562 (build-system r-build-system)
24563 (home-page "https://cran.r-project.org/package=ISOcodes")
24564 (synopsis "Selected ISO codes")
24566 "This package provides ISO language, territory, currency, script and
24567 character codes. It provides ISO 639 language codes, ISO 3166 territory
24568 codes, ISO 4217 currency codes, ISO 15924 script codes, and the ISO 8859
24569 character codes as well as the UN M.49 area codes.")
24570 (license license:gpl2)))
24572 (define-public r-stopwords
24574 (name "r-stopwords")
24579 (uri (cran-uri "stopwords" version))
24582 "1ci1cgxrcvlhhplximsfv0plvjdbcd5kv0nphxnpildsn5m1rv65"))))
24583 (properties `((upstream-name . "stopwords")))
24584 (build-system r-build-system)
24587 (home-page "https://github.com/quanteda/stopwords")
24588 (synopsis "Multilingual stopword lists")
24590 "This package provides multiple sources of stopwords, for use in text
24591 analysis and natural language processing.")
24592 (license license:expat)))
24594 (define-public r-spacyr
24601 (uri (cran-uri "spacyr" version))
24604 "1b2ccgwsiqkvp7w37x8k7699c676q16vfrybkrfvyczyhki4s6nw"))))
24605 (properties `((upstream-name . "spacyr")))
24606 (build-system r-build-system)
24608 (list r-data-table r-reticulate))
24609 (home-page "https://spacyr.quanteda.io")
24610 (synopsis "R wrapper for the spaCy NLP library")
24612 "This package provides an R wrapper to the Python @dfn{natural language
24613 processing} (NLP) library @code{spaCy}, from @url{http://spacy.io}.")
24614 (license license:gpl3)))
24616 (define-public r-snowballc
24618 (name "r-snowballc")
24623 (uri (cran-uri "SnowballC" version))
24626 "1wwm71mp4b2mjb5985x782p6xj519dfrpd40qli7lmig6afyw3xi"))))
24627 (properties `((upstream-name . "SnowballC")))
24628 (build-system r-build-system)
24629 (home-page "https://r-forge.r-project.org/projects/r-temis/")
24630 (synopsis "Snowball stemmers based on the C libstemmer UTF-8 library")
24632 "This package provides an R interface to the C @code{libstemmer} library
24633 that implements Porter's word stemming algorithm for collapsing words to a
24634 common root to aid comparison of vocabulary. Currently supported languages
24635 are Danish, Dutch, English, Finnish, French, German, Hungarian, Italian,
24636 Norwegian, Portuguese, Romanian, Russian, Spanish, Swedish and Turkish.")
24637 (license license:bsd-3)))
24639 (define-public r-quanteda
24641 (name "r-quanteda")
24646 (uri (cran-uri "quanteda" version))
24649 "102wlx6481fskgdr5wv467n29f666q0qg9kjm0ivqfg9xsbvza12"))))
24650 (properties `((upstream-name . "quanteda")))
24651 (build-system r-build-system)
24666 (home-page "https://quanteda.io")
24667 (synopsis "Quantitative analysis of textual data")
24669 "This package provides a fast, flexible, and comprehensive framework for
24670 quantitative text analysis in R. It provides functionality for corpus
24671 management, creating and manipulating tokens and ngrams, exploring keywords in
24672 context, forming and manipulating sparse matrices of documents by features and
24673 feature co-occurrences, analyzing keywords, computing feature similarities and
24674 distances, applying content dictionaries, applying supervised and unsupervised
24675 machine learning, visually representing text and text analyses, and more.")
24676 (license license:gpl3)))
24678 (define-public r-topicmodels
24680 (name "r-topicmodels")
24685 (uri (cran-uri "topicmodels" version))
24688 "1d6iizmn042b59q2y6qc82z19wq3xm0zvgkf8iqf8fdzh51kmn5g"))))
24689 (properties `((upstream-name . "topicmodels")))
24690 (build-system r-build-system)
24694 (list r-modeltools r-slam r-tm))
24695 (home-page "https://cran.r-project.org/package=topicmodels")
24696 (synopsis "Topic models")
24698 "This package provides an interface to the C code for @dfn{Latent
24699 Dirichlet Allocation} (LDA) models and @dfn{Correlated Topics Models} (CTM) by
24700 David M. Blei and co-authors and the C++ code for fitting LDA models using
24701 Gibbs sampling by Xuan-Hieu Phan and co-authors.")
24702 (license license:gpl2)))
24704 (define-public r-stm
24711 (uri (cran-uri "stm" version))
24714 "0qwq4nin2n9fjd06852r8k7arvcgh46kcfb3lm21swgx6j8bgrhb"))))
24715 (properties `((upstream-name . "stm")))
24716 (build-system r-build-system)
24729 (home-page "http://www.structuraltopicmodel.com/")
24730 (synopsis "Estimation of the Structural Topic Model")
24732 "The @dfn{Structural Topic Model} (STM) allows researchers to estimate
24733 topic models with document-level covariates. The package also includes tools
24734 for model selection, visualization, and estimation of topic-covariate
24736 (license license:expat)))
24738 (define-public r-polycor
24745 (uri (cran-uri "polycor" version))
24748 "0285rvx8238qp8dix0jq0cqq7ks8h6cjwsscbc7dx4n9nph56pzh"))))
24749 (properties `((upstream-name . "polycor")))
24750 (build-system r-build-system)
24752 (list r-admisc r-matrix r-mvtnorm))
24753 (home-page "https://r-forge.r-project.org/projects/polycor/")
24754 (synopsis "Polychoric and polyserial correlations")
24756 "This package provides tools to compute polychoric and polyserial
24757 correlations by quick \"two-step\" methods or ML, optionally with standard
24758 errors; tetrachoric and biserial correlations are special cases.")
24759 (license license:gpl2+)))
24761 (define-public r-msm
24768 (uri (cran-uri "msm" version))
24771 "08vhazswyxr3y1zb9y60mbg3bappzlizxml8s08p65mh82xxkz5f"))))
24772 (properties `((upstream-name . "msm")))
24773 (build-system r-build-system)
24775 (list r-expm r-mvtnorm r-survival))
24776 (home-page "https://github.com/chjackson/msm")
24777 (synopsis "Multi-state Markov and hidden Markov models in continuous time")
24779 "This package provides functions for fitting continuous-time Markov and
24780 hidden Markov multi-state models to longitudinal data. It was designed for
24781 processes observed at arbitrary times in continuous time (panel data) but some
24782 other observation schemes are supported. Both Markov transition rates and the
24783 hidden Markov output process can be modelled in terms of covariates, which may
24784 be constant or piecewise-constant in time.")
24785 (license license:gpl2+)))
24787 (define-public r-ltm
24794 (uri (cran-uri "ltm" version))
24797 "0vhgbk6j0z3limsrbjkjkpfn2whiaij5j4jf1gg66mjs9dlylap1"))))
24798 (properties `((upstream-name . "ltm")))
24799 (build-system r-build-system)
24801 (list r-mass r-msm r-polycor))
24802 (home-page "https://github.com/drizopoulos/ltm")
24803 (synopsis "Latent trait models under IRT")
24805 "This is a package supporting the analysis of multivariate dichotomous
24806 and polytomous data using latent trait models under the Item Response Theory
24807 approach. It includes the Rasch, the Two-Parameter Logistic, the Birnbaum's
24808 Three-Parameter, the Graded Response, and the Generalized Partial Credit
24810 (license license:gpl2+)))
24812 (define-public r-mi
24819 (uri (cran-uri "mi" version))
24822 "1h47k5mpbvhid83277dvvj2di493bgzz9iarpyv3r30y219l7x1l"))))
24823 (properties `((upstream-name . "mi")))
24824 (build-system r-build-system)
24826 (list r-arm r-matrix))
24827 (home-page "http://www.stat.columbia.edu/~gelman/")
24828 (synopsis "Missing data imputation and model checking")
24830 "This package provides functions for data manipulation, imputing missing
24831 values in an approximate Bayesian framework, diagnostics of the models used to
24832 generate the imputations, confidence-building mechanisms to validate some of
24833 the assumptions of the imputation algorithm, and functions to analyze multiply
24834 imputed data sets with the appropriate degree of sampling uncertainty.")
24835 (license license:gpl2+)))
24837 (define-public r-matrixcalc
24839 (name "r-matrixcalc")
24844 (uri (cran-uri "matrixcalc" version))
24847 "1jkgl1v1q7cqpl1rf49qahdr9y0f33f0ldsbgby8xhfv0vpy21jr"))))
24848 (properties `((upstream-name . "matrixcalc")))
24849 (build-system r-build-system)
24850 (home-page "https://cran.r-project.org/web/packages/matrixcalc/")
24851 (synopsis "Collection of functions for matrix calculations")
24853 "This package provides a collection of functions to support matrix
24854 calculations for probability, econometric and numerical analysis. There are
24855 additional functions that are comparable to APL functions which are useful for
24856 actuarial models such as pension mathematics.")
24857 (license license:gpl2+)))
24859 (define-public r-matrixextra
24861 (name "r-matrixextra")
24866 (uri (cran-uri "MatrixExtra" version))
24868 (base32 "00f6sgw6p2709gs3df68yr59nvsr429pk9xql71id3kachjzh618"))))
24869 (properties `((upstream-name . "MatrixExtra")))
24870 (build-system r-build-system)
24872 (list r-float r-matrix r-rcpp r-rhpcblasctl))
24875 (home-page "https://github.com/david-cortes/MatrixExtra")
24876 (synopsis "Extra methods for sparse matrices")
24878 "This package extends sparse matrix and vector classes from the Matrix
24879 package by providing:
24882 @item Methods and operators that work natively on CSR formats (compressed
24883 sparse row, a.k.a. @code{RsparseMatrix}) such as slicing/sub-setting,
24884 assignment, @code{rbind()}, mathematical operators for CSR and COO such as
24885 addition or @code{sqrt()}, and methods such as @code{diag()};
24886 @item Multi-threaded matrix multiplication and cross-product for many
24887 @code{<sparse, dense>} types, including the @code{float32} type from
24889 @item Coercion methods between pairs of classes which are not present in
24890 @code{Matrix}, such as from @code{dgCMatrix} to @code{ngRMatrix}, as well as
24891 convenience conversion functions;
24892 @item Utility functions for sparse matrices such as sorting the indices or
24893 removing zero-valued entries;
24894 @item Fast transposes that work by outputting in the opposite storage format;
24895 @item Faster replacements for many @code{Matrix} methods for all sparse types,
24896 such as slicing and elementwise multiplication.
24897 @item Convenience functions for sparse objects, such as @code{mapSparse} or a
24898 shorter @code{show} method.
24901 (license license:gpl2+)))
24903 (define-public r-sem
24910 (uri (cran-uri "sem" version))
24913 "05hk72zxvyv6kkjhk5y6qw253c64108az7030z8j1sz8wq03n0md"))))
24914 (properties `((upstream-name . "sem")))
24915 (build-system r-build-system)
24917 (list r-boot r-mass r-mi))
24918 (home-page "https://cran.r-project.org/package=sem")
24919 (synopsis "Structural equation models")
24921 "This package provides functions for fitting general linear structural
24922 equation models (with observed and latent variables) using the RAM approach,
24923 and for fitting structural equations in observed-variable models by two-stage
24925 (license license:gpl2+)))
24927 (define-public r-semtools
24929 (name "r-semtools")
24934 (uri (cran-uri "semTools" version))
24937 "1wnakz76c4mgkwvx3iycmvgrzqys860jg9zpkba0ln5c08ycw8pm"))))
24938 (properties `((upstream-name . "semTools")))
24939 (build-system r-build-system)
24941 (list r-lavaan r-pbivnorm))
24942 (home-page "https://github.com/simsem/semTools/wiki")
24943 (synopsis "Useful tools for structural equation modeling")
24945 "This package provides useful tools for structural equation modeling.")
24946 (license license:gpl2+)))
24948 (define-public r-regsem
24955 (uri (cran-uri "regsem" version))
24958 "1v33wkrsawcvaa06cijp8ybwi82a0x34y59hdknwdbywplnirzr8"))))
24959 (properties `((upstream-name . "regsem")))
24960 (build-system r-build-system)
24962 (list r-lavaan r-rcpp r-rcpparmadillo r-rsolnp))
24965 (home-page "https://cran.r-project.org/package=regsem")
24966 (synopsis "Regularized structural equation modeling")
24968 "This package uses both ridge and lasso penalties (and extensions) to
24969 penalize specific parameters in structural equation models. The package
24970 offers additional cost functions, cross validation, and other extensions
24971 beyond traditional structural equation models. It also contains a function to
24972 perform @dfn{exploratory mediation} (XMed).")
24973 (license license:gpl2+)))
24975 (define-public r-stanheaders
24977 (name "r-stanheaders")
24978 (version "2.21.0-7")
24982 (uri (cran-uri "StanHeaders" version))
24985 "0srkyawyiykn3p5lw1z3zf18s4ax4iasv1ci3l1px40f9w36wm17"))))
24986 (properties `((upstream-name . "StanHeaders")))
24987 (build-system r-build-system)
24988 (inputs (list pandoc))
24990 (list r-rcppeigen r-rcppparallel))
24992 (list gfortran r-knitr)) ; for vignettes
24993 (home-page "https://mc-stan.org/")
24994 (synopsis "C++ header files for Stan")
24996 "The C++ header files of the Stan project are provided by this package.
24997 There is a shared object containing part of the @code{CVODES} library, but it
24998 is not accessible from R. @code{r-stanheaders} is only useful for developers
24999 who want to utilize the @code{LinkingTo} directive of their package's
25000 DESCRIPTION file to build on the Stan library without incurring unnecessary
25003 The Stan project develops a probabilistic programming language that implements
25004 full or approximate Bayesian statistical inference via Markov Chain Monte
25005 Carlo or variational methods and implements (optionally penalized) maximum
25006 likelihood estimation via optimization. The Stan library includes an advanced
25007 automatic differentiation scheme, templated statistical and linear algebra
25008 functions that can handle the automatically differentiable scalar types (and
25009 doubles, ints, etc.), and a parser for the Stan language. The @code{r-rstan}
25010 package provides user-facing R functions to parse, compile, test, estimate,
25011 and analyze Stan models.")
25012 (license license:bsd-3)))
25014 (define-public r-rpf
25021 (uri (cran-uri "rpf" version))
25024 "1yr1i7kswq57mcxv05lh7bvbicz1djqxcl6f13dlgsf3ww56gzg1"))))
25025 (properties `((upstream-name . "rpf")))
25026 (build-system r-build-system)
25028 (list r-lifecycle r-mvtnorm r-rcpp r-rcppeigen))
25031 (home-page "https://github.com/jpritikin/rpf")
25032 (synopsis "Response probability functions")
25034 "The purpose of this package is to factor out logic and math common to
25035 Item Factor Analysis fitting, diagnostics, and analysis. It is envisioned as
25036 core support code suitable for more specialized IRT packages to build upon.
25037 Complete access to optimized C functions is made available with
25038 @code{R_RegisterCCallable()}.")
25039 (license license:gpl3+)))
25041 (define-public r-openmx
25048 (uri (cran-uri "OpenMx" version))
25051 "1v969100hllh0lwlxd2gv0k7krrsp9gc07iinx0nn04wkzh0rib5"))))
25052 (properties `((upstream-name . "OpenMx")))
25053 (build-system r-build-system)
25065 (native-inputs (list r-knitr gfortran))
25066 (home-page "http://openmx.ssri.psu.edu")
25067 (synopsis "Extended structural equation modelling")
25069 "This package allows for the estimation of a wide variety of advanced
25070 multivariate statistical models. It consists of a library of functions and
25071 optimizers that allow you to quickly and flexibly define an SEM model and
25072 estimate parameters given observed data.")
25073 (license license:asl2.0)))
25075 (define-public r-kutils
25082 (uri (cran-uri "kutils" version))
25085 "06jk66wbq3jmdf2jdhqns6r3yk36l2x7c907x977zv80sqxa1l37"))))
25086 (properties `((upstream-name . "kutils")))
25087 (build-system r-build-system)
25089 (list r-foreign r-openxlsx r-plyr r-runit r-xtable))
25090 (home-page "https://cran.r-project.org/package=kutils")
25091 (synopsis "Project management tools")
25093 "This package provides tools for data importation, recoding, and
25094 inspection. There are functions to create new project folders, R code
25095 templates, create uniquely named output directories, and to quickly obtain a
25096 visual summary for each variable in a data frame. The main feature here is
25097 the systematic implementation of the \"variable key\" framework for data
25098 importation and recoding.")
25099 (license license:gpl2)))
25101 (define-public r-rockchalk
25103 (name "r-rockchalk")
25104 (version "1.8.152")
25108 (uri (cran-uri "rockchalk" version))
25111 "1d15jlgcy35pvaicaddd4zrhwm5ajb9yc3jk6dyxm99gc5wcn6h3"))))
25112 (properties `((upstream-name . "rockchalk")))
25113 (build-system r-build-system)
25115 (list r-cardata r-kutils r-lme4 r-mass))
25116 (home-page "https://cran.r-project.org/package=rockchalk")
25117 (synopsis "Regression estimation and presentation")
25119 "This package provides a collection of functions for interpretation and
25120 presentation of regression analysis. These functions are used to produce the
25121 statistics lectures in @url{http://pj.freefaculty.org/guides}. The package
25122 includes regression diagnostics, regression tables, and plots of interactions
25123 and \"moderator\" variables. The emphasis is on \"mean-centered\" and
25124 \"residual-centered\" predictors. The vignette @code{rockchalk} offers a
25125 fairly comprehensive overview.")
25126 (license license:gpl3+)))
25128 (define-public r-lisreltor
25130 (name "r-lisreltor")
25135 (uri (cran-uri "lisrelToR" version))
25138 "0i51v0x87277ly0kggdd594w6q4zq62b4n7xs9r25j08bzs82nfk"))))
25139 (properties `((upstream-name . "lisrelToR")))
25140 (build-system r-build-system)
25141 (home-page "https://cran.r-project.org/package=lisrelToR")
25142 (synopsis "Import output from LISREL into R")
25144 "This is an unofficial package aimed at automating the import of LISREL
25146 (license license:gpl2)))
25148 (define-public r-bdgraph
25155 (uri (cran-uri "BDgraph" version))
25158 "0s2j4462zlgyjnqvvvxg4lynhmwwnjaw1cr1chzmagfvaj94qhhz"))))
25159 (properties `((upstream-name . "BDgraph")))
25160 (build-system r-build-system)
25165 (home-page "https://www.uva.nl/profile/a.mohammadi")
25166 (synopsis "Bayesian structure learning in graphical models")
25168 "This package provides statistical tools for Bayesian structure learning
25169 in undirected graphical models for continuous, discrete, and mixed data. It
25170 uses a trans-dimensional @dfn{Markov Chain Monte Carlo} (MCMC) approach based
25171 on a continuous-time birth-death process.")
25172 (license license:gpl2+)))
25174 (define-public r-d3network
25176 (name "r-d3network")
25177 (version "0.5.2.1")
25181 (uri (cran-uri "d3Network" version))
25184 "1gh979z9wksyxxxdzlfzibn0ysvf6h1ij7vwpd55fvbwr308syaw"))))
25185 (properties `((upstream-name . "d3Network")))
25186 (build-system r-build-system)
25188 (list r-plyr r-rjson r-whisker))
25189 (home-page "http://christophergandrud.github.io/d3Network/")
25190 (synopsis "Create D3 JavaScript network, tree, dendrogram, and Sankey graphs")
25192 "This package is intended to make it easy to create D3 JavaScript
25193 network, tree, dendrogram, and Sankey graphs from R using data frames.")
25194 (license license:gpl3+)))
25196 (define-public r-qgraph
25203 (uri (cran-uri "qgraph" version))
25206 "0r225b7rnsv6wz41ij0msmqr1xy0iqxh9dbsvjixbi1hvgv91wds"))))
25207 (properties `((upstream-name . "qgraph")))
25208 (build-system r-build-system)
25228 (home-page "http://sachaepskamp.com/qgraph/")
25229 (synopsis "Weighted network visualization and analysis")
25231 "This package implements tools for weighted network visualization and
25232 analysis, as well as Gaussian graphical model computation. It contains graph
25233 plotting methods, and tools for psychometric data visualization and graphical
25234 model estimation. See Epskamp et al. (2012)
25235 @url{doi:10.18637/jss.v048.i04}.")
25236 (license license:gpl2)))
25238 (define-public r-semplot
25245 (uri (cran-uri "semPlot" version))
25248 "0d7v9yqc9nhx3hdrp444w1ah66zai3lg5y778m85r7ngh1prxlvc"))))
25249 (properties `((upstream-name . "semPlot")))
25250 (build-system r-build-system)
25263 (home-page "https://github.com/SachaEpskamp/semPlot")
25264 (synopsis "Unified visualizations of structural equation models")
25266 "Structural equation modeling (SEM) has a long history of representing
25267 models graphically as path diagrams. The semPlot package for R fills the gap
25268 between advanced, but time-consuming, graphical software and the limited
25269 graphics produced automatically by SEM software. In addition, semPlot offers
25270 more functionality than drawing path diagrams: it can act as a common ground
25271 for importing SEM results into R. Any result usable as input to semPlot can
25272 also be represented in any of the three popular SEM frame-works, as well as
25273 translated to input syntax for the R packages @code{sem} and @code{lavaan}.")
25274 (license license:gpl2)))
25276 (define-public r-cdm
25283 (uri (cran-uri "CDM" version))
25286 "1cnk19k09cj81ic43rwbvcalvczfca4ncdyy8r1gyc8fzf2glb0i"))))
25287 (properties `((upstream-name . "CDM")))
25288 (build-system r-build-system)
25290 (list r-mvtnorm r-polycor r-rcpp r-rcpparmadillo))
25292 "https://github.com/alexanderrobitzsch/CDM")
25293 (synopsis "Cognitive diagnosis modeling")
25295 "This package provides functions for cognitive diagnosis modeling and
25296 multidimensional item response modeling for dichotomous and polytomous item
25297 responses. It enables the estimation of the DINA and DINO model, the multiple
25298 group (polytomous) GDINA model, the multiple choice DINA model, the general
25299 diagnostic model (GDM), the structured latent class model (SLCA), and
25300 regularized latent class analysis. See George, Robitzsch, Kiefer, Gross, and
25301 Uenlue (2017) @url{doi:10.18637/jss.v074.i02} for further details on
25302 estimation and the package structure. For tutorials on how to use the CDM
25303 package see George and Robitzsch (2015, @url{doi:10.20982/tqmp.11.3.p189}) as
25304 well as Ravand and Robitzsch (2015).")
25305 (license license:gpl2+)))
25307 (define-public r-tam
25314 (uri (cran-uri "TAM" version))
25317 "00ww277hsyci5rph4gb155h0y95dmjhqgn9amz6g8zbrjb2748dw"))))
25318 (properties `((upstream-name . "TAM")))
25319 (build-system r-build-system)
25321 (list r-cdm r-rcpp r-rcpparmadillo))
25322 (home-page "http://www.edmeasurementsurveys.com/TAM/Tutorials/")
25323 (synopsis "Test analysis modules")
25325 "This package includes tools for marginal maximum likelihood estimation
25326 and joint maximum likelihood estimation for unidimensional and
25327 multidimensional item response models. The package functionality covers the
25328 Rasch model, 2PL model, 3PL model, generalized partial credit model,
25329 multi-faceted Rasch model, nominal item response model, structured latent
25330 class model, mixture distribution IRT models, and located latent class models.
25331 Latent regression models and plausible value imputation are also supported.")
25332 (license license:gpl2+)))
25334 (define-public r-erm
25341 (uri (cran-uri "eRm" version))
25344 "0smym010kswc5vx90qr3x1vl16xj1x1i54rvrj006dc4agc1vmlk"))))
25345 (properties `((upstream-name . "eRm")))
25346 (build-system r-build-system)
25348 (list r-colorspace r-lattice r-mass r-matrix r-psych))
25349 (native-inputs (list gfortran))
25350 (home-page "https://cran.r-project.org/package=eRm")
25351 (synopsis "Extended Rasch modeling")
25353 "This package provides tools to fit @dfn{Rasch models} (RM), @dfn{linear
25354 logistic test models} (LLTM), @dfn{rating scale model} (RSM), @dfn{linear
25355 rating scale models} (LRSM), @dfn{partial credit models} (PCM), and
25356 @dfn{linear partial credit models} (LPCM). Missing values are allowed in the
25357 data matrix. Additional features are the ML estimation of the person
25358 parameters, Andersen's LR-test, item-specific Wald test, Martin-Loef-Test,
25359 nonparametric Monte-Carlo Tests, itemfit and personfit statistics including
25360 infit and outfit measures, ICC and other plots, automated stepwise item
25361 elimination, and a simulation module for various binary data matrices.")
25362 (license license:gpl3)))
25364 (define-public r-irtoys
25371 (uri (cran-uri "irtoys" version))
25374 "1qshz6czykgf53mq6xiswzv5xsjwrkrinpfkf1yavql4v08hs82b"))))
25375 (properties `((upstream-name . "irtoys")))
25376 (build-system r-build-system)
25381 (home-page "https://cran.r-project.org/package=irtoys")
25382 (synopsis "Collection of functions related to Item Response Theory (IRT)")
25384 "This package provides a collection of functions useful in learning and
25385 practicing @dfn{Item Response Theory} (IRT), which can be combined into larger
25386 programs. It provides basic CTT analysis, a simple common interface to the
25387 estimation of item parameters in IRT models for binary responses with three
25388 different programs (ICL, BILOG-MG, and ltm), ability estimation (MLE, BME,
25389 EAP, WLE, plausible values), item and person fit statistics, scaling
25390 methods (MM, MS, Stocking-Lord, and the complete Hebaera method), and a rich
25391 array of parametric and non-parametric (kernel) plots. It estimates and plots
25392 Haberman's interaction model when all items are dichotomously scored.")
25393 (license license:gpl2+)))
25395 (define-public r-iheatmapr
25397 (name "r-iheatmapr")
25402 (uri (cran-uri "iheatmapr" version))
25405 "1pwkwh7ljlpr6zyz6j8knpz3iw60xzkw8amc98x4pc2mw148jvzx"))))
25406 (properties `((upstream-name . "iheatmapr")))
25407 (build-system r-build-system)
25409 (list r-fastcluster
25419 (home-page "https://docs.ropensci.org/iheatmapr")
25420 (synopsis "Interactive, Complex Heatmaps")
25422 "iheatmapr is an R package for building complex, interactive heatmaps
25423 using modular building blocks. \"Complex\" heatmaps are heatmaps in which
25424 subplots along the rows or columns of the main heatmap add more information
25425 about each row or column. For example, a one column additional heatmap may
25426 indicate what group a particular row or column belongs to. Complex heatmaps
25427 may also include multiple side by side heatmaps which show different types of
25428 data for the same conditions. Interactivity can improve complex heatmaps by
25429 providing tooltips with information about each cell and enabling zooming into
25430 interesting features. iheatmapr uses the plotly library for interactivity.")
25431 (license license:expat)))
25433 (define-public r-packrat
25440 (uri (cran-uri "packrat" version))
25443 "1vs4i19x6jdwl3jnanp127k4hk80h1mj56cjn07w1gkl542vj99h"))))
25444 (properties `((upstream-name . "packrat")))
25445 (build-system r-build-system)
25446 (home-page "https://github.com/rstudio/packrat/")
25447 (synopsis "Dependency management R projects")
25449 "This package provides a dependency manager for R projects that allows
25450 you to manage the R packages your project depends on in an isolated, portable,
25451 and reproducible way.")
25452 (license license:gpl2)))
25454 (define-public r-rsconnect
25456 (name "r-rsconnect")
25461 (uri (cran-uri "rsconnect" version))
25464 "1kyr4v7vds2yw3xmkk2yr56ylz1h95944brylwvwmwj5yxvm419w"))))
25465 (properties `((upstream-name . "rsconnect")))
25466 (build-system r-build-system)
25475 (home-page "https://github.com/rstudio/rsconnect")
25476 (synopsis "Deployment interface for R Markdown documents and Shiny applications")
25478 "This package provides a programmatic deployment interface for RPubs,
25479 shinyapps.io, and RStudio Connect. Supported content types include R Markdown
25480 documents, Shiny applications, Plumber APIs, plots, and static web content.")
25481 (license license:gpl2)))
25483 ;; This package includes minified JavaScript files. When upgrading please
25484 ;; check that there are no new minified JavaScript files.
25485 (define-public r-dygraphs
25487 (name "r-dygraphs")
25488 (version "1.1.1.6")
25492 (uri (cran-uri "dygraphs" version))
25495 "022j007mzfa9k2n31yg4aizcsf571vv3jip092h23rqj03rk3ly3"))))
25496 (properties `((upstream-name . "dygraphs")))
25497 (build-system r-build-system)
25499 `(#:modules ((guix build utils)
25500 (guix build r-build-system)
25504 (modify-phases %standard-phases
25505 (add-after 'unpack 'process-javascript
25506 (lambda* (#:key inputs #:allow-other-keys)
25507 (with-directory-excursion "inst/htmlwidgets/lib/"
25511 `(("dygraphs/dygraph-combined-dev.js"
25512 "dygraph-combined.js")
25513 (,(assoc-ref inputs "js-jquery")
25514 "jquery/jquery.min.js")
25515 (,(assoc-ref inputs "js-fquarter")
25516 "fquarter/moment-fquarter.min.js"))))
25517 (lambda (sources targets)
25518 (for-each (lambda (source target)
25519 (format #t "Processing ~a --> ~a~%"
25521 (let ((minified (open-pipe* OPEN_READ "uglifyjs" source)))
25522 (call-with-output-file target
25524 (dump-port minified port)))))
25525 sources targets))))
25528 `(("uglifyjs" ,node-uglify-js)
25529 ;; They actually use version 1.11.1, but this more recent version
25530 ;; should be just fine.
25534 (uri "https://code.jquery.com/jquery-1.12.4.js")
25537 "0x9mrc1668icvhpwzvgafm8xm11x9lfai9nwr66aw6pjnpwkc3s3"))))
25541 (uri (string-append "https://raw.githubusercontent.com/robgallen/"
25542 "moment-fquarter/1.0.1/moment-fquarter.js"))
25545 "01mdnsaibm9jy2f1qpbn692hpv309lhj5si9nagib4dawmrkffij"))))))
25547 (list r-htmltools r-htmlwidgets r-magrittr r-xts r-zoo))
25548 (home-page "https://github.com/rstudio/dygraphs")
25549 (synopsis "Interface to Dygraphs interactive time series charting library")
25551 "This package provides an R interface to the dygraphs JavaScript charting
25552 library (a copy of which is included in the package). It provides rich
25553 facilities for charting time-series data in R, including highly configurable
25554 series- and axis-display and interactive features like zoom/pan and
25555 series/point highlighting.")
25556 (license license:expat)))
25558 (define-public r-shinystan
25560 (name "r-shinystan")
25565 (uri (cran-uri "shinystan" version))
25568 "0afm703zriyqprz1zvypir80lq2ylfff3qvj5i7p9n365mm8b150"))))
25569 (properties `((upstream-name . "shinystan")))
25570 (build-system r-build-system)
25588 (home-page "https://mc-stan.org/")
25589 (synopsis "Interactive visual and numerical analysis for Bayesian models")
25591 "This package provides a graphical user interface for interactive
25592 @dfn{Markov chain Monte Carlo} (MCMC) diagnostics and plots and tables helpful
25593 for analyzing a posterior sample. The interface is powered by the Shiny web
25594 application framework and works with the output of MCMC programs written in
25595 any programming language (and has extended functionality for Stan models fit
25596 using the @code{rstan} and @code{rstanarm} packages).")
25597 (license license:gpl3+)))
25599 (define-public r-rstantools
25601 (name "r-rstantools")
25606 (uri (cran-uri "rstantools" version))
25609 "1dsfgi02hps878n3vimfdbzpm4gr5n3ccrmnc61ncrqcp6p0p0fb"))))
25610 (properties `((upstream-name . "rstantools")))
25611 (build-system r-build-system)
25612 (inputs (list pandoc))
25614 (list r-desc r-rcpp r-rcppparallel))
25617 (home-page "https://mc-stan.org/rstantools/")
25618 (synopsis "Tools for developing R packages interfacing with Stan")
25620 "This package provides various tools for developers of R packages
25621 interfacing with @url{https://mc-stan.org, Stan}, including functions to set
25622 up the required package structure, S3 generics and default methods to unify
25623 function naming across Stan-based R packages, and vignettes with
25624 recommendations for developers.")
25625 (license license:gpl3+)))
25627 (define-public r-loo
25634 (uri (cran-uri "loo" version))
25636 (base32 "1wa5hxk7lkr88mway6b7xd5arrkkl2ldl9rf0v1nqwp8lia2ysl6"))))
25637 (properties `((upstream-name . "loo")))
25638 (build-system r-build-system)
25642 (list r-checkmate r-matrixstats))
25645 (home-page "https://mc-stan.org/loo/")
25646 (synopsis "Leave-One-Out cross-validation and WAIC for Bayesian models")
25648 "This package provides an implementation of efficient approximate
25649 @dfn{leave-one-out} (LOO) cross-validation for Bayesian models fit using
25650 Markov chain Monte Carlo, as described in @url{doi:10.1007/s11222-016-9696-4}.
25651 The approximation uses @dfn{Pareto smoothed importance sampling} (PSIS), a new
25652 procedure for regularizing importance weights. As a byproduct of the
25653 calculations, we also obtain approximate standard errors for estimated
25654 predictive errors and for the comparison of predictive errors between models.
25655 The package also provides methods for using stacking and other model weighting
25656 techniques to average Bayesian predictive distributions.")
25657 (license license:gpl3+)))
25659 (define-public r-rstan
25666 (uri (cran-uri "rstan" version))
25669 "1smr5cjrqvpdnkmjpjp73p96sy581x15mwrn4fqd1p4d5mbgxr46"))))
25670 (properties `((upstream-name . "rstan")))
25671 (build-system r-build-system)
25674 (modify-phases %standard-phases
25675 (add-before 'install 'set-timezone
25676 ;; This package is picky about timezones.
25677 (lambda* (#:key inputs #:allow-other-keys)
25678 (setenv "TZ" "UTC+1")
25680 (search-input-directory inputs
25681 "share/zoneinfo")))))))
25683 (list tzdata-for-tests pandoc r-knitr))
25695 (home-page "https://discourse.mc-stan.org/")
25696 (synopsis "R interface to Stan")
25698 "User-facing R functions are provided to parse, compile, test, estimate,
25699 and analyze Stan models by accessing the header-only Stan library provided by
25700 the StanHeaders package. The Stan project develops a probabilistic
25701 programming language that implements full Bayesian statistical inference via
25702 Markov Chain Monte Carlo, rough Bayesian inference via 'variational'
25703 approximation, and (optionally penalized) maximum likelihood estimation via
25704 optimization. In all three cases, automatic differentiation is used to
25705 quickly and accurately evaluate gradients without burdening the user with the
25706 need to derive the partial derivatives.")
25707 (license license:gpl3+)))
25709 (define-public r-rstanarm
25711 (name "r-rstanarm")
25716 (uri (cran-uri "rstanarm" version))
25719 "19rj396q84maxnd9d2xcd5rblg3310xn7sqbd6k18kwf3dvd7wp9"))))
25720 (properties `((upstream-name . "rstanarm")))
25721 (build-system r-build-system)
25742 (home-page "https://mc-stan.org/rstanarm/")
25743 (synopsis "Bayesian applied regression modeling via Stan")
25745 "This package estimates previously compiled regression models using the
25746 @code{rstan} package, which provides the R interface to the Stan C++ library
25747 for Bayesian estimation. Users specify models via the customary R syntax with
25748 a formula and @code{data.frame} plus some additional arguments for priors.")
25749 (license license:gpl3+)))
25751 (define-public r-kendall
25758 (uri (cran-uri "Kendall" version))
25761 "1xmk95l4i3kj9jn0xh1chi2rj322k29jq14ra5pa7316gwf9vx2m"))))
25762 (properties `((upstream-name . "Kendall")))
25763 (build-system r-build-system)
25768 (home-page "https://cran.r-project.org/web/packages/Kendall/")
25769 (synopsis "Kendall rank correlation and Mann-Kendall trend test")
25771 "This package computes the Kendall rank correlation and Mann-Kendall
25773 (license license:gpl2+)))
25775 (define-public r-keyring
25782 (uri (cran-uri "keyring" version))
25785 "1j8l6nmh4dr70kwybiais8yh687fdwrj134xynq68igw1b1rm8ga"))))
25786 (properties `((upstream-name . "keyring")))
25787 (build-system r-build-system)
25797 (native-inputs (list pkg-config))
25798 (home-page "https://github.com/r-lib/keyring")
25799 (synopsis "Access the system credential store from R")
25801 "This package provides a platform-independent API to access the operating
25802 system's credential store. It currently supports Keychain on macOS,
25803 Credential Store on Windows, the Secret Service API on GNU/Linux, and a
25804 simple, platform independent store implemented with environment variables.
25805 Additional storage back-ends can be added easily.")
25806 (license license:expat)))
25808 (define-public r-zyp
25811 (version "0.10-1.1")
25815 (uri (cran-uri "zyp" version))
25818 "03cxpkfbhrx1fy8l0dl9a13ghz93cqq6877wa8rig09ksdiivaw9"))))
25819 (properties `((upstream-name . "zyp")))
25820 (build-system r-build-system)
25823 (home-page "https://cran.r-project.org/web/packages/zyp/")
25824 (synopsis "Zhang + Yue-Pilon Trends Package")
25826 "This package contains an efficient implementation of Sen's slope
25827 method (Sen, 1968) plus implementation of Xuebin Zhang's (Zhang, 1999) and
25828 Yue-Pilon's (Yue, 2002) pre-whitening approaches to determining trends in
25830 (license license:lgpl2.1)))
25832 (define-public r-rlinsolve
25834 (name "r-rlinsolve")
25839 (uri (cran-uri "Rlinsolve" version))
25842 "1xv500n1480qyakw0isanw1s5ywykhc207hqja4804s5s2m8zfjw"))))
25843 (properties `((upstream-name . "Rlinsolve")))
25844 (build-system r-build-system)
25846 (list r-matrix r-rcpp r-rcpparmadillo r-rdpack))
25847 (home-page "https://cran.r-project.org/web/packages/Rlinsolve/")
25848 (synopsis "Iterative solvers for (sparse) linear system of equations")
25850 "Solving a system of linear equations is one of the most fundamental
25851 computational problems for many fields of mathematical studies, such as
25852 regression problems from statistics or numerical partial differential
25853 equations. This package provides basic stationary iterative solvers such as
25854 Jacobi, Gauss-Seidel, Successive Over-Relaxation and SSOR methods.
25855 Nonstationary, also known as Krylov subspace methods are also provided.
25856 Sparse matrix computation is also supported in that solving large and sparse
25857 linear systems can be manageable using the @code{Matrix} package along with
25858 @code{RcppArmadillo}.")
25859 (license license:gpl3+)))
25861 (define-public r-zvcv
25868 (uri (cran-uri "ZVCV" version))
25871 "0gc76j9i8fkm2v638nyzzb1qxl4zmapbspkkaffb8gi5qyjja448"))))
25872 (properties `((upstream-name . "ZVCV")))
25873 (build-system r-build-system)
25884 (home-page "https://cran.r-project.org/web/packages/ZVCV/")
25885 (synopsis "Zero-Variance Control Variates")
25887 "@dfn{Zero-variance control variates} (ZV-CV) is a post-processing method
25888 to reduce the variance of Monte Carlo estimators of expectations using the
25889 derivatives of the log target. Once the derivatives are available, the only
25890 additional computational effort is in solving a linear regression problem.
25891 This method has been extended to higher dimensions using regularisation. This
25892 package can be used to easily perform ZV-CV or regularised ZV-CV when a set of
25893 samples, derivatives and function evaluations are available. Additional
25894 functions for applying ZV-CV to two estimators for the normalising constant of
25895 the posterior distribution in Bayesian statistics are also supplied.")
25896 (license license:gpl2+)))
25898 (define-public r-ztype
25905 (uri (cran-uri "ztype" version))
25908 "0brbq2rgkl4mhjbb70kkfv47lzs66k9ppfs2klavcbripirxn5fx"))))
25909 (properties `((upstream-name . "ztype")))
25910 (build-system r-build-system)
25919 (home-page "https://cran.r-project.org/web/packages/ztype/")
25920 (synopsis "Run a Ztype game loaded with R functions")
25922 "How fast can you type R functions on your keyboard? Find out by running
25923 a @code{zty.pe} game: export R functions as instructions to type to destroy
25924 opponents' vessels.")
25925 (license license:gpl3)))
25927 (define-public r-zseq
25934 (uri (cran-uri "Zseq" version))
25937 "06dndi2b1q79bmxax11bv0l5ifcz1mhpvbn90y6a6xymrgcq0ivi"))))
25938 (properties `((upstream-name . "Zseq")))
25939 (build-system r-build-system)
25942 (home-page "https://cran.r-project.org/web/packages/Zseq/")
25943 (synopsis "Integer sequence generator")
25945 "This package generates well-known integer sequences. The @code{gmp}
25946 package is adopted for computing with arbitrarily large numbers. Every
25947 function has a hyperlink to its corresponding item in the @dfn{On-Line
25948 Encyclopedia of Integer Sequences} (OEIS) in the function help page.")
25949 (license license:gpl3+)))
25951 (define-public r-isoband
25958 (uri (cran-uri "isoband" version))
25961 "19bbi0n0kz33xdgmdprcmc6raphd1hcm1w1brc16z5phcsh3zxa6"))))
25962 (properties `((upstream-name . "isoband")))
25963 (build-system r-build-system)
25966 (home-page "https://github.com/wilkelab/isoband")
25967 (synopsis "Generate isolines and isobands from regularly spaced elevation grids")
25969 "This package provides a fast C++ implementation to generate contour
25970 lines (isolines) and contour polygons (isobands) from regularly spaced grids
25971 containing elevation data.")
25972 (license license:expat)))
25974 (define-public r-ppcor
25981 (uri (cran-uri "ppcor" version))
25984 "1x9b2kb8s0bp92b17gby0jwzzr3i4cf3ap9c4nq7m8fav72g0y3a"))))
25985 (properties `((upstream-name . "ppcor")))
25986 (build-system r-build-system)
25989 (home-page "https://cran.r-project.org/web/packages/ppcor/")
25990 (synopsis "Partial and semi-partial correlation")
25992 "This package provides users not only with a function to readily
25993 calculate the higher-order partial and semi-partial correlations but also with
25994 statistics and p-values of the correlation coefficients.")
25995 (license license:gpl2)))
25997 (define-public r-hrbrthemes
25999 (name "r-hrbrthemes")
26004 (uri (cran-uri "hrbrthemes" version))
26006 (base32 "057h60b5p53dcyjyfwlgjc1ry968s9s64dw78p443w8717zk7zpc"))))
26007 (properties `((upstream-name . "hrbrthemes")))
26008 (build-system r-build-system)
26020 (home-page "https://github.com/hrbrmstr/hrbrthemes/")
26021 (synopsis "Additional themes, theme components and utilities for @code{ggplot2}")
26023 "This package provides a compilation of extra @code{ggplot2} themes,
26024 scales and utilities, including a spell check function for plot label fields
26025 and an overall emphasis on typography.")
26026 (license license:expat)))
26028 (define-public r-crochet
26035 (uri (cran-uri "crochet" version))
26038 "0zvjaf6cv0nrjb4l4llkr0mmgha7ig31p4ri2rlnqyjlxi5l8hyq"))))
26039 (build-system r-build-system)
26042 (home-page "https://github.com/agrueneberg/crochet")
26043 (synopsis "Implementation Helper for Matrix-Like Types")
26045 "Functions to help implement the extraction / subsetting / indexing
26046 function @code{[} and replacement function @code{[<-} of custom matrix-like
26047 types (based on S3, S4, etc.), modeled as closely to the base matrix class
26048 as possible (with tests to prove it).")
26049 (license license:expat)))
26051 (define-public r-boa
26054 (version "1.1.8-2")
26058 (uri (cran-uri "boa" version))
26061 "04lhqk5qfvaz1jk90glr2yi5vq7cdy0w8m6g2lnzk359l9y41zhp"))))
26062 (properties `((upstream-name . "boa")))
26063 (build-system r-build-system)
26064 (home-page "https://www.jstatsoft.org/v21/i11")
26065 (synopsis "Library for @dfn{Bayesian Output Analysis Program} (BOA) for MCMC")
26067 "This package provides a menu-driven program and library of functions for
26068 carrying out convergence diagnostics and statistical and graphical analysis of
26069 @dfn{Markov chain Monte Carlo} (MCMC) sampling output.")
26070 (license license:gpl2+)))
26072 (define-public r-httpcode
26074 (name "r-httpcode")
26078 (uri (cran-uri "httpcode" version))
26081 "0xig0rvc81hg7mw0iq9s0an1nw24fg0kfs2p2n6dzhwl9w506fjr"))))
26082 (build-system r-build-system)
26083 (home-page "https://github.com/sckott/httpcode")
26084 (synopsis "HTTP status code helper")
26085 (description "@code{httpcode} provides functionality for finding and
26086 explaining the meaning of @code{HTTP} status codes. Functions are included for
26087 searching for codes by full or partial number, by message, and to get
26088 appropriate dog and cat images for many status codes.")
26089 (license license:expat)))
26091 (define-public r-latex2exp
26093 (name "r-latex2exp")
26097 (uri (cran-uri "latex2exp" version))
26100 "0zbbrbgg524lpm733j8qsqk5ssg75c51s6dgzb18c6fk8byrx945"))))
26101 (build-system r-build-system)
26103 (list r-stringr r-magrittr))
26106 (home-page "https://github.com/stefano-meschiari/latex2exp/")
26107 (synopsis "Use LaTeX expressions in plots")
26108 (description "@code{latex2exp} parses and converts LaTeX math formulas to
26109 R's plotmath expressions, used to enter mathematical formulas and symbols to be
26110 rendered as text, axis labels, etc. throughout R's plotting system.")
26111 (license license:expat)))
26113 (define-public r-oai
26119 (uri (cran-uri "oai" version))
26122 "1zcbcxhw692s0y6izvwazyzhgx0iwsxsbcan2nk0mb7n11p7bypb"))))
26123 (build-system r-build-system)
26125 (list r-xml2 r-httr r-plyr r-stringr r-tibble))
26128 (home-page "https://github.com/ropensci/oai/")
26129 (synopsis "General purpose OAI-PMH services client")
26130 (description "@code{oai} provides a general purpose client to work with
26131 any @dfn{Open Archives Initiative Protocol for 'Metadata' Harvesting} (OAI-PMH)
26132 service. Functions are provided to work with the OAI-PMH verbs:
26133 @code{GetRecord}, @code{Identify}, @code{ListIdentifiers},
26134 @code{ListMetadataFormats}, @code{ListRecords}, and @code{ListSets}.")
26135 (license license:expat)))
26137 (define-public r-argon2
26144 (uri (cran-uri "argon2" version))
26147 "09hzl0wz0lw2v7g64rdv0lij2hq36zl37a6rmxwvinmjdzijcsyw"))))
26148 (properties `((upstream-name . "argon2")))
26149 (build-system r-build-system)
26150 (home-page "https://github.com/wrathematics/argon2")
26151 (synopsis "Secure password hashing based on the argon2 algorithm")
26153 "This package provides utilities for secure password hashing via the
26154 argon2 algorithm.")
26155 (license license:bsd-2)))
26157 (define-public r-getpass
26164 (uri (cran-uri "getPass" version))
26167 "03ydafhh0sk3rcnpr3paajyji64x2ddp6p814p9mvbmyrblcgzcc"))))
26168 (properties `((upstream-name . "getPass")))
26169 (build-system r-build-system)
26171 (list r-rstudioapi))
26172 (home-page "https://github.com/wrathematics/getPass")
26173 (synopsis "Masked user input")
26175 "This package provides a micro-package for reading \"passwords\", i.e.
26176 reading user input with masking, so that the input is not displayed as it is
26177 typed. Currently, RStudio, the command line (every OS), and any platform
26178 where tcltk is present are supported.")
26179 (license license:bsd-2)))
26181 (define-public r-remoter
26188 (uri (cran-uri "remoter" version))
26191 "1a7m63l8phv5jnazvdqdrqkaqjwqzaac5y4jm2jn0ypy4n8jvkfl"))))
26192 (properties `((upstream-name . "remoter")))
26193 (build-system r-build-system)
26195 (list r-argon2 r-getpass r-pbdzmq r-png))
26196 (home-page "https://github.com/RBigData/remoter")
26197 (synopsis "Control a remote R session from a local one")
26199 "This package provides a set of utilities for client/server computing
26200 with R, controlling a remote R session (the server) from a local one (the
26202 (license license:bsd-2)))
26204 (define-public r-asd
26211 (uri (cran-uri "asd" version))
26214 "0p3r4qjam3sl3rpcilb0pgx4xx3ly71xqnvkv31vzjs885lgxz4l"))))
26215 (properties `((upstream-name . "asd")))
26216 (build-system r-build-system)
26219 (home-page "https://cran.r-project.org/web/packages/asd")
26220 (synopsis "Simulations for Adaptive Seamless Designs")
26222 "This package provdes means to run simulations for adaptive seamless
26223 designs with and without early outcomes for treatment selection and
26224 subpopulation type designs.")
26225 (license license:gpl3)))
26227 (define-public r-nbconvertr
26229 (name "r-nbconvertr")
26234 (uri (cran-uri "nbconvertR" version))
26237 "0yhmz177r1miain65vspclahhz8cg7638ldbpsw8ylgf7a60l0sg"))))
26238 (properties `((upstream-name . "nbconvertR")))
26239 (build-system r-build-system)
26241 (list python-nbconvert pandoc))
26242 (home-page "https://cran.r-project.org/web/packages/nbconvertR/")
26243 (synopsis "Vignette engine wrapping Jupyter notebooks")
26245 "This package calls the Jupyter script @code{nbconvert} to create
26246 vignettes from notebooks. Those notebooks (@code{.ipynb} files) are files
26247 containing rich text, code, and its output. Code cells can be edited and
26248 evaluated interactively.")
26249 (license license:gpl3)))
26251 (define-public r-bridgesampling
26253 (name "r-bridgesampling")
26258 (uri (cran-uri "bridgesampling" version))
26261 "0sry1xwiv4y52k44hq6z8y2kysp5kxgl4dix3m94svg3ladd7v2l"))))
26263 `((upstream-name . "bridgesampling")))
26264 (build-system r-build-system)
26266 (list r-brobdingnag
26274 (home-page "https://github.com/quentingronau/bridgesampling")
26275 (synopsis "Bridge sampling for marginal likelihoods and Bayes factors")
26277 "This package provides functions for estimating marginal likelihoods,
26278 Bayes factors, posterior model probabilities, and normalizing constants in
26279 general, via different versions of bridge sampling.")
26280 (license license:gpl2+)))
26282 (define-public r-tea
26289 (uri (cran-uri "tea" version))
26292 "0ql7lrxk0ihm49kqsvz79ig8i54rwiy9nxav4v9hy72j9kj5bgjn"))))
26294 `((upstream-name . "tea")))
26295 (build-system r-build-system)
26298 (home-page "https://cran.r-project.org/web/packages/tea/")
26299 (synopsis "Threshold estimation approaches")
26301 "This package provides different approaches for selecting the threshold
26302 in generalized Pareto distributions. Most of them are based on minimizing the
26303 AMSE-criterion or at least by reducing the bias of the assumed GPD-model.
26304 Others are heuristically motivated by searching for stable sample paths, i.e.
26305 a nearly constant region of the tail index estimator with respect to k, which
26306 is the number of data in the tail. The third class is motivated by graphical
26307 inspection. In addition, a sequential testing procedure for GPD-GoF-tests
26308 is also implemented here.")
26309 (license license:gpl3)))
26311 (define-public r-awsmethods
26313 (name "r-awsmethods")
26318 (uri (cran-uri "awsMethods" version))
26321 "0hbmrcpdyg15zg4rysscsmxpxlpy0dkxx2aa63qibq7l1k14v4sh"))))
26323 `((upstream-name . "awsMethods")))
26324 (build-system r-build-system)
26325 (home-page "http://www.wias-berlin.de/software/imaging/")
26326 (synopsis "Class and methods definitions")
26328 "This package defines the generic method @code{extract} and provides
26329 @code{openMP} support as needed in several packages like
26330 @code{aws}, @code{adimpro}, @code{fmri}, and @code{dwi}.")
26331 (license license:gpl2+)))
26333 (define-public r-aws
26340 (uri (cran-uri "aws" version))
26343 "1fhm87iax6bkvd4vszvjbcqw3b2drs11rjxr7zf2w4sgc72svaz8"))))
26345 `((upstream-name . "aws")))
26346 (build-system r-build-system)
26348 (list r-awsmethods r-gsl))
26351 (home-page "https://cran.r-project.org/web/packages/aws/")
26352 (synopsis "Adaptive weights smoothing")
26354 "This package provides a collection of R-functions implementing adaptive
26355 smoothing procedures in 1D, 2D and 3D. This includes the
26356 Propagation-Separation approach to adaptive smoothing, the @dfn{Intersecting
26357 Confidence Intervals} (ICI), variational approaches, and a non-local means
26359 (license license:gpl2+)))
26361 (define-public r-sgloptim
26363 (name "r-sgloptim")
26368 (uri (cran-uri "sglOptim" version))
26371 "15bkkvgp9v9vsp65wps48g3c2fa0fj1025hbrziywq14j7wayyjr"))))
26373 `((upstream-name . "sglOptim")))
26374 (build-system r-build-system)
26385 (home-page "https://github.com/nielsrhansen/sglOptim")
26386 (synopsis "Generic sparse group Lasso solver")
26388 "This package provides a fast generic solver for sparse group lasso
26389 optimization problems. The loss (objective) function must be defined in a C++
26390 module. The optimization problem is solved using a coordinate gradient
26391 descent algorithm. Convergence of the algorithm is established and the
26392 algorithm is applicable to a broad class of loss functions. Use of parallel
26393 computing for cross validation and subsampling is supported through the
26394 @code{foreach} and @code{doParallel} packages.")
26395 (license license:gpl2+)))
26397 (define-public r-grouped
26404 (uri (cran-uri "grouped" version))
26407 "1glxgacpwk7yjbkwg5ci6bmb2il6hf5zhydwi5bbq6hc032m9976"))))
26409 `((upstream-name . "grouped")))
26410 (build-system r-build-system)
26413 (home-page "https://cran.r-project.org/web/packages/grouped/")
26414 (synopsis "Regression analysis of grouped and coarse data")
26416 "This package provides regression models for grouped and coarse data,
26417 under the coarsened at random assumption.")
26418 (license license:gpl2+)))
26420 (define-public r-stam
26427 (uri (cran-uri "stam" version))
26430 "1x1j45fir64kffny0nssb2hwn4rcp8gd2cjv6fw4yy0l4d0xi5iv"))))
26432 `((upstream-name . "stam")))
26433 (build-system r-build-system)
26436 (home-page "https://cran.r-project.org/web/packages/stam")
26437 (synopsis "Spatio-temporal analysis and modelling")
26439 "This package provides various methods to conduct Spatio-Temporal
26440 Analysis and Modelling, including Exploratory Spatio-Temporal Analysis and
26441 Inferred Spatio-Temporal Modelling.")
26442 (license license:gpl2+)))
26444 (define-public r-dcv
26451 (uri (cran-uri "dcv" version))
26454 "12c716x8dnxnqksibpmyysqp2axggvy9dpd55s9bhnsvqvi6dshj"))))
26456 `((upstream-name . "dcv")))
26457 (build-system r-build-system)
26460 (home-page "https://cran.r-project.org/web/packages/dcv/")
26461 (synopsis "Conventional cross-validation statistics for climate-growth model")
26463 "This package performs several conventional cross-validation statistical
26464 methods for climate-growth model in the climate reconstruction from tree
26465 rings, including Sign Test statistic, Reduction of Error statistic, Product
26466 Mean Test, Durbin-Watson statistic etc.")
26467 (license license:gpl2)))
26469 (define-public r-rcdd
26476 (uri (cran-uri "rcdd" version))
26479 "0zxx0qvv26ba30jkm8mvca4h59rqklay4jwazpcw7h9dzp4189jr"))))
26481 `((upstream-name . "rcdd")))
26482 (build-system r-build-system)
26485 (home-page "https://www.stat.umn.edu/geyer/rcdd/")
26486 (synopsis "Computational geometry")
26488 "This package converts back and forth between two representations of a
26489 convex polytope: as solution of a set of linear equalities and inequalities
26490 and as convex hull of set of points and rays. Also does linear programming
26491 and redundant generator elimination. All functions can use exact
26492 infinite-precision rational arithmetic.")
26493 (license license:gpl2)))
26495 (define-public r-rxnat
26502 (uri (cran-uri "Rxnat" version))
26505 "0siylypjd8cgcmr2c443w8krg8sgr5gz4zapbinanp8vsfzivdv2"))))
26507 `((upstream-name . "Rxnat")))
26508 (build-system r-build-system)
26510 (list r-httr r-rcurl r-tibble))
26513 (home-page "https://cran.r-project.org/web/packages/Rxnat/")
26514 (synopsis "Queries and extracts images from neuroimaging datasets")
26516 "This package allows communication with the Extensible Neuroimaging
26517 Archive Toolkit. Rxnat uses the XNAT REST API to perform data queries and
26519 (license license:gpl2)))
26521 (define-public r-rserve
26528 (uri (string-append "http://www.rforge.net/Rserve/snapshot/Rserve_"
26529 version ".tar.gz"))
26532 "017kkzv9lxlz9qhg3gprrf1wcyflxrif6wjk27x9b4bdzylw6bsx"))))
26533 (build-system r-build-system)
26536 (modify-phases %standard-phases
26537 (add-before 'install 'install-server-binary
26538 ;; Makevars tries to install to R's store directory.
26539 (lambda* (#:key outputs #:allow-other-keys)
26540 (let* ((out (assoc-ref outputs "out"))
26541 (bin (string-append out "/bin")))
26542 (substitute* "src/Makevars.in"
26543 (("\\$\\(R_HOME\\)") out))
26544 (mkdir-p bin)))))))
26554 (list openssl zlib))
26555 (home-page "https://github.com/s-u/Rserve")
26557 "Server providing access to R from many languages and systems")
26559 "Rserve acts as a socket server (TCP/IP or local sockets) which allows
26560 binary requests to be sent to R. Every connection has a separate workspace
26561 and working directory. Client-side implementations are available for popular
26562 languages such as C/C++ and Java, allowing any application to use facilities
26563 of R without the need of linking to R code. Rserve supports remote
26564 connection, user authentication and file transfer. A simple R client is
26565 included in this package as well.")
26566 (license license:gpl2)))
26568 (define-public r-gamm4
26575 (uri (cran-uri "gamm4" version))
26578 "128c725y9s07c1m9cvd9hgi9hldrymcs5divd8pw7bdjh9jvdiap"))))
26579 (properties `((upstream-name . "gamm4")))
26580 (build-system r-build-system)
26582 (list r-lme4 r-matrix r-mgcv))
26583 (home-page "https://cran.r-project.org/web/packages/gamm4/")
26584 (synopsis "Generalized additive mixed models using mgcv and lme4")
26586 "Estimate generalized additive mixed models via a version of function
26587 @code{gamm} from the @code{mgcv} package, using the @code{lme4} packagefor
26589 (license license:gpl2+)))
26591 (define-public r-optimx
26594 (version "2022-4.30")
26598 (uri (cran-uri "optimx" version))
26601 "045ls1vl1392ihwln6mngz0zg2w93ym1m607vfrg8v1949x8isgb"))))
26602 (properties `((upstream-name . "optimx")))
26603 (build-system r-build-system)
26604 (propagated-inputs (list r-numderiv))
26605 (native-inputs (list r-knitr))
26606 (home-page "https://cran.r-project.org/web/packages/optimx/")
26607 (synopsis "Expanded replacement and extension of the optim function")
26609 "This package provides a replacement and extension of the @code{optim}
26610 function to call to several function minimization codes in R in a single
26611 statement. These methods handle smooth, possibly box constrained functions of
26612 several or many parameters. Note that the function @code{optimr} was prepared
26613 to simplify the incorporation of minimization codes going forward. This
26614 package also implements some utility codes and some extra solvers, including
26615 safeguarded Newton methods. Many methods previously separate are now included
26617 (license license:gpl2)))
26619 (define-public r-projpred
26621 (name "r-projpred")
26626 (uri (cran-uri "projpred" version))
26629 "1c6gnmknd3vb0fb5h6gd372dk27nzif90b4c1snql49wacg6b2m8"))))
26630 (properties `((upstream-name . "projpred")))
26631 (build-system r-build-system)
26645 (native-inputs (list r-knitr))
26646 (home-page "https://mc-stan.org/projpred/")
26647 (synopsis "Projection predictive feature selection")
26649 "This package performs projection predictive feature selection for
26650 generalized linear models and generalized linear and additive multilevel
26651 models. The package is compatible with the @code{rstanarm} and @code{brms}
26652 packages, but other reference models can also be used. See the package
26653 vignette for more information and examples.")
26654 (license license:gpl3)))
26656 (define-public r-distributional
26658 (name "r-distributional")
26663 (uri (cran-uri "distributional" version))
26666 "1mji8xlhwrw8msih5wdpbzwv4g59kly0xkdklhn8yzb18rrnrczs"))))
26668 `((upstream-name . "distributional")))
26669 (build-system r-build-system)
26681 (home-page "https://pkg.mitchelloharawild.com/distributional/")
26682 (synopsis "Vectorized probability distributions")
26684 "This package provides vectorized distribution objects with tools for
26685 manipulating, visualizing, and using probability distributions. It was
26686 designed to allow model prediction outputs to return distributions rather than
26687 their parameters, allowing users to directly interact with predictive
26688 distributions in a data-oriented workflow. In addition to providing generic
26689 replacements for p/d/q/r functions, other useful statistics can be computed
26690 including means, variances, intervals, and highest density regions.")
26691 (license license:gpl3)))
26693 (define-public r-posterior
26695 (name "r-posterior")
26700 (uri (cran-uri "posterior" version))
26703 "1qdg22l868daqg2axr36szl1m9z0rfpgx8zmv1x1xwm1hmlf0mxp"))))
26704 (properties `((upstream-name . "posterior")))
26705 (build-system r-build-system)
26718 (home-page "https://mc-stan.org/posterior/")
26719 (synopsis "Tools for working with posterior distributions")
26721 "This package provides useful tools for both users and developers of
26722 packages for fitting Bayesian models or working with output from Bayesian
26723 models. The primary goals of the package are to:
26726 @item Efficiently convert between many different useful formats of
26727 draws (samples) from posterior or prior distributions.
26729 @item Provide consistent methods for operations commonly performed on draws,
26730 for example, subsetting, binding, or mutating draws.
26732 @item Provide various summaries of draws in convenient formats.
26734 @item Provide lightweight implementations of state of the art posterior
26735 inference diagnostics.
26738 (license license:bsd-3)))
26740 (define-public r-brms
26747 (uri (cran-uri "brms" version))
26750 "0wff5rld4kgkk2nbllvm1h4c596igzgd0q7nx1cabgl11fja7r94"))))
26751 (properties `((upstream-name . "brms")))
26752 (build-system r-build-system)
26773 (native-inputs (list r-knitr))
26775 "https://github.com/paul-buerkner/brms")
26777 "Bayesian Regression Models using 'Stan'")
26779 "Fit Bayesian generalized (non-)linear multivariate multilevel models
26780 using 'Stan' for full Bayesian inference. A wide range of distributions and
26781 link functions are supported, allowing users to fit -- among others -- linear,
26782 robust linear, count data, survival, response times, ordinal, zero-inflated,
26783 hurdle, and even self-defined mixture models all in a multilevel context.
26784 Further modeling options include non-linear and smooth terms, auto-correlation
26785 structures, censored data, meta-analytic standard errors, and quite a few
26786 more. In addition, all parameters of the response distribution can be
26787 predicted in order to perform distributional regression. Prior specifications
26788 are flexible and explicitly encourage users to apply prior distributions that
26789 actually reflect their beliefs. Model fit can easily be assessed and compared
26790 with posterior predictive checks and leave-one-out cross-validation.")
26791 (license license:gpl2)))
26793 (define-public r-mstate
26800 (uri (cran-uri "mstate" version))
26803 "054dzrd5b0xjjjl7862q3aq1jwgrxbkqz7zpvbdirqsld3zksirw"))))
26804 (properties `((upstream-name . "mstate")))
26805 (build-system r-build-system)
26816 "https://www.lumc.nl/org/bds/research/medische-statistiek/survival-analysis/")
26818 "Data Preparation, Estimation and Prediction in Multi-State Models")
26820 "Contains functions for data preparation, descriptives, hazard estimation
26821 and prediction with Aalen-Johansen or simulation in competing risks and
26822 multi-state models.")
26823 (license license:gpl2+)))
26825 (define-public r-scatterpie
26827 (name "r-scatterpie")
26832 (uri (cran-uri "scatterpie" version))
26835 "1pmspv8a7k20zyd5xvmav2k9mnjrkfhdij3rr9k504zyki8hfy1z"))))
26836 (properties `((upstream-name . "scatterpie")))
26837 (build-system r-build-system)
26839 (list r-ggforce r-ggfun r-ggplot2 r-rlang r-tidyr))
26842 (home-page "https://cran.r-project.org/web/packages/scatterpie/")
26843 (synopsis "Scatter pie plot")
26845 "This package creates scatterpie plots, especially useful for plotting
26847 (license license:artistic2.0)))
26849 (define-public r-scrypt
26856 (uri (cran-uri "scrypt" version))
26859 "12q9d4m7flbvlgssvjh1ga4jswkmqjfshf6pna6qk6v087gmzdsj"))))
26860 (properties `((upstream-name . "scrypt")))
26861 (build-system r-build-system)
26864 (home-page "https://github.com/rstudio/rscrypt")
26865 (synopsis "Key derivation functions for R based on Scrypt")
26867 "This package provides functions for working with the scrypt key
26868 derivation functions. Scrypt is a password-based key derivation function
26869 created by Colin Percival. The algorithm was specifically designed to make it
26870 costly to perform large-scale custom hardware attacks by requiring large
26871 amounts of memory.")
26872 (license license:bsd-2)))
26874 (define-public r-boruta
26881 (uri (cran-uri "Boruta" version))
26884 "0y2w4wb45kfnzrxcrdsiwgal9fsnlr3wad1sqdc70qv8gp921xbg"))))
26885 (properties `((upstream-name . "Boruta")))
26886 (build-system r-build-system)
26887 (propagated-inputs (list r-ranger))
26888 (home-page "https://gitlab.com/mbq/Boruta/")
26889 (synopsis "Wrapper algorithm for all relevant feature selection")
26891 "This package provides an all relevant feature selection wrapper
26892 algorithm. It finds relevant features by comparing original attributes'
26893 importance with importance achievable at random, estimated using their
26894 permuted copies (shadows).")
26895 (license license:gpl2+)))
26897 (define-public r-directlabels
26899 (name "r-directlabels")
26900 (version "2021.1.13")
26904 (uri (cran-uri "directlabels" version))
26907 "0415kh9k2qzdwi8zb32fh2icl5wf5335kyj11cyfdmfxji39zv2w"))))
26908 (build-system r-build-system)
26913 (home-page "http://directlabels.r-forge.r-project.org/")
26914 (synopsis "Direct labels for multicolor plots")
26916 "This package provides an extensible framework for automatically placing
26917 direct labels onto multicolor plots. Label positions are described using
26918 positioning methods that can be re-used across several different plots. There
26919 are heuristics for examining @code{trellis} and @code{ggplot} objects and
26920 inferring an appropriate positioning method.")
26921 (license license:gpl3)))
26923 (define-public r-lsd
26930 (uri (cran-uri "LSD" version))
26932 (base32 "17pbdlcbhzf3v7l42mjikln1ga5xjp5r78gjg6a88iahk0lwwlvm"))))
26933 (properties `((upstream-name . "LSD")))
26934 (build-system r-build-system)
26935 (home-page "https://cran.r-project.org/web/packages/LSD/")
26936 (synopsis "Lots of superior depictions tool creates colorful plots")
26938 "This package creates lots of colorful plots in a multitude of variations.
26939 Try a demo of the LSD by running @code{demotour()}.")
26941 (license (list license:gpl2 license:gpl3))))
26943 (define-public r-phylogram
26945 (name "r-phylogram")
26950 (uri (cran-uri "phylogram" version))
26952 (base32 "1p4h5pirc0m5pzc18q0jk3mcmb5n48gdf9abz03vml3a209xxl2v"))))
26953 (properties `((upstream-name . "phylogram")))
26954 (build-system r-build-system)
26955 (propagated-inputs (list r-ape))
26956 (home-page "https://github.com/ropensci/phylogram/")
26957 (synopsis "Dendrograms for evolutionary analysis")
26959 "The @code{r-phylogram} package is a tool for for developing phylogenetic
26960 trees as deeply-nested lists known as \"dendrogram\" objects. It provides
26961 functions for conversion between \"dendrogram\" and \"phylo\" class objects,
26962 as well as several tools for command-line tree manipulation and import/export
26963 via Newick parenthetic text. This improves accessibility to the comprehensive
26964 range of object-specific analytical and tree-visualization functions found
26965 across a wide array of bioinformatic R packages.")
26966 (license license:gpl3)))
26968 (define-public r-kmer
26975 (uri (cran-uri "kmer" version))
26977 (base32 "0jimn9r0abglwxdl1zqz0lxa99cmj6haydkxjzqfbpx9by80wnww"))))
26978 (properties `((upstream-name . "kmer")))
26979 (build-system r-build-system)
26981 (list r-openssl r-phylogram r-rcpp))
26982 (home-page "https://github.com/shaunpwilkinson/kmer/")
26983 (synopsis "Fast K-Mer counting and clustering for biological sequence analysis")
26985 "@code{r-kmer} is an R package for rapidly computing distance matrices
26986 and clustering large sequence datasets using fast alignment-free k-mer
26987 counting and recursive k-means partitioning.")
26988 (license license:gpl3)))
26990 (define-public r-hardhat
26997 (uri (cran-uri "hardhat" version))
27000 "0a4nq93cmps5xy8h0qsv6xyzrbsz9ka4iwkrvb8m8v10wq7wm5wl"))))
27001 (properties `((upstream-name . "hardhat")))
27002 (build-system r-build-system)
27004 (list r-glue r-rlang r-tibble r-vctrs))
27007 (home-page "https://github.com/tidymodels/hardhat")
27008 (synopsis "Construct modeling packages")
27010 "Building modeling packages is hard. A large amount of effort generally
27011 goes into providing an implementation for a new method that is efficient,
27012 fast, and correct, but often less emphasis is put on the user interface. A
27013 good interface requires specialized knowledge about S3 methods and formulas,
27014 which the average package developer might not have. The goal of
27015 @code{hardhat} is to reduce the burden around building new modeling packages
27016 by providing functionality for preprocessing, predicting, and validating
27018 (license license:expat)))
27020 (define-public r-lightgbm
27022 (name "r-lightgbm")
27027 (uri (cran-uri "lightgbm" version))
27030 "12hbvm1va6sb5yny564jvhhzrkcq4j33rcdhqhwxaac2m08cpi8s"))))
27031 (properties `((upstream-name . "lightgbm")))
27032 (build-system r-build-system)
27034 (list r-data-table r-jsonlite r-matrix r-r6))
27035 (home-page "https://github.com/Microsoft/LightGBM")
27036 (synopsis "Light gradient boosting machine")
27038 "Tree based algorithms can be improved by introducing boosting
27039 frameworks. LightGBM is one such framework, based on Ke, Guolin et
27040 al. (2017). This package offers an R interface to work with it. It is
27041 designed to be distributed and efficient with the following goals:
27044 @item Faster training speed and higher efficiency;
27045 @item lower memory usage;
27046 @item better accuracy;
27047 @item parallel learning supported; and
27048 @item capable of handling large-scale data.
27051 (license license:expat)))
27053 (define-public r-shapforxgboost
27055 (name "r-shapforxgboost")
27060 (uri (cran-uri "SHAPforxgboost" version))
27063 "106nsf02b1w3yshb55lwnyw1rl1a60162v2wk8znjz3b4ln3mqj5"))))
27065 `((upstream-name . "SHAPforxgboost")))
27066 (build-system r-build-system)
27078 (home-page "https://github.com/liuyanguu/SHAPforxgboost")
27079 (synopsis "SHAP Plots for XGBoost")
27081 "The aim of @code{SHAPforxgboost} is to aid in visual data investigations
27082 using @dfn{SHAP} (Shapley additive explanation) visualization plots for
27083 @code{XGBoost}. It provides summary plot, dependence plot, interaction plot,
27084 and force plot. It relies on the @code{XGBoost} package to produce SHAP
27086 (license license:expat)))
27088 (define-public r-rismed
27095 (uri (cran-uri "RISmed" version))
27098 "0vpi88gzi9r85v6nhjz9jbw671zkrmyazwna2z881346wfyr3l8b"))))
27099 (properties `((upstream-name . "RISmed")))
27100 (build-system r-build-system)
27102 (list r-httr r-xml2))
27103 (home-page "https://cran.r-project.org/web/packages/RISmed")
27104 (synopsis "Download content from NCBI databases")
27106 "This package provides a set of tools to extract bibliographic
27107 content from the National Center for Biotechnology Information (NCBI)
27108 databases, including PubMed. The name RISmed is a portmanteau of
27109 RIS (for Research Information Systems, a common tag format for
27110 bibliographic data) and PubMed.")
27111 (license license:gpl2+)))
27113 (define-public r-semver
27120 (uri (cran-uri "semver" version))
27123 "10wpkyms2cix3bsin2q0qhkbl445pwwpa5gm2s4jjw1989namkxy"))))
27124 (properties `((upstream-name . "semver")))
27125 (build-system r-build-system)
27127 (list r-assertthat r-rcpp))
27128 (native-inputs (list r-knitr))
27129 (home-page "https://github.com/johndharrison/semver")
27130 (synopsis "Parser for Semantic Versioning 2.0.0")
27132 "This package provides tools and functions for parsing, rendering and
27133 operating on semantic version strings. Semantic versioning is a simple set of
27134 rules and requirements that dictate how version numbers are assigned and
27135 incremented as outlined at @url{http://semver.org}.")
27136 (license license:expat)))
27138 (define-public r-binman
27145 (uri (cran-uri "binman" version))
27148 "00l7m98h41r67gf0qxqis3vx63j7wylnk9vlgcyk41szkrz8ikkc"))))
27149 (properties `((upstream-name . "binman")))
27150 (build-system r-build-system)
27159 (native-inputs (list r-knitr))
27160 (home-page "https://github.com/ropensci/binman")
27161 (synopsis "Binary download manager")
27163 "This package provides tools and functions for managing the download of
27164 binary files. Binary repositories are defined in the YAML format. Defining
27165 new pre-download, download and post-download templates allow additional
27166 repositories to be added.")
27167 (license license:expat)))
27169 (define-public r-wdman
27176 (uri (cran-uri "wdman" version))
27179 "1yf41lsrr9dbf5n4f5hv9mlmzl736fhnp9gxkm2g9apws6gsig02"))))
27180 (properties `((upstream-name . "wdman")))
27181 (build-system r-build-system)
27183 (list r-assertthat r-binman r-processx r-semver r-yaml))
27184 (native-inputs (list r-knitr))
27185 (home-page "https://docs.ropensci.org/wdman/")
27186 (synopsis "Webdriver/Selenium binary manager")
27188 "There are a number of binary files associated with the
27189 Webdriver/Selenium project (see @url{http://www.seleniumhq.org/download/},
27190 @url{https://sites.google.com/a/chromium.org/chromedriver/},
27191 @url{https://github.com/mozilla/geckodriver},
27192 @url{http://phantomjs.org/download.html}, and
27193 @url{https://github.com/SeleniumHQ/selenium/wiki/InternetExplorerDriver} for
27194 more information). This package provides functions to download these binaries
27195 and to manage processes involving them.")
27196 (license license:expat)))
27198 (define-public r-rselenium
27200 (name "r-rselenium")
27205 (uri (cran-uri "RSelenium" version))
27208 "1xn5fdbzmq7b1f5fc9ls23g177bmnd8bn4p4d8aafr6z3jwkmfir"))))
27209 (properties `((upstream-name . "RSelenium")))
27210 (build-system r-build-system)
27218 (native-inputs (list r-knitr))
27219 (home-page "https://docs.ropensci.org/RSelenium/")
27220 (synopsis "R bindings for Selenium WebDriver")
27222 "This package provides a set of R bindings for the Selenium 2.0
27223 WebDriver (see @url{https://selenium.dev/documentation/en/} for more
27224 information) using the @code{JsonWireProtocol} (see
27225 @url{https://github.com/SeleniumHQ/selenium/wiki/JsonWireProtocol} for more
27226 information). Selenium 2.0 WebDriver allows driving a web browser natively as
27227 a user would either locally or on a remote machine using the Selenium server
27228 it marks a leap forward in terms of web browser automation. Selenium
27229 automates web browsers (commonly referred to as browsers). Using RSelenium
27230 you can automate browsers locally or remotely.")
27231 (license license:agpl3+)))
27233 (define-public r-conquer
27240 (uri (cran-uri "conquer" version))
27243 "1ynmaf7lgqjb8grsifx5dzy29cd5kz4x3yh0abnl2vxdr4c4wddc"))))
27244 (properties `((upstream-name . "conquer")))
27245 (build-system r-build-system)
27247 (list r-matrix r-matrixstats r-rcpp r-rcpparmadillo))
27248 (home-page "https://github.com/XiaoouPan/conquer")
27249 (synopsis "Convolution-type smoothed quantile regression")
27251 "This package provides fast and accurate convolution-type smoothed
27252 quantile regression, implemented using Barzilai-Borwein gradient descent with
27253 a Huber regression warm start. Confidence intervals for regression
27254 coefficients are constructed using multiplier bootstrap.")
27255 (license license:gpl3)))
27257 (define-public r-fastshap
27259 (name "r-fastshap")
27264 (uri (cran-uri "fastshap" version))
27267 "0gxch67i3bj6m8nb94m5hswq058w6n1q9war4dy2qnimlv7cmhdv"))))
27268 (properties `((upstream-name . "fastshap")))
27269 (build-system r-build-system)
27279 (home-page "https://github.com/bgreenwell/fastshap")
27280 (synopsis "Fast approximate Shapley values")
27282 "This package computes fast (relative to other implementations)
27283 approximate Shapley values for any supervised learning model. Shapley values
27284 help to explain the predictions from any black box model using ideas from game
27285 theory; see @url{Strumbel and Kononenko (2014),
27286 doi.org/10.1007/s10115-013-0679-x} for details.")
27287 (license license:gpl2+)))
27289 (define-public r-memuse
27295 (uri (cran-uri "memuse" version))
27298 "1wvwnjaaiv2647561z2b55dss35033ildx4kk8hzxfzgsjmdpsgm"))))
27299 (properties `((upstream-name . "memuse")))
27300 (build-system r-build-system)
27301 (home-page "https://github.com/shinra-dev/memuse")
27302 (synopsis "Memory Estimation Utilities")
27304 "This package provides procedures to answer the following questions:
27305 How much ram do you need to store a 100,000 by 100,000 matrix? How much ram is
27306 your current R session using? How much ram do you even have?")
27307 (license license:bsd-2)))
27309 (define-public r-metrics
27316 (uri (cran-uri "Metrics" version))
27319 "0fh8qbjlwzagh272lgwr4bxcqcjb1qpz53mgs8rzlvncax6nk5bk"))))
27320 (properties `((upstream-name . "Metrics")))
27321 (build-system r-build-system)
27322 (home-page "https://github.com/mfrasco/Metrics")
27323 (synopsis "Evaluation metrics for machine learning")
27325 "This package provides an implementation of evaluation metrics in R that
27326 are commonly used in supervised machine learning. It implements metrics for
27327 regression, time series, binary classification, classification, and
27328 information retrieval problems. It has zero dependencies and a consistent,
27329 simple interface for all functions.")
27330 (license license:bsd-3)))
27332 (define-public r-iml
27339 (uri (cran-uri "iml" version))
27342 "1za7bjnp07i20vyb6vxz2ya5cr8g4p076w61n8m38wnz04lz5yz5"))))
27343 (properties `((upstream-name . "iml")))
27344 (build-system r-build-system)
27355 (native-inputs (list r-knitr))
27356 (home-page "https://github.com/christophM/iml")
27357 (synopsis "Interpretable machine learning")
27359 "This package provides interpretability methods to analyze the behavior
27360 and predictions of any machine learning model. Implemented methods are:
27363 @item Feature importance described by Fisher et al. (2018),
27364 @item accumulated local effects plots described by Apley (2018),
27365 @item partial dependence plots described by Friedman (2001),
27366 @item individual conditional expectation ('ice') plots described by Goldstein
27367 et al. (2013) @url{https://doi.org/10.1080/10618600.2014.907095},
27368 @item local models (variant of 'lime') described by Ribeiro et. al (2016),
27369 @item the Shapley Value described by Strumbelj et. al (2014)
27370 @url{https://doi.org/10.1007/s10115-013-0679-x},
27371 @item feature interactions described by Friedman et. al
27372 @url{https://doi.org/10.1214/07-AOAS148} and tree surrogate models.
27375 (license license:expat)))
27377 (define-public r-goftest
27384 (uri (cran-uri "goftest" version))
27387 "06bz6k7smr4jbvzmb73qc5fkf4my59w5gbl18wlmpkkymsv78prs"))))
27388 (properties `((upstream-name . "goftest")))
27389 (build-system r-build-system)
27390 (home-page "https://github.com/baddstats/goftest")
27391 (synopsis "Classical Goodness-of-Fit tests for univariate distributions")
27393 "This package provides Cramer-Von Mises and Anderson-Darling tests of
27394 goodness-of-fit for continuous univariate distributions, using efficient
27396 (license license:gpl2+)))
27398 (define-public r-tensor
27405 (uri (cran-uri "tensor" version))
27408 "19mfsgr6vz4lgwidm80i4yw0y1dr3n8i6qz7g4n2xa0k74zc5pp1"))))
27409 (properties `((upstream-name . "tensor")))
27410 (build-system r-build-system)
27411 (home-page "https://cran.r-project.org/web/packages/tensor/")
27412 (synopsis "Tensor product of arrays")
27414 "The tensor product of two arrays is notionally an outer product of the
27415 arrays collapsed in specific extents by summing along the appropriate
27416 diagonals. This package allows you to compute the tensor product of arrays.")
27417 (license license:gpl2+)))
27419 (define-public r-spatstat-utils
27421 (name "r-spatstat-utils")
27426 (uri (cran-uri "spatstat.utils" version))
27429 "08pybliv4r3v4rcazmlfr4a07sjfhrkmksdmhhq9k185vw4474av"))))
27431 `((upstream-name . "spatstat.utils")))
27432 (build-system r-build-system)
27433 (home-page "http://www.spatstat.org")
27434 (synopsis "Utility functions for spatstat")
27436 "This package contains utility functions for the @code{spatstat} package
27437 which may also be useful for other purposes.")
27438 (license license:gpl2+)))
27440 (define-public r-spatstat-sparse
27442 (name "r-spatstat-sparse")
27447 (uri (cran-uri "spatstat.sparse" version))
27450 "00vkvv5pnm82gn7vqnzrrp68y46gbkhdq0hbwqx7nxjvf5lssdcs"))))
27452 `((upstream-name . "spatstat.sparse")))
27453 (build-system r-build-system)
27455 (list r-abind r-matrix r-spatstat-utils r-tensor))
27456 (home-page "http://spatstat.org/")
27457 (synopsis "Sparse three-dimensional arrays and linear algebra utilities")
27459 "This package defines sparse three-dimensional arrays and supports
27460 standard operations on them. The package also includes utility functions for
27461 matrix calculations that are common in statistics, such as quadratic forms.")
27462 (license license:gpl2+)))
27464 (define-public r-spatstat-data
27466 (name "r-spatstat-data")
27471 (uri (cran-uri "spatstat.data" version))
27474 "1rf36zy29h9qabpv19hx84gjdiay7i9y9777d2zn17ahyss3p56k"))))
27475 (properties `((upstream-name . "spatstat.data")))
27476 (build-system r-build-system)
27478 (list r-matrix r-spatstat-utils))
27479 (home-page "http://www.spatstat.org")
27480 (synopsis "Datasets for spatstat")
27482 "This package contains all the datasets for the @code{spatstat}
27484 (license license:gpl2+)))
27486 (define-public r-spatstat-geom
27488 (name "r-spatstat-geom")
27493 (uri (cran-uri "spatstat.geom" version))
27496 "0rwysq9a0ylbsr53q5kfh7wjk5mcdji211sc3s8gwzz8ki09mf1j"))))
27497 (properties `((upstream-name . "spatstat.geom")))
27498 (build-system r-build-system)
27500 (list r-deldir r-polyclip r-spatstat-data r-spatstat-utils))
27501 (home-page "http://spatstat.org/")
27502 (synopsis "Geometrical functionality of the spatstat package")
27504 "This is a subset of the original spatstat package, containing the
27505 user-level code from spatstat which performs geometrical operations, except
27506 for the geometry of linear networks.")
27507 (license license:gpl2+)))
27509 (define-public r-spatstat-core
27511 (name "r-spatstat-core")
27516 (uri (cran-uri "spatstat.core" version))
27519 "0fyi8y1z919nzn47kaviln7gflhcp5qdi3gfvf7nwkdix3pkk373"))))
27520 (properties `((upstream-name . "spatstat.core")))
27521 (build-system r-build-system)
27535 (home-page "http://spatstat.org/")
27536 (synopsis "Core functionality of the spatstat package")
27538 "This is a subset of the original spatstat package, containing all of the
27539 user-level code from spatstat, except for the code for linear networks.")
27540 (license license:gpl2+)))
27542 (define-public r-spatstat-linnet
27544 (name "r-spatstat-linnet")
27549 (uri (cran-uri "spatstat.linnet" version))
27552 "0y1py6x0xbw4ad3pjwcspi4ysgfh61f5fd79787zzgyyh2va8y4w"))))
27554 `((upstream-name . "spatstat.linnet")))
27555 (build-system r-build-system)
27564 (home-page "http://spatstat.org/")
27565 (synopsis "Linear networks functionality of the spatstat package")
27567 "This is a subset of the spatstat package, containing its functionality
27568 for spatial data on a linear network.")
27569 (license license:gpl2+)))
27571 (define-public r-spatstat-random
27573 (name "r-spatstat-random")
27578 (uri (cran-uri "spatstat.random" version))
27580 (base32 "0kb01s8k67ydcfqcnz3i55vpiksihh4xsg0w2p2bclxxkpdvpw25"))))
27581 (properties `((upstream-name . "spatstat.random")))
27582 (build-system r-build-system)
27583 (propagated-inputs (list r-spatstat-data r-spatstat-geom r-spatstat-utils))
27584 (home-page "http://spatstat.org/")
27585 (synopsis "Random Generation Functionality for the 'spatstat' Family")
27587 "This package provides functionality for random generation of spatial
27588 data in the spatstat family of packages. It generates random spatial patterns
27589 of points according to many simple rules (complete spatial randomness,
27590 Poisson, binomial, random grid, systematic, cell), randomised alteration of
27591 patterns (thinning, random shift, jittering), simulated realisations of random
27592 point processes (simple sequential inhibition, Matern inhibition models,
27593 Matern cluster process, Neyman-Scott cluster processes, log-Gaussian Cox
27594 processes, product shot noise cluster processes) and simulation of Gibbs point
27595 processes (Metropolis-Hastings birth-death-shift algorithm, alternating Gibbs
27597 (license license:gpl2+)))
27599 (define-public r-spatstat
27601 (name "r-spatstat")
27606 (uri (cran-uri "spatstat" version))
27609 "1nlrp7660y68axlm4pczc5rxbdhbbac1ylh69azr4swj1gbzi82f"))))
27610 (properties `((upstream-name . "spatstat")))
27611 (build-system r-build-system)
27613 (list r-spatstat-core r-spatstat-data r-spatstat-geom
27614 r-spatstat-linnet r-spatstat-random r-spatstat-utils))
27615 (home-page "http://www.spatstat.org")
27616 (synopsis "Spatial Point Pattern analysis, model-fitting, simulation, tests")
27618 "This package provides a comprehensive toolbox for analysing Spatial
27619 Point Patterns. It is focused mainly on two-dimensional point patterns,
27620 including multitype/marked points, in any spatial region. It also supports
27621 three-dimensional point patterns, space-time point patterns in any number of
27622 dimensions, point patterns on a linear network, and patterns of other
27623 geometrical objects. It supports spatial covariate data such as pixel images
27624 and contains over 2000 functions for plotting spatial data, exploratory data
27625 analysis, model-fitting, simulation, spatial sampling, model diagnostics, and
27626 formal inference.")
27627 (license license:gpl2+)))
27629 (define-public r-gaston
27636 (uri (cran-uri "gaston" version))
27639 "14z94dpln4dvgrv2w7w9ik7h6rpvbf02qhq1hqzx8c2cndzxr21i"))))
27640 (properties `((upstream-name . "gaston")))
27641 (build-system r-build-system)
27642 (inputs (list zlib))
27644 (list r-rcpp r-rcppeigen r-rcppparallel))
27645 (native-inputs (list r-knitr))
27646 (home-page "https://cran.r-project.org/web/packages/gaston/")
27647 (synopsis "Genetic data handling (QC, GRM, LD, PCA) and linear mixed models")
27649 "This is a package for the manipulation of genetic data (SNPs).
27650 Computation of @dfn{genetic relationship matrix} (GRM) and dominance matrix,
27651 @dfn{linkage disequilibrium} (LD), and heritability with efficient algorithms
27652 for linear mixed models (AIREML).")
27653 (license license:gpl3)))
27655 (define-public r-cpp11
27662 (uri (cran-uri "cpp11" version))
27665 "16cvjfkbc7c0ymdmbcqg9px6pjsqx6qhyfq5frqj739mhazy0g20"))))
27666 (properties `((upstream-name . "cpp11")))
27667 (build-system r-build-system)
27668 (native-inputs (list r-knitr))
27669 (home-page "https://github.com/r-lib/cpp11")
27670 (synopsis "C++11 Interface for R's C Interface")
27672 "This package provides a header only, C++11 interface to R's C interface.
27673 Compared to other approaches @code{cpp11} strives to be safe against long
27674 jumps from the C API as well as C++ exceptions, conform to normal R function
27675 semantics and supports interaction with @code{ALTREP} vectors.")
27676 (license license:expat)))
27678 (define-public r-rcpptoml
27680 (name "r-rcpptoml")
27685 (uri (cran-uri "RcppTOML" version))
27687 (base32 "0h8517ipwqhqkhcfiyqmvsb585g01p0ra0azbpzyxip6pq6g029g"))))
27688 (properties `((upstream-name . "RcppTOML")))
27689 (build-system r-build-system)
27690 (propagated-inputs (list r-rcpp))
27691 (home-page "http://dirk.eddelbuettel.com/code/rcpp.toml.html")
27692 (synopsis "Rcpp bindings to TOML parser")
27694 "The TOML configuration format specifies an excellent format suitable for
27695 both human editing as well as the common uses of a machine-readable format.
27696 This package provides Rcpp bindings to a TOML parser.")
27697 (license license:gpl2+)))
27699 (define-public r-rcppziggurat
27701 (name "r-rcppziggurat")
27706 (uri (cran-uri "RcppZiggurat" version))
27709 "0wgd1v2p7zajnbrjf3hfi56p3pk3ld6iwkanbb04bjbnlif2ay4w"))))
27710 (properties `((upstream-name . "RcppZiggurat")))
27711 (build-system r-build-system)
27713 (list r-rcpp r-rcppgsl))
27714 (native-inputs (list r-knitr))
27715 (home-page "https://cran.r-project.org/web/packages/RcppZiggurat/")
27716 (synopsis "Rcpp integration of different \"Ziggurat\" normal RNG implementations")
27718 "The Ziggurat generator for normally distributed random numbers,
27719 originally proposed by Marsaglia and Tsang (2000,
27720 @url{https://doi.org/10.18637/jss.v005.i08}) has been improved upon a few
27721 times starting with Leong et al (2005,
27722 @url{https://doi.org/10.18637/jss.v012.i07}). This package provides an
27723 aggregation for comparing different implementations in order to provide a
27724 'faster but good enough' alternative for use with R and C++ code.")
27725 (license license:gpl2+)))
27727 (define-public r-rfast
27734 (uri (cran-uri "Rfast" version))
27737 "0zxykq021h57mq0n6giqbx8ncjsdly0arhmaj3fcp3yfcxf4ns9l"))))
27738 (properties `((upstream-name . "Rfast")))
27739 (build-system r-build-system)
27741 (list r-rcpp r-rcpparmadillo r-rcppziggurat))
27742 (home-page "https://github.com/RfastOfficial/Rfast")
27743 (synopsis "Collection of efficient and fast R functions")
27745 "This package provides a collection of fast (utility) functions for data
27746 analysis. Column- and row- wise means, medians, variances, minimums,
27747 maximums, many t, F and G-square tests, many regressions (normal, logistic,
27748 Poisson), are some of the many fast functions.")
27749 (license license:gpl2+)))
27751 (define-public r-rffc
27757 (uri (string-append
27758 "https://download.r-forge.r-project.org/src/contrib/"
27759 "rfFC_" version ".tar.gz"))
27762 "05x9wgzsmx4vb12lmcspymgmpb2xw8bwryb8ysg7vzg2nkh0ma3g"))))
27763 (build-system r-build-system)
27765 (list r-randomforest))
27766 (home-page "https://r-forge.r-project.org/projects/rffc/")
27767 (synopsis "Random Forest Feature Contributions")
27768 (description "This package provides functions for extracting feature
27769 contributions from a random forest model from package @code{randomForest}.
27770 Feature contributions provide detailed information about the relationship
27771 between data variables and the predicted value returned by random forest
27773 (license license:gpl2)))
27775 (define-public r-clusterr
27777 (name "r-clusterr")
27782 (uri (cran-uri "ClusterR" version))
27785 "00mha8madcba83ix4fc04rb7sagfm0lxlh1wvs7dvjdrngps41jr"))))
27786 (properties `((upstream-name . "ClusterR")))
27787 (build-system r-build-system)
27789 (list r-ggplot2 r-gmp r-gtools r-rcpp r-rcpparmadillo))
27790 (native-inputs (list r-knitr))
27791 (home-page "https://github.com/mlampros/ClusterR")
27792 (synopsis "Clustering")
27794 "This package provides Gaussian mixture models, k-means,
27795 mini-batch-kmeans, k-medoids and affinity propagation clustering with the
27796 option to plot, validate, predict (new data) and estimate the optimal number
27797 of clusters. The package takes advantage of @code{RcppArmadillo} to speed up
27798 the computationally intensive parts of the functions. For more information,
27802 @item \"Clustering in an Object-Oriented Environment\" by Anja Struyf, Mia
27803 Hubert, Peter Rousseeuw (1997), Journal of Statistical Software,
27804 @url{https://doi.org/10.18637/jss.v001.i04};
27805 @item \"Web-scale k-means clustering\" by D. Sculley (2010), ACM Digital
27806 Library, @url{https://doi.org/10.1145/1772690.1772862};
27807 @item \"Armadillo: a template-based C++ library
27808 for linear algebra\" by Sanderson et al (2016), The Journal of Open Source
27809 Software, @url{https://doi.org/10.21105/joss.00026};
27810 @item \"Clustering by Passing Messages Between Data Points\" by Brendan
27811 J. Frey and Delbert Dueck, Science 16 Feb 2007: Vol. 315, Issue 5814,
27812 pp. 972-976, @url{https://doi.org/10.1126/science.1136800}.
27815 (license license:gpl3)))
27817 (define-public r-spectrum
27819 (name "r-spectrum")
27824 (uri (cran-uri "Spectrum" version))
27827 "0n38d360azkck6vvhr771zsh0gbvd9qsf9ygg5r18vhz0pb1xcfw"))))
27828 (properties `((upstream-name . "Spectrum")))
27829 (build-system r-build-system)
27831 (list r-clusterr r-diptest r-ggplot2 r-rfast))
27832 (native-inputs (list r-knitr))
27833 (home-page "https://cran.r-project.org/web/packages/Spectrum/")
27834 (synopsis "Fast adaptive spectral clustering for single and multi-view data")
27836 "This package provides a self-tuning spectral clustering method for
27837 single or multi-view data. Spectrum uses a new type of adaptive density aware
27838 kernel that strengthens connections in the graph based on common nearest
27839 neighbours. It uses a tensor product graph data integration and diffusion
27840 procedure to integrate different data sources and reduce noise. Spectrum uses
27841 either the eigengap or multimodality gap heuristics to determine the number of
27842 clusters. The method is sufficiently flexible so that a wide range of
27843 Gaussian and non-Gaussian structures can be clustered with automatic selection
27845 (license license:agpl3+)))
27847 (define-public r-nabor
27854 (uri (cran-uri "nabor" version))
27857 "1nj39cdfwrmhgsi3cq8imxv3n6xzc1v6dzdb2cf2hybjk368v4s7"))))
27858 (properties `((upstream-name . "nabor")))
27859 (build-system r-build-system)
27861 (list r-bh r-rcpp r-rcppeigen))
27862 (home-page "https://cran.r-project.org/web/packages/nabor/")
27863 (synopsis "Wrapper for K nearest neighbour library for low dimensions")
27865 "This package provides an R wrapper for libnabo, an exact or approximate
27866 k nearest neighbour library which is optimised for low dimensional
27867 spaces (e.g. 3D). @code{nabor} includes a @code{knn} function that is
27868 designed as a drop-in replacement for the RANN function @code{nn2}. In
27869 addition, objects which include the k-d tree search structure can be returned
27870 to speed up repeated queries of the same set of target points.")
27871 (license license:bsd-3)))
27873 (define-public r-naturalsort
27875 (name "r-naturalsort")
27879 (uri (cran-uri "naturalsort" version))
27882 "0mz801y9mzld9ypp3xmsjw2d8l9q97sdnv09wrci9xi3yg2sjf6d"))))
27883 (build-system r-build-system)
27884 (home-page "https://cran.r-project.org/web/packages/naturalsort/")
27885 (synopsis "Natural ordering")
27886 (description "This package provides functions related to human natural
27887 ordering. It handles adjacent digits in a character sequence as a number
27888 so that natural sort function arranges a character vector by their numbers,
27889 not digit characters.")
27890 (license license:bsd-3)))
27892 (define-public r-visdat
27898 (uri (cran-uri "visdat" version))
27901 "1ikqp29nncbw1xlwyb9dqqgcdk9q0bs3wxhnhnjpb11vcjv7cz2j"))))
27902 (build-system r-build-system)
27914 (home-page "https://visdat.njtierney.com/")
27915 (synopsis "Preliminary Visualisation of Data")
27916 (description "This package provides procedures to create preliminary exploratory
27917 data visualisations of an entire dataset to identify problems or unexpected features
27918 using @code{ggplot2}.")
27919 (license license:expat)))
27921 (define-public r-muhaz
27924 (version "1.2.6.4")
27928 (uri (cran-uri "muhaz" version))
27931 "1ddy8ayr4rdhzcipdvxdwd7z5g9hfp0ppacl7xf6f2612cn1185g"))))
27932 (properties `((upstream-name . "muhaz")))
27933 (build-system r-build-system)
27938 (home-page "https://cran.r-project.org/web/packages/muhaz/")
27939 (synopsis "Hazard function estimation in survival analysis")
27941 "This package produces a smooth estimate of the hazard function for
27943 ;; Any version of the GPL.
27944 (license license:gpl3+)))
27946 (define-public r-flexsurv
27948 (name "r-flexsurv")
27953 (uri (cran-uri "flexsurv" version))
27956 "0kwij9nkdvnsn1kn12fj3hjkd2qpgw7bdda4qad7basq5p6divlp"))))
27957 (properties `((upstream-name . "flexsurv")))
27958 (build-system r-build-system)
27981 (home-page "https://github.com/chjackson/flexsurv-dev")
27982 (synopsis "Flexible parametric survival and multi-state models")
27984 "This package provides flexible parametric models for time-to-event data,
27985 including the Royston-Parmar spline model, generalized gamma and generalized F
27986 distributions. Any user-defined parametric distribution can be fitted, given
27987 at least an R function defining the probability density or hazard. There are
27988 also tools for fitting and predicting from fully parametric multi-state
27990 (license license:gpl2+)))
27992 (define-public r-transphylo
27994 (name "r-transphylo")
27999 (uri (cran-uri "TransPhylo" version))
28002 "0g92kwi1nlmpc8m4pc9kv9xhczryr2kn9icfr3js7da7vy8g50xy"))))
28003 (properties `((upstream-name . "TransPhylo")))
28004 (build-system r-build-system)
28006 (list r-ape r-rcpp))
28009 (home-page "https://cran.r-project.org/web/packages/TransPhylo/")
28010 (synopsis "Inference of transmission tree from a dated phylogeny")
28012 "This is a package to infer transmission trees from a dated phylogeny.
28013 It includes methods to simulate and analyze outbreaks. The methodology is
28014 described in @url{https://doi.org/10.1093/molbev/msu121,Didelot et al. (2014)}
28015 and @url{https://doi.org/10.1093/molbev/msw275,Didelot et al. (2017)}.")
28016 (license license:gpl2+)))
28018 (define-public r-km-ci
28025 (uri (cran-uri "km.ci" version))
28028 "18sc9vhbdgks8lhk2nfxkkayh8j4j227hl63fm5p04f7z4wm6wc1"))))
28029 (properties `((upstream-name . "km.ci")))
28030 (build-system r-build-system)
28033 (home-page "https://cran.r-project.org/web/packages/km.ci/")
28034 (synopsis "Confidence intervals for the Kaplan-Meier estimator")
28036 "This package computes various @dfn{confidence intervals} (CI) for the
28037 Kaplan-Meier estimator, namely: Petos CI, Rothman CI, CIs based on Greenwoods
28038 variance, Thomas and Grunkemeier CI and the simultaneous confidence bands by
28039 Nair and Hall and Wellner.")
28040 (license license:gpl2+)))
28042 (define-public r-kmsurv
28049 (uri (cran-uri "KMsurv" version))
28052 "0hi5vvk584rl70gbrr75w9hc775xmbxnaig0dd6hlpi4071pnqjm"))))
28053 (properties `((upstream-name . "KMsurv")))
28054 (build-system r-build-system)
28055 (home-page "https://cran.r-project.org/web/packages/KMsurv/")
28056 (synopsis "Data sets from Klein and Moeschberger (1997), Survival Analysis")
28058 "This package provides data sets and functions for Klein and Moeschberger
28059 (1997), \"Survival Analysis, Techniques for Censored and Truncated Data\",
28061 (license license:gpl3+)))
28063 (define-public r-survmisc
28065 (name "r-survmisc")
28070 (uri (cran-uri "survMisc" version))
28073 "014cf7sfndmib9jmj0p3h67sr750k2pvw7m865zwdpvlqddi44fr"))))
28074 (properties `((upstream-name . "survMisc")))
28075 (build-system r-build-system)
28088 (home-page "https://cran.r-project.org/web/packages/survMisc/")
28089 (synopsis "Miscellaneous functions for survival data")
28091 "This package provides a collection of functions to help in the analysis
28092 of right-censored survival data. These extend the methods available in
28093 the @code{survival} package.")
28094 (license license:gpl2)))
28096 (define-public r-exactranktests
28098 (name "r-exactranktests")
28103 (uri (cran-uri "exactRankTests" version))
28106 "1qv9i57chhz8xiv0j8r47rbigyqs72fa7ssz99inyc0s8gzskd3y"))))
28108 `((upstream-name . "exactRankTests")))
28109 (build-system r-build-system)
28110 (home-page "https://cran.r-project.org/web/packages/exactRankTests/")
28111 (synopsis "Exact distributions for rank and permutation tests")
28113 "This package computes exact conditional p-values and quantiles using an
28114 implementation of the Shift-Algorithm by Streitberg & Roehmel.")
28115 (license license:gpl2+)))
28117 (define-public r-maxstat
28124 (uri (cran-uri "maxstat" version))
28127 "114z1rwxwvk05ijjhdppzm148n1h192fp0w12ky10zkrhf6kphbg"))))
28128 (properties `((upstream-name . "maxstat")))
28129 (build-system r-build-system)
28131 (list r-exactranktests r-mvtnorm))
28132 (home-page "https://cran.r-project.org/web/packages/maxstat/")
28133 (synopsis "Maximally selected rank statistics")
28135 "This package provides maximally selected rank statistics with several
28136 p-value approximations.")
28137 (license license:gpl2+)))
28139 (define-public r-survminer
28141 (name "r-survminer")
28146 (uri (cran-uri "survminer" version))
28149 "0byh0wxdbjfwdrzsnqv4xlmnik6lj0vkkzfxy7lssk8dv5zmj7nz"))))
28150 (properties `((upstream-name . "survminer")))
28151 (build-system r-build-system)
28170 (home-page "https://rpkgs.datanovia.com/survminer/index.html")
28171 (synopsis "Drawing survival curves using ggplot2")
28173 "This package contains the function @code{ggsurvplot()} for easily
28174 drawing beautiful and 'ready-to-publish' survival curves with the 'number at
28175 risk' table and 'censoring count plot'. Other functions are also available to
28176 plot adjusted curves for Cox model and to visually examine Cox model
28178 (license license:gpl2)))
28180 (define-public r-forge
28187 (uri (cran-uri "forge" version))
28190 "0pjfzsc35agkh0zfw2czwajkbsyn6liys5irl5bhz5r1vim3jmwa"))))
28191 (properties `((upstream-name . "forge")))
28192 (build-system r-build-system)
28194 (list r-magrittr r-rlang))
28195 (home-page "https://cran.r-project.org/web/packages/forge/")
28196 (synopsis "Cast values into shape")
28198 "This package provides helper functions with a consistent interface to
28199 coerce and verify the types and shapes of values for input checking.")
28200 (license license:asl2.0)))
28202 (define-public r-config
28209 (uri (cran-uri "config" version))
28212 "0l2zp7v6qaz72dclcbjrlis633zlwp8rsi5azr7iw127iyz7i26l"))))
28213 (properties `((upstream-name . "config")))
28214 (build-system r-build-system)
28219 (home-page "https://github.com/rstudio/config")
28220 (synopsis "Manage environment specific configuration values")
28222 "This package lets you manage configuration values across multiple
28223 environments (e.g. development, test, production). It reads values using a
28224 function that determines the current environment and returns the appropriate
28226 (license license:gpl3)))
28228 (define-public r-adaptivesparsity
28230 (name "r-adaptivesparsity")
28234 (uri (cran-uri "AdaptiveSparsity" version))
28237 "0imr5m8mll9j6n4icsv6z9rl5kbnwsp9wvzrg7n90nnmcxq2cz91"))))
28239 `((upstream-name . "AdaptiveSparsity")))
28240 (build-system r-build-system)
28243 (modify-phases %standard-phases
28244 (add-after 'unpack 'link-against-armadillo
28246 (substitute* "src/Makevars"
28247 (("PKG_LIBS=" prefix)
28248 (string-append prefix "-larmadillo")))
28251 (list r-mass r-matrix r-rcpp r-rcpparmadillo))
28254 (home-page "https://cran.r-project.org/web/packages/AdaptiveSparsity")
28255 (synopsis "Adaptive sparsity models")
28257 "This package implements the Figueiredo machine learning algorithm for
28258 adaptive sparsity and the Wong algorithm for adaptively sparse Gaussian
28259 geometric models.")
28260 (license license:lgpl3+)))
28262 (define-public r-add2ggplot
28264 (name "r-add2ggplot")
28269 (uri (cran-uri "add2ggplot" version))
28271 (base32 "0c94i1cfp2pvplvxmfvvz2fyj026r1jnax05mrzrc7ppnqzy25y0"))))
28272 (properties `((upstream-name . "add2ggplot")))
28273 (build-system r-build-system)
28275 (list r-ggplot2 r-magick r-magrittr r-rcolorbrewer r-zeallot))
28276 (native-inputs (list r-knitr))
28277 (home-page "https://github.com/JiaxiangBU/add2ggplot")
28278 (synopsis "Extension for ggplot2")
28279 (description "This package provides tools to create themes and color
28280 palettes for the package ggplot2.")
28281 (license license:expat)))
28283 (define-public r-diffusionmap
28285 (name "r-diffusionmap")
28290 (uri (cran-uri "diffusionMap" version))
28293 "1rvk7069brlm1s9kqj4c31mwwr3mw4hmhay95cjjjfmw5xclff2j"))))
28294 (properties `((upstream-name . "diffusionMap")))
28295 (build-system r-build-system)
28297 (list r-igraph r-matrix r-scatterplot3d))
28298 (home-page "https://www.r-project.org")
28299 (synopsis "Diffusion map")
28300 (description "This package implements the diffusion map method of data
28301 parametrization, including creation and visualization of diffusion maps,
28302 clustering with diffusion K-means and regression using the adaptive regression
28304 (license license:gpl2)))
28306 (define-public r-igraph
28313 (uri (cran-uri "igraph" version))
28316 "0khl87ncc9hkvx4f1kyzv7w7bg9zbyd1rk20ja3azkhpqjkjnnjh"))))
28317 (build-system r-build-system)
28321 (list gmp glpk libxml2 zlib))
28323 (list r-magrittr r-matrix r-pkgconfig))
28324 (home-page "https://igraph.org")
28325 (synopsis "Network analysis and visualization")
28327 "This package provides routines for simple graphs and network analysis.
28328 It can handle large graphs very well and provides functions for generating
28329 random and regular graphs, graph visualization, centrality methods and much
28331 (license license:gpl2+)))
28333 (define-public r-workflows
28335 (name "r-workflows")
28340 (uri (cran-uri "workflows" version))
28343 "0xhc1j25fjipw8hvcpdbvfm640kp0flwvifj5f7g4n6b3wb8cm6a"))))
28344 (properties `((upstream-name . "workflows")))
28345 (build-system r-build-system)
28358 (home-page "https://github.com/tidymodels/workflows")
28359 (synopsis "Modeling workflows")
28361 "A workflow is an object that can bundle together your pre-processing,
28362 modeling, and post-processing requests. For example, if you have a
28363 @code{recipe} and @code{parsnip} model, these can be combined into a
28364 workflow. The advantages are:
28367 @item You don’t have to keep track of separate objects in your workspace.
28368 @item The recipe prepping and model fitting can be executed using a single
28369 call to @code{fit()}.
28370 @item If you have custom tuning parameter settings, these can be defined using
28371 a simpler interface when combined with @code{tune}.
28372 @item In the future, workflows will be able to add post-processing operations,
28373 such as modifying the probability cutoff for two-class models.
28376 (license license:expat)))
28378 (define-public r-lobstr
28385 (uri (cran-uri "lobstr" version))
28388 "0vkif17825x33cz8r89j0qph4wj5l8fzfgl8nh2g7m2v140cxjdq"))))
28389 (properties `((upstream-name . "lobstr")))
28390 (build-system r-build-system)
28392 (list r-crayon r-rcpp r-rlang))
28393 (home-page "https://github.com/r-lib/lobstr")
28394 (synopsis "Visualize R data structures with trees")
28396 "This package provides a set of tools for inspecting and understanding R
28397 data structures inspired by @code{str}. It includes @code{ast} for
28398 visualizing abstract syntax trees, @code{ref} for showing shared references,
28399 @code{cst} for showing call stack trees, and @code{obj_size} for computing
28401 (license license:gpl3)))
28403 (define-public r-gpfit
28410 (uri (cran-uri "GPfit" version))
28413 "05mpiyi2vxv0wqp422n1mnxa8msc4daq40cwpnpngbcwqhlgqkby"))))
28414 (properties `((upstream-name . "GPfit")))
28415 (build-system r-build-system)
28417 (list r-lattice r-lhs))
28418 (home-page "https://cran.r-project.org/web/packages/GPfit/")
28419 (synopsis "Gaussian Processes modeling")
28421 "This package provides a computationally stable approach of fitting a
28422 @dfn{Gaussian Process} (GP) model to a deterministic simulator.")
28423 (license license:gpl2)))
28425 (define-public r-yardstick
28427 (name "r-yardstick")
28432 (uri (cran-uri "yardstick" version))
28435 "00hv4gk1ba4dab8i3dcq7lim4bll7l572rgc8km9x4ja8by95j8h"))))
28436 (properties `((upstream-name . "yardstick")))
28437 (build-system r-build-system)
28447 (home-page "https://github.com/tidymodels/yardstick")
28448 (synopsis "Tidy characterizations of model performance")
28450 "This package provides tidy tools for quantifying how well a model fits
28451 to a data set such as confusion matrices, class probability curve summaries,
28452 and regression metrics (e.g., RMSE).")
28453 (license license:gpl2)))
28455 (define-public r-warp
28462 (uri (cran-uri "warp" version))
28465 "0s0acddc5h14245hi1faycxp0fyvw6nlgaz2df7da4fpyd2f638f"))))
28466 (properties `((upstream-name . "warp")))
28467 (build-system r-build-system)
28468 (native-inputs (list r-knitr))
28469 (home-page "https://github.com/DavisVaughan/warp")
28470 (synopsis "Group dates")
28472 "This package provides tooling to group dates by a variety of periods
28473 including: yearly, monthly, by second, by week of the month, and more. The
28474 groups are defined in such a way that they also represent the distance between
28475 dates in terms of the period. This extracts valuable information that can be
28476 used in further calculations that rely on a specific temporal spacing between
28478 (license license:expat)))
28480 (define-public r-scico
28487 (uri (cran-uri "scico" version))
28489 (base32 "08grfbjd5s0vdw76ni37yjl2242rr8i2jy72sgpwgra282hpnji3"))))
28490 (properties `((upstream-name . "scico")))
28491 (build-system r-build-system)
28492 (propagated-inputs (list r-scales))
28493 (home-page "https://github.com/thomasp85/scico")
28494 (synopsis "Colour Palettes Based on the Scientific Colour-Maps")
28496 "This package provides colour choice in information visualisation. It
28497 important in order to avoid being mislead by inherent bias in the used colour
28498 palette. This package provides access to the perceptually uniform and
28499 colour-blindness friendly palettes developed by Fabio Crameri and released
28500 under the \"Scientific Colour-Maps\" moniker. The package contains 24
28501 different palettes and includes both diverging and sequential types.")
28502 (license license:expat)))
28504 (define-public r-slider
28511 (uri (cran-uri "slider" version))
28514 "1vxk2bc33svwcki2j8zr5jcxswh27i0fqgzjw2a5a1pp9dh3fmd3"))))
28515 (properties `((upstream-name . "slider")))
28516 (build-system r-build-system)
28518 (list r-ellipsis r-glue r-rlang r-vctrs r-warp))
28519 (native-inputs (list r-knitr))
28520 (home-page "https://github.com/DavisVaughan/slider")
28521 (synopsis "Sliding window functions")
28523 "This package provides type-stable rolling window functions over any R
28524 data type. Cumulative and expanding windows are also supported. For more
28525 advanced usage, an index can be used as a secondary vector that defines how
28526 sliding windows are to be created.")
28527 (license license:expat)))
28529 (define-public r-rlist
28532 (version "0.4.6.2")
28536 (uri (cran-uri "rlist" version))
28538 (base32 "15q99rhbbjq8zd976yjmfnny45dd5fg2p2dv1sljg2kwi66nbppb"))))
28539 (properties `((upstream-name . "rlist")))
28540 (build-system r-build-system)
28541 (propagated-inputs (list r-data-table r-jsonlite r-xml r-yaml))
28542 (home-page "https://renkun-ken.github.io/rlist/")
28543 (synopsis "A Toolbox for Non-Tabular Data Manipulation")
28545 "This package provides a set of functions for data manipulation with
28546 list objects, including mapping, filtering, grouping, sorting, updating,
28547 searching, and other useful functions. Most functions are designed to be
28548 pipeline friendly so that data processing with lists can be chained.")
28549 (license license:expat)))
28551 (define-public r-rsample
28558 (uri (cran-uri "rsample" version))
28561 "01xwhj4zfvxbv9cjb6mbz3aphxqc3cnjjx1xy2yx2wd94fbka42z"))))
28562 (properties `((upstream-name . "rsample")))
28563 (build-system r-build-system)
28579 (home-page "https://rsample.tidymodels.org")
28580 (synopsis "General resampling infrastructure")
28582 "This package provides classes and functions to create and summarize
28583 different types of resampling objects (e.g. bootstrap, cross-validation).")
28584 (license license:gpl2)))
28586 (define-public r-dicedesign
28588 (name "r-dicedesign")
28593 (uri (cran-uri "DiceDesign" version))
28596 "1a8ixa65xgyfri03cviic8qi2plbhdyz8m02bwif8w94w0q3ghlk"))))
28597 (properties `((upstream-name . "DiceDesign")))
28598 (build-system r-build-system)
28599 (home-page "http://dice.emse.fr/")
28600 (synopsis "Designs of computer experiments")
28602 "This package provides tools to create some specific @code{Space-Filling
28603 Design} (SFD) and to test their quality.")
28604 (license license:gpl3)))
28606 (define-public r-dials
28613 (uri (cran-uri "dials" version))
28616 "1h695g9vklqn0vd53j9k03s0989xjpjr11h5qhz3a0v6465fwm8a"))))
28617 (properties `((upstream-name . "dials")))
28618 (build-system r-build-system)
28631 (native-inputs (list r-knitr))
28632 (home-page "https://dials.tidymodels.org/")
28633 (synopsis "Tools for creating tuning parameter values")
28635 "Many models contain tuning parameters (i.e. parameters that cannot be
28636 directly estimated from the data). These tools can be used to define objects
28637 for creating, simulating, or validating values for such parameters.")
28638 (license license:gpl2)))
28640 (define-public r-tune
28647 (uri (cran-uri "tune" version))
28650 "05gxlsaqv6sjk11r5g4nkdd6hlb3bnfmc29cx4vln1blha37jx4i"))))
28651 (properties `((upstream-name . "tune")))
28652 (build-system r-build-system)
28675 (home-page "https://github.com/tidymodels/tune")
28676 (synopsis "Tidy tuning tools")
28678 "The ability to tune models is important. @code{tune} contains functions
28679 and classes to be used in conjunction with other @code{tidymodels} packages
28680 for finding reasonable values of hyper-parameters in models, pre-processing
28681 methods, and post-processing steps.")
28682 (license license:expat)))
28684 (define-public r-workflowsets
28686 (name "r-workflowsets")
28691 (uri (cran-uri "workflowsets" version))
28694 "0q42nhnw0mbivadcfb07v71fp39x8fcnjipvn5l5yhjzc56cfxi8"))))
28695 (properties `((upstream-name . "workflowsets")))
28696 (build-system r-build-system)
28716 (home-page "https://github.com/tidymodels/workflowsets")
28717 (synopsis "Create a collection of tidymodels workflows")
28719 "A workflow is a combination of a model and preprocessors (e.g, a
28720 formula, recipe, etc.). In order to try different combinations of these, an
28721 object can be created that contains many workflows. There are functions to
28722 create workflows en masse as well as training them and visualizing the
28724 (license license:expat)))
28726 (define-public r-tidyposterior
28728 (name "r-tidyposterior")
28733 (uri (cran-uri "tidyposterior" version))
28736 "1h1664sjrg6akph6nrk8ynn2kjiswv6gshy35gamam1h4axf6wah"))))
28737 (properties `((upstream-name . "tidyposterior")))
28738 (build-system r-build-system)
28754 (home-page "https://tidyposterior.tidymodels.org")
28755 (synopsis "Bayesian analysis to compare models using resampling statistics")
28757 "This package can be used to conduct post hoc analyses of resampling
28758 results generated by models. For example, if two models are evaluated with
28759 the @dfn{root mean squared error} (RMSE) using 10-fold cross-validation, there
28760 are 10 paired statistics. These can be used to make comparisons between
28761 models without involving a test set.")
28762 (license license:gpl2)))
28764 (define-public r-tidypredict
28766 (name "r-tidypredict")
28771 (uri (cran-uri "tidypredict" version))
28774 "0x0r36zvny4rqgndx7iqh39yhr53gl4d8wd8wpvdcgg35q6z02z2"))))
28775 (properties `((upstream-name . "tidypredict")))
28776 (build-system r-build-system)
28788 (home-page "https://tidypredict.tidymodels.org")
28789 (synopsis "Run predictions inside the database")
28791 "This package parses a fitted R model object, and returns a formula in
28792 Tidy Eval code that calculates the predictions. It works with several
28793 database backends because it leverages @code{dplyr} and @code{dbplyr} for the
28794 final SQL translation of the algorithm. It currently supports @code{lm()},
28795 @code{glm()}, @code{randomForest()}, @code{ranger()}, @code{earth()},
28796 @code{xgb.Booster.complete()}, @code{cubist()}, and @code{ctree()} models.")
28797 (license license:gpl3)))
28799 (define-public r-janeaustenr
28801 (name "r-janeaustenr")
28806 (uri (cran-uri "janeaustenr" version))
28809 "1wyn4qc28a3sval8shmyi2d7s4nl3jh96s8pzq871brxcmrncbwr"))))
28810 (properties `((upstream-name . "janeaustenr")))
28811 (build-system r-build-system)
28812 (home-page "https://github.com/juliasilge/janeaustenr")
28813 (synopsis "Jane Austen's complete novels")
28815 "This package provides the full texts for Jane Austen's six completed
28816 novels, ready for text analysis. These novels are \"Sense and Sensibility\",
28817 \"Pride and Prejudice\", \"Mansfield Park\", \"Emma\", \"Northanger Abbey\",
28818 and \"Persuasion\".")
28819 (license license:expat)))
28821 (define-public r-tokenizers
28823 (name "r-tokenizers")
28828 (uri (cran-uri "tokenizers" version))
28831 "006xf1vdrmp9skhpss9ldhmk4cwqk512cjp1pxm2gxfybpf7qq98"))))
28832 (properties `((upstream-name . "tokenizers")))
28833 (build-system r-build-system)
28835 (list r-rcpp r-snowballc r-stringi))
28838 (home-page "https://lincolnmullen.com/software/tokenizers/")
28839 (synopsis "Fast, consistent tokenization of natural language text")
28841 "This is a package for converting natural language text into tokens.
28842 It includes tokenizers for shingled n-grams, skip n-grams, words, word stems,
28843 sentences, paragraphs, characters, shingled characters, lines, tweets, Penn
28844 Treebank, regular expressions, as well as functions for counting characters,
28845 words, and sentences, and a function for splitting longer texts into separate
28846 documents, each with the same number of words. The tokenizers have a
28847 consistent interface, and the package is built on the @code{stringi} and
28848 @code{Rcpp} packages for fast yet correct tokenization in UTF-8 encoding.")
28849 (license license:expat)))
28851 (define-public r-hunspell
28853 (name "r-hunspell")
28858 (uri (cran-uri "hunspell" version))
28861 "0ql6y05d4xxpm468rslb0wxdp1x9l3flxzmb5w6pjg617f8vpv8z"))))
28862 (properties `((upstream-name . "hunspell")))
28863 (build-system r-build-system)
28865 (list r-digest r-rcpp))
28868 (home-page "https://github.com/ropensci/hunspell#readme")
28869 (synopsis "High-performance stemmer, tokenizer, and spell checker")
28871 "This package provides a low-level spell checker and morphological
28872 analyzer based on the famous @code{hunspell} library. The package can analyze
28873 or check individual words as well as parse text, LaTeX, HTML or XML documents.
28874 For a more user-friendly interface use the @code{spelling} package which
28875 builds on this package to automate checking of files, documentation and
28876 vignettes in all common formats.")
28877 ;; The hunspell library itself is available under one of GPL2, LGPL2.1, or
28878 ;; MPL; in addition to these licenses the rest of the R wrapper is also
28879 ;; available under the Expat license.
28880 (license (list license:gpl2
28885 (define-public r-tidytext
28887 (name "r-tidytext")
28892 (uri (cran-uri "tidytext" version))
28895 "0kljaxyhhzbcv9jkjdy0wn6gkamh25y2xfb9k11sqhz3lv72nfvm"))))
28896 (properties `((upstream-name . "tidytext")))
28897 (build-system r-build-system)
28913 (home-page "https://github.com/juliasilge/tidytext")
28914 (synopsis "Text mining using dplyr, ggplot2, and other Tidy tools")
28916 "This is a package for text mining for word processing and sentiment
28917 analysis using @code{dplyr}, @code{ggplot2}, and other Tidy tools.")
28918 (license license:expat)))
28920 (define-public r-parsnip
28927 (uri (cran-uri "parsnip" version))
28930 "195i4j38mljv9193yx8lmh65h85yhc52y9vc1mk8zvxi52ks1yln"))))
28931 (properties `((upstream-name . "parsnip")))
28932 (build-system r-build-system)
28952 (home-page "https://parsnip.tidymodels.org")
28953 (synopsis "Common API to modeling and analysis functions")
28955 "This package provides a common interface to allow users to specify a
28956 model without having to remember the different argument names across different
28957 functions or computational engines (e.g. R, Spark, Stan, etc).")
28958 (license license:gpl2)))
28960 (define-public r-infer
28967 (uri (cran-uri "infer" version))
28970 "1qbpcn7jqbvgwnpiyylj021j8m33p58a204yd1pfkpzd3x2lbsm6"))))
28971 (properties `((upstream-name . "infer")))
28972 (build-system r-build-system)
28987 (home-page "https://github.com/tidymodels/infer")
28988 (synopsis "Tidy statistical inference")
28990 "The objective of this package is to perform inference using an
28991 expressive statistical grammar that coheres with the Tidy design framework.")
28992 (license license:cc0)))
28994 (define-public r-modeldata
28996 (name "r-modeldata")
29001 (uri (cran-uri "modeldata" version))
29004 "0jgrwf9k8p9j3ywg3yv2wzwsx3snlwm3dd9vfqwhlr7j63jg3cm4"))))
29005 (properties `((upstream-name . "modeldata")))
29006 (build-system r-build-system)
29007 (home-page "https://modeldata.tidymodels.org")
29008 (synopsis "Data sets useful for modeling packages")
29010 "This package provides data sets used for demonstrating or testing
29011 model-related packages.")
29012 (license license:expat)))
29014 (define-public r-conflicted
29016 (name "r-conflicted")
29021 (uri (cran-uri "conflicted" version))
29024 "1qg9ar114r98wm0pnf65mss4v2ksq3924rlpm13mqp4s3p6j9yi4"))))
29025 (properties `((upstream-name . "conflicted")))
29026 (build-system r-build-system)
29028 (list r-memoise r-rlang))
29029 (home-page "https://github.com/r-lib/conflicted")
29030 (synopsis "Alternative conflict resolution strategy")
29032 "R's default conflict management system gives the most recently loaded
29033 package precedence. This can make it hard to detect conflicts, particularly
29034 when they arise because a package update creates ambiguity that did not
29035 previously exist. The @code{conflicted} package takes a different approach,
29036 making every conflict an error and forcing you to choose which function to
29038 (license license:gpl3)))
29040 (define-public r-tidymodels
29042 (name "r-tidymodels")
29047 (uri (cran-uri "tidymodels" version))
29050 "1xkv4s4kn7k9137svb39zrm5302gxpxyp1jv5bb6z0xrvj5wwa4i"))))
29051 (properties `((upstream-name . "tidymodels")))
29052 (build-system r-build-system)
29077 (home-page "https://github.com/tidymodels/tidymodels")
29078 (synopsis "Tidy collection for modeling and statistical analysis")
29080 "The tidy modeling \"verse\" is a collection of packages for modeling and
29081 statistical analysis that share the underlying design philosophy, grammar, and
29082 data structures of the tidyverse.")
29083 (license license:gpl3)))
29085 (define-public r-lsa
29092 (uri (cran-uri "lsa" version))
29095 "16k1g0kh3yaw7azg76aqf3hn3b6jgqg92xx0syai8l0my9ci2zzh"))))
29096 (properties `((upstream-name . "lsa")))
29097 (build-system r-build-system)
29099 (list r-snowballc))
29100 (home-page "https://cran.r-project.org/package=lsa")
29101 (synopsis "Latent semantic analysis")
29103 "The basic idea of latent semantic analysis (LSA) is, that text do have a
29104 higher order (=latent semantic) structure which, however, is obscured by word
29105 usage (e.g. through the use of synonyms or polysemy). By using conceptual
29106 indices that are derived statistically via a truncated singular value
29107 decomposition (a two-mode factor analysis) over a given document-term matrix,
29108 this variability problem can be overcome.")
29109 (license license:gpl2+)))
29111 (define-public r-mlecens
29118 (uri (cran-uri "MLEcens" version))
29121 "0cdl0y44clds4sg8hikhk354a5xrfbyfg8lxrbh1bfg410rkj186"))))
29122 (properties `((upstream-name . "MLEcens")))
29123 (build-system r-build-system)
29124 (home-page "http://stat.ethz.ch/~maathuis/")
29125 (synopsis "Computation of the MLE for bivariate (interval) censored data")
29127 "This package contains functions to compute the nonparametric
29128 @dfn{maximum likelihood estimator} (MLE) for the bivariate distribution of
29129 @code{(X,Y)}, when realizations of @code{(X,Y)} cannot be observed directly.
29130 To be more precise, we consider the situation where we observe a set of
29131 rectangles that are known to contain the unobservable realizations of (X,Y).
29132 We compute the MLE based on such a set of rectangles. The methods can also be
29133 used for univariate censored data (see data set @code{cosmesis}), and for
29134 censored data with competing risks (see data set @code{menopause}). The
29135 package also provides functions to visualize the observed data and the MLE.")
29136 (license license:gpl2+)))
29138 (define-public r-metafor
29145 (uri (cran-uri "metafor" version))
29148 "1b599fxk7s0brkchmx698fr5k4g1kzkia2rnlvhg349ffs5nfjmn"))))
29149 (properties `((upstream-name . "metafor")))
29150 (build-system r-build-system)
29152 (list r-matrix r-nlme))
29153 (home-page "https://cran.r-project.org/web/packages/metafor/")
29154 (synopsis "Meta-analysis package for R")
29156 "This package provides a comprehensive collection of functions for
29157 conducting meta-analyses in R. The package includes functions to calculate
29158 various effect sizes or outcome measures, fit fixed-, random-, and
29159 mixed-effects models to such data, carry out moderator and meta-regression
29160 analyses, and create various types of meta-analytical plots (e.g., forest,
29161 funnel, radial, L'Abbe, Baujat, GOSH plots). For meta-analyses of binomial
29162 and person-time data, the package also provides functions that implement
29163 specialized methods, including the Mantel-Haenszel method, Peto's method, and
29164 a variety of suitable generalized linear (mixed-effects) models (i.e.
29165 mixed-effects logistic and Poisson regression models). Finally, the package
29166 provides functionality for fitting meta-analytic multivariate/multilevel
29167 models that account for non-independent sampling errors and/or true
29168 effects (e.g. due to the inclusion of multiple treatment studies, multiple
29169 endpoints, or other forms of clustering). Network meta-analyses and
29170 meta-analyses accounting for known correlation structures (e.g. due to
29171 phylogenetic relatedness) can also be conducted.")
29172 (license license:gpl2+)))
29174 (define-public r-altmeta
29181 (uri (cran-uri "altmeta" version))
29184 "17cyiydf4n5j64izj7jph2v43h4x9kfd5b0x6m0ik5ci2aw8xzr5"))))
29185 (properties `((upstream-name . "altmeta")))
29186 (build-system r-build-system)
29188 (list r-coda r-lme4 r-matrix r-metafor r-rjags))
29189 (home-page "https://cran.r-project.org/web/packages/altmeta/")
29190 (synopsis "Alternative meta-analysis methods")
29192 "This package provides alternative statistical methods for meta-analysis,
29196 @item bivariate generalized linear mixed models for synthesizing odds ratios,
29197 relative risks, and risk differences
29198 @item heterogeneity tests and measures that are robust to outliers;
29199 @item measures, tests, and visualization tools for publication bias or
29200 small-study effects;
29201 @item meta-analysis of diagnostic tests for synthesizing sensitivities,
29202 specificities, etc.;
29203 @item meta-analysis methods for synthesizing proportions;
29204 @item models for multivariate meta-analysis.
29207 (license license:gpl2+)))
29209 (define-public r-perm
29212 (version "1.0-0.2")
29216 (uri (cran-uri "perm" version))
29219 "182ac1y91yzb34zwdcmx5fdfr5z0cha0gx2bgk36gwxhgfc994kj"))))
29220 (properties `((upstream-name . "perm")))
29221 (build-system r-build-system)
29222 (home-page "https://cran.r-project.org/web/packages/perm/")
29223 (synopsis "Exact or asymptotic permutation tests")
29225 "This package provides several methods for performing permutation tests.
29226 It has three main functions, to perform linear permutation tests. These tests
29227 are tests where the test statistic is the sum of the product of a
29228 covariate (usually group indicator) and the scores.")
29229 ;; Any version of the GPL
29230 (license license:gpl2+)))
29232 (define-public r-qtl
29239 (uri (cran-uri "qtl" version))
29242 "1mcy9wlp5lj5f3z4mf3n5li7x32vj67rmhjnzsp8fhfw0ipnaf1d"))))
29243 (build-system r-build-system)
29244 (home-page "https://rqtl.org/")
29245 (synopsis "R package for analyzing QTL experiments in genetics")
29246 (description "R/qtl is an extension library for the R statistics system.
29247 It is used to analyze experimental crosses for identifying genes contributing
29248 to variation in quantitative traits (so-called quantitative trait loci, QTLs).
29250 Using a hidden Markov model, R/qtl estimates genetic maps, to identify
29251 genotyping errors, and to perform single-QTL and two-QTL, two-dimensional
29253 (license license:gpl3)))
29255 (define-public r-qtl2
29261 (uri (cran-uri "qtl2" version))
29263 (base32 "0ppc6dzlq77mppxc6bczai9gi40jrbxd1466y2cn2s8a4ah1jg9y"))))
29264 (build-system r-build-system)
29272 (home-page "https://kbroman.org/qtl2/")
29273 (synopsis "Quantitative Trait Locus Mapping in Experimental Crosses")
29275 "This package provides a set of tools to perform @dfn{Quantitative Trait
29276 Locus} (QTL) analysis in experimental crosses. It is a reimplementation of the
29277 @code{R/qtl} package to better handle high-dimensional data and complex cross
29278 designs. Broman et al. (2018) <doi:10.1534/genetics.118.301595>.")
29279 (license license:gpl3)))
29281 (define-public r-seqminer
29283 (name "r-seqminer")
29288 (uri (cran-uri "seqminer" version))
29291 "1mbx1hw9dhgry7hhan43g6aiz2lyd5api7wxq3fwajyzjrc6p1g8"))))
29292 (build-system r-build-system)
29295 (home-page "http://seqminer.genomic.codes")
29296 (synopsis "Read nucleotide sequence data (VCF, BCF, and METAL formats)")
29298 "This package provides tools to integrate nucleotide sequencing
29299 data (variant call format, e.g. VCF or BCF) or meta-analysis results in R.")
29300 ;; Any version of the GPL is acceptable
29301 (license (list license:gpl2+ license:gpl3+))))
29303 (define-public r-maldiquant
29305 (name "r-maldiquant")
29310 (uri (cran-uri "MALDIquant" version))
29313 "1y1g3819ss06dry70kfhg2syddw71682qmzkcyppfsma6hhghw87"))))
29314 (properties `((upstream-name . "MALDIquant")))
29315 (build-system r-build-system)
29318 (home-page "https://cran.r-project.org/web/packages/MALDIquant")
29319 (synopsis "Quantitative analysis of mass spectrometry data")
29321 "This package provides a complete analysis pipeline for matrix-assisted
29322 laser desorption/ionization-time-of-flight (MALDI-TOF) and other
29323 two-dimensional mass spectrometry data. In addition to commonly used plotting
29324 and processing methods it includes distinctive features, namely baseline
29325 subtraction methods such as morphological filters (TopHat) or the
29326 statistics-sensitive non-linear iterative peak-clipping algorithm (SNIP), peak
29327 alignment using warping functions, handling of replicated measurements as well
29328 as allowing spectra with different resolutions.")
29329 (license license:gpl3+)))
29331 (define-public r-scattermore
29333 (name "r-scattermore")
29338 (uri (cran-uri "scattermore" version))
29341 "1rgqm7r1k7j3h2y4i6d1a2y8fzivfcbmr7dj9d367c0w4vc77pfv"))))
29342 (properties `((upstream-name . "scattermore")))
29343 (build-system r-build-system)
29345 (list r-ggplot2 r-scales))
29346 (home-page "https://github.com/exaexa/scattermore")
29347 (synopsis "Scatterplots with more points")
29349 "This package provides C-based tools for converting large scatterplot
29350 data to rasters. It speeds up plotting of data with millions of points.")
29351 (license license:gpl3+)))
29353 (define-public r-seuratobject
29355 (name "r-seuratobject")
29360 (uri (cran-uri "SeuratObject" version))
29363 "018anas8a9m3kh9jn5370v64d93k64z3iic13a75hp6r7g5hd94w"))))
29364 (properties `((upstream-name . "SeuratObject")))
29365 (build-system r-build-system)
29376 (home-page "https://satijalab.org/seurat")
29377 (synopsis "Data structures for single cell data")
29379 "This package defines S4 classes for single-cell genomic data and
29380 associated information, such as dimensionality reduction embeddings,
29381 nearest-neighbor graphs, and spatially-resolved coordinates. It provides data
29382 access methods and R-native hooks to ensure the Seurat object is familiar to
29384 (license license:gpl3)))
29386 (define-public r-seurat
29392 (uri (cran-uri "Seurat" version))
29395 "1klamxk6dj0jgpfwll5frcnj9h8lh8c5fxdn9ky7h8xk35lsj6i0"))))
29396 (properties `((upstream-name . "Seurat")))
29397 (build-system r-build-system)
29442 (home-page "http://www.satijalab.org/seurat")
29443 (synopsis "Seurat is an R toolkit for single cell genomics")
29445 "This package is an R package designed for QC, analysis, and
29446 exploration of single cell RNA-seq data. It easily enables widely-used
29447 analytical techniques, including the identification of highly variable genes,
29448 dimensionality reduction; PCA, ICA, t-SNE, standard unsupervised clustering
29449 algorithms; density clustering, hierarchical clustering, k-means, and the
29450 discovery of differentially expressed genes and markers.")
29451 (license license:gpl3)))
29453 (define-public r-seuratdisk
29454 (let ((commit "163f1aade5bac38ed1e9e9c912283a7e74781610")
29457 (name "r-seuratdisk")
29458 (version (git-version "0.0.0.9019" revision commit))
29462 (uri (git-reference
29463 (url "https://github.com/mojaveazure/seurat-disk")
29465 (file-name (git-file-name name version))
29467 (base32 "1d1v8qi6kknzy5fj6bl8akwy74h5h143i00lyidsnqjbwp9n4qnw"))))
29468 (properties `((upstream-name . "SeuratDisk")))
29469 (build-system r-build-system)
29483 (home-page "https://github.com/mojaveazure/seurat-disk")
29484 (synopsis "Interfaces for HDF5-based single cell file formats")
29486 "The h5Seurat file format is specifically designed for the storage and
29487 analysis of multi-modal single-cell and spatially-resolved expression
29488 experiments, for example, from CITE-seq or 10X Visium technologies. It holds
29489 all molecular information and associated metadata, including (for example)
29490 nearest-neighbor graphs, dimensional reduction information, spatial
29491 coordinates and image data, and cluster labels. This package also supports
29492 rapid and on-disk conversion between h5Seurat and AnnData objects, with the
29493 goal of enhancing interoperability between Seurat and Scanpy.")
29494 (license license:gpl3))))
29496 (define-public r-seuratdata
29497 (let ((commit "b59556b24d7d6728a5744c9c715dd5f7f32ed7a5")
29500 (name "r-seuratdata")
29501 (version (git-version "0.2.1" revision commit))
29505 (uri (git-reference
29506 (url "https://github.com/satijalab/seurat-data")
29508 (file-name (git-file-name name version))
29510 (base32 "1xfdmdmgn4r0z6w4cxa98ic6xk8i6qz054r215dvqbjs1vydsbf9"))))
29511 (properties `((upstream-name . "SeuratData")))
29512 (build-system r-build-system)
29515 (modify-phases %standard-phases
29516 ;; When there is no HOME directory, this package will fail to load
29517 ;; the included list of packages.
29518 (add-after 'unpack 'set-HOME
29519 (lambda _ (setenv "HOME" "/tmp"))))))
29521 (list r-cli r-crayon r-rappdirs))
29522 (home-page "https://github.com/satijalab/seurat-data")
29523 (synopsis "Install and manage Seurat datasets")
29525 "Single cell RNA sequencing datasets can be large, consisting of
29526 matrices that contain expression data for several thousand features across
29527 several thousand cells. This package is designed to easily install, manage,
29528 and learn about various single-cell datasets, provided Seurat objects and
29529 distributed as independent packages.")
29530 (license license:gpl3))))
29532 (define-public r-phangorn
29534 (name "r-phangorn")
29539 (uri (cran-uri "phangorn" version))
29542 "0xfwi7adl1pcfcwk72fj7lkwfm0wiip96ij7m4252xr9mq818ivd"))))
29543 (build-system r-build-system)
29553 (home-page "https://github.com/KlausVigo/phangorn")
29554 (synopsis "Phylogenetic analysis in R")
29556 "Phangorn is a package for phylogenetic analysis in R. It supports
29557 estimation of phylogenetic trees and networks using Maximum Likelihood,
29558 Maximum Parsimony, distance methods and Hadamard conjugation.")
29559 (license license:gpl2+)))
29561 (define-public r-diversitree
29563 (name "r-diversitree")
29568 (uri (cran-uri "diversitree" version))
29571 "0rzrk7xsn4gy271pbcw3azndhx0c06bmsgrg6libjmlfnmq6j8sc"))))
29572 (build-system r-build-system)
29575 (inputs (list fftw gsl))
29577 (list r-ape r-desolve r-rcpp r-subplex))
29578 (home-page "https://www.zoology.ubc.ca/prog/diversitree")
29579 (synopsis "Comparative 'phylogenetic' analyses of diversification")
29580 (description "This package contains a number of comparative \"phylogenetic\"
29581 methods, mostly focusing on analysing diversification and character evolution.
29582 Contains implementations of \"BiSSE\" (Binary State Speciation and Extinction)
29583 and its unresolved tree extensions, \"MuSSE\" (Multiple State Speciation and
29584 Extinction), \"QuaSSE\", \"GeoSSE\", and \"BiSSE-ness\" Other included methods
29585 include Markov models of discrete and continuous trait evolution and constant
29586 rate speciation and extinction.")
29587 (license license:gpl2+)))
29589 (define-public r-calculus
29591 (name "r-calculus")
29596 (uri (cran-uri "calculus" version))
29599 "1fhvr0l2mqik3d95v0vanafxmiab147g5a87q956g2i945wc5f22"))))
29600 (properties `((upstream-name . "calculus")))
29601 (build-system r-build-system)
29606 (home-page "https://github.com/eguidotti/calculus")
29607 (synopsis "High dimensional numerical and symbolic calculus")
29609 "Efficient C++ optimized functions for numerical and symbolic calculus.
29610 It includes basic symbolic arithmetic, tensor calculus, Einstein summing
29611 convention, fast computation of the Levi-Civita symbol and generalized
29612 Kronecker delta, Taylor series expansion, multivariate Hermite polynomials,
29613 accurate high-order derivatives, differential operators (Gradient, Jacobian,
29614 Hessian, Divergence, Curl, Laplacian) and numerical integration in arbitrary
29615 orthogonal coordinate systems: cartesian, polar, spherical, cylindrical,
29616 parabolic or user defined by custom scale factors.")
29617 (license license:gpl3)))
29619 (define-public r-decon
29626 (uri (cran-uri "decon" version))
29629 "036cv56wf42q2p3d5h15hbrp5rc29xxy20qwv4k1qzhkq6hmw0qs"))))
29630 (properties `((upstream-name . "decon")))
29631 (build-system r-build-system)
29635 "https://cran.r-project.org/web/packages/decon/")
29636 (synopsis "Deconvolution Estimation in Measurement Error Models")
29638 "This package contains a collection of functions to deal with
29639 nonparametric measurement error problems using deconvolution
29640 kernel methods. We focus two measurement error models in the
29641 package: (1) an additive measurement error model, where the
29642 goal is to estimate the density or distribution function from
29643 contaminated data; (2) nonparametric regression model with
29644 errors-in-variables. The R functions allow the measurement errors
29645 to be either homoscedastic or heteroscedastic. To make the
29646 deconvolution estimators computationally more efficient in R,
29647 we adapt the \"Fast Fourier Transform\" (FFT) algorithm for
29648 density estimation with error-free data to the deconvolution
29649 kernel estimation. Several methods for the selection of the
29650 data-driven smoothing parameter are also provided in the package.
29651 See details in: Wang, X.F. and Wang, B. (2011). Deconvolution
29652 estimation in measurement error models: The R package decon.
29653 Journal of Statistical Software, 39(10), 1-24.")
29654 (license license:gpl3+)))
29656 (define-public r-densestbayes
29658 (name "r-densestbayes")
29659 (version "1.0-2.1")
29663 (uri (cran-uri "densEstBayes" version))
29665 (base32 "1pzmgn65lv91zg1588qhwczy9f2zgciknlc4l072mvh2i7hncw2b"))))
29666 (properties `((upstream-name . "densEstBayes")))
29667 (build-system r-build-system)
29679 (home-page "https://cran.r-project.org/package=densEstBayes")
29680 (synopsis "Density estimation via Bayesian inference engines")
29682 "Bayesian density estimates for univariate continuous random samples are
29683 provided using the Bayesian inference engine paradigm. The engine options
29684 are: Hamiltonian Monte Carlo, the no U-turn sampler, semiparametric mean field
29685 variational Bayes and slice sampling. The methodology is described in Wand
29686 and Yu (2020), arXiv:2009.06182.")
29687 (license license:gpl2+)))
29689 (define-public r-locpol
29696 (uri (cran-uri "locpol" version))
29699 "1p915n0l09kbwkly627074jslxl01yssp1rf0c7sygvsw6sgy5lm"))))
29700 (properties `((upstream-name . "locpol")))
29701 (build-system r-build-system)
29703 "https://cran.r-project.org/web/packages/locpol/")
29704 (synopsis "Kernel Local Polynomial Regression")
29706 "Computes local polynomial estimators for the regression and
29707 also density. It comprises several different utilities to handle
29708 kernel estimators.")
29709 (license license:gpl2+)))
29711 (define-public r-lpme
29718 (uri (cran-uri "lpme" version))
29721 "1ch11cwjci98m7952p9wdsh9fj5y1mjya6ayq0q4wmbm824qfpzb"))))
29722 (properties `((upstream-name . "lpme")))
29723 (build-system r-build-system)
29725 (list r-decon r-flexmix r-locpol r-rcpp r-rcpparmadillo))
29727 "https://cran.r-project.org/web/packages/lpme/")
29728 (synopsis "Nonparametric Estimation of Measurement Error Models")
29730 "Provide nonparametric methods for mean regression model,
29731 modal regression and conditional density estimation in the
29732 presence/absence of measurement error. Bandwidth selection is
29733 also provided for each method.")
29734 (license license:gpl2+)))
29736 (define-public r-aws-signature
29738 (name "r-aws-signature")
29743 (uri (cran-uri "aws.signature" version))
29746 "15llpcnrdq4y6jsn7079yjmgbr5d1wgy2ymsm3jj3gkrd5l4zzpp"))))
29747 (properties `((upstream-name . "aws.signature")))
29748 (build-system r-build-system)
29750 (list r-base64enc r-digest))
29751 (home-page "https://github.com/cloudyr/aws.signature")
29752 (synopsis "Amazon Web Services Request Signatures")
29754 "This package generates version 2 and 4 request signatures for Amazon Web
29755 Services (AWS) and provides a mechanism for retrieving credentials from
29756 environment variables, AWS credentials files, and EC2 instance metadata. For
29757 use on EC2 instances, the package 'aws.ec2metadata' is suggested.")
29758 (license license:gpl2+)))
29760 (define-public r-aws-s3
29767 (uri (cran-uri "aws.s3" version))
29770 "132cczq0ml7lpp2yl6l4p99dn1zihrncnpa6wyad4m9mnr50a8dx"))))
29771 (properties `((upstream-name . "aws.s3")))
29772 (build-system r-build-system)
29774 (list r-aws-signature
29780 (home-page "https://github.com/cloudyr/aws.s3")
29781 (synopsis "AWS S3 Client Package")
29783 "This package provides a simple client package for the Amazon Web
29784 Services (AWS) Simple Storage Service (S3) REST API.")
29785 (license license:gpl2+)))
29787 (define-public r-lgr
29793 (uri (cran-uri "lgr" version))
29796 "18s92qyakhvp336kk2777ydypwfrfwfz6a1gqkq812zy3kcb4mcc"))))
29797 (build-system r-build-system)
29802 (home-page "https://s-fleck.github.io/lgr/")
29803 (synopsis "Fully featured logging framework")
29804 (description "This package offers a flexible, feature-rich yet
29805 light-weight logging framework based on @code{R6} classes. It supports
29806 hierarchical loggers, custom log levels, arbitrary data fields in log events,
29807 logging to plaintext, JSON, (rotating) files, memory buffers, and databases, as
29808 well as email and push notifications.")
29809 (license license:expat)))
29811 (define-public r-mhg
29818 (uri (cran-uri "mHG" version))
29821 "1rz5ncrvvv9h9grls15apa63v2nh9j87fmp4mwjjil37jx6a5zki"))))
29822 (properties `((upstream-name . "mHG")))
29823 (build-system r-build-system)
29824 (home-page "https://cran.r-project.org/package=mHG")
29825 (synopsis "Minimum-hypergeometric test")
29827 "This package runs a minimum-hypergeometric (mHG) test as described in
29828 \"Discovering Motifs in Ranked Lists of DNA Sequences\" by Eran Eden.")
29829 (license license:gpl2)))
29831 (define-public r-mlr3measures
29833 (name "r-mlr3measures")
29837 (uri (cran-uri "mlr3measures" version))
29840 "1kbw3xd7c9x65v9zzs8i5skmrvl0mf2wsbyssmiif0lvrbzfhcmb"))))
29841 (build-system r-build-system)
29843 (list r-checkmate r-prroc))
29844 (home-page "https://mlr3measures.mlr-org.com/")
29845 (synopsis "Performance measures for mlr3")
29846 (description "This package implements multiple performance measures for
29847 supervised learning. It includes over 40 measures for regression and
29848 classification. Additionally, meta information about the performance measures
29849 can be queried, e.g. what the best and worst possible performances scores
29851 (license license:lgpl3)))
29853 (define-public r-mlr3misc
29855 (name "r-mlr3misc")
29859 (uri (cran-uri "mlr3misc" version))
29862 "1wnzyij1x67smkb3gjb9gpp7iy5andfl0s1c78xx4wylhycc6m11"))))
29863 (build-system r-build-system)
29865 (list r-backports r-checkmate r-data-table r-digest r-r6))
29866 (home-page "https://mlr3misc.mlr-org.com/")
29867 (synopsis "Helper functions for mlr3")
29868 (description "@code{mlr3misc} provides frequently used helper functions
29869 and assertions used in @code{mlr3} and its companion packages. It comes with
29870 helper functions for functional programming, for printing, to work with
29871 @code{data.table}, as well as some generally useful @code{R6} classes. This
29872 package also supersedes the package @code{BBmisc}.")
29873 (license license:lgpl3)))
29875 (define-public r-mlr3pipelines
29877 (name "r-mlr3pipelines")
29881 (uri (cran-uri "mlr3pipelines" version))
29884 "1zz55i8c08znxpcs6gp5inaw96c6la9wnsla0972ankvj1hsrcr2"))))
29885 (build-system r-build-system)
29897 (home-page "https://mlr3pipelines.mlr-org.com/")
29898 (synopsis "Preprocessing Operators and Pipelines for @code{mlr3}")
29899 (description "@code{mlr3pipelines} enriches @code{mlr3} with a diverse
29900 set of pipelining operators (PipeOps) that can be composed into graphs.
29901 Operations exist for data preprocessing, model fitting, and ensemble learning.
29902 Graphs can themselves be treated as @code{mlr3} Learners and can therefore be
29903 resampled, benchmarked, and tuned.")
29904 (license license:lgpl3)))
29906 (define-public r-mlr3ordinal
29907 (let ((commit "9febac983b11b7b1f477e5cf0212e5999cd2ed44")
29910 (name "r-mlr3ordinal")
29911 (version (git-version "0.1.0-9000" revision commit))
29914 (uri (git-reference
29915 (url "https://github.com/mlr-org/mlr3ordinal")
29917 (file-name (git-file-name name version))
29920 "1icfhz1pjm0mlsn2y60gsrbk31b2p7xmpx3xsg7639rcgdb5f9gl"))))
29921 (build-system r-build-system)
29932 (home-page "https://mlr3ordinal.mlr-org.com/")
29933 (synopsis "Ordinal Regression for mlr3")
29934 (description "This package extends @code{mlr3} with support for
29935 performing ordinal regression.")
29936 (license license:expat))))
29938 (define-public r-paradox
29944 (uri (cran-uri "paradox" version))
29947 "0fzq59903fklgj3kblnpzasy13a82s72c1qjsy7d1m0fyj28ahdw"))))
29948 (build-system r-build-system)
29950 (list r-backports r-checkmate r-data-table r-mlr3misc r-r6))
29951 (home-page "https://paradox.mlr-org.com/")
29952 (synopsis "Define and work with parameter spaces for complex algorithms")
29953 (description "With this package it is possible to define parameter spaces,
29954 constraints and dependencies for arbitrary algorithms, and to program on such
29955 spaces. It also includes statistical designs and random samplers. Objects are
29956 implemented as @code{R6} classes.")
29957 (license license:lgpl3)))
29959 (define-public r-mlr3
29965 (uri (cran-uri "mlr3" version))
29968 "010kl51zsgpc0qv63g1fg9kiw9m0wzqskcr14f1j8b9zi1lwi0bf"))))
29969 (build-system r-build-system)
29986 (home-page "https://mlr3.mlr-org.com/")
29987 (synopsis "Machine Learning in R - Next Generation")
29988 (description "@code{mlr3} enables efficient, object-oriented programming
29989 on the building blocks of machine learning. It provides @code{R6} objects for
29990 tasks, learners, resamplings, and measures. The package is geared towards
29991 scalability and larger datasets by supporting parallelization and out-of-memory
29992 data-backends like databases. While @code{mlr3} focuses on the core
29993 computational operations, add-on packages provide additional functionality.")
29994 (license license:lgpl3)))
29996 (define-public r-mlr3learners
29998 (name "r-mlr3learners")
30002 (uri (cran-uri "mlr3learners" version))
30005 "088i2piv7sgxsvc7jyr6mq53vqf8yjdlrysgqphsryq6k50i00zd"))))
30006 (build-system r-build-system)
30014 (home-page "https://mlr3learners.mlr-org.com/")
30015 (synopsis "Recommended Learners for @code{mlr3}")
30016 (description "@code{mlr3learners} extends @code{mlr3} and @code{mlr3proba}
30017 with interfaces to essential machine learning packages on CRAN. This includes,
30018 but is not limited to: (penalized) linear and logistic regression, linear and
30019 quadratic discriminant analysis, k-nearest neighbors, naive Bayes, support
30020 vector machines, and gradient boosting.")
30021 (license license:lgpl3)))
30023 (define-public r-bbotk
30030 (uri (cran-uri "bbotk" version))
30033 "13qj8qysqismv9k9rfw770r7w8jdaw82n71k7sp3wsrlhxjxw734"))))
30034 (properties `((upstream-name . "bbotk")))
30035 (build-system r-build-system)
30045 (home-page "https://bbotk.mlr-org.com")
30046 (synopsis "Black-Box Optimization Toolkit")
30047 (description "This package provides a common framework for optimization of
30048 black-box functions for other packages, e.g. @code{mlr3}. It offers various
30049 optimization methods e.g. grid search, random search and generalized simulated
30051 (license license:lgpl3)))
30053 (define-public r-mlr3tuning
30055 (name "r-mlr3tuning")
30059 (uri (cran-uri "mlr3tuning" version))
30062 "0jfslx6pwk408ydn69grrvsp22jd7gsjmwvss0a1j0zav3q1pvks"))))
30063 (build-system r-build-system)
30073 (home-page "https://mlr3tuning.mlr-org.com/")
30074 (synopsis "Tuning for @code{mlr3}")
30075 (description "@code{mlr3tuning} implements methods for hyperparameter
30076 tuning, e.g. Grid Search, Random Search, or Simulated Annealing. Various
30077 termination criteria can be set and combined. The class @code{AutoTuner} provides a
30078 convenient way to perform nested resampling in combination with @code{mlr3}.")
30079 (license license:lgpl3)))
30081 (define-public r-fontliberation
30083 (name "r-fontliberation")
30088 (uri (cran-uri "fontLiberation" version))
30091 "1w1rl0g4ayyp8lwppmz9yzj9cizg7i50g07216jkm1q5w0is9pmc"))))
30093 `((upstream-name . "fontLiberation")))
30094 (build-system r-build-system)
30095 (home-page "https://cran.r-project.org/package=fontLiberation")
30096 (synopsis "Liberation fonts")
30098 "This package provides a placeholder for the Liberation fontset intended
30099 for the fontquiver package. This fontset covers the 12 combinations of
30100 families (sans, serif, mono) and faces (plain, bold, italic, bold italic)
30101 supported in R graphics devices.")
30102 (license license:silofl1.1)))
30104 (define-public r-fontbitstreamvera
30106 (name "r-fontbitstreamvera")
30111 (uri (cran-uri "fontBitstreamVera" version))
30114 "0nipdlmhjv1wr3aidcl97nk6mppdkd65krgwqnhdsnv0jpfv761j"))))
30116 `((upstream-name . "fontBitstreamVera")))
30117 (build-system r-build-system)
30118 (home-page "https://cran.r-project.org/package=fontBitstreamVera")
30119 (synopsis "Fonts for fontquiver")
30121 "This package is a placeholder for the Bitstream Vera font. It is
30122 intended for the fontquiver package.")
30124 (license:fsdg-compatible
30125 "https://www.gnome.org/fonts/#Final_Bitstream_Vera_Fonts"
30126 "The Font Software may be sold as part of a larger software package but
30127 no copy of one or more of the Font Software typefaces may be sold by
30130 (define-public r-fontquiver
30132 (name "r-fontquiver")
30137 (uri (cran-uri "fontquiver" version))
30140 "0qv3i9hch7cygl9983s3w68wfh5qvym2jkm52pp06p6mq8a1i1wm"))))
30141 (properties `((upstream-name . "fontquiver")))
30142 (build-system r-build-system)
30144 (list r-fontbitstreamvera r-fontliberation))
30145 (home-page "https://cran.r-project.org/package=fontquiver")
30146 (synopsis "Set of installed fonts")
30148 "This package provides a set of fonts. This is useful when you want to
30149 avoid system fonts to make sure your outputs are reproducible.")
30150 (license license:gpl3)))
30152 (define-public r-freetypeharfbuzz
30154 (name "r-freetypeharfbuzz")
30159 (uri (cran-uri "freetypeharfbuzz" version))
30162 "0r3icgnq3jk4fm6z92cmhzdmflbk5df8zsmjg0dzpc4y48xafnk7"))))
30164 `((upstream-name . "freetypeharfbuzz")))
30165 (build-system r-build-system)
30168 (modify-phases %standard-phases
30169 (add-after 'unpack 'prepare-static-libraries
30170 (lambda* (#:key inputs #:allow-other-keys)
30171 (mkdir-p "src/target/include")
30172 (let ((freetype (assoc-ref inputs "static-freetype"))
30173 (harfbuzz (assoc-ref inputs "static-harfbuzz")))
30174 (substitute* "src/Makevars.in"
30175 (("include @MK_FILE@") "") ; do not build static libs
30176 (("^HB_STATIC_LIB =.*")
30177 (string-append "HB_STATIC_LIB = " harfbuzz "/lib/libharfbuzz.a\n"))
30178 (("^FT_STATIC_LIB =.*")
30179 (string-append "FT_STATIC_LIB = " freetype "/lib/libfreetype.a\n")))
30180 (copy-recursively (string-append freetype "/include")
30181 "src/target/include")
30182 (copy-recursively (string-append harfbuzz "/include")
30183 "src/target/include")))))))
30185 (list r-fontquiver))
30186 ;; This may defeat the purpose of this package as our versions of freetype
30187 ;; and harfbuzz obviously differ from the tarballs offered by this
30188 ;; project. On the other hand, Guix arguably does a better job at
30189 ;; "ensur[ing] deterministic computation".
30191 `(("static-freetype"
30193 (inherit (static-package freetype))
30195 `(#:configure-flags
30196 (list "--enable-static=yes"
30201 "--without-harfbuzz")))))
30204 (inherit (static-package harfbuzz))
30206 `(#:tests? #false ; fail because shared library is disabled
30208 (list "--enable-static=yes"
30209 "--enable-shared=no"
30211 "--with-freetype=yes"
30214 "--without-fontconfig"
30215 "--without-glib")))))))
30218 (home-page "https://cran.r-project.org/package=freetypeharfbuzz")
30219 (synopsis "Deterministic computation of text box metrics")
30221 "Unlike other tools that dynamically link to the Cairo stack,
30222 freetypeharfbuzz is statically linked to specific versions of the FreeType and
30223 harfbuzz libraries. This ensures deterministic computation of text box
30224 extents for situations where reproducible results are crucial (for instance
30225 unit tests of graphics).")
30226 (license license:gpl3)))
30228 (define-public r-vdiffr
30235 (uri (cran-uri "vdiffr" version))
30238 "1z8nn8yh6jfzb9r7ylmigwh1p30lrclqm6khmp323qqphzmzfdwy"))))
30239 (properties `((upstream-name . "vdiffr")))
30240 (build-system r-build-system)
30242 (list libpng zlib))
30252 (home-page "https://github.com/r-lib/vdiffr")
30253 (synopsis "Visual regression testing and graphical diffing")
30255 "This package is an extension to the testthat package that makes it easy
30256 to add graphical unit tests. It provides a Shiny application to manage the
30258 (license license:gpl3)))
30260 (define-public r-highlight
30262 (name "r-highlight")
30267 (uri (cran-uri "highlight" version))
30270 "1shar4y07wyixg0ichdrn2xhgwkl3mv2pxkalqzisc69w605b3hf"))))
30271 (properties `((upstream-name . "highlight")))
30272 (build-system r-build-system)
30273 (home-page "https://github.com/hadley/highlight")
30274 (synopsis "Syntax highlighter for R code")
30276 "This package provides a syntax highlighter for R code based on the
30277 results of the R parser. It supports rendering in HTML and LaTeX markup. It
30278 includes a custom Sweave driver performing syntax highlighting of R code
30280 (license license:gpl3+)))
30282 (define-public r-clustree
30284 (name "r-clustree")
30289 (uri (cran-uri "clustree" version))
30292 "0vwmicajl7c0rmjdmf4f857fii0xrxz25vjkn888svlsikw00qbs"))))
30293 (properties `((upstream-name . "clustree")))
30294 (build-system r-build-system)
30307 (home-page "https://github.com/lazappi/clustree")
30308 (synopsis "Visualize clusterings at different resolutions")
30310 "Deciding what resolution to use can be a difficult question when
30311 approaching a clustering analysis. One way to approach this problem is to
30312 look at how samples move as the number of clusters increases. This package
30313 allows you to produce clustering trees, a visualization for interrogating
30314 clusterings as resolution increases.")
30315 (license license:gpl3)))
30317 (define-public r-textshaping
30319 (name "r-textshaping")
30324 (uri (cran-uri "textshaping" version))
30327 "1niaj1dh09rqrg9hrh98ddnc0f2nkyq9iizv24lcwm9gjs3w1ql0"))))
30328 (properties `((upstream-name . "textshaping")))
30329 (build-system r-build-system)
30331 (list freetype fribidi harfbuzz zlib))
30333 (list r-cpp11 r-systemfonts))
30335 (list pkg-config r-knitr))
30336 (home-page "https://github.com/r-lib/textshaping")
30337 (synopsis "Bindings to the HarfBuzz and Fribidi libraries for text shaping")
30339 "This package provides access to the text shaping functionality in the
30340 HarfBuzz library and the bidirectional algorithm in the Fribidi library. This
30341 is a low-level utility package mainly for graphic devices that expands upon
30342 the font tool-set provided by the @code{systemfonts} package.")
30343 (license license:expat)))
30345 (define-public r-ragg
30352 (uri (cran-uri "ragg" version))
30355 "1q43pwmljsqgrikkh2g1n7bpz9c8py5dnj44cfg3y2br7b4m2q9v"))))
30356 (properties `((upstream-name . "ragg")))
30357 (build-system r-build-system)
30359 (list freetype libjpeg-turbo libpng libtiff zlib))
30361 (list r-systemfonts r-textshaping))
30364 (home-page "https://ragg.r-lib.org")
30365 (synopsis "Graphic devices based on AGG")
30367 "Anti-Grain Geometry (AGG) is a high-quality and high-performance 2D
30368 drawing library. The ragg package provides a set of graphic devices based on
30369 AGG to use as alternative to the raster devices provided through the
30370 @code{grDevices} package.")
30371 (license license:expat)))
30373 (define-public r-downlit
30380 (uri (cran-uri "downlit" version))
30383 "10zvrqdpwavdy97h3q26bqh3k63z61fmc04w9vwsnvmnv8hnh3vl"))))
30384 (properties `((upstream-name . "downlit")))
30385 (build-system r-build-system)
30396 (home-page "https://downlit.r-lib.org/")
30397 (synopsis "Syntax highlighting and automatic linking")
30399 "This package provides syntax highlighting of R code, specifically
30400 designed for the needs of RMarkdown packages like @code{pkgdown},
30401 @code{hugodown}, and @code{bookdown}. It includes linking of function calls
30402 to their documentation on the web, and automatic translation of ANSI escapes
30403 in output to the equivalent HTML.")
30404 (license license:expat)))
30406 (define-public r-pkgdown
30413 (uri (cran-uri "pkgdown" version))
30416 "0wqga9bcl7wmvkwpkkmf5hx1cl7rjq5ddvqmxhl4p1dczys3adnr"))))
30417 (properties `((upstream-name . "pkgdown")))
30418 (build-system r-build-system)
30419 (inputs (list pandoc))
30443 (home-page "https://pkgdown.r-lib.org")
30444 (synopsis "Make static HTML documentation for an R package")
30446 "The goal of this package is to generate an attractive and useful website
30447 from a source package. @code{pkgdown} converts your documentation, vignettes,
30448 README file, and more to HTML making it easy to share information about your
30450 (license license:expat)))
30452 (define-public r-prereg
30459 (uri (cran-uri "prereg" version))
30462 "039nrl5cirsx1ysh214dr6xnn1h6h3f90im6k9dgmzfksxdqigpw"))))
30463 (properties `((upstream-name . "prereg")))
30464 (build-system r-build-system)
30466 (list r-rmarkdown))
30467 (home-page "https://github.com/crsh/prereg")
30469 "R Markdown Templates to preregister Scientific Studies")
30471 "This package provides a collection of templates to author
30472 preregistration documents for scientific studies in PDF format.")
30473 (license license:gpl3)))
30475 (define-public r-ez
30482 (uri (cran-uri "ez" version))
30485 "0a58s94x576dfz7wcbivrr2hmdh5x1vy16zwkqp9fmdzqx38pagq"))))
30486 (properties `((upstream-name . "ez")))
30487 (build-system r-build-system)
30499 (home-page "https://github.com/mike-lawrence/ez")
30500 (synopsis "Easy Analysis and Visualization of Factorial Experiments")
30502 "Facilitates easy analysis of factorial experiments, including purely
30503 within-Ss designs (a.k.a. \"repeated measures\"), purely between-Ss designs,
30504 and mixed within-and-between-Ss designs. The functions in this package aim to
30505 provide simple, intuitive and consistent specification of data analysis and
30506 visualization. Visualization functions also include design visualization for
30507 pre-analysis data auditing, and correlation matrix visualization. Finally,
30508 this package includes functions for non-parametric analysis, including
30509 permutation tests and bootstrap resampling. The bootstrap function obtains
30510 predictions either by cell means or by more advanced/powerful mixed effects
30511 models, yielding predictions and confidence intervals that may be easily
30512 visualized at any level of the experiment's design.")
30513 (license license:gpl2+)))
30515 (define-public r-qdapregex
30517 (name "r-qdapregex")
30522 (uri (cran-uri "qdapRegex" version))
30525 "1hdilycwrvi0q6cx7k8vg87bamm2xsafjkya5x4smxysm5k1r4qb"))))
30526 (properties `((upstream-name . "qdapRegex")))
30527 (build-system r-build-system)
30528 (propagated-inputs (list r-stringi))
30530 "https://trinker.github.com/qdapRegex/")
30532 "Regular Expression Removal, Extraction, and Replacement Tools")
30534 "This package provides a collection of regular expression tools
30535 associated with the @code{qdap} package that may be useful outside of the
30536 context of discourse analysis. Tools include removal/extraction/replacement of
30537 abbreviations, dates, dollar amounts, email addresses, hash tags, numbers,
30538 percentages, citations, person tags, phone numbers, times, and zip codes.")
30539 (license license:gpl2)))
30541 (define-public r-mgsub
30548 (uri (cran-uri "mgsub" version))
30551 "1mci6x65h94qiz9cwikx2inbrwkykv43zbs8abfbx416zrh2bbn9"))))
30552 (properties `((upstream-name . "mgsub")))
30553 (build-system r-build-system)
30554 (native-inputs (list r-knitr))
30556 "https://cran.r-project.org/package=mgsub")
30558 "Safe, Multiple, Simultaneous String Substitution")
30560 "Designed to enable simultaneous substitution in strings in a safe
30561 fashion. Safe means it does not rely on placeholders (which can cause errors
30562 in same length matches).")
30563 (license license:expat)))
30565 (define-public r-textshape
30567 (name "r-textshape")
30572 (uri (cran-uri "textshape" version))
30575 "0k9injxykgj2qprc7dygd7gafvcbh3r9x84qzaa1al21pk0dz7ds"))))
30576 (properties `((upstream-name . "textshape")))
30577 (build-system r-build-system)
30579 (list r-data-table r-slam r-stringi))
30580 (home-page "https://github.com/trinker/textshape")
30581 (synopsis "Tools for Reshaping Text")
30583 "Tools that can be used to reshape and restructure text data.")
30584 (license license:gpl2)))
30586 (define-public r-syuzhet
30593 (uri (cran-uri "syuzhet" version))
30596 "16iccqdbw02iw82nah6kwz3gwfghi864j2y698n4b9dyc386ijzv"))))
30597 (properties `((upstream-name . "syuzhet")))
30598 (build-system r-build-system)
30607 (native-inputs (list r-knitr))
30608 (home-page "https://github.com/mjockers/syuzhet")
30610 "Extracts Sentiment and Sentiment-Derived Plot Arcs from Text")
30612 "Extracts sentiment and sentiment-derived plot arcs from text using a
30613 variety of sentiment dictionaries conveniently packaged for consumption by R
30614 users. Implemented dictionaries include @dfn{syuzhet} (default) developed in the
30615 Nebraska Literary Lab, @dfn{afinn} developed by Finn Arup Nielsen, @dfn{bing}
30616 developed by Minqing Hu and Bing Liu, and @dfn{nrc} developed by Mohammad, Saif
30617 M. and Turney, Peter D. Applicable references are available in
30618 @file{README.md} and in the documentation for the @code{get_sentiment}
30619 function. The package also provides a hack for implementing Stanford's coreNLP
30620 sentiment parser. The package provides several methods for plot arc
30622 (license license:gpl3)))
30624 (define-public r-lexicon
30631 (uri (cran-uri "lexicon" version))
30634 "0x7rscsh6par2lj11sby7bmz41cxn63iiw51lgh29z09cg8j606c"))))
30635 (properties `((upstream-name . "lexicon")))
30636 (build-system r-build-system)
30638 (list r-data-table r-syuzhet))
30639 (home-page "https://github.com/trinker/lexicon")
30640 (synopsis "Lexicons for Text Analysis")
30642 "This package provides a collection of lexical hash tables, dictionaries,
30644 (license license:gpl3)))
30646 (define-public r-english
30653 (uri (cran-uri "english" version))
30656 "1g3nmy5p8wj3ix1vp1qmkmy3dyqisrw0md8cjrx4klqkp0wqlms9"))))
30657 (properties `((upstream-name . "english")))
30658 (build-system r-build-system)
30659 (native-inputs (list r-knitr))
30661 "https://cran.r-project.org/package=english")
30662 (synopsis "Translate Integers into English")
30664 "Allow numbers to be presented in an English language version, one, two,
30665 three, ... Ordinals are also available, first, second, third, ... and
30666 indefinite article choice, \"a\" or \"an\".")
30667 (license license:gpl2)))
30669 (define-public r-textclean
30671 (name "r-textclean")
30676 (uri (cran-uri "textclean" version))
30679 "0kgjh6c4f14qkjc4fds7q7rpf4nkma3p0igm54fplmm3p853nvrz"))))
30680 (properties `((upstream-name . "textclean")))
30681 (build-system r-build-system)
30692 "https://github.com/trinker/textclean")
30693 (synopsis "Text Cleaning Tools")
30695 "Tools to clean and process text. Tools are geared at checking for
30696 substrings that are not optimal for analysis and replacing or removing them
30697 (normalizing) with more analysis friendly substrings (see Sproat, Black, Chen,
30698 Kumar, Ostendorf, & Richards (2001) @url{doi:10.1006/csla.2001.0169}) or
30699 extracting them into new variables. For example, emoticons are often used in
30700 text but not always easily handled by analysis algorithms. The
30701 @code{replace_emoticon()} function replaces emoticons with word equivalents.")
30702 (license license:gpl2)))
30704 (define-public r-striprtf
30706 (name "r-striprtf")
30711 (uri (cran-uri "striprtf" version))
30714 "0dqcsh3fb8j0mmmxvxjl77rryhmrjm7a3scqvk2xkgxk4xq6q316"))))
30715 (properties `((upstream-name . "striprtf")))
30716 (build-system r-build-system)
30718 (list r-magrittr r-rcpp r-stringr))
30719 (home-page "https://github.com/kota7/striprtf")
30720 (synopsis "Extract Text from RTF File")
30722 "Extracts plain text from @dfn{Rich Text Format} (RTF) file.")
30723 (license license:expat)))
30725 (define-public r-ndjson
30732 (uri (cran-uri "ndjson" version))
30735 "0lvzbgfi1sg4kya1mvv67z14qk3vz9q57x22qh57xq8ampdkg812"))
30736 (modules '((guix build utils)))
30739 ;; unvendor gzstream
30740 (for-each delete-file '("src/gzstream.cpp" "src/gzstream.h"))
30742 (properties `((upstream-name . "ndjson")))
30743 (build-system r-build-system)
30746 (modify-phases %standard-phases
30747 (add-after 'unpack 'use-system-gzstream
30748 (lambda* (#:key inputs #:allow-other-keys)
30749 (substitute* "src/Makevars"
30750 (("PKG_LIBS = " all)
30751 (string-append all "-lgzstream ")))
30753 (inputs (list zlib gzstream))
30755 (list r-data-table r-rcpp r-tibble))
30756 (home-page "https://gitlab.com/hrbrmstr/ndjson")
30758 "Wicked-Fast @dfn{Streaming JSON} (ndjson) Reader")
30760 "@dfn{Streaming JSON} (ndjson) has one JSON record per-line and many
30761 modern ndjson files contain large numbers of records. These constructs may not
30762 be columnar in nature, but it is often useful to read in these files and
30763 \"flatten\" the structure out to enable working with the data in an R
30764 @code{data.frame}-like context. Functions are provided that make it possible
30765 to read in plain ndjson files or compressed (@code{gz}) ndjson files and either
30766 validate the format of the records or create \"flat\" @code{data.table}
30767 structures from them.")
30768 (license license:expat)))
30770 (define-public r-streamr
30777 (uri (cran-uri "streamR" version))
30780 "1clx3b0j2515r1nmnl6ki7qw5n54q3x2jvqv3zrc00kq71mlj7ix"))))
30781 (properties `((upstream-name . "streamR")))
30782 (build-system r-build-system)
30784 (list r-ndjson r-rcurl r-rjson))
30786 "https://cran.r-project.org/package=streamR")
30788 "Access to Twitter Streaming API via R")
30790 "This package provides functions to access Twitter's filter, sample, and
30791 user streams, and to parse the output into data frames.")
30792 (license license:gpl2)))
30794 (define-public r-readods
30801 (uri (cran-uri "readODS" version))
30804 "1hi217ab7hp15jsbzi5ak57cqf8jn2rv78bnn74q72gn9mrfra7n"))))
30805 (properties `((upstream-name . "readODS")))
30806 (build-system r-build-system)
30808 (list r-cellranger r-readr r-stringi r-xml2))
30809 (native-inputs (list r-knitr))
30811 "https://cran.r-project.org/package=readODS")
30812 (synopsis "Read and Write ODS Files")
30814 "Import @dfn{OpenDocument Spreadsheet} (ODS) into R as a data frame.
30815 Also support writing data frame into ODS file.")
30816 (license license:gpl3)))
30818 (define-public r-qpdf
30825 (uri (cran-uri "qpdf" version))
30828 "03lnfncw8qd1fwfyqh1mjvnsjr3b63wxbah0wp5g7z7gba90dwbi"))
30829 (modules '((guix build utils)))
30832 ;; unvendor libqpdf
30833 (delete-file-recursively "src/libqpdf")
30834 (delete-file-recursively "src/include/qpdf")
30836 (properties `((upstream-name . "qpdf")))
30837 (build-system r-build-system)
30840 (modify-phases %standard-phases
30841 (add-after 'unpack 'configure
30843 (setenv "EXTERNAL_QPDF" "1")
30848 (list r-askpass r-curl r-rcpp))
30849 (native-inputs (list pkg-config))
30850 (home-page "https://github.com/ropensci/qpdf")
30852 "Split, Combine and Compress PDF Files")
30854 "Content-preserving transformations transformations of PDF files such as
30855 split, combine, and compress. This package interfaces directly to the
30856 @code{qpdf} C++ API and does not require any command line utilities. Note that
30857 @code{qpdf} does not read actual content from PDF files: to extract text and
30858 data you need the @code{pdftools} package.")
30859 (license license:asl2.0)))
30861 (define-public r-pdftools
30863 (name "r-pdftools")
30868 (uri (cran-uri "pdftools" version))
30871 "1b9ppdndvlf8nl0i3xy1rx4f9j0j8ic6q9n0c4zn3rv6jdy8zqfi"))))
30872 (properties `((upstream-name . "pdftools")))
30873 (build-system r-build-system)
30874 (inputs (list zlib poppler))
30875 (propagated-inputs (list r-qpdf r-rcpp))
30876 (native-inputs (list pkg-config))
30877 (home-page "https://docs.ropensci.org/pdftools/")
30878 (synopsis "Text Extraction, Rendering and Converting of PDF Documents")
30880 "This package provides utilities based on @code{libpoppler} for
30881 extracting text, fonts, attachments and metadata from a PDF file. It also
30882 supports high quality rendering of PDF documents into PNG, JPEG, TIFF format,
30883 or into raw bitmap vectors for further processing in R.")
30884 (license license:expat)))
30886 (define-public r-antiword
30888 (name "r-antiword")
30893 (uri (cran-uri "antiword" version))
30896 "123v8zlczwh6fr1v3x7dl3885xlmddq1bqlcxih8zh07w0hlk1k2"))
30897 (modules '((guix build utils)))
30900 ;; unvendor libantiword
30901 (delete-file-recursively "src")
30903 (properties `((upstream-name . "antiword")))
30904 (build-system r-build-system)
30907 (modify-phases %standard-phases
30908 (add-after 'unpack 'use-system-antiword
30909 (lambda* (#:key inputs #:allow-other-keys)
30910 (substitute* "R/antiword.R"
30911 (("system.file\\(\"bin\", package = \"antiword\"\\)")
30912 (string-append "\"" (assoc-ref inputs "antiword") "/bin\"")))
30914 (inputs (list antiword))
30915 (propagated-inputs (list r-sys))
30917 "https://github.com/ropensci/antiword#readme")
30919 "Extract Text from Microsoft Word Documents")
30921 "Wraps the @code{AntiWord} utility to extract text from Microsoft Word
30922 documents. The utility only supports the old @code{doc} format, not the new
30923 xml based @code{docx} format. Use the @code{xml2} package to read the
30925 (license license:gpl2)))
30927 (define-public r-readtext
30929 (name "r-readtext")
30934 (uri (cran-uri "readtext" version))
30937 "0k782h5hns5v5h8a6qyfqck2hc15nq0awg8bsp196q4zviv5jw3c"))))
30938 (properties `((upstream-name . "readtext")))
30939 (build-system r-build-system)
30954 (native-inputs (list r-knitr))
30956 "https://github.com/quanteda/readtext")
30958 "Import and Handling for Plain and Formatted Text Files")
30960 "This package provides functions for importing and handling text files
30961 and formatted text files with additional meta-data, such including @code{.csv},
30962 @code{.tab}, @code{.json}, @code{.xml}, @code{.html}, @code{.pdf}, @code{.doc},
30963 @code{.docx}, @code{.rtf}, @code{.xls}, @code{.xlsx}, and others.")
30964 (license license:gpl3)))
30966 (define-public r-packcircles
30968 (name "r-packcircles")
30973 (uri (cran-uri "packcircles" version))
30976 "05pv5c4k4njkr0xw6i6ksiy34hcyx2lbiqpv5gxw81yrkm0rxfyk"))))
30977 (properties `((upstream-name . "packcircles")))
30978 (build-system r-build-system)
30979 (propagated-inputs (list r-rcpp))
30980 (native-inputs (list r-knitr))
30982 "https://github.com/mbedward/packcircles")
30983 (synopsis "Circle Packing")
30985 "Algorithms to find arrangements of non-overlapping circles.")
30986 (license license:expat)))
30988 ;; Cannot unbundle liblwgeom, because PostGIS does not support building it on
30990 (define-public r-lwgeom
30997 (uri (cran-uri "lwgeom" version))
31000 "0d4b1djwrzla91mmyya2m1250mb44fzmq3d36w5mk81d4bg952pl"))))
31001 (properties `((upstream-name . "lwgeom")))
31002 (build-system r-build-system)
31004 (list geos proj sqlite zlib))
31006 (list r-rcpp r-sf r-units))
31007 (native-inputs (list pkg-config))
31008 (home-page "https://github.com/r-spatial/lwgeom/")
31009 (synopsis "Bindings to Selected 'liblwgeom' Functions for Simple Features")
31011 "Access to selected functions found in
31012 @url{https://github.com/postgis/postgis/tree/master/liblwgeom,liblwgeom}, the
31013 light-weight geometry library used by @url{http://postgis.net/,PostGIS}.")
31014 (license license:gpl2)))
31016 (define-public r-stars
31023 (uri (cran-uri "stars" version))
31026 "0hcbzr8c7wk30qjwrvx6bflzwkjpms79pavaxawnq1h8kry5fngk"))))
31027 (properties `((upstream-name . "stars")))
31028 (build-system r-build-system)
31036 (native-inputs (list r-knitr))
31037 (home-page "https://r-spatial.github.io/stars/")
31039 "Spatiotemporal Arrays, Raster and Vector Data Cubes")
31041 "Reading, manipulating, writing and plotting spatiotemporal arrays
31042 (raster and vector data cubes) in @code{R}, using @code{GDAL} bindings provided
31043 by @code{sf}, and @code{NetCDF} bindings by @code{ncmeta} and @code{RNetCDF}.")
31044 (license license:asl2.0)))
31046 (define-public r-tmaptools
31048 (name "r-tmaptools")
31053 (uri (cran-uri "tmaptools" version))
31056 "0bal3czrdr93qig8s5cf5szld5vjbbks67rismfhlkmlgw6wp2gx"))))
31057 (properties `((upstream-name . "tmaptools")))
31058 (build-system r-build-system)
31070 "https://github.com/mtennekes/tmaptools")
31071 (synopsis "Thematic Map Tools")
31073 "Set of tools for reading and processing spatial data. The aim is to
31074 supply the workflow to create thematic maps. This package also facilitates
31075 @code{tmap}, the package for visualizing thematic maps.")
31076 (license license:gpl3)))
31078 (define-public r-rworldmap
31080 (name "r-rworldmap")
31085 (uri (cran-uri "rworldmap" version))
31088 "1q1h0n9qr0m5pdx10swrh9ddsvdj8kv5nqngrf3lnx9rg9iwivjk"))))
31089 (properties `((upstream-name . "rworldmap")))
31090 (build-system r-build-system)
31092 (list r-fields r-maptools r-sp))
31094 "https://github.com/AndySouth/rworldmap/")
31095 (synopsis "Mapping Global Data")
31097 "Enables mapping of country level and gridded user datasets.")
31098 (license license:gpl2+)))
31100 (define-public r-rtweet
31107 (uri (cran-uri "rtweet" version))
31110 "05pbvxm2vmf6935b9s6663k3aifnkr3m52wh2jvnplmrwyrfpn9n"))))
31111 (properties `((upstream-name . "rtweet")))
31112 (build-system r-build-system)
31121 (native-inputs (list r-knitr))
31123 "https://docs.ropensci.org/rtweet/")
31124 (synopsis "Collecting Twitter Data")
31126 "An implementation of calls designed to collect and organize Twitter data
31127 via @url{https://developer.twitter.com/en/docs,Twitter's REST and stream
31128 Application Program Interfaces (API)}.")
31129 (license license:expat)))
31131 (define-public r-intervals
31133 (name "r-intervals")
31138 (uri (cran-uri "intervals" version))
31141 "0mvwfwc03ifb30a3dzbmkv9adwqb8ajxhcw24d8xip8px063plhb"))))
31142 (properties `((upstream-name . "intervals")))
31143 (build-system r-build-system)
31144 (home-page "https://github.com/edzer/intervals")
31146 "Tools for Working with Points and Intervals")
31148 "Tools for working with and comparing sets of points and intervals.")
31149 (license license:artistic2.0)))
31151 (define-public r-eyelinker
31153 (name "r-eyelinker")
31158 (uri (cran-uri "eyelinker" version))
31161 "0wijd45p6j2qal6wnj7zywks8p9v3m9cmyp7axmk44mrjdjx2i71"))))
31162 (properties `((upstream-name . "eyelinker")))
31163 (build-system r-build-system)
31165 (list r-intervals r-readr r-stringi r-stringr r-tibble))
31166 (native-inputs (list r-knitr))
31168 "https://github.com/a-hurst/eyelinker")
31170 "Import ASC Files from EyeLink Eye Trackers")
31172 "Imports plain-text ASC data files from EyeLink eye trackers into
31173 (relatively) tidy data frames for analysis and visualization.")
31174 (license license:gpl3)))
31176 (define-public r-btm
31183 (uri (cran-uri "BTM" version))
31186 "0ab0wr8nbwn1w1j9hpwfz52lm1sw0qk93713y9k0hpm3pw9dq4jr"))))
31187 (properties `((upstream-name . "BTM")))
31188 (build-system r-build-system)
31189 (propagated-inputs (list r-rcpp))
31190 (home-page "https://github.com/bnosac/BTM")
31191 (synopsis "Biterm Topic Models for Short Text")
31193 "Biterm Topic Models find topics in collections of short texts. It is a
31194 word co-occurrence based topic model that learns topics by modeling word-word
31195 co-occurrences patterns which are called biterms. This in contrast to
31196 traditional topic models like Latent Dirichlet Allocation and Probabilistic
31197 Latent Semantic Analysis which are word-document co-occurrence topic models. A
31198 biterm consists of two words co-occurring in the same short text window. This
31199 context window can for example be a twitter message, a short answer on a
31200 survey, a sentence of a text or a document identifier. The techniques are
31201 explained in detail in the paper 'A Biterm Topic Model For Short Text' by
31202 Xiaohui Yan, Jiafeng Guo, Yanyan Lan, Xueqi Cheng (2013)
31203 @url{https://github.com/xiaohuiyan/xiaohuiyan.github.io/blob/master/paper/\
31205 (license license:asl2.0)))
31207 (define-public r-delaporte
31209 (name "r-delaporte")
31214 (uri (cran-uri "Delaporte" version))
31217 "10xsmms2jfw7x4hmgpd35dv4n4azpjzmfid6585kg6qfh2zg23g5"))))
31218 (properties `((upstream-name . "Delaporte")))
31219 (build-system r-build-system)
31220 (native-inputs (list gfortran))
31221 (home-page "https://github.com/aadler/Delaporte")
31222 (synopsis "Statistical functions for the Delaporte distribution")
31224 "This package provides probability mass, distribution, quantile,
31225 random-variate generation, and method-of-moments parameter-estimation
31226 functions for the Delaporte distribution with parameterization based on
31227 Vose (2008). The Delaporte is a discrete probability distribution which can
31228 be considered the convolution of a negative binomial distribution with a
31229 Poisson distribution. Alternatively, it can be considered a counting
31230 distribution with both Poisson and negative binomial components. It has been
31231 studied in actuarial science as a frequency distribution which has more
31232 variability than the Poisson, but less than the negative binomial.")
31233 (license license:bsd-2)))
31235 (define-public r-rjsonio
31238 (version "1.3-1.6")
31242 (uri (cran-uri "RJSONIO" version))
31245 "17x0ayk7daprbc8w2hvb2jl9mfnw4dic9yc3sr5adcjqfzmcklc2"))))
31246 (properties `((upstream-name . "RJSONIO")))
31247 (build-system r-build-system)
31248 (home-page "https://cran.r-project.org/package=RJSONIO")
31249 (synopsis "Serialize R objects to JSON")
31251 "This is a package that allows conversion to and from data in JavaScript
31252 Object Notation (JSON) format. This allows R objects to be inserted into
31253 Javascript/ECMAScript/ActionScript code and allows R programmers to read and
31254 convert JSON content to R objects. This is an alternative to the @code{rjson}
31256 (license license:bsd-3)))
31258 (define-public r-revgeo
31265 (uri (cran-uri "revgeo" version))
31268 "1ns7d1817475lriss6wwgvdm6lj760p40yxqaifla13c2xb73a55"))))
31269 (properties `((upstream-name . "revgeo")))
31270 (build-system r-build-system)
31272 (list r-rcurl r-rjsonio))
31273 (home-page "https://cran.r-project.org/package=revgeo")
31274 (synopsis "Reverse geocoding")
31276 "The @code{revgeo} procedure allows you to use the Photon geocoder for
31277 OpenStreetMap, Google Maps, and Bing to reverse geocode coordinate pairs with
31279 (license license:gpl3+)))
31281 (define-public r-qpcr
31288 (uri (cran-uri "qpcR" version))
31291 "1r01q7jv3w59yx1gc0qw91rq7rvdhqsi8y57sqqkmwyqfw2x2vsv"))))
31292 (properties `((upstream-name . "qpcR")))
31293 (build-system r-build-system)
31295 (list r-mass r-matrix r-minpack-lm r-rgl r-robustbase))
31296 (home-page "https://cran.r-project.org/package=qpcR")
31297 (synopsis "Modelling and analysis of real-time PCR data")
31299 "This is a package for model fitting, optimal model selection and
31300 calculation of various features that are essential in the analysis of
31301 quantitative real-time polymerase chain reaction (qPCR).")
31302 (license license:gpl2+)))
31304 (define-public r-textplot
31306 (name "r-textplot")
31311 (uri (cran-uri "textplot" version))
31314 "10nxh9axhy6kyp6f3rz7smq08yl35ydx9jx47bs7i0bmcl2kwxvl"))))
31315 (properties `((upstream-name . "textplot")))
31316 (build-system r-build-system)
31318 (list r-data-table r-lattice r-matrix))
31319 (native-inputs (list r-knitr))
31320 (home-page "https://github.com/bnosac/textplot")
31321 (synopsis "Text Plots")
31323 "Visualise complex relations in texts. This is done by providing
31324 functionalities for displaying text co-occurrence networks, text correlation
31325 networks, dependency relationships as well as text clustering. Feel free to
31326 join the effort of providing interesting text visualisations.")
31327 (license license:gpl2)))
31329 (define-public r-gsa
31336 (uri (cran-uri "GSA" version))
31339 "1f1mrxxdbdlnibgav6nsvbpniz2x3km2svc0hf43spb4zicn0z8p"))))
31340 (properties `((upstream-name . "GSA")))
31341 (build-system r-build-system)
31342 (home-page "https://statweb.stanford.edu/~tibs/GSA/")
31343 (synopsis "Gene set analysis")
31344 (description "This package lets you determine the significance of
31345 pre-defined sets of genes with respect to an outcome variable, such as a group
31346 indicator, a quantitative variable or a survival time.")
31347 ;; Any version of the LGPL
31348 (license license:lgpl3+)))
31350 (define-public r-randomforestsrc
31352 (name "r-randomforestsrc")
31357 (uri (cran-uri "randomForestSRC" version))
31360 "05ifvj49jv0n5p6k46milpgj9r10sc5aw23fypyyibdgwpwvwixw"))))
31362 `((upstream-name . "randomForestSRC")))
31363 (build-system r-build-system)
31364 (home-page "https://cran.r-project.org/web/packages/randomForestSRC/")
31365 (synopsis "Random forests for survival, regression, and classification")
31367 "This package implements fast OpenMP parallel computing of Breiman's
31368 random forests for survival, competing risks, regression and classification
31369 based on Ishwaran and Kogalur's popular random survival forests (RSF) package.
31370 It handles missing data and now includes multivariate, unsupervised forests,
31371 quantile regression and solutions for class imbalanced data. It provides a
31372 fast interface using subsampling and confidence regions for variable
31374 (license license:gpl3+)))
31376 (define-public r-contfrac
31378 (name "r-contfrac")
31383 (uri (cran-uri "contfrac" version))
31386 "0sq5c7ny235yrkv2xc4insgxby6rvzc1qsj8h301cd2if3lwbgwm"))))
31387 (properties `((upstream-name . "contfrac")))
31388 (build-system r-build-system)
31390 "https://github.com/RobinHankin/contfrac")
31391 (synopsis "Continued Fractions")
31393 "Various utilities for evaluating continued fractions.")
31394 (license license:gpl2)))
31396 (define-public r-elliptic
31398 (name "r-elliptic")
31403 (uri (cran-uri "elliptic" version))
31406 "1dhba0yfxjd5rlqsxp5a7s2hclfkla9wigsr39dlma67l6qjjmxn"))))
31407 (properties `((upstream-name . "elliptic")))
31408 (build-system r-build-system)
31409 (inputs (list pari-gp))
31410 (propagated-inputs (list r-mass))
31412 "https://github.com/RobinHankin/elliptic")
31414 "Weierstrass and Jacobi Elliptic Functions")
31416 "A suite of elliptic and related functions including Weierstrass and
31417 Jacobi forms. Also includes various tools for manipulating and visualizing
31418 complex functions.")
31419 (license license:gpl2)))
31421 (define-public r-hypergeo
31423 (name "r-hypergeo")
31428 (uri (cran-uri "hypergeo" version))
31431 "13jdiy216znwhr91iqnh03mvkmyscw439syb3h4i67dd78sphnvd"))))
31432 (properties `((upstream-name . "hypergeo")))
31433 (build-system r-build-system)
31435 (list r-contfrac r-desolve r-elliptic))
31437 "https://cran.r-project.org/web/packages/hypergeo/")
31438 (synopsis "The Gauss Hypergeometric Function")
31440 "The Gaussian hypergeometric function for complex numbers.")
31441 (license license:gpl2)))
31443 (define-public r-gganimate
31445 (name "r-gganimate")
31450 (uri (cran-uri "gganimate" version))
31453 "046v6j92xxgaghsnh88dy5h8x040qsfa8csvhp4dmsfmrrf0dz0f"))))
31454 (properties `((upstream-name . "gganimate")))
31455 (build-system r-build-system)
31458 (modify-phases %standard-phases
31459 (add-after 'unpack 'absolute-paths
31460 (lambda* (#:key inputs #:allow-other-keys)
31461 (substitute* "R/renderers.R"
31463 (string-append "'" (assoc-ref inputs "ffmpeg") "/bin/ffmpeg'"))))))))
31465 ;; For video output.
31476 ;; For GIF/SVG output. gifski is faster, but depends on Rust.
31478 ;; For HTML output.
31481 (native-inputs (list r-knitr))
31482 (home-page "https://gganimate.com")
31483 (synopsis "Grammar of Animated Graphics")
31485 "This package extends the grammar of graphics as implemented by
31486 @code{ggplot2} to include the description of animation. It does this by
31487 providing a range of new grammar classes that can be added to the plot object
31488 in order to customise how it should change with time.")
31489 (license license:expat)))
31491 ;; This library bundles ‘date’ from (gnu packages calendar). We cannot unbundle
31492 ;; it, because its C++ libtz.so is built with different compiler flags than
31494 (define-public r-tzdb
31501 (uri (cran-uri "tzdb" version))
31504 "0f3h4zaf9f4l371k6nc1mq6z2f9aj1vaf2inni8jnsds3zng16b0"))))
31505 (properties `((upstream-name . "tzdb")))
31506 (build-system r-build-system)
31507 (propagated-inputs (list r-cpp11))
31508 (home-page "https://github.com/r-lib/tzdb")
31509 (synopsis "Time Zone Database Information")
31511 "This package provides an up-to-date copy of the Internet Assigned
31512 Numbers Authority (IANA) Time Zone Database. It is updated periodically to
31513 reflect changes made by political bodies to time zone boundaries, UTC offsets,
31514 and daylight saving time rules. Additionally, this package provides a C++
31515 interface for working with the @code{date} library. @code{date} provides
31516 comprehensive support for working with dates and date-times, which this package
31517 exposes to make it easier for other R packages to utilize. Headers are
31518 provided for calendar specific calculations, along with a limited interface for
31519 time zone manipulations.")
31520 (license license:expat)))
31522 (define-public r-vroom
31529 (uri (cran-uri "vroom" version))
31532 "1plz20x6s01gkkcac51lhx4r2s024pgh778ri7y25hkiiwacp1yh"))))
31533 (properties `((upstream-name . "vroom")))
31534 (build-system r-build-system)
31550 (native-inputs (list r-knitr))
31551 (home-page "https://vroom.r-lib.org")
31553 "Read and Write Rectangular Text Data")
31555 "This package reads and writes data files like @acronym{CSV},
31556 @acronym{TSV} and @acronym{FWF}. When reading it uses a quick initial indexing
31557 step, then reads the values lazily, so only the data you actually use needs to
31558 be read. The writer formats the data in parallel and writes to disk
31559 asynchronously from formatting.")
31560 (license license:expat)))
31562 (define-public r-rmisc
31568 (uri (cran-uri "Rmisc" version))
31571 "1h6jb0xwkyhm9lwm7nj9bhrb5dhrsifvkpqkrd594j1lz74dar8x"))))
31572 (build-system r-build-system)
31574 (list r-plyr r-lattice))
31575 (home-page "https://cran.r-project.org/web/packages/Rmisc/")
31576 (synopsis "Ryan Miscellaneous")
31577 (description "The Rmisc library contains functions for data analysis and
31578 utility operations.")
31579 (license license:gpl3)))
31581 (define-public r-webutils
31583 (name "r-webutils")
31588 (uri (cran-uri "webutils" version))
31590 (base32 "16a6ds0fnb6y8i1r9ba1hf1ydb53am57s070b3hi5jmrs84b9qik"))))
31591 (properties `((upstream-name . "webutils")))
31592 (build-system r-build-system)
31594 (list r-curl r-jsonlite))
31595 (home-page "https://github.com/jeroen/webutils")
31596 (synopsis "Utility functions for developing web applications")
31598 "This package parses HTTP request data in @code{application/json},
31599 @code{multipart/form-data}, or @code{application/x-www-form-urlencoded}
31600 format. It includes an example of hosting and parsing HTML form data in R
31601 using either @code{httpuv} or @code{Rhttpd}.")
31602 (license license:expat)))
31604 (define-public r-protolite
31606 (name "r-protolite")
31611 (uri (cran-uri "protolite" version))
31613 (base32 "0g1r3lzmvx1w44qzqzdvxfn21zmz11srlp6cr76kd7pd5wzjv82p"))))
31614 (properties `((upstream-name . "protolite")))
31615 (build-system r-build-system)
31619 (list r-jsonlite r-rcpp))
31621 (list protobuf pkg-config))
31622 (home-page "https://github.com/jeroen/protolite")
31623 (synopsis "Highly optimized protocol buffer serializers")
31625 "This package provides pure C++ implementations for reading and writing
31626 several common data formats based on Google protocol-buffers. It currently
31627 supports @code{rexp.proto} for serialized R objects, @code{geobuf.proto} for
31628 binary geojson, and @code{mvt.proto} for vector tiles. This package uses the
31629 auto-generated C++ code by protobuf-compiler, hence the entire serialization
31630 is optimized at compile time. The @code{RProtoBuf} package on the other hand
31631 uses the protobuf runtime library to provide a general-purpose toolkit for
31632 reading and writing arbitrary protocol-buffer data in R.")
31633 (license license:expat)))
31635 (define-public r-opencpu
31642 (uri (cran-uri "opencpu" version))
31644 (base32 "1h0s7fbifyf4h1296sdk3amij0m6s12wq32mbky7xg4nz8wj29ni"))))
31645 (properties `((upstream-name . "opencpu")))
31646 (build-system r-build-system)
31666 (home-page "https://www.opencpu.org")
31667 (synopsis "API for embedded scientific computing")
31669 "This package provides a system for embedded scientific computing and
31670 reproducible research with R. The OpenCPU server exposes a simple but
31671 powerful HTTP API for RPC and data interchange with R. This provides a
31672 reliable and scalable foundation for statistical services or building R web
31673 applications. The OpenCPU server runs either as a single-user development
31674 server within the interactive R session, or as a multi-user stack based on
31676 (license license:asl2.0)))
31678 (define-public r-exactextractr
31680 (name "r-exactextractr")
31685 (uri (cran-uri "exactextractr" version))
31688 "0x4axrq9iznvajqy07gcfcrvzniz5yj6wabchgksg0fqz0xancnc"))))
31689 (properties `((upstream-name . "exactextractr")))
31690 (build-system r-build-system)
31691 (inputs (list geos))
31693 (list r-raster r-rcpp r-sf))
31696 (home-page "https://isciences.gitlab.io/exactextractr/")
31697 (synopsis "Fast extraction from raster datasets using polygons")
31699 "This package provides a replacement for the @code{extract} function from
31700 the @code{raster} package that is suitable for extracting raster values using
31701 @code{sf} polygons.")
31702 (license license:asl2.0)))
31704 (define-public r-stringfish
31706 (name "r-stringfish")
31711 (uri (cran-uri "stringfish" version))
31714 "0ddpsi7z0kzqgbq9y646pk9afclq0r7ak22zsdh0i93ni0x71c9l"))))
31715 (properties `((upstream-name . "stringfish")))
31716 (build-system r-build-system)
31718 (list r-rcpp r-rcppparallel))
31720 (list pkg-config r-knitr))
31721 (home-page "https://github.com/traversc/stringfish")
31722 (synopsis "Alternative string implementation")
31724 "This package provides an extendable, performant and multithreaded
31725 @code{alt-string} implementation backed by C++ vectors and strings.")
31726 (license license:gpl3)))
31728 (define-public r-rapiserialize
31730 (name "r-rapiserialize")
31735 (uri (cran-uri "RApiSerialize" version))
31738 "0gm2j8kh40imhncwwx1sx9kmraaxcxycvgwls53lcyy2ap344k9j"))))
31739 (properties `((upstream-name . "RApiSerialize")))
31740 (build-system r-build-system)
31742 "https://cran.r-project.org/package=RApiSerialize")
31743 (synopsis "R API serialization")
31745 "This package provides other packages with access to the internal R
31746 serialization code. Access to this code is provided at the C function level
31747 by using the registration of native function mechanism. Client packages
31748 simply include a single header file RApiSerializeAPI.h provided by this
31750 (license license:gpl2+)))
31752 (define-public r-qs
31759 (uri (cran-uri "qs" version))
31762 "0sxy497v5arjv6lwxng7chkbzrn703waqmgsxv77i7y12ahzdbai"))))
31763 (properties `((upstream-name . "qs")))
31764 (build-system r-build-system)
31765 (inputs (list zlib))
31767 (list r-rapiserialize r-rcpp r-stringfish))
31769 (list pkg-config r-knitr))
31770 (home-page "https://github.com/traversc/qs")
31771 (synopsis "Quick serialization of R objects")
31773 "This package provides functions for quickly writing and reading any R
31774 object to and from disk.")
31775 (license license:gpl3)))
31777 (define-public r-rgeos
31784 (uri (cran-uri "rgeos" version))
31787 "1m73y0nwrdwsjrl48c4fg1kdqnh79835brnmxv9ak01ndbzcp45b"))))
31788 (properties `((upstream-name . "rgeos")))
31789 (build-system r-build-system)
31794 (home-page "https://cran.r-project.org/package=rgeos")
31795 (synopsis "Interface to Geometry Engine (GEOS)")
31797 "This package provides an R interface to Geometry Engine (GEOS) using the
31798 C API for topology operations on geometries.")
31799 (license license:gpl2+)))
31801 (define-public r-tfruns
31808 (uri (cran-uri "tfruns" version))
31811 "04lfckg1if3kfwcl4s4fcc9aw04crwk4m1qr55ag22j2x2jlb2l9"))))
31812 (properties `((upstream-name . "tfruns")))
31813 (build-system r-build-system)
31825 (native-inputs (list r-knitr))
31826 (home-page "https://github.com/rstudio/tfruns")
31827 (synopsis "Training run tools for TensorFlow")
31829 "Create and manage unique directories for each TensorFlow training run.
31830 This package provides a unique, time stamped directory for each run along with
31831 functions to retrieve the directory of the latest run or latest several
31833 (license license:asl2.0)))
31835 (define-public r-tfautograph
31837 (name "r-tfautograph")
31842 (uri (cran-uri "tfautograph" version))
31845 "0fmaq1ggjyxgf2ss7qb8jk74sfwc3s1vc123pd5glclxcy1ib0j2"))))
31846 (properties `((upstream-name . "tfautograph")))
31847 (build-system r-build-system)
31848 (inputs (list tensorflow))
31850 (list r-backports r-reticulate))
31851 (home-page "https://t-kalinowski.github.io/tfautograph/")
31852 (synopsis "Autograph R for Tensorflow")
31854 "This package lets you translate R control flow expressions into
31855 Tensorflow graphs.")
31856 (license license:gpl3)))
31858 (define-public r-tensorflow
31860 (name "r-tensorflow")
31865 (uri (cran-uri "tensorflow" version))
31868 "12c6ndxx4g6fqjakpzp9pgl29ghswhqyr6q9jahpk0cawizh2znj"))))
31869 (properties `((upstream-name . "tensorflow")))
31870 (build-system r-build-system)
31871 (inputs (list tensorflow))
31880 (home-page "https://github.com/rstudio/tensorflow")
31881 (synopsis "R interface to TensorFlow")
31883 "R interface to TensorFlow a library for numerical computation using data
31884 flow graphs. Nodes in the graph represent mathematical operations, while the
31885 graph edges represent the multidimensional data arrays (tensors) communicated
31887 (license license:asl2.0)))
31889 (define-public r-keras
31896 (uri (cran-uri "keras" version))
31899 "06513d1fp7cxk4v03xm9lhgj6xmp9dqqvw3lnzwbzjwdkfj948yc"))))
31900 (properties `((upstream-name . "keras")))
31901 (build-system r-build-system)
31913 (native-inputs (list r-knitr))
31914 (home-page "https://keras.rstudio.com")
31915 (synopsis "R Interface to 'Keras'")
31917 "This package provides an interface to Keras, a high-level neural
31918 networks API. Keras was developed with a focus on enabling fast
31919 experimentation, supports both convolution based networks and recurrent
31920 networks (as well as combinations of the two), and runs seamlessly on both CPU
31922 (license license:expat)))
31924 (define-public r-zzlite
31931 (uri (cran-uri "zzlite" version))
31934 "0vi1slx2s4r5zf82lazqv0c3m12xq73wlgsbz6af4y00h0bkr3ps"))))
31935 (properties `((upstream-name . "zzlite")))
31936 (build-system r-build-system)
31938 (list r-httr r-jsonlite))
31941 (home-page "https://cran.r-project.org/package=zzlite")
31942 (synopsis "Wrapper for the Zamzar file conversion API")
31944 "This package provides a minor collection of HTTP wrappers for the Zamzar
31945 file conversion API. The wrappers makes it easy to utilize the API and thus
31946 convert between more than 100 different file formats (ranging from audio
31947 files, images, movie formats, etc., etc.) through an R session.")
31948 (license license:gpl3)))
31950 (define-public r-ztree
31957 (uri (cran-uri "zTree" version))
31960 "005zk6wpchpss6865ki35yawgf668pn70163ah97rnfkhfaswm6y"))))
31961 (properties `((upstream-name . "zTree")))
31962 (build-system r-build-system)
31965 (home-page "https://cran.r-project.org/package=zTree")
31966 (synopsis "Functions to import data from z-Tree into R")
31968 "This package provides tools for reading @code{.xls} and @code{.sbj}
31969 files which are written by the proprietary program z-Tree for developing and
31970 carrying out economic experiments.")
31971 (license license:gpl3)))
31973 (define-public r-distributionutils
31975 (name "r-distributionutils")
31980 (uri (cran-uri "DistributionUtils" version))
31983 "08vq54pyqxlqsj6q6gsg5ikqa0z3x842j52ld5dxaq272p6xchvl"))))
31985 `((upstream-name . "DistributionUtils")))
31986 (build-system r-build-system)
31989 (home-page "https://cran.r-project.org/package=DistributionUtils")
31990 (synopsis "Distribution utilities")
31992 "This package provides utilities for dealing with distributions.
31993 Functionality includes sample skewness and kurtosis, log-histogram, tail
31994 plots, moments by integration, changing the point about which a moment is
31995 calculated, functions for testing distributions using inversion tests and the
31996 Massart inequality. Also included is an implementation of the incomplete
31997 Bessel K function.")
31998 (license license:gpl2+)))
32000 (define-public r-ztpln
32007 (uri (cran-uri "ztpln" version))
32010 "1b22m72a8117yrgq5k1gzsrbx6yrsrj7bpd49lh7x3vbaz56c0wr"))))
32011 (properties `((upstream-name . "ztpln")))
32012 (build-system r-build-system)
32014 (list r-distributionutils r-mixtools r-rcpp r-rcppeigen
32018 (home-page "https://github.com/mattocci27/ztpln")
32019 (synopsis "Zero-truncated Poisson lognormal distribution")
32021 "This package provides functions for obtaining the density, random
32022 variates and maximum likelihood estimates of the Zero-truncated Poisson
32023 lognormal distribution and their mixture distribution.")
32024 (license license:expat)))
32026 (define-public r-zscorer
32033 (uri (cran-uri "zscorer" version))
32036 "0aijhs0fyird5gq68x4dxchb02mxa7ijk10k9zjhngghxbjj7iqn"))))
32037 (properties `((upstream-name . "zscorer")))
32038 (build-system r-build-system)
32043 (home-page "https://github.com/nutriverse/zscorer")
32044 (synopsis "Child Anthropometry z-Score Calculator")
32046 "This package provides a tool for calculating z-scores and centiles for
32047 weight-for-age, length/height-for-age, weight-for-length/height, BMI-for-age,
32048 head circumference-for-age, age circumference-for-age, subscapular
32049 skinfold-for-age, triceps skinfold-for-age based on the WHO Child Growth
32051 (license license:agpl3+)))
32053 (define-public r-zra
32060 (uri (cran-uri "ZRA" version))
32063 "1sx1q5yf68hhlb5j1hicpj594rmgajqr25llg7ax416j0m2rnagi"))))
32064 (properties `((upstream-name . "ZRA")))
32065 (build-system r-build-system)
32067 (list r-dygraphs r-forecast))
32068 (home-page "https://cran.r-project.org/package=ZRA")
32069 (synopsis "Dynamic plots for time series forecasting")
32071 "This package combines a forecast of a time series, using the function @code{forecast},
32072 with the dynamic plots from @code{dygraphs}.")
32073 (license license:gpl2+)))
32075 (define-public r-rfigshare
32077 (name "r-rfigshare")
32082 (uri (cran-uri "rfigshare" version))
32085 "10shwl1y9220m7ld5w9fjsjzy5yg8myrz9cz97ps9z2bw7bvka5j"))))
32086 (properties `((upstream-name . "rfigshare")))
32087 (build-system r-build-system)
32097 (home-page "https://github.com/ropensci/rfigshare")
32098 (synopsis "R Interface to figshare")
32100 "This package provides an interface to figshare, a scientific repository
32101 to archive and assign DOIs to data, software, figures, and more.")
32102 (license license:cc0)))
32104 (define-public r-dismo
32111 (uri (cran-uri "dismo" version))
32114 "1rqf6h4imbqvs7hjd1k4my6154wg0qnmnp5byan403rcshr1jbl1"))))
32115 (properties `((upstream-name . "dismo")))
32116 (build-system r-build-system)
32118 (list r-raster r-rcpp r-sp r-terra))
32119 (home-page "https://rspatial.org/raster/sdm/")
32120 (synopsis "Species distribution modeling")
32122 "This package provides methods for species distribution modeling, i.e.,
32123 predicting the environmental similarity of any site to that of the locations
32124 of known occurrences of a species.")
32125 (license license:gpl3+)))
32127 (define-public r-zoon
32134 (uri (cran-uri "zoon" version))
32137 "02y29vr2yn8al69km8faiqrwjrc1r3hsvw3dg8lwjr65cxw1krip"))))
32138 (properties `((upstream-name . "zoon")))
32139 (build-system r-build-system)
32154 (home-page "https://github.com/zoonproject/zoon")
32155 (synopsis "Reproducible, accessible and shareable species distribution modelling")
32157 "This package reads user submitted modules from an online repository,
32158 runs full species distribution modelling workflows and returns output that is
32159 fully reproducible.")
32160 (license license:bsd-3)))
32162 (define-public r-paws-common
32164 (name "r-paws-common")
32169 (uri (cran-uri "paws.common" version))
32172 "1dg18hwnrjd6m1vjcxfs2vm1zxciivf4vzhq0z76dmmiqz2yjm28"))))
32173 (properties `((upstream-name . "paws.common")))
32174 (build-system r-build-system)
32176 (list r-base64enc r-digest r-httr r-jsonlite r-xml2))
32177 (home-page "https://cran.r-project.org/package=paws.common")
32178 (synopsis "Paws low-level Amazon Web Services API")
32180 "This package provides functions for making low-level API requests to
32181 Amazon Web Services. The functions handle building, signing, and sending
32182 requests, and receiving responses. They are designed to help build
32183 higher-level interfaces to individual services, such as Simple Storage
32185 (license license:asl2.0)))
32187 (define-public r-paws-customer-engagement
32189 (name "r-paws-customer-engagement")
32194 (uri (cran-uri "paws.customer.engagement" version))
32197 "0ac6hzn4ilfjhzdmc9x80999fl18cz16mky31qd3y09m93w2xkdj"))))
32199 `((upstream-name . "paws.customer.engagement")))
32200 (build-system r-build-system)
32202 (list r-paws-common))
32203 (home-page "https://github.com/paws-r/paws")
32204 (synopsis "Amazon Web Services customer engagement services")
32206 "This package provides an interface to Amazon Web Services customer
32207 engagement services, including Simple Email Service, Connect contact center
32208 service, and more.")
32209 (license license:asl2.0)))
32211 (define-public r-paws-cost-management
32213 (name "r-paws-cost-management")
32218 (uri (cran-uri "paws.cost.management" version))
32221 "0in4f8ygw5g2v6vl3lz2y0v51llglh8b1ymbd04d54xxlgn83knh"))))
32223 `((upstream-name . "paws.cost.management")))
32224 (build-system r-build-system)
32226 (list r-paws-common))
32227 (home-page "https://github.com/paws-r/paws")
32228 (synopsis "Amazon Web Services cost management services")
32230 "This package provides an interface to Amazon Web Services cost
32231 management services, including cost and usage reports, budgets, pricing, and
32233 (license license:asl2.0)))
32235 (define-public r-paws-developer-tools
32237 (name "r-paws-developer-tools")
32242 (uri (cran-uri "paws.developer.tools" version))
32244 (base32 "16gb8g8s67al7qdd95fbigxqkih9a9p7slkyf3cga42wb6miiby2"))))
32245 (properties `((upstream-name . "paws.developer.tools")))
32246 (build-system r-build-system)
32248 (list r-paws-common))
32249 (home-page "https://github.com/paws-r/paws")
32250 (synopsis "Amazon Web Services developer tools services")
32252 "This package provides an interface to Amazon Web Services developer
32253 tools services, including version control, continuous integration and
32254 deployment, and more.")
32255 (license license:asl2.0)))
32257 (define-public r-paws-end-user-computing
32259 (name "r-paws-end-user-computing")
32264 (uri (cran-uri "paws.end.user.computing" version))
32266 (base32 "1xxsz86nx128sizym9np8vldzkbym0p3i6vcy94kq1y0cylaicv3"))))
32267 (properties `((upstream-name . "paws.end.user.computing")))
32268 (build-system r-build-system)
32270 (list r-paws-common))
32271 (home-page "https://github.com/paws-r/paws")
32272 (synopsis "Amazon Web Services end user computing services")
32274 "This package provides an interface to Amazon Web Services end user
32275 computing services, including collaborative document editing, mobile intranet,
32277 (license license:asl2.0)))
32279 (define-public r-paws-application-integration
32281 (name "r-paws-application-integration")
32286 (uri (cran-uri "paws.application.integration" version))
32289 "0llyd9hc679pad1ih0rcc38q5xxpzinhwrl8cvrkgsjgbc3agq42"))))
32291 `((upstream-name . "paws.application.integration")))
32292 (build-system r-build-system)
32294 (list r-paws-common))
32295 (home-page "https://github.com/paws-r/paws")
32296 (synopsis "Amazon Web Services application integration services")
32298 "This package provides an interface to Amazon Web Services application
32299 integration services, including Simple Queue Service (SQS) message queue,
32300 Simple Notification Service (SNS) publish/subscribe messaging, and more.")
32301 (license license:asl2.0)))
32303 (define-public r-paws-security-identity
32305 (name "r-paws-security-identity")
32310 (uri (cran-uri "paws.security.identity" version))
32313 "092lz2ipn5iqr593x7ra8c0bj64yf6315mdc3llgwrjyb4vfxif9"))))
32315 `((upstream-name . "paws.security.identity")))
32316 (build-system r-build-system)
32318 (list r-paws-common))
32319 (home-page "https://github.com/paws-r/paws")
32320 (synopsis "Amazon Web Services security, identity, and compliance services")
32322 "This package provides an interface to Amazon Web Services security,
32323 identity, and compliance services, including the Identity and Access
32324 Management (IAM) service for managing access to services and resources, and
32326 (license license:asl2.0)))
32328 (define-public r-paws-analytics
32330 (name "r-paws-analytics")
32335 (uri (cran-uri "paws.analytics" version))
32338 "04gnaxmj21l312xkrsd9bisi0bz9h6h5fyhwlqylcxi077z1yb2g"))))
32340 `((upstream-name . "paws.analytics")))
32341 (build-system r-build-system)
32343 (list r-paws-common))
32344 (home-page "https://github.com/paws-r/paws")
32345 (synopsis "Amazon Web Services analytics services")
32347 "This package provides an interface to Amazon Web Services analytics
32348 services, including Elastic MapReduce Hadoop and Spark big data service,
32349 Elasticsearch search engine, and more.")
32350 (license license:asl2.0)))
32352 (define-public r-paws-machine-learning
32354 (name "r-paws-machine-learning")
32359 (uri (cran-uri "paws.machine.learning" version))
32362 "01w2y5952pk50xjbzby2pc51xrkrzjpfxbmii1b10cl2xgzfkxsa"))))
32364 `((upstream-name . "paws.machine.learning")))
32365 (build-system r-build-system)
32367 (list r-paws-common))
32368 (home-page "https://github.com/paws-r/paws")
32369 (synopsis "Amazon Web Services machine learning services")
32371 "This package provides an interface to Amazon Web Services machine
32372 learning services, including SageMaker managed machine learning service,
32373 natural language processing, speech recognition, translation, and more.")
32374 (license license:asl2.0)))
32376 (define-public r-paws-management
32378 (name "r-paws-management")
32383 (uri (cran-uri "paws.management" version))
32386 "09k7wg0jlj40zs2yb3vldffpkdcjg7ap98n7c5lxr5plpca08swg"))))
32388 `((upstream-name . "paws.management")))
32389 (build-system r-build-system)
32391 (list r-paws-common))
32392 (home-page "https://github.com/paws-r/paws")
32393 (synopsis "Amazon Web Services management and governance services")
32395 "This package provides an interface to Amazon Web Services management and
32396 governance services, including CloudWatch application and infrastructure
32397 monitoring, Auto Scaling for automatically scaling resources, and more.")
32398 (license license:asl2.0)))
32400 (define-public r-paws-networking
32402 (name "r-paws-networking")
32407 (uri (cran-uri "paws.networking" version))
32410 "02hxaa5nlj70mdggh379ij3fn09xm8h5ldzsyf45c342prpl6zwj"))))
32412 `((upstream-name . "paws.networking")))
32413 (build-system r-build-system)
32415 (list r-paws-common))
32416 (home-page "https://github.com/paws-r/paws")
32417 (synopsis "Amazon Web Services networking and content delivery services")
32419 "This package provides an interface to Amazon Web Services networking and
32420 content delivery services, including Route 53 Domain Name System service,
32421 CloudFront content delivery, load balancing, and more.")
32422 (license license:asl2.0)))
32424 (define-public r-paws-database
32426 (name "r-paws-database")
32431 (uri (cran-uri "paws.database" version))
32434 "08jpwz95fw3f68j0wxh2lg57nn60khflldab0ryhkkbcw1iy0qyz"))))
32435 (properties `((upstream-name . "paws.database")))
32436 (build-system r-build-system)
32438 (list r-paws-common))
32439 (home-page "https://github.com/paws-r/paws")
32441 "Amazon Web Services Database Services")
32443 "This package provides an interface to Amazon Web Services database
32444 services, including Relational Database Service (RDS), DynamoDB NoSQL
32445 database, and more.")
32446 (license license:asl2.0)))
32448 (define-public r-paws-storage
32450 (name "r-paws-storage")
32455 (uri (cran-uri "paws.storage" version))
32458 "06m887vpqp5d6k3zxdlga599dsv8v3rladk7xqaxqnld1f17am04"))))
32459 (properties `((upstream-name . "paws.storage")))
32460 (build-system r-build-system)
32462 (list r-paws-common))
32463 (home-page "https://github.com/paws-r/paws")
32464 (synopsis "Amazon Web Services storage services")
32466 "This package provides an interface to Amazon Web Services storage
32467 services, including Simple Storage Service (S3).")
32468 (license license:asl2.0)))
32470 (define-public r-paws-compute
32472 (name "r-paws-compute")
32477 (uri (cran-uri "paws.compute" version))
32480 "1km6fng6il5fcjlrbbndahsw2dr2ql83hwac9wlpd67zm3wy9lky"))))
32481 (properties `((upstream-name . "paws.compute")))
32482 (build-system r-build-system)
32484 (list r-paws-common))
32485 (home-page "https://github.com/paws-r/paws")
32486 (synopsis "Amazon Web Services compute services")
32488 "This package provides an interface to Amazon Web Services compute
32489 services, including Elastic Compute Cloud (EC2), Lambda
32490 functions-as-a-service, containers, batch processing, and more.")
32491 (license license:asl2.0)))
32493 (define-public r-paws
32500 (uri (cran-uri "paws" version))
32503 "0kn1z045r106fwqcaz52hb02bhrcblh479cajfjiq480s1iljcw6"))))
32504 (properties `((upstream-name . "paws")))
32505 (build-system r-build-system)
32507 (list r-paws-analytics
32508 r-paws-application-integration
32510 r-paws-cost-management
32511 r-paws-customer-engagement
32513 r-paws-developer-tools
32514 r-paws-end-user-computing
32515 r-paws-machine-learning
32518 r-paws-security-identity
32520 (home-page "https://github.com/paws-r/paws")
32521 (synopsis "Amazon Web Services software development kit")
32523 "This package provides an interface to Amazon Web Services, including
32524 storage, database, and compute services, such as Simple Storage Service (S3),
32525 DynamoDB NoSQL database, and Lambda functions-as-a-service.")
32526 (license license:asl2.0)))
32528 (define-public r-zoomgroupstats
32530 (name "r-zoomgroupstats")
32535 (uri (cran-uri "zoomGroupStats" version))
32538 "0gndiq92cy6gi7f833hdjvqii3cn83wz5rjvygcvjl3dw4pwv966"))))
32540 `((upstream-name . "zoomGroupStats")))
32541 (build-system r-build-system)
32552 (native-inputs (list r-knitr))
32553 (home-page "http://zoomgroupstats.org")
32554 (synopsis "Analyze text, audio, and video from Zoom meetings")
32556 "This package provides utilities for processing and analyzing the files
32557 that are exported from a recorded Zoom meeting. This includes analyzing data
32558 captured through video cameras and microphones, the text-based chat, and
32559 meta-data. You can analyze aspects of the conversation among meeting
32560 participants and their emotional expressions throughout the meeting.")
32561 (license license:expat)))
32563 (define-public r-zoom
32570 (uri (cran-uri "zoom" version))
32573 "03f5rxfr6ncf1j6vpn7pip21q7ylj4bx0a5xphqb6x6i33lxf1g5"))))
32574 (properties `((upstream-name . "zoom")))
32575 (build-system r-build-system)
32576 (home-page "https://github.com/cbarbu/R-package-zoom")
32577 (synopsis "Spatial data visualization tool")
32579 "This package provides @code{zm}, a utility that allows you to
32580 zoom/navigate any plot when called with any active plot.")
32581 (license license:gpl3+)))
32583 (define-public r-zoolog
32590 (uri (cran-uri "zoolog" version))
32593 "00fi7czfwr0ll9070w3ijskd0xvilj02gy8wkgqzzrlilij8ah7p"))))
32594 (properties `((upstream-name . "zoolog")))
32595 (build-system r-build-system)
32597 (list r-rdpack r-stringi))
32600 (home-page "https://josempozo.github.io/zoolog/")
32601 (synopsis "Zooarchaeological analysis with log-ratios")
32603 "This package includes functions and reference data to generate and
32604 manipulate log-ratios (also known as @dfn{log size index} (LSI) values) from
32605 measurements obtained on zooarchaeological material. Log ratios are used to
32606 compare the relative (rather than the absolute) dimensions of animals from
32607 archaeological contexts. The zoolog package is also able to seamlessly
32608 integrate data and references with heterogeneous nomenclature, which is
32609 internally managed by a zoolog thesaurus.")
32610 (license license:gpl3)))
32612 (define-public r-filehash
32614 (name "r-filehash")
32619 (uri (cran-uri "filehash" version))
32622 "1ga17smgjd4qsnf5a7qk0giwhpc5969ylqj520favs1k6b4y557k"))))
32623 (properties `((upstream-name . "filehash")))
32624 (build-system r-build-system)
32625 (home-page "http://github.com/rdpeng/filehash")
32626 (synopsis "Simple key-value database")
32628 "This package implements a simple key-value style database where
32629 character string keys are associated with data values that are stored on the
32630 disk. A simple interface is provided for inserting, retrieving, and deleting
32631 data from the database. Utilities are provided that allow filehash databases
32632 to be treated much like environments and lists are already used in R. These
32633 utilities are provided to encourage interactive and exploratory analysis on
32635 (license license:gpl2+)))
32637 (define-public r-mlearning
32639 (name "r-mlearning")
32644 (uri (cran-uri "mlearning" version))
32647 "1zjnh4gcw068li1bks60gazn3205xhmqz67hbkb1san33lmlxya3"))))
32648 (properties `((upstream-name . "mlearning")))
32649 (build-system r-build-system)
32657 (home-page "http://www.sciviews.org/zooimage")
32658 (synopsis "Machine learning algorithms with unified interface")
32660 "This package provides a unified interface to various machine learning
32661 algorithms. Confusion matrices are provided too.")
32662 (license license:gpl2+)))
32664 (define-public r-zooimage
32666 (name "r-zooimage")
32671 (uri (cran-uri "zooimage" version))
32674 "0ck8w0zb9l1n9xvjwqshq9q9l8pigy3yslq2hnfbgcwk17kk9mp8"))))
32675 (properties `((upstream-name . "zooimage")))
32676 (build-system r-build-system)
32690 (home-page "http://www.sciviews.org/zooimage")
32691 (synopsis "Analysis of numerical plankton images")
32693 "This package provides a solution for analyzing digital images of
32694 plankton. In combination with ImageJ, an image analysis system, it processes
32695 digital images, measures individuals, trains for automatic classification of
32696 taxa, and finally, measures plankton samples (abundances, total and partial
32697 size spectra or biomasses, etc.).")
32698 (license license:gpl2+)))
32700 (define-public r-zooarch
32707 (uri (cran-uri "zooaRch" version))
32710 "0grc378xppv0303sf4flfqz5002vq5a23nzbq4bsff41rww7dihc"))))
32711 (properties `((upstream-name . "zooaRch")))
32712 (build-system r-build-system)
32713 (propagated-inputs (list r-ggplot2))
32714 (native-inputs (list r-knitr))
32716 "https://cran.r-project.org/package=zooaRch")
32718 "Analytical Tools for Zooarchaeological Data")
32720 "The analysis and inference of faunal remains recovered from
32721 archaeological sites concerns the field of zooarchaeology. The zooaRch
32722 package provides analytical tools to make inferences on zooarchaeological
32723 data. Functions in this package allow users to read, manipulate, visualize,
32724 and analyze zooarchaeological data.")
32725 (license license:gpl2+)))
32727 (define-public r-zonebuilder
32729 (name "r-zonebuilder")
32734 (uri (cran-uri "zonebuilder" version))
32737 "0mxf3dz0d6bi5wwjilqivdxhy5ypnq5svky8zygha0clv45l4dmn"))))
32738 (properties `((upstream-name . "zonebuilder")))
32739 (build-system r-build-system)
32741 (list r-rcolorbrewer r-sf))
32744 (home-page "https://github.com/zonebuilders/zonebuilder")
32745 (synopsis "Create and explore geographic zoning systems")
32747 "This package provides functions, documentation and example data to help
32748 divide geographic space into discrete polygons (zones). The functions are
32749 motivated by research into the merits of different zoning systems. A flexible
32750 @code{ClockBoard} zoning system is provided, which breaks-up space by
32751 concentric rings and radial lines emanating from a central point.")
32752 (license license:gpl3)))
32754 (define-public r-zonator
32761 (uri (cran-uri "zonator" version))
32764 "1plxchpd4ypp36phl13pi9yvlrqi3lk83lv5rldrhdqynhcgfw2k"))))
32765 (properties `((upstream-name . "zonator")))
32766 (build-system r-build-system)
32768 (list r-ggplot2 r-raster r-rcolorbrewer r-reshape2 r-rgdal))
32769 (native-inputs (list r-knitr))
32770 (home-page "https://cbig.github.io/zonator/")
32771 (synopsis "Utilities for Zonation spatial conservation prioritization")
32773 "Create new analysis setups and deal with results of Zonation
32774 conservation prioritization software.")
32775 (license license:bsd-2)))
32777 (define-public r-mmwrweek
32779 (name "r-mmwrweek")
32784 (uri (cran-uri "MMWRweek" version))
32787 "1l1ks44v52iggw9nhs56lfj6804yab5b17k8fzrc6h1kvj3vda0s"))))
32788 (properties `((upstream-name . "MMWRweek")))
32789 (build-system r-build-system)
32790 (home-page "http://wwwn.cdc.gov/nndss/document/MMWR_Week_overview.pdf")
32791 (synopsis "Convert dates to MMWR day, week, and year")
32793 "The first day of any MMWR week is Sunday. MMWR week numbering is
32794 sequential beginning with 1 and incrementing with each week to a maximum of 52
32795 or 53. MMWR week #1 of an MMWR year is the first week of the year that has at
32796 least four days in the calendar year. This package provides functionality to
32797 convert dates to MMWR day, week, and year and the reverse.")
32798 (license license:gpl2+)))
32800 (define-public r-cccd
32807 (uri (cran-uri "cccd" version))
32809 (base32 "0cxh19jqappc6zq9nz3m40ybdmsp12mf7yvflsz96wks3ly2ld4y"))))
32810 (properties `((upstream-name . "cccd")))
32811 (build-system r-build-system)
32812 (propagated-inputs (list r-deldir r-fnn r-igraph r-proxy))
32813 (home-page "https://cran.r-project.org/package=cccd")
32814 (synopsis "Class cover catch digraphs")
32816 "This package provides tools to create Class Cover Catch Digraphs,
32817 neighborhood graphs, and relatives.")
32818 (license license:gpl2+)))
32820 (define-public r-crul
32827 (uri (cran-uri "crul" version))
32830 "133g0skz4lifl8hm8pqdryd2m2drbrm6mdfzbbsrw8fg46di86my"))))
32831 (properties `((upstream-name . "crul")))
32832 (build-system r-build-system)
32840 (native-inputs (list r-knitr))
32841 (home-page "https://github.com/ropensci/crul")
32842 (synopsis "HTTP client")
32844 "This package provides a simple HTTP client, with tools for making HTTP
32845 requests, and mocking HTTP requests. The package is built on R6, and takes
32846 inspiration from Ruby's @code{faraday} gem.")
32847 (license license:expat)))
32849 (define-public r-gistr
32856 (uri (cran-uri "gistr" version))
32859 "0ac9ikrdg6i8xvlma0gizvsdva46408lk7hvsgkqirhy2ljy02hp"))))
32860 (properties `((upstream-name . "gistr")))
32861 (build-system r-build-system)
32871 (native-inputs (list r-knitr))
32872 (home-page "https://github.com/ropensci/gistr")
32873 (synopsis "Work with Gists in browser")
32875 "This package allows the user to create new Github gists, update gists
32876 with new files, rename files, delete files, get and delete gists, star and
32877 un-star them, fork them, open a gist in your default browser, get an embed
32878 code for a gist, list gist commits, and get rate limit information when
32880 (license license:expat)))
32882 (define-public r-rbokeh
32889 (uri (cran-uri "rbokeh" version))
32892 "1h2fpzqf17pw9d09r1g1iyxsj5qma4fsk8vnar7f1z4fjyypvi6q"))
32894 '(for-each delete-file '("inst/htmlwidgets/lib/bokehjs/bokeh-widgets.min.js"
32895 "inst/htmlwidgets/lib/bokehjs/bokeh.min.js")))))
32896 (properties `((upstream-name . "rbokeh")))
32897 (build-system r-build-system)
32900 (modify-phases %standard-phases
32901 (add-after 'unpack 'process-javascript
32902 (lambda* (#:key inputs #:allow-other-keys)
32903 (with-directory-excursion "inst/htmlwidgets/lib/bokehjs"
32905 `((,(assoc-ref inputs "js-bokeh-widgets")
32906 . "bokeh-widgets.min.js")
32907 (,(assoc-ref inputs "js-bokeh")
32908 . "bokeh.min.js"))))
32909 (for-each (lambda (source target)
32910 (format #true "Processing ~a --> ~a~%"
32912 (invoke "esbuild" source "--minify"
32913 (string-append "--outfile=" target)))
32915 (map cdr mapping)))))))))
32927 ;; Version 0.12.15 is mentioned in lib/htmlwidgets/rbokeh.yaml.
32929 `(("esbuild" ,esbuild)
32930 ("js-bokeh-widgets"
32933 (uri "https://unpkg.com/bokehjs@0.12.15/build/js/bokeh-widgets.js")
32936 "07v9lrkfcbdznpb10qqwi4m660zp65g85vlnfw7kn83zmkxkhhxy"))))
32940 (uri "https://unpkg.com/bokehjs@0.12.15/build/js/bokeh.js")
32943 "1pq0059aad7d2jv50nv9449p3w0gbkxkl0mhblc76m5d9qjqav2q"))))
32944 ("r-knitr" ,r-knitr)))
32945 (home-page "https://cran.r-project.org/web/packages/rbokeh/")
32946 (synopsis "R interface for the Bokeh visualization library")
32948 "This package provides a native R plotting library that provides a
32949 flexible declarative interface for creating interactive web-based graphics,
32950 backed by the @url{https://bokeh.pydata.org/, Bokeh visualization library}.")
32951 (license license:expat)))
32953 (define-public r-fauxpas
32960 (uri (cran-uri "fauxpas" version))
32963 "129fzqb7wsskbn50s8x0marr4wm8jrns6hiycqcsk166k3dnyyy8"))))
32964 (properties `((upstream-name . "fauxpas")))
32965 (build-system r-build-system)
32967 (list r-httpcode r-r6 r-whisker))
32970 (home-page "https://docs.ropensci.org/fauxpas")
32971 (synopsis "HTTP error helpers")
32973 "This package provides HTTP error helpers. Methods are included for
32974 general purpose HTTP error handling, as well as individual methods for every
32975 HTTP status code, both via status code numbers as well as their descriptive
32976 names. It supports the ability to adjust behavior to stop, message or
32977 warning. It includes the ability to use a custom whisker template to have any
32978 configuration of status code, short description, and verbose message.")
32979 (license license:expat)))
32981 (define-public r-webmockr
32983 (name "r-webmockr")
32988 (uri (cran-uri "webmockr" version))
32991 "0j40srwi0yasmllb9wsww4m6zkiyzqd549cis4dxd7c7p24hak8j"))))
32992 (properties `((upstream-name . "webmockr")))
32993 (build-system r-build-system)
33003 (home-page "https://github.com/ropensci/webmockr")
33004 (synopsis "Stubbing and setting expectations on HTTP Requests")
33006 "This is a package for stubbing and setting expectations on HTTP
33007 requests. It includes tools for stubbing HTTP requests, including expected
33008 request conditions and response conditions. You can match on HTTP method,
33009 query parameters, request body, headers and more. It can be used for unit
33010 tests or outside of a testing context.")
33011 (license license:expat)))
33013 (define-public r-iotools
33020 (uri (cran-uri "iotools" version))
33022 (base32 "07q0z0kszm1xx5hfhisfliyrcsxd8dc5mx0a2bwwnv5l1xzmix17"))))
33023 (properties `((upstream-name . "iotools")))
33024 (build-system r-build-system)
33025 (home-page "https://www.rforge.net/iotools")
33026 (synopsis "I/O tools for streaming")
33027 (description "This package provides basic I/O tools for streaming and data
33030 (license license:gpl3)))
33032 (define-public r-wordspace
33034 (name "r-wordspace")
33039 (uri (cran-uri "wordspace" version))
33041 (base32 "0hrjv5mag7gwl4wj7np248sdyns5i623wl37b11hlgalhbmlypyf"))))
33042 (properties `((upstream-name . "wordspace")))
33043 (build-system r-build-system)
33045 (list r-cluster r-iotools r-mass r-matrix r-rcpp r-sparsesvd))
33046 (native-inputs (list r-knitr))
33047 (home-page "https://wordspace.r-forge.r-project.org/")
33048 (synopsis "Distributional semantic models in R")
33050 "The wordspace package turns R into an interactive laboratory for
33051 empirical research on @dfn{distributional semantic models} (DSM). It consists
33052 of a small set of carefully designed functions, most of which
33055 @item encapsulate non-trivial R operations in a user-friendly manner or
33056 @item provide efficient and memory-lean C implementations of key operations.
33059 (license license:gpl3)))
33061 (define-public r-maxlik
33068 (uri (cran-uri "maxLik" version))
33070 (base32 "0pdigfpyiqacj2ydhpn5w1h89dz1ydk0syzs25lsgdi40sz0bvkw"))))
33071 (properties `((upstream-name . "maxLik")))
33072 (build-system r-build-system)
33073 (propagated-inputs (list r-generics r-misctools r-sandwich))
33074 (home-page "https://cran.r-project.org/package=maxLik")
33075 (synopsis "Maximum Likelihood Estimation and related tools")
33077 "This package provides functions for @dfn{Maximum Likelihood} (ML) estimation,
33078 non-linear optimization, and related tools. It includes a unified way to call
33079 different optimizers, and classes and methods to handle the results from the
33080 Maximum Likelihood viewpoint. It also includes a number of convenience tools
33081 for testing and developing your own models.")
33082 (license license:gpl2+)))
33084 (define-public r-misctools
33086 (name "r-misctools")
33091 (uri (cran-uri "miscTools" version))
33093 (base32 "16pwfxpyl0zv3hjxx2kjchkg7p6kbj0s2rrpskj7rkhjr9imlg5y"))))
33094 (properties `((upstream-name . "miscTools")))
33095 (build-system r-build-system)
33096 (propagated-inputs (list r-digest))
33097 (home-page "http://www.micEcon.org")
33098 (synopsis "Miscellaneous tools and utilities")
33100 "This package provides miscellaneous small tools and utilities. Many of
33101 them facilitate the work with matrices, e.g. inserting rows or columns,
33102 creating symmetric matrices, or checking for semidefiniteness. Other tools
33103 facilitate the work with regression models, e.g. extracting the standard
33104 errors, obtaining the number of (estimated) parameters, or calculating
33105 R-squared values.")
33106 (license license:gpl2+)))
33108 (define-public r-mockery
33115 (uri (cran-uri "mockery" version))
33118 "0sj77m9vgn4bzb8c8nq93xb9lm8ih8rcb7sfccripraibibg3jcz"))))
33119 (properties `((upstream-name . "mockery")))
33120 (build-system r-build-system)
33125 (home-page "https://github.com/jfiksel/mockery")
33126 (synopsis "Mocking library for R")
33128 "The two main functionalities of this package are creating mock
33129 objects (functions) and selectively intercepting calls to a given function
33130 that originate in some other function. It can be used with any testing
33131 framework available for R. Mock objects can be injected with either this
33132 package's own @code{stub} function or a similar @code{with_mock} facility
33133 present in the @code{testthat} package.")
33134 (license license:expat)))
33136 (define-public r-zoltr
33143 (uri (cran-uri "zoltr" version))
33146 "12zh7y3pwidclscgvd0b0iaqq9j5y8mc8xd6pz4vs0jy5qs3ahar"))))
33147 (properties `((upstream-name . "zoltr")))
33148 (build-system r-build-system)
33160 (native-inputs (list r-knitr))
33161 (home-page "https://github.com/reichlab/zoltr")
33162 (synopsis "Interface to the Zoltar forecast repository API")
33164 "Zoltar is a website that provides a repository of model forecast results
33165 in a standardized format and a central location. It supports storing,
33166 retrieving, comparing, and analyzing time series forecasts for prediction
33167 challenges of interest to the modeling community. This package provides
33168 functions for working with the Zoltar API, including connecting and
33169 authenticating, getting information about projects, models, and forecasts,
33170 deleting and uploading forecast data, and downloading scores.")
33171 (license license:gpl3)))
33173 (define-public r-zoib
33180 (uri (cran-uri "zoib" version))
33183 "0inm7f2pc68ksqxvq12xp9jc99vj7ydylvs24ip12nksbj5k1n8f"))))
33184 (properties `((upstream-name . "zoib")))
33185 (build-system r-build-system)
33187 (list r-abind r-coda r-formula r-rjags))
33188 (home-page "https://www.r-project.org")
33189 (synopsis "Bayesian inference for beta regression")
33191 "This package lets you fit beta regression and zero-or-one inflated beta
33192 regression and obtain Bayesian inference of the model via the Markov Chain
33193 Monte Carlo approach implemented in JAGS.")
33194 (license license:gpl3+)))
33196 (define-public r-logger
33203 (uri (cran-uri "logger" version))
33205 (base32 "08kym5i5fvbf5xhh9qdszp4jdgyc7j7zpnwzy68wabqz73aff6sg"))))
33206 (properties `((upstream-name . "logger")))
33207 (build-system r-build-system)
33208 (native-inputs (list r-knitr))
33209 (home-page "https://daroczig.github.io/logger/")
33210 (synopsis "Lightweight and flexible logging utility")
33212 "Inspired by the the @code{futile.logger} R package and @code{logging}
33213 Python module, this utility provides a flexible and extensible way of
33214 formatting and delivering log messages with low overhead.")
33215 (license license:agpl3+)))
33217 (define-public r-fasterize
33219 (name "r-fasterize")
33224 (uri (cran-uri "fasterize" version))
33226 (base32 "10bzl77c1b9jhcn1xp467qzp2n8c7s3wpxn53qjh1nwvbri5kd32"))))
33227 (properties `((upstream-name . "fasterize")))
33228 (build-system r-build-system)
33230 (list r-raster r-rcpp r-rcpparmadillo r-sp))
33231 (native-inputs (list r-knitr))
33232 (home-page "https://github.com/ecohealthalliance/fasterize")
33233 (synopsis "Fast Polygon to Raster Conversion")
33235 "This package provides a drop-in replacement for @code{rasterize} from
33236 the @code{raster} package that takes sf-type objects, and is much faster.
33237 There is support for the main options provided by the @code{rasterize}
33238 function, including setting the field used and background value, and
33239 options for aggregating multi-layer rasters.")
33240 (license license:expat)))
33242 (define-public r-bien
33249 (uri (cran-uri "BIEN" version))
33251 (base32 "0s98n6zbf48vssd3h63k6kashcxv1kawcb026n0ngsfpc5dv6i48"))))
33252 (properties `((upstream-name . "BIEN")))
33253 (build-system r-build-system)
33268 (home-page "https://cran.r-project.org/package=BIEN")
33269 (synopsis "Tools for accessing the BIEN database")
33271 "This package provides tools for accessing the Botanical Information and
33272 Ecology Network (BIEN) database. The BIEN database contains cleaned and
33273 standardized botanical data including occurrence, trait, plot and taxonomic
33274 data. This package provides functions that query the BIEN database by
33275 constructing and executing optimized SQL queries.")
33276 (license license:expat)))
33278 (define-public r-varhandle
33280 (name "r-varhandle")
33285 (uri (cran-uri "varhandle" version))
33287 (base32 "1l42d0s6fbjjc9l28a2m3myxkrx2c0p0b9yj8wjjjgilw19yc3lv"))))
33288 (properties `((upstream-name . "varhandle")))
33289 (build-system r-build-system)
33290 (home-page "https://bitbucket.org/mehrad_mahmoudian/varhandle")
33291 (synopsis "Functions for robust variable handling")
33293 "This package contains some functions to help users (especially data
33294 explorers) to make more sense of their variables and take the most out of
33295 variables and hardware resources. Functions in this package are supposed to
33296 be efficient and easy to use.")
33297 (license license:gpl2+)))
33299 (define-public r-ggh4x
33306 (uri (cran-uri "ggh4x" version))
33309 "1r49yfm5fqv5s7jb92ad6rf8hd9plcry6f500czjhnhhrp16cqfp"))))
33310 (properties `((upstream-name . "ggh4x")))
33311 (build-system r-build-system)
33313 (list r-ggplot2 r-gtable r-rlang r-scales r-vctrs))
33316 (home-page "https://github.com/teunbrand/ggh4x")
33317 (synopsis "Extension for ggplot2")
33318 (description "This package is a @code{ggplot2} extension. It provides some
33319 utility functions that do not entirely fit within the grammar of graphics
33320 concept. The package extends @code{ggpplots} facets through customisation, by
33321 setting individual scales per panel, resizing panels and providing nested
33322 facets. It also allows multiple colour, fill scales per plot and hosts a
33323 smaller collection of stats, geoms and axis guides.")
33324 (license license:expat)))
33326 (define-public r-zoeppritz
33328 (name "r-zoeppritz")
33332 (uri (cran-uri "zoeppritz" version))
33335 "1711szx9zz17q6pfinyzlyrw7m9772c8ywlixqar2l165bkjalgm"))))
33336 (properties `((upstream-name . "zoeppritz")))
33337 (build-system r-build-system)
33338 (home-page "https://cran.r-project.org/package=zoeppritz")
33339 (synopsis "Seismic reflection and scattering coefficients for waves")
33341 "The @code{r-zoeppritz} package calculates and plots scattering matrix
33342 coefficients or scattering amplitudes, for seismological P and S-waves at an
33344 (license license:gpl2+)))