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-guix-install
430 (name "r-guix-install")
435 (uri (cran-uri "guix.install" version))
437 (base32 "0s3wb5781yc43c9zwrn7i87zcbrlx7xr0ms0v9hvgs7qsv02id9j"))))
438 (properties `((upstream-name . "guix.install")))
439 (build-system r-build-system)
440 (propagated-inputs (list r-runit))
441 (home-page "https://github.com/BIMSBbioinfo/guix.install")
442 (synopsis "Install R packages with GNU Guix")
444 "This R package provides a single procedure @code{guix.install()}, which
445 allows users to install R packages via Guix right from within their running R
446 session. If the requested R package does not exist in Guix at this time, the
447 package and all its missing dependencies will be imported recursively and the
448 generated package definitions will be written to @file{~/.Rguix/packages.scm}.
449 This record of imported packages can be used later to reproduce the
450 environment, and to add the packages in question to a proper Guix channel (or
451 Guix itself). @code{guix.install()} not only supports installing packages
452 from CRAN, but also from Bioconductor or even arbitrary git or mercurial
453 repositories, replacing the need for installation via @code{devtools}.")
454 (license license:gpl3+)))
463 (uri (cran-uri "ids" version))
466 "1s6ga94gds5ydr9f8qbjfgfpg2dvbnkcrlybqlb33hk3c0c2l8dn"))))
467 (properties `((upstream-name . "ids")))
468 (build-system r-build-system)
470 (list r-openssl r-uuid))
471 (native-inputs (list r-knitr))
472 (home-page "https://github.com/richfitz/ids")
473 (synopsis "Generate random identifiers")
475 "This package lets you generate random or human readable and
476 pronounceable identifiers.")
477 (license license:expat)))
479 (define-public r-googlesheets4
481 (name "r-googlesheets4")
486 (uri (cran-uri "googlesheets4" version))
489 "0yncqwv9l5knyrv88ys5gwcv44hl1j0mbklpins6v7f9m9v7s40a"))))
490 (properties `((upstream-name . "googlesheets4")))
491 (build-system r-build-system)
507 (home-page "https://github.com/tidyverse/googlesheets4")
508 (synopsis "Access Google Sheets using the Sheets API V4")
510 "This package lets you interact with Google Sheets through the
511 @url{https://developers.google.com/sheets/api,Sheets API v4}. This package
512 can read and write both the metadata and the cell data in a Sheet.")
513 (license license:expat)))
515 (define-public r-waldo
522 (uri (cran-uri "waldo" version))
525 "1aky28rn70l24s0sygl36267cf7hjzhchagsz26abfxwr7p8kvjp"))))
526 (properties `((upstream-name . "waldo")))
527 (build-system r-build-system)
536 (home-page "https://github.com/r-lib/waldo")
537 (synopsis "Find differences between R objects")
539 "Compare complex R objects and reveal the key differences. This package
540 was designed particularly for use in testing packages where being able to
541 quickly isolate key differences makes understanding test failures much
543 (license license:expat)))
545 (define-public r-rticles
552 (uri (cran-uri "rticles" version))
555 "1ipblw3rmkma22jl2hf1pyfm6l8k31zcmm3swmwii6k0x7khiav1"))))
556 (properties `((upstream-name . "rticles")))
557 (build-system r-build-system)
559 (list r-knitr r-rmarkdown r-tinytex r-xfun r-yaml))
560 (home-page "https://github.com/rstudio/rticles")
561 (synopsis "Article formats for R Markdown")
563 "This package provides a suite of custom R Markdown formats and templates
564 for authoring journal articles and conference submissions.")
565 (license license:gpl3)))
567 (define-public r-babelwhale
569 (name "r-babelwhale")
574 (uri (cran-uri "babelwhale" version))
576 (base32 "0ph825dwvr48fhamy1l5564linz7cj7b9sj511as77f1yqycv4a2"))))
577 (properties `((upstream-name . "babelwhale")))
578 (build-system r-build-system)
580 (list r-crayon r-dplyr r-dynutils r-processx r-purrr))
581 (home-page "https://github.com/dynverse/babelwhale")
582 (synopsis "Talking to Docker and Singularity containers")
584 "This package provides a unified interface to interact with Docker and
585 Singularity containers. You can execute a command inside a container, mount a
586 volume or copy a file.")
587 (license license:expat)))
589 (define-public r-benchmarkmedata
591 (name "r-benchmarkmedata")
595 (uri (cran-uri "benchmarkmeData" version))
598 "1n4vjkagqlm6kw2hilf4gjfcdjad0bcg652j9nl2ygbq3kdnh1vf"))))
599 (build-system r-build-system)
601 (list r-dplyr r-tibble))
602 (home-page "https://github.com/csgillespie/benchmarkme-data")
603 (synopsis "Data set for the @code{benchmarkme} package")
604 (description "This package contains the data set for the crowd-sourced
605 benchmarks from running the @code{benchmarkme} package.")
606 (license license:gpl2+)))
608 (define-public r-benchmarkme
610 (name "r-benchmarkme")
614 (uri (cran-uri "benchmarkme" version))
617 "0ymgsxzrvnpyvs0cff09d3lrkl12qyqx5bwammsc4vgl5ng9p69p"))))
618 (build-system r-build-system)
622 (list r-benchmarkmedata
629 (home-page "https://csgillespie.github.io/benchmarkme/")
630 (synopsis "Crowd-sourced system benchmarks")
631 (description "This package provides functionality to benchmark your CPU
632 and compare against other CPUs. Also provides functions for obtaining system
633 specifications, such as RAM, CPU type, and R version.")
634 (license license:gpl2+)))
636 (define-public r-bezier
642 (uri (cran-uri "bezier" version))
645 "1vw5128v8h973xwa1fdm9cw2jvrldj87nd55lddlp3qsz3ag4br6"))))
646 (build-system r-build-system)
647 (home-page "https://cran.r-project.org/web/packages/bezier/")
648 (synopsis "Bezier curve and spline toolkit")
650 "This package is a toolkit for working with Bezier curves and splines.
651 The package provides functions for point generation, arc length estimation,
652 degree elevation and curve fitting.")
653 (license license:gpl2+)))
655 (define-public r-bwstest
662 (uri (cran-uri "BWStest" version))
664 (base32 "02amzlfprmw5pyis0dg0kg0x8xqh50a4vfdcxxmklrzik3b1vzzs"))))
665 (properties `((upstream-name . "BWStest")))
666 (build-system r-build-system)
667 (propagated-inputs (list r-memoise r-rcpp))
668 (home-page "https://github.com/shabbychef/BWStest")
669 (synopsis "Baumgartner Weiss Schindler Test of equal distributions")
671 "This package performs the Baumgartner-Weiss-Schindler two-sample test of
672 equal probability distributions (doi:10.2307/2533862). It also performs
673 similar rank-based tests for equal probability distributions due to Neuhauser
674 (doi:10.1080/10485250108832874) and Murakami
675 (doi:10.1080/00949655.2010.551516).")
676 (license license:lgpl3)))
685 (uri (cran-uri "V8" version))
688 "0hs7ajjw6y3q7mp7z00a9712y4cn6wgcnk5dbjbzlc6cfk4zsqkc"))))
689 (properties `((upstream-name . "V8")))
690 (build-system r-build-system)
693 (modify-phases %standard-phases
694 (add-after 'unpack 'find-v8
695 (lambda* (#:key inputs #:allow-other-keys)
696 (substitute* "configure"
698 (string-append "PKG_LIBS="
699 (assoc-ref inputs "libnode")
700 "/lib/libnode.so.64\n")))
701 (setenv "INCLUDE_DIR"
703 (assoc-ref inputs "libnode")
707 (assoc-ref inputs "libnode") "/lib")))))))
711 (list r-curl r-jsonlite r-rcpp))
714 (home-page "https://jeroen.cran.dev/V8")
715 (synopsis "Embedded JavaScript and WebAssembly engine for R")
717 "This package provides an R interface to V8: Google's JavaScript and
718 WebAssembly engine.")
719 (license license:expat)))
728 (uri (cran-uri "DOT" version))
731 "0qh5n57cp9c2n5yn59q4wggz82943pwfanp3kx869aba2x3sj30i"))))
732 (properties `((upstream-name . "DOT")))
733 (build-system r-build-system)
736 (home-page "http://haghish.com/dot")
737 (synopsis "Render and Export DOT Graphs in R")
739 "This package provides tools to render DOT diagram markup language in R
740 and also provides the possibility to export the graphs in PostScript and
741 SVG (Scalable Vector Graphics) formats. In addition, it supports literate
742 programming packages such as @code{knitr} and @code{rmarkdown}.")
743 (license license:expat)))
745 (define-public r-carrier
752 (uri (cran-uri "carrier" version))
754 (base32 "0bqnwnnjqjk9q0lxq6kkz9s75ss10lfyyywyyi24m8wppxpw1vqc"))))
755 (properties `((upstream-name . "carrier")))
756 (build-system r-build-system)
758 (list r-pryr r-rlang))
759 (home-page "https://github.com/r-lib/carrier")
760 (synopsis "Isolate functions for remote execution")
762 "Sending functions to remote processes can be wasteful of resources
763 because they carry their environments with them. With this package, it is
764 easy to create functions that are isolated from their environment. These
765 isolated functions, also called crates, print to the console with their total
766 size and can be easily tested locally before being sent to a remote.")
767 (license license:gpl3)))
769 (define-public r-clipr
776 (uri (cran-uri "clipr" version))
779 "1s9vvv3cxnz8w11gsi8z9ddv9jzib5qf5qqxnwqrrv7vj8cr7hij"))))
780 (build-system r-build-system)
783 (home-page "https://github.com/mdlincoln/clipr")
784 (synopsis "Read and write from the system clipboard")
786 "This package provides simple utility functions to read from and write to
787 the system clipboards.")
788 (license license:gpl3)))
797 (uri (cran-uri "dlm" version))
799 (base32 "1aksm66sfa7ipl5xgs4j5giac7q2m744wjl40mva56xn6i674h4r"))))
800 (properties `((upstream-name . "dlm")))
801 (build-system r-build-system)
802 (home-page "https://cran.r-project.org/package=dlm")
803 (synopsis "Bayesian and Likelihood Analysis of Dynamic Linear Models")
805 "This package provides routines for Maximum likelihood, Kalman filtering
806 and smoothing, and Bayesian analysis of Normal linear State Space models, also
807 known as Dynamic Linear Models.")
808 (license license:gpl2+)))
816 (uri (cran-uri "zoo" version))
819 "0izd66dywq6qd62hdp64apncainrrb9mgmm19wf6a8jc03c858n9"))))
820 (build-system r-build-system)
823 (home-page "http://zoo.R-Forge.R-project.org/")
824 (synopsis "S3 infrastructure for regular and irregular time series")
825 (description "This package contains an S3 class with methods for totally
826 ordered indexed observations. It is particularly aimed at irregular time
827 series of numeric vectors/matrices and factors.")
828 (license license:gpl2+)))
830 (define-public r-fontawesome
832 (name "r-fontawesome")
837 (uri (cran-uri "fontawesome" version))
839 (base32 "0r6zb5175cr4ybqj6bl0mbhadwv9xjxaf32yjc0y76rw3d6vcbap"))))
840 (properties `((upstream-name . "fontawesome")))
841 (build-system r-build-system)
843 (list r-htmltools r-rlang))
844 (home-page "https://github.com/rstudio/fontawesome")
845 (synopsis "Easily work with Font Awesome icons")
847 "Easily and flexibly insert Font Awesome icons into R Markdown documents
848 and Shiny apps. These icons can be inserted into HTML content through inline
849 SVG tags or @code{i} tags. There is also a utility function for exporting
850 Font Awesome icons as PNG images for those situations where raster graphics
852 (license license:expat)))
854 (define-public r-fingerprint
856 (name "r-fingerprint")
861 (uri (cran-uri "fingerprint" version))
863 (base32 "04jcwkydjrs31pia6kq8z2n9s54im950q08hs2ay15xjxxkmb8ic"))))
864 (properties `((upstream-name . "fingerprint")))
865 (build-system r-build-system)
866 (home-page "https://cran.r-project.org/package=fingerprint")
867 (synopsis "Functions to Operate on Binary Fingerprint Data")
869 "This package provides functions to manipulate binary fingerprints of
870 arbitrary length. A fingerprint is represented by an object of S4 class
871 @code{fingerprint}. The bitwise logical functions in R are overridden so that
872 they can be used directly with @code{fingerprint} objects. A number of
873 distance metrics are also available. Fingerprints can be converted to
874 Euclidean vectors (i.e., points on the unit hypersphere) and can also be
875 folded. Arbitrary fingerprint formats can be handled via line handlers.
876 Currently handlers are provided for CDK, MOE and BCI fingerprint data.")
877 ;; Any version of the GPL
878 (license (list license:gpl2+ license:gpl3+))))
880 (define-public r-fpeek
887 (uri (cran-uri "fpeek" version))
889 (base32 "0kv46g21ndxchg3q8ynq7hjjkh6i2zlc21axn5y1jjzigrw047ii"))))
890 (properties `((upstream-name . "fpeek")))
891 (build-system r-build-system)
892 (propagated-inputs (list r-rcpp))
893 (home-page "https://github.com/davidgohel/fpeek")
894 (synopsis "Check text files content at a glance")
896 "This package provides tools to help working with text files. It can
897 return the number of lines; print the first and last lines; convert encoding.
898 Operations are made without reading the entire file before starting, resulting
899 in good performances with large files.")
900 (license license:expat)))
902 (define-public r-ggalluvial
904 (name "r-ggalluvial")
908 (uri (cran-uri "ggalluvial" version))
911 "0mkan9gxg3yxjism22yxbhvlh2lh7wpbrqpb355za790prcmjbh3"))))
912 (properties `((upstream-name . "ggalluvial")))
913 (build-system r-build-system)
923 (home-page "http://corybrunson.github.io/ggalluvial/")
924 (synopsis "Alluvial plots for ggplot2")
925 (description "This package provides alluvial plots for @code{ggplot2}.
926 Alluvial plots use variable-width ribbons and stacked bar plots to represent
927 multi-dimensional or repeated-measures data with categorical or ordinal
929 (license license:gpl3)))
931 (define-public r-ggpp
938 (uri (cran-uri "ggpp" version))
941 "0wcaczxjav5yg8h2197cf288mqk13p3iq675q0x0di9g8lnblvk1"))))
942 (properties `((upstream-name . "ggpp")))
943 (build-system r-build-system)
961 (home-page "https://docs.r4photobiology.info/ggpp/")
962 (synopsis "Grammar extensions to ggplot2")
964 "This package contains extensions to ggplot2.
967 @item Geomas: @code{geom_table}, @code{geom_plot} and @code{geom_grob} add
968 insets to plots using native data coordinates, while @code{geom_table_npc},
969 @code{geom_plot_npc} and @code{geom_grob_npc} do the same using @code{npc}
970 coordinates through new aesthetics @code{npcx} and @code{npcy}.
971 @item Statistics: select observations based on 2D density.
972 @item Positions: radial nudging away from a center point and nudging away from
976 (license license:gpl2+)))
978 (define-public r-lmds
985 (uri (cran-uri "lmds" version))
987 (base32 "130azb0nc2wwxv0qi8v5s4rd02p9lc92zwn634pv7b8awbw81i65"))))
988 (properties `((upstream-name . "lmds")))
989 (build-system r-build-system)
991 (list r-assertthat r-dynutils r-irlba r-matrix))
992 (home-page "https://github.com/dynverse/lmds")
993 (synopsis "Landmark multi-dimensional scaling")
995 "This package provides a fast dimensionality reduction method scalable
996 to large numbers of samples. @dfn{Landmark Multi-Dimensional Scaling} (LMDS)
997 is an extension of classical Torgerson MDS, but rather than calculating a
998 complete distance matrix between all pairs of samples, only the distances
999 between a set of landmarks and the samples are calculated.")
1000 (license license:gpl3)))
1002 (define-public r-lmodel2
1009 (uri (cran-uri "lmodel2" version))
1011 (base32 "1fiin2nkffbihz1s8ixmw9lgf8mn3j9krr8iiflizk10mdv54hnb"))))
1012 (properties `((upstream-name . "lmodel2")))
1013 (build-system r-build-system)
1014 (home-page "https://cran.r-project.org/package=lmodel2")
1015 (synopsis "Model II regression")
1017 "This package computes model II simple linear regression using
1018 @dfn{ordinary least squares} (OLS), @dfn{major axis} (MA), @dfn{standard major
1019 axis} (SMA), and @dfn{ranged major axis} (RMA).")
1020 (license license:gpl2)))
1022 (define-public r-ggpmisc
1028 (uri (cran-uri "ggpmisc" version))
1031 "1iq39rx4nj1lf37hnj4df0c7gbk9374d0mzcnhdr7aqpxaxgs3ys"))))
1032 (build-system r-build-system)
1050 (home-page "https://www.r4photobiology.info/")
1051 (synopsis "Miscellaneous Extensions to @code{ggplot2}")
1052 (description "This package provides extensions to @code{ggplot2},
1053 respecting the grammar of its graphics paradigm.")
1054 (license license:gpl2+)))
1056 (define-public r-ggside
1062 (uri (cran-uri "ggside" version))
1065 "1x505zizv7hf65pxp9j5v92c3bchhxh9dsrkk1m55kwqqnsl5nza"))))
1066 (properties `((upstream-name . "ggside")))
1067 (build-system r-build-system)
1068 (propagated-inputs (list r-ggplot2 r-glue r-gtable r-rlang r-scales))
1069 (native-inputs (list r-knitr))
1070 (home-page "https://cran.r-project.org/package=ggside")
1071 (synopsis "Side grammar graphics that extends @code{ggplot2}")
1073 "The grammar of graphics as shown in @code{ggplot2} has provided an
1074 expressive API for users to build plots. This package @{ggside} extends
1075 @code{ggplot2} by allowing users to add graphical information about one of the
1076 main panel's axis using a familiar @code{ggplot2} style API with tidy data.
1077 This package is particularly useful for visualizing metadata on a discrete
1078 axis, or summary graphics on a continuous axis such as a boxplot or a density
1080 (license license:expat)))
1082 (define-public r-gprofiler
1084 (name "r-gprofiler")
1089 (uri (cran-uri "gProfileR" version))
1092 "1h1v0kgpsn04ald2izznh7fr2riwisj5hcgz4k7h3qc931rf0r4k"))))
1093 (properties `((upstream-name . "gProfileR")))
1094 (build-system r-build-system)
1096 (list r-plyr r-rcurl))
1097 (home-page "https://cran.r-project.org/web/packages/gProfileR/")
1098 (synopsis "Interface to the g:Profiler toolkit")
1100 "This package provides tools for functional enrichment analysis,
1101 gene identifier conversion and mapping homologous genes across related
1102 organisms via the @code{g:Profiler} toolkit.")
1103 (license license:gpl2+)))
1105 (define-public r-gprofiler2
1107 (name "r-gprofiler2")
1112 (uri (cran-uri "gprofiler2" version))
1115 "0r0h34b35xzgd9rh55yndn0anxy0z45zdlqa6qfmpn91b6v1bb1g"))))
1116 (properties `((upstream-name . "gprofiler2")))
1117 (build-system r-build-system)
1128 (native-inputs (list r-knitr))
1129 (home-page "https://cran.r-project.org/web/packages/gprofiler2/")
1130 (synopsis "Interface to the g:Profiler toolset")
1132 "This package provides a toolset for functional enrichment analysis and
1133 visualization, gene/protein/SNP identifier conversion and mapping orthologous
1134 genes across species via @url{https://biit.cs.ut.ee/gprofiler,g:Profiler}.
1138 @item @code{g:GOSt}, functional enrichment analysis and visualization of gene
1140 @item @code{g:Convert}, gene/protein/transcript identifier conversion across
1142 @item @code{g:Orth}, orthology search across species;
1143 @item @code{g:SNPense}, mapping SNP rs identifiers to chromosome positions,
1144 genes and variant effects.
1147 This package is an R interface corresponding to the 2019 update of
1148 @code{g:Profiler} and provides access to versions @code{e94_eg41_p11} and
1150 (license license:gpl2+)))
1152 (define-public r-oenb
1159 (uri (cran-uri "oenb" version))
1162 "1jgxw7ycx2lcdzglg9nix8k08fs4r6i5jdsjzrd6w1dg6smsinl5"))))
1163 (properties `((upstream-name . "oenb")))
1164 (build-system r-build-system)
1166 (list r-dplyr r-xml))
1167 (native-inputs (list r-knitr))
1168 (home-page "https://github.com/franzmohr/oenb")
1169 (synopsis "Tools for the OeNB Data Web Service")
1171 "Tools to access data from the data web service of the
1172 @acronym{OeNB, Oesterreichische Nationalbank},
1173 @url{https://www.oenb.at/en/Statistics/User-Defined-Tables/webservice.html}.")
1174 (license license:gpl2+)))
1176 (define-public r-orgmassspecr
1178 (name "r-orgmassspecr")
1182 (uri (cran-uri "OrgMassSpecR" version))
1185 "1dx9d8rb1dfqyhyc26zhfnxiv3rz2ikvs2mwqnsrq3lsjs9dvyc8"))))
1186 (properties `((upstream-name . "OrgMassSpecR")))
1187 (build-system r-build-system)
1188 (native-inputs (list r-knitr))
1189 (home-page "http://OrgMassSpec.github.io/")
1190 (synopsis "Organic or biological mass spectrometry data analysis")
1192 "This package @code{OrgMassSpecR} is an extension of the @code{R}
1193 statistical computing language. It contains functions to assist with organic
1194 or biological mass spectrometry data analysis. Mass spectral libraries are
1195 available as companion packages.")
1196 (license license:bsd-2)))
1198 (define-public r-scales
1205 (uri (cran-uri "scales" version))
1207 (base32 "1pq2rrix6a5gsi8xw38viiydp1bsxxmcmyy7dv9q8gkb1qj50p8q"))))
1208 (build-system r-build-system)
1218 (home-page "https://github.com/hadley/scales")
1219 (synopsis "Scale functions for visualization")
1221 "This package provides graphical scales that map data to aesthetics, and
1222 provides methods for automatically determining breaks and labels for axes and
1224 (license license:expat)))
1226 (define-public r-pacman
1232 (uri (cran-uri "pacman" version))
1235 "0z7gngd6h83cpjhq1vg75wvzhdjbgjh7gj5d4zvvi9gd2lmagjcy"))))
1236 (build-system r-build-system)
1239 (home-page "https://github.com/trinker/pacman")
1240 (synopsis "Package Management Tool")
1241 (description "This package provides tools to more conveniently perform
1242 tasks associated with add-on packages. @code{pacman} conveniently wraps
1243 library and package related functions and names them in an intuitive and
1244 consistent fashion. It seeks to combine functionality from lower level
1245 functions which can speed up workflow.")
1246 (license license:gpl2)))
1248 (define-public r-paralleldist
1250 (name "r-paralleldist")
1255 (uri (cran-uri "parallelDist" version))
1257 (base32 "01ly4hxwa64a0ya5gla8rvv72s9mcknsfznivjkh937pbjwb7iih"))))
1258 (properties `((upstream-name . "parallelDist")))
1259 (build-system r-build-system)
1260 (propagated-inputs (list r-rcpp r-rcpparmadillo r-rcppparallel))
1261 (home-page "https://github.com/alexeckert/parallelDist")
1262 (synopsis "Parallel Distance Matrix Computation using multiple threads")
1264 "This package provides a fast parallelized alternative to R's native
1265 @code{dist} function to calculate distance matrices for continuous, binary,
1266 and multi-dimensional input matrices, which supports a broad variety of
1267 predefined distance functions from other R packages, as well as user- defined
1268 functions written in C++. For ease of use, the @code{parDist} function
1269 extends the signature of the @code{dist} function and uses the same parameter
1270 naming conventions as distance methods of existing R packages.")
1271 (license license:gpl2+)))
1273 (define-public r-pheatmap
1280 (uri (cran-uri "pheatmap" version))
1283 "1hdh74az3vyzz6dqa311rhxdm74n46lyr03p862kn80p0kp9d7ap"))))
1284 (build-system r-build-system)
1286 (list r-gtable r-rcolorbrewer r-scales))
1287 (home-page "https://cran.r-project.org/web/packages/pheatmap")
1288 (synopsis "Pretty heatmaps")
1290 "This package provides an implementation of heatmaps that offers more
1291 control over dimensions and appearance.")
1292 (license license:gpl2+)))
1294 (define-public r-pnwcolors
1296 (name "r-pnwcolors")
1301 (uri (cran-uri "PNWColors" version))
1304 "1phplnclkficfv8s6wsyrckk4ixzbayiy5iix6dddg40485l9nyj"))))
1305 (properties `((upstream-name . "PNWColors")))
1306 (build-system r-build-system)
1307 (home-page "https://github.com/jakelawlor/PNWColors")
1308 (synopsis "Color palettes for data visualizations")
1310 "This package provides color palettes. They are checked for colorblind
1311 accessibility from hue, saturation, and lightness value scaling using the
1312 Chroma.js Color Palette Helper. See @url{https://gka.github.io/palettes}.")
1313 (license license:cc0)))
1315 (define-public r-plotfunctions
1317 (name "r-plotfunctions")
1322 (uri (cran-uri "plotfunctions" version))
1324 (base32 "0asmxw8283fpvl83h478j5nyg59xqifqaa8f2f6l199gvvswhhg2"))))
1325 (properties `((upstream-name . "plotfunctions")))
1326 (build-system r-build-system)
1327 (native-inputs (list r-knitr))
1328 (home-page "https://jacolienvanrij.com/tutorials.html")
1329 (synopsis "Various functions to facilitate visualization of data and analysis")
1331 "When analyzing data, plots are a helpful tool for visualizing data and
1332 interpreting statistical models. This package provides a set of simple tools
1333 for building plots incrementally, starting with an empty plot region, and
1334 adding bars, data points, regression lines, error bars, gradient legends,
1335 density distributions in the margins, and even pictures. The package builds
1336 further on R graphics by simply combining functions and settings in order to
1337 reduce the amount of code to produce for the user. As a result, the package
1338 does not use formula input or special syntax, but can be used in combination
1339 with default R plot functions.")
1340 (license license:gpl2+)))
1342 (define-public r-polychrome
1344 (name "r-polychrome")
1349 (uri (cran-uri "Polychrome" version))
1351 (base32 "0hyi02m2jpdhk1ky6ihz6dv5pwqwjwk4csjim2qr8ywx8midmrvg"))))
1352 (properties `((upstream-name . "Polychrome")))
1353 (build-system r-build-system)
1355 (list r-colorspace r-scatterplot3d))
1358 (home-page "http://oompa.r-forge.r-project.org/")
1359 (synopsis "Qualitative palettes with many colors")
1361 "This package provides tools for creating, viewing, and assessing
1362 qualitative palettes with many (20-30 or more) colors. See Coombes and
1363 colleagues (2019) @url{https://doi:10.18637/jss.v090.c01}.")
1364 (license license:asl2.0)))
1366 (define-public r-ecp
1372 (uri (cran-uri "ecp" version))
1375 "0n602jssl6rf596nwm6hbl7s9vdlqi20w8mrhxicj373mw5v22m8"))))
1376 (build-system r-build-system)
1379 (home-page "https://cran.r-project.org/web/packages/ecp/")
1380 (synopsis "Multiple change-point analysis of multivariate data")
1382 "This package implements various procedures for finding multiple
1383 change-points. Two methods make use of dynamic programming and pruning, with
1384 no distributional assumptions other than the existence of certain absolute
1385 moments in one method. Hierarchical and exact search methods are included.
1386 All methods return the set of estimated change-points as well as other summary
1388 (license license:gpl2+)))
1390 (define-public r-ellipsis
1397 (uri (cran-uri "ellipsis" version))
1400 "0n0mm9jngklv7j9wa64jdji035z0smmnsp2dfwcz9isrxgjnc0m9"))))
1401 (build-system r-build-system)
1404 (home-page "https://github.com/hadley/ellipsis")
1405 (synopsis "Tools for working with additional arguments")
1407 "In S3 generics, it's useful to take @code{...} so that methods can have
1408 additional arguments. But this flexibility comes at a cost: misspelled
1409 arguments will be silently ignored. The @code{ellipsis} package is an
1410 experiment that allows a generic to warn if any arguments passed in @code{...}
1412 (license license:gpl3)))
1421 (uri (cran-uri "GA" version))
1423 (base32 "135z03lnbj44jihnk6dii5a684jmc666ncpdwyyi910vl4sccib2"))))
1424 (properties `((upstream-name . "GA")))
1425 (build-system r-build-system)
1435 (home-page "https://luca-scr.github.io/GA/")
1436 (synopsis "Genetic algorithms for stochastic optimisation")
1438 "Flexible general-purpose toolbox implementing genetic algorithms (GAs)
1439 for stochastic optimisation. Binary, real-valued, and permutation
1440 representations are available to optimize a fitness function, i.e., a function
1441 provided by users depending on their objective function. Several genetic
1442 operators are available and can be combined to explore the best settings for
1443 the current task. Furthermore, users can define new genetic operators and
1444 easily evaluate their performances. Local search using general-purpose
1445 optimisation algorithms can be applied stochastically to exploit interesting
1446 regions. GAs can be run sequentially or in parallel, using an explicit
1447 master-slave parallelisation or a coarse-grain islands approach.")
1448 (license license:gpl2+)))
1450 (define-public r-grr
1457 (uri (cran-uri "grr" version))
1460 "0arbcgrvhkwb5xk4nry1ffg2qj0v8ivhjghdr505ib4357g0c9i9"))))
1461 (build-system r-build-system)
1462 (home-page "https://cran.r-project.org/web/packages/grr")
1463 (synopsis "Alternative implementations of base R functions")
1465 "This package provides alternative implementations of some base R
1466 functions, including @code{sort}, @code{order}, and @code{match}. The
1467 functions are simplified but can be faster or have other advantages.")
1468 (license license:gpl3)))
1470 (define-public r-matrix-utils
1472 (name "r-matrix-utils")
1477 (uri (cran-uri "Matrix.utils" version))
1480 "0a5fq1scykqk0kc9j051j6fix6j2dqwz5wbgb0amaxsiywz9vigb"))))
1481 (properties `((upstream-name . "Matrix.utils")))
1482 (build-system r-build-system)
1484 (list r-grr r-matrix))
1485 (home-page "https://github.com/cvarrichio/Matrix.utils")
1487 "Data.frame-Like Operations on Sparse and Dense Matrix Objects")
1489 "This package implements data manipulation methods such as @code{cast},
1490 @code{aggregate}, and @code{merge}/@code{join} for Matrix and Matrix-like
1492 (license license:gpl3)))
1494 (define-public r-mboost
1500 (uri (cran-uri "mboost" version))
1503 "01ln0vxbbx1fq77q17sx61si82lhfibbchsnf2yw9032cn8wnhh2"))))
1504 (build-system r-build-system)
1513 (home-page "https://github.com/boost-R/mboost")
1514 (synopsis "Model-based boosting")
1516 "This package provides a functional gradient descent algorithm (boosting)
1517 for optimizing general risk functions utilizing component-wise (penalised)
1518 least squares estimates or regression trees as base-learners for fitting
1519 generalized linear, additive and interaction models to potentially
1520 high-dimensional data.")
1521 (license license:gpl2)))
1523 (define-public r-shadowtext
1525 (name "r-shadowtext")
1529 (uri (cran-uri "shadowtext" version))
1532 "0zdfidrcnmxmfhngv86ppxrjmpmz9kl78l4yfah2lc5vgmrlwg15"))))
1533 (properties `((upstream-name . "shadowtext")))
1534 (build-system r-build-system)
1536 (list r-ggplot2 r-scales))
1539 (home-page "https://github.com/GuangchuangYu/shadowtext/")
1540 (synopsis "Shadow text grob and layer")
1541 (description "This package implements @code{shadowtextGrob()} for
1542 @code{grid} and @code{geom_shadowtext()} layer for @code{ggplot2}.
1543 These functions draw text grob with background shadow.")
1544 (license license:artistic2.0)))
1546 (define-public r-sys
1553 (uri (cran-uri "sys" version))
1556 "11q4zmx62w44p1j34frwmrsp23mc7l4n354i0zyziw92yax8zy0p"))))
1557 (build-system r-build-system)
1558 (home-page "https://github.com/jeroen/sys")
1559 (synopsis "Powerful and reliable tools for running system commands in R")
1561 "This package provides drop-in replacements for the base @code{system2()}
1562 function with fine control and consistent behavior across platforms. It
1563 supports clean interruption, timeout, background tasks, and streaming STDIN /
1564 STDOUT / STDERR over binary or text connections. The package also provides
1565 functions for evaluating expressions inside a temporary fork. Such
1566 evaluations have no side effects on the main R process, and support reliable
1567 interrupts and timeouts. This provides the basis for a sandboxing
1569 (license license:expat)))
1571 (define-public r-ashr
1577 (uri (cran-uri "ashr" version))
1580 "177xs3apnc6yy6737qqv4z8snf0hkpbghab63hrplbyb9wfssfga"))))
1581 (properties `((upstream-name . "ashr")))
1582 (build-system r-build-system)
1593 (home-page "https://github.com/stephens999/ashr")
1594 (synopsis "Methods for adaptive shrinkage, using empirical bayes")
1595 (description "This package implements an empirical Bayes approach for
1596 large-scale hypothesis testing and false discovery rate estimation.")
1597 (license license:gpl3+)))
1599 (define-public r-askpass
1606 (uri (cran-uri "askpass" version))
1609 "07q0ik8jzk44vpwh48rr3fnpd7dzsdhjjsl4l850rffv3dyq4h6v"))))
1610 (build-system r-build-system)
1611 (propagated-inputs (list r-sys))
1612 (home-page "https://github.com/jeroen/askpass")
1613 (synopsis "Safe password entry for R")
1615 "This package provides cross-platform utilities for prompting the user
1616 for credentials or a passphrase, for example to authenticate with a server or
1617 read a protected key.")
1618 (license license:expat)))
1620 (define-public r-astsa
1627 (uri (cran-uri "astsa" version))
1629 (base32 "0mllsq0xdqkviyvs77lq565r1vznsj1qp9cnlj5p48k9v76d7arp"))))
1630 (properties `((upstream-name . "astsa")))
1631 (build-system r-build-system)
1632 (home-page "https://github.com/nickpoison/astsa/")
1633 (synopsis "Applied statistical time series analysis")
1635 "This package provides data sets and scripts to accompany Time Series
1636 Analysis and Its Applications: With R Examples (4th ed), by R.H. Shumway and
1637 D.S. Stoffer. Springer Texts in Statistics, 2017,
1638 @url{https://doi.org/10.1007/978-3-319-52452-8}, and Time Series: A Data
1639 Analysis Approach Using R. Chapman-Hall, 2019,
1640 @url{https://doi.org/10.1201/9780429273285}.")
1641 (license license:gpl3)))
1643 (define-public r-vegan
1650 (uri (cran-uri "vegan" version))
1653 "0nf0ny6jzfy135xiygzzkr0y55y8g27hrbk8c869plarr48d2xxb"))))
1654 (build-system r-build-system)
1656 (list r-knitr ; needed for vignettes
1659 (list r-cluster r-lattice r-mass r-mgcv r-permute))
1660 (home-page "https://cran.r-project.org/web/packages/vegan")
1661 (synopsis "Functions for community ecology")
1663 "The vegan package provides tools for descriptive community ecology. It
1664 has most basic functions of diversity analysis, community ordination and
1665 dissimilarity analysis. Most of its multivariate tools can be used for other
1666 data types as well.")
1667 (license license:gpl2+)))
1669 (define-public r-tidyverse
1671 (name "r-tidyverse")
1676 (uri (cran-uri "tidyverse" version))
1679 "0ck6xmsw5p168jmw2fqv79fzfnw5jckfra7mfii261j6kl89bkw3"))))
1680 (build-system r-build-system)
1713 (home-page "https://tidyverse.tidyverse.org")
1714 (synopsis "Install and load packages from the \"Tidyverse\"")
1716 "The @code{tidyverse} is a set of packages that work in harmony because
1717 they share common data representations and API design. This package is
1718 designed to make it easy to install and load multiple tidyverse packages in a
1720 (license license:gpl3)))
1722 (define-public r-rvest
1729 (uri (cran-uri "rvest" version))
1731 (base32 "1905vxgnj3q09l1wf6rwxpbpydznp06nbkrclnc05j2415z4gfw9"))))
1732 (build-system r-build-system)
1743 (home-page "https://github.com/hadley/rvest")
1744 (synopsis "Simple web scraping for R")
1746 "@code{r-rvest} helps you scrape information from web pages. It is
1747 designed to work with @code{magrittr} to make it easy to express common web
1748 scraping tasks, inspired by libraries like @code{BeautifulSoup}.")
1749 (license license:gpl3)))
1751 (define-public r-selectr
1758 (uri (cran-uri "selectr" version))
1760 (base32 "09y1n3iy297g49xlpl7xrjpwgnm57pskx5991lyfcpizbz8ax22m"))))
1761 (build-system r-build-system)
1763 (list r-stringr r-r6))
1764 (home-page "https://sjp.co.nz/projects/selectr/")
1765 (synopsis "Translate CSS selectors to XPath expressions")
1767 "@code{r-selectr} translates a CSS3 selector into an equivalent XPath
1768 expression. This allows you to use CSS selectors when working with the XML
1769 package as it can only evaluate XPath expressions. Also provided are
1770 convenience functions useful for using CSS selectors on XML nodes. This
1771 package is a port of the Python package @code{cssselect}.")
1772 (license license:bsd-3)))
1774 (define-public r-reprex
1781 (uri (cran-uri "reprex" version))
1784 "09k4rasp7mz6n796dsklcbc5l7prljiznrm7fra16qybr9kqcv8f"))))
1785 (build-system r-build-system)
1799 (home-page "https://github.com/tidyverse/reprex")
1800 (synopsis "Prepare reproducible R code examples for sharing")
1802 "This package provides a convenience wrapper that uses the
1803 @code{rmarkdown} package to render small snippets of code to target formats
1804 that include both code and output. The goal is to encourage the sharing of
1805 small, reproducible, and runnable examples on code-oriented websites or email.
1806 @code{reprex} also extracts clean, runnable R code from various common formats,
1807 such as copy/paste from an R session.")
1808 (license license:expat)))
1810 (define-public r-reordercluster
1812 (name "r-reordercluster")
1816 (uri (cran-uri "ReorderCluster" version))
1819 "0ss750frzvj0bm1w7zblmcsjpszhnbffwlkaw31sm003lbx9hy58"))))
1820 (build-system r-build-system)
1822 (list r-gplots r-rcpp))
1823 (home-page "https://cran.r-project.org/web/packages/ReorderCluster")
1824 (synopsis "Reordering the dendrogram according to the class labels")
1825 (description "This package provides tools for performing the leaf reordering
1826 for the dendrogram that preserves the hierarchical clustering result and at the
1827 same time tries to group instances from the same class together.")
1828 (license license:gpl3+)))
1830 (define-public r-callr
1837 (uri (cran-uri "callr" version))
1840 "02inaf3c7b0hikii7p2zwaphrq5myv4in92d9jxd1ilmhla5awnn"))))
1841 (build-system r-build-system)
1843 (list r-r6 r-processx))
1844 (home-page "https://github.com/r-lib/callr#readme")
1845 (synopsis "Call R from R")
1847 "It is sometimes useful to perform a computation in a separate R process,
1848 without affecting the current R process at all. This package does exactly
1850 (license license:expat)))
1852 (define-public r-depmixs4
1858 (uri (cran-uri "depmixS4" version))
1861 "1pacvhw5m4fsk3ysbal50fdqbvlaz8ywyqp6bn1wh42wipqbb2i8"))))
1863 (list r-nnet r-nlme r-mass r-rsolnp))
1864 (build-system r-build-system)
1865 (home-page "https://cran.r-project.org/web/packages/depmixS4/")
1866 (synopsis "Dependent Mixture Models")
1867 (description "This package fits latent (hidden) Markov models on mixed
1868 categorical and continuous (time series) data, otherwise known as dependent
1870 (license license:gpl2+)))
1872 (define-public r-readxl
1879 (uri (cran-uri "readxl" version))
1882 "1xwi4k5si48hwkgfc59icfmp9dzlvfri59k5fsgn96zp9713k4mb"))))
1883 (build-system r-build-system)
1885 (list r-cellranger r-cpp11 r-progress r-tibble))
1888 (home-page "https://readxl.tidyverse.org")
1889 (synopsis "Read Excel files")
1891 "This package lets you import Excel files into R. It supports
1892 @file{.xls} via the embedded @code{libxls} C library and @file{.xlsx} via
1893 the embedded @code{RapidXML} C++ library.")
1894 ;; XXX: This package bundles a copy of 'libxsl' which is BSD-2 and
1895 ;; 'rapidxml' which is Boost.
1896 (license (list license:gpl3 license:bsd-2 license:boost1.0))))
1898 (define-public r-model4you
1900 (name "r-model4you")
1904 (uri (cran-uri "model4you" version))
1907 "0pni9v3nradvy8sp2m07903vc7z610xrh426lf19dxss12kgrfi8"))))
1908 (build-system r-build-system)
1916 (home-page "https://cran.r-project.org/web/packages/model4you/")
1917 (synopsis "Stratified and personalised models based on trees and forests")
1919 "This package provides procedures for model-based trees for subgroup
1920 analyses in clinical trials and model-based forests for the estimation and
1921 prediction of personalised treatment effects. Currently partitioning of linear
1922 models, @code{lm()}, generalised linear models, @code{glm()}, and
1923 Weibull models, @code{survreg()}, are supported. Advanced plotting functionality is
1924 supported for the trees and a test for parameter heterogeneity is provided for
1925 the personalised models.")
1926 (license license:gpl2+)))
1928 (define-public r-modelr
1935 (uri (cran-uri "modelr" version))
1938 "1i31nff7bqibk6r4hhd4j1vzwbyaf8493v0bjaagn36njmysfnw2"))))
1939 (build-system r-build-system)
1949 (home-page "https://github.com/tidyverse/modelr")
1950 (synopsis "Helper functions for modelling in pipelines")
1952 "Functions for modelling that help you seamlessly integrate modelling
1953 into a pipeline of data manipulation and visualisation.")
1954 (license license:gpl3)))
1956 (define-public r-hmm
1962 (uri (cran-uri "HMM" version))
1965 "03b548bnwqpnd7zypb4gvy9chyi5li2hp99a9vrh4qszxg2ihas7"))))
1966 (properties `((upstream-name . "HMM")))
1967 (build-system r-build-system)
1968 (home-page "https://cran.r-project.org/web/packages/HMM/")
1969 (synopsis "Hidden Markov Models")
1970 (description "This package provides an easy to use library to setup, apply
1971 and make inference with discrete time and discrete space hidden Markov
1973 (license license:gpl2+)))
1975 (define-public r-hiddenmarkov
1977 (name "r-hiddenmarkov")
1981 (uri (cran-uri "HiddenMarkov" version))
1984 "05dm3nl0ffsz2ziw3bz5bivyxk7r5bxs8xhky3hz660qaqzd51ki"))))
1985 (build-system r-build-system)
1988 (home-page "https://cran.r-project.org/web/packages/HiddenMarkov/")
1989 (synopsis "Hidden markov models for R")
1990 (description "This package contains functions for the analysis of Discrete
1991 Time Hidden Markov Models, Markov Modulated GLMs and the Markov Modulated
1992 Poisson Process. It includes functions for simulation, parameter estimation,
1993 and the Viterbi algorithm. The algorithms are based of those of Walter
1995 (license license:gpl2+)))
1997 (define-public r-httpuv
2003 (uri (cran-uri "httpuv" version))
2006 "0mlilxh2mlrsbbrncla2rg02crr8nnajv649d8whx7ayr8lkdxpm"))
2007 ;; Unvendor bundled libraries. As of 1.5.4 the vendored libuv
2008 ;; only contains fixes for building on Solaris.
2009 (patches (search-patches "r-httpuv-1.5.5-unvendor-libuv.patch"))
2010 (modules '((guix build utils)))
2011 ;; Cannot unbundle http-parser, because it contains local
2014 '(delete-file-recursively "src/libuv"))))
2015 (build-system r-build-system)
2018 (modify-phases %standard-phases
2019 (add-after 'unpack 'unbundle-libuv
2020 (lambda* (#:key outputs #:allow-other-keys)
2021 (substitute* (find-files "src" "\\.cpp$|\\.h$")
2022 (("\"libuv/include/uv\\.h\"")
2024 ;; Fix https://github.com/rstudio/httpuv/issues/282
2025 (substitute* "src/http.cpp"
2026 (("uv_pipe_init\\(pLoop, &pSocket->handle\\.pipe, true\\);")
2027 "uv_pipe_init(pLoop, &pSocket->handle.pipe, 0);")))))))
2031 (list r-later r-promises r-r6 r-rcpp))
2032 (home-page "https://github.com/rstudio/httpuv")
2033 (synopsis "HTTP and WebSocket server library for R")
2035 "The httpuv package provides low-level socket and protocol support for
2036 handling HTTP and WebSocket requests directly from within R. It is primarily
2037 intended as a building block for other packages, rather than making it
2038 particularly easy to create complete web applications using httpuv alone.")
2039 ;; This package includes third-party code that was originally released
2040 ;; under various non-copyleft licenses. Full licensing information can be
2041 ;; obtained here: https://github.com/rstudio/httpuv/blob/master/LICENSE
2042 (license license:gpl3+)))
2044 (define-public r-jsonlite
2050 (uri (cran-uri "jsonlite" version))
2053 "0k6dal7gmm19jl5sjsry5gwbnhsbrnn00q3iixig8k6bxgpr463v"))))
2054 (build-system r-build-system)
2057 (home-page "https://arxiv.org/abs/1403.2805")
2058 (synopsis "Robust, high performance JSON parser and generator for R")
2060 "The jsonlite package provides a fast JSON parser and generator optimized
2061 for statistical data and the web. It offers flexible, robust, high
2062 performance tools for working with JSON in R and is particularly powerful for
2063 building pipelines and interacting with a web API. In addition to converting
2064 JSON data from/to R objects, jsonlite contains functions to stream, validate,
2065 and prettify JSON data. The unit tests included with the package verify that
2066 all edge cases are encoded and decoded consistently for use with dynamic data
2067 in systems and applications.")
2068 (license license:expat)))
2070 (define-public r-servr
2076 (uri (cran-uri "servr" version))
2079 "11x0857m3xzdbzr4z0vx4fcdk36arfagyf2qgamvprich0qisknr"))))
2080 (build-system r-build-system)
2082 (list r-httpuv r-jsonlite r-mime r-xfun))
2083 (home-page "https://github.com/yihui/servr")
2084 (synopsis "Simple HTTP server to serve static files or dynamic documents")
2086 "Servr provides an HTTP server in R to serve static files, or dynamic
2087 documents that can be converted to HTML files (e.g., R Markdown) under a given
2089 (license license:expat)))
2091 (define-public r-howmany
2097 (uri (cran-uri "howmany" version))
2100 "045ck8qahfg2swbgyf7dpl32ryq1m4sbalhr7m5qdgpm62vz8h7f"))))
2101 (build-system r-build-system)
2102 (home-page "https://cran.r-project.org/web/packages/howmany/")
2103 (synopsis "Lower bound for the number of correct rejections")
2104 (description "When testing multiple hypotheses simultaneously, this package
2105 provides functionality to calculate a lower bound for the number of correct
2106 rejections (as a function of the number of rejected hypotheses), which holds
2107 simultaneously -with high probability- for all possible number of rejections.
2108 As a special case, a lower bound for the total number of false null hypotheses
2109 can be inferred. Dependent test statistics can be handled for multiple tests
2110 of associations. For independent test statistics, it is sufficient to provide
2111 a list of p-values.")
2112 (license license:gpl2+)))
2114 (define-public r-htmltools
2116 (name "r-htmltools")
2120 (uri (cran-uri "htmltools" version))
2123 "1yv74ydyqm28gfhimmr7825sj1iaawpwsnzq05c2ma756q2dbivx"))))
2124 (build-system r-build-system)
2126 (list r-base64enc r-digest r-fastmap r-rlang))
2127 (home-page "https://cran.r-project.org/web/packages/htmltools")
2128 (synopsis "R tools for HTML")
2130 "This package provides tools for HTML generation and output in R.")
2131 (license license:expat)))
2133 (define-public r-htmlwidgets
2135 (name "r-htmlwidgets")
2139 (uri (cran-uri "htmlwidgets" version))
2142 "1hgz8sx8xrvfcdwa4q15k942w4qsqg8lyxbbf7qyfzbi807wcgqs"))))
2143 (build-system r-build-system)
2145 (list r-htmltools r-jsonlite r-yaml))
2148 (home-page "https://github.com/ramnathv/htmlwidgets")
2149 (synopsis "HTML Widgets for R")
2151 "HTML widgets is a framework for creating HTML widgets that render in
2152 various contexts including the R console, R Markdown documents, and Shiny web
2154 (license license:expat)))
2156 (define-public r-htmltable
2158 (name "r-htmltable")
2163 (uri (cran-uri "htmlTable" version))
2165 (base32 "17csp0ry4iy4m5xy271dn5wd81v4p03l79swmvlfxkvpdmhvb8jc"))))
2166 (properties `((upstream-name . "htmlTable")))
2167 (build-system r-build-system)
2178 (home-page "http://gforge.se/packages/")
2179 (synopsis "Advanced tables for Markdown/HTML")
2181 "This package provides functions to build tables with advanced layout
2182 elements such as row spanners, column spanners, table spanners, zebra
2183 striping, and more. While allowing advanced layout, the underlying
2184 CSS-structure is simple in order to maximize compatibility with word
2185 processors such as LibreOffice. The package also contains a few text
2186 formatting functions that help outputting text compatible with HTML or
2188 (license license:gpl3+)))
2190 (define-public r-curl
2196 (uri (cran-uri "curl" version))
2199 "0s55022hy8shjm1pzax1dqzrg20bv4nvlwnjnddk3dp89g5zmcch"))))
2200 (build-system r-build-system)
2203 (modify-phases %standard-phases
2204 ;; The environment variable CURL_CA_BUNDLE is only respected when
2205 ;; running Windows, so we disable the platform checks.
2206 ;; This can be removed once the libcurl has been patched.
2207 (add-after 'unpack 'allow-CURL_CA_BUNDLE
2209 (substitute* "R/onload.R"
2210 (("if \\(!grepl\\(\"mingw\".*")
2212 (substitute* "src/handle.c"
2213 (("/\\* Only set" m)
2215 const char *_ca_bundle = getenv(\"CURL_CA_BUNDLE\");
2216 if(_ca_bundle != NULL) { curl_easy_setopt(handle, CURLOPT_CAINFO, _ca_bundle); }
2221 (list pkg-config r-knitr))
2222 (home-page "https://github.com/jeroenooms/curl")
2223 (synopsis "HTTP client for R")
2225 "The @code{curl()} and @code{curl_download()} functions provide highly
2226 configurable drop-in replacements for base @code{url()} and
2227 @code{download.file()} with better performance, support for encryption, gzip
2228 compression, authentication, and other @code{libcurl} goodies. The core of
2229 the package implements a framework for performing fully customized requests
2230 where data can be processed either in memory, on disk, or streaming via the
2231 callback or connection interfaces.")
2232 (license license:expat)))
2234 (define-public r-hwriter
2241 (uri (cran-uri "hwriter" version))
2244 "1wxnv8h9cs65m3z01dpnnkgn2cpwfsck70g1jz9nbkr7mdaa4bzd"))))
2245 (build-system r-build-system)
2246 (home-page "https://cran.r-project.org/web/packages/hwriter")
2247 (synopsis "Output R objects in HTML format")
2249 "This package provides easy-to-use and versatile functions to output R
2250 objects in HTML format.")
2251 (license license:lgpl2.1+)))
2253 (define-public r-rjson
2260 (uri (cran-uri "rjson" version))
2263 "1qm27r1w677zg31gsiln60hcciszbymkw78cnaq7s36cbk9mcawq"))))
2264 (build-system r-build-system)
2265 (home-page "https://cran.r-project.org/web/packages/rjson")
2266 (synopsis "JSON library for R")
2268 "This package provides functions to convert R objects into JSON objects
2270 (license license:gpl2+)))
2272 (define-public r-fastmap
2279 (uri (cran-uri "fastmap" version))
2282 "0aw29hnq3ppn7bsnwg9d9sp84k1cvq30lrmfzqn315n0nhkfa4wi"))))
2283 (properties `((upstream-name . "fastmap")))
2284 (build-system r-build-system)
2285 (home-page "https://r-lib.github.io/fastmap/")
2286 (synopsis "Fast implementation of a key-value store")
2288 "This package provides a fast implementation of a key-value store.
2289 Environments are commonly used as key-value stores, but every time a new key
2290 is used, it is added to R's global symbol table, causing a small amount of
2291 memory leakage. This can be problematic in cases where many different keys
2292 are used. Fastmap avoids this memory leak issue by implementing the map using
2293 data structures in C++.")
2294 (license license:expat)))
2296 (define-public r-fastghquad
2298 (name "r-fastghquad")
2303 (uri (cran-uri "fastGHQuad" version))
2306 "1zj7nsbnx4g253m3dpz9vi3zk3jxwrixwjw1ks6n4shpb4dlkp2w"))))
2307 (properties `((upstream-name . "fastGHQuad")))
2308 (build-system r-build-system)
2311 (home-page "https://github.com/awblocker/fastGHQuad")
2312 (synopsis "Fast Rcpp implementation of Gauss-Hermite Quadrature")
2314 "This package implements numerically-stable Gauss-Hermite quadrature
2315 rules and utility functions for adaptive GH quadrature.")
2316 (license license:expat)))
2318 (define-public r-rstpm2
2325 (uri (cran-uri "rstpm2" version))
2328 "17mhzfxh761vl64ar6pynpj3k2jkhjgbacxsjhkrfkbmy3aiv0d1"))))
2329 (properties `((upstream-name . "rstpm2")))
2330 (build-system r-build-system)
2342 (home-page "https://github.com/mclements/rstpm2")
2343 (synopsis "Link-based survival models")
2345 "This package provides R implementations of @dfn{generalized survival
2346 models} (GSMs), smooth @dfn{accelerated failure time} (AFT) models and Markov
2347 multi-state models.")
2348 ;; One of these licenses
2349 (license (list license:gpl2 license:gpl3))))
2351 ;; This package includes minified JavaScript files. When upgrading please
2352 ;; check that there are no new minified JavaScript files.
2353 (define-public r-jquerylib
2355 (name "r-jquerylib")
2360 (uri (cran-uri "jquerylib" version))
2363 "04a40v4znpj98j7y6009d74a6g9dchj5rr3p08cgz9p3rlfw3g7h"))
2365 '(for-each delete-file
2366 '("inst/lib/1.12.4/jquery-1.12.4.min.js"
2367 "inst/lib/2.2.4/jquery-2.2.4.min.js"
2368 "inst/lib/3.6.0/jquery-3.6.0.min.js")))))
2369 (properties `((upstream-name . "jquerylib")))
2370 (build-system r-build-system)
2372 `(#:modules ((guix build utils)
2373 (guix build r-build-system)
2376 (modify-phases %standard-phases
2377 (add-after 'unpack 'process-javascript
2378 (lambda* (#:key inputs #:allow-other-keys)
2379 (with-directory-excursion "inst/lib/"
2383 `(("1.12.4/jquery-1.12.4.js"
2384 "1.12.4/jquery-1.12.4.min.js")
2385 ("2.2.4/jquery-2.2.4.js"
2386 "2.2.4/jquery-2.2.4.min.js")
2387 ("3.6.0/jquery-3.6.0.js"
2388 "3.6.0/jquery-3.6.0.min.js"))))
2389 (lambda (sources targets)
2390 (for-each (lambda (source target)
2391 (format #t "Processing ~a --> ~a~%"
2393 (invoke "esbuild" source "--minify"
2394 (string-append "--outfile=" target)))
2395 sources targets)))))))))
2400 (home-page "https://cran.r-project.org/package=jquerylib")
2401 (synopsis "Obtain jQuery as an HTML dependency object")
2403 "Obtain any major version of jQuery and use it in any webpage generated
2404 by htmltools (e.g. shiny, htmlwidgets, and rmarkdown). Most R users don't
2405 need to use this package directly, but other R packages (e.g. shiny,
2406 rmarkdown, etc.) depend on this package to avoid bundling redundant copies of
2408 (license license:expat)))
2410 (define-public r-sass
2417 (uri (cran-uri "sass" version))
2420 "1fq8wqnxmx10lg0dh4qzmxdkhd22fjh8vhassapxb1chsimwn3w5"))))
2421 (properties `((upstream-name . "sass")))
2422 (build-system r-build-system)
2424 (list r-fs r-htmltools r-r6 r-rappdirs r-rlang))
2425 (native-inputs (list r-knitr))
2426 (home-page "https://github.com/rstudio/sass")
2427 (synopsis "Syntactically Awesome Style Sheets (SASS)")
2429 "This package provides an SCSS compiler, powered by the libsass library.
2430 With this, R developers can use variables, inheritance, and functions to
2431 generate dynamic style sheets. The package uses the Sass CSS extension
2432 language, which is stable, powerful, and CSS compatible.")
2433 (license license:expat)))
2435 (define-public r-saver
2441 (uri (cran-uri "SAVER" version))
2444 "1s1kw8idkaj7j90fw4qn9k0wd4vz0sblsk06ry6lm4afcar0p158"))))
2445 (properties `((upstream-name . "SAVER")))
2446 (build-system r-build-system)
2453 (native-inputs (list r-knitr))
2454 (home-page "https://github.com/mohuangx/SAVER")
2456 "Recovery of gene expression profile in noisy and sparse scRNA-seq data")
2458 "This package is an implementation of a regularized regression prediction
2459 and empirical Bayes method to recover the true gene expression profile in noisy
2460 and sparse single-cell RNA-seq data. In @dfn{single-cell RNA sequencing}
2461 (scRNA-seq) studies, only a small fraction of the transcripts present in each
2462 cell are sequenced. This leads to unreliable quantification of genes with low
2463 or moderate expression, which hinders downstream analysis. This package
2464 @dfn{single-cell analysis via expression recovery} (SAVER) implements an
2465 expression recovery method for unique molecule index (UMI)-based scRNA-seq
2466 data that borrows information across genes and cells to provide accurate
2467 expression estimates for all genes.")
2468 (license license:gpl2)))
2470 ;; This package includes minified JavaScript files. When upgrading please
2471 ;; check that there are no new minified JavaScript files.
2472 (define-public r-bslib
2479 (uri (cran-uri "bslib" version))
2482 "0jcqklry1nkibz0sydsz5xdsnb4wnrrhvmyr9ji3k45bbipbap2z"))
2484 '(for-each delete-file
2485 '("inst/lib/bs-a11y-p/plugins/js/bootstrap-accessibility.min.js"
2486 "inst/lib/bs-colorpicker/js/bootstrap-colorpicker.min.js"
2487 "inst/lib/bs3/assets/javascripts/bootstrap.min.js"
2488 "inst/lib/bs4/dist/js/bootstrap.bundle.min.js"
2489 "inst/lib/bs5/dist/js/bootstrap.bundle.min.js")))))
2490 (properties `((upstream-name . "bslib")))
2491 (build-system r-build-system)
2493 `(#:modules ((guix build utils)
2494 (guix build r-build-system)
2497 (modify-phases %standard-phases
2498 (add-after 'unpack 'process-javascript
2499 (lambda* (#:key inputs #:allow-other-keys)
2500 (with-directory-excursion "inst/lib/"
2504 `(("bs-a11y-p/plugins/js/bootstrap-accessibility.js"
2505 "bs-a11y-p/plugins/js/bootstrap-accessibility.min.js")
2506 ("bs-colorpicker/js/bootstrap-colorpicker.js"
2507 "bs-colorpicker/js/bootstrap-colorpicker.min.js")
2508 ("bs3/assets/javascripts/bootstrap.js"
2509 "bs3/assets/javascripts/bootstrap.min.js")
2510 (,(assoc-ref inputs "js-bootstrap4-bundle")
2511 "bs4/dist/js/bootstrap.bundle.min.js")
2512 (,(assoc-ref inputs "js-bootstrap5-bundle")
2513 "bs5/dist/js/bootstrap.bundle.min.js"))))
2514 (lambda (sources targets)
2515 (for-each (lambda (source target)
2516 (format #t "Processing ~a --> ~a~%"
2518 (invoke "esbuild" source "--minify"
2519 (string-append "--outfile=" target)))
2520 sources targets)))))))))
2522 (list r-htmltools r-jquerylib r-jsonlite r-rlang r-sass))
2524 `(("esbuild" ,esbuild)
2525 ("js-bootstrap4-bundle"
2528 (uri "https://raw.githubusercontent.com/twbs/bootstrap/v4.6.0/dist/js/bootstrap.bundle.js")
2531 "04abvgp923w36qfqkkl2syim3bl119nwxbgials90z1jyb8jgss1"))))
2532 ("js-bootstrap5-bundle"
2535 (uri "https://raw.githubusercontent.com/twbs/bootstrap/v5.0.2/dist/js/bootstrap.bundle.js")
2538 "06vin94nqw1vzs4zrqcms8z9js9fckbj8gwyx07awm8jkjhnqfhl"))))))
2539 (home-page "https://rstudio.github.io/bslib/")
2540 (synopsis "Custom Bootstrap Sass themes for shiny and rmarkdown")
2542 "This package simplifies custom CSS styling of both shiny and rmarkdown
2543 via Bootstrap Sass. It supports both Bootstrap 3 and 4 as well as their
2544 various Bootswatch themes. An interactive widget is also provided for
2545 previewing themes in real time.")
2546 (license license:expat)))
2548 ;; This package includes minified JavaScript files. When upgrading please
2549 ;; check that there are no new minified JavaScript files.
2550 (define-public r-shiny
2558 (url "https://github.com/rstudio/shiny")
2559 (commit (string-append "v" version))))
2560 (file-name (git-file-name name version))
2563 "0wvc6jlgs41p05wbk8gahnl7sfnc4hpliyh9dbi5w52ngsg6wcr7"))
2565 '(for-each delete-file
2566 '("inst/www/shared/bootstrap/js/bootstrap.min.js"
2567 "inst/www/shared/bootstrap/accessibility/js/bootstrap-accessibility.min.js" ; TODO
2568 "inst/www/shared/datatables/js/jquery.dataTables.min.js"
2569 "inst/www/shared/datepicker/js/bootstrap-datepicker.min.js"
2570 "inst/www/shared/highlight/highlight.pack.js"
2571 "inst/www/shared/ionrangeslider/js/ion.rangeSlider.min.js"
2572 "inst/www/shared/jquery.min.js"
2573 "inst/www/shared/jqueryui/jquery-ui.min.js"
2574 "inst/www/shared/legacy/jquery.min.js"
2575 "inst/www/shared/selectize/accessibility/js/selectize-plugin-a11y.min.js"
2576 "inst/www/shared/selectize/js/selectize.min.js"
2577 "inst/www/shared/shiny.min.js"
2578 "inst/www/shared/showdown/compressed/showdown.js"
2579 "inst/www/shared/strftime/strftime-min.js")))))
2580 (build-system r-build-system)
2582 `(#:modules ((guix build r-build-system)
2583 (guix build minify-build-system)
2586 #:imported-modules (,@%r-build-system-modules
2587 (guix build minify-build-system))
2589 (modify-phases (@ (guix build r-build-system) %standard-phases)
2590 (add-after 'unpack 'replace-bundled-minified-JavaScript
2591 (lambda* (#:key inputs #:allow-other-keys)
2592 (let ((replace-file (lambda (old new)
2593 (format #t "replacing ~a with ~a\n" old new)
2594 (symlink new old))))
2595 ;; NOTE: Files in ./inst/www/shared/datepicker/js/locales/
2596 ;; contain just data. They are not minified code, so we don't
2598 (with-directory-excursion "inst/www/shared"
2599 (replace-file "strftime/strftime-min.js"
2600 (search-input-file inputs
2601 "/share/javascript/strftime.min.js"))
2602 (replace-file "highlight/highlight.pack.js"
2603 (search-input-file inputs
2604 "/share/javascript/highlight.min.js"))
2605 (replace-file "datatables/js/jquery.dataTables.min.js"
2606 (search-input-file inputs
2607 "/share/javascript/jquery.dataTables.min.js"))
2608 (replace-file "selectize/js/selectize.min.js"
2609 (search-input-file inputs
2610 "/share/javascript/selectize.min.js"))
2611 (for-each (match-lambda
2613 (minify source #:target target)))
2614 `(("jqueryui/jquery-ui.js" .
2615 "jqueryui/jquery-ui.min.js")
2616 ("datepicker/js/bootstrap-datepicker.js" .
2617 "datepicker/js/bootstrap-datepicker.min.js")
2618 ("ionrangeslider/js/ion.rangeSlider.js" .
2619 "ionrangeslider/js/ion.rangeSlider.min.js")
2620 ("bootstrap/js/bootstrap.js" .
2621 "bootstrap/js/bootstrap.min.js")
2622 (,(assoc-ref inputs "js-bootstrap-accessibility") .
2623 "bootstrap/accessibility/js/bootstrap-accessibility.min.js")
2628 ("legacy/jquery.js" .
2629 "legacy/jquery.min.js")
2630 ("selectize/accessibility/js/selectize-plugin-a11y.js" .
2631 "selectize/accessibility/js/selectize-plugin-a11y.min.js")
2632 ("showdown/src/showdown.js" .
2633 "showdown/compressed/showdown.js"))))))))))
2656 (list js-datatables js-selectize js-strftime js-highlight))
2658 `(("uglifyjs" ,node-uglify-js)
2659 ("gfortran" ,gfortran)
2660 ("js-bootstrap-accessibility"
2663 (uri "https://raw.githubusercontent.com/paypal/bootstrap-accessibility-plugin/\
2664 v1.0.7/_site/plugins/js/bootstrap-accessibility.js")
2667 "1489wyzwrpf86y7vhc13n4v3mszmsfybhd3f75jkpnbvyp5sncm8"))))))
2668 (home-page "https://shiny.rstudio.com")
2669 (synopsis "Easy interactive web applications with R")
2671 "Makes it incredibly easy to build interactive web applications
2672 with R. Automatic \"reactive\" binding between inputs and outputs and
2673 extensive prebuilt widgets make it possible to build beautiful,
2674 responsive, and powerful applications with minimal effort.")
2675 (license license:artistic2.0)))
2677 (define-public r-shinyhelper
2679 (name "r-shinyhelper")
2684 (uri (cran-uri "shinyhelper" version))
2686 (base32 "1c4hvf19j3yyh8r12nx85ldkxs89g98q74csnqs5ml5l79a65vgp"))))
2687 (properties `((upstream-name . "shinyhelper")))
2688 (build-system r-build-system)
2689 (propagated-inputs (list r-markdown r-shiny))
2690 (home-page "https://cran.r-project.org/package=shinyhelper")
2691 (synopsis "Easily add Markdown help files to shiny app elements")
2693 "This package creates a lightweight way to add markdown helpfiles to
2694 Shiny apps, using modal dialog boxes, with no need to observe each help button
2696 (license license:gpl3)))
2698 ;; This package includes minified JavaScript files. When upgrading please
2699 ;; check that there are no new minified JavaScript files.
2700 (define-public r-shinytree
2702 (name "r-shinytree")
2707 (uri (cran-uri "shinyTree" version))
2710 "0jfx2capckv7hf2yx3fn8i4rcmhi222ah91jnmhg497x8wgz31s3"))
2711 (modules '((guix build utils)))
2714 ;; Delete minified JavaScript
2715 (for-each delete-file
2716 '("inst/www/jsTree-3.3.7/libs/require.js"
2717 "inst/www/jsTree-3.3.7/libs/jquery.js"
2718 "inst/www/jsTree-3.3.7/jstree.min.js"))
2720 (properties `((upstream-name . "shinyTree")))
2721 (build-system r-build-system)
2723 `(#:modules ((guix build utils)
2724 (guix build r-build-system)
2728 (modify-phases %standard-phases
2729 (add-after 'unpack 'replace-minified-javascript
2730 (lambda* (#:key inputs #:allow-other-keys)
2731 (with-directory-excursion "inst/www/jsTree-3.3.7/"
2732 (symlink (search-input-file inputs
2733 "/share/javascript/require.min.js")
2738 `((,(assoc-ref inputs "js-jquery")
2742 (lambda (sources targets)
2743 (for-each (lambda (source target)
2744 (format #t "Processing ~a --> ~a~%"
2746 (let ((minified (open-pipe* OPEN_READ "uglifyjs" source)))
2747 (call-with-output-file target
2749 (dump-port minified port)))))
2753 (list r-htmlwidgets r-jsonlite r-promises r-shiny r-stringr))
2755 (list js-requirejs))
2757 `(("uglifyjs" ,node-uglify-js)
2761 (uri "https://code.jquery.com/jquery-3.3.1.js")
2764 "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq"))))))
2765 (home-page "https://cran.r-project.org/web/packages/shinyTree/")
2766 (synopsis "jsTree bindings for Shiny")
2768 "This package exposes R bindings to jsTree, a JavaScript library that
2769 supports interactive trees, to enable rich, editable trees in Shiny.")
2770 (license license:expat)))
2772 (define-public r-shinydashboard
2774 (name "r-shinydashboard")
2778 (uri (cran-uri "shinydashboard" version))
2781 "0hrqkwlpb8rnmp5j74p134g4c4cl16icmwc2ip6k1634fa2y8vm5"))))
2782 (build-system r-build-system)
2783 ;; The directory inst/AdminLTE/ contains a minified JavaScript file.
2784 ;; Regenerate it from the included sources.
2787 (modify-phases %standard-phases
2788 (add-after 'unpack 'generate-minified-javascript
2790 (with-directory-excursion "inst/AdminLTE"
2791 (let ((target "app.min.js")
2793 (format #t "Processing ~a --> ~a~%"
2795 (delete-file target)
2796 (invoke "esbuild" source "--minify"
2797 (string-append "--outfile=" target)))))))))
2799 (list r-htmltools r-promises r-shiny))
2802 (home-page "https://rstudio.github.io/shinydashboard/")
2803 (synopsis "Create dashboards with shiny")
2804 (description "This package provides an extension to the Shiny web
2805 application framework for R, making it easy to create attractive dashboards.")
2806 ;; This package includes software that was released under the Expat
2807 ;; license, but the whole package is released under GPL version 2 or
2809 (license license:gpl2+)))
2811 (define-public r-shinyfiles
2813 (name "r-shinyfiles")
2818 (uri (cran-uri "shinyFiles" version))
2820 (base32 "1l4a4v9ivxkj2vx6xw4z3pk7a8px23icppcgvgpybibq2j74pglg"))))
2821 (properties `((upstream-name . "shinyFiles")))
2822 (build-system r-build-system)
2824 (list r-fs r-htmltools r-jsonlite r-shiny r-tibble))
2825 (home-page "https://github.com/thomasp85/shinyFiles")
2826 (synopsis "Server-side file system viewer for Shiny")
2828 "This package provides functionality for client-side navigation of the
2829 server side file system in shiny apps. In case the app is running locally
2830 this gives the user direct access to the file system without the need to
2831 \"download\" files to a temporary location. Both file and folder selection as
2832 well as file saving is available.")
2833 (license license:gpl2+)))
2835 (define-public r-shinythemes
2837 (name "r-shinythemes")
2842 (uri (cran-uri "shinythemes" version))
2845 "0qr9bfxw8afxns44i2j4msignf6g5qb2nzpay2lpv343rrlqbmip"))))
2846 (properties `((upstream-name . "shinythemes")))
2847 (build-system r-build-system)
2848 (propagated-inputs (list r-shiny))
2849 (home-page "https://rstudio.github.io/shinythemes/")
2850 (synopsis "Themes for Shiny")
2852 "This package provides themes for use with Shiny. It includes several
2853 Bootstrap themes, which are packaged for use with Shiny applications.")
2854 ;; The package is released under version 3 of the GPL, but it includes
2855 ;; source files that are covered by the Expat license. It also includes
2856 ;; fonts under SIL or the ASL.
2857 (license (list license:gpl3 license:expat
2858 license:silofl1.1 license:asl2.0))))
2860 ;; The package sources include minified variants of d3.js and non-minified
2861 ;; source code of d3-jetpack.
2862 (define-public r-d3r
2869 (uri (cran-uri "d3r" version))
2872 "1qijkllfaaw0lb29j8mappm8jz9kg8gkihxq5wqhb4gabsazdwva"))))
2873 (build-system r-build-system)
2875 `(#:modules ((guix build utils)
2876 (guix build r-build-system)
2879 (modify-phases %standard-phases
2880 (add-after 'unpack 'process-javascript
2881 (lambda* (#:key inputs #:allow-other-keys)
2882 (with-directory-excursion "inst/www/d3/"
2886 `((,(assoc-ref inputs "d3.v3.js")
2887 "v3/dist/d3.min.js")
2888 (,(assoc-ref inputs "d3.v4.js")
2889 "v4/dist/d3.min.js")
2890 (,(assoc-ref inputs "d3.v5.js")
2891 "v5/dist/d3.min.js")
2892 (,(assoc-ref inputs "d3.v6.js")
2893 "v6/dist/d3.min.js")
2894 (,(assoc-ref inputs "d3.v7.js")
2895 "v7/dist/d3.min.js"))))
2896 (lambda (sources targets)
2897 (for-each (lambda (source target)
2898 (format #t "Processing ~a --> ~a~%"
2900 (delete-file target)
2901 (invoke "esbuild" source "--minify"
2902 (string-append "--outfile=" target)))
2903 sources targets)))))))))
2905 (list r-dplyr r-htmltools r-rlang r-tidyr))
2907 `(("esbuild" ,esbuild)
2911 (uri "https://d3js.org/d3.v3.js")
2914 "1arr7sr08vy7wh0nvip2mi7dpyjw4576vf3bm45rp4g5lc1k1x41"))))
2918 (uri "https://d3js.org/d3.v4.js")
2921 "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg"))))
2925 (uri "https://d3js.org/d3.v5.js")
2928 "0kxvx5pfagxn6nhavdwsdnzyd26g0z5dsfi1pi5dvcmb0c8ipcdn"))))
2932 (uri "https://d3js.org/d3.v6.js")
2935 "1x6432ca7p1pfxhz3airzw943fincn9izzxkclc1wmphcvv2n2p9"))))
2939 (uri "https://d3js.org/d3.v7.js")
2942 "0sd6vavxs8mx5xyb8xahlqghdiczqd284a7d5wravhqnrj0bw097"))))))
2943 (home-page "https://github.com/timelyportfolio/d3r")
2944 (synopsis "d3.js utilities for R")
2946 "This package provides a suite of functions to help ease the use of the
2947 d3.js visualization library in R. These helpers include
2948 @code{htmltools::htmlDependency} functions, hierarchy builders, and conversion
2949 tools for @code{partykit}, @code{igraph}, @code{table}, and @code{data.frame}
2950 R objects into the JSON format that the d3.js library expects.")
2951 (license license:bsd-3)))
2953 ;; We use the latest commit here because the last release was in 2016 while
2954 ;; the latest commit was in 2018.
2955 (define-public r-sankeyd3
2956 (let ((commit "fd50a74e29056e0d67d75b4d04de47afb2f932bc")
2960 (version (git-version "0.3.2" revision commit))
2965 (url "https://github.com/fbreitwieser/sankeyD3")
2967 (file-name (git-file-name name version))
2970 "0jrcnfax321pszbpjdifnkbrgbjr43bjzvlzv1p5a8wskksqwiyx"))))
2971 (build-system r-build-system)
2973 (list r-d3r r-htmlwidgets r-shiny r-magrittr))
2974 (home-page "https://github.com/fbreitwieser/sankeyD3")
2975 (synopsis "Sankey network graphs from R")
2977 "This package provides an R library to generate Sankey network graphs
2978 in R and Shiny via the D3 visualization library.")
2979 ;; The R code is licensed under GPLv3+. It includes the non-minified
2980 ;; JavaScript source code of d3-sankey, which is released under the
2981 ;; 3-clause BSD license.
2982 (license (list license:gpl3+ license:bsd-3)))))
2984 (define-public r-wesanderson
2986 (name "r-wesanderson")
2991 (uri (cran-uri "wesanderson" version))
2994 "09mr6p2jmqdjq27cz974w5hyxgn929zp9z3inhxqmmh1582fmdi2"))))
2995 (properties `((upstream-name . "wesanderson")))
2996 (build-system r-build-system)
2997 (home-page "https://github.com/karthik/wesanderson")
2998 (synopsis "Wes Anderson color palette generator")
3000 "This package provides color palettes that have been generated mostly
3001 from Wes Anderson movies.")
3002 (license license:expat)))
3004 (define-public r-gg-gap
3011 (uri (cran-uri "gg.gap" version))
3014 "0m66050ryn31xmsmmikjsssllasvjdmp9yjbwfdwfpwdv106zn9h"))))
3015 (properties `((upstream-name . "gg.gap")))
3016 (build-system r-build-system)
3018 (list r-cowplot r-ggplot2))
3019 (home-page "https://github.com/ChrisLou-bioinfo/gg.gap")
3020 (synopsis "Define segments on the y-axis for ggplot2")
3022 "The @code{gg.gap} function enables you to define segments for the y-axis
3023 in a ggplot2 plot.")
3024 (license license:gpl3)))
3026 (define-public r-mbess
3033 (uri (cran-uri "MBESS" version))
3035 (base32 "0qmyvjx2zn5hlzdbz8c94g8l4707swhn7sq9mxkdqiydmflzv0b5"))))
3036 (properties `((upstream-name . "MBESS")))
3037 (build-system r-build-system)
3039 (list r-boot r-lavaan r-mass r-mnormt r-nlme r-openmx r-sem r-semtools))
3040 (home-page "https://www3.nd.edu/~kkelley/site/MBESS.html")
3041 (synopsis "Methods for designing research studies")
3043 "This package implements methods that are useful in designing research
3044 studies and analyzing data, with particular emphasis on methods that are
3045 developed for or used within the behavioral, educational, and social
3046 sciences (broadly defined). That being said, many of the methods implemented
3047 within MBESS are applicable to a wide variety of disciplines. MBESS has a
3048 suite of functions for a variety of related topics, such as effect sizes,
3049 confidence intervals for effect sizes (including standardized effect sizes and
3050 noncentral effect sizes), sample size planning (from the @dfn{accuracy in
3051 parameter estimation} (AIPE), power analytic, equivalence, and minimum-risk
3052 point estimation perspectives), mediation analysis, various properties of
3053 distributions, and a variety of utility functions.")
3054 ;; Either version of the GPL.
3055 (license (list license:gpl2 license:gpl3))))
3057 (define-public r-homologene
3059 (name "r-homologene")
3060 (version "1.4.68.19.3.27")
3064 (uri (cran-uri "homologene" version))
3066 (base32 "0d7wxisk0vqk1n165v1i19bc02zv78h5r5d3jqai5y6nkmwn01sh"))))
3067 (properties `((upstream-name . "homologene")))
3068 (build-system r-build-system)
3070 (list r-dplyr r-magrittr r-purrr r-r-utils r-readr))
3071 (home-page "https://github.com/oganm/homologene")
3072 (synopsis "Quick access to homologene and gene annotation updates")
3074 "This package provides a wrapper for the homologene database by the
3075 National Center for Biotechnology Information (NCBI). It allows searching for
3076 gene homologs across species. The package also includes an updated version of
3077 the homologene database where gene identifiers and symbols are replaced with
3078 their latest (at the time of submission) version and functions to fetch latest
3079 annotation data to keep updated.")
3080 (license license:expat)))
3082 (define-public r-ggtern
3089 (uri (cran-uri "ggtern" version))
3091 (base32 "15hhn8msy0l8zbq8ms0zvg1iajn1c28gd77v3hp6dvwwsla8zzbd"))))
3092 (properties `((upstream-name . "ggtern")))
3093 (build-system r-build-system)
3095 (list r-compositions
3106 (home-page "http://www.ggtern.com")
3107 (synopsis "Extension to ggplot2 for ternary diagrams")
3109 "This package extends the functionality of ggplot2, providing the
3110 capability to plot ternary diagrams for (a subset of) the ggplot2 geometries.
3111 Additionally, ggtern has implemented several new geometries which are
3112 unavailable to the standard ggplot2 release.")
3113 (license license:gpl2)))
3115 (define-public r-tablerdash
3117 (name "r-tablerdash")
3122 (uri (cran-uri "tablerDash" version))
3125 "1mnp6lxa7d669r325aynq1n3f35r9sy4v1fvdh4cymbf33s8mkmm"))
3128 ;; Delete minified JavaScript
3129 (for-each delete-file
3130 '("inst/tablerDash-0.1.0/require.min.js"
3131 "inst/bootstrap-4.0.0/bootstrap.bundle.min.js"))
3133 (properties `((upstream-name . "tablerDash")))
3134 (build-system r-build-system)
3136 `(#:modules ((guix build utils)
3137 (guix build r-build-system)
3140 (modify-phases %standard-phases
3141 (add-after 'unpack 'process-javascript
3142 (lambda* (#:key inputs #:allow-other-keys)
3143 (with-directory-excursion "inst"
3147 `((,(assoc-ref inputs "js-requirejs")
3148 "tablerDash-0.1.0/require.min.js")
3149 (,(assoc-ref inputs "js-bootstrap")
3150 "bootstrap-4.0.0/bootstrap.bundle.min.js"))))
3151 (lambda (sources targets)
3152 (for-each (lambda (source target)
3153 (format #t "Processing ~a --> ~a~%"
3155 (invoke "esbuild" source "--minify"
3156 (string-append "--outfile=" target)))
3160 (list r-htmltools r-knitr r-shiny))
3162 `(("esbuild" ,esbuild)
3166 (uri "https://raw.githubusercontent.com/requirejs/requirejs/2.3.5/require.js")
3169 "06w32mwqii9cx409ivda88z58qbkcdb4p6hf6jawchsgagaziyds"))))
3173 (uri "https://raw.githubusercontent.com/twbs/bootstrap/\
3174 v4.0.0/dist/js/bootstrap.bundle.js")
3177 "0cvfqffn45vfbj3fk6wmrhkyndhk4id89vgydssbbzxjkfwprfrj"))))))
3178 (home-page "https://rinterface.github.io/tablerDash/")
3179 (synopsis "Tabler API for Shiny")
3181 "This package provides an R interface to the
3182 @url{https://tabler.io,Tabler} HTML template. tablerDash is a light Bootstrap
3183 4 dashboard template. There are different layouts available such as a one
3184 page dashboard or a multi-page template, where the navigation menu is
3185 contained in the navigation bar.")
3186 (license license:gpl2+)))
3188 (define-public r-spelling
3195 (uri (cran-uri "spelling" version))
3198 "179nj9w1v27qq9q5240ddvggp0795998sxyqjvbqjvq9dmach3bl"))))
3199 (properties `((upstream-name . "spelling")))
3200 (build-system r-build-system)
3202 (list r-commonmark r-hunspell r-knitr r-xml2))
3203 (home-page "https://docs.ropensci.org/spelling/")
3204 (synopsis "Tools for spell checking in R")
3206 "This is an R package for spell checking common document formats
3207 including LaTeX, markdown, manual pages, and DESCRIPTION files. It includes
3208 utilities to automate checking of documentation and vignettes as a unit test
3209 during @code{R CMD check}. Both British and American English are supported
3210 out of the box and other languages can be added. In addition, packages may
3211 define a wordlist to allow custom terminology without having to abuse
3213 (license license:expat)))
3215 (define-public r-crosstalk
3217 (name "r-crosstalk")
3222 (uri (cran-uri "crosstalk" version))
3225 "180y7mhpj17axpadwhh7s0qvrpdnag7g977vk256l96d6nmvlds2"))))
3226 (build-system r-build-system)
3228 (list r-htmltools r-jsonlite r-lazyeval r-r6))
3229 (home-page "https://rstudio.github.io/crosstalk/")
3230 (synopsis "Inter-widget interactivity for HTML widgets")
3232 "This package provides building blocks for allowing HTML widgets to
3233 communicate with each other, with Shiny or without (i.e. static @code{.html}
3234 files). It currently supports linked brushing and filtering.")
3235 (license license:expat)))
3237 (define-public r-rook
3244 (uri (cran-uri "Rook" version))
3247 "00s9a0kr9rwxvlq433daxjk4ji8m0w60hjdprf502msw9kxfrx00"))))
3248 (properties `((upstream-name . "Rook")))
3249 (build-system r-build-system)
3250 (propagated-inputs (list r-brew))
3251 (home-page "https://cran.r-project.org/web/packages/Rook")
3252 (synopsis "Web server interface for R")
3254 "This package contains the Rook specification and convenience software
3255 for building and running Rook applications. A Rook application is an R
3256 reference class object that implements a @code{call} method or an R closure
3257 that takes exactly one argument, an environment, and returns a list with three
3258 named elements: the @code{status}, the @code{headers}, and the @code{body}.")
3259 (license license:gpl2)))
3261 (define-public r-miniui
3268 (uri (cran-uri "miniUI" version))
3271 "1h5h2sc57h95d6bsgs95l26911g38hvjc1v50bc31xl9689l2as5"))))
3272 (properties `((upstream-name . "miniUI")))
3273 (build-system r-build-system)
3275 (list r-htmltools r-shiny))
3276 (home-page "https://cran.r-project.org/web/packages/miniUI/")
3277 (synopsis "Shiny UI widgets for small screens")
3279 "This package provides UI widget and layout functions for writing Shiny apps that
3280 work well on small screens.")
3281 (license license:gpl3)))
3283 (define-public r-feather
3290 (uri (cran-uri "feather" version))
3293 "1gxd0h2m56sjjlzn4dry6s13nddxc4l5i11gsvavaf2dwbahdzsh"))))
3294 (build-system r-build-system)
3296 (list r-hms r-rcpp r-tibble))
3297 (home-page "https://github.com/wesm/feather")
3298 (synopsis "R Bindings to the Feather API")
3299 (description "Read and write feather files, a lightweight binary columnar
3300 data store designed for maximum speed.")
3301 (license license:asl2.0)))
3303 (define-public r-maps
3310 (uri (cran-uri "maps" version))
3313 "0ispkx1szgwxhr0zzhdzgqqwcgc6psg7vry4sj4rb89w76rcq63r"))))
3314 (build-system r-build-system)
3315 (home-page "https://cran.r-project.org/web/packages/maps")
3316 (synopsis "Draw geographical maps")
3317 (description "This package provides an R module for display of maps.
3318 Projection code and larger maps are in separate packages (@code{mapproj} and
3320 (license license:gpl2)))
3322 (define-public r-mapproj
3329 (uri (cran-uri "mapproj" version))
3332 "10bpib827011fpgvzsmlv4j3i41s0r3cv1hvawwdlk753s7i0pw6"))))
3333 (build-system r-build-system)
3334 (propagated-inputs (list r-maps))
3335 (home-page "https://cran.r-project.org/web/packages/mapproj")
3336 (synopsis "Map projection in R")
3337 (description "This package converts latitude/longitude into projected
3339 (license (list license:gpl2 ; The R interface
3340 (license:non-copyleft ; The C code
3341 "https://www.gnu.org/licenses/license-list.en.html#lucent102"
3342 "Lucent Public License Version 1.02")))))
3344 (define-public r-rgooglemaps
3346 (name "r-rgooglemaps")
3351 (uri (cran-uri "RgoogleMaps" version))
3354 "02v8k0bw70q4qwx4lcdy8p25q7n3ql2ll46lfpqllxa1p26svmfi"))))
3355 (properties `((upstream-name . "RgoogleMaps")))
3356 (build-system r-build-system)
3359 (home-page "https://cran.r-project.org/web/packages/RgoogleMaps")
3360 (synopsis "Use Google Maps in R")
3361 (description "This package serves two purposes:
3363 @item Provide a comfortable R interface to query the Google server for static
3365 @item Use the map as a background image to overlay plots within R. This
3366 requires proper coordinate scaling.
3368 (license license:gpl2+)))
3370 (define-public r-geosphere
3372 (name "r-geosphere")
3377 (uri (cran-uri "geosphere" version))
3380 "0bg4vfmrw140j2ax0p6bflvb77w03ir39wa87l96rj473jpa9hzj"))))
3381 (build-system r-build-system)
3382 (propagated-inputs (list r-sp))
3383 (home-page "https://cran.r-project.org/web/packages/geosphere")
3384 (synopsis "Spherical trigonometry")
3385 (description "This package computes spherical trigonometry for geographic
3386 applications. That is, compute distances and related measures for angular
3387 (longitude/latitude) locations.")
3388 (license license:gpl3+)))
3390 (define-public r-jpeg
3397 (uri (cran-uri "jpeg" version))
3400 "0wihj538wdnr71wdldym83qadb4kh68a6rkallwbh2f25r27b881"))))
3401 (build-system r-build-system)
3402 (inputs (list libjpeg-turbo))
3403 (home-page "https://www.rforge.net/jpeg/")
3404 (synopsis "Read and write JPEG images with R")
3405 (description "This package provides a way to read, write and display
3406 bitmap images stored in the JPEG format with R. It can read and write both
3407 files and in-memory raw vectors.")
3408 (license license:gpl2+)))
3410 (define-public r-ggmap
3417 (uri (cran-uri "ggmap" version))
3420 "13dmzl6z62pzjiffilarkji46vy0sacxa8a7mhrhc3biq3ylzhln"))))
3421 (build-system r-build-system)
3440 (home-page "https://github.com/dkahle/ggmap")
3441 (synopsis "Spatial visualization with ggplot2")
3442 (description "This package provides a collection of functions to visualize
3443 spatial data and models on top of static maps from various online sources (e.g
3444 Google Maps and Stamen Maps). It includes tools common to those tasks,
3445 including functions for geolocation and routing.")
3446 (license license:gpl2)))
3448 (define-public r-haven
3455 (uri (cran-uri "haven" version))
3458 "1x5g6kjrzcyarbjz91f4aaspx7rb50qs6a9y29mzr3mjq4dk305m"))
3459 (modules '((guix build utils)))
3461 ;; unvendor readstat
3462 '(delete-file-recursively "src/readstat"))))
3463 (build-system r-build-system)
3466 (modify-phases %standard-phases
3467 (add-after 'unpack 'unbundle-readstat
3469 ;; Not required, since we’re not building readstat.
3470 (substitute* "src/Makevars"
3471 (("-lz") "-lreadstat")))))))
3487 (home-page "https://haven.tidyverse.org")
3488 (synopsis "Import and export SPSS, Stata and SAS files")
3490 "This package lets you import foreign statistical formats into R via the
3491 @url{https://github.com/WizardMac/ReadStat,ReadStat} C library.")
3492 (license license:expat)))
3494 (define-public r-amap
3500 (uri (cran-uri "amap" version))
3503 "0zpcb73w413na23f6giml9311jh0j0y766w2fh9i40d2h7bbvyvs"))))
3504 (build-system r-build-system)
3507 (home-page "http://mulcyber.toulouse.inra.fr/projects/amap/")
3508 (synopsis "Another multidimensional analysis package")
3509 (description "This package provides tools for clustering and principal
3510 component analysis (with robust methods, and parallelized functions).")
3511 (license license:gpl2+)))
3513 (define-public r-ape
3520 (uri (cran-uri "ape" version))
3523 "0mqjsh7maczd02iwa4fb896q3kgd9jnlilq7y1yz18ch0c54aqlv"))))
3524 (build-system r-build-system)
3526 (list r-lattice r-nlme r-rcpp))
3527 (home-page "http://ape-package.ird.fr/")
3528 (synopsis "Analyses of phylogenetics and evolution")
3530 "This package provides functions for reading, writing, plotting, and
3531 manipulating phylogenetic trees, analyses of comparative data in a
3532 phylogenetic framework, ancestral character analyses, analyses of
3533 diversification and macroevolution, computing distances from DNA sequences,
3534 and several other tools.")
3535 (license license:gpl2+)))
3537 (define-public r-abbyyr
3544 (uri (cran-uri "abbyyR" version))
3547 "1vldnd3dg89aj6a73nhirirqddbfdrnzhb5m3679i60sark8nk6r"))))
3548 (properties `((upstream-name . "abbyyR")))
3549 (build-system r-build-system)
3557 (home-page "https://github.com/soodoku/abbyyR")
3558 (synopsis "Access to Abbyy Optical Character Recognition (OCR) API")
3560 "This package provides tools to get text from images of text using Abbyy
3561 Cloud Optical Character Recognition (OCR) API. With abbyyyR, one can easily
3562 OCR images, barcodes, forms, documents with machine readable zones, e.g.
3563 passports and get the results in a variety of formats including plain text and
3564 XML. To learn more about the Abbyy OCR API, see @url{http://ocrsdk.com/}.")
3565 (license license:expat)))
3567 (define-public r-colorspace
3569 (name "r-colorspace")
3574 (uri (cran-uri "colorspace" version))
3576 (base32 "0zw52s8g2gxp8i1ax96azxmxqrbhb7aad5px0c1vgr6n9p682mp7"))))
3577 (build-system r-build-system)
3580 (home-page "https://cran.r-project.org/web/packages/colorspace")
3581 (synopsis "Color space manipulation")
3583 "This package carries out a mapping between assorted color spaces
3584 including RGB, HSV, HLS, CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB and polar
3585 CIELAB. Qualitative, sequential, and diverging color palettes based on HCL
3586 colors are provided.")
3587 (license license:bsd-3)))
3589 (define-public r-glue
3596 (uri (cran-uri "glue" version))
3599 "1gzxk5jgdh2xq9r7z09xs306ygzf27vhg3pyfl7ck1755gqii9cx"))))
3600 (build-system r-build-system)
3601 ;; knitr depends on glue, so we can't add knitr here to build the
3605 `(("r-knitr" ,r-knitr)))
3606 (home-page "https://github.com/tidyverse/glue")
3607 (synopsis "Interpreted string literals")
3609 "This package provides an implementation of interpreted string literals,
3610 inspired by Python's Literal String Interpolation (PEP-0498) and
3611 Docstrings (PEP-0257) and Julia's Triple-Quoted String Literals.")
3612 (license license:expat)))
3614 (define-public r-palmerpenguins
3616 (name "r-palmerpenguins")
3621 (uri (cran-uri "palmerpenguins" version))
3624 "0q1k3cdkliq7kwrg1n0vs9b6cjwyfarhlgdijhp9c6riy6y5ik7x"))))
3626 `((upstream-name . "palmerpenguins")))
3627 (build-system r-build-system)
3628 (home-page "https://allisonhorst.github.io/palmerpenguins/")
3629 (synopsis "Palmer Archipelago (Antarctica) penguin data")
3631 "This package includes size measurements, clutch observations, and blood
3632 isotope ratios for adult foraging Adélie, Chinstrap, and Gentoo penguins
3633 observed on islands in the Palmer Archipelago near Palmer Station, Antarctica.
3634 Data were collected and made available by Dr. Kristen Gorman and the Palmer
3635 Station Long Term Ecological Research (LTER) Program.")
3636 (license license:cc0)))
3638 (define-public r-pastecs
3644 (uri (cran-uri "pastecs" version))
3647 "0z4dic94ar646w7zc2ggi5hgvf2qnznsani94c5pyql8zspz47lc"))))
3648 (build-system r-build-system)
3651 (home-page "https://github.com/phgrosjean/pastecs")
3652 (synopsis "Analysis of space-time ecological series")
3654 "This package provides functions for regulation, decomposition and analysis
3655 of space-time series. The @code{pastecs} library is a PNEC-Art4 and IFREMER
3656 initiative to bring PASSTEC 2000 functionalities to R.")
3657 (license license:gpl2+)))
3659 (define-public r-partykit
3665 (uri (cran-uri "partykit" version))
3668 "1b73s5l19yicwginqsg5xr7fzb005x372n0wb34kk6jb5x5lbsdj"))))
3669 (build-system r-build-system)
3677 (home-page "http://partykit.R-Forge.R-project.org/partykit")
3678 (synopsis "Toolkit for recursive partytioning")
3680 "This package provides a toolkit with infrastructure for representing,
3681 summarizing, and visualizing tree-structured regression and classification
3683 (license license:gpl2+)))
3685 (define-public r-plogr
3692 (uri (cran-uri "plogr" version))
3695 "0a8dhzlna79ggyhfr0nncgh15a9n6r0dsz664pz0ah323wpblqqf"))))
3696 (build-system r-build-system)
3697 (home-page "https://github.com/krlmlr/plogr")
3698 (synopsis "R bindings for the plog C++ logging library")
3700 "This package provides the header files for a stripped-down version of
3701 the plog header-only C++ logging library, and a method to log to R's standard
3703 (license license:expat)))
3705 (define-public r-pls
3712 (uri (cran-uri "pls" version))
3714 (base32 "1gqq8rcq6p0hs2gfzwfj690rz3pwywmnv8qzcv0wsd6aaqkskwzg"))))
3715 (build-system r-build-system)
3716 (home-page "https://mevik.net/work/software/pls.html")
3717 (synopsis "Partial Least Squares and Principal Component Regression")
3719 "The pls package implements multivariate regression methods: Partial Least
3720 Squares Regression (@dfn{PLSR}), Principal Component Regression (@dfn{PCR}), and
3721 Canonical Powered Partial Least Squares (@dfn{CPPLS}). It supports:
3724 @item several algorithms: the traditional orthogonal scores (@dfn{NIPALS}) PLS
3725 algorithm, kernel PLS, wide kernel PLS, Simpls, and PCR through @code{svd}
3726 @item multi-response models (or @dfn{PLS2})
3727 @item flexible cross-validation
3728 @item Jackknife variance estimates of regression coefficients
3729 @item extensive and flexible plots: scores, loadings, predictions, coefficients,
3730 (R)MSEP, R², and correlation loadings
3731 @item formula interface, modelled after @code{lm()}, with methods for predict,
3732 print, summary, plot, update, etc.
3733 @item extraction functions for coefficients, scores, and loadings
3734 @item MSEP, RMSEP, and R² estimates
3735 @item multiplicative scatter correction (@dfn{MSC})
3737 (license license:gpl2)))
3746 (uri (cran-uri "ps" version))
3748 (base32 "1qaj9gyz7q09aadlnj5al53k2pa4axmzjsbndf5r0b51qqrcy842"))))
3749 (build-system r-build-system)
3750 (home-page "https://ps.r-lib.org")
3751 (synopsis "List, query, and manipulate system processes")
3753 "The ps package implements an API to list, query, and manipulate system
3754 processes. Most of its code is based on the @code{psutil} Python package.")
3755 (license license:bsd-3)))
3757 (define-public r-pkgbuild
3764 (uri (cran-uri "pkgbuild" version))
3766 (base32 "0j6v5nbp8kg1m3j999gd1qsbdmqcqm1mf28ngmm177miwv8q4skw"))))
3767 (build-system r-build-system)
3777 (home-page "https://github.com/r-pkgs/pkgbuild")
3778 (synopsis "Find tools needed to build R packages")
3780 "This package provides functions used to build R packages. It locates
3781 compilers needed to build R packages on various platforms and ensures the PATH
3782 is configured appropriately so R can use them.")
3783 (license license:gpl3)))
3785 (define-public r-pkgload
3792 (uri (cran-uri "pkgload" version))
3795 "03yr9mswx9nij27bp21q6c533zx310xwzhwm52dwr7554k42p4fn"))))
3796 (build-system r-build-system)
3805 (home-page "https://github.com/r-lib/pkgload")
3806 (synopsis "Simulate package installation and attach")
3808 "This package simulates the process of installing a package and then
3809 attaching it. This is a key part of the @code{devtools} package as it allows
3810 you to rapidly iterate while developing a package.")
3811 (license license:gpl3)))
3813 (define-public r-pvclust
3819 (uri (cran-uri "pvclust" version))
3822 "0082icm54k2yq60k06qpr92a626k39j2jr0046lva4ylmhxqb4kq"))))
3823 (build-system r-build-system)
3824 (home-page "https://github.com/shimo-lab/pvclust")
3826 "Hierarchical clustering with P-values via multiscale bootstrap resampling")
3827 (description "This package provides an implementation of multiscale bootstrap
3828 resampling for assessing the uncertainty in hierarchical cluster analysis. It
3829 provides an AU (approximately unbiased) P-value as well as a BP (bootstrap probability)
3830 value for each cluster in a dendrogram.")
3831 (license license:gpl2+)))
3833 (define-public r-rcpp
3840 (uri (cran-uri "Rcpp" version))
3842 (base32 "1gzqfn1xjawzig30ama3rldykqpcn6bd8sg684mrfvpmv96bi9cx"))))
3843 (build-system r-build-system)
3844 (home-page "http://www.rcpp.org")
3845 (synopsis "Seamless R and C++ integration")
3847 "The Rcpp package provides R functions as well as C++ classes which offer
3848 a seamless integration of R and C++. Many R data types and objects can be
3849 mapped back and forth to C++ equivalents which facilitates both writing of new
3850 code as well as easier integration of third-party libraries. Documentation
3851 about Rcpp is provided by several vignettes included in this package, via the
3852 @code{Rcpp Gallery} site at <http://gallery.rcpp.org>, the paper by Eddelbuettel
3853 and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see
3854 @code{citation(\"Rcpp\")} for details on these last two.")
3855 (license license:gpl2+)))
3857 (define-public r-rcppml
3864 (uri (cran-uri "RcppML" version))
3866 (base32 "1ih8i7i6m221iw227mnl3rvnaw2l53h8fpnc4f8yn9sm10anap1j"))))
3867 (properties `((upstream-name . "RcppML")))
3868 (build-system r-build-system)
3869 (propagated-inputs (list r-matrix r-rcpp r-rcppeigen))
3870 (native-inputs (list r-knitr))
3871 (home-page "https://github.com/zdebruine/RcppML")
3872 (synopsis "Rcpp machine learning library")
3874 "This package provides fast machine learning algorithms including matrix
3875 factorization and divisive clustering for large sparse and dense matrices.")
3876 (license license:gpl2+)))
3878 (define-public r-rcppthread
3880 (name "r-rcppthread")
3885 (uri (cran-uri "RcppThread" version))
3888 "0iprpidf7q1wlrgr9dwiikb6apqk80pyjcyni56k64nl7lrkszhj"))))
3889 (properties `((upstream-name . "RcppThread")))
3890 (build-system r-build-system)
3892 "https://github.com/tnagler/RcppThread")
3893 (synopsis "R threading in C++")
3895 "This package provides a C++11-style thread class and thread pool that can
3896 safely be interrupted from R.")
3897 (license license:expat)))
3899 (define-public r-rcppnumerical
3901 (name "r-rcppnumerical")
3905 (uri (cran-uri "RcppNumerical" version))
3908 "1a92fql6mijhnr1kxkcxwivf95pk9lhgmhzkshs51h0ybfv5krik"))))
3909 (build-system r-build-system)
3911 (list r-rcpp r-rcppeigen))
3912 (home-page "https://github.com/yixuan/RcppNumerical")
3913 (synopsis"Numerical computing libraries integration with @code{Rcpp}")
3914 (description "This package provides a collection of libraries for numerical
3915 computing (numerical integration, optimization, etc.) and their integration
3917 (license license:gpl2+)))
3919 (define-public r-rcppxptrutils
3921 (name "r-rcppxptrutils")
3926 (uri (cran-uri "RcppXPtrUtils" version))
3928 (base32 "0hm57nf4dzgsmg4hjj6wikwjx93fgfwkmybw6ly4b58wi6qwml1l"))))
3929 (properties `((upstream-name . "RcppXPtrUtils")))
3930 (build-system r-build-system)
3931 (propagated-inputs (list r-rcpp))
3932 (home-page "https://github.com/Enchufa2/RcppXPtrUtils")
3933 (synopsis "XPtr add-ons for Rcpp")
3935 "This package provides the means to compile user-supplied C++ functions
3936 with Rcpp and retrieve an @code{XPtr} that can be passed to other C++
3938 (license license:expat)))
3940 (define-public r-bindr
3947 (uri (cran-uri "bindr" version))
3950 "1l05fpk2yql3jka321c0bdgx6mqq9pvfrg2844lbjfpbgjkmqy3w"))))
3951 (build-system r-build-system)
3952 (home-page "https://github.com/krlmlr/bindr")
3953 (synopsis "Parametrized active bindings")
3955 "This package provides a simple interface for creating active bindings
3956 where the bound function accepts additional arguments.")
3957 (license license:expat)))
3959 (define-public r-bindrcpp
3966 (uri (cran-uri "bindrcpp" version))
3969 "0rz4ibjdjsxl99ff3ha79z7cnjmilx4rx58fk9kk7ld9xc4hf4s8"))))
3970 (build-system r-build-system)
3972 (list r-bindr r-plogr r-rcpp))
3973 (home-page "https://github.com/krlmlr/bindrcpp")
3974 (synopsis "Rcpp interface to active bindings")
3976 "This package provides an easy way to fill an environment with active
3977 bindings that call a C++ function.")
3978 (license license:expat)))
3980 (define-public r-auc
3987 (uri (cran-uri "AUC" version))
3990 "07xf47kypqbsg2mixmq6mnh4s89aqan9bgl6kfv6lbx8ajv2asw3"))))
3991 (properties `((upstream-name . "AUC")))
3992 (build-system r-build-system)
3993 (home-page "https://cran.r-project.org/web/packages/AUC")
3994 (synopsis "Compute the area under the curve of selected measures")
3996 "This package includes functions to compute the area under the curve of
3997 selected measures: the area under the sensitivity curve (AUSEC), the area
3998 under the specificity curve (AUSPC), the area under the accuracy
3999 curve (AUACC), and the area under the receiver operating characteristic
4000 curve (AUROC). The curves can also be visualized. Support for partial areas
4002 (license license:gpl2+)))
4004 (define-public r-calibrate
4006 (name "r-calibrate")
4011 (uri (cran-uri "calibrate" version))
4013 (base32 "19kgrnsyq67iqv1biyssqi30a6v2836ql20nabpy2m692ns0jfvi"))))
4014 (build-system r-build-system)
4017 (home-page "https://cran.r-project.org/web/packages/calibrate")
4018 (synopsis "Calibration of scatterplot and biplot axes")
4020 "This is a package for drawing calibrated scales with tick marks
4021 on (non-orthogonal) variable vectors in scatterplots and biplots.")
4022 (license license:gpl2)))
4024 (define-public r-shape
4031 (uri (cran-uri "shape" version))
4034 "0yqbrrx2ywmfl99s6d1n6jblc63k1mxbiqyv8y0kq8jws1g3w45r"))))
4035 (build-system r-build-system)
4036 (home-page "https://cran.r-project.org/web/packages/shape")
4037 (synopsis "Functions for plotting graphical shapes")
4039 "This package provides functions for plotting graphical shapes such as
4040 ellipses, circles, cylinders, arrows, ...")
4041 (license license:gpl3+)))
4043 (define-public r-globaloptions
4045 (name "r-globaloptions")
4050 (uri (cran-uri "GlobalOptions" version))
4052 (base32 "0gkm77w6db9ajyncy1xdcivplap06a51zi99m009kylccschd2a7"))))
4053 (properties `((upstream-name . "GlobalOptions")))
4054 (build-system r-build-system)
4057 (home-page "https://github.com/jokergoo/GlobalOptions")
4058 (synopsis "Generate functions to get or set global options")
4060 "This package provides more controls on the option values such as
4061 validation and filtering on the values, making options invisible or private.")
4062 (license license:gpl2+)))
4064 (define-public r-circlize
4071 (uri (cran-uri "circlize" version))
4074 "1iswb7dy08as3pbzxvhx5qlsbnwvp79nwg8m158nfz7y2d9xa0nn"))))
4075 (build-system r-build-system)
4077 (list r-colorspace r-globaloptions r-shape))
4080 (home-page "https://github.com/jokergoo/circlize")
4081 (synopsis "Circular visualization")
4083 "Circular layout is an efficient way to visualise huge amounts of
4084 information. This package provides an implementation of circular layout
4085 generation in R as well as an enhancement of available software. Its
4086 flexibility is based on the usage of low-level graphics functions such that
4087 self-defined high-level graphics can be easily implemented by users for
4088 specific purposes. Together with the seamless connection between the powerful
4089 computational and visual environment in R, it gives users more convenience and
4090 freedom to design figures for better understanding complex patterns behind
4091 multi-dimensional data.")
4092 (license license:gpl2+)))
4094 (define-public r-powerlaw
4101 (uri (cran-uri "poweRlaw" version))
4103 (base32 "14d1myxllvm1grnfiszzzxaiqpb2jpmsi19wq70r8r2wki293h7g"))))
4104 (properties `((upstream-name . "poweRlaw")))
4105 (build-system r-build-system)
4110 (home-page "https://github.com/csgillespie/poweRlaw")
4111 (synopsis "Tools for the analysis of heavy tailed distributions")
4113 "This package provides an implementation of maximum likelihood estimators
4114 for a variety of heavy tailed distributions, including both the discrete and
4115 continuous power law distributions. Additionally, a goodness-of-fit based
4116 approach is used to estimate the lower cut-off for the scaling region.")
4117 ;; Any of these GPL versions.
4118 (license (list license:gpl2 license:gpl3))))
4120 (define-public r-compare
4127 (uri (cran-uri "compare" version))
4130 "0k9zms930b5dz9gy8414li21wy0zg9x9vp7301v5cvyfi0g7xzgw"))))
4131 (build-system r-build-system)
4132 (home-page "https://cran.r-project.org/web/packages/compare")
4133 (synopsis "Comparing objects for differences")
4135 "This package provides functions to compare a model object to a
4136 comparison object. If the objects are not identical, the functions can be
4137 instructed to explore various modifications of the objects (e.g., sorting
4138 rows, dropping names) to see if the modified versions are identical.")
4139 (license license:gpl2+)))
4141 (define-public r-dendextend
4143 (name "r-dendextend")
4148 (uri (cran-uri "dendextend" version))
4151 "06wjs8451hmnimzgngpzbai3yrgy33133vzzapa8jib9crdqi8sb"))))
4152 (build-system r-build-system)
4154 (list r-ggplot2 r-magrittr r-viridis))
4157 (home-page "https://cran.r-project.org/web/packages/dendextend")
4158 (synopsis "Extending 'dendrogram' functionality in R")
4160 "This package offers a set of functions for extending @code{dendrogram}
4161 objects in R, letting you visualize and compare trees of hierarchical
4162 clusterings. You can adjust a tree's graphical parameters (the color, size,
4163 type, etc of its branches, nodes and labels) and visually and statistically
4164 compare different dendrograms to one another.")
4165 ;; Any of these versions
4166 (license (list license:gpl2 license:gpl3))))
4168 (define-public r-getoptlong
4170 (name "r-getoptlong")
4175 (uri (cran-uri "GetoptLong" version))
4178 "00fpm6nd3kqa2ikasxa62jzywi46fvvmx1mdavcp5yrxxn37j8wc"))))
4179 (properties `((upstream-name . "GetoptLong")))
4180 (build-system r-build-system)
4184 (list r-crayon r-globaloptions r-rjson))
4187 (home-page "https://github.com/jokergoo/GetoptLong")
4188 (synopsis "Parsing command-line arguments and variable interpolation")
4190 "This is yet another command-line argument parser which wraps the
4191 powerful Perl module @code{Getopt::Long} and with some adaptation for easier
4192 use in R. It also provides a simple way for variable interpolation in R.")
4193 (license license:gpl2+)))
4195 (define-public r-fastmatch
4197 (name "r-fastmatch")
4202 (uri (cran-uri "fastmatch" version))
4205 "0qcq1gwl9pijgp34giyq5y9rk0ly3d7xza2b7r68xx63ifqa1vqx"))))
4206 (build-system r-build-system)
4207 (home-page "https://www.rforge.net/fastmatch")
4208 (synopsis "Fast match function")
4210 "This package provides a fast @code{match} replacement for cases that
4211 require repeated look-ups. It is slightly faster that R's built-in
4212 @code{match} function on first match against a table, but extremely fast on
4213 any subsequent lookup as it keeps the hash table in memory.")
4214 (license license:gpl2)))
4223 (uri (cran-uri "ff" version))
4226 "1yl3ipzz9bjkfy9bbna7xz5n7iz4lchnw5l7agww7by764yk6iqa"))))
4227 (build-system r-build-system)
4228 (propagated-inputs (list r-bit))
4229 (home-page "http://ff.r-forge.r-project.org/")
4230 (synopsis "Memory-efficient storage of large data on disk and access functions")
4232 "This package provides data structures that are stored on disk but
4233 behave (almost) as if they were in RAM by transparently mapping only a section
4235 ;; error Architecture not supported.
4236 (supported-systems (delete "aarch64-linux" %supported-systems))
4237 (license license:gpl2)))
4239 (define-public r-ffbase
4246 (uri (cran-uri "ffbase" version))
4249 "1dp6lblfq2j7r1b4b8ls47jlx8j27n88d5vp8w116lb8pa01zxmk"))))
4250 (build-system r-build-system)
4252 (list r-bit r-fastmatch r-ff))
4253 (home-page "https://github.com/edwindj/ffbase")
4254 (synopsis "Basic statistical functions for package 'ff'")
4256 "This package extends the out of memory vectors of @code{ff} with
4257 statistical functions and other utilities to ease their usage.")
4258 (license license:gpl3)))
4260 (define-public r-prettyunits
4262 (name "r-prettyunits")
4267 (uri (cran-uri "prettyunits" version))
4270 "1ibmzgknw5896q2i6r59jz2izblxwgb29ivvjzx50pkd1jl9l6cs"))))
4271 (build-system r-build-system)
4272 (home-page "https://github.com/gaborcsardi/prettyunits")
4273 (synopsis "Pretty, human readable formatting of quantities")
4275 "This package provides tools for pretty, human readable formatting of
4277 (license license:expat)))
4279 (define-public r-princurve
4281 (name "r-princurve")
4285 (uri (cran-uri "princurve" version))
4288 "0wzk329bxljkzz57y220lsfckpsn45w348m6dcxh29zbj0ik65h2"))))
4289 (build-system r-build-system)
4292 (home-page "https://github.com/rcannood/princurve")
4293 (synopsis "Fit a principal curve in arbitrary dimension")
4294 (description "This package provides procedures for fitting a principal
4295 curve to a data matrix in arbitrary dimensions.")
4296 (license license:gpl2)))
4298 (define-public r-reshape
4305 (uri (cran-uri "reshape" version))
4308 "0j203qmc076x5lp6q2xi4dq4xdb73jmsa42rpxp1c37knnrph4br"))))
4309 (build-system r-build-system)
4312 (home-page "http://had.co.nz/reshape")
4313 (synopsis "Flexibly reshape data")
4315 "Flexibly restructure and aggregate data using just two functions:
4316 @code{melt} and @code{cast}. This package provides them.")
4317 (license license:expat)))
4319 (define-public r-restrserve
4321 (name "r-restrserve")
4326 (uri (cran-uri "RestRserve" version))
4328 (base32 "1ydsdgy6mxl0zqk7xqf4v6if5nf2qv7k48q340fhaqyjk2gd60p7"))))
4329 (build-system r-build-system)
4341 (home-page "https://restrserve.org")
4342 (synopsis "R web API framework")
4344 "RestRserve is an R web API framework for building high-performance AND
4345 robust microservices and app backends. With Rserve backend on UNIX-like
4346 systems it is parallel by design. It will handle incoming requests in
4347 parallel - each request in a separate fork.")
4348 (license license:gpl2+)))
4350 (define-public r-progress
4357 (uri (cran-uri "progress" version))
4360 "0dgzb362641aqm8xd88iqa8jmpdm43xs0aba0d5kk6fvapnxi95l"))))
4361 (build-system r-build-system)
4363 (list r-crayon r-hms r-prettyunits r-r6))
4364 (home-page "https://github.com/gaborcsardi/progress")
4365 (synopsis "Terminal progress bars")
4367 "This package provides configurable progress bars. They may include
4368 percentage, elapsed time, and/or the estimated completion time. They work in
4369 terminals, in Emacs ESS, RStudio, Windows Rgui, and the macOS R.app. The
4370 package also provides a C++ API, that works with or without Rcpp.")
4371 (license license:expat)))
4373 (define-public r-ggally
4380 (uri (cran-uri "GGally" version))
4383 "1r98zgh2grn8330cf26r1c20gl131zm778szvn5wj6q6pwv2yd9h"))))
4384 (properties `((upstream-name . "GGally")))
4385 (build-system r-build-system)
4401 (home-page "https://ggobi.github.io/ggally")
4402 (synopsis "Extension to ggplot2")
4404 "The R package ggplot2 is a plotting system based on the grammar of
4405 graphics. GGally extends ggplot2 by adding several functions to reduce the
4406 complexity of combining geometric objects with transformed data. Some of
4407 these functions include a pairwise plot matrix, a two group pairwise plot
4408 matrix, a parallel coordinates plot, a survival plot, and several functions to
4410 (license license:gpl2+)))
4412 (define-public r-proxy
4419 (uri (cran-uri "proxy" version))
4422 "0k8sr24mjfvxp12sf1j9228ah3ngy15nqmm0jw14x5s32f1assv7"))))
4423 (build-system r-build-system)
4424 (home-page "https://cran.r-project.org/web/packages/proxy")
4425 (synopsis "Distance and similarity measures")
4427 "This package provides an extensible framework for the efficient
4428 calculation of auto- and cross-proximities, along with implementations of the
4429 most popular ones.")
4430 (license license:gpl2)))
4439 (uri (cran-uri "sp" version))
4441 (base32 "1bdi06n5zkjnnyh0rallf04s0vlcx9rg9p5q7s6vfqvkf19nk501"))))
4442 (build-system r-build-system)
4447 (home-page "https://cran.r-project.org/web/packages/sp")
4448 (synopsis "Classes and methods for spatial data")
4450 "This package provides classes and methods for spatial data; the classes
4451 document where the spatial location information resides, for 2D or 3D data.
4452 Utility functions are provided, e.g. for plotting data as maps, spatial
4453 selection, as well as methods for retrieving coordinates, for subsetting,
4454 print, summary, etc.")
4455 (license license:gpl2+)))
4457 (define-public r-laplacesdemon
4459 (name "r-laplacesdemon")
4464 (uri (cran-uri "LaplacesDemon" version))
4466 (base32 "1dsfp65cg06f25zjzd5ib4qyn1alfhbhpgyvpcw5n6bszn13idap"))))
4467 (properties `((upstream-name . "LaplacesDemon")))
4468 (build-system r-build-system)
4469 (home-page "https://github.com/LaplacesDemonR/LaplacesDemon")
4470 (synopsis "Complete environment for Bayesian inference")
4472 "This package provides a complete environment for Bayesian inference using
4473 a variety of different samplers.")
4474 (license license:expat)))
4476 (define-public r-rmtstat
4483 (uri (cran-uri "RMTstat" version))
4486 "1r1a2sdqv64m9cpm2pz6r8abf7l810126ayd8iq3gx86c7bjfj5v"))))
4487 (properties `((upstream-name . "RMTstat")))
4488 (build-system r-build-system)
4489 (home-page "https://cran.r-project.org/web/packages/RMTstat")
4490 (synopsis "Distributions, statistics and tests derived from random matrix theory")
4492 "This package provides functions for working with the Tracy-Widom laws
4493 and other distributions related to the eigenvalues of large Wishart
4495 (license license:bsd-3)))
4497 (define-public r-rmpi
4503 (uri (cran-uri "Rmpi" version))
4506 "06mxqgrimhfsag5giv810c7ycdbaycqs4qcj41pnfbj0jypw32im"))))
4507 (properties `((upstream-name . "Rmpi")))
4508 (build-system r-build-system)
4510 `(#:configure-flags '("--configure-args=\"--with-Rmpi-type=OPENMPI\"")
4511 #:phases (modify-phases %standard-phases
4512 (add-before 'install 'mpi-setup
4518 (home-page "http://www.stats.uwo.ca/faculty/yu/Rmpi")
4519 (synopsis "R interface to message-passing interface (MPI)")
4521 "This package provides an interface (wrapper) to MPI APIs. It also
4522 provides an interactive R manager and worker environment.")
4523 (license license:gpl2+)))
4525 (define-public r-lmoments
4532 (uri (cran-uri "Lmoments" version))
4535 "0pc63bj9a8hzr5m3yssrc4kin39fffwkl8rggs3sagzr12d4i7bw"))))
4536 (properties `((upstream-name . "Lmoments")))
4537 (build-system r-build-system)
4539 (list r-rcpp r-rcpparmadillo))
4540 (home-page "http://www.tilastotiede.fi/juha_karvanen.html")
4541 (synopsis "L-moments and quantile mixtures")
4543 "This package contains functions to estimate L-moments and trimmed
4544 L-moments from the data. It also contains functions to estimate the
4545 parameters of the normal polynomial quantile mixture and the Cauchy polynomial
4546 quantile mixture from L-moments and trimmed L-moments.")
4547 (license license:gpl2)))
4549 (define-public r-distillery
4551 (name "r-distillery")
4556 (uri (cran-uri "distillery" version))
4559 "1ymmxyamkq0zbz2m4gllln1ihks2hcib6gs0mls92as79srz122b"))))
4560 (build-system r-build-system)
4561 (home-page "https://ral.ucar.edu/staff/ericg/")
4562 (synopsis "Functions for confidence intervals and object information")
4564 "This package provides some very simple method functions for confidence
4565 interval calculation and to distill pertinent information from a potentially
4566 complex object; primarily used in common with the packages extRemes and
4568 (license license:gpl2+)))
4570 (define-public r-etrunct
4576 (uri (cran-uri "etrunct" version))
4579 "0ayazgyqlc8jcqr03cwfmfhm4pck6xri1r6vkgqy4arqkrrnrcqr"))))
4580 (properties `((upstream-name . "etrunct")))
4581 (build-system r-build-system)
4582 (home-page "https://cran.r-project.org/web/packages/etrunct")
4583 (synopsis "Computes moments of univariate truncated T distribution")
4584 (description "This package computes moments of univariate truncated
4585 T distribution. There is only one exported function, @code{e_trunct},
4586 which should be seen for details.")
4587 (license license:expat)))
4589 (define-public r-excelr
4596 (uri (cran-uri "excelR" version))
4598 (base32 "1pb4sy54zjv5vrh7gjjv7qlpab74km6mfsmfyl0yhmr0jx01hrw0"))
4600 '(delete-file "inst/htmlwidgets/lib/jexcel/js/jexcel.min.js"))))
4601 (properties `((upstream-name . "excelR")))
4602 (build-system r-build-system)
4605 (modify-phases %standard-phases
4606 (add-after 'unpack 'process-javascript
4607 (lambda* (#:key inputs #:allow-other-keys)
4608 (with-directory-excursion "inst/htmlwidgets/lib/jexcel/js/"
4609 (let ((source (assoc-ref inputs "js-jexcel"))
4610 (target "jexcel.min.js"))
4611 (format #true "Processing ~a --> ~a~%"
4613 (invoke "esbuild" source "--minify"
4614 (string-append "--outfile=" target)))))))))
4616 `(("esbuild" ,esbuild)
4617 ;; There is no tag for this particular commit, but comparison of the
4618 ;; contents of the JavaScript files point to this commit as the most
4623 (uri (string-append "https://raw.githubusercontent.com/jspreadsheet/ce/"
4624 "8af1960f76e6803bebc5750013d2ebe95354e88a/dist/jexcel.js"))
4627 "0y88hsr9d8cpnvdmbm17m328pc4kc5wbcv02kzmhm0bryzhviw7h"))))))
4628 (propagated-inputs (list r-htmlwidgets r-jsonlite))
4629 (home-page "https://github.com/Swechhya/excelR")
4630 (synopsis "Wrapper of the JavaScript library jExcel")
4632 "This package provides an R interface to the jExcel library to
4633 create web-based interactive tables and spreadsheets compatible with
4634 spreadsheet software.")
4635 (license license:expat)))
4637 (define-public r-extremes
4644 (uri (cran-uri "extRemes" version))
4647 "19q560prq02h3bwk01jb68693qb5bhsv8wiqhia7v5knm34qv8x7"))))
4648 (properties `((upstream-name . "extRemes")))
4649 (build-system r-build-system)
4651 (list r-distillery r-lmoments))
4652 (home-page "https://www.assessment.ucar.edu/toolkit/")
4653 (synopsis "Extreme value analysis")
4655 "ExtRemes is a suite of functions for carrying out analyses on the
4656 extreme values of a process of interest; be they block maxima over long blocks
4657 or excesses over a high threshold.")
4658 (license license:gpl2+)))
4660 (define-public r-lmtest
4667 (uri (cran-uri "lmtest" version))
4670 "15yr2kx08wy085bnziqmj1p6hf9mg3qp2a8465jk2df6di6hsh34"))))
4671 (build-system r-build-system)
4676 (home-page "https://cran.r-project.org/web/packages/lmtest")
4677 (synopsis "Testing linear regression models")
4679 "This package provides a collection of tests, data sets, and examples for
4680 diagnostic checking in linear regression models. Furthermore, some generic
4681 tools for inference in parametric models are provided.")
4682 ;; Either version is okay
4683 (license (list license:gpl2 license:gpl3))))
4685 (define-public r-idr
4691 (uri (cran-uri "idr" version))
4694 "05nvgw1xdg670bsjjrxkgd1mrdkciccpw4krn0zcgdf2r21dzgwb"))))
4695 (build-system r-build-system)
4696 (home-page "https://cran.r-project.org/web/packages/idr/")
4697 (synopsis "Irreproducible discovery rate")
4699 "This is a package for estimating the copula mixture model and plotting
4700 correspondence curves in \"Measuring reproducibility of high-throughput
4701 experiments\" (2011), Annals of Applied Statistics, Vol. 5, No. 3, 1752-1779,
4702 by Li, Brown, Huang, and Bickel")
4703 (license license:gpl2+)))
4705 (define-public r-inline
4711 (uri (cran-uri "inline" version))
4714 "1mcr9hgq6kkq03n7pkcccxa7vg8jma0q7lfxc5vvkc6snydk1s8f"))))
4715 (build-system r-build-system)
4716 (home-page "https://cran.r-project.org/web/packages/inline")
4717 (synopsis "Functions to inline C, C++, Fortran function calls from R")
4719 "This package provides functionality to dynamically define R functions
4720 and S4 methods with inlined C, C++ or Fortran code supporting @code{.C} and
4721 @code{.Call} calling conventions.")
4722 ;; Any version of the LGPL.
4723 (license license:lgpl3+)))
4725 (define-public r-inum
4731 (uri (cran-uri "inum" version))
4734 "1khkzja8lwn9075864vbyajqina9m588ahf1fsrrajrsqilyzssz"))))
4735 (build-system r-build-system)
4738 (home-page "https://cran.r-project.org/web/packages/inum/")
4739 (synopsis "Interval and enum-type representation of vectors")
4741 "This package provides an enum-type representation of vectors and
4742 representation of intervals, including a method of coercing variables
4744 (license license:gpl2)))
4745 (define-public r-invgamma
4751 (uri (cran-uri "invgamma" version))
4754 "12ga2y4wc9bc5zz6vimvxwgjpsx3ys3209nq63gscbw559ydxa5a"))))
4755 (properties `((upstream-name . "invgamma")))
4756 (build-system r-build-system)
4757 (home-page "https://github.com/dkahle/invgamma")
4758 (synopsis "Inverse gamma distribution")
4759 (description "This package provides a light weight implementation of the
4760 standard distribution functions for the inverse gamma distribution, wrapping
4761 those for the gamma distribution in the @code{stats} package.")
4762 (license license:gpl2)))
4764 (define-public r-bdsmatrix
4766 (name "r-bdsmatrix")
4771 (uri (cran-uri "bdsmatrix" version))
4774 "1sh6pg43rgqvips4fx0k4vmp5i9lmniix0bqwj2yq5m06gs227i5"))))
4775 (properties `((upstream-name . "bdsmatrix")))
4776 (build-system r-build-system)
4777 (home-page "https://cran.r-project.org/web/packages/bdsmatrix/")
4778 (synopsis "Routines for block diagonal symmetric matrices")
4780 "This package provides procedures to work with block diagonal symmetric
4781 matrices, a special case of sparse matrices.")
4782 (license license:lgpl2.0)))
4784 (define-public r-bbmle
4791 (uri (cran-uri "bbmle" version))
4794 "0mdj21q7k0fp4cj7la14vmcjmp49zqm57g7r6zrwmxpv0acwda46"))))
4795 (build-system r-build-system)
4805 (home-page "https://cran.r-project.org/web/packages/bbmle")
4806 (synopsis "Tools for General Maximum Likelihood Estimation")
4808 "This package provides methods and functions for fitting maximum
4809 likelihood models in R. This package modifies and extends the @code{mle}
4810 classes in the @code{stats4} package.")
4811 ;; Any version of the GPL
4812 (license license:gpl2+)))
4814 (define-public r-emdbook
4821 (uri (cran-uri "emdbook" version))
4824 "0ls3zxxlwmdv7zn1v9i1y9zc2sn0hbgmyjvsj7zn3ajsw7wwlih6"))))
4825 (build-system r-build-system)
4827 (list r-bbmle r-coda r-lattice r-mass r-plyr))
4828 (home-page "http://www.math.mcmaster.ca/bolker/emdbook")
4829 (synopsis "Support functions and data for \"Ecological Models and Data\"")
4831 "This package provides auxiliary functions and data sets for \"Ecological
4832 Models and Data\", a book presenting maximum likelihood estimation and related
4833 topics for ecologists (ISBN 978-0-691-12522-0).")
4835 (license (list license:gpl2 license:gpl3))))
4837 (define-public r-lpsolve
4844 (uri (cran-uri "lpSolve" version))
4847 "1fpkyjyqykwa1dxnhiky01pm09syxg169lm7hpy39bdbg10vw9s6"))))
4848 (properties `((upstream-name . "lpSolve")))
4849 (build-system r-build-system)
4850 (home-page "https://cran.r-project.org/web/packages/lpSolve")
4851 (synopsis "R interface to Lp_solve to solve linear/integer programs")
4853 "Lp_solve is software for solving linear, integer and mixed integer
4854 programs. This implementation supplies a \"wrapper\" function in C and some R
4855 functions that solve general linear/integer problems, assignment problems, and
4856 transportation problems.")
4857 (license license:lgpl2.0)))
4859 (define-public r-limsolve
4866 (uri (cran-uri "limSolve" version))
4869 "1829rd2cnd8qj80z9a7sgc7gx4sf3kvl5g6d2a0lqqw30f9sjzmr"))))
4870 (properties `((upstream-name . "limSolve")))
4871 (build-system r-build-system)
4873 (list r-lpsolve r-mass r-quadprog))
4874 (native-inputs (list gfortran))
4875 (home-page "https://cran.r-project.org/web/packages/limSolve")
4876 (synopsis "Solving linear inverse models")
4878 "This package provides functions that:
4881 @item find the minimum/maximum of a linear or quadratic function,
4882 @item sample an underdetermined or overdetermined system,
4883 @item solve a linear system Ax=B for the unknown x.
4886 It includes banded and tridiagonal linear systems. The package calls Fortran
4887 functions from LINPACK.")
4889 (license (list license:gpl2+ license:gpl3+))))
4891 (define-public r-fitdistrplus
4893 (name "r-fitdistrplus")
4898 (uri (cran-uri "fitdistrplus" version))
4901 "0nhgjvwya95v6b9khbsgp44lw10xg35w61lmka1v6wq7yh827izk"))))
4902 (build-system r-build-system)
4904 (list r-mass r-survival))
4907 (home-page "http://riskassessment.r-forge.r-project.org")
4908 (synopsis "Fitting a parametric distribution from data")
4910 "This package extends the @code{fitdistr} function of the MASS package
4911 with several functions to help the fit of a parametric distribution to
4912 non-censored or censored data. Censored data may contain left-censored,
4913 right-censored and interval-censored values, with several lower and upper
4914 bounds. In addition to @dfn{maximum likelihood estimation} (MLE), the package
4915 provides moment matching (MME), quantile matching (QME) and maximum
4916 goodness-of-fit estimation (MGE) methods (available only for non-censored
4917 data). Weighted versions of MLE, MME and QME are available.")
4918 (license license:gpl2+)))
4920 (define-public r-energy
4927 (uri (cran-uri "energy" version))
4930 "19xyw5bkyzfk22gly2ca2nsznqnrhaq4a77727kr1k26bj3y8gal"))))
4931 (build-system r-build-system)
4933 (list r-boot r-gsl r-rcpp))
4934 (home-page "https://cran.r-project.org/web/packages/energy")
4935 (synopsis "Multivariate inference via the energy of data")
4937 "This package provides e-statistics (energy) tests and statistics for
4938 multivariate and univariate inference, including distance correlation,
4939 one-sample, two-sample, and multi-sample tests for comparing multivariate
4940 distributions, are implemented. Measuring and testing multivariate
4941 independence based on distance correlation, partial distance correlation,
4942 multivariate goodness-of-fit tests, clustering based on energy distance,
4943 testing for multivariate normality, distance components (disco) for
4944 non-parametric analysis of structured data, and other energy
4945 statistics/methods are implemented.")
4946 (license license:gpl2+)))
4948 (define-public r-suppdists
4950 (name "r-suppdists")
4955 (uri (cran-uri "SuppDists" version))
4958 "025b9nlxz62wk84295csyzbncpn80i3iby3sxdigf3swcgi2fmbb"))))
4959 (properties `((upstream-name . "SuppDists")))
4960 (build-system r-build-system)
4961 (home-page "https://cran.r-project.org/web/packages/SuppDists")
4962 (synopsis "Supplementary distributions")
4964 "This package provides ten distributions supplementing those built into
4965 R. Inverse Gauss, Kruskal-Wallis, Kendall's Tau, Friedman's chi squared,
4966 Spearman's rho, maximum F ratio, the Pearson product moment correlation
4967 coefficient, Johnson distributions, normal scores and generalized
4968 hypergeometric distributions. In addition two random number generators of
4969 George Marsaglia are included.")
4970 (license license:gpl2+)))
4972 (define-public r-ksamples
4979 (uri (cran-uri "kSamples" version))
4982 "1zs22p68d6320kcylisnk0b5wmpapxkyz15py09czxzw7npw8gms"))))
4983 (properties `((upstream-name . "kSamples")))
4984 (build-system r-build-system)
4987 (home-page "https://cran.r-project.org/web/packages/kSamples")
4988 (synopsis "K-Sample rank tests and their combinations")
4990 "This package provides tools to compares k samples using the
4991 Anderson-Darling test, Kruskal-Wallis type tests with different rank score
4992 criteria, Steel's multiple comparison test, and the Jonckheere-Terpstra (JT)
4993 test. It computes asymptotic, simulated or (limited) exact P-values, all
4994 valid under randomization, with or without ties, or conditionally under random
4995 sampling from populations, given the observed tie pattern. Except for Steel's
4996 test and the JT test it also combines these tests across several blocks of
4998 (license license:gpl2+)))
5000 (define-public r-cvst
5007 (uri (cran-uri "CVST" version))
5010 "0bgk0d6w3dyhb5s30idnp6jpb3m8wf3b79wqlg127wwm0cird8pg"))))
5011 (properties `((upstream-name . "CVST")))
5012 (build-system r-build-system)
5014 (list r-kernlab r-matrix))
5015 (home-page "https://cran.r-project.org/web/packages/CVST")
5016 (synopsis "Fast cross-validation via sequential testing")
5018 "This package implements the fast cross-validation via sequential
5019 testing (CVST) procedure. CVST is an improved cross-validation procedure
5020 which uses non-parametric testing coupled with sequential analysis to
5021 determine the best parameter set on linearly increasing subsets of the data.
5022 Additionally to the CVST the package contains an implementation of the
5023 ordinary k-fold cross-validation with a flexible and powerful set of helper
5024 objects and methods to handle the overall model selection process. The
5025 implementations of the Cochran's Q test with permutations and the sequential
5026 testing framework of Wald are generic and can therefore also be used in other
5028 (license license:gpl2+)))
5030 (define-public r-squarem
5037 (uri (cran-uri "SQUAREM" version))
5040 "0n1s32l9p4vdm3h5q6g43s0qbpzry08difsh0yay80wrla6f3rb6"))))
5041 (properties `((upstream-name . "SQUAREM")))
5042 (build-system r-build-system)
5043 (home-page "https://coah.jhu.edu/people/Faculty_personal_Pages/Varadhan.html")
5044 (synopsis "Squared Extrapolation Methods for Accelerating EM-Like Monotone Algorithms")
5046 "This package provides algorithms for accelerating the convergence of
5047 slow, monotone sequences from smooth, contraction mapping such as the EM
5048 algorithm. It can be used to accelerate any smooth, linearly convergent
5049 acceleration scheme. A tutorial style introduction to this package is
5050 available in a vignette.")
5051 (license license:gpl2+)))
5053 (define-public r-progressr
5055 (name "r-progressr")
5060 (uri (cran-uri "progressr" version))
5062 (base32 "1p5s35rzh28n2id2lipgyqmh3wzib66m7x0pz9028y8cql8xr5ac"))))
5063 (properties `((upstream-name . "progressr")))
5064 (build-system r-build-system)
5067 (home-page "https://progressr.futureverse.org")
5068 (synopsis "Inclusive, unifying API for progress updates")
5070 "This package provides a minimal, unifying API for scripts and packages
5071 to report progress updates from anywhere including when using parallel
5072 processing. The package is designed such that the developer can to focus on
5073 what progress should be reported on without having to worry about how to
5074 present it. The end user has full control of how, where, and when to render
5075 these progress updates.")
5076 (license license:gpl3+)))
5078 (define-public r-lava
5085 (uri (cran-uri "lava" version))
5088 "0bi3c1aqwlq7jbz4raz6vga4r264w7lldi0i62xjlbl7hnlgi23s"))))
5089 (build-system r-build-system)
5091 (list r-future-apply r-numderiv r-progressr r-squarem r-survival))
5094 (home-page "https://github.com/kkholst/lava")
5095 (synopsis "Latent variable models")
5097 "This package provides tools for the estimation and simulation of latent
5099 (license license:gpl3)))
5101 (define-public r-drr
5108 (uri (cran-uri "DRR" version))
5111 "1y70si1gig4l7jx5jiqsqliyywfsvimkx53x3zh1lc3yj2j6bqwk"))))
5112 (properties `((upstream-name . "DRR")))
5113 (build-system r-build-system)
5115 (list r-cvst r-kernlab r-matrix))
5116 (home-page "https://cran.r-project.org/web/packages/DRR")
5117 (synopsis "Dimensionality reduction via regression")
5119 "This package provides an implementation of dimensionality reduction via
5120 regression using Kernel Ridge Regression.")
5121 (license license:gpl3)))
5123 (define-public r-prodlim
5126 (version "2019.11.13")
5130 (uri (cran-uri "prodlim" version))
5133 "03wvh3kirp1prac5nky6a5whs97rvaf4hc27x0fnh51sa17r42b8"))))
5134 (build-system r-build-system)
5136 (list r-kernsmooth r-lava r-rcpp r-survival))
5137 (home-page "https://cran.r-project.org/web/packages/prodlim")
5138 (synopsis "Product-limit estimation for censored event history analysis")
5140 "This package provides a fast and user-friendly implementation of
5141 nonparametric estimators for censored event history (survival) analysis with
5142 the Kaplan-Meier and Aalen-Johansen methods.")
5143 (license license:gpl2+)))
5145 (define-public r-dimred
5152 (uri (cran-uri "dimRed" version))
5155 "1z8fqdc8mslvfix8ngxs1y2yrvlanp5581hwp2nzldj6mk5kn15b"))))
5156 (properties `((upstream-name . "dimRed")))
5157 (build-system r-build-system)
5159 (list r-drr r-magrittr))
5162 (home-page "https://github.com/gdkrmr/dimRed")
5163 (synopsis "Framework for dimensionality reduction")
5165 "This package provides a collection of dimensionality reduction
5166 techniques from R packages and provides a common interface for calling the
5168 (license license:gpl3)))
5170 (define-public r-timedate
5173 (version "3043.102")
5177 (uri (cran-uri "timeDate" version))
5180 "0wvl5pq261rvbgly7vilk3x3m9xk3ly6il1i5scwdf6srl1vlz1p"))))
5181 (properties `((upstream-name . "timeDate")))
5182 (build-system r-build-system)
5183 (home-page "https://www.rmetrics.org")
5184 (synopsis "Chronological and calendar objects")
5186 "This package provides an environment for teaching \"Financial
5187 Engineering and Computational Finance\" and for managing chronological and
5189 (license license:gpl2+)))
5191 (define-public r-magic
5198 (uri (cran-uri "magic" version))
5201 "1gybia2aq80ldk1d845y5srncfzbbmpqhgl7vfaz7qqqjs6d85j5"))))
5202 (build-system r-build-system)
5205 (home-page "https://github.com/RobinHankin/magic.git")
5206 (synopsis "Create and investigate magic squares")
5208 "This package provides a collection of efficient, vectorized algorithms
5209 for the creation and investigation of magic squares and hypercubes, including
5210 a variety of functions for the manipulation and analysis of arbitrarily
5211 dimensioned arrays.")
5212 (license license:gpl2)))
5214 (define-public r-rmysql
5221 (uri (cran-uri "RMySQL" version))
5224 "05aavyggyjv46awa7ggbxlfcy9707vak5kh7kj0ljdx8zga7xb7l"))))
5225 (properties `((upstream-name . "RMySQL")))
5226 (build-system r-build-system)
5228 (list `(,mariadb "dev") zlib))
5231 (home-page "https://github.com/r-dbi/RMySQL")
5232 (synopsis "Database interface and MySQL driver for R")
5234 "This package provides a DBI interface to MySQL / MariaDB. The RMySQL
5235 package contains an old implementation based on legacy code from S-PLUS which
5236 is being phased out. A modern MySQL client based on Rcpp is available from
5237 the RMariaDB package.")
5238 (license license:gpl2)))
5240 (define-public r-rpostgresql
5242 (name "r-rpostgresql")
5247 (uri (cran-uri "RPostgreSQL" version))
5250 "1fbixmnjp1kh6yiv8zhg8zi5ryvdf5j2jxv4agq5gcxf541s3g5x"))))
5251 (properties `((upstream-name . "RPostgreSQL")))
5252 (build-system r-build-system)
5257 (home-page "https://github.com/tomoakin/RPostgreSQL")
5258 (synopsis "R interface to the PostgreSQL database system")
5260 "This package provides a Database Interface (DBI) compliant driver for R
5261 to access PostgreSQL database systems.")
5262 ;; The whole package is released under GPL version 2. It includes code
5263 ;; under the PostgreSQL license.
5264 (license license:gpl2)))
5266 (define-public r-linprog
5273 (uri (cran-uri "linprog" version))
5276 "1d34m2nyk7m6j2dci69bhy5mlw479xax1517j7f14pq7vhpsm9l1"))))
5277 (build-system r-build-system)
5278 (propagated-inputs (list r-lpsolve))
5279 (home-page "http://linprog.r-forge.r-project.org/")
5280 (synopsis "Linear programming and optimization")
5282 "This package can be used to solve Linear Programming / Linear
5283 Optimization problems by using the simplex algorithm.")
5284 (license license:gpl2+)))
5286 (define-public r-geometry
5293 (uri (cran-uri "geometry" version))
5296 "1n7m0djqlhrv01l98r76grkki6cv4k4q2z6c7fksqgq4r2l6a14i"))))
5297 (build-system r-build-system)
5299 (list r-magic r-linprog r-lpsolve r-rcpp r-rcppprogress))
5300 (home-page "http://geometry.r-forge.r-project.org/")
5301 (synopsis "Mesh generator and surface tessellator")
5303 "This package makes the qhull library available in R, in a similar manner
5304 as in Octave. Qhull computes convex hulls, Delaunay triangulations, halfspace
5305 intersections about a point, Voronoi diagrams, furthest-site Delaunay
5306 triangulations, and furthest-site Voronoi diagrams. It runs in 2-d, 3-d, 4-d,
5307 and higher dimensions. It implements the Quickhull algorithm for computing
5308 the convex hull. Qhull does not support constrained Delaunay triangulations,
5309 or mesh generation of non-convex objects, but the package does include some R
5310 functions that allow for this. Currently the package only gives access to
5311 Delaunay triangulation and convex hull computation.")
5312 ;; The Qhull sources are included and are distributed under a custom
5313 ;; non-copyleft license. The R sources are released under GPL version 2.
5314 (license (list license:gpl2
5315 (license:non-copyleft "http://www.qhull.org/COPYING.txt")))))
5317 (define-public r-ddalpha
5324 (uri (cran-uri "ddalpha" version))
5327 "1bjfgb3lbzhjb5wx9hzp90jppq7vnj59bmd2n9ymi8sh1570m9p4"))))
5328 (build-system r-build-system)
5339 (home-page "https://cran.r-project.org/web/packages/ddalpha")
5340 (synopsis "Depth-Based classification and calculation of data depth")
5342 "This package contains procedures for depth-based supervised learning,
5343 which are entirely non-parametric, in particular the DDalpha-procedure (Lange,
5344 Mosler and Mozharovskyi, 2014). The training data sample is transformed by a
5345 statistical depth function to a compact low-dimensional space, where the final
5346 classification is done. It also offers an extension to functional data and
5347 routines for calculating certain notions of statistical depth functions. 50
5348 multivariate and 5 functional classification problems are included.")
5349 (license license:gpl2)))
5351 (define-public r-gower
5358 (uri (cran-uri "gower" version))
5361 "0p9qx9aafkdm7wibfwk59jzw6vspsff6zwp84bc40lg0myxbf737"))))
5362 (build-system r-build-system)
5363 (home-page "https://github.com/markvanderloo/gower")
5364 (synopsis "Gower's distance")
5366 "This package provides tools to compute Gower's distance (or similarity)
5367 coefficient between records, and to compute the top-n matches between records.
5368 Core algorithms are executed in parallel on systems supporting OpenMP.")
5369 (license license:gpl3)))
5371 (define-public r-rcpproll
5378 (uri (cran-uri "RcppRoll" version))
5381 "0srzfhzkk42kzrdjnhbb37946jp1p688rgysy6k3i2is8jb21zyb"))))
5382 (properties `((upstream-name . "RcppRoll")))
5383 (build-system r-build-system)
5386 (home-page "https://cran.r-project.org/web/packages/RcppRoll")
5387 (synopsis "Efficient rolling and windowed operations")
5389 "This package provides fast and efficient routines for common rolling /
5390 windowed operations. Routines for the efficient computation of windowed mean,
5391 median, sum, product, minimum, maximum, standard deviation and variance are
5393 (license license:gpl2+)))
5395 (define-public r-ipred
5402 (uri (cran-uri "ipred" version))
5405 "0hsq00382pfd9hzpcgphjxazbxm4zx0k2r6pk6kib56k0ibm7qfn"))))
5406 (build-system r-build-system)
5414 (home-page "https://cran.r-project.org/web/packages/ipred")
5415 (synopsis "Improved predictors")
5417 "This package provides improved predictive models by indirect
5418 classification and bagging for classification, regression and survival
5419 problems as well as resampling based estimators of prediction error.")
5420 (license license:gpl2+)))
5422 (define-public r-psych
5429 (uri (cran-uri "psych" version))
5432 "08f3byqwabgkqcxwpjbsxdcjkdg012iraqinw0fzskfl1srzkhyw"))))
5433 (build-system r-build-system)
5435 (list r-lattice r-mnormt r-nlme))
5438 (home-page "https://cran.r-project.org/web/packages/psych/")
5439 (synopsis "Procedures for psychological, psychometric, and personality research")
5441 "This package provides a general purpose toolbox for personality,
5442 psychometric theory and experimental psychology. Functions are primarily for
5443 multivariate analysis and scale construction using factor analysis, principal
5444 component analysis, cluster analysis and reliability analysis, although others
5445 provide basic descriptive statistics. Item Response Theory is done using
5446 factor analysis of tetrachoric and polychoric correlations. Functions for
5447 analyzing data at multiple levels include within and between group statistics,
5448 including correlations and factor analysis. Functions for simulating and
5449 testing particular item and test structures are included. Several functions
5450 serve as a useful front end for structural equation modeling. Graphical
5451 displays of path diagrams, factor analysis and structural equation models are
5452 created using basic graphics.")
5453 (license license:gpl2+)))
5455 (define-public r-generics
5462 (uri (cran-uri "generics" version))
5465 "162q9hdsnfcwjj255ahbi6v9vnyynvda7gb75p721y28j5xb7sk3"))))
5466 (build-system r-build-system)
5467 (home-page "https://github.com/r-lib/generics")
5468 (synopsis "Common S3 generics not provided by base R methods")
5470 "In order to reduce potential package dependencies and conflicts,
5471 generics provides a number of commonly used S3 generics that are not provided
5472 by base R methods related to model fitting.")
5473 (license license:gpl2)))
5475 (define-public r-broom
5482 (uri (cran-uri "broom" version))
5485 "16grzja9hz5mqpfzbp1r6zif1gp7swfadkm52340si9h8ifhk8b6"))))
5486 (build-system r-build-system)
5501 (home-page "https://github.com/tidyverse/broom")
5502 (synopsis "Convert statistical analysis objects into tidy data frames")
5504 "This package provides tools to convert statistical analysis objects from
5505 R into tidy data frames, so that they can more easily be combined, reshaped
5506 and otherwise processed with tools like @code{dplyr}, @code{tidyr} and
5507 @code{ggplot2}. The package provides three S3 generics: @code{tidy}, which
5508 summarizes a model's statistical findings such as coefficients of a
5509 regression; @code{augment}, which adds columns to the original data such as
5510 predictions, residuals and cluster assignments; and @code{glance}, which
5511 provides a one-row summary of model-level statistics.")
5512 (license license:expat)))
5514 (define-public r-recipes
5521 (uri (cran-uri "recipes" version))
5524 "1950rvva19ms6xy9d3jx94gzy589qprk115zjjd0ib4qxgip601x"))))
5525 (build-system r-build-system)
5548 (home-page "https://github.com/topepo/recipes")
5549 (synopsis "Preprocessing tools to create design matrices")
5551 "Recipes is an extensible framework to create and preprocess design
5552 matrices. Recipes consist of one or more data manipulation and analysis
5553 \"steps\". Statistical parameters for the steps can be estimated from an
5554 initial data set and then applied to other data sets. The resulting design
5555 matrices can then be used as inputs into statistical or machine learning
5557 (license license:gpl2)))
5559 (define-public r-pdist
5566 (uri (cran-uri "pdist" version))
5569 "0bvg8si81hs79v39d7svv4zbv2p0sk2r6m9vamibvkh9qvl4x406"))))
5570 (build-system r-build-system)
5571 (home-page "https://github.com/jeffwong/pdist")
5572 (synopsis "Partitioned distance function")
5574 "Pdist computes the euclidean distance between rows of a matrix X and
5575 rows of another matrix Y. Previously, this could be done by binding the two
5576 matrices together and calling @code{dist}, but this creates unnecessary
5577 computation by computing the distances between a row of X and another row of
5578 X, and likewise for Y. Pdist strictly computes distances across the two
5579 matrices, not within the same matrix, making computations significantly faster
5580 for certain use cases.")
5581 (license license:gpl3+)))
5583 (define-public r-ggrepel
5590 (uri (cran-uri "ggrepel" version))
5593 "1z5xyr5f4aryy0v1gzz9m8m4s5fzzwbrf0fxll1nbflr8xnr3yr9"))))
5594 (build-system r-build-system)
5596 (list r-ggplot2 r-rcpp r-rlang r-scales))
5598 (list r-knitr)) ; for vignettes
5599 (home-page "https://github.com/slowkow/ggrepel")
5600 (synopsis "Repulsive text and label geometries for ggplot2")
5602 "This package provides text and label geometries for ggplot2 that help to
5603 avoid overlapping text labels. Labels repel away from each other and away
5604 from the data points.")
5605 (license license:gpl3)))
5607 (define-public r-coro
5614 (uri (cran-uri "coro" version))
5616 (base32 "14irld29dipgfd34y0k351daqg9vqpnpdx8m3pxmqr1aiyj5f5cv"))))
5617 (properties `((upstream-name . "coro")))
5618 (build-system r-build-system)
5619 (propagated-inputs (list r-rlang))
5620 (native-inputs (list r-knitr))
5621 (home-page "https://github.com/r-lib/coro")
5622 (synopsis "Coroutines for R")
5624 "This package provides coroutines for R, a family of functions that can
5625 be suspended and resumed later on. This includes async functions (which
5626 await) and generators (which yield). Async functions are based on the
5627 concurrency framework of the @code{promises} package. Generators are based on
5628 a dependency free iteration protocol defined in @code{coro} and are compatible
5629 with iterators from the @code{reticulate} package.")
5630 (license license:expat)))
5632 (define-public r-corrplot
5639 (uri (cran-uri "corrplot" version))
5642 "1g98jk6xsl08z4n6sy5vriif99m31zhbz7j3dh1kfj4w7yb9zh78"))))
5643 (build-system r-build-system)
5646 (home-page "https://github.com/taiyun/corrplot")
5647 (synopsis "Visualization of a correlation matrix")
5649 "This package provides a graphical display of a correlation matrix or
5650 general matrix. It also contains some algorithms to do matrix reordering. In
5651 addition, corrplot is good at details, including choosing color, text labels,
5652 color labels, layout, etc.")
5653 ;; Any version of the GPL
5654 (license license:gpl2+)))
5656 (define-public r-stringdist
5658 (name "r-stringdist")
5663 (uri (cran-uri "stringdist" version))
5665 (base32 "1fv1hbdlm8qwx57b2aj50mw0say5k48awzavx65mfk67qp6ddk7g"))))
5666 (build-system r-build-system)
5667 (home-page "https://github.com/markvanderloo/stringdist")
5668 (synopsis "Approximate string matching and string distance functions")
5670 "This package implements an approximate string matching version of R's
5671 native @code{match} function. It can calculate various string distances based
5672 on edits (Damerau-Levenshtein, Hamming, Levenshtein, optimal string alignment),
5673 qgrams (q- gram, cosine, jaccard distance) or heuristic metrics (Jaro,
5674 Jaro-Winkler). An implementation of soundex is provided as well. Distances
5675 can be computed between character vectors while taking proper care of encoding
5676 or between integer vectors representing generic sequences.")
5677 (license license:gpl3+)))
5679 (define-public r-ucminf
5686 (uri (cran-uri "ucminf" version))
5689 "01vggwg1w71k98qs6fhb0x1843vi322mf4g3hbclks94kcpkisx2"))))
5690 (build-system r-build-system)
5691 (native-inputs (list gfortran))
5692 (home-page "https://cran.r-project.org/web/packages/ucminf/")
5693 (synopsis "General-purpose unconstrained non-linear optimization")
5695 "This package provides an implementation of an algorithm for
5696 general-purpose unconstrained non-linear optimization. The algorithm is of
5697 quasi-Newton type with BFGS updating of the inverse Hessian and soft line
5698 search with a trust region type monitoring of the input to the line search
5699 algorithm. The interface of @code{ucminf} is designed for easy interchange
5700 with the package @code{optim}.")
5701 (license license:gpl2+)))
5703 (define-public r-usedist
5710 (uri (cran-uri "usedist" version))
5712 (base32 "0ddf1zcalbrn293qmr9kdzz3x16fzc4k1bwb1pjmwnspisqfi8kj"))))
5713 (properties `((upstream-name . "usedist")))
5714 (build-system r-build-system)
5715 (home-page "https://cran.r-project.org/package=usedist")
5716 (synopsis "Distance matrix utilities")
5718 "This package provides functions to re-arrange, extract, and work with
5720 (license license:gpl3)))
5722 (define-public r-useful
5728 (uri (cran-uri "useful" version))
5731 "0n50v1q75k518sq23id14jphwla35q4sasahrnrnllwrachl67v1"))))
5732 (properties `((upstream-name . "useful")))
5733 (build-system r-build-system)
5743 (home-page "https://github.com/jaredlander/useful")
5744 (synopsis "Collection of handy, useful functions")
5745 (description "This package provides a set of little functions that have been
5746 found useful to do little odds and ends such as plotting the results of K-means
5747 clustering, substituting special text characters, viewing parts of a
5748 @code{data.frame}, constructing formulas from text and building design and
5749 response matrices.")
5750 (license license:bsd-3)))
5752 (define-public r-ordinal
5755 (version "2019.12-10")
5759 (uri (cran-uri "ordinal" version))
5762 "09bpmjmbf4x82kgf6bm4bkncq2apdv9mk20zj4zgma2jx2vyfhbs"))))
5763 (build-system r-build-system)
5765 (list r-mass r-matrix r-numderiv r-ucminf))
5766 (home-page "https://github.com/runehaubo/ordinal")
5767 (synopsis "Regression models for ordinal data")
5769 "This package provides an implementation of cumulative link (mixed)
5770 models also known as ordered regression models, proportional odds models,
5771 proportional hazards models for grouped survival times and ordered models.
5772 Estimation is via maximum likelihood and mixed models are fitted with the
5773 Laplace approximation and adaptive Gauss-Hermite quadrature.")
5774 (license license:gpl2+)))
5776 (define-public r-jomo
5783 (uri (cran-uri "jomo" version))
5786 "0qq03zspmh8x2c8w882ynsw7wshr9b0fyrpwnqx5yc1xlzrqffcx"))))
5787 (build-system r-build-system)
5789 (list r-lme4 r-mass r-ordinal r-survival r-tibble))
5790 (home-page "https://cran.r-project.org/web/packages/jomo/")
5791 (synopsis "Multilevel Joint Modelling Multiple Imputation")
5793 "Similarly to Schafer's package pan, jomo is a package for multilevel
5794 joint modelling multiple imputation @url{Carpenter and Kenward (2013),
5795 http://doi.org/10.1002/9781119942283}. Novel aspects of jomo are the
5796 possibility of handling binary and categorical data through latent normal
5797 variables, the option to use cluster-specific covariance matrices and to
5798 impute compatibly with the substantive model.")
5799 (license license:gpl2)))
5801 (define-public r-pan
5808 (uri (cran-uri "pan" version))
5811 "1dk3jjj826p7xrz10qz04vyc068xnypg7bp0pj4c32z3da0xzh5d"))))
5812 (build-system r-build-system)
5813 (native-inputs (list gfortran))
5814 (home-page "https://cran.r-project.org/web/packages/pan/")
5815 (synopsis "Multiple imputation for multivariate panel or clustered data")
5817 "This package implements multiple imputation for multivariate panel or
5819 (license license:gpl3)))
5821 (define-public r-mitml
5828 (uri (cran-uri "mitml" version))
5831 "00i18nnvrdrg91crgcp2a431xs71cawaip3xkqk2myv0iav3xga9"))))
5832 (build-system r-build-system)
5834 (list r-haven r-jomo r-pan))
5837 (home-page "https://cran.r-project.org/web/packages/mitml/")
5838 (synopsis "Tools for multiple imputation in multilevel modeling")
5840 "This package provides tools for multiple imputation of missing data in
5841 multilevel modeling. It includes a user-friendly interface to the packages
5842 pan and jomo, and several functions for visualization, data management and the
5843 analysis of multiply imputed data sets.")
5844 (license license:gpl2+)))
5846 (define-public r-mice
5853 (uri (cran-uri "mice" version))
5856 "01fnfrr7adp29s5kic95r9q0rdznkz2pjmziyimnrqzyicyvfyzq"))))
5857 (build-system r-build-system)
5868 (home-page "https://cran.r-project.org/web/packages/mice/")
5869 (synopsis "Multivariate imputation by chained equations")
5871 "Multiple imputation using @dfn{Fully Conditional Specification} (FCS)
5872 implemented by the MICE algorithm as described in @url{Van Buuren and
5873 Groothuis-Oudshoorn (2011), http://doi.org/10.18637/jss.v045.i03}. Each
5874 variable has its own imputation model. Built-in imputation models are
5875 provided for continuous data (predictive mean matching, normal), binary
5876 data (logistic regression), unordered categorical data (polytomous logistic
5877 regression) and ordered categorical data (proportional odds). MICE can also
5878 impute continuous two-level data (normal model, pan, second-level variables).
5879 Passive imputation can be used to maintain consistency between variables.
5880 Various diagnostic plots are available to inspect the quality of the
5882 ;; Any of these two versions.
5883 (license (list license:gpl2 license:gpl3))))
5885 (define-public r-truncnorm
5887 (name "r-truncnorm")
5892 (uri (cran-uri "truncnorm" version))
5895 "0zn88wdd58223kibk085rhsikl4yhlrwiyq109hzjg06hy6lwmj9"))))
5896 (build-system r-build-system)
5897 (home-page "https://cran.r-project.org/web/packages/truncnorm/")
5898 (synopsis "Truncated normal distribution")
5899 (description "This package provides functions for the truncated normal
5900 distribution with mean equal to @code{mean} and standard deviation equal to
5901 @code{sd}. It includes density, distribution, quantile, and expected value
5902 functions, as well as a random generation function.")
5903 (license license:gpl2)))
5905 (define-public r-rsolnp
5912 (uri (cran-uri "Rsolnp" version))
5915 "0w7nkj6igr0gi7r7jg950lsx7dj6aipgxi6vbjsf5f5yc9h7fhii"))))
5916 (properties `((upstream-name . "Rsolnp")))
5917 (build-system r-build-system)
5920 (home-page "https://cran.r-project.org/web/packages/Rsolnp/")
5921 (synopsis "General non-linear optimization")
5922 (description "The Rsolnp package implements a general non-linear augmented
5923 Lagrange multiplier method solver, a @dfn{sequential quadratic
5924 programming} (SQP) based solver).")
5925 ;; Any version of the GPL.
5926 (license license:gpl2+)))
5928 (define-public r-hardyweinberg
5930 (name "r-hardyweinberg")
5935 (uri (cran-uri "HardyWeinberg" version))
5938 "0b3szw090dsc3bkas2kvx787ww2i6zzg2qmdyivmqc8amx5arn6g"))))
5939 (properties `((upstream-name . "HardyWeinberg")))
5940 (build-system r-build-system)
5942 (list r-mice r-nnet r-rcpp r-rsolnp))
5943 (home-page "https://cran.r-project.org/package=HardyWeinberg")
5944 (synopsis "Statistical tests and graphics for Hardy-Weinberg equilibrium")
5946 "This package contains tools for exploring Hardy-Weinberg equilibrium for
5947 diallelic genetic marker data. All classical tests (chi-square, exact,
5948 likelihood-ratio and permutation tests) for Hardy-Weinberg equilibrium are
5949 included in the package, as well as functions for power computation and for
5950 the simulation of marker data under equilibrium and disequilibrium. Routines
5951 for dealing with markers on the X-chromosome are included. Functions for
5952 testing equilibrium in the presence of missing data by using multiple
5953 imputation are also provided. Implements several graphics for exploring the
5954 equilibrium status of a large set of diallelic markers: ternary plots with
5955 acceptance regions, log-ratio plots and Q-Q plots.")
5956 (license license:gpl2+)))
5965 (uri (cran-uri "sm" version))
5968 "03z8igsjqr32x407asxvkrbayvm6yhv9xyfs0n8fkmv8zk5a41r6"))))
5969 (build-system r-build-system)
5970 (native-inputs (list gfortran))
5971 (home-page "http://www.stats.gla.ac.uk/~adrian/sm/")
5972 (synopsis "Smoothing methods for nonparametric regression and density estimation")
5974 "This is software accompanying the book 'Applied Smoothing Techniques for
5975 Data Analysis---The Kernel Approach with S-Plus Illustrations', Oxford
5976 University Press. It provides smoothing methods for nonparametric regression
5977 and density estimation")
5978 (license license:gpl2+)))
5980 (define-public r-venndiagram
5982 (name "r-venndiagram")
5986 (uri (cran-uri "VennDiagram" version))
5989 "0ilcxcp8qskmb5cp7fyb7i0qizg42lrx0ny8ws3if90kfrglghp7"))))
5990 (properties `((upstream-name . "VennDiagram")))
5991 (build-system r-build-system)
5993 (list r-futile-logger))
5994 (home-page "https://cran.r-project.org/web/packages/VennDiagram/")
5995 (synopsis "Generate High-Resolution Venn and Euler Plots")
5997 "This package provides a set of functions to generate high-resolution
5998 Venn and Euler plots. It includes handling for several special cases,
5999 including two-case scaling, and extensive customization of plot shape and
6001 (license license:gpl2+)))
6003 (define-public r-vioplot
6010 (uri (cran-uri "vioplot" version))
6013 "1dmdasp3jldc41233z6r08w3j76vyyp9m3jrj7n4ahk48yd5siq6"))))
6014 (build-system r-build-system)
6019 (home-page "http://wsopuppenkiste.wiso.uni-goettingen.de/~dadler")
6020 (synopsis "Violin plot")
6022 "This package provides a violin plot, which is a combination of a box
6023 plot and a kernel density plot.")
6024 (license license:bsd-3)))
6026 (define-public r-rsofia
6032 ;; This package has been removed from CRAN, so we can
6033 ;; only fetch it from the archives.
6034 (uri (string-append "https://cran.r-project.org/src/"
6035 "contrib/Archive/RSofia/RSofia_"
6039 "0q931y9rcf6slb0s2lsxhgqrzy4yqwh8hb1124nxg0bjbxvjbihn"))))
6040 (properties `((upstream-name . "RSofia")))
6041 (build-system r-build-system)
6044 (home-page "https://cran.r-project.org/src/contrib/Archive/RSofia")
6045 (synopsis "Port of sofia-ml to R")
6046 (description "This package is a port of sofia-ml to R. Sofia-ml is a
6047 suite of fast incremental algorithms for machine learning that can be used for
6048 training models for classification or ranking.")
6049 (license license:asl2.0)))
6051 (define-public r-xts
6058 (uri (cran-uri "xts" version))
6061 "0b6a7mpyk9aw6axas7nz01gadczprwwfhii01fz31z26z555i06n"))))
6062 (build-system r-build-system)
6063 (propagated-inputs (list r-zoo))
6064 (home-page "https://github.com/joshuaulrich/xts")
6065 (synopsis "Extensible time series")
6067 "This package provides for uniform handling of R's different time-based
6068 data classes by extending @code{zoo}, maximizing native format information
6069 preservation and allowing for user-level customization and extension, while
6070 simplifying cross-class interoperability.")
6071 (license license:gpl2+)))
6073 (define-public r-performanceanalytics
6075 (name "r-performanceanalytics")
6080 (uri (cran-uri "PerformanceAnalytics" version))
6083 "0ci26hsj4wnw9g0mh4vrn0cg986cpcpx169rvw6v6rbnjxq718bq"))))
6085 `((upstream-name . "PerformanceAnalytics")))
6086 (build-system r-build-system)
6088 (list r-quadprog r-xts r-zoo))
6089 (home-page "https://r-forge.r-project.org/projects/returnanalytics/")
6090 (synopsis "Econometric tools for performance and risk analysis")
6091 (description "This is a collection of econometric functions for
6092 performance and risk analysis. This package aims to aid practitioners and
6093 researchers in utilizing the latest research in analysis of non-normal return
6094 streams. In general, it is most tested on return (rather than price) data on
6095 a regular scale, but most functions will work with irregular return data as
6096 well, and increasing numbers of functions will work with P&L or price data
6098 ;; Either version may be picked.
6099 (license (list license:gpl2 license:gpl3))))
6101 (define-public r-laeken
6108 (uri (cran-uri "laeken" version))
6111 "1p3ccbaydlr52p8qmgmm2l6kryvq6jjjx7mqn2vv0gpjaxqhyy92"))))
6112 (build-system r-build-system)
6114 (list r-boot r-mass))
6115 (home-page "https://cran.r-project.org/web/packages/laeken/")
6116 (synopsis "Estimation of indicators on social exclusion and poverty")
6117 (description "This package provides tools for the estimation of indicators
6118 on social exclusion and poverty, as well as an implementation of Pareto tail
6119 modeling for empirical income distributions.")
6120 (license license:gpl2+)))
6122 (define-public r-vcd
6129 (uri (cran-uri "vcd" version))
6132 "13sn77qdcyll9lz7nab0bxzfvpgj8f5rl2cq5ylpz8pibynj1d55"))))
6133 (build-system r-build-system)
6135 (list r-colorspace r-lmtest r-mass))
6136 (home-page "https://cran.r-project.org/web/packages/vcd/")
6137 (synopsis "Visualizing categorical data")
6138 (description "This package provides visualization techniques, data sets,
6139 summary and inference procedures aimed particularly at categorical data.
6140 Special emphasis is given to highly extensible grid graphics. The package was
6141 originally inspired by the book \"Visualizing Categorical Data\" by Michael
6142 Friendly and is now the main support package for a new book, \"Discrete Data
6143 Analysis with R\" by Michael Friendly and David Meyer (2015).")
6144 (license license:gpl2)))
6146 (define-public r-vcfr
6152 (uri (cran-uri "vcfR" version))
6155 "0lhxb3ac4fafwik9q3cds46svzf0hyca8k54chw3dpk50c0zz1yx"))))
6156 (build-system r-build-system)
6172 (home-page "https://github.com/knausb/vcfR")
6173 (synopsis "Manipulate and visualize VCF data")
6174 (description "This package facilitates easy manipulation of variant call
6175 format (VCF) data. Functions are provided to rapidly read from and write to
6176 VCF files. Once VCF data is read into R, a parser function extracts matrices
6177 of data. This information can then be used for quality control or other
6178 purposes. Additional functions provide visualization of genomic data. Once
6179 processing is complete data may be written to a VCF file. It also may be
6180 converted into other popular R objects. This package provides a link between
6181 VCF data and familiar R software.")
6182 (license license:gpl3)))
6184 (define-public r-ica
6191 (uri (cran-uri "ica" version))
6194 "0ya1nph1zwhad0bfz4yxs27kl45yk1dhnphdlrq34p8pqrpmj8g7"))))
6195 (build-system r-build-system)
6196 (home-page "https://cran.r-project.org/web/packages/ica/")
6197 (synopsis "Independent component analysis")
6198 (description "This package provides tools for @dfn{Independent Component
6199 Analysis} (ICA) using various algorithms: FastICA,
6200 Information-Maximization (Infomax), and @dfn{Joint Approximate Diagonalization
6201 of Eigenmatrices} (JADE).")
6202 (license license:gpl2+)))
6204 (define-public r-dtw
6211 (uri (cran-uri "dtw" version))
6214 "004gm4mzgdzdj807j3bwqsv5lizmnmz5jq514bdjshhkysnzjz6z"))))
6215 (build-system r-build-system)
6216 (propagated-inputs (list r-proxy))
6217 (home-page "http://dtw.r-forge.r-project.org/")
6218 (synopsis "Dynamic Time Warping Algorithms")
6219 (description "This package provides a comprehensive implementation of
6220 @dfn{dynamic time warping} (DTW) algorithms in R. DTW computes the
6221 optimal (least cumulative distance) alignment between points of two time
6222 series. Common DTW variants covered include local (slope) and global (window)
6223 constraints, subsequence matches, arbitrary distance definitions,
6224 normalizations, minimum variance matching, and so on.")
6225 (license license:gpl2+)))
6227 (define-public r-sdmtools
6230 (version "1.1-221.2")
6234 (uri (cran-uri "SDMTools" version))
6237 "1xvcd97ikqsfdpk2fddy3k0z1ajqga7nv9bgac9c1wnjk1gqrpgh"))))
6238 (properties `((upstream-name . "SDMTools")))
6239 (build-system r-build-system)
6240 (propagated-inputs (list r-r-utils))
6241 (home-page "https://www.rforge.net/SDMTools/")
6242 (synopsis "Species distribution modelling tools")
6243 (description "This package provides a set of tools for post processing
6244 the outcomes of species distribution modeling exercises. It includes novel
6245 methods for comparing models and tracking changes in distributions through
6246 time. It further includes methods for visualizing outcomes, selecting
6247 thresholds, calculating measures of accuracy and landscape fragmentation
6249 (license license:gpl3+)))
6251 (define-public r-scatterplot3d
6253 (name "r-scatterplot3d")
6258 (uri (cran-uri "scatterplot3d" version))
6261 "152xqz9c70qab86mpgng049gxsg5f4fpf1m8dh93fb9v1avjd0sc"))))
6262 (build-system r-build-system)
6263 (home-page "https://cran.r-project.org/web/packages/scatterplot3d/")
6264 (synopsis "3D scatter plot")
6265 (description "This package provides an implementation of scatter plots for
6266 plotting. a three dimensional point cloud.")
6267 (license license:gpl2)))
6269 (define-public r-ggridges
6276 (uri (cran-uri "ggridges" version))
6279 "0bmlqy1p6rac90af97ffpdi6php7dblx66l2hcm8ljidgyqzmspm"))))
6280 (build-system r-build-system)
6282 (list r-ggplot2 r-plyr r-scales r-withr))
6285 (home-page "https://github.com/clauswilke/ggridges")
6286 (synopsis "Ridgeline plots in ggplot2")
6288 "Ridgeline plots provide a convenient way of visualizing changes in
6289 distributions over time or space. This package enables the creation of such
6290 plots in @code{ggplot2}.")
6291 (license license:gpl2)))
6293 (define-public r-ggjoy
6300 (uri (cran-uri "ggjoy" version))
6303 "012md2m0jqfcccb933j423m3ck31v3p0pd41gjxpyg9082y7ixyj"))))
6304 (build-system r-build-system)
6306 (list r-ggplot2 r-ggridges))
6307 (home-page "https://github.com/clauswilke/ggjoy")
6308 (synopsis "Joyplots in ggplot2")
6309 (description "Joyplots provide a convenient way of visualizing changes in
6310 distributions over time or space. This package enables the creation of such
6311 plots in @code{ggplot2}.")
6312 (license license:gpl2)))
6314 (define-public r-cli
6321 (uri (cran-uri "cli" version))
6324 "0qqd4mscv8ndjbji7knprdlv2hhyk35gazagvapbjzq1p6yfpaf3"))))
6325 (build-system r-build-system)
6328 (home-page "https://github.com/r-lib/cli#readme")
6329 (synopsis "Helpers for developing command line interfaces")
6330 (description "This package provides a suite of tools designed to build
6331 attractive command line interfaces (CLIs). It includes tools for drawing
6332 rules, boxes, trees, and Unicode symbols with ASCII alternatives.")
6333 (license license:expat)))
6335 (define-public r-argparser
6337 (name "r-argparser")
6342 (uri (cran-uri "argparser" version))
6345 "0xcl0ivsbc4iw8s7027q4cx68j6s5lihbby0xa9pmlv4wjmcvdr6"))))
6346 (build-system r-build-system)
6347 (home-page "https://bitbucket.org/djhshih/argparser")
6348 (synopsis "Command-line argument parser")
6350 "This package provides a cross-platform command-line argument parser
6351 written purely in R with no external dependencies. It is useful with the
6352 Rscript front-end and facilitates turning an R script into an executable
6354 (license license:gpl3+)))
6356 (define-public r-debugme
6363 (uri (cran-uri "debugme" version))
6366 "1c9sg55zvf10h8198jdnpamm6f66lzw3c3jnmdp9ls6na0j0xbjd"))))
6367 (build-system r-build-system)
6368 (propagated-inputs (list r-crayon))
6369 (home-page "https://github.com/r-lib/debugme#readme")
6370 (synopsis "Debug R packages")
6372 "This package allows the user to specify debug messages as special string
6373 constants, and control debugging of packages via environment variables.")
6374 (license license:expat)))
6376 (define-public r-processx
6383 (uri (cran-uri "processx" version))
6385 (base32 "0ail3w8n5g1ibdamgpxcfpla18kqkilmppiasm7ms67cavx2k5k7"))))
6386 (build-system r-build-system)
6389 (home-page "https://github.com/r-lib/processx3")
6390 (synopsis "Execute and control system processes")
6392 "This package provides portable tools to run system processes in the
6393 background. It can check if a background process is running; wait on a
6394 background process to finish; get the exit status of finished processes; kill
6395 background processes and their children; restart processes. It can read the
6396 standard output and error of the processes, using non-blocking connections.
6397 @code{processx} can poll a process for standard output or error, with a
6398 timeout. It can also poll several processes at once.")
6399 (license license:expat)))
6401 (define-public r-tsp
6408 (uri (cran-uri "TSP" version))
6411 "022k0972kcxb0w6qhx09l9cif8fmpkpvwddvgxiy60bx343ywzia"))))
6412 (properties `((upstream-name . "TSP")))
6413 (build-system r-build-system)
6414 (propagated-inputs (list r-foreach))
6415 (home-page "https://cran.r-project.org/web/packages/TSP/")
6416 (synopsis "Traveling salesperson problem (TSP)")
6417 (description "This package provides basic infrastructure and some
6418 algorithms for the @dfn{traveling salesperson problem}(TSP) (also known as the
6419 traveling salesman problem).")
6420 (license license:gpl3)))
6422 (define-public r-qap
6429 (uri (cran-uri "qap" version))
6432 "0d2d1ni1camixyi45lfy00f4pn3p063k7bsi8gj5scp6n15mdgb0"))))
6433 (build-system r-build-system)
6434 (native-inputs (list gfortran))
6435 (home-page "https://cran.r-project.org/web/packages/qap/")
6436 (synopsis "Heuristics for the quadratic assignment problem (QAP)")
6437 (description "This package implements heuristics for the @dfn{quadratic
6438 assignment problem} (QAP). Currently only a simulated annealing heuristic is
6440 (license license:gpl3)))
6442 (define-public r-gclus
6449 (uri (cran-uri "gclus" version))
6452 "1cz0g0i972955hhaji30rx8448x7f3as7z1sww9i5h86ybgirilw"))))
6453 (build-system r-build-system)
6454 (propagated-inputs (list r-cluster))
6455 (home-page "https://cran.r-project.org/web/packages/gclus/")
6456 (synopsis "Clustering graphics")
6457 (description "This package orders panels in scatterplot matrices and
6458 parallel coordinate displays by some merit index. It contains various indices
6459 of merit, ordering functions, and enhanced versions of @code{pairs} and
6460 @code{parcoord} which color panels according to their merit level.")
6461 (license license:gpl2+)))
6463 (define-public r-webshot
6470 (uri (cran-uri "webshot" version))
6473 "1h6v94zwq0ypgi4vf8xlhp5k13j7f9061hx908177i68c6zg5i5p"))))
6474 (build-system r-build-system)
6476 (list r-callr r-jsonlite r-magrittr))
6477 (home-page "https://github.com/wch/webshot/")
6478 (synopsis "Take screenshots of web pages")
6480 "Webshot makes it easy to take screenshots of web pages from within R.
6481 It can also run Shiny applications locally and take screenshots of the
6482 application; and it can render and screenshot static as well as interactive R
6483 Markdown documents.")
6484 (license license:gpl2)))
6486 (define-public r-seriation
6488 (name "r-seriation")
6493 (uri (cran-uri "seriation" version))
6496 "0dlj0mqpg585m6i7yn0h878i8ag6pyqph98xkk42i2nvghpy01gr"))))
6497 (build-system r-build-system)
6506 (native-inputs (list gfortran))
6507 (home-page "https://s2.smu.edu/IDA/seriation/")
6508 (synopsis "Infrastructure for ordering objects using seriation")
6510 "This package provides infrastructure for seriation with an
6511 implementation of several seriation/sequencing techniques to reorder matrices,
6512 dissimilarity matrices, and dendrograms. It also provides (optimally)
6513 reordered heatmaps, color images and clustering visualizations like
6514 dissimilarity plots, and visual assessment of cluster tendency plots (VAT and
6516 (license license:gpl3)))
6518 (define-public r-xfun
6525 (uri (cran-uri "xfun" version))
6527 (base32 "0dgjkrlwl6rxmvdn6s1xrbiaa53hkfx2s7rqrbrc7c6shbkg6sfi"))))
6528 (build-system r-build-system)
6529 ;; knitr itself depends on xfun
6532 `(("r-knitr" ,r-knitr)))
6533 (home-page "https://github.com/yihui/xfun")
6534 (synopsis "Miscellaneous functions")
6536 "This package provides miscellaneous functions commonly used in other
6537 packages maintained by Yihui Xie.")
6538 (license license:expat)))
6540 (define-public r-utf8
6547 (uri (cran-uri "utf8" version))
6550 "1x6qg19z4qih9lk3mvnmx0vailm1khp5lylw4hlwz6rssj3yw6m7"))))
6551 (build-system r-build-system)
6553 (list r-knitr r-rmarkdown)) ; for vignettes
6554 (home-page "https://github.com/patperry/r-utf8")
6555 (synopsis "Unicode text processing")
6557 "This package provides tools to process and print UTF-8 encoded
6558 international text (Unicode). Input, validate, normalize, encode, format, and
6560 (license license:asl2.0)))
6562 (define-public r-zeallot
6569 (uri (cran-uri "zeallot" version))
6572 "1sd1igcfnv27pa3bqxlbyxchi562h7grnjg1l7wxx3bwr49i57s3"))))
6573 (build-system r-build-system)
6574 (home-page "https://github.com/nteetor/zeallot")
6575 (synopsis "Multiple, unpacking, and destructuring assignment")
6577 "This package provides a @code{%<-%} operator to perform multiple,
6578 unpacking, and destructuring assignment in R. The operator unpacks the
6579 right-hand side of an assignment into multiple values and assigns these values
6580 to variables on the left-hand side of the assignment.")
6581 (license license:expat)))
6583 (define-public r-zlog
6589 (uri (cran-uri "zlog" version))
6592 "1d5j31p0h3rrn230087h3ngpvwknlisjv0f1qdbicdj9m177spci"))))
6593 (properties `((upstream-name . "zlog")))
6594 (build-system r-build-system)
6595 (native-inputs (list r-knitr))
6596 (home-page "https://cran.r-project.org/package=zlog")
6597 (synopsis "Transformation for laboratory easurements")
6599 "The @code{zlog} package offers functions to transform laboratory
6600 measurements into standardised z or @math{z(log)-values}. Therefore the lower
6601 and upper reference limits are needed. If these are not known they could be
6602 estimated from a given sample.")
6603 (license license:gpl3+)))
6605 (define-public r-vctrs
6612 (uri (cran-uri "vctrs" version))
6615 "1pb0wjpwix29q8d8p3wi72a9mp9mif7369pk31w238cs00g8hxln"))))
6616 (build-system r-build-system)
6618 (list r-cli r-glue r-rlang))
6621 (home-page "https://github.com/r-lib/vctrs")
6622 (synopsis "Vector helpers")
6624 "There are three main goals to the @code{vctrs} package:
6627 @item To propose @code{vec_size()} and @code{vec_type()} as alternatives to
6628 @code{length()} and @code{class()}. These definitions are paired with a
6629 framework for type-coercion and size-recycling.
6630 @item To define type- and size-stability as desirable function properties, use
6631 them to analyse existing base function, and to propose better alternatives.
6632 This work has been particularly motivated by thinking about the ideal
6633 properties of @code{c()}, @code{ifelse()}, and @code{rbind()}.
6634 @item To provide a new @code{vctr} base class that makes it easy to create new
6635 S3 vectors. @code{vctrs} provides methods for many base generics in terms of
6636 a few new @code{vctrs} generics, making implementation considerably simpler
6639 (license license:gpl3)))
6641 (define-public r-pillar
6648 (uri (cran-uri "pillar" version))
6651 "1fqk18vc9ashf12gdqkdi6n1nj5lh324vwhgiib3b2fcb2bghhbq"))))
6652 (build-system r-build-system)
6665 (home-page "https://github.com/r-lib/pillar")
6666 (synopsis "Coloured formatting for columns")
6668 "This package provides a @code{pillar} generic designed for formatting
6669 columns of data using the full range of colours provided by modern
6671 (license license:gpl3)))
6673 (define-public r-pinfsc50
6679 (uri (cran-uri "pinfsc50" version))
6682 "1547xyxmfb7zi8h9bsm6k67dcw4hpp129xzvmgwfw7r6p4af47zd"))))
6683 (build-system r-build-system)
6684 (home-page "https://cran.r-project.org/web/packages/pinfsc50/")
6685 (synopsis "Genomic data for the plant pathogen Phytophthora infestans")
6686 (description "This package contains genomic data for the plant pathogen
6687 Phytophthora infestans. It includes a variant file, a sequence file and an
6688 annotation file. This package is intended to be used as example data for
6689 packages that work with genomic data.")
6690 (license license:gpl2+)))
6692 (define-public r-uuid
6699 (uri (cran-uri "uuid" version))
6702 "0bzlc2knmr338h4ykx8v8c2a1inizxafj8rh13kwii68gpp50nz7"))))
6703 (build-system r-build-system)
6704 (home-page "https://www.rforge.net/uuid")
6705 (synopsis "Tools for generating and handling of UUIDs")
6707 "This package provides tools for generating and handling of
6708 @dfn{Universally Unique Identifiers} (UUIDs).")
6709 (license license:expat)))
6711 (define-public r-tinytex
6718 (uri (cran-uri "tinytex" version))
6721 "1v95pjxdq0ma90jji5yqh8ihlcf35cmrqx9v0z649zh0q9vrnbpj"))))
6722 (build-system r-build-system)
6725 (home-page "https://github.com/yihui/tinytex")
6726 (synopsis "Helper functions for TeX Live and compiling LaTeX documents")
6728 "This package provides helper functions to install and maintain the LaTeX
6729 distribution named TinyTeX, a lightweight, cross-platform, portable, and
6730 easy-to-maintain version of TeX Live. This package also contains helper
6731 functions to compile LaTeX documents, and install missing LaTeX packages
6733 (license license:expat)))
6735 (define-public r-tinytest
6742 (uri (cran-uri "tinytest" version))
6745 "1mq31f7bzcz5bkgzl9khm1i80axfzra7gcjqxd2yqb4wrw1m3x4s"))))
6746 (properties `((upstream-name . "tinytest")))
6747 (build-system r-build-system)
6748 (home-page "https://github.com/markvanderloo/tinytest")
6749 (synopsis "Lightweight unit testing framework")
6751 "This package provides a lightweight unit testing framework. Main
6755 @item install tests with the package;
6756 @item test results are treated as data that can be stored and manipulated;
6757 @item test files are R scripts interspersed with test commands, that can be
6759 @item fully automated build-install-test sequence for packages;
6760 @item skip tests when not run locally (e.g. on CRAN);
6761 @item flexible and configurable output printing;
6762 @item compare computed output with output stored with the package;
6763 @item run tests in parallel;
6764 @item extensible by other packages;
6765 @item report side effects.
6768 (license license:gpl3)))
6770 (define-public r-network
6777 (uri (cran-uri "network" version))
6780 "1xrhzbci7ls4h05skdlirxl49jsvmylrqivz2kd6i33wh2ca324m"))))
6781 (build-system r-build-system)
6783 (list r-magrittr r-statnet-common r-tibble))
6784 (home-page "https://statnet.org/")
6785 (synopsis "Classes for relational data")
6787 "This package provides tools to create and modify network objects. The
6788 @code{network} class can represent a range of relational data types, and
6789 supports arbitrary vertex/edge/graph attributes.")
6790 (license license:gpl2+)))
6792 (define-public r-stabs
6799 (uri (cran-uri "stabs" version))
6802 "1nf1yg14cgxrs4np1yghpzw1nczaslfv3rvf3918wrlzg0vp6l7q"))))
6803 (build-system r-build-system)
6806 (home-page "https://github.com/hofnerb/stabs")
6807 (synopsis "Stability selection with error control")
6809 "This package provides resampling procedures to assess the stability of
6810 selected variables with additional finite sample error control for
6811 high-dimensional variable selection procedures such as Lasso or boosting.
6812 Both, standard stability selection (Meinshausen & Buhlmann, 2010) and
6813 complementary pairs stability selection with improved error bounds
6814 (Shah & Samworth, 2013) are implemented. The package can be combined with
6815 arbitrary user specified variable selection approaches.")
6816 (license license:gpl2)))
6818 (define-public r-rle
6825 (uri (cran-uri "rle" version))
6828 "0sagl0jggg40lihzy7pfq4593rfvc3b3f7g6ggi85s7n18qvwg40"))))
6829 (properties `((upstream-name . "rle")))
6830 (build-system r-build-system)
6831 (home-page "https://cran.r-project.org/web/packages/rle/")
6832 (synopsis "Common functions for run-length encoded vectors")
6834 "This package provides common @code{base} and @code{stats} methods for
6835 @code{rle} objects, aiming to make it possible to treat them transparently as
6837 (license license:gpl3)))
6839 (define-public r-statnet-common
6841 (name "r-statnet-common")
6846 (uri (cran-uri "statnet.common" version))
6849 "07djgc6qbxahiy5v15lfayxbj4188lxsb8xcs7hnbm2hic953bfx"))))
6851 `((upstream-name . "statnet.common")))
6852 (build-system r-build-system)
6855 (home-page "https://statnet.org")
6856 (synopsis "R scripts and utilities used by the Statnet software")
6857 (description "This package provides non-statistical utilities used by the
6858 software developed by the Statnet Project.")
6859 (license license:gpl3)))
6861 (define-public r-statcheck
6863 (name "r-statcheck")
6868 (uri (cran-uri "statcheck" version))
6871 "0ivybdcrymlsfv6pg6p5bv70qdvgxf2vgp0kf4r0pf2fcvav1mcp"))))
6872 (build-system r-build-system)
6874 (list r-ggplot2 r-plyr r-rmarkdown))
6875 (home-page "https://cran.r-project.org/web/packages/statcheck/")
6876 (synopsis "Extract statistics from articles and recompute p-values")
6877 (description "This package can automatically extract statistical
6878 null-hypothesis significant testing (NHST) results from articles and recompute
6879 the p-values based on the reported test statistic and degrees of freedom to
6880 detect possible inconsistencies.")
6881 (license license:gpl2)))
6883 (define-public r-sna
6890 (uri (cran-uri "sna" version))
6893 "0ai0v4538d30m4wks5s3lch1yfmx1ml0nnrz7ihs097lv586a09s"))))
6894 (build-system r-build-system)
6896 (list r-network r-statnet-common))
6897 (home-page "https://statnet.org")
6898 (synopsis "Tools for social network analysis")
6900 "This package provides a range of tools for social network analysis,
6901 including node and graph-level indices, structural distance and covariance
6902 methods, structural equivalence detection, network regression, random graph
6903 generation, and 2D/3D network visualization.")
6904 (license license:gpl2+)))
6906 (define-public r-tfisher
6913 (uri (cran-uri "TFisher" version))
6916 "0vz74ww1lf1prfwz74hfsi3a8nzq8ss7aqjr85c1d87vss2796xx"))))
6917 (properties `((upstream-name . "TFisher")))
6918 (build-system r-build-system)
6920 (list r-matrix r-mvtnorm r-sn))
6921 (home-page "https://cran.r-project.org/web/packages/TFisher/")
6922 (synopsis "Optimal thresholding Fisher's p-value combination method")
6924 "This package provides the @dfn{cumulative distribution function} (CDF),
6925 quantile, and statistical power calculator for a collection of thresholding
6926 Fisher's p-value combination methods, including Fisher's p-value combination
6927 method, truncated product method and, in particular, soft-thresholding
6928 Fisher's p-value combination method which is proven to be optimal in some
6929 context of signal detection. The p-value calculator for the omnibus version
6930 of these tests are also included.")
6931 (license license:gpl2)))
6933 (define-public r-ttr
6940 (uri (cran-uri "TTR" version))
6943 "11xsmbvmxq2j119j2z58bx1fkkb2xlhmzc35z5fbwr3nchrfz6jd"))))
6944 (properties `((upstream-name . "TTR")))
6945 (build-system r-build-system)
6947 (list r-curl r-xts r-zoo))
6948 (home-page "https://github.com/joshuaulrich/TTR")
6949 (synopsis "Technical trading rules")
6951 "This package provides functions and data to construct technical trading
6953 (license license:gpl2)))
6955 (define-public r-leaflet-providers
6957 (name "r-leaflet-providers")
6962 (uri (cran-uri "leaflet.providers" version))
6964 (base32 "0yynrwv4xd5cdh49cwvfxm4ranarah9iiry2cd3b4fiihdfcg3wy"))))
6965 (properties `((upstream-name . "leaflet.providers")))
6966 (build-system r-build-system)
6967 (home-page "https://github.com/rstudio/leaflet.providers")
6968 (synopsis "Leaflet map tile providers")
6970 "This package contains third-party map tile provider information from
6971 Leaflet.js, to be used with the @code{leaflet} R package. Additionally,
6972 @code{leaflet.providers} enables users to retrieve up-to-date provider
6973 information between package updates.")
6974 (license license:bsd-2)))
6976 ;; This package contains a lot of minified JavaScript with unclear provenance.
6977 ;; When upgrading please make sure that all minified JavaScript files are
6978 ;; removed in a snippet and that the replacement sources correspond to the
6979 ;; original minified scripts.
6980 (define-public r-leaflet
6987 (uri (cran-uri "leaflet" version))
6989 (base32 "0xsng9n08i1w7qj4hbi706m6d8jm9ixrnwq5xac2s3csfm1s1xij"))
6993 (list "inst/htmlwidgets/lib/leaflet/leaflet.js"
6994 "inst/htmlwidgets/lib/leaflet-measure/leaflet-measure.min.js"
6995 "inst/htmlwidgets/lib/leaflet-omnivore/leaflet-omnivore.min.js"
6996 "inst/htmlwidgets/lib/jquery/jquery.min.js"
6997 "inst/htmlwidgets/plugins/Leaflet-MiniMap/Control.MiniMap.min.js"
6998 "inst/htmlwidgets/plugins/Leaflet.awesome-markers/bootstrap.min.js"
6999 "inst/htmlwidgets/plugins/Leaflet.awesome-markers/leaflet.awesome-markers.min.js"
7000 "inst/htmlwidgets/plugins/Leaflet.markercluster/leaflet.markercluster.js"
7001 "inst/htmlwidgets/plugins/Leaflet.markercluster/leaflet.markercluster.freezable.js"
7002 "inst/htmlwidgets/plugins/Leaflet.markercluster/leaflet.markercluster.layersupport.js"
7003 "inst/legacy/www/leaflet.js")))))
7004 (properties `((upstream-name . "leaflet")))
7005 (build-system r-build-system)
7007 `(#:modules ((guix build utils)
7008 (guix build r-build-system)
7011 (modify-phases %standard-phases
7012 (add-after 'unpack 'process-javascript
7013 (lambda* (#:key inputs #:allow-other-keys)
7014 ;; The inst directory contains some minified JavaScript files.
7015 ;; Regenerate them from sources.
7016 (invoke "unzip" "-d" "/tmp" (assoc-ref inputs "js-leaflet"))
7017 (with-directory-excursion "inst/"
7021 `(("/tmp/leaflet-src.js"
7022 "htmlwidgets/lib/leaflet/leaflet.js")
7023 (,(assoc-ref inputs "js-leaflet-measure")
7024 "htmlwidgets/lib/leaflet-measure/leaflet-measure.min.js")
7025 (,(assoc-ref inputs "js-leaflet-omnivore")
7026 "htmlwidgets/lib/leaflet-omnivore/leaflet-omnivore.min.js")
7027 (,(assoc-ref inputs "js-jquery")
7028 "htmlwidgets/lib/jquery/jquery.min.js")
7029 ("htmlwidgets/plugins/Leaflet-MiniMap/Control.MiniMap.js"
7030 "htmlwidgets/plugins/Leaflet-MiniMap/Control.MiniMap.min.js")
7031 (,(assoc-ref inputs "js-bootstrap3")
7032 "htmlwidgets/plugins/Leaflet.awesome-markers/bootstrap.min.js")
7033 ("htmlwidgets/plugins/Leaflet.awesome-markers/leaflet.awesome-markers.js"
7034 "htmlwidgets/plugins/Leaflet.awesome-markers/leaflet.awesome-markers.min.js")
7035 (,(string-append (assoc-ref inputs "js-leaflet-markercluster")
7036 "/dist/leaflet.markercluster-src.js")
7037 "htmlwidgets/plugins/Leaflet.markercluster/leaflet.markercluster.js")
7038 (,(assoc-ref inputs "js-leaflet-markercluster-freezable")
7039 "htmlwidgets/plugins/Leaflet.markercluster/leaflet.markercluster.freezable.js")
7040 (,(assoc-ref inputs "js-leaflet-markercluster-layersupport")
7041 "htmlwidgets/plugins/Leaflet.markercluster/leaflet.markercluster.layersupport.js")
7042 (,(assoc-ref inputs "js-proj4leaflet")
7043 "htmlwidgets/plugins/Proj4Leaflet/proj4.min.js")
7044 ("legacy/www/leaflet-src.js"
7045 "legacy/www/leaflet.js"))))
7046 (lambda (sources targets)
7047 (for-each (lambda (source target)
7048 (format #true "Processing ~a --> ~a~%"
7050 (invoke "esbuild" source "--minify"
7051 (string-append "--outfile=" target)))
7052 sources targets)))))))))
7054 `(("esbuild" ,esbuild)
7059 (uri "https://raw.githubusercontent.com/twbs/bootstrap/v3.3.7/dist/js/bootstrap.js")
7062 "1j1qjagwj0m3q322z9wxxnpkd8zbk6g3kl047dsbmqad6gmqvgha"))))
7066 (uri "https://code.jquery.com/jquery-1.12.4.js")
7069 "0x9mrc1668icvhpwzvgafm8xm11x9lfai9nwr66aw6pjnpwkc3s3"))))
7073 (uri "http://cdn.leafletjs.com/leaflet/v1.3.1/leaflet.zip")
7076 "10phzd2vczy3zm1b64whp2nna69cf9hlj2bndc9yq47vf3ddqx8f"))))
7077 ("js-leaflet-omnivore"
7080 (uri (string-append "https://api.tiles.mapbox.com/mapbox.js/plugins/"
7081 "leaflet-omnivore/v0.3.1/leaflet-omnivore.js"))
7084 "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq"))))
7085 ("js-leaflet-markercluster"
7089 (url "https://github.com/Leaflet/Leaflet.markercluster.git")
7091 (file-name (git-file-name "js-leaflet-markercluster" "1.1.0"))
7094 "0ds8c7picqjmc86bm5n6hm8k71fwsa2cpgib19sbdamzr9hm0rs1"))))
7095 ("js-leaflet-markercluster-freezable"
7099 "https://raw.githubusercontent.com/ghybs/Leaflet.MarkerCluster.Freezable/"
7100 "9db80a3fba7dff4aee940e05d3d4dceaa1fffcf9/src/freezable.js"))
7101 (file-name "leaflet-markercluster-freezable.js")
7104 "1k6sn5n0z2x3an91vwvkzmqq4b8ppswgk5hi5qrr79klas1hbx1k"))))
7105 ("js-leaflet-markercluster-layersupport"
7109 "https://raw.githubusercontent.com/ghybs/Leaflet.MarkerCluster.LayerSupport/"
7110 "87f3848b92e0516d9c98f6d4cd175f7b8a4e3805/src/layersupport.js"))
7111 (file-name "leaflet-markercluster-layersupport.js")
7114 "15qa21xif94y762c65yxxysxykz3mma6y6agw3nxpr3s7wbb75ff"))))
7115 ("js-leaflet-measure"
7118 (uri "https://unpkg.com/leaflet-measure@1.5.2/dist/leaflet-measure.js")
7119 (file-name "js-leaflet-measure-1.5.2.js")
7122 "0ggg3ffmm7pj9ry4gssrh0a17pnad3p6gwi0dg98y819pmpqa7y0"))))
7126 (uri "https://raw.githubusercontent.com/kartena/Proj4Leaflet/1.0.2/lib/proj4.js")
7127 (file-name "js-proj4leaflet-1.0.2.js")
7130 "0vyrbf6gv2lyh4c2bzp5349ivwvvg28gpn87y52a7jdb13rlkpab"))))))
7145 (home-page "https://rstudio.github.io/leaflet/")
7146 (synopsis "Create interactive web maps with the JavaScript Leaflet library")
7148 "Create and customize interactive maps using the Leaflet JavaScript
7149 library and the @code{htmlwidgets} package. These maps can be used directly
7150 from the R console, from RStudio, in Shiny applications and R Markdown
7152 (license license:gpl3)))
7154 (define-public r-leaps
7161 (uri (cran-uri "leaps" version))
7164 "1dn3yl1p03n0iynd1vsdkrr0fhmvgrmfkv37y7n371765h83lz1x"))))
7165 (build-system r-build-system)
7166 (native-inputs (list gfortran))
7167 (home-page "https://cran.r-project.org/web/packages/leaps/")
7168 (synopsis "Regression subset selection")
7170 "This package provides tools for regression subset selection, including
7171 exhaustive search.")
7172 (license license:gpl2+)))
7174 (define-public r-splus2r
7181 (uri (cran-uri "splus2R" version))
7184 "035zd22zcpkh74rik9ws6g8al6vjz7jgrqs5si361bzb5n290p3x"))))
7185 (properties `((upstream-name . "splus2R")))
7186 (build-system r-build-system)
7187 (home-page "https://cran.r-project.org/web/packages/splus2R/")
7188 (synopsis "Supplemental S-PLUS functionality in R")
7190 "Currently there are many functions in S-PLUS that are missing in R. To
7191 facilitate the conversion of S-PLUS packages to R packages, this package
7192 provides some missing S-PLUS functionality in R.")
7193 (license license:gpl2)))
7195 (define-public r-ifultools
7197 (name "r-ifultools")
7202 (uri (cran-uri "ifultools" version))
7205 "16a7rbvlym3bnfm93ikr5kl0l86ppk0s41fva6idvcx765g3fqkk"))))
7206 (build-system r-build-system)
7208 (list r-mass r-splus2r))
7209 (home-page "https://cran.r-project.org/web/packages/ifultools/")
7210 (synopsis "Insightful research tools")
7211 (description "This package provides C code used by the wmtsa, fractal, and
7213 (license license:gpl2)))
7215 (define-public r-sapa
7222 (uri (cran-uri "sapa" version))
7225 "0kj681rd4c2lvqr926lb6f4qwp281x5274dg6vbk8pf5y7s0qlpc"))))
7226 (build-system r-build-system)
7228 (list r-ifultools r-splus2r))
7229 (home-page "https://cran.r-project.org/web/packages/sapa/")
7230 (synopsis "Spectral analysis for physical applications")
7231 (description "This package provides software for the book Spectral
7232 Analysis for Physical Applications, Donald B. Percival and Andrew T. Walden,
7233 Cambridge University Press, 1993.")
7234 (license license:gpl2)))
7236 (define-public r-aggregation
7238 (name "r-aggregation")
7243 (uri (cran-uri "aggregation" version))
7246 "0j9g604m2ccc7hcy02539yja9cf3xcbl25gvp838bp4x8w18my46"))))
7247 (build-system r-build-system)
7248 (home-page "https://cran.r-project.org/web/packages/aggregation/")
7249 (synopsis "Methods for p-value aggregation")
7251 "This package contains functionality for performing the following methods
7252 of p-value aggregation: Fisher's method, the Lancaster method (weighted
7253 Fisher's method), and Sidak correction.")
7254 (license license:gpl3)))
7256 (define-public r-quantmod
7263 (uri (cran-uri "quantmod" version))
7266 "154fqhw46kc7r08zsj5fsg97hg93phsli3z14xwmz22xb50xymzp"))))
7267 (build-system r-build-system)
7269 (list r-curl r-ttr r-xts r-zoo))
7270 (home-page "https://cran.r-project.org/web/packages/quantmod/")
7271 (synopsis "Quantitative financial modelling framework")
7272 (description "This package provides a quantitative financial modelling
7273 framework to allow users to specify, build, trade, and analyse quantitative
7274 financial trading strategies.")
7275 (license license:gpl3)))
7277 (define-public r-tseries
7284 (uri (cran-uri "tseries" version))
7287 "0zr09ikaz96djcvnjbr8ah6waqzjy06f4yd4isshlwc391q20px5"))))
7288 (build-system r-build-system)
7290 (list r-quadprog r-quantmod r-zoo))
7293 (home-page "https://cran.r-project.org/web/packages/tseries/")
7294 (synopsis "Time series analysis and computational finance")
7296 "This package provides functions relating to time series analysis and
7297 computational finance.")
7298 (license license:gpl2)))
7300 (define-public r-wmtsa
7307 (uri (cran-uri "wmtsa" version))
7310 "1q436krz5p1f4a7a7sya6a9rh9x9mi8zzcgq66gbk9w9w4hcqcj6"))))
7311 (build-system r-build-system)
7313 (list r-ifultools r-mass r-splus2r))
7314 (home-page "https://cran.r-project.org/web/packages/wmtsa/")
7315 (synopsis "Wavelet methods for time series analysis")
7317 "This package provides software to accompany the book \"Wavelet Methods
7318 for Time Series Analysis\", Donald B. Percival and Andrew T. Walden, Cambridge
7319 University Press, 2000.")
7320 (license license:gpl2)))
7322 (define-public r-tsa
7329 (uri (cran-uri "TSA" version))
7332 "1bv5q609lhmrcxnjnvcj497fbjlv89zwa8q918hw4iki5nkvwwdb"))))
7333 (properties `((upstream-name . "TSA")))
7334 (build-system r-build-system)
7336 (list r-leaps r-locfit r-mgcv r-tseries))
7337 (home-page "https://homepage.divms.uiowa.edu/~kchan/TSA.htm")
7338 (synopsis "Time series analysis")
7340 "This package contains R functions and datasets detailed in the book
7341 \"Time Series Analysis with Applications in R (second edition)\" by Jonathan
7342 Cryer and Kung-Sik Chan.")
7343 (license license:gpl2+)))
7345 (define-public r-extradistr
7347 (name "r-extradistr")
7352 (uri (cran-uri "extraDistr" version))
7355 "1gypnbvdzczl0mvznvy8r7hzsvc5gvdvi2mmzj21cqdw9n63944r"))))
7356 (properties `((upstream-name . "extraDistr")))
7357 (build-system r-build-system)
7360 (home-page "https://github.com/twolodzko/extraDistr")
7361 (synopsis "Additional univariate and multivariate distributions")
7363 "This package implements density, distribution functions, quantile
7364 functions and random generation functions for a large number of univariate and
7365 multivariate distributions.")
7366 (license license:gpl2)))
7368 (define-public r-fractal
7375 (uri (cran-uri "fractal" version))
7378 "18lr9z0gslvfc3z8vyj3krqj3bfhg60zv1fzinrwwkc4cpk1w7mp"))))
7379 (build-system r-build-system)
7387 (home-page "https://cran.r-project.org/web/packages/fractal/")
7388 (synopsis "Fractal time series modeling and analysis")
7390 "This package provides tools for stochastic fractal and deterministic
7391 chaotic time series analysis.")
7392 (license license:gpl2)))
7394 (define-public r-urca
7401 (uri (cran-uri "urca" version))
7404 "1akaqwf3fvvvx4sgfn641fd4sj51s0701pvfl6s5hnz2k0iwh732"))))
7405 (build-system r-build-system)
7406 (propagated-inputs (list r-nlme))
7407 (native-inputs (list gfortran))
7408 (home-page "https://cran.r-project.org/web/packages/urca/")
7409 (synopsis "Unit root and cointegration tests for time series data")
7411 "This package provides unit root and cointegration tests encountered in
7412 applied econometric analysis.")
7413 (license license:gpl2+)))
7415 (define-public r-cubature
7422 (uri (cran-uri "cubature" version))
7425 "0sfmcy5xpa40w3qn0jbg7b802wksl5k8glz9jpx77n159wn3nyq8"))))
7426 (build-system r-build-system)
7431 (home-page "https://github.com/bnaras/cubature")
7432 (synopsis "Adaptive multivariate integration over hypercubes")
7434 "This package is an R wrapper around the cubature C library for adaptive
7435 multivariate integration over hypercubes. This version provides both
7436 @code{hcubature} and @code{pcubature} routines in addition to a vector
7438 ;; The included cubature C library is released under GPLv2+, but the
7439 ;; wrapper declares the license to be GPLv3+.
7440 (license (list license:gpl2+ license:gpl3+))))
7442 (define-public r-trend
7449 (uri (cran-uri "trend" version))
7452 "1mr5g5gaxiqj6x83ngcbwwh57vhrhcz0x9dh0rmvs9y2ivk29ccs"))))
7453 (build-system r-build-system)
7455 (list r-extradistr))
7458 (home-page "https://cran.r-project.org/web/packages/trend/")
7459 (synopsis "Non-parametric trend tests and change-point detection")
7461 "The analysis of environmental data often requires the detection of
7462 trends and change-points. This package includes tests for trend
7463 detection (Cox-Stuart Trend Test, Mann-Kendall Trend Test, (correlated)
7464 Hirsch-Slack Test, partial Mann-Kendall Trend Test, multivariate (multisite)
7465 Mann-Kendall Trend Test, (Seasonal) Sen's slope, partial Pearson and Spearman
7466 correlation trend test), change-point detection (Lanzante's test procedures,
7467 Pettitt's test, Buishand Range Test, Buishand U Test, Standard Normal
7468 Homogeinity Test), detection of non-randomness (Wallis-Moore Phase Frequency
7469 Test, Bartels rank von Neumann's ratio test, Wald-Wolfowitz Test) and the two
7470 sample Robust Rank-Order Distributional Test.")
7471 (license license:gpl3)))
7473 (define-public r-expm
7480 (uri (cran-uri "expm" version))
7483 "1p5dapwv8ycxaysgi6imnby04i4kh1c5a2czqa4wygz0s8pr2y9c"))))
7484 (build-system r-build-system)
7485 (propagated-inputs (list r-matrix))
7486 (native-inputs (list gfortran))
7487 (home-page "https://r-forge.r-project.org/projects/expm/")
7488 (synopsis "Tools for matrix exponentials and related quantities")
7490 "This package provides tools for the computation of the matrix
7491 exponential, logarithm, square root, and related quantities.")
7492 (license license:gpl2+)))
7494 (define-public r-complexplus
7496 (name "r-complexplus")
7501 (uri (cran-uri "complexplus" version))
7504 "16w9v7d1ckavqmr86l34frr37pkvdn0iqnb17ssb8xaggns5lgqx"))))
7505 (build-system r-build-system)
7507 (list r-expm r-matrix))
7508 (home-page "https://cran.r-project.org/web/packages/complexplus/")
7509 (synopsis "Functions of complex or real variables")
7511 "This package extends several functions to the complex domain, including
7512 the matrix exponential and logarithm, and the determinant.")
7513 (license license:gpl2)))
7515 (define-public r-phontools
7517 (name "r-phontools")
7522 (uri (cran-uri "phonTools" version))
7525 "01i481mhswsys3gpasw9gn6nxkfmi7bz46g5c84m13pg0cv8hxc7"))))
7526 (properties `((upstream-name . "phonTools")))
7527 (build-system r-build-system)
7528 (home-page "http://www.santiagobarreda.com/rscripts.html")
7529 (synopsis "Tools for phonetic and acoustic analyses")
7531 "This package contains tools for the organization, display, and analysis
7532 of the sorts of data frequently encountered in phonetics research and
7533 experimentation, including the easy creation of IPA vowel plots, and the
7534 creation and manipulation of WAVE audio files.")
7535 (license license:bsd-2)))
7544 (uri (cran-uri "np" version))
7547 "1a9kzn37cddwfdki5zjmzanxp75pccdjnsvqfrh84hhcsy51pcx3"))))
7548 (build-system r-build-system)
7550 (list r-boot r-cubature r-quadprog r-quantreg))
7551 (home-page "https://github.com/JeffreyRacine/R-Package-np")
7552 (synopsis "Non-parametric kernel smoothing methods for mixed data types")
7553 (description "This package provides non-parametric (and semi-parametric)
7554 kernel methods that seamlessly handle a mix of continuous, unordered, and
7555 ordered factor data types.")
7556 ;; Any version of the GPL.
7557 (license license:gpl3+)))
7559 (define-public r-powerplus
7561 (name "r-powerplus")
7566 (uri (cran-uri "powerplus" version))
7569 "0ayp6x34hkzgris4j3zbbs0r23n81bhww3wgfyy630ri4sk6brrn"))))
7570 (build-system r-build-system)
7572 (list r-complexplus r-expm r-mass r-matrix r-phontools))
7573 (home-page "https://cran.r-project.org/web/packages/powerplus/")
7574 (synopsis "Exponentiation operations")
7576 "This package provides tools for the computation of matrix and scalar
7578 (license license:gpl2)))
7580 (define-public r-egg
7587 (uri (cran-uri "egg" version))
7590 "1fy7srpiavfn8kyrr1m84an7acgwi6ydzrg71m3b0vk7y9ybmj0m"))))
7591 (properties `((upstream-name . "egg")))
7592 (build-system r-build-system)
7594 (list r-ggplot2 r-gridextra r-gtable))
7595 (home-page "https://cran.r-project.org/web/packages/egg")
7596 (synopsis "Extensions for ggplot2")
7598 "This package provides miscellaneous functions to help customize ggplot2
7599 objects. High-level functions are provided to post-process ggplot2 layouts
7600 and allow alignment between plot panels, as well as setting panel sizes to
7601 fixed values. Other functions include a custom @code{geom}, and helper
7602 functions to enforce symmetric scales or add tags to facetted plots.")
7603 (license license:gpl3)))
7605 (define-public r-heatmap3
7612 (uri (cran-uri "heatmap3" version))
7615 "0sfvizmmwfk1bjhn6zfx5a4qqfgj1ldg8x90b65crqibgfa36k2r"))))
7616 (build-system r-build-system)
7618 (list r-fastcluster))
7621 (home-page "https://cran.r-project.org/web/packages/heatmap3/")
7622 (synopsis "Improved heatmap package")
7624 "This package provides an improved heatmap package. It is completely
7625 compatible with the original R function @code{heatmap}, and provides more
7626 powerful and convenient features.")
7627 (license license:gpl2+)))
7629 (define-public r-heatmaply
7631 (name "r-heatmaply")
7636 (uri (cran-uri "heatmaply" version))
7639 "1w8yyzb68laxd4zxycvgmpqj5wnyidjgv1vbzbxndp9p92f2cp8a"))))
7640 (build-system r-build-system)
7658 (home-page "https://cran.r-project.org/package=heatmaply")
7659 (synopsis "Interactive cluster heat maps using plotly")
7661 "This package enables you to create interactive cluster heatmaps that can
7662 be saved as a stand-alone HTML file, embedded in R Markdown documents or in a
7663 Shiny app, and made available in the RStudio viewer pane. Hover the mouse
7664 pointer over a cell to show details or drag a rectangle to zoom. A heatmap is
7665 a popular graphical method for visualizing high-dimensional data, in which a
7666 table of numbers is encoded as a grid of colored cells. The rows and columns
7667 of the matrix are ordered to highlight patterns and are often accompanied by
7669 ;; Either version of the license.
7670 (license (list license:gpl2 license:gpl3))))
7679 (uri (cran-uri "h5" version))
7682 "14p7i1sj24ky87kd7qr3n9fc9l64s0bp0rwbyl6i2x69xn75gpsx"))))
7683 (build-system r-build-system)
7690 (home-page "https://github.com/mannau/h5")
7691 (synopsis "Interface to the HDF5 Library")
7693 "This package provides an S4 interface to the HDF5 library supporting
7694 fast storage and retrieval of R-objects like vectors, matrices and arrays to
7695 binary files in a language independent format. The HDF5 format can therefore
7696 be used as an alternative to R's save/load mechanism. Since h5 is able to
7697 access only subsets of stored data it can also handle data sets which do not
7699 (license license:bsd-2)))
7701 (define-public r-cgdsr
7708 (uri (cran-uri "cgdsr" version))
7711 "07yc819hkabpzzh0g0cbqza6bcfy67b2marrzz1lj97f9iba78ja"))))
7712 (build-system r-build-system)
7714 (list r-httr r-r-methodss3 r-r-oo))
7715 (home-page "https://github.com/cBioPortal/cgdsr")
7716 (synopsis "R-based API for accessing the MSKCC Cancer Genomics Data Server")
7718 "This package provides a basic set of R functions for querying the Cancer
7719 Genomics Data Server (CGDS), hosted by the Computational Biology Center at
7720 Memorial-Sloan-Kettering Cancer Center (MSKCC).")
7721 (license license:lgpl3)))
7723 (define-public r-import
7730 (uri (cran-uri "import" version))
7733 "19g4jnfg9pkvvsncw62yc15xlb97hfbdqxivpjd9jqi36i6mdjrg"))))
7734 (build-system r-build-system)
7737 (home-page "https://github.com/smbache/import")
7738 (synopsis "Import mechanism for R")
7740 "This is an alternative mechanism for importing objects from packages.
7741 The syntax allows for importing multiple objects from a package with a single
7742 command in an expressive way. The import package bridges some of the gap
7743 between using @code{library} (or @code{require}) and direct (single-object)
7744 imports. Furthermore the imported objects are not placed in the current
7745 environment. It is also possible to import objects from stand-alone @code{.R}
7747 (license license:expat)))
7749 (define-public r-shinyace
7756 (uri (cran-uri "shinyAce" version))
7759 "12mqvdh6rxsr61pc3pzla95r5f4l7xagjs2rcdr7c2lbqyxpx6aa"))))
7760 (properties `((upstream-name . "shinyAce")))
7761 (build-system r-build-system)
7763 (list r-shiny r-jsonlite))
7764 (home-page "https://cran.r-project.org/web/packages/shinyAce/")
7765 (synopsis "Ace editor bindings for Shiny")
7767 "This package provides Ace editor bindings to enable a rich text editing
7768 environment within Shiny.")
7769 (license license:expat)))
7771 (define-public r-rafalib
7778 (uri (cran-uri "rafalib" version))
7780 (base32 "1dmxjl66bfdgrybhwyaa8d4i460liqcdw8b29a6w7shgksh29m0k"))))
7781 (properties `((upstream-name . "rafalib")))
7782 (build-system r-build-system)
7783 (propagated-inputs (list r-rcolorbrewer))
7784 (home-page "https://cran.r-project.org/package=rafalib")
7785 (synopsis "Convenience functions for routine data exploration")
7787 "This package provides a series of shortcuts for routine tasks to
7788 facilitate data exploration.")
7789 (license license:artistic2.0)))
7791 (define-public r-randomizr
7793 (name "r-randomizr")
7798 (uri (cran-uri "randomizr" version))
7801 "1grm0h3xkb0pdbbv0gd531g1kn6njp0gcy5fh153rrmajxgd8hhw"))))
7802 (properties `((upstream-name . "randomizr")))
7803 (build-system r-build-system)
7806 (home-page "https://declaredesign.org/r/randomizr/")
7807 (synopsis "Tools for common forms of random assignment and sampling")
7809 "This package provides tools for generating random assignments for common
7810 experimental designs and random samples for common sampling designs.")
7811 (license license:expat)))
7813 (define-public r-base64url
7815 (name "r-base64url")
7820 (uri (cran-uri "base64url" version))
7823 "0n1c2b68vza1dh7sk38v6biiwm72c4jpl79kpdg1bsb0hq9qy18x"))))
7824 (build-system r-build-system)
7827 (home-page "https://github.com/mllg/base64url")
7828 (synopsis "Fast and URL-safe base64 encoder and decoder")
7830 "This package provides a URL-safe base64 encoder and decoder. In
7831 contrast to RFC3548, the 62nd character (@code{+}) is replaced with @code{-},
7832 the 63rd character (@code{/}) is replaced with @code{_}. Furthermore, the
7833 encoder does not fill the string with trailing @code{=}. The resulting
7834 encoded strings comply to the regular expression pattern @code{[A-Za-z0-9_-]}
7835 and thus are safe to use in URLs or for file names. The package also comes
7836 with a simple base32 encoder/decoder suited for case insensitive file
7838 (license license:gpl3)))
7840 (define-public r-radiant-data
7842 (name "r-radiant-data")
7847 (uri (cran-uri "radiant.data" version))
7850 "0c5c99q13pwv6k0b07x3r2bxmh0h2w15h02xb1pincgs61qwi15k"))
7851 (modules '((guix build utils)))
7854 ;; Delete files that are under CC-NC-SA.
7855 (delete-file-recursively "inst/app/tools/help")
7857 (properties `((upstream-name . "radiant.data")))
7858 (build-system r-build-system)
7892 (home-page "https://github.com/radiant-rstats/radiant.data")
7893 (synopsis "Data menu for Radiant: business analytics using R and Shiny")
7895 "The Radiant Data menu includes interfaces for loading, saving, viewing,
7896 visualizing, summarizing, transforming, and combining data. It also contains
7897 functionality to generate reproducible reports of the analyses conducted in
7899 (license license:agpl3)))
7901 (define-public r-algdesign
7903 (name "r-algdesign")
7908 (uri (cran-uri "AlgDesign" version))
7910 (base32 "01cx63wqr6yvgl5ml1lj6gh9p1sn42b6qcnsppcw7mvba9n652ar"))))
7911 (properties `((upstream-name . "AlgDesign")))
7912 (build-system r-build-system)
7913 (home-page "https://github.com/jvbraun/AlgDesign")
7914 (synopsis "Algorithmic experimental design")
7916 "This package provides tools to calculate exact and approximate theory
7917 experimental designs for D, A, and I criteria. Very large designs may be
7918 created. Experimental designs may be blocked or blocked designs created from
7919 a candidate list, using several criteria. The blocking can be done when whole
7920 and within plot factors interact.")
7921 (license license:gpl2+)))
7923 (define-public r-alluvial
7930 (uri (cran-uri "alluvial" version))
7932 (base32 "039frwrsxq1lb97s7vf2vbyyadimkigs628ymym06fxka53drdkp"))))
7933 (properties `((upstream-name . "alluvial")))
7934 (build-system r-build-system)
7935 (native-inputs (list r-knitr))
7936 (home-page "https://github.com/mbojan/alluvial")
7937 (synopsis "Create parallel sets plots (Alluvial Diagrams)")
7939 "This package creates alluvial diagrams (also known as parallel sets
7940 plots) for multivariate and time series-like data.")
7941 (license license:expat)))
7943 (define-public r-signal
7950 (uri (cran-uri "signal" version))
7953 "0qaf39vfmhn3d0bdjqd805ayfkaj48dkmf5dqd47bpk7dp21b837"))))
7954 (build-system r-build-system)
7955 (propagated-inputs (list r-mass))
7956 (native-inputs (list gfortran))
7957 (home-page "https://cran.r-project.org/web/packages/signal/")
7958 (synopsis "Signal processing")
7960 "This package provides a set of signal processing functions originally
7961 written for Matlab and GNU Octave. It includes filter generation utilities,
7962 filtering functions, resampling routines, and visualization of filter models.
7963 It also includes interpolation functions.")
7964 (license license:gpl2)))
7966 (define-public r-gsubfn
7973 (uri (cran-uri "gsubfn" version))
7976 "00j6b8b6xsx6v370h220x233rpk6asca78165y3d48jpwvwisdc9"))))
7977 (build-system r-build-system)
7978 (propagated-inputs (list r-proto))
7979 (home-page "https://code.google.com/archive/p/gsubfn/")
7980 (synopsis "Utilities for strings and function arguments")
7982 "This package provides @code{gsubfn} which is like @code{gsub} but can
7983 take a replacement function or certain other objects instead of the
7984 replacement string. Matches and back references are input to the replacement
7985 function and replaced by the function output. @code{gsubfn} can be used to
7986 split strings based on content rather than delimiters and for quasi-perl-style
7987 string interpolation. The package also has facilities for translating
7988 formulas to functions and allowing such formulas in function calls instead of
7990 (license license:gpl2+)))
7992 (define-public r-sqldf
7999 (uri (cran-uri "sqldf" version))
8002 "0q12vsb53p2wchgp8wfz5bk08wfnm0jxjrakclj4jyy6x3a7ksff"))))
8003 (build-system r-build-system)
8005 (list r-chron r-dbi r-gsubfn r-proto r-rsqlite))
8006 (home-page "https://github.com/ggrothendieck/sqldf")
8007 (synopsis "Manipulate R data frames using SQL")
8009 "The @code{sqldf} function is typically passed a single argument which is
8010 an SQL select statement where the table names are ordinary R data frame names.
8011 @code{sqldf} transparently sets up a database, imports the data frames into
8012 that database, performs the SQL statement and returns the result using a
8013 heuristic to determine which class to assign to each column of the returned
8014 data frame. The @code{sqldf} or @code{read.csv.sql} functions can also be
8015 used to read filtered files into R even if the original files are larger than
8016 R itself can handle.")
8017 (license license:gpl2)))
8019 (define-public r-abind
8026 (uri (cran-uri "abind" version))
8029 "0b1zd8jbnl6l292cr9rb50m09fy3ylxvzkpgi5lfb1nbzddcwfis"))))
8030 (build-system r-build-system)
8031 (home-page "https://cran.r-project.org/web/packages/abind/")
8032 (synopsis "Combine multidimensional arrays")
8034 "This package provides tools to combine multidimensional arrays into a
8035 single array. This is a generalization of @code{cbind} and @code{rbind}. It
8036 works with vectors, matrices, and higher-dimensional arrays. It also provides
8037 the functions @code{adrop}, @code{asub}, and @code{afill} for manipulating,
8038 extracting and replacing data in arrays.")
8039 (license license:lgpl2.0+)))
8041 (define-public r-prroc
8048 (uri (cran-uri "PRROC" version))
8051 "1m28h8pcd78049lz2qixhkcr9h5b3jik3maqzfbvq9y58z71i4a7"))))
8052 (properties `((upstream-name . "PRROC")))
8053 (build-system r-build-system)
8054 (home-page "https://cran.r-project.org/web/packages/PRROC/")
8055 (synopsis "Precision-Recall and ROC curves for weighted and unweighted data")
8057 "This package computes the areas under the @dfn{precision-recall} (PR)
8058 and ROC curve for weighted (e.g. soft-labeled) and unweighted data. In
8059 contrast to other implementations, the interpolation between points of the PR
8060 curve is done by a non-linear piecewise function. In addition to the areas
8061 under the curves, the curves themselves can also be computed and plotted by a
8062 specific S3-method.")
8063 (license license:gpl3)))
8065 (define-public r-vim
8072 (uri (cran-uri "VIM" version))
8075 "0fbpm6y3hhiw8srnbc38k19b859jcqzsh78ib8yvj86gck5av0bm"))))
8076 (properties `((upstream-name . "VIM")))
8077 (build-system r-build-system)
8094 (home-page "https://github.com/alexkowa/VIM")
8095 (synopsis "Visualization and imputation of missing values")
8097 "This package provides tools for the visualization of missing and/or
8098 imputed values are introduced, which can be used for exploring the data and
8099 the structure of the missing and/or imputed values. Depending on this
8100 structure of the missing values, the corresponding methods may help to
8101 identify the mechanism generating the missing values and explore the
8102 data including missing values. In addition, the quality of imputation can be
8103 visually explored using various univariate, bivariate, multiple and
8104 multivariate plot methods.")
8105 (license license:gpl2+)))
8107 (define-public r-fnn
8114 (uri (cran-uri "FNN" version))
8117 "0nmynpiy3d2dnd5ngjf4m79jy02byhk43gj0xny9a6j8243f5c2j"))))
8118 (properties `((upstream-name . "FNN")))
8119 (build-system r-build-system)
8120 (home-page "https://cran.r-project.org/web/packages/FNN")
8121 (synopsis "Fast nearest neighbor search algorithms and applications")
8123 "This package provides cover-tree and kd-tree fast k-nearest neighbor
8124 search algorithms. Related applications including KNN classification,
8125 regression and information measures are implemented.")
8126 ;; The DESCRIPTION file erroneously states that GPL version 2.1 or
8127 ;; later can be used.
8128 (license license:gpl2+)))
8130 (define-public r-smoother
8137 (uri (cran-uri "smoother" version))
8140 "0nqr1bvlr5bnasqg74zmknjjl4x28kla9h5cxpga3kq5z215pdci"))))
8141 (build-system r-build-system)
8144 (home-page "https://cran.r-project.org/web/packages/smoother")
8145 (synopsis "Functions relating to the smoothing of numerical data")
8147 "This package provides a collection of methods for smoothing numerical
8148 data, commencing with a port of the Matlab gaussian window smoothing function.
8149 In addition, several functions typically used in smoothing of financial data
8151 (license license:gpl2)))
8153 (define-public r-riverplot
8155 (name "r-riverplot")
8160 (uri (cran-uri "riverplot" version))
8163 "04ap1dsa7fx03l73jhv1ql3adaaaz2100qawdplxa9xmrllgcgbj"))))
8164 (build-system r-build-system)
8166 (list r-rcolorbrewer))
8169 (home-page "https://logfc.wordpress.com")
8170 (synopsis "Sankey or ribbon plots")
8172 "Sankey plots are a type of diagram that is convenient to illustrate how
8173 flow of information, resources etc. separates and joins, much like observing
8174 how rivers split and merge. For example, they can be used to compare
8175 different clusterings. This package provides an implementation of Sankey
8177 (license license:gpl2+)))
8179 (define-public r-dyn
8186 (uri (cran-uri "dyn" version))
8189 "16fqv9k7yxdgybwzafjkyqm16qpgqz13lcjpi6a1nc8xbzlzh0gb"))))
8190 (build-system r-build-system)
8193 (home-page "https://cran.r-project.org/web/packages/dyn")
8194 (synopsis "Time series regression")
8196 "This package provides the dyn class interfaces @code{ts}, @code{irts},
8197 @code{zoo} and @code{zooreg} time series classes to @code{lm}, @code{glm},
8198 @code{loess}, @code{quantreg::rq}, @code{MASS::rlm},
8199 @code{MCMCpack::MCMCregress()}, @code{quantreg::rq()},
8200 @code{randomForest::randomForest()} and other regression functions, allowing
8201 those functions to be used with time series including specifications that may
8202 contain lags, diffs and missing values.")
8204 (license license:gpl2+)))
8206 (define-public r-dynutils
8213 (uri (cran-uri "dynutils" version))
8215 (base32 "1pcj4igaw1g898xb42kcpzfmqy80xai5ki5bpnkf8hg738wm00qz"))))
8216 (properties `((upstream-name . "dynutils")))
8217 (build-system r-build-system)
8231 (native-inputs (list r-knitr))
8232 (home-page "https://github.com/dynverse/dynutils")
8233 (synopsis "Common functionality for the dynverse packages")
8235 "This package provides common functionality for the
8236 @url{https://dynverse.org,dynverse} packages. dynverse is created to support
8237 the development, execution, and benchmarking of trajectory inference
8239 (license license:expat)))
8241 (define-public r-catdap
8248 (uri (cran-uri "catdap" version))
8251 "0fyhl69z2lznymvpzxra9qvcg85ggzkfjy68c6mzdmf1ja44d2k5"))))
8252 (build-system r-build-system)
8255 (home-page "https://cran.r-project.org/web/packages/catdap/")
8256 (synopsis "Tools for categorical data analysis")
8258 "This package provides functions for analyzing multivariate data.
8259 Dependencies of the distribution of the specified variable (response
8260 variable) to other variables (explanatory variables) are derived and
8261 evaluated by the @dfn{Akaike Information Criterion} (AIC).")
8262 (license license:gpl2+)))
8264 (define-public r-arules
8271 (uri (cran-uri "arules" version))
8274 "05g6ik4z87g83nlicmb380331f84sqchvv1vch49zb7rq6v8gw6r"))))
8275 (build-system r-build-system)
8277 (list r-generics r-matrix))
8278 (home-page "https://github.com/mhahsler/arules")
8279 (synopsis "Mining association rules and frequent itemsets")
8281 "This package provides an infrastructure for representing, manipulating
8282 and analyzing transaction data and patterns (frequent itemsets and association rules).
8283 It also provides C implementations of the association mining algorithms Apriori
8285 (license license:gpl3)))
8287 (define-public r-parsedate
8289 (name "r-parsedate")
8294 (uri (cran-uri "parsedate" version))
8297 "1c2cpsvma3fkx6zp191bpfvf5rmpsr13g8rzqk6ycyb0n7b9k4qy"))))
8298 (build-system r-build-system)
8299 (home-page "https://github.com/gaborcsardi/parsedate")
8301 "Recognize and parse dates in various formats")
8303 "This package provides three functions for dealing with dates:
8304 @code{parse_iso_8601} recognizes and parses all valid ISO 8601 date and
8305 time formats, @code{parse_date} parses dates in unspecified formats,
8306 and @code{format_iso_8601} formats a date in ISO 8601 format.")
8307 (license license:gpl2)))
8309 (define-public r-abc-data
8316 (uri (cran-uri "abc.data" version))
8319 "1bv1n68ah714ws58cf285n2s2v5vn7382lfjca4jxph57lyg8hmj"))))
8320 (properties `((upstream-name . "abc.data")))
8321 (build-system r-build-system)
8322 (home-page "https://cran.r-project.org/web/packages/abc.data/")
8323 (synopsis "Data for Approximate Bayesian Computation (ABC) package")
8325 "This package contains data which are used by functions of the abc
8326 package which implements several @dfn{Approximate Bayesian Computation} (ABC)
8327 algorithms for performing parameter estimation, model selection, and
8329 (license license:gpl3+)))
8331 (define-public r-abc
8338 (uri (cran-uri "abc" version))
8341 "16753lyzk2dfwgdjfyanwacqw3bvrwby52inq4709804labs6lnv"))))
8342 (build-system r-build-system)
8344 (list r-abc-data r-locfit r-mass r-nnet r-quantreg))
8345 (home-page "https://cran.r-project.org/web/packages/abc/")
8346 (synopsis "Tools for Approximate Bayesian Computation (ABC)")
8348 "This package implements several @dfn{Approximate Bayesian
8349 Computation} (ABC) algorithms for performing parameter estimation, model
8350 selection, and goodness-of-fit. Cross-validation tools are also available for
8351 measuring the accuracy of ABC estimates, and to calculate the
8352 misclassification probabilities of different models.")
8353 (license license:gpl3+)))
8355 (define-public r-zip
8362 (uri (cran-uri "zip" version))
8365 "1n5ryjdj3i16b4mdp29wapgaklz3yzas5k8ffx7q6fa0jry9i5cz"))))
8366 (build-system r-build-system)
8367 (home-page "https://github.com/gaborcsardi/zip")
8368 (synopsis "Cross-platform Zip compression")
8370 "This package provides a cross-platform Zip compression library for R.
8371 It is a replacement for the @code{zip} function, that does not require any
8372 additional external tools on any platform.")
8373 (license license:cc0)))
8375 (define-public r-openxlsx
8382 (uri (cran-uri "openxlsx" version))
8385 "0695b265g7jwiqk5c3vmmfkvagx82bkpwhvqzhqaqmmn34l6vl35"))))
8386 (build-system r-build-system)
8388 (list r-rcpp r-stringi r-zip))
8391 (home-page "https://github.com/awalker89/openxlsx")
8392 (synopsis "Read, write and edit XLSX files")
8394 "This package simplifies the creation of Excel @code{.xlsx} files by
8395 providing a high level interface to writing, styling and editing worksheets.
8396 Through the use of Rcpp, read/write times are comparable to the @code{xlsx}
8397 and @code{XLConnect} packages with the added benefit of removing the
8398 dependency on Java.")
8399 (license license:gpl3)))
8401 (define-public r-rio
8408 (uri (cran-uri "rio" version))
8411 "04jlrhyl0791yxwcpp1s8p1hhkljnijlc5iaxpk56h41w63k39lz"))))
8412 (build-system r-build-system)
8423 (home-page "https://github.com/leeper/rio")
8424 (synopsis "Swiss-army knife for data I/O")
8426 "This package provides streamlined data import and export infrastructure
8427 by making assumptions that the user is probably willing to make: @code{import}
8428 and @code{export} determine the data structure from the file extension,
8429 reasonable defaults are used for data import and export (e.g.,
8430 @code{stringsAsFactors=FALSE}), web-based import is natively
8431 supported (including from SSL/HTTPS), compressed files can be read directly
8432 without explicit decompression, and fast import packages are used where
8433 appropriate. An additional convenience function, @code{convert}, provides a
8434 simple method for converting between file types.")
8435 (license license:gpl2)))
8437 (define-public r-maptools
8444 (uri (cran-uri "maptools" version))
8447 "1jgx8iiirj8qhrmh19mkisa35jcql7352dmc7lvwi5vxg3wjbvpk"))))
8448 (build-system r-build-system)
8450 (list r-foreign r-lattice r-sp))
8451 (home-page "https://r-forge.r-project.org/projects/maptools/")
8452 (synopsis "Tools for reading and handling spatial objects")
8454 "This package provides a set of tools for manipulating and reading
8455 geographic data, in particular ESRI Shapefiles. It includes binary access to
8456 GSHHG shoreline files. The package also provides interface wrappers for
8457 exchanging spatial objects with other R packages.")
8458 ;; The C source files from shapelib are released under the Expat license.
8459 ;; The R code is released under GPL version 2 or later.
8460 (license (list license:gpl2+
8463 (define-public r-later
8470 (uri (cran-uri "later" version))
8473 "0acqg29hcm2iq1418b54np7zb5pnr3xzrwc3ijv2pz9wra10ix88"))))
8474 (build-system r-build-system)
8476 (list r-rcpp r-rlang))
8479 (home-page "https://github.com/r-lib/later")
8480 (synopsis "Utilities for delaying function execution")
8482 "This package provides tools to execute arbitrary R or C functions some
8483 time after the current time, after the R execution stack has emptied.")
8484 (license license:gpl2+)))
8486 (define-public r-promises
8493 (uri (cran-uri "promises" version))
8496 "1dy4cbqw17awh4q8m7cy3anaj0n9iynabfzflb1g94cyj0bq4fld"))))
8497 (build-system r-build-system)
8499 (list r-later r-magrittr r-r6 r-rcpp r-rlang))
8502 (home-page "https://rstudio.github.io/promises")
8503 (synopsis "Abstractions for promise-based asynchronous programming")
8505 "This package provides fundamental abstractions for doing asynchronous
8506 programming in R using promises. Asynchronous programming is useful for
8507 allowing a single R process to orchestrate multiple tasks in the background
8508 while also attending to something else. Semantics are similar to JavaScript
8509 promises, but with a syntax that is idiomatic R.")
8510 (license license:expat)))
8512 (define-public r-dosnow
8519 (uri (cran-uri "doSNOW" version))
8522 "1f5v0k2w0b2478p6iqa3hn2lwd1x3rzc348n57nd38ka2vnsnz4i"))))
8523 (properties `((upstream-name . "doSNOW")))
8524 (build-system r-build-system)
8526 (list r-foreach r-iterators r-snow))
8527 (home-page "https://cran.r-project.org/web/packages/doSNOW")
8528 (synopsis "Foreach parallel adaptor for the snow package")
8530 "This package provides a parallel backend for the @code{%dopar%} function
8531 using the @code{snow} package.")
8532 (license license:gpl2)))
8534 (define-public r-fstcore
8541 (uri (cran-uri "fstcore" version))
8543 (base32 "1a5m68n2dqhi3r8wf5jwg4vjvl550c7wypcf5j0xmkvl836yg1lg"))))
8544 (properties `((upstream-name . "fstcore")))
8545 (build-system r-build-system)
8546 (propagated-inputs (list r-rcpp))
8547 (inputs (list zlib))
8548 (native-inputs (list pkg-config))
8549 (home-page "https://www.fstpackage.org/fstcore/")
8550 (synopsis "R bindings to the fstlib library")
8552 "The fstlib library provides multithreaded serialization of compressed
8553 data frames using the fst format. The fst format allows for random access of
8554 stored data and compression with the LZ4 and ZSTD compressors.")
8555 (license license:mpl2.0)))
8557 (define-public r-fst
8564 (uri (cran-uri "fst" version))
8567 "0r96inwrr960m7wmc80603bw2vvvwab225bh9dq3lalwhy4yiis4"))))
8568 (properties `((upstream-name . "fst")))
8569 (build-system r-build-system)
8570 (propagated-inputs (list r-fstcore r-rcpp))
8571 (home-page "http://www.fstpackage.org")
8572 (synopsis "Fast serialization of data frames")
8574 "The fst package for R provides a fast, easy and flexible way to
8575 serialize data frames. With access speeds of multiple GB/s, fst is
8576 specifically designed to unlock the potential of high speed solid state disks.
8577 Data frames stored in the fst format have full random access, both in column
8578 and rows. The fst format allows for random access of stored data and
8579 compression with the LZ4 and ZSTD compressors.")
8580 (license license:agpl3)))
8582 (define-public r-snowfall
8585 (version "1.84-6.1")
8588 (uri (cran-uri "snowfall" version))
8590 (base32 "13941rlw1jsdjsndp1plzj1cq5aqravizkrqn6l25r9im7rnsi2w"))))
8591 (build-system r-build-system)
8594 (home-page "https://cran.r-project.org/web/packages/snowfall/")
8595 (synopsis "Easier cluster computing")
8596 (description "This package is a usability wrapper around snow for easier
8597 development of parallel R programs. This package offers e.g. extended error
8598 checks, and additional functions. All functions work in sequential mode, too,
8599 if no cluster is present or wished. The package is also designed as connector
8600 to the cluster management tool @code{sfCluster}, but can also used without
8602 (license license:gpl2+)))
8604 (define-public r-rgexf
8611 (uri (cran-uri "rgexf" version))
8614 "00c2zka1n3k7p1l0mlchr063s6x58p9r3fb64d4wgl4rvsq55q3f"))
8615 ;; Delete minified JavaScript files
8617 '(for-each delete-file
8618 '("inst/gexf-js/js/jquery-2.0.2.min.js"
8619 "inst/gexf-js/js/jquery-ui-1.10.3.custom.min.js"
8620 "inst/gexf-js/js/jquery.mousewheel.min.js")))))
8621 (properties `((upstream-name . "rgexf")))
8622 (build-system r-build-system)
8624 `(#:modules ((guix build utils)
8625 (guix build r-build-system)
8629 (modify-phases %standard-phases
8630 (add-after 'unpack 'process-javascript
8631 (lambda* (#:key inputs #:allow-other-keys)
8632 (invoke "unzip" "-d" "/tmp" (assoc-ref inputs "js-jquery-ui"))
8633 (with-directory-excursion "inst/gexf-js/js/"
8637 `((,(assoc-ref inputs "js-jquery")
8638 "jquery-2.0.2.min.js")
8639 ("/tmp/jquery-ui-1.10.3/ui/jquery-ui.js"
8640 "jquery-ui-1.10.3.custom.min.js")
8641 (,(assoc-ref inputs "js-jquery-mousewheel")
8642 "jquery.mousewheel.min.js"))))
8643 (lambda (sources targets)
8644 (for-each (lambda (source target)
8645 (format #true "Processing ~a --> ~a~%"
8647 (invoke "esbuild" source "--minify"
8648 (string-append "--outfile=" target)))
8649 sources targets)))))))))
8651 (list r-igraph r-servr r-xml))
8653 `(("r-knitr" ,r-knitr)
8654 ("esbuild" ,esbuild)
8659 (uri "https://code.jquery.com/jquery-2.0.2.js")
8662 "0v818bxpw48gdk8i95qqqij80r9jcgisi2r4ac6xnxca20h0gvfj"))))
8666 (uri "https://jqueryui.com/resources/download/jquery-ui-1.10.3.zip")
8669 "00xpfy0l69nj2yan4s8k65ldsrlfsjkmyw2dwcg93dc8mv454vxx"))))
8670 ("js-jquery-mousewheel"
8673 (uri "https://raw.githubusercontent.com/jquery/jquery-mousewheel/\
8674 3.0.6/jquery.mousewheel.js")
8677 "19lk5xy2s47bx8hsa7j6bg012f8yw6d770g230bcnm559kf4nc6v"))))))
8678 (home-page "https://gvegayon.github.io/rgexf")
8679 (synopsis "Build, import and export GEXF graph files")
8681 "Create, read and write GEXF (Graph Exchange XML Format) graph
8682 files (used in Gephi and others). It allows the user to easily build/read
8683 graph files including attributes, GEXF visual attributes (such as color, size,
8684 and position), network dynamics (for both edges and nodes) and edge weighting.
8685 Users can build/handle graphs element-by-element or massively through
8686 data-frames, visualize the graph on a web browser through gexf-js (a
8687 JavaScript library) and interact with the igraph package.")
8688 (license license:expat)))
8690 (define-public r-data-tree
8692 (name "r-data-tree")
8697 (uri (cran-uri "data.tree" version))
8700 "0pizmx2312zsym4m42b97q2184bg3hibvbdrblcga05xln84qrs0"))))
8701 (properties `((upstream-name . "data.tree")))
8702 (build-system r-build-system)
8704 (list r-r6 r-stringi))
8707 (home-page "https://github.com/gluc/data.tree")
8708 (synopsis "General purpose hierarchical data structure")
8710 "Create tree structures from hierarchical data, and traverse the tree in
8711 various orders. Aggregate, cumulate, print, plot, convert to and from
8712 data.frame and more. This is useful for decision trees, machine learning,
8713 finance, conversion from and to JSON, and many other applications.")
8714 (license license:gpl2+)))
8716 (define-public r-dtplyr
8723 (uri (cran-uri "dtplyr" version))
8726 "1wyhhn16mvdj55k2xsh7vy489l7xk4mkz7pjrw16z87awk6yjh16"))))
8727 (properties `((upstream-name . "dtplyr")))
8728 (build-system r-build-system)
8742 (home-page "https://github.com/tidyverse/dtplyr")
8743 (synopsis "Data Table back-end for dplyr")
8745 "This package provides a @code{data.table} backend for @code{dplyr}. The
8746 goal of @code{dtplyr} is to allow you to write @code{dplyr} code that is
8747 automatically translated to the equivalent, but usually much faster,
8748 @code{data.table} code.")
8749 (license license:expat)))
8751 (define-public r-collapsibletree
8753 (name "r-collapsibletree")
8758 (uri (cran-uri "collapsibleTree" version))
8761 "0b65pbp1wnpsrayqi630ds4r98jvcvynnlp6wxdqrnnr9nzw5343"))
8764 ;; Delete minified JavaScript file
8765 (delete-file "inst/htmlwidgets/lib/d3-4.10.2/d3.min.js")
8768 `((upstream-name . "collapsibleTree")))
8769 (build-system r-build-system)
8772 (modify-phases %standard-phases
8773 (add-after 'unpack 'process-javascript
8774 (lambda* (#:key inputs #:allow-other-keys)
8775 (with-directory-excursion "inst/htmlwidgets/lib/d3-4.10.2/"
8776 (let ((source (assoc-ref inputs "d3.v4.js"))
8777 (target "d3.min.js"))
8778 (format #t "Processing ~a --> ~a~%"
8780 (invoke "esbuild" source "--minify"
8781 (string-append "--outfile=" target)))))))))
8783 (list r-data-tree r-htmlwidgets))
8785 `(("esbuild" ,esbuild)
8789 (uri "https://d3js.org/d3.v4.js")
8792 "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg"))))))
8793 (home-page "https://github.com/AdeelK93/collapsibleTree")
8794 (synopsis "Interactive collapsible tree diagrams using D3.js")
8796 "This is a package for interactive Reingold-Tilford tree diagrams created
8797 using D3.js, where every node can be expanded and collapsed by clicking on it.
8798 Tooltips and color gradients can be mapped to nodes using a numeric column in
8799 the source data frame.")
8800 (license license:gpl3+)))
8802 (define-public r-rappdirs
8809 (uri (cran-uri "rappdirs" version))
8812 "1161i3jgjvzjv4p8qbz9r976fnggkcrw3mlj4yd1h2svnijrz5a9"))))
8813 (build-system r-build-system)
8814 (home-page "https://cran.r-project.org/web/packages/rappdirs/")
8815 (synopsis "Determine where to save data, caches, and logs")
8817 "This package provides an easy way to determine which directories on the
8818 user's computer should be used to save data, caches and logs. It is a port of
8819 Python's @url{https://github.com/ActiveState/appdirs,Appdirs} to R.")
8820 (license license:expat)))
8822 (define-public r-rastervis
8824 (name "r-rastervis")
8829 (uri (cran-uri "rasterVis" version))
8832 "0kgg6cm7xjqya2d46w0i1i1wjpkb8f99lyqy7rgwa7l9xmwzj5n1"))))
8833 (properties `((upstream-name . "rasterVis")))
8834 (build-system r-build-system)
8845 (home-page "https://oscarperpinan.github.io/rastervis/")
8846 (synopsis "Visualization methods for raster data")
8848 "This package provides methods for enhanced visualization and interaction
8849 with raster data. It implements visualization methods for quantitative data
8850 and categorical data, both for univariate and multivariate rasters. It also
8851 provides methods to display spatiotemporal rasters, and vector fields.")
8852 (license license:gpl3)))
8854 (define-public r-rentrez
8861 (uri (cran-uri "rentrez" version))
8864 "0x1g2f6hvkqqlb39z8m5qxhcvsizddic5i7rpqw0wy77xfbna9gv"))))
8865 (properties `((upstream-name . "rentrez")))
8866 (build-system r-build-system)
8868 (list r-httr r-jsonlite r-xml))
8871 (home-page "https://docs.ropensci.org/rentrez/")
8872 (synopsis "Entrez in R")
8874 "This package provides an R interface to the NCBI's EUtils API,
8875 allowing users to search databases like GenBank PubMed, process the results of
8876 those searches and pull data into their R sessions.")
8877 (license license:expat)))
8879 (define-public r-renv
8886 (uri (cran-uri "renv" version))
8889 "0bjq3ms5dg155clya62m462m93g90sxfxm7b4cqhqbx8vakskwdl"))))
8890 (properties `((upstream-name . "renv")))
8891 (build-system r-build-system)
8894 (home-page "https://rstudio.github.io/renv")
8895 (synopsis "Project environments")
8897 "This package provides a dependency management toolkit for R. Using
8898 renv, you can create and manage project-local R libraries, save the state of
8899 these libraries to a lockfile, and later restore your library as required.
8900 Together, these tools can help make your projects more isolated, portable, and
8902 (license license:expat)))
8904 (define-public r-learnr
8911 (uri (cran-uri "learnr" version))
8914 "08xwmms6x58y3dsfbl9c6d03145hb4ij97nqr1cc9dxxilmr6x31"))))
8915 (build-system r-build-system)
8931 (home-page "https://rstudio.github.io/learnr/")
8932 (synopsis "Interactive tutorials for R")
8934 "This package provides tools to create interactive tutorials using R
8935 Markdown. Use a combination of narrative, figures, videos, exercises, and
8936 quizzes to create self-paced tutorials for learning about R and R packages.")
8937 (license license:asl2.0)))
8939 (define-public r-analytics
8941 (name "r-analytics")
8946 (uri (cran-uri "analytics" version))
8949 "0js3c8lwj3knccb55nq03cbjlf4w390p9aid2mi5x80l3ayd9in1"))))
8950 (build-system r-build-system)
8964 (home-page "https://cran.r-project.org/web/packages/analytics/")
8965 (synopsis "Collection of data analysis tools")
8967 "This package is a collection of data analysis tools. It includes tools
8968 for regression outlier detection in a fitted linear model, stationary
8969 bootstrap using a truncated geometric distribution, a comprehensive test for
8970 weak stationarity, column means by group, weighted biplots, and a heuristic to
8971 obtain a better initial configuration in non-metric MDS.")
8972 (license license:gpl2)))
8974 (define-public r-here
8981 (uri (cran-uri "here" version))
8983 (base32 "0srlr8h8qmr0wrmp7gs4g2ry5dni2hx8n947bik3s3a26f091v88"))))
8984 (properties `((upstream-name . "here")))
8985 (build-system r-build-system)
8986 (propagated-inputs (list r-rprojroot))
8987 (native-inputs (list r-knitr))
8988 (home-page "https://here.r-lib.org/")
8989 (synopsis "Simpler way to find files")
8991 "This package lets you construct paths to your project's files. Use the
8992 @code{here} function as a drop-in replacement for @code{file.path}, it will
8993 always locate the files relative to your project root.")
8994 (license license:expat)))
8996 (define-public r-reticulate
8998 (name "r-reticulate")
9003 (uri (cran-uri "reticulate" version))
9006 "0b1szzsqyc8wcfpkn5517bb1ds064vs2hky71my3p74kfngay991"))))
9007 (build-system r-build-system)
9008 (inputs (list python))
9020 (home-page "https://github.com/rstudio/reticulate")
9021 (synopsis "R interface to Python")
9023 "This package provides an interface from R to Python modules, classes,
9024 and functions. When calling into Python, R data types are automatically
9025 converted to their equivalent Python types. When values are returned from
9026 Python to R they are converted back to R types.")
9027 (license license:asl2.0)))
9029 (define-public r-bibtex
9036 (uri (cran-uri "bibtex" version))
9039 "0vdwx6808r73pk15263f33bkqbfmb08d8jkmr4d7h4ml414ikbbv"))))
9040 (build-system r-build-system)
9041 (propagated-inputs (list r-stringr))
9042 (home-page "https://github.com/romainfrancois/bibtex")
9043 (synopsis "Bibtex parser")
9044 (description "This package provides a utility for R to parse a bibtex
9046 (license license:gpl2+)))
9048 (define-public r-billboarder
9050 (name "r-billboarder")
9055 (uri (cran-uri "billboarder" version))
9057 (base32 "189ngvg84rcwhrivxskmjv3srhadvzr4p1v8pf11axyv2qn01b0x"))
9059 '(delete-file "inst/htmlwidgets/lib/billboard/billboard.pkgd.min.js"))))
9060 (properties `((upstream-name . "billboarder")))
9061 (build-system r-build-system)
9064 (modify-phases %standard-phases
9065 (add-after 'unpack 'process-javascript
9066 (lambda* (#:key inputs #:allow-other-keys)
9067 (with-directory-excursion "inst/htmlwidgets/lib/billboard/"
9068 (let ((source (assoc-ref inputs "js-billboard"))
9069 (target "billboard.pkgd.min.js"))
9070 (format #true "Processing ~a --> ~a~%"
9072 (invoke "esbuild" source "--minify"
9073 (string-append "--outfile=" target)))))))))
9084 `(("r-knitr" ,r-knitr)
9085 ("esbuild" ,esbuild)
9086 ;; It is not ideal to use this concatenated (but not minified)
9087 ;; JavaScript file, as the original source is written in TypeScript.
9088 ;; However, this can still be considered source code as it is readable
9089 ;; and can be modified.
9093 (uri "https://unpkg.com/billboard.js@3.2.0/dist/billboard.js")
9096 "1kx5rqmn87pgal2cwmcij2rrnwa0fgcsw6y99m4i0l2sdm0qffv2"))))))
9097 (home-page "https://github.com/dreamRs/billboarder")
9098 (synopsis "Create interactive charts with the JavaScript Billboard library")
9100 "This package provides an @code{htmlwidgets} interface to billboard.js,
9101 a re-usable easy interface JavaScript chart library, based on D3 v4+. Chart
9102 types include line charts, scatterplots, bar/lollipop charts,
9103 histogram/density plots, pie/donut charts and gauge charts. All charts are
9104 interactive, and a proxy method is implemented to smoothly update a chart
9105 without rendering it again in shiny apps.")
9106 (license license:expat)))
9108 (define-public r-ggseqlogo
9110 (name "r-ggseqlogo")
9115 (uri (cran-uri "ggseqlogo" version))
9118 "13q6kcpxrqxqbji889fx63p0nsi08lk5yymkchig75r5k1d18ky1"))))
9119 (build-system r-build-system)
9120 (propagated-inputs (list r-ggplot2))
9121 (home-page "https://github.com/omarwagih/ggseqlogo")
9122 (synopsis "ggplot2 extension for drawing genetic sequence logos")
9124 "The range of functions provided by this package makes it possible to
9125 draw highly versatile genomic sequence logos. Features include, but are not
9126 limited to, modifying colour schemes and fonts used to draw the logo,
9127 generating multiple logo plots, and aiding the visualisation with annotations.
9128 Sequence logos can easily be combined with other ggplot2 plots.")
9129 ;; Unspecified version of the LGPL.
9130 (license license:lgpl3+)))
9132 (define-public r-ggsci
9139 (uri (cran-uri "ggsci" version))
9142 "0g73x6grbka7ahjh6z23m3wrcifp5rdfdiasbl8lq4sp6rplxwaa"))))
9143 (build-system r-build-system)
9145 (list r-ggplot2 r-scales))
9146 (home-page "https://nanx.me/ggsci/")
9147 (synopsis "Scientific journal and sci-fi themed color palettes for ggplot2")
9149 "This package provides a collection of ggplot2 color palettes inspired by
9150 plots in scientific journals, data visualization libraries, science fiction
9151 movies, and TV shows.")
9152 (license license:gpl3)))
9154 (define-public r-ggsignif
9161 (uri (cran-uri "ggsignif" version))
9164 "1ad774c7s7y4i00xd89lfigr9aybl94q98ch598k3rchanr4b1fa"))))
9165 (build-system r-build-system)
9170 (home-page "https://github.com/const-ae/ggsignif")
9171 (synopsis "Significance brackets for ggplot2")
9173 "Enrich your ggplots with group-wise comparisons. This package provides
9174 an easy way to indicate if two groups are significantly different. Commonly
9175 this is shown by a bracket on top connecting the groups of interest which
9176 itself is annotated with the level of significance. The package provides a
9177 single layer that takes the groups for comparison and the test as arguments
9178 and adds the annotation to the plot.")
9179 (license license:gpl3)))
9181 (define-public r-rstatix
9188 (uri (cran-uri "rstatix" version))
9191 "0330y8iziffqg8j9j5h9zv4qcdyf8ybhmzxrr9fzq9nc6bf1gbm5"))))
9192 (properties `((upstream-name . "rstatix")))
9193 (build-system r-build-system)
9206 (home-page "https://rpkgs.datanovia.com/rstatix/")
9207 (synopsis "Pipe-friendly framework for basic statistical tests")
9209 "This package provides a simple and intuitive pipe-friendly framework,
9210 coherent with the @code{tidyverse} design philosophy, for performing basic
9211 statistical tests, including t-test, Wilcoxon test, ANOVA, Kruskal-Wallis and
9212 correlation analyses. The output of each test is automatically transformed
9213 into a tidy data frame to facilitate visualization. Additional functions are
9214 available for reshaping, reordering, manipulating and visualizing correlation
9216 (license license:gpl2)))
9218 (define-public r-ggpubr
9225 (uri (cran-uri "ggpubr" version))
9228 "0x86lmghr25k8w90yrp360dn42dhp5cjvjpdiv2s2gxfn701xcmb"))))
9229 (build-system r-build-system)
9247 (home-page "http://www.sthda.com/english/rpkgs/ggpubr")
9248 (synopsis "ggplot2-based publication-ready plots")
9250 "The ggplot2 package is an excellent and flexible package for elegant
9251 data visualization in R. However the default generated plots require some
9252 formatting before we can send them for publication. The ggpubr package
9253 provides some easy-to-use functions for creating and customizing ggplot2-based
9254 publication-ready plots.")
9255 (license license:gpl2)))
9257 (define-public r-ellipse
9264 (uri (cran-uri "ellipse" version))
9267 "1wm5v7zdv2drgdba7z96jwsx74mqhlq80qgrvdb4vb5r02dcw68p"))))
9268 (build-system r-build-system)
9269 (home-page "https://cran.r-project.org/web/packages/ellipse/")
9270 (synopsis "Functions for drawing ellipses and ellipse-like confidence regions")
9272 "This package contains various routines for drawing ellipses and
9273 ellipse-like confidence regions, implementing the plots described in Murdoch
9274 and Chow (1996), A graphical display of large correlation matrices, The
9275 American Statistician 50, 178-180. There are also routines implementing the
9276 profile plots described in Bates and Watts (1988), Nonlinear Regression
9277 Analysis and its Applications.")
9278 (license license:gpl2+)))
9280 (define-public r-flashclust
9282 (name "r-flashclust")
9287 (uri (cran-uri "flashClust" version))
9290 "0l4lpz451ll7f7lfxmb7ds24ppzhfg1c3ypvydglcc35p2dq99s8"))))
9291 (properties `((upstream-name . "flashClust")))
9292 (build-system r-build-system)
9293 (native-inputs (list gfortran))
9294 (home-page "https://cran.r-project.org/web/packages/flashClust/")
9295 (synopsis "Implementation of optimal hierarchical clustering")
9297 "This package provides a fast implementation of hierarchical
9299 (license license:gpl2+)))
9301 (define-public r-factominer
9303 (name "r-factominer")
9308 (uri (cran-uri "FactoMineR" version))
9311 "0lg8n9fxxk46nchnj4pbpqqf4swxfsq7r9jzr36dmd36kb7avqxr"))))
9312 (properties `((upstream-name . "FactoMineR")))
9313 (build-system r-build-system)
9328 (home-page "http://factominer.free.fr")
9329 (synopsis "Multivariate exploratory data analysis and data mining")
9331 "This package provides exploratory data analysis methods to summarize,
9332 visualize and describe datasets. The main principal component methods are
9333 available, those with the largest potential in terms of applications:
9334 principal component analysis (PCA) when variables are quantitative,
9335 correspondence analysis (CA) and multiple correspondence analysis (MCA) when
9336 variables are categorical, Multiple Factor Analysis when variables are
9337 structured in groups, etc. and hierarchical cluster analysis.")
9338 (license license:gpl2+)))
9340 (define-public r-factoextra
9342 (name "r-factoextra")
9347 (uri (cran-uri "factoextra" version))
9350 "1allvdjhd3pq8xz30b1cymwcik5iaahghrjrlnn54cwkfhfg0kv2"))))
9351 (build-system r-build-system)
9362 (home-page "http://www.sthda.com/english/rpkgs/factoextra")
9363 (synopsis "Extract and visualize the results of multivariate data analyses")
9365 "This package provides some easy-to-use functions to extract and
9366 visualize the output of multivariate data analyses, including
9367 @code{PCA} (Principal Component Analysis), @code{CA} (Correspondence
9368 Analysis), @code{MCA} (Multiple Correspondence Analysis), @code{FAMD} (Factor
9369 Analysis of Mixed Data), @code{MFA} (Multiple Factor Analysis) and
9370 @code{HMFA} (Hierarchical Multiple Factor Analysis) functions from different R
9371 packages. It contains also functions for simplifying some clustering analysis
9372 steps and provides ggplot2-based elegant data visualization.")
9373 (license license:gpl2)))
9375 (define-public r-fansi
9382 (uri (cran-uri "fansi" version))
9385 "0sn0kflgcn2qrrv646pzqylm02cx8l5ws473ppmvla4xihyvi9w6"))))
9386 (build-system r-build-system)
9388 (list r-knitr)) ; for vignettes
9389 (home-page "https://github.com/brodieG/fansi")
9390 (synopsis "ANSI control sequence aware string functions")
9392 "This package provides counterparts to R string manipulation functions
9393 that account for the effects of ANSI text formatting control sequences.")
9394 (license license:gpl2+)))
9396 (define-public r-nbclust
9403 (uri (cran-uri "NbClust" version))
9406 "0k5hr4zgx4gp1n62xchgz2zvyl35ba2cnczhhvj8rfbg2n4hx6qs"))))
9407 (properties `((upstream-name . "NbClust")))
9408 (build-system r-build-system)
9409 (home-page "https://sites.google.com/site/malikacharrad/research/nbclust-package")
9410 (synopsis "Determine the best number of clusters in a data set")
9412 "NbClust provides 30 indexes for determining the optimal number of
9413 clusters in a data set and offers the best clustering scheme from different
9414 results to the user.")
9415 (license license:gpl2)))
9417 (define-public r-hdf5r
9424 (uri (cran-uri "hdf5r" version))
9427 "0bv2q4ir73sbk5ra2q4mc8wbcmiwkws8k0mjlnx9ysi2mdrm3dw7"))))
9428 (build-system r-build-system)
9432 (list r-bit64 r-r6))
9435 (home-page "https://hhoeflin.github.io/hdf5r")
9436 (synopsis "Interface to the HDF5 binary data format")
9438 "HDF5 is a data model, library and file format for storing and managing
9439 large amounts of data. This package provides a nearly feature complete,
9440 object oriented wrapper for the HDF5 API using R6 classes. Additionally,
9441 functionality is added so that HDF5 objects behave very similar to their
9442 corresponding R counterparts.")
9443 (license license:asl2.0)))
9445 (define-public r-itertools
9447 (name "r-itertools")
9452 (uri (cran-uri "itertools" version))
9455 "1ls5biiva10pb1dj3ph4griykb9vam02hkrdmlr5a5wf660hg6xn"))))
9456 (build-system r-build-system)
9459 (home-page "https://cran.r-project.org/web/packages/itertools/")
9460 (synopsis "Iterator tools")
9462 "This package provides various tools for creating iterators, many
9463 patterned after functions in the Python @code{itertools} module, and others
9464 patterned after functions in the snow package.")
9465 (license license:gpl2)))
9467 (define-public r-itsadug
9474 (uri (cran-uri "itsadug" version))
9476 (base32 "0759l7hhvj05dp92pz59xwrxjm9s1iwkwrdhs68l0fq57550j70l"))))
9477 (properties `((upstream-name . "itsadug")))
9478 (build-system r-build-system)
9479 (propagated-inputs (list r-mgcv r-plotfunctions))
9480 (native-inputs (list r-knitr))
9481 (home-page "https://cran.r-project.org/package=itsadug")
9482 (synopsis "Interpreting time series and autocorrelated data using GAMMs")
9484 "@dfn{Generalized Additive Mixed Modeling} (GAMM; Lin & Zhang, 1999) as
9485 implemented in the R package @code{mgcv} is a nonlinear regression analysis
9486 which is particularly useful for time course data such as EEG, pupil dilation,
9487 gaze data (eye tracking), and articulography recordings, but also for
9488 behavioral data such as reaction times and response data. As time course
9489 measures are sensitive to autocorrelation problems, GAMMs implements methods
9490 to reduce the autocorrelation problems. This package includes functions for
9491 the evaluation of GAMM models (e.g., model comparisons, determining regions of
9492 significance, inspection of autocorrelational structure in residuals) and
9493 interpreting of GAMMs (e.g., visualization of complex interactions, and
9495 (license license:gpl2+)))
9497 (define-public r-polynom
9504 (uri (cran-uri "polynom" version))
9507 "0y4j07syjwpnq5w6a1d90z6h1hjzijmm42pq0f8jk2vcn5xxn7mw"))))
9508 (build-system r-build-system)
9509 (native-inputs (list r-knitr))
9510 (home-page "https://cran.r-project.org/web/packages/polynom/")
9511 (synopsis "Functions for univariate polynomial manipulations")
9513 "This package provides a collection of functions to implement a class for
9514 univariate polynomial manipulations.")
9515 (license license:gpl2)))
9517 (define-public r-pupillometryr
9519 (name "r-pupillometryr")
9524 (uri (cran-uri "PupillometryR" version))
9526 (base32 "0yk30sgl2qqa6pva649swq523vh446ifmydildycfvfmlm1h4qza"))))
9527 (properties `((upstream-name . "PupillometryR")))
9528 (build-system r-build-system)
9541 (native-inputs (list r-knitr))
9542 (home-page "https://cran.r-project.org/package=PupillometryR")
9543 (synopsis "Unified pipeline for pupillometry data")
9545 "This package provides a unified pipeline to clean, prepare, plot, and
9546 run basic analyses on pupillometry experiments.")
9547 (license license:expat)))
9549 (define-public r-gbrd
9556 (uri (cran-uri "gbRd" version))
9559 "06x97rw5i6v6cgjxkfhxnw4dn7lghn5q6ra7ri5ag1x9dkfzcl82"))))
9560 (properties `((upstream-name . "gbRd")))
9561 (build-system r-build-system)
9562 (home-page "https://cran.r-project.org/web/packages/gbRd/")
9563 (synopsis "Utilities for processing Rd objects and files")
9565 "This package provides utilities for processing Rd objects and files.
9566 Extract argument descriptions and other parts of the help pages of
9568 (license license:gpl2+)))
9570 (define-public r-rjags
9577 (uri (cran-uri "rjags" version))
9580 "0cibz6xhmh86fh7ynmdgpmlchizi57pi6dpslgc2if17a56c6p7q"))))
9581 (build-system r-build-system)
9588 (home-page "http://mcmc-jags.sourceforge.net")
9589 (synopsis "Bayesian graphical models using MCMC")
9591 "This package provides an R interface to the JAGS MCMC library. JAGS is
9592 Just Another Gibbs Sampler. It is a program for analysis of Bayesian
9593 hierarchical models using Markov Chain Monte Carlo (MCMC) simulation.")
9594 (license license:gpl2)))
9596 (define-public r-rbibutils
9598 (name "r-rbibutils")
9603 (uri (cran-uri "rbibutils" version))
9606 "0lnia2fk8zlvkkgnl7r7dyi1ip5vqlw448qrvqs2s14rpbpcvbpi"))))
9607 (properties `((upstream-name . "rbibutils")))
9608 (build-system r-build-system)
9609 (home-page "https://geobosh.github.io/rbibutils/")
9610 (synopsis "Convert between bibliography formats")
9612 "This package converts between a number of bibliography formats,
9613 including BibTeX, BibLaTeX and Bibentry. It includes a port of the bibutils
9614 utilities and supports all bibliography formats and character encodings
9615 implemented in bibutils.")
9616 (license license:gpl2)))
9618 (define-public r-rdpack
9625 (uri (cran-uri "Rdpack" version))
9628 "1igpa4hnpiykbdnq57mglby5jsbind6izkkfy81wx4ib6nw1lpn4"))))
9629 (properties `((upstream-name . "Rdpack")))
9630 (build-system r-build-system)
9633 (home-page "https://github.com/GeoBosh/Rdpack")
9634 (synopsis "Update and manipulate Rd documentation objects")
9636 "This package provides functions for manipulation of R documentation
9637 objects, including functions @code{reprompt()} and @code{ereprompt()} for
9638 updating Rd documentation for functions, methods and classes; it also includes
9639 Rd macros for citations and import of references from bibtex files for use in
9640 Rd files and roxygen2 comments, as well as many functions for manipulation of
9641 references and Rd files.")
9642 (license license:gpl2+)))
9644 (define-public r-officer
9651 (uri (cran-uri "officer" version))
9654 "0qmn62srh9zicgizyblanirbdva7f09g967yb86kfrn05ckh5y10"))))
9655 (build-system r-build-system)
9657 (list r-r6 r-uuid r-xml2 r-zip))
9658 (home-page "https://davidgohel.github.io/officer")
9659 (synopsis "Manipulation of Word and PowerPoint documents")
9661 "This package provides tools to access and manipulate Word and PowerPoint
9662 documents from R. The package focuses on tabular and graphical reporting from
9663 R; it also provides two functions that let users get document content into
9664 data objects. A set of functions lets add and remove images, tables and
9665 paragraphs of text in new or existing documents. When working with PowerPoint
9666 presentations, slides can be added or removed; shapes inside slides can also
9667 be added or removed. When working with Word documents, a cursor can be used
9668 to help insert or delete content at a specific location in the document.")
9669 (license license:gpl3)))
9671 (define-public r-profilemodel
9673 (name "r-profilemodel")
9678 (uri (cran-uri "profileModel" version))
9681 "01m5nb8cmq0aq555pxk2a99182si65hhmn68yn9nal2j3zl2bp4i"))))
9682 (properties `((upstream-name . "profileModel")))
9683 (build-system r-build-system)
9684 (home-page "https://github.com/ikosmidis/profileModel")
9685 (synopsis "Profiling inference functions for various model classes")
9687 "This package provides tools that can be used to calculate, evaluate,
9688 plot and use for inference the profiles of *arbitrary* inference functions for
9689 arbitrary @code{glm}-like fitted models with linear predictors. More information
9690 on the methods that are implemented can be found in Kosmidis (2008)
9691 @url{https://www.r-project.org/doc/Rnews/Rnews_2008-2.pdf}.")
9692 (license license:gpl2+)))
9694 (define-public r-brglm
9701 (uri (cran-uri "brglm" version))
9704 "08shcz0j1npdn7xkhsvlzs3z4rdwq3g4rk6a4xx8wirqw8n8s2an"))))
9705 (properties `((upstream-name . "brglm")))
9706 (build-system r-build-system)
9708 (list r-profilemodel))
9709 (home-page "https://github.com/ikosmidis/brglm")
9710 (synopsis "Bias reduction in binomial-response generalized linear models")
9712 "Fit generalized linear models with binomial responses using either an
9713 adjusted-score approach to bias reduction or maximum penalized likelihood
9714 where penalization is by Jeffreys invariant prior. These procedures return
9715 estimates with improved frequentist properties (bias, mean squared error) that
9716 are always finite even in cases where the maximum likelihood estimates are
9717 infinite (data separation). Fitting takes place by fitting generalized linear
9718 models on iteratively updated pseudo-data. The interface is essentially the
9719 same as @code{glm}. More flexibility is provided by the fact that custom
9720 pseudo-data representations can be specified and used for model fitting.
9721 Functions are provided for the construction of confidence intervals for the
9722 reduced-bias estimates.")
9723 (license license:gpl2+)))
9725 (define-public r-entropy
9732 (uri (cran-uri "entropy" version))
9735 "1f0j8jsn6pzf4gi5g0akixx6x5vc69ci5f4m2vnwp40frvsqjnkg"))))
9736 (properties `((upstream-name . "entropy")))
9737 (build-system r-build-system)
9738 (home-page "https://www.strimmerlab.org/software/entropy/")
9739 (synopsis "Estimation of entropy, mutual information and related quantities")
9741 "This package implements various estimators of entropy, such as the
9742 shrinkage estimator by Hausser and Strimmer, the maximum likelihood and the
9743 Millow-Madow estimator, various Bayesian estimators, and the Chao-Shen
9744 estimator. It also offers an R interface to the NSB estimator. Furthermore,
9745 it provides functions for estimating Kullback-Leibler divergence, chi-squared,
9746 mutual information, and chi-squared statistic of independence. In addition
9747 there are functions for discretizing continuous random variables.")
9748 (license license:gpl3+)))
9750 (define-public r-acd
9757 (uri (cran-uri "ACD" version))
9760 "1a67bi3hklq8nlc50r0qnyr4k7m9kpvijy8sqqpm54by5hsysfd6"))))
9761 (properties `((upstream-name . "ACD")))
9762 (build-system r-build-system)
9763 (home-page "https://cran.r-project.org/web/packages/ACD/")
9764 (synopsis "Categorical data analysis with complete or missing responses")
9766 "This package provides tools for categorical data analysis with complete
9767 or missing responses.")
9768 (license license:gpl2+)))
9770 (define-public r-acdm
9777 (uri (cran-uri "ACDm" version))
9780 "0b4f02ga5ra66mbrm79g0bnlzmii82rks9kmxixxqgf18yhlyjil"))))
9781 (properties `((upstream-name . "ACDm")))
9782 (build-system r-build-system)
9784 (list r-dplyr r-ggplot2 r-plyr r-rsolnp r-zoo))
9785 (home-page "https://cran.r-project.org/web/packages/ACDm/")
9786 (synopsis "Tools for Autoregressive Conditional Duration Models")
9788 "ACDm is a package for Autoregressive Conditional Duration (ACD, Engle
9789 and Russell, 1998) models. It creates trade, price or volume durations from
9790 transactions (tic) data, performs diurnal adjustments, fits various ACD models
9792 (license license:gpl2+)))
9794 (define-public r-overlap
9801 (uri (cran-uri "overlap" version))
9804 "1arxprhz035ab78ks88n6scwnlwmnb97mlac5gsx90ipb6gkgcyk"))))
9805 (build-system r-build-system)
9806 (home-page "https://cran.r-project.org/web/packages/overlap/")
9807 (synopsis "Estimates of coefficient of overlapping for animal activity patterns")
9809 "This package provides functions to fit kernel density functions to data
9810 on temporal activity patterns of animals; estimate coefficients of overlapping
9811 of densities for two species; and calculate bootstrap estimates of confidence
9813 (license license:gpl3+)))
9815 (define-public r-snakecase
9817 (name "r-snakecase")
9822 (uri (cran-uri "snakecase" version))
9825 "1ky1x2cp5rd0ffd9m1fji9sq4z4jsrpxzg30brw8bb4ihfjj114r"))))
9826 (build-system r-build-system)
9828 (list r-stringi r-stringr))
9829 (home-page "https://github.com/Tazinho/snakecase")
9830 (synopsis "Convert strings into any case")
9832 "This package provides a consistent, flexible and easy to use tool to
9833 parse and convert strings into cases like snake or camel among others.")
9834 (license license:gpl3)))
9836 (define-public r-prediction
9838 (name "r-prediction")
9843 (uri (cran-uri "prediction" version))
9846 "0awlq5lxfia6m2b91w73rksp93rbwv5gwqb36wbji4rgq41rzbrx"))))
9847 (build-system r-build-system)
9849 (list r-data-table))
9850 (home-page "https://github.com/leeper/prediction")
9851 (synopsis "Tidy, type-safe prediction methods")
9853 "This package provides the @code{prediction()} function, a type-safe
9854 alternative to @code{predict()} that always returns a data frame. The package
9855 currently supports common model types (e.g., @code{\"lm\"}, @code{\"glm\"})
9856 from the @code{stats} package, as well as numerous other model classes from
9857 other add-on packages.")
9858 (license license:expat)))
9860 (define-public r-insight
9867 (uri (cran-uri "insight" version))
9870 "0dffrsimgijdqsgvr9cad4g4w97d5ssjl3l0fm5ssly9l115ag35"))))
9871 (build-system r-build-system)
9874 (home-page "https://easystats.github.io/insight/")
9875 (synopsis "Easy access to model information for various model objects")
9877 "This package provides a tool to provide an easy, intuitive and
9878 consistent access to information contained in various R models, like model
9879 formulas, model terms, information about random effects, data that was used to
9880 fit the model or data from response variables. The package mainly revolves
9881 around two types of functions: Functions that find (the names of) information,
9882 starting with @code{find_}, and functions that get the underlying data,
9883 starting with @code{get_}. The package has a consistent syntax and works with
9884 many different model objects, where otherwise functions to access these
9885 information are missing.")
9886 (license license:gpl3)))
9888 (define-public r-sjlabelled
9890 (name "r-sjlabelled")
9895 (uri (cran-uri "sjlabelled" version))
9898 "1va86q5wddyvqgdpy8d0an2c7v1qbb4hpn0ai6y1v5v1ff87w73k"))))
9899 (build-system r-build-system)
9901 (list r-datawizard r-insight))
9904 (home-page "https://github.com/strengejacke/sjlabelled")
9905 (synopsis "Labelled data utility functions")
9907 "This package provides a collection of functions dealing with labelled
9908 data, like reading and writing data between R and other statistical software
9909 packages. This includes easy ways to get, set or change value and variable
9910 label attributes, to convert labelled vectors into factors or numeric (and
9911 vice versa), or to deal with multiple declared missing values.")
9912 (license license:gpl3)))
9914 (define-public r-sjmisc
9921 (uri (cran-uri "sjmisc" version))
9924 "1gzkq95ckxr0vhrzggflzli9hs7zr8c0yym9zn1wf74yrr0mgc3q"))))
9925 (build-system r-build-system)
9936 (home-page "https://github.com/strengejacke/sjmisc")
9937 (synopsis "Data and variable transformation functions")
9939 "This package is a collection of miscellaneous utility functions,
9940 supporting data transformation tasks like recoding, dichotomizing or grouping
9941 variables, setting and replacing missing values. The data transformation
9942 functions also support labelled data, and all integrate seamlessly into a
9943 tidyverse workflow.")
9944 (license license:gpl3)))
9946 (define-public r-nortest
9953 (uri (cran-uri "nortest" version))
9956 "17r0wpz72z9312c70nwi1i1kp1v9fm1h6jg7q5cx1mc1h420m1d3"))))
9957 (build-system r-build-system)
9958 (home-page "https://cran.r-project.org/web/packages/nortest/")
9959 (synopsis "Tests for normality")
9961 "This package provides five omnibus tests for testing the composite
9962 hypothesis of normality.")
9963 (license license:gpl2+)))
9965 (define-public r-moonbook
9972 (uri (cran-uri "moonBook" version))
9975 "1ml4vvm0mvrprpyi0l50aw38brx18bk2qny4gybmkvlbakalz9bx"))))
9976 (properties `((upstream-name . "moonBook")))
9977 (build-system r-build-system)
9987 (home-page "https://github.com/cardiomoon/moonBook")
9988 (synopsis "Functions and datasets for the book by Keon-Woong Moon")
9990 "This package provides several analysis-related functions for the book
9991 entitled \"R statistics and graph for medical articles\" (written in Korean),
9992 version 1, by Keon-Woong Moon with Korean demographic data with several plot
9994 (license license:gpl2)))
9996 (define-public r-flextable
9998 (name "r-flextable")
10003 (uri (cran-uri "flextable" version))
10006 "15vr5lb87712mymsvv01kz9s1fb54sx5kybsa2x547k5g10dbrbm"))))
10007 (build-system r-build-system)
10021 (home-page "https://davidgohel.github.io/flextable")
10022 (synopsis "Functions for tabular reporting")
10024 "This package provides tools to create pretty tables for HTML documents
10025 and other formats. Functions are provided to let users create tables, modify
10026 and format their content. It extends the @code{officer} package and can be
10027 used within R markdown documents when rendering to HTML and to Word
10029 (license license:gpl3)))
10031 (define-public r-writexl
10038 (uri (cran-uri "writexl" version))
10041 "0mfzyn8n5x5x5gf382bqgq61zpw9dymrp5kzdm2sbszplmxf6xry"))))
10042 (build-system r-build-system)
10043 (inputs (list zlib))
10044 (home-page "https://github.com/ropensci/writexl")
10045 (synopsis "Export data frames to xlsx format")
10047 "This package provides a data frame to xlsx exporter based on
10049 (license license:bsd-2)))
10051 (define-public r-biasedurn
10053 (name "r-biasedurn")
10058 (uri (cran-uri "BiasedUrn" version))
10061 "13i2lgfnjhlbbm2yxfc2l5hswqw6x03pwba5csjmirv8kpjw4xr3"))))
10062 (properties `((upstream-name . "BiasedUrn")))
10063 (build-system r-build-system)
10064 (home-page "https://cran.r-project.org/web/packages/BiasedUrn/")
10065 (synopsis "Biased Urn model distributions")
10067 "This package provides statistical models of biased sampling in the form
10068 of univariate and multivariate noncentral hypergeometric distributions,
10069 including Wallenius' noncentral hypergeometric distribution and Fisher's
10070 noncentral hypergeometric distribution (also called extended hypergeometric
10072 (license license:gpl3)))
10074 (define-public r-goplot
10081 (uri (cran-uri "GOplot" version))
10084 "1y8dv0kbzpr9za91njw0x233vx5d13vqml9hmpddcyi9s6va5nix"))))
10085 (properties `((upstream-name . "GOplot")))
10086 (build-system r-build-system)
10088 (list r-ggdendro r-ggplot2 r-gridextra r-rcolorbrewer))
10089 (home-page "https://github.com/wencke/wencke.github.io")
10090 (synopsis "Visualization of functional analysis data")
10092 "This package provides an implementation of multilayered visualizations
10093 for enhanced graphical representation of functional analysis data. It
10094 combines and integrates omics data derived from expression and functional
10095 annotation enrichment analyses. Its plotting functions have been developed
10096 with an hierarchical structure in mind: starting from a general overview to
10097 identify the most enriched categories (modified bar plot, bubble plot) to a
10098 more detailed one displaying different types of relevant information for the
10099 molecules in a given set of categories (circle plot, chord plot, cluster plot,
10100 Venn diagram, heatmap).")
10101 (license license:gpl2)))
10103 (define-public r-getopt
10110 (uri (cran-uri "getopt" version))
10113 "0zzmzgwl9a4y3s34600vmih22d6y32294f9bvxrnmffnvkgmy7sk"))))
10114 (build-system r-build-system)
10115 (home-page "https://github.com/trevorld/getopt")
10116 (synopsis "Command-line option processor for R")
10118 "This package is designed to be used with Rscript to write shebang
10119 scripts that accept short and long options. Many users will prefer to
10120 use the packages @code{optparse} or @code{argparse} which add extra
10121 features like automatically generated help options and usage texts,
10122 support for default values, positional argument support, etc.")
10123 (license license:gpl2+)))
10125 (define-public r-findpython
10127 (name "r-findpython")
10132 (uri (cran-uri "findpython" version))
10135 "0jf10jpqla90x03kl3k77gnd255zmw9rvr8d724vb17cqawh9yar"))))
10136 (build-system r-build-system)
10137 (home-page "https://github.com/trevorld/findpython")
10138 (synopsis "Functions to find an acceptable Python binary")
10140 "This package was designed to find an acceptable Python binary that
10141 matches version and feature constraints.")
10142 (license license:expat)))
10144 ;; This in not the same as "r-argparser"
10145 (define-public r-argparse
10147 (name "r-argparse")
10152 (uri (cran-uri "argparse" version))
10155 "13b5halfxc7nr57vkz3qmkkcpw1hr4xdk1mjh2cq8cvpnjz15qc3"))))
10156 (build-system r-build-system)
10157 (inputs (list python))
10159 (list r-findpython r-jsonlite r-r6))
10162 (home-page "https://github.com/trevorld/argparse")
10163 (synopsis "Command line optional and positional argument parser")
10165 "This package provides a command line parser to be used with Rscript to
10166 write shebang scripts that gracefully accept positional and optional arguments
10167 and automatically generate usage notices.")
10168 (license license:gpl2+)))
10170 (define-public r-hash
10173 (version "2.2.6.2")
10177 (uri (cran-uri "hash" version))
10180 "17scs675a86c34hjbxmwi8kny4yyv97x3515s449zafj2i0ad8vm"))))
10181 (build-system r-build-system)
10182 (home-page "https://cran.r-project.org/web/packages/hash/")
10183 (synopsis "Implementation of hash/associated arrays/dictionaries")
10185 "This package implements a data structure similar to hashes in Perl and
10186 dictionaries in Python but with a purposefully R flavor. For objects of
10187 appreciable size, access using hashes outperforms native named lists and
10189 (license license:gpl2+)))
10191 (define-public r-orddom
10198 (uri (cran-uri "orddom" version))
10201 "165axs15fvwhrp89xd87l81q3h2qjll1vrwcsap645cwvb85nwsh"))))
10202 (build-system r-build-system)
10203 (propagated-inputs (list r-psych))
10204 (home-page "https://cran.r-project.org/web/packages/orddom/")
10205 (synopsis "Ordinal dominance statistics")
10207 "This package provides tools to compute ordinal, statistics and effect
10208 sizes as an alternative to mean comparison: Cliff's delta or success rate
10209 difference (SRD), Vargha and Delaney's A or the Area Under a Receiver
10210 Operating Characteristic Curve (AUC), the discrete type of McGraw & Wong's
10211 Common Language Effect Size (CLES) or Grissom & Kim's Probability of
10212 Superiority (PS), and the Number needed to treat (NNT) effect size. Moreover,
10213 comparisons to Cohen's d are offered based on Huberty & Lowman's Percentage of
10214 Group (Non-)Overlap considerations.")
10215 (license license:gpl2)))
10217 (define-public r-deriv
10224 (uri (cran-uri "Deriv" version))
10227 "130g3mv0z9sqs6y23a0a94512iiw05yr6fp378vhdxxbignzbnyv"))))
10228 (properties `((upstream-name . "Deriv")))
10229 (build-system r-build-system)
10230 (home-page "https://cran.r-project.org/web/packages/Deriv")
10231 (synopsis "Symbolic differentiation")
10233 "This package provides an R-based solution for symbolic differentiation.
10234 It admits user-defined functions as well as function substitution in arguments
10235 of functions to be differentiated. Some symbolic simplification is part of
10237 (license license:gpl3+)))
10239 (define-public r-doby
10246 (uri (cran-uri "doBy" version))
10249 "0qnfcw4rg5kd1mll3rq6vchz3lgdqfif9469p8x6ixsgrxxpivbz"))))
10250 (properties `((upstream-name . "doBy")))
10251 (build-system r-build-system)
10265 (home-page "https://people.math.aau.dk/~sorenh/software/doBy/")
10266 (synopsis "Groupwise statistics, LSmeans, linear contrasts, and utilities")
10268 "This package contains:
10271 @item facilities for working with grouped data: @code{do}
10272 something to data stratified @code{by} some variables.
10273 @item implementations of least-squares means, general linear contrasts, and
10274 @item miscellaneous other utilities.
10276 (license license:gpl2+)))
10278 (define-public r-refgenome
10280 (name "r-refgenome")
10285 (uri (cran-uri "refGenome" version))
10288 "1za89bn3am1zgvm641qi1ab6kaqpll4rb9p9f1sjwvcgqq6065g5"))))
10289 (properties `((upstream-name . "refGenome")))
10290 (build-system r-build-system)
10292 (list r-dbi r-doby r-rsqlite))
10293 (home-page "https://cran.r-project.org/web/packages/refGenome/")
10295 "Gene and splice site annotation using annotation data from Ensembl and UCSC")
10297 "This package contains functionality for importing and managing of
10298 downloaded genome annotation data from the Ensembl genome browser (European
10299 Bioinformatics Institute) and from the UCSC genome browser (University of
10300 California, Santa Cruz) and annotation routines for genomic positions and
10301 splice site positions.")
10302 (license license:gpl2)))
10304 (define-public r-basix
10311 (uri (cran-uri "BASIX" version))
10314 "18dkvv1iwskfnlpl6xridcgqpalbbpm2616mvc3hfrc0b26v01id"))))
10315 (properties `((upstream-name . "BASIX")))
10316 (build-system r-build-system)
10317 (home-page "https://cran.r-project.org/web/packages/BASIX/")
10318 (synopsis "Efficient C/C++ toolset for R")
10320 "BASIX provides some efficient C/C++ implementations of native R
10321 procedures to speed up calculations in R.")
10322 (license license:gpl2)))
10324 (define-public r-blockfest
10326 (name "r-blockfest")
10331 (uri (cran-uri "BlockFeST" version))
10334 "1fcl3yc1cf09znqbj787d3fd2kl5rp63la7pxawsgmap7nxwkp65"))))
10335 (properties `((upstream-name . "BlockFeST")))
10336 (build-system r-build-system)
10337 (propagated-inputs (list r-basix))
10338 (home-page "https://cran.r-project.org/web/packages/BlockFeST/")
10339 (synopsis "Bayesian calculation of region-specific fixation index")
10341 "This package provides an R implementation of an extension of the
10342 BayeScan software for codominant markers, adding the option to group
10343 individual SNPs into pre-defined blocks. A typical application of this new
10344 approach is the identification of genomic regions, genes, or gene sets
10345 containing one or more SNPs that evolved under directional selection.")
10346 (license license:gpl2)))
10348 (define-public r-proc
10355 (uri (cran-uri "pROC" version))
10358 "1abvbzdss12n64pp9vlgnn0q3abh0nj4n0a8cinwwvhphjrm9vym"))))
10359 (properties `((upstream-name . "pROC")))
10360 (build-system r-build-system)
10362 (list r-plyr r-rcpp))
10363 (home-page "https://web.expasy.org/pROC/")
10364 (synopsis "Display and analyze ROC curves")
10366 "This package provides tools for visualizing, smoothing and comparing
10367 receiver operating characteristic (ROC curves). The area under the
10368 curve (AUC) can be compared with statistical tests based on U-statistics or
10369 bootstrap. Confidence intervals can be computed for (p)AUC or ROC curves.")
10370 (license license:gpl3+)))
10372 (define-public r-rootsolve
10374 (name "r-rootsolve")
10375 (version "1.8.2.3")
10379 (uri (cran-uri "rootSolve" version))
10382 "182bb727sgqi5f3pzmw8jnn328wdjrgj9lfvg49gv8s22rjd3cxm"))))
10383 (properties `((upstream-name . "rootSolve")))
10384 (build-system r-build-system)
10385 (native-inputs (list gfortran))
10386 (home-page "https://cran.r-project.org/web/packages/rootSolve/")
10387 (synopsis "Tools for the analysis of ordinary differential equations")
10389 "This package provides routines to find the root of nonlinear functions,
10390 and to perform steady-state and equilibrium analysis of @dfn{ordinary
10391 differential equations} (ODE). It includes routines that:
10394 @item generate gradient and jacobian matrices (full and banded),
10395 @item find roots of non-linear equations by the Newton-Raphson method,
10396 @item estimate steady-state conditions of a system of (differential) equations
10397 in full, banded or sparse form, using the Newton-Raphson method, or by
10398 dynamically running,
10399 @item solve the steady-state conditions for uni- and multicomponent 1-D, 2-D,
10400 and 3-D partial differential equations, that have been converted to ordinary
10401 differential equations by numerical differencing (using the method-of-lines
10404 (license license:gpl2+)))
10406 (define-public r-abcanalysis
10408 (name "r-abcanalysis")
10413 (uri (cran-uri "ABCanalysis" version))
10415 (base32 "0wac1ksmnxa36v99ca4hv8k0rsh3igwpcllmlv9wf7i9kgqviqwi"))))
10416 (properties `((upstream-name . "ABCanalysis")))
10417 (build-system r-build-system)
10418 (propagated-inputs (list r-plotrix))
10419 (home-page "https://www.uni-marburg.de/fb12/arbeitsgruppen/datenbionik/software-en/")
10420 (synopsis "Computed ABC Analysis")
10422 "Multivariate data sets often differ in several factors or derived statistical
10423 parameters, which have to be selected for a valid interpretation. Basing this
10424 selection on traditional statistical limits leads occasionally to the perception
10425 of losing information from a data set. This package provides tools to calculate
10426 these limits on the basis of the mathematical properties of the distribution of
10427 the analyzed items.")
10428 (license license:gpl3)))
10430 (define-public r-slam
10437 (uri (cran-uri "slam" version))
10439 (base32 "1ggqcf8l1z2hpi7qy4mg0d2ps48bjjb8z1y1xz6fq162cqrbz6bq"))))
10440 (build-system r-build-system)
10441 (home-page "https://cran.r-project.org/web/packages/slam/")
10442 (synopsis "Sparse lightweight arrays and matrices")
10444 "This package contains data structures and algorithms for sparse arrays and matrices,
10445 based on index arrays and simple triplet representations, respectively.")
10446 (license license:gpl2)))
10448 (define-public r-manipulatewidget
10450 (name "r-manipulatewidget")
10455 (uri (cran-uri "manipulateWidget" version))
10457 (base32 "1dpgzmiv08afm57yxr017b014lfn9h3pa4w65prk5k3dgn6p4wsv"))))
10459 `((upstream-name . "manipulateWidget")))
10460 (build-system r-build-system)
10473 (home-page "https://github.com/rte-antares-rpackage/manipulateWidget/")
10474 (synopsis "Add even more interactivity to interactive charts")
10476 "This package lets you create in just a few lines of R code a nice user interface to
10477 modify the data or the graphical parameters of one or multiple interactive
10478 charts. It is useful to quickly explore visually some data or for package
10479 developers to generate user interfaces easy to maintain.")
10480 (license license:gpl2+)))
10482 (define-public r-a3
10489 (uri (cran-uri "A3" version))
10491 (base32 "017hq9pjsv1h9i7cqk5cfx27as54shlhdsdvr6jkhb8jfkpdb6cw"))))
10492 (properties `((upstream-name . "A3")))
10493 (build-system r-build-system)
10495 (list r-pbapply r-xtable))
10496 (home-page "https://cran.r-project.org/web/packages/A3/")
10497 (synopsis "Error metrics for predictive models")
10499 "This package supplies tools for tabulating and analyzing the results of predictive
10500 models. The methods employed are applicable to virtually any predictive model
10501 and make comparisons between different methodologies straightforward.")
10502 (license license:gpl2+)))
10504 (define-public r-infotheo
10506 (name "r-infotheo")
10507 (version "1.2.0.1")
10511 (uri (cran-uri "infotheo" version))
10514 "1m1979vf8rvq3534mp1hihfadikhxrg3p6ac3hirz96kgb4qxyy0"))))
10515 (build-system r-build-system)
10516 (home-page "http://homepage.meyerp.com/software")
10517 (synopsis "Information-theoretic measures")
10519 "This package implements various measures of information theory based on
10520 several entropy estimators.")
10521 (license license:gpl3+)))
10523 (define-public r-nsprcomp
10525 (name "r-nsprcomp")
10526 (version "0.5.1-2")
10530 (uri (cran-uri "nsprcomp" version))
10533 "1zlc1ximx96f235c0l8qfs6vbp1kpnbf943wxsfahnnlnxvwi59f"))))
10534 (properties `((upstream-name . "nsprcomp")))
10535 (build-system r-build-system)
10536 (home-page "https://sigg-iten.ch/research/")
10537 (synopsis "Non-negative and sparse PCA")
10539 "This package implements two methods for performing a constrained
10540 principal component analysis (PCA), where non-negativity and/or sparsity
10541 constraints are enforced on the principal axes (PAs). The function
10542 @code{nsprcomp} computes one principal component (PC) after the other. Each
10543 PA is optimized such that the corresponding PC has maximum additional variance
10544 not explained by the previous components. In contrast, the function
10545 @code{nscumcomp} jointly computes all PCs such that the cumulative variance is
10546 maximal. Both functions have the same interface as the @code{prcomp} function
10547 from the @code{stats} package (plus some extra parameters).")
10548 (license license:gpl2+)))
10550 (define-public r-cmplot
10557 (uri (cran-uri "CMplot" version))
10560 "1h09prpiw7l32mr7jarp8ddrddg1431nfn4kw3bznfnv0sr78zfg"))))
10561 (properties `((upstream-name . "CMplot")))
10562 (build-system r-build-system)
10563 (home-page "https://github.com/YinLiLin/CMplot")
10564 (synopsis "Circle Manhattan plot")
10566 "Circle Manhattan Plot is an R package that can lay out genome-wide
10567 association study P-value results in both traditional rectangular patterns,
10568 QQ-plot and novel circular ones. United in only one bull's eye style plot,
10569 association results from multiple traits can be compared interactively,
10570 thereby to reveal both similarities and differences between signals.
10571 Additional functions include: highlight signals, a group of SNPs, chromosome
10572 visualization and candidate genes around SNPs.")
10573 (license license:gpl2+)))
10575 (define-public r-precrec
10582 (uri (cran-uri "precrec" version))
10585 "1dfz2rqx2ww2l5r40ahg0qdj3rjrwiwh427mw7j5ynhpcj21j2qm"))))
10586 (properties `((upstream-name . "precrec")))
10587 (build-system r-build-system)
10595 (native-inputs (list r-knitr))
10596 (home-page "https://evalclass.github.io/precrec/")
10597 (synopsis "Calculate accurate precision-recall and ROC curves")
10599 "This package provides tools for accurate calculations and visualization
10600 of precision-recall and ROC (Receiver Operator Characteristics) curves.")
10601 (license license:gpl3)))
10603 (define-public r-netrep
10610 (uri (cran-uri "NetRep" version))
10613 "1swlb2k9bc7whvslxbklz864j9ynvna73hvq5rhv61cv5vy05ksd"))))
10614 (properties `((upstream-name . "NetRep")))
10615 (build-system r-build-system)
10625 (native-inputs (list r-knitr))
10626 (home-page "https://cran.r-project.org/package=NetRep")
10627 (synopsis "Permutation testing network module preservation across datasets")
10629 "This package provides functions for assessing the
10630 replication/preservation of a network module's topology across datasets
10631 through permutation testing.")
10632 (license license:gpl2)))
10634 (define-public r-intergraph
10636 (name "r-intergraph")
10641 (uri (cran-uri "intergraph" version))
10644 "18a7xgb2rp0w9jl2rkh8nzyjprrs5w7h2iidvc8c38bzx3qpggkc"))))
10645 (properties `((upstream-name . "intergraph")))
10646 (build-system r-build-system)
10648 (list r-igraph r-network))
10651 (home-page "http://mbojan.github.io/intergraph")
10652 (synopsis "Coercion routines for network data objects")
10654 "Functions implemented in this package allow coercing (i.e. convert)
10655 network data between classes provided by other R packages. Currently
10656 supported classes are those defined in packages @code{network} and
10658 (license license:gpl3)))
10660 (define-public r-abcoptim
10662 (name "r-abcoptim")
10667 (uri (cran-uri "ABCoptim" version))
10669 (base32 "1ih0xk88qhsmpvnxf56041wx5sk8as2f4f2gdnpnwdym9mbr9n4b"))))
10670 (properties `((upstream-name . "ABCoptim")))
10671 (build-system r-build-system)
10672 (propagated-inputs (list r-rcpp))
10673 (home-page "https://github.com/gvegayon/ABCoptim/")
10674 (synopsis "Optimization of Artificial Bee Colony algorithm")
10676 "Artificial Bee Colony (ABC) is one of the most recently defined algorithms by Dervis
10677 Karaboga in 2005, motivated by the intelligent behavior of honey bees. It is as
10678 simple as Particle Swarm Optimization (PSO) and Differential Evolution (DE)
10679 algorithms, and uses only common control parameters such as colony size and
10680 maximum cycle number. The @code{r-abcoptim} implements the Artificial bee
10681 colony optimization algorithm @url{http://mf.erciyes.edu.tr/abc/pub/tr06_2005.pdf}.
10682 This version is a work-in-progress and is written in R code.")
10683 (license license:expat)))
10685 (define-public r-abcp2
10692 (uri (cran-uri "ABCp2" version))
10694 (base32 "1s2skkxpzss7c29i8600psgrp0hl46jcrxqrmy2b4db8hc0kcnbx"))))
10695 (properties `((upstream-name . "ABCp2")))
10696 (build-system r-build-system)
10697 (propagated-inputs (list r-mass))
10698 (home-page "https://cran.r-project.org/web/packages/ABCp2/")
10699 (synopsis "Approximate Bayesian Computational Model for Estimating P2")
10701 "This package tests the goodness of fit of a distribution of offspring to the Normal,
10702 Poisson, and Gamma distribution and estimates the proportional paternity of the
10703 second male (P2) based on the best fit distribution.")
10704 (license license:gpl2)))
10706 (define-public r-abcrf
10713 (uri (cran-uri "abcrf" version))
10715 (base32 "1ghbd24yhqy3xhdxas6ccn84nkavqpgldx5ck8kijknc7qjm8k27"))))
10716 (build-system r-build-system)
10727 (home-page "https://cran.r-project.org/web/packages/abcrf/")
10728 (synopsis "Approximate bayesian computation via random forests")
10730 "This package performs approximate bayesian computation (ABC) model choice and
10731 parameter inference via random forests. This machine learning tool named random
10732 forests (RF) can conduct selection among the highly complex models covered by
10734 (license license:gpl2+)))
10736 (define-public r-abctools
10738 (name "r-abctools")
10743 (uri (cran-uri "abctools" version))
10745 (base32 "07s9dg10i8lsxl73b4n2hynca2fjgb0ykb0dz8c3zv6cgw3cyx97"))))
10746 (build-system r-build-system)
10748 (list r-abc r-abind r-hmisc r-plyr))
10749 (home-page "https://github.com/dennisprangle/abctools/")
10750 (synopsis "Tools for ABC analyses")
10752 "This @code{r-abctools} package provides tools for approximate Bayesian computation
10753 including summary statistic selection and assessing coverage. This includes
10754 recent dimension reduction algorithms to tune the choice of summary statistics,
10755 and coverage methods to tune the choice of threshold.")
10756 (license license:gpl2+)))
10758 (define-public r-ggstance
10760 (name "r-ggstance")
10765 (uri (cran-uri "ggstance" version))
10767 (base32 "0jz9vvnmcc6a38n8nzr458r65sna23bgn5r8mxdhzdlyqibihr7d"))))
10768 (build-system r-build-system)
10770 (list r-ggplot2 r-plyr r-rlang r-withr))
10771 (home-page "https://cran.r-project.org/web/packages/ggstance/")
10772 (synopsis "Horizontal and vertical versions of @code{r-ggplot2}")
10774 "This package is a @code{r-ggplot2} extension that provides flipped components:
10776 @item horizontal versions of @code{r-ggplot2} stats and @code{r-ggplot2} geoms;
10777 @item vertical versions of @code{r-ggplot2} positions.
10779 (license license:gpl3)))
10781 (define-public r-ggnetwork
10783 (name "r-ggnetwork")
10788 (uri (cran-uri "ggnetwork" version))
10791 "0gqdgy5yh700dg0f7xb80hczlnqfisn8l55j7amd1n7fp2x5sr8v"))))
10792 (properties `((upstream-name . "ggnetwork")))
10793 (build-system r-build-system)
10795 (list r-ggplot2 r-ggrepel r-igraph r-network r-sna))
10796 (native-inputs (list r-knitr))
10797 (home-page "https://github.com/briatte/ggnetwork")
10798 (synopsis "Geometries to plot networks with ggplot2")
10800 "This package provides geometries to plot network objects with the
10802 (license license:gpl3)))
10804 (define-public r-cvauc
10811 (uri (cran-uri "cvAUC" version))
10814 "1m2y50a1yapf1c74km9a4r47ds2z2bfp4wwwkqin7swv9v1s7d28"))))
10815 (properties `((upstream-name . "cvAUC")))
10816 (build-system r-build-system)
10818 (list r-data-table r-rocr))
10819 (home-page "https://github.com/ledell/cvAUC")
10820 (synopsis "Cross-validated area under the ROC curve confidence intervals")
10822 "This package contains various tools for working with and evaluating
10823 cross-validated area under the ROC curve (AUC) estimators. The primary
10824 functions of the package are @code{ci.cvAUC} and @code{ci.pooled.cvAUC}, which
10825 report cross-validated AUC and compute confidence intervals for
10826 cross-validated AUC estimates based on influence curves for i.i.d. and pooled
10827 repeated measures data, respectively.")
10828 (license license:asl2.0)))
10830 (define-public r-gam
10837 (uri (cran-uri "gam" version))
10840 "1bbxiqfgi7jc9vw1hspw5q41d69nlw2v6k91zqlvmam5pvxcd1sp"))))
10841 (properties `((upstream-name . "gam")))
10842 (build-system r-build-system)
10847 (home-page "https://cran.r-project.org/package=gam")
10848 (synopsis "Generalized additive models")
10850 "This package provides functions for fitting and working with generalized
10851 additive models, as described in chapter 7 of \"Statistical Models in
10852 S\" (Chambers and Hastie (eds), 1991), and \"Generalized Additive
10853 Models\" (Hastie and Tibshirani, 1990).")
10854 (license license:gpl2)))
10856 (define-public r-superlearner
10858 (name "r-superlearner")
10863 (uri (cran-uri "SuperLearner" version))
10866 "00any24msgflyagy87nznpfjz5g9v15frqda6c679wa8plx26hjz"))))
10867 (properties `((upstream-name . "SuperLearner")))
10868 (build-system r-build-system)
10870 (list r-cvauc r-gam r-nnls))
10873 (home-page "https://github.com/ecpolley/SuperLearner")
10874 (synopsis "Super learner prediction")
10876 "This package implements the super learner prediction method and contains
10877 a library of prediction algorithms to be used in the super learner.")
10878 (license license:gpl3)))
10880 (define-public r-drtmle
10887 (uri (cran-uri "drtmle" version))
10890 "12vplpz9bg5444jy29mbdr70hqby073vb3iw76v2csrwy3ws3f21"))))
10891 (properties `((upstream-name . "drtmle")))
10892 (build-system r-build-system)
10894 (list r-future-apply r-np r-superlearner))
10897 (home-page "https://github.com/benkeser/drtmle")
10898 (synopsis "Doubly-robust nonparametric estimation and inference")
10900 "This package implements targeted minimum loss-based estimators of
10901 counterfactual means and causal effects that are doubly-robust with respect
10902 both to consistency and asymptotic normality.")
10903 (license license:expat)))
10905 (define-public r-dofuture
10907 (name "r-dofuture")
10912 (uri (cran-uri "doFuture" version))
10915 "0w07pmzpsfq4kvfc745s1i9b6dfn1df1wrfi4s9ys4ir3g2s8nk1"))))
10916 (properties `((upstream-name . "doFuture")))
10917 (build-system r-build-system)
10920 (modify-phases %standard-phases
10921 (add-after 'unpack 'set-HOME
10922 (lambda _ (setenv "HOME" "/tmp"))))))
10924 (list r-foreach r-future r-globals r-iterators))
10926 (list r-r-rsp)) ; vignette builder
10927 (home-page "https://github.com/HenrikBengtsson/doFuture")
10928 (synopsis "Foreach parallel adapter using the future API")
10930 "This package provides a @code{%dopar%} adapter such that any type of
10931 futures can be used as backends for the @code{foreach} framework.")
10932 (license license:lgpl2.1+)))
10934 (define-public r-superheat
10936 (name "r-superheat")
10941 (uri (cran-uri "superheat" version))
10944 "01v8s6px1k5fajlm6py3ksr1i853kwwlky1yryzhy3p1cxhwgg83"))))
10945 (properties `((upstream-name . "superheat")))
10946 (build-system r-build-system)
10955 (home-page "https://cran.r-project.org/package=superheat")
10956 (synopsis "Graphical tool for exploring complex datasets using heatmaps")
10958 "This package provides a system for generating extendable and
10959 customizable heatmaps for exploring complex datasets, including big data and
10960 data with multiple data types.")
10961 (license license:cc0)))
10963 (define-public r-qualv
10970 (uri (cran-uri "qualV" version))
10973 "0rkjzva2h158d5c631jmjjh7qjibbyisl0503san80rk9fgxl45b"))))
10974 (properties `((upstream-name . "qualV")))
10975 (build-system r-build-system)
10977 (list r-kernsmooth))
10978 (home-page "http://qualV.R-Forge.R-Project.org/")
10979 (synopsis "Qualitative Validation Methods")
10981 "This package provides qualitative methods for the validation of dynamic
10982 models. It contains
10985 @item an orthogonal set of deviance measures for absolute, relative and
10987 @item approaches accounting for time shifts.
10990 The first approach transforms time to take time delays and speed differences
10991 into account. The second divides the time series into interval units
10992 according to their main features and finds the @dfn{longest common
10993 subsequence} (LCS) using a dynamic programming algorithm.")
10994 (license license:gpl2+)))
10996 (define-public r-mosaiccore
10998 (name "r-mosaiccore")
11003 (uri (cran-uri "mosaicCore" version))
11005 (base32 "1h3ixzna4xy42rdnd89jj0v9q0riy3fnkd33z6l5c0zaidzm58fz"))))
11006 (properties `((upstream-name . "mosaicCore")))
11007 (build-system r-build-system)
11009 (list r-dplyr r-mass r-rlang r-tidyr))
11010 (home-page "https://github.com/ProjectMOSAIC/mosaicCore/")
11011 (synopsis "Common utilities for mosaic family packages")
11013 "Common utilities used in other Mosaic family packages are collected here.")
11014 (license license:gpl2+)))
11016 (define-public r-labelled
11018 (name "r-labelled")
11023 (uri (cran-uri "labelled" version))
11026 "0h7scbyzh7kr51gds222rkhld2b3k36s86hj8rrzpwv4bwj0pccy"))))
11027 (properties `((upstream-name . "labelled")))
11028 (build-system r-build-system)
11039 (home-page "http://larmarange.github.io/labelled/")
11040 (synopsis "Manipulating labelled data")
11042 "This package provides useful functions to deal with the
11043 @code{haven_labelled} and @code{haven_labelled_spss} classes introduced by the
11045 (license license:gpl3)))
11047 (define-public r-ggformula
11049 (name "r-ggformula")
11054 (uri (cran-uri "ggformula" version))
11056 (base32 "1ph5jd8svk8hmshi894vmmpq3zwgdmf4yn3gmdlkad68z8jynhsp"))))
11057 (build-system r-build-system)
11072 (home-page "https://github.com/ProjectMOSAIC/ggformula/")
11073 (synopsis "Formula interface for the @code{r-ggplot2}")
11075 "The @code{r-ggformula} introduces a family of graphics functions, gf_point(),
11076 gf_density(), and so on, bring the formula interface to ggplot(). This captures
11077 and extends the excellent simplicity of the lattice-graphics formula interface,
11078 while providing the intuitive capabilities of @code{r-ggplot2}.")
11079 (license license:expat)))
11081 (define-public r-mosaicdata
11083 (name "r-mosaicdata")
11088 (uri (cran-uri "mosaicData" version))
11090 (base32 "0h3f5fgzkzjfgf3ml0qa5j52921y6wy6jgggxmhs31bs8fd4srg4"))))
11091 (properties `((upstream-name . "mosaicData")))
11092 (build-system r-build-system)
11093 (home-page "https://cran.r-project.org/web/packages/mosaicData/")
11094 (synopsis "Data sets for project Mosaic")
11096 "This package provides data sets from project Mosaic @url{http://mosaic-web.org}
11097 used to teach mathematics, statistics, computation and modeling.")
11098 (license license:gpl2+)))
11100 (define-public r-raster
11107 (uri (cran-uri "raster" version))
11110 "11fnznymwavpph733dayklhcx4phpjgrijfxlaszi122sg2x7ir9"))))
11111 (build-system r-build-system)
11113 (list r-rcpp r-sp r-terra))
11114 (home-page "https://www.rspatial.org/")
11115 (synopsis "Geographic data analysis and modeling")
11117 "The package implements basic and high-level functions for reading,
11118 writing, manipulating, analyzing and modeling of gridded spatial data.
11119 Processing of very large files is supported.")
11120 (license license:gpl3+)))
11122 (define-public r-mosaic
11129 (uri (cran-uri "mosaic" version))
11131 (base32 "1y0isqbva0vi5zlx1xvixbq87n4xp66ljh43qnd0cpzaz0mn21cg"))))
11132 (build-system r-build-system)
11156 (home-page "https://github.com/ProjectMOSAIC/mosaic/")
11157 (synopsis "Mathematics, statistics, and computation teaching utilities")
11159 "This package contain data sets and utilities from
11160 @url{http://mosaic-web.org, Project MOSAIC} used to teach mathematics,
11161 statistics, computation and modeling. Project MOSAIC is a community of
11162 educators working to tie together aspects of quantitative work that students
11163 in science, technology, engineering and mathematics will need in their
11164 professional lives, but which are usually taught in isolation, if at all.")
11165 (license license:gpl2+)))
11167 (define-public r-abd
11174 (uri (cran-uri "abd" version))
11176 (base32 "191gspqzdv573vaw624ri0f5cm6v4j524bjs74d4a1hn3kn6r9b7"))))
11177 (build-system r-build-system)
11179 (list r-lattice r-mosaic r-nlme))
11180 (home-page "https://cran.r-project.org/web/packages/abd/")
11181 (synopsis "Analysis of biological data")
11183 "The @code{r-abd} package contains data sets and sample code for the Analysis of
11184 biological data by Michael Whitlock and Dolph Schluter.")
11185 (license license:gpl2)))
11187 (define-public r-svgui
11194 (uri (cran-uri "svGUI" version))
11196 (base32 "0ch5gdfk834xj9w3vxpm3x4770fz3nnlyn8b0jsw9f3n2as7g979"))))
11197 (properties `((upstream-name . "svGUI")))
11198 (build-system r-build-system)
11201 (home-page "https://github.com/SciViews/svGUI/")
11202 (synopsis "Functions for managing GUI clients in R")
11204 "The SciViews @code{svGUI} package eases the management of Graphical User
11205 Interfaces (GUI) in R. It is independent from any particular GUI widgets. It
11206 centralizes info about GUI elements currently used, and it dispatches GUI
11207 calls to the particular toolkits in use in function of the context.")
11208 (license license:gpl2)))
11210 (define-public r-svdialogs
11212 (name "r-svdialogs")
11217 (uri (cran-uri "svDialogs" version))
11219 (base32 "0z3a5glsi0ab43mdk2yvslxyzg12nbqqqc35jvgzj475mpkbgjif"))))
11220 (properties `((upstream-name . "svDialogs")))
11221 (build-system r-build-system)
11225 (list r-rstudioapi r-svgui))
11228 (home-page "https://github.com/SciViews/svDialogs/")
11229 (synopsis "Portable dialog boxes")
11231 "This package helps to construct standard dialog boxes for your GUI, including
11232 message boxes, input boxes, list, file or directory selection, and others. In
11233 case R cannot display GUI dialog boxes, a simpler command line version of these
11234 interactive elements is also provided as a fallback solution.")
11235 (license license:gpl2)))
11237 (define-public r-abe
11244 (uri (cran-uri "abe" version))
11247 "1f19h3xzzmjhvwc1rrb8z0rai3ip03y4gdi2gg9bfr5sg2nfklk6"))))
11248 (build-system r-build-system)
11249 (home-page "https://cran.r-project.org/web/packages/abe/")
11250 (synopsis "Augmented backward elimination")
11252 "This package performs augmented backward elimination and checks the
11253 stability of the obtained model. Augmented backward elimination combines
11254 significance or information based criteria with the change in estimate to
11255 either select the optimal model for prediction purposes or to serve as a tool
11256 to obtain a practically sound, highly interpretable model.")
11257 (license license:gpl2+)))
11259 (define-public r-abf2
11266 (uri (cran-uri "abf2" version))
11268 (base32 "0d65mc1w4pbiv7xaqzdlw1bfsxf25587rv597hh41vs0j0zlfpxx"))))
11269 (build-system r-build-system)
11270 (home-page "https://cran.r-project.org/web/packages/abf2/")
11271 (synopsis "Load gap-free axon @code{r-abf2} files")
11273 "This package loads electrophysiology data from ABF2 files, as created by
11274 Axon Instruments/Molecular Devices software. Only files recorded in gap-free
11275 mode are currently supported.")
11276 (license license:artistic2.0)))
11278 (define-public r-abhgenotyper
11280 (name "r-abhgenotyper")
11285 (uri (cran-uri "ABHgenotypeR" version))
11287 (base32 "08cpmnaaxsm5c5bjifnfxdlvg5inrf13biqpcl2yq5zpqjmiki0l"))))
11288 (properties `((upstream-name . "ABHgenotypeR")))
11289 (build-system r-build-system)
11291 (list r-ggplot2 r-reshape2))
11292 (home-page "https://github.com/StefanReuscher/ABHgenotypeR/")
11293 (synopsis "Visualize and manipulate ABH genotypes")
11295 "The @code{r-abhgenotyper} package provides simple imputation,
11296 error-correction and plotting capacities for genotype data. The package is
11297 supposed to serve as an intermediate but independent analysis tool between the
11298 TASSEL GBS pipeline and the @code{r-qtl} package. It provides functionalities
11299 not found in either TASSEL or @code{r-qtl} in addition to visualization of
11300 genotypes as \"graphical genotypes\".")
11301 (license license:gpl3)))
11303 (define-public r-furrr
11310 (uri (cran-uri "furrr" version))
11313 "117xj66l14r08macwghgyibzm282ljv1afpa133h952gc70irs9z"))))
11314 (build-system r-build-system)
11322 (home-page "https://github.com/DavisVaughan/furrr")
11323 (synopsis "Apply mapping functions in parallel using futures")
11325 "This package provides implementations of the family of @code{map()}
11326 functions from the @code{purrr} package that can be resolved using any
11327 @code{future}-supported backend, e.g. parallel on the local machine or
11328 distributed on a compute cluster.")
11329 (license license:lgpl2.1+)))
11331 (define-public r-abjutils
11333 (name "r-abjutils")
11338 (uri (cran-uri "abjutils" version))
11340 (base32 "0lmf4va8qnzwg698i2h4fcwvd6dhsgdkqsfh41aa3wg1flimhsr7"))))
11341 (build-system r-build-system)
11351 (home-page "https://github.com/abjur/abjutils/")
11352 (synopsis "Collection of tools for jurimetrical analysis")
11354 "This package implements general purpose tools, such as functions for
11355 sampling and basic manipulation of Brazilian lawsuits identification number.
11356 It also implements functions for text cleaning, such as accentuation
11358 (license license:expat)))
11360 (define-public r-abnormality
11362 (name "r-abnormality")
11367 (uri (cran-uri "abnormality" version))
11369 (base32 "1fzfskl9akl06nliy8hkv2a0pznpj8pwcypg3gj5r2nzvr3kan9v"))))
11370 (build-system r-build-system)
11372 (list r-mass r-matrix))
11373 (home-page "https://cran.r-project.org/web/packages/abnormality/")
11374 (synopsis "Measure a subject's abnormality with respect to a reference population")
11376 "This package contains functions to implement the methodology and
11377 considerations laid out by Marks et al. in the article \"Measuring abnormality
11378 in high dimensional spaces: applications in biomechanical gait analysis\".
11379 Using high-dimensional datasets to measure a subject's overall level of
11380 abnormality as compared to a reference population is often needed in outcomes
11382 (license license:expat)))
11384 (define-public r-abodoutlier
11386 (name "r-abodoutlier")
11391 (uri (cran-uri "abodOutlier" version))
11393 (base32 "1pvhgxmh23br84r0fbmv7g53z2427birdja96a67vqgz18r3fdvj"))))
11394 (properties `((upstream-name . "abodOutlier")))
11395 (build-system r-build-system)
11398 (home-page "https://cran.r-project.org/web/packages/abodOutlier/")
11399 (synopsis "Angle-based outlier detection")
11401 "This package performs angle-based outlier detection on a given data
11402 frame. It offers three methods to process data:
11404 @item full but slow implementation using all the data that has cubic
11406 @item a fully randomized method;
11407 @item a method using k-nearest neighbours.
11409 These algorithms are well suited for high dimensional data outlier
11411 (license license:expat)))
11413 (define-public r-abps
11420 (uri (cran-uri "ABPS" version))
11422 (base32 "0n3f66nmfi5v94il1mxy026mi84w01ph2aljk60vn3mrz8kwf2ll"))))
11423 (properties `((upstream-name . "ABPS")))
11424 (build-system r-build-system)
11425 (propagated-inputs (list r-kernlab))
11426 (home-page "https://cran.r-project.org/web/packages/ABPS/")
11427 (synopsis "Abnormal blood profile score to detect blood doping")
11429 "This package offers an implementation of the @dfn{Abnormal blood profile score} (ABPS).
11430 The ABPS is a part of the Athlete biological passport program of the World
11431 anti-doping agency, which combines several blood parameters into a single
11432 score in order to detect blood doping. The package also contains functions to
11433 calculate other scores used in anti-doping programs, such as the ratio of
11434 hemoglobin to reticulocytes (OFF-score), as well as example data.")
11435 (license license:gpl2+)))
11437 (define-public r-parmigene
11439 (name "r-parmigene")
11444 (uri (cran-uri "parmigene" version))
11447 "067rqxqyzy1fsjj0s1g7af4527whwdhzjzc5b8a8n7683na59ns4"))))
11448 (build-system r-build-system)
11449 (home-page "https://cran.r-project.org/web/packages/parmigene/")
11450 (synopsis "Mutual information estimation for gene network reconstruction")
11452 "This package provides a parallel estimation of the mutual information
11453 based on entropy estimates from k-nearest neighbors distances and algorithms
11454 for the reconstruction of gene regulatory networks.")
11455 (license license:agpl3+)))
11457 (define-public r-pscl
11464 (uri (cran-uri "pscl" version))
11466 (base32 "0vzf5wazs92bhqhqd66v3vwmbfmnh67gb2466g1xxawim649nk05"))))
11467 (build-system r-build-system)
11470 (home-page "https://github.com/atahk/pscl/")
11471 (synopsis "Political science computational laboratory")
11473 "The @code{pscl} is an R package providing classes and methods for:
11475 @item Bayesian analysis of roll call data (item-response models);
11476 @item elementary Bayesian statistics;
11477 @item maximum likelihood estimation of zero-inflated and hurdle models for count
11479 @item utility functions.
11481 (license license:gpl2)))
11483 (define-public r-accelmissing
11485 (name "r-accelmissing")
11490 (uri (cran-uri "accelmissing" version))
11492 (base32 "1nql9inx6azdzi3z4sfm2vdml2mms6krl8wzlf1dn1c97ahn57fy"))))
11493 (build-system r-build-system)
11495 (list r-mice r-pscl))
11496 (home-page "https://cran.r-project.org/web/packages/accelmissing/")
11497 (synopsis "Missing value imputation for accelerometer data")
11499 "This package provides a statistical method to impute the missing values in
11500 accelerometer data. The methodology includes both parametric and
11501 semi-parametric multiple imputations under the zero-inflated Poisson lognormal
11502 model. It also provides multiple functions to preprocess the accelerometer data
11503 previous to the missing data imputation. These include detecting the wearing
11504 and the non-wearing time, selecting valid days and subjects, and creating plots.")
11505 (license license:gpl2+)))
11507 (define-public r-mhsmm
11514 (uri (cran-uri "mhsmm" version))
11516 (base32 "009dj0zkj1zry7jr9hf4cknb686z50a2l967if64xm0dvjmp7dgs"))))
11517 (build-system r-build-system)
11518 (propagated-inputs (list r-mvtnorm))
11519 (home-page "https://github.com/jaredo/mhsmm/")
11520 (synopsis "Inference for hidden Markov and semi-Markov models")
11522 "The @code{r-mhsmm} package implements estimation and prediction methods for
11523 hidden Markov and semi-Markov models for multiple observation sequences. Such
11524 techniques are of interest when observed data is thought to be dependent on some
11525 unobserved (or hidden) state. Also, this package is suitable for equidistant
11526 time series data, with multivariate and/or missing data. Allows user defined
11527 emission distributions.")
11528 (license license:gpl2+)))
11530 (define-public r-nleqslv
11537 (uri (cran-uri "nleqslv" version))
11539 (base32 "1v9znvncyigw9r25wx2ma0b7ib179b488dl0qsrhp5zrcz7mcjgm"))))
11540 (build-system r-build-system)
11541 (native-inputs (list gfortran))
11542 (home-page "https://cran.r-project.org/web/packages/nleqslv/")
11543 (synopsis "Solve systems of nonlinear equations")
11545 "The @code{r-nleqslv} package solves a system of nonlinear equations using a
11546 Broyden or a Newton method with a choice of global strategies such as line
11547 search and trust region. There are options for using a numerical or user
11548 supplied Jacobian, for specifying a banded numerical Jacobian and for allowing a
11549 singular or ill-conditioned Jacobian.")
11550 (license license:gpl2+)))
11552 (define-public r-physicalactivity
11554 (name "r-physicalactivity")
11559 (uri (cran-uri "PhysicalActivity" version))
11561 (base32 "0b27prkv3x6v2afz0y53ccs9scibpc7nj54n0hpd9fgn1wyg4c40"))))
11563 `((upstream-name . "PhysicalActivity")))
11564 (build-system r-build-system)
11565 (home-page "https://cran.r-project.org/web/packages/PhysicalActivity/")
11566 (synopsis "Processing accelerometer data for physical activity measurement")
11568 "This @code{r-physicalactivity} package provides a function @code{wearingMarking}
11569 for classification of monitored wear and nonwear time intervals in accelerometer
11570 data collected to assess physical activity. The package also contains functions
11571 for making plots of accelerometer data and obtaining the summary of various
11572 information including daily monitor wear time and the mean monitor wear time
11573 during valid days. The revised package version 0.2-1 improved the functions
11574 regarding speed, robustness and add better support for time zones and daylight
11575 saving. In addition, several functions were added:
11577 @item the @code{markDelivery} can classify days for ActiGraph delivery by mail;
11578 @item the @code{markPAI} can categorize physical activity intensity level based
11579 on user-defined cut-points of accelerometer counts.
11581 It also supports importing ActiGraph (AGD) files with @code{readActigraph} and
11582 @code{queryActigraph} functions.")
11583 (license license:gpl3+)))
11585 (define-public r-acc
11592 (uri (cran-uri "acc" version))
11594 (base32 "1ii2vm47djxbixa75h690q1s2f9m9x6i8nkygik93j6dayr6kr1m"))))
11595 (build-system r-build-system)
11610 (home-page "https://cran.r-project.org/web/packages/acc/")
11611 (synopsis "Exploring accelerometer data")
11613 "This package processes accelerometer data from uni-axial and tri-axial devices
11614 and generates data summaries. Also, includes functions to plot, analyze, and
11615 simulate accelerometer data.")
11616 (license license:gpl2+)))
11618 (define-public r-rbenchmark
11620 (name "r-rbenchmark")
11625 (uri (cran-uri "rbenchmark" version))
11627 (base32 "010fn3qwnk2k411cbqyvra1d12c3bhhl3spzm8kxffmirj4p2al9"))))
11628 (build-system r-build-system)
11629 (home-page "https://cran.r-project.org/web/packages/rbenchmark/")
11630 (synopsis "Benchmarking routine for R")
11632 "This @code{r-rbenchmark} package is inspired by the Perl module Benchmark,
11633 and is intended to facilitate benchmarking of arbitrary R code. The library
11634 consists of just one function, benchmark, which is a simple wrapper around
11635 system.time. Given a specification of the benchmarking process (counts of
11636 replications, evaluation environment) and an arbitrary number of expressions,
11637 benchmark evaluates each of the expressions in the specified environment,
11638 replicating the evaluation as many times as specified, and returning the results
11639 conveniently wrapped into a data frame.")
11640 (license license:gpl2+)))
11642 (define-public r-mitools
11649 (uri (cran-uri "mitools" version))
11652 "0c2x2n1p53lcw0vx4vmy5j7m2f95i7g2iwbryl89imr99rvz617j"))))
11653 (build-system r-build-system)
11654 (propagated-inputs (list r-dbi))
11655 (home-page "https://cran.r-project.org/web/packages/mitools/")
11656 (synopsis "Tools for multiple imputation of missing data")
11658 "This package provides tools to perform analyses and combine results from
11659 multiple-imputation datasets.")
11660 (license license:gpl2)))
11662 (define-public r-mixsqp
11668 (uri (cran-uri "mixsqp" version))
11671 "1qics04w0swyp216d6g8dmsph8q2kpadpacp66h2qih3521js12q"))))
11672 (properties `((upstream-name . "mixsqp")))
11673 (build-system r-build-system)
11675 (list r-irlba r-rcpp r-rcpparmadillo))
11678 (home-page "https://github.com/stephenslab/mixsqp")
11680 "Sequential quadratic programming for maximum-likelihood estimation")
11682 "This package provides an optimization method based on sequential
11683 quadratic programming for maximum likelihood estimation of the mixture
11684 proportions in a finite mixture model where the component densities are
11685 known. The algorithm is expected to obtain solutions that are at least
11686 as accurate as the state-of-the-art MOSEK interior-point solver, and they
11687 are expected to arrive at solutions more quickly when the number of
11688 samples is large and the number of mixture components is not too large.")
11689 (license license:expat)))
11691 (define-public r-magick
11698 (uri (cran-uri "magick" version))
11701 "0h942bn7wfnzbbgq9hrs75c7igmg5r1c5sad2v0znhza4cp7p1w3"))))
11702 (build-system r-build-system)
11704 (list imagemagick zlib))
11706 (list r-curl r-magrittr r-rcpp))
11708 (list pkg-config r-knitr))
11709 (home-page "https://github.com/ropensci/magick")
11710 (synopsis "Advanced graphics and image-processing in R")
11712 "This package provides bindings to ImageMagick, a comprehensive image
11713 processing library. It supports many common formats (PNG, JPEG, TIFF, PDF,
11714 etc.) and manipulations (rotate, scale, crop, trim, flip, blur, etc). All
11715 operations are vectorized via the Magick++ STL meaning they operate either on
11716 a single frame or a series of frames for working with layers, collages, or
11717 animation. In RStudio, images are automatically previewed when printed to the
11718 console, resulting in an interactive editing environment.")
11719 (license license:expat)))
11721 (define-public r-survey
11728 (uri (cran-uri "survey" version))
11731 "0ljsszybzri531q6xab04r6zq11vchfs7y0snjzk57m3g0b9ms05"))))
11732 (build-system r-build-system)
11740 (home-page "http://r-survey.r-forge.r-project.org/survey/")
11741 (synopsis "Analysis of complex survey samples")
11743 "This package provides tools for the analysis of complex survey samples.
11744 The provided features include: summary statistics, two-sample tests, rank
11745 tests, generalised linear models, cumulative link models, Cox models,
11746 loglinear models, and general maximum pseudolikelihood estimation for
11747 multistage stratified, cluster-sampled, unequally weighted survey samples;
11748 variances by Taylor series linearisation or replicate weights;
11749 post-stratification, calibration, and raking; two-phase subsampling designs;
11750 graphics; PPS sampling without replacement; principal components, and factor
11752 ;; Either version of the GPL.
11753 (license (list license:gpl2 license:gpl3))))
11755 (define-public r-gee
11758 (version "4.13-22")
11762 (uri (cran-uri "gee" version))
11765 "1wbwn7bjqz09l6clh43dy3x5qgv9b9wwn7xnfw9fkkrhn6rvc3rw"))))
11766 (properties `((upstream-name . "gee")))
11767 (build-system r-build-system)
11770 (home-page "https://cran.r-project.org/web/packages/gee/")
11771 (synopsis "Generalized estimation equation solver")
11773 "This package provides a solver for generalized estimation equations.")
11774 (license license:gpl2)))
11776 (define-public r-tab
11783 (uri (cran-uri "tab" version))
11786 "1kg8c1safi9klkx2mdkmsf5dn9piy4jljwd4ma7g4jz2rwl4jzhv"))))
11787 (properties `((upstream-name . "tab")))
11788 (build-system r-build-system)
11790 (list r-dplyr r-kableextra r-knitr r-mass r-survey))
11793 (home-page "https://cran.r-project.org/web/packages/tab/")
11794 (synopsis "Create summary tables for statistical reports")
11796 "This package contains functions for creating various types of summary
11797 tables, e.g. comparing characteristics across levels of a categorical variable
11798 and summarizing fitted generalized linear models, generalized estimating
11799 equations, and Cox proportional hazards models. Functions are available to
11800 handle data from simple random samples as well as complex surveys.")
11801 (license license:gpl3+)))
11803 (define-public r-dvmisc
11810 (uri (cran-uri "dvmisc" version))
11812 (base32 "01v6sixx0f3nrn6ymfifb3pvd2msfrwm21kmdv38laxq29vc4rsi"))))
11813 (build-system r-build-system)
11826 (home-page "https://cran.r-project.org/web/packages/dvmisc/")
11827 (synopsis "Faster computation of common statistics and miscellaneous functions")
11829 "This package implements faster versions of base R functions (e.g. mean, standard
11830 deviation, covariance, weighted mean), mostly written in C++, along with
11831 miscellaneous functions for various purposes (e.g. create the histogram with
11832 fitted probability density function or probability mass function curve, create
11833 the body mass index groups, assess the linearity assumption in logistic
11835 (license license:gpl2)))
11837 (define-public r-accelerometry
11839 (name "r-accelerometry")
11844 (uri (cran-uri "accelerometry" version))
11846 (base32 "13xzrwhr4i1nj9c8vrmfdg2rmrc8n446iihcyxmy99sm99hpzyip"))))
11847 (build-system r-build-system)
11849 (list r-dvmisc r-rcpp))
11850 (home-page "https://cran.r-project.org/web/packages/accelerometry/")
11851 (synopsis "Functions for processing accelerometer data")
11853 "This package provides a collection of functions that perform operations on
11854 time-series accelerometer data, such as identify the non-wear time, flag minutes
11855 that are part of an activity bout, and find the maximum 10-minute average count
11856 value. The functions are generally very flexible, allowing for a variety of
11857 algorithms to be implemented.")
11858 (license license:gpl3)))
11860 (define-public r-absim
11867 (uri (cran-uri "AbSim" version))
11869 (base32 "16ddjk8b6xw80ch4jis1y751i9561wdxh0gifbf15qiz3vjckq8m"))))
11870 (properties `((upstream-name . "AbSim")))
11871 (build-system r-build-system)
11873 (list r-ape r-powerlaw))
11874 (home-page "https://cran.r-project.org/web/packages/AbSim/")
11875 (synopsis "Time resolved simulations of antibody repertoires")
11877 "This package provides simulation methods for the evolution of antibody repertoires.
11878 The heavy and light chain variable region of both human and C57BL/6 mice can
11879 be simulated in a time-dependent fashion. Both single lineages using one set of
11880 V-, D-, and J-genes or full repertoires can be simulated. The algorithm begins
11881 with an initial V-D-J recombination event, starting the first phylogenetic tree.
11882 Upon completion, the main loop of the algorithm begins, with each iteration
11883 representing one simulated time step. Various mutation events are possible at
11884 each time step, contributing to a diverse final repertoire.")
11885 (license license:gpl2)))
11887 (define-public r-quic
11894 (uri (cran-uri "QUIC" version))
11896 (base32 "021bp9xbaih60qmss015ycblbv6d1dvb1z89y93zpqqnc2qhpv3c"))))
11897 (properties `((upstream-name . "QUIC")))
11898 (build-system r-build-system)
11899 (home-page "https://www.cs.utexas.edu/users/sustik/QUIC/")
11900 (synopsis "Regularized sparse inverse covariance matrix estimation")
11902 "This package implements the regularized Gaussian maximum likelihood
11903 estimation of the inverse of a covariance matrix. It uses Newton's method and
11904 coordinate descent to solve the regularized inverse covariance matrix
11905 estimation problem.")
11906 ;; The project home page states that the release is under GPLv3 or later.
11907 ;; The CRAN page only says GPL-3.
11908 (license license:gpl3+)))
11910 (define-public r-abundant
11912 (name "r-abundant")
11917 (uri (cran-uri "abundant" version))
11919 (base32 "15m3ngj5aipjg961yy5kvdg9xlfcpliw30dq6gchzxabhnfzcipd"))))
11920 (build-system r-build-system)
11923 (home-page "https://cran.r-project.org/web/packages/abundant/")
11924 (synopsis "Abundant regression and high-dimensional principal fitted components")
11926 "This package provides tools to fit and predict with the high-dimensional
11927 principal fitted components model. This model is described by Cook, Forzani,
11928 and Rothman (2012) @url{doi:10.1214/11-AOS962}.")
11929 ;; The DESCRIPTION file states GPL-2, but since it directly depends on a
11930 ;; GPLv3+ package (QUIC) this likely means GPLv2+.
11931 (license license:gpl2+)))
11933 (define-public r-ac3net
11940 (uri (cran-uri "Ac3net" version))
11942 (base32 "1ns4n0xxz6p34c11bj0k7nzgmyqr9mis2b0g5nfz37dbikndyqyz"))))
11943 (properties `((upstream-name . "Ac3net")))
11944 (build-system r-build-system)
11946 (list r-data-table))
11947 (home-page "https://cran.r-project.org/web/packages/Ac3net/")
11948 (synopsis "Inferring directional conservative causal core gene networks")
11949 (description "This package infers directional Conservative causal core
11950 (gene) networks (C3NET). This is a version of the algorithm C3NET with
11951 directional network.")
11952 (license license:gpl3+)))
11954 (define-public r-aca
11961 (uri (cran-uri "ACA" version))
11963 (base32 "1i3hm27nvnkvc39xlh0d1blq8q0q02czmvgi3cazmjx3jvxay0vq"))))
11964 (properties `((upstream-name . "ACA")))
11965 (build-system r-build-system)
11966 (home-page "https://cran.r-project.org/web/packages/ACA/")
11967 (synopsis "Abrupt change-point or aberration detection in point series")
11969 "This package offers an interactive function for the detection of breakpoints in
11971 ;; Any version of the GPL
11972 (license (list license:gpl2+ license:gpl3+))))
11974 (define-public r-acceptancesampling
11976 (name "r-acceptancesampling")
11981 (uri (cran-uri "AcceptanceSampling" version))
11983 (base32 "1ja1g0v8qvf7yj81x37wc6i7fkwpc573756jgvazazi8yf1gm12p"))))
11985 `((upstream-name . "AcceptanceSampling")))
11986 (build-system r-build-system)
11987 (home-page "https://cran.r-project.org/web/packages/AcceptanceSampling/")
11988 (synopsis "Creation and evaluation of acceptance sampling plans")
11990 "This @code{r-acceptancesampling} provides functionality for creating and evaluating
11991 acceptance sampling plans. Acceptance sampling is a methodology commonly used
11992 in quality control and improvement. International standards of acceptance
11993 sampling provide sampling plans for specific circumstances. The aim of this
11994 package is to provide an easy-to-use interface to visualize single, double or
11995 multiple sampling plans. In addition, methods have been provided to enable the
11996 user to assess sampling plans against pre-specified levels of performance, as
11997 measured by the probability of acceptance for a given level of quality in the
11999 (license license:gpl3+)))
12001 (define-public r-acclma
12008 (uri (cran-uri "ACCLMA" version))
12010 (base32 "1na27sp18fq12gp6vxgqw1ffsz2yi1d8xvrxbrzx5g1kqxrayy0v"))))
12011 (properties `((upstream-name . "ACCLMA")))
12012 (build-system r-build-system)
12013 (home-page "https://cran.r-project.org/web/packages/ACCLMA/")
12014 (synopsis "ACC & LMA graph plotting")
12016 "This package contains a function that imports data from a @acronym{CSV,
12017 Comma-Separated Values} file, or uses manually entered data from the format (x,
12018 y, weight) and plots the appropriate @acronym{ACC, Absolute Concentration
12019 Curve} vs @acronym{LOI, Line of Independence} graph and
12020 @acronym{LMA, @acronym{LOI} Minus @acronym{ACC}} graph. The main
12021 function is @code{plotLMA} (source file, header) that takes a data set and plots the
12022 appropriate @acronym{LMA} and @acronym{ACC} graphs. If no source file (a
12023 string) was passed, a manual data entry window is opened. The header parameter
12024 indicates by TRUE/FALSE (false by default) if the source @acronym{CSV} file has
12025 a header row or not. The dataset should contain only one independent variable
12026 (x) and one dependent variable (y) and can contain a weight for each
12028 (license license:gpl2)))
12030 (define-public r-aspi
12037 (uri (cran-uri "aspi" version))
12039 (base32 "0rhvxw243vvdv3hxa6pi343gcjc2cbxq1jzqirl9k1l4i3897l87"))))
12040 (build-system r-build-system)
12042 "https://cran.r-project.org/web/packages/aspi/")
12044 "Analysis of symmetry of parasitic infections")
12046 "This package provides tools for the analysis and visualization of bilateral
12047 asymmetry in parasitic infections.")
12048 (license license:gpl3+)))
12050 (define-public r-sandwich
12052 (name "r-sandwich")
12057 (uri (cran-uri "sandwich" version))
12060 "12aa5083k3sfrfq1jy3l94wffss9h0rga8j71jy3n8pkhiq4nn7n"))))
12061 (build-system r-build-system)
12064 (home-page "https://cran.r-project.org/web/packages/sandwich/")
12065 (synopsis "Robust Covariance Matrix Estimators")
12067 "This package provides model-robust standard error estimators for
12068 cross-sectional, time series, clustered, panel, and longitudinal data.")
12069 ;; Either version of the license.
12070 (license (list license:gpl2 license:gpl3))))
12072 (define-public r-th-data
12079 (uri (cran-uri "TH.data" version))
12082 "0ynxacnz002bjsp2ybql7rdqw4zd14af8r7w44nwbx22n4bapwzd"))))
12083 (properties `((upstream-name . "TH.data")))
12084 (build-system r-build-system)
12086 (list r-mass r-survival))
12089 (home-page "https://cran.r-project.org/web/packages/TH.data/")
12090 (synopsis "Shared data sets")
12092 "This package contains supporting data sets that are used in other
12093 packages maintained by Torsten Hothorn.")
12094 (license license:gpl3)))
12096 (define-public r-multcomp
12098 (name "r-multcomp")
12103 (uri (cran-uri "multcomp" version))
12106 "0mz5wdqrqpp2gqijfpp9rgfbq8yvxki4is8fbbc4qwdwryqp6d7h"))))
12107 (build-system r-build-system)
12109 (list r-codetools r-mvtnorm r-sandwich r-survival r-th-data))
12110 (home-page "https://cran.r-project.org/web/packages/multcomp/")
12111 (synopsis "Simultaneous inference in general parametric models")
12113 "Simultaneous tests and confidence intervals for general linear
12114 hypotheses in parametric models, including linear, generalized linear, linear
12115 mixed effects, and survival models. The package includes demos reproducing
12116 analyzes presented in the book \"Multiple Comparisons Using R\" (Bretz,
12117 Hothorn, Westfall, 2010, CRC Press).")
12118 (license license:gpl2)))
12120 (define-public r-multcompview
12122 (name "r-multcompview")
12127 (uri (cran-uri "multcompView" version))
12129 (base32 "1rfq9wvvrghq0542ff40wy8vdmsyd8spzz6ihcywcvxdfa8m6g8j"))))
12130 (properties `((upstream-name . "multcompView")))
12131 (build-system r-build-system)
12132 (home-page "https://cran.r-project.org/package=multcompView")
12133 (synopsis "Visualizations of paired comparisons")
12135 "Convert a logical vector or a vector of p-values or a correlation,
12136 difference, or distance matrix into a display identifying the pairs for which
12137 the differences were not significantly different.")
12138 ;; Any version of the GPL.
12139 (license license:gpl3+)))
12141 (define-public r-emmeans
12144 (version "1.7.4-1")
12148 (uri (cran-uri "emmeans" version))
12151 "08g7ifqhwqa00hc850nwx03dp7isz0281ig6kvixc4xdahmkm8zp"))))
12152 (build-system r-build-system)
12154 (list r-estimability r-mvtnorm r-numderiv r-xtable))
12157 (home-page "https://github.com/rvlenth/emmeans")
12158 (synopsis "Estimated marginal means, aka least-squares means")
12160 "This package provides tools to obtain @dfn{estimated marginal
12161 means} (EMMs) for many linear, generalized linear, and mixed models. It can
12162 be used to compute contrasts or linear functions of EMMs, trends, and
12163 comparisons of slopes.")
12164 ;; Either version of the license.
12165 (license (list license:gpl2 license:gpl3))))
12167 (define-public r-pwr
12174 (uri (cran-uri "pwr" version))
12177 "1kfzy73v3z6ipc3kdfkcjrp4b4p5k54nwk796gqi36srm93hgc2v"))))
12178 (build-system r-build-system)
12181 (home-page "https://github.com/heliosdrm/pwr")
12182 (synopsis "Basic functions for power analysis")
12184 "This package provides power analysis functions along the lines of
12186 (license license:gpl3+)))
12188 (define-public r-libcoin
12195 (uri (cran-uri "libcoin" version))
12197 (base32 "1syrcdj5qg5m3zd3dlxgpfklswbalfg42w058dr09hnzqsvx0z9d"))))
12198 (build-system r-build-system)
12199 (propagated-inputs (list r-mvtnorm))
12200 (home-page "https://cran.r-project.org/web/packages/libcoin")
12201 (synopsis "Linear test statistics for permutation inference")
12203 "This package provides basic infrastructure for linear test statistics
12204 and permutation inference in the framework of Strasser and Weber (1999).")
12205 (license license:gpl2)))
12207 (define-public r-coin
12214 (uri (cran-uri "coin" version))
12217 "1cpv7jx840inzg98bkhrb5yscx0gpag6br237r5qpnc2gbrd2ikm"))))
12218 (build-system r-build-system)
12226 (home-page "http://coin.r-forge.r-project.org")
12227 (synopsis "Conditional inference procedures in a permutation test framework")
12229 "This package provides conditional inference procedures for the general
12230 independence problem including two-sample, K-sample (non-parametric ANOVA),
12231 correlation, censored, ordered and multivariate problems.")
12232 (license license:gpl2)))
12234 (define-public r-bayesplot
12236 (name "r-bayesplot")
12241 (uri (cran-uri "bayesplot" version))
12244 "0hqy597ang53phxnl084hak35ffqz9lw9hygax7370gpkjws908a"))))
12245 (build-system r-build-system)
12260 (home-page "https://mc-stan.org/bayesplot")
12261 (synopsis "Plotting for Bayesian models")
12263 "This package provides plotting functions for posterior analysis, model
12264 checking, and MCMC diagnostics. The package is designed not only to provide
12265 convenient functionality for users, but also a common set of functions that
12266 can be easily used by developers working on a variety of R packages for
12267 Bayesian modeling.")
12268 (license license:gpl3+)))
12270 (define-public r-tmb
12277 (uri (cran-uri "TMB" version))
12280 "1mr5vwamw6ag1fhd83jyy6015296908qwshwq0fcphhiv60x579c"))))
12281 (properties `((upstream-name . "TMB")))
12282 (build-system r-build-system)
12284 (list r-matrix r-rcppeigen))
12285 (home-page "http://tmb-project.org")
12286 (synopsis "Template model builder: a general random effect tool")
12288 "With this tool, a user should be able to quickly implement complex
12289 random effect models through simple C++ templates. The package combines
12290 @code{CppAD} (C++ automatic differentiation), @code{Eigen} (templated
12291 matrix-vector library) and @code{CHOLMOD} (sparse matrix routines available
12292 from R) to obtain an efficient implementation of the applied Laplace
12293 approximation with exact derivatives. Key features are: Automatic sparseness
12294 detection, parallelism through BLAS and parallel user templates.")
12295 (license license:gpl2)))
12297 (define-public r-sjstats
12304 (uri (cran-uri "sjstats" version))
12306 (base32 "1cv80yjnyh6qihxf57zivihhia20gibr5f03x8aspy6382wnwlka"))))
12307 (build-system r-build-system)
12326 (home-page "https://github.com/strengejacke/sjstats")
12327 (synopsis "Functions for common statistical computations")
12329 "This package provides a collection of convenient functions for common
12330 statistical computations, which are not directly provided by R's @code{base}
12331 or @code{stats} packages. This package aims at providing, first, shortcuts
12332 for statistical measures, which otherwise could only be calculated with
12333 additional effort. Second, these shortcut functions are generic, and can be
12334 applied not only to vectors, but also to other objects as well. The focus of
12335 most functions lies on summary statistics or fit measures for regression
12336 models, including generalized linear models, mixed effects models and Bayesian
12338 (license license:gpl3)))
12340 (define-public r-glmmtmb
12347 (uri (cran-uri "glmmTMB" version))
12350 "0xdjc3gx0cj098rrjzlsy9cccxzfvn029xh4ycpya4xjhxsykldr"))))
12351 (properties `((upstream-name . "glmmTMB")))
12352 (build-system r-build-system)
12361 (list r-knitr r-rmarkdown)) ; for vignettes
12362 (home-page "https://github.com/glmmTMB")
12363 (synopsis "Generalized linear mixed models")
12365 "Fit linear and generalized linear mixed models with various extensions,
12366 including zero-inflation. The models are fitted using maximum likelihood
12367 estimation via the Template Model Builder. Random effects are assumed to be
12368 Gaussian on the scale of the linear predictor and are integrated out using the
12369 Laplace approximation. Gradients are calculated using automatic
12371 (license license:agpl3+)))
12373 (define-public r-bayestestr
12375 (name "r-bayestestr")
12380 (uri (cran-uri "bayestestR" version))
12383 "1fbkpagc5zznrafy7h68nhx43a1yg4v7242pbqjkd0h2481c101z"))))
12384 (properties `((upstream-name . "bayestestR")))
12385 (build-system r-build-system)
12387 (list r-datawizard r-insight))
12390 (home-page "https://github.com/easystats/bayestestR")
12391 (synopsis "Describe Bayesian models and posterior distributions")
12393 "This package provides utilities to understand and describe posterior
12394 distributions and Bayesian models. It includes point-estimates such as
12395 @dfn{Maximum A Posteriori} (MAP), measures of dispersion such as @dfn{Highest
12396 Density Interval} (HDI), and indices used for null-hypothesis testing (such as
12397 ROPE percentage and pd).")
12398 (license license:gpl3)))
12400 (define-public r-performance
12402 (name "r-performance")
12407 (uri (cran-uri "performance" version))
12410 "1znr4i1pjv6z3lj6qrma2i3l94rz1z29w92mrxxfy3ch0s71crww"))))
12411 (build-system r-build-system)
12413 (list r-bayestestr r-datawizard r-insight))
12414 (home-page "https://easystats.github.io/performance/")
12415 (synopsis "Assessment of regression models performance")
12417 "This package provides utilities for computing measures to assess model
12418 quality, which are not directly provided by R's @code{base} or @code{stats}
12419 packages. These include e.g. measures like r-squared, intraclass correlation
12420 coefficient, root mean squared error or functions to check models for
12421 overdispersion, singularity or zero-inflation and more. Functions apply to a
12422 large variety of regression models, including generalized linear models, mixed
12423 effects models and Bayesian models.")
12424 (license license:gpl3)))
12426 (define-public r-ggeffects
12428 (name "r-ggeffects")
12433 (uri (cran-uri "ggeffects" version))
12436 "01yyfw7fkbxrp0gpwni5y8m4w9l3xckwc3crnvy1fqs1d6gwx3xx"))))
12437 (build-system r-build-system)
12439 (list r-insight r-mass r-sjlabelled))
12442 (home-page "https://github.com/strengejacke/ggeffects")
12443 (synopsis "Create tidy data frames of marginal effects for ggplot")
12445 "This package provides tools to compute marginal effects from statistical
12446 models and return the result as tidy data frames. These data frames are ready
12447 to use with the @code{ggplot2} package. Marginal effects can be calculated
12448 for many different models. Interaction terms, splines and polynomial terms
12449 are also supported. The two main functions are @code{ggpredict()} and
12450 @code{ggeffect()}. There is a generic @code{plot()} method to plot the
12451 results using @code{ggplot2}.")
12452 (license license:gpl3)))
12454 (define-public r-effectsize
12456 (name "r-effectsize")
12461 (uri (cran-uri "effectsize" version))
12464 "07dbj7n9vwjkb7xrdj224lzc3ppr3jjdgyyilkj7gpkvgjgfrqhz"))))
12465 (properties `((upstream-name . "effectsize")))
12466 (build-system r-build-system)
12468 (list r-bayestestr r-datawizard r-insight r-parameters
12472 (home-page "https://github.com/easystats/effectsize")
12473 (synopsis "Indices of effect size and standardized parameters")
12475 "This package provides utilities to work with indices of effect size and
12476 standardized parameters for a wide variety of models, allowing computation and
12477 conversion of indices such as Cohen's d, r, odds, etc.")
12478 (license license:gpl3)))
12480 (define-public r-sjplot
12487 (uri (cran-uri "sjPlot" version))
12489 (base32 "1rnwhh271xj8xgvvlpqw9ain56mfz37fvl7f6jq9nzx9jxx95bjd"))))
12490 (properties `((upstream-name . "sjPlot")))
12491 (build-system r-build-system)
12513 (home-page "https://strengejacke.github.io/sjPlot/")
12514 (synopsis "Data visualization for statistics in social science")
12516 "This package represents a collection of plotting and table output
12517 functions for data visualization. Results of various statistical
12518 analyses (that are commonly used in social sciences) can be visualized using
12519 this package, including simple and cross tabulated frequencies, histograms,
12520 box plots, (generalized) linear models, mixed effects models, principal
12521 component analysis and correlation matrices, cluster analyses, scatter plots,
12522 stacked scales, effects plots of regression models (including interaction
12523 terms) and much more. This package supports labelled data.")
12524 (license license:gpl3)))
12526 (define-public r-ini
12533 (uri (cran-uri "ini" version))
12536 "04yqij344dwm0xqgara8xia42mlmij3i8711qbb5534w05a1l6bv"))))
12537 (build-system r-build-system)
12538 (home-page "https://github.com/dvdscripter/ini")
12539 (synopsis "Read and write configuration files")
12541 "This package provides tools to parse simple @code{.ini} configuration
12542 files to an structured list. Users can manipulate this resulting list with
12543 @code{lapply()} functions. This same structured list can be used to write
12544 back to file after modifications.")
12545 (license license:gpl3)))
12547 (define-public r-gillespiessa2
12549 (name "r-gillespiessa2")
12554 (uri (cran-uri "GillespieSSA2" version))
12556 (base32 "03ym8qx5yc1a6j9l973lc0rjzs8hiax8fq13j7m1fcb1pvnbvar5"))))
12557 (properties `((upstream-name . "GillespieSSA2")))
12558 (build-system r-build-system)
12571 (native-inputs (list r-knitr))
12572 (home-page "https://github.com/rcannood/GillespieSSA2")
12573 (synopsis "Gillespie's stochastic simulation algorithm")
12575 "This package provides a fast, scalable, and versatile framework for
12576 simulating large systems with Gillespie's @dfn{Stochastic Simulation
12577 Algorithm} (SSA). This package is the spiritual successor to the GillespieSSA
12578 package. Benefits of this package include major speed improvements (>100x),
12579 easier to understand documentation, and many unit tests that try to ensure the
12580 package works as intended.")
12581 (license license:gpl3+)))
12583 (define-public r-gitcreds
12585 (name "r-gitcreds")
12590 (uri (cran-uri "gitcreds" version))
12593 "1snzn7nxy0rwz0bzjsg6k04c0n811dgn8gn9cmn2v78aj57ayjmi"))))
12594 (properties `((upstream-name . "gitcreds")))
12595 (build-system r-build-system)
12596 (inputs (list git-minimal))
12597 (native-inputs (list r-knitr))
12598 (home-page "https://github.com/r-lib/gitcreds")
12599 (synopsis "Query git credentials from R")
12601 "Query, set, and delete credentials from the git credential store.
12602 Manage GitHub tokens and other git credentials. This package is to be used by
12603 other packages that need to authenticate to GitHub and/or other git
12605 (license license:expat)))
12607 (define-public r-gh
12614 (uri (cran-uri "gh" version))
12617 "077drbxz3rx7idv6w24ipj1p6jnzv86a3iyryab699cc9q2kjh54"))))
12618 (build-system r-build-system)
12620 (list r-cli r-gitcreds r-httr r-ini r-jsonlite))
12623 (home-page "https://github.com/r-lib/gh#readme")
12624 (synopsis "Access the GitHub API via R")
12626 "This package provides a minimal R client to access the GitHub API.")
12627 (license license:expat)))
12629 (define-public r-fs
12636 (uri (cran-uri "fs" version))
12639 "11qr3v0xn65vfhgcxl4l6yv48s4w0w3ldp3anpzc25vd3mwd3jim"))))
12640 (build-system r-build-system)
12643 (home-page "https://fs.r-lib.org")
12644 (synopsis "Cross-platform file system operations based on libuv")
12646 "This package provides a cross-platform interface to file system
12647 operations, built on top of the libuv C library.")
12648 (license license:gpl3)))
12650 (define-public r-clisymbols
12652 (name "r-clisymbols")
12657 (uri (cran-uri "clisymbols" version))
12660 "1q7gi2zmykhzas9v8fdnbpdq7pzdcpbhim1yxvd2062l777g4j86"))))
12661 (build-system r-build-system)
12662 (home-page "https://github.com/gaborcsardi/clisymbols")
12663 (synopsis "Unicode symbols at the R prompt")
12665 "This package provides a small subset of Unicode symbols, that are useful
12666 when building command line applications. They fall back to alternatives on
12667 terminals that do not support Unicode.")
12668 (license license:expat)))
12670 (define-public r-credentials
12672 (name "r-credentials")
12677 (uri (cran-uri "credentials" version))
12680 "1f18j3zrq8c9kah57xwahmmljsjg5qphlgamvx507ynvpq8pryig"))))
12681 (properties `((upstream-name . "credentials")))
12682 (build-system r-build-system)
12685 (modify-phases %standard-phases
12686 (add-after 'unpack 'setenv-HOME
12688 ;; This is necessary because git looks for $HOME/.gitconfig
12689 (setenv "HOME" "/tmp"))))))
12691 (list git-minimal))
12693 (list r-askpass r-curl r-jsonlite r-openssl r-sys))
12696 (home-page "https://docs.ropensci.org/credentials/")
12697 (synopsis "Tools for managing SSH and Git credentials")
12699 "This package assists you in setting up and retrieving of HTTPS and SSH
12700 credentials for use with git and other services. For HTTPS remotes the
12701 package interfaces the @command{git-credential} utility which @command{git}
12702 uses to store HTTP usernames and passwords. For SSH remotes this package
12703 provides convenient functions to find or generate appropriate SSH keys. The
12704 package both helps the user to setup a local git installation, and also
12705 provides a back-end for git/ssh client libraries to authenticate with existing
12706 user credentials.")
12707 (license license:expat)))
12709 (define-public r-gert
12716 (uri (cran-uri "gert" version))
12719 "0r19vi77yyjw5gbhgjibdysjlszlw2095v14f6sv675zpbp0li4c"))))
12720 (properties `((upstream-name . "gert")))
12721 (build-system r-build-system)
12723 (list libgit2 zlib))
12732 (list pkg-config r-knitr))
12733 (home-page "https://docs.ropensci.org/gert/")
12734 (synopsis "Simple Git client for R")
12736 "This package provides a simple git client for R based on libgit2 with
12737 support for SSH and HTTPS remotes. All functions in gert use basic R data
12738 types (such as vectors and data-frames) for their arguments and return values.
12739 User credentials are shared with command line git through the
12740 @code{git-credential} store and SSH keys stored on disk or ssh-agent.")
12741 (license license:expat)))
12743 (define-public r-usethis
12750 (uri (cran-uri "usethis" version))
12753 "0638dzl4nm4c36990sf2biy74hjr2fzlqzfb98fsqrbhaw3ngp1i"))))
12754 (build-system r-build-system)
12775 (home-page "https://github.com/r-lib/usethis")
12776 (synopsis "Automate R package and project setup")
12778 "This package helps you to automate R package and project setup tasks
12779 that are otherwise performed manually. This includes setting up unit testing,
12780 test coverage, continuous integration, Git, GitHub integration, licenses,
12781 Rcpp, RStudio projects, and more.")
12782 (license license:gpl3)))
12784 (define-public r-sessioninfo
12786 (name "r-sessioninfo")
12791 (uri (cran-uri "sessioninfo" version))
12794 "1jy7n37qnrb4fgzmn8s8yf7kv29yw27x8zklwf8qdb2kgj2q6qpm"))))
12795 (build-system r-build-system)
12798 (home-page "https://github.com/r-lib/sessioninfo#readme")
12799 (synopsis "R session information")
12801 "This package provides tools to query and print information about the
12802 current R session. It is similar to @code{utils::sessionInfo()}, but includes
12803 more information about packages, and where they were installed from.")
12804 (license license:gpl2)))
12806 (define-public r-remotes
12813 (uri (cran-uri "remotes" version))
12816 "05m5dgv0nba5vhjbdkd8z5lbhpfxgkw31j58am7vz1d44igqgvzj"))))
12817 (build-system r-build-system)
12820 (home-page "https://github.com/r-lib/remotes#readme")
12821 (synopsis "R package installation from remote repositories")
12823 "Download and install R packages stored in GitHub, BitBucket, or plain
12824 subversion or git repositories. This package is a lightweight replacement of
12825 the @code{install_*} functions in the @code{devtools} package. Indeed most of
12826 the code was copied over from @code{devtools}.")
12827 (license license:gpl2+)))
12829 (define-public r-xopen
12836 (uri (cran-uri "xopen" version))
12839 "1vrvgdika1d63dwygynbv2wmd87ll8dji5dy89hj576n8hw601z2"))))
12840 (build-system r-build-system)
12843 (home-page "https://github.com/r-lib/xopen#readme")
12844 (synopsis "Open system files, URLs, anything")
12846 "This package provides a cross-platform solution to open files,
12847 directories or URLs with their associated programs.")
12848 (license license:expat)))
12850 (define-public r-rcmdcheck
12852 (name "r-rcmdcheck")
12857 (uri (cran-uri "rcmdcheck" version))
12860 "1l696byn3kjq2xvz4wxybzaj6ink85h4lz3a35v2132ba5yyzm5v"))))
12861 (build-system r-build-system)
12875 (home-page "https://github.com/r-Lib/rcmdcheck#readme")
12876 (synopsis "Run R CMD check from R and capture results")
12878 "Run @code{R CMD check} from R programmatically, and capture the results
12879 of the individual checks.")
12880 (license license:expat)))
12882 (define-public r-rapportools
12884 (name "r-rapportools")
12889 (uri (cran-uri "rapportools" version))
12892 "0qr86idng12g6hdd764j0wmli700v7rjhw7jdjxj0ka8xm5v7ymm"))))
12893 (build-system r-build-system)
12895 (list r-mass r-pander r-plyr r-reshape2))
12896 (home-page "https://cran.r-project.org/web/packages/rapportools/")
12897 (synopsis "Miscellaneous helper functions with sane defaults for reporting")
12899 "This package provides helper functions that act as wrappers to more
12900 advanced statistical methods with the advantage of having sane defaults for
12902 (license license:agpl3+)))
12904 (define-public r-pander
12911 (uri (cran-uri "pander" version))
12914 "144zkq5w7v6fpzk3x40i0baybbp0y6x2ckh4b9qljryas9mhgp9a"))))
12915 (build-system r-build-system)
12917 (list r-digest r-rcpp))
12920 (home-page "https://rapporter.github.io/pander")
12921 (synopsis "Render R objects into Pandoc's markdown")
12923 "The main aim of the pander R package is to provide a minimal and easy
12924 tool for rendering R objects into Pandoc's markdown. The package is also
12925 capable of exporting/converting complex Pandoc documents (reports) in various
12927 ;; This package is licensed under either the AGPLv3+ or the very rarely
12929 (license license:agpl3+)))
12931 (define-public r-summarytools
12933 (name "r-summarytools")
12938 (uri (cran-uri "summarytools" version))
12941 "0gr95cd1ja8di6s0xghk6w7nj3bh3z4g7j7ixdy7f88q681aixgx"))))
12942 (build-system r-build-system)
12958 (home-page "https://github.com/dcomtois/summarytools")
12959 (synopsis "Tools to quickly and neatly summarize data")
12961 "This package provides tools for data frame summaries, cross-tabulations,
12962 weight-enabled frequency tables and common univariate statistics in concise
12963 tables available in a variety of formats (plain ASCII, Markdown and HTML). A
12964 good point-of-entry for exploring data, both for experienced and new R
12966 (license license:gpl2)))
12968 (define-public r-lsei
12975 (uri (cran-uri "lsei" version))
12978 "1dka0rigfw4vj809qma2dkiwjb3nw5635ynnba5cm299cn7hb2b2"))))
12979 (build-system r-build-system)
12982 (home-page "https://www.stat.auckland.ac.nz/~yongwang")
12983 (synopsis "Solve regression problems under equality/inequality constraints")
12985 "It contains functions that solve least squares linear regression
12986 problems under linear equality/inequality constraints. Functions for solving
12987 quadratic programming problems are also available, which transform such
12988 problems into least squares ones first.")
12989 (license license:gpl2+)))
12991 (define-public r-npsurv
12998 (uri (cran-uri "npsurv" version))
13001 "1ihxhb42cga1hssj2jv4ah0f4hlwsky899ij5261fzh1wxvdp1xw"))))
13002 (build-system r-build-system)
13005 (home-page "https://www.stat.auckland.ac.nz/~yongwang")
13006 (synopsis "Nonparametric survival analysis")
13008 "This package contains functions for non-parametric survival analysis of
13009 exact and interval-censored observations.")
13010 (license license:gpl2+)))
13012 (define-public r-clusteval
13014 (name "r-clusteval")
13019 (uri (cran-uri "clusteval" version))
13022 "1ld0bdl4fy8dsfzm3k7a37cyxc6pfc9qs31x4pxd3z5rslghz7rj"))))
13023 (build-system r-build-system)
13025 (list r-mvtnorm r-rcpp))
13026 (home-page "https://cran.r-project.org/web/packages/clusteval/")
13027 (synopsis "Evaluation of clustering algorithms")
13029 "This R package provides a suite of tools to evaluate clustering
13030 algorithms, clusterings, and individual clusters.")
13031 (license license:expat)))
13033 (define-public r-tweedie
13040 (uri (cran-uri "tweedie" version))
13043 "1nfhaqblvm62j8gfkyrgba5ai0pb2fsnrxp63637mhys2bawlcm0"))))
13044 (build-system r-build-system)
13045 (native-inputs (list gfortran))
13046 (home-page "https://cran.r-project.org/web/packages/tweedie/")
13047 (synopsis "Evaluation of Tweedie exponential family models")
13049 "Maximum likelihood computations for Tweedie families, including the
13050 series expansion (Dunn and Smyth, 2005; <doi10.1007/s11222-005-4070-y>) and
13051 the Fourier inversion (Dunn and Smyth, 2008; <doi:10.1007/s11222-007-9039-6>),
13052 and related methods.")
13053 (license license:gpl2+)))
13055 (define-public r-rcppgsl
13062 (uri (cran-uri "RcppGSL" version))
13064 (base32 "1a5dms0axlzgpv1z2bhfrb77497h0ch1yslq0gidj14vr4kfm57h"))))
13065 (properties `((upstream-name . "RcppGSL")))
13066 (build-system r-build-system)
13069 (home-page "https://cran.r-project.org/web/packages/RcppGSL/")
13070 (synopsis "Rcpp integration for GSL vectors and matrices")
13072 "The GNU Scientific Library (or GSL) is a collection of numerical
13073 routines for scientific computing. It is particularly useful for C and C++
13074 programs as it provides a standard C interface to a wide range of mathematical
13075 routines. There are over 1000 functions in total with an extensive test
13076 suite. The RcppGSL package provides an easy-to-use interface between GSL data
13077 structures and R using concepts from Rcpp which is itself a package that eases
13078 the interfaces between R and C++.")
13079 (license license:gpl2+)))
13081 (define-public r-mvabund
13088 (uri (cran-uri "mvabund" version))
13091 "01kss9dx4an1ir5zs46jypvhj8sdc8wcs00i1223ai09av4lcsgd"))))
13092 (build-system r-build-system)
13094 (list r-mass r-rcpp r-rcppgsl r-statmod r-tweedie))
13095 (home-page "https://cran.r-project.org/web/packages/mvabund/")
13096 (synopsis "Statistical methods for analysing multivariate abundance data")
13098 "This package provides a set of tools for displaying, modeling and
13099 analysing multivariate abundance data in community ecology.")
13100 (license license:lgpl2.1+)))
13102 (define-public r-afex
13109 (uri (cran-uri "afex" version))
13112 "09q426s2zmzxx5ilxy0x5mflpb38pl075ss1s8xvpswkn6cia0b6"))))
13113 (build-system r-build-system)
13114 ;; This is needed for the vignette builder
13117 (modify-phases %standard-phases
13118 (add-after 'unpack 'set-HOME
13119 (lambda _ (setenv "HOME" "/tmp"))))))
13121 (list r-car r-lme4 r-lmertest r-pbkrtest r-reshape2))
13124 r-r-rsp)) ;vignette builder
13125 (home-page "https://afex.singmann.science/")
13126 (synopsis "Analysis of factorial experiments")
13128 "This package provides convenience functions for analyzing factorial
13129 experiments using ANOVA or mixed models.")
13130 (license license:gpl2+)))
13132 (define-public r-lmertest
13134 (name "r-lmertest")
13139 (uri (cran-uri "lmerTest" version))
13142 "1zd8gqjkazhxgpnnr484xwsq30p62fq8592nzyc171zjyplpbaim"))))
13143 (properties `((upstream-name . "lmerTest")))
13144 (build-system r-build-system)
13146 (list r-ggplot2 r-lme4 r-mass r-numderiv))
13147 (home-page "https://github.com/runehaubo/lmerTestR")
13148 (synopsis "Tests in linear mixed effects models")
13150 "This package provides p-values in type I, II or III anova and summary
13151 tables for @code{lmer} model fits via Satterthwaite's degrees of freedom
13152 method. A Kenward-Roger method is also available via the @code{pbkrtest}
13153 package. Model selection methods include step, drop1 and anova-like tables
13154 for random effects (ranova). Methods for Least-Square means (LS-means) and
13155 tests of linear contrasts of fixed effects are also available.")
13156 (license license:gpl2+)))
13158 (define-public r-r2glmm
13165 (uri (cran-uri "r2glmm" version))
13168 "0iim92blpa59vgz97c2pi05yhbjjmaffdbkbmk5kplfb2vmazgiy"))))
13169 (build-system r-build-system)
13181 (home-page "https://github.com/bcjaeger/r2glmm")
13182 (synopsis "Compute R squared for mixed (multilevel) models")
13184 "This package computes model and semi partial R squared with confidence
13185 limits for the linear and generalized linear mixed model (LMM and GLMM). The
13186 R squared measure from L. J. Edwards et al. (2008) is extended to the GLMM
13187 using @dfn{penalized quasi-likelihood} (PQL) estimation (see Jaeger et
13189 (license license:gpl2)))
13191 (define-public r-cmdfun
13198 (uri (cran-uri "cmdfun" version))
13201 "1pbcq7hi2lcmqnghmy3q2fsk0c9fy5m0637acyzmc096fxbx723j"))))
13202 (properties `((upstream-name . "cmdfun")))
13203 (build-system r-build-system)
13213 (home-page "https://snystrom.github.io/cmdfun/")
13214 (synopsis "Framework for building interfaces to shell commands")
13216 "Writing interfaces to command line software is cumbersome. The cmdfun
13217 package provides a framework for building function calls to seamlessly
13218 interface with shell commands by allowing lazy evaluation of command line
13219 arguments. It also provides methods for handling user-specific paths to tool
13220 installs or secrets like API keys. Its focus is to equally serve package
13221 builders who wish to wrap command line software, and to help analysts stay
13222 inside R when they might usually leave to execute non-R software.")
13223 (license license:expat)))
13225 (define-public r-rslurm
13232 (uri (cran-uri "rslurm" version))
13235 "19451icfh7snjbbmpzpr1hrdf52q8ijv0ag1di3y55r2la3jxxcf"))))
13236 (properties `((upstream-name . "rslurm")))
13237 (build-system r-build-system)
13238 (propagated-inputs (list r-whisker))
13239 (native-inputs (list r-knitr))
13240 (home-page "http://cyberhelp.sesync.org/rslurm/")
13241 (synopsis "Submit R calculations to a Slurm cluster")
13243 "This package provides functions that simplify submitting R scripts to a
13244 Slurm workload manager, in part by automating the division of embarrassingly
13245 parallel calculations across cluster nodes.")
13246 (license license:gpl3)))
13248 (define-public r-chk
13255 (uri (cran-uri "chk" version))
13258 "10gcv00mgi88vgxr9jrs0ar67crmdcdi4m9g86cm6pg3ly0v097y"))))
13259 (properties `((upstream-name . "chk")))
13260 (build-system r-build-system)
13262 (list r-lifecycle r-rlang))
13263 (native-inputs (list r-knitr))
13264 (home-page "https://github.com/poissonconsulting/chk")
13265 (synopsis "Check user-supplied function arguments")
13267 "This is a package for developers to check user-supplied function
13268 arguments. It is designed to be simple, fast and customizable. Error
13269 messages follow the tidyverse style guide.")
13270 (license license:expat)))
13272 (define-public r-weights
13279 (uri (cran-uri "weights" version))
13282 "1fnchf7f0hyl514bk8sc3l884kg25kb5xm4mc2l28n6hm7l6bgpg"))))
13283 (build-system r-build-system)
13285 (list r-gdata r-hmisc r-lme4 r-mice))
13286 (home-page "https://cran.r-project.org/web/packages/weights/")
13287 (synopsis "Weighting and weighted statistics")
13288 (description "This package Provides a variety of functions for producing
13289 simple weighted statistics, such as weighted Pearson's correlations, partial
13290 correlations, Chi-Squared statistics, histograms, and t-tests. Also now
13291 includes some software for quickly recoding survey data and plotting point
13292 estimates from interaction terms in regressions (and multiply imputed
13293 regressions). NOTE: Weighted partial correlation calculations pulled to
13295 (license license:gpl2+)))
13297 (define-public r-rcppannoy
13299 (name "r-rcppannoy")
13304 (uri (cran-uri "RcppAnnoy" version))
13307 "12k8ny981dmky5js8yl6bih5r5mq3w43f2f9admhkwqn0n80kcl9"))))
13308 (properties `((upstream-name . "RcppAnnoy")))
13309 (build-system r-build-system)
13312 (home-page "https://cran.r-project.org/web/packages/RcppAnnoy/")
13313 (synopsis "Rcpp bindings for Annoy, a library for Approximate Nearest Neighbors")
13315 "Annoy is a small C++ library for Approximate Nearest Neighbors written
13316 for efficient memory usage as well an ability to load from and save to disk.
13317 This package provides an R interface.")
13318 ;; Annoy is released under ASL 2.0, but this wrapper is released under
13320 (license (list license:gpl2+ license:asl2.0))))
13322 (define-public r-rcpphnsw
13324 (name "r-rcpphnsw")
13329 (uri (cran-uri "RcppHNSW" version))
13332 "01z0plf1i6dyibw4ica8shmijyk1grpqb886hcga72z2cpm4xsx0"))))
13333 (properties `((upstream-name . "RcppHNSW")))
13334 (build-system r-build-system)
13335 (propagated-inputs (list r-rcpp))
13336 (home-page "https://cran.r-project.org/web/packages/RcppHNSW/")
13337 (synopsis "Rcpp bindings for hnswlib, a library for approximate nearest neighbors")
13339 "Hnswlib is a C++ library for approximate nearest neighbors. This
13340 package provides a minimal R interface by relying on the Rcpp package.")
13341 ;; hnswlib is released under Version 2.0 of the Apache License.
13342 (license (list license:gpl3 license:asl2.0))))
13344 (define-public r-rcppparallel
13346 (name "r-rcppparallel")
13351 (uri (cran-uri "RcppParallel" version))
13354 "1sn211ajlb1p12sglxqns175rg078yvww268m8cp0vvd7cmk55k3"))))
13355 (properties `((upstream-name . "RcppParallel")))
13356 (build-system r-build-system)
13357 (home-page "https://rcppcore.github.io/RcppParallel/")
13358 (synopsis "Parallel programming tools for Rcpp")
13360 "This package provides high level functions for parallel programming with
13361 Rcpp. For example, the @code{parallelFor()} function can be used to convert
13362 the work of a standard serial @code{for} loop into a parallel one and the
13363 @code{parallelReduce()} function can be used for accumulating aggregates or
13365 (license license:gpl2)))
13367 (define-public r-ncdf4
13374 (uri (cran-uri "ncdf4" version))
13377 "0qzvin2fjzcb7h2knlnw14s6043pwi1nm7yf6p27ax7w269173fb"))))
13378 (build-system r-build-system)
13380 (list netcdf zlib))
13381 (home-page "https://cran.r-project.org/web/packages/ncdf4/index.html")
13382 (synopsis "R interface to Unidata netCDF format data files")
13384 "This package provides a high-level R interface to data files written
13385 using Unidata's netCDF library (version 4 or earlier), which are binary data
13386 files that are portable across platforms and include metadata information in
13387 addition to the data sets. Using this package, netCDF files can be opened and
13388 data sets read in easily. It is also easy to create new netCDF dimensions,
13389 variables, and files, in either version 3 or 4 format, and manipulate existing
13391 (license license:gpl3+)))
13393 (define-public r-biocmanager
13395 (name "r-biocmanager")
13396 (version "1.30.18")
13400 (uri (cran-uri "BiocManager" version))
13402 (base32 "0dawbd546rznllpw5wq282r0viga4cck398d4s1inkk18mmi4qzp"))))
13403 (properties `((upstream-name . "BiocManager")))
13404 (build-system r-build-system)
13407 (home-page "https://cran.r-project.org/web/packages/BiocManager/")
13408 (synopsis "Access the Bioconductor project package repository")
13410 "This package provides a convenient tool to install and update
13411 Bioconductor packages.")
13412 (license license:artistic2.0)))
13414 (define-public r-rgl
13417 (version "0.108.3.2")
13421 (uri (cran-uri "rgl" version))
13424 "0r9wzhjzl346i37ngs6hqzmizhi53kzqz582lv822v6yxang6fh3"))))
13425 (build-system r-build-system)
13427 (list pkg-config r-knitr))
13442 (home-page "https://r-forge.r-project.org/projects/rgl/")
13443 (synopsis "3D visualization using OpenGL")
13445 "This package provides medium to high level functions for 3D interactive graphics,
13446 including functions modelled on base graphics (@code{plot3d()}, etc.) as well
13447 as functions for constructing representations of geometric
13448 objects (@code{cube3d()}, etc.). Output may be on screen using OpenGL, or to
13449 various standard 3D file formats including WebGL, PLY, OBJ, STL as well as 2D
13450 image formats, including PNG, Postscript, SVG, PGF.")
13451 ;; Any version of the GPL.
13452 (license (list license:gpl2+ license:gpl3+))))
13454 (define-public r-multicool
13456 (name "r-multicool")
13461 (uri (cran-uri "multicool" version))
13464 "0djacq0irfqz4nlnx238kja73yvr1n5qybbfyl6bw1n6qgcjhza8"))))
13465 (build-system r-build-system)
13466 (propagated-inputs (list r-rcpp))
13467 (home-page "https://cran.r-project.org/web/packages/multicool/")
13468 (synopsis "Permutations of multisets in cool-lex order")
13470 "This package provides a set of tools to permute multisets without loops
13471 or hash tables and to generate integer partitions. Cool-lex order is similar
13472 to colexicographical order.")
13473 (license license:gpl2)))
13475 (define-public r-misc3d
13482 (uri (cran-uri "misc3d" version))
13485 "0r9x57s63kx9f6dgam2nhbziq8nrs9wd8pk7g76hds2kw46vnyx0"))))
13486 (build-system r-build-system)
13487 (home-page "https://cran.r-project.org/web/packages/misc3d/")
13488 (synopsis "Miscellaneous 3D Plots")
13490 "This package provides a collection of miscellaneous 3d plots, including
13492 ;; Any version of the GPL.
13493 (license (list license:gpl2+ license:gpl3+))))
13495 (define-public r-ks
13502 (uri (cran-uri "ks" version))
13504 (base32 "05bqrjkbx2kn5aax0hy3xd6pf7nxka9bm1sp8ll1cc2gf1nx1i6i"))))
13505 (build-system r-build-system)
13517 (home-page "https://www.mvstat.net/tduong/")
13518 (synopsis "Kernel smoothing")
13520 "This package provides kernel smoothers for univariate and multivariate
13521 data, including density functions, density derivatives, cumulative
13522 distributions, modal clustering, discriminant analysis, and two-sample
13523 hypothesis testing.")
13524 ;; Either version of the GPL.
13525 (license (list license:gpl2 license:gpl3))))
13527 (define-public r-feature
13534 (uri (cran-uri "feature" version))
13537 "0yzn1w1sasilcp8v0pcjnxjv9l6lspkskqi412i6h040gqmjjf6y"))))
13538 (build-system r-build-system)
13540 (list r-ks r-plot3d))
13543 (home-page "https://www.mvstat.net/tduong/")
13544 (synopsis "Inferential feature significance for kernel density estimation")
13546 "The feature package contains functions to display and compute kernel
13547 density estimates, significant gradient and significant curvature regions.
13548 Significant gradient and/or curvature regions often correspond to significant
13549 features (e.g. local modes).")
13550 ;; Either version of the GPL.
13551 (license (list license:gpl2 license:gpl3))))
13553 (define-public r-arm
13560 (uri (cran-uri "arm" version))
13563 "0pagrc1vkaz460d0lvrgb4xj6gcd920f4mrc8zpzw07c3v1s2sw1"))))
13564 (build-system r-build-system)
13572 (home-page "https://cran.r-project.org/web/packages/arm/")
13573 (synopsis "Data analysis using regression and multilevel/hierarchical models")
13575 "This package provides functions to accompany A. Gelman and J. Hill,
13576 Data Analysis Using Regression and Multilevel/Hierarchical Models, Cambridge
13577 University Press, 2007.")
13578 (license license:gpl3+)))
13580 (define-public r-circular
13582 (name "r-circular")
13587 (uri (cran-uri "circular" version))
13590 "1qmwj1pf37lc2s5r83y7nqckscznqhbsv66bdfgfbby7x4qkwga8"))))
13591 (build-system r-build-system)
13593 (list r-boot r-mvtnorm))
13596 (home-page "https://cran.r-project.org/web/packages/circular/")
13597 (synopsis "Circular statistics")
13599 "This package provides tools for circular statistics, from \"Topics in
13600 circular Statistics\" (2001) S. Rao Jammalamadaka and A. SenGupta, World
13602 (license license:gpl2+)))
13604 (define-public r-activity
13606 (name "r-activity")
13611 (uri (cran-uri "activity" version))
13614 "11n6wmqz7p3428rr615f92m61a5gb908xpn4l8q484h61bwg38c3"))))
13615 (build-system r-build-system)
13617 (list r-insol r-pbapply))
13618 (home-page "https://cran.r-project.org/web/packages/activity/")
13619 (synopsis "Animal activity statistics")
13621 "This package provides functions to fit kernel density functions to
13622 animal activity time data; plot activity distributions; quantify overall
13623 levels of activity; statistically compare activity metrics through
13624 bootstrapping; and evaluate variation in linear variables with time (or other
13625 circular variables).")
13626 (license license:gpl3)))
13628 (define-public r-ouch
13635 (uri (cran-uri "ouch" version))
13638 "119s9llpjy0b4q830xig2xr66fq6izp6mr2k4k79ggmf3gxww8as"))))
13639 (build-system r-build-system)
13640 (propagated-inputs (list r-subplex))
13641 (home-page "https://kingaa.github.io/ouch/")
13642 (synopsis "Ornstein-Uhlenbeck models for phylogenetic comparative hypotheses")
13644 "This package provides tools to fit and compare Ornstein-Uhlenbeck models
13645 for evolution along a phylogenetic tree.")
13646 (license license:gpl2+)))
13648 (define-public r-fmsb
13655 (uri (cran-uri "fmsb" version))
13658 "1gi94xr0b1yk9xzwfprfafxi25yic1lcivd66p73n6iqfzdaimbk"))))
13659 (build-system r-build-system)
13660 (home-page "http://minato.sip21c.org/msb/")
13661 (synopsis "Functions for medical statistics book with demographic data")
13663 "This package provides several utility functions for the book entitled
13664 \"Practices of Medical and Health Data Analysis using R\" (Pearson Education
13665 Japan, 2007) with Japanese demographic data and some demographic analysis
13666 related functions.")
13667 (license license:gpl2+)))
13669 (define-public r-stabledist
13671 (name "r-stabledist")
13676 (uri (cran-uri "stabledist" version))
13679 "0scar396wiq6wkbkvwp4qrxqc1m075y56p37i6iry5rw796p1i86"))))
13680 (build-system r-build-system)
13681 (home-page "https://www.rmetrics.org")
13682 (synopsis "Stable distribution functions")
13684 "This package provides density, probability and quantile functions, and
13685 random number generation for (skew) stable distributions, using the
13686 parametrizations of Nolan.")
13687 (license license:gpl2+)))
13689 (define-public r-gsl
13692 (version "2.1-7.1")
13696 (uri (cran-uri "gsl" version))
13699 "118rj9kjx9rzlynvhrly19qz3yxg8jzws35971ssgzrp5lwd367f"))))
13700 (build-system r-build-system)
13703 (home-page "https://cran.r-project.org/web/packages/gsl")
13704 (synopsis "Wrapper for the GNU Scientific Library")
13706 "This package provides an R wrapper for the special functions and quasi
13707 random number generators of the GNU Scientific Library.")
13708 (license license:gpl2+)))
13710 (define-public r-adgoftest
13712 (name "r-adgoftest")
13717 (uri (cran-uri "ADGofTest" version))
13720 "0ik817qzqp6kfbckjp1z7srlma0w6z2zcwykh0jdiv7nahwk3ncw"))))
13721 (properties `((upstream-name . "ADGofTest")))
13722 (build-system r-build-system)
13723 (home-page "https://cran.r-project.org/web/packages/ADGofTest")
13724 (synopsis "Anderson-Darling GoF test")
13726 "This package provides an implementation of the Anderson-Darling GoF test
13727 with p-value calculation based on Marsaglia's 2004 paper \"Evaluating the
13728 Anderson-Darling Distribution\".")
13729 ;; Any version of the GPL.
13730 (license license:gpl3+)))
13732 (define-public r-admisc
13739 (uri (cran-uri "admisc" version))
13741 (base32 "07hfrhv3pcldsffnyfzpa1q3x32gxr1386r8fik1nhql2w46mm13"))))
13742 (properties `((upstream-name . "admisc")))
13743 (build-system r-build-system)
13744 (home-page "https://github.com/dusadrian/admisc")
13745 (synopsis "Adrian Dusa's miscellaneous")
13747 "This package contains miscellaneous functions used to interpret and
13748 translate, factorize and negate Sum of Products expressions, for both binary
13749 and multi-value crisp sets, and to extract information (set names, set values)
13750 from those expressions. Other functions perform various other checks if
13751 possibly numeric (even if all numbers reside in a character vector) and coerce
13752 to numeric, or check if the numbers are whole. It also offers, among many
13753 others, a highly flexible recoding routine and a more flexible alternative to
13754 the base function @code{with()}.")
13755 (license license:gpl3+)))
13757 (define-public r-sodium
13764 (uri (cran-uri "sodium" version))
13767 "0x4jb3cf1nv1spz1jc9xp8hly2b4a7nj48xr4s33jnfcpdjkmn5q"))))
13768 (properties `((upstream-name . "sodium")))
13769 (build-system r-build-system)
13773 (list pkg-config r-knitr))
13774 (home-page "https://github.com/jeroen/sodium")
13775 (synopsis "R bindings to the libsodium crypto library")
13777 "This package provides bindings to libsodium: a library for encryption,
13778 decryption, signatures, password hashing and more. Sodium uses curve25519, a
13779 Diffie-Hellman function by Daniel Bernstein, which has become very popular
13780 after it was discovered that the NSA had backdoored Dual EC DRBG.")
13781 (license license:expat)))
13783 (define-public r-softimpute
13785 (name "r-softimpute")
13790 (uri (cran-uri "softImpute" version))
13793 "1v2a4d688ij5zcvkzpra9yx40xckdfnllnfnyq2450zf3n1kjk7a"))))
13794 (properties `((upstream-name . "softImpute")))
13795 (build-system r-build-system)
13799 (list gfortran r-knitr))
13800 (home-page "https://cran.r-project.org/web/packages/softImpute")
13801 (synopsis "Matrix completion via iterative soft-thresholded SVD")
13803 "This package provides iterative methods for matrix completion that use
13804 nuclear-norm regularization. The package includes procedures for centering
13805 and scaling rows, columns or both, and for computing low-rank @dfn{single
13806 value decompositions} (SVDs) on large sparse centered matrices (i.e. principal
13808 (license license:gpl2)))
13810 (define-public r-fftwtools
13812 (name "r-fftwtools")
13817 (uri (cran-uri "fftwtools" version))
13820 "0zrchp4l0jdbir2gibjf00x225y9giqk80zvqmr2yyvc12lwkw7i"))))
13821 (build-system r-build-system)
13822 (inputs (list fftw))
13825 (home-page "https://github.com/krahim/fftwtools")
13826 (synopsis "Wrapper for FFTW3")
13828 "This package provides a wrapper for several FFTW functions. It provides
13829 access to the two-dimensional FFT, the multivariate FFT, and the
13830 one-dimensional real to complex FFT using the FFTW3 library. The package
13831 includes the functions @code{fftw()} and @code{mvfftw()} which are designed to
13832 mimic the functionality of the R functions @code{fft()} and @code{mvfft()}.
13833 The FFT functions have a parameter that allows them to not return the
13834 redundant complex conjugate when the input is real data.")
13835 (license license:gpl2+)))
13837 (define-public r-tiff
13844 (uri (cran-uri "tiff" version))
13847 "0xgc7vyndxxahfhc2qqzmwi56bnfyl0pn72l820jz5sd24aymhxq"))))
13848 (build-system r-build-system)
13850 (list libtiff libjpeg-turbo zlib))
13853 (home-page "https://www.rforge.net/tiff/")
13854 (synopsis "Read and write TIFF images")
13856 "This package provides an easy and simple way to read, write and display
13857 bitmap images stored in the TIFF format. It can read and write both files and
13858 in-memory raw vectors.")
13859 ;; Either of these two license versions.
13860 (license (list license:gpl2 license:gpl3))))
13862 (define-public r-nlp
13869 (uri (cran-uri "NLP" version))
13872 "1dpj04fmld2lnhg072ahgjbhmciqqy9h1lrz0wf32mr7mm9s9sh5"))))
13873 (properties `((upstream-name . "NLP")))
13874 (build-system r-build-system)
13875 (home-page "https://cran.r-project.org/web/packages/NLP/")
13876 (synopsis "Natural language processing infrastructure")
13878 "This package provides basic classes and methods for Natural Language
13880 (license license:gpl3)))
13882 (define-public r-tm
13889 (uri (cran-uri "tm" version))
13892 "0mk2lsplynms15nw92vbdgsafg4bw1m0ik31gch1mnsnv61idsxi"))))
13893 (properties `((upstream-name . "tm")))
13894 (build-system r-build-system)
13896 (list r-bh r-nlp r-rcpp r-slam r-xml2))
13897 (home-page "http://tm.r-forge.r-project.org/")
13898 (synopsis "Text mining package")
13900 "This package provides a framework for text mining applications within R.")
13901 (license license:gpl3)))
13903 (define-public r-waveslim
13905 (name "r-waveslim")
13910 (uri (cran-uri "waveslim" version))
13913 "0ibivnhz0l06sss5rrrcvyiwg3qpbyk3qn4vx4pp90kj09x4yg0k"))))
13914 (build-system r-build-system)
13917 (home-page "http://waveslim.blogspot.com")
13918 (synopsis "Basic wavelet routines for signal processing")
13920 "This package provides basic wavelet routines for time series (1D),
13921 image (2D) and array (3D) analysis. The code provided here is based on
13922 wavelet methodology developed in Percival and Walden (2000); Gencay, Selcuk
13923 and Whitcher (2001); the dual-tree complex wavelet transform (DTCWT) from
13924 Kingsbury (1999, 2001) as implemented by Selesnick; and Hilbert wavelet
13925 pairs (Selesnick 2001, 2002).")
13926 (license license:bsd-3)))
13928 (define-public r-wordcloud
13930 (name "r-wordcloud")
13935 (uri (cran-uri "wordcloud" version))
13938 "0j96yyvm6bcrrpbdx4w26piqx44a0vbsr3px9cb4zk8a8da6jwak"))))
13939 (build-system r-build-system)
13941 (list r-rcolorbrewer r-rcpp
13942 ;; The "tm" package is only "suggested" according to CRAN, but the
13943 ;; wordcloud package cannot be loaded without it.
13945 (home-page "https://cran.r-project.org/web/packages/wordcloud")
13946 (synopsis "Word clouds")
13948 "This package provides functionality to create pretty word clouds,
13949 visualize differences and similarity between documents, and avoid
13950 over-plotting in scatter plots with text.")
13951 (license license:lgpl2.1)))
13953 (define-public r-colorramps
13955 (name "r-colorramps")
13960 (uri (cran-uri "colorRamps" version))
13963 "12jnkj50yh2hc5l7j56lrrrmn58akrj9dwj98vzf42iq4h42kwb1"))))
13964 (properties `((upstream-name . "colorRamps")))
13965 (build-system r-build-system)
13966 (home-page "https://cran.r-project.org/web/packages/colorRamps")
13967 (synopsis "Build color tables")
13968 (description "This package provides features to build gradient color
13970 ;; Any version of the GPL
13971 (license license:gpl3+)))
13973 (define-public r-tidytree
13975 (name "r-tidytree")
13980 (uri (cran-uri "tidytree" version))
13982 (base32 "1prfv2jy6z4zp4gyi9krzbysipsbnjrkxcccflm4nwsd9i7mshqj"))))
13983 (build-system r-build-system)
13997 (home-page "https://github.com/GuangchuangYu/tidytree")
13998 (synopsis "Tidy tool for phylogenetic tree data manipulation")
14000 "Phylogenetic trees generally contain multiple components including nodes,
14001 edges, branches and associated data. This package provides an approach to
14002 convert tree objects to tidy data frames. It also provides tidy interfaces to
14003 manipulate tree data.")
14004 (license license:artistic2.0)))
14006 (define-public r-rvcheck
14013 (uri (cran-uri "rvcheck" version))
14015 (base32 "09khjklvzbafd7r55496by01a9g3y291d87hpy43w44dmz9fzn9a"))))
14016 (build-system r-build-system)
14018 (list r-biocmanager r-yulab-utils))
14019 (home-page "https://cran.r-project.org/web/packages/rvcheck")
14020 (synopsis "R package version check")
14022 "This package provides tools to check the latest release version of R and
14023 R packages (on CRAN, Bioconductor or Github).")
14024 (license license:artistic2.0)))
14026 (define-public r-docopt
14033 (uri (cran-uri "docopt" version))
14036 "1zxhwizs916qm5by7nfslqnarl2q5202xc2azlhrnzk0wj3khiwz"))))
14037 (build-system r-build-system)
14038 (home-page "https://github.com/docopt/docopt.R")
14039 (synopsis "Command-line interface specification language")
14041 "This package enables you to define a command-line interface by just
14042 giving it a description in the specific format.")
14043 (license license:expat)))
14045 (define-public r-sparsesvd
14047 (name "r-sparsesvd")
14052 (uri (cran-uri "sparsesvd" version))
14055 "1xm969fjq3fv1p2sqza2apz8picibj4s2agpwf1sx9nwn3b587qs"))))
14056 (build-system r-build-system)
14057 (propagated-inputs (list r-matrix))
14058 (home-page "http://tedlab.mit.edu/~dr/SVDLIBC/")
14059 (synopsis "Sparse truncated singular value decomposition")
14061 "This package provides a Wrapper around the SVDLIBC library
14062 for (truncated) singular value decomposition of a sparse matrix. Currently,
14063 only sparse real matrices in Matrix package format are supported.")
14064 ;; SVDLIBC is released under BSD-2. The R interface is released under
14066 (license (list license:bsd-3 license:bsd-2))))
14068 (define-public r-speedglm
14070 (name "r-speedglm")
14075 (uri (cran-uri "speedglm" version))
14078 "1kj662nfkfhvx37jrbvxd4dyjclz5cm3xh50z7s5rbzapiyxn4hs"))))
14079 (build-system r-build-system)
14081 (list r-mass r-matrix))
14082 (home-page "https://cran.r-project.org/web/packages/speedglm")
14083 (synopsis "Fit linear and generalized linear models to large data sets")
14085 "This package provides tools for fitting linear models and generalized
14086 linear models to large data sets by updating algorithms.")
14087 ;; Any version of the GPL
14088 (license license:gpl2+)))
14090 (define-public r-densityclust
14092 (name "r-densityclust")
14097 (uri (cran-uri "densityClust" version))
14100 "05x2fi1zdnkrg2nimf8k904j3lpyw0f7nmk6ax5p7x7a98wb2iqs"))))
14101 (properties `((upstream-name . "densityClust")))
14102 (build-system r-build-system)
14111 (home-page "https://cran.r-project.org/web/packages/densityClust")
14112 (synopsis "Clustering by fast search and find of density peaks")
14114 "This package provides an improved implementation (based on k-nearest
14115 neighbors) of the density peak clustering algorithm, originally described by
14116 Alex Rodriguez and Alessandro Laio (Science, 2014 vol. 344). It can handle
14117 large datasets (> 100,000 samples) very efficiently.")
14118 (license license:gpl2+)))
14120 (define-public r-combinat
14122 (name "r-combinat")
14127 (uri (cran-uri "combinat" version))
14130 "1h9hr88gigihc4na7lb5i7rn4az1xa7sb34zvnznaj6pdrmwy4qm"))))
14131 (build-system r-build-system)
14132 (home-page "https://cran.r-project.org/web/packages/combinat")
14133 (synopsis "Combinatorics utilities")
14134 (description "This package provides assorted routines for combinatorics.")
14135 (license license:gpl2)))
14137 (define-public r-qlcmatrix
14139 (name "r-qlcmatrix")
14144 (uri (cran-uri "qlcMatrix" version))
14147 "0iqkcvvy8rxlk0s83sjq57dd6fadb18p5z31lzy0gnzv1hsy1x8y"))))
14148 (properties `((upstream-name . "qlcMatrix")))
14149 (build-system r-build-system)
14151 (list r-docopt r-matrix r-slam r-sparsesvd))
14152 (home-page "https://cran.r-project.org/web/packages/qlcMatrix")
14153 (synopsis "Sparse matrix functions for quantitative language comparison")
14155 "This package provides an extension of the functionality of the Matrix
14156 package for using sparse matrices. Some of the functions are very general,
14157 while other are highly specific for the special data format used for
14158 @dfn{quantitative language comparison} (QLC).")
14159 (license license:gpl3)))
14161 (define-public r-ddrtree
14168 (uri (cran-uri "DDRTree" version))
14171 "16s5fjw7kwlxhrkzdny62sx32fvmg3rxjc3wrh6krd31jh1fqlfk"))))
14172 (properties `((upstream-name . "DDRTree")))
14173 (build-system r-build-system)
14175 (list r-bh r-irlba r-rcpp r-rcppeigen))
14176 (home-page "https://cran.r-project.org/web/packages/DDRTree")
14177 (synopsis "Learning principal graphs with DDRTree")
14179 "This package provides an implementation of the framework of
14180 @dfn{reversed graph embedding} (RGE) which projects data into a reduced
14181 dimensional space while constructs a principal tree which passes through the
14182 middle of the data simultaneously. DDRTree shows superiority to
14183 alternatives (Wishbone, DPT) for inferring the ordering as well as the
14184 intrinsic structure of single cell genomics data. In general, it could be
14185 used to reconstruct the temporal progression as well as the bifurcation
14186 structure of any data type.")
14187 (license license:asl2.0)))
14189 (define-public r-corpcor
14196 (uri (cran-uri "corpcor" version))
14199 "028fw61n61i79fhnaqx7gmdifdpbvp3yiaq9vvfrbv4k7i84r83i"))))
14200 (build-system r-build-system)
14201 (home-page "http://strimmerlab.org/software/corpcor/")
14202 (synopsis "Efficient estimation of covariance and (partial) correlation")
14204 "This package implements a James-Stein-type shrinkage estimator for the
14205 covariance matrix, with separate shrinkage for variances and correlations.
14206 Furthermore, functions are available for fast singular value decomposition,
14207 for computing the pseudoinverse, and for checking the rank and positive
14208 definiteness of a matrix.")
14209 (license license:gpl3+)))
14211 (define-public r-rspectra
14213 (name "r-rspectra")
14218 (uri (cran-uri "RSpectra" version))
14221 "16ij84wgpsmqmnxqiii8dgihy3bfxazry9znmckhwzba7m0d79fb"))))
14222 (properties `((upstream-name . "RSpectra")))
14223 (build-system r-build-system)
14225 (list r-matrix r-rcpp r-rcppeigen))
14228 (home-page "https://github.com/yixuan/RSpectra")
14229 (synopsis "Solvers for large-scale Eigenvalue and SVD problems")
14231 "This package provides an R interface to the Spectra library for
14232 large-scale eigenvalue and SVD problems. It is typically used to compute a
14233 few eigenvalues/vectors of an n by n matrix, e.g., the k largest eigenvalues,
14234 which is usually more efficient than @code{eigen()} if k << n.")
14236 (license license:mpl2.0)))
14238 (define-public r-vbsr
14245 (uri (cran-uri "vbsr" version))
14248 "1avskbxxyinjjdga4rnghcfvd4sypv4m39ysfaij5avvmi89bx3b"))))
14249 (build-system r-build-system)
14250 (home-page "https://cran.r-project.org/web/packages/vbsr")
14251 (synopsis "Variational Bayes spike regression regularized linear models")
14253 "This package provides an efficient algorithm for solving ultra-sparse
14254 regularized regression models using a variational Bayes algorithm with a spike
14255 prior. The algorithm is solved on a path, with coordinate updates, and is
14256 capable of generating very sparse models. Very general model
14257 diagnostics for controlling type-1 errors are also provided.")
14258 (license license:gpl2)))
14260 (define-public r-flare
14263 (version "1.7.0.1")
14267 (uri (cran-uri "flare" version))
14270 "1xvrbvq2y7zfp98ijal3z8y1w2xbzfcdykzw4pqc3mnh0qrhq2d5"))))
14271 (build-system r-build-system)
14273 (list r-igraph r-lattice r-mass r-matrix))
14274 (home-page "https://cran.r-project.org/web/packages/flare")
14275 (synopsis "Family of Lasso regression implementations")
14277 "This package provides implementations of a family of Lasso variants
14278 including Dantzig Selector, LAD Lasso, SQRT Lasso, Lq Lasso for estimating
14279 high dimensional sparse linear models.")
14280 (license license:gpl2)))
14282 (define-public r-lassopv
14289 (uri (cran-uri "lassopv" version))
14292 "0yawnjw063jypk3riy9xab9cmliv6c9dnabi18670khd3gzb2r9z"))))
14293 (build-system r-build-system)
14294 (propagated-inputs (list r-lars))
14295 (home-page "https://github.com/lingfeiwang/lassopv")
14296 (synopsis "Non-parametric p-value estimation for predictors in Lasso")
14298 "This package enables you to estimate the p-values for predictors x
14299 against target variable y in Lasso regression, using the regularization
14300 strength when each predictor enters the active set of regularization path for
14301 the first time as the statistic.")
14302 (license license:gpl3)))
14304 (define-public r-splitstackshape
14306 (name "r-splitstackshape")
14311 (uri (cran-uri "splitstackshape" version))
14314 "0mpyf2kkfdl69pdc6brl1r6101vyc6pgr7z17s55ppg3y71k4q35"))))
14315 (build-system r-build-system)
14317 (list r-data-table))
14318 (home-page "https://github.com/mrdwab/splitstackshape")
14319 (synopsis "Stack and reshape datasets after splitting concatenated values")
14321 "Online data collection tools like Google Forms often export
14322 multiple-response questions with data concatenated in cells. The
14323 @code{concat.split} (cSplit) family of functions provided by this package
14324 splits such data into separate cells. This package also includes functions to
14325 stack groups of columns and to reshape wide data, even when the data are
14326 \"unbalanced\"---something which @code{reshape} (from base R) does not handle,
14327 and which @code{melt} and @code{dcast} from @code{reshape2} do not easily
14329 (license license:gpl3)))
14331 (define-public r-tfmpvalue
14333 (name "r-tfmpvalue")
14338 (uri (cran-uri "TFMPvalue" version))
14341 "0h9qkl15k8v17v3g9bdnfwvh2s04ywjgg5y0xn2077dmywlja1bd"))))
14342 (properties `((upstream-name . "TFMPvalue")))
14343 (build-system r-build-system)
14344 (propagated-inputs (list r-rcpp))
14345 (home-page "https://github.com/ge11232002/TFMPvalue")
14346 (synopsis "P-value computation for position weight matrices")
14348 "In putative @dfn{Transcription Factor Binding Sites} (TFBSs)
14349 identification from sequence/alignments, we are interested in the significance
14350 of certain match scores. TFMPvalue provides the accurate calculation of a
14351 p-value with a score threshold for position weight matrices, or the score with
14352 a given p-value. It is an interface to code originally made available by
14353 Helene Touzet and Jean-Stephane Varre, 2007, Algorithms Mol Biol:2, 15.
14354 Touzet and Varre (2007).")
14355 (license license:gpl2)))
14357 (define-public r-rncl
14363 (uri (cran-uri "rncl" version))
14366 "1ywgwqn82z8h6zpcxxq4hgngdpfa6dj0lr7bfq4cwfml9z075jgw"))))
14367 (build-system r-build-system)
14369 (list r-progress r-rcpp))
14370 (home-page "https://github.com/fmichonneau/rncl")
14371 (synopsis "Interface to the Nexus class library")
14372 (description "This package provides an interface to the Nexus class
14373 library which allows parsing of NEXUS, Newick and other phylogenetic tree
14374 file formats. It provides elements of the file that can be used to build
14375 phylogenetic objects such as @code{ape}'s @code{phylo} or @code{phylobase}'s
14376 @code{phylo4(d)}. This functionality is demonstrated with
14377 @code{read_newick_phylo()} and @code{read_nexus_phylo()}.")
14378 (license license:bsd-2)))
14380 (define-public r-phylobase
14382 (name "r-phylobase")
14386 (uri (cran-uri "phylobase" version))
14389 "0jzr1gdvmi4l640hwwzh9bxqmpja69bn3ygnaqx37awvyh7khi2s"))))
14390 (build-system r-build-system)
14392 (list r-ade4 r-ape r-rcpp r-rncl r-rnexml))
14395 (home-page "https://github.com/fmichonneau/phylobase")
14396 (synopsis "Base package for phylogenetic structures and comparative data")
14397 (description "This package provides a base @code{S4} class for comparative
14398 methods, incorporating one or more trees and trait data.")
14399 (license license:gpl2+)))
14401 (define-public r-rnexml
14407 (uri (cran-uri "RNeXML" version))
14410 "1zp6pijsc73jx8cmxb1hng36nvaf5wnhldnzlqhmba9kv9niscfb"))))
14411 (build-system r-build-system)
14428 (home-page "https://docs.ropensci.org/RNeXML/")
14429 (synopsis "Semantically rich I/O for the NeXML Format")
14430 (description "This package provides access to phyloinformatic data in
14431 NeXML format. The package should add new functionality to R such as the
14432 possibility to manipulate NeXML objects in more various and refined way
14433 and compatibility with @code{ape} objects.")
14434 (license license:bsd-3)))
14436 (define-public r-rnifti
14443 (uri (cran-uri "RNifti" version))
14446 "0kkj9dby85iwnlqb7zwrh1xidlvqip7i1mbgckb5qg4b0a3zgibc"))))
14447 (properties `((upstream-name . "RNifti")))
14448 (build-system r-build-system)
14449 (inputs (list zlib))
14450 (propagated-inputs (list r-rcpp))
14451 (home-page "https://github.com/jonclayden/RNifti")
14452 (synopsis "Fast R and C++ access to NIfTI images")
14454 "This package provides very fast read and write access to images stored
14455 in the NIfTI-1 and ANALYZE-7.5 formats, with seamless synchronisation between
14456 compiled C and interpreted R code. It also provides a C/C++ API that can be
14457 used by other packages.")
14458 (license license:gpl2)))
14460 (define-public r-shades
14467 (uri (cran-uri "shades" version))
14470 "1zg95sjhrfvbdlfc387g9p0vnb8nb6agdk1mb3wq3kwkm2da0bqj"))))
14471 (build-system r-build-system)
14472 (home-page "https://github.com/jonclayden/shades")
14473 (synopsis "Simple color manipulation")
14475 "This package provides functions for easily manipulating colors,
14476 creating color scales and calculating color distances.")
14477 (license license:bsd-3)))
14479 (define-public r-ore
14482 (version "1.7.1.1")
14486 (uri (cran-uri "ore" version))
14488 (base32 "0rs5r5h11x4l4nsbl4xqzbl4ahajd5374fq05abcmfjnjr9j64w5"))))
14489 (build-system r-build-system)
14490 (home-page "https://github.com/jonclayden/ore")
14491 (synopsis "R interface to the Onigmo regular expression library")
14493 "This package provides an alternative to R's built-in functionality for
14494 handling regular expressions, based on the Onigmo library. It offers
14495 first-class compiled regex objects, partial matching and function-based
14496 substitutions, amongst other features.")
14497 (license license:bsd-3)))
14499 (define-public r-reportr
14506 (uri (cran-uri "reportr" version))
14509 "0zynplxqvbmf23cm2rsz3wz2jx6mv55z94mn1k44ny3lx625cnpw"))))
14510 (build-system r-build-system)
14511 (propagated-inputs (list r-ore))
14512 (home-page "https://github.com/jonclayden/reportr")
14513 (synopsis "General message and error reporting system")
14515 "This package provides a system for reporting messages, which offers
14516 certain useful features over the standard R system, such as the incorporation
14517 of output consolidation, message filtering, assertions, expression
14518 substitution, automatic generation of stack traces for debugging, and
14519 conditional reporting based on the current \"output level\".")
14520 (license license:gpl2)))
14522 (define-public r-tractor-base
14524 (name "r-tractor-base")
14525 (version "3.3.3.1")
14529 (uri (cran-uri "tractor.base" version))
14532 "0w5jw7pf77npkgig7667yikpbwv4dfk1dcq63qm88l409ga2f95p"))))
14533 (properties `((upstream-name . "tractor.base")))
14534 (build-system r-build-system)
14536 (list r-ore r-reportr r-rnifti r-shades))
14537 (home-page "https://www.tractor-mri.org.uk")
14538 (synopsis "Read, manipulate and visualize magnetic resonance images")
14540 "This package provides functions for working with magnetic resonance
14541 images. It supports reading and writing of popular file formats (DICOM,
14542 Analyze, NIfTI-1, NIfTI-2, MGH); interactive and non-interactive
14543 visualization; flexible image manipulation; metadata and sparse image
14545 (license license:gpl2)))
14547 (define-public r-grimport
14549 (name "r-grimport")
14554 (uri (cran-uri "grImport" version))
14557 "0pbzc45wgp0cpycnw0bzn65ckdszzay0zrp7c7ssxdkifp8bai3a"))))
14558 (properties `((upstream-name . "grImport")))
14559 (build-system r-build-system)
14561 (list ghostscript))
14564 (home-page "https://cran.r-project.org/web/packages/grImport")
14565 (synopsis "Convert, import, and draw PostScript pictures")
14567 "This package provides functions for converting, importing, and drawing
14568 PostScript pictures in R plots.")
14569 (license license:gpl2+)))
14571 (define-public r-grimport2
14573 (name "r-grimport2")
14578 (uri (cran-uri "grImport2" version))
14581 "19q0dd8fpp1g4xf6sg5f8dxybwxjfw553ra6wgjd8b74fzca40m1"))))
14582 (properties `((upstream-name . "grImport2")))
14583 (build-system r-build-system)
14585 (list r-base64enc r-jpeg r-png r-xml))
14586 (home-page "https://cran.r-project.org/web/packages/grImport2/")
14587 (synopsis "Import SVG graphics")
14589 "This package provides functions for importing external vector images and
14590 drawing them as part of R plots. This package is different from the
14591 @code{grImport} package because, where that package imports PostScript format
14592 images, this package imports SVG format images. Furthermore, this package
14593 imports a specific subset of SVG, so external images must be preprocessed
14594 using a package like @code{rsvg} to produce SVG that this package can import.
14595 SVG features that are not supported by R graphics, such as gradient fills, can
14596 be imported and then exported via the @code{gridSVG} package.")
14597 (license license:gpl2+)))
14599 (define-public r-kohonen
14606 (uri (cran-uri "kohonen" version))
14609 "1bk3j0n8w4fhffv89rgyn4n21c0wcx6lr8jv4wbagpxprl585381"))))
14610 (build-system r-build-system)
14613 (home-page "https://cran.r-project.org/web/packages/kohonen")
14614 (synopsis "Supervised and unsupervised self-organising maps")
14616 "This package provides functions to train @dfn{self-organising
14617 maps} (SOMs). Also interrogation of the maps and prediction using trained
14618 maps are supported. The name of the package refers to Teuvo Kohonen, the
14619 inventor of the SOM.")
14620 (license license:gpl2+)))
14622 (define-public r-nnls
14629 (uri (cran-uri "nnls" version))
14632 "07vcrrxvswrvfiha6f3ikn640yg0m2b4yd9lkmim1g0jmsmpfp8f"))))
14633 (build-system r-build-system)
14634 (native-inputs (list gfortran))
14635 (home-page "https://cran.r-project.org/web/packages/nnls")
14636 (synopsis "Lawson-Hanson algorithm for non-negative least squares")
14638 "This package provides an R interface to the Lawson-Hanson implementation
14639 of an algorithm for @dfn{non-negative least squares} (NNLS). It also allows
14640 the combination of non-negative and non-positive constraints.")
14641 (license license:gpl2+)))
14643 (define-public r-iso
14646 (version "0.0-18.1")
14650 (uri (cran-uri "Iso" version))
14653 "0vy6jdyvp751430sf2f690yhasjr70cpk3p3lnaaxjq3fs5gg99g"))))
14654 (properties `((upstream-name . "Iso")))
14655 (build-system r-build-system)
14656 (native-inputs (list gfortran))
14657 (home-page "https://www.stat.auckland.ac.nz/~rolf/")
14658 (synopsis "Functions to perform isotonic regression")
14660 "This package provides support for linear order and unimodal
14661 order (univariate) isotonic regression and bivariate isotonic regression with
14662 linear order on both variables.")
14663 (license license:gpl2+)))
14665 (define-public r-chemometricswithr
14667 (name "r-chemometricswithr")
14672 (uri (cran-uri "ChemometricsWithR" version))
14675 "166va1g3m1wv21qkmw4wpz0bsrclh3jih8smxphdc13l9pqgclpq"))))
14677 `((upstream-name . "ChemometricsWithR")))
14678 (build-system r-build-system)
14680 (list r-devtools r-kohonen r-mass r-pls))
14681 (home-page "https://github.com/rwehrens/CWR")
14682 (synopsis "Chemometrics with R")
14684 "This package provides functions and scripts used in the book
14685 \"Chemometrics with R - Multivariate Data Analysis in the Natural Sciences and
14686 Life Sciences\" by Ron Wehrens, Springer (2011).")
14687 (license license:gpl2+)))
14689 (define-public r-als
14696 (uri (cran-uri "ALS" version))
14699 "1swrn39vy50fazkpf97r7c542gkj6mlvy8gmcxllg7mf2mqx546a"))))
14700 (properties `((upstream-name . "ALS")))
14701 (build-system r-build-system)
14703 (list r-iso r-nnls))
14704 (home-page "https://cran.r-project.org/web/packages/ALS")
14705 (synopsis "Multivariate curve resolution alternating least squares")
14707 "Alternating least squares is often used to resolve components
14708 contributing to data with a bilinear structure; the basic technique may be
14709 extended to alternating constrained least squares. This package provides an
14710 implementation of @dfn{multivariate curve resolution alternating least
14711 squares} (MCR-ALS).
14713 Commonly applied constraints include unimodality, non-negativity, and
14714 normalization of components. Several data matrices may be decomposed
14715 simultaneously by assuming that one of the two matrices in the bilinear
14716 decomposition is shared between datasets.")
14717 (license license:gpl2+)))
14719 (define-public r-strucchange
14721 (name "r-strucchange")
14726 (uri (cran-uri "strucchange" version))
14729 "1y022363a4pp0mnji91sjh1qiyspkh09sybqwj03r9pmwrd7q93x"))))
14730 (build-system r-build-system)
14732 (list r-sandwich r-zoo))
14733 (home-page "https://cran.r-project.org/web/packages/strucchange")
14734 (synopsis "Testing, monitoring, and dating structural changes")
14736 "This package provides tools for testing, monitoring and dating
14737 structural changes in (linear) regression models. It features tests/methods
14738 from the generalized fluctuation test framework as well as from the F
14739 test (Chow test) framework. This includes methods to fit, plot and test
14740 fluctuation processes (e.g., CUSUM, MOSUM, recursive/moving estimates) and F
14741 statistics, respectively. It is possible to monitor incoming data online
14742 using fluctuation processes. Finally, the breakpoints in regression models
14743 with structural changes can be estimated together with confidence intervals.
14744 Emphasis is always given to methods for visualizing the data.")
14745 ;; Either of these two GPL versions
14746 (license (list license:gpl2 license:gpl3))))
14748 (define-public r-pixmap
14755 (uri (cran-uri "pixmap" version))
14758 "1v1a1adsgh5jlvvi98j4nhb1h681s97ip76zdrga12rlsjaahfw9"))))
14759 (build-system r-build-system)
14760 (home-page "https://cran.r-project.org/web/packages/pixmap")
14761 (synopsis "Tools for bitmap images")
14763 "This package provides functions for importing, exporting, plotting and
14764 other manipulations of bitmapped images.")
14765 (license license:gpl2)))
14767 (define-public r-rapidjsonr
14769 (name "r-rapidjsonr")
14774 (uri (cran-uri "rapidjsonr" version))
14777 "07zdirhbzmvq3cp4xn8ngk1lgxbbabzays315zxbs3sxrz6lzjb2"))))
14778 (build-system r-build-system)
14779 (home-page "https://cran.r-project.org/web/packages/rapidjsonr")
14780 (synopsis "JSON parser")
14782 "This package provides JSON parsing capability through the Rapidjson
14784 (license license:expat)))
14786 (define-public r-ontologyindex
14788 (name "r-ontologyindex")
14793 (uri (cran-uri "ontologyIndex" version))
14796 "0j3h1spqwjhh1wbmwivmqcyi042yy7d565c3kxgn70xrmy693x1k"))))
14797 (properties `((upstream-name . "ontologyIndex")))
14798 (build-system r-build-system)
14801 (home-page "https://cran.r-project.org/web/packages/ontologyIndex")
14802 (synopsis "Functions for processing ontologies in R")
14804 "This package provides functions for reading ontologies into R as lists
14805 and manipulating sets of ontological terms.")
14806 (license license:gpl2+)))
14808 (define-public r-gargle
14815 (uri (cran-uri "gargle" version))
14818 "0fypj70c1fjmvs57birik76wfx8a2fs4gzicbb52k57i6clwlijd"))))
14819 (build-system r-build-system)
14832 (home-page "https://gargle.r-lib.org")
14833 (synopsis "Utilities for working with Google APIs")
14835 "This package provides utilities for working with Google APIs. This
14836 includes functions and classes for handling common credential types and for
14837 preparing, executing, and processing HTTP requests.")
14838 (license license:expat)))
14840 (define-public r-bigrquery
14842 (name "r-bigrquery")
14847 (uri (cran-uri "bigrquery" version))
14850 "02msq61l7vamzpvbhvalh3qil1aa7pr68pwpsivbb6pvz6p4zyns"))))
14851 (build-system r-build-system)
14868 (home-page "https://github.com/rstats-db/bigrquery")
14869 (synopsis "R interface to Google's BigQuery API")
14871 "This package provides an R interface to Google's BigQuery database.")
14872 (license license:gpl3)))
14874 (define-public r-gmp
14881 (uri (cran-uri "gmp" version))
14884 "0llyd1wx606vpgvv7d61m0fv2a5yxsmisd38fhzanbjl2wynzrwa"))))
14885 (build-system r-build-system)
14888 (modify-phases %standard-phases
14889 (add-after 'unpack 'set-CC
14890 (lambda _ (setenv "CC" "gcc") #t)))))
14891 (inputs (list gmp))
14892 (home-page "https://cran.r-project.org/web/packages/gmp")
14893 (synopsis "Multiple precision arithmetic")
14895 "This package supports multiple precision arithmetic (big integers and
14896 rationals, prime number tests, matrix computation), \"arithmetic without
14897 limitations\" using the GNU Multiple Precision library.")
14898 ;; Any version of the GPL.
14899 (license license:gpl3+)))
14901 (define-public r-rmpfr
14908 (uri (cran-uri "Rmpfr" version))
14911 "1ljpbxvm4agbxnab5dfffbpw5k964hy3gw57dzydq1gpbxwdphlk"))))
14912 (properties `((upstream-name . "Rmpfr")))
14913 (build-system r-build-system)
14920 (home-page "http://rmpfr.r-forge.r-project.org/")
14921 (synopsis "R bindings to the MPFR library")
14923 "This package supports arithmetic (via S4 classes and methods) for
14924 arbitrary precision floating point numbers, including transcendental
14925 functions. To this end, the package interfaces with the @dfn{Multiple
14926 Precision Floating-Point Reliable} (MPFR) library.")
14927 (license license:gpl2+)))
14929 (define-public r-assertive-base
14931 (name "r-assertive-base")
14936 (uri (cran-uri "assertive.base" version))
14939 "07m0ddz092bgbl2fn1yk932h0iajdcqkri632477wl5a1q5r3w2b"))))
14941 `((upstream-name . "assertive.base")))
14942 (build-system r-build-system)
14943 (home-page "https://bitbucket.org/richierocks/assertive.base")
14944 (synopsis "Core of the assertive package")
14946 "This package provides a minimal set of predicates and assertions used by
14947 the assertive package. This is mainly for use by other package developers who
14948 want to include run-time testing features in their own packages.")
14949 (license license:gpl3+)))
14951 (define-public r-assertive-properties
14953 (name "r-assertive-properties")
14958 (uri (cran-uri "assertive.properties" version))
14961 "1pgljbwwbvbl4kc5c8mcv0qbzq3k6fzi29k88811yml263sm92dn"))))
14963 `((upstream-name . "assertive.properties")))
14964 (build-system r-build-system)
14966 (list r-assertive-base))
14967 (home-page "https://bitbucket.org/richierocks/assertive.properties")
14968 (synopsis "Assertions to check properties of variables")
14970 "This package provides a set of predicates and assertions for checking
14971 the properties of variables, such as length, names and attributes. This is
14972 mainly for use by other package developers who want to include run-time
14973 testing features in their own packages.")
14974 (license license:gpl3+)))
14976 (define-public r-assertive-numbers
14978 (name "r-assertive-numbers")
14983 (uri (cran-uri "assertive.numbers" version))
14986 "0jc3ss64j4m7bjydhagwwmka5n7c72vpw4kfcch0m5jvkq5qrqds"))))
14988 `((upstream-name . "assertive.numbers")))
14989 (build-system r-build-system)
14991 (list r-assertive-base))
14992 (home-page "https://bitbucket.org/richierocks/assertive.numbers")
14993 (synopsis "Assertions to check properties of numbers")
14995 "This package provides a set of predicates and assertions for checking
14996 the properties of numbers. This is mainly for use by other package developers
14997 who want to include run-time testing features in their own packages.")
14998 (license license:gpl3+)))
15000 (define-public r-assertive-sets
15002 (name "r-assertive-sets")
15007 (uri (cran-uri "assertive.sets" version))
15010 "1cqvh2syvh5b6d85h601zjmsdbbf3h8q98ids4dfl4frdshpasc7"))))
15012 `((upstream-name . "assertive.sets")))
15013 (build-system r-build-system)
15015 (list r-assertive-base))
15016 (home-page "https://bitbucket.org/richierocks/assertive.sets")
15017 (synopsis "Assertions to check properties of sets")
15019 "This package provides a set of predicates and assertions for checking
15020 the properties of sets. This is mainly for use by other package developers
15021 who want to include run-time testing features in their own packages.")
15022 (license license:gpl3+)))
15024 (define-public r-assertive-matrices
15026 (name "r-assertive-matrices")
15031 (uri (cran-uri "assertive.matrices" version))
15034 "16sykzcndv6y2d43x6v9n7m95kv76364h39kh10w4z0xw6ksfqil"))))
15036 `((upstream-name . "assertive.matrices")))
15037 (build-system r-build-system)
15039 (list r-assertive-base))
15040 (home-page "https://bitbucket.org/richierocks/assertive.matrices")
15041 (synopsis "Assertions to check properties of matrices")
15043 "This package provides a set of predicates and assertions for checking
15044 the properties of matrices. This is mainly for use by other package
15045 developers who want to include run-time testing features in their own
15047 (license license:gpl3+)))
15049 (define-public r-assertive-models
15051 (name "r-assertive-models")
15056 (uri (cran-uri "assertive.models" version))
15059 "0bn4j4v5qvb2d672cgri61p8d9v258pmz35y3lvm6b9mdxwdi9mr"))))
15061 `((upstream-name . "assertive.models")))
15062 (build-system r-build-system)
15064 (list r-assertive-base))
15065 (home-page "https://bitbucket.org/richierocks/assertive.models")
15066 (synopsis "Assertions to check properties of models")
15068 "This package provides a set of predicates and assertions for checking
15069 the properties of models. This is mainly for use by other package developers
15070 who want to include run-time testing features in their own packages.")
15071 (license license:gpl3+)))
15073 (define-public r-assertive-reflection
15075 (name "r-assertive-reflection")
15080 (uri (cran-uri "assertive.reflection" version))
15083 "1g9lpwzy6r2xmyi2mlbcccnfgyzhzbmx5bsicf3vkffxrlkrpjn2"))))
15085 `((upstream-name . "assertive.reflection")))
15086 (build-system r-build-system)
15088 (list r-assertive-base))
15089 (home-page "https://bitbucket.org/richierocks/assertive.reflection")
15090 (synopsis "Assertions for checking the state of R")
15092 "This package provides a set of predicates and assertions for checking
15093 the state and capabilities of R, the operating system it is running on, and
15094 the IDE being used. This is mainly for use by other package developers who
15095 want to include run-time testing features in their own packages.")
15096 (license license:gpl3+)))
15098 (define-public r-assertive-types
15100 (name "r-assertive-types")
15105 (uri (cran-uri "assertive.types" version))
15108 "0zxq1jfrzgw95ll7alvm0xnk7aihjdksngq4ya2whyvfjbmv4vdb"))))
15110 `((upstream-name . "assertive.types")))
15111 (build-system r-build-system)
15113 (list r-assertive-base r-assertive-properties r-codetools))
15114 (home-page "https://bitbucket.org/richierocks/assertive.types")
15115 (synopsis "Assertions to check types of variables")
15117 "This package provides a set of predicates and assertions for checking
15118 the types of variables. This is mainly for use by other package developers
15119 who want to include run-time testing features in their own packages.")
15120 (license license:gpl3+)))
15122 (define-public r-assertive-files
15124 (name "r-assertive-files")
15129 (uri (cran-uri "assertive.files" version))
15132 "02pfz8j5vwcj5kl6zca46894li7lxwnlrr29j922f14ay6kdssmy"))))
15134 `((upstream-name . "assertive.files")))
15135 (build-system r-build-system)
15137 (list r-assertive-base r-assertive-numbers))
15138 (home-page "https://bitbucket.org/richierocks/assertive.files")
15139 (synopsis "Assertions to check properties of files")
15141 "This package provides a set of predicates and assertions for checking
15142 the properties of files and connections. This is mainly for use by other
15143 package developers who want to include run-time testing features in their own
15145 (license license:gpl3+)))
15147 (define-public r-assertive-code
15149 (name "r-assertive-code")
15154 (uri (cran-uri "assertive.code" version))
15157 "1qhbp668zfvhqs8avkhg9amp4zyazz6dsy4fc6kpdmw3sv8yi07g"))))
15159 `((upstream-name . "assertive.code")))
15160 (build-system r-build-system)
15162 (list r-assertive-base r-assertive-properties r-assertive-types))
15163 (home-page "https://bitbucket.org/richierocks/assertive.code")
15164 (synopsis "Assertions to check properties of code")
15166 "This package provides a set of predicates and assertions for checking
15167 the properties of code. This is mainly for use by other package developers
15168 who want to include run-time testing features in their own packages.")
15169 (license license:gpl3+)))
15171 (define-public r-assertive-datetimes
15173 (name "r-assertive-datetimes")
15178 (uri (cran-uri "assertive.datetimes" version))
15181 "151d05z8n6dpl44pqsa1jfi0ijbigr3zfc43xlw53nd8ymi22kh1"))))
15183 `((upstream-name . "assertive.datetimes")))
15184 (build-system r-build-system)
15186 (list r-assertive-base r-assertive-types))
15187 (home-page "https://bitbucket.org/richierocks/assertive.datetimes")
15188 (synopsis "Assertions to check properties of dates and times")
15190 "This package provides a set of predicates and assertions for checking
15191 the properties of dates and times. This is mainly for use by other package
15192 developers who want to include run-time testing features in their own
15194 (license license:gpl3+)))
15196 (define-public r-assertive-strings
15198 (name "r-assertive-strings")
15203 (uri (cran-uri "assertive.strings" version))
15206 "0n6jrk88670g4ym0r8ii40a08a90z1xadj8wcryk8h0nl04dchfm"))))
15208 `((upstream-name . "assertive.strings")))
15209 (build-system r-build-system)
15211 (list r-assertive-base r-assertive-types r-stringi))
15212 (home-page "https://bitbucket.org/richierocks/assertive.strings")
15213 (synopsis "Assertions to check properties of strings")
15215 "This package provides a set of predicates and assertions for checking
15216 the properties of strings. This is mainly for use by other package developers
15217 who want to include run-time testing features in their own packages.")
15218 (license license:gpl3+)))
15220 (define-public r-assertive-data-us
15222 (name "r-assertive-data-us")
15227 (uri (cran-uri "assertive.data.us" version))
15230 "1bgspn0sccmp9z7s7djvdvprgxlyc5vrxznp4zfjb79kwvgn83hq"))))
15232 `((upstream-name . "assertive.data.us")))
15233 (build-system r-build-system)
15235 (list r-assertive-base r-assertive-strings))
15236 (home-page "https://bitbucket.org/richierocks/assertive.data.us")
15237 (synopsis "Assertions to check properties of strings")
15239 "This package provides a set of predicates and assertions for checking
15240 the properties of US-specific complex data types. This is mainly for use by
15241 other package developers who want to include run-time testing features in
15242 their own packages.")
15243 (license license:gpl3+)))
15245 (define-public r-assertive-data-uk
15247 (name "r-assertive-data-uk")
15252 (uri (cran-uri "assertive.data.uk" version))
15255 "1fzjvhwp7mwkqqix29khvs6zcrc82n6j4czvzzb473vyjyvdlj5b"))))
15257 `((upstream-name . "assertive.data.uk")))
15258 (build-system r-build-system)
15260 (list r-assertive-base r-assertive-strings))
15261 (home-page "https://bitbucket.org/richierocks/assertive.data.uk")
15262 (synopsis "Assertions to check properties of strings")
15264 "This package provides a set of predicates and assertions for checking
15265 the properties of UK-specific complex data types. This is mainly for use by
15266 other package developers who want to include run-time testing features in
15267 their own packages.")
15268 (license license:gpl3+)))
15270 (define-public r-assertive-data
15272 (name "r-assertive-data")
15277 (uri (cran-uri "assertive.data" version))
15280 "00cvg2g36mdl8plrzx40m63qd55742mddqrchwy9n3c7mm4gn02s"))))
15282 `((upstream-name . "assertive.data")))
15283 (build-system r-build-system)
15285 (list r-assertive-base r-assertive-strings))
15286 (home-page "https://bitbucket.org/richierocks/assertive.data")
15287 (synopsis "Assertions to check properties of data")
15289 "This package provides a set of predicates and assertions for checking
15290 the properties of (country independent) complex data types. This is mainly
15291 for use by other package developers who want to include run-time testing
15292 features in their own packages.")
15293 (license license:gpl3+)))
15295 (define-public r-assertive
15297 (name "r-assertive")
15302 (uri (cran-uri "assertive" version))
15305 "02palil82idqhhshcdjsfsja9qkqnd0dczqzj5gbccy4hfg1c0y4"))))
15306 (build-system r-build-system)
15308 (list r-assertive-base
15311 r-assertive-data-uk
15312 r-assertive-data-us
15313 r-assertive-datetimes
15315 r-assertive-matrices
15317 r-assertive-numbers
15318 r-assertive-properties
15319 r-assertive-reflection
15321 r-assertive-strings
15326 (home-page "https://bitbucket.org/richierocks/assertive")
15327 (synopsis "Readable check functions to ensure code integrity")
15329 "This package provides lots of predicates (@code{is_*} functions) to
15330 check the state of your variables, and assertions (@code{assert_*} functions)
15331 to throw errors if they aren't in the right form.")
15332 (license license:gpl3+)))
15334 (define-public r-dotcall64
15336 (name "r-dotcall64")
15341 (uri (cran-uri "dotCall64" version))
15344 "1im5k8jbviwj2i42mq1kmjskh80isa7jr9w8i0fknidrzzy2h2zi"))))
15345 (properties `((upstream-name . "dotCall64")))
15346 (build-system r-build-system)
15347 (native-inputs (list gfortran))
15348 (home-page "https://git.math.uzh.ch/reinhard.furrer/dotCall64")
15349 (synopsis "Enhanced foreign function interface supporting long vectors")
15351 "This package provides @code{.C64()}, an enhanced version of @code{.C()}
15352 and @code{.Fortran()} from the R foreign function interface. @code{.C64()}
15353 supports long vectors, arguments of type 64-bit integer, and provides a
15354 mechanism to avoid unnecessary copies of read-only and write-only arguments.
15355 This makes it a convenient and fast interface to C/C++ and Fortran code.")
15356 (license license:gpl2+)))
15358 (define-public r-spam
15365 (uri (cran-uri "spam" version))
15367 (base32 "1ann2a2ifr3z983fcg1c0pkgmbxz6a0ym5q1dmq1r382bd1pg0fr"))))
15368 (build-system r-build-system)
15370 (list r-dotcall64))
15372 (list gfortran r-knitr))
15373 (home-page "https://www.math.uzh.ch/pages/spam/")
15374 (synopsis "Sparse matrix algebra")
15376 "This package provides a set of functions for sparse matrix algebra.
15377 Differences with other sparse matrix packages are:
15380 @item it only supports (essentially) one sparse matrix format;
15381 @item it is based on transparent and simple structure(s);
15382 @item it is tailored for MCMC calculations within G(M)RF;
15383 @item and it is fast and scalable (with the extension package @code{spam64}).
15385 ;; Either of these licenses
15386 (license (list license:bsd-3 license:lgpl2.0))))
15388 (define-public r-fields
15395 (uri (cran-uri "fields" version))
15397 (base32 "1hs4k5a9hh0r5fsrnpnvs6wvf78xpjzj8a2j6643dsz73a5q6ln6"))))
15398 (build-system r-build-system)
15400 (list r-maps r-spam r-viridis))
15403 (home-page "https://www.image.ucar.edu/fields")
15404 (synopsis "Tools for spatial data")
15406 "This is a package for curve, surface and function fitting with an
15407 emphasis on splines, spatial data and spatial statistics. The major methods
15408 include cubic, and thin plate splines, Kriging, and compactly supported
15409 covariance functions for large data sets.")
15410 (license license:gpl2+)))
15412 (define-public r-spatialextremes
15414 (name "r-spatialextremes")
15419 (uri (cran-uri "SpatialExtremes" version))
15422 "0z1swxp1syz8hdskarjxx4sdd7wx835kcnb783bwqm235yh991j3"))))
15424 `((upstream-name . "SpatialExtremes")))
15425 (build-system r-build-system)
15427 (list r-fields r-maps))
15428 (home-page "http://spatialextremes.r-forge.r-project.org/")
15429 (synopsis "Modelling spatial extremes")
15431 "This package provides tools for the statistical modelling of spatial
15432 extremes using max-stable processes, copula or Bayesian hierarchical models.
15433 More precisely, this package allows (conditional) simulations from various
15434 parametric max-stable models, analysis of the extremal spatial dependence, the
15435 fitting of such processes using composite likelihoods or least square (simple
15436 max-stable processes only), model checking and selection and prediction.")
15437 (license license:gpl2+)))
15439 (define-public r-drc
15446 (uri (cran-uri "drc" version))
15449 "0c8xn8ripzq270hy8d16fcnx02l02alddznd7fqwk3jyi6113h1y"))))
15450 (build-system r-build-system)
15458 (home-page "https://cran.r-project.org/web/packages/drc")
15459 (synopsis "Analysis of dose-response curves")
15461 "This package provides a suite of flexible and versatile model fitting
15462 and after-fitting functions for the analysis of dose-response data.")
15463 (license license:gpl2+)))
15465 (define-public r-rmeta
15472 (uri (cran-uri "rmeta" version))
15475 "0vkbnxp579v8zmcv1isdbzj5swpr6fq17zwparxcvzswjc2x9ydr"))))
15476 (build-system r-build-system)
15477 (home-page "https://cran.r-project.org/web/packages/rmeta")
15478 (synopsis "Tools for meta-analysis")
15480 "This package provides functions for simple fixed and random effects
15481 meta-analysis for two-sample comparisons and cumulative meta-analyses. It
15482 draws standard summary plots, funnel plots, and computes summaries and tests
15483 for association and heterogeneity.")
15484 (license license:gpl2)))
15486 (define-public r-bootstrap
15488 (name "r-bootstrap")
15493 (uri (cran-uri "bootstrap" version))
15496 "1546jqhhw5h177ii8jkdikyd26rv6gwkav816np1zks4p7zgsljj"))))
15497 (build-system r-build-system)
15498 (native-inputs (list gfortran))
15499 (home-page "https://cran.r-project.org/web/packages/bootstrap")
15500 (synopsis "Functions for the book \"An Introduction to the Bootstrap\"")
15502 "This package provides software and data for the book \"An Introduction
15503 to the Bootstrap\" by B. Efron and R. Tibshirani, 1993, Chapman and Hall.
15504 This package is primarily provided for projects already based on it, and for
15505 support of the book. New projects should preferentially use the recommended
15506 package \"boot\".")
15507 (license license:bsd-3)))
15509 (define-public r-survivalroc
15511 (name "r-survivalroc")
15516 (uri (cran-uri "survivalROC" version))
15519 "0wnd65ff5w679hxa1zrpfrx9qg47q21pjxppsga6m3h4iq1yfj8l"))))
15520 (properties `((upstream-name . "survivalROC")))
15521 (build-system r-build-system)
15522 (home-page "https://cran.r-project.org/web/packages/survivalROC")
15523 (synopsis "Time-dependent ROC curve estimation from censored survival data")
15525 "Compute time-dependent ROC curve from censored survival data using
15526 Kaplan-Meier (KM) or Nearest Neighbor Estimation (NNE) method of Heagerty,
15527 Lumley & Pepe (Biometrics, Vol 56 No 2, 2000, PP 337-344)")
15528 (license license:gpl2+)))
15530 (define-public r-locfdr
15536 (uri (cran-uri "locfdr" version))
15539 "1falkbp2xz07am8jlhwlvyqvxnli4nwl188kd0g58vdfjcjy3mj2"))))
15540 (build-system r-build-system)
15541 (home-page "https://cran.r-project.org/web/packages/locfdr/")
15542 (synopsis "Computes local false discovery rates")
15543 (description "This package can be used to compute local false
15545 (license license:gpl2)))
15547 (define-public r-longitudinal
15549 (name "r-longitudinal")
15554 (uri (cran-uri "longitudinal" version))
15557 "046w3xbr535c5jyd68adv42a7limxp1mv57b5w6w673w707lmw2p"))))
15558 (build-system r-build-system)
15559 (propagated-inputs (list r-corpcor))
15560 (home-page "http://strimmerlab.org/software/longitudinal/")
15561 (synopsis "Analysis of multiple time course data")
15563 "This package contains general data structures and functions for
15564 longitudinal data with multiple variables, repeated measurements, and
15565 irregularly spaced time points. It also implements a shrinkage estimator of
15566 dynamical correlation and dynamical covariance.")
15567 (license license:gpl3+)))
15569 (define-public r-genenet
15576 (uri (cran-uri "GeneNet" version))
15579 "1r1khga3nxxjghs4vnbymzp0cwb1q17zw2v3a94qz8fsrirq1sf1"))))
15580 (properties `((upstream-name . "GeneNet")))
15581 (build-system r-build-system)
15583 (list r-corpcor r-fdrtool r-longitudinal))
15584 (home-page "http://strimmerlab.org/software/genenet/")
15585 (synopsis "Modeling and inferring gene networks")
15587 "This package analyzes gene expression (time series) data with focus on
15588 the inference of gene networks. In particular, GeneNet implements the methods
15589 of Schaefer and Strimmer (2005a,b,c) and Opgen-Rhein and Strimmer (2006, 2007)
15590 for learning large-scale gene association networks (including assignment of
15591 putative directions).")
15592 (license license:gpl3+)))
15594 (define-public r-rbamtools
15596 (name "r-rbamtools")
15597 (version "2.16.17")
15601 (uri (cran-uri "rbamtools" version))
15604 "0qj37ljdva3v29s01dkrbg31mcfzy3bl145cp40d54v4h9xhcghc"))))
15605 (build-system r-build-system)
15606 (inputs (list zlib))
15608 (list r-refgenome))
15609 (home-page "https://cran.r-project.org/web/packages/rbamtools")
15610 (synopsis "Read and write BAM (binary alignment) files")
15612 "This package provides an R interface to functions of the SAMtools
15614 (license license:artistic2.0)))
15616 (define-public r-protviz
15623 (uri (cran-uri "protViz" version))
15626 "0f6jwzcqi0w37hvg3i5dlk0c3anpkqh54ibf94vaf17r8sykr4nw"))))
15627 (properties `((upstream-name . "protViz")))
15628 (build-system r-build-system)
15629 (propagated-inputs (list r-rcpp))
15630 (home-page "https://github.com/protViz/protViz/")
15631 (synopsis "Visualizing and analyzing mass spectrometry data in proteomics")
15633 "This package helps with quality checks, visualizations and analysis of
15634 mass spectrometry data, coming from proteomics experiments. The package is
15635 developed, tested and used at the Functional Genomics Center Zurich, where it
15636 is used mainly for prototyping, teaching, and having fun with proteomics data.
15637 But it can also be used to do data analysis for small scale data sets.")
15638 (license license:gpl3)))
15640 (define-public r-cmprsk
15647 (uri (cran-uri "cmprsk" version))
15649 (base32 "050f24l5ab1ds9824c7yjahimf6pg8ih2k83jzpzfb0n5k5jfh44"))))
15650 (build-system r-build-system)
15655 (home-page "https://cran.r-project.org/web/packages/cmprsk")
15656 (synopsis "Subdistribution analysis of competing risks")
15658 "This package provides tool for estimation, testing and regression
15659 modeling of subdistribution functions in competing risks, as described in
15660 Gray (1988), A class of K-sample tests for comparing the cumulative incidence
15661 of a competing risk, Ann. Stat. 16:1141-1154, and Fine JP and Gray RJ (1999),
15662 A proportional hazards model for the subdistribution of a competing risk,
15663 JASA, 94:496-509.")
15664 (license license:gpl2+)))
15666 (define-public r-etm
15673 (uri (cran-uri "etm" version))
15676 "1hvrplmdpjjpjji663rw0vjbbrzj2nvr04d1nkc8bf46p4ixyxgy"))))
15677 (build-system r-build-system)
15679 (list r-data-table r-lattice r-rcpp r-rcpparmadillo r-survival))
15680 (home-page "https://cran.r-project.org/web/packages/etm")
15681 (synopsis "Empirical transition matrix")
15683 "The @dfn{empirical transition matrix} (etm) package estimates
15684 the matrix of transition probabilities for any time-inhomogeneous multistate
15685 model with finite state space using the Aalen-Johansen estimator.")
15686 (license license:expat)))
15688 (define-public r-epi
15695 (uri (cran-uri "Epi" version))
15698 "0s3ij0rya4wd7k97kc4s3pwj1d1ypaxl1s7zqr6sa07hp4a8fzz0"))))
15699 (properties `((upstream-name . "Epi")))
15700 (build-system r-build-system)
15714 (home-page "https://BendixCarstensen.com/Epi/")
15715 (synopsis "Statistical analysis in epidemiology")
15717 "This package provides functions for demographic and epidemiological
15718 analysis in the Lexis diagram, i.e. register and cohort follow-up data, in
15719 particular representation, manipulation and simulation of multistate data -
15720 the Lexis suite of functions, which includes interfaces to the @code{mstate},
15721 @code{etm} and @code{cmprsk} packages. It also contains functions for
15722 Age-Period-Cohort and Lee-Carter modeling and a function for interval censored
15723 data and some useful functions for tabulation and plotting, as well as a
15724 number of epidemiological data sets.")
15725 (license license:gpl2)))
15727 (define-public r-ppls
15730 (version "1.6-1.1")
15734 (uri (cran-uri "ppls" version))
15737 "1zyrisy3c4cz896j1bjh61sf57wdl9p8ywdq268cl819szfq78mx"))))
15738 (build-system r-build-system)
15739 (propagated-inputs (list r-mass))
15740 (home-page "https://cran.r-project.org/web/packages/ppls")
15741 (synopsis "Penalized partial least squares")
15743 "This package contains linear and nonlinear regression methods based on
15744 partial least squares and penalization techniques. Model parameters are
15745 selected via cross-validation, and confidence intervals ans tests for the
15746 regression coefficients can be conducted via jackknifing.")
15747 (license license:gpl2+)))
15749 (define-public r-huge
15756 (uri (cran-uri "huge" version))
15758 (base32 "1sl457a1lndrx98y2j9a2smanawx2iqlhl82iand0g3p5xp8ch4j"))))
15759 (build-system r-build-system)
15761 (list r-igraph r-mass r-matrix r-rcpp r-rcppeigen))
15762 (home-page "https://cran.r-project.org/web/packages/huge")
15763 (synopsis "High-dimensional undirected graph estimation")
15765 "This package provides a general framework for high-dimensional
15766 undirected graph estimation. It integrates data preprocessing, neighborhood
15767 screening, graph estimation, and model selection techniques into a pipeline.")
15768 (license license:gpl2)))
15770 (define-public r-parcor
15777 (uri (cran-uri "parcor" version))
15780 "0vgs6k92vdr0cmb8cwbv2ff6qavw30agskfd8bfh17hsskrisvx0"))))
15781 (build-system r-build-system)
15783 (list r-epi r-genenet r-glmnet r-mass r-ppls))
15784 (home-page "https://cran.r-project.org/web/packages/parcor")
15785 (synopsis "Regularized estimation of partial correlation matrices")
15787 "This package estimates the matrix of partial correlations based on
15788 different regularized regression methods: lasso, adaptive lasso, PLS, and
15789 Ridge Regression. In addition, the package provides model selection for
15790 lasso, adaptive lasso and Ridge regression based on cross-validation.")
15791 (license license:gpl2+)))
15793 (define-public r-mcmc
15800 (uri (cran-uri "mcmc" version))
15803 "0q42m8ab7b6bxhns494ksjdss5f3c5m2jjfdlfj6fk1nz7ax7i5p"))))
15804 (build-system r-build-system)
15805 (home-page "https://www.stat.umn.edu/geyer/mcmc/")
15806 (synopsis "Markov chain Monte Carlo")
15808 "This package simulates continuous distributions of random vectors using
15809 @dfn{Markov chain Monte Carlo} (MCMC). Users specify the distribution by an R
15810 function that evaluates the log unnormalized density. Algorithms are random
15811 walk Metropolis algorithm (function @code{metrop}), simulated
15812 tempering (function @code{temper}), and morphometric random walk
15813 Metropolis (function @code{morph.metrop}), which achieves geometric ergodicity
15814 by change of variable.")
15815 (license license:expat)))
15817 (define-public r-listenv
15824 (uri (cran-uri "listenv" version))
15827 "0ps8bk7zlhbviawrw7vw25skjq81hkk3ijyi6g74dmfqy8zsyapx"))))
15828 (build-system r-build-system)
15831 (modify-phases %standard-phases
15832 (add-after 'unpack 'set-HOME
15833 (lambda _ (setenv "HOME" "/tmp"))))))
15835 (list r-r-rsp)) ; vignette builder
15836 (home-page "https://github.com/HenrikBengtsson/listenv")
15837 (synopsis "Environments behaving (almost) as lists")
15839 "This package implements list environments. List environments are
15840 environments that have list-like properties. For instance, the elements of a
15841 list environment are ordered and can be accessed and iterated over using index
15843 (license license:lgpl2.1+)))
15845 (define-public r-globals
15852 (uri (cran-uri "globals" version))
15855 "15llx4233ihj4w815k7inc17530w9ja0mi29n1i0s2sr42j8jdpq"))))
15856 (build-system r-build-system)
15858 (list r-codetools))
15859 (home-page "https://github.com/HenrikBengtsson/globals")
15860 (synopsis "Identify global objects in R expressions")
15862 "This package provides tools to identify global (\"unknown\" or \"free\")
15863 objects in R expressions by code inspection using various strategies, e.g.
15864 conservative or liberal. The objective of this package is to make it as
15865 simple as possible to identify global objects for the purpose of exporting
15866 them in distributed compute environments.")
15867 (license license:lgpl2.1+)))
15869 (define-public r-parallelly
15871 (name "r-parallelly")
15876 (uri (cran-uri "parallelly" version))
15879 "1nhp66psk3m79is5qm4ppxkj7bdy46jr2h2pir22ia9ghhyzris0"))))
15880 (properties `((upstream-name . "parallelly")))
15881 (build-system r-build-system)
15882 (home-page "https://github.com/HenrikBengtsson/parallelly")
15883 (synopsis "Enhancements of the parallel package")
15885 "This package provides utility functions that enhance the @code{parallel}
15886 package and support the built-in parallel backends of the @code{future}
15887 package. For example, @code{availableCores} gives the number of CPU cores
15888 available to your R process as given by R options and environment variables,
15889 including those set by job schedulers on high-performance compute clusters.
15890 If none is set, it will fall back to @code{parallel::detectCores}. Another
15891 example is @code{makeClusterPSOCK}, which is backward compatible with
15892 @code{parallel::makePSOCKcluster} while doing a better job in setting up
15893 remote cluster workers without the need for configuring the firewall to do
15894 port-forwarding to your local computer.")
15895 (license license:lgpl2.1+)))
15897 (define-public r-future
15904 (uri (cran-uri "future" version))
15907 "1mchjdvvwgs8v0iv8z5m6gav3xzvnq11h8qrc7lfnrb2x3d0np53"))))
15908 (build-system r-build-system)
15911 (modify-phases %standard-phases
15912 (add-after 'unpack 'set-HOME
15913 (lambda _ (setenv "HOME" "/tmp"))))))
15915 (list r-digest r-globals r-listenv r-parallelly))
15917 (list r-r-rsp)) ; vignette builder
15918 (home-page "https://github.com/HenrikBengtsson/future")
15919 (synopsis "Unified parallel and distributed processing in R")
15921 "The purpose of this package is to provide a lightweight and unified
15922 Future API for sequential and parallel processing of R expression via futures.
15923 This package implements sequential, multicore, multisession, and cluster
15924 futures. With these, R expressions can be evaluated on the local machine, in
15925 parallel a set of local machines, or distributed on a mix of local and remote
15926 machines. Extensions to this package implement additional backends for
15927 processing futures via compute cluster schedulers etc. Because of its unified
15928 API, there is no need to modify any code in order to switch from sequential on
15929 the local machine to, say, distributed processing on a remote compute cluster.")
15930 (license license:lgpl2.1+)))
15932 (define-public r-future-apply
15934 (name "r-future-apply")
15939 (uri (cran-uri "future.apply" version))
15942 "1xb7qj8izjwmy4aa92p5f4cdbhgp220hrly3b5879f9hrv2w2rk1"))))
15943 (properties `((upstream-name . "future.apply")))
15944 (build-system r-build-system)
15947 (modify-phases %standard-phases
15948 (add-after 'unpack 'set-HOME
15949 (lambda _ (setenv "HOME" "/tmp"))))))
15951 (list r-future r-globals))
15953 (list r-r-rsp)) ; vignette builder
15954 (home-page "https://github.com/HenrikBengtsson/future.apply")
15955 (synopsis "Apply function to elements in parallel using futures")
15957 "This package provides implementations of @code{apply()},
15958 @code{eapply()}, @code{lapply()}, @code{Map()}, @code{mapply()},
15959 @code{replicate()}, @code{sapply()}, @code{tapply()}, and @code{vapply()} that
15960 can be resolved using any future-supported backend, e.g. parallel on the local
15961 machine or distributed on a compute cluster.")
15962 (license license:gpl2+)))
15964 (define-public r-rsvd
15971 (uri (cran-uri "rsvd" version))
15974 "07p2hjmpcwcsang8z9sjkpy94rydcin7m3hyvcgzgm5cd6w8c1p4"))))
15975 (build-system r-build-system)
15978 (home-page "https://github.com/erichson/rSVD")
15979 (synopsis "Randomized singular value decomposition")
15981 "Low-rank matrix decompositions are fundamental tools and widely used for
15982 data analysis, dimension reduction, and data compression. Classically, highly
15983 accurate deterministic matrix algorithms are used for this task. However, the
15984 emergence of large-scale data has severely challenged our computational
15985 ability to analyze big data. The concept of randomness has been demonstrated
15986 as an effective strategy to quickly produce approximate answers to familiar
15987 problems such as the @dfn{singular value decomposition} (SVD). This package
15988 provides several randomized matrix algorithms such as the randomized singular
15989 value decomposition (@code{rsvd}), randomized principal component
15990 analysis (@code{rpca}), randomized robust principal component
15991 analysis (@code{rrpca}), randomized interpolative decomposition (@code{rid}),
15992 and the randomized CUR decomposition (@code{rcur}). In addition several plot
15993 functions are provided.")
15994 (license license:gpl3+)))
15996 (define-public r-sloop
16003 (uri (cran-uri "sloop" version))
16006 "00fk5fr5zsk2qxc1kfhmshhjxgnamm3401089sx8m2l529zd6r8j"))))
16007 (build-system r-build-system)
16009 (list r-codetools r-crayon r-purrr r-rlang r-tibble))
16010 (home-page "https://github.com/r-lib/sloop")
16011 (synopsis "Helpers for object-oriented programming in R")
16013 "This package provides a collection of helper functions designed to
16014 help you to better understand object oriented programming in R, particularly
16016 (license license:gpl3)))
16018 (define-public r-capushe
16025 (uri (cran-uri "capushe" version))
16028 "1aa76ir1kp67hiz7dr60azyc71yzslshyc640fjh0fpw0sp5kwbc"))))
16029 (build-system r-build-system)
16030 (propagated-inputs (list r-mass))
16031 (home-page "https://cran.r-project.org/web/packages/capushe/index.html")
16032 (synopsis "Calibrating penalties using slope heuristics")
16034 "This package provides tools for the calibration of penalized criteria
16035 for model selection. The calibration methods available are based on the slope
16037 (license license:gpl2+)))
16039 (define-public r-dorng
16046 (uri (cran-uri "doRNG" version))
16049 "1jff27zzrvd1fd61x2m9468h8xn3s1c9f6wibviy5zdhj5dx9s9k"))))
16050 (properties `((upstream-name . "doRNG")))
16051 (build-system r-build-system)
16053 (list r-foreach r-iterators r-rngtools))
16054 (home-page "https://renozao.github.io/doRNG/")
16055 (synopsis "Generic reproducible parallel backend for foreach loops")
16057 "This package provides functions to perform reproducible parallel
16058 @code{foreach} loops, using independent random streams as generated by
16059 L'Ecuyer's combined multiple-recursive generator. It enables to easily
16060 convert standard @code{%dopar%} loops into fully reproducible loops,
16061 independently of the number of workers, the task scheduling strategy, or the
16062 chosen parallel environment and associated foreach backend.")
16063 (license license:gpl2+)))
16065 (define-public r-blockmodeling
16067 (name "r-blockmodeling")
16072 (uri (cran-uri "blockmodeling" version))
16075 "1vc8gy4slsywcwxq532373i0dq73fhs5cac9mr6zz2pjaaxjghhq"))))
16076 (build-system r-build-system)
16079 (native-inputs (list gfortran))
16080 (home-page "https://cran.r-project.org/web/packages/blockmodeling")
16081 (synopsis "Generalized and classical blockmodeling of valued networks")
16083 "This package is primarily meant as an implementation of generalized
16084 blockmodeling for valued networks. In addition, measures of similarity or
16085 dissimilarity based on structural equivalence and regular equivalence (REGE
16086 algorithms) can be computed and partitioned matrices can be plotted.")
16087 (license license:gpl2+)))
16089 (define-public r-upsetr
16096 (uri (cran-uri "UpSetR" version))
16099 "007i0njnjjy7vbrxabwav7a1kk2n0hn2mkvqsdzzfk10ckp5y7im"))))
16100 (properties `((upstream-name . "UpSetR")))
16101 (build-system r-build-system)
16103 (list r-ggplot2 r-gridextra r-plyr r-scales))
16104 (home-page "https://github.com/hms-dbmi/UpSetR")
16105 (synopsis "Visualize intersecting sets")
16107 "This package provides a more scalable alternative to Venn and Euler
16108 diagrams for visualizing intersecting sets. Create visualizations of
16109 intersecting sets using a novel matrix design, along with visualizations of
16110 several common set, element and attribute related tasks.")
16111 (license license:expat)))
16113 ;; This package includes a JavaScript file, which is not minified. When
16114 ;; upgrading please check that there are no new minified JavaScript files.
16115 (define-public r-shinybs
16122 (uri (cran-uri "shinyBS" version))
16125 "0h51685a9qll4agayldjyryi60ih969219ibg071slv0613p5v8a"))))
16126 (properties `((upstream-name . "shinyBS")))
16127 (build-system r-build-system)
16128 ;; The tests spawn Shiny browser apps. They cannot be run
16129 ;; non-interactively.
16130 (arguments '(#:tests? #f))
16132 (list r-htmltools r-shiny))
16133 (home-page "https://ebailey78.github.io/shinyBS/")
16134 (synopsis "Twitter Bootstrap components for Shiny")
16136 "This package adds additional Twitter Bootstrap components to Shiny.")
16137 (license license:gpl3)))
16139 (define-public r-shinyjqui
16141 (name "r-shinyjqui")
16146 (uri (cran-uri "shinyjqui" version))
16149 "135gwz7syyb6pbn0lkvmq0v1c6r1zivavnqhi1rnzbbzlysi27v1"))
16151 '(for-each delete-file
16152 (list "inst/www/shinyjqui.min.js"
16153 "inst/www/jquery.ui.touch-punch.min.js")))))
16154 (properties `((upstream-name . "shinyjqui")))
16155 (build-system r-build-system)
16158 (modify-phases %standard-phases
16159 (add-after 'unpack 'process-javascript
16160 (lambda* (#:key inputs #:allow-other-keys)
16161 (with-directory-excursion "inst/www"
16163 `((,(string-append (assoc-ref inputs "js-jquery.ui.touch-punch")
16164 "/jquery.ui.touch-punch.js")
16165 . "jquery.ui.touch-punch.min.js")
16167 . "shinyjqui.min.js"))))
16168 (for-each (lambda (source target)
16169 (format #true "Processing ~a --> ~a~%"
16171 (invoke "esbuild" source "--minify"
16172 (string-append "--outfile=" target)))
16174 (map cdr mapping)))))))))
16176 (list r-htmltools r-htmlwidgets r-jsonlite r-rlang r-shiny))
16178 `(("r-knitr" ,r-knitr)
16179 ("esbuild" ,esbuild)
16180 ("js-jquery.ui.touch-punch"
16183 (uri (git-reference
16184 (url "https://github.com/furf/jquery-ui-touch-punch")
16185 (commit "8f7559b6e65cdc3ee3648d5fe76d38c653f87ff5")))
16188 "1lzywp2q9hwx6d5fqjla95vp7ra2lahr5dam7lsqjmch9d98r48q"))))))
16189 (home-page "https://github.com/yang-tang/shinyjqui")
16190 (synopsis "jQuery UI interactions and effects for Shiny")
16192 "This is an extension to Shiny that brings interactions and animation
16193 effects from the jQuery UI library.")
16194 (license license:expat)))
16196 (define-public r-shinymanager
16198 (name "r-shinymanager")
16199 (version "1.0.400")
16203 (uri (cran-uri "shinymanager" version))
16205 (base32 "1np2yp5pn8g9i4jhysfgprmdn13cpw4vaaagrd72rnk2r4hpmyx4"))))
16206 (properties `((upstream-name . "shinymanager")))
16207 (build-system r-build-system)
16209 (list r-billboarder
16219 (native-inputs (list r-knitr))
16220 (home-page "https://github.com/datastorm-open/shinymanager")
16221 (synopsis "Authentication management for Shiny applications")
16223 "This package provides simple and secure authentification mechanism for
16224 single Shiny applications. Credentials are stored in an encrypted SQLite
16226 (license license:gpl3)))
16228 (define-public r-outliers
16230 (name "r-outliers")
16235 (uri (cran-uri "outliers" version))
16238 "1yrmwvjjb0a6sbx940k9svf23cykcxz8rrwcgyic7lpgzbrdfcfc"))))
16239 (build-system r-build-system)
16240 (home-page "https://cran.r-project.org/web/packages/outliers/index.html")
16241 (synopsis "Tests for outliers")
16243 "This package provides a collection of some tests commonly used for
16244 identifying outliers.")
16245 (license license:gpl2+)))
16247 (define-public r-bayesm
16254 (uri (cran-uri "bayesm" version))
16256 (base32 "154glks7rsjkza0sfi1kj7wj727py9sl1ba6sswflwmwc9n226q6"))))
16257 (build-system r-build-system)
16259 (list r-rcpp r-rcpparmadillo))
16260 (home-page "http://www.perossi.org/home/bsm-1")
16261 (synopsis "Bayesian inference for marketing/micro-econometrics")
16263 "This package covers many important models used in marketing and
16264 micro-econometrics applications, including Bayes Regression (univariate or
16265 multivariate dep var), Bayes Seemingly Unrelated Regression (SUR), Binary and
16266 Ordinal Probit, Multinomial Logit (MNL) and Multinomial Probit (MNP),
16267 Multivariate Probit, Negative Binomial (Poisson) Regression, Multivariate
16268 Mixtures of Normals (including clustering), Dirichlet Process Prior Density
16269 Estimation with normal base, Hierarchical Linear Models with normal prior and
16270 covariates, Hierarchical Linear Models with a mixture of normals prior and
16271 covariates, Hierarchical Multinomial Logits with a mixture of normals prior
16272 and covariates, Hierarchical Multinomial Logits with a Dirichlet Process prior
16273 and covariates, Hierarchical Negative Binomial Regression Models, Bayesian
16274 analysis of choice-based conjoint data, Bayesian treatment of linear
16275 instrumental variables models, Analysis of Multivariate Ordinal survey data
16276 with scale usage heterogeneity, and Bayesian Analysis of Aggregate Random
16277 Coefficient Logit Models.")
16278 (license license:gpl2+)))
16280 (define-public r-tensora
16287 (uri (cran-uri "tensorA" version))
16290 "19wwh654qlja4z1n7afjpzsrrm53p8ddysa2vra5mdnkddb4g2cf"))))
16291 (properties `((upstream-name . "tensorA")))
16292 (build-system r-build-system)
16293 (home-page "http://www.stat.boogaart.de/tensorA")
16294 (synopsis "Advanced tensor arithmetic with named indices")
16296 "This package provides convenience functions for advanced linear algebra
16297 with tensors and computation with datasets of tensors on a higher level
16298 abstraction. It includes Einstein and Riemann summing conventions, dragging,
16299 co- and contravariate indices, and parallel computations on sequences of
16301 (license license:gpl2+)))
16303 (define-public r-rarpack
16310 (uri (cran-uri "rARPACK" version))
16313 "12h2y46xcfldhjdmm960swgn9b23zvkj5vg2bi42s9qxwgi02d63"))))
16314 (properties `((upstream-name . "rARPACK")))
16315 (build-system r-build-system)
16316 (propagated-inputs (list r-rspectra))
16317 (home-page "https://github.com/yixuan/rARPACK")
16318 (synopsis "Solvers for large scale eigenvalue and SVD problems")
16320 "This package was previously an R wrapper of the ARPACK library, and now
16321 a shell of the R package RSpectra, an R interface to the Spectra library for
16322 solving large scale eigenvalue/vector problems. The current version of
16323 rARPACK simply imports and exports the functions provided by RSpectra. New
16324 users of rARPACK are advised to switch to the RSpectra package.")
16325 (license license:bsd-3)))
16327 (define-public r-compositions
16329 (name "r-compositions")
16334 (uri (cran-uri "compositions" version))
16337 "1bqg0qqzsf92q0jb7hdjycr54bwv8rk7ajhvxgch5yslyqxpm73v"))))
16338 (build-system r-build-system)
16340 (list r-bayesm r-mass r-robustbase r-tensora))
16343 (home-page "http://www.stat.boogaart.de/compositions")
16344 (synopsis "Compositional data analysis")
16346 "This package provides functions for the consistent analysis of
16347 compositional data (e.g. portions of substances) and positive
16348 numbers (e.g. concentrations).")
16349 (license license:gpl2+)))
16351 (define-public r-cobs
16358 (uri (cran-uri "cobs" version))
16361 "0hiw5smk6kgk0gb9840kcqkhkybl7n30s77xhjc395x09izbgix1"))))
16362 (build-system r-build-system)
16364 (list r-quantreg r-sparsem))
16365 (home-page "https://cran.r-project.org/web/packages/cobs")
16366 (synopsis "Constrained B-Splines (sparse matrix based)")
16368 "This package provides qualitatively constrained (regression) smoothing
16369 splines via linear programming and sparse matrices.")
16370 (license license:gpl2+)))
16372 (define-public r-drimpute
16374 (name "r-drimpute")
16379 (uri (cran-uri "DrImpute" version))
16382 "1adzarrwqb282pqgx2yqswp9rpwd1naxsmar54kddr6qyd6b923b"))))
16383 (properties `((upstream-name . "DrImpute")))
16384 (build-system r-build-system)
16386 (list r-rcpp r-rcpparmadillo))
16387 (home-page "https://github.com/ikwak2/DrImpute")
16388 (synopsis "Imputing dropout events in single-cell RNA-Seq data")
16390 "This is an R package for imputing dropout events. Many statistical
16391 methods in cell type identification, visualization and lineage reconstruction
16392 do not account for dropout events. DrImpute can improve the performance of
16393 such software by imputing dropout events.")
16394 (license license:gpl3)))
16396 (define-public r-gamlss-dist
16398 (name "r-gamlss-dist")
16403 (uri (cran-uri "gamlss.dist" version))
16405 (base32 "1gqjr419v8z2ygh0h1xz7bipnsbp820njzwq7z3r9f41rn1ym47c"))))
16406 (properties `((upstream-name . "gamlss.dist")))
16407 (build-system r-build-system)
16408 (propagated-inputs (list r-mass))
16409 (home-page "http://www.gamlss.org/")
16410 (synopsis "Distributions for Generalized Additive Models for location scale and shape")
16412 "This package provides a set of distributions which can be used for
16413 modelling the response variables in Generalized Additive Models for Location
16414 Scale and Shape. The distributions can be continuous, discrete or mixed
16415 distributions. Extra distributions can be created, by transforming, any
16416 continuous distribution defined on the real line, to a distribution defined on
16417 ranges 0 to infinity or 0 to 1, by using a @code{log} or a @code{logit}
16418 transformation, respectively.")
16419 ;; Either version of the GPL.
16420 (license (list license:gpl2 license:gpl3))))
16422 ;; This package includes JavaScript files, which are not minified. When
16423 ;; upgrading please check that there are no new minified JavaScript files.
16424 (define-public r-shinyjs
16431 (uri (cran-uri "shinyjs" version))
16434 "1id9gsrkr28xl80a8794in17rxmmz06zqvd5hlns7mqz3fzhrhky"))))
16435 (build-system r-build-system)
16437 (list r-digest r-jsonlite r-shiny))
16440 (home-page "https://deanattali.com/shinyjs")
16441 (synopsis "Improve the user experience of your Shiny apps")
16443 "Perform common useful JavaScript operations in Shiny apps that will
16444 greatly improve your apps without having to know any JavaScript. Examples
16445 include: hiding an element, disabling an input, resetting an input back to its
16446 original value, delaying code execution by a few seconds, and many more useful
16447 functions for both the end user and the developer. Shinyjs can also be used
16448 to easily call your own custom JavaScript functions from R.")
16449 (license license:agpl3+)))
16451 ;; This package includes minified JavaScript files. When upgrading please
16452 ;; check that there are no new minified JavaScript files.
16453 (define-public r-colourpicker
16455 (name "r-colourpicker")
16460 (uri (cran-uri "colourpicker" version))
16463 "1q1wi3g403fbzp4ys3gsjbwdc86x770cx323qgi47ca8n219kl50"))))
16464 (build-system r-build-system)
16467 (modify-phases %standard-phases
16468 (add-after 'unpack 'process-javascript
16469 (lambda* (#:key inputs #:allow-other-keys)
16470 (with-directory-excursion "inst"
16472 `((,(assoc-ref inputs "js-salvattore")
16473 . "examples/colourInput/www/salvattore.min.js")
16474 (,(assoc-ref inputs "js-jquery")
16475 . "htmlwidgets/lib/jquery/jquery.min.js")
16476 ("www/shared/colourpicker/js/colourpicker.js"
16477 . "www/shared/colourpicker/js/colourpicker.min.js"))))
16478 (for-each (lambda (source target)
16479 (format #true "Processing ~a --> ~a~%"
16481 (delete-file target)
16482 (invoke "esbuild" source "--minify"
16483 (string-append "--outfile=" target)))
16485 (map cdr mapping)))))))))
16495 `(("esbuild" ,esbuild)
16499 (uri "https://code.jquery.com/jquery-1.11.3.js")
16502 "1v956yf5spw0156rni5z77hzqwmby7ajwdcd6mkhb6zvl36awr90"))))
16506 (uri "https://raw.githubusercontent.com/rnmp/salvattore/v1.0.9/dist/salvattore.js")
16509 "0lfrbx7l9w5x89jpc6njmd0pk7h8fpvg537vklai2vf7b1r2nnk5"))))))
16510 (home-page "https://github.com/daattali/colourpicker")
16511 (synopsis "Color picker tool for Shiny and for selecting colors in plots")
16513 "This package provides a color picker that can be used as an input in
16514 Shiny apps or Rmarkdown documents. The color picker supports alpha opacity,
16515 custom color palettes, and many more options. A plot color helper tool is
16516 available as an RStudio Addin, which helps you pick colors to use in your
16517 plots. A more generic color picker RStudio Addin is also provided to let you
16518 select colors to use in your R code.")
16519 (license license:expat)))
16521 (define-public r-ggextra
16528 (uri (cran-uri "ggExtra" version))
16531 "1rd3qv6ah3zphr1jicjhgxms73vi496mjnxnsrcgl7z8nyxmas6w"))))
16532 (properties `((upstream-name . "ggExtra")))
16533 (build-system r-build-system)
16535 (list r-colourpicker
16545 (home-page "https://github.com/daattali/ggExtra")
16546 (synopsis "Marginal histograms for ggplot2 and other enhancements")
16548 "This package is a collection of functions and layers to enhance ggplot2.
16549 The flagship function is @code{ggMarginal()}, which can be used to add
16550 marginal histograms/boxplots/density plots to ggplot2 scatterplots.")
16551 (license license:expat)))
16553 (define-public r-minpack-lm
16555 (name "r-minpack-lm")
16560 (uri (cran-uri "minpack.lm" version))
16563 "11yz6hk2r33571d16kq01cb1x6sgdzi6jmksqlrm8mr84l95c2f7"))))
16564 (properties `((upstream-name . "minpack.lm")))
16565 (build-system r-build-system)
16566 (native-inputs (list gfortran))
16567 (home-page "https://cran.r-project.org/web/packages/minpack.lm")
16568 (synopsis "Levenberg-Marquardt Nonlinear Least-Squares algorithm")
16570 "The @code{nls.lm} function provides an R interface to @code{lmder} and
16571 @code{lmdif} from the MINPACK library, for solving nonlinear least-squares
16572 problems by a modification of the Levenberg-Marquardt algorithm, with support
16573 for lower and upper parameter bounds. The implementation can be used via
16574 @code{nls}-like calls using the @code{nlsLM} function.")
16575 (license license:gpl3)))
16577 (define-public r-moments
16584 (uri (cran-uri "moments" version))
16587 "0r6qf3i1rzh2822bx1p0h8mh91gsbgg6asl2rzh2l4ys094bilif"))))
16588 (build-system r-build-system)
16589 (home-page "https://cran.r-project.org/web/packages/moments")
16590 (synopsis "Moments, cumulants, skewness, kurtosis and related tests")
16592 "This package provides functions to calculate: moments, Pearson's
16593 kurtosis, Geary's kurtosis and skewness; it also includes tests related to
16594 them (Anscombe-Glynn, D'Agostino, Bonett-Seier).")
16595 (license license:gpl2+)))
16597 (define-public r-msir
16604 (uri (cran-uri "msir" version))
16607 "1wm83m3cqd6llxb9p2jwim0wb81v84pgdmgcznygzaaq6kbn3n84"))))
16608 (build-system r-build-system)
16613 (home-page "https://cran.r-project.org/web/packages/msir")
16614 (synopsis "Model-based sliced inverse regression")
16616 "This is an R package for dimension reduction based on finite Gaussian
16617 mixture modeling of inverse regression.")
16618 (license license:gpl2+)))
16620 (define-public r-pbivnorm
16622 (name "r-pbivnorm")
16627 (uri (cran-uri "pbivnorm" version))
16630 "05jzrjqxzbcf6z245hlk7sjxiszv9paadaaimvcx5y5qgi87vhq7"))))
16631 (build-system r-build-system)
16632 (native-inputs (list gfortran))
16633 (home-page "https://github.com/brentonk/pbivnorm")
16634 (synopsis "Vectorized bivariate normal CDF")
16636 "This package provides a vectorized R function for calculating
16637 probabilities from a standard bivariate normal CDF.")
16638 (license license:gpl2+)))
16640 (define-public r-lavaan
16647 (uri (cran-uri "lavaan" version))
16650 "026k32paf51lpy6zxm9m81zg9szx14j37dxdip6nba334jw97h9c"))))
16651 (build-system r-build-system)
16653 (list r-mass r-mnormt r-numderiv r-pbivnorm))
16654 (home-page "https://lavaan.ugent.be")
16655 (synopsis "Latent variable analysis")
16657 "This package provides tools to fit a variety of latent variable models,
16658 including confirmatory factor analysis, structural equation modeling and
16659 latent growth curve models.")
16660 (license license:gpl2+)))
16662 (define-public r-nonnest2
16664 (name "r-nonnest2")
16669 (uri (cran-uri "nonnest2" version))
16672 "1ddaqwx8i3ygwvxf11mc8xhgk4nkvnail99nr5szq8i168752zq2"))))
16673 (build-system r-build-system)
16675 (list r-compquadform r-lavaan r-mvtnorm r-sandwich))
16678 (home-page "https://cran.r-project.org/web/packages/nonnest2/")
16679 (synopsis "Tests of non-nested models")
16681 "This package allows for testing of non-nested models. It includes tests
16682 of model distinguishability and of model fit that can be applied to both
16683 nested and non-nested models. The package also includes functionality to
16684 obtain confidence intervals associated with AIC and BIC.")
16685 ;; Either version of the GPL.
16686 (license (list license:gpl2 license:gpl3))))
16688 (define-public r-penalized
16690 (name "r-penalized")
16695 (uri (cran-uri "penalized" version))
16698 "08badmgygppbqzay20qijyww028yw6s8dyd8ijcp8g4r9rn8xqyq"))))
16699 (build-system r-build-system)
16701 (list r-rcpp r-rcpparmadillo r-survival))
16702 (home-page "https://cran.r-project.org/web/packages/penalized/")
16703 (synopsis "Penalized estimation in GLMs and in the Cox model")
16705 "This package provides tools for fitting possibly high dimensional
16706 penalized regression models. The penalty structure can be any combination of
16707 an L1 penalty (lasso and fused lasso), an L2 penalty (ridge) and a positivity
16708 constraint on the regression coefficients. The supported regression models
16709 are linear, logistic and Poisson regression and the Cox Proportional Hazards
16710 model. Cross-validation routines allow optimization of the tuning
16712 (license license:gpl2+)))
16714 (define-public r-zim
16721 (uri (cran-uri "ZIM" version))
16724 "0scyfjn4ilsvha3x41c3b8bcfi31hlhwm77wn2a8hj5dsvnnmzig"))))
16725 (properties `((upstream-name . "ZIM")))
16726 (build-system r-build-system)
16727 (propagated-inputs (list r-mass))
16728 (home-page "https://github.com/biostatstudio/ZIM")
16729 (synopsis "Zero-inflated models (ZIM) for count time series with excess zeros")
16731 "Analyze count time series with excess zeros. Two types of statistical
16732 models are supported: Markov regression and state-space models. They are also
16733 known as observation-driven and parameter-driven models respectively in the
16734 time series literature. The functions used for Markov regression or
16735 observation-driven models can also be used to fit ordinary regression models
16736 with independent data under the zero-inflated Poisson (ZIP) or zero-inflated
16737 negative binomial (ZINB) assumption. The package also contains miscellaneous
16738 functions to compute density, distribution, quantile, and generate random
16739 numbers from ZIP and ZINB distributions.")
16740 (license license:gpl3)))
16742 (define-public r-nor1mix
16749 (uri (cran-uri "nor1mix" version))
16752 "1817wcvlmxs70vs4db0jkxd7i037744zz8ay3c2a9949z29fxr4w"))))
16753 (build-system r-build-system)
16754 (home-page "https://cran.r-project.org/web/packages/nor1mix/")
16755 (synopsis "Normal (1-d) mixture models")
16757 "This package provides S3 classes and methods for one-dimensional normal
16758 mixture models, for, e.g., density estimation or clustering algorithms
16759 research and teaching; it provides the widely used Marron-Wand densities. It
16760 also provides tools for efficient random number generation and graphics.")
16761 (license license:gpl2+)))
16763 (define-public r-beanplot
16765 (name "r-beanplot")
16770 (uri (cran-uri "beanplot" version))
16773 "1b8mvlcsv5l9g08ag92hndsvk8jmgxvznhzgazc8y4296kp8l5a9"))))
16774 (build-system r-build-system)
16775 (home-page "https://cran.r-project.org/web/packages/beanplot/")
16776 (synopsis "Visualization via beanplots")
16778 "This package provides beanplots, an alternative to
16779 boxplot/stripchart/violin plots. It can be used to plot univariate comparison
16781 (license license:gpl2)))
16783 (define-public r-pbdzmq
16790 (uri (cran-uri "pbdZMQ" version))
16793 "020qy6fq8w8wq0j3bii14ahrlg8wzl0lrnndfr6scmrg9ghjnbfz"))))
16794 (properties `((upstream-name . "pbdZMQ")))
16795 (build-system r-build-system)
16797 (list zeromq zlib))
16800 (home-page "https://pbdr.org/")
16801 (synopsis "R interface to ZeroMQ")
16803 "ZeroMQ is a well-known library for high-performance asynchronous
16804 messaging in scalable, distributed applications. This package provides high
16805 level R wrapper functions to easily utilize ZeroMQ. The main focus is on
16806 interactive client/server programming frameworks. A few wrapper functions
16807 compatible with @code{rzmq} are also provided.")
16808 (license license:gpl3)))
16810 (define-public r-repr
16817 (uri (cran-uri "repr" version))
16820 "0h3h14ybamcbwmm31ib66fx13v75vkzn4bn2v26n2h097sl9qybg"))))
16821 (build-system r-build-system)
16823 (list r-base64enc r-htmltools r-jsonlite r-pillar))
16824 (home-page "https://cran.r-project.org/web/packages/repr/")
16825 (synopsis "Serializable representations")
16827 "This package provides string and binary representations of objects for
16828 several formats and MIME types.")
16829 (license license:gpl3)))
16831 (define-public r-irdisplay
16833 (name "r-irdisplay")
16838 (uri (cran-uri "IRdisplay" version))
16841 "0awdiv4rr93y8jb1d64sm1iy37ywyniqm7w98yv6qm0zz47h7sw3"))))
16842 (properties `((upstream-name . "IRdisplay")))
16843 (build-system r-build-system)
16846 (home-page "https://cran.r-project.org/web/packages/IRdisplay/")
16847 (synopsis "Jupyter display machinery")
16849 "This package provides an interface to the rich display capabilities of
16850 Jupyter front-ends (e.g. Jupyter Notebook). It is designed to be used from a
16851 running IRkernel session.")
16852 (license license:expat)))
16854 (define-public r-irkernel
16856 (name "r-irkernel")
16861 (uri (cran-uri "IRkernel" version))
16864 "00qrmsywpzw2hfp88020zjaijma7q4hqm9h2cz53rywdjzywnzss"))))
16865 (properties `((upstream-name . "IRkernel")))
16866 (build-system r-build-system)
16869 (modify-phases %standard-phases
16870 (add-after 'install 'install-kernelspec
16871 (lambda* (#:key outputs #:allow-other-keys)
16872 (let ((out (assoc-ref outputs "out")))
16873 (setenv "HOME" "/tmp")
16874 (invoke "jupyter" "kernelspec" "install"
16877 (string-append out "/site-library/IRkernel/kernelspec"))
16878 ;; Record the absolute file name of the 'R' executable in
16880 (substitute* (string-append out "/share/jupyter"
16881 "/kernels/ir/kernel.json")
16883 (string-append "[\"" (which "R") "\",")))
16893 ;; sets R_LIBS_SITE, so R can actually find this package (IRkernel)
16898 (home-page "https://cran.r-project.org/web/packages/IRkernel/")
16899 (synopsis "Native R kernel for Jupyter")
16901 "The R kernel for the Jupyter environment executes R code which the
16902 front-end (Jupyter Notebook or other front-ends) submits to the kernel via the
16904 (license license:expat)))
16906 (define-public r-gmodels
16909 (version "2.18.1.1")
16913 (uri (cran-uri "gmodels" version))
16916 "158y7yh4maawn9vki8cq4sil48xib2bbpl6qgj5gvlkw3c14hzfs"))))
16917 (build-system r-build-system)
16919 (list r-gdata r-mass))
16920 (home-page "https://cran.r-project.org/web/packages/gmodels/")
16921 (synopsis "Various R programming tools for model fitting")
16923 "This package provides various R programming tools for model fitting.")
16924 (license license:gpl2)))
16926 (define-public r-apcluster
16928 (name "r-apcluster")
16933 (uri (cran-uri "apcluster" version))
16936 "0wnbb3kj9m7rfq63xr43jjf6n8jxm1r2wvvx6g0qkss0wvipbb1s"))))
16937 (build-system r-build-system)
16939 (list r-matrix r-rcpp))
16940 (native-inputs (list r-knitr))
16941 (home-page "https://cran.r-project.org/web/packages/apcluster/")
16942 (synopsis "Affinity propagation clustering")
16944 "This package implements affinity propagation clustering introduced by
16945 Frey and Dueck (2007). The package further provides leveraged affinity
16946 propagation and an algorithm for exemplar-based agglomerative clustering that
16947 can also be used to join clusters obtained from affinity propagation. Various
16948 plotting functions are available for analyzing clustering results.")
16949 (license license:gpl2+)))
16951 (define-public r-rematch2
16953 (name "r-rematch2")
16958 (uri (cran-uri "rematch2" version))
16961 "1fzpz8vhghw8ygwg6rsvfy3783pqk7ch029i5851lwypkplvz77y"))))
16962 (build-system r-build-system)
16965 (home-page "https://github.com/r-lib/rematch2")
16966 (synopsis "Tidy output from regular expression matching")
16968 "This package provides wrappers on @code{regexpr} and @code{gregexpr} to
16969 return the match results in tidy data frames.")
16970 (license license:expat)))
16972 (define-public r-picante
16979 (uri (cran-uri "picante" version))
16982 "19savjzj44b7ifdxcp02ynj22z4n4ikq2aipc74ljzy3yykmqmjn"))))
16983 (build-system r-build-system)
16985 (list r-ape r-nlme r-vegan))
16986 (home-page "https://cran.r-project.org/web/packages/picante/")
16987 (synopsis "Integrating phylogenies and ecology")
16989 "This package provides functions for phylocom integration, community
16990 analyses, null-models, traits and evolution. It implements numerous
16991 ecophylogenetic approaches including measures of community phylogenetic and
16992 trait diversity, phylogenetic signal, estimation of trait values for
16993 unobserved taxa, null models for community and phylogeny randomizations, and
16994 utility functions for data input/output and phylogeny plotting. A full
16995 description of package functionality and methods are provided by Kembel et
16997 (license license:gpl2)))
16999 (define-public r-reinforcelearn
17001 (name "r-reinforcelearn")
17006 (uri (cran-uri "reinforcelearn" version))
17009 "176z2q69p24i29a8sh19xxn2zl3h1z2ixdssr5i6m4yvkvdrvv3b"))))
17010 (build-system r-build-system)
17012 (list r-checkmate r-nnet r-purrr r-r6))
17013 (home-page "https://markusdumke.github.io/reinforcelearn")
17014 (synopsis "Reinforcement learning")
17016 "This package implements reinforcement learning environments and
17017 algorithms as described in Sutton & Barto (1998). The Q-Learning algorithm
17018 can be used with function approximation, eligibility traces (Singh & Sutton,
17019 1996) and experience replay (Mnih et al., 2013).")
17020 (license license:expat)))
17022 (define-public r-lemon
17029 (uri (cran-uri "lemon" version))
17032 "1y3ljidhqdakxlya2npj2w0az820g8kw6gl1cfm4f0cxvzgd1ly4"))))
17033 (build-system r-build-system)
17045 (home-page "https://github.com/stefanedwards/lemon")
17046 (synopsis "Freshen up your ggplot2 plots")
17048 "This package provides functions for working with legends and axis lines
17049 of ggplot2, facets that repeat axis lines on all panels, and some knitr
17051 (license license:gpl3)))
17053 (define-public r-wgaim
17060 (uri (cran-uri "wgaim" version))
17062 (base32 "1qiyfkpsbzjr9xsq5kqq6rlqpndngkn2irdfh3gyi45h6hn118j4"))))
17063 (build-system r-build-system)
17065 (list r-ggplot2 r-qtl))
17066 (home-page "https://cran.r-project.org/web/packages/wgaim")
17067 (synopsis "Whole genome average interval mapping for QTL detection")
17069 "This package integrates sophisticated mixed modelling methods with a
17070 whole genome approach to detecting significant QTL in linkage maps.")
17071 (license license:gpl2+)))
17073 (define-public r-bedr
17080 (uri (cran-uri "bedr" version))
17083 "0zpqvyjgwyqawxm8qrhcv8zq2b3yxgcqkkc87br29yrl7sjb8h6j"))))
17084 (build-system r-build-system)
17093 htslib)) ; for tabix
17095 (list r-knitr)) ; for vignettes
17096 (home-page "https://cran.r-project.org/web/packages/bedr")
17097 (synopsis "Genomic region processing")
17099 "This package is for genomic regions processing using command line tools
17100 such as BEDTools, BEDOPS and Tabix. These tools offer scalable and efficient
17101 utilities to perform genome arithmetic e.g indexing, formatting and merging.
17102 The bedr package's API enhances access to these tools as well as offers
17103 additional utilities for genomic regions processing.")
17104 (license license:gpl2)))
17106 (define-public r-sets
17113 (uri (cran-uri "sets" version))
17116 "1h1a03b1850kh5hd3gxbspx2nxqxvk2gb0wm0s60b70qb6zg0csp"))))
17117 (properties `((upstream-name . "sets")))
17118 (build-system r-build-system)
17119 (home-page "https://cran.r-project.org/web/packages/sets")
17120 (synopsis "Sets, generalized sets, customizable sets and intervals")
17122 "This package provides data structures and basic operations for ordinary
17123 sets, generalizations such as fuzzy sets, multisets, and fuzzy multisets,
17124 customizable sets, and intervals.")
17125 (license license:gpl2)))
17127 (define-public r-partitions
17129 (name "r-partitions")
17134 (uri (cran-uri "partitions" version))
17137 "1qqy4df28wy4q0g572azrj171jlhvrnzbh7x0wr2g7v6gr20y0ns"))))
17138 (build-system r-build-system)
17140 (list r-gmp r-polynom r-sets))
17141 (home-page "https://cran.r-project.org/web/packages/partitions")
17142 (synopsis "Additive partitions of integers")
17144 "This package provides tools to enumerates the partitions, unequal
17145 partitions, and restricted partitions of an integer; the three corresponding
17146 partition functions are also given.")
17147 ;; Any version of the GPL
17148 (license license:gpl2+)))
17150 (define-public r-brobdingnag
17152 (name "r-brobdingnag")
17157 (uri (cran-uri "Brobdingnag" version))
17160 "0hnp5nrpnscykvgrrbgp7987660hcbv92zc2q8lmpnin4ws399vk"))))
17161 (properties `((upstream-name . "Brobdingnag")))
17162 (build-system r-build-system)
17163 (home-page "https://github.com/RobinHankin/Brobdingnag.git")
17164 (synopsis "Very large numbers in R")
17166 "This package handles very large numbers in R. Real numbers are held
17167 using their natural logarithms, plus a logical flag indicating sign. The
17168 package includes a vignette that gives a step-by-step introduction to using S4
17170 ;; Any version of the GPL
17171 (license license:gpl2+)))
17173 (define-public r-untb
17180 (uri (cran-uri "untb" version))
17183 "1i7m4vfslsix98dwx4jlrsldm7fhhfp25gr7aapcxqxms7ryaby6"))))
17184 (build-system r-build-system)
17186 (list r-brobdingnag r-partitions r-polynom))
17187 (home-page "https://github.com/RobinHankin/untb.git")
17188 (synopsis "Ecological drift under the UNTB")
17190 "This package provides numerical simulations, and visualizations, of
17191 Hubbell's @dfn{Unified Neutral Theory of Biodiversity} (UNTB).")
17192 (license license:gpl2+)))
17194 (define-public r-stepwise
17196 (name "r-stepwise")
17201 (uri (cran-uri "stepwise" version))
17204 "1lbx1bxwkf9dw6q46w40pp7h5nkxgghmx8rkpaymm6iybc7gyir2"))))
17205 (build-system r-build-system)
17206 (home-page "https://stat.sfu.ca/statgen/research/stepwise.html")
17207 (synopsis "Stepwise detection of recombination breakpoints")
17209 "This package provides a stepwise approach to identifying recombination
17210 breakpoints in a genomic sequence alignment.")
17211 (license license:gpl2+)))
17213 (define-public r-snpmaxsel
17215 (name "r-snpmaxsel")
17220 (uri (cran-uri "SNPmaxsel" version))
17223 "0pjvixwqzjd3jwccc8yqq9c76afvbmfq0z1w0cwyj8bblrjpx13z"))))
17224 (properties `((upstream-name . "SNPmaxsel")))
17225 (build-system r-build-system)
17227 (list r-combinat r-mvtnorm))
17228 (home-page "https://cran.r-project.org/web/packages/SNPmaxsel/index.html")
17229 (synopsis "Maximally selected statistics for SNP data")
17231 "This package implements asymptotic methods related to maximally selected
17232 statistics, with applications to @dfn{single-nucleotide polymorphism} (SNP)
17234 (license license:gpl2+)))
17236 (define-public r-acsnminer
17238 (name "r-acsnminer")
17239 (version "0.16.8.25")
17242 (uri (cran-uri "ACSNMineR" version))
17245 "0gh604s8qall6zfjlwcg2ilxjvz08dplf9k5g47idhv43scm748l"))))
17246 (properties `((upstream-name . "ACSNMineR")))
17247 (build-system r-build-system)
17249 (list r-ggplot2 r-gridextra))
17250 (home-page "https://cran.r-project.org/web/packages/ACSNMineR")
17251 (synopsis "Gene enrichment analysis")
17253 "This package provides tools to compute and represent gene set enrichment
17254 or depletion from your data based on pre-saved maps from the @dfn{Atlas of
17255 Cancer Signalling Networks} (ACSN) or user imported maps. The gene set
17256 enrichment can be run with hypergeometric test or Fisher exact test, and can
17257 use multiple corrections. Visualization of data can be done either by
17258 barplots or heatmaps.")
17259 (license license:gpl2+)))
17261 (define-public r-seqinr
17268 (uri (cran-uri "seqinr" version))
17271 "0cj07b7km5mla63qhbkxg1mnqq6vh79lsyyfpnbm29gw68w2bwy4"))))
17272 (build-system r-build-system)
17274 (list r-ade4 r-segmented))
17277 (home-page "http://seqinr.r-forge.r-project.org/")
17278 (synopsis "Biological sequences retrieval and analysis")
17280 "This package provides tools for exploratory data analysis and data
17281 visualization of biological sequence (DNA and protein) data. It also includes
17282 utilities for sequence data management under the ACNUC system.")
17283 (license license:gpl2+)))
17285 (define-public r-units
17292 (uri (cran-uri "units" version))
17295 "06mjprqi06xprj6185k5cmrrdl025x0pd1r6a4x3s74ciq9zwilw"))))
17296 (build-system r-build-system)
17303 (home-page "https://github.com/r-quantities/units/")
17304 (synopsis "Measurement Units for R Vectors")
17306 "This package provides support for measurement units in R vectors,
17307 matrices and arrays: automatic propagation, conversion, derivation and
17308 simplification of units; raising errors in case of unit incompatibility. It
17309 is compatible with the @code{POSIXct}, @code{Date} and @code{difftime}
17311 (license license:gpl2)))
17313 (define-public r-udunits2
17315 (name "r-udunits2")
17316 (version "0.13.2.1")
17320 (uri (cran-uri "udunits2" version))
17323 "00prsy8m41v1camcsz94d7gm8qab2mdnwl3x0dyhz4r49b02jm4z"))))
17324 (properties `((upstream-name . "udunits2")))
17325 (build-system r-build-system)
17328 (home-page "https://cran.r-project.org/package=udunits2")
17329 (synopsis "Udunits-2 bindings for R")
17331 "This package provides simple bindings to Unidata's udunits library.")
17332 (license license:gpl2)))
17334 (define-public r-classint
17336 (name "r-classint")
17341 (uri (cran-uri "classInt" version))
17344 "1b1lqhpzxm6b8pza8l3s0cxy74mm9y45lcd3354i2v3bg8m7mply"))))
17345 (properties `((upstream-name . "classInt")))
17346 (build-system r-build-system)
17348 (list r-class r-e1071 r-kernsmooth))
17350 (list gfortran r-knitr))
17351 (home-page "https://github.com/r-spatial/classInt/")
17352 (synopsis "Choose univariate class intervals")
17354 "This package provides selected commonly used methods for choosing
17355 univariate class intervals for mapping or other graphics purposes.")
17356 (license license:gpl2+)))
17358 (define-public r-spdata
17365 (uri (cran-uri "spData" version))
17368 "1z4hp5ivwzyvl8mkp98j2ng1cl1xksqbjxv85vdlqfqjwpia6df6"))))
17369 (properties `((upstream-name . "spData")))
17370 (build-system r-build-system)
17372 (list r-raster r-sp))
17373 (home-page "https://github.com/Nowosad/spData")
17374 (synopsis "Datasets for spatial analysis")
17376 "This a package containing diverse spatial datasets for demonstrating,
17377 benchmarking and teaching spatial data analysis. It includes R data of class
17378 @code{sf}, @code{Spatial}, and @code{nb}. It also contains data stored in a
17379 range of file formats including GeoJSON, ESRI Shapefile and GeoPackage. Some
17380 of the datasets are designed to illustrate specific analysis techniques.
17381 @code{cycle_hire()} and @code{cycle_hire_osm()}, for example, are designed to
17382 illustrate point pattern analysis techniques.")
17383 (license license:cc0)))
17385 (define-public r-learnbayes
17387 (name "r-learnbayes")
17392 (uri (cran-uri "LearnBayes" version))
17395 "0ch54v2zz2yyyk0lvn5rfikdmyz1qh9j1wk3585wl8v58mc0h4cv"))))
17396 (properties `((upstream-name . "LearnBayes")))
17397 (build-system r-build-system)
17398 (home-page "https://cran.r-project.org/web/packages/LearnBayes")
17399 (synopsis "Functions for learning Bayesian inference")
17401 "This package provides a collection of functions helpful in learning the
17402 basic tenets of Bayesian statistical inference. It contains functions for
17403 summarizing basic one and two parameter posterior distributions and predictive
17404 distributions. It contains MCMC algorithms for summarizing posterior
17405 distributions defined by the user. It also contains functions for regression
17406 models, hierarchical models, Bayesian tests, and illustrations of Gibbs
17408 (license license:gpl2+)))
17410 (define-public r-deldir
17417 (uri (cran-uri "deldir" version))
17420 "1igq0l2knsbhizncgydcsidgkvvlwwlkrifbcdyhnzk0bhrdixkd"))))
17421 (build-system r-build-system)
17422 (native-inputs (list gfortran))
17423 (home-page "https://cran.r-project.org/web/packages/deldir")
17424 (synopsis "Delaunay triangulation and Dirichlet (Voronoi) tessellation")
17426 "This package provides tools for calculating the Delaunay triangulation
17427 and the Dirichlet or Voronoi tessellation (with respect to the entire plane)
17428 of a planar point set. It plots triangulations and tessellations in various
17429 ways, clips tessellations to sub-windows, calculates perimeters of
17430 tessellations, and summarizes information about the tiles of the
17432 (license license:gpl2+)))
17434 (define-public r-wk
17441 (uri (cran-uri "wk" version))
17444 "1xga4rrqsr190g55by39az4nimnn06bf5b6mcjgwqvba0lvjhb5g"))))
17445 (properties `((upstream-name . "wk")))
17446 (build-system r-build-system)
17447 (home-page "https://paleolimbot.github.io/wk/")
17448 (synopsis "Lightweight well-known geometry parsing")
17450 "This package provides a minimal R and C++ API for parsing well-known
17451 binary and well-known text representation of geometries to and from R-native
17452 formats. Well-known binary is compact and fast to parse; well-known text is
17453 human-readable and is useful for writing tests. These formats are only useful
17454 in R if the information they contain can be accessed in R, for which
17455 high-performance functions are provided here.")
17456 (license license:expat)))
17458 (define-public r-s2
17465 (uri (cran-uri "s2" version))
17468 "0gwydn6wdl675ydkcckrci6ylcx30qn8nfhmrp4qx4r9mv3c2410"))))
17469 (properties `((upstream-name . "s2")))
17470 (build-system r-build-system)
17472 (list r-rcpp r-wk))
17477 (home-page "https://r-spatial.github.io/s2/")
17478 (synopsis "Spherical geometry operators using the S2 geometry library")
17480 "This package provides R bindings for Google's s2 library for geometric
17481 calculations on the sphere. High-performance constructors and exporters
17482 provide high compatibility with existing spatial packages, transformers
17483 construct new geometries from existing geometries, predicates provide a means
17484 to select geometries based on spatial relationships, and accessors extract
17485 information about geometries.")
17486 (license license:asl2.0)))
17488 (define-public r-sf
17495 (uri (cran-uri "sf" version))
17498 "0lsl4rh4lbv386hxlsnnwsjb5x1n9d3z0ckjmxakmmrqjjmiywyh"))))
17499 (build-system r-build-system)
17501 (list gdal geos proj sqlite zlib))
17510 (list pkg-config r-knitr))
17511 (home-page "https://github.com/r-spatial/sf/")
17512 (synopsis "Simple features for R")
17514 "This package provides support for simple features, a standardized way to
17515 encode spatial vector data. It binds to GDAL for reading and writing data, to
17516 GEOS for geometrical operations, and to PROJ for projection conversions and
17517 datum transformations.")
17518 ;; Either of these licenses
17519 (license (list license:gpl2 license:expat))))
17521 (define-public r-spdep
17527 (uri (cran-uri "spdep" version))
17530 "0xx6k3rsvsz1hwj0ny8aqfi9ca54x38f8pz8sfya5cggaspxbx59"))
17532 '(for-each delete-file '("inst/doc/CO69.html"
17536 "inst/doc/nb_sf.html"
17538 "inst/doc/nb_sf.Rmd"
17539 "inst/doc/sids.html"
17540 "inst/doc/sids.R")))))
17541 (build-system r-build-system)
17553 (home-page "https://github.com/r-spatial/spdep/")
17554 (synopsis "Spatial dependence: weighting schemes, statistics and models")
17556 "This package provides a collection of functions to create spatial
17557 weights matrix objects from polygon contiguities, from point patterns by
17558 distance and tessellations, for summarizing these objects, and for permitting
17559 their use in spatial data analysis, including regional aggregation by minimum
17561 (license license:gpl2+)))
17563 (define-public r-adegenet
17565 (name "r-adegenet")
17570 (uri (cran-uri "adegenet" version))
17573 "0sx25p7bgz0h9mc3jsdnnjhvmb7sy8nb3r0z923vhk336d4xw8vq"))))
17574 (build-system r-build-system)
17587 (home-page "https://github.com/thibautjombart/adegenet")
17588 (synopsis "Exploratory analysis of genetic and genomic data")
17590 "This package provides a toolset for the exploration of genetic and
17591 genomic data. Adegenet provides formal (S4) classes for storing and handling
17592 various genetic data, including genetic markers with varying ploidy and
17593 hierarchical population structure (@code{genind} class), alleles counts by
17594 populations (@code{genpop}), and genome-wide SNP data (@code{genlight}). It
17595 also implements original multivariate methods (DAPC, sPCA), graphics,
17596 statistical tests, simulation tools, distance and similarity measures, and
17597 several spatial methods. A range of both empirical and simulated datasets is
17598 also provided to illustrate various methods.")
17599 (license license:gpl2+)))
17601 (define-public r-pegas
17608 (uri (cran-uri "pegas" version))
17610 (base32 "0ngd0laqbs139ji9hm9kwsm9rm56agw2yyfcplxgqva936l93fl7"))))
17611 (build-system r-build-system)
17614 (home-page "http://ape-package.ird.fr/pegas.html")
17615 (synopsis "Population and evolutionary genetics analysis system")
17617 "This package provides functions for reading, writing, plotting,
17618 analysing, and manipulating allelic and haplotypic data, including from VCF
17619 files, and for the analysis of population nucleotide sequences and
17620 micro-satellites including coalescent analyses, linkage disequilibrium,
17621 population structure (Fst, Amova) and equilibrium (HWE), haplotype networks,
17622 minimum spanning tree and network, and median-joining networks.")
17623 (license license:gpl2+)))
17625 (define-public r-rmetasim
17627 (name "r-rmetasim")
17632 (uri (cran-uri "rmetasim" version))
17635 "0rdkhfgyr97r2d1kd9g8ipb2pn563qxm1y4m9z678q0kqan2ddl0"))))
17636 (build-system r-build-system)
17638 (list r-ade4 r-adegenet r-gtools r-pegas))
17639 (home-page "https://cran.r-project.org/web/packages/rmetasim")
17640 (synopsis "Individual-based population genetic simulation environment")
17642 "This package provides an interface between R and the metasim simulation
17643 engine. The simulation environment is documented in: Strand, A.(2002),
17644 Metasim 1.0: an individual-based environment for simulating population
17645 genetics of complex population dynamics.")
17647 (license license:gpl2+)))
17649 (define-public r-genetics
17651 (name "r-genetics")
17652 (version "1.3.8.1.3")
17656 (uri (cran-uri "genetics" version))
17659 "0lljxvz7nc6y2z303icphar2niir0i407w5cyhy2pwspd9gwkwpy"))))
17660 (build-system r-build-system)
17662 (list r-combinat r-gdata r-gtools r-mass r-mvtnorm))
17663 (home-page "https://cran.r-project.org/web/packages/genetics/")
17664 (synopsis "Population genetics")
17666 "This package provides classes and methods for handling genetic data.
17667 It includes classes to represent genotypes and haplotypes at single markers up
17668 to multiple markers on multiple chromosomes. Function include allele
17669 frequencies, flagging homo/heterozygotes, flagging carriers of certain
17670 alleles, estimating and testing for Hardy-Weinberg disequilibrium, estimating
17671 and testing for linkage disequilibrium, ...")
17672 ;; Any GPL version.
17673 (license license:gpl2+)))
17675 (define-public r-snp-plotter
17677 (name "r-snp-plotter")
17682 (uri (cran-uri "snp.plotter" version))
17685 "16apsqvkah5l0d5qcwp3lq2jspkb6n62wzr0wskmj84jblx483vv"))))
17686 (properties `((upstream-name . "snp.plotter")))
17687 (build-system r-build-system)
17688 (propagated-inputs (list r-genetics))
17689 (home-page "https://cran.r-project.org/web/packages/snp.plotter/")
17690 (synopsis "Plot p-values using single SNP and/or haplotype data")
17692 "This package helps you create plots of p-values using single SNP and/or
17693 haplotype data. Main features of the package include options to display a
17694 @dfn{linkage disequilibrium} (LD) plot and the ability to plot multiple
17695 datasets simultaneously. Plots can be created using global and/or individual
17696 haplotype p-values along with single SNP p-values. Images are created as
17697 either PDF/EPS files.")
17698 (license license:gpl2+)))
17700 (define-public r-polspline
17702 (name "r-polspline")
17707 (uri (cran-uri "polspline" version))
17709 (base32 "1dd1jwiaglkkhajzvqfkd1x5r3wzjlk5ww0yxzmns0s1kr74i4k9"))))
17710 (build-system r-build-system)
17711 (native-inputs (list gfortran))
17712 (home-page "https://cran.r-project.org/web/packages/polspline/")
17713 (synopsis "Polynomial spline routines")
17715 "This package provides routines for the polynomial spline fitting
17716 routines hazard regression, hazard estimation with flexible tails, logspline,
17717 lspec, polyclass, and polymars.")
17718 (license license:gpl2+)))
17720 (define-public r-rms
17727 (uri (cran-uri "rms" version))
17729 (base32 "1yfk800q4mgmrjkh0hqjkiv907sr1bi1jaigrj8l6pmg1mkynhbc"))))
17730 (build-system r-build-system)
17747 (native-inputs (list gfortran))
17748 (home-page "http://biostat.mc.vanderbilt.edu/rms")
17749 (synopsis "Regression modeling strategies")
17751 "This is a package for regression modeling, testing, estimation,
17752 validation, graphics, prediction, and typesetting by storing enhanced model
17753 design attributes in the fit. The rms package is a collection of functions
17754 that assist with and streamline modeling. It also contains functions for
17755 binary and ordinal logistic regression models, ordinal models for continuous Y
17756 with a variety of distribution families, and the Buckley-James multiple
17757 regression model for right-censored responses, and implements penalized
17758 maximum likelihood estimation for logistic and ordinary linear models. The
17759 package works with almost any regression model, but it was especially written
17760 to work with binary or ordinal regression models, Cox regression, accelerated
17761 failure time models, ordinary linear models, the Buckley-James model,
17762 generalized least squares for serially or spatially correlated observations,
17763 generalized linear models, and quantile regression.")
17764 (license license:gpl2+)))
17766 (define-public r-arsenal
17773 (uri (cran-uri "arsenal" version))
17776 "0qvs3ld28djnjnggdhqjwq8sbv8zz322qahlvf7dnx35yqf6xkms"))))
17777 (properties `((upstream-name . "arsenal")))
17778 (build-system r-build-system)
17779 (propagated-inputs (list r-knitr))
17780 (native-inputs (list r-knitr))
17781 (home-page "https://github.com/mayoverse/arsenal")
17782 (synopsis "Functions for large-scale statistical summaries")
17784 "This package provides an arsenal of R functions for large-scale
17785 statistical summaries, which are streamlined to work within the latest
17786 reporting tools in R and RStudio and which use formulas and versatile
17787 summary statistics for summary tables and models. The primary functions
17791 @item @code{tableby}, a Table-1-like summary of multiple variable types by the
17792 levels of one or more categorical variables;
17793 @item @code{paired}, a Table-1-like summary of multiple variable types paired
17794 across two time points;
17795 @item @code{modelsum}, which performs simple model fits on one or more
17796 endpoints for many variables (univariate or adjusted for covariates);
17797 @item @code{freqlist}, a powerful frequency table across many categorical
17799 @item @code{comparedf}, a function for comparing @code{data.frames}; and
17800 @item @code{write2}, a function to output tables to a document.
17803 (license license:gpl2+)))
17805 (define-public r-haplo-stats
17807 (name "r-haplo-stats")
17812 (uri (cran-uri "haplo.stats" version))
17815 "1q2zn72j92bwhcdswk4qqfgzch56p9pcy2xhkd3safvqp3l9rzpw"))))
17816 (properties `((upstream-name . "haplo.stats")))
17817 (build-system r-build-system)
17819 (list r-arsenal r-rms))
17821 (list r-r-rsp)) ; for vignettes
17822 (home-page "https://www.mayo.edu/research/labs/statistical-genetics-genetic-epidemiology/software")
17823 (synopsis "Analysis of haplotypes when linkage phase is ambiguous")
17825 "This package provides routines for the analysis of indirectly measured
17826 haplotypes. The statistical methods assume that all subjects are unrelated
17827 and that haplotypes are ambiguous (due to unknown linkage phase of the genetic
17828 markers). The main functions are: @code{haplo.em()}, @code{haplo.glm()},
17829 @code{haplo.score()}, and @code{haplo.power()}; all of which have detailed
17830 examples in the vignette.")
17831 (license license:gpl2+)))
17833 (define-public r-bqtl
17840 (uri (cran-uri "bqtl" version))
17843 "1sbzpi9z94f010lw2y1gmifjrvpmiqs4m26za7vr1xz72azrqvs9"))))
17844 (build-system r-build-system)
17845 (native-inputs (list gfortran))
17846 (home-page "http://famprevmed.ucsd.edu/faculty/cberry/bqtl/")
17847 (synopsis "Bayesian QTL mapping toolkit")
17849 "This is a QTL mapping toolkit for inbred crosses and recombinant inbred
17850 lines. It includes maximum likelihood and Bayesian tools.")
17851 (license license:gpl2+)))
17853 (define-public r-ibdreg
17860 (uri (cran-uri "ibdreg" version))
17863 "1x8z0vr2cmdks12hxfm0wwxskb0cr669w5j5rpa2ln8q704yy41g"))))
17864 (build-system r-build-system)
17865 (home-page "https://www.mayo.edu/research/labs/\
17866 statistical-genetics-genetic-epidemiology/software")
17867 (synopsis "Regression methods for IBD linkage with covariates")
17869 "This package provides a method to test genetic linkage with covariates
17870 by regression methods with response IBD sharing for relative pairs. Account
17871 for correlations of IBD statistics and covariates for relative pairs within
17872 the same pedigree.")
17873 (license license:gpl2+)))
17875 (define-public r-dlmap
17882 (uri (cran-uri "dlmap" version))
17885 "0s6wlkggkm3qndwyvw72xv1n0mcjb7ss3ajbq2ll6rv30splq0db"))))
17886 (build-system r-build-system)
17888 (list r-ibdreg r-mgcv r-nlme r-qtl r-wgaim))
17889 (home-page "https://cran.r-project.org/web/packages/dlmap/")
17890 (synopsis "Detection localization mapping for QTL")
17892 "This is package for QTL mapping in a mixed model framework with separate
17893 detection and localization stages. The first stage detects the number of QTL
17894 on each chromosome based on the genetic variation due to grouped markers on
17895 the chromosome; the second stage uses this information to determine the most
17896 likely QTL positions. The mixed model can accommodate general fixed and
17897 random effects, including spatial effects in field trials and pedigree
17898 effects. It is applicable to backcrosses, doubled haploids, recombinant
17899 inbred lines, F2 intercrosses, and association mapping populations.")
17900 (license license:gpl2)))
17902 (define-public r-hwde
17909 (uri (cran-uri "hwde" version))
17912 "0wb2f9i5qi7w77ygh8bvydfpr7j5x8dyvnnhdkajaz0wdcpkyaqy"))))
17913 (build-system r-build-system)
17914 (home-page "https://cran.r-project.org/web/packages/hwde/")
17915 (synopsis "Models and tests for departure from Hardy-Weinberg equilibrium")
17917 "This package fits models for genotypic disequilibria, as described in
17918 Huttley and Wilson (2000), Weir (1996) and Weir and Wilson (1986). Contrast
17919 terms are available that account for first order interactions between loci.
17920 It also implements, for a single locus in a single population, a conditional
17921 exact test for Hardy-Weinberg equilibrium.")
17922 (license license:gpl2+)))
17924 (define-public r-tdthap
17931 (uri (cran-uri "tdthap" version))
17934 "15qlj2bivvz3pizd8dq34wczbkbxhzqh3cqp1ixkdkprlyvcxj5k"))))
17935 (build-system r-build-system)
17936 (home-page "https://cran.r-project.org/web/packages/tdthap/")
17937 (synopsis "TDT tests for extended haplotypes")
17939 "Functions and examples are provided for transmission/disequilibrium
17940 tests for extended marker haplotypes, as in Clayton, D. and Jones, H. (1999)
17941 \"Transmission/disequilibrium tests for extended marker haplotypes\".")
17942 (license license:artistic2.0)))
17944 (define-public r-sparql
17950 (uri (cran-uri "SPARQL" version))
17953 "0gak1q06yyhdmcxb2n3v0h9gr1vqd0viqji52wpw211qp6r6dcrc"))))
17954 (properties `((upstream-name . "SPARQL")))
17955 (build-system r-build-system)
17957 (list r-rcurl r-xml))
17958 (home-page "https://cran.r-project.org/web/packages/SPARQL")
17959 (synopsis "SPARQL client for R")
17960 (description "This package provides an interface to use SPARQL to pose
17961 SELECT or UPDATE queries to an end-point.")
17962 ;; The only license indication is found in the DESCRIPTION file,
17963 ;; which states GPL-3. So we cannot assume GPLv3+.
17964 (license license:gpl3)))
17966 (define-public r-bookdown
17968 (name "r-bookdown")
17972 (uri (cran-uri "bookdown" version))
17975 "11din9h2sgzvg44627xc5is4psbq2b34km5sbiaprskjrf474866"))))
17976 (build-system r-build-system)
17986 ;; We cannot add knitr because this package depends on xfun, which is an
17991 (home-page "https://github.com/rstudio/bookdown")
17992 (synopsis "Authoring books and technical documents with R markdown")
17993 (description "This package provides output formats and utilities for
17994 authoring books and technical documents with R Markdown.")
17995 (license license:gpl3)))
17997 (define-public r-optparse
17999 (name "r-optparse")
18004 (uri (cran-uri "optparse" version))
18007 "1rqz0y4r94y3mwbb9kyz97cjqpnprka96qbncvbnbmgg2d630kij"))))
18008 (build-system r-build-system)
18013 (home-page "https://github.com/trevorld/optparse")
18014 (synopsis "Command line option parser")
18016 "This package provides a command line parser inspired by Python's
18017 @code{optparse} library to be used with Rscript to write shebang scripts
18018 that accept short and long options.")
18019 (license license:gpl2+)))
18021 (define-public r-kernlab
18028 (uri (cran-uri "kernlab" version))
18030 (base32 "10gfb542nbl1d5pfy6r7gcg3j1ikra9l18r6xjv8lzp5ka1kmz28"))))
18031 (build-system r-build-system)
18032 (home-page "https://cran.r-project.org/web/packages/kernlab")
18033 (synopsis "Kernel-based machine learning tools")
18035 "This package provides kernel-based machine learning methods for
18036 classification, regression, clustering, novelty detection, quantile regression
18037 and dimensionality reduction. Among other methods @code{kernlab} includes
18038 Support Vector Machines, Spectral Clustering, Kernel PCA, Gaussian Processes
18040 (license license:gpl2)))
18042 (define-public r-hierfstat
18044 (name "r-hierfstat")
18049 (uri (cran-uri "hierfstat" version))
18052 "0nyb5091lr8ma9vydbssyx9503601rynlrbldv98mmrmh74h6v41"))))
18053 (build-system r-build-system)
18055 (list r-ade4 r-adegenet r-gaston r-gtools))
18058 (home-page "https://cran.r-project.org/web/packages/hierfstat/")
18059 (synopsis "Estimation and tests of hierarchical F-statistics")
18061 "This package allows the estimation of hierarchical F-statistics from
18062 haploid or diploid genetic data with any numbers of levels in the hierarchy,
18063 following the algorithm of Yang (Evolution, 1998, 52(4):950-956). Functions
18064 are also given to test via randomisations the significance of each F and
18065 variance components, using the likelihood-ratio statistics G.")
18066 (license license:gpl2+)))
18068 (define-public r-hapassoc
18070 (name "r-hapassoc")
18075 (uri (cran-uri "hapassoc" version))
18078 "09ijc4sbw743z74fzklmvig11ndkycg6j86k4214wfsj1yj6j9x6"))))
18079 (build-system r-build-system)
18080 (home-page "https://stat.sfu.ca/statgen/research/hapassoc.html")
18081 (synopsis "Inference of trait associations with SNP haplotypes")
18083 "Hapassoc performs likelihood inference of trait associations with
18084 haplotypes and other covariates in @dfn{generalized linear models} (GLMs). The
18085 functions are developed primarily for data collected in cohort or
18086 cross-sectional studies. They can accommodate uncertain haplotype phase and
18087 handle missing genotypes at some SNPs.")
18088 (license license:gpl2)))
18090 (define-public r-sampling
18092 (name "r-sampling")
18097 (uri (cran-uri "sampling" version))
18100 "11xis4vzn2ga8ml9xrgfgqzccvwbnabq35aidzdvpnvciybsanvz"))))
18101 (build-system r-build-system)
18103 (list r-lpsolve r-mass))
18104 (home-page "https://cran.r-project.org/web/packages/sampling/")
18105 (synopsis "Survey sampling")
18107 "This package provides functions for drawing and calibrating samples.")
18108 (license license:gpl2+)))
18110 (define-public r-r2html
18117 (uri (cran-uri "R2HTML" version))
18120 "12qg9rp1j26h2f48dfg5k9jds26ycacv3f3ymk686ks43hd1hzja"))))
18121 (properties `((upstream-name . "R2HTML")))
18122 (build-system r-build-system)
18123 (home-page "https://github.com/nalimilan/R2HTML")
18124 (synopsis "HTML export for R objects")
18126 "This package includes HTML functions and methods to write in an HTML
18127 file. Thus, making HTML reports is easy. It includes a function that allows
18128 redirection on the fly, which appears to be very useful for teaching purposes,
18129 as the student can keep a copy of the produced output to keep all that they
18130 did during the course. The package comes with a vignette describing how to
18131 write HTML reports for statistical analysis. Finally, a driver for Sweave
18132 parses HTML flat files containing R code and to automatically write
18133 the corresponding outputs (tables and graphs).")
18134 (license license:gpl2+)))
18136 (define-public r-rjava
18143 (uri (cran-uri "rJava" version))
18146 "1ijqhvnb8ab38cp9pwdf7zq7xqqlm6x94gkrab2dd98p6d4x1472"))))
18147 (properties `((upstream-name . "rJava")))
18148 (build-system r-build-system)
18150 `(#:modules ((guix build utils)
18151 (guix build r-build-system)
18154 (modify-phases %standard-phases
18155 (add-after 'unpack 'set-JAVA_HOME
18156 (lambda* (#:key inputs #:allow-other-keys)
18157 (let ((jdk (assoc-ref inputs "jdk")))
18158 (setenv "JAVA_HOME" jdk)
18159 (setenv "JAVA" (which "java"))
18160 (setenv "JAR" (which "jar"))
18161 (setenv "JAVAC" (which "javac"))
18162 (setenv "JAVAH" (which "javah"))
18163 (setenv "JAVA_CPPFLAGS"
18164 (string-append "-I" jdk "/include "
18165 "-I" jdk "/include/linux"))
18166 (match (find-files (string-append jdk "/jre/lib/") "libjvm.so")
18167 ((lib) (setenv "JAVA_LIBS" lib))
18168 (_ (error "Could not find libjvm.so"))))
18172 ("jdk" ,icedtea-8 "jdk")
18174 (home-page "https://www.rforge.net/rJava/")
18175 (synopsis "Low-Level R to Java interface")
18177 "This package provides a low-level interface to the Java VM very much
18178 like .C/.Call and friends. It allows the creation of objects, calling methods
18179 and accessing fields.")
18180 (license license:gpl2)))
18182 (define-public r-svmisc
18189 (uri (cran-uri "svMisc" version))
18192 "1r3kih5bnr4plnzdn5f2gg3xl3krgyl7gkdlf58a2l8vk13j3m9d"))))
18193 (properties `((upstream-name . "svMisc")))
18194 (build-system r-build-system)
18197 (home-page "https://github.com/SciViews/svMisc")
18198 (synopsis "Miscellaneous functions for SciViews")
18200 "This package provides miscellaneous functions for SciViews or general
18201 use, including tools to manage a temporary environment attached to the search
18202 path for temporary variables you do not want to @code{save()} or
18203 @code{load()}; test the current platform; showing progress bars, etc.")
18204 (license license:gpl2)))
18206 (define-public r-xyz
18213 (uri (cran-uri "xyz" version))
18216 "13w4sb4pvgciwr8wsz785dafj2k2kpx7znz46r5d32wx88vkycp4"))))
18217 (build-system r-build-system)
18220 (home-page "https://cran.r-project.org/web/packages/xyz/")
18221 (synopsis "Algorithm for fast interaction search in high-dimensional data")
18223 "High dimensional interaction search by brute force requires a quadratic
18224 computational cost in the number of variables. The xyz algorithm provably
18225 finds strong interactions in almost linear time. For details of the algorithm
18226 see: G. Thanei, N. Meinshausen and R. Shah (2016). The xyz algorithm for fast
18227 interaction search in high-dimensional data.")
18228 ;; Any version of the GPL.
18229 (license license:gpl2+)))
18231 (define-public r-rttf2pt1
18233 (name "r-rttf2pt1")
18238 (uri (cran-uri "Rttf2pt1" version))
18241 "1fp1y0kxa5xg8w0dplm12wfm8h78az4k6ql1758wwhb3d17np241"))))
18242 (properties `((upstream-name . "Rttf2pt1")))
18243 (build-system r-build-system)
18244 (home-page "https://github.com/wch/Rttf2pt1")
18245 (synopsis "Font conversion utility")
18247 "This package contains the program @code{ttf2pt1}, for use with the
18248 @code{extrafont} package.")
18249 ;; Most of the files are covered under the Expat license. Some files are
18250 ;; covered under BSD-3. Deviations for individual files are recorded in
18251 ;; the LICENSE file.
18252 (license (list license:bsd-3 license:expat
18253 (license:non-copyleft "file://LICENSE")))))
18255 (define-public r-extrafontdb
18257 (name "r-extrafontdb")
18262 (uri (cran-uri "extrafontdb" version))
18265 "115n42hfvv5h4nn4cfkfmkmn968py4lpy8zd0d6w5yylwpzbm8gs"))))
18266 (build-system r-build-system)
18267 (home-page "https://github.com/wch/extrafontdb")
18268 (synopsis "Database for the extrafont package")
18270 "This package holds the database for the @code{extrafont} package.")
18271 (license license:gpl2)))
18273 (define-public r-extrafont
18275 (name "r-extrafont")
18280 (uri (cran-uri "extrafont" version))
18283 "0mx810mld67vb1w3wkl4fhpjmkq32lgpq5x1c0a9rf8li5wskrj4"))))
18284 (build-system r-build-system)
18286 (list r-extrafontdb r-rttf2pt1))
18287 (home-page "https://github.com/wch/extrafont")
18288 (synopsis "Tools for using fonts in R")
18290 "The extrafont package makes it easier to use fonts other than the basic
18291 PostScript fonts that R uses. Fonts that are imported into extrafont can be
18292 used with PDF or PostScript output files. There are two hurdles for using
18293 fonts in PDF (or Postscript) output files:
18296 @item Making R aware of the font and the dimensions of the characters.
18297 @item Embedding the fonts in the PDF file so that the PDF can be displayed
18298 properly on a device that doesn't have the font. This is usually needed if
18299 you want to print the PDF file or share it with others.
18302 The extrafont package makes both of these things easier.")
18303 (license license:gpl2)))
18305 (define-public r-xkcd
18312 (uri (cran-uri "xkcd" version))
18315 "1z2y0ihn68ppay7xkglhw7djki5654g6z4bbpyy41if57z9q554f"))))
18316 (build-system r-build-system)
18318 (list r-extrafont r-ggplot2 r-hmisc))
18319 (home-page "https://cran.r-project.org/web/packages/xkcd/")
18320 (synopsis "Plot ggplot2 graphics in the XKCD style")
18322 "This package provides the means to plot ggplot2 graphs in the style of
18323 the XKCD web comic.")
18324 (license license:gpl3)))
18326 (define-public r-babelgene
18328 (name "r-babelgene")
18333 (uri (cran-uri "babelgene" version))
18336 "1735h4s2vahv55pmq65zkgxq8d5x71i1is03rf17dric8yynjjhg"))))
18337 (properties `((upstream-name . "babelgene")))
18338 (build-system r-build-system)
18340 (list r-dplyr r-rlang))
18344 "https://igordot.github.io/babelgene/")
18345 (synopsis "Gene orthologs for model organisms in a Tidy data format")
18347 "Genomic analysis of model organisms often requires the use of databases
18348 based on human data or making comparisons to patient-derived resources. This
18349 requires converting genes between human and non-human analogues. The
18350 babelgene R package provides predicted gene orthologs/homologs for frequently
18351 studied model organisms in an R-friendly tidy/long format. The package
18352 integrates orthology assertion predictions sourced from multiple databases as
18353 compiled by the HGNC Comparison of Orthology Predictions (HCOP).")
18354 (license license:expat)))
18356 (define-public r-msigdbr
18363 (uri (cran-uri "msigdbr" version))
18366 "1jna9bkq0a7r6f8nhxziyiw75kfhsyh1rv7sx5d4551mvxxlhc6w"))))
18367 (build-system r-build-system)
18377 (home-page "https://github.com/igordot/msigdbr")
18378 (synopsis "MSigDB gene sets for multiple organisms")
18380 "This package provides the @dfn{Molecular Signatures Database} (MSigDB)
18381 gene sets typically used with the @dfn{Gene Set Enrichment Analysis} (GSEA)
18382 software in a standard R data frame with key-value pairs. Included are the
18383 original human gene symbols and Entrez IDs as well as the equivalents for
18384 various frequently studied model organisms such as mouse, rat, pig, fly, and
18386 ;; The package is covered under the Expat license, but the upstream MSigDB
18387 ;; files are made available under the Creative Commons Attribution 4.0
18388 ;; International license.
18389 (license (list license:expat license:cc-by4.0))))
18391 (define-public r-gridgraphics
18393 (name "r-gridgraphics")
18398 (uri (cran-uri "gridGraphics" version))
18401 "12yswy02j3h5wir7m5jnkhpjmb0sa4snn61vjd68i49qwsa6w219"))))
18402 (properties `((upstream-name . "gridGraphics")))
18403 (build-system r-build-system)
18404 (home-page "https://github.com/pmur002/gridgraphics")
18405 (synopsis "Redraw base graphics using @code{grid} graphics")
18407 "This package provides functions to convert a page of plots drawn with
18408 the @code{graphics} package into identical output drawn with the @code{grid}
18409 package. The result looks like the original @code{graphics}-based plot, but
18410 consists of @code{grid} grobs and viewports that can then be manipulated with
18411 @code{grid} functions (e.g., edit grobs and revisit viewports).")
18412 (license license:gpl2+)))
18414 (define-public r-farver
18421 (uri (cran-uri "farver" version))
18424 "1x6ffwxqbrwlylnk995jz2a6nz2y9z59jaq0ncpni7q40w367j75"))))
18425 (build-system r-build-system)
18426 (home-page "https://github.com/thomasp85/farver")
18427 (synopsis "Vectorized color conversion and comparison")
18429 "The encoding of color can be handled in many different ways, using
18430 different color spaces. As different color spaces have different uses,
18431 efficient conversion between these representations are important. This
18432 package provides a set of functions that gives access to very fast color space
18433 conversion and comparisons implemented in C++, and offers 100-fold speed
18434 improvements over the @code{convertColor} function in the @code{grDevices}
18436 (license license:expat)))
18438 (define-public r-yulab-utils
18440 (name "r-yulab-utils")
18445 (uri (cran-uri "yulab.utils" version))
18448 "1bj93gnj7j4b7dgkbr5v22rsbwfcw5dvipl5irmidaakvrihd19q"))))
18449 (properties `((upstream-name . "yulab.utils")))
18450 (build-system r-build-system)
18451 (home-page "https://cran.r-project.org/package=yulab.utils")
18452 (synopsis "Supporting functions for packages maintained by YuLab-SMU")
18454 "Miscellaneous functions commonly used by YuLab-SMU, such as
18455 @code{install_zip_gh} to install R packages from Github ZIP files.")
18456 (license license:artistic2.0)))
18458 (define-public r-ggplotify
18460 (name "r-ggplotify")
18465 (uri (cran-uri "ggplotify" version))
18468 "12mk3fa8fdjxj7xxz21jkr7h91w5wdgwjqhszcz1qffwsgb773qp"))))
18469 (build-system r-build-system)
18471 (list r-ggplot2 r-gridgraphics r-yulab-utils))
18474 (home-page "https://github.com/GuangchuangYu/ggplotify")
18475 (synopsis "Convert plots to @code{grob} or @code{ggplot} object")
18477 "This package provides tools to convert plot function calls (using
18478 expression or formula) to @code{grob} or @code{ggplot} objects that are
18479 compatible with the @code{grid} and @code{ggplot2} environment. With this
18480 package, we are able to e.g. use @code{cowplot} to align plots produced by
18481 @code{base} graphics, @code{grid}, @code{lattice}, @code{vcd} etc. by
18482 converting them to @code{ggplot} objects.")
18483 (license license:artistic2.0)))
18485 (define-public r-triebeard
18487 (name "r-triebeard")
18492 (uri (cran-uri "triebeard" version))
18495 "1hqyz57gph02c9fdc07lxz113bbklif3g18sw8jan6pakhhdc7dz"))))
18496 (build-system r-build-system)
18497 (propagated-inputs (list r-rcpp))
18498 (home-page "https://github.com/Ironholds/triebeard/")
18499 (synopsis "Radix trees in Rcpp")
18501 "Radix trees, or tries, are key-value data structures optimized for
18502 efficient lookups, similar in purpose to hash tables. This package provides
18503 an implementation of radix trees for use in R programming and in developing
18504 packages with Rcpp.")
18505 (license license:expat)))
18507 (define-public r-tweenr
18514 (uri (cran-uri "tweenr" version))
18517 "17znizh4yabh2zs9mzyr0sl6p0pw49961i61br7cl1b7v9sza18q"))))
18518 (build-system r-build-system)
18520 (list r-farver r-magrittr r-rcpp r-rlang))
18521 (home-page "https://github.com/thomasp85/tweenr")
18522 (synopsis "Interpolate data for smooth animations")
18524 "In order to create smooth animation between states of data, tweening is
18525 necessary. This package provides a range of functions for creating tweened
18526 data that can be used as basis for animation. Furthermore it adds a number of
18527 vectorized interpolaters for common R data types such as numeric, date and
18529 (license license:expat)))
18531 (define-public r-polyclip
18533 (name "r-polyclip")
18538 (uri (cran-uri "polyclip" version))
18541 "0jyk4maqiblvj095jd59dr76kbniyli3v3xvy0a72ljszq6vrnkl"))))
18542 (build-system r-build-system)
18543 (native-inputs (list pkg-config))
18544 (home-page "http://www.angusj.com/delphi/clipper.php")
18545 (synopsis "Polygon clipping")
18547 "This package provides an R port of the library Clipper. It performs
18548 polygon clipping operations (intersection, union, set minus, set difference)
18549 for polygonal regions of arbitrary complexity, including holes. It computes
18550 offset polygons (spatial buffer zones, morphological dilations, Minkowski
18551 dilations) for polygonal regions and polygonal lines. It computes the
18552 Minkowski Sum of general polygons. There is a function for removing
18553 self-intersections from polygon data.")
18554 (license license:boost1.0)))
18556 (define-public r-urltools
18558 (name "r-urltools")
18563 (uri (cran-uri "urltools" version))
18566 "04x3my655dd287cbsszbnf75q0swmjlxxrblcsay7a8n3df3a830"))))
18567 (build-system r-build-system)
18569 (list r-rcpp r-triebeard))
18570 (home-page "https://github.com/Ironholds/urltools/")
18571 (synopsis "Vectorized tools for URL handling and parsing")
18573 "This package provides a toolkit for all URL-handling needs, including
18574 encoding and decoding, parsing, parameter extraction and modification. All
18575 functions are designed to be both fast and entirely vectorized. It is
18576 intended to be useful for people dealing with web-related datasets, such as
18577 server-side logs, although may be useful for other situations involving large
18579 (license license:expat)))
18581 (define-public r-ggforce
18588 (uri (cran-uri "ggforce" version))
18591 "0bwzjbjl678xvc2ihm80dwn9pidwafqjdab3k299csys16s3na1a"))))
18592 (build-system r-build-system)
18605 (home-page "https://ggforce.data-imaginist.com")
18606 (synopsis "Accelerating ggplot2")
18608 "The aim of the ggplot2 package is to aid in visual data investigations.
18609 This focus has led to a lack of facilities for composing specialized plots.
18610 This package aims to be a collection of mainly new statistics and geometries
18611 that fills this gap.")
18612 (license license:expat)))
18614 (define-public r-europepmc
18616 (name "r-europepmc")
18621 (uri (cran-uri "europepmc" version))
18624 "16japbndid34shqg8n0bmjrxn84xmhrylvz832zclcllm6i93fn1"))))
18625 (build-system r-build-system)
18640 (home-page "https://github.com/ropensci/europepmc/")
18641 (synopsis "R Interface to the Europe PubMed Central RESTful Web Service")
18643 "This package provides an R Client for the
18644 @url{https://europepmc.org/RestfulWebService,Europe PubMed Central RESTful Web
18645 Service}. It gives access to both metadata on life science literature and
18646 open access full texts. Europe PMC indexes all PubMed content and other
18647 literature sources including Agricola, a bibliographic database of citations
18648 to the agricultural literature, or Biological Patents. In addition to
18649 bibliographic metadata, the client allows users to fetch citations and
18650 reference lists. Links between life-science literature and other EBI
18651 databases, including ENA, PDB or ChEMBL are also accessible.")
18652 (license license:gpl3)))
18654 (define-public r-ggraph
18661 (uri (cran-uri "ggraph" version))
18664 "0m4n8iw2b9jk8hcy5blg5w59zsqcpsbv27wbw598dvljpafx8sp3"))))
18665 (build-system r-build-system)
18684 (home-page "https://cran.r-project.org/web/packages/ggraph/")
18685 (synopsis "Implementation of grammar of graphics for graphs and networks")
18687 "The grammar of graphics as implemented in ggplot2 is a poor fit for
18688 graph and network visualizations due to its reliance on tabular data input.
18689 The ggraph package is an extension of the ggplot2 API tailored to graph
18690 visualizations and provides the same flexible approach to building up plots
18692 (license license:gpl3)))
18694 (define-public r-gkmsvm
18701 (uri (cran-uri "gkmSVM" version))
18704 "119g5rhc7ffyviz04r04aj5z1g6abnj3ddd01g7db505sdr6lapj"))))
18705 (properties `((upstream-name . "gkmSVM")))
18706 (build-system r-build-system)
18708 (list r-kernlab r-rcpp r-rocr r-seqinr))
18709 (home-page "https://cran.r-project.org/web/packages/gkmSVM")
18710 (synopsis "Gapped-kmer support vector machine")
18712 "This R package provides tools for training gapped-kmer SVM classifiers
18713 for DNA and protein sequences. This package supports several sequence
18714 kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.")
18715 (license license:gpl2+)))
18717 (define-public r-varselrf
18719 (name "r-varselrf")
18724 (uri (cran-uri "varSelRF" version))
18727 "0h49rl1j13yfh97rsfsyh9s2c4wajny4rzms2qw77d0cavxqg53i"))))
18728 (properties `((upstream-name . "varSelRF")))
18729 (build-system r-build-system)
18731 (list r-randomforest))
18732 (home-page "https://www.ligarto.org/rdiaz/software/software")
18733 (synopsis "Variable selection using random forests")
18735 "This package provides tools for the variable selection from random
18736 forests using both backwards variable elimination (for the selection of small
18737 sets of non-redundant variables) and selection based on the importance
18738 spectrum (somewhat similar to scree plots; for the selection of large,
18739 potentially highly-correlated variables). The main applications are in
18740 high-dimensional data (e.g., microarray data, and other genomics and
18741 proteomics applications).")
18742 (license license:gpl2+)))
18744 (define-public r-pamr
18751 (uri (cran-uri "pamr" version))
18754 "0ycpgkk23y3zzkb42n2skcyl35ps1n7jmyzfj7pbxr3f6gr2grfh"))))
18755 (build-system r-build-system)
18757 (list r-cluster r-survival))
18758 (native-inputs (list gfortran))
18759 (home-page "https://cran.r-project.org/web/packages/pamr/")
18760 (synopsis "Prediction Analysis for Microarrays")
18762 "This package provides some functions for sample classification in
18764 (license license:gpl2)))
18766 (define-public r-rda
18769 (version "1.0.2-2.1")
18773 (uri (cran-uri "rda" version))
18776 "1y4fawslr3i6crjaxhsdb47kfsqkyszdx6avq3r5far5a4pvc639"))))
18777 (build-system r-build-system)
18778 (home-page "https://cran.r-project.org/web/packages/rda/")
18779 (synopsis "Shrunken centroids regularized discriminant analysis")
18781 "This package provides tools for shrunken centroids regularized
18782 discriminant analysis for the purpose of classifying high dimensional data.")
18783 (license license:gpl2+)))
18785 (define-public r-ggvis
18792 (uri (cran-uri "ggvis" version))
18795 "1qv512pd4x5vmx15y9nvqmabbbw14h75fmi1sjbcg5yl25z0cswy"))))
18796 (build-system r-build-system)
18805 (home-page "https://ggvis.rstudio.com/")
18806 (synopsis "Interactive grammar of graphics")
18808 "This package is a data visualization package for R providing an
18809 implementation of an interactive grammar of graphics, taking the best parts of
18810 ggplot2, combining them with the reactive framework of Shiny and drawing web
18811 graphics using Vega.")
18812 (license license:gpl2)))
18814 (define-public r-gbm
18821 (uri (cran-uri "gbm" version))
18824 "1h9f4ww9yc3nsvghgr2q7jjrlz29ibabxjbax1sk5wmqh2wy6pbx"))))
18825 (build-system r-build-system)
18827 (list r-lattice r-survival))
18830 (home-page "https://github.com/gbm-developers/gbm")
18831 (synopsis "Generalized boosted regression models")
18833 "This package is an implementation of extensions to Freund and Schapire's
18834 AdaBoost algorithm and Friedman's gradient boosting machine. It includes
18835 regression methods for least squares, absolute loss, t-distribution loss,
18836 quantile regression, logistic, multinomial logistic, Poisson, Cox proportional
18837 hazards partial likelihood, AdaBoost exponential loss, Huberized hinge loss,
18838 and Learning to Rank measures (LambdaMart).")
18839 (license license:gpl2+)))
18841 (define-public r-threejs
18848 (uri (cran-uri "threejs" version))
18851 "1711h351nzxfkbbdwvfzyhciyvi9c6wx3jq1g97lzcqgnb45kivn"))))
18852 (build-system r-build-system)
18854 `(#:modules ((guix build utils)
18855 (guix build r-build-system)
18859 (modify-phases %standard-phases
18860 (add-after 'unpack 'process-javascript
18861 (lambda* (#:key inputs #:allow-other-keys)
18862 (with-directory-excursion "inst"
18866 `((,(assoc-ref inputs "js-jquery")
18867 "htmlwidgets/lib/jquery/jquery.min.js")
18868 (,(assoc-ref inputs "js-threejs-111")
18869 "htmlwidgets/lib/threejs-111/three.min.js"))))
18870 (lambda (sources targets)
18871 (for-each (lambda (source target)
18872 (format #t "Processing ~a --> ~a~%"
18874 (delete-file target)
18875 (let ((minified (open-pipe* OPEN_READ "uglifyjs" source)))
18876 (call-with-output-file target
18878 (dump-port minified port)))))
18879 sources targets))))
18882 (list r-base64enc r-crosstalk r-htmlwidgets r-igraph))
18884 `(("uglifyjs" ,node-uglify-js)
18888 (uri "https://code.jquery.com/jquery-1.12.4.js")
18891 "0x9mrc1668icvhpwzvgafm8xm11x9lfai9nwr66aw6pjnpwkc3s3"))))
18895 (uri "https://raw.githubusercontent.com/mrdoob/three.js/r111/build/three.js")
18898 "1cxdkw3plmlw1xvhbx5dm39gqczgzxip2dm887v6whhsxqxl9cky"))))))
18899 (home-page "https://bwlewis.github.io/rthreejs")
18900 (synopsis "Interactive 3D scatter plots, networks and globes")
18902 "Create interactive 3D scatter plots, network plots, and globes in R
18903 using the three.js visualization library.")
18904 (license license:expat)))
18906 (define-public r-mlbench
18913 (uri (cran-uri "mlbench" version))
18916 "157iqsld0wj8g8cbs7nh6p2x6kasmkhs3078hsmqac946gk2pydi"))))
18917 (build-system r-build-system)
18918 (home-page "https://cran.r-project.org/web/packages/mlbench/")
18919 (synopsis "Machine learning benchmark problems")
18921 "This package provides a collection of artificial and real-world machine
18922 learning benchmark problems, including, e.g., several data sets from the UCI
18924 (license license:gpl2)))
18926 (define-public r-mpm
18933 (uri (cran-uri "mpm" version))
18936 "1jpv2ddmw7aarqbbyfys1yb840arw33319wnny3v2hk84hldmayj"))))
18937 (build-system r-build-system)
18939 (list r-kernsmooth r-mass))
18940 (home-page "http://mpm.r-forge.r-project.org")
18941 (synopsis "Multivariate projection methods")
18943 "This is a package for exploratory graphical analysis of multivariate
18944 data, specifically gene expression data with different projection methods:
18945 principal component analysis, correspondence analysis, spectral map
18947 (license license:gpl2+)))
18949 (define-public r-png
18955 (uri (cran-uri "png" version))
18958 "0g2mcp55lvvpx4kd3mn225mpbxqcq73wy5qx8b4lyf04iybgysg2"))))
18959 (build-system r-build-system)
18961 (list libpng zlib))
18962 (home-page "https://www.rforge.net/png/")
18963 (synopsis "Read and write PNG images")
18965 "This package provides an easy and simple way to read, write and display
18966 bitmap images stored in the PNG format. It can read and write both files and
18967 in-memory raw vectors.")
18968 ;; Any of these GPL versions.
18969 (license (list license:gpl2 license:gpl3))))
18971 (define-public r-ggcorrplot
18973 (name "r-ggcorrplot")
18978 (uri (cran-uri "ggcorrplot" version))
18981 "0hi9lz121ya1l2lbm7rqlxg6fs6bvxck396dngnidrhl5fvqb41b"))))
18982 (build-system r-build-system)
18984 (list r-ggplot2 r-reshape2))
18985 (home-page "http://www.sthda.com/english/wiki/ggcorrplot")
18986 (synopsis "Visualization of a correlation matrix using ggplot2")
18988 "The ggcorrplot package can be used to visualize easily a correlation
18989 matrix using ggplot2. It provides a solution for reordering the correlation
18990 matrix and displays the significance level on the plot. It also includes a
18991 function for computing a matrix of correlation p-values.")
18992 (license license:gpl2)))
18994 (define-public r-ggfun
19001 (uri (cran-uri "ggfun" version))
19004 "06si42b60hp8wprs5nbks93qlb9s269k9kw7akcirizwc399x62r"))))
19005 (properties `((upstream-name . "ggfun")))
19006 (build-system r-build-system)
19008 (list r-ggplot2 r-rlang))
19009 (native-inputs (list r-knitr))
19010 (home-page "https://cran.r-project.org/package=ggfun")
19011 (synopsis "Miscellaneous functions for ggplot2")
19013 "This package provides useful functions to edit ggplot object (e.g.,
19014 setting fonts for theme and layers, adding rounded rectangle as background for
19015 each of the legends).")
19016 (license license:artistic2.0)))
19018 (define-public r-gridtext
19020 (name "r-gridtext")
19025 (uri (cran-uri "gridtext" version))
19028 "131kw7nkfwksviwfifd2kk7lyvhxzzzv1nnj8rahkr3dik3akk61"))))
19029 (properties `((upstream-name . "gridtext")))
19030 (build-system r-build-system)
19040 (home-page "https://wilkelab.org/gridtext/")
19041 (synopsis "Improved text rendering support for Grid graphics")
19043 "This package provides support for rendering of formatted text using Grid
19044 graphics. Text can be formatted via a minimal subset of Markdown, HTML, and
19045 inline CSS directives, and it can be rendered both with and without word
19047 (license license:expat)))
19049 (define-public r-ggtext
19056 (uri (cran-uri "ggtext" version))
19059 "0n19dlcys8v7myfyckr6dnq0kx79k3sbh8nwx1jsx8pgzfbi8a2b"))))
19060 (properties `((upstream-name . "ggtext")))
19061 (build-system r-build-system)
19063 (list r-ggplot2 r-gridtext r-rlang r-scales))
19064 (native-inputs (list r-knitr))
19065 (home-page "https://wilkelab.org/ggtext/")
19066 (synopsis "Improved text rendering support for ggplot2")
19068 "This package provides a ggplot2 extension that enables the rendering of
19069 complex formatted plot labels (titles, subtitles, facet labels, axis labels,
19070 etc.). Text boxes with automatic word wrap are also supported.")
19071 (license license:gpl2)))
19073 ;; This package includes minified JavaScript files. When upgrading please
19074 ;; check that there are no new minified JavaScript files.
19075 (define-public r-flexdashboard
19077 (name "r-flexdashboard")
19082 (uri (cran-uri "flexdashboard" version))
19085 "1bh759llp15fxrx2rwvxd8p3w84vjmkid32ism7zg49a127fjib4"))
19086 (modules '((guix build utils)))
19089 ;; Delete bundled minified JavaScript files
19090 (delete-file "inst/htmlwidgets/lib/raphael/raphael-2.1.4.min.js")
19091 (delete-file "inst/www/sly/sly.min.js")
19092 (delete-file "inst/www/stickytableheaders/jquery.stickytableheaders.min.js")
19093 (delete-file "inst/www/prism/prism.js")
19095 (build-system r-build-system)
19097 `(#:modules ((guix build utils)
19098 (guix build r-build-system)
19102 (ice-9 textual-ports))
19104 (modify-phases %standard-phases
19105 (add-after 'unpack 'process-javascript
19106 (lambda* (#:key inputs #:allow-other-keys)
19107 (with-directory-excursion "inst"
19108 ;; Concatenate all components of prism.js
19109 (let ((contents (string-join
19110 (map (lambda (name)
19111 (call-with-input-file
19112 (assoc-ref inputs name)
19116 "js-prism-line-numbers"))
19118 (call-with-output-file "prism-src.js"
19119 (cut display contents <>)))
19123 `(("www/stickytableheaders/jquery.stickytableheaders.js"
19124 "www/stickytableheaders/jquery.stickytableheaders.min.js")
19126 "www/sly/sly.min.js")
19128 "www/prism/prism.js")
19129 (,(assoc-ref inputs "js-raphael")
19130 "htmlwidgets/lib/raphael/raphael-2.1.4.min.js")
19131 (,(assoc-ref inputs "js-featherlight")
19132 "www/featherlight/featherlight.min.js"))))
19133 (lambda (sources targets)
19134 (for-each (lambda (source target)
19135 (format #t "Processing ~a --> ~a~%"
19137 (let ((minified (open-pipe* OPEN_READ "uglifyjs" source)))
19138 (call-with-output-file target
19140 (dump-port minified port)))))
19141 sources targets))))
19151 `(("uglifyjs" ,node-uglify-js)
19155 (uri "https://raw.githubusercontent.com/DmitryBaranovskiy/raphael/v2.1.4/raphael.js")
19158 "1h4c4akrgcj7wra9j1z1rv2406j0yf68y9c0wg8v7w9ibw2iwf1x"))))
19162 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/prism.js")
19165 "0gqa9irbp9k8p5r3d98cszajzhjnssnl43nrsc5aiy7ki52z500c"))))
19169 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/components/prism-r.js")
19172 "1x31glci7wdgr2305njy0bm2lncb0jyn0j1s2g72rqi29xid9aki"))))
19173 ("js-prism-line-numbers"
19176 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/plugins/line-numbers/prism-line-numbers.js")
19179 "1543wgf3iynrilyb27jq8px3h5gvfz5xmdib5ik2ki400c1sl991"))))
19183 (uri "https://raw.githubusercontent.com/noelboss/featherlight/1.3.4/src/featherlight.js")
19186 "14kkhwzvp8rxq2mrck5i0xcm8v5rqwqhwnmncbng8h4qq42zx3sb"))))))
19187 (home-page "https://rmarkdown.rstudio.com/flexdashboard")
19188 (synopsis "R Markdown format for flexible dashboards")
19190 "This package provides an R Markdown format for converting an R Markdown
19191 document to a grid-oriented dashboard. The dashboard flexibly adapts the size
19192 of its components to the containing web page.")
19193 (license license:expat)))
19195 (define-public r-preseqr
19202 (uri (cran-uri "preseqR" version))
19205 "1g2rnnmi45649vpy6z45v5i3wxm54s138ajqrzwi3a5r7x3xnhq1"))))
19206 (properties `((upstream-name . "preseqR")))
19207 (build-system r-build-system)
19210 (home-page "https://cran.r-project.org/web/packages/preseqR/")
19211 (synopsis "Predicting species accumulation curves")
19213 "This package can be used to predict the r-species accumulation
19214 curve (r-SAC), which is the number of species represented at least r times as
19215 a function of the sampling effort. When r = 1, the curve is known as the
19216 species accumulation curve, or the library complexity curve in high-throughput
19217 genomic sequencing. The package includes both parametric and nonparametric
19218 methods, as described by Deng C, et al. (2018).")
19219 (license license:gpl3)))
19221 (define-public r-mapplots
19223 (name "r-mapplots")
19228 (uri (cran-uri "mapplots" version))
19231 "18s2y66f8vi8g2r8a25zbgp2xm079r8v8qxv0w71h8krycs6vs9p"))))
19232 (build-system r-build-system)
19233 (home-page "https://cran.r-project.org/web/packages/mapplots/")
19234 (synopsis "Data visualization on maps")
19236 "This package helps you create simple maps; add sub-plots like pie plots
19237 to a map or any other plot; format, plot and export gridded data. The package
19238 was developed for displaying fisheries data but most functions can be used for
19239 more generic data visualisation.")
19240 (license license:gpl2+)))
19242 (define-public r-pmcmr
19249 (uri (cran-uri "PMCMR" version))
19252 "05n13pp5yff6pzk4ry07crddfaj3jlglrd1vkcnacyd8jpaxkd77"))))
19253 (properties `((upstream-name . "PMCMR")))
19254 (build-system r-build-system)
19255 (home-page "https://cran.r-project.org/web/packages/PMCMR/")
19256 (synopsis "Calculate pairwise multiple comparisons of mean rank sums")
19258 "This is a deprecated package for calculating pairwise multiple
19259 comparisons of mean rank sums. This package is superseded by the novel
19260 PMCMRplus package. The PMCMR package is no longer maintained, but kept for
19261 compatibility of dependent packages for some time.")
19262 (license license:gpl3+)))
19264 (define-public r-downloader
19266 (name "r-downloader")
19271 (uri (cran-uri "downloader" version))
19274 "1axggnsc27zzgr7snf41j3zd1vp3nfpmq4zj4d01axc709dyg40q"))))
19275 (build-system r-build-system)
19278 (home-page "https://github.com/wch/downloader")
19279 (synopsis "Download files over HTTP and HTTPS")
19281 "This package provides a wrapper for the @code{download.file} function,
19282 making it possible to download files over HTTPS across platforms. The
19283 @code{RCurl} package provides this functionality (and much more) but has
19284 external dependencies. This package has is implemented purely in R.")
19285 (license license:gpl2)))
19287 (define-public r-aplot
19294 (uri (cran-uri "aplot" version))
19297 "1b4jjj05a602dgn6yr1bsmbzlzkj6wf6af3k3w63g3mkqv0xzsfd"))))
19298 (properties `((upstream-name . "aplot")))
19299 (build-system r-build-system)
19306 (home-page "https://github.com/YuLab-SMU/aplot")
19307 (synopsis "Decorate a ggplot with associated information")
19309 "Users may want to align plots with associated information that requires
19310 axes to be exactly matched in subplots, e.g. hierarchical clustering with a
19311 heatmap. This package provides utilities to align associated subplots to a
19312 main plot at different sides (left, right, top and bottom) with axes exactly
19314 (license license:artistic2.0)))
19316 (define-public r-ggnewscale
19318 (name "r-ggnewscale")
19323 (uri (cran-uri "ggnewscale" version))
19326 "108a7y6sqqvzyfk247lbmnacfpwdl405rf1b3fa62cgx8ycsq4kb"))))
19327 (properties `((upstream-name . "ggnewscale")))
19328 (build-system r-build-system)
19331 (home-page "https://cran.r-project.org/package=ggnewscale")
19332 (synopsis "Multiple fill and color scales in ggplot2")
19334 "This package lets you use multiple fill and color scales in ggplot2.")
19335 (license license:gpl3)))
19337 (define-public r-ggpointdensity
19339 (name "r-ggpointdensity")
19344 (uri (cran-uri "ggpointdensity" version))
19347 "0c9a14j3b0hvamqylhzldw2hjdxmfbllwahjkf3gg2rw337ld9iy"))))
19349 `((upstream-name . "ggpointdensity")))
19350 (build-system r-build-system)
19353 (home-page "https://github.com/LKremer/ggpointdensity")
19354 (synopsis "Cross between a 2D density plot and a scatter plot")
19356 "This package provides a cross between a 2D density plot and a scatter
19357 plot, implemented as a ggplot2 @code{geom}. Points in the scatter plot are
19358 colored by the number of neighboring points. This is useful to visualize the
19359 2D-distribution of points in case of overplotting.")
19360 (license license:gpl3)))
19362 (define-public r-arrow
19369 (uri (cran-uri "arrow" version))
19372 "1b85vc5ld7nibqgsdkl5kbzc0rm5jh5lqfdrssvrrcxpd26a16kc"))))
19373 (properties `((upstream-name . "arrow")))
19374 (build-system r-build-system)
19376 (list `(,apache-arrow "lib") zlib))
19387 (list pkg-config r-knitr))
19388 (home-page "https://github.com/apache/arrow/")
19389 (synopsis "R integration to Apache Arrow")
19391 "Apache Arrow is a cross-language development platform for in-memory
19392 data. It specifies a standardized language-independent columnar memory format
19393 for flat and hierarchical data, organized for efficient analytic operations on
19394 modern hardware. This package provides an R interface to the Arrow C++
19396 (license license:asl2.0)))
19398 (define-public r-rex
19405 (uri (cran-uri "rex" version))
19408 "1mmzlc3j7xa0rbjxa369f4sr0iw3gq58g8fmjjxbsjvfq14ychmg"))))
19409 (build-system r-build-system)
19414 (home-page "https://github.com/kevinushey/rex")
19415 (synopsis "Friendly regular expressions")
19417 "This package provides a friendly interface for the construction of
19418 regular expressions. Regular expressions are a very powerful feature, however
19419 they are often difficult to interpret. Rex allows you to build complex
19420 regular expressions from human readable expressions")
19421 (license license:expat)))
19423 (define-public r-mlapi
19430 (uri (cran-uri "mlapi" version))
19433 "1qyiii6x9b89i4pd4yi2zd23aabpmnpj18gqi5va0zy0l8r7kknr"))))
19434 (properties `((upstream-name . "mlapi")))
19435 (build-system r-build-system)
19437 (list r-matrix r-r6))
19440 (home-page "https://cran.r-project.org/package=mlapi")
19441 (synopsis "Abstract classes for building scikit-learn like API")
19443 "This package provides R6 abstract classes for building machine learning
19444 models with a scikit-learn like API. Scikit-learn is a popular module for the
19445 Python programming language whose design became a de facto standard in
19446 industry for machine learning tasks.")
19447 (license license:expat)))
19449 (define-public r-float
19456 (uri (cran-uri "float" version))
19459 "0m7bf3548vlgkk1c78jyrgj72ngwg0gsccap2iqinm3l3qrm4zbs"))))
19460 (properties `((upstream-name . "float")))
19461 (build-system r-build-system)
19464 (home-page "https://github.com/wrathematics/float")
19465 (synopsis "32-bit floats")
19467 "R comes with a suite of utilities for linear algebra with
19468 \"numeric\" (double precision) vectors/matrices. However, sometimes single
19469 precision (or less!) is more than enough for a particular task. This package
19470 extends R's linear algebra facilities to include 32-bit float (single
19471 precision) data. Float vectors/matrices have half the precision of their
19472 \"numeric\"-type counterparts but are generally faster to numerically operate
19473 on, for a performance vs accuracy trade-off.")
19474 (license license:bsd-2)))
19476 (define-public r-rsparse
19483 (uri (cran-uri "rsparse" version))
19486 "0d05h47j29zipyxbkv9cwzv2dzj894z6hh9dqfhwswwjbv6ciwpq"))))
19487 (properties `((upstream-name . "rsparse")))
19488 (build-system r-build-system)
19498 (home-page "https://github.com/rexyai/rsparse")
19499 (synopsis "Statistical learning on sparse matrices")
19501 "This package implements many algorithms for statistical learning on
19502 sparse matrices: matrix factorizations, matrix completion, elastic net
19503 regressions, factorization machines. The rsparse package also enhances the
19504 Matrix package by providing methods for multithreaded <sparse, dense> matrix
19505 products and native slicing of the sparse matrices in @dfn{Compressed Sparse
19506 Row} (CSR) format.")
19507 (license license:gpl2+)))
19509 (define-public r-text2vec
19511 (name "r-text2vec")
19516 (uri (cran-uri "text2vec" version))
19519 "0bisr31051hnshw26rp9r4bm8ksr977dl9k1d3fb1x79pq5aa2pi"))))
19520 (properties `((upstream-name . "text2vec")))
19521 (build-system r-build-system)
19534 (home-page "http://text2vec.org")
19535 (synopsis "Text mining framework for R")
19537 "This package provides fast and memory-friendly tools for text
19538 vectorization, topic modeling (LDA, LSA), word embeddings (GloVe),
19539 similarities. It provides a source-agnostic streaming API, which allows
19540 researchers to perform analysis of collections of documents which are larger
19541 than available RAM. All core functions are parallelized to benefit from
19542 multicore machines.")
19543 (license license:gpl2+)))
19545 (define-public r-mcmcpack
19547 (name "r-mcmcpack")
19552 (uri (cran-uri "MCMCpack" version))
19555 "1cwdjn43b9hxpxf9mnas583myhk6r2258mh57f0zsc8bd4hbl56b"))))
19556 (properties `((upstream-name . "MCMCpack")))
19557 (build-system r-build-system)
19559 (list r-coda r-lattice r-mass r-mcmc r-quantreg))
19560 (home-page "https://cran.r-project.org/package=MCMCpack")
19561 (synopsis "Markov Chain Monte Carlo (MCMC) package")
19563 "This package contains functions to perform Bayesian inference using
19564 posterior simulation for a number of statistical models. Most simulation is
19565 done in compiled C++ written in the Scythe Statistical Library. All models
19566 return @code{coda} @code{mcmc} objects that can then be summarized using the
19567 @code{coda} package. Some useful utility functions such as density functions,
19568 pseudo-random number generators for statistical distributions, a general
19569 purpose Metropolis sampling algorithm, and tools for visualization are
19571 (license license:gpl3)))
19573 (define-public r-xmlparsedata
19575 (name "r-xmlparsedata")
19580 (uri (cran-uri "xmlparsedata" version))
19583 "1c6bnz3ng1qw7sfip8wq3a4dn36a4d6rbja0sadn0a4pbsmk8q3n"))))
19584 (properties `((upstream-name . "xmlparsedata")))
19585 (build-system r-build-system)
19586 (home-page "https://github.com/r-lib/xmlparsedata#readme")
19587 (synopsis "Parse data of @code{R} code as an @code{XML} tree")
19589 "This package provides tools to convert the output of
19590 @code{utils::getParseData()} to an @code{XML} tree, that one can search via
19591 @code{XPath}, and is easier to manipulate in general.")
19592 (license license:expat)))
19594 (define-public r-cyclocomp
19596 (name "r-cyclocomp")
19601 (uri (cran-uri "cyclocomp" version))
19604 "0gky3svk02wiajw7nfjh30684h3qxili4bvsab0m7b6cggw6bgyd"))))
19605 (properties `((upstream-name . "cyclocomp")))
19606 (build-system r-build-system)
19608 (list r-callr r-crayon r-desc r-remotes r-withr))
19609 (home-page "https://github.com/MangoTheCat/cyclocomp")
19610 (synopsis "Cyclomatic complexity of R code")
19612 "Cyclomatic complexity is a software metric, used to indicate the
19613 complexity of a program. It is a quantitative measure of the number of
19614 linearly independent paths through a program's source code. This package
19615 provides tools to compute this metric.")
19616 (license license:expat)))
19618 (define-public r-lintr
19625 (uri (cran-uri "lintr" version))
19628 "14yfh641afg6griaadbdciyr3k94fl55s055qwzghgk5gdsj61zy"))))
19629 (properties `((upstream-name . "lintr")))
19630 (build-system r-build-system)
19644 (home-page "https://github.com/jimhester/lintr")
19645 (synopsis "Linter for R code")
19646 (description "This package checks adherence to a given style, syntax
19647 errors and possible semantic issues. It supports on the fly checking of R
19648 code edited with @code{RStudio IDE}, @code{Emacs} and @code{Vim}.")
19649 (license license:expat)))
19651 (define-public r-sctransform
19653 (name "r-sctransform")
19658 (uri (cran-uri "sctransform" version))
19661 "0aqbcarsvvzkh5h4i65f08y4b8dfcs3zi62hmvfy24gj81f15bw3"))))
19662 (build-system r-build-system)
19677 (home-page "https://github.com/ChristophH/sctransform")
19678 (synopsis "Variance stabilizing transformations for Single Cell UMI Data")
19680 "This package provides a normalization method for single-cell UMI count
19681 data using a variance stabilizing transformation. The transformation is based
19682 on a negative binomial regression model with regularized parameters. As part
19683 of the same regression framework, this package also provides functions for
19684 batch correction, and data correction.")
19685 (license license:gpl3)))
19687 (define-public r-styler
19694 (uri (cran-uri "styler" version))
19697 "1ki260ga0jrmayhdlx2sl788yp5kkmi4wyl32nmvvyb55sng6j9y"))))
19698 (build-system r-build-system)
19699 ;; This is needed by R.cache.
19702 (modify-phases %standard-phases
19703 (add-after 'unpack 'set-HOME
19704 (lambda _ (setenv "HOME" "/tmp"))))))
19717 (home-page "https://github.com/r-lib/styler")
19718 (synopsis "Non-invasive pretty printing of R code")
19720 "This is a package for pretty-printing R code without changing the user's
19721 formatting intent.")
19722 (license license:gpl3)))
19724 (define-public r-scrime
19731 (uri (cran-uri "scrime" version))
19734 "0y2mh9fsffjf3i15bafpasa17z99c1s75r8g6h4hgcwfgpjx75sx"))))
19735 (build-system r-build-system)
19736 (home-page "https://cran.r-project.org/web/packages/scrime/")
19737 (synopsis "Analysis of high-dimensional categorical data such as SNP data")
19739 "This package provides tools for the analysis of high-dimensional data
19740 developed/implemented at the group \"Statistical Complexity Reduction In
19741 Molecular Epidemiology\" (SCRIME). The main focus is on SNP data, but most of
19742 the functions can also be applied to other types of categorical data.")
19743 (license license:gpl2)))
19745 (define-public r-pbmcapply
19747 (name "r-pbmcapply")
19752 (uri (cran-uri "pbmcapply" version))
19755 "1p8jf7c4k45482w72sr0jw4jkz787krrxai3sl6jz5l4lda2iz3z"))))
19756 (build-system r-build-system)
19757 (home-page "https://github.com/kvnkuang/pbmcapply")
19758 (synopsis "Track the progress of apply procedures with a progress bar")
19760 "This light-weight package helps you track and visualize the progress of
19761 parallel versions of vectorized R functions of the @code{mc*apply} family.")
19762 (license license:expat)))
19764 (define-public r-blme
19771 (uri (cran-uri "blme" version))
19774 "0413j7gwr5yj14jamkizj55q7xii1a0kgazzj0ilqn2ascclz6k7"))))
19775 (build-system r-build-system)
19776 (propagated-inputs (list r-lme4))
19777 (home-page "https://github.com/vdorie/blme")
19778 (synopsis "Bayesian linear mixed-effects models")
19780 "This package provides tools for maximum a posteriori estimation for
19781 linear and generalized linear mixed-effects models in a Bayesian setting. It
19782 extends the lme4 package.")
19783 (license license:gpl2+)))
19785 (define-public r-batchtools
19787 (name "r-batchtools")
19792 (uri (cran-uri "batchtools" version))
19795 "0d2xy77hkzhcnyz8zxcv98i80fx6ripjw4rvyx4ww1d0vjjgqf52"))))
19796 (build-system r-build-system)
19812 (home-page "https://github.com/mllg/batchtools")
19813 (synopsis "Tools for computation on batch systems")
19815 "As a successor of the packages BatchJobs and BatchExperiments, this
19816 package provides a parallel implementation of the Map function for high
19817 performance computing systems managed by various schedulers. A multicore and
19818 socket mode allow the parallelization on a local machines, and multiple
19819 machines can be hooked up via SSH to create a makeshift cluster. Moreover,
19820 the package provides an abstraction mechanism to define large-scale computer
19821 experiments in a well-organized and reproducible way.")
19822 (license license:lgpl3)))
19824 (define-public r-clue
19831 (uri (cran-uri "clue" version))
19834 "0apgpdnn74mqg2bnr8yjyxgyvdl411h0r2b1r2xd67k21pyxs8bd"))))
19835 (build-system r-build-system)
19836 (propagated-inputs (list r-cluster))
19837 (home-page "https://cran.r-project.org/web/packages/clue/")
19838 (synopsis "Tools for analyzing cluster ensembles")
19839 (description "Cluster ensembles are collections of individual solutions to
19840 a given clustering problem which are useful or necessary to consider in a wide
19841 range of applications. This R package provides an extensible computational
19842 environment for creating and analyzing cluster ensembles, with basic data
19843 structures for representing partitions and hierarchies, and facilities for
19844 computing on them, including methods for measuring proximity and obtaining
19845 consensus and secondary clusterings.")
19846 (license license:gpl2)))
19848 (define-public r-sitmo
19855 (uri (cran-uri "sitmo" version))
19858 "1hm89zi38ldgbskyx1cn7gm87yqy7zrxli8q05a36y1ndvazi3j4"))))
19859 (build-system r-build-system)
19860 (propagated-inputs (list r-rcpp))
19863 (home-page "https://github.com/coatless/sitmo/")
19864 (synopsis "Parallel pseudo random number generator header files")
19866 "This package provides two high quality and fast PPRNGs that may be used
19867 in an OpenMP parallel environment. In addition, there is a generator for one
19868 dimensional low-discrepancy sequence.")
19869 (license license:expat)))
19871 (define-public r-dqrng
19878 (uri (cran-uri "dqrng" version))
19881 "1fwsldqcri2lccna4icbmmlqic3w4xyjm7rn0xmikrsw4kzapvjb"))))
19882 (build-system r-build-system)
19884 (list r-bh r-rcpp r-sitmo))
19887 (home-page "https://www.daqana.org/dqrng")
19888 (synopsis "Fast pseudo random number generators")
19890 "Several fast random number generators are provided as C++ header-only
19891 libraries: the PCG family as well as Xoroshiro128+ and Xoshiro256+.
19892 Additionally, fast functions for generating random numbers according to a
19893 uniform, normal and exponential distribution are included. The latter two use
19894 the Ziggurat algorithm originally proposed by Marsaglia and Tsang. These
19895 functions are exported to R and as a C++ interface and are enabled for use
19896 with the default 64 bit generator from the PCG family, Xoroshiro128+ and
19897 Xoshiro256+ as well as the 64 bit version of the 20 rounds Threefry
19898 engine (Salmon et al., 2011) as provided by the package @code{sitmo}.")
19899 ;; This package includes code under CC0 and Apache 2.0 or Expat, but as a
19900 ;; whole is distributed under the terms of the AGPL 3.
19901 (license license:agpl3)))
19903 (define-public r-ingredients
19905 (name "r-ingredients")
19910 (uri (cran-uri "ingredients" version))
19913 "11bv4l4fn9kr7y2nfzrwnaya8fi9w3nwcm9vzlqb7dva83rkqbsc"))))
19914 (properties `((upstream-name . "ingredients")))
19915 (build-system r-build-system)
19917 (list r-ggplot2 r-gridextra r-scales))
19918 (native-inputs (list r-knitr))
19919 (home-page "https://ModelOriented.github.io/ingredients/")
19920 (synopsis "Effects and importances of model ingredients")
19922 "This is a collection of tools for assessment of feature importance and
19923 feature effects. Key functions are:
19926 @item @code{feature_importance()} for assessment of global level feature
19928 @item @code{ceteris_paribus()} for calculation of the what-if plots,
19929 @item @code{partial_dependence()} for partial dependence plots,
19930 @item @code{conditional_dependence()} for conditional dependence plots,
19931 @item @code{accumulated_dependence()} for accumulated local effects plots,
19932 @item @code{aggregate_profiles()} and @code{cluster_profiles()} for
19933 aggregation of ceteris paribus profiles,
19934 @item generic @code{print()} and @code{plot()} for better usability of
19935 selected explainers,
19936 @item generic @code{plotD3()} for interactive, D3 based explanations, and
19937 @item generic @code{describe()} for explanations in natural language.
19939 (license license:gpl3)))
19941 (define-public r-ibreakdown
19943 (name "r-ibreakdown")
19948 (uri (cran-uri "iBreakDown" version))
19951 "00jzrndb3ahsv6ihp2pvs732n9cc944m83vdinrl9v1pxd82prkh"))))
19952 (properties `((upstream-name . "iBreakDown")))
19953 (build-system r-build-system)
19954 (propagated-inputs (list r-ggplot2))
19955 (native-inputs (list r-knitr))
19956 (home-page "https://ModelOriented.github.io/iBreakDown/")
19957 (synopsis "Model agnostic instance level variable attributions")
19959 "This package provides a model agnostic tool for decomposition of
19960 predictions from black boxes. It supports additive attributions and
19961 attributions with interactions. The Break Down Table shows contributions of
19962 every variable to a final prediction. The Break Down Plot presents variable
19963 contributions in a concise graphical way. This package works for
19964 classification and regression models.")
19965 (license license:gpl3)))
19967 (define-public r-dae
19974 (uri (cran-uri "dae" version))
19977 "0mq94ah21p1glvsbvdmi2p7nlgz1bvq7w3rz2z3mdqq18kz6nkjw"))))
19978 (build-system r-build-system)
19980 (list r-ggplot2 r-plyr))
19982 (list r-r-rsp)) ; vignette builder
19983 (home-page "http://chris.brien.name")
19984 (synopsis "Functions useful in the design and ANOVA of experiments")
19986 "This package provides functions useful in the design and ANOVA of
19987 experiments. The content falls into the following groupings:
19991 @item factor manipulation functions,
19992 @item design functions,
19993 @item ANOVA functions,
19994 @item matrix functions,
19995 @item projector and canonical efficiency functions, and
19996 @item miscellaneous functions.
19999 There is a vignette called @code{DesignNotes} describing how to use the design
20000 functions for randomizing and assessing designs. The ANOVA functions
20001 facilitate the extraction of information when the @code{Error} function has
20002 been used in the call to @code{aov}.")
20003 (license license:gpl2)))
20005 (define-public r-dalex
20012 (uri (cran-uri "DALEX" version))
20015 "0mcdd2bd8zlsz7x174g87dp8vy4wc06w58dyr27f6lgv9shzya8j"))))
20016 (properties `((upstream-name . "DALEX")))
20017 (build-system r-build-system)
20019 (list r-ggplot2 r-ibreakdown r-ingredients))
20020 (home-page "https://pbiecek.github.io/DALEX/")
20021 (synopsis "Descriptive machine learning explanations")
20023 "Machine Learning models are widely used and have various applications in
20024 classification or regression. Models created with boosting, bagging, stacking
20025 or similar techniques are often used due to their high performance, but such
20026 black-box models usually lack interpretability. The DALEX package contains
20027 various explainers that help to understand the link between input variables
20028 and model output.")
20029 ;; Any version of the GPL
20030 (license license:gpl3+)))
20032 (define-public r-enrichr
20039 (uri (cran-uri "enrichR" version))
20042 "0i3kfq4fkmx47n61zj5f87iv8ci6gbgy90a7s8dy9zbndzvbgya3"))))
20043 (properties `((upstream-name . "enrichR")))
20044 (build-system r-build-system)
20046 (list r-ggplot2 r-httr r-rjson))
20049 (home-page "https://cran.r-project.org/web/packages/enrichR/")
20050 (synopsis "R Interface to Enrichr database for analyzing gene sets")
20052 "This package provides an R interface to all Enrichr databases, a
20053 web-based tool for analyzing gene sets and returns any enrichment of common
20054 annotated biological functions.")
20055 (license license:gpl2+)))
20057 (define-public r-plot3d
20064 (uri (cran-uri "plot3D" version))
20067 "1h59zlsyzbjylaziwavppl9bjmnba4iiq34772y3dys6fqclajnh"))))
20068 (properties `((upstream-name . "plot3D")))
20069 (build-system r-build-system)
20070 (propagated-inputs (list r-misc3d))
20071 (home-page "https://cran.r-project.org/web/packages/plot3D")
20072 (synopsis "Plot multi-dimensional data")
20074 "This package provides functions for viewing 2D and 3D data, including
20075 perspective plots, slice plots, surface plots, scatter plots, etc. It
20076 includes data sets from oceanography.")
20077 (license license:gpl3+)))
20079 (define-public r-ggfortify
20081 (name "r-ggfortify")
20086 (uri (cran-uri "ggfortify" version))
20089 "038m74azpy43869ax1yi6wxbl1kr59iaxl8raiikjg749vcx6njw"))))
20090 (build-system r-build-system)
20101 (home-page "https://github.com/sinhrks/ggfortify")
20102 (synopsis "Data visualization tools for statistical analysis results")
20104 "This package provides unified plotting tools for statistics commonly
20105 used, such as GLM, time series, PCA families, clustering and survival
20106 analysis. The package offers a single plotting interface for these analysis
20107 results and plots in a unified style using the @code{ggplot2} package.")
20108 (license license:gpl2)))
20110 (define-public r-refmanager
20112 (name "r-refmanager")
20117 (uri (cran-uri "RefManageR" version))
20120 "1spzdp5ni52dybcaxqnhwdphh27wjyrsfy4hsxsplpg9rqwfqfps"))))
20121 (properties `((upstream-name . "RefManageR")))
20122 (build-system r-build-system)
20132 (home-page "https://github.com/ropensci/RefManageR/")
20133 (synopsis "Straightforward BibTeX and BibLaTeX bibliography management")
20135 "This package provides tools for importing and working with bibliographic
20136 references. It greatly enhances the @code{bibentry} class by providing a
20137 class @code{BibEntry} which stores BibTeX and BibLaTeX references, supports
20138 UTF-8 encoding, and can be easily searched by any field, by date ranges, and
20139 by various formats for name lists (author by last names, translator by full
20140 names, etc.). Entries can be updated, combined, sorted, printed in a number
20141 of styles, and exported. BibTeX and BibLaTeX @code{.bib} files can be read
20142 into R and converted to @code{BibEntry} objects.")
20143 ;; Any of these licenses may be picked.
20144 (license (list license:gpl2 license:gpl3 license:bsd-3))))
20146 (define-public r-citr
20153 (uri (cran-uri "citr" version))
20156 "1qbarvafjb8jgkrnrhh6jw7mcglmjwf7dpdiibxf39jkmlhf7las"))))
20157 (build-system r-build-system)
20168 (home-page "https://github.com/crsh/citr")
20169 (synopsis "RStudio add-in to insert Markdown citations")
20171 "This package provides functions and an RStudio add-in that search a
20172 BibTeX or BibLaTeX file to create and insert formatted Markdown citations into
20173 the current document.")
20174 (license license:expat)))
20176 (define-public r-xgboost
20179 (version "1.6.0.1")
20183 (uri (cran-uri "xgboost" version))
20186 "1gafjv6vcpny03lqw8s68xszalsylniavaqwsbzh46vyk4h9mscs"))))
20187 (build-system r-build-system)
20189 (list r-data-table r-jsonlite r-matrix))
20192 (home-page "https://github.com/dmlc/xgboost")
20193 (synopsis "Extreme gradient boosting")
20195 "This package provides an R interface to Extreme Gradient Boosting, which
20196 is an efficient implementation of the gradient boosting framework from Chen
20197 and Guestrin (2016). The package includes efficient linear model solver and
20198 tree learning algorithms. The package can automatically do parallel
20199 computation on a single machine. It supports various objective functions,
20200 including regression, classification and ranking. The package is made to be
20201 extensible, so that users are also allowed to define their own objectives
20203 (license license:asl2.0)))
20205 (define-public r-umap
20208 (version "0.2.8.0")
20212 (uri (cran-uri "umap" version))
20215 "0aiarnzc8gl932gi8fxd9f9rshaiwh9vj570l135fkiaja3q2wap"))))
20216 (build-system r-build-system)
20218 (list r-matrix r-openssl r-rcpp r-reticulate r-rspectra))
20221 (home-page "https://github.com/tkonopka/umap")
20222 (synopsis "Uniform manifold approximation and projection")
20224 "Uniform manifold approximation and projection is a technique for
20225 dimension reduction. This package provides an interface to the UMAP algorithm
20226 in R, including a translation of the original algorithm into R.")
20227 (license license:expat)))
20229 (define-public r-uwot
20236 (uri (cran-uri "uwot" version))
20239 "06ylzxmdh8jipbrzgqaiivd2lnqmbcva41cyvc0iyals6vqr1ksg"))))
20240 (build-system r-build-system)
20250 (home-page "https://github.com/jlmelville/uwot")
20251 (synopsis "Uniform manifold approximation and projection")
20253 "This package provides an implementation of the Uniform Manifold
20254 Approximation and Projection dimensionality reduction by McInnes et
20255 al. (2018). It also provides means to transform new data and to carry out
20256 supervised dimensionality reduction. An implementation of the related
20257 LargeVis method of Tang et al. (2016) is also provided.")
20258 (license license:gpl3)))
20260 (define-public r-kableextra
20262 (name "r-kableextra")
20267 (uri (cran-uri "kableExtra" version))
20270 "1c5vzy95cbz36jwyssr927qicrayifinv861rvnmg4nghb1gl7q9"))))
20271 (properties `((upstream-name . "kableExtra")))
20272 (build-system r-build-system)
20290 (home-page "https://haozhu233.github.io/kableExtra/")
20291 (synopsis "Construct complex tables with pipe syntax")
20293 "Build complex HTML or LaTeX tables using @code{kable()} from
20294 @code{knitr} and the piping syntax from @code{magrittr}. The function
20295 @code{kable()} is a light weight table generator coming from @code{knitr}.
20296 This package simplifies the way to manipulate the HTML or LaTeX codes
20297 generated by @code{kable()} and allows users to construct complex tables and
20298 customize styles using a readable syntax.")
20299 (license license:expat)))
20301 (define-public r-glasso
20308 (uri (cran-uri "glasso" version))
20310 (base32 "02p3612rpydk195n2qr77lp1j2w8zsw1ckkk98c8angm4r5q8dsc"))))
20311 (build-system r-build-system)
20312 (native-inputs (list gfortran))
20313 (home-page "https://statweb.stanford.edu/~tibs/glasso/")
20314 (synopsis "Graphical Lasso: estimation of Gaussian graphical models")
20316 "This is a package for estimation of a sparse inverse covariance matrix
20317 using a lasso (L1) penalty. Facilities are provided for estimates along a
20318 path of values for the regularization parameter.")
20319 (license license:gpl2)))
20321 (define-public r-rhpcblasctl
20323 (name "r-rhpcblasctl")
20324 (version "0.21-247.1")
20328 (uri (cran-uri "RhpcBLASctl" version))
20331 "0scpr6jq25xx7wmqyc380ann4h536ll0g7wblikk25yqvpamzrav"))))
20332 (properties `((upstream-name . "RhpcBLASctl")))
20333 (build-system r-build-system)
20334 (home-page "https://prs.ism.ac.jp/~nakama/Rhpc/")
20335 (synopsis "Control the number of threads on BLAS")
20337 "This package allows you to control the number of threads the BLAS
20338 library uses. It is also possible to control the number of threads in
20340 (license license:agpl3+)))
20342 (define-public r-lda
20349 (uri (cran-uri "lda" version))
20352 "03r4h5kgr8mfy44p66mfj5bp4k00g8zh4a1mhn46jw14pkhs21jn"))))
20353 (build-system r-build-system)
20354 (home-page "https://cran.r-project.org/web/packages/lda/")
20355 (synopsis "Collapsed Gibbs sampling methods for topic models")
20357 "This package implements @dfn{latent Dirichlet allocation} (LDA) and
20358 related models. This includes (but is not limited to) sLDA, corrLDA, and the
20359 mixed-membership stochastic blockmodel. Inference for all of these models is
20360 implemented via a fast collapsed Gibbs sampler written in C. Utility
20361 functions for reading/writing data typically used in topic models, as well as
20362 tools for examining posterior distributions are also included.")
20363 ;; Any version of the LGPL
20364 (license license:lgpl3+)))
20366 (define-public r-rann-l1
20373 (uri (cran-uri "RANN.L1" version))
20376 "1hanh3my84mdr5wy6b89fawqzfc184vff1y65wy4l5ld9qza1n44"))))
20377 (properties `((upstream-name . "RANN.L1")))
20378 (build-system r-build-system)
20379 (home-page "https://github.com/jefferis/RANN/tree/master-L1")
20380 (synopsis "Fast nearest neighbour search using L1 metric")
20382 "This package provides tools to find the k nearest neighbours for every
20383 point in a given dataset in O(N log N) time using Arya and Mount's ANN
20384 library. There is support for approximate as well as exact searches, fixed
20385 radius searches and @code{bd} as well as @code{kd} trees. The distance is
20386 computed using the L1 (Manhattan, taxicab) metric.")
20387 (license license:gpl3+)))
20389 (define-public r-leiden
20396 (uri (cran-uri "leiden" version))
20399 "1gg24afwbz818041bhmswmdqgxv35zp5h1i1102p58aaiis8dkna"))))
20400 (properties `((upstream-name . "leiden")))
20401 (build-system r-build-system)
20403 (list r-igraph r-matrix r-reticulate))
20406 (home-page "https://github.com/TomKellyGenetics/leiden")
20407 (synopsis "R implementation of Leiden clustering algorithm")
20409 "This package implements the Python @code{leidenalg} module to be called
20410 in R. It enables clustering using the Leiden algorithm for partitioning a
20411 graph into communities. See also Traag et al (2018) \"From Louvain to Leiden:
20412 guaranteeing well-connected communities.\" <arXiv:1810.08473>.")
20413 (license license:gpl3)))
20415 (define-public r-patchwork
20417 (name "r-patchwork")
20422 (uri (cran-uri "patchwork" version))
20425 "10glgkf58lcykcwda1hj6xdps02m3i247qynk6s2jmwljagps3fg"))))
20426 (build-system r-build-system)
20428 (list r-ggplot2 r-gtable))
20431 (home-page "https://github.com/thomasp85/patchwork")
20432 (synopsis "Compose ggplot2 plots")
20434 "The @code{ggplot2} package provides a strong API for sequentially
20435 building up a plot, but does not concern itself with composition of multiple
20436 plots. Patchwork is a package that expands the API to allow for arbitrarily
20437 complex composition of plots by providing mathematical operators for combining
20439 (license license:expat)))
20441 (define-public r-liger
20448 (uri (git-reference
20449 (url "https://github.com/MacoskoLab/liger")
20450 (commit (string-append "v" version))))
20451 (file-name (git-file-name name version))
20454 "16dzwwcpw6n78pxlc5w3kraigki35ix7zhd2cbx5f3y60bbkhlmx"))
20455 (modules '((guix build utils)))
20458 (delete-file "inst/java/ModularityOptimizer.jar")
20460 (build-system r-build-system)
20463 (modify-phases %standard-phases
20464 (add-after 'unpack 'build-java-part
20465 (lambda* (#:key inputs #:allow-other-keys)
20466 (invoke "unzip" (assoc-ref inputs "optimizer-src"))
20467 (for-each (lambda (file) (invoke "javac" file))
20468 (find-files "." "\\.java$"))
20469 (apply invoke "jar" "cf" "inst/java/ModularityOptimizer.jar"
20470 (find-files "." "\\.class$"))
20494 `(("jdk" ,icedtea "jdk")
20495 ;; See https://github.com/MacoskoLab/liger/issues/96
20496 ;; The optimizer is released under the Expat license.
20500 (uri "http://www.ludowaltman.nl/slm/modularity_optimizer_source.zip")
20503 "01hmm6sapcmldvayknqx2w4cav3qv71mwwkdkwj4qgq6dss09g18"))))
20505 ("r-knitr" ,r-knitr))) ; for vignettes
20506 (home-page "https://github.com/MacoskoLab/liger")
20507 (synopsis "Integrate and analyze multiple single-cell datasets")
20509 "LIGER is a package for integrating and analyzing multiple single-cell
20510 datasets, developed and maintained by the Macosko lab. It relies on
20511 integrative non-negative matrix factorization to identify shared and
20512 dataset-specific factors.")
20513 (license license:gpl3)))
20515 (define-public r-harmony
20522 (uri (git-reference
20523 (url "https://github.com/immunogenomics/harmony")
20525 (file-name (git-file-name name version))
20528 "05r401q09rbr6fqhb9mbd95082cjdi3nag1cv6zn96xkr0f6imq9"))
20529 (modules '((guix build utils)))
20532 (for-each delete-file '("config.status" "configure"))
20534 (build-system r-build-system)
20549 (home-page "https://github.com/immunogenomics/harmony")
20550 (synopsis "Integration of single cell sequencing data")
20552 "This package provides an implementation of the Harmony algorithm for
20553 single cell integration, described in Korsunsky et al
20554 @url{doi.org/10.1101/461954}. The package includes a standalone Harmony
20555 function and interfaces to external frameworks.")
20556 (license license:gpl3)))
20558 (define-public r-covr
20565 (uri (cran-uri "covr" version))
20567 (base32 "0v5cv3cw2kpdr6wxmkbd3wclavr17zipypdcb10hhmpa4cvgqk55"))))
20568 (properties `((upstream-name . "covr")))
20569 (build-system r-build-system)
20579 (list r-knitr)) ; for vignettes
20580 (home-page "https://github.com/r-lib/covr")
20581 (synopsis "Test coverage for R packages")
20583 "Thisp package enables you to track and report code coverage for your
20584 package and (optionally) upload the results to a coverage service. Code
20585 coverage is a measure of the amount of code being exercised by a set of tests.
20586 It is an indirect measure of test quality and completeness. This package is
20587 compatible with any testing methodology or framework and tracks coverage of
20588 both R code and compiled C/C++/FORTRAN code.")
20589 (license license:gpl3)))
20591 (define-public r-systemfonts
20593 (name "r-systemfonts")
20598 (uri (cran-uri "systemfonts" version))
20601 "1h44bal845jp7ya8i7ff1kz1n3wklkb00jk6hb9lgwa2p5snqxpg"))))
20602 (properties `((upstream-name . "systemfonts")))
20603 (build-system r-build-system)
20607 (list fontconfig freetype zlib))
20609 (list pkg-config r-knitr))
20610 (home-page "https://github.com/r-lib/systemfonts")
20611 (synopsis "System native font finding")
20613 "This package provides system native access to the font catalogue. As
20614 font handling varies between systems it is difficult to correctly locate
20615 installed fonts across different operating systems. The 'systemfonts' package
20616 provides bindings to the native libraries for finding font files that can then
20617 be used further by e.g. graphic devices.")
20618 (license license:expat)))
20620 (define-public r-graphlayouts
20622 (name "r-graphlayouts")
20627 (uri (cran-uri "graphlayouts" version))
20630 "1l7gkn0r1ijllv3w7cbwcbi0jggs7wlkq9b2lykprng4g1kjc96p"))))
20631 (properties `((upstream-name . "graphlayouts")))
20632 (build-system r-build-system)
20634 (list r-igraph r-rcpp r-rcpparmadillo))
20635 (home-page "https://github.com/schochastics/graphlayouts")
20636 (synopsis "Additional layout algorithms for network visualizations")
20638 "This package provides several layout algorithms to visualize networks
20639 which are not part of the igraph library. Most are based on the concept of
20640 stress majorization by Gansner et al. (2004)
20641 <doi:10.1007/978-3-540-31843-9_25>. Some more specific algorithms
20642 emphasize hidden group structures in networks or focus on specific nodes.")
20643 (license license:expat)))
20645 (define-public r-terra
20652 (uri (cran-uri "terra" version))
20655 "0gzl0ka19jjw0dmaghjk2sgwi78kkz4w3rlfkym62rdarhlfj7h9"))))
20656 (properties `((upstream-name . "terra")))
20657 (build-system r-build-system)
20662 sqlite ; needed for proj
20668 (home-page "https://rspatial.org/terra")
20669 (synopsis "Spatial data analysis")
20671 "This package provides methods for spatial data analysis, especially
20672 raster data. The included methods allow for low-level data manipulation as
20673 well as high-level global, local, zonal, and focal computation. The predict
20674 and interpolate methods facilitate the use of regression type (interpolation,
20675 machine learning) models for spatial prediction. Processing of very large
20676 files is supported.")
20677 (license license:gpl3+)))
20679 (define-public r-tidygraph
20681 (name "r-tidygraph")
20686 (uri (cran-uri "tidygraph" version))
20689 "0dmdff3bkg53xn0c51xd6k2d9c7l250x1lhl5z3libf533dw5g9g"))))
20690 (properties `((upstream-name . "tidygraph")))
20691 (build-system r-build-system)
20703 (home-page "https://github.com/thomasp85/tidygraph")
20704 (synopsis "Tidy API for graph manipulation")
20706 "This package provides a graph implementation that can be thought of as
20707 two tidy data frames describing node and edge data respectively. It provides
20708 an approach to manipulate these two virtual data frames using the API defined
20709 in the @code{dplyr} package, and it also provides tidy interfaces to a lot of
20710 common graph algorithms.")
20711 (license license:expat)))
20713 (define-public r-soupx
20714 (let ((commit "a3354be76fb52fd795be6ddf163cf056c05c6cb8")
20718 (version (git-version "0.3.1" revision commit))
20722 (uri (git-reference
20723 (url "https://github.com/constantAmateur/SoupX")
20725 (file-name (git-file-name name version))
20728 "1zmlyzrl0fz6l79gn2wswid670p88mm3y292is89sa5p3h7frr99"))))
20729 (properties `((upstream-name . "SoupX")))
20730 (build-system r-build-system)
20732 (list r-ggplot2 r-matrix r-seurat))
20733 (home-page "https://github.com/constantAmateur/SoupX")
20734 (synopsis "Single cell mRNA Soup eXterminator")
20736 "This package provides a package for quantifying, profiling and
20737 removing cell free mRNA contamination (the \"soup\") from droplet based single
20738 cell RNA-seq experiments.")
20739 (license license:gpl2))))
20741 (define-public r-assertr
20748 (uri (cran-uri "assertr" version))
20751 "00764vv86r3bn4r85in4w637harffyw605fgq0dj6mrbrwcfb650"))))
20752 (build-system r-build-system)
20754 (list r-dplyr r-mass r-rlang))
20756 (list r-knitr)) ; needed for vignette
20757 (home-page "https://github.com/ropensci/assertr")
20758 (synopsis "Assertive programming for R analysis pipelines")
20760 "This package provides functionality to assert conditions that have to be
20761 met so that errors in data used in analysis pipelines can fail quickly. It is
20762 similar to @code{stopifnot()} but more powerful, friendly, and easier for use
20764 (license license:expat)))
20766 (define-public r-parameters
20768 (name "r-parameters")
20773 (uri (cran-uri "parameters" version))
20776 "0r6bj29frhqyv75cviw0p8kns6h8z10n7g7khyk0hzq2fqjsjrwh"))))
20777 (properties `((upstream-name . "parameters")))
20778 (build-system r-build-system)
20780 (list r-bayestestr r-datawizard r-insight))
20783 (home-page "https://cran.r-project.org/web/packages/parameters")
20784 (synopsis "Processing of model parameters")
20786 "This package provides utilities for processing the parameters of various
20787 statistical models. Beyond computing p values, CIs, and other indices for a
20788 wide variety of models, this package implements features like standardization
20789 or bootstrapping of parameters and models, feature reduction (feature
20790 extraction and variable selection) as well as conversion between indices of
20792 (license license:gpl3)))
20794 (define-public r-rgdal
20801 (uri (cran-uri "rgdal" version))
20803 (base32 "1vbkyhw8nd7dw1r53qisphav31x6zvpbzilvnlvbjbj9hzhs90s5"))))
20804 (properties `((upstream-name . "rgdal")))
20805 (build-system r-build-system)
20807 (list gdal proj zlib))
20811 (list pkg-config r-knitr))
20812 (home-page "http://rgdal.r-forge.r-project.org")
20813 (synopsis "Bindings for the Geospatial Data Abstraction Library")
20815 "This package provides bindings to the Geospatial Data Abstraction
20816 Library (GDAL) and access to projection/transformation operations from the
20818 (license license:gpl2+)))
20820 (define-public r-insol
20827 (uri (cran-uri "insol" version))
20830 "166kgxgzbh55y2qqya6c2si22x0v7asi70im054g6xxwc5187kh3"))))
20831 (properties `((upstream-name . "insol")))
20832 (build-system r-build-system)
20837 (home-page "https://meteoexploration.com/R/insol/index.html")
20838 (synopsis "Tools for calculating solar radiation")
20840 "This package provides functions to compute insolation on tilted
20841 surfaces, computes atmospheric transmittance and related parameters such as:
20842 Earth radius vector, declination, sunset and sunrise, daylength, equation of
20843 time, vector in the direction of the sun, vector normal to surface, and some
20844 atmospheric physics.")
20845 (license license:gpl2+)))
20847 (define-public r-lifecycle
20849 (name "r-lifecycle")
20854 (uri (cran-uri "lifecycle" version))
20857 "183v1z1h037pvsgrj6vakpwhnhsr29hsw8p16k59dgpi00f6x9qx"))))
20858 (properties `((upstream-name . "lifecycle")))
20859 (build-system r-build-system)
20861 (list r-glue r-rlang))
20863 (list r-knitr)) ; for vignettes
20864 (home-page "https://github.com/r-lib/lifecycle")
20865 (synopsis "Manage the life cycle of your package functions")
20867 "Manage the life cycle of your exported functions with shared
20868 conventions, documentation badges, and non-invasive deprecation warnings. The
20869 lifecycle package defines four development stages (experimental, maturing,
20870 stable, and questioning) and three deprecation stages (soft-deprecated,
20871 deprecated, and defunct). It makes it easy to insert badges corresponding to
20872 these stages in your documentation. Usage of deprecated functions are
20873 signalled with increasing levels of non-invasive verbosity.")
20874 (license license:gpl3)))
20876 (define-public r-assertable
20878 (name "r-assertable")
20883 (uri (cran-uri "assertable" version))
20886 "1cciil1nzxd8gbj49w99jiv077lbpb59vx7bmb4p218aj2h5hqq4"))))
20887 (build-system r-build-system)
20889 (list r-data-table))
20892 (home-page "https://cran.r-project.org/web/packages/assertable/")
20893 (synopsis "Verbose assertions for tabular data (data.frames and data.tables)")
20894 (description "This package provides simple, flexible assertions on
20895 data.frame or data.table objects with verbose output for vetting. While other
20896 assertion packages apply towards more general use-cases, @code{assertable} is
20897 tailored towards tabular data. It includes functions to check variable names
20898 and values, whether the dataset contains all combinations of a given set of
20899 unique identifiers, and whether it is a certain length. In addition,
20900 @code{assertable} includes utility functions to check the existence of target
20901 files and to efficiently import multiple tabular data files into one
20903 (license license:gpl3)))
20905 (define-public r-quadprog
20907 (name "r-quadprog")
20912 (uri (cran-uri "quadprog" version))
20914 (base32 "1ka9g8zak8sg4y2xbz93dfrldznlk9qpd4pq9z21cdcdn3b8s4i2"))))
20915 (build-system r-build-system)
20918 (home-page "https://cran.r-project.org/web/packages/quadprog")
20919 (synopsis "Functions to solve quadratic programming problems")
20921 "This package contains routines and documentation for solving quadratic
20922 programming problems.")
20923 (license license:gpl3+)))
20925 (define-public r-desolve
20932 (uri (cran-uri "deSolve" version))
20934 (base32 "1bfr4w760nr7mjhpmf32z39swr6isnn1665cld2d1pdgx8b0yrvl"))))
20935 (properties `((upstream-name . "deSolve")))
20936 (build-system r-build-system)
20939 (home-page "https://desolve.r-forge.r-project.org/")
20940 (synopsis "Solvers for initial value problems of differential equations")
20941 (description "This package provides functions that solve initial value
20942 problems of a system of first-order @dfn{ordinary differential
20943 equations} (ODE), of @dfn{partial differential equations} (PDE), of
20944 @dfn{differential algebraic equations} (DAE), and of delay differential
20945 equations. The functions provide an interface to the FORTRAN functions
20946 @code{lsoda}, @code{lsodar}, @code{lsode}, @code{lsodes} of the ODEPACK
20947 collection, to the FORTRAN functions @code{dvode} and @code{daspk} and a
20948 C-implementation of solvers of the Runge-Kutta family with fixed or variable
20949 time steps. The package contains routines designed for solving ODEs resulting
20950 from 1-D, 2-D and 3-D partial differential equations that have been converted
20951 to ODEs by numerical differencing.")
20952 (license license:gpl2+)))
20954 (define-public r-pmcmrplus
20956 (name "r-pmcmrplus")
20961 (uri (cran-uri "PMCMRplus" version))
20963 (base32 "16m1pdrzjq9vnx5v7zv56mz9r1205rkw92883cxaqbvdpds6dhqy"))))
20964 (properties `((upstream-name . "PMCMRplus")))
20965 (build-system r-build-system)
20966 (inputs (list gmp))
20976 (native-inputs (list gfortran r-knitr))
20977 (home-page "https://cran.r-project.org/package=PMCMRplus")
20978 (synopsis "Calculate pairwise multiple comparisons of mean rank sums extended")
20980 "This package provides multiple pairwise tests.")
20981 (license license:gpl3+)))
20983 (define-public r-pracma
20989 (uri (cran-uri "pracma" version))
20991 (base32 "0r17siivm37k4gp253v9mlg5m7cwqp85h9kk2hbp2wkf81ad80i3"))))
20992 (build-system r-build-system)
20993 (home-page "https://cran.r-project.org/web/packages/pracma/")
20994 (synopsis "Practical numerical math functions")
20995 (description "This package provides functions for numerical analysis and
20996 linear algebra, numerical optimization, differential equations, plus some
20997 special functions. It uses Matlab function names where appropriate to simplify
20999 (license license:gpl3+)))
21001 (define-public r-subplex
21008 (uri (cran-uri "subplex" version))
21011 "19g5bd39gmcn27xdsklkzxg99x1r5v5q8zcw1iwry31qj24ivhrv"))))
21012 (build-system r-build-system)
21015 (home-page "https://cran.r-project.org/web/packages/subplex")
21016 (synopsis "Unconstrained optimization using the subplex algorithm")
21018 "This package implements the Subplex optimization algorithm.
21019 It solves unconstrained optimization problems using a simplex method on
21020 subspaces. The method is well suited for optimizing objective functions that
21021 are noisy or are discontinuous at the solution.")
21022 (license license:gpl3+)))
21024 (define-public r-txtplot
21031 (uri (cran-uri "txtplot" version))
21034 "00sriml48y70j18jz235dsfm5x3a81bnzskfp3hnv6cbjwwsmca4"))))
21035 (build-system r-build-system)
21036 (home-page "https://cran.r-project.org/web/packages/txtplot/")
21037 (synopsis "Text-based plotting")
21038 (description "This package provides functions to produce rudimentary ASCII
21039 graphics directly in the terminal window. This package provides a basic
21040 plotting function (and equivalents of curve, density, acf and barplot) as well
21041 as a boxplot function.")
21042 (license license:lgpl3+)))
21044 (define-public r-bio3d
21051 (uri (cran-uri "bio3d" version))
21054 "0x3apqxbk4lvvcnvvdsyjd9f6qh9f9qgml3ih69hl9ikj06iy0y6"))))
21055 (properties `((upstream-name . "bio3d")))
21056 (build-system r-build-system)
21057 (inputs (list zlib))
21058 (propagated-inputs (list r-rcpp))
21061 (home-page "http://thegrantlab.org/bio3d/")
21062 (synopsis "Biological structure analysis")
21064 "This package provides utilities to process, organize and explore protein
21065 structure, sequence and dynamics data. Features include the ability to read
21066 and write structure, sequence and dynamic trajectory data, perform sequence
21067 and structure database searches, data summaries, atom selection, alignment,
21068 superposition, rigid core identification, clustering, torsion analysis,
21069 distance matrix analysis, structure and sequence conservation analysis, normal
21070 mode analysis, principal component analysis of heterogeneous structure data,
21071 and correlation network analysis from normal mode and molecular dynamics data.
21072 In addition, various utility functions are provided to enable the statistical
21073 and graphical power of the R environment to work with biological sequence and
21075 (license license:gpl2+)))
21077 (define-public r-bios2cor
21079 (name "r-bios2cor")
21084 (uri (cran-uri "Bios2cor" version))
21087 "1wkj9vr33m9jilidil9jpw5rzr3pf7gkimxdvch22ks4bgkx7l1w"))))
21088 (properties `((upstream-name . "Bios2cor")))
21089 (build-system r-build-system)
21091 (list r-bigmemory r-bio3d r-circular r-igraph))
21092 (home-page "https://cran.r-project.org/web/packages/Bios2cor/")
21093 (synopsis "From biological sequences and simulations to correlation analysis")
21095 "This package provides utilities for computation and analysis of
21096 correlation/covariation in multiple sequence alignments and in side chain
21097 motions during molecular dynamics simulations. Features include the
21098 computation of correlation/covariation scores using a variety of scoring
21099 functions between either sequence positions in alignments or side chain
21100 dihedral angles in molecular dynamics simulations and utilities to analyze the
21101 correlation/covariation matrix through a variety of tools including network
21102 representation and principal components analysis. In addition, several
21103 utility functions are based on the R graphical environment to provide friendly
21104 tools for help in data interpretation.")
21105 (license license:gpl2+)))
21107 ;; This package includes minified JavaScript files. When upgrading please
21108 ;; check that there are no new minified JavaScript files.
21109 (define-public r-networkd3
21111 (name "r-networkd3")
21116 (uri (cran-uri "networkD3" version))
21119 "02wxki67drppgfka1is1ykg1f2rxf0x0657c0crj7ipfy62jbf1k"))
21122 (delete-file "inst/htmlwidgets/lib/d3-4.5.0/d3.min.js")
21124 (properties `((upstream-name . "networkD3")))
21125 (build-system r-build-system)
21127 `(#:modules ((guix build utils)
21128 (guix build r-build-system)
21132 (modify-phases %standard-phases
21133 (add-after 'unpack 'process-javascript
21134 (lambda* (#:key inputs #:allow-other-keys)
21135 (with-directory-excursion "inst/htmlwidgets/lib/"
21139 `((,(assoc-ref inputs "d3.v4.js")
21140 "d3-4.5.0/d3.min.js"))))
21141 (lambda (sources targets)
21142 (for-each (lambda (source target)
21143 (format #t "Processing ~a --> ~a~%"
21145 (let ((minified (open-pipe* OPEN_READ "uglifyjs" source)))
21146 (call-with-output-file target
21148 (dump-port minified port)))))
21149 sources targets))))
21152 `(("uglifyjs" ,node-uglify-js)
21153 ;; NOTE: Make sure that this version of d3 is still valid when
21154 ;; upgrading the package.
21158 (uri "https://d3js.org/d3.v4.js")
21161 "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg"))))))
21163 (list r-htmlwidgets r-igraph r-magrittr))
21164 (home-page "https://cran.r-project.org/package=networkD3")
21165 (synopsis "D3 JavaScript network graphs from R")
21167 "This package creates D3 JavaScript network, tree, dendrogram, and Sankey
21169 (license license:gpl3+)))
21171 (define-public r-aasea
21178 (uri (cran-uri "aaSEA" version))
21181 "0him4r8qyp0xssgrmdxjs45yn4d28h5anv4jyxxbbs9phb0m6j3h"))))
21182 (properties `((upstream-name . "aaSEA")))
21183 (build-system r-build-system)
21194 (home-page "https://cran.r-project.org/web/packages/aaSEA/")
21195 (synopsis "Amino acid substitution effect analyzer")
21197 "Given a protein multiple sequence alignment, it is a daunting task to
21198 assess the effects of substitutions along sequence length. The aaSEA package
21199 is intended to help researchers to rapidly analyze property changes caused by
21200 single, multiple and correlated amino acid substitutions in proteins.")
21201 (license license:gpl3)))
21203 (define-public r-abacus
21210 (uri (cran-uri "ABACUS" version))
21213 "0m1dnkwjr1522l9ddbzzx7ayxvli17sbmk6s28adpmzzjwh2kd1i"))))
21214 (properties `((upstream-name . "ABACUS")))
21215 (build-system r-build-system)
21217 (list r-ggplot2 r-shiny))
21218 (home-page "https://shiny.abdn.ac.uk/Stats/apps/")
21219 (synopsis "Apps-based activities for communicating and understanding statistics")
21221 "This package provides a set of Shiny apps for effective communication
21222 and understanding in statistics. The current version includes properties of
21223 normal distribution, properties of sampling distribution, one-sample z and t
21224 tests, two samples independent (unpaired) t test and analysis of variance.")
21225 (license license:gpl3)))
21227 (define-public r-abc-rap
21234 (uri (cran-uri "ABC.RAP" version))
21237 "1kdspln17v0krvahcd55vib4dv5azp60b3r1zf489x10qqbp1mxk"))))
21238 (properties `((upstream-name . "ABC.RAP")))
21239 (build-system r-build-system)
21240 (home-page "https://cran.r-project.org/web/packages/ABC.RAP/")
21241 (synopsis "Array-based CpG region analysis pipeline")
21243 "This package aims to identify candidate genes that are differentially
21244 methylated between cases and controls. It applies Student's t-test and delta
21245 beta analysis to identify candidate genes containing multiple CpG sites.")
21246 (license license:gpl3)))
21248 (define-public r-abcadm
21255 (uri (cran-uri "abcADM" version))
21258 "0vcabnnnwc0psv9v3rda5aap9s8cq1pjh02zva3ki64hlavf2a10"))))
21259 (properties `((upstream-name . "abcADM")))
21260 (build-system r-build-system)
21262 (list r-bh r-rcpp))
21263 (home-page "https://cran.r-project.org/web/packages/abcADM/")
21264 (synopsis "Fit accumulated damage models and estimate reliability using ABC")
21266 "This package provides tools to estimate parameters of accumulated
21267 damage (load duration) models based on failure time data under a Bayesian
21268 framework, using @dfn{Approximate Bayesian Computation} (ABC), and to assess
21269 long-term reliability under stochastic load profiles.")
21270 (license license:gpl3)))
21272 (define-public r-rglpk
21279 (uri (cran-uri "Rglpk" version))
21282 "19mzpyimzq9zqnbi05j79b2di3nzaln8swggs9p8sqdr60qvr3d2"))))
21283 (properties `((upstream-name . "Rglpk")))
21284 (build-system r-build-system)
21289 (home-page "https://r-forge.r-project.org/projects/rglp/")
21290 (synopsis "R interface to the GNU Linear Programming Kit")
21292 "This package provides an R interface to the GNU Linear Programming Kit,
21293 software for solving large-scale @dfn{linear programming} (LP), @dfn{mixed
21294 integer linear programming} (MILP) and other related problems.")
21296 (license (list license:gpl2 license:gpl3))))
21298 (define-public r-abcdefba
21300 (name "r-abcdefba")
21305 (uri (cran-uri "abcdeFBA" version))
21308 "1rxjripy8v6bxi25vdfjnbk24zkmf752qbl73cin6nvnqflwxkx4"))))
21309 (properties `((upstream-name . "abcdeFBA")))
21310 (build-system r-build-system)
21312 (list r-corrplot r-lattice r-rgl r-rglpk))
21313 (home-page "https://cran.r-project.org/web/packages/abcdeFBA/")
21314 (synopsis "A-Biologist-Can-Do-Everything of Flux Balance Analysis with this package")
21316 "This package provides functions for Constraint Based Simulation using
21317 Flux Balance Analysis and informative analysis of the data generated during
21319 (license license:gpl2)))
21321 (define-public r-abcrlda
21328 (uri (cran-uri "abcrlda" version))
21331 "04pcdnk2szfpc2ylcw5ds7y895ivy03bycal03kxw7cwylzxasks"))))
21332 (properties `((upstream-name . "abcrlda")))
21333 (build-system r-build-system)
21334 (home-page "https://ieeexplore.ieee.org/document/8720003/")
21335 (synopsis "Asymptotically bias-corrected regularized linear discriminant analysis")
21337 "This package offers methods to perform @dfn{asymptotically
21338 bias-corrected regularized linear discriminant analysis} (ABC_RLDA) for
21339 cost-sensitive binary classification. The bias-correction is an estimate of
21340 the bias term added to regularized discriminant analysis that minimizes the
21342 (license license:gpl3)))
21344 (define-public r-abemus
21351 (uri (cran-uri "abemus" version))
21354 "1dhllb184byp1yl15rg2w02zgw3iajag7cxshirg47mnmm7n70bb"))))
21355 (properties `((upstream-name . "abemus")))
21356 (build-system r-build-system)
21358 (list r-data-table))
21359 (home-page "https://cran.r-project.org/web/packages/abemus/")
21360 (synopsis "Adaptive base error model in ultra-deep sequencing data")
21362 "This package provides an implementation of @dfn{Adaptive Base Error
21363 Model in Ultra-deep Sequencing data} (ABEMUS), which combines
21364 platform-specific genetic knowledge and empirical signal to readily detect and
21365 quantify somatic @dfn{single nucleotide variants} (SNVs) in @dfn{circulating
21366 cell free DNA} (cfDNA).")
21367 (license license:gpl3)))
21369 ;; This package includes minified JavaScript files. When upgrading please
21370 ;; check that there are no new minified JavaScript files.
21371 (define-public r-rintrojs
21373 (name "r-rintrojs")
21378 (uri (cran-uri "rintrojs" version))
21381 "00l5mk80gj3xkbf3m1kip566ic98bhd88lh0bg69ybkpk4gifpyw"))
21383 '(delete-file "inst/javascript/introjs/intro.min.js"))))
21384 (properties `((upstream-name . "rintrojs")))
21385 (build-system r-build-system)
21388 (modify-phases %standard-phases
21389 (add-after 'unpack 'process-javascript
21390 (lambda* (#:key inputs #:allow-other-keys)
21391 (with-directory-excursion "inst/javascript/introjs/"
21392 (let ((source (assoc-ref inputs "intro.js"))
21393 (target "intro.min.js"))
21394 (format #true "Processing ~a --> ~a~%"
21396 (invoke "esbuild" source "--minify"
21397 (string-append "--outfile=" target)))))))))
21399 `(("esbuild" ,esbuild)
21403 (uri "https://cdn.jsdelivr.net/npm/intro.js@3.2.1/intro.js")
21406 "0vh5n7hqqyx2pdvlqq6xadfqibcn78h5961rwhpf817kpxfzv8v7"))))))
21408 (list r-jsonlite r-shiny))
21409 (home-page "https://github.com/carlganz/rintrojs")
21410 (synopsis "Wrapper for the Intro.js library")
21412 "This package provides a wrapper for the @url{http://www.introjs.com,
21413 Intro.js} library. This package makes it easy to include step-by-step
21414 introductions, and clickable hints in a Shiny application. It supports both
21415 static introductions in the UI, and programmatic introductions from the
21417 ;; The intro.js library is licensed under Expat.
21418 (license (list license:agpl3+ license:expat))))
21420 (define-public r-sysfonts
21422 (name "r-sysfonts")
21427 (uri (cran-uri "sysfonts" version))
21430 "1fq5dn4l09sgrbznfz9cakf4vgc3761zwicvqaazh0s8mzbaicpn"))))
21431 (properties `((upstream-name . "sysfonts")))
21432 (build-system r-build-system)
21434 (list freetype libpng zlib))
21437 (home-page "https://github.com/yixuan/sysfonts")
21438 (synopsis "Loading fonts into R")
21440 "This is a package to simplify loading of system fonts and Google Fonts
21441 into R, in order to support other packages.")
21442 (license license:gpl2)))
21444 (define-public r-showtextdb
21446 (name "r-showtextdb")
21451 (uri (cran-uri "showtextdb" version))
21454 "0hlnc3fhgrdkd46n7hb6id0gg1v0bf8s4679nrr7rchyp455szq2"))))
21455 (properties `((upstream-name . "showtextdb")))
21456 (build-system r-build-system)
21459 (home-page "https://cran.r-project.org/web/packages/showtextdb/")
21460 (synopsis "Font files for the 'showtext' package")
21462 "This package provides font files that can be used by the @code{showtext}
21464 (license license:asl2.0)))
21466 (define-public r-showtext
21468 (name "r-showtext")
21473 (uri (cran-uri "showtext" version))
21476 "1larnqxn9nanbqiadm35ah5hh89xrzm4fdj9pfc93zzzhlfrvhb3"))))
21477 (properties `((upstream-name . "showtext")))
21478 (build-system r-build-system)
21480 (list freetype libpng zlib))
21482 (list r-showtextdb r-sysfonts))
21484 (list pkg-config r-knitr))
21485 (home-page "https://github.com/yixuan/showtext")
21486 (synopsis "Using fonts more easily in R graphs")
21488 "This package aims to make it easy to use various types of
21489 fonts (TrueType, OpenType, Type 1, web fonts, etc.) in R graphs, and supports
21490 most output formats of R graphics including PNG, PDF and SVG. Text glyphs
21491 will be converted into polygons or raster images, hence after the plot has
21492 been created, it no longer relies on the font files. No external software
21493 such as Ghostscript is needed to use this package.")
21494 (license license:asl2.0)))
21496 (define-public r-emojifont
21498 (name "r-emojifont")
21503 (uri (cran-uri "emojifont" version))
21506 "1hhrwilv36hd9gs1kcl2zsi6519md0h9aixjrm6lfclxvz8r6k1i"))))
21507 (properties `((upstream-name . "emojifont")))
21508 (build-system r-build-system)
21510 (list r-ggplot2 r-proto r-showtext r-sysfonts))
21513 (home-page "https://guangchuangyu.github.io/emojifont")
21514 (synopsis "Emoji and Font Awesome in R graphics")
21516 "This package enables the use of emoji and the Font Awesome glyphs in
21517 both base and ggplot2 graphics.")
21518 (license license:artistic2.0)))
21520 (define-public r-abstractr
21522 (name "r-abstractr")
21527 (uri (cran-uri "abstractr" version))
21530 "1ymwp7syrynwd4i8aj2x5n8jdi9d96fjzl6jb09n0bnr5fgl7vig"))))
21531 (properties `((upstream-name . "abstractr")))
21532 (build-system r-build-system)
21534 (list r-colourpicker
21541 (home-page "https://matt-kumar.shinyapps.io/portfolio")
21542 (synopsis "R-Shiny application for creating visual abstracts")
21544 "This package provides an R Shiny application to create visual abstracts
21545 for original research. A variety of user defined options and formatting are
21547 (license license:gpl3)))
21549 (define-public r-qgam
21556 (uri (cran-uri "qgam" version))
21559 "1jyamamdffaks89rspyhmg18b4iik0nb1j0vgqzvfnm890514cvn"))))
21560 (properties `((upstream-name . "qgam")))
21561 (build-system r-build-system)
21563 (list r-doparallel r-mgcv r-plyr r-shiny))
21564 (native-inputs (list r-knitr))
21565 (home-page "https://cran.r-project.org/web/packages/qgam/")
21566 (synopsis "Smooth additive quantile regression models")
21568 "This package provides smooth additive quantile regression models, fitted
21569 using the methods of Fasiolo et al. (2017). Differently from @code{quantreg},
21570 the smoothing parameters are estimated automatically by marginal loss
21571 minimization, while the regression coefficients are estimated using either
21572 PIRLS or Newton algorithm. The learning rate is determined so that the
21573 Bayesian credible intervals of the estimated effects have approximately the
21574 correct coverage. The main function is @code{qgam()} which is similar to
21575 @code{gam()} in the @code{mgcv} package, but fits non-parametric quantile
21576 regression models.")
21577 (license license:gpl2+)))
21579 (define-public r-abtest
21586 (uri (cran-uri "abtest" version))
21589 "0jz2ry5364p8h8xlk5a5sycn8xlpxd1iasfg99bcr4jqzd92jfqg"))))
21590 (properties `((upstream-name . "abtest")))
21591 (build-system r-build-system)
21601 (home-page "https://cran.r-project.org/web/packages/abtest/")
21602 (synopsis "Bayesian A/B testing")
21604 "This package provides functions for Bayesian A/B testing including prior
21605 elicitation options based on Kass and Vaidyanathan (1992)
21606 @url{doi:10.1111/j.2517-6161.1992.tb01868.x}.")
21607 (license license:gpl2+)))
21609 (define-public r-reldist
21616 (uri (cran-uri "reldist" version))
21619 "17kbqqapqmckghv7jizibmicv3bzbycfr3mz4xg3yjp3c2bap4r6"))))
21620 (properties `((upstream-name . "reldist")))
21621 (build-system r-build-system)
21623 (list r-densestbayes r-mgcv))
21624 (home-page "http://www.stat.ucla.edu/~handcock/RelDist")
21625 (synopsis "Relative distribution methods")
21627 "This package provides tools for the comparison of distributions. This
21628 includes nonparametric estimation of the relative distribution PDF and CDF and
21629 numerical summaries as described in \"Relative Distribution Methods in the
21630 Social Sciences\" by Mark S. Handcock and Martina Morris, Springer-Verlag,
21631 1999, Springer-Verlag, ISBN 0387987789.")
21632 ;; See also https://cran.r-project.org/web/packages/reldist/LICENSE for
21633 ;; attribution requirements.
21634 (license license:gpl3)))
21636 (define-public r-accept
21643 (uri (cran-uri "accept" version))
21646 "13kx8fbnbpasjklgbq2rf4n73j2s8rvy5v77ywqhfzln24937qgh"))))
21647 (properties `((upstream-name . "accept")))
21648 (build-system r-build-system)
21650 (list r-dplyr r-reldist))
21651 (home-page "https://cran.r-project.org/web/packages/accept/")
21652 (synopsis "Acute COPD Exacerbation Prediction Tool (ACCEPT)")
21654 "This package allows clinicians to predict the rate and severity of
21655 future acute exacerbation in @dfn{Chronic Obstructive Pulmonary
21656 Disease} (COPD) patients, based on the clinical prediction model published in
21657 Adibi et al. (2019) @url{doi:10.1101/651901}.")
21658 (license license:gpl3)))
21660 (define-public r-smpracticals
21662 (name "r-smpracticals")
21667 (uri (cran-uri "SMPracticals" version))
21670 "0zxq84f9i3b86xx6msb25b61gyj9k09iab2b7wg4d93yas9qzayf"))))
21671 (properties `((upstream-name . "SMPracticals")))
21672 (build-system r-build-system)
21674 (list r-ellipse r-mass r-nlme r-survival))
21675 (home-page "http://statwww.epfl.ch/davison/SM/")
21676 (synopsis "Practicals for use with Davison (2003) Statistical Models")
21678 "This package contains the datasets and a few functions for use with the
21679 practicals outlined in Appendix A of the book Statistical Models (Davison,
21680 2003, Cambridge University Press). The practicals themselves can be found at
21681 @url{http://statwww.epfl.ch/davison/SM/}.")
21682 (license license:gpl2+)))
21684 (define-public r-fgui
21691 (uri (cran-uri "fgui" version))
21694 "024fzd1c7iwqprn26hwjb9l2qlvvyzl449d7iixy0x69djwsrysv"))))
21695 (properties `((upstream-name . "fgui")))
21696 (build-system r-build-system)
21698 "https://sites.google.com/site/thomashoffmannproject/software/fgui")
21699 (synopsis "Create GUI for R functions")
21701 "Rapidly create a GUI for a function you created by automatically
21702 creating widgets for arguments of the function. This package automatically
21703 parses help routines for context-sensitive help to these arguments. The
21704 interface is essentially a wrapper to some Tcl/Tk routines to both simplify
21705 and facilitate GUI creation. More advanced Tcl/Tk routines/GUI objects can be
21706 incorporated into the interface for greater customization for the more
21708 ;; Any version of the GPL.
21709 (license (list license:gpl2+ license:gpl3+))))
21711 (define-public r-tcltk2
21718 (uri (cran-uri "tcltk2" version))
21721 "1ibxld379600xx7kiqq3fck083s8psry12859980218rnzikl65d"))))
21722 (properties `((upstream-name . "tcltk2")))
21723 (build-system r-build-system)
21726 (home-page "https://www.sciviews.org/SciViews-R")
21727 (synopsis "Tcl/Tk additions")
21729 "This package provides a series of additional Tcl commands and Tk widgets
21730 with style and various functions to supplement the tcltk package")
21731 (license license:lgpl3)))
21733 (define-public r-accrual
21740 (uri (cran-uri "accrual" version))
21743 "11clm9s5c5518nmp6hd6pjnp0s28y92b2i2x0xgj4j5g816p4j3z"))))
21744 (properties `((upstream-name . "accrual")))
21745 (build-system r-build-system)
21747 (list r-fgui r-smpracticals r-tcltk2))
21748 (home-page "https://cran.r-project.org/web/packages/accrual/")
21749 (synopsis "Bayesian accrual prediction")
21751 "Subject recruitment for medical research is challenging. Slow patient
21752 accrual leads to delay in research. Accrual monitoring during the process of
21753 recruitment is critical. Researchers need reliable tools to manage the
21754 accrual rate. This package provides an implementation of a Bayesian method
21755 that integrates researcher's experience on previous trials and data from the
21756 current study, providing reliable prediction on accrual rate for clinical
21757 studies. It provides functions for Bayesian accrual prediction which can be
21758 easily used by statisticians and clinical researchers.")
21759 (license license:gpl2)))
21761 (define-public r-accrued
21768 (uri (cran-uri "accrued" version))
21771 "05g1jb5914z18rcai1ahn7nihn27vr2rnadwv94gc1j7ivvikvs5"))))
21772 (properties `((upstream-name . "accrued")))
21773 (build-system r-build-system)
21774 (home-page "https://cran.r-project.org/web/packages/accrued/")
21775 (synopsis "Data quality visualization tools for partially accruing data")
21777 "This is a package for visualizing data quality of partially accruing
21779 (license license:gpl3)))
21781 (define-public r-mda
21788 (uri (cran-uri "mda" version))
21791 "0qw4scc2w7jmnxssj5w2mdxb9rrl4dscqn54gplzm1gk2yf419mx"))))
21792 (properties `((upstream-name . "mda")))
21793 (build-system r-build-system)
21794 (propagated-inputs (list r-class))
21795 (native-inputs (list gfortran))
21796 (home-page "https://cran.r-project.org/web/packages/mda/")
21797 (synopsis "Mixture and flexible discriminant analysis")
21799 "This is a package for mixture and flexible discriminant analysis,
21800 @dfn{multivariate adaptive regression splines} (MARS), BRUTO, and so on.")
21801 (license license:gpl2)))
21803 (define-public r-elasticnet
21805 (name "r-elasticnet")
21810 (uri (cran-uri "elasticnet" version))
21813 "0nxcw06d0cp2mbqzg2fm9yys5xm6xx7bfcfvr0avcs8afkvz29j8"))))
21814 (properties `((upstream-name . "elasticnet")))
21815 (build-system r-build-system)
21818 (home-page "http://users.stat.umn.edu/~zouxx019/")
21819 (synopsis "Elastic-Net for sparse estimation and sparse PCA")
21821 "This package provides functions for fitting the entire solution path of
21822 the Elastic-Net and also provides functions for estimating sparse Principal
21823 Components. The Lasso solution paths can be computed by the same function.")
21824 (license license:gpl2+)))
21826 (define-public r-sparselda
21828 (name "r-sparselda")
21833 (uri (cran-uri "sparseLDA" version))
21836 "1k3sw9kc40yxnfss4vrsx34qxmv8ssddyhbfjhxrdldvblhbwchb"))))
21837 (properties `((upstream-name . "sparseLDA")))
21838 (build-system r-build-system)
21840 (list r-elasticnet r-mass r-mda))
21841 (home-page "https://www.imm.dtu.dk/~lkhc/")
21842 (synopsis "Sparse discriminant analysis")
21844 "This package performs sparse linear discriminant analysis for Gaussians
21845 and mixture of Gaussian models.")
21846 (license license:gpl2+)))
21848 (define-public r-accsda
21855 (uri (cran-uri "accSDA" version))
21858 "104xdz63mnibh6827xm0pfr9zbhbi2a7iw4m1x27xjqi7zqvbky6"))))
21859 (properties `((upstream-name . "accSDA")))
21860 (build-system r-build-system)
21866 (home-page "https://github.com/gumeo/accSDA/wiki")
21867 (synopsis "Accelerated sparse discriminant analysis")
21869 "This package provides an implementation of sparse linear discriminant
21870 analysis, which is a supervised classification method for multiple classes.
21871 Various novel optimization approaches to this problem are implemented
21872 including @dfn{alternating direction method of multipliers} (ADMM),
21873 @dfn{proximal gradient} (PG) and @dfn{accelerated proximal gradient} (APG).
21874 Functions for performing cross validation are also supplied along with basic
21875 prediction and plotting functions. @dfn{Sparse zero variance
21876 discriminant} (SZVD) analysis is also included in the package.")
21877 (license license:gpl2+)))
21879 (define-public r-ace2fastq
21881 (name "r-ace2fastq")
21886 (uri (cran-uri "ace2fastq" version))
21889 "09kk3yyqnr2xp820g0p3aai9a21figigjr9lxkr3zjq2d8gzwfic"))))
21890 (properties `((upstream-name . "ace2fastq")))
21891 (build-system r-build-system)
21894 (home-page "https://github.com/c5sire/ace2fastq")
21895 (synopsis "ACE file to FASTQ converter")
21897 "The ACE file format is used in genomics to store contigs from sequencing
21898 machines. This tools converts it into FASTQ format. Both formats contain the
21899 sequence characters and their corresponding quality information. Unlike the
21900 FASTQ file, the ACE file stores the quality values numerically. The
21901 conversion algorithm uses the standard Sanger formula. The package
21902 facilitates insertion into pipelines, and content inspection.")
21903 (license license:gpl3)))
21905 (define-public r-rngwell
21912 (uri (cran-uri "rngWELL" version))
21915 "0f1dxxaimfb0fww8ym9ciqf6q760ai46wxldl37m5mfpd57ca00c"))))
21916 (properties `((upstream-name . "rngWELL")))
21917 (build-system r-build-system)
21918 (home-page "https://cran.r-project.org/web/packages/rngWELL/")
21919 (synopsis "Toolbox for WELL random number generators")
21921 "This is a dedicated package to WELL pseudo random generators, which were
21922 introduced in Panneton et al. (2006), ``Improved Long-Period Generators Based
21923 on Linear Recurrences Modulo 2'', ACM Transactions on Mathematical Software.")
21924 (license license:bsd-3)))
21926 (define-public r-rnmf
21932 (uri (cran-uri "rNMF" version))
21935 "1nz6h0j5ywdh48m0swmhp34hbkycd7n13rclrxaw85qi9wc42597"))))
21936 (build-system r-build-system)
21938 (list r-knitr r-nnls))
21939 (home-page "https://cran.r-project.org/web/packages/rNMF/")
21940 (synopsis "Robust nonnegative matrix factorization")
21942 "This package provides an implementation of robust nonnegative matrix
21943 factorization (rNMF). The rNMF algorithm decomposes a nonnegative high
21944 dimension data matrix into the product of two low rank nonnegative matrices,
21945 while detecting and trimming outliers. The main function is @code{rnmf()}.
21946 The package also includes a visualization tool, @code{see()}, that arranges
21947 and prints vectorized images.")
21948 (license license:gpl2+)))
21950 (define-public r-randtoolbox
21952 (name "r-randtoolbox")
21957 (uri (cran-uri "randtoolbox" version))
21960 "005x2igljc6vm0nsmkld9aqjqz1ccwapc8z3aw5c3ivh4n2bghf9"))))
21961 (properties `((upstream-name . "randtoolbox")))
21962 (build-system r-build-system)
21965 (home-page "https://cran.r-project.org/web/packages/randtoolbox/")
21966 (synopsis "Toolbox for pseudo and quasi random number generation")
21968 "This package provides
21971 @item pseudo random generators, such as general linear
21972 congruential generators, multiple recursive generators and generalized
21973 feedback shift register (SF-Mersenne Twister algorithm and WELL
21976 @item quasi random generators, such as the Torus algorithm, the Sobol
21977 sequence, the Halton sequence (including the Van der Corput sequence), and
21979 @item some generator tests: the gap test, the serial test, the poker test.
21982 See e.g. Gentle (2003) @url{doi:10.1007/b97336}.")
21983 (license license:bsd-3)))
21985 (define-public r-lhs
21992 (uri (cran-uri "lhs" version))
21995 "0fb3bc3s5pbwg92qkjbg7v8ah36wm6qs05vf098hwjakr7f6yg3s"))))
21996 (properties `((upstream-name . "lhs")))
21997 (build-system r-build-system)
21998 (propagated-inputs (list r-rcpp))
22001 (home-page "https://github.com/bertcarnell/lhs")
22002 (synopsis "Latin Hypercube Samples")
22004 "This package provides a number of methods for creating and augmenting
22005 Latin Hypercube Samples.")
22006 (license license:gpl3)))
22008 (define-public r-acebayes
22010 (name "r-acebayes")
22015 (uri (cran-uri "acebayes" version))
22018 "11bffz430gdfdaxjx3simig66vhynmx6l1ylac4q2shcmj52nx73"))))
22019 (properties `((upstream-name . "acebayes")))
22020 (build-system r-build-system)
22022 (list r-compare r-lhs r-randtoolbox r-rcpp r-rcpparmadillo))
22023 (home-page "https://cran.r-project.org/web/packages/acebayes/")
22024 (synopsis "Optimal Bayesian experimental design using the ACE algorithm")
22026 "Finding an optimal Bayesian experimental design involves maximizing an
22027 objective function given by the expectation of some appropriately chosen
22028 utility function with respect to the joint distribution of unknown
22029 quantities (including responses). This objective function is usually not
22030 available in closed form and the design space can be continuous and of high
22031 dimensionality. This package uses @dfn{Approximate Coordinate Exchange} (ACE)
22032 to maximise an approximation to the expectation of the utility function.")
22033 (license license:gpl2)))
22035 (define-public r-acet
22042 (uri (cran-uri "ACEt" version))
22045 "0b5lfpnppyk0237phr2aybhx29nhm8ngwk2qa1y4lshrvsw97wg4"))))
22046 (properties `((upstream-name . "ACEt")))
22047 (build-system r-build-system)
22049 (list r-bh r-mass r-rcpp r-rcpparmadillo))
22050 (home-page "https://cran.r-project.org/web/packages/ACEt/")
22051 (synopsis "Estimating dynamic heritability and twin model comparison")
22053 "This package supports twin models that are able to estimate the dynamic
22054 behaviour of the variance components in the classical twin models with respect
22055 to age using B-splines and P-splines.")
22056 (license license:gpl2+)))
22058 (define-public r-acfmperiod
22060 (name "r-acfmperiod")
22065 (uri (cran-uri "acfMPeriod" version))
22068 "1yww8isfrbs2v9s94hx7p2imyszcgadwafdgpj438n2ik0q6p9d5"))))
22069 (properties `((upstream-name . "acfMPeriod")))
22070 (build-system r-build-system)
22073 (home-page "https://cran.r-project.org/web/packages/acfMPeriod/")
22074 (synopsis "Estimation of the ACF from the M-periodogram")
22076 "This package support non-robust and robust computations of the sample
22077 autocovariance (ACOVF) and sample autocorrelation functions (ACF) of
22078 univariate and multivariate processes. The methodology consists in reversing
22079 the diagonalization procedure involving the periodogram or the
22080 cross-periodogram and the Fourier transform vectors, and, thus, obtaining the
22081 ACOVF or the ACF as discussed in Fuller (1995)
22082 @url{doi:10.1002/9780470316917}. The robust version is obtained by fitting
22083 robust M-regressors to obtain the M-periodogram or M-cross-periodogram as
22084 discussed in Reisen et al. (2017) @url{doi:10.1016/j.jspi.2017.02.008}.")
22085 (license license:gpl2+)))
22087 (define-public r-gamlss-data
22089 (name "r-gamlss-data")
22094 (uri (cran-uri "gamlss.data" version))
22097 "07mpdl4h9rwmnpl9jmsn6ig8ji11an6pyjfsvg62h2alapwbdcyv"))))
22098 (properties `((upstream-name . "gamlss.data")))
22099 (build-system r-build-system)
22100 (home-page "http://www.gamlss.org/")
22101 (synopsis "GAMLSS data")
22103 "This package provides data used as examples to demonstrate GAMLSS
22105 ;; Either version of the license
22106 (license (list license:gpl2 license:gpl3))))
22108 (define-public r-gamlss
22115 (uri (cran-uri "gamlss" version))
22118 "0xih19zqgpjl5qv5j38ana6x29y84shn2jfl2lk4kaw3q7yx86b6"))))
22119 (properties `((upstream-name . "gamlss")))
22120 (build-system r-build-system)
22122 (list r-gamlss-data r-gamlss-dist r-mass r-nlme r-survival))
22123 (home-page "http://www.gamlss.org/")
22124 (synopsis "Generalized additive models for location scale and shape")
22126 "This package provides functions for fitting the generalized additive
22127 models for location scale and shape introduced by Rigby and
22128 Stasinopoulos (2005), @url{doi:10.1111/j.1467-9876.2005.00510.x}. The models
22129 use a distributional regression approach where all the parameters of the
22130 conditional distribution of the response variable are modelled using
22131 explanatory variables.")
22132 ;; Either version of the license
22133 (license (list license:gpl2 license:gpl3))))
22135 (define-public r-acid
22142 (uri (cran-uri "acid" version))
22145 "030i0y8s283ivbsmjccpbv9v7mgbcg2jk9df7vgcbbns74swf9hd"))))
22146 (properties `((upstream-name . "acid")))
22147 (build-system r-build-system)
22149 (list r-gamlss r-gamlss-dist r-hmisc))
22150 (home-page "https://cran.r-project.org/web/packages/acid/")
22151 (synopsis "Analysing conditional income distributions")
22153 "This package provides functions for the analysis of income distributions
22154 for subgroups of the population as defined by a set of variables like age,
22155 gender, region, etc. This entails a Kolmogorov-Smirnov test for a mixture
22156 distribution as well as functions for moments, inequality measures, entropy
22157 measures and polarisation measures of income distributions. This package thus
22158 aides the analysis of income inequality by offering tools for the exploratory
22159 analysis of income distributions at the disaggregated level.")
22160 (license license:gpl3)))
22162 (define-public r-acm4r
22169 (uri (cran-uri "acm4r" version))
22172 "1wqzc35i1rshx0zlmas8y4qkkvy6h9r4i4apscjjv1xg2wjflzxa"))))
22173 (properties `((upstream-name . "acm4r")))
22174 (build-system r-build-system)
22175 (propagated-inputs (list r-mass))
22176 (home-page "https://cran.r-project.org/web/packages/acm4r/")
22177 (synopsis "Align-and-count method comparisons of RFLP data")
22179 "This is a package to compare sequence fragment lengths or molecular
22180 weights from pairs of lanes. The number of matching bands in the
22181 @dfn{Restriction Fragment Length Polymorphism} (RFLP) data is calculated using
22182 the align-and-count method.")
22183 ;; Any version of the GPL
22184 (license (list license:gpl2+ license:gpl3+))))
22186 (define-public r-filelock
22188 (name "r-filelock")
22193 (uri (cran-uri "filelock" version))
22196 "00ql5fw1hidpfnm0szaavf43ahmsnvdbi8i5lr1nrcc90yaiaadc"))))
22197 (properties `((upstream-name . "filelock")))
22198 (build-system r-build-system)
22199 (home-page "https://github.com/r-lib/filelock")
22200 (synopsis "Portable file locking")
22202 "This library lets you place an exclusive or shared lock on a file using
22203 the appropriate system call provided by the underlying operating system.")
22204 (license license:expat)))
22206 (define-public r-filematrix
22208 (name "r-filematrix")
22213 (uri (cran-uri "filematrix" version))
22216 "1v3aj1ng742msb0sfdnjsbqb508mqjf8jlq2v33vxldhradw5w0b"))))
22217 (properties `((upstream-name . "filematrix")))
22218 (build-system r-build-system)
22219 ;; These inputs are needed for vignettes
22221 (list r-knitr r-rmarkdown))
22222 (home-page "https://github.com/andreyshabalin/filematrix")
22223 (synopsis "File-backed matrix class with convenient read and write access")
22225 "This package provides an interface for working with large matrices
22226 stored in files, not in computer memory. It supports multiple non-character
22227 data types (double, integer, logical and raw) of various sizes (e.g. 8 and 4
22228 byte real values). Access to parts of the matrix is done by indexing, exactly
22229 as with usual R matrices. It supports very large matrices; the package has
22230 been tested on multi-terabyte matrices. It allows for more than 2^32 rows or
22231 columns, ad allows for quick addition of extra columns to a filematrix.")
22232 (license license:lgpl3)))
22234 (define-public r-acmeeqtl
22236 (name "r-acmeeqtl")
22241 (uri (cran-uri "ACMEeqtl" version))
22244 "049xjv2ym35bbn43zwi68cq27fwdh404vp0r2ca5gxgmmx8kj1cz"))))
22245 (properties `((upstream-name . "ACMEeqtl")))
22246 (build-system r-build-system)
22248 (list r-filematrix))
22249 (home-page "https://github.com/andreyshabalin/ACMEeqtl")
22250 (synopsis "Estimation of interpretable eQTL effect sizes")
22252 "This package provides a non-linear model, termed ACME, that reflects a
22253 parsimonious biological model for allelic contributions of cis-acting eQTLs.
22254 With non-linear least-squares algorithm the maximum likelihood parameters can
22255 be estimated. The ACME model provides interpretable effect size estimates and
22256 p-values with well controlled Type-I error.")
22257 (license license:lgpl3)))
22259 (define-public r-acmer
22266 (uri (cran-uri "acmeR" version))
22269 "000b2hqlhj93958nddw0fqb15ahigs08najv2miivym046x04mf7"))))
22270 (properties `((upstream-name . "acmeR")))
22271 (build-system r-build-system)
22272 (propagated-inputs (list r-foreign))
22273 (home-page "https://cran.r-project.org/web/packages/acmeR/")
22274 (synopsis "ACME estimator of bird and bat mortality by wind turbines")
22276 "This package provides an implementation of the ACME estimator, described
22277 in Wolpert (2015), ACME: A Partially Periodic Estimator of Avian & Chiropteran
22278 Mortality at Wind Turbines. Unlike most other models, this estimator supports
22279 decreasing-hazard Weibull model for persistence; decreasing search proficiency
22280 as carcasses age; variable bleed-through at successive searches; and interval
22281 mortality estimates. The package provides, based on search data, functions
22282 for estimating the mortality inflation factor in Frequentist and Bayesian
22284 (license license:expat)))
22286 (define-public r-r-huge
22293 (uri (cran-uri "R.huge" version))
22296 "13p558qalv60pgr24nsm6mi92ryj65rsbqa6pgdwy0snjqx12bgi"))))
22297 (properties `((upstream-name . "R.huge")))
22298 (build-system r-build-system)
22300 (list r-r-methodss3 r-r-oo r-r-utils))
22301 (home-page "https://github.com/HenrikBengtsson/R.huge")
22302 (synopsis "Methods for accessing huge amounts of data")
22304 "This is a deprecated package for accessing huge amounts of data.
22305 Cross-platform alternatives are the following packages: bigmemory (CRAN),
22306 ff (CRAN), or BufferedMatrix (Bioconductor). The main usage of it was inside
22307 the @code{aroma.affymetrix} package.")
22308 (license license:lgpl2.1+)))
22310 (define-public r-r-filesets
22312 (name "r-r-filesets")
22317 (uri (cran-uri "R.filesets" version))
22320 "08xv8b3c81nf54viyr3w912al18483k5gfnjpg7bxbdfk70dfzbh"))))
22321 (properties `((upstream-name . "R.filesets")))
22322 (build-system r-build-system)
22325 (modify-phases %standard-phases
22326 (add-after 'unpack 'set-HOME
22327 (lambda _ (setenv "HOME" "/tmp"))))))
22329 (list r-digest r-r-cache r-r-methodss3 r-r-oo r-r-utils))
22330 (home-page "https://github.com/HenrikBengtsson/R.filesets")
22331 (synopsis "Easy handling of and access to files")
22333 "This package provides classes and methods to locate, setup, subset,
22334 navigate and iterate file sets, i.e. sets of files located in one or more
22335 directories on the file system. The API is designed such that these classes
22336 can be extended via inheritance to provide a richer API for special file
22337 formats. Moreover, a specific name format is defined such that filenames and
22338 directories can be considered to have full names which consists of a name
22339 followed by comma-separated tags. This adds additional flexibility to
22340 identify file sets and individual files.")
22341 (license license:lgpl2.1+)))
22343 (define-public r-r-devices
22345 (name "r-r-devices")
22350 (uri (cran-uri "R.devices" version))
22353 "1djz6vm1b7sjvx1q319dl47gbnz9kvipaxcz9i0spyp094lv3m62"))))
22354 (properties `((upstream-name . "R.devices")))
22355 (build-system r-build-system)
22357 (list r-base64enc r-r-methodss3 r-r-oo r-r-utils))
22358 (home-page "https://github.com/HenrikBengtsson/R.devices")
22359 (synopsis "Unified handling of graphics devices")
22361 "This package provides functions for creating plots and image files in a
22362 unified way regardless of output format (EPS, PDF, PNG, SVG, TIFF, WMF, etc.).
22363 Default device options as well as scales and aspect ratios are controlled in a
22364 uniform way across all device types. Switching output format requires minimal
22365 changes in code. This package is ideal for large-scale batch processing,
22366 because it will never leave open graphics devices or incomplete image files
22367 behind, even on errors or user interrupts.")
22368 (license license:lgpl2.1+)))
22370 (define-public r-acnr
22377 (uri (cran-uri "acnr" version))
22380 "087hq4i7jp67ba2finzsqjfnqbiprl33na6ryjv9zqzsdawj9cym"))))
22381 (properties `((upstream-name . "acnr")))
22382 (build-system r-build-system)
22383 (home-page "https://github.com/mpierrejean/acnr")
22384 (synopsis "Annotated copy-number regions")
22386 "This package provides SNP array data from different types of copy-number
22387 regions. These regions were identified manually by the authors of the package
22388 and may be used to generate realistic data sets with known truth.")
22389 (license license:lgpl2.1+)))
22391 (define-public r-acopula
22398 (uri (cran-uri "acopula" version))
22401 "0vvbbw8pfs9jwfz5c57lw48pr0qj661r0ys007q6zf9jmlrhx1ln"))))
22402 (properties `((upstream-name . "acopula")))
22403 (build-system r-build-system)
22404 (home-page "https://cran.r-project.org/web/packages/acopula/")
22405 (synopsis "Modelling dependence with multivariate Archimax copulas")
22407 "Archimax copulas are a mixture of Archimedean and EV copulas. This
22408 package provides definitions of several parametric families of generator and
22409 dependence function, computes CDF and PDF, estimates parameters, tests for
22410 goodness of fit, generates random sample and checks copula properties for
22411 custom constructs. In the 2-dimensional case explicit formulas for density
22412 are used, contrary to higher dimensions when all derivatives are linearly
22413 approximated. Several non-archimax families (normal, FGM, Plackett) are
22414 provided as well.")
22415 (license license:gpl2)))
22417 (define-public r-tuner
22424 (uri (cran-uri "tuneR" version))
22427 "1sd0drxzbdy71bh35fccg9ajhpdhdpy0m9nja2lw82p1pzhyl7jn"))))
22428 (properties `((upstream-name . "tuneR")))
22429 (build-system r-build-system)
22430 (propagated-inputs (list r-signal))
22431 (home-page "https://cran.r-project.org/web/packages/tuneR/")
22432 (synopsis "Analysis of music and speech")
22434 "This is a package for the analysis of music and speech. Analyze music
22435 and speech, extract features like MFCCs, handle wave files and their
22436 representation in various ways, read MP3, read MIDI, perform steps of a
22437 transcription, ...")
22438 ;; Either of these versions.
22439 (license (list license:gpl2 license:gpl3))))
22441 (define-public r-seewave
22448 (uri (cran-uri "seewave" version))
22451 "0bi1l47l3846c18k6h2vrv0xp9xh00n544a578jrndahzrj1hfwl"))))
22452 (properties `((upstream-name . "seewave")))
22453 (build-system r-build-system)
22458 (home-page "http://rug.mnhn.fr/seewave")
22459 (synopsis "Sound analysis and synthesis")
22461 "This package provides functions for analysing, manipulating, displaying,
22462 editing and synthesizing time waves (particularly sound). This package
22463 processes time analysis (oscillograms and envelopes), spectral content,
22464 resonance quality factor, entropy, cross correlation and autocorrelation,
22465 zero-crossing, dominant frequency, analytic signal, frequency coherence, 2D
22466 and 3D spectrograms and many other analyses.")
22467 (license license:gpl2+)))
22469 (define-public r-acousticndlcoder
22471 (name "r-acousticndlcoder")
22476 (uri (cran-uri "AcousticNDLCodeR" version))
22479 "1fgzgwanpv2pzy74xdk3hamc44p8qch467wh163dxby8jr9ik0sb"))))
22481 `((upstream-name . "AcousticNDLCodeR")))
22482 (build-system r-build-system)
22484 (list r-seewave r-tuner r-zoo))
22485 (home-page "https://cran.r-project.org/web/packages/AcousticNDLCodeR/")
22486 (synopsis "Coding sound files for use with NDL")
22488 "Make acoustic cues to use with the R package @code{ndl}.
22489 The package implements functions used in the PLoS ONE paper \"Words from
22490 spontaneous conversational speech can be recognized with human-like accuracy
22491 by an error-driven learning algorithm that discriminates between meanings
22492 straight from smart acoustic features, bypassing the phoneme as recognition
22493 unit.\" @url{doi:10.1371/journal.pone.0174623}")
22494 (license license:gpl2+)))
22496 (define-public r-acp
22503 (uri (cran-uri "acp" version))
22506 "0lcwbjcyyr32m6qjmjqh25qjwrbyqj1n092xhgbhxzd8fslppnmn"))))
22507 (properties `((upstream-name . "acp")))
22508 (build-system r-build-system)
22510 (list r-quantmod r-tseries))
22511 (home-page "https://cran.r-project.org/web/packages/acp/")
22512 (synopsis "Autoregressive conditional Poisson")
22514 "This package supports the analysis of count data exhibiting
22515 autoregressive properties, using the @dfn{Autoregressive Conditional Poisson}
22516 model (ACP(p,q)) proposed by Heinen (2003).")
22517 (license license:gpl2)))
22519 (define-public r-ada
22526 (uri (cran-uri "ada" version))
22529 "1h3a07czp0w3hrhjcg1fz721y8vsfclzqi3rq8qfzgpfb4h1f06r"))))
22530 (properties `((upstream-name . "ada")))
22531 (build-system r-build-system)
22532 (propagated-inputs (list r-rpart))
22533 (home-page "https://cran.r-project.org/web/packages/ada/")
22534 (synopsis "Stochastic boosting")
22536 "This package provides a straightforward, well-documented, and broad
22537 boosting routine for classification, ideally suited for small to
22538 moderate-sized data sets. It performs discrete, real, and gentle boost under
22539 both exponential and logistic loss on a given data set.")
22540 ;; Any version of the GPL.
22541 (license (list license:gpl2+ license:gpl3+))))
22543 (define-public r-genalg
22550 (uri (cran-uri "genalg" version))
22553 "1y4qz1s85zpd1r3259gr542arssf2vpd4drhy0wnq5q47ignrvna"))))
22554 (properties `((upstream-name . "genalg")))
22555 (build-system r-build-system)
22556 (home-page "https://github.com/egonw/genalg")
22557 (synopsis "R based genetic algorithm")
22559 "This package provides an R based genetic algorithm for binary and
22560 floating point chromosomes.")
22561 (license license:gpl2)))
22563 (define-public r-kernelfactory
22565 (name "r-kernelfactory")
22570 (uri (cran-uri "kernelFactory" version))
22573 "001kw9k3ivd4drd4mwqapkkk3f4jgljiaprhg2630hmll064s89j"))))
22574 (properties `((upstream-name . "kernelFactory")))
22575 (build-system r-build-system)
22577 (list r-auc r-genalg r-kernlab r-randomforest))
22578 (home-page "https://cran.r-project.org/web/packages/kernelFactory/")
22579 (synopsis "Ensemble of kernel machines")
22581 "Kernel factory is an ensemble method where each base classifier (random
22582 forest) is fit on the kernel matrix of a subset of the training data.")
22583 (license license:gpl2+)))
22585 (define-public r-dummies
22592 (uri (cran-uri "dummies" version))
22595 "01f84crqx17xd6xy55qxlvsj3knm8lhw7jl26p2rh2w3y0nvqlbm"))))
22596 (properties `((upstream-name . "dummies")))
22597 (build-system r-build-system)
22598 (home-page "https://decisionpatterns.com")
22599 (synopsis "Create dummy/indicator variables flexibly and efficiently")
22601 "This package lets you expand factors, characters and other eligible
22602 classes into dummy/indicator variables.")
22603 (license license:gpl2+)))
22605 (define-public r-acrm
22612 (uri (cran-uri "aCRM" version))
22615 "0kzp568hd9c9a9qgniia5s5gv0q5f89xfvvwpzb197gqhs3x092v"))))
22616 (properties `((upstream-name . "aCRM")))
22617 (build-system r-build-system)
22619 (list r-ada r-dummies r-kernelfactory r-randomforest))
22620 (home-page "https://cran.r-project.org/web/packages/aCRM/")
22621 (synopsis "Convenience functions for analytical customer relationship management")
22623 "This package provides convenience functions for data preparation and
22624 modeling often used in @dfn{analytical customer relationship
22625 management} (aCRM).")
22626 (license license:gpl2+)))
22628 (define-public r-tree
22634 (uri (cran-uri "tree" version))
22637 "13jwdxx3na16mly176n01zdkaqn4a8x9fc43rq5xx5vx31drkkr1"))))
22638 (build-system r-build-system)
22639 (home-page "https://cran.r-project.org/web/packages/tree/")
22640 (synopsis "Classification and regression trees")
22641 (description "This package provides procedures to work with classification
22642 and regression trees.")
22643 (license license:gpl2+)))
22645 (define-public r-treeclust
22647 (name "r-treeclust")
22652 (uri (cran-uri "treeClust" version))
22655 "1s7kh6q0bkixsygrip95zf1bi10ihddsa5lq9dfxd68yh8rsby6z"))))
22656 (properties `((upstream-name . "treeClust")))
22657 (build-system r-build-system)
22659 (list r-cluster r-rpart))
22660 (home-page "https://cran.r-project.org/web/packages/treeClust/")
22661 (synopsis "Cluster distances through trees")
22663 "This package provides tools to create a measure of inter-point
22664 dissimilarity useful for clustering mixed data, and, optionally, perform the
22666 (license license:gpl2+)))
22668 (define-public r-acrosstic
22670 (name "r-acrosstic")
22675 (uri (cran-uri "AcrossTic" version))
22678 "03180h79jhjd66ibrnsfp3yyp2jlfysp7cymw46phzj2palghsc0"))))
22679 (properties `((upstream-name . "AcrossTic")))
22680 (build-system r-build-system)
22682 (list r-lpsolve r-treeclust))
22683 (home-page "https://cran.r-project.org/web/packages/AcrossTic/")
22684 (synopsis "Cost-minimal regular spanning subgraph with TreeClust")
22686 "This is a package for constructing minimum-cost regular spanning
22687 subgraph as part of a non-parametric two-sample test for equality of
22689 (license license:gpl2+)))
22691 (define-public r-acrt
22698 (uri (cran-uri "acrt" version))
22701 "0y9ndcq8ffpfrv7w9rikm4zn68jpsj6baqisq9kp2433xrwzdb6s"))))
22702 (properties `((upstream-name . "acrt")))
22703 (build-system r-build-system)
22705 (list r-rcpp r-rcppeigen r-sandwich))
22706 (home-page "https://cran.r-project.org/web/packages/acrt/")
22707 (synopsis "Autocorrelation robust testing")
22709 "This package provides functions for testing affine hypotheses on the
22710 regression coefficient vector in regression models with autocorrelated
22712 (license license:gpl2)))
22714 (define-public r-acs
22721 (uri (cran-uri "acs" version))
22724 "0ajw9rf8l8akcvgqvbxjvryc6wjx74521xyxswz2b0bky3m6kah5"))))
22725 (properties `((upstream-name . "acs")))
22726 (build-system r-build-system)
22728 (list r-httr r-plyr r-rcpp r-stringr r-xml))
22729 (home-page "https://dusp.mit.edu/faculty/ezra-haber-glenn")
22730 (synopsis "Work with data from the US Census")
22732 "This package provides a general toolkit for downloading, managing,
22733 analyzing, and presenting data from the
22734 @url{https://www.census.gov/data/developers/data-sets.html, U.S. Census},
22735 including SF1 (Decennial short-form), SF3 (Decennial long-form), and the
22736 American Community Survey (ACS). Confidence intervals provided with ACS data
22737 are converted to standard errors to be bundled with estimates in complex
22738 @code{acs} objects. The package provides new methods to conduct standard
22739 operations on @code{acs} objects and present/plot data in statistically
22740 appropriate ways.")
22741 (license license:gpl3)))
22743 (define-public r-acss-data
22745 (name "r-acss-data")
22750 (uri (cran-uri "acss.data" version))
22753 "09kl4179ipr8bq19g89xcdi1xxs397zcx5cvgp6viy8gn687ilgv"))))
22754 (properties `((upstream-name . "acss.data")))
22755 (build-system r-build-system)
22756 (home-page "http://complexitycalculator.com/methodology.html")
22757 (synopsis "Data for algorithmic complexity of short strings")
22759 "This is a data only package providing the algorithmic complexity of
22760 short strings, computed using the coding theorem method. For a given set of
22761 symbols in a string, all possible or a large number of random samples of
22762 Turing machines with a given number of states (e.g., 5) and number of symbols
22763 corresponding to the number of symbols in the strings were simulated until
22764 they reached a halting state or failed to end. This package contains data on
22765 4.5 million strings from length 1 to 12 simulated on Turing machines with 2,
22766 4, 5, 6, and 9 symbols. The complexity of the string corresponds to the
22767 distribution of the halting states.")
22768 (license license:gpl2+)))
22770 (define-public r-acss
22777 (uri (cran-uri "acss" version))
22780 "0cqa60544f58l5qd7h6xmsir40b9hqnq6pqgd5hfx2j2l5n7qhmk"))))
22781 (properties `((upstream-name . "acss")))
22782 (build-system r-build-system)
22784 (list r-acss-data r-zoo))
22785 (home-page "http://complexitycalculator.com/methodology.html")
22786 (synopsis "Algorithmic complexity for short strings")
22788 "The main purpose of this package is to provide the algorithmic
22789 complexity for short strings, an approximation of the Kolmogorov Complexity of
22790 a short string using the coding theorem method. While the database containing
22791 the complexity is provided in the data only package @code{acss.data}, this
22792 package provides functions accessing the data such as @code{prob_random}
22793 returning the posterior probability that a given string was produced by a
22794 random process. In addition, two traditional (but problematic) measures of
22795 complexity are also provided: entropy and change complexity.")
22796 (license license:gpl2+)))
22798 (define-public r-acswr
22805 (uri (cran-uri "ACSWR" version))
22808 "195vjrkang5cl7gwsna0aq4p0h4jym9xg9yh94bnf8vq6wf8j83n"))))
22809 (properties `((upstream-name . "ACSWR")))
22810 (build-system r-build-system)
22813 (home-page "https://cran.r-project.org/web/packages/ACSWR/")
22814 (synopsis "Companion package for the book \"A Course in Statistics with R\"")
22816 "This is a companion package for the book \"A Course in Statistics with
22817 R\" (ISBN 978-1-119-15272-9.)")
22818 (license license:gpl2)))
22820 (define-public r-alabama
22823 (version "2022.4-1")
22827 (uri (cran-uri "alabama" version))
22830 "0v6kl6ndm8wvp9xzya3x4gj5kh03qgx13x5vyzn410wsndcjiim8"))))
22831 (properties `((upstream-name . "alabama")))
22832 (build-system r-build-system)
22833 (propagated-inputs (list r-numderiv))
22834 (home-page "https://cran.r-project.org/web/packages/alabama/")
22835 (synopsis "Constrained nonlinear optimization")
22837 "Alabama stands for Augmented Lagrangian Adaptive Barrier Minimization
22838 Algorithm; it is used for optimizing smooth nonlinear objective functions with
22839 constraints. Linear or nonlinear equality and inequality constraints are
22841 (license license:gpl2+)))
22843 (define-public r-gdina
22850 (uri (cran-uri "GDINA" version))
22853 "1slq1npsq8s8aghnrpm6vvc6kxj4svz0kr2x0akblndrcr25wxjr"))))
22854 (properties `((upstream-name . "GDINA")))
22855 (build-system r-build-system)
22868 (home-page "https://github.com/Wenchao-Ma/GDINA")
22869 (synopsis "Generalized DINA model framework")
22871 "This package provides a set of psychometric tools for cognitive
22872 diagnosis modeling based on the generalized deterministic inputs, noisy and
22873 gate (G-DINA) model by de la Torre (2011) @url{doi:10.1007/s11336-011-9207-7}
22874 and its extensions, including the sequential G-DINA model by Ma and de la
22875 Torre (2016) @url{doi:10.1111/bmsp.12070} for polytomous responses, and the
22876 polytomous G-DINA model by Chen and de la Torre
22877 @url{doi:10.1177/0146621613479818} for polytomous attributes. Joint attribute
22878 distribution can be independent, saturated, higher-order, loglinear smoothed
22879 or structured. Q-matrix validation, item and model fit statistics, model
22880 comparison at test and item level and differential item functioning can also
22881 be conducted. A graphical user interface is also provided.")
22882 (license license:gpl3)))
22884 (define-public r-actcd
22891 (uri (cran-uri "ACTCD" version))
22894 "0mzjxxr2zfdidw8ibh6w8mvpkw3q3nvngqi05g9ind26ckvk053p"))))
22895 (properties `((upstream-name . "ACTCD")))
22896 (build-system r-build-system)
22898 (list r-gdina r-r-methodss3))
22901 (home-page "https://cran.r-project.org/web/packages/ACTCD/")
22902 (synopsis "Asymptotic classification theory for cognitive diagnosis")
22904 "This is a package supporting cluster analysis for cognitive diagnosis
22905 based on the Asymptotic Classification Theory (Chiu, Douglas & Li, 2009;
22906 @url{doi:10.1007/s11336-009-9125-0}). Given the sample statistic of
22907 sum-scores, cluster analysis techniques can be used to classify examinees into
22908 latent classes based on their attribute patterns. In addition to the
22909 algorithms used to classify data, three labeling approaches are proposed to
22910 label clusters so that examinees' attribute profiles can be obtained.")
22911 (license license:gpl2+)))
22913 (define-public r-ineq
22920 (uri (cran-uri "ineq" version))
22923 "09fsxyrh0j7mwmb5hkhmrzgcy7kf85jxkh7zlwpgqgcsyl1n91z0"))))
22924 (properties `((upstream-name . "ineq")))
22925 (build-system r-build-system)
22926 (home-page "https://cran.r-project.org/web/packages/ineq/")
22927 (synopsis "Measuring inequality, concentration, and poverty")
22929 "This package provides tools for measuring inequality, concentration, and
22930 poverty measures. It provides both empirical and theoretical Lorenz curves.")
22931 ;; Either of these two versions.
22932 (license (list license:gpl2 license:gpl3))))
22934 (define-public r-actfrag
22941 (uri (cran-uri "ActFrag" version))
22944 "08r3gwjz4fkyy85dxqix0ffm5xyq45032qv3snnzxnlqxslxbqn1"))))
22945 (properties `((upstream-name . "ActFrag")))
22946 (build-system r-build-system)
22948 (list r-accelerometry r-dplyr r-ineq r-survival r-tidyr))
22949 (home-page "https://github.com/junruidi/ActFrag")
22950 (synopsis "Activity fragmentation metrics extraction")
22952 "This package provides functions to extract commonly used fragmentation
22953 metrics to quantify time accumulation strategies based on minute level
22954 actigraphy-measured activity counts data.")
22955 (license license:gpl3)))
22957 (define-public r-ash
22964 (uri (cran-uri "ash" version))
22967 "1ay2a2agdmiz7zzvn26mli0x0iwk09g5pp4yy1r23knhkp1pn2lb"))))
22968 (properties `((upstream-name . "ash")))
22969 (build-system r-build-system)
22970 (native-inputs (list gfortran))
22971 (home-page "https://cran.r-project.org/web/packages/ash/")
22972 (synopsis "David Scott's ASH routines")
22974 "This package provides David Scott's ASH routines ported from S-PLUS to
22976 (license license:gpl2+)))
22978 (define-public r-hdrcde
22985 (uri (cran-uri "hdrcde" version))
22988 "16qlk44cjvn2s0vzaf915df65ksdx20dbxhy7fpdqins46hccha3"))))
22989 (properties `((upstream-name . "hdrcde")))
22990 (build-system r-build-system)
22998 (native-inputs (list gfortran))
22999 (home-page "http://pkg.robjhyndman.com/hdrcde")
23000 (synopsis "Highest density regions and conditional density estimation")
23002 "This is a package for the computation of highest density regions in one
23003 and two dimensions, kernel estimation of univariate density functions
23004 conditional on one covariate, and multimodal regression.")
23005 (license license:gpl3)))
23007 (define-public r-rainbow
23014 (uri (cran-uri "rainbow" version))
23017 "11vfcck17d2xjc049ci5i8l1nqv345anmd110gdz7654i1pj9lb3"))))
23018 (properties `((upstream-name . "rainbow")))
23019 (build-system r-build-system)
23027 (home-page "https://cran.r-project.org/web/packages/rainbow/")
23028 (synopsis "Bagplots, boxplots and rainbow plots for functional data")
23030 "This is a package for visualizing functional data and identifying
23031 functional outliers with bagplots, boxplots and rainbow plots.")
23032 (license license:gpl3)))
23034 (define-public r-fds
23041 (uri (cran-uri "fds" version))
23044 "1284vncixrzrz9x6b52gslrbrbia07sd0xac7nwdqhp5f5v5wfi0"))))
23045 (properties `((upstream-name . "fds")))
23046 (build-system r-build-system)
23048 (list r-rainbow r-rcurl))
23049 (home-page "https://cran.r-project.org/web/packages/fds/")
23050 (synopsis "Functional data sets")
23051 (description "This package contains a list of functional time series,
23052 sliced functional time series, and functional data sets. Functional time
23053 series is a special type of functional data observed over time. Sliced
23054 functional time series is a special type of functional time series with a time
23055 variable observed over time.")
23056 (license license:gpl2+)))
23058 (define-public r-fda
23065 (uri (cran-uri "fda" version))
23068 "1lvp4i4hqz650k27sa5flbdlkalihc79xy9128hfhr16h6wi8n10"))))
23069 (properties `((upstream-name . "fda")))
23070 (build-system r-build-system)
23072 (list r-desolve r-fds))
23075 (home-page "https://www.functionaldata.org")
23076 (synopsis "Functional data analysis")
23078 "These functions were developed to support functional data analysis as
23079 described in Ramsay, J. O. and Silverman, B. W. (2005) Functional Data
23080 Analysis. The package includes data sets and script files working many
23082 (license license:gpl2+)))
23084 (define-public r-actigraphy
23086 (name "r-actigraphy")
23091 (uri (cran-uri "Actigraphy" version))
23094 "0bpmvszzv5fm72nar3wgnmfl5am7znqfajmlbv38ihkbi7jbwk20"))))
23095 (properties `((upstream-name . "Actigraphy")))
23096 (build-system r-build-system)
23099 (home-page "https://cran.r-project.org/web/packages/Actigraphy/")
23100 (synopsis "Actigraphy data analysis")
23102 "This package provides tools for functional linear modeling and analysis
23103 of actigraphy data.")
23104 (license license:asl2.0)))
23106 (define-public r-activedriver
23108 (name "r-activedriver")
23113 (uri (cran-uri "ActiveDriver" version))
23116 "10c7ga48fwvpd5mc4dqiyw4kc2l0iz5qn4hg7xk15r1qmm5rsipa"))))
23117 (properties `((upstream-name . "ActiveDriver")))
23118 (build-system r-build-system)
23121 (home-page "https://cran.r-project.org/web/packages/ActiveDriver/")
23122 (synopsis "Tools for finding cancer driver proteins")
23124 "This package provides a mutation analysis tool that discovers cancer
23125 driver genes with frequent mutations in protein signalling sites such as
23126 post-translational modifications (phosphorylation, ubiquitination, etc). The
23127 Poisson generalized linear regression model identifies genes where cancer
23128 mutations in signalling sites are more frequent than expected from the
23129 sequence of the entire gene. Integration of mutations with signalling
23130 information helps find new driver genes and propose candidate mechanisms to
23132 (license license:gpl2+)))
23134 (define-public r-activitycounts
23136 (name "r-activitycounts")
23141 (uri (cran-uri "activityCounts" version))
23144 "0zgxr2sk3a8kmygfxx1p5hnrfwdkxx7php6jlrhm8wv6052ck8jz"))))
23146 `((upstream-name . "activityCounts")))
23147 (build-system r-build-system)
23149 (list r-lubridate r-magrittr r-seewave r-signal r-tibble))
23150 (home-page "https://github.com/walkabillylab/activityCounts")
23151 (synopsis "Generate ActiLife counts")
23153 "ActiLife generates activity counts from data collected by Actigraph
23154 accelerometers. Actigraph is one of the most common research-grade
23155 accelerometers. There is considerable research validating and developing
23156 algorithms for human activity using ActiLife counts. Unfortunately, ActiLife
23157 counts are proprietary and difficult to implement if researchers use different
23158 accelerometer brands. The code creates ActiLife counts from raw acceleration
23159 data for different accelerometer brands.")
23160 (license license:gpl3)))
23162 (define-public r-activityindex
23164 (name "r-activityindex")
23169 (uri (cran-uri "ActivityIndex" version))
23172 "1zj2b6x31a1kxl80rarmkrlm7ack4154mrkbqs3fpi48zpmjbgd5"))))
23173 (properties `((upstream-name . "ActivityIndex")))
23174 (build-system r-build-system)
23176 (list r-data-table r-matrixstats r-r-utils))
23179 (home-page "https://cran.r-project.org/web/packages/ActivityIndex/")
23180 (synopsis "Activity Index calculation using raw accelerometry data")
23182 "This is a package to read raw accelerometry from GT3X+ accelerometry
23183 data and plain table data to calculate the Activity Index from Bai et
23184 al. (2016) @url{doi:10.1371/journal.pone.0160644}.")
23185 (license license:gpl3)))
23187 (define-public r-activpal
23189 (name "r-activpal")
23194 (uri (cran-uri "activPAL" version))
23197 "1h6hp5z89ji73gdzxy1dgbfwjysiy5lvcqh90xagpb7sa7ahs3na"))))
23198 (properties `((upstream-name . "activPAL")))
23199 (build-system r-build-system)
23207 (home-page "https://cran.r-project.org/web/packages/activPAL")
23208 (synopsis "Processing and chart generation from activPAL events files")
23210 "This package contains functions to generate pre-defined summary
23211 statistics from activPAL events files. The package also contains functions to
23212 produce informative graphics that visualize physical activity behaviour and
23213 trends. This includes generating graphs that align physical activity
23214 behaviour with additional time based observations described by other data
23215 sets, such as sleep diaries and continuous glucose monitoring data.")
23216 (license license:gpl3)))
23218 (define-public r-activpalprocessing
23220 (name "r-activpalprocessing")
23225 (uri (cran-uri "activpalProcessing" version))
23228 "1y0bjx2qx53iy930y9iww4q1yzjj8y16cwgixk1mq3w4g1f116d1"))))
23230 `((upstream-name . "activpalProcessing")))
23231 (build-system r-build-system)
23234 (home-page "https://cran.r-project.org/web/packages/activpalProcessing/")
23235 (synopsis "Process activPAL events files")
23237 "This package performs estimation of physical activity and sedentary
23238 behavior variables from activPAL events files.")
23239 ;; Either version of the GPL.
23240 (license (list license:gpl2 license:gpl3))))
23242 (define-public r-actogrammr
23244 (name "r-actogrammr")
23249 (uri (cran-uri "actogrammr" version))
23252 "1jzvarmd41yqlrkagzlc8m19n5mn0w0b36fy50lyvgrfsafjfbqa"))))
23253 (properties `((upstream-name . "actogrammr")))
23254 (build-system r-build-system)
23256 (list r-dplyr r-ggplot2 r-lubridate r-readr r-tidyr))
23257 (home-page "https://cran.r-project.org/web/packages/actogrammr/")
23258 (synopsis "Read in activity data and plot actograms")
23260 "Read in activity measurements from standard file formats used by
23261 circadian rhythm researchers, currently only ClockLab format, and process and
23262 plot the data. The central type of plot is the actogram, as first described
23263 in \"Activity and distribution of certain wild mice in relation to biotic
23264 communities\" by MS Johnson (1926) @url{doi:10.2307/1373575}.")
23265 (license license:gpl3)))
23267 (define-public r-expint
23274 (uri (cran-uri "expint" version))
23277 "01d0a7pc4qx7044a0cymnv5ld88r90vdvlqjbnzg9qlfbizdgyvw"))))
23278 (properties `((upstream-name . "expint")))
23279 (build-system r-build-system)
23280 (home-page "https://gitlab.com/vigou3/expint")
23281 (synopsis "Exponential integral and incomplete Gamma function")
23283 "This package provides the exponential integrals @code{E_1(x)},
23284 @code{E_2(x)}, @code{E_n(x)} and @code{Ei(x)}, and the incomplete gamma
23285 function @code{G(a, x)} defined for negative values of its first argument.
23286 The package also gives easy access to the underlying C routines through an
23287 API; see the package vignette for details.")
23288 (license license:gpl2+)))
23290 (define-public r-actuar
23297 (uri (cran-uri "actuar" version))
23300 "0dhpaivyga0jwvw1csagbx74biy9jfkw4a8sa871579njxl1x7p1"))))
23301 (properties `((upstream-name . "actuar")))
23302 (build-system r-build-system)
23303 (propagated-inputs (list r-expint))
23304 (home-page "https://gitlab.com/vigou3/actuar")
23305 (synopsis "Actuarial functions and heavy tailed distributions")
23307 "This package provides functions and data sets for actuarial science:
23308 modeling of loss distributions; risk theory and ruin theory; simulation of
23309 compound models, discrete mixtures and compound hierarchical models;
23310 credibility theory. It boasts support for many additional probability
23311 distributions to model insurance loss amounts and loss frequency: 19
23312 continuous heavy tailed distributions; the Poisson-inverse Gaussian discrete
23313 distribution; zero-truncated and zero-modified extensions of the standard
23314 discrete distributions. It also supports phase-type distributions commonly
23315 used to compute ruin probabilities.")
23316 (license license:gpl2+)))
23318 (define-public r-bmp
23325 (uri (cran-uri "bmp" version))
23328 "0jd67r11bn98hjwgyr6gas423787xy7ji2hq7ay80blkkcj91xxx"))))
23329 (properties `((upstream-name . "bmp")))
23330 (build-system r-build-system)
23331 (home-page "https://cran.r-project.org/web/packages/bmp/")
23332 (synopsis "Read Bitmap (BMP) images")
23334 "This package provides pure R tools to read BMP format images. It is
23335 currently limited to 8 bit greyscale images and 24, 32 bit (A)RGB images.")
23336 (license license:gpl2+)))
23338 (define-public r-readbitmap
23340 (name "r-readbitmap")
23345 (uri (cran-uri "readbitmap" version))
23348 "14825906l326w59g6apy00j55jg3h5kx2r6s031f4gdkbrc7szbk"))))
23349 (properties `((upstream-name . "readbitmap")))
23350 (build-system r-build-system)
23352 (list libjpeg-turbo libpng))
23354 (list r-bmp r-jpeg r-png r-tiff))
23355 (home-page "https://github.com/jefferis/readbitmap")
23356 (synopsis "Unified interface to read bitmap images (BMP, JPEG, PNG, TIFF)")
23358 "This package provides tools to identify and read BMP, JPEG, PNG, and
23359 TIFF format bitmap images. Identification defaults to the use of the magic
23360 number embedded in the file rather than the file extension.")
23361 (license license:gpl2+)))
23363 (define-public r-imager
23366 (version "0.42.13")
23370 (uri (cran-uri "imager" version))
23373 "0zygnmxwbbmj5i2l2affzdz90xvsa7b5pbkzkhjbm40is69rh2nr"))))
23374 (properties `((upstream-name . "imager")))
23375 (build-system r-build-system)
23377 (list fftw libtiff libx11 zlib))
23389 (list pkg-config r-knitr))
23390 (home-page "https://dahtah.github.io/imager/")
23391 (synopsis "Image processing library")
23393 "This is a package for fast image processing for images in up to 4
23394 dimensions (two spatial dimensions, one time/depth dimension, one color
23395 dimension). It provides most traditional image processing tools (filtering,
23396 morphology, transformations, etc.) as well as various functions for easily
23397 analyzing image data using R. The package wraps @url{http://cimg.eu, CImg}, a
23398 simple, modern C++ library for image processing.")
23399 (license license:lgpl3)))
23401 (define-public r-acuityview
23403 (name "r-acuityview")
23408 (uri (cran-uri "AcuityView" version))
23411 "0f0iclmnwdc8ixiiai4svk4x1g3pjy7dhm3cm58fv6ckx12d3d2l"))))
23412 (properties `((upstream-name . "AcuityView")))
23413 (build-system r-build-system)
23415 (list r-fftwtools r-imager r-plotrix))
23416 (home-page "https://cran.r-project.org/web/packages/AcuityView/")
23417 (synopsis "Display scenes as seen by an animal with less acute vision")
23419 "This package provides a simple method for representing a visual scene as
23420 it may be seen by an animal with less acute vision.")
23421 (license license:gpl2+)))
23423 (define-public r-caret
23430 (uri (cran-uri "caret" version))
23433 "048mp325ndfl83a8p4dkd1b6zh5bws4gg9kxka5ss8qsj8m4m08x"))))
23434 (build-system r-build-system)
23449 (home-page "https://github.com/topepo/caret")
23450 (synopsis "Classification and regression training")
23452 "This package provides miscellaneous functions for training and plotting
23453 classification and regression models.")
23454 (license license:gpl2+)))
23456 (define-public r-adabag
23463 (uri (cran-uri "adabag" version))
23466 "109wrl1pwvmyv2l909hrvk7dg4aa9pv449mvdycp50zwrsw9w0a7"))))
23467 (properties `((upstream-name . "adabag")))
23468 (build-system r-build-system)
23470 (list r-caret r-doparallel r-foreach r-rpart))
23471 (home-page "https://cran.r-project.org/web/packages/adabag/")
23472 (synopsis "Multiclass AdaBoost.M1, SAMME and Bagging")
23474 "This package implements Freund and Schapire's Adaboost.M1 algorithm and
23475 Breiman's Bagging algorithm using classification trees as individual
23476 classifiers. Once these classifiers have been trained, they can be used to
23477 predict on new data. Also, cross validation estimation of the error can be
23479 (license license:gpl2+)))
23481 (define-public r-adagio
23488 (uri (cran-uri "adagio" version))
23491 "0ihv05402iq003m0338f85pnqnlnrmx0pf1mg8cz9sgi5h98mbnl"))))
23492 (properties `((upstream-name . "adagio")))
23493 (build-system r-build-system)
23496 (home-page "https://cran.r-project.org/web/packages/adagio/")
23497 (synopsis "Discrete and global optimization routines")
23499 "This package provides methods and algorithms for discrete optimization,
23500 e.g. knapsack and subset sum procedures, derivative-free Nelder-Mead and
23501 Hooke-Jeeves minimization, and some (evolutionary) global optimization
23503 (license license:gpl3+)))
23505 (define-public r-univoutl
23507 (name "r-univoutl")
23512 (uri (cran-uri "univOutl" version))
23515 "1hhpxrpmp2wbrynx9xjndnp2sccirgky2x6ksd6yk6phmk0rbzjp"))))
23516 (properties `((upstream-name . "univOutl")))
23517 (build-system r-build-system)
23519 (list r-hmisc r-robustbase))
23520 (home-page "https://github.com/marcellodo/univOutl")
23521 (synopsis "Detection of univariate outliers")
23523 "This package provides well-known outlier detection techniques in the
23524 univariate case. Methods to deal with skewed distribution are included too.
23525 The Hidiroglou-Berthelot (1986) method to search for outliers in ratios of
23526 historical data is implemented as well. When available, survey weights can be
23527 used in outliers detection.")
23528 (license license:gpl2+)))
23530 (define-public r-tolerance
23532 (name "r-tolerance")
23537 (uri (cran-uri "tolerance" version))
23540 "001snzr2ipag3zprynydlbi9prkjzrllc054qh7m0qwkb3r19jjd"))))
23541 (properties `((upstream-name . "tolerance")))
23542 (build-system r-build-system)
23544 (list r-mass r-rgl))
23545 (home-page "https://cran.r-project.org/web/packages/tolerance/")
23546 (synopsis "Statistical tolerance intervals and regions")
23548 "This package provides functions for estimating tolerance
23549 limits (intervals) for various univariate distributions (binomial, Cauchy,
23550 discrete Pareto, exponential, two-parameter exponential, extreme value,
23551 hypergeometric, Laplace, logistic, negative binomial, negative hypergeometric,
23552 normal, Pareto, Poisson-Lindley, Poisson, uniform, and Zipf-Mandelbrot),
23553 Bayesian normal tolerance limits, multivariate normal tolerance regions,
23554 nonparametric tolerance intervals, tolerance bands for regression
23555 settings (linear regression, nonlinear regression, nonparametric regression,
23556 and multivariate regression), and analysis of variance tolerance intervals.
23557 Visualizations are also available for most of these settings.")
23558 (license license:gpl2+)))
23560 ;; Keep this in sync with the liblantern package.
23561 (define-public r-torch
23568 (uri (cran-uri "torch" version))
23570 (base32 "163pvl3gyz7l2fmqhgg4k6pw4dmvfir71yp9l5ra2k4zc32lz166"))))
23571 (properties `((upstream-name . "torch")))
23572 (build-system r-build-system)
23576 #~(modify-phases %standard-phases
23577 (add-after 'install 'link-libraries
23578 (lambda* (#:key inputs #:allow-other-keys)
23579 (let ((deps (string-append #$output "/site-library/torch/deps")))
23583 inputs "/lib/python3.9/site-packages/torch/lib/libtorch.so")
23584 (string-append deps "/libtorch.so"))
23587 inputs "/lib/liblantern.so")
23588 (string-append deps "/liblantern.so"))))))))
23590 (list python-pytorch-for-r-torch
23603 (native-inputs (list r-knitr))
23604 (home-page "https://torch.mlverse.org/docs")
23605 (synopsis "Tensors and neural networks with GPU acceleration")
23607 "This package provides functionality to define and train neural networks
23608 similar to PyTorch but written entirely in R using the libtorch library. It
23609 also supports low-level tensor operations and GPU acceleration.")
23610 (license license:expat)))
23612 (define-public r-additivitytests
23614 (name "r-additivitytests")
23619 (uri (cran-uri "additivityTests" version))
23622 "048ds90wqjdjy1nyhna3m06asdklbh8sx1n556kss2j1r1pma1sw"))))
23624 `((upstream-name . "additivityTests")))
23625 (build-system r-build-system)
23626 (home-page "https://github.com/simecek/additivityTests")
23627 (synopsis "Additivity tests in the two way Anova with single sub-class numbers")
23629 "This package provides an implementation of the Tukey, Mandel,
23630 Johnson-Graybill, LBI, Tusell and modified Tukey non-additivity tests.")
23631 (license license:gpl3)))
23633 (define-public r-flexclust
23635 (name "r-flexclust")
23640 (uri (cran-uri "flexclust" version))
23643 "13akk3w6a76jpws5v9108c3hdmb8i6gm0sc06lr2hqly0pgpfyfn"))))
23644 (properties `((upstream-name . "flexclust")))
23645 (build-system r-build-system)
23647 (list r-class r-lattice r-modeltools))
23648 (home-page "https://cran.r-project.org/web/packages/flexclust/")
23649 (synopsis "Flexible cluster algorithms")
23651 "The main function @code{kcca} implements a general framework for
23652 k-centroids cluster analysis supporting arbitrary distance measures and
23653 centroid computation. Further cluster methods include hard competitive
23654 learning, neural gas, and QT clustering. There are numerous visualization
23655 methods for cluster results (neighborhood graphs, convex cluster hulls,
23656 barcharts of centroids, ...), and bootstrap methods for the analysis of
23657 cluster stability.")
23658 (license license:gpl2)))
23660 (define-public r-biclust
23667 (uri (cran-uri "biclust" version))
23670 "0lgyc2f04dhr65cwga78pradxsdzgjrpp8vphchqn60ab1z95dlp"))))
23671 (properties `((upstream-name . "biclust")))
23672 (build-system r-build-system)
23674 (list r-additivitytests
23681 (home-page "https://cran.r-project.org/web/packages/biclust/")
23682 (synopsis "BiCluster algorithms")
23684 "The main function @code{biclust()} provides several algorithms to find
23685 biclusters in two-dimensional data, spectral, plaid model, xmotifs, and bimax.
23686 In addition, the package provides methods for data
23687 preprocessing (normalization and discretization), visualization, and
23688 validation of bicluster solutions.")
23689 (license license:gpl3)))
23691 (define-public r-icge
23698 (uri (cran-uri "ICGE" version))
23701 "0w6hbi3h98q6gsxqbb43p95v6xykgrasxcjivwm8hw9fly4avxyi"))))
23702 (properties `((upstream-name . "ICGE")))
23703 (build-system r-build-system)
23705 (list r-cluster r-fastcluster r-mass))
23706 (home-page "https://cran.r-project.org/web/packages/ICGE/")
23707 (synopsis "Cluster estimation and identification of atypical units")
23709 "ICGE is a package that helps to estimate the number of real clusters in
23710 data as well as to identify atypical units. The underlying methods are based
23711 on distances rather than on unit x variables.")
23712 (license license:gpl2+)))
23714 (define-public r-depth
23717 (version "2.1-1.1")
23721 (uri (cran-uri "depth" version))
23724 "0szy0027nh4ps1z919i740i50app5q7cfyg1fj7pdyl45nbl8k6m"))))
23725 (properties `((upstream-name . "depth")))
23726 (build-system r-build-system)
23728 (list r-abind r-circular r-rgl))
23731 (home-page "https://cran.r-project.org/web/packages/depth/")
23732 (synopsis "Nonparametric depth functions for multivariate analysis")
23734 "This package provides tools for depth functions methodology applied to
23735 multivariate analysis. Besides allowing calculation of depth values and
23736 depth-based location estimators, the package includes functions or drawing
23737 contour plots and perspective plots of depth functions. Euclidean and
23738 spherical depths are supported.")
23739 (license license:gpl2)))
23741 (define-public r-archetypes
23743 (name "r-archetypes")
23744 (version "2.2-0.1")
23748 (uri (cran-uri "archetypes" version))
23751 "0ibxsr173ib77gjhid91m85s8gjii4mi2w3d52q5301igv20p7r0"))))
23752 (properties `((upstream-name . "archetypes")))
23753 (build-system r-build-system)
23755 (list r-modeltools r-nnls))
23756 (home-page "https://cran.r-project.org/web/packages/archetypes")
23757 (synopsis "Archetypal analysis")
23759 "The main function @code{archetypes} implements a framework for
23760 archetypal analysis supporting arbitrary problem solving mechanisms for the
23761 different conceptual parts of the algorithm.")
23762 (license license:gpl2+)))
23764 (define-public r-shapes
23771 (uri (cran-uri "shapes" version))
23774 "1p9fr95zk3q2v277c5ksb0nh26mcpzwjzjb2lmag51z6hck8cb66"))))
23775 (properties `((upstream-name . "shapes")))
23776 (build-system r-build-system)
23778 (list r-mass r-minpack-lm r-rgl r-scatterplot3d))
23779 (home-page "http://www.maths.nottingham.ac.uk/~ild/shapes")
23780 (synopsis "Statistical shape analysis")
23782 "This package provides routines for the statistical analysis of landmark
23783 shapes, including Procrustes analysis, graphical displays, principal
23784 components analysis, permutation and bootstrap tests, thin-plate spline
23785 transformation grids and comparing covariance matrices. See Dryden, I.L. and
23786 Mardia, K.V. (2016). Statistical shape analysis, with Applications in R (2nd
23787 Edition), John Wiley and Sons.")
23788 (license license:gpl2)))
23790 (define-public r-anthropometry
23792 (name "r-anthropometry")
23797 (uri (cran-uri "Anthropometry" version))
23800 "0vxjlzxv16bygw8n57f25msq5bd1dydg41my92ximah0nzzvbg41"))))
23801 (properties `((upstream-name . "Anthropometry")))
23802 (build-system r-build-system)
23815 (home-page "https://cran.r-project.org/web/packages/Anthropometry/")
23816 (synopsis "Statistical methods for anthropometric data")
23818 "This package provides statistical methods especially developed to
23819 analyze anthropometric data. These methods are aimed at providing effective
23820 solutions to some commons problems related to Ergonomics and Anthropometry.
23821 They are based on clustering, the statistical concept of data depth,
23822 statistical shape analysis and archetypal analysis.")
23823 (license license:gpl2+)))
23825 (define-public r-anndata
23828 (version "0.7.5.3")
23832 (uri (cran-uri "anndata" version))
23834 (base32 "115v7gdilayd18hd519vzkixp2s6rvvrd1inc1i6amn7d0spy8r1"))))
23835 (properties `((upstream-name . "anndata")))
23836 (build-system r-build-system)
23837 (propagated-inputs (list r-assertthat r-matrix r-r6 r-reticulate))
23838 (native-inputs (list r-knitr))
23839 (home-page "https://anndata.dynverse.org")
23840 (synopsis "Anndata for R")
23842 "This package provides a reticulate wrapper for the Python package
23843 @code{anndata}. It provides a scalable way of keeping track of data and
23844 learned annotations. It is used to read from and write to the h5ad file
23846 (license license:expat)))
23848 (define-public r-adamethods
23850 (name "r-adamethods")
23855 (uri (cran-uri "adamethods" version))
23858 "150awbd3skb1mqca18bqjykhyycqw8crviw66s6qrcnmcsbk77pj"))))
23859 (properties `((upstream-name . "adamethods")))
23860 (build-system r-build-system)
23862 (list r-anthropometry
23869 (home-page "https://cran.r-project.org/web/packages/adamethods/")
23870 (synopsis "Archetypoid algorithms and anomaly detection")
23872 "This package is a collection of several algorithms to obtain
23873 archetypoids with small and large databases and with both classical
23874 multivariate data and functional data (univariate and multivariate). Some of
23875 these algorithms also detect anomalies (outliers).")
23876 (license license:gpl2+)))
23878 (define-public r-idpmisc
23885 (uri (cran-uri "IDPmisc" version))
23888 "0zy6mxqa8arq0vvhsdcifzm3085c23rnwa1n36fhircph1xwvfdw"))))
23889 (properties `((upstream-name . "IDPmisc")))
23890 (build-system r-build-system)
23893 (home-page "https://cran.r-project.org/web/packages/IDPmisc/")
23894 (synopsis "Functions for data analyses and visualization")
23896 "This package provides different high-level graphics functions for
23897 displaying large datasets, displaying circular data in a very flexible way,
23898 finding local maxima, brewing color ramps, drawing nice arrows, zooming
23899 2D-plots, creating figures with differently colored margin and plot region.
23900 In addition, the package contains auxiliary functions for data manipulation
23901 like omitting observations with irregular values or selecting data by logical
23902 vectors, which include NAs. Other functions are especially useful in
23903 spectroscopy and analyses of environmental data: robust baseline fitting,
23904 finding peaks in spectra, converting humidity measures.")
23905 (license license:gpl3+)))
23907 (define-public r-qqman
23914 (uri (cran-uri "qqman" version))
23917 "1a6qp5wv9bvwjchfw8x4jh48hkynlnfr21a8vqgnswldvwbq7njq"))))
23918 (properties `((upstream-name . "qqman")))
23919 (build-system r-build-system)
23921 (list r-calibrate))
23924 (home-page "https://cran.r-project.org/web/packages/qqman/")
23925 (synopsis "Q-Q and Manhattan plots for GWAS data")
23927 "This package allows you to create Q-Q and Manhattan plots for GWAS data
23928 from PLINK results.")
23929 (license license:gpl3)))
23931 (define-public r-gghighlight
23933 (name "r-gghighlight")
23938 (uri (cran-uri "gghighlight" version))
23940 (base32 "0bxgn4srxz1qhawqa8ck57p8hg5ikwfa9ll03zmnn8fb19akwm2v"))))
23941 (properties `((upstream-name . "gghighlight")))
23942 (build-system r-build-system)
23944 (list r-dplyr r-ggplot2 r-ggrepel r-lifecycle r-purrr r-rlang r-tibble))
23945 (native-inputs (list r-knitr))
23946 (home-page "https://github.com/yutannihilation/gghighlight/")
23947 (synopsis "Highlight lines and points in ggplot2")
23948 (description "Suppose we have data that has so many series that it is hard
23949 to identify them by their colors as the differences are so subtle. With
23950 gghighlight we can highlight those lines that match certain criteria. The
23951 result is a usual @code{ggplot} object, so it is fully customizable and can be
23952 used with custom themes and facets.")
23953 (license license:expat)))
23955 (define-public r-ggplot-multistats
23957 (name "r-ggplot-multistats")
23962 (uri (cran-uri "ggplot.multistats" version))
23965 "1afzfa86vc484bcwpg7m1ky03jpax584rigzgai8w06pifkmz0il"))))
23967 `((upstream-name . "ggplot.multistats")))
23968 (build-system r-build-system)
23970 (list r-ggplot2 r-hexbin r-rlang r-scales))
23971 (home-page "https://github.com/flying-sheep/ggplot.multistats")
23972 (synopsis "Multiple summary statistics for binned stats/geometries")
23974 "This package provides the ggplot binning layer @code{stat_summaries_hex()},
23975 which functions similar to its singular form, but allows the use of multiple
23976 statistics per bin. Those statistics can be mapped to multiple bin
23978 (license license:gpl3)))
23980 (define-public r-knn-covertree
23982 (name "r-knn-covertree")
23987 (uri (cran-uri "knn.covertree" version))
23990 "0msfcmwydws7q7m5jdb0dxab0nkbl7mq5llg6v3r4qrnlvrdggvz"))))
23991 (properties `((upstream-name . "knn.covertree")))
23992 (build-system r-build-system)
23994 (list r-matrix r-rcpp r-rcppeigen))
23995 (home-page "https://github.com/flying-sheep/knn.covertree")
23996 (synopsis "Accurate kNN Implementation with multiple distance measures")
23998 "Similarly to the FNN package, this package allows calculation of the k
23999 nearest neighbors (kNN) of a data matrix. The implementation is based on
24000 cover trees introduced by Alina Beygelzimer, Sham Kakade, and John
24001 Langford (2006) @url{doi:10.1145/1143844.1143857}.")
24002 (license license:agpl3+)))
24004 (define-public r-poibin
24011 (uri (cran-uri "poibin" version))
24014 "1sxryvwwz6ldsnkzdy56p8c895s5yvpcai9ndyjv1x5q3l05wf9v"))))
24015 (properties `((upstream-name . "poibin")))
24016 (build-system r-build-system)
24017 (home-page "https://cran.r-project.org/web/packages/poibin/")
24018 (synopsis "Poisson binomial distribution")
24020 "This package provides an implementation of both the exact and
24021 approximation methods for computing the @dfn{cumulative distribution
24022 function} (CDF) of the Poisson binomial distribution. It also provides the
24023 @dfn{probability mass function} (PMF), quantile function, and random number
24024 generation for the Poisson binomial distribution.")
24025 (license license:gpl2)))
24027 (define-public r-diagram
24034 (uri (cran-uri "diagram" version))
24037 "1r3lyl0h7mk9cfg8smr3jydfkjdawaphnxibkxfjqa7029vkxh79"))))
24038 (properties `((upstream-name . "diagram")))
24039 (build-system r-build-system)
24042 (home-page "https://cran.r-project.org/web/packages/diagram/")
24043 (synopsis "Visualize simple graphs (networks) and plot flow diagrams")
24045 "This package provides tools to visualize simple graphs (networks) based
24046 on a transition matrix, utilities to plot flow diagrams, visualizing webs,
24047 electrical networks, etc. It also includes supporting material for the book
24048 \"A practical guide to ecological modelling - using R as a simulation
24049 platform\" by Karline Soetaert and Peter M.J. Herman (2009) and the book
24050 \"Solving Differential Equations in R\" by Karline Soetaert, Jeff Cash and
24051 Francesca Mazzia (2012).")
24052 (license license:gpl2+)))
24054 (define-public r-lim
24061 (uri (cran-uri "LIM" version))
24064 "0d9bgyd0mnag8wds993dsvlbpkhyakydlzwc3nghxzv2n8504hjj"))))
24065 (properties `((upstream-name . "LIM")))
24066 (build-system r-build-system)
24068 (list r-diagram r-limsolve))
24069 (home-page "https://cran.r-project.org/web/packages/LIM/")
24070 (synopsis "Linear inverse model examples and solution methods")
24072 "This package provides functions that read and solve linear inverse
24073 problems (food web problems, linear programming problems).")
24074 (license license:gpl2+)))
24076 (define-public r-shinycssloaders
24078 (name "r-shinycssloaders")
24083 (uri (cran-uri "shinycssloaders" version))
24086 "0r3xm273lhdhzbs2mkgw1m2kwb7z1dh1pzya8yxy5vacda1l2ikl"))))
24088 `((upstream-name . "shinycssloaders")))
24089 (build-system r-build-system)
24091 (list r-digest r-glue r-shiny))
24092 (home-page "https://github.com/andrewsali/shinycssloaders")
24093 (synopsis "Add CSS loading animations to Shiny outputs")
24095 "This package provides tools to create a lightweight Shiny wrapper for
24096 the css-loaders created by Luke Hass
24097 @url{https://github.com/lukehaas/css-loaders}. Wrapping a Shiny output will
24098 automatically show a loader when the output is (re)calculating.")
24099 (license license:gpl3)))
24101 (define-public r-rsvg
24108 (uri (cran-uri "rsvg" version))
24111 "096w4d1gvfc65d4jg7ykp23k9f7cf7f8zvzfhvhd7qkfsbjpxqkj"))))
24112 (properties `((upstream-name . "rsvg")))
24113 (build-system r-build-system)
24115 (list librsvg zlib))
24117 (list pkg-config r-knitr))
24118 (home-page "https://github.com/jeroen/rsvg#readme")
24119 (synopsis "Render SVG images into PDF, PNG, PostScript, or Bitmap arrays")
24121 "This package allows you to render vector-based SVG images into
24122 high-quality custom-size bitmap arrays using the librsvg2 library. The
24123 resulting bitmap can be written to e.g. PNG, JPEG or WEBP format. In
24124 addition, the package can convert images directly to various formats such as
24125 PDF or PostScript.")
24126 (license license:expat)))
24128 (define-public r-influencer
24130 (name "r-influencer")
24131 (version "0.1.0.1")
24135 (uri (cran-uri "influenceR" version))
24138 "0rj7rm236vn3v8302nwl12s0kvpv6xpdbm3q3gxk7vgwfl8nzi33"))))
24139 (properties `((upstream-name . "influenceR")))
24140 (build-system r-build-system)
24142 (list r-igraph r-matrix))
24143 (home-page "https://github.com/rcc-uchicago/influenceR")
24144 (synopsis "Tools to quantify structural importance of nodes in a network")
24146 "This package provides functionality to compute various node centrality
24147 measures on networks. Included are functions to compute betweenness
24148 centrality (by utilizing Madduri and Bader's SNAP library), implementations of
24149 Burt's constraint and @dfn{effective network size} (ENS) metrics, Borgatti's
24150 algorithm to identify key players, and Valente's bridging metric. The
24151 betweenness, Key Players, and bridging implementations are parallelized with
24153 (license license:gpl2)))
24155 (define-public r-emplik
24162 (uri (cran-uri "emplik" version))
24165 "1kw8g8j075bsicdvgkjf4870rfv5c30gvmw6qkkaz3ki22x74w77"))))
24166 (properties `((upstream-name . "emplik")))
24167 (build-system r-build-system)
24170 (home-page "https://www.ms.uky.edu/~mai/EmpLik.html")
24171 (synopsis "Empirical likelihood ratio for censored/truncated data")
24173 "This package provides empirical likelihood ratio tests for
24174 means/quantiles/hazards from possibly censored and/or truncated data. It also
24176 (license license:gpl2+)))
24178 (define-public r-imputeyn
24180 (name "r-imputeyn")
24185 (uri (cran-uri "imputeYn" version))
24188 "1b21w1aa5f7yiq8k0wa86wvbg4ij7f6ldwn6asfqwb0b90rvsgvs"))))
24189 (properties `((upstream-name . "imputeYn")))
24190 (build-system r-build-system)
24192 (list r-boot r-emplik r-mvtnorm r-quadprog r-survival))
24193 (home-page "https://cran.r-project.org/web/packages/imputeYn/")
24194 (synopsis "Impute last largest censored observation under weighted least squares")
24196 "This package allows for the imputation of the last largest censored
24197 observantions. This method brings less bias and more efficient estimates for
24199 (license license:gpl2)))
24201 (define-public r-adapenetclass
24203 (name "r-adapenetclass")
24208 (uri (cran-uri "AdapEnetClass" version))
24211 "01k3mj4g1ckbng7wkzzn9h0k9yf01cpnnkly0sjda574c5jhj0rc"))))
24212 (properties `((upstream-name . "AdapEnetClass")))
24213 (build-system r-build-system)
24215 (list r-glmnet r-imputeyn r-lars r-quadprog))
24216 (home-page "https://cran.r-project.org/web/packages/AdapEnetClass/")
24217 (synopsis "Class of adaptive elastic net methods for censored data")
24219 "This package provides methods for variable selection for AFT models.")
24220 (license license:gpl2)))
24222 (define-public r-flock
24229 (uri (cran-uri "flock" version))
24232 "1zg93p74icj4bhxnmnssj2xp6vw4yaksyavq03497v33xfpdxss7"))))
24233 (properties `((upstream-name . "flock")))
24234 (build-system r-build-system)
24235 (propagated-inputs (list r-rcpp))
24236 (home-page "https://cran.r-project.org/web/packages/flock/")
24237 (synopsis "Process synchronization using file locks")
24239 "This package implements synchronization between R processes (spawned by
24240 using the @code{parallel} package for instance) using file locks. It supports
24241 both exclusive and shared locking.")
24242 (license license:asl2.0)))
24244 (define-public r-archivist
24246 (name "r-archivist")
24251 (uri (cran-uri "archivist" version))
24254 "0q1qysack30xzxdbvvi56rk7r85hsj4ghls9r70ki7bl3rqwr4c9"))))
24255 (properties `((upstream-name . "archivist")))
24256 (build-system r-build-system)
24268 (home-page "https://pbiecek.github.io/archivist/")
24269 (synopsis "Tools for storing, restoring and searching for R objects")
24271 "Data exploration and modelling is a process in which a lot of data
24272 artifacts are produced. Artifacts like: subsets, data aggregates, plots,
24273 statistical models, different versions of data sets and different versions of
24274 results. Archivist helps to store and manage artifacts created in R. It
24275 allows you to store selected artifacts as binary files together with their
24276 metadata and relations. Archivist allows sharing artifacts with others. It
24277 can look for already created artifacts by using its class, name, date of the
24278 creation or other properties. It also makes it easy to restore such
24280 (license license:gpl2)))
24282 (define-public r-versions
24284 (name "r-versions")
24289 (uri (cran-uri "versions" version))
24292 "0zm49j785dgv7fyr1yl9q5f0dsk8hhpim5q5bpkgrkzv7pwjribd"))))
24293 (properties `((upstream-name . "versions")))
24294 (build-system r-build-system)
24295 (home-page "https://cran.r-project.org/web/packages/versions/")
24296 (synopsis "Query and install specific versions of CRAN packages")
24298 "This package allows you to install specified versions of R packages
24299 hosted on CRAN and provides functions to list available versions and the
24300 versions of currently installed packages.")
24301 (license license:bsd-3)))
24303 (define-public r-adapr
24310 (uri (cran-uri "adapr" version))
24313 "1s57jdbi5pik56xjz1d4438ax6cywg2yq2s47h5g6wrwvpgr1qfw"))))
24314 (properties `((upstream-name . "adapr")))
24315 (build-system r-build-system)
24332 (home-page "https://cran.r-project.org/web/packages/adapr/")
24333 (synopsis "Implementation of an accountable data analysis process")
24335 "This package tracks reading and writing within R scripts that are
24336 organized into a directed acyclic graph. It contains an interactive Shiny
24337 application @code{adaprApp()}. It uses Git and file hashes to track version
24338 histories of inputs and outputs.")
24339 (license license:lgpl2.0)))
24341 (define-public r-adapsamp
24343 (name "r-adapsamp")
24348 (uri (cran-uri "AdapSamp" version))
24351 "1jayjrsiib2ij4rxxj59g71r3xhzl5yqh0lhi8k6cfy03i7dkvis"))))
24352 (properties `((upstream-name . "AdapSamp")))
24353 (build-system r-build-system)
24354 (propagated-inputs (list r-pracma))
24355 (home-page "https://cran.r-project.org/web/packages/AdapSamp/")
24356 (synopsis "Adaptive sampling algorithms")
24358 "For distributions whose probability density functions are log-concave,
24359 the adaptive rejection sampling algorithm can be used to build envelope
24360 functions for sampling. For others, the modified adaptive rejection sampling
24361 algorithm, the concave-convex adaptive rejection sampling algorithm, and the
24362 adaptive slice sampling algorithm can be used. This R package mainly includes
24363 these four functions: @code{rARS()}, @code{rMARS()}, @code{rCCARS()}, and
24364 @code{rASS()}. These functions can realize sampling based on the algorithms
24366 (license license:gpl2)))
24368 (define-public r-adaptalint
24370 (name "r-adaptalint")
24375 (uri (cran-uri "adaptalint" version))
24378 "15qdcvnnbgcps8j5k79354wsc9alswijv8lcafg2i3lghaw536yf"))))
24379 (properties `((upstream-name . "adaptalint")))
24380 (build-system r-build-system)
24382 (list r-dplyr r-lintr r-purrr))
24383 (home-page "https://cran.r-project.org/web/packages/adaptalint/")
24384 (synopsis "Check R code style")
24386 "This package provides tools to infer the code style (which style rules
24387 are followed and which ones are not) from one package and use it to check
24388 another. This makes it easier to find and correct the most important problems
24390 (license license:gpl3)))
24392 (define-public r-fracdiff
24394 (name "r-fracdiff")
24399 (uri (cran-uri "fracdiff" version))
24402 "1dhfjlhr9sb38qgpsx0sm73l9lgc13d0fk32l7fmjfnalhr3n45q"))))
24403 (properties `((upstream-name . "fracdiff")))
24404 (build-system r-build-system)
24405 (home-page "https://github.com/mmaechler/fracdiff")
24407 "Fractionally differenced ARIMA aka ARFIMA(P,d,q) models")
24409 "This package provides tools for the maximum likelihood estimation of the
24410 parameters of a fractionally differenced ARIMA(p,d,q) model (Haslett and
24411 Raftery, Appl.Statistics, 1989); it includes inference and basic methods.")
24412 (license license:gpl2+)))
24414 (define-public r-forecast
24416 (name "r-forecast")
24421 (uri (cran-uri "forecast" version))
24424 "0zvn44k7npxai8kj0hgxaaqv1hgd8rxicnvj4cg7wfl8ba4yn0cz"))))
24425 (properties `((upstream-name . "forecast")))
24426 (build-system r-build-system)
24441 (list r-knitr)) ; needed for vignettes
24442 (home-page "https://pkg.robjhyndman.com/forecast/")
24443 (synopsis "Forecasting functions for time series and linear models")
24445 "This package provides methods and tools for displaying and analysing
24446 univariate time series forecasts including exponential smoothing via state
24447 space models and automatic ARIMA modelling.")
24448 (license license:gpl3)))
24450 (define-public r-formattable
24452 (name "r-formattable")
24457 (uri (cran-uri "formattable" version))
24459 (base32 "1vdxi0xmg019qyzjrp8bkjxciz245jcxsrkhfzd44ynqcwi4s3ag"))))
24460 (properties `((upstream-name . "formattable")))
24461 (build-system r-build-system)
24463 (list r-htmltools r-htmlwidgets r-lifecycle r-rmarkdown))
24466 (home-page "https://github.com/renkun-ken/formattable")
24467 (synopsis "Print vectors and data frames with text fromatting")
24469 "This R package provides functions to create formattable vectors and data
24470 frames. @emph{Formattable} vectors are printed with text formatting, and
24471 formattable data frames are printed with multiple types of formatting in HTML
24472 to improve the readability of data presented in tabular form rendered in web
24474 (license license:expat)))
24476 (define-public r-xmisc
24483 (uri (cran-uri "Xmisc" version))
24486 "11gwlcyxhz1p50m68cnqrxmisdk99v8vrsbvyr7k67f0kvsznzs1"))))
24487 (properties `((upstream-name . "Xmisc")))
24488 (build-system r-build-system)
24489 (home-page "https://cran.r-project.org/package=Xmisc")
24491 "Xiaobei's miscellaneous classes and functions")
24493 "This package provides Xiaobei's miscellaneous classes and functions,
24494 which are useful when developing R packages for @dfn{object oriented
24495 programming} (OOP) using R Reference Class.")
24496 (license license:gpl2+)))
24498 (define-public r-proxyc
24505 (uri (cran-uri "proxyC" version))
24508 "1mcimswrx1cjjm7wsgkzfrgh3jpf4sncwfvdvg2f14fzfzy7afd6"))))
24509 (properties `((upstream-name . "proxyC")))
24510 (build-system r-build-system)
24512 (list r-matrix r-rcpp r-rcpparmadillo r-rcppparallel))
24513 (home-page "https://cran.r-project.org/package=proxyC")
24514 (synopsis "Compute proximity in large sparse matrices")
24516 "This package provides efficient tools to compute the proximity between
24517 rows or columns of large matrices. Functions are optimised for large sparse
24518 matrices using the Armadillo and Intel TBB libraries. Among several built-in
24519 similarity/distance measures, computation of correlation, cosine similarity
24520 and Euclidean distance is particularly fast.")
24521 (license license:gpl3)))
24523 (define-public r-isocodes
24525 (name "r-isocodes")
24526 (version "2022.01.10")
24530 (uri (cran-uri "ISOcodes" version))
24533 "0gy7n5bgxnl4rawry0pg078bkks9lzsbsrwjq8q5cvxl4k3dwpdj"))))
24534 (properties `((upstream-name . "ISOcodes")))
24535 (build-system r-build-system)
24536 (home-page "https://cran.r-project.org/package=ISOcodes")
24537 (synopsis "Selected ISO codes")
24539 "This package provides ISO language, territory, currency, script and
24540 character codes. It provides ISO 639 language codes, ISO 3166 territory
24541 codes, ISO 4217 currency codes, ISO 15924 script codes, and the ISO 8859
24542 character codes as well as the UN M.49 area codes.")
24543 (license license:gpl2)))
24545 (define-public r-stopwords
24547 (name "r-stopwords")
24552 (uri (cran-uri "stopwords" version))
24555 "1ci1cgxrcvlhhplximsfv0plvjdbcd5kv0nphxnpildsn5m1rv65"))))
24556 (properties `((upstream-name . "stopwords")))
24557 (build-system r-build-system)
24560 (home-page "https://github.com/quanteda/stopwords")
24561 (synopsis "Multilingual stopword lists")
24563 "This package provides multiple sources of stopwords, for use in text
24564 analysis and natural language processing.")
24565 (license license:expat)))
24567 (define-public r-spacyr
24574 (uri (cran-uri "spacyr" version))
24577 "1b2ccgwsiqkvp7w37x8k7699c676q16vfrybkrfvyczyhki4s6nw"))))
24578 (properties `((upstream-name . "spacyr")))
24579 (build-system r-build-system)
24581 (list r-data-table r-reticulate))
24582 (home-page "https://spacyr.quanteda.io")
24583 (synopsis "R wrapper for the spaCy NLP library")
24585 "This package provides an R wrapper to the Python @dfn{natural language
24586 processing} (NLP) library @code{spaCy}, from @url{http://spacy.io}.")
24587 (license license:gpl3)))
24589 (define-public r-snowballc
24591 (name "r-snowballc")
24596 (uri (cran-uri "SnowballC" version))
24599 "1wwm71mp4b2mjb5985x782p6xj519dfrpd40qli7lmig6afyw3xi"))))
24600 (properties `((upstream-name . "SnowballC")))
24601 (build-system r-build-system)
24602 (home-page "https://r-forge.r-project.org/projects/r-temis/")
24603 (synopsis "Snowball stemmers based on the C libstemmer UTF-8 library")
24605 "This package provides an R interface to the C @code{libstemmer} library
24606 that implements Porter's word stemming algorithm for collapsing words to a
24607 common root to aid comparison of vocabulary. Currently supported languages
24608 are Danish, Dutch, English, Finnish, French, German, Hungarian, Italian,
24609 Norwegian, Portuguese, Romanian, Russian, Spanish, Swedish and Turkish.")
24610 (license license:bsd-3)))
24612 (define-public r-quanteda
24614 (name "r-quanteda")
24619 (uri (cran-uri "quanteda" version))
24622 "102wlx6481fskgdr5wv467n29f666q0qg9kjm0ivqfg9xsbvza12"))))
24623 (properties `((upstream-name . "quanteda")))
24624 (build-system r-build-system)
24639 (home-page "https://quanteda.io")
24640 (synopsis "Quantitative analysis of textual data")
24642 "This package provides a fast, flexible, and comprehensive framework for
24643 quantitative text analysis in R. It provides functionality for corpus
24644 management, creating and manipulating tokens and ngrams, exploring keywords in
24645 context, forming and manipulating sparse matrices of documents by features and
24646 feature co-occurrences, analyzing keywords, computing feature similarities and
24647 distances, applying content dictionaries, applying supervised and unsupervised
24648 machine learning, visually representing text and text analyses, and more.")
24649 (license license:gpl3)))
24651 (define-public r-topicmodels
24653 (name "r-topicmodels")
24658 (uri (cran-uri "topicmodels" version))
24661 "1d6iizmn042b59q2y6qc82z19wq3xm0zvgkf8iqf8fdzh51kmn5g"))))
24662 (properties `((upstream-name . "topicmodels")))
24663 (build-system r-build-system)
24667 (list r-modeltools r-slam r-tm))
24668 (home-page "https://cran.r-project.org/package=topicmodels")
24669 (synopsis "Topic models")
24671 "This package provides an interface to the C code for @dfn{Latent
24672 Dirichlet Allocation} (LDA) models and @dfn{Correlated Topics Models} (CTM) by
24673 David M. Blei and co-authors and the C++ code for fitting LDA models using
24674 Gibbs sampling by Xuan-Hieu Phan and co-authors.")
24675 (license license:gpl2)))
24677 (define-public r-stm
24684 (uri (cran-uri "stm" version))
24687 "0qwq4nin2n9fjd06852r8k7arvcgh46kcfb3lm21swgx6j8bgrhb"))))
24688 (properties `((upstream-name . "stm")))
24689 (build-system r-build-system)
24702 (home-page "http://www.structuraltopicmodel.com/")
24703 (synopsis "Estimation of the Structural Topic Model")
24705 "The @dfn{Structural Topic Model} (STM) allows researchers to estimate
24706 topic models with document-level covariates. The package also includes tools
24707 for model selection, visualization, and estimation of topic-covariate
24709 (license license:expat)))
24711 (define-public r-polycor
24718 (uri (cran-uri "polycor" version))
24721 "0285rvx8238qp8dix0jq0cqq7ks8h6cjwsscbc7dx4n9nph56pzh"))))
24722 (properties `((upstream-name . "polycor")))
24723 (build-system r-build-system)
24725 (list r-admisc r-matrix r-mvtnorm))
24726 (home-page "https://r-forge.r-project.org/projects/polycor/")
24727 (synopsis "Polychoric and polyserial correlations")
24729 "This package provides tools to compute polychoric and polyserial
24730 correlations by quick \"two-step\" methods or ML, optionally with standard
24731 errors; tetrachoric and biserial correlations are special cases.")
24732 (license license:gpl2+)))
24734 (define-public r-msm
24741 (uri (cran-uri "msm" version))
24744 "08vhazswyxr3y1zb9y60mbg3bappzlizxml8s08p65mh82xxkz5f"))))
24745 (properties `((upstream-name . "msm")))
24746 (build-system r-build-system)
24748 (list r-expm r-mvtnorm r-survival))
24749 (home-page "https://github.com/chjackson/msm")
24750 (synopsis "Multi-state Markov and hidden Markov models in continuous time")
24752 "This package provides functions for fitting continuous-time Markov and
24753 hidden Markov multi-state models to longitudinal data. It was designed for
24754 processes observed at arbitrary times in continuous time (panel data) but some
24755 other observation schemes are supported. Both Markov transition rates and the
24756 hidden Markov output process can be modelled in terms of covariates, which may
24757 be constant or piecewise-constant in time.")
24758 (license license:gpl2+)))
24760 (define-public r-ltm
24767 (uri (cran-uri "ltm" version))
24770 "0vhgbk6j0z3limsrbjkjkpfn2whiaij5j4jf1gg66mjs9dlylap1"))))
24771 (properties `((upstream-name . "ltm")))
24772 (build-system r-build-system)
24774 (list r-mass r-msm r-polycor))
24775 (home-page "https://github.com/drizopoulos/ltm")
24776 (synopsis "Latent trait models under IRT")
24778 "This is a package supporting the analysis of multivariate dichotomous
24779 and polytomous data using latent trait models under the Item Response Theory
24780 approach. It includes the Rasch, the Two-Parameter Logistic, the Birnbaum's
24781 Three-Parameter, the Graded Response, and the Generalized Partial Credit
24783 (license license:gpl2+)))
24785 (define-public r-mi
24792 (uri (cran-uri "mi" version))
24795 "1h47k5mpbvhid83277dvvj2di493bgzz9iarpyv3r30y219l7x1l"))))
24796 (properties `((upstream-name . "mi")))
24797 (build-system r-build-system)
24799 (list r-arm r-matrix))
24800 (home-page "http://www.stat.columbia.edu/~gelman/")
24801 (synopsis "Missing data imputation and model checking")
24803 "This package provides functions for data manipulation, imputing missing
24804 values in an approximate Bayesian framework, diagnostics of the models used to
24805 generate the imputations, confidence-building mechanisms to validate some of
24806 the assumptions of the imputation algorithm, and functions to analyze multiply
24807 imputed data sets with the appropriate degree of sampling uncertainty.")
24808 (license license:gpl2+)))
24810 (define-public r-matrixcalc
24812 (name "r-matrixcalc")
24817 (uri (cran-uri "matrixcalc" version))
24820 "1jkgl1v1q7cqpl1rf49qahdr9y0f33f0ldsbgby8xhfv0vpy21jr"))))
24821 (properties `((upstream-name . "matrixcalc")))
24822 (build-system r-build-system)
24823 (home-page "https://cran.r-project.org/web/packages/matrixcalc/")
24824 (synopsis "Collection of functions for matrix calculations")
24826 "This package provides a collection of functions to support matrix
24827 calculations for probability, econometric and numerical analysis. There are
24828 additional functions that are comparable to APL functions which are useful for
24829 actuarial models such as pension mathematics.")
24830 (license license:gpl2+)))
24832 (define-public r-matrixextra
24834 (name "r-matrixextra")
24839 (uri (cran-uri "MatrixExtra" version))
24841 (base32 "00f6sgw6p2709gs3df68yr59nvsr429pk9xql71id3kachjzh618"))))
24842 (properties `((upstream-name . "MatrixExtra")))
24843 (build-system r-build-system)
24845 (list r-float r-matrix r-rcpp r-rhpcblasctl))
24848 (home-page "https://github.com/david-cortes/MatrixExtra")
24849 (synopsis "Extra methods for sparse matrices")
24851 "This package extends sparse matrix and vector classes from the Matrix
24852 package by providing:
24855 @item Methods and operators that work natively on CSR formats (compressed
24856 sparse row, a.k.a. @code{RsparseMatrix}) such as slicing/sub-setting,
24857 assignment, @code{rbind()}, mathematical operators for CSR and COO such as
24858 addition or @code{sqrt()}, and methods such as @code{diag()};
24859 @item Multi-threaded matrix multiplication and cross-product for many
24860 @code{<sparse, dense>} types, including the @code{float32} type from
24862 @item Coercion methods between pairs of classes which are not present in
24863 @code{Matrix}, such as from @code{dgCMatrix} to @code{ngRMatrix}, as well as
24864 convenience conversion functions;
24865 @item Utility functions for sparse matrices such as sorting the indices or
24866 removing zero-valued entries;
24867 @item Fast transposes that work by outputting in the opposite storage format;
24868 @item Faster replacements for many @code{Matrix} methods for all sparse types,
24869 such as slicing and elementwise multiplication.
24870 @item Convenience functions for sparse objects, such as @code{mapSparse} or a
24871 shorter @code{show} method.
24874 (license license:gpl2+)))
24876 (define-public r-sem
24883 (uri (cran-uri "sem" version))
24886 "05hk72zxvyv6kkjhk5y6qw253c64108az7030z8j1sz8wq03n0md"))))
24887 (properties `((upstream-name . "sem")))
24888 (build-system r-build-system)
24890 (list r-boot r-mass r-mi))
24891 (home-page "https://cran.r-project.org/package=sem")
24892 (synopsis "Structural equation models")
24894 "This package provides functions for fitting general linear structural
24895 equation models (with observed and latent variables) using the RAM approach,
24896 and for fitting structural equations in observed-variable models by two-stage
24898 (license license:gpl2+)))
24900 (define-public r-semtools
24902 (name "r-semtools")
24907 (uri (cran-uri "semTools" version))
24910 "1wnakz76c4mgkwvx3iycmvgrzqys860jg9zpkba0ln5c08ycw8pm"))))
24911 (properties `((upstream-name . "semTools")))
24912 (build-system r-build-system)
24914 (list r-lavaan r-pbivnorm))
24915 (home-page "https://github.com/simsem/semTools/wiki")
24916 (synopsis "Useful tools for structural equation modeling")
24918 "This package provides useful tools for structural equation modeling.")
24919 (license license:gpl2+)))
24921 (define-public r-regsem
24928 (uri (cran-uri "regsem" version))
24931 "1v33wkrsawcvaa06cijp8ybwi82a0x34y59hdknwdbywplnirzr8"))))
24932 (properties `((upstream-name . "regsem")))
24933 (build-system r-build-system)
24935 (list r-lavaan r-rcpp r-rcpparmadillo r-rsolnp))
24938 (home-page "https://cran.r-project.org/package=regsem")
24939 (synopsis "Regularized structural equation modeling")
24941 "This package uses both ridge and lasso penalties (and extensions) to
24942 penalize specific parameters in structural equation models. The package
24943 offers additional cost functions, cross validation, and other extensions
24944 beyond traditional structural equation models. It also contains a function to
24945 perform @dfn{exploratory mediation} (XMed).")
24946 (license license:gpl2+)))
24948 (define-public r-stanheaders
24950 (name "r-stanheaders")
24951 (version "2.21.0-7")
24955 (uri (cran-uri "StanHeaders" version))
24958 "0srkyawyiykn3p5lw1z3zf18s4ax4iasv1ci3l1px40f9w36wm17"))))
24959 (properties `((upstream-name . "StanHeaders")))
24960 (build-system r-build-system)
24961 (inputs (list pandoc))
24963 (list r-rcppeigen r-rcppparallel))
24965 (list gfortran r-knitr)) ; for vignettes
24966 (home-page "https://mc-stan.org/")
24967 (synopsis "C++ header files for Stan")
24969 "The C++ header files of the Stan project are provided by this package.
24970 There is a shared object containing part of the @code{CVODES} library, but it
24971 is not accessible from R. @code{r-stanheaders} is only useful for developers
24972 who want to utilize the @code{LinkingTo} directive of their package's
24973 DESCRIPTION file to build on the Stan library without incurring unnecessary
24976 The Stan project develops a probabilistic programming language that implements
24977 full or approximate Bayesian statistical inference via Markov Chain Monte
24978 Carlo or variational methods and implements (optionally penalized) maximum
24979 likelihood estimation via optimization. The Stan library includes an advanced
24980 automatic differentiation scheme, templated statistical and linear algebra
24981 functions that can handle the automatically differentiable scalar types (and
24982 doubles, ints, etc.), and a parser for the Stan language. The @code{r-rstan}
24983 package provides user-facing R functions to parse, compile, test, estimate,
24984 and analyze Stan models.")
24985 (license license:bsd-3)))
24987 (define-public r-rpf
24994 (uri (cran-uri "rpf" version))
24997 "1yr1i7kswq57mcxv05lh7bvbicz1djqxcl6f13dlgsf3ww56gzg1"))))
24998 (properties `((upstream-name . "rpf")))
24999 (build-system r-build-system)
25001 (list r-lifecycle r-mvtnorm r-rcpp r-rcppeigen))
25004 (home-page "https://github.com/jpritikin/rpf")
25005 (synopsis "Response probability functions")
25007 "The purpose of this package is to factor out logic and math common to
25008 Item Factor Analysis fitting, diagnostics, and analysis. It is envisioned as
25009 core support code suitable for more specialized IRT packages to build upon.
25010 Complete access to optimized C functions is made available with
25011 @code{R_RegisterCCallable()}.")
25012 (license license:gpl3+)))
25014 (define-public r-openmx
25021 (uri (cran-uri "OpenMx" version))
25024 "1v969100hllh0lwlxd2gv0k7krrsp9gc07iinx0nn04wkzh0rib5"))))
25025 (properties `((upstream-name . "OpenMx")))
25026 (build-system r-build-system)
25038 (native-inputs (list r-knitr gfortran))
25039 (home-page "http://openmx.ssri.psu.edu")
25040 (synopsis "Extended structural equation modelling")
25042 "This package allows for the estimation of a wide variety of advanced
25043 multivariate statistical models. It consists of a library of functions and
25044 optimizers that allow you to quickly and flexibly define an SEM model and
25045 estimate parameters given observed data.")
25046 (license license:asl2.0)))
25048 (define-public r-kutils
25055 (uri (cran-uri "kutils" version))
25058 "06jk66wbq3jmdf2jdhqns6r3yk36l2x7c907x977zv80sqxa1l37"))))
25059 (properties `((upstream-name . "kutils")))
25060 (build-system r-build-system)
25062 (list r-foreign r-openxlsx r-plyr r-runit r-xtable))
25063 (home-page "https://cran.r-project.org/package=kutils")
25064 (synopsis "Project management tools")
25066 "This package provides tools for data importation, recoding, and
25067 inspection. There are functions to create new project folders, R code
25068 templates, create uniquely named output directories, and to quickly obtain a
25069 visual summary for each variable in a data frame. The main feature here is
25070 the systematic implementation of the \"variable key\" framework for data
25071 importation and recoding.")
25072 (license license:gpl2)))
25074 (define-public r-rockchalk
25076 (name "r-rockchalk")
25077 (version "1.8.152")
25081 (uri (cran-uri "rockchalk" version))
25084 "1d15jlgcy35pvaicaddd4zrhwm5ajb9yc3jk6dyxm99gc5wcn6h3"))))
25085 (properties `((upstream-name . "rockchalk")))
25086 (build-system r-build-system)
25088 (list r-cardata r-kutils r-lme4 r-mass))
25089 (home-page "https://cran.r-project.org/package=rockchalk")
25090 (synopsis "Regression estimation and presentation")
25092 "This package provides a collection of functions for interpretation and
25093 presentation of regression analysis. These functions are used to produce the
25094 statistics lectures in @url{http://pj.freefaculty.org/guides}. The package
25095 includes regression diagnostics, regression tables, and plots of interactions
25096 and \"moderator\" variables. The emphasis is on \"mean-centered\" and
25097 \"residual-centered\" predictors. The vignette @code{rockchalk} offers a
25098 fairly comprehensive overview.")
25099 (license license:gpl3+)))
25101 (define-public r-lisreltor
25103 (name "r-lisreltor")
25108 (uri (cran-uri "lisrelToR" version))
25111 "0i51v0x87277ly0kggdd594w6q4zq62b4n7xs9r25j08bzs82nfk"))))
25112 (properties `((upstream-name . "lisrelToR")))
25113 (build-system r-build-system)
25114 (home-page "https://cran.r-project.org/package=lisrelToR")
25115 (synopsis "Import output from LISREL into R")
25117 "This is an unofficial package aimed at automating the import of LISREL
25119 (license license:gpl2)))
25121 (define-public r-bdgraph
25128 (uri (cran-uri "BDgraph" version))
25131 "0s2j4462zlgyjnqvvvxg4lynhmwwnjaw1cr1chzmagfvaj94qhhz"))))
25132 (properties `((upstream-name . "BDgraph")))
25133 (build-system r-build-system)
25138 (home-page "https://www.uva.nl/profile/a.mohammadi")
25139 (synopsis "Bayesian structure learning in graphical models")
25141 "This package provides statistical tools for Bayesian structure learning
25142 in undirected graphical models for continuous, discrete, and mixed data. It
25143 uses a trans-dimensional @dfn{Markov Chain Monte Carlo} (MCMC) approach based
25144 on a continuous-time birth-death process.")
25145 (license license:gpl2+)))
25147 (define-public r-d3network
25149 (name "r-d3network")
25150 (version "0.5.2.1")
25154 (uri (cran-uri "d3Network" version))
25157 "1gh979z9wksyxxxdzlfzibn0ysvf6h1ij7vwpd55fvbwr308syaw"))))
25158 (properties `((upstream-name . "d3Network")))
25159 (build-system r-build-system)
25161 (list r-plyr r-rjson r-whisker))
25162 (home-page "http://christophergandrud.github.io/d3Network/")
25163 (synopsis "Create D3 JavaScript network, tree, dendrogram, and Sankey graphs")
25165 "This package is intended to make it easy to create D3 JavaScript
25166 network, tree, dendrogram, and Sankey graphs from R using data frames.")
25167 (license license:gpl3+)))
25169 (define-public r-qgraph
25176 (uri (cran-uri "qgraph" version))
25179 "0r225b7rnsv6wz41ij0msmqr1xy0iqxh9dbsvjixbi1hvgv91wds"))))
25180 (properties `((upstream-name . "qgraph")))
25181 (build-system r-build-system)
25201 (home-page "http://sachaepskamp.com/qgraph/")
25202 (synopsis "Weighted network visualization and analysis")
25204 "This package implements tools for weighted network visualization and
25205 analysis, as well as Gaussian graphical model computation. It contains graph
25206 plotting methods, and tools for psychometric data visualization and graphical
25207 model estimation. See Epskamp et al. (2012)
25208 @url{doi:10.18637/jss.v048.i04}.")
25209 (license license:gpl2)))
25211 (define-public r-semplot
25218 (uri (cran-uri "semPlot" version))
25221 "0d7v9yqc9nhx3hdrp444w1ah66zai3lg5y778m85r7ngh1prxlvc"))))
25222 (properties `((upstream-name . "semPlot")))
25223 (build-system r-build-system)
25236 (home-page "https://github.com/SachaEpskamp/semPlot")
25237 (synopsis "Unified visualizations of structural equation models")
25239 "Structural equation modeling (SEM) has a long history of representing
25240 models graphically as path diagrams. The semPlot package for R fills the gap
25241 between advanced, but time-consuming, graphical software and the limited
25242 graphics produced automatically by SEM software. In addition, semPlot offers
25243 more functionality than drawing path diagrams: it can act as a common ground
25244 for importing SEM results into R. Any result usable as input to semPlot can
25245 also be represented in any of the three popular SEM frame-works, as well as
25246 translated to input syntax for the R packages @code{sem} and @code{lavaan}.")
25247 (license license:gpl2)))
25249 (define-public r-cdm
25256 (uri (cran-uri "CDM" version))
25259 "1cnk19k09cj81ic43rwbvcalvczfca4ncdyy8r1gyc8fzf2glb0i"))))
25260 (properties `((upstream-name . "CDM")))
25261 (build-system r-build-system)
25263 (list r-mvtnorm r-polycor r-rcpp r-rcpparmadillo))
25265 "https://github.com/alexanderrobitzsch/CDM")
25266 (synopsis "Cognitive diagnosis modeling")
25268 "This package provides functions for cognitive diagnosis modeling and
25269 multidimensional item response modeling for dichotomous and polytomous item
25270 responses. It enables the estimation of the DINA and DINO model, the multiple
25271 group (polytomous) GDINA model, the multiple choice DINA model, the general
25272 diagnostic model (GDM), the structured latent class model (SLCA), and
25273 regularized latent class analysis. See George, Robitzsch, Kiefer, Gross, and
25274 Uenlue (2017) @url{doi:10.18637/jss.v074.i02} for further details on
25275 estimation and the package structure. For tutorials on how to use the CDM
25276 package see George and Robitzsch (2015, @url{doi:10.20982/tqmp.11.3.p189}) as
25277 well as Ravand and Robitzsch (2015).")
25278 (license license:gpl2+)))
25280 (define-public r-tam
25287 (uri (cran-uri "TAM" version))
25290 "00ww277hsyci5rph4gb155h0y95dmjhqgn9amz6g8zbrjb2748dw"))))
25291 (properties `((upstream-name . "TAM")))
25292 (build-system r-build-system)
25294 (list r-cdm r-rcpp r-rcpparmadillo))
25295 (home-page "http://www.edmeasurementsurveys.com/TAM/Tutorials/")
25296 (synopsis "Test analysis modules")
25298 "This package includes tools for marginal maximum likelihood estimation
25299 and joint maximum likelihood estimation for unidimensional and
25300 multidimensional item response models. The package functionality covers the
25301 Rasch model, 2PL model, 3PL model, generalized partial credit model,
25302 multi-faceted Rasch model, nominal item response model, structured latent
25303 class model, mixture distribution IRT models, and located latent class models.
25304 Latent regression models and plausible value imputation are also supported.")
25305 (license license:gpl2+)))
25307 (define-public r-erm
25314 (uri (cran-uri "eRm" version))
25317 "0smym010kswc5vx90qr3x1vl16xj1x1i54rvrj006dc4agc1vmlk"))))
25318 (properties `((upstream-name . "eRm")))
25319 (build-system r-build-system)
25321 (list r-colorspace r-lattice r-mass r-matrix r-psych))
25322 (native-inputs (list gfortran))
25323 (home-page "https://cran.r-project.org/package=eRm")
25324 (synopsis "Extended Rasch modeling")
25326 "This package provides tools to fit @dfn{Rasch models} (RM), @dfn{linear
25327 logistic test models} (LLTM), @dfn{rating scale model} (RSM), @dfn{linear
25328 rating scale models} (LRSM), @dfn{partial credit models} (PCM), and
25329 @dfn{linear partial credit models} (LPCM). Missing values are allowed in the
25330 data matrix. Additional features are the ML estimation of the person
25331 parameters, Andersen's LR-test, item-specific Wald test, Martin-Loef-Test,
25332 nonparametric Monte-Carlo Tests, itemfit and personfit statistics including
25333 infit and outfit measures, ICC and other plots, automated stepwise item
25334 elimination, and a simulation module for various binary data matrices.")
25335 (license license:gpl3)))
25337 (define-public r-irtoys
25344 (uri (cran-uri "irtoys" version))
25347 "1qshz6czykgf53mq6xiswzv5xsjwrkrinpfkf1yavql4v08hs82b"))))
25348 (properties `((upstream-name . "irtoys")))
25349 (build-system r-build-system)
25354 (home-page "https://cran.r-project.org/package=irtoys")
25355 (synopsis "Collection of functions related to Item Response Theory (IRT)")
25357 "This package provides a collection of functions useful in learning and
25358 practicing @dfn{Item Response Theory} (IRT), which can be combined into larger
25359 programs. It provides basic CTT analysis, a simple common interface to the
25360 estimation of item parameters in IRT models for binary responses with three
25361 different programs (ICL, BILOG-MG, and ltm), ability estimation (MLE, BME,
25362 EAP, WLE, plausible values), item and person fit statistics, scaling
25363 methods (MM, MS, Stocking-Lord, and the complete Hebaera method), and a rich
25364 array of parametric and non-parametric (kernel) plots. It estimates and plots
25365 Haberman's interaction model when all items are dichotomously scored.")
25366 (license license:gpl2+)))
25368 (define-public r-iheatmapr
25370 (name "r-iheatmapr")
25375 (uri (cran-uri "iheatmapr" version))
25378 "1pwkwh7ljlpr6zyz6j8knpz3iw60xzkw8amc98x4pc2mw148jvzx"))))
25379 (properties `((upstream-name . "iheatmapr")))
25380 (build-system r-build-system)
25382 (list r-fastcluster
25392 (home-page "https://docs.ropensci.org/iheatmapr")
25393 (synopsis "Interactive, Complex Heatmaps")
25395 "iheatmapr is an R package for building complex, interactive heatmaps
25396 using modular building blocks. \"Complex\" heatmaps are heatmaps in which
25397 subplots along the rows or columns of the main heatmap add more information
25398 about each row or column. For example, a one column additional heatmap may
25399 indicate what group a particular row or column belongs to. Complex heatmaps
25400 may also include multiple side by side heatmaps which show different types of
25401 data for the same conditions. Interactivity can improve complex heatmaps by
25402 providing tooltips with information about each cell and enabling zooming into
25403 interesting features. iheatmapr uses the plotly library for interactivity.")
25404 (license license:expat)))
25406 (define-public r-packrat
25413 (uri (cran-uri "packrat" version))
25416 "1vs4i19x6jdwl3jnanp127k4hk80h1mj56cjn07w1gkl542vj99h"))))
25417 (properties `((upstream-name . "packrat")))
25418 (build-system r-build-system)
25419 (home-page "https://github.com/rstudio/packrat/")
25420 (synopsis "Dependency management R projects")
25422 "This package provides a dependency manager for R projects that allows
25423 you to manage the R packages your project depends on in an isolated, portable,
25424 and reproducible way.")
25425 (license license:gpl2)))
25427 (define-public r-rsconnect
25429 (name "r-rsconnect")
25434 (uri (cran-uri "rsconnect" version))
25437 "1kyr4v7vds2yw3xmkk2yr56ylz1h95944brylwvwmwj5yxvm419w"))))
25438 (properties `((upstream-name . "rsconnect")))
25439 (build-system r-build-system)
25448 (home-page "https://github.com/rstudio/rsconnect")
25449 (synopsis "Deployment interface for R Markdown documents and Shiny applications")
25451 "This package provides a programmatic deployment interface for RPubs,
25452 shinyapps.io, and RStudio Connect. Supported content types include R Markdown
25453 documents, Shiny applications, Plumber APIs, plots, and static web content.")
25454 (license license:gpl2)))
25456 ;; This package includes minified JavaScript files. When upgrading please
25457 ;; check that there are no new minified JavaScript files.
25458 (define-public r-dygraphs
25460 (name "r-dygraphs")
25461 (version "1.1.1.6")
25465 (uri (cran-uri "dygraphs" version))
25468 "022j007mzfa9k2n31yg4aizcsf571vv3jip092h23rqj03rk3ly3"))))
25469 (properties `((upstream-name . "dygraphs")))
25470 (build-system r-build-system)
25472 `(#:modules ((guix build utils)
25473 (guix build r-build-system)
25477 (modify-phases %standard-phases
25478 (add-after 'unpack 'process-javascript
25479 (lambda* (#:key inputs #:allow-other-keys)
25480 (with-directory-excursion "inst/htmlwidgets/lib/"
25484 `(("dygraphs/dygraph-combined-dev.js"
25485 "dygraph-combined.js")
25486 (,(assoc-ref inputs "js-jquery")
25487 "jquery/jquery.min.js")
25488 (,(assoc-ref inputs "js-fquarter")
25489 "fquarter/moment-fquarter.min.js"))))
25490 (lambda (sources targets)
25491 (for-each (lambda (source target)
25492 (format #t "Processing ~a --> ~a~%"
25494 (let ((minified (open-pipe* OPEN_READ "uglifyjs" source)))
25495 (call-with-output-file target
25497 (dump-port minified port)))))
25498 sources targets))))
25501 `(("uglifyjs" ,node-uglify-js)
25502 ;; They actually use version 1.11.1, but this more recent version
25503 ;; should be just fine.
25507 (uri "https://code.jquery.com/jquery-1.12.4.js")
25510 "0x9mrc1668icvhpwzvgafm8xm11x9lfai9nwr66aw6pjnpwkc3s3"))))
25514 (uri (string-append "https://raw.githubusercontent.com/robgallen/"
25515 "moment-fquarter/1.0.1/moment-fquarter.js"))
25518 "01mdnsaibm9jy2f1qpbn692hpv309lhj5si9nagib4dawmrkffij"))))))
25520 (list r-htmltools r-htmlwidgets r-magrittr r-xts r-zoo))
25521 (home-page "https://github.com/rstudio/dygraphs")
25522 (synopsis "Interface to Dygraphs interactive time series charting library")
25524 "This package provides an R interface to the dygraphs JavaScript charting
25525 library (a copy of which is included in the package). It provides rich
25526 facilities for charting time-series data in R, including highly configurable
25527 series- and axis-display and interactive features like zoom/pan and
25528 series/point highlighting.")
25529 (license license:expat)))
25531 (define-public r-shinystan
25533 (name "r-shinystan")
25538 (uri (cran-uri "shinystan" version))
25541 "0afm703zriyqprz1zvypir80lq2ylfff3qvj5i7p9n365mm8b150"))))
25542 (properties `((upstream-name . "shinystan")))
25543 (build-system r-build-system)
25561 (home-page "https://mc-stan.org/")
25562 (synopsis "Interactive visual and numerical analysis for Bayesian models")
25564 "This package provides a graphical user interface for interactive
25565 @dfn{Markov chain Monte Carlo} (MCMC) diagnostics and plots and tables helpful
25566 for analyzing a posterior sample. The interface is powered by the Shiny web
25567 application framework and works with the output of MCMC programs written in
25568 any programming language (and has extended functionality for Stan models fit
25569 using the @code{rstan} and @code{rstanarm} packages).")
25570 (license license:gpl3+)))
25572 (define-public r-rstantools
25574 (name "r-rstantools")
25579 (uri (cran-uri "rstantools" version))
25582 "1dsfgi02hps878n3vimfdbzpm4gr5n3ccrmnc61ncrqcp6p0p0fb"))))
25583 (properties `((upstream-name . "rstantools")))
25584 (build-system r-build-system)
25585 (inputs (list pandoc))
25587 (list r-desc r-rcpp r-rcppparallel))
25590 (home-page "https://mc-stan.org/rstantools/")
25591 (synopsis "Tools for developing R packages interfacing with Stan")
25593 "This package provides various tools for developers of R packages
25594 interfacing with @url{https://mc-stan.org, Stan}, including functions to set
25595 up the required package structure, S3 generics and default methods to unify
25596 function naming across Stan-based R packages, and vignettes with
25597 recommendations for developers.")
25598 (license license:gpl3+)))
25600 (define-public r-loo
25607 (uri (cran-uri "loo" version))
25609 (base32 "1wa5hxk7lkr88mway6b7xd5arrkkl2ldl9rf0v1nqwp8lia2ysl6"))))
25610 (properties `((upstream-name . "loo")))
25611 (build-system r-build-system)
25615 (list r-checkmate r-matrixstats))
25618 (home-page "https://mc-stan.org/loo/")
25619 (synopsis "Leave-One-Out cross-validation and WAIC for Bayesian models")
25621 "This package provides an implementation of efficient approximate
25622 @dfn{leave-one-out} (LOO) cross-validation for Bayesian models fit using
25623 Markov chain Monte Carlo, as described in @url{doi:10.1007/s11222-016-9696-4}.
25624 The approximation uses @dfn{Pareto smoothed importance sampling} (PSIS), a new
25625 procedure for regularizing importance weights. As a byproduct of the
25626 calculations, we also obtain approximate standard errors for estimated
25627 predictive errors and for the comparison of predictive errors between models.
25628 The package also provides methods for using stacking and other model weighting
25629 techniques to average Bayesian predictive distributions.")
25630 (license license:gpl3+)))
25632 (define-public r-rstan
25639 (uri (cran-uri "rstan" version))
25642 "1smr5cjrqvpdnkmjpjp73p96sy581x15mwrn4fqd1p4d5mbgxr46"))))
25643 (properties `((upstream-name . "rstan")))
25644 (build-system r-build-system)
25647 (modify-phases %standard-phases
25648 (add-before 'install 'set-timezone
25649 ;; This package is picky about timezones.
25650 (lambda* (#:key inputs #:allow-other-keys)
25651 (setenv "TZ" "UTC+1")
25653 (search-input-directory inputs
25654 "share/zoneinfo")))))))
25656 (list tzdata-for-tests pandoc r-knitr))
25668 (home-page "https://discourse.mc-stan.org/")
25669 (synopsis "R interface to Stan")
25671 "User-facing R functions are provided to parse, compile, test, estimate,
25672 and analyze Stan models by accessing the header-only Stan library provided by
25673 the StanHeaders package. The Stan project develops a probabilistic
25674 programming language that implements full Bayesian statistical inference via
25675 Markov Chain Monte Carlo, rough Bayesian inference via 'variational'
25676 approximation, and (optionally penalized) maximum likelihood estimation via
25677 optimization. In all three cases, automatic differentiation is used to
25678 quickly and accurately evaluate gradients without burdening the user with the
25679 need to derive the partial derivatives.")
25680 (license license:gpl3+)))
25682 (define-public r-rstanarm
25684 (name "r-rstanarm")
25689 (uri (cran-uri "rstanarm" version))
25692 "19rj396q84maxnd9d2xcd5rblg3310xn7sqbd6k18kwf3dvd7wp9"))))
25693 (properties `((upstream-name . "rstanarm")))
25694 (build-system r-build-system)
25715 (home-page "https://mc-stan.org/rstanarm/")
25716 (synopsis "Bayesian applied regression modeling via Stan")
25718 "This package estimates previously compiled regression models using the
25719 @code{rstan} package, which provides the R interface to the Stan C++ library
25720 for Bayesian estimation. Users specify models via the customary R syntax with
25721 a formula and @code{data.frame} plus some additional arguments for priors.")
25722 (license license:gpl3+)))
25724 (define-public r-kendall
25731 (uri (cran-uri "Kendall" version))
25734 "1xmk95l4i3kj9jn0xh1chi2rj322k29jq14ra5pa7316gwf9vx2m"))))
25735 (properties `((upstream-name . "Kendall")))
25736 (build-system r-build-system)
25741 (home-page "https://cran.r-project.org/web/packages/Kendall/")
25742 (synopsis "Kendall rank correlation and Mann-Kendall trend test")
25744 "This package computes the Kendall rank correlation and Mann-Kendall
25746 (license license:gpl2+)))
25748 (define-public r-keyring
25755 (uri (cran-uri "keyring" version))
25758 "1j8l6nmh4dr70kwybiais8yh687fdwrj134xynq68igw1b1rm8ga"))))
25759 (properties `((upstream-name . "keyring")))
25760 (build-system r-build-system)
25770 (native-inputs (list pkg-config))
25771 (home-page "https://github.com/r-lib/keyring")
25772 (synopsis "Access the system credential store from R")
25774 "This package provides a platform-independent API to access the operating
25775 system's credential store. It currently supports Keychain on macOS,
25776 Credential Store on Windows, the Secret Service API on GNU/Linux, and a
25777 simple, platform independent store implemented with environment variables.
25778 Additional storage back-ends can be added easily.")
25779 (license license:expat)))
25781 (define-public r-zyp
25784 (version "0.10-1.1")
25788 (uri (cran-uri "zyp" version))
25791 "03cxpkfbhrx1fy8l0dl9a13ghz93cqq6877wa8rig09ksdiivaw9"))))
25792 (properties `((upstream-name . "zyp")))
25793 (build-system r-build-system)
25796 (home-page "https://cran.r-project.org/web/packages/zyp/")
25797 (synopsis "Zhang + Yue-Pilon Trends Package")
25799 "This package contains an efficient implementation of Sen's slope
25800 method (Sen, 1968) plus implementation of Xuebin Zhang's (Zhang, 1999) and
25801 Yue-Pilon's (Yue, 2002) pre-whitening approaches to determining trends in
25803 (license license:lgpl2.1)))
25805 (define-public r-rlinsolve
25807 (name "r-rlinsolve")
25812 (uri (cran-uri "Rlinsolve" version))
25815 "1xv500n1480qyakw0isanw1s5ywykhc207hqja4804s5s2m8zfjw"))))
25816 (properties `((upstream-name . "Rlinsolve")))
25817 (build-system r-build-system)
25819 (list r-matrix r-rcpp r-rcpparmadillo r-rdpack))
25820 (home-page "https://cran.r-project.org/web/packages/Rlinsolve/")
25821 (synopsis "Iterative solvers for (sparse) linear system of equations")
25823 "Solving a system of linear equations is one of the most fundamental
25824 computational problems for many fields of mathematical studies, such as
25825 regression problems from statistics or numerical partial differential
25826 equations. This package provides basic stationary iterative solvers such as
25827 Jacobi, Gauss-Seidel, Successive Over-Relaxation and SSOR methods.
25828 Nonstationary, also known as Krylov subspace methods are also provided.
25829 Sparse matrix computation is also supported in that solving large and sparse
25830 linear systems can be manageable using the @code{Matrix} package along with
25831 @code{RcppArmadillo}.")
25832 (license license:gpl3+)))
25834 (define-public r-zvcv
25841 (uri (cran-uri "ZVCV" version))
25844 "0gc76j9i8fkm2v638nyzzb1qxl4zmapbspkkaffb8gi5qyjja448"))))
25845 (properties `((upstream-name . "ZVCV")))
25846 (build-system r-build-system)
25857 (home-page "https://cran.r-project.org/web/packages/ZVCV/")
25858 (synopsis "Zero-Variance Control Variates")
25860 "@dfn{Zero-variance control variates} (ZV-CV) is a post-processing method
25861 to reduce the variance of Monte Carlo estimators of expectations using the
25862 derivatives of the log target. Once the derivatives are available, the only
25863 additional computational effort is in solving a linear regression problem.
25864 This method has been extended to higher dimensions using regularisation. This
25865 package can be used to easily perform ZV-CV or regularised ZV-CV when a set of
25866 samples, derivatives and function evaluations are available. Additional
25867 functions for applying ZV-CV to two estimators for the normalising constant of
25868 the posterior distribution in Bayesian statistics are also supplied.")
25869 (license license:gpl2+)))
25871 (define-public r-ztype
25878 (uri (cran-uri "ztype" version))
25881 "0brbq2rgkl4mhjbb70kkfv47lzs66k9ppfs2klavcbripirxn5fx"))))
25882 (properties `((upstream-name . "ztype")))
25883 (build-system r-build-system)
25892 (home-page "https://cran.r-project.org/web/packages/ztype/")
25893 (synopsis "Run a Ztype game loaded with R functions")
25895 "How fast can you type R functions on your keyboard? Find out by running
25896 a @code{zty.pe} game: export R functions as instructions to type to destroy
25897 opponents' vessels.")
25898 (license license:gpl3)))
25900 (define-public r-zseq
25907 (uri (cran-uri "Zseq" version))
25910 "06dndi2b1q79bmxax11bv0l5ifcz1mhpvbn90y6a6xymrgcq0ivi"))))
25911 (properties `((upstream-name . "Zseq")))
25912 (build-system r-build-system)
25915 (home-page "https://cran.r-project.org/web/packages/Zseq/")
25916 (synopsis "Integer sequence generator")
25918 "This package generates well-known integer sequences. The @code{gmp}
25919 package is adopted for computing with arbitrarily large numbers. Every
25920 function has a hyperlink to its corresponding item in the @dfn{On-Line
25921 Encyclopedia of Integer Sequences} (OEIS) in the function help page.")
25922 (license license:gpl3+)))
25924 (define-public r-isoband
25931 (uri (cran-uri "isoband" version))
25934 "19bbi0n0kz33xdgmdprcmc6raphd1hcm1w1brc16z5phcsh3zxa6"))))
25935 (properties `((upstream-name . "isoband")))
25936 (build-system r-build-system)
25939 (home-page "https://github.com/wilkelab/isoband")
25940 (synopsis "Generate isolines and isobands from regularly spaced elevation grids")
25942 "This package provides a fast C++ implementation to generate contour
25943 lines (isolines) and contour polygons (isobands) from regularly spaced grids
25944 containing elevation data.")
25945 (license license:expat)))
25947 (define-public r-ppcor
25954 (uri (cran-uri "ppcor" version))
25957 "1x9b2kb8s0bp92b17gby0jwzzr3i4cf3ap9c4nq7m8fav72g0y3a"))))
25958 (properties `((upstream-name . "ppcor")))
25959 (build-system r-build-system)
25962 (home-page "https://cran.r-project.org/web/packages/ppcor/")
25963 (synopsis "Partial and semi-partial correlation")
25965 "This package provides users not only with a function to readily
25966 calculate the higher-order partial and semi-partial correlations but also with
25967 statistics and p-values of the correlation coefficients.")
25968 (license license:gpl2)))
25970 (define-public r-hrbrthemes
25972 (name "r-hrbrthemes")
25977 (uri (cran-uri "hrbrthemes" version))
25979 (base32 "057h60b5p53dcyjyfwlgjc1ry968s9s64dw78p443w8717zk7zpc"))))
25980 (properties `((upstream-name . "hrbrthemes")))
25981 (build-system r-build-system)
25993 (home-page "https://github.com/hrbrmstr/hrbrthemes/")
25994 (synopsis "Additional themes, theme components and utilities for @code{ggplot2}")
25996 "This package provides a compilation of extra @code{ggplot2} themes,
25997 scales and utilities, including a spell check function for plot label fields
25998 and an overall emphasis on typography.")
25999 (license license:expat)))
26001 (define-public r-crochet
26008 (uri (cran-uri "crochet" version))
26011 "0zvjaf6cv0nrjb4l4llkr0mmgha7ig31p4ri2rlnqyjlxi5l8hyq"))))
26012 (build-system r-build-system)
26015 (home-page "https://github.com/agrueneberg/crochet")
26016 (synopsis "Implementation Helper for Matrix-Like Types")
26018 "Functions to help implement the extraction / subsetting / indexing
26019 function @code{[} and replacement function @code{[<-} of custom matrix-like
26020 types (based on S3, S4, etc.), modeled as closely to the base matrix class
26021 as possible (with tests to prove it).")
26022 (license license:expat)))
26024 (define-public r-boa
26027 (version "1.1.8-2")
26031 (uri (cran-uri "boa" version))
26034 "04lhqk5qfvaz1jk90glr2yi5vq7cdy0w8m6g2lnzk359l9y41zhp"))))
26035 (properties `((upstream-name . "boa")))
26036 (build-system r-build-system)
26037 (home-page "https://www.jstatsoft.org/v21/i11")
26038 (synopsis "Library for @dfn{Bayesian Output Analysis Program} (BOA) for MCMC")
26040 "This package provides a menu-driven program and library of functions for
26041 carrying out convergence diagnostics and statistical and graphical analysis of
26042 @dfn{Markov chain Monte Carlo} (MCMC) sampling output.")
26043 (license license:gpl2+)))
26045 (define-public r-httpcode
26047 (name "r-httpcode")
26051 (uri (cran-uri "httpcode" version))
26054 "0xig0rvc81hg7mw0iq9s0an1nw24fg0kfs2p2n6dzhwl9w506fjr"))))
26055 (build-system r-build-system)
26056 (home-page "https://github.com/sckott/httpcode")
26057 (synopsis "HTTP status code helper")
26058 (description "@code{httpcode} provides functionality for finding and
26059 explaining the meaning of @code{HTTP} status codes. Functions are included for
26060 searching for codes by full or partial number, by message, and to get
26061 appropriate dog and cat images for many status codes.")
26062 (license license:expat)))
26064 (define-public r-latex2exp
26066 (name "r-latex2exp")
26070 (uri (cran-uri "latex2exp" version))
26073 "0zbbrbgg524lpm733j8qsqk5ssg75c51s6dgzb18c6fk8byrx945"))))
26074 (build-system r-build-system)
26076 (list r-stringr r-magrittr))
26079 (home-page "https://github.com/stefano-meschiari/latex2exp/")
26080 (synopsis "Use LaTeX expressions in plots")
26081 (description "@code{latex2exp} parses and converts LaTeX math formulas to
26082 R's plotmath expressions, used to enter mathematical formulas and symbols to be
26083 rendered as text, axis labels, etc. throughout R's plotting system.")
26084 (license license:expat)))
26086 (define-public r-oai
26092 (uri (cran-uri "oai" version))
26095 "1zcbcxhw692s0y6izvwazyzhgx0iwsxsbcan2nk0mb7n11p7bypb"))))
26096 (build-system r-build-system)
26098 (list r-xml2 r-httr r-plyr r-stringr r-tibble))
26101 (home-page "https://github.com/ropensci/oai/")
26102 (synopsis "General purpose OAI-PMH services client")
26103 (description "@code{oai} provides a general purpose client to work with
26104 any @dfn{Open Archives Initiative Protocol for 'Metadata' Harvesting} (OAI-PMH)
26105 service. Functions are provided to work with the OAI-PMH verbs:
26106 @code{GetRecord}, @code{Identify}, @code{ListIdentifiers},
26107 @code{ListMetadataFormats}, @code{ListRecords}, and @code{ListSets}.")
26108 (license license:expat)))
26110 (define-public r-argon2
26117 (uri (cran-uri "argon2" version))
26120 "09hzl0wz0lw2v7g64rdv0lij2hq36zl37a6rmxwvinmjdzijcsyw"))))
26121 (properties `((upstream-name . "argon2")))
26122 (build-system r-build-system)
26123 (home-page "https://github.com/wrathematics/argon2")
26124 (synopsis "Secure password hashing based on the argon2 algorithm")
26126 "This package provides utilities for secure password hashing via the
26127 argon2 algorithm.")
26128 (license license:bsd-2)))
26130 (define-public r-getpass
26137 (uri (cran-uri "getPass" version))
26140 "03ydafhh0sk3rcnpr3paajyji64x2ddp6p814p9mvbmyrblcgzcc"))))
26141 (properties `((upstream-name . "getPass")))
26142 (build-system r-build-system)
26144 (list r-rstudioapi))
26145 (home-page "https://github.com/wrathematics/getPass")
26146 (synopsis "Masked user input")
26148 "This package provides a micro-package for reading \"passwords\", i.e.
26149 reading user input with masking, so that the input is not displayed as it is
26150 typed. Currently, RStudio, the command line (every OS), and any platform
26151 where tcltk is present are supported.")
26152 (license license:bsd-2)))
26154 (define-public r-remoter
26161 (uri (cran-uri "remoter" version))
26164 "1a7m63l8phv5jnazvdqdrqkaqjwqzaac5y4jm2jn0ypy4n8jvkfl"))))
26165 (properties `((upstream-name . "remoter")))
26166 (build-system r-build-system)
26168 (list r-argon2 r-getpass r-pbdzmq r-png))
26169 (home-page "https://github.com/RBigData/remoter")
26170 (synopsis "Control a remote R session from a local one")
26172 "This package provides a set of utilities for client/server computing
26173 with R, controlling a remote R session (the server) from a local one (the
26175 (license license:bsd-2)))
26177 (define-public r-asd
26184 (uri (cran-uri "asd" version))
26187 "0p3r4qjam3sl3rpcilb0pgx4xx3ly71xqnvkv31vzjs885lgxz4l"))))
26188 (properties `((upstream-name . "asd")))
26189 (build-system r-build-system)
26192 (home-page "https://cran.r-project.org/web/packages/asd")
26193 (synopsis "Simulations for Adaptive Seamless Designs")
26195 "This package provdes means to run simulations for adaptive seamless
26196 designs with and without early outcomes for treatment selection and
26197 subpopulation type designs.")
26198 (license license:gpl3)))
26200 (define-public r-nbconvertr
26202 (name "r-nbconvertr")
26207 (uri (cran-uri "nbconvertR" version))
26210 "0yhmz177r1miain65vspclahhz8cg7638ldbpsw8ylgf7a60l0sg"))))
26211 (properties `((upstream-name . "nbconvertR")))
26212 (build-system r-build-system)
26214 (list python-nbconvert pandoc))
26215 (home-page "https://cran.r-project.org/web/packages/nbconvertR/")
26216 (synopsis "Vignette engine wrapping Jupyter notebooks")
26218 "This package calls the Jupyter script @code{nbconvert} to create
26219 vignettes from notebooks. Those notebooks (@code{.ipynb} files) are files
26220 containing rich text, code, and its output. Code cells can be edited and
26221 evaluated interactively.")
26222 (license license:gpl3)))
26224 (define-public r-bridgesampling
26226 (name "r-bridgesampling")
26231 (uri (cran-uri "bridgesampling" version))
26234 "0sry1xwiv4y52k44hq6z8y2kysp5kxgl4dix3m94svg3ladd7v2l"))))
26236 `((upstream-name . "bridgesampling")))
26237 (build-system r-build-system)
26239 (list r-brobdingnag
26247 (home-page "https://github.com/quentingronau/bridgesampling")
26248 (synopsis "Bridge sampling for marginal likelihoods and Bayes factors")
26250 "This package provides functions for estimating marginal likelihoods,
26251 Bayes factors, posterior model probabilities, and normalizing constants in
26252 general, via different versions of bridge sampling.")
26253 (license license:gpl2+)))
26255 (define-public r-tea
26262 (uri (cran-uri "tea" version))
26265 "0ql7lrxk0ihm49kqsvz79ig8i54rwiy9nxav4v9hy72j9kj5bgjn"))))
26267 `((upstream-name . "tea")))
26268 (build-system r-build-system)
26271 (home-page "https://cran.r-project.org/web/packages/tea/")
26272 (synopsis "Threshold estimation approaches")
26274 "This package provides different approaches for selecting the threshold
26275 in generalized Pareto distributions. Most of them are based on minimizing the
26276 AMSE-criterion or at least by reducing the bias of the assumed GPD-model.
26277 Others are heuristically motivated by searching for stable sample paths, i.e.
26278 a nearly constant region of the tail index estimator with respect to k, which
26279 is the number of data in the tail. The third class is motivated by graphical
26280 inspection. In addition, a sequential testing procedure for GPD-GoF-tests
26281 is also implemented here.")
26282 (license license:gpl3)))
26284 (define-public r-awsmethods
26286 (name "r-awsmethods")
26291 (uri (cran-uri "awsMethods" version))
26294 "0hbmrcpdyg15zg4rysscsmxpxlpy0dkxx2aa63qibq7l1k14v4sh"))))
26296 `((upstream-name . "awsMethods")))
26297 (build-system r-build-system)
26298 (home-page "http://www.wias-berlin.de/software/imaging/")
26299 (synopsis "Class and methods definitions")
26301 "This package defines the generic method @code{extract} and provides
26302 @code{openMP} support as needed in several packages like
26303 @code{aws}, @code{adimpro}, @code{fmri}, and @code{dwi}.")
26304 (license license:gpl2+)))
26306 (define-public r-aws
26313 (uri (cran-uri "aws" version))
26316 "1fhm87iax6bkvd4vszvjbcqw3b2drs11rjxr7zf2w4sgc72svaz8"))))
26318 `((upstream-name . "aws")))
26319 (build-system r-build-system)
26321 (list r-awsmethods r-gsl))
26324 (home-page "https://cran.r-project.org/web/packages/aws/")
26325 (synopsis "Adaptive weights smoothing")
26327 "This package provides a collection of R-functions implementing adaptive
26328 smoothing procedures in 1D, 2D and 3D. This includes the
26329 Propagation-Separation approach to adaptive smoothing, the @dfn{Intersecting
26330 Confidence Intervals} (ICI), variational approaches, and a non-local means
26332 (license license:gpl2+)))
26334 (define-public r-sgloptim
26336 (name "r-sgloptim")
26341 (uri (cran-uri "sglOptim" version))
26344 "15bkkvgp9v9vsp65wps48g3c2fa0fj1025hbrziywq14j7wayyjr"))))
26346 `((upstream-name . "sglOptim")))
26347 (build-system r-build-system)
26358 (home-page "https://github.com/nielsrhansen/sglOptim")
26359 (synopsis "Generic sparse group Lasso solver")
26361 "This package provides a fast generic solver for sparse group lasso
26362 optimization problems. The loss (objective) function must be defined in a C++
26363 module. The optimization problem is solved using a coordinate gradient
26364 descent algorithm. Convergence of the algorithm is established and the
26365 algorithm is applicable to a broad class of loss functions. Use of parallel
26366 computing for cross validation and subsampling is supported through the
26367 @code{foreach} and @code{doParallel} packages.")
26368 (license license:gpl2+)))
26370 (define-public r-grouped
26377 (uri (cran-uri "grouped" version))
26380 "1glxgacpwk7yjbkwg5ci6bmb2il6hf5zhydwi5bbq6hc032m9976"))))
26382 `((upstream-name . "grouped")))
26383 (build-system r-build-system)
26386 (home-page "https://cran.r-project.org/web/packages/grouped/")
26387 (synopsis "Regression analysis of grouped and coarse data")
26389 "This package provides regression models for grouped and coarse data,
26390 under the coarsened at random assumption.")
26391 (license license:gpl2+)))
26393 (define-public r-stam
26400 (uri (cran-uri "stam" version))
26403 "1x1j45fir64kffny0nssb2hwn4rcp8gd2cjv6fw4yy0l4d0xi5iv"))))
26405 `((upstream-name . "stam")))
26406 (build-system r-build-system)
26409 (home-page "https://cran.r-project.org/web/packages/stam")
26410 (synopsis "Spatio-temporal analysis and modelling")
26412 "This package provides various methods to conduct Spatio-Temporal
26413 Analysis and Modelling, including Exploratory Spatio-Temporal Analysis and
26414 Inferred Spatio-Temporal Modelling.")
26415 (license license:gpl2+)))
26417 (define-public r-dcv
26424 (uri (cran-uri "dcv" version))
26427 "12c716x8dnxnqksibpmyysqp2axggvy9dpd55s9bhnsvqvi6dshj"))))
26429 `((upstream-name . "dcv")))
26430 (build-system r-build-system)
26433 (home-page "https://cran.r-project.org/web/packages/dcv/")
26434 (synopsis "Conventional cross-validation statistics for climate-growth model")
26436 "This package performs several conventional cross-validation statistical
26437 methods for climate-growth model in the climate reconstruction from tree
26438 rings, including Sign Test statistic, Reduction of Error statistic, Product
26439 Mean Test, Durbin-Watson statistic etc.")
26440 (license license:gpl2)))
26442 (define-public r-rcdd
26449 (uri (cran-uri "rcdd" version))
26452 "0zxx0qvv26ba30jkm8mvca4h59rqklay4jwazpcw7h9dzp4189jr"))))
26454 `((upstream-name . "rcdd")))
26455 (build-system r-build-system)
26458 (home-page "https://www.stat.umn.edu/geyer/rcdd/")
26459 (synopsis "Computational geometry")
26461 "This package converts back and forth between two representations of a
26462 convex polytope: as solution of a set of linear equalities and inequalities
26463 and as convex hull of set of points and rays. Also does linear programming
26464 and redundant generator elimination. All functions can use exact
26465 infinite-precision rational arithmetic.")
26466 (license license:gpl2)))
26468 (define-public r-rxnat
26475 (uri (cran-uri "Rxnat" version))
26478 "0siylypjd8cgcmr2c443w8krg8sgr5gz4zapbinanp8vsfzivdv2"))))
26480 `((upstream-name . "Rxnat")))
26481 (build-system r-build-system)
26483 (list r-httr r-rcurl r-tibble))
26486 (home-page "https://cran.r-project.org/web/packages/Rxnat/")
26487 (synopsis "Queries and extracts images from neuroimaging datasets")
26489 "This package allows communication with the Extensible Neuroimaging
26490 Archive Toolkit. Rxnat uses the XNAT REST API to perform data queries and
26492 (license license:gpl2)))
26494 (define-public r-rserve
26501 (uri (string-append "http://www.rforge.net/Rserve/snapshot/Rserve_"
26502 version ".tar.gz"))
26505 "017kkzv9lxlz9qhg3gprrf1wcyflxrif6wjk27x9b4bdzylw6bsx"))))
26506 (build-system r-build-system)
26509 (modify-phases %standard-phases
26510 (add-before 'install 'install-server-binary
26511 ;; Makevars tries to install to R's store directory.
26512 (lambda* (#:key outputs #:allow-other-keys)
26513 (let* ((out (assoc-ref outputs "out"))
26514 (bin (string-append out "/bin")))
26515 (substitute* "src/Makevars.in"
26516 (("\\$\\(R_HOME\\)") out))
26517 (mkdir-p bin)))))))
26527 (list openssl zlib))
26528 (home-page "https://github.com/s-u/Rserve")
26530 "Server providing access to R from many languages and systems")
26532 "Rserve acts as a socket server (TCP/IP or local sockets) which allows
26533 binary requests to be sent to R. Every connection has a separate workspace
26534 and working directory. Client-side implementations are available for popular
26535 languages such as C/C++ and Java, allowing any application to use facilities
26536 of R without the need of linking to R code. Rserve supports remote
26537 connection, user authentication and file transfer. A simple R client is
26538 included in this package as well.")
26539 (license license:gpl2)))
26541 (define-public r-gamm4
26548 (uri (cran-uri "gamm4" version))
26551 "128c725y9s07c1m9cvd9hgi9hldrymcs5divd8pw7bdjh9jvdiap"))))
26552 (properties `((upstream-name . "gamm4")))
26553 (build-system r-build-system)
26555 (list r-lme4 r-matrix r-mgcv))
26556 (home-page "https://cran.r-project.org/web/packages/gamm4/")
26557 (synopsis "Generalized additive mixed models using mgcv and lme4")
26559 "Estimate generalized additive mixed models via a version of function
26560 @code{gamm} from the @code{mgcv} package, using the @code{lme4} packagefor
26562 (license license:gpl2+)))
26564 (define-public r-optimx
26567 (version "2022-4.30")
26571 (uri (cran-uri "optimx" version))
26574 "045ls1vl1392ihwln6mngz0zg2w93ym1m607vfrg8v1949x8isgb"))))
26575 (properties `((upstream-name . "optimx")))
26576 (build-system r-build-system)
26577 (propagated-inputs (list r-numderiv))
26578 (native-inputs (list r-knitr))
26579 (home-page "https://cran.r-project.org/web/packages/optimx/")
26580 (synopsis "Expanded replacement and extension of the optim function")
26582 "This package provides a replacement and extension of the @code{optim}
26583 function to call to several function minimization codes in R in a single
26584 statement. These methods handle smooth, possibly box constrained functions of
26585 several or many parameters. Note that the function @code{optimr} was prepared
26586 to simplify the incorporation of minimization codes going forward. This
26587 package also implements some utility codes and some extra solvers, including
26588 safeguarded Newton methods. Many methods previously separate are now included
26590 (license license:gpl2)))
26592 (define-public r-projpred
26594 (name "r-projpred")
26599 (uri (cran-uri "projpred" version))
26602 "1c6gnmknd3vb0fb5h6gd372dk27nzif90b4c1snql49wacg6b2m8"))))
26603 (properties `((upstream-name . "projpred")))
26604 (build-system r-build-system)
26618 (native-inputs (list r-knitr))
26619 (home-page "https://mc-stan.org/projpred/")
26620 (synopsis "Projection predictive feature selection")
26622 "This package performs projection predictive feature selection for
26623 generalized linear models and generalized linear and additive multilevel
26624 models. The package is compatible with the @code{rstanarm} and @code{brms}
26625 packages, but other reference models can also be used. See the package
26626 vignette for more information and examples.")
26627 (license license:gpl3)))
26629 (define-public r-distributional
26631 (name "r-distributional")
26636 (uri (cran-uri "distributional" version))
26639 "1mji8xlhwrw8msih5wdpbzwv4g59kly0xkdklhn8yzb18rrnrczs"))))
26641 `((upstream-name . "distributional")))
26642 (build-system r-build-system)
26654 (home-page "https://pkg.mitchelloharawild.com/distributional/")
26655 (synopsis "Vectorized probability distributions")
26657 "This package provides vectorized distribution objects with tools for
26658 manipulating, visualizing, and using probability distributions. It was
26659 designed to allow model prediction outputs to return distributions rather than
26660 their parameters, allowing users to directly interact with predictive
26661 distributions in a data-oriented workflow. In addition to providing generic
26662 replacements for p/d/q/r functions, other useful statistics can be computed
26663 including means, variances, intervals, and highest density regions.")
26664 (license license:gpl3)))
26666 (define-public r-posterior
26668 (name "r-posterior")
26673 (uri (cran-uri "posterior" version))
26676 "1qdg22l868daqg2axr36szl1m9z0rfpgx8zmv1x1xwm1hmlf0mxp"))))
26677 (properties `((upstream-name . "posterior")))
26678 (build-system r-build-system)
26691 (home-page "https://mc-stan.org/posterior/")
26692 (synopsis "Tools for working with posterior distributions")
26694 "This package provides useful tools for both users and developers of
26695 packages for fitting Bayesian models or working with output from Bayesian
26696 models. The primary goals of the package are to:
26699 @item Efficiently convert between many different useful formats of
26700 draws (samples) from posterior or prior distributions.
26702 @item Provide consistent methods for operations commonly performed on draws,
26703 for example, subsetting, binding, or mutating draws.
26705 @item Provide various summaries of draws in convenient formats.
26707 @item Provide lightweight implementations of state of the art posterior
26708 inference diagnostics.
26711 (license license:bsd-3)))
26713 (define-public r-brms
26720 (uri (cran-uri "brms" version))
26723 "0wff5rld4kgkk2nbllvm1h4c596igzgd0q7nx1cabgl11fja7r94"))))
26724 (properties `((upstream-name . "brms")))
26725 (build-system r-build-system)
26746 (native-inputs (list r-knitr))
26748 "https://github.com/paul-buerkner/brms")
26750 "Bayesian Regression Models using 'Stan'")
26752 "Fit Bayesian generalized (non-)linear multivariate multilevel models
26753 using 'Stan' for full Bayesian inference. A wide range of distributions and
26754 link functions are supported, allowing users to fit -- among others -- linear,
26755 robust linear, count data, survival, response times, ordinal, zero-inflated,
26756 hurdle, and even self-defined mixture models all in a multilevel context.
26757 Further modeling options include non-linear and smooth terms, auto-correlation
26758 structures, censored data, meta-analytic standard errors, and quite a few
26759 more. In addition, all parameters of the response distribution can be
26760 predicted in order to perform distributional regression. Prior specifications
26761 are flexible and explicitly encourage users to apply prior distributions that
26762 actually reflect their beliefs. Model fit can easily be assessed and compared
26763 with posterior predictive checks and leave-one-out cross-validation.")
26764 (license license:gpl2)))
26766 (define-public r-mstate
26773 (uri (cran-uri "mstate" version))
26776 "054dzrd5b0xjjjl7862q3aq1jwgrxbkqz7zpvbdirqsld3zksirw"))))
26777 (properties `((upstream-name . "mstate")))
26778 (build-system r-build-system)
26789 "https://www.lumc.nl/org/bds/research/medische-statistiek/survival-analysis/")
26791 "Data Preparation, Estimation and Prediction in Multi-State Models")
26793 "Contains functions for data preparation, descriptives, hazard estimation
26794 and prediction with Aalen-Johansen or simulation in competing risks and
26795 multi-state models.")
26796 (license license:gpl2+)))
26798 (define-public r-scatterpie
26800 (name "r-scatterpie")
26805 (uri (cran-uri "scatterpie" version))
26808 "1pmspv8a7k20zyd5xvmav2k9mnjrkfhdij3rr9k504zyki8hfy1z"))))
26809 (properties `((upstream-name . "scatterpie")))
26810 (build-system r-build-system)
26812 (list r-ggforce r-ggfun r-ggplot2 r-rlang r-tidyr))
26815 (home-page "https://cran.r-project.org/web/packages/scatterpie/")
26816 (synopsis "Scatter pie plot")
26818 "This package creates scatterpie plots, especially useful for plotting
26820 (license license:artistic2.0)))
26822 (define-public r-scrypt
26829 (uri (cran-uri "scrypt" version))
26832 "12q9d4m7flbvlgssvjh1ga4jswkmqjfshf6pna6qk6v087gmzdsj"))))
26833 (properties `((upstream-name . "scrypt")))
26834 (build-system r-build-system)
26837 (home-page "https://github.com/rstudio/rscrypt")
26838 (synopsis "Key derivation functions for R based on Scrypt")
26840 "This package provides functions for working with the scrypt key
26841 derivation functions. Scrypt is a password-based key derivation function
26842 created by Colin Percival. The algorithm was specifically designed to make it
26843 costly to perform large-scale custom hardware attacks by requiring large
26844 amounts of memory.")
26845 (license license:bsd-2)))
26847 (define-public r-boruta
26854 (uri (cran-uri "Boruta" version))
26857 "0y2w4wb45kfnzrxcrdsiwgal9fsnlr3wad1sqdc70qv8gp921xbg"))))
26858 (properties `((upstream-name . "Boruta")))
26859 (build-system r-build-system)
26860 (propagated-inputs (list r-ranger))
26861 (home-page "https://gitlab.com/mbq/Boruta/")
26862 (synopsis "Wrapper algorithm for all relevant feature selection")
26864 "This package provides an all relevant feature selection wrapper
26865 algorithm. It finds relevant features by comparing original attributes'
26866 importance with importance achievable at random, estimated using their
26867 permuted copies (shadows).")
26868 (license license:gpl2+)))
26870 (define-public r-directlabels
26872 (name "r-directlabels")
26873 (version "2021.1.13")
26877 (uri (cran-uri "directlabels" version))
26880 "0415kh9k2qzdwi8zb32fh2icl5wf5335kyj11cyfdmfxji39zv2w"))))
26881 (build-system r-build-system)
26886 (home-page "http://directlabels.r-forge.r-project.org/")
26887 (synopsis "Direct labels for multicolor plots")
26889 "This package provides an extensible framework for automatically placing
26890 direct labels onto multicolor plots. Label positions are described using
26891 positioning methods that can be re-used across several different plots. There
26892 are heuristics for examining @code{trellis} and @code{ggplot} objects and
26893 inferring an appropriate positioning method.")
26894 (license license:gpl3)))
26896 (define-public r-lsd
26903 (uri (cran-uri "LSD" version))
26905 (base32 "17pbdlcbhzf3v7l42mjikln1ga5xjp5r78gjg6a88iahk0lwwlvm"))))
26906 (properties `((upstream-name . "LSD")))
26907 (build-system r-build-system)
26908 (home-page "https://cran.r-project.org/web/packages/LSD/")
26909 (synopsis "Lots of superior depictions tool creates colorful plots")
26911 "This package creates lots of colorful plots in a multitude of variations.
26912 Try a demo of the LSD by running @code{demotour()}.")
26914 (license (list license:gpl2 license:gpl3))))
26916 (define-public r-phylogram
26918 (name "r-phylogram")
26923 (uri (cran-uri "phylogram" version))
26925 (base32 "1p4h5pirc0m5pzc18q0jk3mcmb5n48gdf9abz03vml3a209xxl2v"))))
26926 (properties `((upstream-name . "phylogram")))
26927 (build-system r-build-system)
26928 (propagated-inputs (list r-ape))
26929 (home-page "https://github.com/ropensci/phylogram/")
26930 (synopsis "Dendrograms for evolutionary analysis")
26932 "The @code{r-phylogram} package is a tool for for developing phylogenetic
26933 trees as deeply-nested lists known as \"dendrogram\" objects. It provides
26934 functions for conversion between \"dendrogram\" and \"phylo\" class objects,
26935 as well as several tools for command-line tree manipulation and import/export
26936 via Newick parenthetic text. This improves accessibility to the comprehensive
26937 range of object-specific analytical and tree-visualization functions found
26938 across a wide array of bioinformatic R packages.")
26939 (license license:gpl3)))
26941 (define-public r-kmer
26948 (uri (cran-uri "kmer" version))
26950 (base32 "0jimn9r0abglwxdl1zqz0lxa99cmj6haydkxjzqfbpx9by80wnww"))))
26951 (properties `((upstream-name . "kmer")))
26952 (build-system r-build-system)
26954 (list r-openssl r-phylogram r-rcpp))
26955 (home-page "https://github.com/shaunpwilkinson/kmer/")
26956 (synopsis "Fast K-Mer counting and clustering for biological sequence analysis")
26958 "@code{r-kmer} is an R package for rapidly computing distance matrices
26959 and clustering large sequence datasets using fast alignment-free k-mer
26960 counting and recursive k-means partitioning.")
26961 (license license:gpl3)))
26963 (define-public r-hardhat
26970 (uri (cran-uri "hardhat" version))
26973 "0a4nq93cmps5xy8h0qsv6xyzrbsz9ka4iwkrvb8m8v10wq7wm5wl"))))
26974 (properties `((upstream-name . "hardhat")))
26975 (build-system r-build-system)
26977 (list r-glue r-rlang r-tibble r-vctrs))
26980 (home-page "https://github.com/tidymodels/hardhat")
26981 (synopsis "Construct modeling packages")
26983 "Building modeling packages is hard. A large amount of effort generally
26984 goes into providing an implementation for a new method that is efficient,
26985 fast, and correct, but often less emphasis is put on the user interface. A
26986 good interface requires specialized knowledge about S3 methods and formulas,
26987 which the average package developer might not have. The goal of
26988 @code{hardhat} is to reduce the burden around building new modeling packages
26989 by providing functionality for preprocessing, predicting, and validating
26991 (license license:expat)))
26993 (define-public r-lightgbm
26995 (name "r-lightgbm")
27000 (uri (cran-uri "lightgbm" version))
27003 "12hbvm1va6sb5yny564jvhhzrkcq4j33rcdhqhwxaac2m08cpi8s"))))
27004 (properties `((upstream-name . "lightgbm")))
27005 (build-system r-build-system)
27007 (list r-data-table r-jsonlite r-matrix r-r6))
27008 (home-page "https://github.com/Microsoft/LightGBM")
27009 (synopsis "Light gradient boosting machine")
27011 "Tree based algorithms can be improved by introducing boosting
27012 frameworks. LightGBM is one such framework, based on Ke, Guolin et
27013 al. (2017). This package offers an R interface to work with it. It is
27014 designed to be distributed and efficient with the following goals:
27017 @item Faster training speed and higher efficiency;
27018 @item lower memory usage;
27019 @item better accuracy;
27020 @item parallel learning supported; and
27021 @item capable of handling large-scale data.
27024 (license license:expat)))
27026 (define-public r-shapforxgboost
27028 (name "r-shapforxgboost")
27033 (uri (cran-uri "SHAPforxgboost" version))
27036 "106nsf02b1w3yshb55lwnyw1rl1a60162v2wk8znjz3b4ln3mqj5"))))
27038 `((upstream-name . "SHAPforxgboost")))
27039 (build-system r-build-system)
27051 (home-page "https://github.com/liuyanguu/SHAPforxgboost")
27052 (synopsis "SHAP Plots for XGBoost")
27054 "The aim of @code{SHAPforxgboost} is to aid in visual data investigations
27055 using @dfn{SHAP} (Shapley additive explanation) visualization plots for
27056 @code{XGBoost}. It provides summary plot, dependence plot, interaction plot,
27057 and force plot. It relies on the @code{XGBoost} package to produce SHAP
27059 (license license:expat)))
27061 (define-public r-rismed
27068 (uri (cran-uri "RISmed" version))
27071 "0vpi88gzi9r85v6nhjz9jbw671zkrmyazwna2z881346wfyr3l8b"))))
27072 (properties `((upstream-name . "RISmed")))
27073 (build-system r-build-system)
27075 (list r-httr r-xml2))
27076 (home-page "https://cran.r-project.org/web/packages/RISmed")
27077 (synopsis "Download content from NCBI databases")
27079 "This package provides a set of tools to extract bibliographic
27080 content from the National Center for Biotechnology Information (NCBI)
27081 databases, including PubMed. The name RISmed is a portmanteau of
27082 RIS (for Research Information Systems, a common tag format for
27083 bibliographic data) and PubMed.")
27084 (license license:gpl2+)))
27086 (define-public r-semver
27093 (uri (cran-uri "semver" version))
27096 "10wpkyms2cix3bsin2q0qhkbl445pwwpa5gm2s4jjw1989namkxy"))))
27097 (properties `((upstream-name . "semver")))
27098 (build-system r-build-system)
27100 (list r-assertthat r-rcpp))
27101 (native-inputs (list r-knitr))
27102 (home-page "https://github.com/johndharrison/semver")
27103 (synopsis "Parser for Semantic Versioning 2.0.0")
27105 "This package provides tools and functions for parsing, rendering and
27106 operating on semantic version strings. Semantic versioning is a simple set of
27107 rules and requirements that dictate how version numbers are assigned and
27108 incremented as outlined at @url{http://semver.org}.")
27109 (license license:expat)))
27111 (define-public r-binman
27118 (uri (cran-uri "binman" version))
27121 "00l7m98h41r67gf0qxqis3vx63j7wylnk9vlgcyk41szkrz8ikkc"))))
27122 (properties `((upstream-name . "binman")))
27123 (build-system r-build-system)
27132 (native-inputs (list r-knitr))
27133 (home-page "https://github.com/ropensci/binman")
27134 (synopsis "Binary download manager")
27136 "This package provides tools and functions for managing the download of
27137 binary files. Binary repositories are defined in the YAML format. Defining
27138 new pre-download, download and post-download templates allow additional
27139 repositories to be added.")
27140 (license license:expat)))
27142 (define-public r-wdman
27149 (uri (cran-uri "wdman" version))
27152 "1yf41lsrr9dbf5n4f5hv9mlmzl736fhnp9gxkm2g9apws6gsig02"))))
27153 (properties `((upstream-name . "wdman")))
27154 (build-system r-build-system)
27156 (list r-assertthat r-binman r-processx r-semver r-yaml))
27157 (native-inputs (list r-knitr))
27158 (home-page "https://docs.ropensci.org/wdman/")
27159 (synopsis "Webdriver/Selenium binary manager")
27161 "There are a number of binary files associated with the
27162 Webdriver/Selenium project (see @url{http://www.seleniumhq.org/download/},
27163 @url{https://sites.google.com/a/chromium.org/chromedriver/},
27164 @url{https://github.com/mozilla/geckodriver},
27165 @url{http://phantomjs.org/download.html}, and
27166 @url{https://github.com/SeleniumHQ/selenium/wiki/InternetExplorerDriver} for
27167 more information). This package provides functions to download these binaries
27168 and to manage processes involving them.")
27169 (license license:expat)))
27171 (define-public r-rselenium
27173 (name "r-rselenium")
27178 (uri (cran-uri "RSelenium" version))
27181 "1xn5fdbzmq7b1f5fc9ls23g177bmnd8bn4p4d8aafr6z3jwkmfir"))))
27182 (properties `((upstream-name . "RSelenium")))
27183 (build-system r-build-system)
27191 (native-inputs (list r-knitr))
27192 (home-page "https://docs.ropensci.org/RSelenium/")
27193 (synopsis "R bindings for Selenium WebDriver")
27195 "This package provides a set of R bindings for the Selenium 2.0
27196 WebDriver (see @url{https://selenium.dev/documentation/en/} for more
27197 information) using the @code{JsonWireProtocol} (see
27198 @url{https://github.com/SeleniumHQ/selenium/wiki/JsonWireProtocol} for more
27199 information). Selenium 2.0 WebDriver allows driving a web browser natively as
27200 a user would either locally or on a remote machine using the Selenium server
27201 it marks a leap forward in terms of web browser automation. Selenium
27202 automates web browsers (commonly referred to as browsers). Using RSelenium
27203 you can automate browsers locally or remotely.")
27204 (license license:agpl3+)))
27206 (define-public r-conquer
27213 (uri (cran-uri "conquer" version))
27216 "1ynmaf7lgqjb8grsifx5dzy29cd5kz4x3yh0abnl2vxdr4c4wddc"))))
27217 (properties `((upstream-name . "conquer")))
27218 (build-system r-build-system)
27220 (list r-matrix r-matrixstats r-rcpp r-rcpparmadillo))
27221 (home-page "https://github.com/XiaoouPan/conquer")
27222 (synopsis "Convolution-type smoothed quantile regression")
27224 "This package provides fast and accurate convolution-type smoothed
27225 quantile regression, implemented using Barzilai-Borwein gradient descent with
27226 a Huber regression warm start. Confidence intervals for regression
27227 coefficients are constructed using multiplier bootstrap.")
27228 (license license:gpl3)))
27230 (define-public r-fastshap
27232 (name "r-fastshap")
27237 (uri (cran-uri "fastshap" version))
27240 "0gxch67i3bj6m8nb94m5hswq058w6n1q9war4dy2qnimlv7cmhdv"))))
27241 (properties `((upstream-name . "fastshap")))
27242 (build-system r-build-system)
27252 (home-page "https://github.com/bgreenwell/fastshap")
27253 (synopsis "Fast approximate Shapley values")
27255 "This package computes fast (relative to other implementations)
27256 approximate Shapley values for any supervised learning model. Shapley values
27257 help to explain the predictions from any black box model using ideas from game
27258 theory; see @url{Strumbel and Kononenko (2014),
27259 doi.org/10.1007/s10115-013-0679-x} for details.")
27260 (license license:gpl2+)))
27262 (define-public r-memuse
27268 (uri (cran-uri "memuse" version))
27271 "1wvwnjaaiv2647561z2b55dss35033ildx4kk8hzxfzgsjmdpsgm"))))
27272 (properties `((upstream-name . "memuse")))
27273 (build-system r-build-system)
27274 (home-page "https://github.com/shinra-dev/memuse")
27275 (synopsis "Memory Estimation Utilities")
27277 "This package provides procedures to answer the following questions:
27278 How much ram do you need to store a 100,000 by 100,000 matrix? How much ram is
27279 your current R session using? How much ram do you even have?")
27280 (license license:bsd-2)))
27282 (define-public r-metrics
27289 (uri (cran-uri "Metrics" version))
27292 "0fh8qbjlwzagh272lgwr4bxcqcjb1qpz53mgs8rzlvncax6nk5bk"))))
27293 (properties `((upstream-name . "Metrics")))
27294 (build-system r-build-system)
27295 (home-page "https://github.com/mfrasco/Metrics")
27296 (synopsis "Evaluation metrics for machine learning")
27298 "This package provides an implementation of evaluation metrics in R that
27299 are commonly used in supervised machine learning. It implements metrics for
27300 regression, time series, binary classification, classification, and
27301 information retrieval problems. It has zero dependencies and a consistent,
27302 simple interface for all functions.")
27303 (license license:bsd-3)))
27305 (define-public r-iml
27312 (uri (cran-uri "iml" version))
27315 "1za7bjnp07i20vyb6vxz2ya5cr8g4p076w61n8m38wnz04lz5yz5"))))
27316 (properties `((upstream-name . "iml")))
27317 (build-system r-build-system)
27328 (native-inputs (list r-knitr))
27329 (home-page "https://github.com/christophM/iml")
27330 (synopsis "Interpretable machine learning")
27332 "This package provides interpretability methods to analyze the behavior
27333 and predictions of any machine learning model. Implemented methods are:
27336 @item Feature importance described by Fisher et al. (2018),
27337 @item accumulated local effects plots described by Apley (2018),
27338 @item partial dependence plots described by Friedman (2001),
27339 @item individual conditional expectation ('ice') plots described by Goldstein
27340 et al. (2013) @url{https://doi.org/10.1080/10618600.2014.907095},
27341 @item local models (variant of 'lime') described by Ribeiro et. al (2016),
27342 @item the Shapley Value described by Strumbelj et. al (2014)
27343 @url{https://doi.org/10.1007/s10115-013-0679-x},
27344 @item feature interactions described by Friedman et. al
27345 @url{https://doi.org/10.1214/07-AOAS148} and tree surrogate models.
27348 (license license:expat)))
27350 (define-public r-goftest
27357 (uri (cran-uri "goftest" version))
27360 "06bz6k7smr4jbvzmb73qc5fkf4my59w5gbl18wlmpkkymsv78prs"))))
27361 (properties `((upstream-name . "goftest")))
27362 (build-system r-build-system)
27363 (home-page "https://github.com/baddstats/goftest")
27364 (synopsis "Classical Goodness-of-Fit tests for univariate distributions")
27366 "This package provides Cramer-Von Mises and Anderson-Darling tests of
27367 goodness-of-fit for continuous univariate distributions, using efficient
27369 (license license:gpl2+)))
27371 (define-public r-tensor
27378 (uri (cran-uri "tensor" version))
27381 "19mfsgr6vz4lgwidm80i4yw0y1dr3n8i6qz7g4n2xa0k74zc5pp1"))))
27382 (properties `((upstream-name . "tensor")))
27383 (build-system r-build-system)
27384 (home-page "https://cran.r-project.org/web/packages/tensor/")
27385 (synopsis "Tensor product of arrays")
27387 "The tensor product of two arrays is notionally an outer product of the
27388 arrays collapsed in specific extents by summing along the appropriate
27389 diagonals. This package allows you to compute the tensor product of arrays.")
27390 (license license:gpl2+)))
27392 (define-public r-spatstat-utils
27394 (name "r-spatstat-utils")
27399 (uri (cran-uri "spatstat.utils" version))
27402 "08pybliv4r3v4rcazmlfr4a07sjfhrkmksdmhhq9k185vw4474av"))))
27404 `((upstream-name . "spatstat.utils")))
27405 (build-system r-build-system)
27406 (home-page "http://www.spatstat.org")
27407 (synopsis "Utility functions for spatstat")
27409 "This package contains utility functions for the @code{spatstat} package
27410 which may also be useful for other purposes.")
27411 (license license:gpl2+)))
27413 (define-public r-spatstat-sparse
27415 (name "r-spatstat-sparse")
27420 (uri (cran-uri "spatstat.sparse" version))
27423 "00vkvv5pnm82gn7vqnzrrp68y46gbkhdq0hbwqx7nxjvf5lssdcs"))))
27425 `((upstream-name . "spatstat.sparse")))
27426 (build-system r-build-system)
27428 (list r-abind r-matrix r-spatstat-utils r-tensor))
27429 (home-page "http://spatstat.org/")
27430 (synopsis "Sparse three-dimensional arrays and linear algebra utilities")
27432 "This package defines sparse three-dimensional arrays and supports
27433 standard operations on them. The package also includes utility functions for
27434 matrix calculations that are common in statistics, such as quadratic forms.")
27435 (license license:gpl2+)))
27437 (define-public r-spatstat-data
27439 (name "r-spatstat-data")
27444 (uri (cran-uri "spatstat.data" version))
27447 "1rf36zy29h9qabpv19hx84gjdiay7i9y9777d2zn17ahyss3p56k"))))
27448 (properties `((upstream-name . "spatstat.data")))
27449 (build-system r-build-system)
27451 (list r-matrix r-spatstat-utils))
27452 (home-page "http://www.spatstat.org")
27453 (synopsis "Datasets for spatstat")
27455 "This package contains all the datasets for the @code{spatstat}
27457 (license license:gpl2+)))
27459 (define-public r-spatstat-geom
27461 (name "r-spatstat-geom")
27466 (uri (cran-uri "spatstat.geom" version))
27469 "0rwysq9a0ylbsr53q5kfh7wjk5mcdji211sc3s8gwzz8ki09mf1j"))))
27470 (properties `((upstream-name . "spatstat.geom")))
27471 (build-system r-build-system)
27473 (list r-deldir r-polyclip r-spatstat-data r-spatstat-utils))
27474 (home-page "http://spatstat.org/")
27475 (synopsis "Geometrical functionality of the spatstat package")
27477 "This is a subset of the original spatstat package, containing the
27478 user-level code from spatstat which performs geometrical operations, except
27479 for the geometry of linear networks.")
27480 (license license:gpl2+)))
27482 (define-public r-spatstat-core
27484 (name "r-spatstat-core")
27489 (uri (cran-uri "spatstat.core" version))
27492 "0fyi8y1z919nzn47kaviln7gflhcp5qdi3gfvf7nwkdix3pkk373"))))
27493 (properties `((upstream-name . "spatstat.core")))
27494 (build-system r-build-system)
27508 (home-page "http://spatstat.org/")
27509 (synopsis "Core functionality of the spatstat package")
27511 "This is a subset of the original spatstat package, containing all of the
27512 user-level code from spatstat, except for the code for linear networks.")
27513 (license license:gpl2+)))
27515 (define-public r-spatstat-linnet
27517 (name "r-spatstat-linnet")
27522 (uri (cran-uri "spatstat.linnet" version))
27525 "0y1py6x0xbw4ad3pjwcspi4ysgfh61f5fd79787zzgyyh2va8y4w"))))
27527 `((upstream-name . "spatstat.linnet")))
27528 (build-system r-build-system)
27537 (home-page "http://spatstat.org/")
27538 (synopsis "Linear networks functionality of the spatstat package")
27540 "This is a subset of the spatstat package, containing its functionality
27541 for spatial data on a linear network.")
27542 (license license:gpl2+)))
27544 (define-public r-spatstat-random
27546 (name "r-spatstat-random")
27551 (uri (cran-uri "spatstat.random" version))
27553 (base32 "0kb01s8k67ydcfqcnz3i55vpiksihh4xsg0w2p2bclxxkpdvpw25"))))
27554 (properties `((upstream-name . "spatstat.random")))
27555 (build-system r-build-system)
27556 (propagated-inputs (list r-spatstat-data r-spatstat-geom r-spatstat-utils))
27557 (home-page "http://spatstat.org/")
27558 (synopsis "Random Generation Functionality for the 'spatstat' Family")
27560 "This package provides functionality for random generation of spatial
27561 data in the spatstat family of packages. It generates random spatial patterns
27562 of points according to many simple rules (complete spatial randomness,
27563 Poisson, binomial, random grid, systematic, cell), randomised alteration of
27564 patterns (thinning, random shift, jittering), simulated realisations of random
27565 point processes (simple sequential inhibition, Matern inhibition models,
27566 Matern cluster process, Neyman-Scott cluster processes, log-Gaussian Cox
27567 processes, product shot noise cluster processes) and simulation of Gibbs point
27568 processes (Metropolis-Hastings birth-death-shift algorithm, alternating Gibbs
27570 (license license:gpl2+)))
27572 (define-public r-spatstat
27574 (name "r-spatstat")
27579 (uri (cran-uri "spatstat" version))
27582 "1nlrp7660y68axlm4pczc5rxbdhbbac1ylh69azr4swj1gbzi82f"))))
27583 (properties `((upstream-name . "spatstat")))
27584 (build-system r-build-system)
27586 (list r-spatstat-core r-spatstat-data r-spatstat-geom
27587 r-spatstat-linnet r-spatstat-random r-spatstat-utils))
27588 (home-page "http://www.spatstat.org")
27589 (synopsis "Spatial Point Pattern analysis, model-fitting, simulation, tests")
27591 "This package provides a comprehensive toolbox for analysing Spatial
27592 Point Patterns. It is focused mainly on two-dimensional point patterns,
27593 including multitype/marked points, in any spatial region. It also supports
27594 three-dimensional point patterns, space-time point patterns in any number of
27595 dimensions, point patterns on a linear network, and patterns of other
27596 geometrical objects. It supports spatial covariate data such as pixel images
27597 and contains over 2000 functions for plotting spatial data, exploratory data
27598 analysis, model-fitting, simulation, spatial sampling, model diagnostics, and
27599 formal inference.")
27600 (license license:gpl2+)))
27602 (define-public r-gaston
27609 (uri (cran-uri "gaston" version))
27612 "14z94dpln4dvgrv2w7w9ik7h6rpvbf02qhq1hqzx8c2cndzxr21i"))))
27613 (properties `((upstream-name . "gaston")))
27614 (build-system r-build-system)
27615 (inputs (list zlib))
27617 (list r-rcpp r-rcppeigen r-rcppparallel))
27618 (native-inputs (list r-knitr))
27619 (home-page "https://cran.r-project.org/web/packages/gaston/")
27620 (synopsis "Genetic data handling (QC, GRM, LD, PCA) and linear mixed models")
27622 "This is a package for the manipulation of genetic data (SNPs).
27623 Computation of @dfn{genetic relationship matrix} (GRM) and dominance matrix,
27624 @dfn{linkage disequilibrium} (LD), and heritability with efficient algorithms
27625 for linear mixed models (AIREML).")
27626 (license license:gpl3)))
27628 (define-public r-cpp11
27635 (uri (cran-uri "cpp11" version))
27638 "16cvjfkbc7c0ymdmbcqg9px6pjsqx6qhyfq5frqj739mhazy0g20"))))
27639 (properties `((upstream-name . "cpp11")))
27640 (build-system r-build-system)
27641 (native-inputs (list r-knitr))
27642 (home-page "https://github.com/r-lib/cpp11")
27643 (synopsis "C++11 Interface for R's C Interface")
27645 "This package provides a header only, C++11 interface to R's C interface.
27646 Compared to other approaches @code{cpp11} strives to be safe against long
27647 jumps from the C API as well as C++ exceptions, conform to normal R function
27648 semantics and supports interaction with @code{ALTREP} vectors.")
27649 (license license:expat)))
27651 (define-public r-rcpptoml
27653 (name "r-rcpptoml")
27658 (uri (cran-uri "RcppTOML" version))
27660 (base32 "0h8517ipwqhqkhcfiyqmvsb585g01p0ra0azbpzyxip6pq6g029g"))))
27661 (properties `((upstream-name . "RcppTOML")))
27662 (build-system r-build-system)
27663 (propagated-inputs (list r-rcpp))
27664 (home-page "http://dirk.eddelbuettel.com/code/rcpp.toml.html")
27665 (synopsis "Rcpp bindings to TOML parser")
27667 "The TOML configuration format specifies an excellent format suitable for
27668 both human editing as well as the common uses of a machine-readable format.
27669 This package provides Rcpp bindings to a TOML parser.")
27670 (license license:gpl2+)))
27672 (define-public r-rcppziggurat
27674 (name "r-rcppziggurat")
27679 (uri (cran-uri "RcppZiggurat" version))
27682 "0wgd1v2p7zajnbrjf3hfi56p3pk3ld6iwkanbb04bjbnlif2ay4w"))))
27683 (properties `((upstream-name . "RcppZiggurat")))
27684 (build-system r-build-system)
27686 (list r-rcpp r-rcppgsl))
27687 (native-inputs (list r-knitr))
27688 (home-page "https://cran.r-project.org/web/packages/RcppZiggurat/")
27689 (synopsis "Rcpp integration of different \"Ziggurat\" normal RNG implementations")
27691 "The Ziggurat generator for normally distributed random numbers,
27692 originally proposed by Marsaglia and Tsang (2000,
27693 @url{https://doi.org/10.18637/jss.v005.i08}) has been improved upon a few
27694 times starting with Leong et al (2005,
27695 @url{https://doi.org/10.18637/jss.v012.i07}). This package provides an
27696 aggregation for comparing different implementations in order to provide a
27697 'faster but good enough' alternative for use with R and C++ code.")
27698 (license license:gpl2+)))
27700 (define-public r-rfast
27707 (uri (cran-uri "Rfast" version))
27710 "0zxykq021h57mq0n6giqbx8ncjsdly0arhmaj3fcp3yfcxf4ns9l"))))
27711 (properties `((upstream-name . "Rfast")))
27712 (build-system r-build-system)
27714 (list r-rcpp r-rcpparmadillo r-rcppziggurat))
27715 (home-page "https://github.com/RfastOfficial/Rfast")
27716 (synopsis "Collection of efficient and fast R functions")
27718 "This package provides a collection of fast (utility) functions for data
27719 analysis. Column- and row- wise means, medians, variances, minimums,
27720 maximums, many t, F and G-square tests, many regressions (normal, logistic,
27721 Poisson), are some of the many fast functions.")
27722 (license license:gpl2+)))
27724 (define-public r-rffc
27730 (uri (string-append
27731 "https://download.r-forge.r-project.org/src/contrib/"
27732 "rfFC_" version ".tar.gz"))
27735 "05x9wgzsmx4vb12lmcspymgmpb2xw8bwryb8ysg7vzg2nkh0ma3g"))))
27736 (build-system r-build-system)
27738 (list r-randomforest))
27739 (home-page "https://r-forge.r-project.org/projects/rffc/")
27740 (synopsis "Random Forest Feature Contributions")
27741 (description "This package provides functions for extracting feature
27742 contributions from a random forest model from package @code{randomForest}.
27743 Feature contributions provide detailed information about the relationship
27744 between data variables and the predicted value returned by random forest
27746 (license license:gpl2)))
27748 (define-public r-clusterr
27750 (name "r-clusterr")
27755 (uri (cran-uri "ClusterR" version))
27758 "00mha8madcba83ix4fc04rb7sagfm0lxlh1wvs7dvjdrngps41jr"))))
27759 (properties `((upstream-name . "ClusterR")))
27760 (build-system r-build-system)
27762 (list r-ggplot2 r-gmp r-gtools r-rcpp r-rcpparmadillo))
27763 (native-inputs (list r-knitr))
27764 (home-page "https://github.com/mlampros/ClusterR")
27765 (synopsis "Clustering")
27767 "This package provides Gaussian mixture models, k-means,
27768 mini-batch-kmeans, k-medoids and affinity propagation clustering with the
27769 option to plot, validate, predict (new data) and estimate the optimal number
27770 of clusters. The package takes advantage of @code{RcppArmadillo} to speed up
27771 the computationally intensive parts of the functions. For more information,
27775 @item \"Clustering in an Object-Oriented Environment\" by Anja Struyf, Mia
27776 Hubert, Peter Rousseeuw (1997), Journal of Statistical Software,
27777 @url{https://doi.org/10.18637/jss.v001.i04};
27778 @item \"Web-scale k-means clustering\" by D. Sculley (2010), ACM Digital
27779 Library, @url{https://doi.org/10.1145/1772690.1772862};
27780 @item \"Armadillo: a template-based C++ library
27781 for linear algebra\" by Sanderson et al (2016), The Journal of Open Source
27782 Software, @url{https://doi.org/10.21105/joss.00026};
27783 @item \"Clustering by Passing Messages Between Data Points\" by Brendan
27784 J. Frey and Delbert Dueck, Science 16 Feb 2007: Vol. 315, Issue 5814,
27785 pp. 972-976, @url{https://doi.org/10.1126/science.1136800}.
27788 (license license:gpl3)))
27790 (define-public r-spectrum
27792 (name "r-spectrum")
27797 (uri (cran-uri "Spectrum" version))
27800 "0n38d360azkck6vvhr771zsh0gbvd9qsf9ygg5r18vhz0pb1xcfw"))))
27801 (properties `((upstream-name . "Spectrum")))
27802 (build-system r-build-system)
27804 (list r-clusterr r-diptest r-ggplot2 r-rfast))
27805 (native-inputs (list r-knitr))
27806 (home-page "https://cran.r-project.org/web/packages/Spectrum/")
27807 (synopsis "Fast adaptive spectral clustering for single and multi-view data")
27809 "This package provides a self-tuning spectral clustering method for
27810 single or multi-view data. Spectrum uses a new type of adaptive density aware
27811 kernel that strengthens connections in the graph based on common nearest
27812 neighbours. It uses a tensor product graph data integration and diffusion
27813 procedure to integrate different data sources and reduce noise. Spectrum uses
27814 either the eigengap or multimodality gap heuristics to determine the number of
27815 clusters. The method is sufficiently flexible so that a wide range of
27816 Gaussian and non-Gaussian structures can be clustered with automatic selection
27818 (license license:agpl3+)))
27820 (define-public r-nabor
27827 (uri (cran-uri "nabor" version))
27830 "1nj39cdfwrmhgsi3cq8imxv3n6xzc1v6dzdb2cf2hybjk368v4s7"))))
27831 (properties `((upstream-name . "nabor")))
27832 (build-system r-build-system)
27834 (list r-bh r-rcpp r-rcppeigen))
27835 (home-page "https://cran.r-project.org/web/packages/nabor/")
27836 (synopsis "Wrapper for K nearest neighbour library for low dimensions")
27838 "This package provides an R wrapper for libnabo, an exact or approximate
27839 k nearest neighbour library which is optimised for low dimensional
27840 spaces (e.g. 3D). @code{nabor} includes a @code{knn} function that is
27841 designed as a drop-in replacement for the RANN function @code{nn2}. In
27842 addition, objects which include the k-d tree search structure can be returned
27843 to speed up repeated queries of the same set of target points.")
27844 (license license:bsd-3)))
27846 (define-public r-naturalsort
27848 (name "r-naturalsort")
27852 (uri (cran-uri "naturalsort" version))
27855 "0mz801y9mzld9ypp3xmsjw2d8l9q97sdnv09wrci9xi3yg2sjf6d"))))
27856 (build-system r-build-system)
27857 (home-page "https://cran.r-project.org/web/packages/naturalsort/")
27858 (synopsis "Natural ordering")
27859 (description "This package provides functions related to human natural
27860 ordering. It handles adjacent digits in a character sequence as a number
27861 so that natural sort function arranges a character vector by their numbers,
27862 not digit characters.")
27863 (license license:bsd-3)))
27865 (define-public r-visdat
27871 (uri (cran-uri "visdat" version))
27874 "1ikqp29nncbw1xlwyb9dqqgcdk9q0bs3wxhnhnjpb11vcjv7cz2j"))))
27875 (build-system r-build-system)
27887 (home-page "https://visdat.njtierney.com/")
27888 (synopsis "Preliminary Visualisation of Data")
27889 (description "This package provides procedures to create preliminary exploratory
27890 data visualisations of an entire dataset to identify problems or unexpected features
27891 using @code{ggplot2}.")
27892 (license license:expat)))
27894 (define-public r-muhaz
27897 (version "1.2.6.4")
27901 (uri (cran-uri "muhaz" version))
27904 "1ddy8ayr4rdhzcipdvxdwd7z5g9hfp0ppacl7xf6f2612cn1185g"))))
27905 (properties `((upstream-name . "muhaz")))
27906 (build-system r-build-system)
27911 (home-page "https://cran.r-project.org/web/packages/muhaz/")
27912 (synopsis "Hazard function estimation in survival analysis")
27914 "This package produces a smooth estimate of the hazard function for
27916 ;; Any version of the GPL.
27917 (license license:gpl3+)))
27919 (define-public r-flexsurv
27921 (name "r-flexsurv")
27926 (uri (cran-uri "flexsurv" version))
27929 "0kwij9nkdvnsn1kn12fj3hjkd2qpgw7bdda4qad7basq5p6divlp"))))
27930 (properties `((upstream-name . "flexsurv")))
27931 (build-system r-build-system)
27954 (home-page "https://github.com/chjackson/flexsurv-dev")
27955 (synopsis "Flexible parametric survival and multi-state models")
27957 "This package provides flexible parametric models for time-to-event data,
27958 including the Royston-Parmar spline model, generalized gamma and generalized F
27959 distributions. Any user-defined parametric distribution can be fitted, given
27960 at least an R function defining the probability density or hazard. There are
27961 also tools for fitting and predicting from fully parametric multi-state
27963 (license license:gpl2+)))
27965 (define-public r-transphylo
27967 (name "r-transphylo")
27972 (uri (cran-uri "TransPhylo" version))
27975 "0g92kwi1nlmpc8m4pc9kv9xhczryr2kn9icfr3js7da7vy8g50xy"))))
27976 (properties `((upstream-name . "TransPhylo")))
27977 (build-system r-build-system)
27979 (list r-ape r-rcpp))
27982 (home-page "https://cran.r-project.org/web/packages/TransPhylo/")
27983 (synopsis "Inference of transmission tree from a dated phylogeny")
27985 "This is a package to infer transmission trees from a dated phylogeny.
27986 It includes methods to simulate and analyze outbreaks. The methodology is
27987 described in @url{https://doi.org/10.1093/molbev/msu121,Didelot et al. (2014)}
27988 and @url{https://doi.org/10.1093/molbev/msw275,Didelot et al. (2017)}.")
27989 (license license:gpl2+)))
27991 (define-public r-km-ci
27998 (uri (cran-uri "km.ci" version))
28001 "18sc9vhbdgks8lhk2nfxkkayh8j4j227hl63fm5p04f7z4wm6wc1"))))
28002 (properties `((upstream-name . "km.ci")))
28003 (build-system r-build-system)
28006 (home-page "https://cran.r-project.org/web/packages/km.ci/")
28007 (synopsis "Confidence intervals for the Kaplan-Meier estimator")
28009 "This package computes various @dfn{confidence intervals} (CI) for the
28010 Kaplan-Meier estimator, namely: Petos CI, Rothman CI, CIs based on Greenwoods
28011 variance, Thomas and Grunkemeier CI and the simultaneous confidence bands by
28012 Nair and Hall and Wellner.")
28013 (license license:gpl2+)))
28015 (define-public r-kmsurv
28022 (uri (cran-uri "KMsurv" version))
28025 "0hi5vvk584rl70gbrr75w9hc775xmbxnaig0dd6hlpi4071pnqjm"))))
28026 (properties `((upstream-name . "KMsurv")))
28027 (build-system r-build-system)
28028 (home-page "https://cran.r-project.org/web/packages/KMsurv/")
28029 (synopsis "Data sets from Klein and Moeschberger (1997), Survival Analysis")
28031 "This package provides data sets and functions for Klein and Moeschberger
28032 (1997), \"Survival Analysis, Techniques for Censored and Truncated Data\",
28034 (license license:gpl3+)))
28036 (define-public r-survmisc
28038 (name "r-survmisc")
28043 (uri (cran-uri "survMisc" version))
28046 "014cf7sfndmib9jmj0p3h67sr750k2pvw7m865zwdpvlqddi44fr"))))
28047 (properties `((upstream-name . "survMisc")))
28048 (build-system r-build-system)
28061 (home-page "https://cran.r-project.org/web/packages/survMisc/")
28062 (synopsis "Miscellaneous functions for survival data")
28064 "This package provides a collection of functions to help in the analysis
28065 of right-censored survival data. These extend the methods available in
28066 the @code{survival} package.")
28067 (license license:gpl2)))
28069 (define-public r-exactranktests
28071 (name "r-exactranktests")
28076 (uri (cran-uri "exactRankTests" version))
28079 "1qv9i57chhz8xiv0j8r47rbigyqs72fa7ssz99inyc0s8gzskd3y"))))
28081 `((upstream-name . "exactRankTests")))
28082 (build-system r-build-system)
28083 (home-page "https://cran.r-project.org/web/packages/exactRankTests/")
28084 (synopsis "Exact distributions for rank and permutation tests")
28086 "This package computes exact conditional p-values and quantiles using an
28087 implementation of the Shift-Algorithm by Streitberg & Roehmel.")
28088 (license license:gpl2+)))
28090 (define-public r-maxstat
28097 (uri (cran-uri "maxstat" version))
28100 "114z1rwxwvk05ijjhdppzm148n1h192fp0w12ky10zkrhf6kphbg"))))
28101 (properties `((upstream-name . "maxstat")))
28102 (build-system r-build-system)
28104 (list r-exactranktests r-mvtnorm))
28105 (home-page "https://cran.r-project.org/web/packages/maxstat/")
28106 (synopsis "Maximally selected rank statistics")
28108 "This package provides maximally selected rank statistics with several
28109 p-value approximations.")
28110 (license license:gpl2+)))
28112 (define-public r-survminer
28114 (name "r-survminer")
28119 (uri (cran-uri "survminer" version))
28122 "0byh0wxdbjfwdrzsnqv4xlmnik6lj0vkkzfxy7lssk8dv5zmj7nz"))))
28123 (properties `((upstream-name . "survminer")))
28124 (build-system r-build-system)
28143 (home-page "https://rpkgs.datanovia.com/survminer/index.html")
28144 (synopsis "Drawing survival curves using ggplot2")
28146 "This package contains the function @code{ggsurvplot()} for easily
28147 drawing beautiful and 'ready-to-publish' survival curves with the 'number at
28148 risk' table and 'censoring count plot'. Other functions are also available to
28149 plot adjusted curves for Cox model and to visually examine Cox model
28151 (license license:gpl2)))
28153 (define-public r-forge
28160 (uri (cran-uri "forge" version))
28163 "0pjfzsc35agkh0zfw2czwajkbsyn6liys5irl5bhz5r1vim3jmwa"))))
28164 (properties `((upstream-name . "forge")))
28165 (build-system r-build-system)
28167 (list r-magrittr r-rlang))
28168 (home-page "https://cran.r-project.org/web/packages/forge/")
28169 (synopsis "Cast values into shape")
28171 "This package provides helper functions with a consistent interface to
28172 coerce and verify the types and shapes of values for input checking.")
28173 (license license:asl2.0)))
28175 (define-public r-config
28182 (uri (cran-uri "config" version))
28185 "0l2zp7v6qaz72dclcbjrlis633zlwp8rsi5azr7iw127iyz7i26l"))))
28186 (properties `((upstream-name . "config")))
28187 (build-system r-build-system)
28192 (home-page "https://github.com/rstudio/config")
28193 (synopsis "Manage environment specific configuration values")
28195 "This package lets you manage configuration values across multiple
28196 environments (e.g. development, test, production). It reads values using a
28197 function that determines the current environment and returns the appropriate
28199 (license license:gpl3)))
28201 (define-public r-adaptivesparsity
28203 (name "r-adaptivesparsity")
28207 (uri (cran-uri "AdaptiveSparsity" version))
28210 "0imr5m8mll9j6n4icsv6z9rl5kbnwsp9wvzrg7n90nnmcxq2cz91"))))
28212 `((upstream-name . "AdaptiveSparsity")))
28213 (build-system r-build-system)
28216 (modify-phases %standard-phases
28217 (add-after 'unpack 'link-against-armadillo
28219 (substitute* "src/Makevars"
28220 (("PKG_LIBS=" prefix)
28221 (string-append prefix "-larmadillo")))
28224 (list r-mass r-matrix r-rcpp r-rcpparmadillo))
28227 (home-page "https://cran.r-project.org/web/packages/AdaptiveSparsity")
28228 (synopsis "Adaptive sparsity models")
28230 "This package implements the Figueiredo machine learning algorithm for
28231 adaptive sparsity and the Wong algorithm for adaptively sparse Gaussian
28232 geometric models.")
28233 (license license:lgpl3+)))
28235 (define-public r-add2ggplot
28237 (name "r-add2ggplot")
28242 (uri (cran-uri "add2ggplot" version))
28244 (base32 "0c94i1cfp2pvplvxmfvvz2fyj026r1jnax05mrzrc7ppnqzy25y0"))))
28245 (properties `((upstream-name . "add2ggplot")))
28246 (build-system r-build-system)
28248 (list r-ggplot2 r-magick r-magrittr r-rcolorbrewer r-zeallot))
28249 (native-inputs (list r-knitr))
28250 (home-page "https://github.com/JiaxiangBU/add2ggplot")
28251 (synopsis "Extension for ggplot2")
28252 (description "This package provides tools to create themes and color
28253 palettes for the package ggplot2.")
28254 (license license:expat)))
28256 (define-public r-diffusionmap
28258 (name "r-diffusionmap")
28263 (uri (cran-uri "diffusionMap" version))
28266 "1rvk7069brlm1s9kqj4c31mwwr3mw4hmhay95cjjjfmw5xclff2j"))))
28267 (properties `((upstream-name . "diffusionMap")))
28268 (build-system r-build-system)
28270 (list r-igraph r-matrix r-scatterplot3d))
28271 (home-page "https://www.r-project.org")
28272 (synopsis "Diffusion map")
28273 (description "This package implements the diffusion map method of data
28274 parametrization, including creation and visualization of diffusion maps,
28275 clustering with diffusion K-means and regression using the adaptive regression
28277 (license license:gpl2)))
28279 (define-public r-igraph
28286 (uri (cran-uri "igraph" version))
28289 "0khl87ncc9hkvx4f1kyzv7w7bg9zbyd1rk20ja3azkhpqjkjnnjh"))))
28290 (build-system r-build-system)
28294 (list gmp glpk libxml2 zlib))
28296 (list r-magrittr r-matrix r-pkgconfig))
28297 (home-page "https://igraph.org")
28298 (synopsis "Network analysis and visualization")
28300 "This package provides routines for simple graphs and network analysis.
28301 It can handle large graphs very well and provides functions for generating
28302 random and regular graphs, graph visualization, centrality methods and much
28304 (license license:gpl2+)))
28306 (define-public r-workflows
28308 (name "r-workflows")
28313 (uri (cran-uri "workflows" version))
28316 "0xhc1j25fjipw8hvcpdbvfm640kp0flwvifj5f7g4n6b3wb8cm6a"))))
28317 (properties `((upstream-name . "workflows")))
28318 (build-system r-build-system)
28331 (home-page "https://github.com/tidymodels/workflows")
28332 (synopsis "Modeling workflows")
28334 "A workflow is an object that can bundle together your pre-processing,
28335 modeling, and post-processing requests. For example, if you have a
28336 @code{recipe} and @code{parsnip} model, these can be combined into a
28337 workflow. The advantages are:
28340 @item You don’t have to keep track of separate objects in your workspace.
28341 @item The recipe prepping and model fitting can be executed using a single
28342 call to @code{fit()}.
28343 @item If you have custom tuning parameter settings, these can be defined using
28344 a simpler interface when combined with @code{tune}.
28345 @item In the future, workflows will be able to add post-processing operations,
28346 such as modifying the probability cutoff for two-class models.
28349 (license license:expat)))
28351 (define-public r-lobstr
28358 (uri (cran-uri "lobstr" version))
28361 "0vkif17825x33cz8r89j0qph4wj5l8fzfgl8nh2g7m2v140cxjdq"))))
28362 (properties `((upstream-name . "lobstr")))
28363 (build-system r-build-system)
28365 (list r-crayon r-rcpp r-rlang))
28366 (home-page "https://github.com/r-lib/lobstr")
28367 (synopsis "Visualize R data structures with trees")
28369 "This package provides a set of tools for inspecting and understanding R
28370 data structures inspired by @code{str}. It includes @code{ast} for
28371 visualizing abstract syntax trees, @code{ref} for showing shared references,
28372 @code{cst} for showing call stack trees, and @code{obj_size} for computing
28374 (license license:gpl3)))
28376 (define-public r-gpfit
28383 (uri (cran-uri "GPfit" version))
28386 "05mpiyi2vxv0wqp422n1mnxa8msc4daq40cwpnpngbcwqhlgqkby"))))
28387 (properties `((upstream-name . "GPfit")))
28388 (build-system r-build-system)
28390 (list r-lattice r-lhs))
28391 (home-page "https://cran.r-project.org/web/packages/GPfit/")
28392 (synopsis "Gaussian Processes modeling")
28394 "This package provides a computationally stable approach of fitting a
28395 @dfn{Gaussian Process} (GP) model to a deterministic simulator.")
28396 (license license:gpl2)))
28398 (define-public r-yardstick
28400 (name "r-yardstick")
28405 (uri (cran-uri "yardstick" version))
28408 "00hv4gk1ba4dab8i3dcq7lim4bll7l572rgc8km9x4ja8by95j8h"))))
28409 (properties `((upstream-name . "yardstick")))
28410 (build-system r-build-system)
28420 (home-page "https://github.com/tidymodels/yardstick")
28421 (synopsis "Tidy characterizations of model performance")
28423 "This package provides tidy tools for quantifying how well a model fits
28424 to a data set such as confusion matrices, class probability curve summaries,
28425 and regression metrics (e.g., RMSE).")
28426 (license license:gpl2)))
28428 (define-public r-warp
28435 (uri (cran-uri "warp" version))
28438 "0s0acddc5h14245hi1faycxp0fyvw6nlgaz2df7da4fpyd2f638f"))))
28439 (properties `((upstream-name . "warp")))
28440 (build-system r-build-system)
28441 (native-inputs (list r-knitr))
28442 (home-page "https://github.com/DavisVaughan/warp")
28443 (synopsis "Group dates")
28445 "This package provides tooling to group dates by a variety of periods
28446 including: yearly, monthly, by second, by week of the month, and more. The
28447 groups are defined in such a way that they also represent the distance between
28448 dates in terms of the period. This extracts valuable information that can be
28449 used in further calculations that rely on a specific temporal spacing between
28451 (license license:expat)))
28453 (define-public r-scico
28460 (uri (cran-uri "scico" version))
28462 (base32 "08grfbjd5s0vdw76ni37yjl2242rr8i2jy72sgpwgra282hpnji3"))))
28463 (properties `((upstream-name . "scico")))
28464 (build-system r-build-system)
28465 (propagated-inputs (list r-scales))
28466 (home-page "https://github.com/thomasp85/scico")
28467 (synopsis "Colour Palettes Based on the Scientific Colour-Maps")
28469 "This package provides colour choice in information visualisation. It
28470 important in order to avoid being mislead by inherent bias in the used colour
28471 palette. This package provides access to the perceptually uniform and
28472 colour-blindness friendly palettes developed by Fabio Crameri and released
28473 under the \"Scientific Colour-Maps\" moniker. The package contains 24
28474 different palettes and includes both diverging and sequential types.")
28475 (license license:expat)))
28477 (define-public r-slider
28484 (uri (cran-uri "slider" version))
28487 "1vxk2bc33svwcki2j8zr5jcxswh27i0fqgzjw2a5a1pp9dh3fmd3"))))
28488 (properties `((upstream-name . "slider")))
28489 (build-system r-build-system)
28491 (list r-ellipsis r-glue r-rlang r-vctrs r-warp))
28492 (native-inputs (list r-knitr))
28493 (home-page "https://github.com/DavisVaughan/slider")
28494 (synopsis "Sliding window functions")
28496 "This package provides type-stable rolling window functions over any R
28497 data type. Cumulative and expanding windows are also supported. For more
28498 advanced usage, an index can be used as a secondary vector that defines how
28499 sliding windows are to be created.")
28500 (license license:expat)))
28502 (define-public r-rlist
28505 (version "0.4.6.2")
28509 (uri (cran-uri "rlist" version))
28511 (base32 "15q99rhbbjq8zd976yjmfnny45dd5fg2p2dv1sljg2kwi66nbppb"))))
28512 (properties `((upstream-name . "rlist")))
28513 (build-system r-build-system)
28514 (propagated-inputs (list r-data-table r-jsonlite r-xml r-yaml))
28515 (home-page "https://renkun-ken.github.io/rlist/")
28516 (synopsis "A Toolbox for Non-Tabular Data Manipulation")
28518 "This package provides a set of functions for data manipulation with
28519 list objects, including mapping, filtering, grouping, sorting, updating,
28520 searching, and other useful functions. Most functions are designed to be
28521 pipeline friendly so that data processing with lists can be chained.")
28522 (license license:expat)))
28524 (define-public r-rsample
28531 (uri (cran-uri "rsample" version))
28534 "01xwhj4zfvxbv9cjb6mbz3aphxqc3cnjjx1xy2yx2wd94fbka42z"))))
28535 (properties `((upstream-name . "rsample")))
28536 (build-system r-build-system)
28552 (home-page "https://rsample.tidymodels.org")
28553 (synopsis "General resampling infrastructure")
28555 "This package provides classes and functions to create and summarize
28556 different types of resampling objects (e.g. bootstrap, cross-validation).")
28557 (license license:gpl2)))
28559 (define-public r-dicedesign
28561 (name "r-dicedesign")
28566 (uri (cran-uri "DiceDesign" version))
28569 "1a8ixa65xgyfri03cviic8qi2plbhdyz8m02bwif8w94w0q3ghlk"))))
28570 (properties `((upstream-name . "DiceDesign")))
28571 (build-system r-build-system)
28572 (home-page "http://dice.emse.fr/")
28573 (synopsis "Designs of computer experiments")
28575 "This package provides tools to create some specific @code{Space-Filling
28576 Design} (SFD) and to test their quality.")
28577 (license license:gpl3)))
28579 (define-public r-dials
28586 (uri (cran-uri "dials" version))
28589 "1h695g9vklqn0vd53j9k03s0989xjpjr11h5qhz3a0v6465fwm8a"))))
28590 (properties `((upstream-name . "dials")))
28591 (build-system r-build-system)
28604 (native-inputs (list r-knitr))
28605 (home-page "https://dials.tidymodels.org/")
28606 (synopsis "Tools for creating tuning parameter values")
28608 "Many models contain tuning parameters (i.e. parameters that cannot be
28609 directly estimated from the data). These tools can be used to define objects
28610 for creating, simulating, or validating values for such parameters.")
28611 (license license:gpl2)))
28613 (define-public r-tune
28620 (uri (cran-uri "tune" version))
28623 "05gxlsaqv6sjk11r5g4nkdd6hlb3bnfmc29cx4vln1blha37jx4i"))))
28624 (properties `((upstream-name . "tune")))
28625 (build-system r-build-system)
28648 (home-page "https://github.com/tidymodels/tune")
28649 (synopsis "Tidy tuning tools")
28651 "The ability to tune models is important. @code{tune} contains functions
28652 and classes to be used in conjunction with other @code{tidymodels} packages
28653 for finding reasonable values of hyper-parameters in models, pre-processing
28654 methods, and post-processing steps.")
28655 (license license:expat)))
28657 (define-public r-workflowsets
28659 (name "r-workflowsets")
28664 (uri (cran-uri "workflowsets" version))
28667 "0q42nhnw0mbivadcfb07v71fp39x8fcnjipvn5l5yhjzc56cfxi8"))))
28668 (properties `((upstream-name . "workflowsets")))
28669 (build-system r-build-system)
28689 (home-page "https://github.com/tidymodels/workflowsets")
28690 (synopsis "Create a collection of tidymodels workflows")
28692 "A workflow is a combination of a model and preprocessors (e.g, a
28693 formula, recipe, etc.). In order to try different combinations of these, an
28694 object can be created that contains many workflows. There are functions to
28695 create workflows en masse as well as training them and visualizing the
28697 (license license:expat)))
28699 (define-public r-tidyposterior
28701 (name "r-tidyposterior")
28706 (uri (cran-uri "tidyposterior" version))
28709 "1h1664sjrg6akph6nrk8ynn2kjiswv6gshy35gamam1h4axf6wah"))))
28710 (properties `((upstream-name . "tidyposterior")))
28711 (build-system r-build-system)
28727 (home-page "https://tidyposterior.tidymodels.org")
28728 (synopsis "Bayesian analysis to compare models using resampling statistics")
28730 "This package can be used to conduct post hoc analyses of resampling
28731 results generated by models. For example, if two models are evaluated with
28732 the @dfn{root mean squared error} (RMSE) using 10-fold cross-validation, there
28733 are 10 paired statistics. These can be used to make comparisons between
28734 models without involving a test set.")
28735 (license license:gpl2)))
28737 (define-public r-tidypredict
28739 (name "r-tidypredict")
28744 (uri (cran-uri "tidypredict" version))
28747 "0x0r36zvny4rqgndx7iqh39yhr53gl4d8wd8wpvdcgg35q6z02z2"))))
28748 (properties `((upstream-name . "tidypredict")))
28749 (build-system r-build-system)
28761 (home-page "https://tidypredict.tidymodels.org")
28762 (synopsis "Run predictions inside the database")
28764 "This package parses a fitted R model object, and returns a formula in
28765 Tidy Eval code that calculates the predictions. It works with several
28766 database backends because it leverages @code{dplyr} and @code{dbplyr} for the
28767 final SQL translation of the algorithm. It currently supports @code{lm()},
28768 @code{glm()}, @code{randomForest()}, @code{ranger()}, @code{earth()},
28769 @code{xgb.Booster.complete()}, @code{cubist()}, and @code{ctree()} models.")
28770 (license license:gpl3)))
28772 (define-public r-janeaustenr
28774 (name "r-janeaustenr")
28779 (uri (cran-uri "janeaustenr" version))
28782 "1wyn4qc28a3sval8shmyi2d7s4nl3jh96s8pzq871brxcmrncbwr"))))
28783 (properties `((upstream-name . "janeaustenr")))
28784 (build-system r-build-system)
28785 (home-page "https://github.com/juliasilge/janeaustenr")
28786 (synopsis "Jane Austen's complete novels")
28788 "This package provides the full texts for Jane Austen's six completed
28789 novels, ready for text analysis. These novels are \"Sense and Sensibility\",
28790 \"Pride and Prejudice\", \"Mansfield Park\", \"Emma\", \"Northanger Abbey\",
28791 and \"Persuasion\".")
28792 (license license:expat)))
28794 (define-public r-tokenizers
28796 (name "r-tokenizers")
28801 (uri (cran-uri "tokenizers" version))
28804 "006xf1vdrmp9skhpss9ldhmk4cwqk512cjp1pxm2gxfybpf7qq98"))))
28805 (properties `((upstream-name . "tokenizers")))
28806 (build-system r-build-system)
28808 (list r-rcpp r-snowballc r-stringi))
28811 (home-page "https://lincolnmullen.com/software/tokenizers/")
28812 (synopsis "Fast, consistent tokenization of natural language text")
28814 "This is a package for converting natural language text into tokens.
28815 It includes tokenizers for shingled n-grams, skip n-grams, words, word stems,
28816 sentences, paragraphs, characters, shingled characters, lines, tweets, Penn
28817 Treebank, regular expressions, as well as functions for counting characters,
28818 words, and sentences, and a function for splitting longer texts into separate
28819 documents, each with the same number of words. The tokenizers have a
28820 consistent interface, and the package is built on the @code{stringi} and
28821 @code{Rcpp} packages for fast yet correct tokenization in UTF-8 encoding.")
28822 (license license:expat)))
28824 (define-public r-hunspell
28826 (name "r-hunspell")
28831 (uri (cran-uri "hunspell" version))
28834 "0ql6y05d4xxpm468rslb0wxdp1x9l3flxzmb5w6pjg617f8vpv8z"))))
28835 (properties `((upstream-name . "hunspell")))
28836 (build-system r-build-system)
28838 (list r-digest r-rcpp))
28841 (home-page "https://github.com/ropensci/hunspell#readme")
28842 (synopsis "High-performance stemmer, tokenizer, and spell checker")
28844 "This package provides a low-level spell checker and morphological
28845 analyzer based on the famous @code{hunspell} library. The package can analyze
28846 or check individual words as well as parse text, LaTeX, HTML or XML documents.
28847 For a more user-friendly interface use the @code{spelling} package which
28848 builds on this package to automate checking of files, documentation and
28849 vignettes in all common formats.")
28850 ;; The hunspell library itself is available under one of GPL2, LGPL2.1, or
28851 ;; MPL; in addition to these licenses the rest of the R wrapper is also
28852 ;; available under the Expat license.
28853 (license (list license:gpl2
28858 (define-public r-tidytext
28860 (name "r-tidytext")
28865 (uri (cran-uri "tidytext" version))
28868 "0kljaxyhhzbcv9jkjdy0wn6gkamh25y2xfb9k11sqhz3lv72nfvm"))))
28869 (properties `((upstream-name . "tidytext")))
28870 (build-system r-build-system)
28886 (home-page "https://github.com/juliasilge/tidytext")
28887 (synopsis "Text mining using dplyr, ggplot2, and other Tidy tools")
28889 "This is a package for text mining for word processing and sentiment
28890 analysis using @code{dplyr}, @code{ggplot2}, and other Tidy tools.")
28891 (license license:expat)))
28893 (define-public r-parsnip
28900 (uri (cran-uri "parsnip" version))
28903 "195i4j38mljv9193yx8lmh65h85yhc52y9vc1mk8zvxi52ks1yln"))))
28904 (properties `((upstream-name . "parsnip")))
28905 (build-system r-build-system)
28925 (home-page "https://parsnip.tidymodels.org")
28926 (synopsis "Common API to modeling and analysis functions")
28928 "This package provides a common interface to allow users to specify a
28929 model without having to remember the different argument names across different
28930 functions or computational engines (e.g. R, Spark, Stan, etc).")
28931 (license license:gpl2)))
28933 (define-public r-infer
28940 (uri (cran-uri "infer" version))
28943 "1qbpcn7jqbvgwnpiyylj021j8m33p58a204yd1pfkpzd3x2lbsm6"))))
28944 (properties `((upstream-name . "infer")))
28945 (build-system r-build-system)
28960 (home-page "https://github.com/tidymodels/infer")
28961 (synopsis "Tidy statistical inference")
28963 "The objective of this package is to perform inference using an
28964 expressive statistical grammar that coheres with the Tidy design framework.")
28965 (license license:cc0)))
28967 (define-public r-modeldata
28969 (name "r-modeldata")
28974 (uri (cran-uri "modeldata" version))
28977 "0jgrwf9k8p9j3ywg3yv2wzwsx3snlwm3dd9vfqwhlr7j63jg3cm4"))))
28978 (properties `((upstream-name . "modeldata")))
28979 (build-system r-build-system)
28980 (home-page "https://modeldata.tidymodels.org")
28981 (synopsis "Data sets useful for modeling packages")
28983 "This package provides data sets used for demonstrating or testing
28984 model-related packages.")
28985 (license license:expat)))
28987 (define-public r-conflicted
28989 (name "r-conflicted")
28994 (uri (cran-uri "conflicted" version))
28997 "1qg9ar114r98wm0pnf65mss4v2ksq3924rlpm13mqp4s3p6j9yi4"))))
28998 (properties `((upstream-name . "conflicted")))
28999 (build-system r-build-system)
29001 (list r-memoise r-rlang))
29002 (home-page "https://github.com/r-lib/conflicted")
29003 (synopsis "Alternative conflict resolution strategy")
29005 "R's default conflict management system gives the most recently loaded
29006 package precedence. This can make it hard to detect conflicts, particularly
29007 when they arise because a package update creates ambiguity that did not
29008 previously exist. The @code{conflicted} package takes a different approach,
29009 making every conflict an error and forcing you to choose which function to
29011 (license license:gpl3)))
29013 (define-public r-tidymodels
29015 (name "r-tidymodels")
29020 (uri (cran-uri "tidymodels" version))
29023 "1xkv4s4kn7k9137svb39zrm5302gxpxyp1jv5bb6z0xrvj5wwa4i"))))
29024 (properties `((upstream-name . "tidymodels")))
29025 (build-system r-build-system)
29050 (home-page "https://github.com/tidymodels/tidymodels")
29051 (synopsis "Tidy collection for modeling and statistical analysis")
29053 "The tidy modeling \"verse\" is a collection of packages for modeling and
29054 statistical analysis that share the underlying design philosophy, grammar, and
29055 data structures of the tidyverse.")
29056 (license license:gpl3)))
29058 (define-public r-lsa
29065 (uri (cran-uri "lsa" version))
29068 "16k1g0kh3yaw7azg76aqf3hn3b6jgqg92xx0syai8l0my9ci2zzh"))))
29069 (properties `((upstream-name . "lsa")))
29070 (build-system r-build-system)
29072 (list r-snowballc))
29073 (home-page "https://cran.r-project.org/package=lsa")
29074 (synopsis "Latent semantic analysis")
29076 "The basic idea of latent semantic analysis (LSA) is, that text do have a
29077 higher order (=latent semantic) structure which, however, is obscured by word
29078 usage (e.g. through the use of synonyms or polysemy). By using conceptual
29079 indices that are derived statistically via a truncated singular value
29080 decomposition (a two-mode factor analysis) over a given document-term matrix,
29081 this variability problem can be overcome.")
29082 (license license:gpl2+)))
29084 (define-public r-mlecens
29091 (uri (cran-uri "MLEcens" version))
29094 "0cdl0y44clds4sg8hikhk354a5xrfbyfg8lxrbh1bfg410rkj186"))))
29095 (properties `((upstream-name . "MLEcens")))
29096 (build-system r-build-system)
29097 (home-page "http://stat.ethz.ch/~maathuis/")
29098 (synopsis "Computation of the MLE for bivariate (interval) censored data")
29100 "This package contains functions to compute the nonparametric
29101 @dfn{maximum likelihood estimator} (MLE) for the bivariate distribution of
29102 @code{(X,Y)}, when realizations of @code{(X,Y)} cannot be observed directly.
29103 To be more precise, we consider the situation where we observe a set of
29104 rectangles that are known to contain the unobservable realizations of (X,Y).
29105 We compute the MLE based on such a set of rectangles. The methods can also be
29106 used for univariate censored data (see data set @code{cosmesis}), and for
29107 censored data with competing risks (see data set @code{menopause}). The
29108 package also provides functions to visualize the observed data and the MLE.")
29109 (license license:gpl2+)))
29111 (define-public r-metafor
29118 (uri (cran-uri "metafor" version))
29121 "1b599fxk7s0brkchmx698fr5k4g1kzkia2rnlvhg349ffs5nfjmn"))))
29122 (properties `((upstream-name . "metafor")))
29123 (build-system r-build-system)
29125 (list r-matrix r-nlme))
29126 (home-page "https://cran.r-project.org/web/packages/metafor/")
29127 (synopsis "Meta-analysis package for R")
29129 "This package provides a comprehensive collection of functions for
29130 conducting meta-analyses in R. The package includes functions to calculate
29131 various effect sizes or outcome measures, fit fixed-, random-, and
29132 mixed-effects models to such data, carry out moderator and meta-regression
29133 analyses, and create various types of meta-analytical plots (e.g., forest,
29134 funnel, radial, L'Abbe, Baujat, GOSH plots). For meta-analyses of binomial
29135 and person-time data, the package also provides functions that implement
29136 specialized methods, including the Mantel-Haenszel method, Peto's method, and
29137 a variety of suitable generalized linear (mixed-effects) models (i.e.
29138 mixed-effects logistic and Poisson regression models). Finally, the package
29139 provides functionality for fitting meta-analytic multivariate/multilevel
29140 models that account for non-independent sampling errors and/or true
29141 effects (e.g. due to the inclusion of multiple treatment studies, multiple
29142 endpoints, or other forms of clustering). Network meta-analyses and
29143 meta-analyses accounting for known correlation structures (e.g. due to
29144 phylogenetic relatedness) can also be conducted.")
29145 (license license:gpl2+)))
29147 (define-public r-altmeta
29154 (uri (cran-uri "altmeta" version))
29157 "17cyiydf4n5j64izj7jph2v43h4x9kfd5b0x6m0ik5ci2aw8xzr5"))))
29158 (properties `((upstream-name . "altmeta")))
29159 (build-system r-build-system)
29161 (list r-coda r-lme4 r-matrix r-metafor r-rjags))
29162 (home-page "https://cran.r-project.org/web/packages/altmeta/")
29163 (synopsis "Alternative meta-analysis methods")
29165 "This package provides alternative statistical methods for meta-analysis,
29169 @item bivariate generalized linear mixed models for synthesizing odds ratios,
29170 relative risks, and risk differences
29171 @item heterogeneity tests and measures that are robust to outliers;
29172 @item measures, tests, and visualization tools for publication bias or
29173 small-study effects;
29174 @item meta-analysis of diagnostic tests for synthesizing sensitivities,
29175 specificities, etc.;
29176 @item meta-analysis methods for synthesizing proportions;
29177 @item models for multivariate meta-analysis.
29180 (license license:gpl2+)))
29182 (define-public r-perm
29185 (version "1.0-0.2")
29189 (uri (cran-uri "perm" version))
29192 "182ac1y91yzb34zwdcmx5fdfr5z0cha0gx2bgk36gwxhgfc994kj"))))
29193 (properties `((upstream-name . "perm")))
29194 (build-system r-build-system)
29195 (home-page "https://cran.r-project.org/web/packages/perm/")
29196 (synopsis "Exact or asymptotic permutation tests")
29198 "This package provides several methods for performing permutation tests.
29199 It has three main functions, to perform linear permutation tests. These tests
29200 are tests where the test statistic is the sum of the product of a
29201 covariate (usually group indicator) and the scores.")
29202 ;; Any version of the GPL
29203 (license license:gpl2+)))
29205 (define-public r-qtl
29212 (uri (cran-uri "qtl" version))
29215 "1mcy9wlp5lj5f3z4mf3n5li7x32vj67rmhjnzsp8fhfw0ipnaf1d"))))
29216 (build-system r-build-system)
29217 (home-page "https://rqtl.org/")
29218 (synopsis "R package for analyzing QTL experiments in genetics")
29219 (description "R/qtl is an extension library for the R statistics system.
29220 It is used to analyze experimental crosses for identifying genes contributing
29221 to variation in quantitative traits (so-called quantitative trait loci, QTLs).
29223 Using a hidden Markov model, R/qtl estimates genetic maps, to identify
29224 genotyping errors, and to perform single-QTL and two-QTL, two-dimensional
29226 (license license:gpl3)))
29228 (define-public r-qtl2
29234 (uri (cran-uri "qtl2" version))
29236 (base32 "0ppc6dzlq77mppxc6bczai9gi40jrbxd1466y2cn2s8a4ah1jg9y"))))
29237 (build-system r-build-system)
29245 (home-page "https://kbroman.org/qtl2/")
29246 (synopsis "Quantitative Trait Locus Mapping in Experimental Crosses")
29248 "This package provides a set of tools to perform @dfn{Quantitative Trait
29249 Locus} (QTL) analysis in experimental crosses. It is a reimplementation of the
29250 @code{R/qtl} package to better handle high-dimensional data and complex cross
29251 designs. Broman et al. (2018) <doi:10.1534/genetics.118.301595>.")
29252 (license license:gpl3)))
29254 (define-public r-seqminer
29256 (name "r-seqminer")
29261 (uri (cran-uri "seqminer" version))
29264 "1mbx1hw9dhgry7hhan43g6aiz2lyd5api7wxq3fwajyzjrc6p1g8"))))
29265 (build-system r-build-system)
29268 (home-page "http://seqminer.genomic.codes")
29269 (synopsis "Read nucleotide sequence data (VCF, BCF, and METAL formats)")
29271 "This package provides tools to integrate nucleotide sequencing
29272 data (variant call format, e.g. VCF or BCF) or meta-analysis results in R.")
29273 ;; Any version of the GPL is acceptable
29274 (license (list license:gpl2+ license:gpl3+))))
29276 (define-public r-maldiquant
29278 (name "r-maldiquant")
29283 (uri (cran-uri "MALDIquant" version))
29286 "1y1g3819ss06dry70kfhg2syddw71682qmzkcyppfsma6hhghw87"))))
29287 (properties `((upstream-name . "MALDIquant")))
29288 (build-system r-build-system)
29291 (home-page "https://cran.r-project.org/web/packages/MALDIquant")
29292 (synopsis "Quantitative analysis of mass spectrometry data")
29294 "This package provides a complete analysis pipeline for matrix-assisted
29295 laser desorption/ionization-time-of-flight (MALDI-TOF) and other
29296 two-dimensional mass spectrometry data. In addition to commonly used plotting
29297 and processing methods it includes distinctive features, namely baseline
29298 subtraction methods such as morphological filters (TopHat) or the
29299 statistics-sensitive non-linear iterative peak-clipping algorithm (SNIP), peak
29300 alignment using warping functions, handling of replicated measurements as well
29301 as allowing spectra with different resolutions.")
29302 (license license:gpl3+)))
29304 (define-public r-scattermore
29306 (name "r-scattermore")
29311 (uri (cran-uri "scattermore" version))
29314 "1rgqm7r1k7j3h2y4i6d1a2y8fzivfcbmr7dj9d367c0w4vc77pfv"))))
29315 (properties `((upstream-name . "scattermore")))
29316 (build-system r-build-system)
29318 (list r-ggplot2 r-scales))
29319 (home-page "https://github.com/exaexa/scattermore")
29320 (synopsis "Scatterplots with more points")
29322 "This package provides C-based tools for converting large scatterplot
29323 data to rasters. It speeds up plotting of data with millions of points.")
29324 (license license:gpl3+)))
29326 (define-public r-seuratobject
29328 (name "r-seuratobject")
29333 (uri (cran-uri "SeuratObject" version))
29336 "018anas8a9m3kh9jn5370v64d93k64z3iic13a75hp6r7g5hd94w"))))
29337 (properties `((upstream-name . "SeuratObject")))
29338 (build-system r-build-system)
29349 (home-page "https://satijalab.org/seurat")
29350 (synopsis "Data structures for single cell data")
29352 "This package defines S4 classes for single-cell genomic data and
29353 associated information, such as dimensionality reduction embeddings,
29354 nearest-neighbor graphs, and spatially-resolved coordinates. It provides data
29355 access methods and R-native hooks to ensure the Seurat object is familiar to
29357 (license license:gpl3)))
29359 (define-public r-seurat
29365 (uri (cran-uri "Seurat" version))
29368 "1klamxk6dj0jgpfwll5frcnj9h8lh8c5fxdn9ky7h8xk35lsj6i0"))))
29369 (properties `((upstream-name . "Seurat")))
29370 (build-system r-build-system)
29415 (home-page "http://www.satijalab.org/seurat")
29416 (synopsis "Seurat is an R toolkit for single cell genomics")
29418 "This package is an R package designed for QC, analysis, and
29419 exploration of single cell RNA-seq data. It easily enables widely-used
29420 analytical techniques, including the identification of highly variable genes,
29421 dimensionality reduction; PCA, ICA, t-SNE, standard unsupervised clustering
29422 algorithms; density clustering, hierarchical clustering, k-means, and the
29423 discovery of differentially expressed genes and markers.")
29424 (license license:gpl3)))
29426 (define-public r-seuratdisk
29427 (let ((commit "163f1aade5bac38ed1e9e9c912283a7e74781610")
29430 (name "r-seuratdisk")
29431 (version (git-version "0.0.0.9019" revision commit))
29435 (uri (git-reference
29436 (url "https://github.com/mojaveazure/seurat-disk")
29438 (file-name (git-file-name name version))
29440 (base32 "1d1v8qi6kknzy5fj6bl8akwy74h5h143i00lyidsnqjbwp9n4qnw"))))
29441 (properties `((upstream-name . "SeuratDisk")))
29442 (build-system r-build-system)
29456 (home-page "https://github.com/mojaveazure/seurat-disk")
29457 (synopsis "Interfaces for HDF5-based single cell file formats")
29459 "The h5Seurat file format is specifically designed for the storage and
29460 analysis of multi-modal single-cell and spatially-resolved expression
29461 experiments, for example, from CITE-seq or 10X Visium technologies. It holds
29462 all molecular information and associated metadata, including (for example)
29463 nearest-neighbor graphs, dimensional reduction information, spatial
29464 coordinates and image data, and cluster labels. This package also supports
29465 rapid and on-disk conversion between h5Seurat and AnnData objects, with the
29466 goal of enhancing interoperability between Seurat and Scanpy.")
29467 (license license:gpl3))))
29469 (define-public r-seuratdata
29470 (let ((commit "b59556b24d7d6728a5744c9c715dd5f7f32ed7a5")
29473 (name "r-seuratdata")
29474 (version (git-version "0.2.1" revision commit))
29478 (uri (git-reference
29479 (url "https://github.com/satijalab/seurat-data")
29481 (file-name (git-file-name name version))
29483 (base32 "1xfdmdmgn4r0z6w4cxa98ic6xk8i6qz054r215dvqbjs1vydsbf9"))))
29484 (properties `((upstream-name . "SeuratData")))
29485 (build-system r-build-system)
29488 (modify-phases %standard-phases
29489 ;; When there is no HOME directory, this package will fail to load
29490 ;; the included list of packages.
29491 (add-after 'unpack 'set-HOME
29492 (lambda _ (setenv "HOME" "/tmp"))))))
29494 (list r-cli r-crayon r-rappdirs))
29495 (home-page "https://github.com/satijalab/seurat-data")
29496 (synopsis "Install and manage Seurat datasets")
29498 "Single cell RNA sequencing datasets can be large, consisting of
29499 matrices that contain expression data for several thousand features across
29500 several thousand cells. This package is designed to easily install, manage,
29501 and learn about various single-cell datasets, provided Seurat objects and
29502 distributed as independent packages.")
29503 (license license:gpl3))))
29505 (define-public r-phangorn
29507 (name "r-phangorn")
29512 (uri (cran-uri "phangorn" version))
29515 "0xfwi7adl1pcfcwk72fj7lkwfm0wiip96ij7m4252xr9mq818ivd"))))
29516 (build-system r-build-system)
29526 (home-page "https://github.com/KlausVigo/phangorn")
29527 (synopsis "Phylogenetic analysis in R")
29529 "Phangorn is a package for phylogenetic analysis in R. It supports
29530 estimation of phylogenetic trees and networks using Maximum Likelihood,
29531 Maximum Parsimony, distance methods and Hadamard conjugation.")
29532 (license license:gpl2+)))
29534 (define-public r-diversitree
29536 (name "r-diversitree")
29541 (uri (cran-uri "diversitree" version))
29544 "0rzrk7xsn4gy271pbcw3azndhx0c06bmsgrg6libjmlfnmq6j8sc"))))
29545 (build-system r-build-system)
29548 (inputs (list fftw gsl))
29550 (list r-ape r-desolve r-rcpp r-subplex))
29551 (home-page "https://www.zoology.ubc.ca/prog/diversitree")
29552 (synopsis "Comparative 'phylogenetic' analyses of diversification")
29553 (description "This package contains a number of comparative \"phylogenetic\"
29554 methods, mostly focusing on analysing diversification and character evolution.
29555 Contains implementations of \"BiSSE\" (Binary State Speciation and Extinction)
29556 and its unresolved tree extensions, \"MuSSE\" (Multiple State Speciation and
29557 Extinction), \"QuaSSE\", \"GeoSSE\", and \"BiSSE-ness\" Other included methods
29558 include Markov models of discrete and continuous trait evolution and constant
29559 rate speciation and extinction.")
29560 (license license:gpl2+)))
29562 (define-public r-calculus
29564 (name "r-calculus")
29569 (uri (cran-uri "calculus" version))
29572 "1fhvr0l2mqik3d95v0vanafxmiab147g5a87q956g2i945wc5f22"))))
29573 (properties `((upstream-name . "calculus")))
29574 (build-system r-build-system)
29579 (home-page "https://github.com/eguidotti/calculus")
29580 (synopsis "High dimensional numerical and symbolic calculus")
29582 "Efficient C++ optimized functions for numerical and symbolic calculus.
29583 It includes basic symbolic arithmetic, tensor calculus, Einstein summing
29584 convention, fast computation of the Levi-Civita symbol and generalized
29585 Kronecker delta, Taylor series expansion, multivariate Hermite polynomials,
29586 accurate high-order derivatives, differential operators (Gradient, Jacobian,
29587 Hessian, Divergence, Curl, Laplacian) and numerical integration in arbitrary
29588 orthogonal coordinate systems: cartesian, polar, spherical, cylindrical,
29589 parabolic or user defined by custom scale factors.")
29590 (license license:gpl3)))
29592 (define-public r-decon
29599 (uri (cran-uri "decon" version))
29602 "036cv56wf42q2p3d5h15hbrp5rc29xxy20qwv4k1qzhkq6hmw0qs"))))
29603 (properties `((upstream-name . "decon")))
29604 (build-system r-build-system)
29608 "https://cran.r-project.org/web/packages/decon/")
29609 (synopsis "Deconvolution Estimation in Measurement Error Models")
29611 "This package contains a collection of functions to deal with
29612 nonparametric measurement error problems using deconvolution
29613 kernel methods. We focus two measurement error models in the
29614 package: (1) an additive measurement error model, where the
29615 goal is to estimate the density or distribution function from
29616 contaminated data; (2) nonparametric regression model with
29617 errors-in-variables. The R functions allow the measurement errors
29618 to be either homoscedastic or heteroscedastic. To make the
29619 deconvolution estimators computationally more efficient in R,
29620 we adapt the \"Fast Fourier Transform\" (FFT) algorithm for
29621 density estimation with error-free data to the deconvolution
29622 kernel estimation. Several methods for the selection of the
29623 data-driven smoothing parameter are also provided in the package.
29624 See details in: Wang, X.F. and Wang, B. (2011). Deconvolution
29625 estimation in measurement error models: The R package decon.
29626 Journal of Statistical Software, 39(10), 1-24.")
29627 (license license:gpl3+)))
29629 (define-public r-densestbayes
29631 (name "r-densestbayes")
29632 (version "1.0-2.1")
29636 (uri (cran-uri "densEstBayes" version))
29638 (base32 "1pzmgn65lv91zg1588qhwczy9f2zgciknlc4l072mvh2i7hncw2b"))))
29639 (properties `((upstream-name . "densEstBayes")))
29640 (build-system r-build-system)
29652 (home-page "https://cran.r-project.org/package=densEstBayes")
29653 (synopsis "Density estimation via Bayesian inference engines")
29655 "Bayesian density estimates for univariate continuous random samples are
29656 provided using the Bayesian inference engine paradigm. The engine options
29657 are: Hamiltonian Monte Carlo, the no U-turn sampler, semiparametric mean field
29658 variational Bayes and slice sampling. The methodology is described in Wand
29659 and Yu (2020), arXiv:2009.06182.")
29660 (license license:gpl2+)))
29662 (define-public r-locpol
29669 (uri (cran-uri "locpol" version))
29672 "1p915n0l09kbwkly627074jslxl01yssp1rf0c7sygvsw6sgy5lm"))))
29673 (properties `((upstream-name . "locpol")))
29674 (build-system r-build-system)
29676 "https://cran.r-project.org/web/packages/locpol/")
29677 (synopsis "Kernel Local Polynomial Regression")
29679 "Computes local polynomial estimators for the regression and
29680 also density. It comprises several different utilities to handle
29681 kernel estimators.")
29682 (license license:gpl2+)))
29684 (define-public r-lpme
29691 (uri (cran-uri "lpme" version))
29694 "1ch11cwjci98m7952p9wdsh9fj5y1mjya6ayq0q4wmbm824qfpzb"))))
29695 (properties `((upstream-name . "lpme")))
29696 (build-system r-build-system)
29698 (list r-decon r-flexmix r-locpol r-rcpp r-rcpparmadillo))
29700 "https://cran.r-project.org/web/packages/lpme/")
29701 (synopsis "Nonparametric Estimation of Measurement Error Models")
29703 "Provide nonparametric methods for mean regression model,
29704 modal regression and conditional density estimation in the
29705 presence/absence of measurement error. Bandwidth selection is
29706 also provided for each method.")
29707 (license license:gpl2+)))
29709 (define-public r-aws-signature
29711 (name "r-aws-signature")
29716 (uri (cran-uri "aws.signature" version))
29719 "15llpcnrdq4y6jsn7079yjmgbr5d1wgy2ymsm3jj3gkrd5l4zzpp"))))
29720 (properties `((upstream-name . "aws.signature")))
29721 (build-system r-build-system)
29723 (list r-base64enc r-digest))
29724 (home-page "https://github.com/cloudyr/aws.signature")
29725 (synopsis "Amazon Web Services Request Signatures")
29727 "This package generates version 2 and 4 request signatures for Amazon Web
29728 Services (AWS) and provides a mechanism for retrieving credentials from
29729 environment variables, AWS credentials files, and EC2 instance metadata. For
29730 use on EC2 instances, the package 'aws.ec2metadata' is suggested.")
29731 (license license:gpl2+)))
29733 (define-public r-aws-s3
29740 (uri (cran-uri "aws.s3" version))
29743 "132cczq0ml7lpp2yl6l4p99dn1zihrncnpa6wyad4m9mnr50a8dx"))))
29744 (properties `((upstream-name . "aws.s3")))
29745 (build-system r-build-system)
29747 (list r-aws-signature
29753 (home-page "https://github.com/cloudyr/aws.s3")
29754 (synopsis "AWS S3 Client Package")
29756 "This package provides a simple client package for the Amazon Web
29757 Services (AWS) Simple Storage Service (S3) REST API.")
29758 (license license:gpl2+)))
29760 (define-public r-lgr
29766 (uri (cran-uri "lgr" version))
29769 "18s92qyakhvp336kk2777ydypwfrfwfz6a1gqkq812zy3kcb4mcc"))))
29770 (build-system r-build-system)
29775 (home-page "https://s-fleck.github.io/lgr/")
29776 (synopsis "Fully featured logging framework")
29777 (description "This package offers a flexible, feature-rich yet
29778 light-weight logging framework based on @code{R6} classes. It supports
29779 hierarchical loggers, custom log levels, arbitrary data fields in log events,
29780 logging to plaintext, JSON, (rotating) files, memory buffers, and databases, as
29781 well as email and push notifications.")
29782 (license license:expat)))
29784 (define-public r-mhg
29791 (uri (cran-uri "mHG" version))
29794 "1rz5ncrvvv9h9grls15apa63v2nh9j87fmp4mwjjil37jx6a5zki"))))
29795 (properties `((upstream-name . "mHG")))
29796 (build-system r-build-system)
29797 (home-page "https://cran.r-project.org/package=mHG")
29798 (synopsis "Minimum-hypergeometric test")
29800 "This package runs a minimum-hypergeometric (mHG) test as described in
29801 \"Discovering Motifs in Ranked Lists of DNA Sequences\" by Eran Eden.")
29802 (license license:gpl2)))
29804 (define-public r-mlr3measures
29806 (name "r-mlr3measures")
29810 (uri (cran-uri "mlr3measures" version))
29813 "1kbw3xd7c9x65v9zzs8i5skmrvl0mf2wsbyssmiif0lvrbzfhcmb"))))
29814 (build-system r-build-system)
29816 (list r-checkmate r-prroc))
29817 (home-page "https://mlr3measures.mlr-org.com/")
29818 (synopsis "Performance measures for mlr3")
29819 (description "This package implements multiple performance measures for
29820 supervised learning. It includes over 40 measures for regression and
29821 classification. Additionally, meta information about the performance measures
29822 can be queried, e.g. what the best and worst possible performances scores
29824 (license license:lgpl3)))
29826 (define-public r-mlr3misc
29828 (name "r-mlr3misc")
29832 (uri (cran-uri "mlr3misc" version))
29835 "1wnzyij1x67smkb3gjb9gpp7iy5andfl0s1c78xx4wylhycc6m11"))))
29836 (build-system r-build-system)
29838 (list r-backports r-checkmate r-data-table r-digest r-r6))
29839 (home-page "https://mlr3misc.mlr-org.com/")
29840 (synopsis "Helper functions for mlr3")
29841 (description "@code{mlr3misc} provides frequently used helper functions
29842 and assertions used in @code{mlr3} and its companion packages. It comes with
29843 helper functions for functional programming, for printing, to work with
29844 @code{data.table}, as well as some generally useful @code{R6} classes. This
29845 package also supersedes the package @code{BBmisc}.")
29846 (license license:lgpl3)))
29848 (define-public r-mlr3pipelines
29850 (name "r-mlr3pipelines")
29854 (uri (cran-uri "mlr3pipelines" version))
29857 "1zz55i8c08znxpcs6gp5inaw96c6la9wnsla0972ankvj1hsrcr2"))))
29858 (build-system r-build-system)
29870 (home-page "https://mlr3pipelines.mlr-org.com/")
29871 (synopsis "Preprocessing Operators and Pipelines for @code{mlr3}")
29872 (description "@code{mlr3pipelines} enriches @code{mlr3} with a diverse
29873 set of pipelining operators (PipeOps) that can be composed into graphs.
29874 Operations exist for data preprocessing, model fitting, and ensemble learning.
29875 Graphs can themselves be treated as @code{mlr3} Learners and can therefore be
29876 resampled, benchmarked, and tuned.")
29877 (license license:lgpl3)))
29879 (define-public r-mlr3ordinal
29880 (let ((commit "9febac983b11b7b1f477e5cf0212e5999cd2ed44")
29883 (name "r-mlr3ordinal")
29884 (version (git-version "0.1.0-9000" revision commit))
29887 (uri (git-reference
29888 (url "https://github.com/mlr-org/mlr3ordinal")
29890 (file-name (git-file-name name version))
29893 "1icfhz1pjm0mlsn2y60gsrbk31b2p7xmpx3xsg7639rcgdb5f9gl"))))
29894 (build-system r-build-system)
29905 (home-page "https://mlr3ordinal.mlr-org.com/")
29906 (synopsis "Ordinal Regression for mlr3")
29907 (description "This package extends @code{mlr3} with support for
29908 performing ordinal regression.")
29909 (license license:expat))))
29911 (define-public r-paradox
29917 (uri (cran-uri "paradox" version))
29920 "0fzq59903fklgj3kblnpzasy13a82s72c1qjsy7d1m0fyj28ahdw"))))
29921 (build-system r-build-system)
29923 (list r-backports r-checkmate r-data-table r-mlr3misc r-r6))
29924 (home-page "https://paradox.mlr-org.com/")
29925 (synopsis "Define and work with parameter spaces for complex algorithms")
29926 (description "With this package it is possible to define parameter spaces,
29927 constraints and dependencies for arbitrary algorithms, and to program on such
29928 spaces. It also includes statistical designs and random samplers. Objects are
29929 implemented as @code{R6} classes.")
29930 (license license:lgpl3)))
29932 (define-public r-mlr3
29938 (uri (cran-uri "mlr3" version))
29941 "010kl51zsgpc0qv63g1fg9kiw9m0wzqskcr14f1j8b9zi1lwi0bf"))))
29942 (build-system r-build-system)
29959 (home-page "https://mlr3.mlr-org.com/")
29960 (synopsis "Machine Learning in R - Next Generation")
29961 (description "@code{mlr3} enables efficient, object-oriented programming
29962 on the building blocks of machine learning. It provides @code{R6} objects for
29963 tasks, learners, resamplings, and measures. The package is geared towards
29964 scalability and larger datasets by supporting parallelization and out-of-memory
29965 data-backends like databases. While @code{mlr3} focuses on the core
29966 computational operations, add-on packages provide additional functionality.")
29967 (license license:lgpl3)))
29969 (define-public r-mlr3learners
29971 (name "r-mlr3learners")
29975 (uri (cran-uri "mlr3learners" version))
29978 "088i2piv7sgxsvc7jyr6mq53vqf8yjdlrysgqphsryq6k50i00zd"))))
29979 (build-system r-build-system)
29987 (home-page "https://mlr3learners.mlr-org.com/")
29988 (synopsis "Recommended Learners for @code{mlr3}")
29989 (description "@code{mlr3learners} extends @code{mlr3} and @code{mlr3proba}
29990 with interfaces to essential machine learning packages on CRAN. This includes,
29991 but is not limited to: (penalized) linear and logistic regression, linear and
29992 quadratic discriminant analysis, k-nearest neighbors, naive Bayes, support
29993 vector machines, and gradient boosting.")
29994 (license license:lgpl3)))
29996 (define-public r-bbotk
30003 (uri (cran-uri "bbotk" version))
30006 "13qj8qysqismv9k9rfw770r7w8jdaw82n71k7sp3wsrlhxjxw734"))))
30007 (properties `((upstream-name . "bbotk")))
30008 (build-system r-build-system)
30018 (home-page "https://bbotk.mlr-org.com")
30019 (synopsis "Black-Box Optimization Toolkit")
30020 (description "This package provides a common framework for optimization of
30021 black-box functions for other packages, e.g. @code{mlr3}. It offers various
30022 optimization methods e.g. grid search, random search and generalized simulated
30024 (license license:lgpl3)))
30026 (define-public r-mlr3tuning
30028 (name "r-mlr3tuning")
30032 (uri (cran-uri "mlr3tuning" version))
30035 "0jfslx6pwk408ydn69grrvsp22jd7gsjmwvss0a1j0zav3q1pvks"))))
30036 (build-system r-build-system)
30046 (home-page "https://mlr3tuning.mlr-org.com/")
30047 (synopsis "Tuning for @code{mlr3}")
30048 (description "@code{mlr3tuning} implements methods for hyperparameter
30049 tuning, e.g. Grid Search, Random Search, or Simulated Annealing. Various
30050 termination criteria can be set and combined. The class @code{AutoTuner} provides a
30051 convenient way to perform nested resampling in combination with @code{mlr3}.")
30052 (license license:lgpl3)))
30054 (define-public r-fontliberation
30056 (name "r-fontliberation")
30061 (uri (cran-uri "fontLiberation" version))
30064 "1w1rl0g4ayyp8lwppmz9yzj9cizg7i50g07216jkm1q5w0is9pmc"))))
30066 `((upstream-name . "fontLiberation")))
30067 (build-system r-build-system)
30068 (home-page "https://cran.r-project.org/package=fontLiberation")
30069 (synopsis "Liberation fonts")
30071 "This package provides a placeholder for the Liberation fontset intended
30072 for the fontquiver package. This fontset covers the 12 combinations of
30073 families (sans, serif, mono) and faces (plain, bold, italic, bold italic)
30074 supported in R graphics devices.")
30075 (license license:silofl1.1)))
30077 (define-public r-fontbitstreamvera
30079 (name "r-fontbitstreamvera")
30084 (uri (cran-uri "fontBitstreamVera" version))
30087 "0nipdlmhjv1wr3aidcl97nk6mppdkd65krgwqnhdsnv0jpfv761j"))))
30089 `((upstream-name . "fontBitstreamVera")))
30090 (build-system r-build-system)
30091 (home-page "https://cran.r-project.org/package=fontBitstreamVera")
30092 (synopsis "Fonts for fontquiver")
30094 "This package is a placeholder for the Bitstream Vera font. It is
30095 intended for the fontquiver package.")
30097 (license:fsdg-compatible
30098 "https://www.gnome.org/fonts/#Final_Bitstream_Vera_Fonts"
30099 "The Font Software may be sold as part of a larger software package but
30100 no copy of one or more of the Font Software typefaces may be sold by
30103 (define-public r-fontquiver
30105 (name "r-fontquiver")
30110 (uri (cran-uri "fontquiver" version))
30113 "0qv3i9hch7cygl9983s3w68wfh5qvym2jkm52pp06p6mq8a1i1wm"))))
30114 (properties `((upstream-name . "fontquiver")))
30115 (build-system r-build-system)
30117 (list r-fontbitstreamvera r-fontliberation))
30118 (home-page "https://cran.r-project.org/package=fontquiver")
30119 (synopsis "Set of installed fonts")
30121 "This package provides a set of fonts. This is useful when you want to
30122 avoid system fonts to make sure your outputs are reproducible.")
30123 (license license:gpl3)))
30125 (define-public r-freetypeharfbuzz
30127 (name "r-freetypeharfbuzz")
30132 (uri (cran-uri "freetypeharfbuzz" version))
30135 "0r3icgnq3jk4fm6z92cmhzdmflbk5df8zsmjg0dzpc4y48xafnk7"))))
30137 `((upstream-name . "freetypeharfbuzz")))
30138 (build-system r-build-system)
30141 (modify-phases %standard-phases
30142 (add-after 'unpack 'prepare-static-libraries
30143 (lambda* (#:key inputs #:allow-other-keys)
30144 (mkdir-p "src/target/include")
30145 (let ((freetype (assoc-ref inputs "static-freetype"))
30146 (harfbuzz (assoc-ref inputs "static-harfbuzz")))
30147 (substitute* "src/Makevars.in"
30148 (("include @MK_FILE@") "") ; do not build static libs
30149 (("^HB_STATIC_LIB =.*")
30150 (string-append "HB_STATIC_LIB = " harfbuzz "/lib/libharfbuzz.a\n"))
30151 (("^FT_STATIC_LIB =.*")
30152 (string-append "FT_STATIC_LIB = " freetype "/lib/libfreetype.a\n")))
30153 (copy-recursively (string-append freetype "/include")
30154 "src/target/include")
30155 (copy-recursively (string-append harfbuzz "/include")
30156 "src/target/include")))))))
30158 (list r-fontquiver))
30159 ;; This may defeat the purpose of this package as our versions of freetype
30160 ;; and harfbuzz obviously differ from the tarballs offered by this
30161 ;; project. On the other hand, Guix arguably does a better job at
30162 ;; "ensur[ing] deterministic computation".
30164 `(("static-freetype"
30166 (inherit (static-package freetype))
30168 `(#:configure-flags
30169 (list "--enable-static=yes"
30174 "--without-harfbuzz")))))
30177 (inherit (static-package harfbuzz))
30179 `(#:tests? #false ; fail because shared library is disabled
30181 (list "--enable-static=yes"
30182 "--enable-shared=no"
30184 "--with-freetype=yes"
30187 "--without-fontconfig"
30188 "--without-glib")))))))
30191 (home-page "https://cran.r-project.org/package=freetypeharfbuzz")
30192 (synopsis "Deterministic computation of text box metrics")
30194 "Unlike other tools that dynamically link to the Cairo stack,
30195 freetypeharfbuzz is statically linked to specific versions of the FreeType and
30196 harfbuzz libraries. This ensures deterministic computation of text box
30197 extents for situations where reproducible results are crucial (for instance
30198 unit tests of graphics).")
30199 (license license:gpl3)))
30201 (define-public r-vdiffr
30208 (uri (cran-uri "vdiffr" version))
30211 "1z8nn8yh6jfzb9r7ylmigwh1p30lrclqm6khmp323qqphzmzfdwy"))))
30212 (properties `((upstream-name . "vdiffr")))
30213 (build-system r-build-system)
30215 (list libpng zlib))
30225 (home-page "https://github.com/r-lib/vdiffr")
30226 (synopsis "Visual regression testing and graphical diffing")
30228 "This package is an extension to the testthat package that makes it easy
30229 to add graphical unit tests. It provides a Shiny application to manage the
30231 (license license:gpl3)))
30233 (define-public r-highlight
30235 (name "r-highlight")
30240 (uri (cran-uri "highlight" version))
30243 "1shar4y07wyixg0ichdrn2xhgwkl3mv2pxkalqzisc69w605b3hf"))))
30244 (properties `((upstream-name . "highlight")))
30245 (build-system r-build-system)
30246 (home-page "https://github.com/hadley/highlight")
30247 (synopsis "Syntax highlighter for R code")
30249 "This package provides a syntax highlighter for R code based on the
30250 results of the R parser. It supports rendering in HTML and LaTeX markup. It
30251 includes a custom Sweave driver performing syntax highlighting of R code
30253 (license license:gpl3+)))
30255 (define-public r-clustree
30257 (name "r-clustree")
30262 (uri (cran-uri "clustree" version))
30265 "0vwmicajl7c0rmjdmf4f857fii0xrxz25vjkn888svlsikw00qbs"))))
30266 (properties `((upstream-name . "clustree")))
30267 (build-system r-build-system)
30280 (home-page "https://github.com/lazappi/clustree")
30281 (synopsis "Visualize clusterings at different resolutions")
30283 "Deciding what resolution to use can be a difficult question when
30284 approaching a clustering analysis. One way to approach this problem is to
30285 look at how samples move as the number of clusters increases. This package
30286 allows you to produce clustering trees, a visualization for interrogating
30287 clusterings as resolution increases.")
30288 (license license:gpl3)))
30290 (define-public r-textshaping
30292 (name "r-textshaping")
30297 (uri (cran-uri "textshaping" version))
30300 "1niaj1dh09rqrg9hrh98ddnc0f2nkyq9iizv24lcwm9gjs3w1ql0"))))
30301 (properties `((upstream-name . "textshaping")))
30302 (build-system r-build-system)
30304 (list freetype fribidi harfbuzz zlib))
30306 (list r-cpp11 r-systemfonts))
30308 (list pkg-config r-knitr))
30309 (home-page "https://github.com/r-lib/textshaping")
30310 (synopsis "Bindings to the HarfBuzz and Fribidi libraries for text shaping")
30312 "This package provides access to the text shaping functionality in the
30313 HarfBuzz library and the bidirectional algorithm in the Fribidi library. This
30314 is a low-level utility package mainly for graphic devices that expands upon
30315 the font tool-set provided by the @code{systemfonts} package.")
30316 (license license:expat)))
30318 (define-public r-ragg
30325 (uri (cran-uri "ragg" version))
30328 "1q43pwmljsqgrikkh2g1n7bpz9c8py5dnj44cfg3y2br7b4m2q9v"))))
30329 (properties `((upstream-name . "ragg")))
30330 (build-system r-build-system)
30332 (list freetype libjpeg-turbo libpng libtiff zlib))
30334 (list r-systemfonts r-textshaping))
30337 (home-page "https://ragg.r-lib.org")
30338 (synopsis "Graphic devices based on AGG")
30340 "Anti-Grain Geometry (AGG) is a high-quality and high-performance 2D
30341 drawing library. The ragg package provides a set of graphic devices based on
30342 AGG to use as alternative to the raster devices provided through the
30343 @code{grDevices} package.")
30344 (license license:expat)))
30346 (define-public r-downlit
30353 (uri (cran-uri "downlit" version))
30356 "10zvrqdpwavdy97h3q26bqh3k63z61fmc04w9vwsnvmnv8hnh3vl"))))
30357 (properties `((upstream-name . "downlit")))
30358 (build-system r-build-system)
30369 (home-page "https://downlit.r-lib.org/")
30370 (synopsis "Syntax highlighting and automatic linking")
30372 "This package provides syntax highlighting of R code, specifically
30373 designed for the needs of RMarkdown packages like @code{pkgdown},
30374 @code{hugodown}, and @code{bookdown}. It includes linking of function calls
30375 to their documentation on the web, and automatic translation of ANSI escapes
30376 in output to the equivalent HTML.")
30377 (license license:expat)))
30379 (define-public r-pkgdown
30386 (uri (cran-uri "pkgdown" version))
30389 "0wqga9bcl7wmvkwpkkmf5hx1cl7rjq5ddvqmxhl4p1dczys3adnr"))))
30390 (properties `((upstream-name . "pkgdown")))
30391 (build-system r-build-system)
30392 (inputs (list pandoc))
30416 (home-page "https://pkgdown.r-lib.org")
30417 (synopsis "Make static HTML documentation for an R package")
30419 "The goal of this package is to generate an attractive and useful website
30420 from a source package. @code{pkgdown} converts your documentation, vignettes,
30421 README file, and more to HTML making it easy to share information about your
30423 (license license:expat)))
30425 (define-public r-prereg
30432 (uri (cran-uri "prereg" version))
30435 "039nrl5cirsx1ysh214dr6xnn1h6h3f90im6k9dgmzfksxdqigpw"))))
30436 (properties `((upstream-name . "prereg")))
30437 (build-system r-build-system)
30439 (list r-rmarkdown))
30440 (home-page "https://github.com/crsh/prereg")
30442 "R Markdown Templates to preregister Scientific Studies")
30444 "This package provides a collection of templates to author
30445 preregistration documents for scientific studies in PDF format.")
30446 (license license:gpl3)))
30448 (define-public r-ez
30455 (uri (cran-uri "ez" version))
30458 "0a58s94x576dfz7wcbivrr2hmdh5x1vy16zwkqp9fmdzqx38pagq"))))
30459 (properties `((upstream-name . "ez")))
30460 (build-system r-build-system)
30472 (home-page "https://github.com/mike-lawrence/ez")
30473 (synopsis "Easy Analysis and Visualization of Factorial Experiments")
30475 "Facilitates easy analysis of factorial experiments, including purely
30476 within-Ss designs (a.k.a. \"repeated measures\"), purely between-Ss designs,
30477 and mixed within-and-between-Ss designs. The functions in this package aim to
30478 provide simple, intuitive and consistent specification of data analysis and
30479 visualization. Visualization functions also include design visualization for
30480 pre-analysis data auditing, and correlation matrix visualization. Finally,
30481 this package includes functions for non-parametric analysis, including
30482 permutation tests and bootstrap resampling. The bootstrap function obtains
30483 predictions either by cell means or by more advanced/powerful mixed effects
30484 models, yielding predictions and confidence intervals that may be easily
30485 visualized at any level of the experiment's design.")
30486 (license license:gpl2+)))
30488 (define-public r-qdapregex
30490 (name "r-qdapregex")
30495 (uri (cran-uri "qdapRegex" version))
30498 "1hdilycwrvi0q6cx7k8vg87bamm2xsafjkya5x4smxysm5k1r4qb"))))
30499 (properties `((upstream-name . "qdapRegex")))
30500 (build-system r-build-system)
30501 (propagated-inputs (list r-stringi))
30503 "https://trinker.github.com/qdapRegex/")
30505 "Regular Expression Removal, Extraction, and Replacement Tools")
30507 "This package provides a collection of regular expression tools
30508 associated with the @code{qdap} package that may be useful outside of the
30509 context of discourse analysis. Tools include removal/extraction/replacement of
30510 abbreviations, dates, dollar amounts, email addresses, hash tags, numbers,
30511 percentages, citations, person tags, phone numbers, times, and zip codes.")
30512 (license license:gpl2)))
30514 (define-public r-mgsub
30521 (uri (cran-uri "mgsub" version))
30524 "1mci6x65h94qiz9cwikx2inbrwkykv43zbs8abfbx416zrh2bbn9"))))
30525 (properties `((upstream-name . "mgsub")))
30526 (build-system r-build-system)
30527 (native-inputs (list r-knitr))
30529 "https://cran.r-project.org/package=mgsub")
30531 "Safe, Multiple, Simultaneous String Substitution")
30533 "Designed to enable simultaneous substitution in strings in a safe
30534 fashion. Safe means it does not rely on placeholders (which can cause errors
30535 in same length matches).")
30536 (license license:expat)))
30538 (define-public r-textshape
30540 (name "r-textshape")
30545 (uri (cran-uri "textshape" version))
30548 "0k9injxykgj2qprc7dygd7gafvcbh3r9x84qzaa1al21pk0dz7ds"))))
30549 (properties `((upstream-name . "textshape")))
30550 (build-system r-build-system)
30552 (list r-data-table r-slam r-stringi))
30553 (home-page "https://github.com/trinker/textshape")
30554 (synopsis "Tools for Reshaping Text")
30556 "Tools that can be used to reshape and restructure text data.")
30557 (license license:gpl2)))
30559 (define-public r-syuzhet
30566 (uri (cran-uri "syuzhet" version))
30569 "16iccqdbw02iw82nah6kwz3gwfghi864j2y698n4b9dyc386ijzv"))))
30570 (properties `((upstream-name . "syuzhet")))
30571 (build-system r-build-system)
30580 (native-inputs (list r-knitr))
30581 (home-page "https://github.com/mjockers/syuzhet")
30583 "Extracts Sentiment and Sentiment-Derived Plot Arcs from Text")
30585 "Extracts sentiment and sentiment-derived plot arcs from text using a
30586 variety of sentiment dictionaries conveniently packaged for consumption by R
30587 users. Implemented dictionaries include @dfn{syuzhet} (default) developed in the
30588 Nebraska Literary Lab, @dfn{afinn} developed by Finn Arup Nielsen, @dfn{bing}
30589 developed by Minqing Hu and Bing Liu, and @dfn{nrc} developed by Mohammad, Saif
30590 M. and Turney, Peter D. Applicable references are available in
30591 @file{README.md} and in the documentation for the @code{get_sentiment}
30592 function. The package also provides a hack for implementing Stanford's coreNLP
30593 sentiment parser. The package provides several methods for plot arc
30595 (license license:gpl3)))
30597 (define-public r-lexicon
30604 (uri (cran-uri "lexicon" version))
30607 "0x7rscsh6par2lj11sby7bmz41cxn63iiw51lgh29z09cg8j606c"))))
30608 (properties `((upstream-name . "lexicon")))
30609 (build-system r-build-system)
30611 (list r-data-table r-syuzhet))
30612 (home-page "https://github.com/trinker/lexicon")
30613 (synopsis "Lexicons for Text Analysis")
30615 "This package provides a collection of lexical hash tables, dictionaries,
30617 (license license:gpl3)))
30619 (define-public r-english
30626 (uri (cran-uri "english" version))
30629 "1g3nmy5p8wj3ix1vp1qmkmy3dyqisrw0md8cjrx4klqkp0wqlms9"))))
30630 (properties `((upstream-name . "english")))
30631 (build-system r-build-system)
30632 (native-inputs (list r-knitr))
30634 "https://cran.r-project.org/package=english")
30635 (synopsis "Translate Integers into English")
30637 "Allow numbers to be presented in an English language version, one, two,
30638 three, ... Ordinals are also available, first, second, third, ... and
30639 indefinite article choice, \"a\" or \"an\".")
30640 (license license:gpl2)))
30642 (define-public r-textclean
30644 (name "r-textclean")
30649 (uri (cran-uri "textclean" version))
30652 "0kgjh6c4f14qkjc4fds7q7rpf4nkma3p0igm54fplmm3p853nvrz"))))
30653 (properties `((upstream-name . "textclean")))
30654 (build-system r-build-system)
30665 "https://github.com/trinker/textclean")
30666 (synopsis "Text Cleaning Tools")
30668 "Tools to clean and process text. Tools are geared at checking for
30669 substrings that are not optimal for analysis and replacing or removing them
30670 (normalizing) with more analysis friendly substrings (see Sproat, Black, Chen,
30671 Kumar, Ostendorf, & Richards (2001) @url{doi:10.1006/csla.2001.0169}) or
30672 extracting them into new variables. For example, emoticons are often used in
30673 text but not always easily handled by analysis algorithms. The
30674 @code{replace_emoticon()} function replaces emoticons with word equivalents.")
30675 (license license:gpl2)))
30677 (define-public r-striprtf
30679 (name "r-striprtf")
30684 (uri (cran-uri "striprtf" version))
30687 "0dqcsh3fb8j0mmmxvxjl77rryhmrjm7a3scqvk2xkgxk4xq6q316"))))
30688 (properties `((upstream-name . "striprtf")))
30689 (build-system r-build-system)
30691 (list r-magrittr r-rcpp r-stringr))
30692 (home-page "https://github.com/kota7/striprtf")
30693 (synopsis "Extract Text from RTF File")
30695 "Extracts plain text from @dfn{Rich Text Format} (RTF) file.")
30696 (license license:expat)))
30698 (define-public r-ndjson
30705 (uri (cran-uri "ndjson" version))
30708 "0lvzbgfi1sg4kya1mvv67z14qk3vz9q57x22qh57xq8ampdkg812"))
30709 (modules '((guix build utils)))
30712 ;; unvendor gzstream
30713 (for-each delete-file '("src/gzstream.cpp" "src/gzstream.h"))
30715 (properties `((upstream-name . "ndjson")))
30716 (build-system r-build-system)
30719 (modify-phases %standard-phases
30720 (add-after 'unpack 'use-system-gzstream
30721 (lambda* (#:key inputs #:allow-other-keys)
30722 (substitute* "src/Makevars"
30723 (("PKG_LIBS = " all)
30724 (string-append all "-lgzstream ")))
30726 (inputs (list zlib gzstream))
30728 (list r-data-table r-rcpp r-tibble))
30729 (home-page "https://gitlab.com/hrbrmstr/ndjson")
30731 "Wicked-Fast @dfn{Streaming JSON} (ndjson) Reader")
30733 "@dfn{Streaming JSON} (ndjson) has one JSON record per-line and many
30734 modern ndjson files contain large numbers of records. These constructs may not
30735 be columnar in nature, but it is often useful to read in these files and
30736 \"flatten\" the structure out to enable working with the data in an R
30737 @code{data.frame}-like context. Functions are provided that make it possible
30738 to read in plain ndjson files or compressed (@code{gz}) ndjson files and either
30739 validate the format of the records or create \"flat\" @code{data.table}
30740 structures from them.")
30741 (license license:expat)))
30743 (define-public r-streamr
30750 (uri (cran-uri "streamR" version))
30753 "1clx3b0j2515r1nmnl6ki7qw5n54q3x2jvqv3zrc00kq71mlj7ix"))))
30754 (properties `((upstream-name . "streamR")))
30755 (build-system r-build-system)
30757 (list r-ndjson r-rcurl r-rjson))
30759 "https://cran.r-project.org/package=streamR")
30761 "Access to Twitter Streaming API via R")
30763 "This package provides functions to access Twitter's filter, sample, and
30764 user streams, and to parse the output into data frames.")
30765 (license license:gpl2)))
30767 (define-public r-readods
30774 (uri (cran-uri "readODS" version))
30777 "1hi217ab7hp15jsbzi5ak57cqf8jn2rv78bnn74q72gn9mrfra7n"))))
30778 (properties `((upstream-name . "readODS")))
30779 (build-system r-build-system)
30781 (list r-cellranger r-readr r-stringi r-xml2))
30782 (native-inputs (list r-knitr))
30784 "https://cran.r-project.org/package=readODS")
30785 (synopsis "Read and Write ODS Files")
30787 "Import @dfn{OpenDocument Spreadsheet} (ODS) into R as a data frame.
30788 Also support writing data frame into ODS file.")
30789 (license license:gpl3)))
30791 (define-public r-qpdf
30798 (uri (cran-uri "qpdf" version))
30801 "03lnfncw8qd1fwfyqh1mjvnsjr3b63wxbah0wp5g7z7gba90dwbi"))
30802 (modules '((guix build utils)))
30805 ;; unvendor libqpdf
30806 (delete-file-recursively "src/libqpdf")
30807 (delete-file-recursively "src/include/qpdf")
30809 (properties `((upstream-name . "qpdf")))
30810 (build-system r-build-system)
30813 (modify-phases %standard-phases
30814 (add-after 'unpack 'configure
30816 (setenv "EXTERNAL_QPDF" "1")
30821 (list r-askpass r-curl r-rcpp))
30822 (native-inputs (list pkg-config))
30823 (home-page "https://github.com/ropensci/qpdf")
30825 "Split, Combine and Compress PDF Files")
30827 "Content-preserving transformations transformations of PDF files such as
30828 split, combine, and compress. This package interfaces directly to the
30829 @code{qpdf} C++ API and does not require any command line utilities. Note that
30830 @code{qpdf} does not read actual content from PDF files: to extract text and
30831 data you need the @code{pdftools} package.")
30832 (license license:asl2.0)))
30834 (define-public r-pdftools
30836 (name "r-pdftools")
30841 (uri (cran-uri "pdftools" version))
30844 "1b9ppdndvlf8nl0i3xy1rx4f9j0j8ic6q9n0c4zn3rv6jdy8zqfi"))))
30845 (properties `((upstream-name . "pdftools")))
30846 (build-system r-build-system)
30847 (inputs (list zlib poppler))
30848 (propagated-inputs (list r-qpdf r-rcpp))
30849 (native-inputs (list pkg-config))
30850 (home-page "https://docs.ropensci.org/pdftools/")
30851 (synopsis "Text Extraction, Rendering and Converting of PDF Documents")
30853 "This package provides utilities based on @code{libpoppler} for
30854 extracting text, fonts, attachments and metadata from a PDF file. It also
30855 supports high quality rendering of PDF documents into PNG, JPEG, TIFF format,
30856 or into raw bitmap vectors for further processing in R.")
30857 (license license:expat)))
30859 (define-public r-antiword
30861 (name "r-antiword")
30866 (uri (cran-uri "antiword" version))
30869 "123v8zlczwh6fr1v3x7dl3885xlmddq1bqlcxih8zh07w0hlk1k2"))
30870 (modules '((guix build utils)))
30873 ;; unvendor libantiword
30874 (delete-file-recursively "src")
30876 (properties `((upstream-name . "antiword")))
30877 (build-system r-build-system)
30880 (modify-phases %standard-phases
30881 (add-after 'unpack 'use-system-antiword
30882 (lambda* (#:key inputs #:allow-other-keys)
30883 (substitute* "R/antiword.R"
30884 (("system.file\\(\"bin\", package = \"antiword\"\\)")
30885 (string-append "\"" (assoc-ref inputs "antiword") "/bin\"")))
30887 (inputs (list antiword))
30888 (propagated-inputs (list r-sys))
30890 "https://github.com/ropensci/antiword#readme")
30892 "Extract Text from Microsoft Word Documents")
30894 "Wraps the @code{AntiWord} utility to extract text from Microsoft Word
30895 documents. The utility only supports the old @code{doc} format, not the new
30896 xml based @code{docx} format. Use the @code{xml2} package to read the
30898 (license license:gpl2)))
30900 (define-public r-readtext
30902 (name "r-readtext")
30907 (uri (cran-uri "readtext" version))
30910 "0k782h5hns5v5h8a6qyfqck2hc15nq0awg8bsp196q4zviv5jw3c"))))
30911 (properties `((upstream-name . "readtext")))
30912 (build-system r-build-system)
30927 (native-inputs (list r-knitr))
30929 "https://github.com/quanteda/readtext")
30931 "Import and Handling for Plain and Formatted Text Files")
30933 "This package provides functions for importing and handling text files
30934 and formatted text files with additional meta-data, such including @code{.csv},
30935 @code{.tab}, @code{.json}, @code{.xml}, @code{.html}, @code{.pdf}, @code{.doc},
30936 @code{.docx}, @code{.rtf}, @code{.xls}, @code{.xlsx}, and others.")
30937 (license license:gpl3)))
30939 (define-public r-packcircles
30941 (name "r-packcircles")
30946 (uri (cran-uri "packcircles" version))
30949 "05pv5c4k4njkr0xw6i6ksiy34hcyx2lbiqpv5gxw81yrkm0rxfyk"))))
30950 (properties `((upstream-name . "packcircles")))
30951 (build-system r-build-system)
30952 (propagated-inputs (list r-rcpp))
30953 (native-inputs (list r-knitr))
30955 "https://github.com/mbedward/packcircles")
30956 (synopsis "Circle Packing")
30958 "Algorithms to find arrangements of non-overlapping circles.")
30959 (license license:expat)))
30961 ;; Cannot unbundle liblwgeom, because PostGIS does not support building it on
30963 (define-public r-lwgeom
30970 (uri (cran-uri "lwgeom" version))
30973 "0d4b1djwrzla91mmyya2m1250mb44fzmq3d36w5mk81d4bg952pl"))))
30974 (properties `((upstream-name . "lwgeom")))
30975 (build-system r-build-system)
30977 (list geos proj sqlite zlib))
30979 (list r-rcpp r-sf r-units))
30980 (native-inputs (list pkg-config))
30981 (home-page "https://github.com/r-spatial/lwgeom/")
30982 (synopsis "Bindings to Selected 'liblwgeom' Functions for Simple Features")
30984 "Access to selected functions found in
30985 @url{https://github.com/postgis/postgis/tree/master/liblwgeom,liblwgeom}, the
30986 light-weight geometry library used by @url{http://postgis.net/,PostGIS}.")
30987 (license license:gpl2)))
30989 (define-public r-stars
30996 (uri (cran-uri "stars" version))
30999 "0hcbzr8c7wk30qjwrvx6bflzwkjpms79pavaxawnq1h8kry5fngk"))))
31000 (properties `((upstream-name . "stars")))
31001 (build-system r-build-system)
31009 (native-inputs (list r-knitr))
31010 (home-page "https://r-spatial.github.io/stars/")
31012 "Spatiotemporal Arrays, Raster and Vector Data Cubes")
31014 "Reading, manipulating, writing and plotting spatiotemporal arrays
31015 (raster and vector data cubes) in @code{R}, using @code{GDAL} bindings provided
31016 by @code{sf}, and @code{NetCDF} bindings by @code{ncmeta} and @code{RNetCDF}.")
31017 (license license:asl2.0)))
31019 (define-public r-tmaptools
31021 (name "r-tmaptools")
31026 (uri (cran-uri "tmaptools" version))
31029 "0bal3czrdr93qig8s5cf5szld5vjbbks67rismfhlkmlgw6wp2gx"))))
31030 (properties `((upstream-name . "tmaptools")))
31031 (build-system r-build-system)
31043 "https://github.com/mtennekes/tmaptools")
31044 (synopsis "Thematic Map Tools")
31046 "Set of tools for reading and processing spatial data. The aim is to
31047 supply the workflow to create thematic maps. This package also facilitates
31048 @code{tmap}, the package for visualizing thematic maps.")
31049 (license license:gpl3)))
31051 (define-public r-rworldmap
31053 (name "r-rworldmap")
31058 (uri (cran-uri "rworldmap" version))
31061 "1q1h0n9qr0m5pdx10swrh9ddsvdj8kv5nqngrf3lnx9rg9iwivjk"))))
31062 (properties `((upstream-name . "rworldmap")))
31063 (build-system r-build-system)
31065 (list r-fields r-maptools r-sp))
31067 "https://github.com/AndySouth/rworldmap/")
31068 (synopsis "Mapping Global Data")
31070 "Enables mapping of country level and gridded user datasets.")
31071 (license license:gpl2+)))
31073 (define-public r-rtweet
31080 (uri (cran-uri "rtweet" version))
31083 "05pbvxm2vmf6935b9s6663k3aifnkr3m52wh2jvnplmrwyrfpn9n"))))
31084 (properties `((upstream-name . "rtweet")))
31085 (build-system r-build-system)
31094 (native-inputs (list r-knitr))
31096 "https://docs.ropensci.org/rtweet/")
31097 (synopsis "Collecting Twitter Data")
31099 "An implementation of calls designed to collect and organize Twitter data
31100 via @url{https://developer.twitter.com/en/docs,Twitter's REST and stream
31101 Application Program Interfaces (API)}.")
31102 (license license:expat)))
31104 (define-public r-intervals
31106 (name "r-intervals")
31111 (uri (cran-uri "intervals" version))
31114 "0mvwfwc03ifb30a3dzbmkv9adwqb8ajxhcw24d8xip8px063plhb"))))
31115 (properties `((upstream-name . "intervals")))
31116 (build-system r-build-system)
31117 (home-page "https://github.com/edzer/intervals")
31119 "Tools for Working with Points and Intervals")
31121 "Tools for working with and comparing sets of points and intervals.")
31122 (license license:artistic2.0)))
31124 (define-public r-eyelinker
31126 (name "r-eyelinker")
31131 (uri (cran-uri "eyelinker" version))
31134 "0wijd45p6j2qal6wnj7zywks8p9v3m9cmyp7axmk44mrjdjx2i71"))))
31135 (properties `((upstream-name . "eyelinker")))
31136 (build-system r-build-system)
31138 (list r-intervals r-readr r-stringi r-stringr r-tibble))
31139 (native-inputs (list r-knitr))
31141 "https://github.com/a-hurst/eyelinker")
31143 "Import ASC Files from EyeLink Eye Trackers")
31145 "Imports plain-text ASC data files from EyeLink eye trackers into
31146 (relatively) tidy data frames for analysis and visualization.")
31147 (license license:gpl3)))
31149 (define-public r-btm
31156 (uri (cran-uri "BTM" version))
31159 "0ab0wr8nbwn1w1j9hpwfz52lm1sw0qk93713y9k0hpm3pw9dq4jr"))))
31160 (properties `((upstream-name . "BTM")))
31161 (build-system r-build-system)
31162 (propagated-inputs (list r-rcpp))
31163 (home-page "https://github.com/bnosac/BTM")
31164 (synopsis "Biterm Topic Models for Short Text")
31166 "Biterm Topic Models find topics in collections of short texts. It is a
31167 word co-occurrence based topic model that learns topics by modeling word-word
31168 co-occurrences patterns which are called biterms. This in contrast to
31169 traditional topic models like Latent Dirichlet Allocation and Probabilistic
31170 Latent Semantic Analysis which are word-document co-occurrence topic models. A
31171 biterm consists of two words co-occurring in the same short text window. This
31172 context window can for example be a twitter message, a short answer on a
31173 survey, a sentence of a text or a document identifier. The techniques are
31174 explained in detail in the paper 'A Biterm Topic Model For Short Text' by
31175 Xiaohui Yan, Jiafeng Guo, Yanyan Lan, Xueqi Cheng (2013)
31176 @url{https://github.com/xiaohuiyan/xiaohuiyan.github.io/blob/master/paper/\
31178 (license license:asl2.0)))
31180 (define-public r-delaporte
31182 (name "r-delaporte")
31187 (uri (cran-uri "Delaporte" version))
31190 "10xsmms2jfw7x4hmgpd35dv4n4azpjzmfid6585kg6qfh2zg23g5"))))
31191 (properties `((upstream-name . "Delaporte")))
31192 (build-system r-build-system)
31193 (native-inputs (list gfortran))
31194 (home-page "https://github.com/aadler/Delaporte")
31195 (synopsis "Statistical functions for the Delaporte distribution")
31197 "This package provides probability mass, distribution, quantile,
31198 random-variate generation, and method-of-moments parameter-estimation
31199 functions for the Delaporte distribution with parameterization based on
31200 Vose (2008). The Delaporte is a discrete probability distribution which can
31201 be considered the convolution of a negative binomial distribution with a
31202 Poisson distribution. Alternatively, it can be considered a counting
31203 distribution with both Poisson and negative binomial components. It has been
31204 studied in actuarial science as a frequency distribution which has more
31205 variability than the Poisson, but less than the negative binomial.")
31206 (license license:bsd-2)))
31208 (define-public r-rjsonio
31211 (version "1.3-1.6")
31215 (uri (cran-uri "RJSONIO" version))
31218 "17x0ayk7daprbc8w2hvb2jl9mfnw4dic9yc3sr5adcjqfzmcklc2"))))
31219 (properties `((upstream-name . "RJSONIO")))
31220 (build-system r-build-system)
31221 (home-page "https://cran.r-project.org/package=RJSONIO")
31222 (synopsis "Serialize R objects to JSON")
31224 "This is a package that allows conversion to and from data in JavaScript
31225 Object Notation (JSON) format. This allows R objects to be inserted into
31226 Javascript/ECMAScript/ActionScript code and allows R programmers to read and
31227 convert JSON content to R objects. This is an alternative to the @code{rjson}
31229 (license license:bsd-3)))
31231 (define-public r-revgeo
31238 (uri (cran-uri "revgeo" version))
31241 "1ns7d1817475lriss6wwgvdm6lj760p40yxqaifla13c2xb73a55"))))
31242 (properties `((upstream-name . "revgeo")))
31243 (build-system r-build-system)
31245 (list r-rcurl r-rjsonio))
31246 (home-page "https://cran.r-project.org/package=revgeo")
31247 (synopsis "Reverse geocoding")
31249 "The @code{revgeo} procedure allows you to use the Photon geocoder for
31250 OpenStreetMap, Google Maps, and Bing to reverse geocode coordinate pairs with
31252 (license license:gpl3+)))
31254 (define-public r-qpcr
31261 (uri (cran-uri "qpcR" version))
31264 "1r01q7jv3w59yx1gc0qw91rq7rvdhqsi8y57sqqkmwyqfw2x2vsv"))))
31265 (properties `((upstream-name . "qpcR")))
31266 (build-system r-build-system)
31268 (list r-mass r-matrix r-minpack-lm r-rgl r-robustbase))
31269 (home-page "https://cran.r-project.org/package=qpcR")
31270 (synopsis "Modelling and analysis of real-time PCR data")
31272 "This is a package for model fitting, optimal model selection and
31273 calculation of various features that are essential in the analysis of
31274 quantitative real-time polymerase chain reaction (qPCR).")
31275 (license license:gpl2+)))
31277 (define-public r-textplot
31279 (name "r-textplot")
31284 (uri (cran-uri "textplot" version))
31287 "10nxh9axhy6kyp6f3rz7smq08yl35ydx9jx47bs7i0bmcl2kwxvl"))))
31288 (properties `((upstream-name . "textplot")))
31289 (build-system r-build-system)
31291 (list r-data-table r-lattice r-matrix))
31292 (native-inputs (list r-knitr))
31293 (home-page "https://github.com/bnosac/textplot")
31294 (synopsis "Text Plots")
31296 "Visualise complex relations in texts. This is done by providing
31297 functionalities for displaying text co-occurrence networks, text correlation
31298 networks, dependency relationships as well as text clustering. Feel free to
31299 join the effort of providing interesting text visualisations.")
31300 (license license:gpl2)))
31302 (define-public r-gsa
31309 (uri (cran-uri "GSA" version))
31312 "1f1mrxxdbdlnibgav6nsvbpniz2x3km2svc0hf43spb4zicn0z8p"))))
31313 (properties `((upstream-name . "GSA")))
31314 (build-system r-build-system)
31315 (home-page "https://statweb.stanford.edu/~tibs/GSA/")
31316 (synopsis "Gene set analysis")
31317 (description "This package lets you determine the significance of
31318 pre-defined sets of genes with respect to an outcome variable, such as a group
31319 indicator, a quantitative variable or a survival time.")
31320 ;; Any version of the LGPL
31321 (license license:lgpl3+)))
31323 (define-public r-randomforestsrc
31325 (name "r-randomforestsrc")
31330 (uri (cran-uri "randomForestSRC" version))
31333 "05ifvj49jv0n5p6k46milpgj9r10sc5aw23fypyyibdgwpwvwixw"))))
31335 `((upstream-name . "randomForestSRC")))
31336 (build-system r-build-system)
31337 (home-page "https://cran.r-project.org/web/packages/randomForestSRC/")
31338 (synopsis "Random forests for survival, regression, and classification")
31340 "This package implements fast OpenMP parallel computing of Breiman's
31341 random forests for survival, competing risks, regression and classification
31342 based on Ishwaran and Kogalur's popular random survival forests (RSF) package.
31343 It handles missing data and now includes multivariate, unsupervised forests,
31344 quantile regression and solutions for class imbalanced data. It provides a
31345 fast interface using subsampling and confidence regions for variable
31347 (license license:gpl3+)))
31349 (define-public r-contfrac
31351 (name "r-contfrac")
31356 (uri (cran-uri "contfrac" version))
31359 "0sq5c7ny235yrkv2xc4insgxby6rvzc1qsj8h301cd2if3lwbgwm"))))
31360 (properties `((upstream-name . "contfrac")))
31361 (build-system r-build-system)
31363 "https://github.com/RobinHankin/contfrac")
31364 (synopsis "Continued Fractions")
31366 "Various utilities for evaluating continued fractions.")
31367 (license license:gpl2)))
31369 (define-public r-elliptic
31371 (name "r-elliptic")
31376 (uri (cran-uri "elliptic" version))
31379 "1dhba0yfxjd5rlqsxp5a7s2hclfkla9wigsr39dlma67l6qjjmxn"))))
31380 (properties `((upstream-name . "elliptic")))
31381 (build-system r-build-system)
31382 (inputs (list pari-gp))
31383 (propagated-inputs (list r-mass))
31385 "https://github.com/RobinHankin/elliptic")
31387 "Weierstrass and Jacobi Elliptic Functions")
31389 "A suite of elliptic and related functions including Weierstrass and
31390 Jacobi forms. Also includes various tools for manipulating and visualizing
31391 complex functions.")
31392 (license license:gpl2)))
31394 (define-public r-hypergeo
31396 (name "r-hypergeo")
31401 (uri (cran-uri "hypergeo" version))
31404 "13jdiy216znwhr91iqnh03mvkmyscw439syb3h4i67dd78sphnvd"))))
31405 (properties `((upstream-name . "hypergeo")))
31406 (build-system r-build-system)
31408 (list r-contfrac r-desolve r-elliptic))
31410 "https://cran.r-project.org/web/packages/hypergeo/")
31411 (synopsis "The Gauss Hypergeometric Function")
31413 "The Gaussian hypergeometric function for complex numbers.")
31414 (license license:gpl2)))
31416 (define-public r-gganimate
31418 (name "r-gganimate")
31423 (uri (cran-uri "gganimate" version))
31426 "046v6j92xxgaghsnh88dy5h8x040qsfa8csvhp4dmsfmrrf0dz0f"))))
31427 (properties `((upstream-name . "gganimate")))
31428 (build-system r-build-system)
31431 (modify-phases %standard-phases
31432 (add-after 'unpack 'absolute-paths
31433 (lambda* (#:key inputs #:allow-other-keys)
31434 (substitute* "R/renderers.R"
31436 (string-append "'" (assoc-ref inputs "ffmpeg") "/bin/ffmpeg'"))))))))
31438 ;; For video output.
31449 ;; For GIF/SVG output. gifski is faster, but depends on Rust.
31451 ;; For HTML output.
31454 (native-inputs (list r-knitr))
31455 (home-page "https://gganimate.com")
31456 (synopsis "Grammar of Animated Graphics")
31458 "This package extends the grammar of graphics as implemented by
31459 @code{ggplot2} to include the description of animation. It does this by
31460 providing a range of new grammar classes that can be added to the plot object
31461 in order to customise how it should change with time.")
31462 (license license:expat)))
31464 ;; This library bundles ‘date’ from (gnu packages calendar). We cannot unbundle
31465 ;; it, because its C++ libtz.so is built with different compiler flags than
31467 (define-public r-tzdb
31474 (uri (cran-uri "tzdb" version))
31477 "0f3h4zaf9f4l371k6nc1mq6z2f9aj1vaf2inni8jnsds3zng16b0"))))
31478 (properties `((upstream-name . "tzdb")))
31479 (build-system r-build-system)
31480 (propagated-inputs (list r-cpp11))
31481 (home-page "https://github.com/r-lib/tzdb")
31482 (synopsis "Time Zone Database Information")
31484 "This package provides an up-to-date copy of the Internet Assigned
31485 Numbers Authority (IANA) Time Zone Database. It is updated periodically to
31486 reflect changes made by political bodies to time zone boundaries, UTC offsets,
31487 and daylight saving time rules. Additionally, this package provides a C++
31488 interface for working with the @code{date} library. @code{date} provides
31489 comprehensive support for working with dates and date-times, which this package
31490 exposes to make it easier for other R packages to utilize. Headers are
31491 provided for calendar specific calculations, along with a limited interface for
31492 time zone manipulations.")
31493 (license license:expat)))
31495 (define-public r-vroom
31502 (uri (cran-uri "vroom" version))
31505 "1plz20x6s01gkkcac51lhx4r2s024pgh778ri7y25hkiiwacp1yh"))))
31506 (properties `((upstream-name . "vroom")))
31507 (build-system r-build-system)
31523 (native-inputs (list r-knitr))
31524 (home-page "https://vroom.r-lib.org")
31526 "Read and Write Rectangular Text Data")
31528 "This package reads and writes data files like @acronym{CSV},
31529 @acronym{TSV} and @acronym{FWF}. When reading it uses a quick initial indexing
31530 step, then reads the values lazily, so only the data you actually use needs to
31531 be read. The writer formats the data in parallel and writes to disk
31532 asynchronously from formatting.")
31533 (license license:expat)))
31535 (define-public r-rmisc
31541 (uri (cran-uri "Rmisc" version))
31544 "1h6jb0xwkyhm9lwm7nj9bhrb5dhrsifvkpqkrd594j1lz74dar8x"))))
31545 (build-system r-build-system)
31547 (list r-plyr r-lattice))
31548 (home-page "https://cran.r-project.org/web/packages/Rmisc/")
31549 (synopsis "Ryan Miscellaneous")
31550 (description "The Rmisc library contains functions for data analysis and
31551 utility operations.")
31552 (license license:gpl3)))
31554 (define-public r-webutils
31556 (name "r-webutils")
31561 (uri (cran-uri "webutils" version))
31563 (base32 "16a6ds0fnb6y8i1r9ba1hf1ydb53am57s070b3hi5jmrs84b9qik"))))
31564 (properties `((upstream-name . "webutils")))
31565 (build-system r-build-system)
31567 (list r-curl r-jsonlite))
31568 (home-page "https://github.com/jeroen/webutils")
31569 (synopsis "Utility functions for developing web applications")
31571 "This package parses HTTP request data in @code{application/json},
31572 @code{multipart/form-data}, or @code{application/x-www-form-urlencoded}
31573 format. It includes an example of hosting and parsing HTML form data in R
31574 using either @code{httpuv} or @code{Rhttpd}.")
31575 (license license:expat)))
31577 (define-public r-protolite
31579 (name "r-protolite")
31584 (uri (cran-uri "protolite" version))
31586 (base32 "0g1r3lzmvx1w44qzqzdvxfn21zmz11srlp6cr76kd7pd5wzjv82p"))))
31587 (properties `((upstream-name . "protolite")))
31588 (build-system r-build-system)
31592 (list r-jsonlite r-rcpp))
31594 (list protobuf pkg-config))
31595 (home-page "https://github.com/jeroen/protolite")
31596 (synopsis "Highly optimized protocol buffer serializers")
31598 "This package provides pure C++ implementations for reading and writing
31599 several common data formats based on Google protocol-buffers. It currently
31600 supports @code{rexp.proto} for serialized R objects, @code{geobuf.proto} for
31601 binary geojson, and @code{mvt.proto} for vector tiles. This package uses the
31602 auto-generated C++ code by protobuf-compiler, hence the entire serialization
31603 is optimized at compile time. The @code{RProtoBuf} package on the other hand
31604 uses the protobuf runtime library to provide a general-purpose toolkit for
31605 reading and writing arbitrary protocol-buffer data in R.")
31606 (license license:expat)))
31608 (define-public r-opencpu
31615 (uri (cran-uri "opencpu" version))
31617 (base32 "1h0s7fbifyf4h1296sdk3amij0m6s12wq32mbky7xg4nz8wj29ni"))))
31618 (properties `((upstream-name . "opencpu")))
31619 (build-system r-build-system)
31639 (home-page "https://www.opencpu.org")
31640 (synopsis "API for embedded scientific computing")
31642 "This package provides a system for embedded scientific computing and
31643 reproducible research with R. The OpenCPU server exposes a simple but
31644 powerful HTTP API for RPC and data interchange with R. This provides a
31645 reliable and scalable foundation for statistical services or building R web
31646 applications. The OpenCPU server runs either as a single-user development
31647 server within the interactive R session, or as a multi-user stack based on
31649 (license license:asl2.0)))
31651 (define-public r-exactextractr
31653 (name "r-exactextractr")
31658 (uri (cran-uri "exactextractr" version))
31661 "0x4axrq9iznvajqy07gcfcrvzniz5yj6wabchgksg0fqz0xancnc"))))
31662 (properties `((upstream-name . "exactextractr")))
31663 (build-system r-build-system)
31664 (inputs (list geos))
31666 (list r-raster r-rcpp r-sf))
31669 (home-page "https://isciences.gitlab.io/exactextractr/")
31670 (synopsis "Fast extraction from raster datasets using polygons")
31672 "This package provides a replacement for the @code{extract} function from
31673 the @code{raster} package that is suitable for extracting raster values using
31674 @code{sf} polygons.")
31675 (license license:asl2.0)))
31677 (define-public r-stringfish
31679 (name "r-stringfish")
31684 (uri (cran-uri "stringfish" version))
31687 "0ddpsi7z0kzqgbq9y646pk9afclq0r7ak22zsdh0i93ni0x71c9l"))))
31688 (properties `((upstream-name . "stringfish")))
31689 (build-system r-build-system)
31691 (list r-rcpp r-rcppparallel))
31693 (list pkg-config r-knitr))
31694 (home-page "https://github.com/traversc/stringfish")
31695 (synopsis "Alternative string implementation")
31697 "This package provides an extendable, performant and multithreaded
31698 @code{alt-string} implementation backed by C++ vectors and strings.")
31699 (license license:gpl3)))
31701 (define-public r-rapiserialize
31703 (name "r-rapiserialize")
31708 (uri (cran-uri "RApiSerialize" version))
31711 "0gm2j8kh40imhncwwx1sx9kmraaxcxycvgwls53lcyy2ap344k9j"))))
31712 (properties `((upstream-name . "RApiSerialize")))
31713 (build-system r-build-system)
31715 "https://cran.r-project.org/package=RApiSerialize")
31716 (synopsis "R API serialization")
31718 "This package provides other packages with access to the internal R
31719 serialization code. Access to this code is provided at the C function level
31720 by using the registration of native function mechanism. Client packages
31721 simply include a single header file RApiSerializeAPI.h provided by this
31723 (license license:gpl2+)))
31725 (define-public r-qs
31732 (uri (cran-uri "qs" version))
31735 "0sxy497v5arjv6lwxng7chkbzrn703waqmgsxv77i7y12ahzdbai"))))
31736 (properties `((upstream-name . "qs")))
31737 (build-system r-build-system)
31738 (inputs (list zlib))
31740 (list r-rapiserialize r-rcpp r-stringfish))
31742 (list pkg-config r-knitr))
31743 (home-page "https://github.com/traversc/qs")
31744 (synopsis "Quick serialization of R objects")
31746 "This package provides functions for quickly writing and reading any R
31747 object to and from disk.")
31748 (license license:gpl3)))
31750 (define-public r-rgeos
31757 (uri (cran-uri "rgeos" version))
31760 "1m73y0nwrdwsjrl48c4fg1kdqnh79835brnmxv9ak01ndbzcp45b"))))
31761 (properties `((upstream-name . "rgeos")))
31762 (build-system r-build-system)
31767 (home-page "https://cran.r-project.org/package=rgeos")
31768 (synopsis "Interface to Geometry Engine (GEOS)")
31770 "This package provides an R interface to Geometry Engine (GEOS) using the
31771 C API for topology operations on geometries.")
31772 (license license:gpl2+)))
31774 (define-public r-tfruns
31781 (uri (cran-uri "tfruns" version))
31784 "04lfckg1if3kfwcl4s4fcc9aw04crwk4m1qr55ag22j2x2jlb2l9"))))
31785 (properties `((upstream-name . "tfruns")))
31786 (build-system r-build-system)
31798 (native-inputs (list r-knitr))
31799 (home-page "https://github.com/rstudio/tfruns")
31800 (synopsis "Training run tools for TensorFlow")
31802 "Create and manage unique directories for each TensorFlow training run.
31803 This package provides a unique, time stamped directory for each run along with
31804 functions to retrieve the directory of the latest run or latest several
31806 (license license:asl2.0)))
31808 (define-public r-tfautograph
31810 (name "r-tfautograph")
31815 (uri (cran-uri "tfautograph" version))
31818 "0fmaq1ggjyxgf2ss7qb8jk74sfwc3s1vc123pd5glclxcy1ib0j2"))))
31819 (properties `((upstream-name . "tfautograph")))
31820 (build-system r-build-system)
31821 (inputs (list tensorflow))
31823 (list r-backports r-reticulate))
31824 (home-page "https://t-kalinowski.github.io/tfautograph/")
31825 (synopsis "Autograph R for Tensorflow")
31827 "This package lets you translate R control flow expressions into
31828 Tensorflow graphs.")
31829 (license license:gpl3)))
31831 (define-public r-tensorflow
31833 (name "r-tensorflow")
31838 (uri (cran-uri "tensorflow" version))
31841 "12c6ndxx4g6fqjakpzp9pgl29ghswhqyr6q9jahpk0cawizh2znj"))))
31842 (properties `((upstream-name . "tensorflow")))
31843 (build-system r-build-system)
31844 (inputs (list tensorflow))
31853 (home-page "https://github.com/rstudio/tensorflow")
31854 (synopsis "R interface to TensorFlow")
31856 "R interface to TensorFlow a library for numerical computation using data
31857 flow graphs. Nodes in the graph represent mathematical operations, while the
31858 graph edges represent the multidimensional data arrays (tensors) communicated
31860 (license license:asl2.0)))
31862 (define-public r-keras
31869 (uri (cran-uri "keras" version))
31872 "06513d1fp7cxk4v03xm9lhgj6xmp9dqqvw3lnzwbzjwdkfj948yc"))))
31873 (properties `((upstream-name . "keras")))
31874 (build-system r-build-system)
31886 (native-inputs (list r-knitr))
31887 (home-page "https://keras.rstudio.com")
31888 (synopsis "R Interface to 'Keras'")
31890 "This package provides an interface to Keras, a high-level neural
31891 networks API. Keras was developed with a focus on enabling fast
31892 experimentation, supports both convolution based networks and recurrent
31893 networks (as well as combinations of the two), and runs seamlessly on both CPU
31895 (license license:expat)))
31897 (define-public r-zzlite
31904 (uri (cran-uri "zzlite" version))
31907 "0vi1slx2s4r5zf82lazqv0c3m12xq73wlgsbz6af4y00h0bkr3ps"))))
31908 (properties `((upstream-name . "zzlite")))
31909 (build-system r-build-system)
31911 (list r-httr r-jsonlite))
31914 (home-page "https://cran.r-project.org/package=zzlite")
31915 (synopsis "Wrapper for the Zamzar file conversion API")
31917 "This package provides a minor collection of HTTP wrappers for the Zamzar
31918 file conversion API. The wrappers makes it easy to utilize the API and thus
31919 convert between more than 100 different file formats (ranging from audio
31920 files, images, movie formats, etc., etc.) through an R session.")
31921 (license license:gpl3)))
31923 (define-public r-ztree
31930 (uri (cran-uri "zTree" version))
31933 "005zk6wpchpss6865ki35yawgf668pn70163ah97rnfkhfaswm6y"))))
31934 (properties `((upstream-name . "zTree")))
31935 (build-system r-build-system)
31938 (home-page "https://cran.r-project.org/package=zTree")
31939 (synopsis "Functions to import data from z-Tree into R")
31941 "This package provides tools for reading @code{.xls} and @code{.sbj}
31942 files which are written by the proprietary program z-Tree for developing and
31943 carrying out economic experiments.")
31944 (license license:gpl3)))
31946 (define-public r-distributionutils
31948 (name "r-distributionutils")
31953 (uri (cran-uri "DistributionUtils" version))
31956 "08vq54pyqxlqsj6q6gsg5ikqa0z3x842j52ld5dxaq272p6xchvl"))))
31958 `((upstream-name . "DistributionUtils")))
31959 (build-system r-build-system)
31962 (home-page "https://cran.r-project.org/package=DistributionUtils")
31963 (synopsis "Distribution utilities")
31965 "This package provides utilities for dealing with distributions.
31966 Functionality includes sample skewness and kurtosis, log-histogram, tail
31967 plots, moments by integration, changing the point about which a moment is
31968 calculated, functions for testing distributions using inversion tests and the
31969 Massart inequality. Also included is an implementation of the incomplete
31970 Bessel K function.")
31971 (license license:gpl2+)))
31973 (define-public r-ztpln
31980 (uri (cran-uri "ztpln" version))
31983 "1b22m72a8117yrgq5k1gzsrbx6yrsrj7bpd49lh7x3vbaz56c0wr"))))
31984 (properties `((upstream-name . "ztpln")))
31985 (build-system r-build-system)
31987 (list r-distributionutils r-mixtools r-rcpp r-rcppeigen
31991 (home-page "https://github.com/mattocci27/ztpln")
31992 (synopsis "Zero-truncated Poisson lognormal distribution")
31994 "This package provides functions for obtaining the density, random
31995 variates and maximum likelihood estimates of the Zero-truncated Poisson
31996 lognormal distribution and their mixture distribution.")
31997 (license license:expat)))
31999 (define-public r-zscorer
32006 (uri (cran-uri "zscorer" version))
32009 "0aijhs0fyird5gq68x4dxchb02mxa7ijk10k9zjhngghxbjj7iqn"))))
32010 (properties `((upstream-name . "zscorer")))
32011 (build-system r-build-system)
32016 (home-page "https://github.com/nutriverse/zscorer")
32017 (synopsis "Child Anthropometry z-Score Calculator")
32019 "This package provides a tool for calculating z-scores and centiles for
32020 weight-for-age, length/height-for-age, weight-for-length/height, BMI-for-age,
32021 head circumference-for-age, age circumference-for-age, subscapular
32022 skinfold-for-age, triceps skinfold-for-age based on the WHO Child Growth
32024 (license license:agpl3+)))
32026 (define-public r-zra
32033 (uri (cran-uri "ZRA" version))
32036 "1sx1q5yf68hhlb5j1hicpj594rmgajqr25llg7ax416j0m2rnagi"))))
32037 (properties `((upstream-name . "ZRA")))
32038 (build-system r-build-system)
32040 (list r-dygraphs r-forecast))
32041 (home-page "https://cran.r-project.org/package=ZRA")
32042 (synopsis "Dynamic plots for time series forecasting")
32044 "This package combines a forecast of a time series, using the function @code{forecast},
32045 with the dynamic plots from @code{dygraphs}.")
32046 (license license:gpl2+)))
32048 (define-public r-rfigshare
32050 (name "r-rfigshare")
32055 (uri (cran-uri "rfigshare" version))
32058 "10shwl1y9220m7ld5w9fjsjzy5yg8myrz9cz97ps9z2bw7bvka5j"))))
32059 (properties `((upstream-name . "rfigshare")))
32060 (build-system r-build-system)
32070 (home-page "https://github.com/ropensci/rfigshare")
32071 (synopsis "R Interface to figshare")
32073 "This package provides an interface to figshare, a scientific repository
32074 to archive and assign DOIs to data, software, figures, and more.")
32075 (license license:cc0)))
32077 (define-public r-dismo
32084 (uri (cran-uri "dismo" version))
32087 "1rqf6h4imbqvs7hjd1k4my6154wg0qnmnp5byan403rcshr1jbl1"))))
32088 (properties `((upstream-name . "dismo")))
32089 (build-system r-build-system)
32091 (list r-raster r-rcpp r-sp r-terra))
32092 (home-page "https://rspatial.org/raster/sdm/")
32093 (synopsis "Species distribution modeling")
32095 "This package provides methods for species distribution modeling, i.e.,
32096 predicting the environmental similarity of any site to that of the locations
32097 of known occurrences of a species.")
32098 (license license:gpl3+)))
32100 (define-public r-zoon
32107 (uri (cran-uri "zoon" version))
32110 "02y29vr2yn8al69km8faiqrwjrc1r3hsvw3dg8lwjr65cxw1krip"))))
32111 (properties `((upstream-name . "zoon")))
32112 (build-system r-build-system)
32127 (home-page "https://github.com/zoonproject/zoon")
32128 (synopsis "Reproducible, accessible and shareable species distribution modelling")
32130 "This package reads user submitted modules from an online repository,
32131 runs full species distribution modelling workflows and returns output that is
32132 fully reproducible.")
32133 (license license:bsd-3)))
32135 (define-public r-paws-common
32137 (name "r-paws-common")
32142 (uri (cran-uri "paws.common" version))
32145 "1dg18hwnrjd6m1vjcxfs2vm1zxciivf4vzhq0z76dmmiqz2yjm28"))))
32146 (properties `((upstream-name . "paws.common")))
32147 (build-system r-build-system)
32149 (list r-base64enc r-digest r-httr r-jsonlite r-xml2))
32150 (home-page "https://cran.r-project.org/package=paws.common")
32151 (synopsis "Paws low-level Amazon Web Services API")
32153 "This package provides functions for making low-level API requests to
32154 Amazon Web Services. The functions handle building, signing, and sending
32155 requests, and receiving responses. They are designed to help build
32156 higher-level interfaces to individual services, such as Simple Storage
32158 (license license:asl2.0)))
32160 (define-public r-paws-customer-engagement
32162 (name "r-paws-customer-engagement")
32167 (uri (cran-uri "paws.customer.engagement" version))
32170 "0ac6hzn4ilfjhzdmc9x80999fl18cz16mky31qd3y09m93w2xkdj"))))
32172 `((upstream-name . "paws.customer.engagement")))
32173 (build-system r-build-system)
32175 (list r-paws-common))
32176 (home-page "https://github.com/paws-r/paws")
32177 (synopsis "Amazon Web Services customer engagement services")
32179 "This package provides an interface to Amazon Web Services customer
32180 engagement services, including Simple Email Service, Connect contact center
32181 service, and more.")
32182 (license license:asl2.0)))
32184 (define-public r-paws-cost-management
32186 (name "r-paws-cost-management")
32191 (uri (cran-uri "paws.cost.management" version))
32194 "0in4f8ygw5g2v6vl3lz2y0v51llglh8b1ymbd04d54xxlgn83knh"))))
32196 `((upstream-name . "paws.cost.management")))
32197 (build-system r-build-system)
32199 (list r-paws-common))
32200 (home-page "https://github.com/paws-r/paws")
32201 (synopsis "Amazon Web Services cost management services")
32203 "This package provides an interface to Amazon Web Services cost
32204 management services, including cost and usage reports, budgets, pricing, and
32206 (license license:asl2.0)))
32208 (define-public r-paws-developer-tools
32210 (name "r-paws-developer-tools")
32215 (uri (cran-uri "paws.developer.tools" version))
32217 (base32 "16gb8g8s67al7qdd95fbigxqkih9a9p7slkyf3cga42wb6miiby2"))))
32218 (properties `((upstream-name . "paws.developer.tools")))
32219 (build-system r-build-system)
32221 (list r-paws-common))
32222 (home-page "https://github.com/paws-r/paws")
32223 (synopsis "Amazon Web Services developer tools services")
32225 "This package provides an interface to Amazon Web Services developer
32226 tools services, including version control, continuous integration and
32227 deployment, and more.")
32228 (license license:asl2.0)))
32230 (define-public r-paws-end-user-computing
32232 (name "r-paws-end-user-computing")
32237 (uri (cran-uri "paws.end.user.computing" version))
32239 (base32 "1xxsz86nx128sizym9np8vldzkbym0p3i6vcy94kq1y0cylaicv3"))))
32240 (properties `((upstream-name . "paws.end.user.computing")))
32241 (build-system r-build-system)
32243 (list r-paws-common))
32244 (home-page "https://github.com/paws-r/paws")
32245 (synopsis "Amazon Web Services end user computing services")
32247 "This package provides an interface to Amazon Web Services end user
32248 computing services, including collaborative document editing, mobile intranet,
32250 (license license:asl2.0)))
32252 (define-public r-paws-application-integration
32254 (name "r-paws-application-integration")
32259 (uri (cran-uri "paws.application.integration" version))
32262 "0llyd9hc679pad1ih0rcc38q5xxpzinhwrl8cvrkgsjgbc3agq42"))))
32264 `((upstream-name . "paws.application.integration")))
32265 (build-system r-build-system)
32267 (list r-paws-common))
32268 (home-page "https://github.com/paws-r/paws")
32269 (synopsis "Amazon Web Services application integration services")
32271 "This package provides an interface to Amazon Web Services application
32272 integration services, including Simple Queue Service (SQS) message queue,
32273 Simple Notification Service (SNS) publish/subscribe messaging, and more.")
32274 (license license:asl2.0)))
32276 (define-public r-paws-security-identity
32278 (name "r-paws-security-identity")
32283 (uri (cran-uri "paws.security.identity" version))
32286 "092lz2ipn5iqr593x7ra8c0bj64yf6315mdc3llgwrjyb4vfxif9"))))
32288 `((upstream-name . "paws.security.identity")))
32289 (build-system r-build-system)
32291 (list r-paws-common))
32292 (home-page "https://github.com/paws-r/paws")
32293 (synopsis "Amazon Web Services security, identity, and compliance services")
32295 "This package provides an interface to Amazon Web Services security,
32296 identity, and compliance services, including the Identity and Access
32297 Management (IAM) service for managing access to services and resources, and
32299 (license license:asl2.0)))
32301 (define-public r-paws-analytics
32303 (name "r-paws-analytics")
32308 (uri (cran-uri "paws.analytics" version))
32311 "04gnaxmj21l312xkrsd9bisi0bz9h6h5fyhwlqylcxi077z1yb2g"))))
32313 `((upstream-name . "paws.analytics")))
32314 (build-system r-build-system)
32316 (list r-paws-common))
32317 (home-page "https://github.com/paws-r/paws")
32318 (synopsis "Amazon Web Services analytics services")
32320 "This package provides an interface to Amazon Web Services analytics
32321 services, including Elastic MapReduce Hadoop and Spark big data service,
32322 Elasticsearch search engine, and more.")
32323 (license license:asl2.0)))
32325 (define-public r-paws-machine-learning
32327 (name "r-paws-machine-learning")
32332 (uri (cran-uri "paws.machine.learning" version))
32335 "01w2y5952pk50xjbzby2pc51xrkrzjpfxbmii1b10cl2xgzfkxsa"))))
32337 `((upstream-name . "paws.machine.learning")))
32338 (build-system r-build-system)
32340 (list r-paws-common))
32341 (home-page "https://github.com/paws-r/paws")
32342 (synopsis "Amazon Web Services machine learning services")
32344 "This package provides an interface to Amazon Web Services machine
32345 learning services, including SageMaker managed machine learning service,
32346 natural language processing, speech recognition, translation, and more.")
32347 (license license:asl2.0)))
32349 (define-public r-paws-management
32351 (name "r-paws-management")
32356 (uri (cran-uri "paws.management" version))
32359 "09k7wg0jlj40zs2yb3vldffpkdcjg7ap98n7c5lxr5plpca08swg"))))
32361 `((upstream-name . "paws.management")))
32362 (build-system r-build-system)
32364 (list r-paws-common))
32365 (home-page "https://github.com/paws-r/paws")
32366 (synopsis "Amazon Web Services management and governance services")
32368 "This package provides an interface to Amazon Web Services management and
32369 governance services, including CloudWatch application and infrastructure
32370 monitoring, Auto Scaling for automatically scaling resources, and more.")
32371 (license license:asl2.0)))
32373 (define-public r-paws-networking
32375 (name "r-paws-networking")
32380 (uri (cran-uri "paws.networking" version))
32383 "02hxaa5nlj70mdggh379ij3fn09xm8h5ldzsyf45c342prpl6zwj"))))
32385 `((upstream-name . "paws.networking")))
32386 (build-system r-build-system)
32388 (list r-paws-common))
32389 (home-page "https://github.com/paws-r/paws")
32390 (synopsis "Amazon Web Services networking and content delivery services")
32392 "This package provides an interface to Amazon Web Services networking and
32393 content delivery services, including Route 53 Domain Name System service,
32394 CloudFront content delivery, load balancing, and more.")
32395 (license license:asl2.0)))
32397 (define-public r-paws-database
32399 (name "r-paws-database")
32404 (uri (cran-uri "paws.database" version))
32407 "08jpwz95fw3f68j0wxh2lg57nn60khflldab0ryhkkbcw1iy0qyz"))))
32408 (properties `((upstream-name . "paws.database")))
32409 (build-system r-build-system)
32411 (list r-paws-common))
32412 (home-page "https://github.com/paws-r/paws")
32414 "Amazon Web Services Database Services")
32416 "This package provides an interface to Amazon Web Services database
32417 services, including Relational Database Service (RDS), DynamoDB NoSQL
32418 database, and more.")
32419 (license license:asl2.0)))
32421 (define-public r-paws-storage
32423 (name "r-paws-storage")
32428 (uri (cran-uri "paws.storage" version))
32431 "06m887vpqp5d6k3zxdlga599dsv8v3rladk7xqaxqnld1f17am04"))))
32432 (properties `((upstream-name . "paws.storage")))
32433 (build-system r-build-system)
32435 (list r-paws-common))
32436 (home-page "https://github.com/paws-r/paws")
32437 (synopsis "Amazon Web Services storage services")
32439 "This package provides an interface to Amazon Web Services storage
32440 services, including Simple Storage Service (S3).")
32441 (license license:asl2.0)))
32443 (define-public r-paws-compute
32445 (name "r-paws-compute")
32450 (uri (cran-uri "paws.compute" version))
32453 "1km6fng6il5fcjlrbbndahsw2dr2ql83hwac9wlpd67zm3wy9lky"))))
32454 (properties `((upstream-name . "paws.compute")))
32455 (build-system r-build-system)
32457 (list r-paws-common))
32458 (home-page "https://github.com/paws-r/paws")
32459 (synopsis "Amazon Web Services compute services")
32461 "This package provides an interface to Amazon Web Services compute
32462 services, including Elastic Compute Cloud (EC2), Lambda
32463 functions-as-a-service, containers, batch processing, and more.")
32464 (license license:asl2.0)))
32466 (define-public r-paws
32473 (uri (cran-uri "paws" version))
32476 "0kn1z045r106fwqcaz52hb02bhrcblh479cajfjiq480s1iljcw6"))))
32477 (properties `((upstream-name . "paws")))
32478 (build-system r-build-system)
32480 (list r-paws-analytics
32481 r-paws-application-integration
32483 r-paws-cost-management
32484 r-paws-customer-engagement
32486 r-paws-developer-tools
32487 r-paws-end-user-computing
32488 r-paws-machine-learning
32491 r-paws-security-identity
32493 (home-page "https://github.com/paws-r/paws")
32494 (synopsis "Amazon Web Services software development kit")
32496 "This package provides an interface to Amazon Web Services, including
32497 storage, database, and compute services, such as Simple Storage Service (S3),
32498 DynamoDB NoSQL database, and Lambda functions-as-a-service.")
32499 (license license:asl2.0)))
32501 (define-public r-zoomgroupstats
32503 (name "r-zoomgroupstats")
32508 (uri (cran-uri "zoomGroupStats" version))
32511 "0gndiq92cy6gi7f833hdjvqii3cn83wz5rjvygcvjl3dw4pwv966"))))
32513 `((upstream-name . "zoomGroupStats")))
32514 (build-system r-build-system)
32525 (native-inputs (list r-knitr))
32526 (home-page "http://zoomgroupstats.org")
32527 (synopsis "Analyze text, audio, and video from Zoom meetings")
32529 "This package provides utilities for processing and analyzing the files
32530 that are exported from a recorded Zoom meeting. This includes analyzing data
32531 captured through video cameras and microphones, the text-based chat, and
32532 meta-data. You can analyze aspects of the conversation among meeting
32533 participants and their emotional expressions throughout the meeting.")
32534 (license license:expat)))
32536 (define-public r-zoom
32543 (uri (cran-uri "zoom" version))
32546 "03f5rxfr6ncf1j6vpn7pip21q7ylj4bx0a5xphqb6x6i33lxf1g5"))))
32547 (properties `((upstream-name . "zoom")))
32548 (build-system r-build-system)
32549 (home-page "https://github.com/cbarbu/R-package-zoom")
32550 (synopsis "Spatial data visualization tool")
32552 "This package provides @code{zm}, a utility that allows you to
32553 zoom/navigate any plot when called with any active plot.")
32554 (license license:gpl3+)))
32556 (define-public r-zoolog
32563 (uri (cran-uri "zoolog" version))
32566 "00fi7czfwr0ll9070w3ijskd0xvilj02gy8wkgqzzrlilij8ah7p"))))
32567 (properties `((upstream-name . "zoolog")))
32568 (build-system r-build-system)
32570 (list r-rdpack r-stringi))
32573 (home-page "https://josempozo.github.io/zoolog/")
32574 (synopsis "Zooarchaeological analysis with log-ratios")
32576 "This package includes functions and reference data to generate and
32577 manipulate log-ratios (also known as @dfn{log size index} (LSI) values) from
32578 measurements obtained on zooarchaeological material. Log ratios are used to
32579 compare the relative (rather than the absolute) dimensions of animals from
32580 archaeological contexts. The zoolog package is also able to seamlessly
32581 integrate data and references with heterogeneous nomenclature, which is
32582 internally managed by a zoolog thesaurus.")
32583 (license license:gpl3)))
32585 (define-public r-filehash
32587 (name "r-filehash")
32592 (uri (cran-uri "filehash" version))
32595 "1ga17smgjd4qsnf5a7qk0giwhpc5969ylqj520favs1k6b4y557k"))))
32596 (properties `((upstream-name . "filehash")))
32597 (build-system r-build-system)
32598 (home-page "http://github.com/rdpeng/filehash")
32599 (synopsis "Simple key-value database")
32601 "This package implements a simple key-value style database where
32602 character string keys are associated with data values that are stored on the
32603 disk. A simple interface is provided for inserting, retrieving, and deleting
32604 data from the database. Utilities are provided that allow filehash databases
32605 to be treated much like environments and lists are already used in R. These
32606 utilities are provided to encourage interactive and exploratory analysis on
32608 (license license:gpl2+)))
32610 (define-public r-mlearning
32612 (name "r-mlearning")
32617 (uri (cran-uri "mlearning" version))
32620 "1zjnh4gcw068li1bks60gazn3205xhmqz67hbkb1san33lmlxya3"))))
32621 (properties `((upstream-name . "mlearning")))
32622 (build-system r-build-system)
32630 (home-page "http://www.sciviews.org/zooimage")
32631 (synopsis "Machine learning algorithms with unified interface")
32633 "This package provides a unified interface to various machine learning
32634 algorithms. Confusion matrices are provided too.")
32635 (license license:gpl2+)))
32637 (define-public r-zooimage
32639 (name "r-zooimage")
32644 (uri (cran-uri "zooimage" version))
32647 "0ck8w0zb9l1n9xvjwqshq9q9l8pigy3yslq2hnfbgcwk17kk9mp8"))))
32648 (properties `((upstream-name . "zooimage")))
32649 (build-system r-build-system)
32663 (home-page "http://www.sciviews.org/zooimage")
32664 (synopsis "Analysis of numerical plankton images")
32666 "This package provides a solution for analyzing digital images of
32667 plankton. In combination with ImageJ, an image analysis system, it processes
32668 digital images, measures individuals, trains for automatic classification of
32669 taxa, and finally, measures plankton samples (abundances, total and partial
32670 size spectra or biomasses, etc.).")
32671 (license license:gpl2+)))
32673 (define-public r-zooarch
32680 (uri (cran-uri "zooaRch" version))
32683 "0grc378xppv0303sf4flfqz5002vq5a23nzbq4bsff41rww7dihc"))))
32684 (properties `((upstream-name . "zooaRch")))
32685 (build-system r-build-system)
32686 (propagated-inputs (list r-ggplot2))
32687 (native-inputs (list r-knitr))
32689 "https://cran.r-project.org/package=zooaRch")
32691 "Analytical Tools for Zooarchaeological Data")
32693 "The analysis and inference of faunal remains recovered from
32694 archaeological sites concerns the field of zooarchaeology. The zooaRch
32695 package provides analytical tools to make inferences on zooarchaeological
32696 data. Functions in this package allow users to read, manipulate, visualize,
32697 and analyze zooarchaeological data.")
32698 (license license:gpl2+)))
32700 (define-public r-zonebuilder
32702 (name "r-zonebuilder")
32707 (uri (cran-uri "zonebuilder" version))
32710 "0mxf3dz0d6bi5wwjilqivdxhy5ypnq5svky8zygha0clv45l4dmn"))))
32711 (properties `((upstream-name . "zonebuilder")))
32712 (build-system r-build-system)
32714 (list r-rcolorbrewer r-sf))
32717 (home-page "https://github.com/zonebuilders/zonebuilder")
32718 (synopsis "Create and explore geographic zoning systems")
32720 "This package provides functions, documentation and example data to help
32721 divide geographic space into discrete polygons (zones). The functions are
32722 motivated by research into the merits of different zoning systems. A flexible
32723 @code{ClockBoard} zoning system is provided, which breaks-up space by
32724 concentric rings and radial lines emanating from a central point.")
32725 (license license:gpl3)))
32727 (define-public r-zonator
32734 (uri (cran-uri "zonator" version))
32737 "1plxchpd4ypp36phl13pi9yvlrqi3lk83lv5rldrhdqynhcgfw2k"))))
32738 (properties `((upstream-name . "zonator")))
32739 (build-system r-build-system)
32741 (list r-ggplot2 r-raster r-rcolorbrewer r-reshape2 r-rgdal))
32742 (native-inputs (list r-knitr))
32743 (home-page "https://cbig.github.io/zonator/")
32744 (synopsis "Utilities for Zonation spatial conservation prioritization")
32746 "Create new analysis setups and deal with results of Zonation
32747 conservation prioritization software.")
32748 (license license:bsd-2)))
32750 (define-public r-mmwrweek
32752 (name "r-mmwrweek")
32757 (uri (cran-uri "MMWRweek" version))
32760 "1l1ks44v52iggw9nhs56lfj6804yab5b17k8fzrc6h1kvj3vda0s"))))
32761 (properties `((upstream-name . "MMWRweek")))
32762 (build-system r-build-system)
32763 (home-page "http://wwwn.cdc.gov/nndss/document/MMWR_Week_overview.pdf")
32764 (synopsis "Convert dates to MMWR day, week, and year")
32766 "The first day of any MMWR week is Sunday. MMWR week numbering is
32767 sequential beginning with 1 and incrementing with each week to a maximum of 52
32768 or 53. MMWR week #1 of an MMWR year is the first week of the year that has at
32769 least four days in the calendar year. This package provides functionality to
32770 convert dates to MMWR day, week, and year and the reverse.")
32771 (license license:gpl2+)))
32773 (define-public r-cccd
32780 (uri (cran-uri "cccd" version))
32782 (base32 "0cxh19jqappc6zq9nz3m40ybdmsp12mf7yvflsz96wks3ly2ld4y"))))
32783 (properties `((upstream-name . "cccd")))
32784 (build-system r-build-system)
32785 (propagated-inputs (list r-deldir r-fnn r-igraph r-proxy))
32786 (home-page "https://cran.r-project.org/package=cccd")
32787 (synopsis "Class cover catch digraphs")
32789 "This package provides tools to create Class Cover Catch Digraphs,
32790 neighborhood graphs, and relatives.")
32791 (license license:gpl2+)))
32793 (define-public r-crul
32800 (uri (cran-uri "crul" version))
32803 "133g0skz4lifl8hm8pqdryd2m2drbrm6mdfzbbsrw8fg46di86my"))))
32804 (properties `((upstream-name . "crul")))
32805 (build-system r-build-system)
32813 (native-inputs (list r-knitr))
32814 (home-page "https://github.com/ropensci/crul")
32815 (synopsis "HTTP client")
32817 "This package provides a simple HTTP client, with tools for making HTTP
32818 requests, and mocking HTTP requests. The package is built on R6, and takes
32819 inspiration from Ruby's @code{faraday} gem.")
32820 (license license:expat)))
32822 (define-public r-gistr
32829 (uri (cran-uri "gistr" version))
32832 "0ac9ikrdg6i8xvlma0gizvsdva46408lk7hvsgkqirhy2ljy02hp"))))
32833 (properties `((upstream-name . "gistr")))
32834 (build-system r-build-system)
32844 (native-inputs (list r-knitr))
32845 (home-page "https://github.com/ropensci/gistr")
32846 (synopsis "Work with Gists in browser")
32848 "This package allows the user to create new Github gists, update gists
32849 with new files, rename files, delete files, get and delete gists, star and
32850 un-star them, fork them, open a gist in your default browser, get an embed
32851 code for a gist, list gist commits, and get rate limit information when
32853 (license license:expat)))
32855 (define-public r-rbokeh
32862 (uri (cran-uri "rbokeh" version))
32865 "1h2fpzqf17pw9d09r1g1iyxsj5qma4fsk8vnar7f1z4fjyypvi6q"))
32867 '(for-each delete-file '("inst/htmlwidgets/lib/bokehjs/bokeh-widgets.min.js"
32868 "inst/htmlwidgets/lib/bokehjs/bokeh.min.js")))))
32869 (properties `((upstream-name . "rbokeh")))
32870 (build-system r-build-system)
32873 (modify-phases %standard-phases
32874 (add-after 'unpack 'process-javascript
32875 (lambda* (#:key inputs #:allow-other-keys)
32876 (with-directory-excursion "inst/htmlwidgets/lib/bokehjs"
32878 `((,(assoc-ref inputs "js-bokeh-widgets")
32879 . "bokeh-widgets.min.js")
32880 (,(assoc-ref inputs "js-bokeh")
32881 . "bokeh.min.js"))))
32882 (for-each (lambda (source target)
32883 (format #true "Processing ~a --> ~a~%"
32885 (invoke "esbuild" source "--minify"
32886 (string-append "--outfile=" target)))
32888 (map cdr mapping)))))))))
32900 ;; Version 0.12.15 is mentioned in lib/htmlwidgets/rbokeh.yaml.
32902 `(("esbuild" ,esbuild)
32903 ("js-bokeh-widgets"
32906 (uri "https://unpkg.com/bokehjs@0.12.15/build/js/bokeh-widgets.js")
32909 "07v9lrkfcbdznpb10qqwi4m660zp65g85vlnfw7kn83zmkxkhhxy"))))
32913 (uri "https://unpkg.com/bokehjs@0.12.15/build/js/bokeh.js")
32916 "1pq0059aad7d2jv50nv9449p3w0gbkxkl0mhblc76m5d9qjqav2q"))))
32917 ("r-knitr" ,r-knitr)))
32918 (home-page "https://cran.r-project.org/web/packages/rbokeh/")
32919 (synopsis "R interface for the Bokeh visualization library")
32921 "This package provides a native R plotting library that provides a
32922 flexible declarative interface for creating interactive web-based graphics,
32923 backed by the @url{https://bokeh.pydata.org/, Bokeh visualization library}.")
32924 (license license:expat)))
32926 (define-public r-fauxpas
32933 (uri (cran-uri "fauxpas" version))
32936 "129fzqb7wsskbn50s8x0marr4wm8jrns6hiycqcsk166k3dnyyy8"))))
32937 (properties `((upstream-name . "fauxpas")))
32938 (build-system r-build-system)
32940 (list r-httpcode r-r6 r-whisker))
32943 (home-page "https://docs.ropensci.org/fauxpas")
32944 (synopsis "HTTP error helpers")
32946 "This package provides HTTP error helpers. Methods are included for
32947 general purpose HTTP error handling, as well as individual methods for every
32948 HTTP status code, both via status code numbers as well as their descriptive
32949 names. It supports the ability to adjust behavior to stop, message or
32950 warning. It includes the ability to use a custom whisker template to have any
32951 configuration of status code, short description, and verbose message.")
32952 (license license:expat)))
32954 (define-public r-webmockr
32956 (name "r-webmockr")
32961 (uri (cran-uri "webmockr" version))
32964 "0j40srwi0yasmllb9wsww4m6zkiyzqd549cis4dxd7c7p24hak8j"))))
32965 (properties `((upstream-name . "webmockr")))
32966 (build-system r-build-system)
32976 (home-page "https://github.com/ropensci/webmockr")
32977 (synopsis "Stubbing and setting expectations on HTTP Requests")
32979 "This is a package for stubbing and setting expectations on HTTP
32980 requests. It includes tools for stubbing HTTP requests, including expected
32981 request conditions and response conditions. You can match on HTTP method,
32982 query parameters, request body, headers and more. It can be used for unit
32983 tests or outside of a testing context.")
32984 (license license:expat)))
32986 (define-public r-iotools
32993 (uri (cran-uri "iotools" version))
32995 (base32 "07q0z0kszm1xx5hfhisfliyrcsxd8dc5mx0a2bwwnv5l1xzmix17"))))
32996 (properties `((upstream-name . "iotools")))
32997 (build-system r-build-system)
32998 (home-page "https://www.rforge.net/iotools")
32999 (synopsis "I/O tools for streaming")
33000 (description "This package provides basic I/O tools for streaming and data
33003 (license license:gpl3)))
33005 (define-public r-wordspace
33007 (name "r-wordspace")
33012 (uri (cran-uri "wordspace" version))
33014 (base32 "0hrjv5mag7gwl4wj7np248sdyns5i623wl37b11hlgalhbmlypyf"))))
33015 (properties `((upstream-name . "wordspace")))
33016 (build-system r-build-system)
33018 (list r-cluster r-iotools r-mass r-matrix r-rcpp r-sparsesvd))
33019 (native-inputs (list r-knitr))
33020 (home-page "https://wordspace.r-forge.r-project.org/")
33021 (synopsis "Distributional semantic models in R")
33023 "The wordspace package turns R into an interactive laboratory for
33024 empirical research on @dfn{distributional semantic models} (DSM). It consists
33025 of a small set of carefully designed functions, most of which
33028 @item encapsulate non-trivial R operations in a user-friendly manner or
33029 @item provide efficient and memory-lean C implementations of key operations.
33032 (license license:gpl3)))
33034 (define-public r-maxlik
33041 (uri (cran-uri "maxLik" version))
33043 (base32 "0pdigfpyiqacj2ydhpn5w1h89dz1ydk0syzs25lsgdi40sz0bvkw"))))
33044 (properties `((upstream-name . "maxLik")))
33045 (build-system r-build-system)
33046 (propagated-inputs (list r-generics r-misctools r-sandwich))
33047 (home-page "https://cran.r-project.org/package=maxLik")
33048 (synopsis "Maximum Likelihood Estimation and related tools")
33050 "This package provides functions for @dfn{Maximum Likelihood} (ML) estimation,
33051 non-linear optimization, and related tools. It includes a unified way to call
33052 different optimizers, and classes and methods to handle the results from the
33053 Maximum Likelihood viewpoint. It also includes a number of convenience tools
33054 for testing and developing your own models.")
33055 (license license:gpl2+)))
33057 (define-public r-misctools
33059 (name "r-misctools")
33064 (uri (cran-uri "miscTools" version))
33066 (base32 "16pwfxpyl0zv3hjxx2kjchkg7p6kbj0s2rrpskj7rkhjr9imlg5y"))))
33067 (properties `((upstream-name . "miscTools")))
33068 (build-system r-build-system)
33069 (propagated-inputs (list r-digest))
33070 (home-page "http://www.micEcon.org")
33071 (synopsis "Miscellaneous tools and utilities")
33073 "This package provides miscellaneous small tools and utilities. Many of
33074 them facilitate the work with matrices, e.g. inserting rows or columns,
33075 creating symmetric matrices, or checking for semidefiniteness. Other tools
33076 facilitate the work with regression models, e.g. extracting the standard
33077 errors, obtaining the number of (estimated) parameters, or calculating
33078 R-squared values.")
33079 (license license:gpl2+)))
33081 (define-public r-mockery
33088 (uri (cran-uri "mockery" version))
33091 "0sj77m9vgn4bzb8c8nq93xb9lm8ih8rcb7sfccripraibibg3jcz"))))
33092 (properties `((upstream-name . "mockery")))
33093 (build-system r-build-system)
33098 (home-page "https://github.com/jfiksel/mockery")
33099 (synopsis "Mocking library for R")
33101 "The two main functionalities of this package are creating mock
33102 objects (functions) and selectively intercepting calls to a given function
33103 that originate in some other function. It can be used with any testing
33104 framework available for R. Mock objects can be injected with either this
33105 package's own @code{stub} function or a similar @code{with_mock} facility
33106 present in the @code{testthat} package.")
33107 (license license:expat)))
33109 (define-public r-zoltr
33116 (uri (cran-uri "zoltr" version))
33119 "12zh7y3pwidclscgvd0b0iaqq9j5y8mc8xd6pz4vs0jy5qs3ahar"))))
33120 (properties `((upstream-name . "zoltr")))
33121 (build-system r-build-system)
33133 (native-inputs (list r-knitr))
33134 (home-page "https://github.com/reichlab/zoltr")
33135 (synopsis "Interface to the Zoltar forecast repository API")
33137 "Zoltar is a website that provides a repository of model forecast results
33138 in a standardized format and a central location. It supports storing,
33139 retrieving, comparing, and analyzing time series forecasts for prediction
33140 challenges of interest to the modeling community. This package provides
33141 functions for working with the Zoltar API, including connecting and
33142 authenticating, getting information about projects, models, and forecasts,
33143 deleting and uploading forecast data, and downloading scores.")
33144 (license license:gpl3)))
33146 (define-public r-zoib
33153 (uri (cran-uri "zoib" version))
33156 "0inm7f2pc68ksqxvq12xp9jc99vj7ydylvs24ip12nksbj5k1n8f"))))
33157 (properties `((upstream-name . "zoib")))
33158 (build-system r-build-system)
33160 (list r-abind r-coda r-formula r-rjags))
33161 (home-page "https://www.r-project.org")
33162 (synopsis "Bayesian inference for beta regression")
33164 "This package lets you fit beta regression and zero-or-one inflated beta
33165 regression and obtain Bayesian inference of the model via the Markov Chain
33166 Monte Carlo approach implemented in JAGS.")
33167 (license license:gpl3+)))
33169 (define-public r-logger
33176 (uri (cran-uri "logger" version))
33178 (base32 "08kym5i5fvbf5xhh9qdszp4jdgyc7j7zpnwzy68wabqz73aff6sg"))))
33179 (properties `((upstream-name . "logger")))
33180 (build-system r-build-system)
33181 (native-inputs (list r-knitr))
33182 (home-page "https://daroczig.github.io/logger/")
33183 (synopsis "Lightweight and flexible logging utility")
33185 "Inspired by the the @code{futile.logger} R package and @code{logging}
33186 Python module, this utility provides a flexible and extensible way of
33187 formatting and delivering log messages with low overhead.")
33188 (license license:agpl3+)))
33190 (define-public r-fasterize
33192 (name "r-fasterize")
33197 (uri (cran-uri "fasterize" version))
33199 (base32 "10bzl77c1b9jhcn1xp467qzp2n8c7s3wpxn53qjh1nwvbri5kd32"))))
33200 (properties `((upstream-name . "fasterize")))
33201 (build-system r-build-system)
33203 (list r-raster r-rcpp r-rcpparmadillo r-sp))
33204 (native-inputs (list r-knitr))
33205 (home-page "https://github.com/ecohealthalliance/fasterize")
33206 (synopsis "Fast Polygon to Raster Conversion")
33208 "This package provides a drop-in replacement for @code{rasterize} from
33209 the @code{raster} package that takes sf-type objects, and is much faster.
33210 There is support for the main options provided by the @code{rasterize}
33211 function, including setting the field used and background value, and
33212 options for aggregating multi-layer rasters.")
33213 (license license:expat)))
33215 (define-public r-bien
33222 (uri (cran-uri "BIEN" version))
33224 (base32 "0s98n6zbf48vssd3h63k6kashcxv1kawcb026n0ngsfpc5dv6i48"))))
33225 (properties `((upstream-name . "BIEN")))
33226 (build-system r-build-system)
33241 (home-page "https://cran.r-project.org/package=BIEN")
33242 (synopsis "Tools for accessing the BIEN database")
33244 "This package provides tools for accessing the Botanical Information and
33245 Ecology Network (BIEN) database. The BIEN database contains cleaned and
33246 standardized botanical data including occurrence, trait, plot and taxonomic
33247 data. This package provides functions that query the BIEN database by
33248 constructing and executing optimized SQL queries.")
33249 (license license:expat)))
33251 (define-public r-varhandle
33253 (name "r-varhandle")
33258 (uri (cran-uri "varhandle" version))
33260 (base32 "1l42d0s6fbjjc9l28a2m3myxkrx2c0p0b9yj8wjjjgilw19yc3lv"))))
33261 (properties `((upstream-name . "varhandle")))
33262 (build-system r-build-system)
33263 (home-page "https://bitbucket.org/mehrad_mahmoudian/varhandle")
33264 (synopsis "Functions for robust variable handling")
33266 "This package contains some functions to help users (especially data
33267 explorers) to make more sense of their variables and take the most out of
33268 variables and hardware resources. Functions in this package are supposed to
33269 be efficient and easy to use.")
33270 (license license:gpl2+)))
33272 (define-public r-ggh4x
33279 (uri (cran-uri "ggh4x" version))
33282 "1r49yfm5fqv5s7jb92ad6rf8hd9plcry6f500czjhnhhrp16cqfp"))))
33283 (properties `((upstream-name . "ggh4x")))
33284 (build-system r-build-system)
33286 (list r-ggplot2 r-gtable r-rlang r-scales r-vctrs))
33289 (home-page "https://github.com/teunbrand/ggh4x")
33290 (synopsis "Extension for ggplot2")
33291 (description "This package is a @code{ggplot2} extension. It provides some
33292 utility functions that do not entirely fit within the grammar of graphics
33293 concept. The package extends @code{ggpplots} facets through customisation, by
33294 setting individual scales per panel, resizing panels and providing nested
33295 facets. It also allows multiple colour, fill scales per plot and hosts a
33296 smaller collection of stats, geoms and axis guides.")
33297 (license license:expat)))
33299 (define-public r-zoeppritz
33301 (name "r-zoeppritz")
33305 (uri (cran-uri "zoeppritz" version))
33308 "1711szx9zz17q6pfinyzlyrw7m9772c8ywlixqar2l165bkjalgm"))))
33309 (properties `((upstream-name . "zoeppritz")))
33310 (build-system r-build-system)
33311 (home-page "https://cran.r-project.org/package=zoeppritz")
33312 (synopsis "Seismic reflection and scattering coefficients for waves")
33314 "The @code{r-zoeppritz} package calculates and plots scattering matrix
33315 coefficients or scattering amplitudes, for seismological P and S-waves at an
33317 (license license:gpl2+)))